in - University of California, Berkeley...1 Abstract Production and Photodissociation of Neutral...

Production and Photodissociation of Neutral Free Radicals

by

Neil Charles Cole-Filipiak

A dissertation submitted in partial satisfaction of the

requirements for the degree of

Doctor of Philosophy

in

Chemistry

in the

Graduate Division

of the

University of California, Berkeley

Committee in charge:

Professor Daniel M. Neumark, ChairProfessor Richard SaykallyProfessor C. Bradley Moore

Professor Robert Dibble

Fall 2015

1

Abstract


by


Doctor of Philosophy in Chemistry

University of California, Berkeley

Professor Daniel M. Neumark, Chair

The primary photochemistry of several combustion-relevant free radicals have been in-vestigated via photofragment translational spectroscopy. The relevance of radical photo-chemistry will be discussed, along with methodologies and details of each experiment. Theexperimental apparatus will also be described, especially with regard to the recent installa-tion of a tunable energy electron ionizer. The upgraded ionizer has been a significant advance,allowing for more detailed characterization of the radical source employed in this thesis.

The photochemistry of the phenyl radical (c-C6H5), a combustion intermediate and pre-cursor to polycyclic aromatic hydrocarbons, was investigated at 248 and 193 nm. At 248nm, an H-atom loss pathway was found, while at 193 nm both H-atom loss and C2H2 losspathways were observed. For both wavelengths, P(ET) distributions suggested internal con-version to the ground electronic state followed by energy randomization and dissociation. Thebranching ratio between the two 193 nm dissociation pathways was found to be 0.2 ± 0.1 infavor of H-atom loss, in good agreement with statistical Rice–Rampsperger–Kassel–Marcus(RRKM) theory.

An initial investigation of the methyl perthiyl radical (CH3SS) at 248 nm suggested thesurprising results of both CH3+SS and CH2S+SH dissociation channels with no evidence forS-atom loss. In both cases, the translational energy distributions were inconsistent with theexpected energetics. Upon reinvestigation, the assumption of radical production—and there-fore radical photodissociation—was shown to be incorrect. The new results demonstratedS-loss and CH3 loss pathways, with the former appearing to involve a repulsive electronicexcited state.

i

“Photochemical determinations which pretend to anything more than a roughapproximation, are surrounded by difficulties of so considerable a nature, thatup to the present time all attempts to gain a knowledge of the laws of the chemicalaction of light have been fruitless.”

R. W. E. Bunsen and H. E. Roscoe, Q. J. Chem. Soc. 8, 193 (1856).

http://doi.org/10.1039/QJ8560800193

ii

Contents

Contents ii

List of Figures v

List of Tables vii

1 Introduction 11.1 Neutral Free Radicals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11.2 Photochemistry and Photodissociation . . . . . . . . . . . . . . . . . . . . . 2

1.2.1 Photodissociation Dynamics . . . . . . . . . . . . . . . . . . . . . . . 21.2.2 Dissociation on an Electronic Excited State . . . . . . . . . . . . . . 21.2.3 Dissociation on the Electronic Ground State . . . . . . . . . . . . . . 41.2.4 Experimental Observables . . . . . . . . . . . . . . . . . . . . . . . . 51.2.5 Photofragment Translational Spectroscopy . . . . . . . . . . . . . . . 6

1.3 Kinematics of Photodissociation . . . . . . . . . . . . . . . . . . . . . . . . . 61.3.1 Fundamental Overview . . . . . . . . . . . . . . . . . . . . . . . . . . 61.3.2 Determination of Translational Energy Distributions . . . . . . . . . 71.3.3 Product Branching Ratios . . . . . . . . . . . . . . . . . . . . . . . . 10

1.4 Systems Discussed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

2 Experiment 132.1 Experimental Considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . 132.2 The Crossed Beam Machine . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

2.2.1 History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132.2.2 Apparatus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142.2.3 Lasers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162.2.4 Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162.2.5 Machine Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

2.3 Radical Production . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192.3.1 General Considerations . . . . . . . . . . . . . . . . . . . . . . . . . . 192.3.2 Photolysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192.3.3 Electric Discharge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

iii

2.3.4 Flash Pyrolysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

3 Tunable Energy Electron Ionization 233.1 Electron Ionization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233.2 New Ionizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

3.2.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253.2.2 Filament . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263.2.3 Ion Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

3.3 Electron Energy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283.4 Cautions, Caveats, and Constraints . . . . . . . . . . . . . . . . . . . . . . . 28

3.4.1 TOF Dependence on Iem . . . . . . . . . . . . . . . . . . . . . . . . . 283.4.2 IEC Dependence on Iem . . . . . . . . . . . . . . . . . . . . . . . . . 303.4.3 Ion Optic Bias . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

3.5 Implementation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323.5.1 Radical Characterization . . . . . . . . . . . . . . . . . . . . . . . . . 323.5.2 Low Energy Electron Ionization of Photofragments . . . . . . . . . . 37

4 The Phenyl Radical 394.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 394.2 Experimental . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 424.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 434.4 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 464.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 514.6 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 534.7 Supplemental Material . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

4.7.1 Investigating Experimental Parameters . . . . . . . . . . . . . . . . . 544.7.2 TOF Feature Assignment . . . . . . . . . . . . . . . . . . . . . . . . 564.7.3 Effect of Carrier Gas . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

5 The Methyl Perthiyl Radical, Part I 605.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 605.2 Experimental . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 625.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 635.4 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 655.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 675.6 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

6 The Methyl Perthiyl Radical, Part II 706.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 706.2 Experimental . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 726.3 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 736.4 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

iv

6.5 Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 816.6 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 836.7 Supporting Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

6.7.1 Reproduction of Previous Experiment . . . . . . . . . . . . . . . . . . 836.7.2 Dimethyl Trisulfide Photodissociation . . . . . . . . . . . . . . . . . . 866.7.3 Thiomethoxy Radical Photodissociation . . . . . . . . . . . . . . . . 886.7.4 Additional Methyl Perthiyl Radical Results . . . . . . . . . . . . . . 906.7.5 BEB Model Calculation . . . . . . . . . . . . . . . . . . . . . . . . . 93

Bibliography 94

A Summary for a Broader Audience 104A.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104

A.1.1 Free Radicals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104A.1.2 Photochemistry and Photodissociation . . . . . . . . . . . . . . . . . 104

A.2 Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105A.2.1 Technique . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105A.2.2 Apparatus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

A.3 The Phenyl (c-C6H5) Radical . . . . . . . . . . . . . . . . . . . . . . . . . . 107A.4 The Methyl Perthiyl (CH3SS) Radical . . . . . . . . . . . . . . . . . . . . . 108A.5 Concluding Remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109

B Abbreviations and Definitions 110

C Data Acquisition and Analysis Programs 112C.1 Automated Ionization Efficiency Curve Collection . . . . . . . . . . . . . . . 112

C.1.1 iec_mass.pml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112C.2 Ionization Efficiency Curve Normalization . . . . . . . . . . . . . . . . . . . 116

C.2.1 iec_norm.m . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116C.3 Binary-Encounter-Bethe Model for Electron Ionization Cross Sections . . . . 120

C.3.1 BEB.m . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120C.4 Product Branching Ratios . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121

C.4.1 branching_ratio.m . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

D Publications Resulting From Graduate Work 125

v

List of Figures

1.1 Examples of photoexcitation to several possible electronic excited states . . . . . 31.2 Prototypical potential energy curves along the ground electronic state . . . . . . 41.3 Newton diagram for the photodissociation of ABC . . . . . . . . . . . . . . . . . 8

2.1 Schematic of B Machine as used for the experiments described in this thesis . . 152.2 Schematic of the trigger system and temporal contributions to measured TOF on

B Machine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172.3 Schematic of the flash pyrolysis source . . . . . . . . . . . . . . . . . . . . . . . 212.4 Example mass spectra demonstrating radical generation via pyrolysis . . . . . . 22

3.1 Schematic of a Brink-type ionizer . . . . . . . . . . . . . . . . . . . . . . . . . . 243.2 Picture and schematic of the axial ionizer . . . . . . . . . . . . . . . . . . . . . 253.3 Schematic cross-sectional view of filament and ion region . . . . . . . . . . . . . 263.4 Ionization efficiency curves for He, Ne, Ar, and Kr . . . . . . . . . . . . . . . . . 293.5 Time-of-flight dependence upon electron emission current . . . . . . . . . . . . . 303.6 Ionization efficiency curve dependence upon electron emission current . . . . . . 313.7 Scheme for the pyrolytic production of the benzyl radical . . . . . . . . . . . . . 323.8 Example mass spectra of the benzyl radical and precursor with an electron ion-

ization energy of 70 eV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333.9 Example mass spectra of the benzyl radical and precursor with an electron ion-

ization energy of 17 eV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343.10 Ionization efficiency curve of the benzyl radical . . . . . . . . . . . . . . . . . . 343.11 Appearance energies of several m/z values relevant to benzyl radical decomposi-

tion as a function of pyrolysis source power . . . . . . . . . . . . . . . . . . . . . 353.12 Ionization efficiency curves for dissociative ionization fragments . . . . . . . . . 363.13 Proof-of-concept photofragment ionization efficiency curve . . . . . . . . . . . . 37

4.1 Simplified ground state potential energy diagram of the phenyl radical . . . . . 414.2 Representative m/z = 76 TOF spectra at 248 and 193 nm . . . . . . . . . . . . 444.3 Sample TOF spectra taken at m/z = 51 and m/z = 26 at 193 nm . . . . . . . . 454.4 Representative m/z = 50 TOF spectra at 193 nm . . . . . . . . . . . . . . . . . 454.5 Time-of-flight dependence on carrier gas . . . . . . . . . . . . . . . . . . . . . . 46

vi

4.6 Newton diagram for the phenyl radical photodissociation at 193 nm . . . . . . . 474.7 Translational energy distribution for C6H4 + H channel from the phenyl radical

at 248 nm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 484.8 Translational energy distribution for C6H4 + H channel from the phenyl radical

at 193 nm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 494.9 Translational energy distribution for C4H3+C2H2 channel from the phenyl radical

at 193 nm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 504.10 Sample TOF spectra under previous experimental conditions . . . . . . . . . . . 554.11 Sample TOF spectra taken at m/z = 76 using the Ar/He carrier gas mixture at

193 nm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 564.12 Time-of-flight spectra taken at m/z = 152 and 193 nm . . . . . . . . . . . . . . 574.13 Translational energy distributions assuming biphenyl photodissociation . . . . . 584.14 Time-of-flight simulations assuming biphenyl photodissociation . . . . . . . . . . 58

5.1 Ground state potential energy surface for the isomerization and dissociation ofthe methyl perthiyl radical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

5.2 Sample TOF spectra m/z = 64 (SS+) collected at various Θlab . . . . . . . . . . 645.3 TOF spectra showing evidence for CH2S + SH . . . . . . . . . . . . . . . . . . . 645.4 Center-of-mass P(ET) distribution for C–S fission of CH3SS . . . . . . . . . . . 665.5 Center-of-mass P(ET) distribution for SH loss from CH3SS . . . . . . . . . . . . 66

6.1 Mass spectra and IEC identifying the production of CH3SS . . . . . . . . . . . . 746.2 Example TOF spectra of the m/z = 47 and 32 photoproducts from CH3SS . . . 756.3 Example TOF spectra of m/z = 64 . . . . . . . . . . . . . . . . . . . . . . . . . 766.4 Photofragment intensity dependence on laser polarization . . . . . . . . . . . . . 776.5 Center-of-mass P(ET) assuming anisotropic S–S bond fission from the methyl

perthiyl radical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 786.6 Center-of-mass P(ET) assuming isotropic C–S bond fission from the methyl

perthiyl radical . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 796.7 Very low electron ionization energy DMDS mass spectra . . . . . . . . . . . . . 846.8 Appearance energies of several relevant m/z values during the pyrolysis of DMDS 856.9 Example TOF spectra testing dimethyl disulfide as a precursor for CH3SS . . . 866.10 Example TOF spectra of the m/z = 79 and 47 photoproducts observed in the

photodissociation of DMTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 876.11 Center-of-mass P(ET) for the primary and secondary dissociation of dimethyl

trisulfide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 876.12 Example m/z = 64 TOF spectra from the dissociation of dimethyl trisulfide . . 886.13 Example m/z = 46 TOF spectra . . . . . . . . . . . . . . . . . . . . . . . . . . 896.14 Center-of-mass P(ET) assuming H-atom loss from CH3S . . . . . . . . . . . . . 896.15 Center-of-mass P(ET) assuming S-atom loss from CH3S . . . . . . . . . . . . . . 906.16 TOF spectra of the S-atom loss from CH3SS using two different electron energies 906.17 Laser pulse energy dependence of dimethyl trisulfide, CH3SS, and CH3S . . . . . 91

vii

6.18 TOF spectra taken with a “very hot” pyrolysis source . . . . . . . . . . . . . . . 926.19 TOF spectrum at m/z = 64 showing the second, slow feature . . . . . . . . . . 92

List of Tables

4.1 Characteristics of the P(ET) distributions derived for the phenyl radical . . . . . 50

6.1 Total electron ionization cross sections for CH3S and S2 at various levels of theory 93

viii

Acknowledgments

First and foremost, I am tremendously grateful to Dan Neumark for his mentorshipand support. I have learned a great deal from his experience and through his approach toscientific inquiry, and cannot imagine grad school with another advisor.

Bogdan “B” Negru was the senior student on X-Beam when I joined, and I owe him agreat many thanks as well. B not only taught me a lot about the project, but how to takeit easy and enjoy my time in grad school. I miss our dart games. I would also like to thankGab Just and Dayong Park, the other two X-Beamers when I joined, for welcoming me andhelping me learn the ropes.

Madeline Elkins and Sarah King-Zimmer were my classmates in the Neumark group.The three of us relied on each other during our time here, and I owe them many thanks fortheir help, kindness, tolerance, and support.

I’ve had the great pleasure of working with Mark Shapero for the past few years. Notonly is he an intelligent and engaging co-worker, but he has taught me much about how tobe a mentor. He has helped me try new things with the experiment (and been patient whenthey didn’t work). I have come to rely on his opinion, and will miss our discussions.

I must also thank the many members of the Neumark group over the years. While thepeople have changed, this has always been a driven, intelligent group of people willing tohelp change pump oil or talk through an interpretation. I am also thankful that this groupknows when it’s time to quit and go have fun, and I will miss drinking with Alex Shreve andmaintaining awkward eye contact with Holly Williams. Despite being a synthetic chemist, Imust also thank Mike Lipshutz for being a willing collaborator and supportive friend.

I am grateful to my friends outside of the chemistry department (particularly Rachelfor living with me and Chris and Andrea for the backpacking) for their support and helpkeeping me a sane and happy person.

I would like to thank my family, especially my parents, for their continuous support andlove during my 20 some years in school. I would not be here if they hadn’t nurtured mycuriosity in the world and shown me the pleasures of thinking and learning.

Finally, I would like to thank Mari Hsu for deciding that she liked spending time withme. She’s been supportive and patient while I’ve blundered through the end of grad school.I am looking forward to having her along for the next adventure.

1

Chapter 1

Introduction

1.1 Neutral Free RadicalsThe term “radical” was first introduced in 1785 by Louis-Bernard Guyton de Morveau1

and later published in Antoine Lavoisier’s Triaté Élémentaire de Chimie.2 The term, how-ever, described the “the acidifiable base” of an acid. By the 19th century, “radical” was moreanalogous to the modern definition of functional group,1 and chemists were attempting toisolate these radicals, often producing the stable dimer instead (e.g. Bunsen’s work on ca-codyl3 or Frankland’s attempts to isolate ethyl4). The first example of a modern free radicalis generally attributed to Moses Gomberg’s observation of the triphenyl methyl radical in1900.5 By the mid-20th century, the free radical as a reactive intermediate had become widelyaccepted (see, for example, Ref. [6]) and has become a central concept in many disciplinesof chemistry.

While free radicals are important to many fields of modern chemistry, their roles in at-mospheric7 and combustion chemistries have implications for the environment and humanhealth.8 To understand these chemically rich and complex systems, it is important to un-derstand the chemical reactivity of the individual components. How are radicals formed ina car engine? How do radicals react in the troposphere? How do radicals dissociate? Whatare the dissociation products? These last two questions in particular have driven chemicaldynamics research for years9 and are the primary questions of interest in this thesis.

The unpaired electron of a free radical results in a unique electronic structure, namely theavailability of low-lying electronic excited states. These states provide a valuable tool to studyradical unimolecular decomposition by investigating dissociation induced by absorption ofa photon. These photodissociation events yield information about the fundamental radicalphotochemistry and dissociation dynamics on the ground or excited electronic states.

CHAPTER 1: Introduction 2

1.2 Photochemistry and PhotodissociationPhotochemistry is the interrogation of molecular structure and dynamics through the

interaction of molecules and light.10 In a static picture, absorption of light provides infor-mation about molecular structure, relative energy levels, and populations of a molecule oran ensemble of molecules. Dynamically, energized molecules may have different chemicalreactivity than their ground state counterparts (e.g. the reactivity of triplet versus singletO2). From a unimolecular perspective, the processes of photon absorption and energy dis-posal are of considerable interest, and many experimental techniques have been designed toinvestigate these unimolecular processes.

1.2.1 Photodissociation DynamicsWithin the field of photochemistry is the study of photodissociation, whereby bond rup-

ture occurs after a photon of sufficient energy is absorbed by a molecule. For the case of ageneric molecule ABC, the photodissociation may result in many products:

ABC + hν → ABC∗ → A + BC→ AB + C→ AC + B...

with the fragments populating several electronic, vibrational, rotational, and translationalenergies. The shape of potential energy surface (PES) upon which the molecule dissociateswill determine this energy partitioning, making photodissociation studies a powerful meansof interrogating the PES of a molecule. Thus, by investigating fragments A or BC (e.g.the vibrational energy of fragment BC), the PES of ABC may be elucidated through itsphotochemistry.

Following photoexcitation of a molecule, several possible events may occur. The moleculemay fluoresce or (if coupled to a bath) undergo collisional deactivation, and these non-dissociative relaxation processes are extensively studied in and of themselves. Conversely, aphotoexcited molecule may relax via dissociation. Following photoexcitation with an ultra-violet photon, dissociation may occur on an electronic excited state or the electronic groundstate and, in either case, will generally follow a few prototypical reaction mechanisms.

1.2.2 Dissociation on an Electronic Excited StateThe photon shown in Fig. 1.1a) will excite molecule ABC to a repulsive electronic excited

state. This state is not bound along the A–B coordinate, and so will lead directly to theelectronic ground state products A and BC. Since the excited ABC cannot spend muchtime on this part of the surface and redistribute the photon energy into internal degrees offreedom, a majority of the available energy is partitioned into relative translational energy of

CHAPTER 1: Introduction 3Energy

Reaction Coordinate

a)

En

erg

yReaction Coordinate

b)

Figure 1.1: Examples of photoexcitation to several possible electronic excited states. Disso-ciation on either repulsive state will result in most of the available energy partitioned intotranslation. At higher photon energies than shown, dissociation to produce A + BC∗ willresult in substantial energy partitioning into photofragment internal (electronic) energy. Thedashed circles highlight the conical intersections between these states.

the dissociating products (the photofragments). The photodissociation of water from the firstelectronic excited state is an example of dissociation on a repulsive surface.11 Sulfur atomloss from the methyl perthiyl radical, discussed in Chapter 6, also exhibits the characteristicsof dissociation along a repulsive surface to form products in the electronic ground state.

The photon shown in Fig. 1.1b) will excite ABC to a bound electronic excited state.This “predissociative”12 state may couple to either of the two repulsive states through aconical intersection (CI), indicated by the dashed circles in Fig. 1.1b). Passage through aconical intersection, a degenerate seam between two or more adiabatic electronic potentialenergy surfaces, is a ubiquitous mechanism whereby an electronically excited molecule maynonradiatively change electronic states.13 In the case of Fig. 1.1b), the photoexcited ABCmay couple to the A + BC or the A∗ + BC states and dissociate to form either or bothsets of photoproducts. The product channels A + BC and A∗ + BC may be distinguishedby the internal energy of A or the translational energy of A and BC, as the A∗ + BCchannel will have less available energy to partition into translation. By varying the photonenergy, coupling to the repulsive surfaces may be tuned and the predissociation mechanismexplored. For example, the predissociative, first electronic excited state of the thiomethoxyradical (CH3S) intersects several repulsive states along the C–S coordinate.14,15 The finestructure population of S(3Pj) produced after photoexcitation to the predissociative statedepends upon which of the repulsive states is accessed during the dissociation.16

The final, prototypical excited state dissociation mechanism is the formation of A +


Energ

y

Reaction Coordinate

Figure 1.2: Prototypical potential energy curves along the ground electronic state. Dissoci-ation may occur over an exit barrier (AB + C) or may be “barrierless” along the reactioncoordinate (A + BC). Conical intersections are again highlighted by dashed circles.

BC∗. While this process will require a higher photon energy than depicted in Fig. 1.1b), dissociation along this surface can occur and may again be characterized by the BCinternal energy or A and BC translational energies. With a high enough photon energy, thephotodissociation of CH3S may proceed along the first electronic excited state to produce S(1D).14,15

1.2.3 Dissociation on the Electronic Ground StateDepending on the shape and energies of the electronic excited states of ABC, relaxation

of the electronic excited state may be competitive with, or out compete, dissociation. Whiledissociation may occur on a lower excited state, ultimately the electronic relaxation willreturn ABC to the electronic ground state. Internal conversion to the electronic groundstate will occur through conical intersections to other excited states,13 shown schematicallyin Fig. 1.2, ultimately resulting in highly internally excited, vibrationally “hot” molecules inthe electronic ground state.

Depending upon the shape of the potential energy surfaces and the dynamics of thetransition through the CI, internal conversion to the ground state may occur along thereaction coordinate. In these cases, dissociation may be prompt and feature a high degreeof translational energy in the photoproducts. For instance, the repulsive H-atom loss fromheterocycles such as phenol17 or pyrrole18 may pass through a CI with the electronic groundstate, yet result in photoproducts with high translational energy.


Internal conversion may occur through conical intersections to regions of the potentialenergy surface that, despite the vibrational excitation, remain bound (such as the electronicrelaxation of many biomolecules, see Ref. [19] for example). For dissociation to occur, thevibrational energy must migrate to the dissociation coordinate via intramolecular vibrationalenergy redistribution (IVR). To describe IVR in a molecule, models that randomize the en-ergy among the vibrational modes using statistical theory—where all of the accessible phasespace is statistically populated and continuously maintaining a microcanonical ensemble20—are often used. These models, such as the Rice-Ramsperger-Kassel-Marcus theory,21 may beused to describe how a system explores the potential energy surface by calculating unimolec-ular rate constants. During a dissociation, these rate constants yield the relative importanceof each product channel (the product branching ratio), thus providing a conceptual andtheoretical framework to describe dissociation on the electronic ground state.

As the photon energy in Fig. 1.2 is greater than the asymptotic dissociation energy of theA–B bond and the activation energy for B–C bond cleavage, dissociation will occur whenenough energy has “collected” into an appropriate coordinate via IVR. The case of A–Bcleavage shown in Fig. 1.2, is an example of simple bond fission. There is no well-definedtransition state along the A–B reaction coordinate, implying that the reverse addition pro-cess would not encounter an energetic barrier. Dissociations along these “barrierless” coor-dinates will result in large internal energies and near-zero translational energy as the bondwill break once sufficient energy has collected in the reactive mode. The loss of a hydrogenatom from the phenyl radical (see Chapter 4) or vibrationally excited toluene22 are examplesof this dissociation mechanism.

The other prototypical ground state dissociation mechanism occurs along the B–C co-ordinate shown in Fig. 1.2. In this case, the reaction has a well defined transition state anda small “exit barrier” is present. As ABC dissociates along this coordinate, the differencein energy between the top of the barrier and the asymptotic energy will be partitioned intotranslation. The fragments will still have a relatively large amount of internal energy butthe translational energy will be slightly greater than the “barrierless” case. The productionof acetylene and C4H3 from the dissociation of the phenyl radical in Chapter 4 occurs oversuch an exit barrier.

1.2.4 Experimental ObservablesIt is apparent from the above discussion that interrogating final photoproduct states is a

powerful tool for exploring the potential energy landscape of a molecule and the dynamicsthat can occur. As such, many techniques have been developed to look at photodissociationprocesses and interrogate an aspect of the system. Absorption23 and fluorescence24 spectro-scopies are powerful tools to investigate photofragment internal energy distributions. Thesetechniques are both readily adapted to monitor the time-dependent evolution of reactant orproduct state populations, providing yet further information about dissociation processes andmechanisms. Photoproduct translational energies, as discussed above, will also be controlled


by the dissociation mechanisms and provide another tool to investigate the photochemistry,known as photofragment translational spectroscopy.

1.2.5 Photofragment Translational SpectroscopyPhotofragment translational spectroscopy (PTS) is a technique whereby photodissocia-

tion dynamics are inferred from distributions of product translational energies.25 Based onthe conservation of energy and momenta from the absorption of a photon with known energy,the final product translational energies can be related to the energy partitioning during areaction. As techniques to measure translational energy require information about the massof a photoproduct, PTS is a useful tool for determining photoproduct identities and eluci-dating the dissociation channels of a given molecule. By comparing the experimental resultsfor different pathways, product branching ratios can be determined. When combined, thesepieces of information provide a rich picture of the dissociation mechanisms of a molecule.

Under the umbrella of PTS, there are a variety of experimental implementations all basedon letting the photodissociated system evolve for some time prior to detection. Velocity mapimaging is often employed to measure the photoproduct center-of-mass velocities26 and canbe used to capture the entire dynamics.27 Photoionization may be used to ionize specificphotoproducts, which in turn provides mass information. Both techniques can be operatedin a time-resolved fashion,26 allowing for the real time dynamics of a photodissociation tobe determined.

The oldest techniques use time-of-flight spectrometry coupled to an electron ionizer andmass filter to measure photoproduct velocities.25,28 These “universal” machines (used inthe experiments presented herein) allow for detailed information about all photoproductchannels and product branching ratios without prior knowledge of the photochemistry orphotoproducts. The following discussions, while mostly generalizable to any PTS experiment,will include considerations for these apparatuses.

1.3 Kinematics of Photodissociation1.3.1 Fundamental Overview

As discussed in the previous section, PTS is based on energy balance and conservation ofmomentum in the center-of-mass (CM) frame. The energy partitioning during a photodisso-ciation event may be written as follows:

Eavail = hν −D + E = Eint + ET , (1.1)

where the photon energy hν is set by the photon frequency ν, D is the asymptotic disso-ciation energy, E is the (nascent) rovibrational energy of the radical immediately beforephotoexcitation, and Eint and ET are the photofragment internal and translational energies.For PTS experiments carried out using a molecular beam, the supersonic expansion results


in internally cold molecules.29,30 As such, E is usually approximated as zero—further dis-cussion of this point may be found in Chapter 4.

The prototypical molecule ABC photodissociating along the A–B coordinate yields frag-ments A and BC. In the CM frame, these two fragments are related by conservation of linearand angular momentum and energy:

mAuA +mBCuBC = 0 (1.2)

J = jA + jBC + l (1.3)

ET =1

2mAu2

A +1

2mBCu2

BC (1.4)

where mi is the mass and ui is the CM velocity of fragment i, J is the total angular momentumof the system, ji is the rotational angular momentum of fragment i, and l is the orbital angularmomentum. For a known D, Eqs. (1.1)–(1.4) demonstrate that measuring the CM velocityof one fragment provides enough information to determine the photodissociation dynamicsof the system. For the experiments described in this thesis, however, the laboratory framephotofragment velocities vi are measured and so a conversion between the CM and laboratoryframe velocities must be achieved.

Conversion between the laboratory and CM frames is done by knowing the velocity ofmolecule ABC in the laboratory frame (vlab). For molecules entrained in a molecular beam,the beam velocity is used. Newton diagrams, such as the one shown in Fig. 1.3, demonstratethe conversion process via classical scattering: through vector addition, measured vi can berelated to specific ui by the angle between vi and vlab (Θlab). In the CM frame, it can easilybe seen that fragment BC is heavier than fragment A as |uA| is larger, as related by Eq.(1.2). In the laboratory frame, photofragments recoil off of the molecular beam axis and areconfined to a maximum laboratory scattering angle Θmax when all of Eavail is partitionedinto translational energy (Eint = 0). As will be seen in subsequent chapters, this Θmax is auseful tool for identifying photoproduct channels.

Figure 1.3 implies that different values of ui may be sampled by observing photofragmentsover a range of Θlab. By measuring the photofragment number densities as a function of timesince irradiation—i.e. a time-of-flight (TOF) spectrum—for several Θlab, the probability thata photodissociation event will produce photofragments with a given translational energycan be determined. These translational energy distributions (P(ET)) provide a wealth ofinformation about the dissociation mechanisms discussed in the previous sections and arethe desired information from a PTS experiment.

1.3.2 Determination of Translational Energy DistributionsWhile the above discussion provides an intuitive framework for understanding photofrag-

ment translational spectroscopy through classical scattering, the full relationship between alaboratory time-of-flight and the CM translational energy distribution is much more involved.Details of the molecule, photon absorption, position of a detector, etc. must all be considered


Figure 1.3: Newton diagram for the photodissociation of ABC along the A–B coordinate.

in order to accurately determine the P(ET) from experimental observables. The followingdiscussion will highlight the key points of this calculation. For a full discussion, the thesis ofXinsheng Zhao31 is particularly useful.

The systems of interest to this thesis are typically photodissociated by one photon oflight and each channel produces two fragments. In this framework, the photodissociation ofreactant molecule R may be described as:

R + hν → An + Bn; n = 1, 2, . . . , Np (1.5)

where n is the primary reaction channel and Np is the total number of reaction channels.The reactant molecules may be described by laboratory velocity vR, laboratory solid angleωR, laboratory position X, and quantum state ri as NR(vR, ωR,X, ri).

It is useful to incorporate some approximations based on experimental considerations; amore complete description of the experiment may be found in Chapter 2. Typical photofrag-ment translational spectroscopy experiments are performed with a nanosecond pulsed laser,focused to ca. 1 mm at the region of intersection with a molecular beam (the interactionregion). Laboratory molecular beam velocities are typically ∼ 103 m/s, so molecule R willhave moved approximately 1% of the interaction length during the laser pulse. For the ex-periments described herein, the photon momentum is small compared to the momentumof molecule R. For a single photon absorption, molecule R is instantaneously photoexcitedand the reaction time after photoexcitation is typically a femto- to picosecond timescale,occurring much faster than the nanosecond laser pulse. With a final assumption that the


experiment cannot distinguish between molecules photoexcited at different times in the laserpulse or with different values of X in the interaction region, the photoproduct number densitymay be described by:

NAn(vAn , ωAn)dvAndωAn =

∫vAn ,dvAn ,ωAn ,dωAn

CnPn(ET,n,Ωn)N

R(vR, ωR) dvR dωR dET,n dΩn, (1.6)

where Pn(ET,n,Ωn) is the normalized, center-of-mass (i.e. constant with respect to vR andωR) translational energy and solid angle distribution for dissociation channel n; N

R(vR, ωR)is density of all initial reactant states ri in the interaction volume of the laser and molecularbeams prior to irradiation; C

n describes the photoexcitation and is a normalization factorfor Pn(ET,n,Ωn); and the brackets denote the constraints on the integrals. As mentioned inthe previous section, the Pn(ET,n,Ωn) are the desired information from a PTS experiment.Equation (1.6) may be similarly written for products Bn.

As mentioned in the previous section, detection of photofragments is measured as afunction of time since the laser interacted with the molecular beam, defined as T. WhileEq. (1.6) describes the photoproduct laboratory velocities in terms of the CM translationalenergies, it does not yet relate to the laboratory observables used in this thesis. To determinea photofragment laboratory velocity, T can be measured and divided into a known flightlength L:

vAn =L

T. (1.7)

For products An with laboratory velocities in the range of vAn to vAn + dvAn entering adetector with solid angle ωD, the number of photoproducts entering the detector may bewritten as:

NTAn(T, ωD) dT =

∫ωD

NAn(vAn , ωAn)vAn

T dωAn

dT, (1.8)

where vAn/T is the Jacobian from the transformation to time. The CM frame translationalenergies and solid angles in Eq. (1.6) must be converted to the laboratory frame:

ET,n =1

2

mRmAn

mBn

u2An

(1.9)

and ∣∣∣∣ ∂(uAn ,Ωn)

∂(vAn , ωAn)

∣∣∣∣ = v2An

u2An

, (1.10)

where mi and ui are the mass and CM velocity of species i, and Eq. (1.10) is the Jacobianfor the coordinate transformation.29 The time-of-flight spectrum for product An may thus


be expressed as:

NTAn(T, ωD) = C

n

v3An

TmRmAn

mBn

∫T,ωD

Pn(ET,n,Ωn)

uAn

NR(vR, ωR) dvR dωR dωAn . (1.11)

Finally, as it is difficult to determine neutral molecule translational energies, the detectionscheme used involves ionization of the photofragments. For electron ionization, the ionizationefficiency is dependent upon fragment velocity32,33 and may be written as:

ηAn(vAn) =ηAn

vAn

, (1.12)

where ηAnis a collection of constants related to ionizer parameters (e.g. emission current) and

the properties of species An (e.g. electron ionization cross section). With this last considera-tion, the ion signal NT,+

An(T, ωD) may be written in terms of the center-of-mass translational

and angular distributions:

NT,+An

(T, ωD) = Cnη

An

v2An

TmRmAn

mBn

∫T,ωD

Pn(ET,n,Ωn)

uAn

NR(vR, ωR) dvR dωR dωAn . (1.13)

Equation (1.13) thus allows for ion counts as a function of time since laser irradiation (aTOF spectrum) to be related to the primary photochemistry of a molecule through theconstruction of a CM translational energy distribution.

For the experiments described herein, only photoproducts scattered into a plane areaccepted by the detector. As such, the scattering and detector solid angles discussed above areadequately described by angles with respect to the molecular beam or laser. Thus, laboratoryTOF are acquired as a function of laboratory scattering angles Θlab. The translational energyand angular distribution may be written in terms of the CM scattering angle θ as P(ET , θ),further simplified by assuming separable distributions:

P(ET , θ) = P(ET )I(θ), (1.14)

where the angular distribution I(θ) has a known form.34 Typically, a computer program isused to numerically evaluate a trial P(ET) in Eq. (1.13) for a given set of experimental con-ditions, producing a “forward convolution” simulation of the observed TOF spectrum. Thetrial distribution may then be iteratively adjusted until the TOF simulation is in agreementwith the observed data.

1.3.3 Product Branching RatiosIn any field of chemistry, one of the fundamental characteristics of a reaction is the

competition between different possible product channels. For reactions that can proceed via


several mechanisms, the relative weight of each channel is the product branching ratio (BR).The TOF spectra may be used to determine a product branching ratio, once experimentalobservables and the conversion to the laboratory frame have been taken into account. Thefollowing is a brief overview of this calculation; details may be found in Refs. [35] and [36].

For a reactant molecule with two-body dissociation channels A and B (with productmasses m1 +m2 and m3 +m4, respectively), the laboratory product ratio may be related tothe experimental observables by:

NTm1

(Θlab)

NTm3

(Θlab)=

NT,+m1

(Θlab)

NT,+m3 (Θlab)

×ηm3

ηm1

, (1.15)

where NTmi(Θlab) is the total neutral TOF signal for a given laboratory angle from Eq. (1.11)

and NT,+mi

(Θlab) is the total ion TOF signal from Eq. (1.13). The right side of Eq. (1.15) isnormalized by the photoproduct-dependent components of ηAn

to yield the ratio of neutralphotofragments at a given laboratory scattering angle. Equation (1.15) is thus related to theCM translational energy distributions by:

NTm1

(Θlab)

NTm3

(Θlab)= R× m1m4

m2m3

×∫

PA(ET , θ)v1

u1dv1∫

PB(ET , θ)v3

u3dv3

, (1.16)

where R is the product channel branching ratio. The ratio of integrals evaluates which CMtranslational energies will contribute to a given laboratory frame velocity and thus appear inthe TOF spectrum. A BR calculation using Eqs. (1.15) and (1.16) may be found in Chapter6; the corresponding computer code to perform the calculation may be found in AppendixC.

As will be discussed in Chapter 3 a photoproduct may further fragment upon ionization,making it possible that both m1 and m3 will be observable in the same time-of-flight spec-trum. For this case, multiple P(ET) will contribute to the observed TOF and the branchingratio may be expressed as the relative weight of the translational energy distributions usedin the TOF simulations discussed above. An example of this branching ratio calculation maybe found in Chapter 4.

1.4 Systems DiscussedThe particular radical systems discussed in this thesis are the phenyl radical (c-C6H5) and

the methyl perthiyl radical (CH3SS). While the photochemistry and decomposition pathwaysof each radical is unique, the first attempts to study these radicals were based on assumptionslater shown to be incorrect. Taken as a whole, the investigations presented herein highlightthe importance of control and repeatability in scientific investigations.

In the case of the phenyl radical, a previous investigation revealed the surprising re-sult that the ring opening was the dominant dissociation pathway.37 The work describedin Chapter 4 revealed that the observed photochemistry was dependent upon the nascent


radical internal energy, testing the assumptions presented in Sec. 1.3.1. The implicationsand consequences for radical production techniques are explored in some detail.

Chapters 5 and 6 detail two attempts to study the photodissociation dynamics of themethyl perthiyl radical. In the initial investigation, production of CH3SS was never con-firmed, however the photodissociation results were interpreted as such. A subsequent inves-tigation by a different PTS experiment found severe disagreement with the photodissociationresults of Chapter 5. The reinvestigation presented in Chapter 6 found that the assumptionof radical production in the original experiment was incorrect.

The need to have more tools to quantify radical production prompted the experimen-tal upgrade to measure the ionization energies of molecular beam constituents, discussed inChapter 3. Coincident with an investigation of the benzyl radical,38 this upgrade has dra-matically improved the confidence of experimental results. The theory, testing, and use ofthe new electron ionizer will be detailed and discussed.

13

Chapter 2

Experiment

The following section gives an overview of the primary techniques and instrumentation usedthroughout this thesis. Starting with the concepts presented in the Introduction, the exper-imental apparatus is described. Several techniques for the clean production of free radicalsare discussed.

2.1 Experimental ConsiderationsAs discussed in the Introduction, photofragment translational spectroscopy relies upon

the ability to experimentally determine the translational energies of all products after aphotodissociation. Any collisions experienced by a photofragment will destroy informationabout the photoproduct translational energy, and as the species studied are reactive radi-cals, the experiments must be done in a collision-free environment. Moreover, the ability todetermine photofragment mass must be included. In order to accurately determine producttranslational energies, the reactants must be prepared so as to all have the same initial states(i.e. internal energy and laboratory velocities). Taken together, these considerations mandatea vacuum chamber apparatus. A molecular beam can be used to prepare radicals with lowinternal energy and uniform laboratory velocity. Time-of-flight spectrometry, coupled to anionizer and quadrupole mass filter, will allow for the determination of photoproduct trans-lational energies. These requirements are satisfied by a universal crossed molecular beammachine39 modified for photofragment translational spectroscopy.25

2.2 The Crossed Beam Machine2.2.1 History

First described by Yuan T. Lee in 1969,39 the universal crossed beam machine is a remark-able piece of equipment. The second iteration, Machine B (or B Machine), is the apparatusused for the experiments described in this thesis. Originally built at the University of Chicago

CHAPTER 2: Experiment 14

in the 1970s, B Machine moved with Lee to the University of California, Berkeley. While atBerkeley, B Machine was used for a variety of experiments, from crossed beam reactions ofO(3P ) + hydrocarbons40 to infrared photodissociation of halocarbons.36

When Lee left Berkeley in 1999, B Machine was entrusted to Lee’s former graduate stu-dent (now professor) Daniel Neumark. Jason Robinson, the first Neumark group studenton B Machine, moved the apparatus from C level Giauque Hall to D level Latimer Hallwith a quick stop at Lawrence Berkeley National Laboratory for cleaning.41 By this point, BMachine had been modified to study photodissociation processes via photofragment trans-lational spectroscopy—accomplished by replacing one of the molecular beam sources with alaser. While the first Neumark group projects on B Machine studied the photochemistry ofclosed shell molecules, the machine was soon (slightly) modified to perform PTS experimentson free radicals; a role it continues to this day.

2.2.2 ApparatusB Machine itself is a large vacuum chamber approximately 1 m3 in pumped volume. The

machine is divided into two differentially pumped regions: the main (or scattering) chamberand a source chamber. A series of differentially pumped detector chambers, mounted on arotating flange, are housed inside the main chamber (see Fig. 2.1). Briefly, a gas sample isintroduced into vacuum by supersonic expansion from a piezoelectric pulsed valve housed inthe source chamber. The resulting molecular beam is collimated by two skimmers and entersthe main chamber. A slotted chopper wheel allows for beam velocity measurements. Afterthe chopper, the molecular beam is intersected by a laser beam at 90 in a volume of spacetermed the “interaction region.” Photoproducts leave the interaction region and enter thedetector, where they are ionized, mass selected, and detected.

The main chamber is box-like, with inner dimensions of 96 × 96 × 76 cm. The volume ispumped out by a 2200 L/s turbomolecular pump (TMP). A recirculating helium cryopumpattached to a copper coldhead provides additional pumping surface near the interactionregion: most gas molecules that come into contact with the ∼10 K surface will not returnto the gas phase. The top of the main chamber is dominated by a 63.5 cm diameter roundflange that supports the detector. The detector flange can rotate while maintaining vacuumin the main chamber via two spring loaded graphite/PFTE gaskets evacuated by a separateroughing pump. With all of these systems running, typical pressures in the main chamberare 2–5 ×10−7 torr.

The source chamber consists of a 10” ASA Tee chamber and a portion of the main chamberisolated by a removable stainless steel enclosure. The former supports another 2200 L/s TMPused to evacuate gas from the source chamber while the latter houses the mount for a gasvalve. Without a molecular beam, the source chamber may reach pressures of ∼ 5 × 10−8

torr. Typical operating pressures with a molecular beam are around 10−5 torr; the exactpressure will depend on the repetition rate of the pulsed valve and system studied.

The detector is the pride and joy (and terror) of B Machine. The detector consists ofthree, nested, differentially pumped chambers. Each chamber is evacuated by a ∼400 L/s


RIII

trigger input

gas inlet Θlab

electron ionizer

quadrupole

ion detector

copper cooling block

pulsed valve

source

chamber

main

chamber

RI

RII

hν

Figure 2.1: Schematic of B Machine as used for the experiments described in this thesis.

TMP and these pumps are, in turn, backed by a fourth 400 L/s TMP prior to the roughingpump. The first chamber (Region I, RI) interfaces to the main chamber via a small aperture;typical operating pressures are ≤ 10−10 torr. Region II (RII) houses a quadrupole mass filterand the ion detector; typical operating pressures are ≤ 10−12 torr. The third chamber, RegionIII (RIII), is nested in Region II between Region I and the quadrupole. Region III housesthe ionizer and the walls of Region III are filled with liquid nitrogen to increase the pumpingsurface; typical operating pressures are ≤ 5 × 10−11 torr. The ultrahigh vacuum conditions(terror) mean that background gases have minimal contributions to acquired data (pride andjoy).

Species entering the detector are ionized via electron ionization, a process discussedmore thoroughly in Chapter 3. Cations are extracted from the ionizer and passed into aquadrupole mass filter which selects ions of a specific mass-to-charge ratio (m/z). Each endof the quadrupole has a short length of electrically isolated rods forming a “trifilter” (with themisnomers “front trifilter” and “rear trifilter” to denote the first and last sections) designedto minimize fringe field effects and ensure ion transmission into and out of the quadrupole.Mass selected cations leave the quadrupole and are accelerated towards a −30 kV metal plate(the “doorknob,” shown in Fig. 2.2). As the cations strike the doorknob, secondary electronsare ejected from the surface and accelerated away from the doorknob to a scintillator andphotomultiplier tube (PMT). Output from the PMT is passed through a discriminator andlevel adapter, producing TTL pulses. These TTL pulses are then recorded by a multichannel


scaler (MCS) as a function of time since the laser interacted with the molecular beam. Acomputer program periodically records the time and intensity information and stores thesedata.42 Repeating this process approximately 106 times results in a time-of-flight (TOF)spectrum. These TOF spectra are used to determine the center-of-mass translational energydistributions using the relationships described in Chapter 1.

2.2.3 LasersThe ultraviolet photon sources for B Machine are excimer lasers: a GAM EX100/500

and a Lambda Physik LPX 220i. Excimer (or exciplex) lasers use a high voltage electricdischarge to produce an excited state complex of fluorine and a rare gas atom. This “exciteddimer” is weakly bound on the electronic excited state and repulsive on the electronic groundstate. Spontaneous emission starts laser action and all excimers decay to produce a pulseof ultraviolet light. The photon energy may be tuned by choice of rare gas or halogen; amixture of Ar and F2 produces light at 193 nm while Xe and Cl2 are used to make 308 nm.As a consequence of using a gas as the lasing medium, excimer lasers produce unpolarized,incoherent light. Polarization of the excimer laser light is achieved by a stack of eight quartzplates held at the Brewster angle. This stack is then placed in a rotating mount at the laserbeam entrance to the vacuum chamber. Thus, the electric field may be rotated relative tothe plane defined by the laser and molecular beams.

2.2.4 AlignmentSince the photodissociation processes studied on B Machine involve neutral molecules,

the molecular beam, laser beam, and detector must all be carefully aligned to each other.For the molecular and laser beams, grooves were cut into the sides of the apparatus aroundeach flange. By running thread through opposing grooves, crosshairs are set up on oppositesides of the machine, defining one of the principal axes. A level scope is placed on one sideof the apparatus and aligned to the crosshairs. Thus, an object (e.g. the pulsed vale) maybe brought into alignment at any point within the machine.

Similarly, the ionizer may be aligned by replacing the quadrupole and ion detector housingwith a window. Regions I–III may then be evacuated and the cryogen cooling reapplied toRegion III. Adjustment of the Region III position in Region II will bring the ionizer intoposition as determined by the crosshairs. During an experiment, the scattering angle selectedby matching angle demarkations on the rotating flange to an aligned and known Θlab = 0

position.

2.2.5 Machine ParametersThe laboratory frame velocity of the reactant vlab, vR in Eq. (1.13), must be known

to determine the translational energy distribution. The molecular beam velocity may be


PV

laser

point of

ionization

doorknob

quadrupole

PMT

e-

rate ÷ 2

L'

L

user delay

laser

MCS

TOF

rotating chopper

wheel ( )

photo-

diode

( )

user delay ( ) rate ÷ 2

user delay user delay

Figure 2.2: Schematic of the trigger system and temporal contributions to measured TOF onB Machine: PV is the pulsed valve, PMT is the photomultiplier tube, MCS is the multichannelscalar, and TOF is the resulting time-of-flight spectrum.

determined by acquiring a TOF spectrum of a known m/z value at Θlab = 0; the neutralflight time (ttrue) is related to the velocity by a known neutral flight length (L′):

ttrue =L′

vlab. (2.1)

However, to accurately determine the velocity, timing contributions from the apparatus mustbe removed from the measured flight time tmeas to acquire the true flight time. As such, thefollowing discussion focuses on obtaining accurate ttrue and L′.

To facilitate laboratory velocity measurements, a slotted chopper wheel is inserted intothe molecular beam at a fixed distance from the ionizer (L′, see Fig. 2.2). A photodiodepair measures when a chopper slot is 90 off of the molecular beam. As there are four slotsseparated by 90, this photodiode produces a trigger signal every time a slot is aligned withthe molecular beam. Since the photodiode does not respond instantaneously and there arephysical variations in the chopper wheel slots, the chopper wheel/photodiode setup intro-duces two timing paramenters: an electronic offset (E) and a mechanical offset (M). Whilethese offsets would account for the flight time of the neutral molecule, Fig. 2.2 suggests thatthe ion flight time through the detector must also be considered. For ions with a given kineticenergy, the ion’s velocity (and thus flight time) will be related to the mass of the ion. Taking


these considerations together, contributions to the measured flight times may be written as:

tmeas = ttrue + αion√m+ E ±M, (2.2)

where m is the mass-to-charge (m/z) value of the ion detected and the ion flight constastαion provides the relationship between ion kinetic energy and ion flight time.

The last term in Eq. (2.2) deals with the chopper wheel. The mechanical offset accountsfor any misalignments between the chopper wheel slots, the photodiode, and the detectoraperture. M is easily determined by recording tmeas while spinning the chopper wheel clock-wise and counter-clockwise. M is half the difference between these two time values andthe sign of M is determined by which direction the wheel spins during an experiment. Thecurrent chopper wheel has a measured M = 7.4 µs.

The electronic offset has two components to correct for the difference between when thephotodiode is triggered and when a chopper wheel slot is centered on the molecular beam.The first factor in E stems from the physical widths of the chopper slots; the rising edge ofthe trigger signal is a few µs off of the center of the chopper slot. A delay generator (see Fig.2.2) allows the user to overlap the photodiode pulse with the trigger for the MCS, reducingthis E contribution to zero. A second component to E comes from the transformation ofthe photodiode pulse into a usable TTL pulse. The model photodiode pair used has a built inamplifier with a propagation delay time of 5.0 µs.43 Thus, the electronic offset for B Machineis 5.0 µs.

To determine αion, a molecule with distinct dissociative ionization features (see Chapter3 for further discussion) spanning the mass range of the quadrupole is entrained in themolecular beam. Since all m/z values were originally from the same molecule in the beam—and thus moving at the same velocity—any m/z dependent differences in the value of tmeasare due to ions in the detector. A linear regression of tmeas versus

√m thus yields αion as

the slope of the line. For B Machine, typical values of αion range from 5 to 7 µs · amu−1/2

depending on the ion energy.To determine the flight length L′, tmeas for several neat rare gas beams must be measured.

For the expansion of a rare gas, the flow velocity v∞ is related to the enthalpy by:29

v∞ =

√5kBT

m, (2.3)

where kB is Boltzmann’s constant, T is the nozzle temperature, and m is the mass of the raregas used. After accounting for αion, a linear regression of tmeas versus

√m contains L′ in the

slope. The previous value of L′ on B Machine was 22.8 cm. However, with the installation ofa new ionizer (see Sec. 3.2), a new flight length of 22.1 cm was measured. As shown in Fig.2.2 photofragments generated by the laser have a flight length L, determined by subtractingthe distance between the chopper wheel and the interaction region from L′; this value is 2cm, resulting in a photofragment flight length L = 20.1 cm.

The above discussion is based upon an ideal molecular beam that has one velocity. Whilemolecular beams do have an exceptionally narrow velocity spread (compared to a Boltzmann


distribution), there is some spread in the velocities. As photodissociation can occur from amolecule with any one of those velocities, the velocity spread must be determined. DouglasKrajnovich’s thesis36 spends some time on this subject. In short, a TOF spectrum at Θlab =0 is fit42 to the following equation:

N(vlab) ∝ v2lab exp

[−S2

(vlab − V

V

)2]

, (2.4)

where N(vlab) is the velocity dependent number density in the beam, vlab is the beamvelocity, V is the flow velocity, and S is the speed ratio (flow velocity divided by the spreadin velocities). The velocity from Eq. (2.4) may be used for vR in Eq. (1.13), allowing the TOFspectra to be used to determine the photodissociation dynamics via the process discussed inSec. 1.3.1.

2.3 Radical Production2.3.1 General Considerations

While the photodissociation of closed shell species is not trivial, investigating open shellradicals adds another layer of difficulty to the experiment. As highly reactive species, radicalsmust be made in the gas phase and cannot collide with a reactive parter prior to their arrivalat the interaction region. Having uniform velocity in the direction of beam propagationmakes molecular beams attractive for radical study, as any radicals entrained in the beamwill not undergo any collisions. Molecular beams are principally composed of a rare gas sosufficiently low concentrations of radicals will only have non-reactive collisions during theexpansion. What this implies, however, is that radicals must be created just prior to or duringthe expansion. Radicals must also be produced from a precursor molecule at sufficiently lowconcentration (i.e. ≤ 1%) so as to minimize reactive (e.g. radical-radical) collisions.

In general, a radical is produced by dissociating a suitable precursor, such as a moleculewith one weak bond. Typical examples include the C–X bond of halocarbons; nitro (RNO2)or nitroso (RNO) compounds; or molecules that, upon dissociation, form one or more sta-bilized products, such as acetone dissociation into CO + 2CH3.44 Dissociation is usuallyinduced via a photon, a high voltage electric discharge, or flash pyrolysis.

2.3.2 PhotolysisFormation of a radical via photon initiated dissociation of a radical precursor will be

termed “photolysis” to avoid confusion with the radical photodissociation experiment. Es-sentially, a second laser is used in the experiment to photodissociate the precursor moleculeand produce the radical. The steel insert that separates the main and source chambers of BMachine has windows to allow for this configuration. The photolysis laser is focused either in


the expansion45 or in a quartz tube attached to the end of the pulsed valve. The radical inter-nal energy is then immediately quenched by the expansion and, ideally, remain entrained inthe molecular beam. If the carrier gas contains a specific reactive partner (e.g. O2), radicalsformed by photolysis may react to form new species, such as peroxy (CnH2n+1O2) radicalsor Criegee intermediates (CnH2nO2).

Photolysis is an extremely attractive means of producing a radical. Halocarbons, for ex-ample, are readily available from commercial sources and often have a dissociative electronicexcited state in the UV (e.g. Ref. [46]), selectively producing the radical of choice. Addition-ally, by running the photolysis laser every other molecular beam pulse and photodissociatingevery pulse, photodissociation of the precursor molecule can be subtracted from the total sig-nal. This subtraction can be aided by careful selection of precursor, such that the precursorand radical absorption spectra do not overlap.

While photolysis has been successfully used on B Machine,45 it is not without problems.Precursors that have overlapping absorption bands with the radical can present large back-ground signals for subtraction, resulting in TOF spectra with high noise. Photolysis in theexpansion may not entrain sufficient numbers of the radicals, especially if the counter frag-ment is heavy compared to the radical (as is the case for halocarbons). While a quartz tubemay ameliorate this last problem, the tubes reduce the number of photons actually interact-ing with the gas. Finally, as the photolysis laser is typically a nanosecond laser, only a smallfraction of the gas pulse has been photolyzed. This small portion of the pulse must thenbe hit a second time with the photodissociation laser, an experimentally challenging featas the radicals are typically difficult to observe due to precursor dissociative ionization (seeChapter 3). For these reasons, photolysis is not usually employed on B Machine to produceradicals.

2.3.3 Electric DischargeHigh voltage electric discharge sources are near and dear to the Neumark group’s heart.

Many projects in the group use these sources to generate anions which, after photodetachingthe extra electron, are a convenient source of mass selectable species of interest.47 As dis-charge sources will also produce cations and neutrals, the molecular beam could be passedthrough ion optics to remove ions, leaving a neutral radical beam for photodissociation.

In general, two isolated electrodes are placed on the end of the pulsed gas source. Dis-charge is achieved by either continuously holding a large potential difference (the “DC”method) or pulsing a high potential difference (for a user-selectable duration and delay,pulsed method) across the electrodes. In both methods, the discharge will occur when thegas pressure between the electrodes has increased enough to allow electrical breakdown. Theformer method will undergo breakdown every pulse while the latter method allows for sub-traction of precursor photodissociation by limiting the discharge to alternating gas pulses.For either method, the discharge would ideally excite the precursor and cause dissociationof the weakest bond just prior to supersonic expansion.


SiC tube

Mo electrodes

alumina spacers

steel spacer

cooled Cu spacer

mounting flange

heat shield

cooling water

gas inlet

trigger input

1

2

3

4

5

6

7

8

9

10

power

supply

1

3

2

345

6

788

9

10

Figure 2.3: Schematic of the flash pyrolysis source.

As discussed in Bogdan Negru’s thesis,48 several discharge sources were tried on B Ma-chine. Many designs, including those used in the Neumark group49 or the Endo group,50 wereattempted using both the DC and pulsed methods. Unfortunately, the designed dischargesources were at best an inconsistent success. It was ultimately decided that without the massselection capabilities afforded by ionization, the discharge source was not well suited to BMachine.

2.3.4 Flash PyrolysisFor nearly the past decade, pyrolysis has been the primary tool for producing radicals

on B Machine. While the dynamics in a pyrolysis source are quite complex,51 the principlesmay first be understood via thermal decomposition. For a thermally equilibrated molecule,every vibrational mode will have kBT of energy, where kB is the Boltzmann constant. Withn vibrational modes, the total energy of the molecule is E = nkBT . In a statistical picture,20energy will be randomly distributed throughout all of the oscillators in a molecule. Bondcleavage will thus occur once sufficient energy has accumulated in a bond to overcome theactivation energy Ea. Complete dissociation will occur for T ≫ Ea/nkB. For suitable radicalprecursors with one weak bond, the weakened bond will dissociate first leaving at least tworadicals. With careful selection of precursor, one of these radicals will be of interest (e.g. thephenyl radical) while the other will be a spectator in the photochemistry experiment (e.g.NO).

In contrast to both photolysis or electric discharge sources, pyrolysis sources are a meansof continuously producing radicals. As with many groups that use pyrolysis, the source designis modeled after the work of Peter Chen.52,53 A resistively heated silicon carbide (SiC) tube


40 50 60 70 80 90 100 1100

2

4

6

8

m/z

10

4 C

ounts

Pyrolysis Source OffPyrolysis Source On

Figure 2.4: Example mass spectra showing pyrolysis off (black trace) and on (red trace). Theprecursor parent mass at m/z = 107 is fully depleted, and the resulting radical signal at m/z= 77 is one of the dominant components in the molecular beam. A contaminant at m/z = 78is also present, though was not in sufficient quantities to affect the photodissociation results(see Chapter 4).

is placed at the end of the gas valve. Precursor molecules in the gas mixture are thus heateduntil thermolysis occurs, then promptly cooled by supersonic expansion into vacuum.30 Thepyrolysis tube length is short (e.g. 1.5 cm) so that gas residence time in the tube is kept toa few 10s of µs. As a consequence of the short residence time, radicals formed do not havea chance to encounter a reactive partner. These flash pyrolysis sources may be used witheither pulsed or continuous gas beams, increasing their versatility compared to photolysisor electric discharge. A more complete description of the theory behind these flash pyrolysissources may be found in Ref. [51].

Figure 2.3 shows a schematic of the flash pyrolysis source used on B Machine. The SiCtube is held between two molybdenum electrodes and electrically isolated by alumina spacers.A stainless steel and a water-cooled copper spacer sit between the alumina and a small flangeat the end of the pulsed valve. A more detailed drawing of the source may be found in BogdanNegru’s thesis.48 An aluminum and copper heat shield around the electrodes and additionalwater cooling on the pulsed valve mount were recently added, yielding dramatic increases inpulsed valve stability.

Operation of the pyrolysis source is relatively simple. The detector is rotated to Θlab =0 and a m/z value exclusively attributable to the precursor is monitored. An external powersupply is used to regulate the power dissipated by the SiC tube; power is increased whilemonitoring depletion of the precursor. Any remaining m/z values will be due to precursordecomposition products, ideally the radical of choice as shown in Fig. 2.4. Photodissociationof the precursor may also be used to monitor depletion, especially if the on-axis precursorsignal is low.

23

Chapter 3

Tunable Energy Electron Ionization

3.1 Electron IonizationFirst described in 1921,54 electron ionization (EI)—or electron impact ionization or

electron bombardment ionization—is a technique whereby atoms or molecules are ionizedthrough interactions with high kinetic energy electrons. An extremely versatile technique,EI is widely used in the mass spectrometry community as a “universal” ionization source.55Generally, a hot tungsten or iridium filament is resistively heated, resulting in thermionicemission of electrons. By placing the filament in an electric field, the electrons can be acceler-ated to a desired energy, typically around 100 eV. As these electrons interact with neutrals,secondary electrons and cations are produced. The latter are then extracted and may beused as desired.

ABC + e− → ABC+ + 2e−

By utilizing electrons with energies far above the ionization energy of most any species, EIis a “universal” detection method. The ionization cross section for most species is typicallymaximized around 100 eV, with small variations in electron energy having minimal effectson the cross section.56 From an operational standpoint, the ionizers are small and requireonly a few power supplies to operate. The use of EI on B Machine is especially important,as the ionization of all photoproducts is desired. The rotating detector geometry would alsomake other ionization methods (namely photoionization) difficult to perform.

Use of EI is not without drawbacks. While the method will ionize any molecule, the largeenergy excess will often partition into other molecular degrees of freedom, typically resultingin dissociation. This “dissociative ionization” (DI) results in daughter ions at smaller m/z

CHAPTER 3: Tunable Energy Electron Ionization 24

power

supply

grid

extraction

focus

+

linear filament

Figure 3.1: Schematic of a Brink-type ionizer. Electrons generated from the filament areaccelerated to the grid. Ions generated are removed by the extractor and passed into thequadrupole.

values than the parent mass, resulting in spectral congestion (as seen in Fig. 2.4).

ABC + e− → ABC+ + 2e−

→ AB+ + C + 2e−

→ A+ + BC + 2e−

→ AC+ + B + 2e−

...

Fortunately, DI fragmentation patterns are quite reproducible, and since these patternsdepend on both stoichiometry and structure, DI thus becomes a powerful tool for speciesidentification.55 As will be discussed in the following chapters, DI can be used to deter-mine photodissociation product channel branching ratios—an extremely important part ofa molecule’s photochemistry. The main detraction of DI is the spectral congestion due todaughter ions. When a molecule will produce multiple m/z values, determining which m/zis due to the parent ion can be difficult, especially for cases when the parent ion has littleor no signal. Dissociative ionization is thus particularly troublesome for determining radicalproduction. As the precursor molecules typically have one weak bond, the radical m/z valueis often present (and, in some cases, dominant) with the radical source both off and on. Thislast consideration has driven the recent upgrade of B Machine to include an ionizer thatallows for tunable electron kinetic energies.

Although EI is primarily performed with ∼100 eV electrons, any electron energy abovethe ionization energy of the target molecule may be used and a variety of possible experimentsbecome available. With control over the electron energy, ionization energies may be measured,


(a) Picture

ring filament

ion region

extractor

lenses 1–3

(Einzel lens)+

(b) Axial Schematic

Figure 3.2: The axial ionizer.

providing another tool for determining radical production. Reducing the electron energy willreduce DI, allowing for parent molecular ions to be more easily distinguished. Reducedelectron energies may also help limit background gas ionization and improve the signal-to-noise ratio during TOF measurements.57 Because of the possible advantages, in Septemberof 2014 the Brink-type ionizer in B Machine was replaced with an Extrel Axial MolecularBeam Ionizer designed for use with tunable energy electrons.33,58

3.2 New Ionizer3.2.1 Overview

The geometry of the axial ionizer is fairly different from the Brink-type ionizer dia-grammed in Fig. 3.1. As diagrammed in Fig. 3.2, the axial ionizer filament runs perpendic-ular to the neutral/ion flight path and the volume in which ionization may occur is shorter.As with the Brink-type ionizer, though, the filament is biased negative with respect to the“grid” (the ion region, IR) and electrons produced by the filament are accelerated towardsthe IR. To a first approximation, this “filament bias” will be the resulting electron energy.Ions formed in the IR are extracted, focused by an Einzel lens, and pass out of the ionizertowards the quadrupole.

As mentioned in Sec. 2.2.5, the neutral photofragment flight length is the distance betweenthe interaction region and the center of the IR. While the total length of the previous andnew ionizer set-ups is approximately the same, the axial ionizer IR is substantially shorter(1 cm compared to the previous 3.1 cm). As such, a new flight length had to be calculatedand was found to be 0.7 cm shorter—a reasonable change given the difference in ionizergeometry.

In addition to a new ionizer, the Merlin 3500 quadrupole computer was replaced withthe new Merlin 5221. The new Merlin includes computer-controlled power supplies for each


Ion Region

Supply

Filament Bias

Supply

Filament Power

Supply

ion region

ring filament

Figure 3.3: Schematic cross-sectional view of filament and ion region. An example powersupply configuration is shown to demonstrate the general mechanism for biasing of ion optics.

ion optic in the ionizer which replace the stand alone manual units used previously. Alongwith the addition of a new MCS and data acquisition software,42 the new Merlin completedthe transition to a new data acquisition computer. While the complete upgrade has been animprovement, the new Merlin has some disadvantages as discussed in a later section.

3.2.2 FilamentThe filament in the axial ionizer consists of four thoriated iridium wires connected in a

loop perpendicular to the central axis. The filaments in B Machine are currently wired in a4-series-parallel configuration: two filaments are run in series with the two resulting pairs inparallel.59 Power, controlled and regulated by the Merlin 5221, is dissipated by the filamentas heat and electron emission. The “filament current” and “filament voltage” are defined asthe current passed through and potential drop across the filament wire itself. For B Machine,typical filament currents are 3–6 A while filament voltages are approximately 5V.

Thermionic emission of electrons would normally result in a Boltzmann distribution ofelectron kinetic energies. In EI, the filament is held at a negative potential (the “filamentbias”) with respect to the grid so that electrons generated from the filament are acceleratedtowards the IR with known energy: Eelec = IR potential − filament bias.

The emission current (Iem, the number of electrons emitted) can be regulated by adjustingthe power dissipated by the filament. Emission of electrons from the filament, however, alsodepends upon the filament bias. The work function of the filament decreases with increasingfilament bias and more electrons are emitted for a given power. In other words, a decrease inelectron energy results in a decrease in emission current for a given filament power. Decreasedemission current means fewer ions produced in the IR. This reduction is compounded by thefact that EI cross sections decrease with decreasing electron energy. Unfortunately, arbitraryemission currents are not possible. Care must be taken to prevent the filament from “burningout” by attempting to dissipate too much power. The Merlin 5221 has safeguards in place


to prevent such an occurrence and Extrel has published safe, maximum emission currents asa function of electron energy.58

3.2.3 Ion OpticsAfter selecting a filament bias and emission current, the remaining ion optics must be

optimized. The goal of optimization is to achieve a stable tune, where small changes in opticpotential will have little to no effect on the ion trajectories.58 Practically, several ion signalsshould be monitored as a function of ion optic potential. Stable potentials will show smallintensity changes while unstable potentials may have different effects for different m/z values.While this may raise concerns about DI pattern reproducibility, it seems that stable tuneswill result in mass spectra that match literature DI patterns.

During an optimization of the ion optics, it is important to be observing the molecularbeam as ionization efficiency is dependent upon neutral velocity.32 A simple choice would be amolecule (or several) with m/z values that span the mass range and include both parent m/zvalues as well as DI. While DI will be reduced at low electron energies, suitable calibrantswill still undergo some DI. The optimum tune has been found to vary little for Eelec ≲ 20eV, sufficient energy to expect some DI features.

In general, optimization is performed by adjusting the bias on each optic in order of ionpath through the ionizer.33 Several stable tune profiles may exist, so initial exploration ofthe possible configurations is important. Optimization of the optics may need to be iteratedseveral times to find the highest signal without sacrificing stability. Conventionally, the IR isbiased positive with respect to ground and all other optics are referenced to the ion region.The following discussion will follow that convention unless otherwise noted.

The first optics to be set will be the IR and pole bias as the difference in potentialbetween these optics defines the ion energy. Ion energies in the low 10s of eV seem to beappropriate for B Machine; a 14 eV ion energy is currently used for low electron energytunes. The extractor, the next optic, is responsible for helping to remove cations from theIR. Typical extractor potentials are approximately the opposite potential of the IR (−VIR),though the exact value may vary. The extractor potential may need to be increased withincreasing emission current, as discussed in Sec. 3.4.

The next three optics form an einzel lens, responsible for focusing the ions into thequadrupole.60 The lens consists of two controllable potentials: lens 1&3 and lens 2. Thesetwo potentials should be iteratively adjusted to find the optimum prior to the next optics.Typical values are around −150V and −300V for lenses 1&3 and 2, respectively. The optimalsettings for the einzel lens do not seem to change significantly for large changes in Eelec.

A standard instrument would have adjustable quadrupole entrance and exit lenses, how-ever the detector housing in B Machine was designed such that these lenses are at groundpotential. The roles of the entrance and exit lenses are mostly filled by independently biasingthe front and rear trifilters (see Sec. 2.2.2). Lack of entrance and exit lens flexibility does,however, introduce an added constraint as discussed in Sec. 3.4. Ion signal is particularlysensitive to the potential of the front trifilter. While the highest signal seems to be at ap-


proximately −VIR, this region is relatively unstable. Stability may be found over a broaderpotential range around −2VIR. The rear trifilter has little effect on ion signal; large, negativepotentials are routine.

Once all of the optics have been tuned, the new mass spectrum should be comparedto a spectrum taken previously or to a literature spectrum. If the ion energy was changed(e.g. changing the pole bias without adjusting the ion region), a new value of αion should bedetermined (see Sec. 2.2.5).

3.3 Electron EnergyWhile the electron energy is defined as the difference between the filament bias and IR

potential (Eelec = filament bias − IR potential), there are a few factors that influence theactual energy, the foremost being the filament voltage. Since electrons may be ejected atany point along the filament, the location of an electron’s birth will alter the potential itexperiences. For large electron energies (e.g. ∼100 eV), this effect is negligible as the filamentvoltage is small compared to the filament bias and, at these energies, ionization cross sectionsare relatively constant. However, at low electron energies, this effect can be quite pronounced.While the average electron energy will be correct, there will be a comparatively large spreadin energies. To minimize this spread, the emission current must be reduced to the minimumneeded to perform the experiment, as a reduction in power dissipated by the filament willreduce the filament voltage. Charge density in the IR will also have an influence on theelectron energy, but this effect seems to be negligible compared to the filament voltage.From a user’s perspective, the commands to the Merlin 5221 that set the filament bias andIR potential result in actual potentials ∼1V closer to ground.

The electron energy may be calibrated by measuring the ionization energy of knownspecies, such as the rare gases. In these experiments, signal intensity is measured as a functionof electron energy, producing an ionization efficiency curve (IEC, see Fig. 3.4). For a oneelectron process, the appearance energy may be determined by least-squares fit to the linearportion of the IEC and extrapolating to zero intensity. The measured appearance energy maythen be compared to the literature value to determine an offset between measured electronenergy and actual electron energy. A linear extrapolation is used as IEC measured via EIhave a small, nonlinear tail due in part to the inherent spread in electron energies from ahot filament.

3.4 Cautions, Caveats, and ConstraintsUnfortunately, there are some additional caveats and constraints to the above discussion.

Some of the following discussion is true of the ionizer geometry or configuration of the BMachine detector. Other constraints are due to the Merlin 5221 itself.


15 20 25 30 350

2

4

6

8

10

Electron Energy (eV)

10

5 C

ou

nts

KrArNeHe

15 18 21 2421

24

27

30

33

True I.P. (eV)

Measure

d I.P

. (e

V)

Regression:slope = 1.01 ± 0.05int. = 8.1 ± 1.0

Figure 3.4: Corrected IEC of rare gases He, Ne, Ar, and Kr. The average offset from all fourmeasurements was used to correct the measured values; the resulting correction was foundto be sufficient as shown in the inset.

3.4.1 TOF Dependence on Iem

Within the bounds of safe operation of the filament, large values of Iem may not berecommended for applications where electron energy accuracy is needed or when timinginformation is critical. For applications based on timings, such as the TOF experimentsdescribed in this thesis, the emission current will have an effect on the shape and locationof an observed TOF feature. Two examples of TOF data are shown in Fig. 3.5, where theblack curve is a forward convolution simulation from the same P(ET). The higher emissioncurrent clearly has more intensity at longer flight times, in addition to a substantially lowersignal-to-noise ratio.

This effect of emission current on TOF features can be justified by considering the chargein the ion region due to the electrons.33 For the current ionizer geometry, 100 eV electronsmay spend a few nanoseconds in the IR before hitting the grid. For lower emission currents,e.g. ≤ 2 mA, this results in approximately 107 electrons in the IR, or an average chargedensity of ca. −10−5 C/m3. If one assumes homogeneous charge distribution in a cylinder(the shape of the IR), the radial potential in the IR has a parabolic shape:

|V (r)− Vaxis| ∝|ρ|ϵ

r2 (3.1)

where Vaxis is the axial potential of the IR, r is the distance from the axis, ρ is the averagecharge density, and ϵ is the permittivity of free space. Equation (3.1) implies that, for largeelectron emission currents, the axis of the IR can be O(10V) more negative than the edgeof the cylinder (the grid, one of the optics that determines the electron kinetic energy).


0 100 200

0

50

100

150

Time of Flight (µs)

Co

un

ts

0 100 200 300

Iem

= 4 mA

300k shots

Iem

= 8 mA

500k shots

Figure 3.5: Example TOF with two different emission currents and otherwise identical con-ditions. The emission current and number of laser shots is noted in each spectrum. The blackcurve is a forward convolution simulation from the same P(ET), highlighting the additionalsignal at longer flight times using 8 mA.

If the extractor potential is also O(10V) negative with respect to the IR then it becomesapparent that excess negative charge in the IR will retard ion extraction. Indeed, if no opticsare adjusted, increasing Iem will eventually lead to a decrease in observed signal. This effectis observable in the TOF spectra shown in Fig. 3.5, where doubling the emission currenthas a reduction in ion signal per laser shot. While ion signal intensity may be recovered byincreasing the magnitude of the extractor potential, the effect on signal timing will remain.In general, emission currents of 4 mA (∼100 eV electrons) or 1 mA (≤ 20 eV electrons) arereasonable values for accurate TOF spectra on B Machine.

3.4.2 IEC Dependence on Iem

For cases where accurate Eelec are desired, such as IEC measurements, the emission cur-rent may produce severe distortions in the measured appearance energy. When the ionizerwas first installed—before the Merlin 5221—the optics were operated using manually con-trolled, stand alone power supplies. Accurate IEC measurements could be performed with upto 0.5 mA of emission current. With the Merlin 5221, however, emission currents of ≤0.13mA are needed to accurately measure appearance energies below ∼10 eV. The IEC in Fig.3.6 demonstrate the dependence of the measured appearance energy on the filament emissioncurrent. As the figure shows, even Iem = 0.195 mA results in a slightly high measurement ofthe acetone ionization energy. Currently, Extrel has no explanation for this behavior; theirrecommendation for appearance energy measurements are for Iem = 0.5 mA. It should alsobe noted that there is a large discrepancy (∼0.125 mA) between the Merlin 5221 “em_cmd”and the measured emission current. To achieve a measured 0.13 mA, an em_cmd = 0.01mA must be used. Again, Extrel has no explanation for this behavior.


6 8 10 12 14 16 180

0.2

0.4

0.6

0.8

1


Norm

aliz

ed Inte

nsity

m/z = 58, Iem

= 0.3 mA

m/z = 58, Iem

= 0.195 mA

m/z = 28, Iem

= 0.3 mA

m/z = 28, Iem

= 0.195 mA

Figure 3.6: IEC of acetone (m/z = 58, IE = 9.703 eV) and molecular nitrogen (m/z = 28,IE = 15.581 eV) with an emission current of 0.3 mA (red) and 0.195 mA (black).

Emission currents this small make for extremely difficult experiments on radicals; indi-vidual points on an IEC must be acquired for longer times to produce curves of reasonablequality (see Appendix C). It is unclear whether this effect is due to filament voltage, space-charge effects, or some other aspect of the ionizer or Merlin 5221. It is known that the4-parallel configuration,59 where all four filaments are connected in parallel, is best suitedto low IE studies. A possible solution would be to rewire the ionizer to allow for selection ofeither configuration outside of vacuum.

3.4.3 Ion Optic BiasThe Merlin 5221 filament bias setting cannot be arbitrarily chosen while maintaining

electron emission, even for cases of “safe” electron energies. For example, the ion regionand filament bias—with respect to ground—cannot be set to +80V and 0V, respectively,despite the resulting electron energy of 80 eV. This forces the ion region to be held at asmall potential above ground so that the filament bias may be accordingly set to achieve lowelectron energies while still biased negative with respect to ground. The functional limitsare filament bias ≳ 3V while still maintaining emission and IR ≳ 4V while still maintainingsignal. Extrel does have an explanation for this behavior, though it is rather unsatisfactorilytied to the design of the power supplies in the Merlin 5221.

Given no other constraints, the limitation on the filament bias would be a minor im-pediment as the rest of the system could be floated arbitrarily with respect to ground. Asmentioned in Sec. 3.2.3, though, the entrance and exit lenses to the quadrupole are fixed atground potential. Taken together, these limitations force the user to have a subset of configu-rations over which the tune may be optimized. In the short term, stand-alone power suppliesmay be used for experiments requiring tune conditions not currently allowed by the Merlin.


C

CH2

ONO CH2•

•

+

+

+ H

CH3

∆

∆Ho = 39.4 kcal/mol

∆Ho = 80 kcal/mol

∆Ho = 91 kcal/mol

∆Ho = 66 kcal/mol

NO

CH2O+

Figure 3.7: 2-phenylethyl nitrite was used to pyrolytically generate the benzyl radical.61Three example benzyl decomposition channels are also shown.62,63

In the long term, the entrance and exit lenses should be redesigned to allow for independentcontrol of the bias. This latter option may alleviate some of the signal level issues due to thelow filament bias and low electron energies needed to achieve accurate appearance energies.

3.5 ImplementationDespite the problems discussed in the previous section, the addition of tunable energy

EI to B Machine has been a welcome change. The following section will detail some of thetechniques available in the context of actual experiments. Since the new ionizer was installedduring a study of the benzyl radical, much of the initial exploration of the ionizer’s capabil-ities were tested with this system.* Details of the benzyl radical photochemistry experimentmay be found in Ref. [38]; Fig. 3.7 outlines the production and possible decomposition prod-ucts of the benzyl radical.

3.5.1 Radical CharacterizationThe most significant advantage of the new ionizer has been the ability to characterize the

molecular beam in more detail, namely by reduction of dissociative ionization and measuringthe appearance energy of molecular beam constituents. These tools are particularly relevantfor determining radical production from a precursor molecule. With new tools, radical pre-cursors can be evaluated more rapidly and with greater confidence. The following will discussboth methods for characterization of the molecular beam in the context of pyrolysis.

For some molecules, dissociative ionization in an EI setup results in a weak or completelack of the parent molecular ion (e.g. 1-butanol). As radical precursors usually feature a

*Reproduced in part with permission from Shapero, M.; Cole-Filipiak, N. C.; Haibach-Morris, C.; Neu-mark, D. M. Benzyl Radical Photodissociation Dynamics at 248 nm. J. Phys. Chem. A., 2015, ASAP.Copyright 2015 American Chemical Society.

http://dx.doi.org/10.1021/acs.jpca.5b07125



40 60 80 100 120 140 1600

0.2

0.4

0.6

0.8

1

m/z

Rela

tive Inte

nsity

Radical

Precursor

Precursor Parent Mass

Precursor D.I.

Radical Parent Mass

Radical and Precursor D.I.

Figure 3.8: Example mass spectra of the benzyl radical and precursor taken with 70 eVelectrons showing pyrolysis off (black trace) and on (red trace). The precursor parent massat m/z = 151 is fully depleted.

weak bond, DI will often result in the radical parent m/z value appearing prior to radicalproduction. Fig. 3.8 shows an example of both of these cases for the benzyl radical precursor2-phenylethyl nitrite (PEN). In this case the peak at m/z = 91, corresponding to C7H7

+

and the nominal benzyl radical parent peak, is the dominant feature with pyrolysis bothoff and on. The PEN precursor peak appears as a relatively small feature at m/z = 151.While the relative importance of other peaks changes—e.g. the m/z = 65 (C5H5

+) contribu-tion dramatically increases with pyrolysis—confirmation of precursor depletion and radicalproduction is difficult and potentially ambiguous.

Reduction of the electron kinetic energy Eelec means that there is less energy available toionize and dissociate a molecule. When applied to the pyrolysis of PEN, the mass spectra aresubstantially less congested as shown in Fig. 3.9. At lower electron energies the PEN parentfeature is still quite visible. While there is still some dissociative ionization, the contributionsat lower m/z values are gone for m/z < 91. The appearance of a completely new feature atm/z = 65 with the pyrolysis source on is a promising indication that radical production istaking place. Example near-threshold mass spectra (complete removal of DI features) maybe found in Fig. 6.7.

While decreasing contributions from dissociative ionization is a helpful tool, unambiguousassignment of all the features in Fig. 3.9 is not possible for that value of Eelec. For example,one of the possible benzyl decomposition products is the cyclopentadienyl radical (c-C5H5),which would appear at m/z = 65. To determine the source of a peak in a mass spectrum—i.e. neutral ionization or dissociative ionization—the appearance energy of a feature may bedetermined, a tool that has already made substantial contributions to the lab.

The procedure for collecting IEC discussed in Sec. 3.3 may be used on any m/z value


40 60 80 100 120 140 1600

0.2

0.4

0.6

0.8

1

m/z

Rela

tive Inte

nsity

RadicalPrecursor

Precursor Parent Mass

Precursor D.I.

Radical Parent MassRadical Only D.I.

Figure 3.9: Example mass spectra of the benzyl radical and precursor taken with 17 eVelectrons showing pyrolysis off (black trace) and on (red trace). Depletion of the precursorparent mass at m/z = 151 is apparent. A “radical only” dissociative ionization feature atm/z = 65 is now apparent.

observed in an experiment. For clarity, if the m/z value is due to the ionization of a parentneutral molecule, it will be referred to as the ionization energy IE (or ionization potential,IP). If the observed feature is due to dissociative ionization of a molecule or is of unknownorigin, the measured energy will be referred to as the appearance energy AE. Programs tocollect and analyze ionization efficiency curves may be found in Appendix C.

To confirm that PEN pyrolysis was producing the benzyl radical, ionization efficiencycurves at m/z = 91, such as the ones shown in Fig. 3.10, were taken. The results from theseIEC look very promising: the benzyl radical has an ionization energy of 7.2 eV.64 The cleardifference in appearance energies suggests that, with the pyrolysis source on and depletionof the PEN precursor, the benzyl radical is produced. The expected accuracy for an EIappearance energy measurement is around 1 eV (Refs. [65, 66]) and results with the ionizerin B Machine suggest that calibrated energies within 500 meV of the literature values areroutine. The expected accuracy is especially important as the next most stable C7H7 isomer isthe tropyl (cycloheptatrienyl) radical.62 With an ionization energy of approximately 6.4 eV,64contribution from the tropyl radical appears to be minimal. Thus, not only does it appearthat we are producing the benzyl radical, but it appears to be the dominant contribution tothe feature at m/z = 91.

In addition to producing radicals, these flash pyrolysis micro-reactors have been usedto study radical thermal decomposition.67,68 Indeed, as is observed in Chapters 5 and 6,thermolysis of the target radical may limit the usable range of pyrolysis source powers. Fromthe benzyl radical spectrum in Fig. 3.9, the peak at m/z = 65 could be due to dissociationof the benzyl radical in the pyrolysis source. To confirm clean production of radicals, IEC


8 10 12 14 16 180

0.2

0.4

0.6

0.8

1

1.2


No

rmaliz

ed I

nte

nsity

Pyrolysis OffPyrolysis On

AE = 10.7 eV

IE = 7.8 eV

Figure 3.10: Ionization efficiency curves for m/z = 91 with the pyrolysis source off (blackpoints) and on (red points).

at several (or all) m/z values can be taken at several pyrolysis source powers. The resultingappearance energy values, shown in Fig. 3.11, can yield insight into the pyrolysis and informchoice of source conditions.

Figure 3.11 reveals that, as the power dissipated by the pyrolysis source is increased,the appearance energies of all benzyl-related m/z values decreases. Molecular nitrogen wasused to calibrate the electron energies. The appearance energy measurements clearly showthat the dominant contribution to m/z = 91 is the benzyl radical starting at 30W. Them/z = 65 AE similarly shows a plateau, but at ∼4 eV higher than the ionization energy forfree cyclopentadienyl radical suggesting that the m/z = 65 feature observed in Fig. 3.9 isfrom dissociative ionization of the benzyl radical. Thus, through a combination of reduceddissociative ionization and appearance energy measurements, the tunable energy electronionizer allows for confirmation of precursor and source conditions to cleanly produce thebenzyl radical.

While a linear extrapolation is a simple means of quantifying IEC changes due to py-rolysis, the dissociative ionization appearance energies derived using this method are notequivalent to the equilibrium thermochemical values for daughter ion formation.69 Based onthe near-threshold ionization cross section behavior,70,71 an estimate of the heat of formationmay be determined by fitting the threshold region of an ionization efficiency curve to thefollowing functional form:72

f(E) =

b if E ≤ EAE,b+ c (E − EAE)

p if E > EAE,(3.2)


0 10 20 30 40 506

8

10

12

14

16

18

20

22

Pyrolysis Source Power (W)

Ap

peara

nce E

nerg

y (

eV

)

m/z = 28 (N2

+)

m/z = 65 (C5H

5+)

m/z = 89 (C7H

5+)

m/z = 90 (C7H

6+)

m/z = 91 (C7H

7+)

N2

benzyl radical

cyclopentadienyl radicalfulvenallene

CH2

C•

CH2•

Figure 3.11: Appearance energies of several m/z values relevant to benzyl radical decompo-sition as a function of pyrolysis source power. The dashed lines are the neutral ionizationenergies of the indicated fragments.

where b is the baseline signal below threshold, c is a scaling factor, and p is a fit parameter.In the case of low signal-to-noise, a weighting factor of 1/(N+1) may be used where N is theion count in the energy bin. Examples of this fit are shown in Fig. 3.12 for the production ofm/z = 91 from PEN and m/z = 65 from the benzyl radical, yielding respective appearanceenergies of 8.2 ± 0.6 eV and 11.5 ± 0.6 eV. Based on the bond dissociation and ionizationenergies, the expected appearance energies are 8.9 eV (PEN→ C7H7

++NO+CH2O)61,73 and11.3 eV (benzyl radical → C5H5

+ + C2H2),63,64 in good agreement with the derived valuesfrom the IEC and supporting the conclusion that PEN is pyrolyzing to produce the benzylradical.

3.5.2 Low Energy Electron Ionization of PhotofragmentsFor some species, an ionization efficiency curve may be taken of the photoproducts. A

potentially powerful tool to identify species from the photodissociation, the proof of conceptfor this experiment is shown in Fig. 3.13. Here, off-axis photodissociation spectra were takenwhile varying the electron energy. While each point was only taken once (except for thenormalization spectra) and ion optic tunes with higher signal levels have been found sincethese data were taken, Fig. 3.13 demonstrates that appearance energies may be used to assistin determining photofragment identities in addition to molecular beam constituents.

Off-axis IEC would be a difficult experiment for many systems and may not be gen-erally useful. While a reduction of background gas ionization and DI was only somewhatuseful for analyzing the molecular beam, these features are advantageous to TOF spectral


8 10 12 14 16 18


Inte

nsity (

arb

. units)

10 12 14 16 18 20

a)m/z = 91Pyrolysis Off

b)m/z = 65Pyrolysis On

AE = 8.2 eVAE = 11.5 eV

Figure 3.12: Ionization efficiency curves for the dissociative ionization of a) PEN to formm/z = 91 and b) the benzyl radical to form m/z = 65. The nonlinear fit using Eq. (3.2) isshown as a solid line.

6 8 10 12 14 16 180

0.2

0.4

0.6

0.8

1

1.2

1.4


Inte

nsity (

Arb

. U

nits)

Included in Fit

Excluded

I.P. = 9.5 eV

Figure 3.13: IEC of the m/z = 47 photoproduct from the 248 nm photodissociation ofdimethyl disulfide (CH3SSCH3). The measured ionization energy of 9.5 eV is in good agree-ment with the literature value64 of 9.2 eV for the thiomethoxy radical (CH3S).


collection and assignment. At reduced electron energies, photofragment parent m/z valuesare observable while DI features are minimized. This reduction in DI is useful in assigningphotoproduct parent masses, an important part of determining a molecule’s photochemistry.Reduction in dissociative ionization is also useful for TOF spectra taken at low laboratoryscattering angle, as DI contamination from the molecular beam can increase the noise in aTOF spectrum.

As demonstrated in Chapter 6, reduction of background gas ionization can be extremelyhelpful for some m/z values. Gases such as N2, O2, and H2O persist in the scattering chamberand will contribute to TOF background counts and increasing the subtraction noise. For somecases, the IE of the desired photoproduct is lower than the background signal AE, and areduced Eelec can “turn off” background gas signal, as shown in Fig. 6.16.

While reducing the electron energy was quite successful for observation of S atoms, itis unlikely to help for m/z = 28 or 15. These m/z values have substantial background dueto N2 ionization and hydrocarbon DI, respectively. And while the appearance energies forthese are higher than the ionization energy for ethylene or the methyl radical,64 these smallhydrocarbons have very small electron ionization cross sections at “background free” electronenergies.74,75 Indeed, results thus far have shown no improvement in acquiring signal at m/z= 15 using reduced electron energies.

39

Chapter 4

Revisiting the photodissociationdynamics of the phenyl radical

We have reinvestigated the photodissociation dynamics of the phenyl radical at 248 nmand 193 nm via photofragment translational spectroscopy under a variety of experimentalconditions aimed at reducing the nascent internal energy of the phenyl radical and eliminatingsignal from contaminants. Under these optimized conditions, slower translational energy(P(ET)) distributions for H-atom loss were seen at both wavelengths than in previouslyreported work. At 193 nm, the branching ratio for C2H2 loss vs. H-atom loss was found tobe 0.2 ± 0.1, a significantly lower value than was obtained previously in our laboratory. Thenew branching ratio agrees with calculated Rice-Ramsperger-Kassel-Marcus rate constants,suggesting that the photodissociation of the phenyl radical at 193 nm can be treated usingstatistical models. The effects of experimental conditions on the P(ET) distributions andproduct branching ratios are discussed. †

4.1 IntroductionThe phenyl radical, c-C6H5, is a key intermediate in the combustion of aromatic hydrocar-

bons and formation of polycyclic aromatic hydrocarbons (PAH).76–78 The role of the phenylradical in soot79,80formation has been of particular interest, as soot particles, which can beformed from PAH,81,82 have been implicated in both health and environmental issues.83,84The phenyl radical has also been implicated in the chemistry of the interstellar medium,particularly in the formation of PAH.85–87 In this work, we focus on the unimolecular chem-istry of the phenyl radical by re-investigating its ultraviolet photodissociation at excitationwavelengths of 248 nm and 193 nm, with particular emphasis on product branching at 193nm.

†Originally published as: Cole-Filipiak, N. C.; Shapero, M.; Negru, B.; Neumark, D. M. Revisiting thephotodissociation dynamics of the phenyl radical J. Chem. Phys., 2014, 141, 104307.

http://dx.doi.org/10.1063/1.4894398

http://dx.doi.org/10.1063/1.4894398

CHAPTER 4: The Phenyl Radical 40

The spectroscopy of the phenyl radical is fairly well characterized. Several of its electronicproperties have been measured, including its ultraviolet absorption spectrum,88,89 ionizationpotential,90,91 photoionization cross section,92 and electron affinity.93 The electronic statesand vibronic spectra of the phenyl radical have also been calculated.94 The 12B1 ← X2A1

transition of the phenyl radical was recently studied using cavity ring-down spectroscopy.95Rotationally resolved infrared spectra have been measured96,97 and investigated theoreti-cally.98

The reactions of the phenyl radical are also of considerable interest. Early theoretical workfocused on its ring-opening and subsequent dissociation or bimolecular cyclization.99,100101,102From the ring-opened structure, two dissociation pathways can occur: C–H bond cleavage toform l-C6H4 +H and C–C bond cleavage to form C2H2 +C4H3. Madden et al.103 calculated aground state potential energy surface (PES), shown in Fig. 4.1, along with Rice-Ramsperger-Kassel-Marcus (RRKM) rate constants for the phenyl radical that demonstrated the impor-tance of C–H bond cleavage from the cyclic species to form o-benzyne + H,103 the lowestenergy product channel. The energetics for these three channels, based on calculations byMebel and Landera,104 are as follows:

c-C6H5 → o-C6H4 + H ∆H0K = 79.9 kcal/mol, (4.1)c-C6H5 → n-C4H3 + C2H2 ∆H0K = 103.4 kcal/mol, (4.2)c-C6H5 → l-C6H4 + H ∆H0K = 96.1 kcal/mol. (4.3)

Later work by Olivella and Solé105 focused on the ring opening and cyclization pathwaysof the phenyl radical. A small exit barrier (∼4 kcal/mol)102 for channel 4.1 that was notpresent in the PES from Madden et al.103 has been reported by several groups.106,107 Wanget al.106 further explored the RRKM rate constants for the direct H-atom loss channel athigher temperatures than the previous work.103 The PES was later expanded upon102,108,109

to include an additional acetylene loss channel and a C4H4 + C2H channel.110Early experimental work identified the role of the phenyl radical in combustion subse-

quent to the thermolysis of aromatic molecules such as benzene,111–114 thereby stimulatinginterest in the reactions of the phenyl radical itself. Kinetics of reactions with the phenylradical have been performed in the liquid phase,115,116 and several gas phase bimolecularkinetics and dynamics experiments have been carried out, most notably by the Lin117–119

and Kaiser85,86 groups. The photodissociation of benzene120 and nitrosobenzene107 have beenshown to produce vibrationally excited phenyl radicals, which then spontaneously decayto form a hydrogen atom and a C6H4 fragment. These studies concluded that o-benzynewas the most likely C6H4 fragment. Recent investigations of the reactions of the phenylradical have included the crossed molecular beam study of phenyl with propene and trans-2-butene121 as well as several further experimental and computational studies by Kaiser andco-workers.87,122–124

In work from our laboratory, Negru et al.37 investigated the photodissociation of thephenyl radical at 248 and 193 nm via photofragment translational spectroscopy. The radi-cals were produced by flash pyrolysis53 of nitrosobenzene (C6H5NO). At 248 nm, the phenyl


0

20

40

60

80

100

En

erg

y (

kca

l/m

ol)

103.4107

61.9

101.796.1

79.9

0

66.8

c-C6H5

l-C6H5

n-C4H3 +

C2H2l-C6H4 + H

o-C6H4 +

H+

Figure 4.1: Simplified ground state potential energy diagram of the phenyl radical showingthe three primary dissociation pathways. Energies are from Ref. [104], structures are fromRefs. [103] and [104].

radical was found to dissociate to C6H4 + H and the resulting translational energy distri-bution suggested that dissociation occurred via channel 4.1, a result consistent with thePES and RRKM rate constants of Madden et al.103 At 193 nm, both H-atom and acetyleneloss pathways were observed. Signal from channels 4.1 and 4.3 could not be distinguishedand was thus referred to as “combined H-atom loss.” Translational energy distributions forboth product channels suggested statistical ground state dissociation dynamics. However,the product branching ratio between acetylene loss and the combined H-atom loss channelwas determined to be 5.3 in favor of acetylene loss, a somewhat surprising result given thatchannel 4.2 is higher in energy than channels 4.1 and 4.3. Using the PES and vibrationalfrequencies of Lin and co-workers,103 we were unable to reproduce the experimental branch-ing ratio with RRKM rate constants and speculated that the lower energy i-C4H3 + C2H2channel102 would allow for more product flux into acetylene loss. As RRKM rate constantswere unavailable for this channel, this proposal was not tested.

Our investigation was followed by a study of phenyl radical photodissociation by Songet al.125 via H-atom time-of-flight using resonance enhanced multiphoton ionization. In thewavelength range of 215 nm to 268 nm, their translational energy distributions were consis-tent with ground state dissociation dynamics. The distributions also indicated that eitheronly channel 4.1 was accessed or that both channels 4.1 and 4.3 were accessed but thechannel 4.3 contribution was small, a conclusion supported by the available RRKM rateconstants.103,125 As only H-atoms are detected using this technique, Song et al.125 were un-able to investigate the acetylene loss channel.

Motivated by the results of Negru et al.,37 recent theoretical work by Mebel and Lan-dera104 examined a larger number of channels for phenyl radical dissociation. Detailed RRKMcalculations at a variety of energies were also carried out in an effort to characterize therelative importance of each product channel, finding that the three channels originally in-


vestigated by Madden et al.103 to be of greatest importance over a wide range of excitationenergies. Dissociation via the i-C4H3 +C2H2 channel was found to be insignificant, owing to asubstantial isomerization barrier along the reaction coordinate to form these products. Mebeland Landera were unable to reproduce the experimental branching ratio with their calcu-lated surface and the absorption of only one 193 nm photon (148 kcal/mol): their calculatedchannel 4.2 to channels (4.1 + 4.3) branching ratio was 0.17, favoring the combined H-atomloss channel. Significantly, they found that channel 4.2 becomes dominant at higher excita-tion energies, e.g., 182 kcal/mol corresponding to absorption by one photon at 157 nm. In afinal effort to explain the experimental results, they calculated several conical intersectionsbetween the first excited and ground electronic states, two of which would place substan-tial vibrational energy into the acetylene loss coordinate, and suggested that these conicalintersections might result in non-statistical dynamics that could explain the experimentalresults of Negru et al. However, no excited state dynamics calculations were performed, sothe importance of these conical intersections could not be quantified.

In an effort to reconcile the experimental and theoretical results, we have reinvestigatedthe photodissociation of the phenyl radical at 193 nm and 248 nm using photofragmenttranslational spectroscopy. Results were obtained under a variety of different experimentalconditions aimed at reducing the radical internal energy. We find that a minor modification ofsource conditions, using 10% N2 in He for the carrier gas instead of pure He, yields noticeablyslower translational energy distributions for H-atom loss at 193 nm and 248 nm. Under theseconditions, and taking steps to insure that all the nitrosobenzene precursor molecules werepyrolyzed in our radical source, we find a C2H2 loss vs. H-atom loss branching ratio at 193nm of 0.2 ± 0.1, largely in agreement with statistical theoretical results.104 Our results willbe discussed in light of previous work, particularly the results from Negru et al.37

4.2 ExperimentalPhenyl radical photodissociation was studied on a modified crossed molecular beam ma-

chine using a fixed source and rotating time-of-flight (TOF) detector with electron impact(EI) ionization and a quadrupole mass filter. Details of this apparatus have been describedpreviously.37,39,126,127 As in our previous investigation,37 phenyl radicals were produced viaflash pyrolysis of nitrosobenzene (Sigma, ≥97%) using a resistively heated SiC pyrolysissource based on the design by Kohn et al.53 The source was recently modified to includeadditional water cooling lines on the pulsed valve assembly and an aluminum heat shieldaround the SiC tube and electrodes, resulting in a significant increase in source stabilityand thus allowing for increased TOF integration times. A gas mixture of 1.6 atm of ∼10%N2 in He was flowed over a room temperature sample of nitrosobenzene, resulting in a ni-trosobenzene concentration of ∼0.5%, and was introduced into vacuum by expansion througha piezoelectric pulsed valve with the pyrolysis source attached (further discussion of sourceconditions may be found in Sec. 4.7).

The resulting phenyl radical beam was skimmed and collimated by two skimmers that


isolate the source from the scattering chamber. The collimated molecular beam was crossedat 90 with the 1 × 3 mm2 focused output of a GAM EX100/500 excimer laser operatingat either 193 nm with typical pulse energies of 4 mJ, or 248 nm with typical pulse energiesof 12 mJ; corresponding fluences were 133 and 400 mJ cm−2. The fluence at 193 nm wasconsiderably lower than the 500 mJ cm−2 used by Negru et al.37 The pulsed valve and laserwere operated at 200 and 100 Hz, respectively, in order to perform background subtraction.Scattered photofragments were detected as a function of laboratory angle Θlab in the planedefined by the laser and molecular beams. After entering the detector, photofragments wereionized via EI ionization, mass-selected with a quadrupole mass filter, and ultimately de-tected with a Daly-style ion detector.128 Ion counts as a function of time relative to the laserpulse were recorded with a multichannel scaler interfaced to a computer and the resultingTOF spectra were acquired for 105–106 laser shots at each laboratory angle. TOF spectrawere simulated using an iterative forward convolution method to determine the center-of-mass translational energy distributions.

The molecular beam was characterized using a spinning, slotted chopper disk. Typicalbeam velocities were∼1700 m/s with speed ratios of 4–5. The beam was further characterizedby monitoring the nitrosobenzene signal (m/z = 107) and phenyl radical signal (m/z = 77)while the pyrolysis source was incrementally heated until the nitrosobenzene signal was fullydepleted. Incomplete depletion of the precursor may have been a possible source of errorin our previous work,37 as discussed in Sec. 4.5. Any remaining signal at m/z = 77 wasattributed to the phenyl radical, an assumption tested in Sec. 4.3. For comparison to ourprevious investigation, the experiments were also repeated with 1.6 atm of pure He. Underthese conditions, typical beam velocities were ∼2500 m/s with speed ratios of 6–7, similarto the beam characteristics described by Negru et al.37

Further experiments aimed at testing the effect of carrier gas composition were carriedout using 1.6 atm of 10% Ar in He or 10% CO2 in He, again directly applied to both thesample and pulsed valve. These source conditions resulted in beam velocities ∼200 m/sslower than the N2/He mixture but had otherwise similar beam characteristics.

4.3 ResultsTOF spectra were taken at multiple angles for m/z = 76 (C6H4

+), m/z = 51 (C4H3+),

and m/z = 26 (C2H2+), representing parent ions of photoproducts from channels 4.1–4.3,

and for m/z = 50 (C4H2+), a possible daughter ion from all three channels resulting from

dissociative ionization in the EI ionizer. At 248 nm, spectra taken at m/z = 76 for Θlab = 3–7 were found to have one feature; no signal was observed in spectra taken at larger scatteringangles. Representative spectra are shown in Figs. 4.2(a) and 4.2(b). The data are shown asopen circles while the solid line is from a forward convolution simulation of a translationalenergy distribution (see Sec. 4.4). No other photoproducts were observed, and all spectra atm/z ≤ 76 appeared to be from dissociative ionization of the C6H4 photofragment. As in ourprevious work,37 all of the signal at 248 nm is attributed to channel 4.1.


0

500

1000

1500

2000

2500

3000

0 100 200−200

0

200

400

600

800

0 100 200 300

×2


Counts

248 nm4°

248 nm6°

193 nm4°

193 nm7°

(a) (b)

(c) (d)

Figure 4.2: Representative m/z = 76 TOF spectra taken in the N2/He carrier gas mixtureat 248 nm, (a) and (b), or 193 nm, (c) and (d). The data are shown as open circles while thesolid line shows the simulation from either the 248 nm P(ET) distribution in Fig. 4.7 or the193 nm P(ET) distribution in Fig. 4.8. The number of laser shots is 300000 and 500000 forpanels (a) and (b), respectively; and 200000 and 400000 for panels (c) and (d), respectively.

At 193 nm, spectra at m/z = 76 were observed for Θlab = 3–9 and representative TOFspectra are shown in Figs. 4.2(c) and 4.2(d). These spectra are attributed to channels 4.1 and4.3. TOF spectra for H-atoms at m/z = 1 were not recorded due to unfavorable kinematicsand high background levels. Figure 4.3 shows representative TOF spectra for m/z = 51 andm/z = 26. These spectra are assigned to the C4H3 and C2H2 photofragments from phenylradical dissociation via channel 4.2.

Sample TOF spectra for m/z = 50 and Θlab < 10 at 193 nm are shown in Figure 4.4.These spectra show two features, attributed to the dissociative ionization of the C6H4 andC4H3 photofragments and can be used to determine the product branching ratio. Comparedto our previous work in pure He,37 the two features are better-resolved because the molecularbeam velocity is slower using the 10% N2 in He carrier gas mixture. Details of all channelassignments and the product branching ratio will be discussed in Sec. 4.4.

Similar m/z = 76 and m/z = 50 TOF spectra to those shown in Figures 2 and 4 weretaken with the current experimental conditions using a pure He carrier gas. Figure 4.5shows representative results for m/z = 76 and compares them to forward convolutions fromtwo translational energy distributions (Sec. 4.4). Experiments with the Ar/He and CO2/Hecarrier gas mixtures resulted in TOF spectra similar to those shown in Figures 4.2 and 4.3;sample 193 nm Ar/He spectra are shown and discussed in Sec. 4.7.


−50

0

50

100

150

200

250

0 100 200−200

−100

0

100

200

300

0 100 200 300

m/z = 5115°

m/z = 5125°

m/z = 2615°

m/z = 2625°


Counts

Figure 4.3: Sample TOF spectra taken at m/z = 51 (top row) and m/z = 26 (bottom row)in the N2/He carrier gas mixture and 193 nm photoexcitation. The data are shown as opencircles while the solid line shows the simulation from the P(ET) in Fig. 4.9. All spectra weresimultaneously simulated with a single P(ET) distribution. All spectra shown were averagedfor 106 laser shots.

0 100 200 300

0

500

1000

1500

Co

un

ts

0 100 200 300


0 100 200 300 400

8°7°6°

×2

Figure 4.4: Representative m/z = 50 TOF spectra taken at Θlab = 6–8 in N2/He carriergas mixture and 193 nm photoexcitation. Data are shown as open circles. The fast feature(dashed line) is simulated by the channel 4.2 P(ET) shown in Fig. 4.9 while the slow feature(dotted line) is simulated by the channel (4.1 + 4.3) P(ET) shown in Fig. 4.8. The solid lineis the total TOF simulation. The number of laser shots is 500000 for the 6 and 7 TOFspectra and 400000 for the 8 TOF spectrum.


0 100 200


0 100 200 300

Inte

nsity (

arb

. u

nits)

(a) (b)

Figure 4.5: (a) TOF spectrum (open circles) of m/z = 76 and 6 at 193 nm in He withsimulations from N2/He (solid line) and pure He (dotted line) P(ET) distributions shown inFig. 4.8. (b) An equivalent spectrum taken with the N2/He carrier gas mixture at m/z = 76and 6.

4.4 AnalysisThe results presented in Sec. 4.3 suggest that phenyl radical photodissociation at 193 nm

occurs via two main pathways—an apparent C–C bond fission pathway and an H-atom losschannel—while only H-atom loss appears at 248 nm. These assignments are consistent withthe kinematics of phenyl radical dissociation after excitation from one photon, as illustratedby the Newton diagram in Fig. 4.6 where the circles represent the maximum center-of-mass frame velocity for each specified photofragment after photodissociation at 193 nm. TheC6H4 products from channels 4.1 and 4.3 are confined to a very small angular range whilephotofragments from channel 4.2 are scattered over a larger angular range with scattering ofthe acetylene fragment unconstrained to a maximum Θlab. TOF spectra at m/z = 76 werenot observed beyond 9 at 193 nm or 7 at 248 nm, supporting their assignment to a phenylradical H-atom loss pathway. Signals at m/z = 51 and m/z = 26 were observed outside ofthe maximum laboratory angle for the C6H4 fragments, eliminating the possibility that thesespectra are due to dissociative ionization of the m/z = 76 photofragment and supportingtheir assignment to channel 4.2. This assignment can be confirmed by determining if theTOF spectra for the two fragments are “momentum-matched,” as discussed below.

To analyze these results quantitatively, center-of-mass photofragment translational en-ergy and angular distributions, P(ET,θ), were generated for each channel by simulating theobserved TOF spectra. These P(ET,θ) distributions can then be rewritten as uncoupledcenter-of-mass translational energy distributions P(ET) and angular distributions I(θ,ET),

P(ET,θ) = P(ET)I(θ,ET). (4.4)To simulate the TOF spectra, assumed P(ET) and I(θ,ET) distributions were used withthe PHOTRAN forward convolution program.129 The P(ET) distribution was then adjusted


C6H4

C4H3

9.2°

10.6°

68.1°

vlab = 1700 m/s

Figure 4.6: Newton diagram for the phenyl radical dissociation at 193 nm under the currentexperimental conditions. Each circle represents the maximum center-of-mass velocity for aphotofragment based on channels 4.1–4.3 and Eq. (4.5). The dotted circle corresponds tothe heavy fragment of channel 4.1, the dashed circle to the heavy fragment of channel 4.2,and the solid circle corresponds to the heavy fragment of channel 4.3. Maximum scatteringangles are shown.

point-wise until satisfactory agreement between the TOF data and the simulation for thatchannel was achieved. While an anisotropic angular distribution is possible, satisfactoryagreement between spectral data and the simulations was achieved assuming isotropic dis-tributions for all center-of-mass translational energies ET.

By conservation of energy, ET is given by

ET = hν −D + E − Eint, (4.5)

where hν is the photon energy, D is the bond dissociation energy for a given channel, E isthe nascent internal energy of the phenyl radicals, and Eint is the total internal energy of theresulting photofragments. In the limit of cold radicals (E = 0), each channel’s maximumtranslational energy is Eavail, given by hν−D, and is used to generate the Newton diagramin Fig. 4.6.

Figure 4.7 shows the P(ET) distribution for H-atom loss via channel 4.1 at 248 nm usedto simulate the observed TOF feature in Figures 4.2(a) and 4.2(b). The assignment of thesefeatures to channel 4.1 is substantiated by the result that there appear to be no other phenylradical photodissociation products at 248 nm. The TOF simulations for H-atom loss at193 nm, shown as a solid line in Figures 4.2(c) and 4.2(d), were generated by the P(ET)distribution shown as a black line in Fig. 4.8. As in our previous investigation,37 we wereunable to distinguish between channels 4.1 and 4.3, since most of the signal occurs below


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Figure 4.7: Translational energy distribution for channel 4.1 at 248 nm. Due to the minimumexperimental scattering angle of 3, energies below 6 kcal/mol are less certain than highertranslational energies. Characteristics of this distribution are given in Table 4.1. The dashed,gray line shows the prior distribution for this channel as discussed in Sec. 4.4.

Eavail for both channels. Thus, this P(ET) distribution represents the combined channels(4.1 + 4.3). While the probability of translational energies greater than 30 kcal/mol is quitesmall (see Fig. 4.8 inset), a trial P(ET) distribution with zero probability at these energiesresulted in noticeably poorer agreement between simulations and experimental data. As m/z= 76 TOF data were not acquired for Θlab< 3, energies below 5 kcal/mol are uncertain.Adjustments to the 3 kcal/mol point, however, still had an effect on the TOF simulationsand the current placement was found to produce the best agreement with experimental data.The probability at ET = 0 kcal/mol was assumed to be zero based on previous work37,125

and functional forms for translational energy distributions.20TOF spectra at m/z = 76 taken in pure He carrier gas are not simulated by the P(ET)

distribution used to fit the N2/He data, as can be seen in Fig. 4.5(a), but these data arewell-simulated by the somewhat faster distribution given in Figure 4.8 (dark gray line). ThisP(ET) distribution is slower than our previously published distribution at 193 nm,37 buthas a higher probability than the N2/He distribution for all ET > 6 kcal/mol. The panelin Fig. 4.5(b) shows that this faster distribution does not simulate the N2/He data. TOFspectra taken using Ar/He and CO2/He mixes, on the other hand, were fit well using thedistribution that simulated the N2/He data. Hence, the P(ET) distribution for H atom lossclearly depends on whether a pure He or mixed carrier gas is used, but does not dependnoticeably on which gas is mixed with the He.

The P(ET) distribution for channel 4.2 is shown in Fig. 4.9 and the respective TOFsimulations are overlaid on Fig. 4.3. Refinements to the distribution were made by simulatingspectra at m/z = 50 and Θlab > 10, where there is no contribution from channels 4.1 or4.3, as the signal at m/z = 50 is substantially higher than at either m/z = 51 or m/z = 26.


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Figure 4.8: Translational energy distribution for the combined H-atom loss channel at 193 nmfor the N2/He (black line) and pure He (dark gray line) carrier gases. Due to the minimumscattering angle of 3, energies below 5 kcal/mol are less certain than higher translationalenergies. The probability from 35 kcal/mol to 80 kcal/mol for the N2/He distribution isshown in the inset. Characteristics of these distributions are given in Table 4.1. The dashed,gray line shows the prior distribution as discussed in Sec. 4.4.

The result that both the m/z = 51 and m/z = 26 TOF spectra are simulated by the sameP(ET) distribution indicates that these fragments are momentum-matched, which supportsthe conclusions that the spectra in Fig. 4.3 are the result of acetylene loss from the phenylradical.

Characteristics of all P(ET) distributions are given in Table 4.1. At 193 nm, the averagetranslational energy ⟨ET⟩ for H-atom loss in the N2/He mixture is 4 kcal/mol below that forpure He. In fact, it is slower than our previously published P(ET) for H-atom loss at 248 nm.37While ⟨ET⟩ for channel 4.2 has not changed, the P(ET) distribution in Fig. 4.9 does havehigher probability at the peak translational energy and slightly decreased probability above25 kcal/mol compared to our previous distribution.37 At 248 nm, the P(ET) distributionfor H-atom loss is also slower than previously published distributions.37,125 Although ourexperiment does not distinguish between channels 4.1 and 4.3 at 193 nm, it is of interest tonote from Table 4.1 that the ⟨fT⟩ = ⟨ET⟩/Eavail for H-atom loss is smaller at 193 nm than248 nm. Such a result could occur if there were significant channel 4.3 production at 193 nm,since the available energy for this channel is 16 kcal/mol lower than for channel 4.1.

For comparison to experiment, prior distributions for the H-atom loss P(ET) distributionsat 248 nm and 193 nm were calculated. The prior distribution has the functional form20

P(ET|Eavail) ∝ E1/2T ρvr(Eavail − ET), (4.6)

where ET is the translational energy of the photofragment, Eavail is the available energy givenby hν − D in Eq. (4.5), and ρvr(Eavail − ET) is the total rotational-vibrational density of


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Figure 4.9: Channel 4.2 translational energy distribution used to simultaneously simulatethe m/z = 51 and m/z = 26 TOF spectra. Characteristics of this distribution are given inTable 4.1.

Table 4.1: Characteristics of the P(ET) distributions derived in this work: available energyEavail, the maximum translational energy of the distribution ET,max, the average translationalenergy ⟨ET⟩, and the average fraction of Eavail partitioned into translational energy ⟨fT⟩.Wavelengths are given in nm and energy values are in kcal/mol.

Channel Wavelength Carrier gas Figure Eavail ET,max ⟨ET⟩ ⟨fT⟩4.1 248 N2/He 6 35 35 6 0.17(4.1 + 4.3) 193 N2/He 7, black line 68 65 7 0.10(4.1 + 4.3) 193 He 7, dark gray line 68 70 11 0.16(4.1 + 4.3) 193 He Fig. 9 of Ref. [37] 68 66 16 0.244.2 193 N2/He 8 46 46 13 0.28

states for the pair of fragments. All vibrational degrees of freedom were treated as classicalharmonic oscillators, i.e., ρv ∝ Es−1, and Eavail was calculated for channel 4.1. The resultingprior distributions for H-atom loss at 193 nm and 248 nm are shown as dashed, light graylines in Figures 4.7 and 4.8. These distributions are slightly slower than the experimentallydetermined P(ET) distributions at both photon energies. A prior distribution was not cal-culated for channel 4.2 as Eq. (4.6) is generally not applicable to reactions proceeding overa barrier.

The assignment of the two features observed in the TOF spectra at m/z = 50 and Θlab< 10 to dissociative ionization of the m/z = 51 and m/z = 76 photofragments is supportedby the agreement between the TOF data and the simulations for each channel as well as thedependence of the slower feature on Θlab. Thus, these spectra can be used to calculate the


product branching ratio. The channel 4.2/channel (4.1 + 4.3) branching ratio (BR) can becalculated using the following equation:

BR = R× σC6H4

σC4H3

× fC6H4

fC4H3

. (4.7)

Here, R represents the ratio of contributions from each P(ET) distribution used in the totalTOF simulation. The second term, denoted by σ, is the relative ionization cross section foreach photofragment and is estimated using the additive method of Fitch and Sauter.130 Thefinal variable in Eq. (4.7), f , is the fraction of the total photofragment signal for each channelthat appears at m/z = 50. To determine the value of f for each channel, TOF spectra weretaken at Θlab= 7 for all values of m/z that yield measurable signal (m/z = 76, 75, 74, 73,61, 51, 50, 49, 37, and 36). The amount of signal from each channel was then determined foreach mass-to-charge ratio: 40% of the total C6H4 signal and 52% of the total C4H3 signalappear at m/z = 50, compared to 11% and 10% at the parent ion masses of 76 and 51.

Using the P(ET) distributions in Figures 8 and 9 for the N2/He gas mixture, Eq. (4.7)gives a channel 4.2/channel (4.1 + 4.3) branching ratio of 0.2, a BR in favor of the combinedH-atom loss pathway. Similarly, using our published37 f values in Eq. (4.7) and the pureHe P(ET) distribution in Fig. 4.8, simulations of TOF spectra for m/z = 50 taken in Heyield BR = 0.8. In order to estimate the error for each branching ratio, we calculated theparameter R in Eq. (4.7) over a range of P(ET) distributions for H-atom loss that producedreasonable agreement with each set of m/z = 76 TOF spectra. This procedure yields BR =0.2 ± 0.1 for N2/He and BR = 0.8 ± 0.2 for pure He.

It thus appears that the branching ratio is remarkably and reproducibly sensitive to thecarrier gas composition. There also appears to be a strong correlation between the form ofthe P(ET) distribution for H-atom loss and the overall branching ratio. In simulating theN2/He data at m/z = 50, such as that in Fig. 4.4, the slower P(ET) distribution for channels(4.1 + 4.3) relative to that in pure He necessitates increasing the contribution from H-atomloss (dotted line in Fig. 4.4) in order to achieve satisfactory agreement between the overallsimulation and the TOF spectra.

4.5 DiscussionThe primary question of this investigation is whether the phenyl radical dissociation at

193 nm proceeds via internal conversion to the ground electronic state followed by statis-tical dissociation. The N2/He P(ET) distributions for H-atom loss are only slightly fasterthan the prior distributions, consistent with statistical dissociation with no exit barrier. Thecorresponding distribution for channel 4.2 peaks further away from ET = 0, as expected fordissociation over a small exit barrier as shown in Fig. 4.1. The branching ratio of 0.2 ± 0.1for channel 4.2/channels (4.1 + 4.3) is in reasonable agreement with the value of 0.17 fromthe RRKM calculations of Mebel and Landera.104 This set of observations implies that thephenyl radical dissociates statistically on the ground state surface.


The branching ratio obtained using the N2/He mix, however, is considerably lower thanthat obtained here for pure He (0.8), and is in serious disagreement with our previous exper-imental result of 5.3 in favor of channel 4.2.37 Moreover, the P(ET) distributions for H-atomloss are considerably slower than those reported in our previous work at both 193 nm and 248nm. To understand these differences, we examine the current results in detail and comparethem to previous experimental and theoretical work.

The theoretical study by Mebel104 showed that channels associated with ring-opening,i.e., channels 4.2 and 4.3, become progressively more important as the available energy ofthe phenyl radical increases. Specifically, they found channel 4.2 to be the dominant channelwhen the available energy is equivalent to two-photon absorption at either 248 nm or 193nm. Along the reaction coordinates for channels 4.2 and 4.3, the RRKM rate constant forring opening increases by over four orders of magnitude as the internal energy is raised from115.3 kcal/mol (one photon at 248 nm) to 296.3 kcal/mol (two-photon absorption at 193nm), whereas the ring closure rate constant rises by less than a factor of three over the sameenergy range. This result reflects the fact that in the statistical limit, the electronic energyfrom photoexcitation is rapidly converted to internal energy on the ground state surfaceand that with increasing excitation energy the entropically favored—but higher energy—ring-opened dissociation channels become dominant. Essentially, once ring-opening occursat high internal energy, ring-closure is highly unlikely.

In order to test whether the branching ratio reported by Negru et al.37 resulted from two-photon excitation at 193 nm, we reduced (see Sec. 4.7) the laser fluence from 500 to <100mJ/cm2 using our original experimental conditions: high pressure pure He as the carriergas.37 Reducing the photon fluence had a negligible effect on the branching ratio and theshape of TOF spectral features, suggesting that two-photon excitation was unimportant inour original experiments.

However, the work by Mebel104 and the calculated rate constants by Madden et al.103imply that channel 4.2 is also favored if the nascent internal energy E (see Eq. (4.5)) ofthe phenyl radical is raised. This consideration motivated our attempts to produce colderphenyl radicals from our pyrolysis source by adjusting the composition of the carrier gas.Here, we found a significant effect. Using 10% N2 in He resulted in slower P(ET) distributionsfor H-atom loss at both photodissociation wavelengths and, at 193 nm, a branching ratiomuch closer to the H-atom loss dominant ratio predicted by Mebel’s RRKM calculations.As shown in Sec. 4.7, experiments with 10% Ar in He and 10% CO2 in He carrier gasmixtures gave similar results. When we reverted to a pure He carrier gas while holding allother experimental conditions constant, as shown in Fig. 4.5(a), the resulting TOF spectraat 193 nm could only be adequately simulated using the faster, pure He P(ET) distributionin Fig. 4.8, and the branching ratio again showed channel 4.2 to be dominant (although notas dominant as seen previously37).

The choice of carrier gas is known to have an effect on the internal energy of a seededmolecule in a molecular beam (see, for example, Ref. [131]). It thus appears that since N2is a heavier collider and has more degrees of freedom than He, the phenyl radicals are moreeffectively cooled by the N2/He carrier gas mixture than by pure He, thus lowering E and


reducing the energy available to the photofragments. The lowered nascent internal energyresults in a slower P(ET) distribution for H-atom loss and, at 193 nm, contributes to a shiftin branching ratio favoring H-atom loss over acetylene loss. Note that the P(ET) distributionfor channel 4.2 is largely unchanged, perhaps reflecting the presence of the exit barrier forthis channel.

Based on the RRKM results of Mebel,104 a BR ≈ 1 would result from a phenyl radicalinternal energy of ∼180 kcal/mol, ∼30 kcal/mol higher than a 193 nm photoexcited phenylradical. The cooling of vibrationally excited benzyl radicals by collisions with N2 is knownto reduce the internal energy by 140 cm−1 per collision.132 A 30 kcal/mol decrease in Ewould thus require less than 100 collisions with N2. From our experimental parameters, weestimate the number of collisions during the expansion29 to be several thousand, suggestingthat this decrease in E due to the addition of 10% N2 is reasonable.

The BR of 0.8 ± 0.2 found here using pure He as the carrier gas is considerably lowerthan our previously reported value of 5.3.37 Close examination of the original m/z = 50 TOFspectra shows that simulations from the published H-atom loss P(ET) distribution do nothave sufficient intensity along the trailing edge of the observed feature. A slower H-atomloss distribution could account for this discrepancy and would also increase the contribu-tion from this channel in the BR. However, the sensitivity of the BR to small differencesin P(ET) distributions was not appreciated at the time, and the overall simulations werethought to provide reasonable agreement with the data. Moreover, as discussed in Sec. 4.2,the photodissociation of any remaining nitrosobenzene in the molecular beam yields signalin the m/z = 50 TOF spectra that strongly overlaps the contribution from channel 4.2.Simulations of these spectra in which only phenyl dissociation is assumed would appear torequire higher contribution from channel 4.2 to match the total signal, i.e., a larger valuefor R in Eq. (4.7). It is thus possible that our previously published m/z = 50 TOF spectrawere contaminated in this way, resulting in an additional contribution to erroneously highBR in favor of channel 4.2.

The P(ET) distribution reported here for H-atom loss at 248 nm is slower than thosemeasured by Song et al.125 from 226 nm to 255 nm (245 nm is the closest point of comparison),whereas our earlier distribution37 was somewhat faster. In their experiment, phenyl wasproduced by photolysis of chlorobenzene or bromobenzene seeded in Ar at a backing pressureof∼1.2 atm. The UV photolysis of chlorobenzene is known to produce phenyl with substantialinternal energy,92 so it is possible that the discrepancies between this measurement and oursalso reflect the extent of cooling by the carrier gas once the phenyl radicals are formed. Songet al. also observed a decrease in ⟨fT⟩ with increasing photon energy, consistent with ourresults at 248 and 193 nm.

4.6 ConclusionsWe have re-evaluated the photodissociation of the phenyl radical, optimizing experimental

conditions to cool the radicals and to reduce signal from any contaminants in the phenyl


radical beam. This work is particularly concerned with the product branching ratio for thephotodissociation of the phenyl radical at 193 nm and the implications that this ratio hasfor the photodissociation mechanism. We find that the branching ratio of acetylene lossto combined H-atom is 0.2, in agreement with the RRKM result of 0.17 (Ref. [104]) andconsistent with a statistical dissociation on the ground state surface. This value resultsfrom experiments in which the phenyl radical is formed in N2/He carrier gas mixture; aconsiderably higher value of 0.8 is found when pure He is used as the carrier gas. In addition,the mixed carrier gas results in P(ET) distributions for H-atom loss at 248 nm and 193nm with decreased average translational energies. The dependence of the BR on P(ET)distributions implies that the addition of N2 results in more effective cooling of the phenylradicals after pyrolysis. While these results suggest that the previous work by Negru et al.37was also affected by excess internal energy in the phenyl radicals, the considerably higherbranching ratio reported therein most likely reflects two additional effects: an overly fastP(ET) distribution for H-atom loss and incomplete pyrolysis of the nitrosobenzene precursorin the radical source. The conclusions presented here represent a cautionary note when usingflash pyrolysis sources to generate radicals and show that extra care must be taken to ensurecontaminant-free production and sufficient cooling of the radical.

AcknowledgementsThis work was supported by the Director, Office of Basic Energy Sciences, Chemical

Sciences, Geosciences, and Biosciences Division of the U.S. Department of Energy underContract No. DE-AC02-05CH11231.

4.7 Supplemental Material4.7.1 Investigating Experimental Parameters

The original experimental conditions of Negru et al.37 were 4 atm of pure He appliedto the nitrosobenzene sample which then passed through a vacuum regulator to reduce thepressure to 1.1 atm behind the pulsed valve. The laser fluence in those experiments was 500mJ cm−2. Our initial reinvestigation of the phenyl radical used these source conditions andlaser fluence. While these source conditions provided enough signal with a pure He carriergas, the addition of 10% N2 resulted in reduced signal. As the addition of nitrogen to thecarrier gas was an attempt at decreasing the initial radical internal energy, it was criticalto the experiment and could not be eliminated. Thus, the current configuration of 1.6 atmof carrier gas directly applied to both the sample and pulsed valve was used to increase theconcentration of phenyl radicals in the molecular beam and thus increase photodissociationsignal. Laser power studies were also performed in both He and the N2/He experiments usingthe 2 × 4mm2 focused output of a Lambda Physik LPX 220i excimer laser. Pulse energieswere varied from 40 mJ cm−2 to 500 mJ cm−2, the laser fluence used prevously.37 Under


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m/z = 764°, 300k

m/z = 507°, 300k

(a) (b)

Figure 4.10: Sample TOF spectra taken at (a) m/z = 76 and (b) m/z = 50 using experimentalconditions similar to those of Negru et al.:37 4 atm of 10% N2 in He were applied to thenitrosobenzene sample with 1.1 atm of the resulting mixture backing the pulsed valve anda laser fluence of 500 mJ cm−2. Simulations are from the N2/He P(ET) distributions shownin Figures 4.8 and 4.9, and the relative P(ET) weight used in (b) was derived from the 1.6atm N2/He experiments at 133 mJ cm−2.

the source conditions of Negru et al., i.e. a less concentrated molecular beam, TOF spectralfeatures remained constant over all laser powers: only the intensity of the signal varied andall spectra were well simulated by the same translational energy distribution. However, m/z= 76 TOF spectra taken with the current, higher phenyl molecular beam concentration anda 193 nm laser fluence of 500 mJ cm−2 resulted in additional photodissociation signal atshorter flight times that was not simulated by the published energy distributions, suggestingcontamination in the molecular beam. Using a pure He carrier gas, laser power was reduceduntil the observed TOF data were again well simulated by the published translational energydistributions,1 thus determining the laser fluence of 133 mJ cm−2 for the rest of the 193 nmexperiment as described in Sec. 4.2. A similarly fast photodissociation signal was observedwhen using the N2/He carrier gas mixture and high laser fluence, suggesting that a fluenceof 133 mJ cm−2 is appropriate for all source conditions. This procedure was also carried outat 248 nm, resulting in a fluence of 400 mJ cm−2.

Despite the reduced signal, sample TOF spectra at 193 nm were also taken applying4 atm of the N2/He mixture to the sample and 1.1 atm behind the pulsed valve with aphoton fluence of 500 mJ cm−2. Simulations of these spectra were performed using P(ET)distributions and P(ET) weighting values (see Sec. 4.4) derived from the 1.6 atm N2/He and133 mJ cm−2 experiment. As shown in Fig. 4.10, these simulations were found to be in goodagreement with those data. These results suggest that the contaminating signal observed athigher laser fluence does not have an effect on our low laser fluence results. Further, theseresults demonstrate that changes in nitrosobenzene concentration and pulsed valve pressurecannot be responsible for the observed difference between the previously published1 and


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4°, 250k 6°, 400k

Figure 4.11: Sample TOF spectra taken at m/z = 76 using 1.6 atm of the Ar/He carrier gasmixture and a 193 nm laser fluence of 125 mJ cm−2. The simulations are from the N2/HeP(ET) distribution shown in Fig. 4.7.

current P(ET) distributions.As discussed in Sec. 4.2, additional experiments were performed with 10% Ar in He and

10% CO2 in He carrier gas mixtures at 193 nm. These experiments were performed to checkthe results of the N2/He experiments against a heavier carrier gas. Figure 4.11 shows samplem/z = 76 TOF spectra taken using the Ar/He carrier gas mixture. These spectra weresimulated with the N2/He P(ET) distribution shown in Fig. 4.7. The agreement betweenthese data and the simulations suggest that the Ar/He mixture is not cooling the radicalsany further than the N2/He carrier gas and that the latter mixture is sufficient.

4.7.2 TOF Feature AssignmentBefore assigning the observed TOF spectral features to phenyl radical photofragments,

we must carefully consider contaminants in the molecular beam. This is especially importantas TOF spectra taken at high laser fluence contained unassigned spectral features, as dis-cussed in the previous section. In particular, dimerization of the phenyl radical will becomeincreasingly important with increasing radical concentration. With the pyrolysis source on,a small amount of signal at m/z = 154 was observed within the molecular beam and wasattributed to the biphenyl molecule. While the gas-phase photodissociation of biphenyl doesnot appear to have been studied, thin films133 of solid biphenyl absorb at 193 nm and 248nm and so we must consider possible photoproducts. Previous work on the thermolysis ofbiphenyl suggests benzene as a dissociation product134 while H-atom loss appears to be thefirst step of biphenyl radiolysis in neat aqueous solutions.135 No photodissociation signal wasobserved at m/z = 78 (C6H6

+) or m/z = 77 (C6H5+), eliminating the possibility of benzene

or phenyl radical production from biphenyl. The loss of a hydrogen atom from biphenyl isexpected to have a bond dissociation energy of ca. 110 kcal/mol (Ref. [136]) resulting in amaximum laboratory scattering angle of approximately 4 for the C12H9 fragment at 193nm. TOF spectra at m/z = 153 (C12H9

+), m/z = 152 (C12H8+), m/z = 139 (C11H7

+),


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Figure 4.12: TOF spectra at m/z = 152. Overlaid are simulations assuming either H-atomloss (dashed line) or H2 loss (dotted line) from biphenyl at 193 nm. P(ET) distributions usedto simulate these spectra are shown in Fig. 4.13.

and m/z = 128 (C10H8+) were taken for Θlab = 3–5 at 193 nm. Spectra taken at m/z

= 152 showed one relatively slow peak and are shown in Fig. 4.12; all other spectra werefeatureless. Coarse simulations of the m/z = 152 spectra assuming either H-atom or H2 lossfrom biphenyl were performed and the resulting P(ET) distributions are shown in Fig. 4.13.The resulting translational energy distributions were used to simulate m/z = 76 and m/z= 50 spectra and, in all cases, biphenyl dissociation simulations peak at flight times longerthan the observed features (see Fig. 4.14). As such, the possibility of biphenyl dissociationcontributing to the observed TOF spectra for m/z ≤ 76 at 193 nm can be eliminated. Asbiphenyl absorption is weaker at 248 nm than at 193 nm,133 and the less energetic 248 nmphoton will result in smaller maximum photofragment scattering angles, it is reasonable toassume biphenyl dissociation does not contribute to the observed signal at m/z ≤ 76 at 248nm.

No photodissociation signal at either wavelength was observed in spectra at m/z = 77or at m/z = 30 (NO+), eliminating the possibility of contamination from nitrosobenzenephotodissociation.107 These results confirm that the nitrosobenzene precursor has been com-pletely depleted by the pyrolysis source when all m/z = 107 signal has been depleted. Whilebenzene is produced in the pyrolysis source, the concentration and photon fluence are toolow to observe photodissociation signal at 193 nm as, again, no signal was observed at m/z= 77. H2 loss from benzene is the primary photodissociation pathway at 248 nm, yielding aC6H4 photofragment.120 To confirm that neither benzene nor nitrosobenzene are contribut-ing to the observed TOF spectra at either wavelength, TOF spectra were simulated usingpreviously published translational energy distributions for each species.107,120 The resultingsimulations did not match the observed signal at m/z ≤ 76 at either 193 nm or 248 nm,further suggesting that the observed photofragment signal is from the phenyl radical.


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T⟩ = 4 kcal/mol

Figure 4.13: (a) P(ET) distribution used to simulate the TOF spectra shown in Fig. 4.11assuming H-atom loss from biphenyl. (b) P(ET) distribution used to simulate the TOFspectra shown in Fig. 4.11 assuming H2 loss from biphenyl.

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Figure 4.14: An m/z = 76 TOF spectrum at 4 using 1.6 atm of the N2/He carrier gasmixture and a laser fluence of 133 mJ cm−2. The simulations are from the biphenyl P(ET)distributions in Fig. 4.13. As with Fig. 4.12, H-atom loss is the dashed line and H2 loss isthe dotted line.


4.7.3 Effect of Carrier GasSlower photofragments due to a heavier carrier gas could be due to the formation of

clusters; e.g. phenyl·N2 or phenyl·Ar. This possibility can be eliminated for two main reasons.First, in their study of radical formation and temperature via flash pyrolysis, Rohrs et al.30did not see evidence for cluster formation under source conditions similar to those employedin the present study. Second, if clusters were being formed during the expansion, some shouldsurvive EI ionization and there was no evidence of clustering in any molecular beam massspectrum. Thus, a change in E due to carrier gas remains the most reasonable explanationof our results.

60

Chapter 5

Photodissociation dynamics of themethyl perthiyl radical at 248 nm viaphotofragment translationalspectroscopy

Photofragment translational spectroscopy was used to study the photodissociation of themethyl perthiyl radical CH3SS at 248 nm. The radical was produced by flash pyrolysis ofdimethyl disulfide (CH3SSCH3). Two channels were observed: CH3 + S2 and CH2S + SH.Photofragment translational energy distributions indicate that CH3 + S2 results from C–Sbond fission on the ground state surface. The CH2S + SH channel can proceed throughisomerization to CH2SSH on the ground state surface but also may involve production ofelectronically excited CH2S.‡

5.1 IntroductionThe disulfide bond plays a key role in diverse areas of chemistry ranging from chemical

biology, where it plays a critical role in protein folding and structure as the cysteine bond,137to atmospheric chemistry, where it is found in atmospherically relevant species that take partin the sulfur cycle.138 These considerations have motivated fundamental studies of the gas-phase chemistry and photochemistry of alkyl disulfides, with dimethyl disulfide (DMDS) atthe forefront of many investigations.139–153 Depending on the wavelength used, the competingdissociation pathways for DMDS are as follows:151

‡Originally published as: Cole-Filipiak, N. C.; Negru, B.; Just, G. M. P.; Park, D.; Neumark, D. M.Photodissociation dynamics of the methyl perthiyl radical at 248 nm via photofragment translational spec-troscopy J. Chem. Phys., 2013, 138, 054301.

http://dx.doi.org/10.1063/1.4789485

http://dx.doi.org/10.1063/1.4789485

http://dx.doi.org/10.1063/1.4789485

CHAPTER 5: The Methyl Perthiyl Radical, Part I 61

CH3SSCH3 + hν → 2 CH3S (X2E) ∆H = 70 kcal/mol, (5.1)CH3SSCH3 + hν → CH3SS (X2A′′) + CH3 (X

2A′′2) ∆H = 55 kcal/mol. (5.2)

Channel 5.2 has been of special interest due to the CH3SS (methyl perthiyl) radical pro-duced. Callear and Dickson studied this pathway at ca. 195 nm, and observed CH3 and S2photoproducts.140 Pressure dependence studies for this channel demonstrated that internallyexcited CH3SS from channel 5.2 decayed spontaneously to produce the S2 fragment. Subse-quently, Ng and co-workers150 observed both the methyl perthiyl radical and S2 fragmentsfrom the 193 nm photodissociation of DMDS and attributed the S2 signal to absorption ofa second photon rather than a secondary process. Additional studies at 193 nm by Lee etal.151 and Martínez-Haya et al.152 showed that spontaneous decay of hot CH3SS was theprimary source of S2, but that there was a smaller contribution from photoexcitation ofCH3SS. Kumar et al.154 studied the 248 nm photodissociation of DMDS via transient ab-sorption spectroscopy in a static cell. They reported several UV absorption bands that theyassigned to CH3S and S2 photofragments. The more recent work by Lee et al.151 showedthat the collisionless photodissociation of DMDS at 248 nm exclusively occurs via channel5.1. They attributed the exclusivity to a σ∗

SS ← nS electronic excitation, resulting in a rapid,bond-specific dissociation.

In this work, we investigate the photodissociation of the methyl perthiyl radical itself at248 nm. Several experimental and theoretical studies of CH3SS have been reported previ-ously. Moran and Ellison155 measured the electron affinity of CH3SS via negative-ion pho-toelectron spectroscopy. Ma et al.156 measured the photoionization efficiency of the methylperthiyl radical in a supersonic beam and carried out ab initio calculations to explore pos-sible isomerization on its ground state surface. Subsequent theoretical work by Cheung etal.157 found several stable conformers of the methyl perthiyl radical with CH3SS as themost stable. More recently, Maofa et al.158 studied the ionization of CH3SS using photoelec-tron spectroscopy and Martin-Diaconescu and Kennepohl159 measured its X-ray absorptionspectrum. While the above studies were concerned with the energetics and spectroscopy ofthe methyl perthiyl radical, none probed the specific photochemistry of the radical itself.The only previous study of perthiyl photodissociation was performed by Mikhailik et al. onthe tert-butyl perthiyl radical in a hydrocarbon matrix at 365 nm.160 Appearance of thetert-butyl radical was monitored using EPR, and the group concluded that the tert-butylperthiyl radical was undergoing C–S bond fission to produce S and the tert-butyl radical.The methyl perthiyl radical is of further interest as an isovalent analog to the methyl peroxyradical (CH3OO), an important atmospheric and combustion intermediate.7,161,162

The ultraviolet absorption spectrum of CH3SS has not been characterized. By analogyto CH3O2,163 excitation at 248 nm may access the B (2A′′) state of the radical.

At this wavelength, corresponding to a photon energy of 115 kcal/mol, there are several


CH3SS (Cs)

CH3 + SS

CH3S + S

CH2S + SH

TS2 (Cs)

TS1 (C1)

TS3 (C1)

CH2SHS (C1)

CH2SSH (C1)

C S

S

H

HH

C S

SH

H

H

C S

S

H

H

H

C S

S

H

H

H

0

20

40

60

80

En

erg

y (

kca

l/m

ol)

Figure 5.1: Ground state potential energy surface for the isomerization and dissociation ofthe methyl perthiyl radical. Stationary points were calculated at the MP2(full)/6-31G(d)level of theory. Symmetries are given in parentheses. Exact structures can be found in Ref.[157].

energetically allowed products from the photodissociation of the methyl perthiyl radical:

CH3SS (X 2A′′)→ CH3 (X2A′′

2) + SS (X 3−g ) ∆H = 47.5 kcal/mol, (5.3)CH3SS (X 2A′′)→ CH3S (X 2E) + S (3P ) ∆H = 83.2 kcal/mol, (5.4)CH3SS (X 2A′′)→ CH2S (X 1A1) + SH (X 2) ∆H = 45.9 kcal/mol. (5.5)

Figure 5.1 shows asymptotic energetics and barrier heights for these channels on the groundstate potential energy surface taken from previous experimental151,164 and theoretical157 work.On this surface, channels 5.3 and 5.4164 involve simple C–S or S–S bond fission, respectively,while channel 5.5157 requires isomerization prior to dissociation. As will be discussed in Sec.5.3, only channels 5.3 and 5.5 are observed in the 248 nm photodissociation of CH3SS.

5.2 ExperimentalA molecular beam of CH3SS was produced by flash pyrolysis of DMDS and photodis-

sociated; the photoproducts were mass-analyzed using a rotatable detector. Details aboutthis instrument have been described elsewhere.39,126 A piezo-electric valve produced a pulsedbeam of 0.5% DMDS seeded in 2 atm of 10% N2 in He. The N2 was added to slow the molec-ular beam in order to facilitate detection of slower photofragments and to achieve bettertemporal separation of photofragments (see Sec. 5.3). Methyl perthiyl radicals were gener-ated using a resistively heated SiC flash pyrolysis source based on the design of Kohn et


al.53 and previously used by our laboratory to study the phenyl and tert-butyl radicals.37,127The radical beam was collimated by two skimmers that separate the source and main cham-bers of the machine. The beam was then crossed at 90 with the 248 nm output of a GAMEX100/500 excimer laser focused into a 3 × 1 mm2 beam spot. Typical pulse energies werearound 20 mJ/pulse. The laser and pulsed valve were operated at repetition rates of 100 Hzand 200 Hz, respectively, to allow for background subtraction. The scattered photofragmentswere detected as a function of laboratory scattering angle, Θlab, relative to the molecularbeam in the plane defined by the molecular and laser beams. After entering the detector,photofragments were ionized by an electron impact ionizer, mass selected with a quadrupolemass filter, and detected with a Daly style ion detector.128 Ion counts were recorded as afunction of time relative to the laser pulse. The resulting time-of-flight (TOF) spectra werecollected using a multichannel scaler interfaced to a computer. Typical TOF spectra were av-eraged over 100000 to 200000 laser shots. An iterative forward convolution program was usedto simulate the TOF spectra for photoproducts over all angles, resulting in a photofragmenttranslational energy distribution in the center-of-mass frame of reference.

The radical beam was characterized using a rotating, slotted chopper disk. Typical beamvelocities were around 1500 m/s with speed ratios between 5 and 6. The beam was furthercharacterized by taking mass spectra at Θlab = 0 as the SiC tube temperature was increased.Intensities of the CH3SSCH3

+ (m/z = 94) and CH3SS+ (m/z = 79) signals were monitoredas a function of current passing through the tube.

While complete removal of the precursor ion signal at m/z = 94 was possible, the remain-ing CH3SS+ signal at m/z = 79 was insubstantial under these very hot source conditionsand the only photodissociation signal observed was m/z = 32 (S+) from S2 produced inthe pyrolysis source; this signal was not observed under any other source conditions. Assuch, photodissociation data were taken under a variety of pyrolysis source conditions whilemonitoring the m/z = 64 photoproduct signal. Since m/z = 64, corresponding to the S2photoproduct, is not produced from the photodissociation of DMDS,151 ion signal at thismass was assumed to be from the methyl perthiyl radical. This assumption was tested ex-perimentally and will be discussed in Sec. 5.4. Because of incomplete precursor depletionfrom the beam and the large absorption cross section of dimethyl disulfide at 248 nm,149DMDS photodissociation experiments (pyrolysis source off) at 248 nm were also performed.

5.3 ResultsTOF spectra were taken for m/z = 64 (SS+), m/z = 47 (CH3S+), m/z = 46 (CH2S+),

m/z = 45 (CHS+), m/z = 33 (SH+), m/z = 32 (S+), and m/z = 15 (CH3+), representing

possible photofragments from channels 5.3–5.5 and daughter ions from dissociative ionizationin the electron impact ionizer.

Figure 5.2 shows sample TOF spectra for m/z = 64 at Θlab = 10 with and withoutflash pyrolysis as well as spectra at selected larger scattering angles. Signal from m/z =64 ions was seen over at laboratory angles as low as Θlab = 6 (the lowest angle spectrum


−50

0

50

100

150

200

250

300

0 100 200 300−50

0

50

100

150

200

250

0 100 200 300 400


Counts

50k, 10°pyrolysis off

100k, 10°pyrolysis on



Figure 5.2: Sample TOF spectra m/z = 64 (SS+) collected at various Θlab. The top spectrashow photodissociation signal without and with the pyrolysis source at Θlab = 10. TheP(ET) shown in Fig. 5.4 was used to simulate the signal attributed to the methyl perthiylradical (solid line). The number of laser shots averaged over is given in each TOF.

0 100 200 300

0

500

1000

1500

2000

0 100 200 300 0 100 200 300 400

Counts


m/z = 4750k, 15°

m/z = 46200k, 15°

m/z = 45200k, 15°

×2

Figure 5.3: TOF spectra showing evidence for channel 5.5. The fast, sharp peak appearing inall three spectra (dotted-dashed line) was well simulated as DMDS photodissociation usinga P(ET) similar to that reported by Lee et al.151 The second feature appearing in the m/z =46 and 45 spectra was attributed to the CH2S fragment from channel 5.5 and was simulated(dashed line) using the P(ET) in Fig. 5.5.

recorded) and disappeared by Θlab = 30. These spectra were attributed to channel 5.3, anassignment discussed in Sec. 5.4. TOF data are represented by the open circles while the solidlines represent simulations obtained by forward convolution of a center-of-mass translationalenergy distribution (see Sec. 5.4). While we attempted to observe the corresponding CH3signal from radical photodissociation at m/z = 15, there was too much background fromresidual DMDS photodissociation to do so.

Evidence for a second channel can be observed in Fig. 5.3. At Θlab = 15, two peaks


are resolved in the m/z = 46 and 45 TOF spectra but only one is seen at m/z = 47. Thesingle peak at m/z = 47 and the larger, faster peaks at m/z = 46 and 45 are present up toΘlab = 30, the largest angle collected. The second, smaller peak is seen up to Θlab = 25.As discussed in more detail in Sec. 5.4, we attribute the slower peaks at m/z = 46 and 45to the parent and daughter ion signals from the CH2S photofragment produced via channel5.5, while the faster peaks at these two masses and the single peak at m/z = 47 appear tobe from DMDS photodissociation via channel 5.1. TOF spectra taken at m/z = 33 (SH+)were inconclusive due to low signal levels, while m/z = 32 spectra were unusable due tocontributions from DMDS photodissociation and high background gas signal.

5.4 AnalysisThe results in Sec. 5.3 suggest that CH3SS undergoes photodissociation via channels

5.3 and 5.5. In this section, we first analyze our data based on this assumption and thenconsider alternative interpretations. Center-of-mass photofragment translational and angulardistributions, P(ET,θ) were obtained by simulating the TOF spectra of the photoproducts.For each channel, this distribution can be written as a product of uncoupled center-of-masstranslational energy and angular distributions,

P(ET,θ) = P(ET)I(ET,θ) (5.6)

where I(ET,θ) is the angular distribution and P(ET) is the translational energy distribution.The PHOTRAN129 forward convolution program was used to simulate all TOF spectra usingassumed P(ET) distributions. The input P(ET) was adjusted point-wise until a satisfactoryTOF simulation was achieved for all spectra. The experimental configuration used in thisstudy has the detector rotating in the plane defined by the molecular and laser beams, soan anisotropic distribution is possible with unpolarized laser light. However, satisfactoryagreement between simulation and experimental data was achieved by assuming isotropicdistributions for all ET. By conservation of energy, the total ET available is given by

ET = hν + E − Eint −D (5.7)

where hν is the photon energy, E is the initial internal energy of the methyl perthiyl radicals,Eint is the internal energy of the photoproducts, and D is the bond dissociation energy. Inthe limit of cold radicals (Eint = 0), the maximum translational energy ET,max is given byhν − D. For channel 5.3, ET,max = 67.5 kcal/mol whereas for channel 5.5, ET,max = 69.1kcal/mol.

The best TOF simulations for channels 5.3 and 5.5 are shown in Figures 5.2 and 5.3, re-spectively. The P(ET) distribution shown in Fig. 5.4, used to simulate channel 5.3, peaks at6.1 kcal/mol and extends to 34 kcal/mol, 33.5 kcal/mol below the maximum allowable trans-lational energy. The distribution has an average translational energy ⟨ET⟩ = 10.4 kcal/mol.The P(ET) distribution shown in Fig. 5.5 peaks at 5 kcal/mol and extends to 12 kcal/mol,


0 5 10 15 20 25 30 35 40 450

0.01

0.02

0.03

0.04

0.05

0.06

0.07


Pro

ba

bili

ty

Figure 5.4: Center-of-mass P(ET) distribution for C–S fission (black curve). For this channel,ET,max = 67.5 kcal/mol. The prior distribution as described in Sec. 5.4 is also shown (dashed,grey curve).

0 2 4 6 8 10 12 140

0.05

0.1

0.15

0.2

0.25

0.3

0.35


Pro

ba

bili

ty

Figure 5.5: Center-of-mass P(ET) distribution for SH loss. For this channel, ET,max = 69.1kcal/mol assuming ground state fragments.

which is 57.1 kcal/mol below the maximum allowable translational energy. This distribu-tion has an average translational energy ⟨ET⟩ = 5.8 kcal/mol, implications of these P(ET)distributions will be discussed in Sec. 5.4.

The interpretation of our TOF data in terms of channels 5.3 and 5.5 is based on theobservation of only a single fragment from each channel, rather than momentum-matchedpairs of fragments as would be preferred when carrying out radical photodissociation experi-ments. Consideration must be given to sources of signal other than perthiyl photodissociationcontributing to an observed TOF spectrum. In particular, owing to incomplete eliminationof DMDS from the molecular beam, the 248 nm photodissociation of this species must be


accounted for in all TOF spectra. As DMDS exclusively undergoes dissociation by channel5.1 at 248 nm, the pyrolysis source-dependent peak at m/z = 64 is a strong indication ofmethyl perthiyl production and dissociation via channel 5.3.

The assignment of channel 5.5 is not as straightforward, especially in light of its best-fitP(ET) distribution (see Sec. 5.4). Dissociative ionization of CH3S from DMDS channel 5.1yields daughter ions in the m/z = 46 and 45 spectra in Fig. 5.3, partly obscuring the slowerfeatures. However, since the slower peaks in those spectra were not observed in the 248 nmphotodissociation of DMDS (both in the present work and by Lee et al.151), these slowerfeatures are not from direct dissociation of the precursor. Another possibility is that thissignal is from secondary photodissociation of CH3S produced from DMDS via channel 5.1.While H-atom loss from CH3S is energetically allowed at 248 nm,15 the slower peaks in Fig.5.3 were not observed in the DMDS photodissociation experiments where further photodis-sociation would have been obvious. Finally, it is possible that the signal in question couldbe from photodissociation of other DMDS pyrolysis products generated in the source, suchas CH3S or CH2S. Attempts to simulate the signal as H + CH2S from the photodissociationof CH3S were unsuccessful. Trial P(ET) functions ranged from low translational energy dis-tributions similar to the work by Zheng et al.165 to a distribution peaking at the maximumavailable translational energy of 67.5 kcal/mol. All of these yielded TOF simulations withphotofragment arrival times later than the slower peak in the experimental spectra, particu-larly at larger laboratory angles. It thus appears that CH3S photodissociation is an unlikelyexplanation for the slower feature in the m/z = 46 and 45 TOF spectra. If this signal werefrom CH2S photodissociation, then there would only be signal at m/z = 45 and not m/z= 46. Overall, the slower peaks in Fig. 5.3 are most reasonably assigned to methyl perthiylradical photodissociation via channel 5.5.

5.5 DiscussionThe primary objectives of this study were (a) to probe the primary photochemistry of

the methyl perthiyl radical and (b) to gain insight into the photodissociation mechanism at248 nm. A key question is whether photodissociation occurs on an excited state surface or ifthe excited radical undergoes internal conversion to the ground state followed by statisticaldissociation. This issue can be addressed by examining the translational energy distributionsfor the observed channels to see if they are consistent with statistical decay on the groundstate surface.

Based on the schematic for the ground state surface in Fig. 5.1, no exit barriers are in-volved in the simple bond fission channels 5.3 and 5.4. In a statistical picture, the resultingP(ET) distributions should be most intense at low translational energy with most of theenergy distributed among the internal degrees of freedom. While channel 5.4 was not ob-served, channel 5.3 does peak at low translational energy, consistent with the high degree ofinternal excitation expected with ground state dissociation. To further test the hypothesis


that channel 5.3 is statistical, a prior distribution was calculated using the functional form20

P(ET|Eavail) ∝ E1/2T ρvr(Eavail − ET), (5.8)

where ET is the translational energy and ρvr(Eavail − ET) is the rotational-vibrational den-sity of states for the pair of fragments. To implement Eq. (5.8) for channel 5.3, five totalrotational degrees of freedom and seven total vibrational degrees of freedom (treated as clas-sical harmonic oscillators) were used. The resulting prior distribution for channel 5.3, shownin Fig. 5.4 as the dashed grey line, agrees reasonably well with the experimentally derivedP(ET), suggesting that dissociation for this channel occurs statistically on the ground statesurface.

The P(ET) distribution for channel 5.5 falls off more rapidly as ET → 0 than the distri-bution for channel 5.3, a result suggesting ground state dissociation over a small exit barrier.Such a result can be rationalized with reference to Fig. 5.1, which shows that the lowerenergy pathway to channel 5.3 involves isomerization over TS2 and then passage through ashallow well (19.8 kcal/mol with respect to products) coresponding to the CH2SSH struc-ture. Under these circumstances, energy randomization in this well may not occur, with theoverall P(ET) distribution still reflecting the effect of TS2. However, the form of this distri-bution is still unusual, as it implies a significant degree of product internal energy confinedwithin a narrow range of only a few kcal/mol. It is possible that this signal corresponds toCH2S in its first electronic excited state (A 1A2), which lies only 47 kcal/mol166 above thethioformaldehyde ground state with a corresponding ET,max of 22 kcal/mol. Full elucidationof the dissociation mechanism requires more information than is presently available. Obser-vation of the SH photofragment and a determination of the translational energy (or internalenergy distribution via techniques such as laser induced fluorescence) would provide furtherinsight into the exact dynamical process. Calculation of the excited state potential energysurfaces for CH3SS would also provide valuable insight.

The results for the methyl perthiyl radical can be compared to the 248 nm photofrag-mentation of the methyl peroxy (CH3O2) radical by Hartmann et al.167 In that experiment,ground state OH and CH3O products were seen by laser-induced fluorescence, and emissionfrom electronically excited OH(A2Σ+) was also observed. These are the analogues to chan-nels 5.4 and 5.5 in CH3SS photodissociation. Although Hartmann et al. were not set up todetect CH3 + O2 products, the analogue to channel 5.3, they proposed, based on quantumyield measurements, that this was in fact the dominant channel (74%), followed by CH3O +O (20%) and CH2O + OH (6%). However, the asymptotic energetics for CH3O2 dissociationare very different than for CH3SS; the lowest energy channel is production of CH2O + OH,which lies 21 kcal/mol below CH3O2, 52 kcal/mol below CH3 + O2 and 80 kcal/mol belowCH3O+O. The observation of OH(A2Σ+) indicates that at least some dissociation of CH3O2occurs on an excited state surface. Direct characterization of the CH3 + O2 channel wouldbe of considerable interest to see if that channel is indeed dominant and if so, whether itsdynamics are consistent with ground state dissociation.


5.6 ConclusionThe photodissociation dynamics of the methyl perthiyl radical has been explored at 248

nm using photofragment translational spectroscopy. Two channels were observed, CH3 + SSand CH2S+SH. The translational energy distribution for channel 5.3, CH3 +SS, is similar tothat expected for a simple statistical distribution, suggesting that the methyl perthiyl radicalundergoes internal conversion to the ground state prior to dissociation to these products.Channel 5.5, CH2S + SH, can occur via isomerization on the ground state surface but couldalso involve production of electronically excited CH2S.

AcknowledgementsThis work was supported by the Director, Office of Basic Energy Sciences, Chemical

Sciences, Geosciences, and Biosciences Division of the U.S. Department of Energy underContract No. DE-AC02-05CH11231.

70

Chapter 6

Production and Photodissociation ofthe Methyl Perthiyl Radical

The photodissociation dynamics of the methyl perthiyl (CH3SS) radical are investigated viamolecular beam photofragment translational spectroscopy, using “soft” electron ionizationto detect the radicals and their photofragments. With this new capability, we have shownthat CH3SS can be generated from flash pyrolysis of dimethyl trisulfide. Utilizing this sourceof radicals and the advantages afforded by soft electron ionization, we have reinvestigatedthe photodissociation dynamics of CH3SS at 248 nm, finding CH3S + S to be the dominantdissociation channel with CH3 + SS as a minor process. These results differ from previouswork reported in our laboratory in which we found CH3 + SS and CH2S + SH as the maindissociation channels. The difference in results is discussed in the light of our new capabilitiesfor characterization of radical production.§

6.1 IntroductionPolysulfides and the sulfur-centered radicals resulting from their decomposition occur

in diverse fields of chemistry. Low-valence sulfur compounds play important roles in sul-fur cycle chemistry,138,168 the cystine bond in proteins,137 and the Venusian atmosphere.169Due to the prevalence of the disulfide bond in particular, alkyl disulfides have been studiedextensively, with recent investigations focusing on the dynamics of alkyl disulfide photodis-sociation.152,153,170–173 Dimethyl disulfide (DMDS) is known to undergo two main dissociationpathways, cleaving either the C–S or S–S bond.140,150–152 While the photochemistry of thethiomethoxy radical (CH3S) has been studied,15,16,165 the methyl perthiyl radical (CH3SS)has received less attention. Apart from roles the methyl perthiyl radical may play in disulfidechemistry, the radical is of additional interest as an isovalent analog to the methyl peroxy

§Reprinted with permission from Cole-Filipiak, N. C.; Shapero, M.; Haibach-Morris, C.; Neumark, D. M.Production and Photodissociation of the Methyl Perthiyl Radical. J. Phys. Chem. A, Submitted. Copyright2015 American Chemical Society.

http://pubs.acs.org/journal/jpcafh

CHAPTER 6: The Methyl Perthiyl Radical, Part II 71

radical (CH3OO), an important species in combustion and atmospheric chemistry.7,161,162In this work, we investigate the ultraviolet photodissociation of CH3SS with improved ex-perimental capabilities compared to an earlier report from our laboratory, finding markedlydifferent results.

The electronic ground state of the methyl perthiyl radical is the X 2A′′ state, in whichthe radical electron is delocalized over the two S atoms in a π∗-like orbital.174,175 The ul-traviolet (UV) absorption spectrum of CH3SS has not been experimentally characterized,though spectra of HS2 and tert-butyl perthiyl radicals have been measured to ∼320 nmwith intensity maxima around 340−370 nm.146,176 Ionization energies and electron affini-ties of the methyl perthiyl radical have been characterized experimentally155,156,158,177 andtheoretically.156,157,175,178,179

The three lowest energy dissociation channels for the methyl perthiyl radical are:

CH3SS (X 2A′′)→ CH3 (X2A′′

2) + SS (X 3−g ) D = 48.6 kcal/mol,156,180,181 (6.1)CH3SS (X 2A′′)→ CH3S (X 2E) + S (3P ) D = 79.5 kcal/mol,16,156,182 (6.2)CH3SS (X 2A′′)→ CH2S (X 1A1) + SH (X 2) D = 46 kcal/mol.156,157 (6.3)

The CH3 +SS channel has been observed to occur from vibrationally hot CH3SS produced bythe photodissociation of dimethyl disulfide at 193 nm.140,150–152 While the SH loss channel islower in energy, the minimum energy pathway on the electronic ground state for this channelinvolves passage over a 50 kcal/mol isomerization barrier en route to the CH2SSH well.157An S2 loss pathway has been observed in the photodissociation of the tert-butyl perthiylradical at 365 nm using EPR spectroscopy in a hydrocarbon matrix.160

Recent theoretical work has explored electronic excitation of the methyl perthiyl radi-cal,175 finding two doublet states at 1.176 eV (1 2A′) and 3.422 eV (2 2A′′) above the groundstate. A bound quartet state (1 4A′′) was also found at 4.216 eV with dramatic elongation ofthe S–S bond. An additional 4A′ state was found to be repulsive along the S–S coordinateresulting in CH3S + S, but no excitation energy to this state was given.

Our laboratory reported the first investigation of the primary photochemistry of themethyl perthiyl radical.183 In that work, we attempted to generate CH3SS by flash pyrol-ysis of DMDS, photodissociate the radical at 248 nm, and characterize the products withphotofragment translational spectroscopy.184 The results indicated both CH3 loss (channel6.1) and SH loss (channel 6.3); there was no evidence for S–S cleavage, the only photodis-sociation channel for DMDS at 248 nm.150,151 Analysis was hindered by substantial radicalprecursor contamination and a lack of momentum-matched photofragment pairs from eitherdissociation channel. These concerns prompted our group to probe the radical photochemistrystarting from the methyl perthiyl anion185 using our fast radical beam (FRBM) photodisso-ciation instrument,47 a technique that allows for mass selection of the desired anion prior tophotodetachment and photodissociation. That investigation revealed a very different methylperthiyl photochemistry than our initial report: S-atom loss, channel 6.2, was the dominantdissociation pathway with CH3 loss as a minor contribution.


This discrepancy has led us to re-investigate the photodissociation of methyl perthiylvia flash pyrolysis and photofragment translational spectroscopy. Using a different radicalprecursor, dimethyl trisulfide, and a newly installed tunable energy electron ionizer,38 we wereable to optimize conditions for CH3SS production and determine its primary photochemistryat 248 nm. The results show the dominant channel to be CH3S + S, with evidence for a smallamount of CH3 + SS production.

6.2 ExperimentalThe experiments described herein were performed on a universal crossed molecular beam

machine with a fixed-source and rotatable detector, modified to perform photofragmenttranslational spectroscopy; further details may be found elsewhere.39,126 Room temperaturedimethyl trisulfide (DMTS, CH3S3CH3) was seeded in 1.2 bar of 10% N2 in He, resultingin ∼1% DMTS. The resulting gas mixture passed through a piezoelectric pulsed valve andthen through a resistively heated SiC flash pyrolysis source into the source vacuum chamber,resulting in a supersonic expansion. The pyrolysis source is based on the design of Kohnet al.53 and has been used previously in our lab to successfully produce several radicalspecies.38,127,186 Power dissipated by the source is controlled by a current regulated powersupply. DMTS was chosen as a radical precursor since, for alkyl sulfides with more thantwo sulfur atoms, the S–S bond is expected to have a dissociation energy of approximately34 kcal/mol, ∼20 kcal/mol weaker than the C–S bond in DMTS (and DMDS, the radicalprecursor used in our previous work).164

The free jet emerging from the source passes through two skimmers that serve to separatethe source and scattering chambers and to form a collimated molecular beam in the scatteringchamber. The radical beam was crossed at 90 with the 2 × 8 mm2 focused output of aLambda Physik LPX 220i laser at 248 nm; typical pulse energies were 60 mJ/pulse resultingin a photon fluence of 375 mJ cm−2. Pulse energies were also varied to perform photon fluencedependence studies as discussed in Sec. 6.7. The laser and pulsed valve were operated at 200and 400 Hz, respectively, to enable isolation of the photodissociation signal via backgroundsubtraction.

Photofragments were collected as a function of the laboratory scattering angle, Θlab,relative to the molecular beam in the scattering plane defined by the molecular and laserbeams. Upon entering the detector, photofragments were ionized using a “soft” electronionization (EI) source33 capable of producing electrons with tunable energy as low as 7 eV.Soft ionization has been shown by Casavecchia and co-workers57 to be a powerful tool inreactive scattering experiments, since it reduces dissociative ionization (DI) in the ionizerand, as discussed below, provides a useful means for optimizing radical production.

Cations produced in the ionizer were mass-selected using a quadrupole mass filter anddetected with a Daly style ion counter.128 Ion counts were recorded and binned as a func-tion of time relative to the laser pulse interacting with the molecular beam. The resultingtime-of-flight (TOF) spectra were collected using a multichannel scalar interfaced to a com-


puter and were typically averaged over 105−106 laser shots. All photofragment TOF spectrawere simulated using an iterative forward convolution program, producing center-of-masstranslational energy distributions as discussed in Sec. 6.4.

The radical beam was characterized by a spinning, slotted chopper wheel. Typical beamvelocities were around 1800 m/s with speed ratios, defined as the ratio of beam velocity tothe spread in velocities, of ∼5. Further characterization was performed by acquiring on-axis(Θlab = 0) mass spectra at a variety of pyrolysis source powers and monitoring depletion ofthe precursor parent signal at m/z = 126 (C2H6S3

+). For selected pyrolysis source powers,appearance energy measurements were carried out for several m/z values by taking ionizationefficiency curves (IEC), in which ion signal intensity was recorded as a function of electronenergy for fixed electron emission current. The linear portion of the resulting curve maythen be extrapolated to zero intensity, yielding the appearance energy of each ion mass.Appearance energies were used to find pyrolysis source conditions under which the CH3S2

+

signal at m/z = 79 originated from ionization of CH3SS as opposed to DI of the DMTSprecursor.

To determine the photofragment angular distribution, laser polarization studies wereperformed by passing the unpolarized excimer laser light through a stack of eight quartzplates at Brewster’s angle. The stack was held in a rotatable mount, allowing for rotation ofthe electric field with respect to the plane defined by the molecular beam and detector axis.The laser polarization was rotated in 20 increments while monitoring photodissociationsignal at fixed laboratory scattering angle, similar to the work described by Butler andco-workers.187,188 The polarization purity was determined by passing the output from thequartz stack through a birefringent MgF2 prism, resulting in two spatially separated, linearlypolarized spots. Measuring the intensity of each spot indicated that the combined outputfrom the quartz stack is a 9:1 mixture of the two linear polarizations.

Pyrolysis and photodissociation experiments were also performed under the conditionsof our previous study in which DMDS was used as the radical precursor183 and on thephotodissociation of DMTS itself; details of these experiments may be found in Sec. 6.7.

6.3 ResultsFigure 6.1 a) shows mass spectra of the molecular beam at two different pyrolysis source

conditions: a “cold” pyrolysis source (dissipating 0W), and a “hot” pyrolysis source (dissi-pating 45W). As the power dissipated by the source is increased, the DMTS parent peakat m/z = 126 disappears, leaving peaks at m/z = 79 (CH3S2

+), 64 (S2+), and 47 (CH3S+).

Under a third set of conditions at even higher power (80W), termed “very hot,” the m/z =79 contribution in the molecular beam is depleted, leaving a dominant feature at m/z = 64.

Figure 6.1 b) shows the ionization efficiency curves at m/z = 79 under cold and hotpyrolysis source conditions. An appearance energy of 12.1 eV at m/z = 79 was found withthe cold source, in agreement with the previously reported189 value of 12.3 ± 0.3 eV. Witha hot pyrolysis source, the curve visibly shifts and the appearance energy decreases to 8.7


40 60 80 100 1200

0.5

1

m/z

No

rma

lize

d I

nte

nsity

cold pyrolysis source

hot pyrolysis source

6 8 10 12 14 160

0.2

0.4

0.6

0.8


cold source

hot source

8.7 eV

12.1 eV

a) b) m/z = 79

No

rma

lize

d I

nte

nsity

Figure 6.1: a) Mass spectra of the molecular beam taken at two different pyrolysis sourcepowers normalized to the signal at m/z = 79. The black trace (cold pyrolysis source) showsthe precursor mass spectrum using an electron ionization energy of 19 eV. The red trace (hotpyrolysis source) shows depletion of the precursor peak. b) Ionization efficiency curves forthe m/z = 79 component of the molecular beam with the pyrolysis source cold (black) andhot (red).

eV, in good agreement with the known ionization energy of 8.63 eV for CH3SS.158 Similarly,m/z = 47 shows an appearance energy of 12.5 eV with a cold pyrolysis source (previouslyreported189 as 12.9± 0.2 eV), dropping to 9.2 eV with a hot pyrolysis source, consistent withthe production of CH3S.190 It is important to note that, for dissociative ionization, an ap-pearance energy derived from a linear extrapolation is not equivalent to the thermochemicalthreshold for daughter ion formation.69 A more rigorous fit of the threshold region using apower law, as discussed in detail elsewhere,72 yields dissociative ionization appearance ener-gies of 10.6±0.6 eV and 10.4±0.6 eV, respectively, in excellent agreement with the expectedvalues of 10.8 eV for CH3S+ + CH3SS and 10.1 eV for CH3S + CH3SS+ from DMTS.158,164,191Similar measurements were performed with the DMDS precursor as discussed in Sec. 6.7.Unlike DMTS, pyrolysis of DMDS appears to only produce small quantities of CH3SS beforedecomposing to S2.

TOF spectra were taken for photofragment signals at m/z = 79, 64, 47, 46 (CH2S+),45 (CHS+), 44 (CS+), 33 (SH+), 32 (S+), and 15 (CH3

+), accounting for the dissociationchannels 6.1–6.3 and daughter ions from dissociative ionization (DI) during EI. With acold pyrolysis source, DMTS photodissociation using an electron ionization energy of 16 eVrevealed one TOF feature at m/z = 79 and 47; further discussion may be found in Sec.6.7. With a hot pyrolysis source, no photodissociation signal was observed at m/z = 79 forspectra averaged for 106 laser shots, consistent with total depletion of the DMTS under theseconditions.

Sample TOF spectra taken with a hot pyrolysis source and an electron ionization energy


−20

0

20

40

60

80

100

50 100 150

0

200

400

600

50 100 150


Counts

m/z = 4715°

200k shots

m/z = 3225°

1M shots

m/z = 3215°

500k shots

m/z = 4740°

500k shots

Figure 6.2: Example TOF spectra taken at m/z = 47 (top row, 2 µs bin width) and m/z = 32(bottom row, 1 µs bin width) using unpolarized laser light and an electron ionization energyof 19 eV. The open circles are data while the solid line is a forward convolution simulationfrom the P(ET) in Fig. 6.5. The dashed lines at m/z = 32 are a forward convolution simulationfrom the P(ET) in Fig. 6.15 assuming CH3S photodissociation.

of 19 eV are shown in Figs. 6.2 and 6.3. Figure 6.2 shows TOF spectra at m/z = 47 at Θlab= 15 and 40. These spectra exhibit one sharp peak; similar spectra are seen from Θlab =15−45. TOF spectra at m/z = 47 and Θlab < 15 exhibit an additional slow peak. Figure6.2 also shows TOF spectra at m/z = 32 at Θlab = 15 and 25; the two features seen herepersist out to Θlab =45, the highest angle taken at this m/z value. TOF spectra taken atm/z = 32 and high electron energy (100 eV) do not have well resolved features, most likelydue to ionization of background O2; example spectra are shown in Sec. 6.7. TOF spectralfeatures at m/z = 46 and 45, as well as the second TOF feature at m/z = 32 and 47, areattributed to CH3S photodissociation and are discussed in Sec. 6.7. Spectra at m/z = 33comprise several overlapping, unresolved features.

The TOF spectra in Fig. 6.3 show one broad feature at m/z = 64 at Θlab = 20 and 35,observed over Θlab = 5−35 that could arise from dissociation of CH3SS to CH3 + SS. Theonly TOF feature found at m/z = 15 appears to be DI of the fast feature at m/z = 47. Owingto unfavorable kinematics and either high background signal (due to large background gasDI at high electron ionization energies) or a low EI cross section at low electron ionizationenergies,75 no CH3 photofragment signal from CH3 + SS is observed.

TOF spectra were also taken using the very hot pyrolysis source conditions that depleteCH3SS from the molecular beam; representative spectra may be found in Fig. 6.18 in Sec. 6.7.


0 100 200−20

0

20

40

60

80


Counts

0 100 200 300

m/z = 6420°

°m/z = 6435°

Figure 6.3: Example TOF spectra taken at m/z = 64 using unpolarized laser light and anelectron ionization energy of 19 eV. The open circles are data while the solid line is a forwardconvolution simulation from the P(ET) in Fig. 6.6.

Multiple photodissociation features present with a hot source were absent with a very hotsource, including: the faster half of the m/z = 64 TOF feature at Θlab ≤ 15, the entire m/z= 64 feature for Θlab ≥ 20, and the fast peaks at m/z = 47 and m/z = 32. Conversely, them/z = 33 TOF spectra were relatively unchanged compared to the results with a hot source.The correlation between the depletion of CH3SS from the molecular beam and the loss ofthe fast contributions to the m/z = 64, 47, and 32 TOF spectra supports the assignment ofthese features to methyl perthiyl radical photodissociation. These results also suggest thatTOF features observed under both hot and very hot pyrolysis source conditions, namely theobserved m/z = 33 signal and the slower contributions to the m/z = 64, 47, and 32 TOFspectra, are not due to photodissociation of the methyl perthiyl radical and may be ignoredin the analysis.

Figure 6.4 shows the results of the laser polarization study for m/z = 47 photoproductat Θlab = 15 and the m/z = 64 photoproduct at Θlab = 20. To determine the signalintensity, the entire m/z = 47 TOF spectrum was integrated while, at m/z = 64, a 50 µswindow centered at the peak was integrated. These signals are plotted as a function of φ, theangle between the laser polarization and the scattering plane. At m/z = 47, a clear drop inphotofragment intensity is observed as φ increases from 0 to 90. Conversely, the intensityat m/z = 64 appears to have no dependence upon the laser polarization angle.

The attempt to replicate previous experimental results using DMDS as the radical pre-cursor is found in Sec. 6.7. Briefly, a pyrolysis source dependent photodissociation featureat m/z = 64 was again observed, along with a feature at m/z = 79 and m/z = 47, 46, and45. Very low energy electron ionization mass spectra and appearance energy measurementsof molecular beam constituents taken at a variety of pyrolysis source powers show little tono production of CH3SS from DMDS.


0 20 40 60 80 100 120

0.4

0.6

0.8

1

1.2

ϕ (degrees)

Norm

aliz

ed Inte

nsity

m/z = 47

β = 0.6

β = 0.8

β = 1.0

m/z = 64

β = 0

Figure 6.4: Photofragment intensity at m/z = 47 (black) and m/z = 64 (red) as a functionof φ. Intensities are normalized to φ = 0, the lowest angle recorded. Error bars representthe standard deviation from the average intensity for repeated values of φ. The curves areplots of Eq. (6.6) for the indicated values of β, also normalized to φ = 0.

6.4 AnalysisTaken together, the results presented above strongly indicate that DMTS is pyrolyzing to

produce the methyl perthiyl radical and that we observe clear photodissociation signal un-der the source conditions that produce this radical. To analyze these laboratory-frame data,we determine the corresponding center-of-mass translational energy and angular distribu-tions P(ET, θ). These distributions are generated by simulating the observed TOF featuresassuming uncoupled center-of-mass translational and angular distributions,

P(ET, θ) = P(ET ) I(θ), (6.4)where P(ET) is the CM translational energy distribution and I(θ) is the photofragmentangular distribution. The photofragment intensity dependence on the laser polarization incenter-of-mass coordinates has the functional form:34

I(θ) = 1

4π[1 + β P2(cos θ)], (6.5)

where β is the anisotropy parameter, P2(x) is the second degree Legendre polynomial, and θis the CM scattering angle (the angle between the electric field vector and the CM productrecoil axis). The anisotropy parameter ranges in value from 2 to −1 depending on whetherthe transition dipole is parallel or perpendicular to the dissociation axis. For incompletepolarization of the laser light, the observed TOF intensities will have contributions fromboth linear polarizations and Eq. (6.5) must be rewritten to account for the incompletepolarization. For the experimental geometry used herein, Eq. (6.5) becomes:

I(θ) ∝ 3

2β(cos2 ω)[x cos2 φ+ (1− x) sin2(φ)], (6.6)


0 10 20 30 400

0.05

0.1

0.15

0.2

0.25

0.3


Pro

babili

ty

⟨ET⟩ = 27.4 kcal/mol

Eavail

Figure 6.5: Center-of-mass P(ET) assuming anisotropic S–S bond fission (β = 0.8) fromthe methyl perthiyl radical used to simulate the TOF spectra in Fig. 6.2 (solid line). Themaximum observed translational energy is 38 kcal/mol.

where ω is the angle between the CM recoil axis and the molecular beam in the scatteringplane, φ is the angle between the electric field vector and the scattering plane, cos θ =cosω cosφ, and x is the dominant fraction of light polarization (x = 0.9 for this experiment).To determine ω, the TOF signal at each m/z value was assumed to come from a single CMvelocity corresponding to the peak of the TOF spectrum, yielding ω = 35 at m/z = 47and 68 at m/z = 64. The value of β may be determined by plotting Eq. (6.6) along withphotofragment intensity for fixed laboratory scattering angle versus φ, as shown in Fig. 6.4for the m/z = 47 photofragment at Θlab = 15 and m/z = 64 photofragment at Θlab =20.18746 The best overall agreement between the CH3S TOF intensity data and Eq. (6.6)appears to be for β = 0.8. To estimate the error in the anisotropy parameter, Eq. (6.6) wasplotted for several values of β that still simulated the experimental data, yielding β = 0.8 ±0.2. The m/z = 64 intensity data shown in Fig. 6.4 have no clear dependence on the laserpolarization, suggesting an isotropic angular distribution.

The PHOTRAN forward convolution program129 was used to produce the CM transla-tional energy distributions shown in Figs. 6.5 and 6.6. Trial forms of the distribution areiteratively adjusted point-wise until TOF simulations agree with all photofragment data forall scattering angles acquired with unpolarized laser light. For the CH3S + S distributionin Fig. 6.5, a value of β = 0.8 was used while the CH3 + SS P(ET) shown in Fig. 6.6 wasproduced using an isotropic (β = 0) angular distribution.

By conservation of energy, the available energy (Eavail) in photodissociation is given by:

Eavail = hν −D + E = ET + Eint, (6.7)

where hν is the photon energy, D is the bond dissociation energy, E is the nascent radicalinternal energy, ET is the photoproduct translational energy, and Eint is the photoproduct


0 10 20 30 40 50 60 700

0.02

0.04

0.06

0.08


Pro

babili

ty

⟨ET⟩ = 24 kcal/mol

Eavail

Figure 6.6: Center-of-mass P(ET) assuming isotropic C–S bond fission from the methylperthiyl radical used to simulate the TOF spectra in Fig. 6.3. The maximum translationalenergy is 67 kcal/mol in agreement with the expected Eavail = 66 kcal/mol. Translationalenergies below ∼17 kcal/mol (shaded gray) are uncertain due to a slower contribution to thephotodissociation feature appearing at lower laboratory scattering angles and m/z = 64.

internal energy. In the limit of internally cold radicals (E = 0) and photoproducts (Eint =0), the maximum translational energy is given by Eavail = hν −D = ET.

The simulations shown in Fig. 6.2 were generated using the P(ET) shown in Fig. 6.5. Thedistribution peaks at 28 kcal/mol with an average translational energy ⟨ET⟩ = 27.4 kcal/moland extends to 38 kcal/mol. A key feature of the TOF assignments is that counter-fragmentsfrom a dissociation channel must be described by the same translational energy distribution.As shown in Fig. 6.2, the fast features at m/z = 47 and m/z = 32 can be simulated as“momentum-matched” CH3S and S-atom fragments from CH3SS dissociation. Further ev-idence of the assignment is the agreement between the observed maximum translationalenergy and the expected Eavail.

Assignment of the m/z = 64 TOF spectra of Fig. 6.3 is not as straightforward. Withoutobservation of the CH3 counter fragment, the observed feature can only be tentatively as-signed to the CH3 + SS product channel. Caution is required as spectra for Θlab ≤ 15 showan increasingly prominent contribution at longer flight times (see Figure 6.19 in Sec. 6.7for an example TOF spectrum) that persists under the very hot pyrolysis source conditionsthat deplete CH3SS from the molecular beam. While this contribution to the TOF does notappear to be from the methyl perthiyl radical, it obscures signal from CH3SS at long flighttimes. The TOF data for Θlab ≥ 20 in Fig. 6.3 were simulated with the P(ET) shown inFig. 6.6. This distribution has an average translational energy ⟨ET ⟩ = 24 kcal/mol, peaksaround 17 kcal/mol, and extends to the expected Eavail. Attempts to simulate the slowercontribution assuming methyl perithyl photodissociation were unsuccessful, consistent withthe interpretation that this TOF contribution is not from CH3SS.


For the TOF features currently attributed to CH3SS photodissociation, other sources ofsignal must be considered, as DMTS not only pyrolyzes to methyl perthiyl radical, but alsoto CH3S (by necessity) and possibly S2 (based our results with a very hot source). Eitherof these may absorb a photon at 248 nm12,192 and CH3S photodissociation does appear tocontribute to some of the observed TOF signal, but neither can account for all of the observedphotodissociation features. Small amounts of DMDS are present in our DMTS sample, butthe observed TOF features are not consistent with DMDS photodissociation at 248 nm.151,183CS2 and S3 appear as minor contributions in the mass spectrum in Fig. 6.1 with the pyrolysissource on. CS2 does not absorb 248 nm light,193,19457,58 and there was no evidence for themomentum-matched m/z = 32 counter fragment assuming that S3 dissociation produces thefeatures at m/z = 64. As such, the most reasonable conclusion is that the methyl perthiylradical photodissociates via the CH3S + S and CH3 + SS pathways.

We next consider the branching ratio for these two channels. In previous work in our lab,most recently on the benzyl radical,38 product branching ratios were determined by finding atleast one m/z value with TOF contributions from all photoproduct channels. Here, however,no single m/z value shows features from both CH3SS dissociation pathways. Nonetheless,the photodissociation product channel branching ratio may be calculated using the followingequation:35

N+1 (Θlab, Eelec)

N+3 (Θlab, Eelec)

× σ3(Eelec)

σ1(Eelec)× f3(Eelec)

f1(Eelec)× T3

T1

= BR(A/B)×(m1 ×m4

m2 ×m3

)×

∫PA(ET )IA(θ)v1/u1dv1∫PB(ET )IB(θ)v3/u3dv3

. (6.8)

The notation in Eq. (6.8) assumes two photodissociation channels, with masses m1+m2 fromchannel A and m3 +m4 from channel B. For the analysis below, channel A will be CH3S +S with m1 = 47 amu as the detected mass and channel B will be CH3 + SS with m3 = 64amu. The left side of Eq. (6.8) calculates the ratio of neutral photofragment intensities fromtwo channels at a given laboratory scattering angle: N+

i (Θlab,Eelec) is the laboratory TOFsignal of the species of interest at Θlab and electron ionization energy Eelec, σi is the electronionization cross section, fi is the probability of the fragment appearing at that m/z value, andTi is the ion transmission probability through the quadrupole. On the right side of Eq. (6.8),BR(A/B) is the product branching ratio of channel A to channel B, mi is the mass of speciesi, and vi and ui are the laboratory and CM velocities of photofragment i, respectively. Foreach point in the integration, ui and θ are determined by the velocity of the molecular beam,the photofragment laboratory velocity vi, and the laboratory scattering angle Θlab. Eachintegral evaluates the probability that a CM velocity will result in a laboratory velocity thatcontributes to the TOF at a given Θlab. Further details and a derivation of this relationshipmay be found in Appendix B of Ref. [35].

The electron ionization cross section σi may be calculated using the Binary-Encounter-Bethe (BEB) Model;195 details of this calculation may be found in Sec. 6.7. Briefly, the BEBmodel takes an orbital binding energy and electron kinetic energy (calculated using the Q-Chem software package196) to calculate an electron ionization cross section for each orbital


for a given electron ionization energy. The total electron ionization cross section is thendetermined by summing all orbital cross sections. As the calculated cross sections showed adependence on the theoretical method employed, all combinations of the cross section ratioin Eq. (6.8) were calculated and an average ionization cross section ratio of 1.4 ± 0.2 wasfound. The third term in Eq. (6.8), fi, was determined by collecting TOF spectra at eachm/z value with measurable signal; values of 44% for CH3S at m/z = 47 and 100% for S2at m/z = 64 were found using an electron ionization energy of 19 eV. As the differencein m/z for the two fragments is small compared to the mass range of the radio frequencyoscillator used in these experiments, the ratio of transmission probabilities is approximatedas unity. The translational energy distributions shown in Figs. 6.5 and 6.6 were used forPA(ET) and PB(ET), respectively, with β = 0.8 or 0 for the respective angular distributions.The molecular beam was assumed to have a uniform velocity of 1800 m/s. Averaging overall of the calculated cross sections and the BR determined at Θlab = 20−35, the productbranching ratio is 15 ± 10 in favor of the CH3S + S pathway. The error in the branchingratio was estimated by calculating the BR using a range of CH3 + SS translational energydistributions that still produce reasonable simulations of the m/z = 64 TOF spectra for Θlab= 20−35.

6.5 DiscussionThe principal objective of this study was to reconcile the differences between our previous

investigation of the methyl perthiyl radical183 with recent results from our group.185 Ouroriginal investigation suggested dissociation via C–S bond cleavage and an apparent SH losschannel while the FRBM results revealed almost exclusive S–S bond fission. As mentionedabove and discussed in Sec. 6.7, our current results suggest that flash pyrolysis of our originalprecursor, dimethyl disulfide, did not produce sufficient quantities of CH3SS to determine theradical’s photochemistry. DMTS appears to be a superior precursor for CH3SS productionbecause S–S bond cleavage requires less energy than the C–S bond cleavage required whenusing DMDS.164

It is important to note that the data previously presented do not appear to be in error:replication of our previous experiment again revealed a pyrolysis source dependent TOFfeature at m/z = 64 and m/z = 46. In the original investigation, TOF spectra acquired atm/z = 79 showed no discernible photofragment signal. These TOF spectra, though, were notacquired for a sufficient number of laser shots to observe the photodissociation signal at thism/z value as shown in Fig. 6.9 in Sec. 6.7—evidence that would have called into question theassumption of methyl perthiyl radical photodissociation. Information about the ionizationenergy of species in the molecular beam was not available at the time. Thus, our primary errorappears to have been the assumption of methyl perthiyl production and photodissociation.Taken with the results from our investigations of the phenyl radical,37,186 this work againhighlights the exceptional care that must be taken when attempting to produce and studythese reactive intermediates.


In the present work, analysis of the molecular beam shows good agreement between themeasured and literature vales for the methyl perthiyl radical ionization energy. Photodis-sociation at m/z = 47 and 32 show momentum-matched photofragments with the resultingP(ET) in agreement with the most recent results from our group.185 Disappearance of thephotodissociation features attributed to the methyl perthiyl radical under the “very hot” py-rolytic conditions that remove the m/z = 79 contribution from the molecular beam stronglysuggests that these photofragments are from CH3SS. The preponderance of evidence pre-sented herein thus indicates CH3SS production and photodissociation and we now proceedonto our original goal of determining this radical’s primary photochemistry.

For the CH3S+S channel, the P(ET) in Fig. 6.5 is peaked far away from zero translationalenergy and very close to the available energy for electronic ground state photoproducts. Thistype of behavior is indicative of dissociation on a repulsive electronic state.184 This inter-pretation is supported by the measurable photofragment anisotropy, a signature of rapiddissociation prior to substantial energy redistribution or rotational motion of the photoex-cited radical.197 If dissociation is occurring on a repulsive surface, an impulsive model ofthe dissociation may be used to describe the product energy partitioning.20,198 For a pureimpulsive dissociation of an initially stationary, nonlinear, triatomic species ABC along theA–B coordinate, ET may be given by:

ET =µa

µf

Eavail, (6.9)

where µa is the reduced mass of atoms A and B, and µf is the reduced mass of fragments Aand BC. The total internal energy is thus:

Eint =

(1− µa

µf

)Eavail. (6.10)

Approximating the methyl perthiyl radical as a triatomic and using the value Eavail = 35kcal/mol, Eqs. (6.9) and (6.10) yield ET = 29 kcal/mol and Eint = 6 kcal/mol. This modelvalue of ET is in good agreement with the peak value of ET = 28 kcal/mol for the P(ET)shown in Fig. 6.5 and supports the conclusion that S-atom loss is occurring on a repulsiveelectronic state.

The CH3 + SS channel is less straightforward to assess than the S-atom loss channel.The broad, unstructured translational energy distribution shown in Fig. 6.6 is peaked awayfrom either ET = 0 or Eavail and is not consistent with dissociation on a repulsive state nordoes complete vibrational energy redistribution seem to have occurred. The isotropic angulardistribution also suggests that prompt dissociation does not occur. Further dynamical infor-mation cannot be inferred without the portion of the P(ET) below 17 kcal/mol. Nonetheless,given that CH3 + SS is a low energy dissociation channel, it is possible it arises from internalconversion to the electronic ground state followed by dissociation to these products.

While TOF spectra at m/z = 46 and m/z = 33 exhibit photodissociation signal notattributed to S-atom loss, these features remain under the very hot pyrolysis source condi-tions that remove CH3SS from the molecular beam. Trial translational energy distributions


assuming CH2S + SH (channel 6.3) could not simultaneously simulate the observed spec-tral features, supporting the conclusion that these photofragments are not from the methylperthiyl radical. Thus our current results suggest that SH loss is at most a very minor processafter photoexcitation at 248 nm.

The current CH3SS photodissociation results are in agreement with the FRBM study185

at 248 nm. Both experiments conclude that S-atom loss occurs on a repulsive excited state toproduce ground state photoproducts. The measured anisotropy parameter of 0.8 is consistentwith a parallel transition and in qualitative agreement with the FRBM value of 1.4. Thereported branching ratio of (S-atom loss/CH3 loss) = 15 (i.e. 94% S-atom loss) is also inexcellent agreement with the FRBM result of 96% S-atom loss.

6.6 ConclusionThe photodissociation dynamics of the methyl perthiyl radical have been reinvestigated at

248 nm. With a new precursor and the ability to characterize our radical pyrolysis source withsoft electron ionization, we have been able to verify CH3SS production and photodissociation.We find clear evidence through the observation of momentum-matched photofragments thatthe major dissociation channel is CH3S + S on a repulsive surface, and additional indicationsthat CH3 + SS occurs as a minor channel. These results are in overall agreement with recentresults in our laboratory on another instrument. The work presented herein showcases theadvantages of using a tunable energy electron ionizer for both radical characterization andsimplification of photodissociation spectra.

AcknowledgementsThe authors would like to thank Narbe Mardirossian and Yuezhi Mao for assistance with

Q-Chem, Patrick W. Smith for synthesis of a potential radical precursor, and Drs. AaronW. Harrison and Mikhail Ryazanov for helpful discussions. This work was supported by theDirector, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and BiosciencesDivision of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

6.7 Supporting Information6.7.1 Reproduction of Previous Experiment

The conditions of our original investigation were repeated.183 Briefly, 1.8 bar of eitherpure He or 10% N2 in He was bubbled through 0C dimethyl disulfide (CH3SSCH3, DMDS).The resulting gas mixture was used as described in the main article as a radical source. In ourprevious investigation, pyrolysis source powers were chosen such that the m/z = 94 signal waspartially depleted while preserving intensity at m/z = 79 and maximizing photodissociation


60 65 70 75 80 85 90 95 100

0

500

1000

1500

2000

2500

3000

m/z

Counts

0W

50W

75W

×2

×5

Figure 6.7: Very low electron ionization energy (∼10 eV) DMDS mass spectra taken at severalpyrolysis powers.

intensity at m/z = 64, a feature not observed from DMDS photodissociation. The highestpyrolysis powers investigated, resulting in full depletion of DMDS from the molecular beam,showed no TOF signal at m/z = 64 but substantial signal at m/z = 32 assigned to S2photodissociation.

Matching the results of our original investigation,183 the DMDS parent peak at m/z =94 is depleted by heating the pyrolysis source. At the powers needed to completely eliminatethe precursor feature, the m/z = 79 peak is also depleted. Fig. 6.7 shows example massspectra taken at very low electron energies, showing only modest growth of the m/z = 79feature by 50W and complete removal of both m/z = 94 and 79 by 75W. With our tunableenergy electron ionizer, the appearance energy (AE) of several m/z values were measuredas a function of pyrolysis source power. As evidenced by Fig. 6.8, there does not appearto be a pyrolysis source power where the primary contribution to the m/z = 79 feature isthe methyl perthiyl radical until the end of the plotted range. These powers, however, haveinsubstantial signal at this m/z value compared to the (still dominant) m/z = 94 precursorfeature as seen in Fig. 6.7. No larger species (e.g. CH3S4CH3) were detected in the molecularbeam during pyrolysis.

With the pyrolysis source off (0W), DMDS photodissociation was observed; the onlyfeature was a fast, sharp TOF peak at m/z = 47 due to cleavage of the S–S bond. This resulthas been established in the literature150,151 and was observed in our original investigation.183For pyrolysis source powers of 15W to 70W, a TOF feature at m/z = 64 was observed (seeFig. 6.9). This feature disappears when the m/z = 79 component of the molecular beam isdepleted—e.g. the 75W mass spectrum shown in Fig. 6.7—in agreement with the behaviorseen in our original experiment. Two TOF features were observed at m/z = 46 and 45.Longer TOF integration times than were previously used revealed a second feature at m/z= 47. TOF spectra at m/z = 79 were taken to check for contaminant photodissociation.


0 10 20 30 40 508

10

12

14

16

Pyrolysis Source Power (W)

Ap

pe

ara

nce

En

erg

y (

eV

) m/z = 47m/z = 64m/z = 79m/z = 94

S2

CH3SS

Original Power

Range

Figure 6.8: Appearance energies of several relevant m/z values during the pyrolysis of DMDS.The dashed lines indicate the ionization energies of the corresponding neutral species. Thegray lines show the range of pyrolysis source powers with photodissociation signal attributedto CH3SS in the original investigation.183

For spectra taken with the conditions of our original experiment (pyrolysis source power,number of laser shots, etc.) no features were observed. However, integration of these spectrafor additional laser shots revealed one TOF peak as shown in Fig. 6.9.

Several dissociation channels and trial translational energy distributions were tested to de-termine the source of the m/z = 79 TOF feature, however no counter fragment was observed.Without a counter fragment or obvious contaminant in the molecular beam, assignment ofthe photodissociating molecule was not possible. Nonetheless, a stand-in P(ET) producedsatisfactory m/z = 79 TOF simulations for testing TOF spectra at other m/z values. Thesesimulations suggest that the feature at m/z = 64 and the slower feature at m/z = 47−45may be due to dissociative ionization (DI) of the m/z = 79 photoproduct. As a TOF featureat m/z = 79 over the observed angular range cannot be from photodissociation of the methylperthiyl radical and the appearance energy measurements do not indicate significant CH3SSproduction, it is unlikely that our previously reported1 TOF features are primarily due toCH3SS photodissociation.


0 100 200−100

0

100

200

300

400

500

Co

un

ts

0 100 200 0 100 200 300


m/z = 4715°

50k shots

m/z = 6425°

300k shots

m/z = 7925°

1M shots

Figure 6.9: Example m/z = 47, 64, and 79 spectra taken with a pyrolysis power of 35W andan electron ionization energy of 100 eV. The number of laser shots is given in each spectrum.The simulation shown at m/z = 47 is for DMDS photodissociation using the known P(ET).151

6.7.2 Dimethyl Trisulfide PhotodissociationPhotodissociation of dimethyl trisulfide (DMTS) was performed using 169 mJ cm−2 of

248 nm laser light under the experimental conditions outlined in Sec. 6.2. Photoexcitationat this wavelength most likely accesses an electronic excited state at 5.2 eV with primarilyσ∗SS character.199 One primary channel was found, S–S fission resulting in CH3SS and CH3S

photofragments. Selected TOF spectra at m/z = 79 and 47 are shown in Fig. 6.10 withsimulations from the translational energy distribution shown in Fig. 6.11 a). TOF spectraat m/z = 64 are dominated by DI of the m/z = 79 photofragment, however there is addi-tional TOF signal at longer flight times (see Fig. 6.12). Low electron energy TOF spectra(i.e. without dissociative ionization) reveal that the m/z = 47 feature also extends to longerflight times than is simulated by the P(ET) from the m/z = 79 feature. Taken together, theseresults suggest that some of the CH3SS photoproduct is produced with enough internal exci-tation to undergo spontaneous secondary dissociation to produce SS + CH3, analogous to thephotodissociation of DMDS at 193 nm.140,150–152 Simulations including the secondary pho-toproduct (Fig. 6.12) were performed using the CMLAB3 software package;200 the resultingP(ET) may be found in Fig. 6.11 b). TOF spectra at m/z = 15 were inconclusive due tohigh background or low photodissociation signal.


0

50

100

150

0 100 200

0

50

100

0 100 200 300


Counts

m/z = 7910°

m/z = 7930°

m/z = 4715°

m/z = 4725°

Figure 6.10: Example TOF spectra of the m/z = 79 (top row, 19 eV electron ionizationenergy) and m/z = 47 (bottom row, 16 eV electron ionization energy) observed in thephotodissociation of DMTS. The open circles are data while the lines are simulations fromthe P(ET) shown in Fig. 6.11.

0 10 20 30 400

0.05

0.1

0.15

0.2


Pro

babili

ty

0 5 10 15 200

0.1

0.2

0.3

0.4

0.5

0.6

0.7a) b)

Figure 6.11: a) P(ET) for the S–S bond fission of DMTS. The black trace was used to simulatethe m/z = 79 spectra while the gray line indicates the additional probability for simulationof the low electron energy m/z = 47 spectra. The two P(ET) have been normalized to thesame height for ease of visualization. b) P(ET) for the secondary dissociation of internallyexcited CH3SS.


0 100 200

0

50

100

150

Counts

0 100 200 0 100 200 300


m/z = 6410°

m/z = 6420°

m/z = 6430°

Figure 6.12: Example TOF spectra taken with 19 eV electron ionization energy at m/z =64. The open circles are data while the dashed line is a forward simulation from black P(ET)in Fig. 6.11 a). The dotted line is a simulation from the P(ET) in Fig. 6.11 b).

6.7.3 Thiomethoxy Radical PhotodissociationDirect photodissociation of the thiomethoxy radical (CH3S) has been limited to a handful

of studies. Utilizing a 2 + 1 REMPI scheme to ionize sulfur atoms, Hsu et al.15 determinedthat CH3S dissociation at 193 nm produces both S(3Pj) and S(1D) with a branching ratio of15:85 in favor of S(1D) production. Our group investigated the CH3 + S channel in two UVranges (315−366 nm and ∼220 nm).16 The results around 220 nm suggested dissociation onthe repulsive B 2A2 state with CH3 + S(3Pj) as the primary dissociation channel. Excitationto the A 2A1 state, below the CH3 + S(1D) asymptotic energy, was found to dissociate toCH3 + S(3Pj) via photon energy dependent coupling to the 4A2 and 4E states. Recently, theH-atom loss channel has been investigated from the A 2A1 state165 after excitation at 351nm, finding a broad, structureless P(ET) peaked at low translational energy, consistent withelectronic ground state CH2S + H dissociation.

Pyrolytic production of CH3SS from DMTS also produces the thiomethoxy radical (seeSec. 6.3), and some of our results may be attributed to the photodissociation of this species.TOF spectra at m/z = 46 and m/z = 45 exhibit two features; example m/z = 46 spectraare shown in Fig. 6.13. A fast, sharp peak (attributed to DI of the m/z = 47 fragment)is observed from Θlab = 10 to 45. For Θlab ≤ 16 a second, slow, broad feature at m/z= 46 and m/z = 45 is observed. This slow feature suggests H-atom loss from CH3S andthe TOF spectra shown in Fig. 6.13 were simulated by the P(ET) in Fig. 6.14 assumingCH2S + H. The P(ET) is qualitatively similar to the previous H-atom loss P(ET) at 351nm:165 the distribution is broad, extends to the maximum available energy, and is peaked atlow translational energies. TOF at m/z = 47 had an additional small, slow feature Θlab <15. Due to the relatively abundant sulfur isotopes, H-atom loss from CH3S is assigned tothis second m/z = 47 feature.


0 100 200

0

500

1000


Counts

0 100 200 300

×2

m/z = 467°

m/z = 4612°

Figure 6.13: Example m/z = 46 TOF spectra. The open circles are data while the lines areforward convolution simulations using the P(ET) shown in Fig. 6.5 (fast feature, dashed line)or Fig. 6.14 (slow feature, solid line).

0 10 20 30 40 50 60 700

0.05

0.1

0.15


Pro

babili

ty

⟨ET⟩ = 19 kcal/mol

Eavail

Figure 6.14: Center-of-mass P(ET) derived from the TOF spectra in Fig. 6.13 assumingisotropic H-atom loss from CH3S.


0 5 10 15 20 25 30 35 400

0.1

0.2

0.3

0.4

0.5


Pro

babili

ty

Eavail

⟨ET⟩ = 16.3 kcal/mol

Figure 6.15: Center-of-mass P(ET) derived from the m/z = 32 TOF spectra shown in Fig.6.2 assuming isotropic S-atom loss from CH3S.

6.7.4 Additional Methyl Perthiyl Radical Results6.7.4.1 Use of low electron ionization energy for TOF acquisition

0 100 200−1000

−500

0

500

1000

1500

2000


Counts

0 100 200 300

×20

m/z = 32100 eV

500k shots

m/z = 3216 eV

300k shots

Figure 6.16: Example TOF spectra of the S-atom loss from CH3SS using two different electronenergies. While the total signal using 16 eV electrons is reduced, the signal-to-noise ratio issubstantially improved.

6.7.4.2 Laser pulse energy studies

Laser pulse energy studies of DMTS at m/z = 79 and the “hot” pyrolysis source m/z =47 and m/z = 46 TOF spectra showed markedly different results. DMTS photodissociationwas linear over the range of 56−169 mJ cm−2 with TOF intensity plateauing at higher laserpulse energies. The m/z = 47 spectra taken with a hot pyrolysis source show a linear response


100 200 300 400 500 6000

20

40

60

80

100

120

Photon Fluence (mJ cm-2)

Counts

/1000 L

aser

Shots

DMTS, m/z = 79

CH3S, m/z = 46

CH3SS, m/z = 47

Figure 6.17: Laser pulse energy studies at m/z = 79 (circles), m/z = 46 (+), and m/z = 47(diamonds). Intensities have been normalized to number of laser shots.

over the entire range tested (56−560 mJ cm−2) while the slow feature from the m/z = 46spectra (see above) show a slight plateau for ≥ 375 mJ cm−2; all three traces are shown inFig. 6.17. The different responses strongly suggest that the observed m/z = 47 and m/z =46 signals are from different photodissociating molecules and that neither is due to DMTSphotodissociation. Photon fluence studies at m/z = 64 and 32 were less conclusive due tolow signal or overlapping signal contributions.

6.7.4.3 Depletion of CH3SS from the molecular beam

As mentioned in Sec. 6.4, experiments were performed under pyrolysis conditions wherethe m/z = 79 component of the molecular beam was depleted. Under these “very hot”conditions, the faster TOF feature at m/z = 64 and Θlab ≤ 15 was depleted and spectra atm/z = 47, 46, and 32 lacked the fast feature observed under the “hot” pyrolytic conditions,example spectra are shown in Fig. 6.18.


0 50 100

0

200

400

600

Co

un

ts

0 100 200


0 100 200 300

m/z = 3215°

m/z = 4710°

m/z = 6410°

×3

Figure 6.18: Example m/z = 32, 47, and 64 TOF spectra. The open circles are the datawhile the black line is the forward simulation from Fig. 6.5 (m/z = 32 and 47) or Fig. 6.6(m/z = 64).

6.7.4.4 Additional m/z = 64 TOF signal

0 50 100 150 200 250 300−50

0

50

100

150

200


Cou

nts

m/z = 6410°

700k shots

Figure 6.19: Example m/z = 64 TOF spectrum showing the slower TOF feature observedfor Θlab ≤ 15 mentioned in Sec. 6.4. The open circles are data while the solid line is asimulation using the P(ET) shown in Fig. 6.6.


6.7.5 BEB Model CalculationThe integrated cross section per orbital may be calculated by the following equation:195

σBEB =S

t+ u+ 1

[ln t

2

(1− 1

t2

)+ 1− 1

t− ln t

t+ 1

]. (6.11)

Here, S = 4πa2NR2/B2, B is the electron binding energy, t = T/B and T is the electronkinetic energy, u = U/B and the average kinetic energy U = ⟨p2/2m⟩ of the bound electronwith momentum p and mass m, a = 0.5292 Å, and R = 13.61 eV. Electron binding energiesand orbital kinetic energies were calculated using the Q-Chem software package196 at theHF/6-311G and HF/6-311++G(3df,3pd) levels of theory. Orbital energies were used as theelectron binding energy as prescribed by Koopman’s theorem. In the case of UHF orbitalsyielding different energies, the average value was taken. Since the BEB model is sensitive tothe lowest electron binding energy, the experimentally determined ionization energy was usedin lieu of the calculated value.190 For orbitals of primarily atomic character (as determined bya LOBA population analysis201 of the HF/6-311G results) with a principal quantum numbern ≥ 3, the u+1 term in the denominator of Eq. (6.11) was replaced by (u+1)/n.202 For S2,the orbital assignments from NIST Electron Impact Cross Section Database191 were used.Table 6.1 outlines the results from these calculations.

Table 6.1: Total electron ionization cross sections for CH3S and S2 at various levels of theory.

Species Theoretical Method Total Cross Section (Å) at 19 eVS2 HF/6-311G 3.957

HF/6-311++G(3df,3pd) 3.6543NIST 3.985

Experimental (Ref. [203]) 4.93CH3S HF/6-311G 3.6216

HF/6-311++G(3df,3pd) 3.5938

94

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atomic Molecules, Radicals, and Ions”, in Atomic and Molecular Data and Their Appli-cations: ICAMDATA - Second International Conference, edited by K. A. Berringtonand K. L. Bell (American Institute of Physics, 2000).

[203] R. S. Freund, R. C. Wetzel, and R. J. Shul, Phys. Rev. A 41, 5861 (1990).

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http://stacks.iop.org/0953-4075/31/i=11/a=004




104

Appendix A

Summary for a Broader Audience

Author’s Note: The following is a brief summary of my thesis, written for a broader audience.I have tried to convey the important ideas and concepts of the project as a whole in additionto summaries of each molecule I examined. I have provided some explanatory commentsand background information in the footnotes, but I encourage you to consult introductorychemistry or physics textbooks for further information.

A.1 IntroductionA.1.1 Free Radicals

Free radicals, a class of “partially formed” molecules, are found in many chemical reactions(e.g. combustion chemistry) as a very reactive intermediate species. Understanding a radical’sfundamental chemistry is therefore important to understanding larger chemical systems.Radical reactivity is due to the existence of an unpaired electron,1 making the study ofradical chemistry quite difficult. This is particularly true if one seeks to understand a radical’sunimolecular chemistry, i.e. how the radical itself will dissociate to form new species. Thework described in this thesis looks at these processes for several radical species relevant tocombustion, atmospheric, and interstellar chemistries.

A.1.2 Photochemistry and PhotodissociationLight absorption by a molecule results in an incredible diversity of chemical reactions.

From ultraviolet light causing DNA damage to photovoltaics to ozone depletion, the role oflight in chemistry is important to many aspects of life. Several things can happen when a

1Electrons are considered “paired” when two electrons stably occupy the same atomic or molecularorbital. For example, a “chemical bond” is generally two electrons shared between two atoms. Conversely,an unpaired electron is considered unstable and will be quite reactive as it “seeks” a way to become paired.

APPENDICES 105

molecule (such as the generic molecule ABC) absorbs a photon:2

ABC + hν → ABC∗ + M→ ABC, (A.1)ABC + hν1 → ABC + hν2, (A.2)ABC + hν → AB + C, (A.3)ABC + hν → A + BC. (A.4)

In Eq. (A.1), molecule ABC becomes photoexcited (ABC∗) and then undergoes a collisionwith M (another molecule, an atom, a surface, etc.). Regardless of the identity of M, theexcited ABC∗ loses at least some of its energy and goes to a lower energy state (such asthe “ground state,” the lowest energy state of a molecule). This process is studied to learnabout energy transfer due to atomic or molecular collisions. Equation (A.2) describes aprocess where light is absorbed and then re-emitted (fluorescence). If the molecule retainssome of that energy, the photon coming out will be of lower energy in a process that isan incredibly important tool to many fields, such as the study of protein behavior in cellsor the identification of product quantum states after a chemical reaction. However, for theexperiments described in this thesis, Eqs. (A.1) and (A.2) are irrelevant.

Equations (A.3) and (A.4) describe a situation where the photon is energetic enoughto break a chemical bond. These light-matter interactions, termed “photodissociations,” arekey to understanding the stability and reactivity of molecule ABC. The photodissociationinvestigations in this thesis focus on two, mutually informative, main questions: identifyingthe photoproducts and determining how the dissociation occurred (the mechanism). In otherwords, we wish to determine if either or both Eqs. (A.3) and (A.4) happen and, if so, how. Ifboth occur, then we want to know which “pathway” or “channel” is dominant by determiningthe “product branching ratio.” The branching ratio helps inform an answer to the questionof dissociation mechanism; dominance of one product versus another3 yields clues about howthe photoexcited molecule behaves.

A.2 ExperimentA.2.1 Technique

The technique used to study radical photodissociation in this thesis is called “photofrag-ment translational spectroscopy” (PTS). To understand the basics of PTS, consider Eq.(A.4). In the center-of-mass reference frame,4 ABC is sitting still when it absorbs one pho-ton of energy. Some of the energy may be used to break the A–B bond, and any extra energy

2Photons, units of light, are characterized by their frequency (ν) or wavelength (λ). Either of these,in turn, describe the energy of said photon through Planck’s constant (h). In chemical reactions, a photon“reactant” is specified by its energy hν.

3Suppose that ABC has a branching ratio of 2 in favor of AB + C. This would mean that, for every 3molecules of ABC that dissociate, two will become AB + C and one will become A + BC.

4“Reference frames” are a way of describing how one is examining a problem. To a person on the street,a car and everything inside is moving past them. Meanwhile, to the people in the car, everything in the car

APPENDICES 106

must—by the law of conservation of energy—be divided between A and BC (the photofrag-ments) as either internal energy (“heating up” the photofragments) or translational energy(movement). How the energy is divided depends upon the chemistry and physics underlyingthat particular molecule and how much energy was absorbed. Using Eq. (A.4) as an example,photofragments A and BC will move away from each other with some velocity, determinedby how much translational energy was imparted to them.5 Thus, by measuring the velocityof A or BC (determining a distribution of translational energies), the underlying chemistryand physics of molecule ABC may be investigated.

A.2.2 ApparatusIn order to accurately measure the velocity of a photofragment, the experiment must be

performed such that the fragments will not collide with anything prior to detection. Sinceradicals are extremely reactive, they must also be prevented from colliding with anothermolecule. As such, PTS experiments are carried out in vacuum chambers to minimize thechances of a collision. The experimental apparatus used in this thesis is a large (approxi-mately one cubic meter) vacuum chamber that, for historical reasons, is called “B Machine.”6

Radicals must be made in the vacuum chamber just prior to photodissociation. To makethese radicals we first start with a suitable precursor, a designer molecule that will readilyreact to form the radical of interest. To introduce molecules into the vacuum chamber, aninert gas—typically a helium/nitrogen mixture for these experiments—is mixed with theradical precursor so that the final gas mixture is at most 1% precursor. This gas mixture ispassed through a short length of very hot (around 1500C) silicon carbide tube just beforethe gas is released into vacuum. The high temperature tube (the pyrolysis source) will causethermal dissociation of the radical precursor and, ideally, form the radical of choice. The gasis then sent into the vacuum chamber by a process called “supersonic expansion,” wherebyall of the internal energy is converted into unidirectional translational energy. In other words,the gas is now very cold (with all of the radicals in their ground state) and traveling in astraight line at one velocity as a “molecular beam” of radicals.

An ultraviolet laser beam then intersects the molecular beam at 90. The energy in anultraviolet (UV) photon is greater than a typical chemical bond, so UV light will often resultin photodissociation. Photofragments scatter away from the molecular beam at particularvelocities and angles determined by the velocity of the molecular beam and the translationalenergy imparted to the photofragment during dissociation.7 As such, these velocities andscattering angles are necessary to determine the translational energy, and the detector usedin B Machine rotates around the point where the laser and molecular beams intersect.8

is stationary and the world is moving past. The latter is like the center-of-mass frame, where a collection ofobjects all moving at the same speed are stationary with respect to each other.

5A “half collision,” as A and BC behave as if they’ve just bounced off of each other like billiard balls.6See section 2.2.1 on page 13 for a brief history of B Machine.7Figure 1.3 on page 8 may be helpful to visualize this relationship.8See Fig. 2.1 on page 15 for a schematic of B Machine.

APPENDICES 107

At a given angle, the detector counts the number of photofragments it “sees” as a functionof time since the interaction with the laser. The photofragments fly over a known distanceto the detector, so measuring their flight time gives us their velocity. A mass spectrometer isused in the detector to help assign the photofragment mass (and thus the chemical formulaof the fragment). From these data, the partitioning of energy during a photodissociationevent may be determined, revealing a molecule’s photochemistry.

A.3 The Phenyl (c-C6H5) RadicalPolycyclic aromatic hydrocarbons (PAH, soot) are an important class of chemicals in

the atmosphere and the interstellar medium. One of the fundamental building blocks ofPAH is the phenyl radical, a six carbon ring with the radical electron located on one ofthe carbon atoms. The phenyl radical is also an intermediate in the combustion of aromatichydrocarbons. As such, a great deal of theoretical work9 and experimental investigationshave been done, probing the properties and the reactivity of this radical.

Theoretical work on the decomposition of the phenyl radical predicts two main path-ways: a C2H2 loss channel and an H-atom loss pathway (with two possible C6H4 structures),pictured below.

C

C

C

C

C

C

H

H

H

H

H

C CH H

C

CCCH

H

H

+

C

C

C

C

C

C

H

HH

HC C

C C

C C

H H

H H

+ Hor

c-C6H5C2H2

C4H3

c-C6H4 l-C6H4

Based on the photochemistry of similar molecules, the phenyl radical is expected to behaveas if it were “hot” from the absorption of a UV photon.10 If this is the case, the dissocia-tion of the phenyl radical would behave as if it had been thermally excited (such as in acombustion reaction) and its decomposition can be modeled using RRKM theory.11 RRKMtheory predicts that, at an energy of 1.03 × 10−18J,12 the product branching ratio will beapproximately 6 in favor of the H-atom loss channel.

9Theory, in this instance, refers to the computational modeling of chemistry from the fundamentalprinciples of quantum mechanics.

10While this is the expectation, every molecule is unique and subtle changes may result in very differentproperties—hence the reason we do experiments.

11Rice-Rampsberger-Kassel-Marcus theory is a framework for modeling the thermal (hot) dissociation ofa molecule. While it is technically inappropriate to use RRKM to model a photodissociation, it can be auseful comparison for the cases when photodissociation “looks” like thermal dissociation.

12Equivalent to the absorption of one ultraviolet photon with a wavelength of 193 nm, as used in theexperiment.

APPENDICES 108

A previous investigation of the phenyl radical photochemistry on B Machine found bothof the proposed dissociation channels. The translational energy distributions found in thatstudy suggested that the dissociation does indeed “look” like a thermal dissociation. However,the measured branching ratio was approximately 5 in favor of the C2H2 + C4H3 pathway, theopposite of the RRKM prediction. This result was an unexpected finding and, in response,additional theory and a detailed RRKM analysis was performed by another group to explorepossible explanations (e.g. that the dissociation may have been caused by the absorption oftwo photons instead of one).

Prompted by the unusual results and the additional theory work, we reinvestigated thephotodissociation of the phenyl radical. The same products were found as in the originalinvestigation, supporting the original product channel assignments. However, when work-ing through the experimental parameters, we found different photofragment translationalenergies depending on the gas used in the molecular beam. When we used a heavier gas(a helium/nitrogen mixture) than was used in the original experiment (pure helium), thephotofragments moved more slowly (a decrease in translational energy). Additionally, wefound a new branching ratio of 5 in favor of H-atom loss, in good agreement with the valueof 6 from RRKM theory but in direct conflict with our previous finding. Ultimately, weconcluded that the heavier gases, which take away more energy from the radicals during acollision, were better at cooling the phenyl radical than the pure helium used in the origi-nal experiment. Thus the original investigation had not been working with cold radicals, incontradiction with one of their assumptions. Overall, the reinvestigation helped show howmuch care must be taken when attempting to produce and study radicals.

A.4 The Methyl Perthiyl (CH3SS) RadicalThe disulfide bond, a chemical bond between two sulfur atoms, is important in many

fields of chemistry (disulfide bonds help hold proteins together, for example). Ultravioletphotoexcitation of alkyl13 disulfides will typically break the S–S or C–S bond, depending onthe photon energy. The latter process will produce an alkyl perthiyl radical, with the simplestof these being the methyl perthiyl radical (CH3SS). There are three proposed dissociationpathways for CH3SS:

CH3SS + hν → CH3S + S→ CH3 + SS→ CH2SSH→ CH2S + SH

Our investigation was the first attempt to study the photodissociation of the methylperthiyl radical. We choose dimethyl disulfide (DMDS, CH3SSCH3) as the radical precursorbecause its photochemistry is well known. Unfortunately, we could not find a setting for

13“Alkyl” refers to simple hydrocarbon groups (e.g. methyl, ethyl). The exact identity of the alkyl groupis unimportant as, for example, dimethyl disulfide has nearly identical photochemistry as diethyl disulfide.

APPENDICES 109

the pyrolysis source that eliminated the precursor yet still had plenty of radicals. We did,however, find that the observed photochemistry changed with use of the pyrolysis source.Since radical production is likely the first step of DMDS decomposition in the pyrolysissource, we assumed the molecular beam was a mixture of radical and precursor. In thiscase, any observed photodissociation that is not DMDS would be due to the methyl perthiylradical. The photodissociation results produced evidence of CH3 loss and SH loss. Therewas no evidence of S-atom loss, but photodissociation of the remaining DMDS may haveobscured any signal from this channel.

Following our work, another lab in our group—using a different experimental implemen-tation of the principles underlying photofragment translational spectroscopy—examined themethyl perthiyl radical photochemistry and found almost exclusively S-atom loss with CH3loss a minor contribution. These results were in direct contradiction with our original find-ings, so we tried again. By this point, we had upgraded the detector in B Machine to giveus more information about the identity of molecules in the molecular beam. Repeating theoriginal experiment, we found the same results as before, but now with the knowledge thatDMDS was not producing significant quantities of the methyl perthiyl radical, making itapparent that our assumptions of CH3SS production and photodissociation were incorrect.

Using a new precursor, dimethyl trisulfide (CH3SSSCH3), and the new capabilities ofthe detector, we were able to confirm production of CH3SS. Unsurprisingly, we found S-atom loss to be the dominant pathway with a small amount of CH3 loss, in agreement withthe other experiment in our group. The photofragment translational energies suggested thatthese dissociation processes are linked more closely to the photon absorption and may not becompared to a thermal dissociation. The results of these two methyl perthiyl investigationsreiterates the difficulty of ensuring radical production.

A.5 Concluding RemarksIndividually, the results of investigations of the phenyl and methyl perthiyl radical pho-

tochemistries have relevance to atmospheric or combustion processes. The results of theseexperiments also demonstrate that scientists make mistakes. However, scientific inquiry isself-correcting and those mistakes are part of the learning process. Looking forward, the workdescribed in this thesis may be used by other scientists to interpret photodissociation exper-iments or help other labs produce radicals. Occasionally research produces groundbreakingresults, but the slow, collective contributions of many people building on previous researchis the most common mechanism for exploring and understanding the world around us.

110

Appendix B

Abbreviations and Definitions

AE appearance energyαion ion flight constantBR photoproduct branching ratioCI conical intersectionCM center-of-mass reference frameDI dissociative ionizationE nascent radical internal energy (photodissociation)E the electronic offset (experimental)Eavail the energy available after bond cleavageEelec electron kinetic energy used in the ionizerEI electron ionization (or electron impact ionization)ET photofragment translational energyET,max largest observed photofragment translational energyIE ionization energy (or ionization potential, IP)IEC ionization efficiency curveIem electron emission currentIR ion regionIVR intramolecular vibrational energy redistributionm/z mass-to-charge ratioMCS multichannel scalarP(ET) center-of-mass translational energy distributionPMT photomultiplier tube

APPENDICES 111

PTS photofragment translational spectroscopyΘlab the angle between the molecular beam and detector axisΘmax maximum photoproduct laboratory scattering angleTOF time-of-flightUHV ultrahigh vacuum; < 10−8 torr

112

Appendix C

Data Acquisition and AnalysisPrograms

C.1 Automated Ionization Efficiency Curve CollectionThe following is a computer program to collect ionization efficiency curves as discussed

in Chapter 3. The program is written to run on the Merlin 5221 using the PAW MacroLanguage supplied with the instrument. Briefly, over a given range of electron energies theprogram will “fish” for ion signal at particular m/z values. A “spectrum” consists of all m/zvalues at a particular electron energy, and one run through the energy range is a “pass.” Eachspectrum gets its own file, with the date, the nominal electron energy (ev_cmd), the filamentbias reading, and the ion counts. Spectra are taken with 1 V filament bias steps, making one“run” through the range before repeating the range with a 0.5 V offset. A spectrum withelectron energy energy_norm is taken every third spectrum for normalization. User inputsinclude the m/z values to record, the number of scans to take at each m/z value, the SIMwidth, emission current, and electron energy range.

C.1.1 iec_mass.pml

1 # PAW macro to automate ionization efficiency curves.2 #3 # written May 2015 by N. C. Cole -Filipiak4 # edited November 2015 NCCF5 #6 # This macro draws upon the slow_scan.pml and7 # ev_ramp.pml written by Extrel.8 #9 # This macro modifies iec3.pml to only acquire specific m/z

values.

APPENDICES 113

10

11 if cent; prof; end12 list_clear13

14 if %1;else;%1=3;end # number of passes input with program15

16 #### BEGIN USER INPUT17

18 # Assign specific m/z values to take to list(x,3).19 # For each m/z, specify number of fish averages in list(x,4).20 # Copy , paste , and edit for desired number of m/z values.21

22 # m/z value : fish averages23 list(1,3) = 15 : list(1,4) = 50 : end24 list(2,3) = 28 : list(2,4) = 10 : end25 list(3,3) = 43 : list(3,4) = 200 : end26 list(4,3) = 57 : list(4,4) = 200 : end27

28 num_mass = 4 # number of m/z values to analyze29

30 # set scan variables31 simwid = 0.232 scan_time = 0.0533

34 # set energy paratmeters35 I_em = 0.01 # set emission current (mA), must be very low36 mlens 511 = I_em37 energy_max = -20 # set filament bias potentials38 energy_min = -4 # unstable above -2V39 energy_norm = -20 # set E_elec for normalization40

41 #### END USER INPUT42

43 old_scan_time = scan_time44 pass = 1;s_mass = 1;end45

46 repeat %1 # repeat the IEC measurement %1 times47 spec = 1 # start at first spectrum48

49 volt = energy_min # used to control filament bias50 run = 1 # used to control movement through the IEC51 norm = 2 # used to count spectra for normalization

APPENDICES 114

52

53 while run > 054

55 if norm = 2 # if taking a normalization scan56 old_volt = volt # store the old voltage57 volt = energy_norm # and set to norm58 mlens 510 = volt59 else60 mlens 510 = volt # otherwise , set the new filament bias61 end62

63 energy_readback = mlens 99940264 doze 4 # let optics stabilize65 energy_readback = mlens 99940266

67 # start the file68 file_start:"pass":?pass:"spec":?spec:".csv":CR69 file_write:"pass":?pass:"spec":?spec:".csv":CR:?month:"/":?

day:"/":?year:CR70 file_write:"pass":?pass:"spec":?spec:".csv":CR:?volt:CR71 file_write:"pass":?pass:"spec":?spec:".csv":CR:?

energy_readback:CR72

73 list_clear(1)74

75 # acquire and write spectrum76 while s_mass <= num_mass77

78 # sets mass dependent averaging79 avmode = 2:average = list(s_mass ,4)80 "Pass: ":?pass:", ":"Spectrum: ":?spec:", ":"ev_cmd =":?volt:

", ":"m/z =":?list(s_mass ,3):CR81

82 # acquire ion signal83 ions:ions list(s_mass ,3)84 repeat list(s_mass ,4): fish: end85 prof_to_list(1)86 file_write:"pass":?pass:"spec":?spec:".csv":CR:?list(s_mass

,3):",":?list_sum(1):CR87 s_mass +=188 end89 s_mass=1

APPENDICES 115

90

91 # need to call readback twice to get right answer92 energy_readback = mlens 999402: energy_readback = mlens 99940293 file_write:"pass":?pass:"spec":?spec:".csv":CR:?

energy_readback:CR94

95 if run = 3 # ends the pass after final normalizing spectrum96 run = 097 end98

99 # if the spectrum just acquired was for normalization100 if norm = 2 & run != 3101 volt = old_volt # restore previous voltage102 norm = 0 # restart normalization counting103 else104 norm += 1 # otherwise , keep counting spectra105 end106

107 # if taking a normal spectrum108 if volt > energy_max & norm != 2 & run !=3 & spec != 1109 volt -= 1 # change filament bias by 1V110 end111

112 # if finished with integer bias run113 if volt = energy_max & run = 1 & norm != 2114 volt = energy_min -0.5 # offset bias by 0.5V115 run = 2116 end117

118 # if finished both runs , but need another normalizationspectrum

119 if volt = energy_max+0.5 & run = 2 & norm = 2120 run = 3 # set run to stop after spectrum121 volt = energy_norm # set bias to norm122 end123

124 # if finished both runs and do not need another normalizationspectrum

125 if volt = energy_max -0.5 & run = 2 & norm != 2126 run = 0 # end pass127 end128

APPENDICES 116

129 spec += 1 : end # voltage scan130

131 pass += 1 : end # pass132

133 "IEC passes finished.":CR134 beep 440 0.3135

136 # Restarts profile scanning the input mass range.137 avmode = 1:scan_time=old_scan_time138 ions:ions list(1,3) list(num_mass ,3)

C.2 Ionization Efficiency Curve NormalizationThe following is MATLAB code to process IEC data from iec3.pml, iec3mass.pml, or

iec_mass.pml (see above). The first section orients the program to file location and providesinformation about the number of passes to analyze. The program then reads the m/z valuesand begins running through each pass. For a given pass, the program reads the nominalelectron energy (either the filament bias or the “ev_cmd” for the Merlin 5221). The pass’intensities are normalized and both the raw and normalized intensities are written out to files(intensity and normintensity, respectively). The program then averages all normalizedintensities and writes a master file (average_norm.csv). The final section (lines 108–141,currently commented out) is a rough draft to acquire non-calibrated appearance energieswithin MATLAB. In practice, this has been done outside of MATLAB using a spreadsheetapplication.

C.2.1 iec_norm.m

1 % MATLAB program to concatenate and normalize2 % IEC curve spectra produced by3 % iec3.pml, iec3mass.pml, or iec_mass.pml.4 % Written by N. C. Cole -Filipiak May 2015.5

6 clear;7

8 %%%% BEGIN USER INPUT9

10 % path to data11 path = 'C:\Merlin Automation\data\My Files\';12

13 first_pass = 1; % first pass to analyze14 num_pass = 5; % number of passes to analyze15 spec = 1; % first spectrum number

APPENDICES 117

16

17 %%%% END USER INPUT18

19 % introduce matricies , etc.20 spectrum = [];long=0;linregion=[]; %#ok<NASGU >21

22 % acquire masses23 s1=strcat(path ,'pass',int2str(first_pass),'spec');24 s2=int2str(spec);25 s3='.csv';26 spectrum = csvread(strcat(s1,s2,s3),3,0);27

28 mass(1,:)=spectrum(:,1);29 mass(length(mass))=[]; % remove last entry30

31 for pass=first_pass:num_pass32

33 files = length(dir(strcat(path ,'pass',int2str(pass),'spec','*.csv')));

34

35 % preallocate some of the matricies36 normintensity = zeros(files ,length(mass));37 energy=zeros(length(files)+1,1);38

39 % acquire the intensity of each mass in each spectrum40 m=1;41 for num=1:files42 s1=strcat(path ,'pass',int2str(pass),'spec');43 s2=int2str(num);44 s3='.csv';45 spectrum = csvread(strcat(s1,s2,s3),1,0); % read file46

47 intensity(num ,:)=spectrum(3:end -1,2);%#ok<SAGROW >48

49 % use ev_cmd for energy50 %energy(num+1,1)=spectrum(1,1);51

52 % use filament bias readback for energy53 energy(num+1,1)=(spectrum(2,1)+spectrum(length(spectrum),1))

/2;54 spectrum=zeros;55 end

APPENDICES 118

56

57 % normalize the intensity matrix58 incr=3; % for the pattern: norm spec spec norm spec spec...59 for o = 1:length(mass)60 % if the last spectrum is a normalization spectrum61 if mod(files ,3) == 162 long=files -1;63 % if there is one spectrum after the last normalization

spectrum64 elseif mod(files ,3) == 265 long=files -2;66 end67

68 for n = 1:incr:long69 normintensity(n+1,o) = intensity(n+1,o)/intensity(n,o);70 normintensity(n+2,o) = intensity(n+2,o)/intensity(n+3,o);71 normintensity(n,o) = intensity(n,o)/intensity(n,o);72 end73

74 % if the last spectrum is a normalization spectrum75 if mod(files ,3) == 176 normintensity(files ,o) = intensity(files ,o)/intensity

(files ,o);77 % if there is one spectrum after the last normalization

spectrum78 elseif mod(files ,3) == 279 normintensity(files ,o) = intensity(files ,o)/intensity

(files -1,o);80 normintensity(files -1,o) = intensity(files -1,o)/

intensity(files -1,o);81 end82 end83

84 temp=cat(1,mass ,intensity);85 temp=cat(2,energy ,temp);86 temp2=cat(1,mass ,normintensity);87 temp2=cat(2,energy ,temp2);88

89 % add the normalized intensity to a larger array90 totalnorm(pass ,:,:)=temp2;%#ok<SAGROW >91

92 % write the output file of normalized intensities

APPENDICES 119

93 dlmwrite(strcat(path ,'intensity',int2str(pass),'.csv'),temp);94 dlmwrite(strcat(path ,'normintensity',int2str(pass),'.csv'),

temp2);95

96 end97

98 % average the pass intensities99 for j=1:length(mass)+1100 for k=1:length(energy)101 average_norm(k,j)=mean(totalnorm(:,k,j));%#ok<SAGROW >102 end103 end104

105 % write the output file of average normalized intensities106 dlmwrite(strcat(path ,'average_norm.csv'),average_norm);107

108 % perform linear regressions109 %110 for m=1:length(mass) % which value in mass vector111

112 fig_handle=figure;113 scatter(energy ,average_norm(:,m+1));114 title(strcat('m/z = ',num2str(mass(m))));115 x = inputdlg('Enter comma -separated energy values:',...116 'Linear Range ', [1 50]);117 range = str2num(x:);118 close(fig_handle);119

120 e=1;cal=0;121 for en=1:length(energy)122 if (range(1)<=energy(en)==1) && (energy(en)<=range(2)==1)123 if (round(energy(en),0)~=round(mode(energy),0))124 linregion(e,1)=energy(en); %#ok<*SAGROW >125 linregion(e,2)=average_nom(en,m+1);126 e = e+1;127 elseif (round(energy(en),0)==round(mode(energy),0)) &&

(cal==0)128 linregion(e,1)=energy(en);129 linregion(e,2)=average_norm(en,m+1);130 e = e+1;131 cal=1;132 end

APPENDICES 120

133 end134 end135 fitobject=fit(linregion(:,1),linregion(:,2),'poly1 ');136 %plot(fitobject ,energy ,average_norm(:,m+1));137 fits(m,:)=coeffvalues(fitobject);138 ap(m,1)=mass(m);139 ap(m,2)=abs(fits(m,2)/fits(m,1));140 end141 %

C.3 Binary-Encounter-Bethe Model for ElectronIonization Cross Sections

The following code implements the Binary-Encounter-Bethe Model195 for calculating elec-tron ionization cross sections as discussed in Chapter 6. The model requires orbital bindingenergies B in eV, single electron kinetic energies U in eV, orbital occupation number N, andprincipal quantum number n. The input is a .csv file with columns for each of those vari-ables. Plots of cross sections as a function of electron energy may be generated by placingthe calculation (lines 30–41) in a for loop over the desired range of T. These plots are usefulfor benchmarking results against the cross section data from NIST.

C.3.1 BEB.m

1 clear;2


5 % calculate for a particular electron energy T in eV6 T=19;7

8 % Import parameters needed in calc.9 % Format of 4 columns: B, U, N, n10 calc=csvread('calc.csv');11

12 %%%% END USER INPUT13

14 % binding energy for each orbital15 B = calc(:,1); S = zeros(1,length(B));16 % average kinetic energy for each orbital17 U = calc(:,2); u = zeros(1,length(U));18 % occupation number for each orbital

APPENDICES 121

19 N = calc(:,3);20 % principal quantum number of the orbital21 % n = 1; % for principle quantum numbers of 2 or 122 n = calc(:,4);23

24 % constants25 a0 = 0.52918; % Angstroms26 R = 13.6057; % eV27 Q = 1; % an approximation28 sigma = [];29

30 for orbital=1:length(B)31 % only orbitals with binding energies less than T32 if T>=B(orbital)==133 t = T/B(orbital);34 S = 4*pi*(a0^2)*N(orbital)*(R/B(orbital))^2;35 u = U(orbital)/B(orbital);36 term1 = S/(t+(u+1)/n(orbital));37 term2 = Q*log(t)*0.5*(1-t^-2);38 term3 = (2-Q)*(1-(1/t)-log(t)/(t+1));39 sigma(1,orbital) = term1 * (term2 + term3);40 end41 end42

43 % display total cross section for electron energy T44 sigmatot=sum(sigma)

C.4 Product Branching RatiosInformation about calculating a product branching ratio from laboratory TOF intensities

may be found in Douglas Krajnovich’s thesis.36 The following code integrates experimentalP(ET) and β parameters over laboratory-frame velocities for a given Θlab. The required inputsare information about the experiment (e.g. molecular beam velocity, vlab), the photoproductmasses, the P(ET) for each channel, the anisotropy parameter for each channel, and thelaboratory intensity ratio R_lab. Following the arguments of Krajnovich,36 R_lab is the ratioof ion counts for each channel, normalized by electron ionization cross section, dissociativeionization fractioning, and ion transmission through the quadrupole.

Due to the variety of cross sections calculated using the BEB Model195, this branchingratio program was written to produce the range of product branching ratios in order toestimate error. As such, the laboratory intensity ratio is currently written to read a .csvcolumn of numbers (line 29). If there are only a few values of R_lab to test, this line may bereplaced with a number and the program rerun.

APPENDICES 122

C.4.1 branching_ratio.m

1 % MATLAB program to calculate CM branching ratios fromlaboratory frame

2 % TOF intensities3 %4 % For more info: Krajnovich et al., J. Chem. Phys. 77, 5977

(1982).5 %6 clear;7


10 % input beginning parameters11 L = 0.201; % flight length in meters12 vlab = 1800; % laboratory frame beam velocity , m/s13 thetalab = 25; % laboratory scattering angle , degrees14 m1 = 47; % channel A, measured mass15 m2 = 32; % channel A, counterfragment16 m3 = 64; % channel B, measured mass17 m4 = 15; % channel B, counterfragment18

19 % P(E_T) names20 name_a = 'ch3s s norm';21 name_b = 'ch3 ss norm';22

23 % input anisotropy parameter for angle between24 % electric field and CM scattering angle25 beta_a = 1.4; % channel A anisotropy parameter26 beta_b = 0; % channel B anisotropy parameter27

28 % lab intensity ratio after accounting for ionization , etc.29 R_lab = csvread(strcat(num2str(thetalab),'d.csv'));30

31 %%%% END USER INPUTS32

33 % read P(E_T) in kcal/mol34 poe_a = csvread(strcat(name_a ,'.dat'),1,0); %ignore first row35 poe_b = csvread(strcat(name_b ,'.dat'),1,0); %ignore first row36

37 % convert P(E_T) into Joules38 for i=1:length(poe_a)

APPENDICES 123

39 poe_a(i,1)=4.184*poe_a(i,1)/6.022E20;40 end41 for i=1:length(poe_b)42 poe_b(i,1)=4.184*poe_b(i,1)/6.022E20;43 end44

45 M=(m1*m4)/(m2*m3); % lab mass ratio46 % CM mass ratios in kg47 Ma=(0.5*m1 + 0.5*(m1^2)/m2)*1.66E-27;48 Mb=(0.5*m3 + 0.5*(m3^2)/m4)*1.66E-27;49

50 % generate velocities for first 500us of TOF, m/s51 v1 = 20000:-10:400;52 v3 = 20000:-10:400;53

54 % evaluate integrals for specified beam velocity55 for j=1:length(v1)-156 delta_v1=v1(j)-v1(j+1);57 delta_v3=v3(j)-v3(j+1);58 for i=1:259 % CM velocity60 u1(i) = sqrt(v1(j+i-1)^2 + vlab^2 - 2*v1(j+i-1)*vlab*cosd(

thetalab));61 u3(i) = sqrt(v3(j+i-1)^2 + vlab^2 - 2*v3(j+i-1)*vlab*cosd(

thetalab));62 % CM angular distribution , for CM angle w.r.t. laser

propogation direction63 % ASSUMES UNPOLARIZED LIGHT64 angle_a(i) = atand(abs(vlab -v1(j+i-1)*cosd(thetalab))/(v1(j+

i-1)*sind(thetalab)));65 Ia(i) = 1-0.5*beta_a*(1.5*(cosd(angle_a(i))^2) -0.5);66 angle_b(i) = atand(abs(vlab -v3(j+i-1)*cosd(thetalab))/(v3(j+

i-1)*sind(thetalab)));67 Ib(i) = 1-0.5*beta_b*(1.5*(cosd(angle_b(i))^2) -0.5);68

69 % get probability of CM velocity70 Ea = Ma*u1(i)^2;71 if Ea <= poe_a(length(poe_a))72 proba(i) = interp1(poe_a(:,1),poe_a(:,2),Ea);73 else74 proba(i) = 0;75 end

APPENDICES 124

76

77 Eb = Mb*u3(i)^2;78 if Eb <= poe_b(length(poe_b))79 probb(i) = interp1(poe_b(:,1),poe_b(:,2),Eb);80 else81 probb(i) = 0;82 end83 end % i84

85 % calculate product of probability*angular dist*Jacobian*delta_v

86 prodA(j) = mean(proba)*mean(Ia)*mean(v1(j),v1(j+1))*delta_v1/mean(u1);

87 prodB(j) = mean(probb)*mean(Ib)*mean(v3(j),v3(j+1))*delta_v3/mean(u3);

88 end % j89

90 % calculate total product for all lab velocities91 ProdA = sum(prodA);92 ProdB = sum(prodB);93

94 % calculate and display CM branching ratio for given R_lab95 for j=1:length(R_lab)96 R_cm(j) = (R_lab(j)*ProdB)/(M*ProdA);97 end98

99 % write the branching ratios to a .csv file100 csvwrite(strcat('R_cm',num2str(thetalab),'.csv'),transpose(

R_cm));

125

Appendix D

Publications Resulting FromGraduate Work

1. Cole-Filipiak, N. C.; Shapero, M. Haibach-Morris, C.; Neumark, D. M. Productionand Photodissociation of the Methyl Perthiyl Radical. J. Phys. Chem. A., Submitted.

2. Shapero, M.; Cole-Filipiak, N. C.; Haibach-Morris, C.; Neumark, D. M. Benzyl RadicalPhotodissociation Dynamics at 248 nm. J. Phys. Chem. A., 2015, ASAP.

3. Cole-Filipiak, N. C.; Shapero, M.; Negru, B.; Neumark, D. M. Revisiting the Photodis-sociation Dynamics of the Phenyl Radical. J. Chem. Phys., 2014, 141, 104307.

4. Cole-Filipiak, N. C.; Negru, B.; Just, G. M. P.; Park, D.; Neumark, D. M. Photodis-sociation Dynamics of the Methyl Perthiyl Radical at 248 nm via PhotofragmentTranslational Spectroscopy. J. Chem. Phys., 2013, 138, 054301.



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