Photoelectron spectroscopy and density functional theory studies on theuridine homodimer radical anionsYeon Jae Ko Piotr Storoniak Haopeng Wang Kit H Bowen and Janusz Rak Citation J Chem Phys 137 205101 (2012) doi 10106314767053 View online httpdxdoiorg10106314767053 View Table of Contents httpjcpaiporgresource1JCPSA6v137i20 Published by the American Institute of Physics Additional information on J Chem PhysJournal Homepage httpjcpaiporg Journal Information httpjcpaiporgaboutabout_the_journal Top downloads httpjcpaiporgfeaturesmost_downloaded Information for Authors httpjcpaiporgauthors

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THE JOURNAL OF CHEMICAL PHYSICS 137 205101 (2012)

Photoelectron spectroscopy and density functional theory studieson the uridine homodimer radical anions

Yeon Jae Ko1a) Piotr Storoniak2b) Haopeng Wang1 Kit H Bowen1b) and Janusz Rak2

1Department of Chemistry Johns Hopkins University Baltimore Maryland 21218 USA2Department of Chemistry University of Gdansk Sobieskiego 18 80-952 Gdansk Poland

(Received 14 September 2012 accepted 28 October 2012 published online 26 November 2012)

We report the photoelectron spectrum (PES) of the homogeneous dimer anion radical of uridine(rU)2

bullminus It features a broad band consisting of an onset of sim12 eV and a maximum at the elec-tron binding energy (EBE) ranging from 20 to 25 eV Calculations performed at the B3LYP6-31++G level of theory suggest that the PES is dominated by dimeric radical anions in whichone uridine nucleoside hosting the excess charge on the base moiety forms hydrogen bonds viaits O8 atom with hydroxyl of the other neutral nucleosidersquos ribose The calculated adiabatic elec-tron affinities (AEAGs) and vertical detachment energies (VDEs) of the most stable homodimersshow an excellent agreement with the experimental values The anionic complexes consisting of twointermolecular uracil-uracil hydrogen bonds appeared to be substantially less stable than the uracil-ribose dimers Despite the fact that uracil-uracil anionic homodimers are additionally stabilized bybarrier-free electron-induced proton transfer their relative thermodynamic stabilities and the calcu-lated VDEs suggest that they do not contribute to the experimental PES spectrum of (rU)2

bullminus copy 2012American Institute of Physics [httpdxdoiorg10106314767053]

I INTRODUCTION

Since Sanchersquos et al1 discovery that dry DNA is highlysusceptible to degradation by low energy electrons (LEEs)great quantity of data have been collected on damaging ac-tion of LEEs to DNA and its components2ndash14 These findingsmotivated a tremendous interest in electron attachment to nu-cleobases (NB) since the anions of purines and pyrimidinesare perceived as intermediates in the radiation-induced dam-age of nucleic acids Initially it was proposed that such tran-sient anionic states appear as molecular resonances3 Indeedemploying electron transmission spectroscopy (ETS) Burrowet al15 found the negative vertical electron affinities for thefour DNA bases Similarly most of computational studies inthe nineties inferred lack of the gas phase stability of valence-bound (VB) anions as indicated by their computed negativecomputational adiabatic electron affinities16ndash20

On the other hand the gas phase photoelectron spec-troscopy (PES)21 22 and Rydberg electron transfer spec-troscopy (RET)23 experiments revealed that the isolatedpyrimidines (uracil thymine and cytosine) may trap the ex-cess electron in their dipole field forming adiabatically sta-ble dipole-bound (DB) anions Indeed the CCSD(T)MP2(single-point coupled-cluster with single double and non-iterative triple excitation at the second order Moslashller-Plessetgeometry) adiabatic electron affinity for the DB anion ofuracil was calculated to be 0069 eV24 Moreover small(014ndash025 eV) but positive adiabatic electron affinities ofuracil and thymine VB anions were later computed with theB3LYP functional and different basis sets augmented with

a)Present address Rowland Institute at Harvard 100 Edwin H Land BlvdCambridge Massachusetts 02142 USA

b)Authors to whom correspondence should be addressed Electronicaddresses pondroschemunivgdapl and kbowenjhuedu

diffuse functions25ndash28 At that level of methodology the AEAvalues of cytosine and guanine VB anions were predicted tobe around zero26ndash28 and significantly negative for adenine (inthe range of minus035 eV to minus017 eV)26ndash28 The most accurateRI-MP2-R12CCSD(T) value of 004 eV for the VB anionof uracil was calculated by Bachorz et al29 Nevertheless thevertical electron affinities (VEAs) of all the nucleobases seemto be negative25 26 28 The experimental and computational re-sults concerning the electrophilic properties of nucleobasesare summarized in several excellent reviews30ndash32

The well-established fact that the parent valence anionsof nucleobases exist in the condensed phase33 suggests thatinteractions with the environment support their covalent an-ionic form Indeed the PES experiments of Hendricks et al34

and Schiedt et al22 demonstrated a transformation of DB toVB anions of isolated uracil upon even marginal solvation bya single atom of rare gas or water molecule34 The conver-sion of the dipole-bound to valence uracil and thymine an-ions upon rare gas atom solvation were also observed in thecrossed beam RET studies35 Similarly gas phase hydrogen-bonded complexes of nucleobases with various inorganic36

and organic (alcohols acids aminoacids)37 proton donorswere studied both computationally and experimentally Inthose systems the strong thermodynamic stabilization of re-sulting valence anions was often accompanied by the barrier-free proton transfer

The hydrogen-bonded Watson-Crick AT38ndash42 andGC40 43ndash47 base pairs were also shown to form stable valenceanions in the gas phase The influence of stabilizing hydrogenbonds on the electrophilic properties of AT and GC pairsas well as the nucleoside pairs of dAdT and dGdC wasdiscussed in detail by Gu et al42 47

The increased stability of nucleobases VB anions inthe presence of even a single solvent molecule suggests

0021-96062012137(20)2051018$3000 copy 2012 American Institute of Physics137 205101-1

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205101-2 Ko et al J Chem Phys 137 205101 (2012)

that the sugar moiety chemically attached to the NB viaN-glycosidic bonding should exert a similar effect In-deed the B3LYPDZP++ calculations pertaining to 2prime-deoxyribonucleosides predicted positive electron affinities forall of them48 Later on Stokes et al49 employing a com-bination of infrared desorption electron photoemission andgas jet expansion recorded the anion photoelectron spectra ofthe nucleoside parent anions of 2prime-deoxythymidinebullminus (dTbullminus)2prime-deoxycytidinebullminus (dCbullminus) 2prime-deoxyadenosinebullminus (dAbullminus)uridinebullminus (rUbullminus) cytidinebullminus (rCbullminus) adenosinebullminus (rAbullminus) andguanosinebullminus (rGbullminus) Their measurements proved the appear-ance of stable valence radical anions of nucleosides in the gasphase VDEs and AEAs of dT dC and dA extracted fromthe spectra matched quite well those calculated by Richard-son et al48 and by Li et al50

The attachment of the phosphate group to a nucleosideconverting it to a nucleotide further strengthens its tendencyto bind an excess electron by sim008 to 027 eV as was con-cluded by Gu et al at the DFT level51

As to the best of our knowledge there have been no ex-perimental studies on the parent (intact) anions of the nu-cleotides in the gas phase except of the report by Stokeset al52 concerning adenosine-5prime-monophosphate (5prime-AMPH)and 2prime-deoxyadenosine-5prime-monophosphate (5prime-dAMPH) Thephotoelectron spectra revealed that both nucleotides form sta-ble valence-bound radical anions in the gas phase The com-putational study by Kobyłecka et al demonstrated that in theanionic (5prime-dAMPH)bullminus the excess electron on a π orbital ofpurine is stabilized by the spontaneous intramolecular protontransfer from the phosphate group53

Non-canonical base pairs such as the homogeneousdimer of U U commonly occur in RNA molecules that donot transfer sequence information54 Tandem U U base pairsincrease the stability of duplexes allowing for the formation ofspecific biologically relevant RNA conformations54 Hereinemploying infrared desorption electron photoemission anda gas jet expansion we were able to generate intact stableradical anionic species (uridine)2

bullminus in the gas phase andrecord its photoelectron spectrum In order to interpret themeasured spectrum we conducted density functional theory(DFT) calculations On the basis of the relative stabilities ofconceivable complexes and their propensity to attach and de-tach the excess electron we have identified species whichdominate under the experimental conditions The most stableradical anionic homodimer exhibits the arrangement whereone monomer (hosting an excess electron on the base moiety)is hydrogen-bonded via O8 to the sugar hydroxyl groups ofthe other nucleoside The calculated VDE values for the mostthermodynamically favorable structures are in good agree-ment with the values extracted from the spectrum A com-mon feature of the investigated anionic structures is unevencharge distribution which can be perceived as the solvationof the negatively charged nucleoside with the electron den-sity localized entirely within the base moiety by the neutralmonomer Surprisingly the hydrogen-bonded radical anioniccomplexes utilizing the typical uracil proton-donor N3H cen-ter and the proton-acceptor O8 O7 sites are highly unstablein comparison with the structures featuring uracil-ribose in-teractions We have also identified radical anionic complexes

stabilized by barrier free intermolecular proton transfer be-tween base moieties but in contrast to our previous studiessuch structures are not the lowest energy configurations andtherefore should not exhibit in the spectrum of (uridine)2

bullminus

II METHODS

A Experimental details

Uridine (rU) radical dimer anions were generated usinga novel pulsed infrared desorption-pulsed visible photoemis-sion anion source which has been described previously49 52

Anion photoelectron spectroscopy (PES) is conductedby crossing beams of mass-selected negative ions and fixedfrequency photons followed by energy-analysis the resultantphotodetached electrons This technique is governed by theenergy conserving relationship hν = EBE + EKE where hν

is the photon energy EBE is the electron binding energy andEKE is the measured electron kinetic energy

Low-power infrared laser pulses (117 eVphoton) froma NdYAG laser were used to desorb neutral uridine from aslowly moving graphite rod which was thinly coated withthe sample Almost simultaneously electrons were generatedby visible laser pulses (another NdYAG laser operated at532 nm 233 eVphoton) striking a rotating yttrium oxidedisk Since yttriumrsquos work function of sim2 eV is slightly belowthe photon energy of the visible laser low energy electronswere produced and this process is critical to the formationof intact biomolecular ions At the same time a pulsed valveprovided a collisionally cooled jet of helium to carry away ex-cess energy and stabilize the resulting parent radical anionsThe photoelectron spectrum of the intact uridine dimer rad-ical anions was recorded by crossing a mass-selected beamof (rU)2

bullminus parent anions with a fixed-frequency photon beam(third NdYAG laser operated at 355 nm 349 eVphoton)The resultant photodetached electrons were energy-analyzedusing a magnetic bottle energy analyzer with a resolution of35 meV at EKE = 1 eV

B Computational details

We have applied the density functional theory methodwith Beckersquos three-parameter hybrid functional (B3LYP)55ndash57

and the 6-31++G basis set58 59 The usefulness of theB3LYP6-31++G method to describe intra- and inter-molecular hydrogen bonds has been demonstrated throughcomparison with the second order Moslashller-Plesset (MP2)predictions60 The ability of the B3LYP method to predictexcess electron binding energies was reviewed and the re-sults were found to be satisfactory for valence-type molecularanions61

All geometries presented here have been fully optimizedwithout geometrical constraints and the analysis of harmonicfrequencies proved that all of them are also geometrically sta-ble (all force constants were positive)

The relative energies E and Gibbs free energies Gof the neutral and anionic complexes are defined with respectto the energy of the most stable neutral or anionic configu-ration The stabilization free energies Gstab of neutral com-plexes are calculated as a difference between the energy of

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205101-3 Ko et al J Chem Phys 137 205101 (2012)

the complex and the sum of the energies of fully optimizedisolated monomers

The adiabatic electron affinities AEAG are defined asthe Gibbs free energies difference between the neutral andthe anion for both species at their fully relaxed geometriesThe free energies of the neutral and anionic species resultfrom correcting the relevant values of electronic energies forzero-point vibration terms thermal contributions to energythe pV term and the entropy terms These terms were calcu-lated in the rigid rotor-harmonic oscillator approximation atT = 298 K and p = 1 atm

Electron VDEsmdashdirect observables in photoelectronspectroscopy experimentsmdashwere defined as the energy ofneutral dimer minus the energy of the anionic dimer at thegeometry of the fully relaxed anion

In the past calculations at the B3LYP6-31++Glevel36(a) for the valence-bound (uracil middot middot middot water)minus clusterswas shown to reproduce very well the VDE value ex-tracted from the photoelectron spectrum34 For these sys-tems the B3LYP6-31++G approach appeared as goodas the MP26-31++G(2df2p)MP26-311++G level oftheory62 However in order to improve our predictions wecorrected the calculated VDE values by minus015 eV Introduc-ing such an increment can be justified by juxtaposing theVDE value of 075 eV obtained at the B3LYP6-31++Glevel for isolated valence-bound uracil with the VDE of060 eV calculated for this system at the coupled-clusterlevel of theory29

All quantum chemical calculations have been carried outwith the GAUSSIAN 0363 and GAUSSIAN 0964 codes The pic-tures of molecules and molecular orbitals and were plottedusing the GaussView 41 program65

III RESULTS AND DISCUSSION

A Photoelectron results

Photoelectron spectrum of the uridine dimer radical an-ion is presented in Figure 1 The broad peak indicative ofvalence-bound anions results from the vertical photodetach-ment of the excess electron from a ground vibronic state ofmass-selected nucleoside dimer radical anions to the groundvibronic state of the resulting neutrals The maximal photo-electron intensities correspond to the optimal Franck-Condonoverlaps of the vibrational wave functions between anion andneutral ground states The photoelectron spectrum of (rU)2

bullminus

features an onset at EBE around 12 eV and exhibits a broadpeak covering the range of sim12ndash3 eV (see Figure 1) withmaximum intensity at the EBE of 20ndash25 eV Thus the verti-cal detachment energy (VDE) is in the range of 20ndash25 eV inagreement with our computational result The electron affinity(EA) is more difficult to determine explicitly Since there areoften vibrational hot bands present in spectra such as thesethe threshold EBE energy is probably not exactly equivalentto the value of the EA As a reasonable approximation how-ever one can estimate the EA value as corresponding to theEBE at sim10 of the rising photoelectron intensity This putsthe value of EA at sim15 eV in an excellent agreement withthe computational value of 145 eV

FIG 1 Photoelectron spectrum of (uridine)2bullminus recorded with 349 eV

photons

The photoelectron spectrum of the radical anionic uri-dine monomer (rUbullminus)49 resembles that of (rU)2

bullminus but issubstantially shifted to lower electron binding energies In-deed the rUbullminus PES exhibits a maximum intensity at theEBE range of sim12ndash16 and an onset at sim07 eV49 On theother hand the photoelectron spectrum of the anionic homod-imer form of uracil (U2

bullminus)66 similarly to (rU)2bullminus exhibits

a dominant broad peak with the maximum covering almostidentical range 2ndash25 eV with gradually increasing inten-sity toward the high electron binding energy (EBE) end ofthe spectrum however its onset falls at a significantly lowerEBE (sim07 eV)

B Computational results

The starting geometries of uridine were taken from Leul-liot et al67 where the complete geometry optimizations ofthe representative for RNA uridine conformations were per-formed at the DFT level We have found the neutral C2prime-endoanti monomer to be the most stable while C3prime-endoantito be the least stable at the B3LYP6-31++G level of the-ory and all four considered conformers span a narrow rangeof 07 kcalmol in terms of both the relative energy and Gibbsfree energy (see Table I and Figure 2) Thus the selection of a

TABLE I Values of relative electronic energy free energy (E and G)for the four conformations of the neutral and anion radical uridine verticaldetachment energies (VDEs) and adiabatic electron affinities (AEAs) of an-ion radical uridine calculated at the B3LYP6-31++G level E G aregiven in kcalmol and AEAG and VDE in eV

Neutrals Anions

Conformation E G E G AEAG VDE

C2prime-endoanti 0 0 0 0 073 162C2prime-endosyn 029 113 509 384 061 121

C3prime-endoanti 073 072 Converges to C2prime-endoantiC3prime-endosyn 093 139 745 573 054 101

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205101-4 Ko et al J Chem Phys 137 205101 (2012)

FIG 2 Neutral conformations of uridine optimized at the B3LYP6-31++G level

monomeric model for further studies by using the stability ofthe particular neutral conformers does not seem to be justifiedHowever photoelectron spectrum measured by Stokes et alrevealed that the VDE and AEA values of isolated valence-bound uridine amounts to 139 and sim07 eV respectively49

Upon re-optimization of the four monomeric uridine con-formers listed in Table I as anion radicals we found out thatVDE equal to 147 eV (after correction with minus015 eV) andAEAG = 073 eV for the C2prime-endoanti structure remain ingood accordance with experimental VDE and AEA of rUbullminusMoreover the C2prime-endoanti radical anion was also identifiedas the most stable among the considered anionic structures(see Table I) The next most stable anionic conformer C2prime-endosyn is separated from C2prime-endoanti by as much as 51and 38 kcalmol in terms of E and G respectively The calcu-lated VDE and AEAG values of the C2prime-endosyn conformeramount to 106 (after correction with minus015 eV) and 061 eVrespectively Thus the thermodynamic stability and the elec-trophilic characteristics of C2prime-endosyn do not support theexistence of this radical anion in the gas phase

Noticing that the neutral geometries do not change dras-tically upon electron attachment (except for C3prime-endoanti)and what is more important that the relative stability orderis the same for both neutrals and anions we assume that therelative stabilities of neutral uridine conformations in the gasphase may be deduced from the stability of anionic radicalsIn view of foregoing we decided that the C2prime-endoanti ge-ometry of neutral uridine is the proper choice for the currentstudy The fact that the isolated ribose C2prime-endo conformationis slightly more stable than C3prime-endo67 also speaks in favor ofthe C2prime-endoanti geometry

1 Neutral dimer conformations

Uracil nucleoside dimers can be stabilized by hydrogenbonding via proton acceptor sites (O7 or O8) and protondonor sites (N3) of the nucleobases as well as the OH protondonor groups of the ribose moiety Figure 3 displays the neu-tral complexes optimized at the B3LYP6-31++G levelAll involve the C2prime-endoanti conformation of uridine

There are three conceivable hydrogen-bonded structuresinvolving interactions exclusively among the two uracils Wenamed them n1 n2 and n3 with the supplementary labeling ofthe proton acceptor atoms participating in the hydrogen bond-ing scheme The complexes n1_O8-O8 (both uracils engagetheir O8 and N3H atoms) and n3_O7-O7 (both uracils en-

gage the same O7 and N3H centers) are ldquosymmetricalrdquo whilethe n2_O8-O7 structure features an ldquoasymmetricalrdquo schemeof hydrogen bonds O8middot middot middotHndashN3 O7middot middot middotHndashN3

Homodimers involving uracil-ribose hydrogen bondinginteractions are depicted on the lower half of Figure 3 Uponrotation of uridine with respect to the hydroxyl groups ofsugar we obtained several structures of similar energy Herewe show only four of these conformers which were se-lected to illustrate the most significant geometrical differ-ences within the current hydrogen bonding scheme Thesestructures are numbered from n4 to n7 and in contrast to the

FIG 3 Structures of neutral uridine dimers optimized at the B3LYP6-31++G level

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205101-5 Ko et al J Chem Phys 137 205101 (2012)

TABLE II Values of relative electronic energy and free energy (E andG) with respect to the most stable neutral uridine dimer and stabilizationfree energies (Gstab) of the neutral uridine dimers calculated at the B3LYP6-31++G level All values given in kcalmol

Complex E G Gstab

n1_O8-O8 000 000 004n2_O8-O7 219 113 118n3_O7-O7 363 246 250n4_O8 654 504 509n5_O8 707 452 456n6_O8 722 354 358n7_O8 755 545 550

previous uracil-uracil bonding motif only one O8 label isused in the nomenclature since the conformers are stabilizedby a single hydrogen bond The relative energies and Gibbsfree energies (E and G) as well as the stabilization en-thalpies (Gstab) of the neutral uridine homodimers gatheredin Table II are sorted according to their energy values TheGstab values ranging from 0 to 55 kcalmol (see Table II)suggest that dimerization is not thermodynamically favored

2 Anions resulting from electron attachment

The fully optimized neutral complexes described inSec III B 1 (see Figure 3) were used as starting pointsfor the investigation of the electrophilic properties of (rU)2The results of B3LYP6-31++G calculations for (rU)2

bullminus

are summarized in Table III and the respective structures areshown in Figure 4 Using the seven neutral parents we haveobtained a large number of anionic geometries as the systemunder investigation is characterized by a large number of con-formational degrees of freedom particularly the complexeswhere the nucleosides interact with each other through thesugar moiety (structures ax_O8 where x = 1ndash7) Fortunatelymost of these conformers lie close to each other on the po-tential energy surface and exhibit similar electrophilic proper-ties Thus the fourteen structures displayed in Figure 4 are therepresentative geometries of the thoroughly scrutinized con-formational space of the uridine homodimer anionic radicalcomplex

Attachment of the excess electron to the neutral uracil-uracil arrangements (structures n1_O8-O8 n2_O8-O7 andn3_O7-O7) leads to the structures stabilized by two hydro-gen bonds which do not allow for a large change of mutualpositions of monomers Two types of anions are formed inthis casendashstructures that resemble the neutral parent showingsimilar double hydrogen bonding motifs and structures whereelectron-induced proton transfer occurs in one of the two H-bonds (a8_O8-O8-pt and a9_O8-O7-pt) The proton acceptorsite is exclusively the O8 atom which is not surprising basedon the SOMO shapes plotted in Figure 4 The complete lackof the electron density on the O7 atom of uridine makes theO8 atom the only available proton-accepting center within theconsidered dimers

As expected from the broad shape of photoelectron spec-trum shown in the current report and from previous stud-ies demonstrating that nucleobase anions (and other anionic

TABLE III Values of relative electronic energy and free energy (E andG) with respect to the most stable uridine homodimer radical anion stabi-lization free energies (Gstab) vertical detachment energies (VDEs) and adi-abatic electron affinities (AEAs) of anion radical uridine homodimers cal-culated at the B3LYP6-31++G level E G and Gstab are given inkcalmol and AEAG and VDE in eV

Complex E G Gstab AEAG VDEa

a1_O8 000 000 minus 1343 146b 261 (246)a2_O8 169 004 minus 1338 146b 245 (230)a3_O8 377 055 minus 1288 144b 246 (231)a4_O8 408 020 minus 1323 145b 242 (227)a5_O8 410 104 minus 1239 142b 243 (228)a6_O8 464 091 minus 1252 142b 242 (227)a7_O8 481 132 minus 1210 141b 241 (226)a8_O8-O8-pt 673 420 minus 923 113c 269 (254)a9_O8-O7-pt 852 568 minus 774 111d 276 (261)a10_O8-O8 936 612 minus 730 104c 193 (178)a11_O8-O7 1041 785 minus 558 102d 196 (181)a12_O8-O8 1057 546 minus 797 107c 109 (094)a13_O7-O7 1518 1134 minus 208 092e 117 (102)a14_O7-O7 1663 1403 060 081e 165 (150)

aIn parentheses are given VDE values corrected by minus015 eV For details see Sec IIbAEAG calculated from the difference in Gibbs free energies of the neutral structuren6_O8 and the given anionic structurecAEAG calculated from the difference in Gibbs free energies of the neutral structuren1_O8-O8 and the given anionic structuredAEAG calculated from the difference in Gibbs free energies of the neutral structuren2_O8-O7 and the given anionic structureeAEAG calculated from the difference in Gibbs free energies of the neutral structuren3_O7-O7 and the given anionic structure

DNARNA subunits) are thermodynamically stable in the gasphase provided that the solvent molecule is present in thevicinity22 34ndash51 all (rU)2

bullminus complexes reported here exhibitvalence-bound character Inspection of the anionic wave func-tions of complexes reveals that in most cases the excess elec-tron locates on a π orbital of uracil of only one of theinteracting monomers Therefore the dimer structures maybe perceived as uridine radical anions solvated by neutralcounterparts

All considered homodimers form adiabatically stable an-ions as indicated by the AEAG values in Table III which spanthe range of 081ndash146 eV

According to the relative stabilities of the anionic radicalcomplexes (Table III) a clear picture emerges that dominat-ing in the gas phase should be the geometries of the ax_O8family where one of the nucleoside is hydrogen bonded viathe O8 atom of its uracil to one or two OH groups of the sec-ond nucleosidersquos sugar (uracil-ribose pattern of interactions)In such geometries the excess electron is completely local-ized on the uracil moiety of one nucleoside which is interact-ing with the second neutral monomer via its O8 atom For theseven most stable structures (ax_O8 where x = 1ndash7) the Gstab

values lie between minus1343 and minus1210 kcalmol In contrastto the relatively unstable uracil-ribose nx_O8 neutral dimers(characterized by positive Gstab values in the range of 358 to55 kcalmol) the corresponding anionic dimers ax_O8 ex-hibit significant stability

For the most stable geometries a1_O8 and a2_O8 wehave unexpectedly found that the neutral monomers adopt theC2prime-endosyn conformation Additionally the C3prime-endoanti

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205101-6 Ko et al J Chem Phys 137 205101 (2012)

FIG 4 Structures of anion radical uridine dimers optimized at the B3LYP6-31++G level with corresponding VDE values and their singly occupiedmolecular orbitals plotted with a contour value of 005 bohrminus32

conformer was identified in a5_O8 The four remaining an-ionic dimers of the ax_O8 family as well as the seven homod-imers from the other family shown in Figure 4 are uniformlycomposed of the C2prime-endoanti monomers The least stablestructure among the ax_O8 structures that is a7_O8 is sepa-rated by 48 and 13 kcalmol from the most stable a1_O8 inthe energy and free energy scale respectively (see Table III)The calculated VDE values (incremented by minus015 eV)246 eV for the most stable a1_O8 and 226 eV for the leaststable a7_O8 agree very well with the broad feature of thePES spectrum at maximum EBE range of 20 to 25 eV

The least stable member of ldquouracil-riboserdquo family is sep-arated from the next structure (which is a8_O8-O8-pt) by 192and 288 kcalmol in the term of E and G (see Table III) re-spectively The anionic a8_O8-O8-pt and a9_O8-O7-pt struc-tures are stabilized by electron-induced intermolecular pro-ton transfer (PT) occurring between the complementary uracilmoieties Based on our earlier experiences with anionic com-plexes of biomolecules in the gas phase we expected the PTstructures to be the most stable geometries among consideredradical anions However the data gathered in Table III demon-strate unequivocally that both PT homodimers should not bepopulated in the gas phase Despite of the favorable Gstab

values equal to minus93 and minus77 kcalmol and positive AEAGrsquosof sim11 eV both a8_O8-O8-pt and a9_O8-O7-pt are too highon the energy (67 and 85 kcalmol respectively) and free en-ergy scale (42 and 57 kcalmol) to compete with any of theax_O8 geometries

Similarly the relatively small stabilities for the non-PTldquouracil-uracilrdquo anions (a10 to a14 structures see Table III)suggest that such anionic complexes do not form under theconditions of the photoelectron experiment

IV DISCUSSION

The calculations carried out on conceivable neutral ho-modimers enabled the fourteen anionic (uridine)2

bullminus structuresdepicted in Figure 4 to be identified and characterized Thecharge distribution of the unpaired electron in uridine homod-imers is uneven one of the two nucleosides accepts the excesselectron which is accompanied by pyrimidine ring distortionwhile its counterpart monomer stays neutral The main partof the excess electron density resides on the C4 C5 andC6 sites of uracil and smaller amounts on the N1 N3 andO8 atoms An identical shape of the unpaired electron orbital

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205101-7 Ko et al J Chem Phys 137 205101 (2012)

was found for the isolated 1-methyluracil and non-methylateduracil anions29

Since dimerization is not favorable for the neutralmonomers (see positive Gstab values gathered in Table II)the formation of anionic radical dimers probably begins withelectron capture by a single nucleoside rather than by a neutraldimer The resulting monomeric anion radical could be sub-sequently stabilized by dimerization with the neutral uridineThe Gstab values predicted for the anionic homodimers (seeTable III) are in favor of such a mechanism Strong stabiliza-tion of the (rU)2

bullminus complexes characterized by the negativeGstab and positive AEAG values results in VDEs much largerthan 2 eV In our previous studies36 37 41 53 VDEs close to2 eV were computed exclusively for the radical anions sta-bilized by proton transfer (PT) Here we demonstrated thatVDEs above 2 eV can occur for non-PT anions Moreoversuch non-PT complexes turned out to be the most stable an-ionic geometries (ax_O8 family) and therefore should have adominating contribution to the main PES signal covering theEBEs of 226ndash246 eV On the other hand the PT-structureswere shown to be significantly unstable with respect to theax_O8 geometries although characterized by similarly highVDEs (sim25 eV)

The prevailing stability of the ax_O8 family with regardto ax_O8-O8 ax_O7-O7 and ax_O8-O7 is surprising giventhe fact that the uracil-ribose interactions involve a singleO8middot middot middotHO or a bifurcated hydrogen bond while each struc-ture featuring a uracil-uracil interaction contains two inter-molecular (O8middot middot middotHN3 or O7middot middot middotHN3) hydrogen bonds Theintermolecular hydrogen bonds in which the hydroxyl groupsof ribose participate are not unusual in biological systemsIt was observed that certain conformations of RNA are ex-traordinarily stable and conserved due to the presence of suchinter-strand interactions54 What is also important is that theformation of hydrogen bonds involving sugar OH groups maybe correlated to the conformational change of sugar puckeringfrom C3prime-endo to C2prime-endo68 69

The most stable structures a1_O8 and a2_O8 differfrom the other ax_O8 (x = 3ndash7) geometries (as well as fromthe other ldquouracil-uracilrdquo structures) by the presence of thesyn conformer The syn orientation of the OH-donating neu-tral nucleoside enables the bifurcated H-bond between O2primeHand O3primeH of ribose and the O8 atom of the anionic uri-dine (both OHmiddot middot middotO8 distances are similar to each other andamount to sim17 Aring see Figure 4) to be formed in a1_O8and a2_O8 Both structures are almost identical energeti-cally (free energy difference of 004 kcalmol difference inGstab equal to 005 kcalmol and identical AEAG) Sincethe thermodynamic characteristics of the ax_O8 structures donot vary substantially one may draw a conclusion that the(uracil)O8middot middot middotHO(ribose) interaction rather than syn or C3prime-endo conformation is responsible for the extraordinary stabi-lization of the excess charge in this family of geometries

V SUMMARY

In the present work we report on the electrophilic proper-ties of uridine homodimers in the gas phase that were charac-

terized with photoelectron spectroscopy and quantum chem-istry modeling

Photoelectron spectrum of uridine homodimer radi-cal anions (rU)2

bullminus was registered using infrared desorp-tionphotoemission anion generation and pulsed laser pho-todetachment The spectrum exhibits a broad signal with athreshold at sim12 eV and a maximum intensity at 20ndash25 eV(Figure 1) The shape of photoelectron spectrum of uridineanions (rUbullminus) registered previously resembles that of (rU)2

bullminusHowever dimerization process shifts the (rU)2

bullminus PES maxi-mum by around 08 eV to the higher EBEs when compared torUbullminus On the other hand the photoelectron spectra of uracil2bullndash

(U2bullminus) and (rU)2

bullminus are characterized by the maximum inten-sity lying within the same EBE range

The results of our computational studies suggest that for-mation of the neutral uridine homodimers in the gas phaseis thermodynamically improbable while the existence of thehighly stable valence radical anions of this dimer is plau-sibe in agreement with the experimental observations Acommon feature of the investigated anionic structures is anuneven charge distribution which suggests that the nega-tively charged nucleoside with the electron density local-ized entirely within the base moiety is solvated by a neutralmonomer In the most stable radical anionic homodimer thathas a predominant contribution to the PES signal the nucle-oside hosting the excess charge on the base moiety forms abifurcated hydrogen bond via its O8 atom with two hydroxylgroups of the other neutral nucleosidersquos ribose Its calculatedVDE of 246 eV fits perfectly the VDE measured by PES

The anionic radical complexes consisting of two inter-molecular uracil-uracil hydrogen bonds are substantially lessstable than the uracil-ribose dimers Despite the fact that theuracil-uracil anionic radical homodimers are additionally sta-bilized by barrier-free electron-induced proton transfer theirrelative thermodynamic stabilities and the calculated VDEssuggest that they do not contribute to the experimental PESspectrum of (rU)2

bullminus

ACKNOWLEDGMENTS

The experimental results reported here are based uponwork supported by the National Science Foundation grant toKHB (Grant No CHE-1111693) and the theoretical partswere supported by the Polish Ministry of Science and HigherEducation grant to JR (Grant No DS8221-4-0140-12) Thecalculations have been carried out at the Wrocław Center forNetworking and Supercomputing (httpwwwwcsswrocpl)(Grant No 196) and at the Academic Computer Center inGdansk (TASK)

1B Boudaiumlffa P Cloutier D Hunting M A Huels and L Sanche Science287 1658 (2000)

2B Boudaiumlffa P Cloutier D Hunting M A Huels and L Sanche RadiatRes 157 227 (2002)

3M A Huels B Boudaiumlffa P Cloutier D Hunting M A Huels andL Sanche J Am Chem Soc 125 4467 (2003)

4F Martin P D Burrow Z Cai P Cloutier D Hunting and L SanchePhys Rev Lett 93 068101 (2004)

5Y Zheng P Cloutier D J Hunting L Sanche and J R Wagner J AmChem Soc 127 16592 (2005)

6Z Cai P Cloutier D Hunting and L Sanche J Phys Chem B 109 4796(2005)

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-3 Ko et al J Chem Phys 137 205101 (2012)

the complex and the sum of the energies of fully optimizedisolated monomers

The adiabatic electron affinities AEAG are defined asthe Gibbs free energies difference between the neutral andthe anion for both species at their fully relaxed geometriesThe free energies of the neutral and anionic species resultfrom correcting the relevant values of electronic energies forzero-point vibration terms thermal contributions to energythe pV term and the entropy terms These terms were calcu-lated in the rigid rotor-harmonic oscillator approximation atT = 298 K and p = 1 atm

Electron VDEsmdashdirect observables in photoelectronspectroscopy experimentsmdashwere defined as the energy ofneutral dimer minus the energy of the anionic dimer at thegeometry of the fully relaxed anion

In the past calculations at the B3LYP6-31++Glevel36(a) for the valence-bound (uracil middot middot middot water)minus clusterswas shown to reproduce very well the VDE value ex-tracted from the photoelectron spectrum34 For these sys-tems the B3LYP6-31++G approach appeared as goodas the MP26-31++G(2df2p)MP26-311++G level oftheory62 However in order to improve our predictions wecorrected the calculated VDE values by minus015 eV Introduc-ing such an increment can be justified by juxtaposing theVDE value of 075 eV obtained at the B3LYP6-31++Glevel for isolated valence-bound uracil with the VDE of060 eV calculated for this system at the coupled-clusterlevel of theory29

All quantum chemical calculations have been carried outwith the GAUSSIAN 0363 and GAUSSIAN 0964 codes The pic-tures of molecules and molecular orbitals and were plottedusing the GaussView 41 program65

III RESULTS AND DISCUSSION

A Photoelectron results

Photoelectron spectrum of the uridine dimer radical an-ion is presented in Figure 1 The broad peak indicative ofvalence-bound anions results from the vertical photodetach-ment of the excess electron from a ground vibronic state ofmass-selected nucleoside dimer radical anions to the groundvibronic state of the resulting neutrals The maximal photo-electron intensities correspond to the optimal Franck-Condonoverlaps of the vibrational wave functions between anion andneutral ground states The photoelectron spectrum of (rU)2

bullminus

features an onset at EBE around 12 eV and exhibits a broadpeak covering the range of sim12ndash3 eV (see Figure 1) withmaximum intensity at the EBE of 20ndash25 eV Thus the verti-cal detachment energy (VDE) is in the range of 20ndash25 eV inagreement with our computational result The electron affinity(EA) is more difficult to determine explicitly Since there areoften vibrational hot bands present in spectra such as thesethe threshold EBE energy is probably not exactly equivalentto the value of the EA As a reasonable approximation how-ever one can estimate the EA value as corresponding to theEBE at sim10 of the rising photoelectron intensity This putsthe value of EA at sim15 eV in an excellent agreement withthe computational value of 145 eV

FIG 1 Photoelectron spectrum of (uridine)2bullminus recorded with 349 eV

photons

The photoelectron spectrum of the radical anionic uri-dine monomer (rUbullminus)49 resembles that of (rU)2

bullminus but issubstantially shifted to lower electron binding energies In-deed the rUbullminus PES exhibits a maximum intensity at theEBE range of sim12ndash16 and an onset at sim07 eV49 On theother hand the photoelectron spectrum of the anionic homod-imer form of uracil (U2

bullminus)66 similarly to (rU)2bullminus exhibits

a dominant broad peak with the maximum covering almostidentical range 2ndash25 eV with gradually increasing inten-sity toward the high electron binding energy (EBE) end ofthe spectrum however its onset falls at a significantly lowerEBE (sim07 eV)

B Computational results

The starting geometries of uridine were taken from Leul-liot et al67 where the complete geometry optimizations ofthe representative for RNA uridine conformations were per-formed at the DFT level We have found the neutral C2prime-endoanti monomer to be the most stable while C3prime-endoantito be the least stable at the B3LYP6-31++G level of the-ory and all four considered conformers span a narrow rangeof 07 kcalmol in terms of both the relative energy and Gibbsfree energy (see Table I and Figure 2) Thus the selection of a

TABLE I Values of relative electronic energy free energy (E and G)for the four conformations of the neutral and anion radical uridine verticaldetachment energies (VDEs) and adiabatic electron affinities (AEAs) of an-ion radical uridine calculated at the B3LYP6-31++G level E G aregiven in kcalmol and AEAG and VDE in eV

Neutrals Anions

Conformation E G E G AEAG VDE

C2prime-endoanti 0 0 0 0 073 162C2prime-endosyn 029 113 509 384 061 121

C3prime-endoanti 073 072 Converges to C2prime-endoantiC3prime-endosyn 093 139 745 573 054 101

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-4 Ko et al J Chem Phys 137 205101 (2012)

FIG 2 Neutral conformations of uridine optimized at the B3LYP6-31++G level

monomeric model for further studies by using the stability ofthe particular neutral conformers does not seem to be justifiedHowever photoelectron spectrum measured by Stokes et alrevealed that the VDE and AEA values of isolated valence-bound uridine amounts to 139 and sim07 eV respectively49

Upon re-optimization of the four monomeric uridine con-formers listed in Table I as anion radicals we found out thatVDE equal to 147 eV (after correction with minus015 eV) andAEAG = 073 eV for the C2prime-endoanti structure remain ingood accordance with experimental VDE and AEA of rUbullminusMoreover the C2prime-endoanti radical anion was also identifiedas the most stable among the considered anionic structures(see Table I) The next most stable anionic conformer C2prime-endosyn is separated from C2prime-endoanti by as much as 51and 38 kcalmol in terms of E and G respectively The calcu-lated VDE and AEAG values of the C2prime-endosyn conformeramount to 106 (after correction with minus015 eV) and 061 eVrespectively Thus the thermodynamic stability and the elec-trophilic characteristics of C2prime-endosyn do not support theexistence of this radical anion in the gas phase

Noticing that the neutral geometries do not change dras-tically upon electron attachment (except for C3prime-endoanti)and what is more important that the relative stability orderis the same for both neutrals and anions we assume that therelative stabilities of neutral uridine conformations in the gasphase may be deduced from the stability of anionic radicalsIn view of foregoing we decided that the C2prime-endoanti ge-ometry of neutral uridine is the proper choice for the currentstudy The fact that the isolated ribose C2prime-endo conformationis slightly more stable than C3prime-endo67 also speaks in favor ofthe C2prime-endoanti geometry

1 Neutral dimer conformations

Uracil nucleoside dimers can be stabilized by hydrogenbonding via proton acceptor sites (O7 or O8) and protondonor sites (N3) of the nucleobases as well as the OH protondonor groups of the ribose moiety Figure 3 displays the neu-tral complexes optimized at the B3LYP6-31++G levelAll involve the C2prime-endoanti conformation of uridine

There are three conceivable hydrogen-bonded structuresinvolving interactions exclusively among the two uracils Wenamed them n1 n2 and n3 with the supplementary labeling ofthe proton acceptor atoms participating in the hydrogen bond-ing scheme The complexes n1_O8-O8 (both uracils engagetheir O8 and N3H atoms) and n3_O7-O7 (both uracils en-

gage the same O7 and N3H centers) are ldquosymmetricalrdquo whilethe n2_O8-O7 structure features an ldquoasymmetricalrdquo schemeof hydrogen bonds O8middot middot middotHndashN3 O7middot middot middotHndashN3

Homodimers involving uracil-ribose hydrogen bondinginteractions are depicted on the lower half of Figure 3 Uponrotation of uridine with respect to the hydroxyl groups ofsugar we obtained several structures of similar energy Herewe show only four of these conformers which were se-lected to illustrate the most significant geometrical differ-ences within the current hydrogen bonding scheme Thesestructures are numbered from n4 to n7 and in contrast to the

FIG 3 Structures of neutral uridine dimers optimized at the B3LYP6-31++G level

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-5 Ko et al J Chem Phys 137 205101 (2012)

TABLE II Values of relative electronic energy and free energy (E andG) with respect to the most stable neutral uridine dimer and stabilizationfree energies (Gstab) of the neutral uridine dimers calculated at the B3LYP6-31++G level All values given in kcalmol

Complex E G Gstab

n1_O8-O8 000 000 004n2_O8-O7 219 113 118n3_O7-O7 363 246 250n4_O8 654 504 509n5_O8 707 452 456n6_O8 722 354 358n7_O8 755 545 550

previous uracil-uracil bonding motif only one O8 label isused in the nomenclature since the conformers are stabilizedby a single hydrogen bond The relative energies and Gibbsfree energies (E and G) as well as the stabilization en-thalpies (Gstab) of the neutral uridine homodimers gatheredin Table II are sorted according to their energy values TheGstab values ranging from 0 to 55 kcalmol (see Table II)suggest that dimerization is not thermodynamically favored

2 Anions resulting from electron attachment

The fully optimized neutral complexes described inSec III B 1 (see Figure 3) were used as starting pointsfor the investigation of the electrophilic properties of (rU)2The results of B3LYP6-31++G calculations for (rU)2

bullminus

are summarized in Table III and the respective structures areshown in Figure 4 Using the seven neutral parents we haveobtained a large number of anionic geometries as the systemunder investigation is characterized by a large number of con-formational degrees of freedom particularly the complexeswhere the nucleosides interact with each other through thesugar moiety (structures ax_O8 where x = 1ndash7) Fortunatelymost of these conformers lie close to each other on the po-tential energy surface and exhibit similar electrophilic proper-ties Thus the fourteen structures displayed in Figure 4 are therepresentative geometries of the thoroughly scrutinized con-formational space of the uridine homodimer anionic radicalcomplex

Attachment of the excess electron to the neutral uracil-uracil arrangements (structures n1_O8-O8 n2_O8-O7 andn3_O7-O7) leads to the structures stabilized by two hydro-gen bonds which do not allow for a large change of mutualpositions of monomers Two types of anions are formed inthis casendashstructures that resemble the neutral parent showingsimilar double hydrogen bonding motifs and structures whereelectron-induced proton transfer occurs in one of the two H-bonds (a8_O8-O8-pt and a9_O8-O7-pt) The proton acceptorsite is exclusively the O8 atom which is not surprising basedon the SOMO shapes plotted in Figure 4 The complete lackof the electron density on the O7 atom of uridine makes theO8 atom the only available proton-accepting center within theconsidered dimers

As expected from the broad shape of photoelectron spec-trum shown in the current report and from previous stud-ies demonstrating that nucleobase anions (and other anionic

TABLE III Values of relative electronic energy and free energy (E andG) with respect to the most stable uridine homodimer radical anion stabi-lization free energies (Gstab) vertical detachment energies (VDEs) and adi-abatic electron affinities (AEAs) of anion radical uridine homodimers cal-culated at the B3LYP6-31++G level E G and Gstab are given inkcalmol and AEAG and VDE in eV

Complex E G Gstab AEAG VDEa

a1_O8 000 000 minus 1343 146b 261 (246)a2_O8 169 004 minus 1338 146b 245 (230)a3_O8 377 055 minus 1288 144b 246 (231)a4_O8 408 020 minus 1323 145b 242 (227)a5_O8 410 104 minus 1239 142b 243 (228)a6_O8 464 091 minus 1252 142b 242 (227)a7_O8 481 132 minus 1210 141b 241 (226)a8_O8-O8-pt 673 420 minus 923 113c 269 (254)a9_O8-O7-pt 852 568 minus 774 111d 276 (261)a10_O8-O8 936 612 minus 730 104c 193 (178)a11_O8-O7 1041 785 minus 558 102d 196 (181)a12_O8-O8 1057 546 minus 797 107c 109 (094)a13_O7-O7 1518 1134 minus 208 092e 117 (102)a14_O7-O7 1663 1403 060 081e 165 (150)

aIn parentheses are given VDE values corrected by minus015 eV For details see Sec IIbAEAG calculated from the difference in Gibbs free energies of the neutral structuren6_O8 and the given anionic structurecAEAG calculated from the difference in Gibbs free energies of the neutral structuren1_O8-O8 and the given anionic structuredAEAG calculated from the difference in Gibbs free energies of the neutral structuren2_O8-O7 and the given anionic structureeAEAG calculated from the difference in Gibbs free energies of the neutral structuren3_O7-O7 and the given anionic structure

DNARNA subunits) are thermodynamically stable in the gasphase provided that the solvent molecule is present in thevicinity22 34ndash51 all (rU)2

bullminus complexes reported here exhibitvalence-bound character Inspection of the anionic wave func-tions of complexes reveals that in most cases the excess elec-tron locates on a π orbital of uracil of only one of theinteracting monomers Therefore the dimer structures maybe perceived as uridine radical anions solvated by neutralcounterparts

All considered homodimers form adiabatically stable an-ions as indicated by the AEAG values in Table III which spanthe range of 081ndash146 eV

According to the relative stabilities of the anionic radicalcomplexes (Table III) a clear picture emerges that dominat-ing in the gas phase should be the geometries of the ax_O8family where one of the nucleoside is hydrogen bonded viathe O8 atom of its uracil to one or two OH groups of the sec-ond nucleosidersquos sugar (uracil-ribose pattern of interactions)In such geometries the excess electron is completely local-ized on the uracil moiety of one nucleoside which is interact-ing with the second neutral monomer via its O8 atom For theseven most stable structures (ax_O8 where x = 1ndash7) the Gstab

values lie between minus1343 and minus1210 kcalmol In contrastto the relatively unstable uracil-ribose nx_O8 neutral dimers(characterized by positive Gstab values in the range of 358 to55 kcalmol) the corresponding anionic dimers ax_O8 ex-hibit significant stability

For the most stable geometries a1_O8 and a2_O8 wehave unexpectedly found that the neutral monomers adopt theC2prime-endosyn conformation Additionally the C3prime-endoanti

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-6 Ko et al J Chem Phys 137 205101 (2012)

FIG 4 Structures of anion radical uridine dimers optimized at the B3LYP6-31++G level with corresponding VDE values and their singly occupiedmolecular orbitals plotted with a contour value of 005 bohrminus32

conformer was identified in a5_O8 The four remaining an-ionic dimers of the ax_O8 family as well as the seven homod-imers from the other family shown in Figure 4 are uniformlycomposed of the C2prime-endoanti monomers The least stablestructure among the ax_O8 structures that is a7_O8 is sepa-rated by 48 and 13 kcalmol from the most stable a1_O8 inthe energy and free energy scale respectively (see Table III)The calculated VDE values (incremented by minus015 eV)246 eV for the most stable a1_O8 and 226 eV for the leaststable a7_O8 agree very well with the broad feature of thePES spectrum at maximum EBE range of 20 to 25 eV

The least stable member of ldquouracil-riboserdquo family is sep-arated from the next structure (which is a8_O8-O8-pt) by 192and 288 kcalmol in the term of E and G (see Table III) re-spectively The anionic a8_O8-O8-pt and a9_O8-O7-pt struc-tures are stabilized by electron-induced intermolecular pro-ton transfer (PT) occurring between the complementary uracilmoieties Based on our earlier experiences with anionic com-plexes of biomolecules in the gas phase we expected the PTstructures to be the most stable geometries among consideredradical anions However the data gathered in Table III demon-strate unequivocally that both PT homodimers should not bepopulated in the gas phase Despite of the favorable Gstab

values equal to minus93 and minus77 kcalmol and positive AEAGrsquosof sim11 eV both a8_O8-O8-pt and a9_O8-O7-pt are too highon the energy (67 and 85 kcalmol respectively) and free en-ergy scale (42 and 57 kcalmol) to compete with any of theax_O8 geometries

Similarly the relatively small stabilities for the non-PTldquouracil-uracilrdquo anions (a10 to a14 structures see Table III)suggest that such anionic complexes do not form under theconditions of the photoelectron experiment

IV DISCUSSION

The calculations carried out on conceivable neutral ho-modimers enabled the fourteen anionic (uridine)2

bullminus structuresdepicted in Figure 4 to be identified and characterized Thecharge distribution of the unpaired electron in uridine homod-imers is uneven one of the two nucleosides accepts the excesselectron which is accompanied by pyrimidine ring distortionwhile its counterpart monomer stays neutral The main partof the excess electron density resides on the C4 C5 andC6 sites of uracil and smaller amounts on the N1 N3 andO8 atoms An identical shape of the unpaired electron orbital

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-7 Ko et al J Chem Phys 137 205101 (2012)

was found for the isolated 1-methyluracil and non-methylateduracil anions29

Since dimerization is not favorable for the neutralmonomers (see positive Gstab values gathered in Table II)the formation of anionic radical dimers probably begins withelectron capture by a single nucleoside rather than by a neutraldimer The resulting monomeric anion radical could be sub-sequently stabilized by dimerization with the neutral uridineThe Gstab values predicted for the anionic homodimers (seeTable III) are in favor of such a mechanism Strong stabiliza-tion of the (rU)2

bullminus complexes characterized by the negativeGstab and positive AEAG values results in VDEs much largerthan 2 eV In our previous studies36 37 41 53 VDEs close to2 eV were computed exclusively for the radical anions sta-bilized by proton transfer (PT) Here we demonstrated thatVDEs above 2 eV can occur for non-PT anions Moreoversuch non-PT complexes turned out to be the most stable an-ionic geometries (ax_O8 family) and therefore should have adominating contribution to the main PES signal covering theEBEs of 226ndash246 eV On the other hand the PT-structureswere shown to be significantly unstable with respect to theax_O8 geometries although characterized by similarly highVDEs (sim25 eV)

The prevailing stability of the ax_O8 family with regardto ax_O8-O8 ax_O7-O7 and ax_O8-O7 is surprising giventhe fact that the uracil-ribose interactions involve a singleO8middot middot middotHO or a bifurcated hydrogen bond while each struc-ture featuring a uracil-uracil interaction contains two inter-molecular (O8middot middot middotHN3 or O7middot middot middotHN3) hydrogen bonds Theintermolecular hydrogen bonds in which the hydroxyl groupsof ribose participate are not unusual in biological systemsIt was observed that certain conformations of RNA are ex-traordinarily stable and conserved due to the presence of suchinter-strand interactions54 What is also important is that theformation of hydrogen bonds involving sugar OH groups maybe correlated to the conformational change of sugar puckeringfrom C3prime-endo to C2prime-endo68 69

The most stable structures a1_O8 and a2_O8 differfrom the other ax_O8 (x = 3ndash7) geometries (as well as fromthe other ldquouracil-uracilrdquo structures) by the presence of thesyn conformer The syn orientation of the OH-donating neu-tral nucleoside enables the bifurcated H-bond between O2primeHand O3primeH of ribose and the O8 atom of the anionic uri-dine (both OHmiddot middot middotO8 distances are similar to each other andamount to sim17 Aring see Figure 4) to be formed in a1_O8and a2_O8 Both structures are almost identical energeti-cally (free energy difference of 004 kcalmol difference inGstab equal to 005 kcalmol and identical AEAG) Sincethe thermodynamic characteristics of the ax_O8 structures donot vary substantially one may draw a conclusion that the(uracil)O8middot middot middotHO(ribose) interaction rather than syn or C3prime-endo conformation is responsible for the extraordinary stabi-lization of the excess charge in this family of geometries

V SUMMARY

In the present work we report on the electrophilic proper-ties of uridine homodimers in the gas phase that were charac-

terized with photoelectron spectroscopy and quantum chem-istry modeling

Photoelectron spectrum of uridine homodimer radi-cal anions (rU)2

bullminus was registered using infrared desorp-tionphotoemission anion generation and pulsed laser pho-todetachment The spectrum exhibits a broad signal with athreshold at sim12 eV and a maximum intensity at 20ndash25 eV(Figure 1) The shape of photoelectron spectrum of uridineanions (rUbullminus) registered previously resembles that of (rU)2

bullminusHowever dimerization process shifts the (rU)2

bullminus PES maxi-mum by around 08 eV to the higher EBEs when compared torUbullminus On the other hand the photoelectron spectra of uracil2bullndash

(U2bullminus) and (rU)2

bullminus are characterized by the maximum inten-sity lying within the same EBE range

The results of our computational studies suggest that for-mation of the neutral uridine homodimers in the gas phaseis thermodynamically improbable while the existence of thehighly stable valence radical anions of this dimer is plau-sibe in agreement with the experimental observations Acommon feature of the investigated anionic structures is anuneven charge distribution which suggests that the nega-tively charged nucleoside with the electron density local-ized entirely within the base moiety is solvated by a neutralmonomer In the most stable radical anionic homodimer thathas a predominant contribution to the PES signal the nucle-oside hosting the excess charge on the base moiety forms abifurcated hydrogen bond via its O8 atom with two hydroxylgroups of the other neutral nucleosidersquos ribose Its calculatedVDE of 246 eV fits perfectly the VDE measured by PES

The anionic radical complexes consisting of two inter-molecular uracil-uracil hydrogen bonds are substantially lessstable than the uracil-ribose dimers Despite the fact that theuracil-uracil anionic radical homodimers are additionally sta-bilized by barrier-free electron-induced proton transfer theirrelative thermodynamic stabilities and the calculated VDEssuggest that they do not contribute to the experimental PESspectrum of (rU)2

bullminus

ACKNOWLEDGMENTS

The experimental results reported here are based uponwork supported by the National Science Foundation grant toKHB (Grant No CHE-1111693) and the theoretical partswere supported by the Polish Ministry of Science and HigherEducation grant to JR (Grant No DS8221-4-0140-12) Thecalculations have been carried out at the Wrocław Center forNetworking and Supercomputing (httpwwwwcsswrocpl)(Grant No 196) and at the Academic Computer Center inGdansk (TASK)

1B Boudaiumlffa P Cloutier D Hunting M A Huels and L Sanche Science287 1658 (2000)

2B Boudaiumlffa P Cloutier D Hunting M A Huels and L Sanche RadiatRes 157 227 (2002)

3M A Huels B Boudaiumlffa P Cloutier D Hunting M A Huels andL Sanche J Am Chem Soc 125 4467 (2003)

4F Martin P D Burrow Z Cai P Cloutier D Hunting and L SanchePhys Rev Lett 93 068101 (2004)

5Y Zheng P Cloutier D J Hunting L Sanche and J R Wagner J AmChem Soc 127 16592 (2005)

6Z Cai P Cloutier D Hunting and L Sanche J Phys Chem B 109 4796(2005)

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-4 Ko et al J Chem Phys 137 205101 (2012)

FIG 2 Neutral conformations of uridine optimized at the B3LYP6-31++G level

monomeric model for further studies by using the stability ofthe particular neutral conformers does not seem to be justifiedHowever photoelectron spectrum measured by Stokes et alrevealed that the VDE and AEA values of isolated valence-bound uridine amounts to 139 and sim07 eV respectively49

Upon re-optimization of the four monomeric uridine con-formers listed in Table I as anion radicals we found out thatVDE equal to 147 eV (after correction with minus015 eV) andAEAG = 073 eV for the C2prime-endoanti structure remain ingood accordance with experimental VDE and AEA of rUbullminusMoreover the C2prime-endoanti radical anion was also identifiedas the most stable among the considered anionic structures(see Table I) The next most stable anionic conformer C2prime-endosyn is separated from C2prime-endoanti by as much as 51and 38 kcalmol in terms of E and G respectively The calcu-lated VDE and AEAG values of the C2prime-endosyn conformeramount to 106 (after correction with minus015 eV) and 061 eVrespectively Thus the thermodynamic stability and the elec-trophilic characteristics of C2prime-endosyn do not support theexistence of this radical anion in the gas phase

Noticing that the neutral geometries do not change dras-tically upon electron attachment (except for C3prime-endoanti)and what is more important that the relative stability orderis the same for both neutrals and anions we assume that therelative stabilities of neutral uridine conformations in the gasphase may be deduced from the stability of anionic radicalsIn view of foregoing we decided that the C2prime-endoanti ge-ometry of neutral uridine is the proper choice for the currentstudy The fact that the isolated ribose C2prime-endo conformationis slightly more stable than C3prime-endo67 also speaks in favor ofthe C2prime-endoanti geometry

1 Neutral dimer conformations

Uracil nucleoside dimers can be stabilized by hydrogenbonding via proton acceptor sites (O7 or O8) and protondonor sites (N3) of the nucleobases as well as the OH protondonor groups of the ribose moiety Figure 3 displays the neu-tral complexes optimized at the B3LYP6-31++G levelAll involve the C2prime-endoanti conformation of uridine

There are three conceivable hydrogen-bonded structuresinvolving interactions exclusively among the two uracils Wenamed them n1 n2 and n3 with the supplementary labeling ofthe proton acceptor atoms participating in the hydrogen bond-ing scheme The complexes n1_O8-O8 (both uracils engagetheir O8 and N3H atoms) and n3_O7-O7 (both uracils en-

gage the same O7 and N3H centers) are ldquosymmetricalrdquo whilethe n2_O8-O7 structure features an ldquoasymmetricalrdquo schemeof hydrogen bonds O8middot middot middotHndashN3 O7middot middot middotHndashN3

Homodimers involving uracil-ribose hydrogen bondinginteractions are depicted on the lower half of Figure 3 Uponrotation of uridine with respect to the hydroxyl groups ofsugar we obtained several structures of similar energy Herewe show only four of these conformers which were se-lected to illustrate the most significant geometrical differ-ences within the current hydrogen bonding scheme Thesestructures are numbered from n4 to n7 and in contrast to the

FIG 3 Structures of neutral uridine dimers optimized at the B3LYP6-31++G level

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-5 Ko et al J Chem Phys 137 205101 (2012)

TABLE II Values of relative electronic energy and free energy (E andG) with respect to the most stable neutral uridine dimer and stabilizationfree energies (Gstab) of the neutral uridine dimers calculated at the B3LYP6-31++G level All values given in kcalmol

Complex E G Gstab

n1_O8-O8 000 000 004n2_O8-O7 219 113 118n3_O7-O7 363 246 250n4_O8 654 504 509n5_O8 707 452 456n6_O8 722 354 358n7_O8 755 545 550

previous uracil-uracil bonding motif only one O8 label isused in the nomenclature since the conformers are stabilizedby a single hydrogen bond The relative energies and Gibbsfree energies (E and G) as well as the stabilization en-thalpies (Gstab) of the neutral uridine homodimers gatheredin Table II are sorted according to their energy values TheGstab values ranging from 0 to 55 kcalmol (see Table II)suggest that dimerization is not thermodynamically favored

2 Anions resulting from electron attachment

The fully optimized neutral complexes described inSec III B 1 (see Figure 3) were used as starting pointsfor the investigation of the electrophilic properties of (rU)2The results of B3LYP6-31++G calculations for (rU)2

bullminus

are summarized in Table III and the respective structures areshown in Figure 4 Using the seven neutral parents we haveobtained a large number of anionic geometries as the systemunder investigation is characterized by a large number of con-formational degrees of freedom particularly the complexeswhere the nucleosides interact with each other through thesugar moiety (structures ax_O8 where x = 1ndash7) Fortunatelymost of these conformers lie close to each other on the po-tential energy surface and exhibit similar electrophilic proper-ties Thus the fourteen structures displayed in Figure 4 are therepresentative geometries of the thoroughly scrutinized con-formational space of the uridine homodimer anionic radicalcomplex

Attachment of the excess electron to the neutral uracil-uracil arrangements (structures n1_O8-O8 n2_O8-O7 andn3_O7-O7) leads to the structures stabilized by two hydro-gen bonds which do not allow for a large change of mutualpositions of monomers Two types of anions are formed inthis casendashstructures that resemble the neutral parent showingsimilar double hydrogen bonding motifs and structures whereelectron-induced proton transfer occurs in one of the two H-bonds (a8_O8-O8-pt and a9_O8-O7-pt) The proton acceptorsite is exclusively the O8 atom which is not surprising basedon the SOMO shapes plotted in Figure 4 The complete lackof the electron density on the O7 atom of uridine makes theO8 atom the only available proton-accepting center within theconsidered dimers

As expected from the broad shape of photoelectron spec-trum shown in the current report and from previous stud-ies demonstrating that nucleobase anions (and other anionic

TABLE III Values of relative electronic energy and free energy (E andG) with respect to the most stable uridine homodimer radical anion stabi-lization free energies (Gstab) vertical detachment energies (VDEs) and adi-abatic electron affinities (AEAs) of anion radical uridine homodimers cal-culated at the B3LYP6-31++G level E G and Gstab are given inkcalmol and AEAG and VDE in eV

Complex E G Gstab AEAG VDEa

a1_O8 000 000 minus 1343 146b 261 (246)a2_O8 169 004 minus 1338 146b 245 (230)a3_O8 377 055 minus 1288 144b 246 (231)a4_O8 408 020 minus 1323 145b 242 (227)a5_O8 410 104 minus 1239 142b 243 (228)a6_O8 464 091 minus 1252 142b 242 (227)a7_O8 481 132 minus 1210 141b 241 (226)a8_O8-O8-pt 673 420 minus 923 113c 269 (254)a9_O8-O7-pt 852 568 minus 774 111d 276 (261)a10_O8-O8 936 612 minus 730 104c 193 (178)a11_O8-O7 1041 785 minus 558 102d 196 (181)a12_O8-O8 1057 546 minus 797 107c 109 (094)a13_O7-O7 1518 1134 minus 208 092e 117 (102)a14_O7-O7 1663 1403 060 081e 165 (150)

aIn parentheses are given VDE values corrected by minus015 eV For details see Sec IIbAEAG calculated from the difference in Gibbs free energies of the neutral structuren6_O8 and the given anionic structurecAEAG calculated from the difference in Gibbs free energies of the neutral structuren1_O8-O8 and the given anionic structuredAEAG calculated from the difference in Gibbs free energies of the neutral structuren2_O8-O7 and the given anionic structureeAEAG calculated from the difference in Gibbs free energies of the neutral structuren3_O7-O7 and the given anionic structure

DNARNA subunits) are thermodynamically stable in the gasphase provided that the solvent molecule is present in thevicinity22 34ndash51 all (rU)2

bullminus complexes reported here exhibitvalence-bound character Inspection of the anionic wave func-tions of complexes reveals that in most cases the excess elec-tron locates on a π orbital of uracil of only one of theinteracting monomers Therefore the dimer structures maybe perceived as uridine radical anions solvated by neutralcounterparts

All considered homodimers form adiabatically stable an-ions as indicated by the AEAG values in Table III which spanthe range of 081ndash146 eV

According to the relative stabilities of the anionic radicalcomplexes (Table III) a clear picture emerges that dominat-ing in the gas phase should be the geometries of the ax_O8family where one of the nucleoside is hydrogen bonded viathe O8 atom of its uracil to one or two OH groups of the sec-ond nucleosidersquos sugar (uracil-ribose pattern of interactions)In such geometries the excess electron is completely local-ized on the uracil moiety of one nucleoside which is interact-ing with the second neutral monomer via its O8 atom For theseven most stable structures (ax_O8 where x = 1ndash7) the Gstab

values lie between minus1343 and minus1210 kcalmol In contrastto the relatively unstable uracil-ribose nx_O8 neutral dimers(characterized by positive Gstab values in the range of 358 to55 kcalmol) the corresponding anionic dimers ax_O8 ex-hibit significant stability

For the most stable geometries a1_O8 and a2_O8 wehave unexpectedly found that the neutral monomers adopt theC2prime-endosyn conformation Additionally the C3prime-endoanti

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-6 Ko et al J Chem Phys 137 205101 (2012)

FIG 4 Structures of anion radical uridine dimers optimized at the B3LYP6-31++G level with corresponding VDE values and their singly occupiedmolecular orbitals plotted with a contour value of 005 bohrminus32

conformer was identified in a5_O8 The four remaining an-ionic dimers of the ax_O8 family as well as the seven homod-imers from the other family shown in Figure 4 are uniformlycomposed of the C2prime-endoanti monomers The least stablestructure among the ax_O8 structures that is a7_O8 is sepa-rated by 48 and 13 kcalmol from the most stable a1_O8 inthe energy and free energy scale respectively (see Table III)The calculated VDE values (incremented by minus015 eV)246 eV for the most stable a1_O8 and 226 eV for the leaststable a7_O8 agree very well with the broad feature of thePES spectrum at maximum EBE range of 20 to 25 eV

The least stable member of ldquouracil-riboserdquo family is sep-arated from the next structure (which is a8_O8-O8-pt) by 192and 288 kcalmol in the term of E and G (see Table III) re-spectively The anionic a8_O8-O8-pt and a9_O8-O7-pt struc-tures are stabilized by electron-induced intermolecular pro-ton transfer (PT) occurring between the complementary uracilmoieties Based on our earlier experiences with anionic com-plexes of biomolecules in the gas phase we expected the PTstructures to be the most stable geometries among consideredradical anions However the data gathered in Table III demon-strate unequivocally that both PT homodimers should not bepopulated in the gas phase Despite of the favorable Gstab

values equal to minus93 and minus77 kcalmol and positive AEAGrsquosof sim11 eV both a8_O8-O8-pt and a9_O8-O7-pt are too highon the energy (67 and 85 kcalmol respectively) and free en-ergy scale (42 and 57 kcalmol) to compete with any of theax_O8 geometries

Similarly the relatively small stabilities for the non-PTldquouracil-uracilrdquo anions (a10 to a14 structures see Table III)suggest that such anionic complexes do not form under theconditions of the photoelectron experiment

IV DISCUSSION

The calculations carried out on conceivable neutral ho-modimers enabled the fourteen anionic (uridine)2

bullminus structuresdepicted in Figure 4 to be identified and characterized Thecharge distribution of the unpaired electron in uridine homod-imers is uneven one of the two nucleosides accepts the excesselectron which is accompanied by pyrimidine ring distortionwhile its counterpart monomer stays neutral The main partof the excess electron density resides on the C4 C5 andC6 sites of uracil and smaller amounts on the N1 N3 andO8 atoms An identical shape of the unpaired electron orbital

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-7 Ko et al J Chem Phys 137 205101 (2012)

was found for the isolated 1-methyluracil and non-methylateduracil anions29

Since dimerization is not favorable for the neutralmonomers (see positive Gstab values gathered in Table II)the formation of anionic radical dimers probably begins withelectron capture by a single nucleoside rather than by a neutraldimer The resulting monomeric anion radical could be sub-sequently stabilized by dimerization with the neutral uridineThe Gstab values predicted for the anionic homodimers (seeTable III) are in favor of such a mechanism Strong stabiliza-tion of the (rU)2

bullminus complexes characterized by the negativeGstab and positive AEAG values results in VDEs much largerthan 2 eV In our previous studies36 37 41 53 VDEs close to2 eV were computed exclusively for the radical anions sta-bilized by proton transfer (PT) Here we demonstrated thatVDEs above 2 eV can occur for non-PT anions Moreoversuch non-PT complexes turned out to be the most stable an-ionic geometries (ax_O8 family) and therefore should have adominating contribution to the main PES signal covering theEBEs of 226ndash246 eV On the other hand the PT-structureswere shown to be significantly unstable with respect to theax_O8 geometries although characterized by similarly highVDEs (sim25 eV)

The prevailing stability of the ax_O8 family with regardto ax_O8-O8 ax_O7-O7 and ax_O8-O7 is surprising giventhe fact that the uracil-ribose interactions involve a singleO8middot middot middotHO or a bifurcated hydrogen bond while each struc-ture featuring a uracil-uracil interaction contains two inter-molecular (O8middot middot middotHN3 or O7middot middot middotHN3) hydrogen bonds Theintermolecular hydrogen bonds in which the hydroxyl groupsof ribose participate are not unusual in biological systemsIt was observed that certain conformations of RNA are ex-traordinarily stable and conserved due to the presence of suchinter-strand interactions54 What is also important is that theformation of hydrogen bonds involving sugar OH groups maybe correlated to the conformational change of sugar puckeringfrom C3prime-endo to C2prime-endo68 69

The most stable structures a1_O8 and a2_O8 differfrom the other ax_O8 (x = 3ndash7) geometries (as well as fromthe other ldquouracil-uracilrdquo structures) by the presence of thesyn conformer The syn orientation of the OH-donating neu-tral nucleoside enables the bifurcated H-bond between O2primeHand O3primeH of ribose and the O8 atom of the anionic uri-dine (both OHmiddot middot middotO8 distances are similar to each other andamount to sim17 Aring see Figure 4) to be formed in a1_O8and a2_O8 Both structures are almost identical energeti-cally (free energy difference of 004 kcalmol difference inGstab equal to 005 kcalmol and identical AEAG) Sincethe thermodynamic characteristics of the ax_O8 structures donot vary substantially one may draw a conclusion that the(uracil)O8middot middot middotHO(ribose) interaction rather than syn or C3prime-endo conformation is responsible for the extraordinary stabi-lization of the excess charge in this family of geometries

V SUMMARY

In the present work we report on the electrophilic proper-ties of uridine homodimers in the gas phase that were charac-

terized with photoelectron spectroscopy and quantum chem-istry modeling

Photoelectron spectrum of uridine homodimer radi-cal anions (rU)2

bullminus was registered using infrared desorp-tionphotoemission anion generation and pulsed laser pho-todetachment The spectrum exhibits a broad signal with athreshold at sim12 eV and a maximum intensity at 20ndash25 eV(Figure 1) The shape of photoelectron spectrum of uridineanions (rUbullminus) registered previously resembles that of (rU)2

bullminusHowever dimerization process shifts the (rU)2

bullminus PES maxi-mum by around 08 eV to the higher EBEs when compared torUbullminus On the other hand the photoelectron spectra of uracil2bullndash

(U2bullminus) and (rU)2

bullminus are characterized by the maximum inten-sity lying within the same EBE range

The results of our computational studies suggest that for-mation of the neutral uridine homodimers in the gas phaseis thermodynamically improbable while the existence of thehighly stable valence radical anions of this dimer is plau-sibe in agreement with the experimental observations Acommon feature of the investigated anionic structures is anuneven charge distribution which suggests that the nega-tively charged nucleoside with the electron density local-ized entirely within the base moiety is solvated by a neutralmonomer In the most stable radical anionic homodimer thathas a predominant contribution to the PES signal the nucle-oside hosting the excess charge on the base moiety forms abifurcated hydrogen bond via its O8 atom with two hydroxylgroups of the other neutral nucleosidersquos ribose Its calculatedVDE of 246 eV fits perfectly the VDE measured by PES

The anionic radical complexes consisting of two inter-molecular uracil-uracil hydrogen bonds are substantially lessstable than the uracil-ribose dimers Despite the fact that theuracil-uracil anionic radical homodimers are additionally sta-bilized by barrier-free electron-induced proton transfer theirrelative thermodynamic stabilities and the calculated VDEssuggest that they do not contribute to the experimental PESspectrum of (rU)2

bullminus

ACKNOWLEDGMENTS

The experimental results reported here are based uponwork supported by the National Science Foundation grant toKHB (Grant No CHE-1111693) and the theoretical partswere supported by the Polish Ministry of Science and HigherEducation grant to JR (Grant No DS8221-4-0140-12) Thecalculations have been carried out at the Wrocław Center forNetworking and Supercomputing (httpwwwwcsswrocpl)(Grant No 196) and at the Academic Computer Center inGdansk (TASK)

1B Boudaiumlffa P Cloutier D Hunting M A Huels and L Sanche Science287 1658 (2000)

2B Boudaiumlffa P Cloutier D Hunting M A Huels and L Sanche RadiatRes 157 227 (2002)

3M A Huels B Boudaiumlffa P Cloutier D Hunting M A Huels andL Sanche J Am Chem Soc 125 4467 (2003)

4F Martin P D Burrow Z Cai P Cloutier D Hunting and L SanchePhys Rev Lett 93 068101 (2004)

5Y Zheng P Cloutier D J Hunting L Sanche and J R Wagner J AmChem Soc 127 16592 (2005)

6Z Cai P Cloutier D Hunting and L Sanche J Phys Chem B 109 4796(2005)

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-5 Ko et al J Chem Phys 137 205101 (2012)

TABLE II Values of relative electronic energy and free energy (E andG) with respect to the most stable neutral uridine dimer and stabilizationfree energies (Gstab) of the neutral uridine dimers calculated at the B3LYP6-31++G level All values given in kcalmol

Complex E G Gstab

n1_O8-O8 000 000 004n2_O8-O7 219 113 118n3_O7-O7 363 246 250n4_O8 654 504 509n5_O8 707 452 456n6_O8 722 354 358n7_O8 755 545 550

previous uracil-uracil bonding motif only one O8 label isused in the nomenclature since the conformers are stabilizedby a single hydrogen bond The relative energies and Gibbsfree energies (E and G) as well as the stabilization en-thalpies (Gstab) of the neutral uridine homodimers gatheredin Table II are sorted according to their energy values TheGstab values ranging from 0 to 55 kcalmol (see Table II)suggest that dimerization is not thermodynamically favored

2 Anions resulting from electron attachment

The fully optimized neutral complexes described inSec III B 1 (see Figure 3) were used as starting pointsfor the investigation of the electrophilic properties of (rU)2The results of B3LYP6-31++G calculations for (rU)2

bullminus

are summarized in Table III and the respective structures areshown in Figure 4 Using the seven neutral parents we haveobtained a large number of anionic geometries as the systemunder investigation is characterized by a large number of con-formational degrees of freedom particularly the complexeswhere the nucleosides interact with each other through thesugar moiety (structures ax_O8 where x = 1ndash7) Fortunatelymost of these conformers lie close to each other on the po-tential energy surface and exhibit similar electrophilic proper-ties Thus the fourteen structures displayed in Figure 4 are therepresentative geometries of the thoroughly scrutinized con-formational space of the uridine homodimer anionic radicalcomplex

Attachment of the excess electron to the neutral uracil-uracil arrangements (structures n1_O8-O8 n2_O8-O7 andn3_O7-O7) leads to the structures stabilized by two hydro-gen bonds which do not allow for a large change of mutualpositions of monomers Two types of anions are formed inthis casendashstructures that resemble the neutral parent showingsimilar double hydrogen bonding motifs and structures whereelectron-induced proton transfer occurs in one of the two H-bonds (a8_O8-O8-pt and a9_O8-O7-pt) The proton acceptorsite is exclusively the O8 atom which is not surprising basedon the SOMO shapes plotted in Figure 4 The complete lackof the electron density on the O7 atom of uridine makes theO8 atom the only available proton-accepting center within theconsidered dimers

As expected from the broad shape of photoelectron spec-trum shown in the current report and from previous stud-ies demonstrating that nucleobase anions (and other anionic

TABLE III Values of relative electronic energy and free energy (E andG) with respect to the most stable uridine homodimer radical anion stabi-lization free energies (Gstab) vertical detachment energies (VDEs) and adi-abatic electron affinities (AEAs) of anion radical uridine homodimers cal-culated at the B3LYP6-31++G level E G and Gstab are given inkcalmol and AEAG and VDE in eV

Complex E G Gstab AEAG VDEa

a1_O8 000 000 minus 1343 146b 261 (246)a2_O8 169 004 minus 1338 146b 245 (230)a3_O8 377 055 minus 1288 144b 246 (231)a4_O8 408 020 minus 1323 145b 242 (227)a5_O8 410 104 minus 1239 142b 243 (228)a6_O8 464 091 minus 1252 142b 242 (227)a7_O8 481 132 minus 1210 141b 241 (226)a8_O8-O8-pt 673 420 minus 923 113c 269 (254)a9_O8-O7-pt 852 568 minus 774 111d 276 (261)a10_O8-O8 936 612 minus 730 104c 193 (178)a11_O8-O7 1041 785 minus 558 102d 196 (181)a12_O8-O8 1057 546 minus 797 107c 109 (094)a13_O7-O7 1518 1134 minus 208 092e 117 (102)a14_O7-O7 1663 1403 060 081e 165 (150)

aIn parentheses are given VDE values corrected by minus015 eV For details see Sec IIbAEAG calculated from the difference in Gibbs free energies of the neutral structuren6_O8 and the given anionic structurecAEAG calculated from the difference in Gibbs free energies of the neutral structuren1_O8-O8 and the given anionic structuredAEAG calculated from the difference in Gibbs free energies of the neutral structuren2_O8-O7 and the given anionic structureeAEAG calculated from the difference in Gibbs free energies of the neutral structuren3_O7-O7 and the given anionic structure

DNARNA subunits) are thermodynamically stable in the gasphase provided that the solvent molecule is present in thevicinity22 34ndash51 all (rU)2

bullminus complexes reported here exhibitvalence-bound character Inspection of the anionic wave func-tions of complexes reveals that in most cases the excess elec-tron locates on a π orbital of uracil of only one of theinteracting monomers Therefore the dimer structures maybe perceived as uridine radical anions solvated by neutralcounterparts

All considered homodimers form adiabatically stable an-ions as indicated by the AEAG values in Table III which spanthe range of 081ndash146 eV

According to the relative stabilities of the anionic radicalcomplexes (Table III) a clear picture emerges that dominat-ing in the gas phase should be the geometries of the ax_O8family where one of the nucleoside is hydrogen bonded viathe O8 atom of its uracil to one or two OH groups of the sec-ond nucleosidersquos sugar (uracil-ribose pattern of interactions)In such geometries the excess electron is completely local-ized on the uracil moiety of one nucleoside which is interact-ing with the second neutral monomer via its O8 atom For theseven most stable structures (ax_O8 where x = 1ndash7) the Gstab

values lie between minus1343 and minus1210 kcalmol In contrastto the relatively unstable uracil-ribose nx_O8 neutral dimers(characterized by positive Gstab values in the range of 358 to55 kcalmol) the corresponding anionic dimers ax_O8 ex-hibit significant stability

For the most stable geometries a1_O8 and a2_O8 wehave unexpectedly found that the neutral monomers adopt theC2prime-endosyn conformation Additionally the C3prime-endoanti

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-6 Ko et al J Chem Phys 137 205101 (2012)

FIG 4 Structures of anion radical uridine dimers optimized at the B3LYP6-31++G level with corresponding VDE values and their singly occupiedmolecular orbitals plotted with a contour value of 005 bohrminus32

conformer was identified in a5_O8 The four remaining an-ionic dimers of the ax_O8 family as well as the seven homod-imers from the other family shown in Figure 4 are uniformlycomposed of the C2prime-endoanti monomers The least stablestructure among the ax_O8 structures that is a7_O8 is sepa-rated by 48 and 13 kcalmol from the most stable a1_O8 inthe energy and free energy scale respectively (see Table III)The calculated VDE values (incremented by minus015 eV)246 eV for the most stable a1_O8 and 226 eV for the leaststable a7_O8 agree very well with the broad feature of thePES spectrum at maximum EBE range of 20 to 25 eV

The least stable member of ldquouracil-riboserdquo family is sep-arated from the next structure (which is a8_O8-O8-pt) by 192and 288 kcalmol in the term of E and G (see Table III) re-spectively The anionic a8_O8-O8-pt and a9_O8-O7-pt struc-tures are stabilized by electron-induced intermolecular pro-ton transfer (PT) occurring between the complementary uracilmoieties Based on our earlier experiences with anionic com-plexes of biomolecules in the gas phase we expected the PTstructures to be the most stable geometries among consideredradical anions However the data gathered in Table III demon-strate unequivocally that both PT homodimers should not bepopulated in the gas phase Despite of the favorable Gstab

values equal to minus93 and minus77 kcalmol and positive AEAGrsquosof sim11 eV both a8_O8-O8-pt and a9_O8-O7-pt are too highon the energy (67 and 85 kcalmol respectively) and free en-ergy scale (42 and 57 kcalmol) to compete with any of theax_O8 geometries

Similarly the relatively small stabilities for the non-PTldquouracil-uracilrdquo anions (a10 to a14 structures see Table III)suggest that such anionic complexes do not form under theconditions of the photoelectron experiment

IV DISCUSSION

The calculations carried out on conceivable neutral ho-modimers enabled the fourteen anionic (uridine)2

bullminus structuresdepicted in Figure 4 to be identified and characterized Thecharge distribution of the unpaired electron in uridine homod-imers is uneven one of the two nucleosides accepts the excesselectron which is accompanied by pyrimidine ring distortionwhile its counterpart monomer stays neutral The main partof the excess electron density resides on the C4 C5 andC6 sites of uracil and smaller amounts on the N1 N3 andO8 atoms An identical shape of the unpaired electron orbital

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-7 Ko et al J Chem Phys 137 205101 (2012)

was found for the isolated 1-methyluracil and non-methylateduracil anions29

Since dimerization is not favorable for the neutralmonomers (see positive Gstab values gathered in Table II)the formation of anionic radical dimers probably begins withelectron capture by a single nucleoside rather than by a neutraldimer The resulting monomeric anion radical could be sub-sequently stabilized by dimerization with the neutral uridineThe Gstab values predicted for the anionic homodimers (seeTable III) are in favor of such a mechanism Strong stabiliza-tion of the (rU)2

bullminus complexes characterized by the negativeGstab and positive AEAG values results in VDEs much largerthan 2 eV In our previous studies36 37 41 53 VDEs close to2 eV were computed exclusively for the radical anions sta-bilized by proton transfer (PT) Here we demonstrated thatVDEs above 2 eV can occur for non-PT anions Moreoversuch non-PT complexes turned out to be the most stable an-ionic geometries (ax_O8 family) and therefore should have adominating contribution to the main PES signal covering theEBEs of 226ndash246 eV On the other hand the PT-structureswere shown to be significantly unstable with respect to theax_O8 geometries although characterized by similarly highVDEs (sim25 eV)

The prevailing stability of the ax_O8 family with regardto ax_O8-O8 ax_O7-O7 and ax_O8-O7 is surprising giventhe fact that the uracil-ribose interactions involve a singleO8middot middot middotHO or a bifurcated hydrogen bond while each struc-ture featuring a uracil-uracil interaction contains two inter-molecular (O8middot middot middotHN3 or O7middot middot middotHN3) hydrogen bonds Theintermolecular hydrogen bonds in which the hydroxyl groupsof ribose participate are not unusual in biological systemsIt was observed that certain conformations of RNA are ex-traordinarily stable and conserved due to the presence of suchinter-strand interactions54 What is also important is that theformation of hydrogen bonds involving sugar OH groups maybe correlated to the conformational change of sugar puckeringfrom C3prime-endo to C2prime-endo68 69

The most stable structures a1_O8 and a2_O8 differfrom the other ax_O8 (x = 3ndash7) geometries (as well as fromthe other ldquouracil-uracilrdquo structures) by the presence of thesyn conformer The syn orientation of the OH-donating neu-tral nucleoside enables the bifurcated H-bond between O2primeHand O3primeH of ribose and the O8 atom of the anionic uri-dine (both OHmiddot middot middotO8 distances are similar to each other andamount to sim17 Aring see Figure 4) to be formed in a1_O8and a2_O8 Both structures are almost identical energeti-cally (free energy difference of 004 kcalmol difference inGstab equal to 005 kcalmol and identical AEAG) Sincethe thermodynamic characteristics of the ax_O8 structures donot vary substantially one may draw a conclusion that the(uracil)O8middot middot middotHO(ribose) interaction rather than syn or C3prime-endo conformation is responsible for the extraordinary stabi-lization of the excess charge in this family of geometries

V SUMMARY

In the present work we report on the electrophilic proper-ties of uridine homodimers in the gas phase that were charac-

terized with photoelectron spectroscopy and quantum chem-istry modeling

Photoelectron spectrum of uridine homodimer radi-cal anions (rU)2

bullminus was registered using infrared desorp-tionphotoemission anion generation and pulsed laser pho-todetachment The spectrum exhibits a broad signal with athreshold at sim12 eV and a maximum intensity at 20ndash25 eV(Figure 1) The shape of photoelectron spectrum of uridineanions (rUbullminus) registered previously resembles that of (rU)2

bullminusHowever dimerization process shifts the (rU)2

bullminus PES maxi-mum by around 08 eV to the higher EBEs when compared torUbullminus On the other hand the photoelectron spectra of uracil2bullndash

(U2bullminus) and (rU)2

bullminus are characterized by the maximum inten-sity lying within the same EBE range

The results of our computational studies suggest that for-mation of the neutral uridine homodimers in the gas phaseis thermodynamically improbable while the existence of thehighly stable valence radical anions of this dimer is plau-sibe in agreement with the experimental observations Acommon feature of the investigated anionic structures is anuneven charge distribution which suggests that the nega-tively charged nucleoside with the electron density local-ized entirely within the base moiety is solvated by a neutralmonomer In the most stable radical anionic homodimer thathas a predominant contribution to the PES signal the nucle-oside hosting the excess charge on the base moiety forms abifurcated hydrogen bond via its O8 atom with two hydroxylgroups of the other neutral nucleosidersquos ribose Its calculatedVDE of 246 eV fits perfectly the VDE measured by PES

The anionic radical complexes consisting of two inter-molecular uracil-uracil hydrogen bonds are substantially lessstable than the uracil-ribose dimers Despite the fact that theuracil-uracil anionic radical homodimers are additionally sta-bilized by barrier-free electron-induced proton transfer theirrelative thermodynamic stabilities and the calculated VDEssuggest that they do not contribute to the experimental PESspectrum of (rU)2

bullminus

ACKNOWLEDGMENTS

The experimental results reported here are based uponwork supported by the National Science Foundation grant toKHB (Grant No CHE-1111693) and the theoretical partswere supported by the Polish Ministry of Science and HigherEducation grant to JR (Grant No DS8221-4-0140-12) Thecalculations have been carried out at the Wrocław Center forNetworking and Supercomputing (httpwwwwcsswrocpl)(Grant No 196) and at the Academic Computer Center inGdansk (TASK)

1B Boudaiumlffa P Cloutier D Hunting M A Huels and L Sanche Science287 1658 (2000)

2B Boudaiumlffa P Cloutier D Hunting M A Huels and L Sanche RadiatRes 157 227 (2002)

3M A Huels B Boudaiumlffa P Cloutier D Hunting M A Huels andL Sanche J Am Chem Soc 125 4467 (2003)

4F Martin P D Burrow Z Cai P Cloutier D Hunting and L SanchePhys Rev Lett 93 068101 (2004)

5Y Zheng P Cloutier D J Hunting L Sanche and J R Wagner J AmChem Soc 127 16592 (2005)

6Z Cai P Cloutier D Hunting and L Sanche J Phys Chem B 109 4796(2005)

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-6 Ko et al J Chem Phys 137 205101 (2012)

FIG 4 Structures of anion radical uridine dimers optimized at the B3LYP6-31++G level with corresponding VDE values and their singly occupiedmolecular orbitals plotted with a contour value of 005 bohrminus32

conformer was identified in a5_O8 The four remaining an-ionic dimers of the ax_O8 family as well as the seven homod-imers from the other family shown in Figure 4 are uniformlycomposed of the C2prime-endoanti monomers The least stablestructure among the ax_O8 structures that is a7_O8 is sepa-rated by 48 and 13 kcalmol from the most stable a1_O8 inthe energy and free energy scale respectively (see Table III)The calculated VDE values (incremented by minus015 eV)246 eV for the most stable a1_O8 and 226 eV for the leaststable a7_O8 agree very well with the broad feature of thePES spectrum at maximum EBE range of 20 to 25 eV

The least stable member of ldquouracil-riboserdquo family is sep-arated from the next structure (which is a8_O8-O8-pt) by 192and 288 kcalmol in the term of E and G (see Table III) re-spectively The anionic a8_O8-O8-pt and a9_O8-O7-pt struc-tures are stabilized by electron-induced intermolecular pro-ton transfer (PT) occurring between the complementary uracilmoieties Based on our earlier experiences with anionic com-plexes of biomolecules in the gas phase we expected the PTstructures to be the most stable geometries among consideredradical anions However the data gathered in Table III demon-strate unequivocally that both PT homodimers should not bepopulated in the gas phase Despite of the favorable Gstab

values equal to minus93 and minus77 kcalmol and positive AEAGrsquosof sim11 eV both a8_O8-O8-pt and a9_O8-O7-pt are too highon the energy (67 and 85 kcalmol respectively) and free en-ergy scale (42 and 57 kcalmol) to compete with any of theax_O8 geometries

Similarly the relatively small stabilities for the non-PTldquouracil-uracilrdquo anions (a10 to a14 structures see Table III)suggest that such anionic complexes do not form under theconditions of the photoelectron experiment

IV DISCUSSION

The calculations carried out on conceivable neutral ho-modimers enabled the fourteen anionic (uridine)2

bullminus structuresdepicted in Figure 4 to be identified and characterized Thecharge distribution of the unpaired electron in uridine homod-imers is uneven one of the two nucleosides accepts the excesselectron which is accompanied by pyrimidine ring distortionwhile its counterpart monomer stays neutral The main partof the excess electron density resides on the C4 C5 andC6 sites of uracil and smaller amounts on the N1 N3 andO8 atoms An identical shape of the unpaired electron orbital

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-7 Ko et al J Chem Phys 137 205101 (2012)

was found for the isolated 1-methyluracil and non-methylateduracil anions29

Since dimerization is not favorable for the neutralmonomers (see positive Gstab values gathered in Table II)the formation of anionic radical dimers probably begins withelectron capture by a single nucleoside rather than by a neutraldimer The resulting monomeric anion radical could be sub-sequently stabilized by dimerization with the neutral uridineThe Gstab values predicted for the anionic homodimers (seeTable III) are in favor of such a mechanism Strong stabiliza-tion of the (rU)2

bullminus complexes characterized by the negativeGstab and positive AEAG values results in VDEs much largerthan 2 eV In our previous studies36 37 41 53 VDEs close to2 eV were computed exclusively for the radical anions sta-bilized by proton transfer (PT) Here we demonstrated thatVDEs above 2 eV can occur for non-PT anions Moreoversuch non-PT complexes turned out to be the most stable an-ionic geometries (ax_O8 family) and therefore should have adominating contribution to the main PES signal covering theEBEs of 226ndash246 eV On the other hand the PT-structureswere shown to be significantly unstable with respect to theax_O8 geometries although characterized by similarly highVDEs (sim25 eV)

The prevailing stability of the ax_O8 family with regardto ax_O8-O8 ax_O7-O7 and ax_O8-O7 is surprising giventhe fact that the uracil-ribose interactions involve a singleO8middot middot middotHO or a bifurcated hydrogen bond while each struc-ture featuring a uracil-uracil interaction contains two inter-molecular (O8middot middot middotHN3 or O7middot middot middotHN3) hydrogen bonds Theintermolecular hydrogen bonds in which the hydroxyl groupsof ribose participate are not unusual in biological systemsIt was observed that certain conformations of RNA are ex-traordinarily stable and conserved due to the presence of suchinter-strand interactions54 What is also important is that theformation of hydrogen bonds involving sugar OH groups maybe correlated to the conformational change of sugar puckeringfrom C3prime-endo to C2prime-endo68 69

The most stable structures a1_O8 and a2_O8 differfrom the other ax_O8 (x = 3ndash7) geometries (as well as fromthe other ldquouracil-uracilrdquo structures) by the presence of thesyn conformer The syn orientation of the OH-donating neu-tral nucleoside enables the bifurcated H-bond between O2primeHand O3primeH of ribose and the O8 atom of the anionic uri-dine (both OHmiddot middot middotO8 distances are similar to each other andamount to sim17 Aring see Figure 4) to be formed in a1_O8and a2_O8 Both structures are almost identical energeti-cally (free energy difference of 004 kcalmol difference inGstab equal to 005 kcalmol and identical AEAG) Sincethe thermodynamic characteristics of the ax_O8 structures donot vary substantially one may draw a conclusion that the(uracil)O8middot middot middotHO(ribose) interaction rather than syn or C3prime-endo conformation is responsible for the extraordinary stabi-lization of the excess charge in this family of geometries

V SUMMARY

In the present work we report on the electrophilic proper-ties of uridine homodimers in the gas phase that were charac-

terized with photoelectron spectroscopy and quantum chem-istry modeling

Photoelectron spectrum of uridine homodimer radi-cal anions (rU)2

bullminus was registered using infrared desorp-tionphotoemission anion generation and pulsed laser pho-todetachment The spectrum exhibits a broad signal with athreshold at sim12 eV and a maximum intensity at 20ndash25 eV(Figure 1) The shape of photoelectron spectrum of uridineanions (rUbullminus) registered previously resembles that of (rU)2

bullminusHowever dimerization process shifts the (rU)2

bullminus PES maxi-mum by around 08 eV to the higher EBEs when compared torUbullminus On the other hand the photoelectron spectra of uracil2bullndash

(U2bullminus) and (rU)2

bullminus are characterized by the maximum inten-sity lying within the same EBE range

The results of our computational studies suggest that for-mation of the neutral uridine homodimers in the gas phaseis thermodynamically improbable while the existence of thehighly stable valence radical anions of this dimer is plau-sibe in agreement with the experimental observations Acommon feature of the investigated anionic structures is anuneven charge distribution which suggests that the nega-tively charged nucleoside with the electron density local-ized entirely within the base moiety is solvated by a neutralmonomer In the most stable radical anionic homodimer thathas a predominant contribution to the PES signal the nucle-oside hosting the excess charge on the base moiety forms abifurcated hydrogen bond via its O8 atom with two hydroxylgroups of the other neutral nucleosidersquos ribose Its calculatedVDE of 246 eV fits perfectly the VDE measured by PES

The anionic radical complexes consisting of two inter-molecular uracil-uracil hydrogen bonds are substantially lessstable than the uracil-ribose dimers Despite the fact that theuracil-uracil anionic radical homodimers are additionally sta-bilized by barrier-free electron-induced proton transfer theirrelative thermodynamic stabilities and the calculated VDEssuggest that they do not contribute to the experimental PESspectrum of (rU)2

bullminus

ACKNOWLEDGMENTS

The experimental results reported here are based uponwork supported by the National Science Foundation grant toKHB (Grant No CHE-1111693) and the theoretical partswere supported by the Polish Ministry of Science and HigherEducation grant to JR (Grant No DS8221-4-0140-12) Thecalculations have been carried out at the Wrocław Center forNetworking and Supercomputing (httpwwwwcsswrocpl)(Grant No 196) and at the Academic Computer Center inGdansk (TASK)

1B Boudaiumlffa P Cloutier D Hunting M A Huels and L Sanche Science287 1658 (2000)

2B Boudaiumlffa P Cloutier D Hunting M A Huels and L Sanche RadiatRes 157 227 (2002)

3M A Huels B Boudaiumlffa P Cloutier D Hunting M A Huels andL Sanche J Am Chem Soc 125 4467 (2003)

4F Martin P D Burrow Z Cai P Cloutier D Hunting and L SanchePhys Rev Lett 93 068101 (2004)

5Y Zheng P Cloutier D J Hunting L Sanche and J R Wagner J AmChem Soc 127 16592 (2005)

6Z Cai P Cloutier D Hunting and L Sanche J Phys Chem B 109 4796(2005)

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-7 Ko et al J Chem Phys 137 205101 (2012)

was found for the isolated 1-methyluracil and non-methylateduracil anions29

Since dimerization is not favorable for the neutralmonomers (see positive Gstab values gathered in Table II)the formation of anionic radical dimers probably begins withelectron capture by a single nucleoside rather than by a neutraldimer The resulting monomeric anion radical could be sub-sequently stabilized by dimerization with the neutral uridineThe Gstab values predicted for the anionic homodimers (seeTable III) are in favor of such a mechanism Strong stabiliza-tion of the (rU)2

bullminus complexes characterized by the negativeGstab and positive AEAG values results in VDEs much largerthan 2 eV In our previous studies36 37 41 53 VDEs close to2 eV were computed exclusively for the radical anions sta-bilized by proton transfer (PT) Here we demonstrated thatVDEs above 2 eV can occur for non-PT anions Moreoversuch non-PT complexes turned out to be the most stable an-ionic geometries (ax_O8 family) and therefore should have adominating contribution to the main PES signal covering theEBEs of 226ndash246 eV On the other hand the PT-structureswere shown to be significantly unstable with respect to theax_O8 geometries although characterized by similarly highVDEs (sim25 eV)

The prevailing stability of the ax_O8 family with regardto ax_O8-O8 ax_O7-O7 and ax_O8-O7 is surprising giventhe fact that the uracil-ribose interactions involve a singleO8middot middot middotHO or a bifurcated hydrogen bond while each struc-ture featuring a uracil-uracil interaction contains two inter-molecular (O8middot middot middotHN3 or O7middot middot middotHN3) hydrogen bonds Theintermolecular hydrogen bonds in which the hydroxyl groupsof ribose participate are not unusual in biological systemsIt was observed that certain conformations of RNA are ex-traordinarily stable and conserved due to the presence of suchinter-strand interactions54 What is also important is that theformation of hydrogen bonds involving sugar OH groups maybe correlated to the conformational change of sugar puckeringfrom C3prime-endo to C2prime-endo68 69

The most stable structures a1_O8 and a2_O8 differfrom the other ax_O8 (x = 3ndash7) geometries (as well as fromthe other ldquouracil-uracilrdquo structures) by the presence of thesyn conformer The syn orientation of the OH-donating neu-tral nucleoside enables the bifurcated H-bond between O2primeHand O3primeH of ribose and the O8 atom of the anionic uri-dine (both OHmiddot middot middotO8 distances are similar to each other andamount to sim17 Aring see Figure 4) to be formed in a1_O8and a2_O8 Both structures are almost identical energeti-cally (free energy difference of 004 kcalmol difference inGstab equal to 005 kcalmol and identical AEAG) Sincethe thermodynamic characteristics of the ax_O8 structures donot vary substantially one may draw a conclusion that the(uracil)O8middot middot middotHO(ribose) interaction rather than syn or C3prime-endo conformation is responsible for the extraordinary stabi-lization of the excess charge in this family of geometries

V SUMMARY

In the present work we report on the electrophilic proper-ties of uridine homodimers in the gas phase that were charac-

terized with photoelectron spectroscopy and quantum chem-istry modeling

Photoelectron spectrum of uridine homodimer radi-cal anions (rU)2

bullminus was registered using infrared desorp-tionphotoemission anion generation and pulsed laser pho-todetachment The spectrum exhibits a broad signal with athreshold at sim12 eV and a maximum intensity at 20ndash25 eV(Figure 1) The shape of photoelectron spectrum of uridineanions (rUbullminus) registered previously resembles that of (rU)2

bullminusHowever dimerization process shifts the (rU)2

bullminus PES maxi-mum by around 08 eV to the higher EBEs when compared torUbullminus On the other hand the photoelectron spectra of uracil2bullndash

(U2bullminus) and (rU)2

bullminus are characterized by the maximum inten-sity lying within the same EBE range

The results of our computational studies suggest that for-mation of the neutral uridine homodimers in the gas phaseis thermodynamically improbable while the existence of thehighly stable valence radical anions of this dimer is plau-sibe in agreement with the experimental observations Acommon feature of the investigated anionic structures is anuneven charge distribution which suggests that the nega-tively charged nucleoside with the electron density local-ized entirely within the base moiety is solvated by a neutralmonomer In the most stable radical anionic homodimer thathas a predominant contribution to the PES signal the nucle-oside hosting the excess charge on the base moiety forms abifurcated hydrogen bond via its O8 atom with two hydroxylgroups of the other neutral nucleosidersquos ribose Its calculatedVDE of 246 eV fits perfectly the VDE measured by PES

The anionic radical complexes consisting of two inter-molecular uracil-uracil hydrogen bonds are substantially lessstable than the uracil-ribose dimers Despite the fact that theuracil-uracil anionic radical homodimers are additionally sta-bilized by barrier-free electron-induced proton transfer theirrelative thermodynamic stabilities and the calculated VDEssuggest that they do not contribute to the experimental PESspectrum of (rU)2

bullminus

ACKNOWLEDGMENTS

The experimental results reported here are based uponwork supported by the National Science Foundation grant toKHB (Grant No CHE-1111693) and the theoretical partswere supported by the Polish Ministry of Science and HigherEducation grant to JR (Grant No DS8221-4-0140-12) Thecalculations have been carried out at the Wrocław Center forNetworking and Supercomputing (httpwwwwcsswrocpl)(Grant No 196) and at the Academic Computer Center inGdansk (TASK)

1B Boudaiumlffa P Cloutier D Hunting M A Huels and L Sanche Science287 1658 (2000)

2B Boudaiumlffa P Cloutier D Hunting M A Huels and L Sanche RadiatRes 157 227 (2002)

3M A Huels B Boudaiumlffa P Cloutier D Hunting M A Huels andL Sanche J Am Chem Soc 125 4467 (2003)

4F Martin P D Burrow Z Cai P Cloutier D Hunting and L SanchePhys Rev Lett 93 068101 (2004)

5Y Zheng P Cloutier D J Hunting L Sanche and J R Wagner J AmChem Soc 127 16592 (2005)

6Z Cai P Cloutier D Hunting and L Sanche J Phys Chem B 109 4796(2005)

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions

205101-8 Ko et al J Chem Phys 137 205101 (2012)

7R Panajotovic F Martin P Cloutier D Hunting and L Sanche RadiatRes 165 452 (2006)

8Y Zheng P Cloutier D J Hunting J R Wagner and L Sanche J ChemPhys 124 064710 (2006)

9Y Zheng J R Wagner and L Sanche Phys Rev Lett 96 208101 (2006)10Z Li Y Zheng P Cloutier L Sanche and J R Wagner J Am Chem

Soc 130 5612 (2008)11H Abdoul-Carime and L Sanche Int J Radiat Biol 78 89 (2002)12L Sanche Mass Spectrom Rev 21 349 (2002)13X Pan P Cloutier D Hunting and L Sanche Phys Rev Lett 90 208102

(2003)14X Pan and L Sanche Phys Rev Lett 94 198104 (2005)15K Aflatooni G Gallup and P Burrow J Phys Chem A 102 6205 (1998)16N Oyler and L Adamowicz J Phys Chem 97 11122 (1993)17N Oyler and L Adamowicz Chem Phys Lett 219 223 (1994)18C Desfrancois H Abdoul-Carime S Carles V Periquet J Schermann

D Smith and L Adamowicz J Chem Phys 110 11876 (1999)19D Smith J Smets Y Elkadi and L Adamowicz J Phys Chem A 101

8123 (1997)20O Dolgounitcheva V Zakrzewski and J Ortiz Chem Phys Lett 307

220 (1999)21J H Hendricks S A Lyapustina H L de Clercq J T Snodgrass and

K H Bowen J Chem Phys 104 7788 (1996)22J Schiedt R Weinkauf D Neumark and E Schlag Chem Phys 239 511

(1998)23C Desfranccedilois H Abdoul-Carime and J Schermann J Chem Phys 104

7792 (1996)24R A Bachorz J Rak and M Gutowski Phys Chem Chem Phys 7 2116

(2005)25S Wetmore R Boyd and L Eriksson Chem Phys Lett 322 129 (2000)26N Russo M Toscano and A Grand J Comput Chem 21 1243 (2000)27S Wesolowski M Leininger P Pentchev and H Schaefer J Am Chem

Soc 123 4023 (2001)28X Li Z Cai and M Sevilla J Phys Chem A 106 1596 (2002)29R A Bachorz W Klopper and M Gutowski J Chem Phys 126 085101

(2007)30D Svozil P Jungwirth and Z Havlas Collect Czech Chem Commun

69 1395 (2004)31J Gu J Leszczynski and H F Schaefer ldquoInteractions of electrons with

bare and hydrated biomolecules From nucleic acid bases to DNA seg-mentsrdquo Chem Rev (in press)

32A Kumar and M D Sevilla ldquoRadiation effects on DNA Theoretical inves-tigations of electron hole and excitation pathways to DNA damagerdquo in Ra-diation Induced Molecular Phenomena in Nucleic Acids A ComprehensiveTheoretical and Experimental Analysis (Challenges and Advances in Com-putational Chemistry and Physics) edited by M Shukla and J Leszczynski(Springer 2008) pp 577ndash617

33M Yan D Becker S Summerfield P Renke and M D Sevilla J PhysChem 96 1983 (1992) M D Sevilla ibid 75 626 (1971) M D SevillaD Becker M Yan and S R Summerfield ibid 95 3409 (1991) M DSevilla and D Becker in Royal Society of Chemistry Specialist PeriodicalReport Electron Spin Resonance edited by B C Gilbert M J Davies andD M Murphy (RSC Cambridge 2004) Vol 19 pp 243

34J H Hendricks S A Lyapustina H L de Clercq and K H BowenJ Chem Phys 108 8 (1998)

35C Desfranccedilois V Periquet Y Bouteiller and J P Schermann J PhysChem A 102 1274 (1998)

36(a) M Haranczyk R Bachorz J Rak M Gutowski D Radisic S TStokes J M Nilles and K H Bowen J Phys Chem B 107 7889 (2003)(b) M Haranczyk J Rak M Gutowski D Radisic S T Stokes J M

Nilles and K H Bowen Isr J Chem 44 157 (2004)37M Haranczyk J Rak M Gutowski D Radisic S T Stokes and K H

Bowen J Phys Chem B 109 13383 (2005) M Haranczyk I DabkowskaJ Rak M Gutowski J M Nilles S T Stokes D Radisic and K HBowen ibid 108 6919 (2004) K Mazurkiewicz M Haranczyk M

Gutowski J Rak D Radisic S N Eustis D Wang and K H BowenJ Am Chem Soc 129 1216 (2007) K Mazurkiewicz M HaranczykP Storoniak M Gutowski J Rak D Radisic S N Eustis D Wang andK H Bowen Chem Phys 342 215 (2007) M Gutowski I DabkowskaJ Rak S Xu J M Nilles D Radisic and K H Bowen Eur Phys JD 20 431 (2002) I Dabkowska J Rak M Gutowski J M Nilles DRadisic and K H Bowen J Chem Phys 120 6064 (2004) I DabkowskaJ Rak M Gutowski D Radisic S T Stokes J M Nilles and K HBowen Phys Chem Chem Phys 6 4351 (2004)

38N A Richardson S S Wesolowski and H F Schaefer J Phys Chem B107 848 (2003)

39I Al-Jihad J Smets and L Adamowicz J Phys Chem A 104 2994(2000)

40A Kumar M Knapp-Mohammady P C Mishra and S Suhai J ComputChem 25 1047 (2004)

41D Radisic K H Bowen I Dabkowska P Storoniak J Rak andM Gutowski J Am Chem Soc 127 6443 (2005)

42J Gu Y Xie and H F Schaefer J Phys Chem B 109 13067 (2005)43A-O Colson B Besler D M Close and M D Sevilla J Phys Chem

96 661 (1992)44J Smets A F Jalbout and L Adamowicz Chem Phys Lett 342 342

(2001)45X Li Z Cai and M D Sevilla J Phys Chem B 105 10115 (2001)46N A Richardson S S Wesolowski and H F Schaefer III J Am Chem

Soc 124 10163 (2002)47J Gu Y Xie and H F Schaefer III J Chem Phys 127 155107 (2007)48N A Richardson J Gu S Wang Y Xie and H F Schaefer III J Am

Chem Soc 126 4404 (2004)49S T Stokes X Li A Grubisic Y J Ko and K H Bowen J Chem Phys

127 084321 (2007)50X Li L Sanche and M D Sevilla Radiat Res 165 721 (2006)51J Gu Y Xie and H F Schaefer Nucleic Acids Res 35 5165 (2007)52S T Stokes A Grubisic X Li Y J Ko and K H Bowen J Chem Phys

128 044314 (2008)53M Kobyłecka J Gu J Rak and J Leszczynski J Chem Phys 128

044315 (2008)54S E Lietzke C L Barnes J A Berglund and C E Kundrot Structure 4

917 (1996)55A D Becke Phys Rev A 38 3098 (1988)56A D Becke J Chem Phys 98 5648 (1993)57C Lee W Yang and R G Parr Phys Rev B 37 785 (1988)58R Ditchfield W J Hehre and J A Pople J Chem Phys 54 724 (1971)59W J Hehre R Ditchfield and J A Pople J Chem Phys 56 2257 (1972)60T van Mourik S L Price and D C Clary J Phys Chem A 103 1611

(1999)61J C Rienstra-Kiracofe G S Tschumper and H F Schaefer Chem Rev

102 231 (2002)62O Dolgounitcheva V Zakrzewski and J Ortiz J Phys Chem A 103

7912 (1999)63M J Frisch G W Trucks H B Schlegel et al GAUSSIAN 03 Revision

B05 Gaussian Inc Pittsburgh PA 200364M J Frisch G W Trucks H B Schlegel et al GAUSSIAN 09 Revision

B01 Gaussian Inc Pittsburgh PA 201065R Dennington II T Keith J Millam K Eppinnett W Lee Hovell and R

Gilliland GAUSSVIEW Version 309 Semichem Inc Shawnee MissionKS 2003

66Y J Ko H Wang R Cao D Radisic S N Eustis S T StokesS Lyapustina S X Tian and K H Bowen Phys Chem Chem Phys12 3535 (2010)

67N Leulliot M Ghomi G Scalmani and G Berthier J Phys Chem A103 8716 (1999)

68M Chastain and I Tinoco Jr Biochemistry 32 14220 (1993)69R F Setlik M Shibata R H Sarma M H Sarma A L Kazim R L

Ornstein T B Tomasi and R J Rein J Biomol Struct Dyn 13 515(1995)

Downloaded 27 Nov 2012 to 1282201593 Redistribution subject to AIP license or copyright see httpjcpaiporgaboutrights_and_permissions