Victor Salvador Batista - Yale Universityxbeams.chem.yale.edu/~batista/cv.pdf · quantum dynamics...

Victor Salvador Batista

Yale University, Department of Chemistry Phone: (203) 432-6672 P.O. Box 208107, Sterling Chemistry Laboratory Fax:(203) 432-6144 New Haven, CT 06520-8107, U.S.A. E-mail: [email protected]

TEACHING AND RESEARCH POSITIONS:

2008-: Professor , Yale University, Department of Chemistry.

2005-2008: Associate Professor , Yale University, Department of Chemistry.

2001-2005: Assistant Professor , Yale University, Department of Chemistry.

Research interests include: development and application of semiclassical and quantum dynamics methods for studies of excited state reaction dynamics and relaxation phenomena in polyatomic systems and sensitized semiconductor materials; developments and applications of quantum mechanics/molecular mechanics computational methods to study ligand binding interactions and reactivity in biomolecules.

2000-2001: Postdoctoral Research Associate , University of Toronto, Department of Chemistry.

Postdoctoral research performed with Professor Paul Brumer on the development of coherent control techniques and simulations of quantum control of reaction dynamics based on semiclassical initial value representation methods.

1997-1999: Postdoctoral Research Associate , University of California, Berkeley, Department of Chemistry.

Postdoctoral research performed with Professor William H. Miller. Development and implementation of semiclassical initial value representation methods to investigate photoinduced reaction dynamics and ultrafast spectroscopy of polyatomic molecules in excited electronic states.

1994-1996: Research Assistant in Theoretical Chemistry , Boston University, Department of Chemistry.

1991-1993: Teaching Assistant in General Chemistry , Boston University, Department of Chemistry.

1989-1991: Teaching Assistant in Theoretical Physics , Department of Physics, University of Buenos Aires [Universidad de Buenos Aires (UBA)], College of Natural and Exact Sciences [Facultad de Ciencias Exactas y Naturales (FCEyN)].

1986-1989: Teaching Assistant in Organic Chemistry , Department of Organic Chemistry, University of Buenos Aires [Universidad de Buenos Aires (UBA)], College of Natural and Exact Sciences [Facultad de Ciencias Exactas y Naturales (FCEyN)].

Curriculum Vitae – July 2008 Victor S. Batista (Yale University)

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EDUCATION:

1991-1996: Ph.D. in Theoretical Chemistry , Boston University, Department of Chemistry. Thesis advisor: Professor David F. Coker. Thesis title: “Nonadiabatic Dynamics Simulations of Quantum Reaction Dynamics in the Condensed Phase“.

1984-1989: B.Sc. in Chemistry [Licenciado en Ciencias Químicas ], University of Buenos Aires [Universidad de Buenos Aires (UBA)], College of Natural and Exact Sciences [Facultad de Ciencias Exactas y Naturales (FCEyN)].

AWARDS AND HONORS:

• 2005: Camille and Henry Dreyfus Teacher-Scholar Award. • 2005: Alfred P. Sloan Research Fellowship. • 2005: Yale University Junior Faculty Fellowship in the Natural Sciences. • 2004: NSF CAREER Award. • 2004: NSF Nanoscale Exploratory Research Award. • 2002: Petroleum Research Fund, American Chemical Society. • 2002: F. Hellman Family Foundation Award, Yale University. • 2001: Research Innovation Award, Research Corporation. • 1995: Sugata Ray Award, Boston University.

SOCIETY MEMBER:

• American Chemical Society. • American Physical Society. • Biophysical Society.

PROFESSIONAL AND SYNERGISTIC ACTIVITIES SINCE 2001:

Scientific Review Panelist:

• 2007: Ph.D. External Committee Member, Columbia University. • 2007: Panel on Computation Research Needs for Alternative and

Renewable Energy, DOE Office of Science. • 2005: Collaborative Research in Chemistry NSF Review Panel. • 2005: Career Program NSF Review Panel. • 2004: Major Research Instrumentation (MRI) NSF Review Panel. • 2004: Ph.D. External Committee Member, University of Toronto.

Conference Organizer:

• 2007: APS March Meeting, Denver, CO. Symposium on Quantum Mechanics/Molecular Mechanics (QM/MM) Methodologies.

• 2006: 37th Winter Colloquium PQE, Symposium on Coherent Control. • 2006: 36th Winter Colloquium PQE, Symposium on Quantum Control.


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Scientific Journal Reviewer:

Proteins; Science; Annual Review of Physical Chemistry; Proceedings of the National Academy of Science (U.S.A); Journal of Computational and Theoretical Chemistry; Journal of the American Chemical Society; Journal of Chemical Physics; Chemical Physics Letters; Journal of Chemical Theory and Computations; Chemical Physics; Molecular Physics; Journal of Physical Chemistry; Journal of Inorganic Biochemistry; Biophysical Journal.

Grant Proposal Reviewer:

National Science Foundation (NSF); Department of Energy (DOE); American Chemical Society (ACS); Research Corporation; National Commission of Scientific and Technological Research [Comisión Nacional de Investigaciones Científicas y Técnicas (CONICET)].

Departmental Committee Services at Yale:

2008/2009: Director of Undergraduate Studies

2007/2008: Building Committee Information Technology Committee Jr. Faculty Search Committee (Diversity Liaison Officer) Undergrad Placement and Advising 2006/2007: Graduate Admissions (Diversity Liaison Office) Undergraduate Placement and Advising 2005/2006: Yale Junior Faculty Fellow in the Physical & Natural Sciences 2004/2005: Graduate Admissions Library Information Technology 2003/2004: Space and Finance Library Information Technology 2002/2003: Graduate Admissions Corporate Relations Information Technology 2001/2002: Graduate Admissions Library Information Technology

STARS Program: Undergraduate Research Mentorship:

The STARS program gives underrepresented minority students an opportunity to work in research laboratories at Yale early in their college careers.

2002, 2003: Mr. Devon Philips . Project title: “Electronic structure calculations for studies of hydrated ozone complexes”. Poster presentation at the 227th National Meeting of the American Chemical Society; Research


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Poster Award at the Yale Bouchet Conference on Diversity in Graduate Education, 2003.

2003: Ms. Grace Kalisha . Project title: “Quantum Mechanics/Molecular Mechanics (QM/MM) studies of the photoabsorption of visual rhodopsin and pathological phenotypes responsible for inducing photoabsorption spectral shifts”.

Classes Lectured at Yale:

Fall 2007, 2006, 2004: General Chemistry (Chemistry 113). A lecture class offered exclusively for freshmen.

Chemistry 113 introduces the fundamentals of chemistry and chemical reactivity with emphasis on scientific problem solving and quantitative reasoning.

Spring 2007, 2006, 2004-2002: Introduction to Stati stical Mechanics (Chemistry 430b/530b). A lecture course for advanced undergraduates and graduate students in the Physical Sciences.

Chemistry 430b/530b combines Quantum Mechanics, Classical Mechanics, and introduces the fundamentals of classical and quantum statistical mechanics. Topics include ensembles, Fermi, Bose and Boltzmann statistics, density matrices, mean field theories, phase transitions, chemical reaction dynamics, time-correlation functions, Monte Carlo simulations, and Molecular Dynamics simulations.

Fall 2003, 2002, 2001: Introduction to Quantum Che mistry (Chemistry 470a/570a). A lecture course for advanced undergraduates and graduate students in the Physical Sciences.

The course introduces the fundamentals of Quantum Mechanics and applications to the description of atoms and molecules, and their interactions with other molecular systems and electromagnetic radiation.

Pedagogical Web-Site Developments:

Courses: Complete online Chemistry classes. Introduction on Quantum Chemistry (Chemistry 470a/ 570a): http://xbeams.chem.yale.edu/~batista/vvv/index.html Introduction to Statistical Mechanics(Chemistry 430 b/530b) http://xbeams.chem.yale.edu/~batista/vaa/index.html General Chemistry (Chemistry 113) : http://xbeams.chem.yale.edu/~batista/113/index.html Summer School on Quantum Dynamics :


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http://xbeams.chem.yale.edu/~batista/summer.pdf http://xbeams.chem.yale.edu/~batista/solutions.pdf

WikiSites: User maintained World Wide Web (WWW) sites providing agency for the rapid exchange, communication and efficient distribution of pedagogical materials (e.g., lectures, problem sets, solutions, exams, and computational assignments) among the entire chemistry community.

WikidChem: http://www.wikidchem.org/ Bulldog Biophysics: http://www.wikidchem.org/index.php/Yale_Biophysics

Freshmen Advisor:

Saybrook College, Yale University.

K-12 Teacher Mentorship:

K-12 educational program e-mentoring initiative, Society for Advancement of Chicanos and Native Americans in Science (SACNAS).

Undergraduate Research Mentorship:

Undergraduate students involved in computational research in the Batista research group, including students enrolled in Chemistry 490, a credit course offered by the Department of Chemistry at Yale University for students interested in gaining undergraduate research experience:

Fall 2006-present: Mr. Nobu Iguchi: Project title: “Quantum mechanical/molecular mechanics (QM/MM) hybrid studies of siloxane molecular adsorbates covalently functionalizing TiO2 semiconductor surfaces”.

Summer 2005-present: Mr. Justin Kim. Project title: “Computational Studies of Excited State Intramolecular Proton Transfer (ESIPT) in 2-(2'-hydroxyphenyl) benzothiazole (HBT)”.

Summer 2005-Spring 2006: Mr. Xiao Ying: Project title: “Computational studies of O3 adsorbed on Ice Ih”. Awarded the Yale College Dean's Research Fellowship.

Summer 2005: Ms. Cheryl Suet-Lee Leung: Project title: “Development of molecular mechanics force fields for modeling TiO2 semiconductors functionalized with organic molecules”.

Summer 2004-Spring 2005: Ms. Heather Wittels: Project title: “Density Functional Theory (DFT) studies of electronic structure and vibrational spectroscopy of hydrated O3 complexes”. Awarded the Brigitte Prusoff Summer Fellowship. Awarded the Yale College Dean's Research Fellowship.


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Graduate Biophysical Research Mentorship:

2006, Fall: Ms. Katherine Shinolopoulos: Project title: “Computational Studies of substrate water binding to the Oxygen Evolving Complex of photosystem II”.

2005, Fall: Mr. Michael Newcomer: Project title: “Quantum Mechanics Molecular Mechanics Methodologies: Applications to the Oxygen Evolving Complex of photosystem II and visual rhodopsin”.

2005, Fall: Mr. Eric Watt: Project title: “Multi-Configurational Continuum Electrostatics Studies of pKa’s of Amino Acid Residues in contact with the Oxygen Evolving Complex of photosystem II”.

2004, Spring: Christina Regain: Project title: “Quantum Mechanics/Molecular Mechanics Studies of the 1H and 205Tl NMR spectra of Thallium bound G-quadruplex from Oxytricha Nova”.

2003, Fall: Siegfried Leung: Project title: “Quantum Mechanics Molecular Mechanics Methodologies for Computations of Protein Electrostatic Potentials”.

Dissertation Thesis Mentorship:

2006- : Mr. Robert Snoeberger : Ph.D. candidate, Department of Chemistry, Yale University. Thesis title: “Computational Studies of Functionalized Semiconductor Materials for Green Photocatalytic Chemistry”.

2005- : Mr. Michael Newcomer: Ph.D. candidate, Department of Chemistry, Yale University. Thesis title: “Quantum Mechanics/Molecular Mechanics Methodologies for Modeling Structural Refinement and Ligand-Protein Binding Interactions”.

2004-2008: Mr. Xin Chen: Ph.D. candidate, Department of Chemistry, Yale University. Thesis title: “Greedy Algorithms for Computations of Thermal Correlation Functions and Simulations of Nonadiabatic Quantum Dynamics”. Future position: Postdoctoral Research Associate, Department of Chemistry, Massachussetts Institute of Technology.

2002-2007: Mr. Sabas Abuabara: Ph.D. candidate, Department of Physics, Yale University. Thesis title: “Computational Studies of Interfacial Electron Transfer Coherent Control of Electronic Excitations in Sensitized TiO2 Surfaces”. Current position: Business Analyst at HBK Capital Management, Dallas/Fort Worth Area.

2001-2004: Dr. Yinghua Wu: Thesis title: ”Rigorous Time-Dependent Methods for Simulations of Quantum Processes in Multidimensional Systems”. Current position: Postdoctoral Research Associate, Department of Chemistry and Biochemistry, Georgia Institute of Technology.


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Post-Doctoral Research Mentorship :

02/05 – 01/08: Dr. Eduardo Sproviero: Postdoctoral Research Associate, Yale University, Department of Chemistry.

08/03 – 08/06: Dr. Jose A. Gascon: Current Position: Assistant Professor of Chemistry, University of Connecticut, Department of Chemistry.

03/03 – 05/04: Dr. Sergio D. Dalosto: Current Position: Adjunct Investigator, CONICET, Department of Physics, University of Litoral, Santa Fé, Argentina.

01/02 – 12/02: Dr. Luis G.C. Rego: Current Position: Associate Professor of Physics, Universidade Federal de Santa Catarina (UFSC), Florianópolis, SC, Brazil.

LIST OF COLLABORATORS SINCE 2001, IN ALPHABETICAL O RDER:

• Enrique R. Batista, Los Alamos National Laboratory, USA. • Jean-Luc Bredás, Georgia Institute of Technology, USA. • David Britt, University of California, Davis, USA. • Doug Bruce, Brock University, Canada. • Gary W. Brudvig, Yale University, USA. • Paul Brumer, University of Toronto, Canada. • Robert H. Crabtree, Yale University, USA. • Holger Dau, Freie Universität Berlin, Germany. • José A. Gascon, University of Connecticut, USA. • Victor Guallar, Barcelona Supercomputing Center, Spain. • Marilyn Gunner, City College of New York, USA. • Michael F. Herman, Tulane University, USA. • Casey Hynes, University of Colorado, Boulder, USA. • Daniel Laria, University of Buenos Aires, Argentina. • Kevin Leung, Sandia National Laboratories, USA • J. Patrick Loria, Yale University, USA. • Krishna C. Mandal, EIC Lab. Inc, USA. • James P. McEvoy, Regis University, USA. • Latika Menon, Northeastern Universtiy, USA. • William H. Miller, University of California, Berkeley, USA. • Erik T.J. Nibbering, Max-Born Institut, Berlin, Germany. • Lou Noodleman, The Scripps Research Institute, USA. • Ehud Pines, University of the Negev, Beer-Sheva, Israel. • Tijana Rajh, Argonne National Lab, IL, USA. • Luis G.C. Rego, Universidade Federal de Santa Catarina, Florianopolis, Brazil • Susan B. Rempe, Sandia National Laboratories, USA. • Charles A. Schmuttenmaer, Yale University, USA. • Per Siegbahn, Stockholm University, Sweden. • Scott A. Strobel, Yale University, USA. • Ann Valentine, Yale University, USA. • Yinghua Wu, Georgia Institute of Technology, USA.


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PUBLICATIONS (TOTAL 43 SINCE JOINING THE YALE FACUL TY IN 2001):

54. Iguchi N, Cady CW, Snoeberger RC, Hunter BM, Sproviero EM, Schmuttenmaer CA, Crabtree RH, Brudvig GW, Batista VS. Characterization of Siloxane Adsorbates Covalently Attached to TiO2. Proc. of SPIE (2008) 7034:7034 R.

53. McNamara WR, Snoeberger RC, Li G, Schleicher JM, Cady CW, Povatos M, Schmuttenmaer CA, Crabtree RH, Brudvig GW, Batista VS. Acetylacetonate anchors for robust functionalization of TiO2 nanoparticles with Mn(II)-terpyridine complexes. J. Am. Chem. Soc. (2008) in press.

52. Rego L.G.C, Santos LF, Batista VS. Coherent Control of Quantum Dynamics with Sequences of Unitary Phase-Kick Pulses. Ann Rev. Phys. Chem. (2009) 60:xxxx-xxxx.

51. Sproviero EM, Gascon JA, McEvoy JP, Brudvig GW, Batista VS. A Model of the O2-evolving complex of photosystem II predicted by structural refinement based on EXAFS simulations.J. Am. Chem. Soc. (2008) 130:6728-6730.

50. Sproviero EM, Gascon JA, McEvoy JP, Brudvig GW, Batista VS. Computational insights into the O2-evolving complex of photosystem II. Photosynth. Res. (2008) 97:91-114.

49. Sproviero EM, Gascon JA, McEvoy JP, Brudvig GW, Batista VS. Computational studies of the O2-evolving complex of photosystem II and biomimetic oxomanganese complexes. Coord. Chem. Rev. (2008) 252:295-415.

48. Sproviero EM, Gascon JA, McEvoy JP, Brudvig GW, Batista VS. QM/MM Study of Water-Splitting in Photosystem II. J. Am. Chem. Soc. (2008) 130: 3428-3442.

47. Sproviero EM, Shinopoulos K, Gascon JA, McEvoy JP, Brudvig GW, Batista VS. QM/MM computational studies of substrate water binding to the oxygen-evolving complex of Photosystem II. Phil. Trans. Royal Soc. London B (2008) 363:1149-1156.

46. Gascon JA, Sproviero EM, McEvoy JP, Brudvig GW, Batista VS. Ligation of the C-terminus of the D1 polypeptide of photosystem II to the oxygen-evolving complex: A DFT-QM/MM study. In Photosynthesis. Energy from the Sun 14th International Congress on Photosynthesis Research Allen, J.F.; Gantt, E.; Golbeck, J.H.; Osmond, B. (Eds.) p. 363-368 (2008).

45. Rego LGC, Abuabara SG, Batista VS. Multiple Unitary Pulses for Coherent Control of Tunneling and Decoherence. J Mod Opt (2007) 54:2617-2627.

44. Chen X, Batista VS. The MP/SOFT methodology for simulations of quantum dynamics: Model study of the photoisomerization of the retinyl chromophore in visual rhodopsin. J. Photochem Photobiol (2007) 190:274-282.

43. Abuabara SG, Cady CW, Baxter JB, Schmuttenmaer CA, Crabtree RH, Brudvig GW, Batista VB. Ultrafast Photooxidation of a Mn(II)-terpyridine complex covalently attached to TiO2 nanoparticles. J Phys Chem C (2007) 111:11982-11990.

42. Sproviero EM, Gascon JA, McEvoy JP, Brudvig GW, Batista VS. Structural Models of the Oxygen-Evolving Complex of Photosystem II. Curr. Opinions Struct. Biol. (2007) 17:173-180.


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41. Chen X, Batista VS. Matching Pursuit Split Operator Fourier Transform Simulations of Excited State Nonadiabatic Quantum Dynamics in Pyrazine. J Chem Phys (2006) 125:124313.

40. Abuabara SG, Gascon, JA, Leung, SY, Rego LGC, Batista VS. Force Field Parameters for Large-Scale Computational Modeling of Sensitized TiO2 Surfaces. Proc. of SPIE (2006) 6325:63250R.

39. Wu Y, Batista VS. Matching-Pursuit Split Operator Fourier Transform Simulations of Excited-State Intramolecular Proton Transfer in 2-(2`-hydroxyphenyl)-oxazole. J Chem Phys (2006) 124:224305.

38. Rego LGC, Abuabara SG, Batista VS. Coherent-Control of Tunneling Dynamics in Functionalized Semiconductor Nanostructures: A Quantum-Control Scenario Based on Stochastic Unitary Pulses. J Mod Opt (2006) 53:2519-2532.

37. Leung K, Rempe SB, Schultz PA, Sproviero EM, Batista VS, Chandross ME, Medforth CJ. Density functional theory and DFT+U study of transition metal porphine adsorbed on Au (111) surfaces and effects of applied electric fields. J. Am. Chem. Soc. (2006) 128:3659-3668.

36. Sproviero EM, Gascon JA, McEvoy JP, Brudvig GW, Batista VS. QM/MM Model of the Oxygen-Evolving Complex of Photosystem II. J. Chem. Theor. Comput. (2006) 4:1119-1134.

35. Sproviero EM, Gascon JA, McEvoy JP, Brudvig GW, Batista VS. Characterization of Synthetic Oxomanganese Complexes and the Inorganic-Core of the O2-Evolving Complex in Photosystem II: Evaluation of the DFT/B3LYP Level of Theory. J. Inorg. Biochem. (2006) 100:786-800.

34. Gascon JA, Sproviero EM, Batista VS. Computational studies of the primary photo-transduction event in visual rhodopsin. Acc. Chem. Res. (2006) 39:184-193.

33. Gascon JA, Leung SSF, Batista ER, Batista VS. A Self-Consistent Space-Domain Decomposition Method for QM/MM computations of protein electrostatic potentials. J Chem Theor Comput (2006) 2:175-186.

32. Abuabara SG, Rego LGC, Batista VS. Influence of thermal fluctuations on interfacial electron transfer in functionalized TiO2 semiconductors. J Am Chem Soc (2005) 127:18234-18242.

31. McEvoy JP, Gascon JA, Batista VS, Brudvig GW. The mechanism of photosynthetic water splitting. Photochem. Photobiol. (2005) 4:940-949.

30. Rego LGC, Abuabara SG, Batista VS. Coherent Optical Control of Electronic Excitations in Functionalized Semiconductor Nanostructures. Quant Inform Compu (2005) 5:318-334.

29. Spanner M, Batista VS, Brumer P. Is the Filinov integral conditioning technique useful in semiclassical IVR methods? J Chem Phys (2005) 122:084111.

28. Gascon JA, Sproviero EM, Batista VS. QM/MM study of the 1H and 13C NMR spectra of the retinylidene chromophore in visual rhodopsin. J Chem Theory Comput (2005) 1:674-685.


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27. Wu Y, Herman M, Batista VS. Matching pursuit split operator Fourier transform simulations of nonadiabatic quantum dynamics. J Chem Phys (2005) 122:114114.

26. Rego LGC, Abuabara SG, Batista VS. Model study of coherent quantum dynamics of hole states in functionalized semiconductor nanostructures. J Chem Phys (2005) 122:154709.

25. McEvoy JP, Gascon J, Batista VS, Brudvig G. Computational structural model of the oxygen evolving complex in Photosystem II: complete ligation by protein, water and chloride. In “Photosynthesis: Fundamental Aspects to global perspectives”, vol 1 (D. Bruce and A. van der Est, ed.) Allen Press Inc., Lawrence, Kansas, pp. 278-280 (2005).

24. Chen X, Wu Y, Batista VS. Matching-pursuit split operator Fourier transform computations of thermal correlation functions. J Chem Phys (2005) 121:64102.

23. Batista VS, Brumer P. Coherent control: principles and semiclassical implementations, in Quantum control: mathematical and numerical challenges (Andre Bandrauk and Claude de Bris, Eds.) Oxford University Press, 2004.

22. Wu Y, Batista VS. Quantum tunneling in multidimensional systems: a matching-pursuit description. J Chem Phys (2004) 121:1676-1680.

21. Gascon JA, Batista VS. QM/MM study of energy storage and molecular rearrangements due to the primary event in vision. Biophys J (2004) 87:2931-29411.

20. Flores SC, Batista VS. Model study of coherent control of the femtosecond primary event of vision. J Phys Chem B (2004) 108: 6745-6749.

19. Rego LGC, Batista VS. Quantum dynamics simulations of the interfacial electron transfer in sensitized TiO2 semiconductors. J Am Chem Soc (2003) 125:7989-7997.

18. Wu Y, Batista VS. Matching pursuit for simulations of quantum processes. J Chem Phys (2003) 117:6720-6724.

17. Wu Y, Batista VS. Semiclassical molecular dynamics simulations of the excited state photodissociation dynamics of H2O in the A 1B1 band. J Phys Chem B (2002) 106:8271-8277.

16. Burant JC, Batista VS. Real time path integrals using the Herman-Kluk propagator. J Chem Phys (2002) 116:2748-2756.

15. Guallar V, Harris DL, Batista VS, Miller WH. Proton transfer dynamics in the activation of cytochrome P450eryF. J Am Chem Soc (2002) 124:1430-1437.

14. Batista, VS, Brumer, P. On Coherent control in the presence of intrinsic decoherence: proton transfer in large molecular systems (vol 89, art no 143201, 2002). Phys Rev Lett (2002) 89:249903.

13. Batista VS, Brumer P. Coherent control in the presence of intrinsic decoherence: proton transfer in large molecular systems. Phys Rev Lett (2002) 89:143201.


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12. Batista V.S., Brumer P. A direct approach to one photon interference contributions in the coherent control of photodissociation. J Chem Phys (2001) 114:10321-10331.

11. Batista VS, Brumer P. Semiclassical Dynamics in the Coherent Control of Nonadiabatic ICN Photodissociation. J Phys Chem A (2001) 105:2591-2598.

10. Guallar V, Batista VS, Miller WH. Semiclassical molecular dynamics simulations of the excited state intramolecular proton transfer reaction in 2-(2'-hydroxyphenyl)-oxazole. J Chem Phys (2000) 113: 9510-9522.

9. Coronado EA, Batista VS, Miller WH. Nonadiabatic photodissociation dynamics of ICN in the A continuum: a semiclassical initial value representation study. J Chem Phys (2000) 112: 5566-5575.

8. Guallar V, Batista VS, Miller WH. Semiclassical Molecular Dynamics Simulations of Double Proton Transfer Dynamics in 7-Azaindole dimers. J Chem Phys (1999) 110: 9922-9936.

7. Zanni MT, Batista VS, Greenblatt BJ, Miller WH, Neumark DM. Femtosecond Photoelectron Spectroscopy of the I2

- anion: characterization of the Ã’ 2g,1/2

excited state. J Chem Phys (1999) 110: 3748-3755.

6. Batista VS, Coker DF. Erratum: On nonadiabatic molecular dynamics simulations of the photofragmentation and geminate recombination dynamics in size-selected I2

-Arn cluster ions. J Chem Phys (1999) 105: 6583-6584.

5. Batista VS, Zanni MT, Greenblatt BJ, Neumark DM, Miller WH. Femtosecond Photoelectron Spectroscopy of the I2

- anion: A semiclassical molecular dynamics simulation method. J Chem Phys (1999) 110: 3736-3747.

4. Batista VS, Miller WH. Semiclassical molecular dynamics simulations of ultrafast photodissociation dynamics associated with the Chappuis band of ozone. J Chem Phys (1998) 108: 498-510.

3. Batista VS, Coker DF. Nonadiabatic molecular dynamics simulation of the photofragmentation and geminate recombination dynamics in size selected I2

-.Arn cluster ions. J Chem Phys (1997) 105: 7102-7116.

2. Batista VS, Coker DF. Nonadiabatic molecular dynamics simulation of pump-probe experiments on I2 in solid rare gases. J Chem Phys (1997) 106: 6923-6941.

1. Batista VS, Coker DF. Nonadiabatic molecular dynamics simulation of photodissociation and geminate recombination of I2 liquid xenon. J Chem Phys (1996) 105: 4033-4054.


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INVITED TALKS SINCE JOINING THE YALE FACULTY IN 200 1 (TOTAL 80)

2008, September 28: NSF CIAM Workshop, Guaruja, Brazil.

2008, August 17: 236th ACS Meeting, Philadelphia, PA.

2008, August 10: SPIE Optics and Photonics, San Diego, CA.

2008, July 19: American Conference on Theoretical Chemistry, Evanston, IL.

2008, July 7: Telluride Workshop on Condensed Phase Dynamics, Telluride, CO.

2008, June 3: Physical Chemistry Symposium, Department of Chemistry, Boston University, Boston, MA.

2008, April 30: Department of Chemistry, University of Maryland, College Park, MD.

2008, April 18: 25th Eastern Regional Photosynthesis Conference, Woods Hole, MA.

2008, April 6: 235th ACS Meeting, New Orleans, LA.

2008, March 11: APS Meeting, New Orleans, LA.

2008, March 7: Department of Chemistry, University of Toronto, Toronto, ON.

2008, February 21: Optical Properties of Surfaces, Sanibel Symposium, University of Florida, FL.

2008, February 15: Department of Chemistry, University of Missouri, Columbia, MI.

2008, February 1: Department of Chemistry, University of Colorado, Boulder, CO.

2008, January 13: Meeting on Diffusion, Solvation and Transport of Protons in Complex and Biological Systems, Eilat Hilton Hotel, Israel.

2008, January 5: Winter Workshop on New Challenges for Theory in Chemical Dynamics, Telluride, CO.

2007, November 23: Department of Physics, University of Florianopolis, Florianopolis, Brazil.

2007, November 9: Department of Chemistry, Colby College, ME.

2007, November 6: Department of Chemistry & Chemical Biology, Rensselaer Polytechnic Institute, NY.


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2007, October 17: Department of Chemistry, Boston University, Boston, MA.

2007, October 5: Department of Photochemistry & Molecular Science, Swedish Consortium for Artificial Photosynthesis, Uppsala, Uppsala, Sweden.

2007, October 2: 2nd PRC workshop on Energy Flow Dynamics in Biomaterial Systems, Paris, France.

2007, September 28: Barcelona Supercomputer Center, Barcelona, Spain.

2007, September 26: Department of Mathematics and Computer Science, Free University of Berlin, Berlin, Germany.

2007, September 23: International Retinal Symposium 2007, Bremen, Germany.

2007, August 19: 234th ACS Meeting, Boston, MA.

2007, August 7: CECAM workshop on quantum dynamics in condensed phase chemical systems, Dublin, Ireland.

2007, July 22: 14th International Photosynthesis Congress, Glasgow, UK.

2007, May 8: Boston College, Department of Chemistry, Newton, MA.

2007, April 30: NSF ECCS Workshop, University of Nevada, Reno, NV.

2007, April 23: Royal Society Meeting on Water Splitting by photosystem II, London, UK.

2007, April 5: Temple University, Department of Chemistry, Philadelphia, PA.

2007, March 19: Argonne National Lab, Chemistry Division, Argonne, IL.

2007, March 5: APS March Meeting, Denver, CO.

2007, March 2: Northwestern University, Dept. of Chemistry, Evanston, IL.

2007, February 6: Georgia Tech, Dept. of Chemistry, Atlanta, GA.

2007, February 5: Emory University, Department of Chemistry, Atlanta, GA.

2007, January 6: 37th Winter Colloquium on the Physics of Quantum Electronics.

2006, November 29: The City University of New York (CUNY), New York

2006, October 10: UC Davis, Department of Chemistry, Davis, CA.

2006, September 10: 232nd ACS Meeting, San Francisco, CA.


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2006, August 18: The Scripps Research Institute, La Jolla, CA.

2006, August 13: SPIE Conference. Phys. Chem. of Interfaces and Nanomaterials V, San Diego,CA.

2006, August 6: Summer-School Workshop on Computational Materials Science, University of Illinois at Urbana Champaign.

2006, July 2: GRC on Photosynthesis, Bryant University, RI.

2006, April 21: 23rd Eastern Regional Photosynthesis Conference, Woods Hole College, MA.

2006, March 26: 231st ACS Meeting, Atlanta, G.A., U.S.A.

2006, January 18: University of Montreal, Department of Chemistry, Montreal, Canada.

2006, January 6: 36th Winter Colloquium on the Physics of Quantum Electronics, Snowbird, Utah.

2005, December 15: Pacifichem 2005, Honolulu, Hawaii, U.S.A.

2005, August 27 : 230th ACS Meeting, Washington D.C., U.S.A.

2005, June 23: MMQ2005 Meeting, Barcelona, Spain.

2005, June 18: From H3 to Biocatalysis International Conference, Stockholm, Sweden.

2005, April 1: Trinity College, Department of Chemistry, Hartford, CT.

2005, March 21: APS March Meeting 2005, Los Angeles, CA.

2005, March 16: 229th ACS Meeting, San Diego, California.

2005, January 3: 35rd Winter Colloquium on the Physics of Quantum Electronics, Snowbird, Utah.

2004, September 28 : University of Wisconsin-Madison, Department of Chemistry, Madison.

2004, September 16: CECAM Quantum Dynamics Workshop, Lyon, France.

2004, August 22: 228th ACS Meeting, Philadelphia, Pennsylvania.

2004, August 1: Workshop on Nonadiabatic Dynamics, Telluride, Colorado.


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2004, July 19: Quantum Information and Quantum Control Conference, Toronto.

2004, July 15: Workshop on Quantum and Semiclassical Molecular Dynamics of Nanostructures, Los Alamos National Laboratory, Los Alamos.

2004, March 28: 227th ACS Meeting, Anaheim, California.

2004, February 2: Boston University, Department of Chemistry, Boston.

2004, January 28: MIT, Department of Chemistry, Boston.

2003, December 3: Washington University, Department of Biochemistry, St. Louis.

2003, September 7: 226th ACS Meeting, New York University, New York.

2003, July 27: 5th Canadian Computational Chemistry Conference, University of Toronto.

2003, May 2: Baylor College of Medicine, Department of Biochemistry and Structural Biology.

2003, January 6: 33rd Winter Colloquium on the Physics of Quantum Electronics, Snowbird, Utah.

2002, August 21: 224th ACS Meeting, Hynes Convention Center, Boston.

2002, January 6: 32nd Winter Colloquium on the Physics of Quantum Electronics, Snowbird, Utah.

2001, November 16: Wesleyan University, Department of Chemistry.

2001, March 28: University of California, Berkeley, Miller Symposium on Chemical Dynamics.

2001, March 12: APS Meeting, Washington State Convention Center, Seattle.


16

ACTIVE RESEARCH GRANTS:

(6) MRI-0821132 (08/31/08-08/31/10)

Girvin listed as PI (Batista, Ismail-Beigi, Basu and Smooke, co-PI)

National Science Foundation (NSF) $500,000

MRI: Acquisition of a High Performance Computational Cluster for Yale University.

The MRI equipment acquisition involves a large-scale computing system for the physical, biological and social sciences under the umbrella of one of our High Performance Computing (HPC) centers.

(5) BSF-2006276 (10/01/07-09/30/11)

Batista listed as PI (other co-PI’s: Hynes and Pines)

U.S.-Israel Binational Science Foundation (BSF) $60,000

Solute-solvent interactions and proton transfer reactions of Physiologically protonable groups in aqueous solutions and their biochemical significance.

Objectives: Studies of photoacids and proton transfer reactions in liquids, including QM/MM simulations of vibrational and electronic spectroscopy.

(4) ECCS-0725118 (08/01/07-07/31/10)

Batista listed as PI


Studies of Electronic Relaxation and Coherent Control in Functionalized Semiconductors.

Development of methods to describe quantum dynamics in extended semiconductor nanostructures, and the application of these methods to explore ultrafast quantum dynamical phenomena associated with photoinduced electronic excitations in TiO2 and ZnO nanostructures. The project includes the characterization of photoinduced electron-hole pair relaxation pathways in functionalized semiconductor surfaces; the investigation of photoexcitation methods for laser manipulation of electronic relaxation; and the integration of the proposed research with an outreach education progrm for minority students.

(3) DE-FG02-07ER15909 (09/01/07-08/31/10)

Brudvig listed as PI on this grant (Batista listed as Co-PI).

Department of Energy (DOE) $330,000

Oxomanganese Catalysts for Solar Fuel Production.

The specific objectives of the proposed research program are: (I) to investigate surface arrangements of oxo-Mn catalysts on Ti02 surfaces that are stable in catalytic turnover and give fast electron injection upon visible-light excitation; (II) to determine the chemical nature of ligands and linkers that suppress detrimental reactions, including recombination, charge-trapping pathways and catalyst degradation; (III) to investigate water-oxidation chemistry as couples to photon-driven single-electron transfer at the photoanode; and (IV) to correlate the efficiency of the photocatalytic steps to the nature of surface complexes and


17

reaction mechanisms, as characterized by spectroscopic and synthetic methods applied in conjunction with theoretical and computational studies.

(2) 2R01-GM043278-14 (07/01/07-06/30/12) Noodleman listed as PI (Batista listed as Co-PI)

National Institute of Health (NIH) $390,140

Yale University -The Scripps Research Institute Con sortion

Electronic Structure and Reactions of Fe-oxo Enzymes.

The objectives of the proposed research are to calculate accurate geometries, associated energies, and protonation states of critical intermediates for the reaction cycles of important iron-oxo and iron-peroxo enzymes. Our focus will be on Class I ribonuleotide reductase (RNR), with detailed comparisons to methane monooxygenase (MMO), toluene monooxygenase (Tolo), and to the Rieske oxygenases. Connections with spectroscopy, evaluation of reaction pathways and development of computational methods are also proposed.

(1) CHE-0345984 (02/01/04-01/31/09) Batista listed as PI


CAREER: Matching Pursuit For Simulation of Quantum Processes.

The research and education program established under the auspices of this CAREER Award has three important objectives. The first goal is the development of rigorous time-dependent methods for simulations of quantum processes, based on matching pursuit wavefunction representations. The second goal is the development of computational studies of hydrated complexes, with emphasis on O3(H2O)n molecular complexes. The third goal is the development of educational activities to introduce several aspects of the proposed research program into the undergraduate curriculum; encourage the participation of underrepresented minority students in the sciences; and facilitate the exchange and distribution of pedagogical material on the World Wide Web.

COMPLETED RESEARCH GRANTS:

(6) ECS-0404191 (12/01/01-01/01/06)



Nanoscale Exploratory Research Award: NER: Modeling Quantum-Coherent Electronic Excitations in Functionalized Semiconductor Nanostructures.

Objectives: Development of methods to describe quantum dynamics in extended semiconductor nanostructures, and the application of these methods to explore quantum dynamical phenomena associated with the behavior of electronic excitations in nanostructures.


18

(5) PRF-37789-G6 (12/01/01-01/01/07)

Batista listed as PI $35,000

American Chemical Society (ACS)-Petroleum Research Fund (PRF)

The Influence of the Condensed Phase on Quantum Reaction Dynamics: The Photodissociation of Ozone on Ice Ih

Objectives: Development of quantum dynamics methods for simulations of atmospheric chemical reactions and the development of electronic structure calculations for the characterization of hydrated ozone complexes.

(4) R-010702 (12/01/01-01/01/07)


Research Corporation

Coherent Control of Ultrafast Phototransduction Dynamics.

Objectives: Development of semiclassical and quantum mechanical computational methods for simulations of coherent control and applications to studies of cis/trans isomerization dynamics relevant to natural and artificial photochromic compounds, including biomolecules of technological interest such as rhodopsin.

(3) Sloan Research Fellowship Award (04/01/05-04/01/06)


Sloan Foundation

Computational studies of visual rhodopsin.

Objectives: Development of QM/MM methodologies and applications to studies of cis/trans isomerization in visual rhodopsin.

(2) Henry and Camille Dreyfus Teacher-Scholar Award (04/01/05-04/01/07)


Henry and Camille Dreyfus Foundation $75,000

Computational methods for simulations of quantum reaction dynamics.

Objectives: Development of time-dependent semiclassical and quantum mechanical methods for simulations of quantum reaction dynamics and applications to photoinduced reactions of polyatomic molecules in excited electronic states.

(1) F. Hellman Family Award (09/01/02-01/01/07)


Hellman Family, Yale University

Interfacial electron transfer dynamics in sensitized semiconductor nanostructures.

Objectives: Studies of sensitized semiconductor surfaces, including electronic structure calculations and simulations of excited state electronic relaxation dynamics.


19

RESEARCH AND EDUCATIONAL PROGRAM ESTABLISHED AT YAL E:

Time-Dependent Methods for Simulations of Quantum R eaction Dynamics

The Batista group has developed time-dependent methods for simulations of quantum reaction dynamics in polyatomic systems, including algorithms based on time-sliced semiclassical and full quantum-mechanical propagators.1-11 Applications of these methods were focused on ultrafast relaxation processes that produce broad and structureless absorption spectra of polyatomic systems, including nonadiabatic dynamics, excited state intramolecular proton transfer, and photoinduced isomerization processes in excited electronic states. It was found that the spectral consequence of ultrafast relaxation processes is to mask the structural and dynamical information necessary to describe chemical reactivity at the molecular level, and that computational modeling is essential to provide insight into the nature of reaction dynamics and rigorous assignments of spectroscopic measurements.

Modeling quantum reaction dynamics at the most fundamental level of theory requires the propagation of multidimensional wavepackets by numerical integration of the time-dependent Schrödinger equation. Until very recently, however, studies of complex polyatomic systems have relied upon approximate methods since rigorous propagation schemes were limited to systems with very few degrees of freedom (e.g., molecules with 3 or 4 atoms). This scenario is rapidly changing with the development of powerful computational methods, capable of propagating multidimensional wavepackets. One such method is the matching pursuit split operator Fourier transform (MP/SOFT) algorithm, developed by the Batista group.2-6, 8-11

The MP/SOFT method has been applied to investigate quantum reaction dynamics in polyatomic systems,6, 8-10 including the photophysics of pyrazine described by a 2-state 24-dimensional wavepacket scattering at the S1/S2 conical intersection of potential energy surfaces9 and the excited-state intramolecular proton transfer (ESIPT) associated with the keto-enolic tautomerization of 2-2’-hydroxyphenyl-oxazole (HPO) shown in Fig. 1;6 the photoisomerization of the retinal chromophore in visual rhodopsin, modeled by a 2-state 25-dimensional wavepacket evolving on electronically coupled potential energy surfaces10 (see Fig. 2) and the photophysics of 2-(2'-hydroxyphenyl)-benzothiazole (HBT) modeled by the propagation of a 69-dimensional wavepacket describing the keto-enolic tautomerization coupled to ESIPT (see Fig. 3).8

A general dynamical picture has emerged from the MP/SOFT simulations of excited state reaction dynamics. It was found that photoinduced reaction dynamics in polyatomic systems often results from photoexcitation of molecular chromophores to highly unstable configurations, leading to ultrafast relaxation of reaction coordinates usually tuned by the dynamics of low-frequency modes. Examples of tuning modes include the internal- bending coordinates in HPO and HBT that change the intermoiety proton donor-acceptor separation during ESITP.6, 8 Analogously, nonadiabatic internal conversion is tuned by vibronic modes that change the strength of the couplings between excited electronic states, including ring-breathing modes in pyrazine,9 and the stretching mode of the polyene chain in the retinyl chromophore of visual rhodopsin.10 The coupling between reaction coordinates and tuning modes induces


20

(a)

Nonadiabatic quantum dynamics of Pyrazine24-dimensional wave packet propagation

MP/SOFT

Nonadiabatic quantum dynamics of Pyrazine24-dimensional wave packet propagation

MP/SOFT

(b)

ESIPT in HPO 35-dimensional wave packet propagation

SC-IVR

MP/SOFT

ESIPT in HPO 35-dimensional wave packet propagation

SC-IVR

MP/SOFT

Figure 1. (a) MP/SOFT simulations of the photoabsorption of pyrazine (with n the number of basis functions in the coherent state expansions of the time-dependent wavepacket); (b) MP/SOFT simulation of the photoabsorption spectrum of 2-2’-hydroxyphenyl-oxazole (HPO) due to excited-state intramolecular proton transfer (ESIPT) coupled to keto-enolic tautomerization.

decohernece and is spectroscopically manifested by diffuse vibronic structures superimposed to the photoabsorption bands (Figs. 1 and 3). Product formation is usually stabilized by ultrafast vibrational energy redistribution and is manifested by large Stokes shifts in the fluorescence spectra.

In addition to the description of photoinduced reaction mechanisms, the MP/SOFT studies have allowed the characterization of the time-scales for decoherence induced by interactions between the reaction coordinates (e.g., the proton motion, the isomerization coordinate, etc.) and the remaining degrees of freedom in the system. To this end, the decoherence measure Tr[ (t)2] was examined, with (t) the time-dependent reduced density matrix associated with the reaction coordinates (Fig. 3).6, 8 It was found that quantum mechanical coherences affect the overall reaction rates and efficiencies, even in the presence of ultrafast decoherence, since the reaction times in excited electronic states of polyatomic systems are often comparable to, or shorter than, the decoherence times. Furthermore, coherent-control of excited state reaction dynamics was found to be feasible whenever the photoinduced reactions were faster than the decoherence dynamics induced by the vibronic activity.12, 13

The methods and applications developed by the Batista group represent significant contributions to the field of Chemical Dynamics where for many years progress has been hindered by the complexity of nonintegrable systems and the intrinsic limitations of theoretical and experimental methods. In addition to advancing our understanding of specific systems, the MP/SOFT simulations served to establish the range of validity of theoretical studies based on semiclassical


21

(a)

(b)

Figure 2. MP/SOFT simulations of the ultrafast cis/trans-isomerization of the retinyl chromophore in visual rhodopsin, and relaxation dynamics at the S0/S1 conical intersection of potential energy surfaces; (b) time-dependent reactant and product populations predicting a 200 fs reaction time and 67% product yield as described by MP/SOFT and TDSCF simulations of the photoexcitation of the retinyl chromophore triggering excited-state cis/trans isomerization.

methods,14-17 and introduced general methods to model reaction dynamics in polyatomic systems. In particular, MP/SOFT is a greedy algorithm that generates compact coherent-state expansions of multidimensional wavepackets (or density matrices in dual space) by using matching pursuit, and propagates the time-dependent states analytically (in real- or imaginary-time) by using the Trotter expansion of the time evolution operator. The application studies have shown that high-dimensional wavepackets can be efficiently propagated whenever they remain sufficiently localized, since the MP/SOFT propagation simultaneously achieves sparsity (i.e., compact representations), superresolution (i.e., resolution higher than possible with traditional nonadaptive methods, such as Fourier representations) and speed (i.e., expansions obtained in O(n) or O(n log(n)) steps, where n is the number of basis functions in the basis set). Furthermore, the Fourier (and inverse Fourier) transform operations, required by the Trotter expansion, can be computed analytically overcoming the intrinsic limitations of the standard SOFT approach (i.e., the exponential scaling of storage and computational effort demanded by grid-based representations and the fast-Fourier transform (FFT) algorithm).


22

(a)

(b)

Figure 3. (a) MP/SOFT calculations of time-dependent reactant population PR(t), after photoexcitation of 2-2’-hydroxyphenyl-benzothiazole (HBT), triggering excited-state intramolecular proton transfer (ESIPT) coupled to keto-enolic tautomerization. The decoherence dynamics is measured by the Tr[ (t)2], with (t) the time-dependent reduced density matrix associated with the transfering hydrogen; (b) UV-vis photoabsorption spectrum of HBT, predicted by MP/SOFT simulations, including a broad band with a superimposed diffused vibronic structure.

One may think of MP/SOFT as the SOFT method implemented in matching pursuit coherent state representations, or as a numerically exact quantum mechanical version of the time-sliced coherent-state propagation method, previously developed by the Batista group.1 The MP/SOFT efficiency results from focusing the computational effort on generating (and dynamically adapting) compact coherent state expansions. The strategy ensures accuracy and efficiency, complementing traditional propagation schemes based on orthogonal representations, methods based on ad hoc truncation procedures, and approximate semiclassical or mixed quantum-classical algorithms. When compared to alternative time-dependent methods (e.g., the multi-configurational-time-dependent Hartree (MCTDH) method, or other approaches based on coherent state expansions), MP/SOFT is usually easier to implement since it avoids the need of propagating time-dependent expansion coefficients. The main drawback of MP/SOFT is that the propagation requires new coherent-state expansions of the time-evolving state for each propagation time step. While the underlying computational task is demanding, it can be trivially parallelized overcoming the limitations of memory/storage bandwidth with readily available computational power.


23

Figure 4. Real (a) and imaginary (b) parts of the position-position correlation function for a particle at finite temperature in an asymmetric quartic potential, as described by the generalized MP/SOFT method (solid lines), benchmark grid-based SOFT calculations (dots), and classical Boltzmann ensemble averages (thin- lines). These results show that the generalized MP/SOFT avoids the “sign problem” that usually defies the capabilities of real-time path-integral Monte Carlo, and properly describes not only the early time dephasing dynamics but also the quantum-mechanical recurrencies induced by interference at longer times that often defy the capabilities of approximate semiclassical approaches.

Thermal Correlation Functions:

In addition to quantum dynamics studies based on propagation of multidimensional wavefunctions, the Batista group has generalized the MP/SOFT algorithm to evaluate thermal-equilibrium density matrices, thermal correlation functions, and finite-temperature time-dependent expectation values.4 The generalized MP/SOFT method exploits the analogy between the time-dependent Schrödinger equation and the Bloch equation and computes finite-temperature density matrices via imaginary-time propagation, avoiding the “sign problem” that usually defies the capabilities of real-time path-integral Monte Carlo. The Heisenberg time-evolution operators, involved in thermal correlation functions, are analogously computed by real-time propagation.

The accuracy and efficiency of the generalized MP/SOFT approach have been demonstrated as compared to benchmark quantum mechanical calculations for model systems, including systems at finite temperature in asymmetric quartic potentials (Fig. 4). The reported results show that MP/SOFT provides a quantitative description of both classical dephasing dynamics and quantum recoherence as well as the effect of temperature on the classical and quantum relaxation time scales.

Computational Studies of Electronic Relaxation in S ensitized Semiconductors

Computational studies of sensitized semiconductor surfaces by the Batista group focused on TiO2 anatase surfaces functionalized with organic and inorganic molecules, including molecular linkers commonly used in Grätzel cells.18-25 The studies characterized the nature of interfacial electron transfer mechanisms that for many years have challenged conventional electron transfer theories formulated in the weak-coupling limit. The studies addressed the dynamics of photoinduced electron-


24

(a)

(b)

Figure 5. (a): Through-space electron injection mechanism proposed by the Batista group, for interfacial electron transfer in TiO2 surfaces functionalized with catechol adsorbates; and (b):energy diagram for the underlying photoinduced interfacial electron injection.

hole pair relaxation at the molecular level, and the subsequent carrier diffusion mechanism after electron injection in the conduction band.19-22, 25 In addition, coherent control scenarios based on sequences of ultrafast unitary laser pulses were computationally demonstrated, predicting the feasibility of creating and manipulating coherent electronic excitations on monolayers of adsorbate molecules covalently attached to TiO2 semiconductor surfaces.18, 23, 24

Interfacial Electron Transfer:

A computational methodology combining mean-field DFT molecular dynamics simulations of nuclear motion and quantum dynamics propagation of electronic excitations was developed and implemented to study interfacial electron transfer and hole relaxation in sensitized surfaces. The approach was particularly suited for modeling ultrafast electronic relaxation pathways in extended sensitized TiO2 supercells, providing fundamental insight on the nature of interfacial electron injection mechanisms (see Fig. 5). Contrary to electron transfer between redox species in homogeneous phases, where the rates are determined by nuclear reorganization energies, Batista’s simulations of electronic relaxation showed that the time scales and mechanisms for interfacial electron transfer are mainly determined by the electronic couplings between excited states localized in the molecular adsorbates and states in the TiO2 conduction band.

Fully atomistic simulations provided a detailed description of the primary electron injection event, including ultrafast through-space electron transfer into Ti4+ ions next to the molecular adsorbate, similar to ligand-to-metal intramolecular electron transfer in transition metal coordination complexes. The analysis of the subsequent charge delocalization mechanism, after electron injection into the TiO2 crystal, revealed a highly anisotropic carrier diffusion process that can be up to an order of magnitude slower along certain directions in the anatase crystal.19-22, 25 These results, explaining the origin of ultrashort time scales, are particularly relevant for the optimization of interfacial charge transfer and surface charge separation in photovoltaic devices.


25

Force Field Parameters:

Force field parameters for large-scale computational modeling of sensitized TiO2 surfaces have been developed from the energetic analysis of minimum energy configurations and ensembles of thermal configurations generated by DFT molecular dynamics simulations.20 The resulting force field, composed of Coulomb, van der Waals and harmonic interactions is an extension of Amber and reproduces ab initio minimum energy structures and phonon spectra density profiles of sensitized TiO2-anatase nanostructures. Furthermore, simulations of interfacial electron injection and electron-hole relaxation dynamics have demonstrated the capabilities of the resulting molecular mechanics force field parameters for accurate modeling nuclear fluctuations responsible for speeding up the interfacial electron transfer dynamics in sensitized semiconductor surfaces at finite temperature. The resulting force field thus offers an opportunity to study models beyond the capabilities of DFT molecular dynamics methods, including adsorbate molecules covalently attached to semiconductor surfaces in complex molecular environments (liquids).

Photocatalysis:

Computational studies of TiO2 surfaces sensitized with oxomanganese surfaces, by the Batista group, predicted visible-light sensitization based on TiO2 surface functionalization with oxomanganese complexes. The simulations also suggested the possibility of visible-light photoactivation of Mn catalysts attached to semiconductor surfaces (Fig 6). These results motivated Batista to initiate a collaboration with 3 experimental groups at Yale (including Brudvig, Crabtree and Schmuttenmaer) in a joint experimental and theoretical effort to investigate TiO2 functionalization for solar-light water-splitting and other applications of green-oxidation chemistry in the absence of primary oxidants. The team has already demonstrated, in practice, the feasibility of sensitizing TiO2 to absorption of visible light by surface functionalization with Mn-catalysts, and the possibility of activating Mn(III) catalysts by ultrafast interfacial electron injection.25 As a result of these research findings, the team has been recently awarded a $1.44 million grant from the DOE to pursue research on photocatalytic water splitting based on TiO2 surfaces functionalized with Mn complexes.

0 fs 15 fs 30 fs 45 fs0 fs 15 fs 30 fs 45 fs

Figure 6. Snapshots of the electronic charge distribution, during the ultrafast interfacial electron injection from [MnII(H2O)3(catechol-terpy)]2+ (terpy = 2,2’:6,2”-terpyridine), activating a Mn(III) surface catalyst by visible light photoexcitation.


26

(a) (b)

0 20 40 60 80 1000.0

0.2

0.4

0.6

0.8

1.0

SU

RV

IVA

L P

RO

BA

BIL

ITY

TIME (PS)

2-π pulses (200 fs spacing)

14 fs 60 fs

0 20 40 60 80 1000.0

0.2

0.4

0.6

0.8

1.0

SU

RV

IVA

L P

RO

BA

BIL

ITY

TIME (PS)

2-π pulses (200 fs spacing)

14 fs 60 fs

Figure 7. (a) Coherent control scenario, based on frequent unitary laser pulses, proposed by the Batista group for laser manipulation of quantum tunneling dynamics; (b) Quantum control of Rabi oscillations by a sequence of 2- Π pulses that freeze superexchange electron tunneling in sensitized TiO2 surfaces.

Coherent Control:

The Batista group has developed quantum control scenarios for laser manipulation of electronic excitations in sensitized semiconductor surfaces.18, 23, 24 Building on earlier work on coherent-control of reaction dynamics in excited electronic states,12 it was found that superexchange hole tunneling through adsorbate molecules can be inhibited and eventually halted by applying sufficiently frequent unitary pulses that exchange energy with the system but do not collapse the coherent evolution, or affect the underlying electron transfer energy barriers (see Fig. 7).

The discovered coherent control scenarios were also demonstrated as applied to control of decoherence in archetype model systems, including a quantum dot structure coupled to a free standing quasi 2-dimensional phonon cavity.18 These structures are physical realizations of artificial atoms and molecules with structural and transport properties that can be modulated in the presence of external fields, and engineered for specific applications. The reported studies are, therefore, particularly relevant to advance our understanding of coherent optical control of electronic excitations in semiconductor devices where performance might be limited by quantum mechanical effects such as tunneling and decoherence.


27

Figure 8. Schematic representation of the iterative self-consistent `mod-QM/MM’ algorithm developed by the Batista group for addressing polarization effects in macrobiomolecules.

QM/MM Methods for Modeling Polarization Effects Studies of Structure/Function Relations in Biomolec ules

Mod-QM/MM: A practical, yet rigorous, self-consistent QM/MM protocol has been developed to compute ab initio quality electrostatic potentials of extended molecular systems, including polymers, proteins and other macromolecules.26 The method (called Mod-QM/MM) involves a linear scaling algorithm that models polarization effects in complex molecular systems by iteratively computing electroStatic-Potential (ESP) atomic-charges of the constituent domains (see Fig. 8). The method is thus a general approach for addressing the problem of electrostatic interactions at QM and MM interfaces, bypassing the need of empirical parametrization or rescaling of partial atomic charges.

The Mod-QM/MM method implements a space-domain decomposition scheme, partitioning extended molecular systems into molecular domains R1 ... Rn capped with nearest neighbor molecular fragments, or hydrogen atoms. ESP atomic charges are computed by using a least square fit procedure, similar to the Besler-Merz-Kollman method but with different holonomic constraints, so that the total charge is conserved for both the individual fragments and the molecular caps. The calculation of partial atomic charges iteratively minimizes the error in the evaluation of the electrostatic potentials computed over extended grids and considers the polarization due to the surrounding fragments as described by the partial atomic charges obtained in previous computational steps. The entire computational cycle is iterated several times until reaching self-consistency.

The mod-QM/MM program is now available in the public domain,27 as a versatile software interface with external calls to QM/MM calculations with popular quantum chemistry packages, including Gaussian and Schrodinger’s Q-site. The algorithm complements a variety of other linear-scaling ’divide-and-conquer’ methods, previously proposed for modeling polarization effects and contributes with computational aspects that are crucial to obtain ab initio quality electrostatic potentials. Typically, the effect of polarization corrects the values of partial atomic charges provided by popular force fields by only 10–20%. However, the sum of these small corrections from multiple residues at QM/MM interfaces is important since it can account for 10-15 kcal mol-1 energy corrections to the total interaction between the QM and MM layers.

Mod-QM/MM has already been applied to the description of polarization effects in several systems of biological interest, including the oxygen evolving complex of photosystem II,28-36 the binding site of the retinyl chromophore in visual rhodopsin12,


28

(a)

(b)

Figure 9. (a) DFT-QM/MM structural model of the O2-evolving complex (OEC) of photosystem II (PSII) proposed by the Batista group, including substrate water molecules (`slow’ and `fast’) that form O2 upon oxidation and deprotonation; (b)Comparison between the experimental EXAFS spectrum of the OEC of PSII and the simulated spectra based on two high-valent redox isomers (a) and (b) of the QM/MM model.

37-39 and, more recently, the description of DNA quadruplexes polarized by monovalent cations. These studies showed that including polarization effects in the description of electrostatic interactions is essential for a proper description of structure/function relations.

Water Splitting in Photosystem II: The DFT-QM/MM studies of photosystem II (PSII) by Batista and coworkers addressed the development of chemically sensible models of the oxygen-evolving complex (OEC) in the S0 S4 states (Fig. 9).28, 30-36, 40,

41 The OEC of PSII is a paradigm system for engineering direct solar fuel production systems since it involves a catalyst with inexpensive and abundant metals (calcium and manganese) and is capable of splitting water by accumulating sufficient oxidizing power. The resulting scientific insight on structure/function relations provided by these computational studies of PSII has been useful not only to understand fundamental chemistry of oxygen evolution by natural photosynthesis, but also for studies of water splitting by artificial photosynthetic systems, including TiO2 sacrificial electron-acceptor surfaces functionalized with oxomanganese catalysts.

Previous theoretical studies of the OEC of PSII were limited to the energetic analysis of biomimetic model complexes in the gas phase (or embedded in a dielectric continuum) since the protein structure was unknown. The contributions of DFT-QM/MM models exploited recent breakthroughs in X-ray crystallography and explicitly considered the perturbational influence of the protein environment on the electronic and structural properties of the OEC. In addition, the DFT-QM/MM models have suggested models with complete coordination of metal centers by proteinaceous ligands, water and chloride and have identified potential substrate water molecules coordinated as terminal ligands to the Mn4Ca metal cluster. The resulting structures significantly improved the X-ray diffraction models, suffering from incomplete coordination of metal centers and unresolved substrate water molecules.

The QM/MM models were validated by comparisons with a wide range of experiments providing spectroscopic and mechanistic data,


29

Figure 10: Catalytic cycle of water splitting proposed by DFT QM/MM structural models of the OEC of PSII, developed by the Batista group. The blue circles highlight substrate water molecules that form O2. Dashed brown arrows indicate transformations (e.g., proton movements) leading to the following S-state in the cycle. Changes caused by an S-state transition are highlighted in red. Coordination bonds elongated by the Jahn-Teller distortion, marked in green.

including first-principle simulations of extended X-ray absorption fine structure (EXAFS) spectra and direct comparisons with high-resolution spectroscopy. The resulting models are thus particularly useful for rationalizing a wide range of spectroscopic and crystallographic data and for building a complete structure-based mechanism of water splitting. The catalytic cycle is described by oxidation state transitions and deprotonation events leading to structural changes in the metal cluster. The QM/MM models thus provide fundamental understanding on the molecular origin of structural rearrangements in the oxomanganese metal cluster and on the specific functional roles of structural motifs formed by changes in the nature of the ligands along the catalytic cycle (Fig. 10). These findings, have advanced our current understanding of photosynthetic water oxidation, as described by the S-state cycle proposed by Joliot and Kok,42, 43 establishing the foundation for further studies on the chemical nature of the reaction intermediates and the electronic state transitions responsible for the accumulation of oxidizing equivalents.

The QM/MM models were consistent with a mechanism based on dioxygen evolution during the S4 S0 transition, involving a nucleophilic attack of the calcium-bound water molecule on the electrophilic oxyl radical MnIV –O· species. The reaction is similar to earlier proposals (e.g., Pecoraro44 and Brudvig45) with the difference that in the QM/MM model the nucleophilic water attacks an oxyl radical rather than the oxo-MnV species. Another distinct aspect is that the reaction is


30

Figure 11. Detailed structure of the binding cavity of rhodopsin, predicted by Batista’s QM/MM models, indicating that isomerization must occur only along the <0 direction due to steric impediments in the binding pocket.

promoted by water exchange in the coordination sphere of Ca2+ and that the nucleophilic water is activated not only by Ca2+ but also by two other basic species, including CP43-R357 and a basic µ-oxo bridge linking Mn(4) and Mn(3). The QM/MM models also showed that the most significant structural rearrangements in the metal cluster are due to formation (or opening) of such a basic µ-oxo bridge linking Mn(4) and Mn(3), a structural motif that is essential for deprotonation of Ca2+

bound water molecules.

The proposed DFT-QM/MM mechanism is also significantly different from earlier proposals where the oxidation reaction involves species near the Mn cluster (Sauer-Yachandra,46 Siegbahn47), or a manganese bridging oxo group (Yachandra48). The overall DFT cycle also disagrees with other proposed mechanisms where manganese bridging oxo ligands react with one another during the O–O bond forming step (e.g., Brudvig-Crabtree,49 Sauer-Yachandra50), where oxyl radicals react with µ-oxo bridges instead of reacting with terminal Ca2+-bound water molecules (Hillier & Messinger,51 Messinger,52 Siegbahn & Lundberg53) or where basic µ-oxo ligands deprotonate manganese-bound terminal water molecules.54

Studies of Visual Rhodopsin: Computational studies of visual rhodopsin by Batista and coworkers have addressed the molecular rearrangements induced by the primary photochemical event responsible for phototransduction and energy storage.12,

37-39 These studies provided fundamental insight on long-standing problems regarding the assembly and function of the individual amino acid residues and bound water molecules at the active site of this prototypical G-protein coupled receptor (GPCR) that is responsible for triggering the signal transmission cascade in vertebrate vision.

The QM/MM structural models were based on recent high resolution X-ray structures of bovine visual rhodopsin and provided fundamental insight concerning the molecular structure of the chromophore binding pocket, the role of bound water molecules in close contact with the retinyl chromophore, the detailed molecular rearrangements responsible for the primary photoactivation event (Figs. 11 and 12), the underlying energy storage mechanism and the assignment of spectroscopic features in both the 1H and 13C NMR spectra, and the photoabsorption spectrum of the retinyl chromophore in rhodopsin (Fig. 12).


31

(a)

(b)

Energy Storage

*Exp Value :

Dihedral angle

11-cis rhodopsin

all-trans bathorhodopsin

Intermediate conformation

34 kcal/mol

Energy Storage

*Exp Value :

Dihedral angle

11-cis rhodopsin

all-trans bathorhodopsin

Intermediate conformation

34 kcal/mol

Figure 9. (a) Calculated 13C-NMR chemical-shifts of the retinyl chromophore, validating the QM/MM models; (b) cis/transisomerization QM/MM energy profile and detailed molecular rearrangements responsible for the primary photoactivation event.

The DFT-QM/MM models suggested that the isomerization proceeds only clockwise, due to steric constraints, and that half of the photoabsorbed energy is stored as strain energy in the polyene chain due to steric interactions with the binding cavity adapted to the 11-cis retinyl form. The other half of the stored energy is predicted to be electrostatic, due to charge separation induced by torsion of the polyene chain. Torsional strain induces reorientation of the polarized bonds N-H(+) and C15-H, producing a displacement of the net positive charge of the chromophore relative to the negatively charged counterion Glu-113. These structural rearrangements thus suggested a simple energy storage mechanism based on torsion of the polyene chain induced by steric interactions. The process is significantly different from previously postulated energy storage mechanisms, based upon displacement of the polyene chain away from the negative counterion toward a nonpolar environment. The QM/MM models were also validated by rigorous comparisons with experimental data, including calorimetry measurements of energy storage and NMR chemical shifts.


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Pedagogical Developments

Courses for graduate and undergraduate students, introducing a selection of problems and methodologies to modernize Theoretical Physical Chemistry courses and the General Chemistry curriculum, were developed. Pedagogical websites were created for General Chemistry [http://xbeams.chem.yale.edu/~batista/113/index.html], Introductory Quantum Chemistry [http://xbeams.chem.yale.edu/~batista/vvv/index.html], Introduction to Statistical Mechanics [http://xbeams.chem.yale.edu/~batista/vva/index.html] and a Summer School on Quantum Dynamics [http://xbeams.chem.yale.edu/~batista/summer.pdf]. These pedagogical resources were made available not only to the students enrolled in the classes but also to the entire community and are consulted extensively by students and teachers from many universities around the world. In recognition for these contributions to education, Batista was awarded the Yale Junior Faculty Fellowship in the Natural Sciences 2005.

The classes introduced innovations for college science education that fit in with the existing infrastructure at Yale and complement existing programs for diversity students. The activities were inspired by a wide range of pedagogical proposals for improvements in science education, ranging from including every aspect of modern technology in the classroom and beyond to incorporating the latest findings of sociological studies as well as other approaches that fall somewhere in between. Written assignments in science classes, case studies, computational projects, as well as a tutoring and mentoring program for underrepresented minority students, were introduced. In addition, the user maintained website www.wikidchem.org was developed, providing:

• Multiple pedagogical approaches • Agency for the rapid exchange and distribution of

pedagogical materials • Smooth implementation of research topics into the

standard curriculum • A platform for scholars from different institutions to

share their own approaches and experiences. • An open access wikisite (Bulldog Biophysics) for

the biophysical community at Yale and beyond.

These developments address natural limitations of the traditional pedagogical approach where the presentation of the subject matter is usually limited to the perspective of the teacher responsible for the class and the textbook of choice. The very individual nature of the process of learning, however, makes a presentation that is optimum for some students not ideal for others and vice-versa. In addition, only a few possible textbooks are usually appropriate for a specific course and often none of them covers all of the topics updated with the most recent discoveries. Wikidchem addresses these limitations by making available to students and teachers multiple pedagogical approaches and by complementing the textbooks with up-to-date materials uploaded by the scientific community. Wikidchem also provides a wealth of pedagogical information for writing new textbooks as well as an efficient way to estimate the need for a new textbook, or a new edition of an existing text. Therefore, wikidchem offers valuable information to overcome some of the gaps and shortcomings of the current pedagogical system.


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Chemistry 113: This has been the first class at Yale that introduced the powerful online Webassign management system [www.webassign.net] for the efficient distribution and collection of homework assignments over the Internet. In addition, the class included lectures with computer simulations, movies and laboratory demonstrations. The application of these new technological advances offers educational technology at its best for grading, leaving teachers with as much time as possible to meet personally with students and address their individual and specific needs with science education. Chemistry 113 also includes a tutoring mentoring program for students with learning difficulties due to little or no previous exposure to physical sciences.

Chemistry 430b/530b and Chem 470a/570a: The computational projects introduced in the course Introduction to Statistical Mechanics (Chemistry 430b/530b), http://xbeams.chem.yale.edu/~batista/vva/index.html and Introduction to Quantum Chemistry (Chemistry 470a/570a) http://xbeams.chem.yale.edu/~batista/vvv/index.html were met with great enthusiasm. The assignments offered an opportunity for advanced undergraduates and graduate students to study to multidisciplinary frontier research problems and gain experience in the development of computer simulations with an experimental motivation, including electronic structure calculations, as well as Monte Carlo and Molecular Dynamics simulations. Contrary to traditionally courses that mostly relied on calculus, Chemistry 430b/530b and Chemistry 470a/570a exploited the accessibility that both undergraduate and graduate students at Yale have to computational resources, including the computer laboratory at the Chemistry Department, the possibility of remote access to departmental computers, and the popularity of owning personal computers. In addition, the computational assignments were designed to make students interact with instructors and researchers. Causing, encouraging, and stimulating interactions between students, as well as with other people in the department, including post-doctoral fellows and other faculty members, was an essential aspect that fosters the possibility of learning from other students and researchers, to become familiar with their own research interests, and to develop skills that would later allow them to participate in specific research projects. These activities were crucial for students to become actively integrated in the educational program, modernizing the traditional school where students were not supposed to consult with anybody while working on their assignments since the grade was a measure of individual and isolated accomplishment. In contrast, the assignments motivated students to consult with others as much as possible with the intention that the more ideas they would exchange the more they would learn. The program also required a non-traditional approach for submitting assignments. Rather than simply dropping their assignments in mailboxes, students were required to meet with the instructor in small groups for about 10–15 minutes to go over their work. These specific office hours dedicated to receive assignments were part of the grading process and were crucial for getting direct feedback from each student, to find out how much the students were working and learning, what kind of difficulties they had, and what topics needed more attention.

Undergraduate Mentorship: In addition to the development of courses and to the mentorship of graduate students and post-doctoral fellows, Batista has maintained an active research mentorship program for outstanding undergraduate students. Mentees included undergraduate students awarded by the Brigitte Prusoff Summer Fellowship, the Yale College Dean’s Research Fellowship (Mr. Justin Kim; Ms. Heather Wittels; Mr. Xiao Ying) and the STARS program fellowship (Mr. Devon


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Philips; Ms. Grace Kalisha) designed to give underrepresented minority students an opportunity to work in research laboratories at Yale University early in their college careers. Mr. Devon Philip presented his research at the 227th ACS Meeting, Anaheim, CA, March 28-April 1, 2004 and was awarded for the best poster presentation at the Yale Bouchet Conference on Diversity in Graduate Education, April 23-25, 2004. The research program also served as a tutoring and mentoring initiative, carried out mostly by the graduate students and post-doctoral fellows in the Batista group. The main goal was to support members of minority groups to remain and achieve success in higher education and naturally broaden the participation of underrepresented minorities.

In addition to his participation in undergraduate research mentorship, Batista has been a member of the freshman advising program at one of the residential colleges (Saybrook College, Yale University). This is an initiative to help students select a program of study for their first year, taking into account their interests, goals, and the composition of the course schedule as a whole, including aspects of what constitutes the liberal arts education at Yale. Furthermore, Batista has been an active member of the Society for Advancement of Chicanos and Native Americans in Science (SACNAS), the K-12 education program e-mentoring initiative that aims to create meaningful, collaborative partnerships between pre-college teachers and professional minority scientists in order to cause a positive impact on the achievement of underrepresented minority students in the sciences.


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References:

1. Burant, J.C. and V.S. Batista, Real time path integrals using the Herman-Kluk propagator. J. Chem. Phys., 2002. 116(7): p. 2748-2756.

2. Wu, Y.H. and V.S. Batista, Matching-pursuit for simulations of quantum processes. J. Chem. Phys., 2003. 118(15): p. 6720-6724.

3. Wu, Y.H., M.F. Herman, and V.S. Batista, Matching-pursuit/split-operator Fourier-transform simulations of nonadiabatic quantum dynamics. J. Chem. Phys., 2005. 122(11): p. 114114.

4. Chen, X., Y.H. Wu, and V.S. Batista, Matching-pursuit/split-operator-Fourier-transform computations of thermal correlation functions. J. Chem. Phys., 2005. 122(6): p. 64102.

5. Wu, Y.H. and V.S. Batista, Quantum tunneling dynamics in multidimensional systems: A matching-pursuit description. J. Chem. Phys., 2004. 121(4): p. 1676-1680.

6. Wu, Y. and V.S. Batista, Matching-pursuit split-operator Fourier-transform simulations of excited-state intramolecular proton transfer in 2-(2'-hydroxyphenyl)-oxazole. J. Chem. Phys., 2006. 124: p. 224305.

7. Wu, Y. and V.S. Batista, Semiclassical molecular dynamics simulations of the excited state photodissociation dynamics of H2O in the A 1B1 band. J. Phys. Chem. B, 2002. 106: p. 8271-8277.

8. Wu, Y., J. Kim, and V.S. Batista, MP/SOFT study of the excited-state intramolecular proton transfer in 2-(2'-hydroxyphenyl)-benzothiazole in full dimensionality. J. Chem. Phys., 2007: p. in prep.

9. Chen, X. and V.S. Batista, Matching-pursuit/split-operator-Fourier-transform simulations of excited-state nonadiabatic quantum dynamics in pyrazine. J. Chem. Phys., 2006. 125(12): p. 124313.

10. Chen, X. and V.S. Batista, The MP/SOFT Methodology for Simulations of Nonadiabatic Quantum Dynamics: Application to the Photoisomerization of the Retinyl Chromophore in Rhodopsin. J. Photochem. Photobiol., 2007. 190: p. 274-282.

11. Wu, Y.H. and V.S. Batista, Matching-pursuit for simulations of quantum processes (vol 118, pg 6720, 2003). J. Chem. Phys., 2003. 119(14): p. 7606-7606.

12. Flores, S.C. and V.S. Batista, Model study of coherent-control of the femtosecond primary event of vision. J. Phys. Chem. B, 2004. 108(21): p. 6745-6749.

13. Batista, V.S. and P. Brumer, Coherent control in the presence of intrinsic decoherence: Proton transfer in large molecular systems. Phys. Rev. Lett., 2002. 89(24): p. 143201.

14. Batista, V.S. and W.H. Miller, Semiclassical molecular dynamics simulations of ultrafast photodissociation dynamics associated with the Chappuis band of ozone. J. Chem. Phys., 1998. 108(2): p. 498-510.

15. Coronado, E.A., V.S. Batista, and W.H. Miller, Nonadiabatic photodissociation dynamics of ICN in the A continuum: a semiclassical initial value representation study. J. Chem. Phys., 2000. 112: p. 5566-5575.


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16. Guallar, V., V.S. Batista, and W.H. Miller, Semiclassical molecular dynamics simulations of excited state double-proton transfer in 7-azaindole dimers. J. Chem. Phys., 1999. 110(20): p. 9922-9936.

17. Guallar, V., V.S. Batista, and W.H. Miller, Semiclassical molecular dynamics simulations of intramolecular proton transfer in photoexcited 2-(2 '-hydroxyphenyl)-oxazole. J. Chem. Phys., 2000. 113(21): p. 9510-9522.

18. Rego, L.G.C., S.G. Abuabara, and V.S. Batista, Multiple Unitary Pulses for Coherent Control of Tunneling and Decoherence. J. Mod. Optics, 2007. 54: p. 2617-2627.

19. Abuabara, S.G., L.G.C. Rego, and V.S. Batista, Influence of thermal fluctuations on interfacial electron transfer in functionalized TiO2 semiconductors. J. Am. Chem. Soc., 2005. 127(51): p. 18234-18242.

20. Abuabara, S.G., J.A. Gascon, S.Y. Leung, L.G.C. Rego, and V.S. Batista, Force Field Parameters for Large-Scale Computational Modeling of Sensitized TiO2 Surfaces. Proceedings of SPIE, 2006. 6325: p. 63250R.

21. Rego, L.G.C. and V.S. Batista, Quantum Dynamics Simulations of the Interfacial Electron Transfer in Sensitized TiO2 Semiconductors. J. Am. Chem. Soc., 2003. 125: p. 7989-7997.

22. Rego, L.G.C., S.G. Abuabara, and V.S. Batista, Model study of coherent quantum dynamics of hole states in functionalized semiconductor nanostructures. J. Chem. Phys., 2005. 122(15): p. 154709.

23. Rego, L.G.C., S.G. Abuabara, and V.S. Batista, Coherent optical control of electronic excitations in functionalized semiconductor nanostructures. Quant. Inform. Comput., 2005. 5(4-5): p. 318-334.

24. Rego, L.G.C., S.G. Abuabara, and V.S. Batista, Coherent-Control of Tunneling Dynamics in Functionalized Semiconductor Nanostructures: A Quantum-Control Scenario Based on Stochastic Unitary Pulses. J. Mod. Opt., 2006. 53: p. 2519-2532.

25. Abuabara, S.G., C.W. Cady, J.B. Baxter, C.A. Schmuttenmaer, R.H. Crabtree, G.W. Brudvig, and V.S. Batista, Ultrafast Interfacial Electron Transfer drives Mn(II) photooxidation on TiO2 Nanoparticles. J. Phys. Chem. C, 2007. 111: p. 11982-11990.

26. Gascon, J.A., S.S.F. Leung, E.R. Batista, and V.S. Batista, A self-consistent space-domain decomposition method for QM/MM computations of protein electrostatic potentials. J. Chem. Theory Comput., 2006. 2(1): p. 175-186.

27. Gascon, J.A., S.S.F. Leung, E.R. Batista, and V.S. Batista, MODQ3M release 1.0. 2006.

28. Sproviero, E.M., J.A. Gascon, J.P. McEvoy, G.W. Brudvig, and V.S. Batista, QM/MM study of the catalytic cycle for water splitting in photosystem II. J. Am. Chem. Soc., 2008. 130: p. 3428-3442.

29. Sproviero, E.M., K. Shinopoulos, J.A. Gascon, J.P. McEvoy, G.W. Brudvig, and V.S. Batista, QM/MM computational studies of substrate water binding to the oxygen evolving complex of Photosystem II. Phil. Trans. Royal Soc. London Series B - Biol. Sci., 2008. 363: p. 1149-1156.


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30. Sproviero, E.M., J.A. Gascon, J.P. McEvoy, G.W. Brudvig, and V.S. Batista, Computational studies of the O2-evolving complex of photosystem II and biomimetic oxomanganese complexes. Coord. Chem. Rev., 2007. 252: p. 395-415.

31. Gascon, J.A., E.M. Sproviero, J.P. McEvoy, G.W. Brudvig, and V.S. Batista, Ligation of the C-terminus of the D1 polypeptide of photosystem II to the oxygen-evolving complex: A DFT-QM/MM study, in Photosynthesis. Energy from the Sun. 2008, Allen Press Inc: London. p. 363-358.

32. Sproviero, E.M., J.A. Gascon, J.P. McEvoy, G.W. Brudvig, and V.S. Batista, QM/MM models of the O2-evolving complex of photosystem II. J. Chem. Theory Comput., 2006. 2(4): p. 1119-1134.

33. Sproviero, E.M., J.A. Gascon, J.P. McEvoy, G.W. Brudvig, and V.S. Batista, Characterization of synthetic oxomanganese complexes and the inorganic core of the O2-evolving complex in photosystem - II: Evaluation of the DFT/B3LYP level of theory. J. Inorg. Biochem., 2006. 100(4): p. 786-800.

34. Sproviero, E.M., J.A. Gascon, J.P. McEvoy, G.W. Brudvig, and V.S. Batista, Structural Models of the Oxygen-Evolving Complex of Photosystem II. Curr. Op. Struct. Biol., 2007. 17: p. 173-180.

35. McEvoy, J.P., J.A. Gascon, V.S. Batista, and G.W. Brudvig, Computational structural model of the oxygen evolving complex in Photosystem II: complete ligation by protein, water and chloride, in Photosynthesis: Fundamental Aspects to global perspectives. 2005, Allen Press Inc: Kansas. p. 278-280.

36. McEvoy, J.P., J.A. Gascon, V.S. Batista, and G.W. Brudvig, The mechanism of photosynthetic water splitting. Photochem. Photobiol., 2005. 4: p. 940-949.

37. Gascon, J.A. and V.S. Batista, QM/MM study of energy storage and molecular rearrangements due to the primary event in vision. Biophys. J., 2004. 87(5): p. 2931-2941.

38. Gascon, J.A., E.M. Sproviero, and V.S. Batista, QM/MM study of the NMR spectroscopy of the retinyl chromophore in visual rhodopsin. J. Chem. Theory Comput., 2005. 1(4): p. 674-685.

39. Gascon, J.A., E.M. Sproviero, and V.S. Batista, Computational studies of the primary phototransduction event in visual rhodopsin. Acc. Chem. Res., 2006. 39(3): p. 184-193.

40. Sproviero, E.M., J.A. Gascon, J.P. McEvoy, G.W. Brudvig, and V.S. Batista, Computational Insights into the Oxygen-Evolving Complex of Photosystem II. Photosyn. Res., 2008. In press .

41. Sproviero, E.M., J.A. Gascon, J.P. McEvoy, G.W. Brudvig, and V.S. Batista, QM/MM computational studies of substrate water binding to the oxygen-evolving complex of Photosystem II. Phil. Trans. Royal Soc. London B, 2007. 363: p. in press (online since Oct. 30).

42. Kok, B., B. Forbush, and M. McGloin, Cooperation of charges in photosynthetic O2 evolution. 1. A linear four step mechanism. Photochem. Photobiol., 1970. 11(6): p. 457-475.

43. Joliot, P., G. Barbieri, and R. Chabaud, Un nouveau modele des centres photochimiques du systeme II. Photochem. Photobiol., 1969. 10: p. 309-329.


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44. Pecoraro, V.L., M.J. Baldwin, M.T. Caudle, W.Y. Hsieh, and N.A. Law, A proposal for water oxidation in photosystem II. Pure and Applied Chemistry, 1998. 70(4): p. 925-929.

45. Vrettos, J.S., J. Limburg, and G.W. Brudvig, Mechanism of photosynthetic water oxidation: combining biophysical studies of photosystem II with inorganic model chemistry. Biochim. Biophys. Acta, 2001. 1503(1-2): p. 229-245.

46. Roelofs, T.A., W.C. Liang, M.J. Latimer, R.M. Cinco, A. Rompel, J.C. Andrews, K. Sauer, V.K. Yachandra, and M.P. Klein, Oxidation states of the manganese cluster during the flash-induced S-state cycle of the photosynthetic oxygen-evolving complex. Proc. Natl. Acad. Sci. U.S.A., 1996. 93(8): p. 3335-3340.

47. Siegbahn, P.E.M., Quantum chemical studies of manganese centers in biology. Curr. Op. Chem. Biol., 2002. 6(2): p. 227-235.

48. Robblee, J.H., R.M. Cinco, and V.K. Yachandra, X-ray spectroscopy-based structure of the Mn cluster and mechanism of photosynthetic oxygen evolution. Biochimica Et Biophysica Acta, 2001. 1503(1-2): p. 7-23.

49. Brudvig, G.W. and R.H. Crabtree, Mechanism For Photosynthetic O2 Evolution. Proc. Natl. Acad. Sci. U.S.A., 1986. 83(13): p. 4586-4588.

50. Yachandra, V.K., K. Sauer, and M.P. Klein, Manganese cluster in photosynthesis: Where plants oxidize water to dioxygen. Chem. Rev., 1996. 96(7): p. 2927-2950.

51. Hillier, W. and J. Messinger, Mechanism of Photosynthetic Oxygen Evolution, in Photosystem II: The Light-Driven Water:Plastoquinone Oxidoreductase, T.J. Wydrzynski and K. Satoh, Editors. 2005, Springer: Dordrecht. p. 567-608.

52. Messinger, J., Evaluation of different mechanistic proposals for water oxidation in photosynthesis on the basis of Mn4OxCa structures for the catalytic site and spectroscopic data. Phys. Chem. Chem. Phys., 2004. 6: p. 4764-4771.

53. Siegbahn, P.E.M. and M. Lundberg, The mechanism for dioxygen formation in PSII studied by quantum chemical methods. Photochem. Photobiol. Sci., 2005. 4: p. 1035-1043.

54. Dau, H., L. Iuzzolino, and J. Dittmer, The tetra-manganese complex of photosystem II during its redox cycle - X-ray absorption results and mechanistic implications. Biochim. Biophys. Acta, 2001. 1503(1-2): p. 24-39.

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