Publications List
Last updated September 20, 2012


158. B. L. Golden, S. Hammes-Schiffer, P. R. Carey, P. C. Bevilacqua, "An Integrated Picture of Ribozyme Catalysis" in Biophysics of RNA Folding, ed. R. Russell (Springer Science + Business Media, New York, 2013).
157. B. H. Solis and S. Hammes-Schiffer, "Computational study of anomalous reduction potentials for hydrogen evolution catalyzed by cobalt dithiolene complexes," J. Am. Chem. Soc. 134, 15253-15256 (2012).
156. B. Auer, A. V. Soudackov, and S. Hammes-Schiffer, "Nonadiabatic dynamics of photoinduced proton-coupled electron transfer: Comparison of explicit and implicit solvent simulations," J. Phys. Chem. B 116, 7695-7708 (2012).
155. A. Sirjoosingh, M. V. Pak, and S. Hammes-Schiffer, "Multicomponent density functional theory study of the interplay between electron-electron and electron-proton correlation," J. Chem. Phys. 136, 174114 (2012).
154. C. Swalina, M. V. Pak, and S. Hammes-Schiffer, "Analysis of electron-positron wavefunctions in the nuclear-electronic orbital framework," J. Chem. Phys. 136, 164105 (2012).
153. S. Horvath, L. E. Fernandez, and S. Hammes-Schiffer, "Insights into proton-coupled electron transfer mechanisms of electrocatalytic H2 oxidation and production," Proc. Natl. Acad. Sci. USA (in press).
152. S. Hammes-Schiffer, "Proton-coupled electron transfer: Classification scheme and guide to theoretical methods," Energy and Environ. Sci. 5, 7696-7703 (2012).
151. L. E. Fernandez, S. Horvath, and S. Hammes-Schiffer, "Theoretical analysis of the sequential proton-coupled electron transfer mechanisms for H2 oxidation and production pathways catalyzed by nickel molecular electrocatalysts," J. Phys. Chem. C 116, 3171-3180 (2012).
150. A. Ganguly, P. C. Bevilacqua, and S. Hammes-Schiffer, "Quantum mechanical/molecular mechanical study of the HDV ribozyme: Impact of the catalytic metal ion on the mechanism," J. Phys. Chem. Lett. 2, 2906-2911 (2011).
149. G. G. Hammes, S. J. Benkovic, and S. Hammes-Schiffer, "Flexibility, diversity, and cooperativity: Pillars of enzyme catalysis" Biochemistry 50, 10422-10430 (2011).
148. B. H. Solis and S. Hammes-Schiffer, "Substituent effects on cobalt diglyoxime catalysts for hydrogen evolution," J. Am. Chem. Soc. 133, 19036-19039 (2011).
147. A. V. Soudackov, A. Hazra, and S. Hammes-Schiffer, "Multidimensional treatment of stochastic solvent dynamics in photoinduced proton-coupled electron transfer processes: Sequential, concerted, and complex branching mechanisms," J. Chem. Phys. 135, 144115 (2011).
146. B. H. Solis and S. Hammes-Schiffer, "Theoretical analysis of mechanistic pathways for hydrogen evolution catalyzed by cobaloximes," Inorg. Chem. 50, 11252-11262 (2011).
145. A. Sirjoosingh, M. V. Pak, and S. Hammes-Schiffer, "Derivation of an electron-proton correlation functional for multicomponent density functional theory within the nuclear-electronic orbital approach," J. Chem. Theory Comput. 7, 2689-2693 (2011).
144. A. Sirjoosingh and S. Hammes-Schiffer, "Diabatization schemes for generating charge-localized electron-proton vibronic states in proton-coupled electron transfer systems," J. Chem. Theory Comput. 7, 2831-2841 (2011).
143. P. Hanoian, and S. Hammes-Schiffer, "Water in the active site of ketosteroid isomerase," Biochemistry 50, 6689-6700 (2011).
142. C. Ko, M. V. Pak, C. Swalina, and S. Hammes-Schiffer, "Alternative wavefunction ansatz for including explicit electron-proton correlation in the nuclear-electronic orbital approach," J. Chem. Phys. 135, 054106 (2011).
141. N. Veeraraghavan, A. Ganguly, B. L. Golden, P. C. Bevilacqua, and S. Hammes-Schiffer, "Mechanistic strategies in the HDV ribozyme: Chelated and diffuse metal ion interactions and active site protonation," J. Phys.Chem. B 115, 8346-8357 (2011).
140. S. Hammes-Schiffer, "When electrons and protons get excited," Proc. Nat. Acad. Sci. USA 108, 8531-8532 (2011).
139. B. Auer, L. E. Fernandez, and S. Hammes-Schiffer, "Theoretical analysis of proton relays in electrochemical proton-coupled electron transfer," J. Am. Chem. Soc. 133, 8282-8292 (2011).
138. S. Hammes-Schiffer, "Current theoretical challenges in proton-coupled electron transfer: Electron-proton nonadiabaticity, proton relays, and ultrafast dynamics," J. Phys. Chem. Lett. 2, 1410-1416 (2011).
137. N. Veeraraghavan, A. Ganguly, J.-H. Chen, P. C. Bevilacqua, S. Hammes-Schiffer, and B. L. Golden, "Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions," Biochemistry 50, 2672-2682 (2011).
136. A. Sirjoosingh and S. Hammes-Schiffer, "Proton-coupled electron transfer versus hydrogen atom transfer: Generation of charge-localized diabatic states," J. Phys. Chem. A 115, 2367-2377 (2011).
135. A. Hazra, A. V. Soudackov, and S. Hammes-Schiffer, "Isotope effects on the nonequilibrium dynamics of ultrafast photoinduced proton-coupled electron transfer reactions in solution," J. Phys. Chem. Lett. 2, 36-40 (2011).
134. P. Hanoian, P. A. Sigala, D. Herschlag, and S. Hammes-Schiffer, "Hydrogen bonding in the active site of ketosteroid isomerase: Electronic inductive effects and hydrogen bond coupling," Biochemistry 49, 10339-10348 (2010).
133. S. Hammes-Schiffer, "Introduction: Proton-coupled electron transfer," Chem. Rev. 110, 6937-6938 (2010).
132. S. Hammes-Schiffer and A. A. Stuchebrukhov, "Theory of coupled electron and proton transfer reactions," Chem. Rev. 110, 6939-6960 (2010).
131. V. C. Nashine, S. Hammes-Schiffer, and S. J. Benkovic, "Coupled motions in enzyme catalysis," Curr. Op. Chem. Biol. 14, 644-651 (2010).
130. A. Hazra, A. V. Soudackov, and S. Hammes-Schiffer, "Role of solvent dynamics in ultrafast photoinduced proton-coupled electron transfer reactions in solution," J. Phys. Chem. B 114, 12319-12332 (2010).
129. N. Veeraraghavan, P. C. Bevilacqua, and S. Hammes-Schiffer, "Long distance communication in the HDV ribozyme: Insights from molecular dynamics and experiments," J. Mol. Biol. 402, 278-291 (2010).
128. S. Hammes-Schiffer, "Theoretical studies of DNA: Editorial," J. Phys. Chem. Lett. 1, 1906 (2010).
127. D.K. Chakravorty and S. Hammes-Schiffer, "Impact of mutation on proton transfer reactions in ketosteroid isomerase: Insights from molecular dynamics simulations," J. Am. Chem. Soc. 132, 7549-7555 (2010).
126. S. J. Edwards, A. V. Soudackov, and S. Hammes-Schiffer, "Impact of distal mutation on hydrogen transfer interface and substrate conformation in soybean lipoxygenase," J. Phys. Chem. B 114, 6653-6660 (2010).
125. B. Auer and S. Hammes-Schiffer, "Localized Hartree product treatment of multiple protons in the nuclear-electronic orbital framework," J. Chem. Phys. 132, 084110 (2010).
124. M. K. Ludlow, A. V. Soudackov, and S. Hammes-Schiffer, "Electrochemical proton-coupled electron transfer of an osmium aquo complex: Theoretical analysis of asymmetric Tafel plots and transfer coefficients," J. Am. Chem. Soc. 132, 1234-1235 (2010).
123. B. Auer, M.V. Pak, and S. Hammes-Schiffer, "Nuclear-electronic orbital method within the fragment molecular orbital approach," J. Phys. Chem. C 114, 5582-5588 (2010).
122. C. Venkataraman, A.V. Soudackov, and S. Hammes-Schiffer, "Dynamics of photoinduced proton-coupled electron transfer at molecule-semiconductor interfaces: A reduced density approach," J. Phys. Chem. C 114, 487-496 (2010).
121. D.K. Chakravorty, A.V. Soudackov, and S. Hammes-Schiffer, "Hybrid quantum/classical molecular dynamics simulations of the proton transfer reactions catalyzed by ketosteroid isomerase: Analysis of hydrogen bonding, conformational motions, and electrostatics," Biochemistry 48, 10608-10619 (2009).
120. S.J. Edwards, A.V. Soudackov, and S. Hammes-Schiffer, "Driving force dependence of rates for nonadiabatic proton and proton-coupled electron transfer: Conditions for inverted region behavior," J. Phys. Chem. B 113, 14545-14548 (2009).
119. C. Venkataraman, A.V. Soudackov, and S. Hammes-Schiffer, "Photoinduced homogeneous proton-coupled electron transfer: Model study of isotope effects on reaction dynamics," J. Chem. Phys. 131, 154502 (2009).
118. A. Chakraborty, M.V. Pak, and S. Hammes-Schiffer, "Properties of the exact universal functional in multicomponent density functional theory," J. Chem. Phys. 131, 124115 (2009).
117. L. Hammarström and S. Hammes-Schiffer, "Artificial photosynthesis and solar fuels: Guest editorial," Acc. Chem. Res. 42, 1859-1860 (2009).
116. S. Hammes-Schiffer, "Theory of proton-coupled electron transfer in energy conversion processes," Acc. Chem. Res. 42, 1881-1889 (2009).
115. I. Navrotskaya and S. Hammes-Schiffer, "Electrochemical proton-coupled electron transfer: Beyond the golden rule," J. Chem. Phys. 131, 024112 (2009).
114. M. K. Ludlow, A.V. Soudackov, and S. Hammes-Schiffer, "Theoretical analysis of the unusual temperature dependence of the kinetic isotope effect in quinol oxidation," J. Am. Chem. Soc. 131, 7094-7102 (2009).
113. M. Kumarasiri, G.A. Baker, A.V. Soudackov, and S. Hammes-Schiffer, "Computational approach for ranking mutant enzymes according to catalytic reaction rates," J. Phys. Chem. B 113, 3579-3583 (2009).
112. M.V. Pak, A. Chakraborty, and S. Hammes-Schiffer, "Calculation of the positron annihilation rate in PsH with the positronic extension of the explicitly correlated nuclear-electronic orbital method," J. Phys. Chem. A 113, 4004-4008 (2009).
111. A. Hazra, J.H. Skone, and S. Hammes-Schiffer, "Combining the nuclear-electronic orbital approach with vibronic coupling theory: Calculation of the tunneling splitting for malonaldehyde," J. Chem. Phys. 130, 054108 (2009).
110. S.J. Edwards, A.V. Soudackov, and S. Hammes-Schiffer, "Analysis of kinetic isotope effects for proton-coupled electron transfer reactions," J. Phys. Chem. A 113, 2117-2126 (2009).
109. S. Hammes-Schiffer, "Selected Theoretical Models and Computational Methods for Enzymatic Tunnelling," pp. 79-104 in Quantum Tunnelling in Enzyme-Catalysed Reactions, eds. R.K. Allemann and N.S. Scrutton (Royal Society of Chemistry, Cambridge, 2009)
108. A. Chakraborty, and S. Hammes-Schiffer, "Density matrix formulation of the nuclear-electronic orbital approach with explicit electron-proton correlation," J. Chem. Phys. 129, 204101 (2008).
107. D.K. Chakravorty, M. Kumarasiri, A.V. Soudackov, and S. Hammes-Schiffer, "Implementation of umbrella integration within the framework of the empirical valence bond approach," J. Chem. Theory Comput. 4, 1974-1990 (2008).
106. S. Hammes-Schiffer and A.V. Soudackov, "Proton-coupled electron transfer in solution, proteins, and electrochemistry," J. Phys. Chem. B 112, 14108-14123 (2008) (Centennial Feature article).
105. A. Chakraborty, M.V. Pak, and S. Hammes-Schiffer, "Development of electron-proton density functionals for multicomponent density functional theory," Phys. Rev. Lett. 101, 153001 (2008).
104. I. Navrotskaya, A.V. Soudackov, and S. Hammes-Schiffer, "Model system-bath Hamiltonian and nonadiabatic rate constants for proton-coupled electron transfer at electrode solution interfaces," J. Chem. Phys. 128, 244712 (2008).
103. A. Chakraborty, M.V. Pak, and S. Hammes-Schiffer, "Inclusion of explicit electron-proton correlation in the nuclear-electronic orbital approach using Gaussian type geminal functions," J. Chem. Phys. 129, 014101 (2008).
102. C. Venkataraman, A.V. Soudackov, and S. Hammes-Schiffer, "Theoretical formulation of nonadiabatic electrochemical proton-coupled electron transfer at metal-solution interfaces," J. Phys. Chem. C 112, 12386-12397 (2008).
101. S. J. Benkovic, G. G. Hammes, and S. Hammes-Schiffer, "Free energy landscape of enzyme catalysis," Biochemistry 47, 3317-3321 (2008).
100. P. E. Adamson, X. F. Duan, L. W. Burggraf, M. V. Pak, C. Swalina, and S. Hammes-Schiffer, "Modeling positrons in molecular electronic structure calculations with the nuclear-electronic orbital method," J. Phys. Chem. A 112, 1346-1351 (2008).
99. S. Hammes-Schiffer, E. Hatcher, H. Ishikita, J. H. Skone, A. V. Soudackov, "Theoretical studies of proton-coupled electron transfer: Models and concepts relevant to bioenergetics," Coordination Chemistry Reviews 252, 384-394 (2008).
98. M. K. Ludlow, J. H. Skone, and S. Hammes-Schiffer, "Substituent effects on the vibronic coupling for the phenoxyl/phenol self-exchange reaction," J. Phys. Chem. B 112, 336-343 (2008).
97. H. Ishikita, A. V. Soudackov, and S. Hammes-Schiffer, "Buffer-assisted proton-coupled electron transfer in a model rhenium-tyrosine complex," J. Am. Chem. Soc. 129, 11146-11152 (2007).
96. M. V. Pak, A. Chakraborty, and S. Hammes-Schiffer, "Density functional theory treatment of electron correlation in the nuclear-electronic orbital approach," J. Phys. Chem. A 111, 4522-4526 (2007).
95. C. Swalina, Q. Wang, A. Chakraborty, and S. Hammes-Schiffer, "Analysis of nuclear quantum effects on hydrogen bonding," J. Phys. Chem. A 111, 2206-2212 (2007).

94. M. Kumarasiri, C. Swalina, and S. Hammes-Schiffer, "Anharmonic effects in ammonium nitrate and hydroxylammonium nitrate clusters," J. Phys. Chem. B 111, 4653-4658 (2007).

93. E. Hatcher, A. V. Soudackov, and S. Hammes-Schiffer, "Proton-coupled electron transfer in soybean lipoxygenase: Dynamical behavior and temperature dependence of kinetic isotope effects," J. Am. Chem. Soc. 129, 187-196 (2007).

92. S. J. Benkovic and S. Hammes-Schiffer, "Dihydrofolate reductase: Hydrogen tunneling and protein motion," pp. 1439-1454 in Handbook of Hydrogen Transfer. Volume 4: Biological Aspects of Hydrogen Transfer, eds. J.T. Hynes, J.P. Klinman, H.-H. Limbach, and R.L. Schowen (Wiley-VCH, Weinheim, 2007).

91. S. Hammes-Schiffer, "Proton-coupled electron transfer reactions: Theoretical formulation and applications" pp. 479-502 in Handbook of Hydrogen Transfer. Volume 2: Physical and Chemical Aspects of Hydrogen Transfer, eds. J.T. Hynes, J.P. Klinman, H.-H. Limbach, and R.L. Schowen (Wiley-VCH, Weinheim, 2007).

90. J. H. Skone, A. V. Soudackov, and S. Hammes-Schiffer, "Calculation of vibronic couplings for phenoxyl/phenol and benzyl/toluene self-exchange reactions: Implications for proton-coupled electron transfer mechanisms," J. Am. Chem. Soc. 128, 16655-16663 (2006).

89. Q. Wang and S. Hammes-Schiffer, "Hybrid quantum/classical path integral approach for simulation of hydrogen transfer reactions in enzymes," J. Chem. Phys. 125, 184102 (2006).

88. Y. Ohta, A. V. Soudackov, and S. Hammes-Schiffer, "Extended spin-boson model for nonadiabatic hydrogen tunneling in the condensed phase," J. Chem. Phys. 125, 144522 (2006).

87. Y. A. Small, V. Guallar, A. V. Soudackov, and S. Hammes-Schiffer, "Hydrogen bonding pathways in human dihydroorotate dehydrogenase," J. Phys. Chem. B 110, 19704-19710 (2006).

86. C. Swalina, M. V. Pak, A. Chakraborty, and S. Hammes-Schiffer, "Explicit dynamical electron-proton correlation in the nuclear-electronic orbital framework," J. Phys. Chem. A 110, 9983-9987 (2006).

85. S. Y. Kim and S. Hammes-Schiffer, "Hybrid quantum/classical molecular dynamics for a proton transfer reaction coupled to a dissipative bath," J. Chem. Phys. 124, 244102 (2006).

84. S. Hammes-Schiffer and J. B. Watney, "Hydride transfer catalyzed by Escherichia coli and Bacillus subtilis dihydrofolate reductase: Coupled motions and distal mutations," Phil. Trans. R. Soc. B 361, 1365-1373 (2006).

83. J. B. Watney and S. Hammes-Schiffer, "Comparison of coupled motions in Escherichia coli and Bacillus subtilis dihydrofolate reductase," J. Phys. Chem. B 110, 10130-10138 (2006).

82. S. J. Benkovic and S. Hammes-Schiffer, "Enzyme motions inside and out," Science 312, 208-209 (2006).

81. S. Hammes-Schiffer and S. J. Benkovic, "Relating protein motion to catalysis," Annual Reviews of Biochemistry 75, 519-541 (2006).

80. A. Sergi, J. B. Watney, K. F. Wong, and S. Hammes-Schiffer, "Freezing a single distal motion in dihydrofolate reductase," J. Phys. Chem. B 110, 2435-2441 (2006).

79. S. Hammes-Schiffer, "Hydrogen tunneling and protein motion in enzyme reactions," Acc. Chem. Res. 39, 93-100 (2006).

78. J. B. Watney, A. V. Soudackov, K. F. Wong, and S. Hammes-Schiffer, "Calculation of the transition state theory rate constant for a general reaction coordinate: Application to hydride transfer in an enzyme," Chem. Phys. Lett. 418, 264-267 (2005).

77. E. Hatcher, A. Soudackov, S. Hammes-Schiffer, "Comparison of dynamical aspects of nonadiabatic electron, proton, and proton-coupled electron transfer reactions," Chemical Physics 319, 93-100 (2005).

76. C. Swalina and S. Hammes-Schiffer, "Impact of nuclear quantum effects on the molecular structure of bihalides and the hydrogen fluoride dimer," J. Phys. Chem. A 109, 10410-10417 (2005).

75. J. H. Skone, M. V. Pak, and S. Hammes-Schiffer, "Nuclear-electronic orbital nonorthogonal configuration interaction approach," J. Chem. Phys. 123, 134108 (2005).

74. E. Hatcher, A. Soudackov, and S. Hammes-Schiffer, "Nonadiabatic proton-coupled electron transfer reactions: Impact of donor-acceptor vibrations, reorganization energies, and couplings on dynamics and rates," J. Phys. Chem. B 109 18565-18574 (2005).

73. A. Reyes, M. V. Pak, and S. Hammes-Schiffer, "Investigation of isotope effects with the nuclear-electronic orbital approach", J. Chem. Phys. 123, Art. No. 064104 (2005).

72. C. Swalina, M. V. Pak, and S. Hammes-Schiffer, "Analysis of the nuclear-electronic orbital method for model hydrogen transfer systems," J. Chem. Phys. 123, Art. No. 014303 (2005).

71. K. F. Wong, T. Selzer, S. J. Benkovic, and S. Hammes-Schiffer, "Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase," Proc. Nat. Acad. Sci. USA 102, 6807-6812 (2005).

70. C. Swalina, M. V. Pak, and S. Hammes-Schiffer, "Alternative formulation of many-body perturbation theory for electron-proton correlation," Chem. Phys. Lett. 404, 394-399 (2005).

69. A. Soudackov, E. Hatcher, and S. Hammes-Schiffer, "Quantum and dynamical effects of proton donor-acceptor vibrational motion in nonadiabatic proton-coupled electron transfer reactions," J. Chem. Phys. 122, Art. No. 014505 (2005).

68. S. Hammes-Schiffer, "Kinetic isotope effects for proton-coupled electron transfer reactions" in Isotope Effects in Chemistry and Biology, eds. H. Limbach and A. Kohen (CRC Press LLC, Boca Raton, 2005).

67. K. F. Wong, J. B. Watney, and S. Hammes-Schiffer, "Analysis of electrostatics and correlated motions for hydride transfer in dihydrofolate reductase," J. Phys. Chem. B 108, 12231-12241 (2004).

66. M. V. Pak, C. Swalina, S. P. Webb, and S. Hammes-Schiffer, "Application of the nuclear-electronic orbital method to hydrogen transfer systems: Multiple centers and multiconfigurational wavefunctions," Chemical Physics 304, 227-236 (2004).

65. O. Vendrell, M. Moreno, J. M. Lluch, and S. Hammes-Schiffer, "Molecular dynamics of excited state intramolecular proton transfer: 2-(2'-hydroxyphenyl)-4-methyloxazole in gas phase, solution and protein environments," J. Phys. Chem. B 108, 6616-6623 (2004).

64. E. Hatcher, A. V. Soudackov, and S. Hammes-Schiffer, "Proton-coupled electron transfer in soybean lipoxygenase," J. Am. Chem. Soc. 126, 5763-5775 (2004).

63. S. Hammes-Schiffer, "Quantum-classical simulation methods for hydrogen transfer in enzymes: A case study of dihydrofolate reductase," Curr. Opin. Struct. Biol. 14, 192-201 (2004).

62. M. V. Pak and S. Hammes-Schiffer, "Electron-proton correlation for hydrogen tunneling systems," Phys. Rev. Lett. 92, Art. No. 103002 (2004).

61. S. Hammes-Schiffer and N. Iordanova, "Theoretical studies of proton-coupled electron transfer reactions," Biochim. Biophys. Acta. 1655, 29-36 (2004).

60. C. Carra, N. Iordanova, and S. Hammes-Schiffer, "Proton-coupled electron transfer in a model for tyrosine oxidation in photosystem II," J. Am. Chem. Soc. 125, 10429-10436 (2003).

59. S. Y. Kim and S. Hammes-Schiffer, "Molecular dynamics with quantum transitions for proton transfer: Quantum treatment of hydrogen and donor-acceptor motions," J. Chem. Phys. 119, 4389-4398 (2003).

58. S. J. Benkovic and S. Hammes-Schiffer, "A perspective on enzyme catalysis," Science 301, 1196-1202 (2003). [Abstract]     [Full Article - PDF]

57. T. Iordanov and S. Hammes-Schiffer, "Vibrational analysis for the nuclear-electronic orbital method," J. Chem. Phys. 118, 9489-9496 (2003).

56. J. B. Watney, P. K. Agarwal, and S. Hammes-Schiffer, "Effect of mutation on enzyme motion in dihydrofolate reductase," J. Am. Chem. Soc. 125, 3745-3750 (2003).

55. S. Hammes-Schiffer, "Impact of enzyme motion on activity," Biochemistry 41, 13335-13343 (2002).

54. S. Webb, T. Iordanov, and S. Hammes-Schiffer, "Multiconfigurational nuclear-electronic orbital approach: Incorporation of nuclear quantum effects in electronic structure calculations," J. Chem. Phys. 117, 4106-4118 (2002).

53. C. Carra, N. Iordanova and S. Hammes-Schiffer, "Proton-coupled electron transfer in DNA-acrylamide complexes," J. Phys. Chem. B 106, 8415-8421 (2002).

52. N. Iordanova and S. Hammes-Schiffer, "Theoretical investigation of large kinetic isotope effects for proton-coupled electron transfer in ruthenium polypyridyl complexes," J. Am. Chem. Soc. 124, 4848-4856 (2002).

51. P. K. Agarwal, S. R. Billeter,and S. Hammes-Schiffer, "Nuclear quantum effects and enzyme dynamics in dihydrofolate reductase catalysis," J. Phys. Chem. B 106, 3283-3293 (2002).

50. P. K. Agarwal, S. R. Billeter, P. T. Rajagopalan, S. J. Benkovic, and S. Hammes- Schiffer, "Network of coupled promoting motions in enzyme catalysis," Proc. Nat. Acad. Sci. USA 99, 2794-2799 (2002).

49. S. Hammes-Schiffer, "Comparison of hydride, hydrogen atom, and proton-coupled electron transfer reactions," Chem. Phys. Chem. 3, 33-42 (2002).

48. S. R. Billeter, S. P. Webb, P. K. Agarwal, T. Iordanov, and S. Hammes-Schiffer, "Hydride transfer in liver alcohol dehydrogenase: Quantum dynamics, kinetic isotope effects, and the role of enzyme motion," J. Am. Chem. Soc. 123, 11262-11272 (2001).

47. M. Kobrak and S. Hammes-Schiffer, "Molecular dynamics simulation of proton-coupled electron transfer in solution," J. Phys. Chem. B 105, 10435-10445 (2001).

46. S. Hammes-Schiffer and S. Billeter, "Hybrid approach for the dynamical simulation of proton and hydride transfer in solution and proteins," Int. Rev. Phys. Chem. 20, 591-616 (2001).

45. I. Rostov and S. Hammes-Schiffer, "Theoretical formulation for electron transfer coupled to multiple protons: Application to amidinium-carboxylate interfaces," J. Chem. Phys. 115, 285-296 (2001).

44. N. Iordanova, H. Decornez, and S. Hammes-Schiffer, "Theoretical study of electron, proton, and proton-coupled electron transfer reactions in iron bi-imidazoline complexes," J. Am. Chem. Soc. 123, 3723-3733 (2001).

43. S. Hammes-Schiffer, "Theoretical perspectives on proton-coupled electron transfer reactions," Acc. Chem. Res. 34, 273-281 (2001).

42. T. Iordanov, S. R. Billeter, S. P. Webb, and S. Hammes-Schiffer, "Partial multidimensional grid generation method for efficient calculation of nuclear wavefunctions," Chem. Phys. Lett. 338, 389-397 (2001).

41. S. R. Billeter, S. P. Webb, T. Iordanov, P. K. Agarwal, and S. Hammes-Schiffer, "Hybrid approach for including electronic and nuclear quantum effects in molecular dynamics simulations of hydrogen transfer reactions in enzymes," J. Chem. Phys. 114, 6925-6936 (2001).

40. S. Hammes-Schiffer, ""Proton-coupled electron transfer," in Electron Transfer in Chemistry Vol. I. Principles, Theories, Methods and Techniques, ed. V. Balzani (Wiley-VCH, Weinheim, 2001).

39. H. Decornez and S. Hammes-Schiffer, "Model proton-coupled electron transfer reactions in solution: Predictions of rates, mechanisms, and kinetic isotope effects," J. Phys. Chem. A 104, 9370-9384 (2000).

38. S.P. Webb and S. Hammes-Schiffer, "Fourier grid Hamiltonian multiconfigurational self-consistent-field: A method to calculate multidimensional hydrogen vibrational wavefunctions," J. Chem. Phys. 113, 5214-5227 (2000).

37. S. P. Webb, P. K. Agarwal, and S. Hammes-Schiffer, "Combining electronic structure methods with the calculation of hydrogen vibrational wavefunctions: Applications to hydride transfer in liver alcohol dehydrogenase," J. Phys. Chem. B 104, 8884-8894 (2000).

36. H. Hu, M. Kobrak, C. Xu, and S. Hammes-Schiffer, "Reaction path Hamiltonian analysis of dynamical solvent effects for a Claisen rearrangement and a Diels Alder reaction," J.Phys. Chem. A 104, 8058-8066 (2000).

35. A. Soudackov and S. Hammes-Schiffer, "Derivation of rate expressions for nonadiabatic proton-coupled electron transfer reactions in solution," J. Chem. Phys. 113, 2385-2396 (2000).

34. P. K. Agarwal, S. P. Webb, and S. Hammes-Schiffer, "Computational studies of the mechanism for proton and hydride transfer in liver alcohol dehydrogenase," J. Am. Chem. Soc. 122 , 4803-4812 (2000).

33. A. V. Soudackov and S. Hammes-Schiffer, "Theoretical study of photoinduced proton-coupled electron transfer through asymmetric salt bridges," J. Am. Chem. Soc. 121, 10598-10607 (1999).

32. J.-Y. Fang and S. Hammes-Schiffer, "Improvement of the internal consistency in trajectory surface hopping," J. Phys. Chem. A 103, 9399-9407 (1999).

31. H. Decornez and S. Hammes-Schiffer, "Effects of model protein environments on the dynamics of proton wires," Israel J. of Chem. 39, 397-407 (1999) (special issue on Proton Solvation and Proton Mobility).

30. A. Soudackov and S. Hammes-Schiffer, "Multistate continuum theory for multiple charge transfer reactions in solution," J. Chem. Phys. 111, 4672-4687 (1999).

29. J.-Y. Fang and S. Hammes-Schiffer, "Comparison of surface hopping and mean field approaches for model proton transfer reactions," J. Chem. Phys. 110, 11166-11175 (1999).

28. H. Decornez, K. Drukker, and S. Hammes-Schiffer, "Solvation and hydrogen-bonding effects on proton wires," J. Phys. Chem. A 103, 2891-2898 (1999).

27. A. V. Soudackov and S. Hammes-Schiffer, "Removal of the double adiabatic approximation for proton-coupled electron transfer reactions in solution", Chem. Phys. Lett. 299, 503-510 (1999).

26. S. Hammes-Schiffer, "Mixed quantum/classical dynamics of hydrogen transfer reactions", J. Phys. Chem. A 102, 10443-10454 (1998).

25. S. Hammes-Schiffer, "Quantum dynamics of multiple modes for reactions in complex systems", Faraday Discuss. 110, 391-406 (1998).

24. S. Hammes-Schiffer, "Mixed quantum/classical dynamics of single proton, multiple proton, and proton-coupled electron transfer reactions in the condensed phase," pp. 73-119 in Comparisons of Classical and Quantum Dynamics, Volume II of Advances in Classical Trajectory Methods, ed. W. L. Hase (JAI Press, Inc., Greenwich, 1998)

23. J.-Y. Fang and S. Hammes-Schiffer, "Time-dependent self-consistent-field dynamics based on a reaction path Hamiltonian. II. Numerical tests", J. Chem. Phys. 109, 7051-7063 (1998).

22. J.-Y. Fang and S. Hammes-Schiffer, "Time-dependent self-consistent-field dynamics based on a reaction path Hamiltonian. I. Theory", J. Chem. Phys. 108, 7085-7099 (1998).

21. K. Drukker, S. de Leeuw, and S. Hammes-Schiffer, "Proton transport along water chains in an electric field ", J. Chem. Phys. 108, 6799-6808 (1998).

20. H. Decornez, K. Drukker, M. M. Hurley, and S. Hammes-Schiffer, "Proton transport along water chains and NADH hydride transfer in solution," Berichte der Bunsengesellschaft für Physikalische Chemie (special issue on hydrogen transfer) 102, 533-543 (1998).

19. J.-Y. Fang and S. Hammes-Schiffer, "Nonadiabatic dynamics for processes involving multiple avoided curve crossings: Double proton transfer and proton-coupled electron transfer reactions ", J. Chem. Phys. 107, 8933-8939 (1997).

18. J.-Y. Fang and S. Hammes-Schiffer, "Excited state dynamics with nonadiabatic transitions for model photoinduced proton-coupled electron transfer reactions ", J. Chem. Phys. 107, 5727-5739 (1997).

17. K. Drukker and S. Hammes-Schiffer, "An analytical derivation of MC-SCF vibrational wavefunctions for the quantum dynamical simulation of multiple proton transfer reactions: Initial application to protonated water chains", J. Chem. Phys. 107, 363-374 (1997).

16. M. M. Hurley and S. Hammes-Schiffer, "Development of a potential surface for simulation of proton and hydride transfer in solution: Application to NADH hydride transfer," J. Phys. Chem. A 101, 3977-3989 (1997).

15. J.-Y. Fang and S. Hammes-Schiffer, "Proton-coupled electron transfer reactions in solution: molecular dynamics with quantum transitions for model systems ", J. Chem. Phys. 106, 8442-8454 (1997).

14. J. Morelli and S. Hammes-Schiffer, "Surface hopping and fully quantum dynamical wavepacket propagation on multiple coupled adiabatic potential surfaces for proton transfer reactions," Chem. Phys. Lett. 269, 161-170 (1997).

13. S. Hammes-Schiffer, "Multiconfigurational molecular dynamics with quantum transitions: Multiple proton transfer reactions," J. Chem. Phys. 105, 2236-2246 (1996).

12. S. Hammes-Schiffer and J.C. Tully, "Nonadiabatic transition state theory and multiple potential energy surface molecular dynamics of infrequent events," J. Chem. Phys. 103, 8528-8537 (1995).

11. S. Hammes-Schiffer and J.C. Tully, "Vibrationally enhanced proton transfer," J. Phys. Chem. 99, 5793-5797 (1995).

10. S. Hammes-Schiffer and J.C. Tully, "Proton transfer in solution: molecular dynamics with quantum transitions," J. Chem. Phys. 101, 4657-4667 (1994).

9. S. Hammes-Schiffer and H.C. Andersen, "A new formulation of the Hartree-Fock- Roothaan method for electronic structure calculations on crystals," J. Chem. Phys. 101, 375-393 (1994).

8. S. Hammes-Schiffer and H.C. Andersen, "Ab initio and semiempirical methods for molecular dynamics simulations based on general Hartree-Fock theory," J. Chem. Phys. 99, 523-532 (1993).

7. S. Hammes-Schiffer and H.C. Andersen, "The advantages of the general Hartree- Fock method for future computer simulation of materials," J. Chem. Phys. 99, 1901-1913 (1993).

6. D.J. Lockhart, S.L. Hammes, S. Franzen, and S.G. Boxer, "Electric field effects on emission line shapes when electron transfer competes with emission: An example from photosynthetic reaction centers," J. Phys. Chem. 95, 2217-2226 (1991).

5. S. Han, Y-C. Ching, S.L. Hammes, and D.L. Rousseau, "Vibrational structure of the formyl group on heme A: Implications on the properties of cytochrome c oxidase," Biophys. J. 60, 45-52 (1991).

4. S.L. Hammes, L. Mazzola, S.G. Boxer, D.F. Gaul, and C.C. Schenck, "Stark spectroscopy of the Rhodobacter sphaeroides reaction center heterodimer mutant," Proc. Natl. Acad. Sci. 87, 5682-5686 (1990).

3. W.S. Warren, S.L. Hammes, and J.L. Bates, "Dynamics of radiation damping in nuclear magnetic resonance," J. Chem. Phys. 91, 5895-5904 (1989).

2. A. Hasenfeld, S.L. Hammes, and W.S. Warren, "Understanding of phase modulation in two-level systems through inverse scattering," Phys. Rev. A 38, 2678-2681 (1988).

1. F. Loaiza, M.A. McCoy, S.L. Hammes, and W.S. Warren, "Selective excitation without phase distortion using self-refocused amplitude- and amplitude/phase modulated pulses," J. Mag. Res. 77, 175-181 (1988).

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