Source: https://www.hammes-schiffer-group.org/publications/
Timestamp: 2019-04-25 06:34:41+00:00

Document:
239. Y. Yang, T. Culpitt, Z. Tao, and S. Hammes-Schiffer, “Stability conditions and local minima in multicomponent Hartree-Fock and density functional theory,” J. Chem. Phys. 149, 084105 (2018).
234. S. Ghosh, A. V. Soudackov, and S. Hammes-Schiffer, “Role of proton diffusion in the kinetics of proton-coupled electron transfer from photoreduced ZnO nanocrystals,” ACS Nano 11, 10295-10302 (2017).
233. S. Ghosh, J. Castillo-Lora, A. V. Soudackov, J. M. Mayer, and S. Hammes-Schiffer, “Theoretical insights into proton-coupled electron transfer from a photoreduced ZnO nanocrystal to an organic radical,” Nano Lett. 17, 5762-5767 (2017).
229. M. T. Huynh, S. J. Mora, M. Villalba, M. E. Tejeda-Ferrari, P. A. Liddell, B. R. Cherry, A.-L. Teillout, C. W. Machan, C. P. Kubiak, D. Gust, T. A. Moore, S. Hammes-Schiffer, and A. L. Moore, “Concerted one-electron two-proton transfer processes in models inspired by the Tyr-His couple of photosystem II,” ACS Cent. Sci. 3, 372-380 (2017).
227. K. R. Brorsen, Y. Yang, M.V. Pak, and S. Hammes-Schiffer, “Is the accuracy of density functional theory for atomization energies and densities in bonding regions correlated?” J. Phys. Chem. Lett. 8, 2076-2081 (2017).
220. K. R. Brorsen, M. V. Pak, and S. Hammes-Schiffer, “Calculation of positron binding energies and electron-positron annihilation rates for atomic systems with the reduced explicitly correlated Hartree-Fock method within the nuclear-electronic orbital framework,” J. Phys. Chem. A 121, 515-522 (2017).
219. M. Horitani, A. R. Offenbacher, C. M. Carr, T. Yu, V. Hoeke, G. E. Cutsail III, S. Hammes-Schiffer, J. P. Klinman, and B. M. Hoffman, “13C ENDOR spectroscopy of lipoxygenase-substrate complexes reveals the structural basis for C-H activation by tunneling,” J. Am. Chem. Soc. 139, 1984-1997 (2017).
216. A. V. Soudackov and S. Hammes-Schiffer, “Proton-coupled electron transfer reactions: Analytical rate constants and case study of kinetic isotope effects in lipoxygenase,” Farad. Discuss. 195, 171-189 (2016).
214. S. Zhang, D. R. Stevens, P. Goyal, J. L. Bingaman, P. C. Bevilacqua, and S. Hammes-Schiffer, “Assessing the potential effects of active site Mg2+ ions in the glmS ribozyme-cofactor complex,” J. Phys. Chem. Lett. 7, 3984-3988 (2016).
213. T. Yu, A. V. Soudackov, and S. Hammes-Schiffer, “Computational insights into five- versus six-coordinate iron center in ferrous soybean lipoxygenase,” J. Phys. Chem. Lett. 7, 3429-3433 (2016).
210. M. N. Ucisik, P. C. Bevilacqua, and S. Hammes-Schiffer, “Molecular dynamics study of twister ribozyme: Role of Mg2+ ions and the hydrogen-bonding network in the active site,” Biochemistry 55, 3834-3846 (2016).
206. C. W. Anson, S. Ghosh, S. Hammes-Schiffer, and S. S. Stahl, “Co(salophen)-catalyzed aerobic oxidation of para-hydroquinone: Mechanism and implications for aerobic oxidation catalysis,” J. Am. Chem. Soc. 138, 4186–4193 (2016).
204. S. Kennedy, P. Goyal, M. Kozar, H. Yennawar, S. Hammes-Schiffer, and B. Lear, “Effect of protonation upon electron coupling in the mixed valence and mixed protonated complex, [Ni(2,3-pyrazinedithiol)2],” Inorg. Chem. 55, 1433-1445 (2016).
203. S. Raugei, M. L. Helm, S. Hammes-Schiffer, A. M. Appel, M. O’Hagan, E. S. Wiedner, and R. M. Bullock, “Experimental and computational mechanistic studies guiding the rational design of molecular electrocatalysts for production and oxidation of hydrogen,” Inorg. Chem. 55, 445-460 (2016).
202. B. H. Solis, A. G. Maher, D. K. Dogutan, D. G. Nocera, and S. Hammes-Schiffer, “Nickel phlorin intermediate formed by proton-coupled electron transfer in hydrogen evolution mechanism,” Proc. Nat. Acad. Sci. USA 113, 485-492 (2016).
201. G. M. Chambers, M. T. Huynh, Y. Li, S. Hammes-Schiffer, T. B. Rauchfuss, E. Reijerse, and W. Lubitz, “Models of the Ni-L and Ni-SIastates of the [NiFe]-hydrogenase active site,” Inorg. Chem. 55, 419-431 (2016).
198. M. N. Ucisik and S. Hammes-Schiffer, “Relative binding free energies of adenine and guanine to damaged and undamaged DNA in human DNA polymerase η: Clues for fidelity and overall efficiency,” J. Am. Chem. Soc. 137, 13240-13243 (2015).
196. Y. Yang, I. Kylänpää, N. M. Tubman, J. T. Krogel, S. Hammes-Schiffer, and D. Ceperley, “How large are nonadiabatic effects in atomic and diatomic systems?” J. Chem. Phys. 143, 124308 (2015).
194. S. Hammes-Schiffer, “Proton-coupled electron transfer: Moving together and charging forward,” J. Am. Chem. Soc. 137, 8860-8871 (2015).
189. P. Goyal, C. A. Schwerdtfeger, A. V. Soudackov, and S. Hammes-Schiffer, “Nonadiabatic dynamics of photoinduced proton-coupled electron transfer in a solvated phenol-amine complex,” J. Phys. Chem. B 119, 2758-2768 (2015) .
188. S. Zhang, A. Ganguly, P. Goyal, J. Bingaman, P. C. Bevilacqua, and S. Hammes-Schiffer, “Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: Quantum mechanical/molecular mechanical free energy simulations,” J. Am. Chem. Soc. 137, 784-798 (2015).
185. C. T. Liu, K. Francis, J. Layfield, X. Huang, S. Hammes-Schiffer, A. Kohen, and S. J. Benkovic, “Escherichia coli dihydrofolate reductase catalyzed proton and hydride transfers: Temporal order and the roles of Asp27 and Tyr100,” Proc. Nat. Acad. Sci. USA 111, 18231-18236 (2014).
178. S. Hu, S. C. Sharma, A. D. Scouras, A. V. Soudackov, C. A. M. Carr, S. Hammes-Schiffer, T. Alber, and J.P. Klinman, “Extremely elevated room-temperature kinetic isotope effects quantify the critical role of barrier width in enzymatic C-H activation,” J. Am. Chem. Soc. 136, 8157-8160 (2014).
175. J. P. Schwans, P. Hanoian, B. J. Lengerich, F. Sunden, A. Gonzalez, Y. Tsai, S. Hammes-Schiffer, and D. Herschlag, “Experimental and computational mutagenesis to investigate the positioning of a general base within an enzyme active site,” Biochemistry 53, 2541-2555 (2014).
172. S. Chakraborty, J. Reed, M. Ross, M. J. Nilges, I. D. Petrik, S. Ghosh, S. Hammes-Schiffer, J. T. Sage, Y. Zhang, C. E. Schulz, and Y. Lu, “Spectroscopic and computational study of a nonheme iron nitrosyl center in a biosynthetic model of nitric oxide reductase,” Angew. Chem. Int. Ed. 53, 2417-2421 (2014).
167. A. Sirjoosingh, M. V. Pak, C. Swalina, and S. Hammes-Schiffer, “Reduced explicitly correlated Hartree-Fock approach within the nuclear-electronic orbital framework: Theoretical formulation,” J. Chem. Phys. 139, 034102 (2013).
161. S. Hammes-Schiffer, “Catalytic efficiency of enzymes: A theoretical analysis,” Biochemistry 52, 2012-2020 (2013).
160. C. Ko, B. H. Solis, A. V. Soudackov, and S. Hammes-Schiffer, “Photoinduced Proton-Coupled Electron Transfer of Hydrogen-Bonded p‐Nitrophenylphenol−Methylamine Complex in Solution,” J. Phys. Chem. B 117, 316-325 (2013).
153. S. Horvath, L. E. Fernandez, A. V. Soudackov, and S. Hammes-Schiffer, “Insights into proton-coupled electron transfer mechanisms of electrocatalytic H2 oxidation and production,” Proc. Natl. Acad. Sci. USA 109, 15663-15668 (2012).
152. S. Hammes-Schiffer, “Proton-coupled electron transfer: Classification scheme and guide to theoretical methods,” Energy and Environ. Sci. 5, 7696-7703 (2012).
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).
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).
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).
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).
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).
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).
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).
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).
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,” Coord. Chem. Rev. 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).
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).
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).
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).
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,” Annu. Rev. Biochem. 75, 519-541 (2006).
77. E. Hatcher, A. Soudackov, S. Hammes-Schiffer, “Comparison of dynamical aspects of nonadiabatic electron, proton, and proton-coupled electron transfer reactions,” Chem. Phys. 319, 93-100 (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. Natl. Acad. Sci. USA 102, 6807-6812 (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, 014505 (2005).
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,” Chem. Phys. 304, 227-236 (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).
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).
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 role of enzyme motion,” J. Am. Chem. Soc. 123, 11262-11272 (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).
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).
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).
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).
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).
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).
20. H. Decornez, K. Drukker, M. M. Hurley, and S. Hammes-Schiffer, “Proton transport along water chains and NADH hydride transfer in solution,” Ber. Bunsenges. Phys. Chem. (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).
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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