2024

375. R. E. Warburton, A. V. Soudackov, and S. Hammes-Schiffer, “Interfacial proton-coupled electron transfer via localized trap states on metal oxide surfaces,” J. Phys. Chem. C (in press). DOI: 10.1021/acs.jpcc.4300458

374. N. E. Gentry, A. Kurimoto, K. Cui, J. L. Cleron, C. M. Xiang, S. Hammes-Schiffer, and J. M. Mayer, “Hydrogen on colloidal gold nanoparticles,” J. Am. Chem. Soc. (in press). 

373. J. L. Alvarez-Hernandez, X. Zhang, K. Cui, A. P. Deziel, S. Hammes-Schiffer, N. Hazari, N. Piekut, and M. Zhong, “Long-range electrostatic effects from intramolecular Lewis acid binding influence the redox properties of cobalt-porphyrin complexes,” Chem. Sci. (in press). DOI: 10.1039/D3SC06177A

372. E. Lambros, J. H. Fetherolf, S. Hammes-Schiffer, and X. Li, “A many-body perspective of nuclear quantum effects in aqueous clusters,” J. Phys. Chem. Lett. 15, 4070-4075 (2024). DOI: 10.1021/acs.jpclett.4c00439

371. A. Nilsen-Moe, C. R. Reinhardt, P. Huang, H. Agarwala, R. Lopes, M. Lasagna, S. Glover, S. Hammes-Schiffer, C. Tommos, and L. Hammarström, “Switching the proton-coupled electron transfer mechanism for non-canonical tyrosine residues in a de novo protein,” Chem. Sci. 15, 3957-3970 (2024). DOI: 10.1039/d3sc05450k

370. J. Zhong, A. V. Soudackov, and S. Hammes-Schiffer, “Probing nonadiabaticity of proton-coupled electron transfer in ribonucleotide reductase,” J. Phys. Chem. Lett. 15, 1686-1693 (2024). DOI: 10.1021/acs.jpclett.3c03552

369. D. Konstantinovsky, T. Santiago, M. Tremblay, G. J. Simpson, S. Hammes-Schiffer, and E. C. Y. Yan, “Theoretical basis for interpreting heterodyne chirality-selective sum frequency generation spectra of water,” J. Chem. Phys. 160, 055102 (2024). DOI: 10.1063/5.0181718

368. T. E. Li, E. Paenurk, and S. Hammes-Schiffer, “Squeezed protons and infrared plasmonic resonance energy transfer,” J. Phys. Chem. Lett. 15, 751-757 (2024). DOI: 10.1021/acs.jpclett.3c03112

367. M. C. Kessinger, J. Xu, K. Cui, Q. Loague, A. V. Soudackov, S. Hammes-Schiffer, and G. J. Meyer, “Direct evidence for a sequential electron transfer–proton transfer mechanism in the PCET reduction of a metal hydroxide catalyst,” J. Am. Chem. Soc. 146, 1742-1747 (2024). DOI: 10.1021/jacs.3c10742

2023

366. J. Xu, R. Zhou, V. Blum, T. E. Li, S. Hammes-Schiffer, and Y. Kanai, “First-principles approach for coupled quantum dynamics of electrons and protons in heterogeneous systems,” Phys. Rev. Lett. 131, 238002 (2023). DOI: 10.1103/PhysRevLett.131.238002

365. E. Lambros, B. Link, M. Chow, F. Lipparini, S. Hammes-Schiffer, and X. Li, “Assessing implicit and explicit polarizable solvation models for nuclear-electronic orbital systems: Quantum proton polarization and solvation energetics,” J. Phys. Chem. A 127, 9322-9333 (2023). DOI: 10.1021/acs.jpca.3c03153

364. K. Cui, A. V. Soudackov, and S. Hammes-Schiffer, “Modeling the weak pH dependence of proton-coupled electron transfer for tryptophan derivatives,” J. Phys. Chem. Lett. 14, 10980-10987 (2023). DOI: 10.1021/acs.jpclett.3c02282

363. M. Chow, T. E. Li, and S. Hammes-Schiffer, “Nuclear-electronic orbital quantum mechanical/molecular mechanical real-time dynamics,” J. Phys. Chem. Lett. 14, 9556-9562 (2023). DOI: 10.1021/acs.jpclett.3c02275

362. W. R. Lake, J. Meng, J. M. Dawlaty, T. Lian, and S. Hammes-Schiffer, “Electro-inductive effect dominates vibrational frequency shifts of conjugated probes on gold electrodes,” J. Am. Chem. Soc. 145, 22548-22554 (2023). DOI: 10.1021/jacs.3c07489

361. A. Liu, T. Zhang, S. Hammes-Schiffer, and X. Li, “Multicomponent Cholesky decomposition: Application to nuclear-electronic orbital theory,” J. Chem. Theory Comput. 19, 6255-6262 (2023). DOI: 10.1021/acs.jctc.3c00686

360. X. Jia, K. Cui, J. L. Alvarez-Hernandez, C. L. Donley, A. Gang, S. Hammes-Schiffer, N. Hazari, S. Jeon, J. M. Mayer, H. S. Nedzbala, B. Shang, E. A. Stach, E. Stewart-Jones, H. Wang, and A. Williams, “Synthesis and surface attachment of molecular Re(I) hydride species with silatrane functionalized bipyridyl ligands,” Organometallics 42, 2238-2250 (2023). DOI: 10.1021/acs.organomet.3c00235

359. K. Cui, A. V. Soudackov, M. C. Kessinger, J. Xu, G. J. Meyer, and S. Hammes-Schiffer, “General kinetic model for pH dependence of proton-coupled electron transfer: Application to an electrochemical water oxidation system,” J. Am. Chem. Soc. 145, 19321-29332 (2023). DOI: 10.1021/jacs.3c04927

358. T. E. Li and S. Hammes-Schiffer, “Nuclear-electronic orbital quantum dynamics of plasmon-driven H2 photodissociation,” J. Am. Chem. Soc. 145, 18210-18214 (2023). DOI: 10.1021/jacs.3c04927

357. M. Secor, A. V. Soudackov, and S. Hammes-Schiffer, “Density matrix based features as descriptors for oxygen reduction and evolution catalysts,” J. Phys. Chem. C 127, 15246-15256 (2023). DOI: 10.1021/acs.jpcc.3c03392

356. R. Feng, Y. Chen, X. Zhang, B. J. G. Rousseau, P. Gao, P. Chen, S. T. Mergelsberg, L. Zhong, A. Hollas, Y. Liang, V. Murugesan, Q. Huang, S. Hammes-Schiffer, Y. Shao, and W. Wang, “Proton-regulated alcohol oxidation for high-capacity ketone-based flow battery anolyte,” Joule 7, 1609-1622 (2023). DOI: 10.1016/j.joule.2023.06.013

355. M. Chow, E. Lambros, X. Li, and S. Hammes-Schiffer, “Nuclear-electronic orbital QM/MM approach: Geometry optimizations and molecular dynamics,” J. Chem. Theory Comput. 19, 3839-3848 (2023). DOI: 10.1021/acs.jctc.3c00361

354. J. A. Dickinson, Q. Yu, and S. Hammes-Schiffer, “Generalized nuclear-electronic orbital multistate density functional theory for multiple proton transfer processes,” J. Phys. Chem. Lett. 14, 6170-6178 (2023). DOI: 10.1021/acs.jpclett.3c01422

353. D. Konstantinovsky, E. C. Y. Yan, and S. Hammes-Schiffer, “Characterizing interfaces by Voronai tessellation,” J. Phys. Chem. Lett. 14, 5260-5266 (2023). DOI: 10.1021/acs.jpclett.3c01159

352. E. C. Y. Yan, E. A. Perets, D. Konstantinovsky, and S. Hammes-Schiffer, “Detecting interplay of chirality, water, and interfaces for elucidating biological functions,” Acc. Chem. Res. 56, 1494-1504 (2023). DOI: 10.1021/acs.accounts.3c00088

351. B. J. G. Rousseau, A. V. Soudackov, R. R. Tuttle, M. M. Reynolds, R. G. Finke, and S. Hammes-Schiffer, “Computational insights into the mechanism of nitric oxide generation from S-nitrosoglutathione catalyzed by a copper metal-organic framework, J. Am. Chem. Soc. 145, 10285-10294 (2023). DOI: 10.1021/jacs.3c01569

350. P. Hutchison, C. J. Kaminsky, Y. Surendranath, and S. Hammes-Schiffer, “Concerted PCET to a graphite adsorbed metalloporphyrin occurs by band-to-bond electron redistribution,” ACS Cent. Sci. 9, 927-936 (2023). DOI: 10.1021/acscentsci.3c00186

349. E. Lambros, B. Link, M. Chow, S. Hammes-Schiffer, and X. Li, “Solvent induced proton polarization within the nuclear-electronic orbital framework,” J. Phys. Chem. Lett. 14, 2990-2995 (2023). DOI: 10.1021/acs.jpclett.3c00471

348. T. E. Li and S. Hammes-Schiffer, “Electronic Born-Oppenheimer approximation in nuclear-electronic orbital dynamics,” J. Chem. Phys. 158, 114118 (2023). DOI: 10.1063/5.0142007

347. S. Menachekanian, M. Voegtle, R. E. Warburton, S. Hammes-Schiffer, and J. M. Dawlaty, “Inductive effect alone cannot explain Lewis adduct formation and dissociation at electrode interfaces,” J. Am. Chem. Soc. 145, 5759-5768 (2023). DOI: 10.1021/jacs.2c12370

346. S. Hammes-Schiffer, “Exploring proton-coupled electron transfer at multiple scales,” Nat. Comp. Sci. 3, 291-300 (2023). DOI: 10.1038/s43588-023-00422-5

345. D. Konstantinovsky, E. A. Perets, T. Santiago, K. Olesen, Z. Wang, A. V. Soudackov, E. C. Y. Yan, S. Hammes-Schiffer, “Design of an electrostatic frequency map for the NH stretch of the protein backbone and application to chiral sum frequency generation spectroscopy,” J. Phys. Chem. B 127, 2418-2429 (2023). DOI: 10.1021/acs.jpcb.3c00217

344. J. Zhong, C. R. Reinhardt, and S. Hammes-Schiffer, “Direct proton-coupled electron transfer between interfacial tyrosines in ribonucleotide reductase,” J. Am. Chem. Soc.145, 4784-4790 (2023). DOI: 10.1021/jacs.2c13615

343. A. Mohamed, S. C. Edington, M. Secor, J. R. Breton, S. Hammes-Schiffer, and M. A. Johnson, “Spectroscopic characterization of the divalent metal docking motif to isolated cyanobenzoate: Direct observation of tridentate binding to ortho-cyanobenzoate and implications for the CN response,” J. Phys. Chem. A 127, 1413-1421 (2023). DOI: 10.1021/acs.jpca.2c07658

342. T. E. Li and S. Hammes-Schiffer, “QM/MM modeling of vibrational polariton induced energy transfer and chemical dynamics,” J. Am. Chem. Soc. 145, 377-384 (2023). DOI: 10.1021/jacs.2c10170

341. Y. Yang, R. G. Agarwal, P. Hutchison, R. Rizo, A. V. Soudackov, X. Lu, E. Herrero, J. M. Feliu, S. Hammes-Schiffer, J. M. Mayer, and H. D. Abruña, “Inverse kinetic isotope effects in the oxygen reduction reaction at platinum single crystals,” Nat. Chem. 15, 271-277 (2023). DOI: 10.1038/s41557-022-01084-y

2022

340. Q. Yu, S. Roy, and S. Hammes-Schiffer, “Nonadiabatic dynamics of hydrogen tunneling with nuclear-electronic orbital multistate density functional theory,” J. Chem. Theory Comput. 18, 7132-7141 (2022). DOI: 10.1021/acs.jctc.2c00938

339. Q. Yu and S. Hammes-Schiffer, “Multidimensional quantum dynamical simulation of infrared spectra under polaritonic vibrational strong coupling,” J. Phys. Chem. Lett. 13, 11253-11261 (2022). DOI: 10.1021/acs.jpclett.2c03245

338. P. Hutchison, R. E. Warburton, Y. Surendranath, and S. Hammes-Schiffer, “Correlation between electronic descriptor and proton-coupled electron transfer thermodynamics in doped graphite-conjugated catalysts,” J. Phys. Chem. Lett. 13, 11216-11222 (2022). DOI: 10.1021/acs.jpclett.2c03278

337. M. Kessinger, A. V. Soudackov, J. Schneider, R. E. Bangle, S. Hammes-Schiffer, and G. J. Meyer, “Reorganization energies for interfacial proton-coupled electron transfer to a water oxidation catalyst,” J. Am. Chem. Soc. 144, 20514-20524 (2022). DOI: 10.1021/jacs.2c09672

336. A. Liu, M. Chow, A. Wildman, M. J. Frisch, S. Hammes-Schiffer, and X. Li, “Simultaneous optimization of nuclear-electronic orbitals,” J. Phys. Chem. A 126, 7033-7039 (2022). DOI: 10.1021/acs.jpca.2c05172

335. D. Konstantinovsky, E. A. Perets, T. Santiago, L. Velarde, S. Hammes-Schiffer, and E. C. Y. Yan, “Detecting first hydration shell structure around biomolecules at interfaces,” ACS Cent. Sci. 8, 1404-1414 (2022). DOI: 10.1021/acscentsci.2c00702

334. E. Odella, M. Secor, E. A. R. Cruz, W. D. Guerra, M. N. Urrutia, P. A. Liddell, T. A. Moore, G. F. Moore, S. Hammes-Schiffer, and A. L. Moore, “Managing the redox potential of PCET in Grotthuss-type proton wires,” J. Am. Chem. Soc. 144, 15672-15679 (2022). DOI: 10.1021/jacs.2c05820

333. P. Hutchison, P. S. Rice, R. E. Warburton, S. Raugei, and S. Hammes-Schiffer, “Multilevel computational studies reveal importance of axial ligand for oxygen reduction reaction on Fe-N-C materials,” J. Am. Chem. Soc. 144, 16524-16534 (2022). DOI: 10.1021/jacs.2c05779

332. F. Pavošević and S. Hammes-Schiffer, “Triple electron-electron-proton excitations and second-order approximations in nuclear-electronic orbital coupled cluster methods,” J. Chem. Phys. 157, 074104 (2022). DOI: 10.1063/5.0106173

331. B. P. Rimgard, Z. Tao, G. A. Parada, L. F. Cotter, S. Hammes-Schiffer, J. M. Mayer, and L. Hammarström, “Proton-coupled energy transfer in molecular triads,” Science 377, 742-747 (2022). DOI: 10.1126/science.abq5173

330. C. R. Reinhardt, D. Konstantinovsky, A. V. Soudackov, and S. Hammes-Schiffer, “Kinetic model for reversible radical transfer in ribonucleotide reductase,” Proc. Nat. Acad. Sci. USA 119, e2202022119 (2022). DOI: 10.1073/pnas.2202022119

329. J. H. Fetherolf, F. Pavošević, Z. Tao, and S. Hammes-Schiffer, “Multicomponent orbital optimized perturbation theory with density fitting: Anharmonic zero-point energies in protonated water clusters,” J. Phys. Chem. Lett. 13, 5563-5570 (2022). DOI: 10.1021/acs.jpclett.2c01357

328. J. Xu, R. Zhou, Z. Tao, C. Malbon, V. Blum, S. Hammes-Schiffer, and Y. Kanai, “Nuclear-electronic orbital approach to quantization of protons in periodic electronic structure calculations,” J. Chem. Phys. 156, 224111 (2022). DOI: 10.48550/arXiv.2205.06328

327. T. E. Li, Z. Tao, and S. Hammes-Schiffer, “Semiclassical real-time nuclear-electronic orbital approach for molecular polaritons: Unified theory of electronic and vibrational strong couplings,” J. Chem. Theory Comput. 18, 2774–2784 (2022). DOI: 10.1021/acs.jctc.2c00096

326. T. E. Li, A. Nitzan, S. Hammes-Schiffer, and J. E. Subotnik, “Quantum simulations of vibrational strong coupling via path integrals,” J. Phys. Chem. Lett. 13, 3890-3895 (2022). DOI: 10.48550/arXiv.2203.03001

325. J. Zhong, C. R. Reinhardt, and S. Hammes-Schiffer, “Role of water in proton-coupled electron transfer between tyrosine and cysteine in ribonucleotide reductase,” J. Am. Chem. Soc. 144, 7208-7214 (2022). DOI: 10.1021/jacs.1c13455

324. F. Pavošević, S. Hammes-Schiffer, A. Rubio, and J. Flick, “Cavity-modulated proton transfer reactions,” J. Am. Chem. Soc. 144, 4995-5002 (2022).DOI: 10.1021/jacs.1c13201

323. R. E. Warburton, A. V. Soudackov, and S. Hammes-Schiffer, “Theoretical modeling of electrochemical proton-coupled electron transfer,” Chem. Rev. 122, 10599-10650 (2022). DOI: 10.1021/acs.chemrev.1c00929

322. S. Hammes-Schiffer, “Theoretical perspectives on non-Born-Oppenheimer effects in chemistry,” Phil. Trans. A. 380, 20200377 (2022). DOI: 10.1098/rsta.2020.0377

321. Y. Yang et al. “Electrocatalysis in alkaline media and alkaline membrane-based energy technologies,” Chem. Rev. 122, 6117-6321 (2022). DOI: 10.1021/acs.chemrev.1c00331

320. A. Wildman, Z. Tao, L. Zhao, S. Hammes-Schiffer, and X. Li, “Solvated nuclear-electronic orbital structure and dynamics,” J. Chem. Theory Comp. 18, 1340-1346 (2022). DOI: 10.1021/acs.jctc.1c01285

319. Q. Yu, P. E. Schneider, and S. Hammes-Schiffer, “Analytical gradients for nuclear-electronic orbital multistate density functional theory: Geometry optimizations and reaction paths,” J. Chem. Phys. 156, 114115 (2022). DOI: 10.1063/5.0085344

318. B. Koronkiewicz, E. R. Sayfutyarova, S. C. Coste, B. Q. Mercado, S. Hammes-Schiffer, and J. M. Mayer, “Structural and thermodynamic effects on the kinetics of C–H oxidation by multisite proton-coupled electron transfer in fluorenyl benzoates,” J. Org. Chem. 87, 2997-3006 (2022). DOI: 10.1021/acs.joc.1c02834

2021

317. M. T. Bender, R. Warburton, S. Hammes-Schiffer, and K.-S. Choi, “Understanding hydrogen atom and hydride transfer processes during electrochemical alcohol and aldehyde oxidation,” ACS Catal. 11, 15110-15124 (2021).DOI: 10.1021/acscatal.1c04163

316. Z. Tao, Q. Yu, S. Roy, and S. Hammes-Schiffer, “Direct dynamics with nuclear-electronic orbital density functional theory,” Acc. Chem. Res. 54, 4131-4141 (2021). DOI: 10.1021/acs.accounts.1c00516

315. D. Konstantinovsky, E. A. Perets, E. C. Y. Yan, and S. Hammes-Schiffer, “Simulation of the chiral sum frequency generation response of supramolecular structures requires vibrational couplings,” J. Phys. Chem. B 125, 12072-12081 (2021). DOI: 10.1021/acs.jpcb.1c06360

314.  A. J. Veenis, P. Li, A. V. Soudackov, S. Hammes-Schiffer, and P. C. Bevilacqua, “Investigation of the pKa of the nucleophilic O2′ of the hairpin ribozyme,” J. Phys. Chem. B 125, 11869-11883 (2021). DOI: 10.1021/acs.jpcb.1c06546

313. M. Secor, A. V. Soudackov, and S. Hammes-Schiffer, “Artificial neural networks as propagators in quantum dynamics,” J. Phys. Chem. Lett. 12, 10654-10662 (2021). DOI: 10.1021/acs.jpclett.1c03117

312. E. Odella, M. Secor, M. Elliot, T. L. Groy, T. A. Moore, S. Hammes-Schiffer, and A. L. Moore, “Multi PCET in symmetrically substituted benzimidazoles,” Chem. Sci. 12, 12667-12675 (2021). DOI: 10.1039/D1SC03782J

311. P. Hutchison, R. E. Warburton, A. V. Soudackov, and S. Hammes-Schiffer, “Multicapacitor approach to interfacial proton-coupled electron transfer thermodynamics at constant potential,” J. Phys. Chem. C 125, 21891-21901 (2021). DOI: 10.1021/acs.jpcc.1c04464

310. R. E. Warburton, J. M. Mayer, and S. Hammes-Schiffer, “Proton-coupled defects impact O—H bond dissociation free energies on metal oxide surfaces,” J. Phys. Chem. Lett. 12, 9761-9767 (2021). DOI: 10.1021/acs.jpclett.1c02837

309. Epifanovsky et al. (Q-Chem collaboration), “Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package,” J. Chem. Phys. 155, 084801 (2021). DOI: 10.1063/5.0055522

308. Z. Tao,  S. Roy, P. E. Schneider, F. Pavošević, and S. Hammes-Schiffer, “Analytical gradients for nuclear-electronic orbital time-dependent density functional theory: Excited state geometry optimizations and adiabatic excitation energies,” J. Chem. Theory Comp.17, 5110-5122 (2021) . DOI: 10.1021/acs.jctc.1c00454

307. D. Sun, A. K. Harshan, J. Pécaut, S. Hammes-Schiffer, C. Costentin, and V. Artero, “Hydrogen evolution mediated by cobalt diimine-dioxime complexes: Insights into the role of the ligand acid/base functionalities,” ChemElectroChem 8, 2671-2679 (2021). DOI: 10.1002/celc.202100413

306. S. Hammes-Schiffer, “Nuclear-electronic orbital methods: Foundations and prospects,” J. Chem. Phys. 143, 8381-8390 (2021). DOI: 10.1063/5.0053576

305. S. Sarkar, A. Maitra, W. R. Lake, R. E. Warburton, S. Hammes-Schiffer, and J. M. Dawlaty, “Mechanistic insights about electrochemical proton-coupled electron transfer derived from a vibrational probe,” J. Am. Chem. Soc. 143, 8381-8390 (2021). DOI: 10.1021/jacs.1c01977

304. S. P. Heins, P. E. Schneider, A. L Speelman, S. Hammes-Schiffer, and A. M. Appel, “Electrocatalytic oxidation of alcohol with cobalt triphosphine complexes,” ACS Catalyl. 11, 6384-6389 (2021). DOI: 10.1021/acscatal.1c00781

303. S. Hammes-Schiffer and G. Galli, “Integration of theory and experiment in the modelling of heterogeneous electrocatalysis,” Nat. Energy 6700-705 (2021). DOI: 10.1038/s41560-021-00827-4

302. F. Pavošević and S. Hammes-Schiffer, “Multicomponent unitary coupled cluster and equation-of-motion for quantum computation,” J. Chem. Theory Comp. 17, 3252-3258 (2021). DOI: 10.1021/acs.jctc.1c00220

301. C. R. Reinhardt, E. Sayfutyarova, J. Zhong, and S. Hammes-Schiffer, “Glutamate mediates proton-coupled electron transfer between tyrosines 730 and 731 in Escherichia coli ribonucleotide reductase,” J. Am. Chem. Soc. 143, 6054-6059 (2021). DOI: 10.1021/jacs.1c02152

300. L. Zhao, A. Wildman, F. Pavošević, J. C. Tully, S. Hammes-Schiffer, and X. Li, “Excited state intramolecular proton transfer with nuclear-electronic orbital Ehrenfest dynamics,” J. Phys. Chem. Lett. 12, 3497-3502 (2021). DOI: 10.1021/acs.jpclett.1c00564

299. M. Secor, A. V. Soudackov, and S. Hammes-Schiffer, “Artificial neural networks as mappings between proton potentials, wave functions, densities, and energy levels,” J. Phys. Chem. Lett. 12, 2206-2212 (2021). DOI: 10.1021/acs.jpclett.1c00229

298. F. Pavošević, Z. Tao, and S. Hammes-Schiffer, “Multicomponent coupled cluster singles and doubles with density fitting: Protonated water tetramers with quantized protons,” J. Phys. Chem. Lett. 12, 1631-1637 (2021). DOI: 10.1021/acs.jpclett.0c03771

297. P. E. Schneider, Z. Tao,  F. Pavošević, E. Epifanovsky, X. Feng, and S. Hammes-Schiffer, “Transition states, reaction paths, and thermochemistry using the nuclear-electronic orbital analytic Hessian,” J. Chem. Phys. 154, 054108 (2021). DOI: 10.1063/5.0033540

296. A. Barragan, A. V. Soudackov, Z. Luthey-Schulten, S. Hammes-Schiffer, K. Schulten, and I. Solov’yov, “Theoretical description of the primary proton-coupled electron transfer reaction in the cytochrome bc1 complex,” J. Am. Chem. Soc. 143, 715-723 (2021). DOI: 10.1021/jacs.0c07799

295. C.  R. Reinhardt, R. Sequeira, C. Tommos, and S. Hammes-Schiffer, “Computing proton-coupled redox potentials of fluorotyrosines in a protein environment,” J. Phys. Chem. B. 125, 128-136 (2021). DOI: 10.1021/acs.jpcb.0c09974

2020

294. W. D. Guerra, E. Odella, M. Secor, J. J. Goings, M. N. Urrutia, B. L. Wadsworth, M. Gervaldo, L. E. Sereno, T. A. Moore, G. F. Moore, S. Hammes-Schiffer, and A. L. Moore, “The role of intact hydrogen-bond networks in multiproton-coupled electron transfer,” J. Am. Chem. Soc. 142, 21842-21851 (2020). DOI: 10.1021/jacs.0c10474

293. E. A. Perets, D. Konstantinovsky, L. Fu, J. Chen, H.-F. Wang, S. Hammes-Schiffer, and E. C.-Y. Yan, “Mirror-image antiparallel β-sheets organize water molecules into superstructures with opposite chirality,” Proc. Nat. Acad. Sci. USA 11732902-32909 (2020)DOI: 10.1073/pnas.2015567117

292. M. T. Bender, Y. C. Lam, S. Hammes-Schiffer, and K.-S. Choi, “Unraveling two pathways for electrochemical alcohol and aldehyde oxidation on NiOOH,” J. Am. Chem. Soc. 142, 21538-21547 (2020). DOI: 10.1021/jacs.0c10924

291. L. Zhao, A. Wildman, Z. Tao, P. Schneider, S. Hammes-Schiffer, and X. Li, “Nuclear-electronic orbital Ehrenfest dynamics,” J. Chem. Phys. 153, 224111 (2020). DOI: 10.1063/5.0031019

290. Y.-C. Lam, A. V. Soudackov, and S. Hammes-Schiffer, “Theory of electrochemical proton-coupled electron transfer in diabatic vibronic representation: Application to proton discharge on metal electrodes in alkaline solution,” J. Phys. Chem. C 124, 27309-27322 (2020). DOI: 10.1021/acs.jpcc.0c08096

289. R. E. Warburton, P. Hutchison, M. N. Jackson, M. L. Pegis, Y. Surendranath, and S. Hammes-Schiffer, “Interfacial field-driven proton-coupled electron transfer at graphite-conjugated organic acids,” J. Am. Chem. Soc. 142, 20855-20864 (2020). DOI: 10.1021/jacs.0c10632

288. Q. Yu and S. Hammes-Schiffer, “Nuclear-electronic orbital multistate density functional theory,” J. Phys. Chem. Lett. 11, 10106-10113 (2020). DOI: 10.1021/acs.jpclett.0c02923

287. J. J. Goings, P. Li, Q. Zhu, and S. Hammes-Schiffer, “Formation of an unusual glutamine tautomer in a blue-light using flavin photocycle characterizes the light-adapted state,” Proc. Nat. Acad. Sci. USA  117, 26626-26632 (2020). DOI: 10.1073/pnas.2016719117

286. J. J. Goings and S. Hammes-Schiffer, “Nonequilibrium dynamics of proton-coupled electron transfer in proton wires: Concerted but asynchronous mechanisms,” ACS Cent. Sci. 6, 1594-1601 (2020). DOI: 10.1021/acscentsci.0c00756

285. K. Sakaushi, T. Kumeda, S. Hammes-Schiffer, M. M. Melander, and O. Sugino, “Advances and challenges for experiment and theory for multi-electron multi-proton at electrified solid-liquid interfaces,” Phys. Chem. Chem. Phys. 22, 19401-19442 (2020). DOI: 10.1039/D0CP02741C

284. E. R. Sayfutyarova and S. Hammes-Schiffer, “Excited state molecular dynamics of photoinduced proton-coupled electron transfer in anthracene-phenol-pyridine triads,” J. Phys. Chem. Lett. 11, 7109-7115 (2020). DOI: 10.1021/acs.jpclett.0c02012

283. A. Proppe, Y. Li, A. Aspuru-Guzik, C. Berlinguette, C. Chang, R. Cogdell, A. Doyle, J. Flick, N. Gabor, R. van Grondelle, S. Hammes-Schiffer, S. Jaffer, S. Kelley, M. Leclerc, K. Leo, T. Mallouk, P. Narang, G. Schlau-Cohen, G. Scholes, A. Vojvodic, V. W. W. Yam, J. Yang, and E. Sargent, “Bioinspiration in light harvesting and catalysis,” Nat. Rev. Mater. 5, 828-846 (2020). DOI: 10.1038/s41578-020-0222-0

282. F. Pavošević, Z. Tao, T. Culpitt, L. Zhao, X. Li, and S. Hammes-Schiffer, “Frequency and time domain nuclear-electronic orbital equation-of-motion coupled cluster methods: Combination bands and electronic-protonic double excitations,” J. Phys. Chem. Lett. 11, 6435-6442 (2020). DOI: 10.1021/acs.jpclett.0c01891

281. P. Li, A. V. Soudackov, B. Koronkiewicz, J. M. Mayer, and S. Hammes-Schiffer, “Theoretical study of shallow distance dependence of proton-coupled electron transfer in oligoproline metallopeptides,” J. Am. Chem. Soc. 142, 13795-13804 (2020). DOI: 10.1021/jacs.0c04716

280. Q. Yu, F. Pavošević, and S. Hammes-Schiffer, “Development of nuclear basis sets for multicomponent quantum chemistry methods,” J. Chem. Phys. 152, 244123 (2020). DOI: 10.1063/5.0009233

279. C. R. Reinhardt, P. Li, G. Kang, J. Stubbe, C. L. Drennan, and S. Hammes-Schiffer, “Conformational motions and water networks at the α/β interface in E. coli ribonucleotide reductase,” J. Am. Chem. Soc. 142, 13768-13778 (2020). DOI: 10.1021/jacs.0c04325

278. A. Nilsen-Moe, C. R. Reinhardt, S. D. Glover, L. Liang, S. Hammes-Schiffer, L. Hammarström, and C. Tommos, “Proton-coupled electron transfer from tyrosine in the interior of a de novoprotein: Mechanisms and primary proton acceptor,” J. Am. Chem. Soc. 142, 11550-11559 (2020). DOI: 10.1021/jacs.0c04655

277. P. Li, A. Rangadurai, H. M. Al-Hashimi, and S. Hammes-Schiffer, “Environmental effects on guanine-thymine mispair tautomerization explored with quantum mechanical/molecular mechanical free energy simulations,” J. Am. Chem. Soc. 142, 11183-11191 (2020). DOI: 10.1021/jacs.0c03774 

276. A. J. Coffman, W. Dou, S. Hammes-Schiffer, and J. E. Subotnik, “Modeling voltammetry curves for proton-coupled electron transfer: The importance of nuclear quantum effects,” J. Chem. Phys. 152, 234108 (2020). DOI: 10.1063/5.0010412

275. L. Zhao, Z. Tao, F. Pavošević, A. Wildman, S. Hammes-Schiffer, and X. Li, “Real-time time-dependent nuclear-electronic orbital approach: Dynamics beyond the Born-Oppenheimer approximation,” J. Phys. Chem. Lett. 11, 4052-4058 (2020). DOI: 10.1021/acs.jpclett.0c00701

274. E. Odella, S. J. Mora, B. L. Wadsworth, J. J. Goings, M. A. Gervaldo, L. E. Sereno, T. L. Groy, D. Gust, T. A. Moore, G. F. Moore, S. Hammes-Schiffer, and A. L. Moore, “Proton coupled electron transfer across benzimidazole bridges in bioinspired proton wires,” Chem. Sci. 11, 3820 (2020). DOI: 10.1039/C9SC06010C

273. F.Pavošević, T. Culpitt, and S. Hammes-Schiffer, “Multicomponent quantum chemistry: Integrating electronic and nuclear quantum effects via the nuclear-electronic orbital method,” Chem. Rev. 120, 4222-4253 (2020). DOI: 10.1021/acs.chemrev.9b00798

272. Z. K. Goldsmith, M. Secor, and S. Hammes-Schiffer, “Inhomogeneity of interfacial electric fields at vibrational probes on electrode surfaces,” ACS Cent. Sci. 6, 304-311 (2020). DOI: 10.1021/acscentsci.9b01297

271. D. R. Stevens and S. Hammes-Schiffer, “Examining the mechanism of phosphite dehydrogenase with quantum mechanical/molecular mechanical free energy simulations,” Biochemistry 59, 943-954 (2020). DOI: 10.1021/acs.biochem.9b01089

270. F. Pavošević, B. J. G. Rousseau, and S. Hammes-Schiffer, “Multicomponent orbital-optimized perturbation theory methods: Approaching coupled cluster accuracy at lower cost,” J. Phys. Chem. Lett. 11, 1578-1583 (2020). DOI: 10.1021/acs.jpclett.0c00090

269. E. Sayfutyarova, and S. Hammes-Schiffer, “Substituent effects on photochemistry of anthracene‒phenol‒pyridine triads revealed by multireference calculations,” J. Am. Chem. Soc. 142, 487-494 (2020). DOI: 10.1021/jacs.9b11425

268. S. Hammes-Schiffer, “Quantum effects in complex systems: Summarizing remarks,” Faraday Discuss. 221, 582-588 (2020). DOI: 10.1039/C9FD00097F

2019

267. J. J. Goings and S. Hammes-Schiffer, “Early photocycle of Slr1694 blue-light using flavin photoreceptor unraveled through adiabatic excited state quantum mechanical/molecular mechanical dynamics,” J. Am. Chem. Soc. 141, 20470-20479 (2019). DOI: 10.1021/jacs.9b11196

266. T. Culpitt, Y. Yang, P. E. Schneider, F. Pavošević, and S. Hammes-Schiffer, “Molecular vibrational frequencies with multiple quantum protons within the nuclear-electronic orbital framework,” J. Chem. Theory Comput. 15, 6840-6849 (2019). DOI: 10.1021/acs.jctc.9b00665

265. D. Ess, L. Gagliardi, and S. Hammes-Schiffer, “Introduction: Computational design of catalysts from molecules to materials,” Chem. Rev. 119, 6507-6508 (2019). DOI: 10.1021/acs.chemrev.9b00296

264. Z. Tao, Y. Yang, and S. Hammes-Schiffer, “Multicomponent density functional theory: Including the density gradient in the electron-proton correlation functional for hydrogen and deuterium,” J. Chem. Phys. 151, 124102 (2019). DOI: 10.1063/1.5119124

263. E. Sayfutyarova, Y. C. Lam, and S. Hammes-Schiffer, “Strategies for enhancing the rate constant of C—H bond cleavage by concerted proton-coupled electron transfer,” J. Am. Chem. Soc. 141, 15183-15189 (2019). DOI: 10.1021/jacs.9b06849

262. P. Li and S. Hammes-Schiffer, “Substrate-to-product conversion facilitates active site loop opening in yeast enolase: A molecular dynamics study,” ACS Catal. 9, 8985-8990 (2019). DOI: 10.1021/acscatal.9b03249

261.E. Odella, B. L. Wadsworth, S. J. Mora, J. J. Goings, M. T. Huynh, D. Gust, T. A. Moore, G. F. Moore, S. Hammes-Schiffer, and A. L. Moore, “Proton-coupled electron transfer drives long-range proton translocation in bioinspired systems,” J. Am. Chem. Soc. 141, 14057-14061 (2019). DOI: 10.1021/jacs.9b06978

260. Y. C. Lam, A. V. Soudackov, and S. Hammes-Schiffer, “Kinetics of proton discharge on metal electrodes: Effects of vibrational nonadiabaticity and solvent dynamics,” J. Phys. Chem. Lett. 10, 5312-5217 (2019). DOI: 10.1021/acs.jpclett.9b01984

259. F. Pavošević and S. Hammes-Schiffer, “Multicomponent coupled cluster singles and doubles and Brueckner doubles methods: Proton densities and energies,” J. Chem. Phys. 151, 074104 (2019). DOI: 10.1063/1.5116113

258. P. E. Schneider, F. Pavošević, and S. Hammes-Schiffer, “Diagonal Born-Oppenheimer corrections within the nuclear-electronic orbital framework,” J. Phys. Chem. Lett. 10, 4639-4643 (2019). DOI: 10.1021/acs.jpclett.9b01803

257. Y.-H. Wang, P. E. Schneider, Z. K. Goldsmith, B. Mondal, S. Hammes-Schiffer, and S. S. Stahl, “Brønsted acid scaling relationships enable control over product selectivity from Oreduction with a mononuclear cobalt porphyrin catalyst,” ACS Cent. Sci. 5, 1024-1034 (2019). DOI: 10.1021/acscentsci.9b00194

256. A. J. Coffman, A. K. Harshan, S. Hammes-Schiffer, and J. E. Subotnik, “Modeling electron transfer in diffusive multidimensional electrochemical systems,” J. Phys. Chem. C 123, 13304-13317 (2019). DOI: 10.1021/acs.jpcc.9b02068

255. T. Culpitt, Y. Yang, F. Pavošević, Z. Tao, and S. Hammes-Schiffer, “Enhancing the applicability of multicomponent time-dependent density functional theory,” J. Chem. Phys. 150, 201101 (2019). DOI: 10.1063/1.5099093

254. Y.-C. Lam, A. V. Soudackov, Z. K. Goldsmith, and S. Hammes-Schiffer, “Theory of proton discharge on metal electrodes: Electronically adiabatic model,” J. Phys. Chem.123, 12335-12345 (2019). DOI:10.1021/acs.jpcc.9b02148

253. Z. K. Goldsmith, A. V. Soudackov, and S. Hammes-Schiffer, “Theoretical analysis of the inverted region in photoinduced proton-coupled electron transfer,” Faraday Discuss. 216, 363-378 (2019). DOI: 10.1039/C8FD00240A

252. F. Pavošević and S. Hammes-Schiffer, “Multicomponent equation-of-motion coupled cluster singles and doubles: Theory and calculation of excitation energies for positronium hydride,” J. Chem. Phys. 150, 161102 (2019). DOI: 10.1063/1.5094035

251. G. A. Parada, Z. K. Goldsmith, S. Kolmar, B. P. Rimgard, B. Q. Mercado, L. Hammarström, S. Hammes-Schiffer, and J. M. Mayer, “Concerted proton-electron transfer reactions in the Marcus inverted region,” Science 364, 471-475 (2019). DOI: 10.1126/science.aaw4675.

250. Y. Yang, P. E. Schneider, T. Culpitt, F. Pavošević, and S. Hammes-Schiffer, “Molecular vibrational frequencies within the nuclear-electronic orbital framework,” J. Phys. Chem. Lett. 10, 1167-1172 (2019). DOI: 10.1021/acs.jpclett.9b00299

249. E. R. Sayfutyarova and S. Hammes-Schiffer, “Constructing molecular π-orbital active spaces for multireference calculations of conjugated systems,” J. Chem. Theory Comput. 15, 1679-1689 (2019). DOI: 10.1021/acs.jctc.8b01196

248. Z. K. Goldsmith, Y. C. Lam, A V. Soudackov, and S. Hammes-Schiffer, “Proton discharge on a gold electrode from triethylammonium in acetonitrile: Theoretical modeling of potential-dependent kinetic isotope effects,” J. Am. Chem. Soc. 141, 1084-1090 (2019). DOI: 10.1021/jacs.8b11826

247. E. R. Sayfutyarova, J. J. Goings, and S. Hammes-Schiffer, “Electron-coupled double proton transfer in the Slr1694 BLUF photoreceptor: A multireference electronic structure study,” J. Phys. Chem. B 123, 439-447 (2019). DOI: 10.1021/acs.jpcb.8b10973

246. F. Pavošević, T. Culpitt, and S. Hammes-Schiffer, “Multicomponent coupled cluster singles and doubles theory within the nuclear-electronic orbital framework,” J. Chem. Theory Comput. 15, 338-347 (2019). DOI: 10.1021/acs.jctc.8b01120

2018

245. E. R. Sayfutyarova, Z. K. Goldsmith, and S. Hammes-Schiffer, “Theoretical study of C-H bond cleavage via concerted proton-coupled electron transfer in fluorenyl-benzoates,” J. Am. Chem. Soc. 140, 15641-15645 (2018). DOI: 10.1021/jacs.8b10461

244. P. Li, A. V. Soudackov, and S. Hammes-Schiffer, “Impact of mutations on the binding pocket of soybean lipoxygenase: Implications for proton-coupled electron transfer,” J. Phys. Chem. Lett. 96444-6449 (2018). DOI: 10.1021/acs.jpclett.8b02945

243. E. Odella, S. J. Mora, B. L. Wadsworth, M. T. Huynh, J. J. Goings, P. A. Liddell, T. L. Groy, M. Gervaldo, L. E. Sereno, D. Gust, T. A. Moore, G. F. Moore, S. Hammes-Schiffer, and A. L. Moore, “Controlling proton-coupled electron transfer in bio-inspired artificial photosynthetic relays,” J. Am. Chem. Soc. 14015450-15460 (2018). DOI: 10.1021/jacs.8b09724

242. J. J. Goings, C. R. Reinhardt, and S. Hammes-Schiffer, “Propensity for proton relay and electrostatic impact of protein reorganization in Slr1694 BLUF photoreceptor,” J. Am. Chem. Soc. 14015241-15251 (2018)DOI: 10.1021/jacs.8b07456

241. Y.-H. Wang, Z. K. Goldsmith, P. E. Schneider, C. W. Anson, J. B. Gerken, S. Ghosh, S. Hammes-Schiffer, and S. S. Stahl, “Kinetic and mechanistic characterization of low-overpotential, H2O2-selective reduction of O2 catalyzed by N2O2-ligated cobalt complexes,” J. Am. Chem. Soc14010890-10899 (2018)DOI: 10.1021/jacs.8b06394

240. S. Hammes-Schiffer, “Controlling electrons and protons through theory: Molecular electrocatalysts to nanoparticles,” Acc. Chem. Res. 51, 1975-1983 (2018). DOI: 10.1021/acs.accounts.8b00240

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). DOI: 10.1063/1.5040353

238. K. R. Brorsen, P. Schneider, and S. Hammes-Schiffer, “Alternative forms and transferability of electron-proton correlation functionals in nuclear-electronic orbital density functional theory,” J. Chem. Phys. 149044110 (2018). DOI: 10.1063/1.5037945

237. D. R. Stevens and S. Hammes-Schiffer, “Exploring the role of the third active site metal ion in DNA polymerase η with QM/MM free energy simulations,” J. Am. Chem. Soc. 140, 8965-8969 (2018). DOI: 10.1021/jacs.8b05177

236. Y. Yang, T. Culpitt, and S. Hammes-Schiffer, “Multicomponent time-dependent density functional theory: Proton and electron excitation energies,” J. Phys. Chem. Lett. 91765-1770 (2018). DOI: 10.1021/acs.jpclett.8b00547

235.  P. Li, A. V. Soudackov, and S. Hammes-Schiffer, “Fundamental insights into proton-coupled electron transfer in soybean lipoxygenase from quantum mechanical/molecular mechanical free energy simulations,” J. Am. Chem. Soc. 1403068-3076 (2018). DOI: 10.1021/jacs.7b13642

2017 

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). DOI: 10.1021/acsnano.7b05009

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). DOI: 10.1021/acs.nanolett.7b02642

232. K. R. Brorsen, Y. Yang, and S. Hammes-Schiffer, “Multicomponent density functional theory: Impact of nuclear quantum effects on proton affinities and geometries,” J. Phys. Chem. Lett. 8, 3488-3493 (2017). DOI: 10.1021/acs.jpclett.7b01442

231. Y. Yang, K. R. Brorsen, T. Culpitt, M. V. Pak, and S. Hammes-Schiffer, “Development of a practical multicomponent density functional for electron-proton correlation to produce accurate proton densities,” J. Chem. Phys. 147, 114113 (2017). DOI: 10.1063/1.4996038

230. X. Yu, C.-H Tung, W. Wang, M. T. Huynh, D. L. Gray, S. Hammes-Schiffer, and T. B. Rauchfuss, “Interplay between terminal and bridging diiron hydrides in neutral and oxidized states,” Organometallics 36, 2245-2253 (2017). DOI: 10.1021/acs.organomet.7b00297

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). DOI: 10.1021/acscentsci.7b00125

228. T. Culpitt, K. R. Brorsen, and S. Hammes-Schiffer, “Density functional theory embedding with the orthogonality constrained basis set expansion procedure,” J. Chem. Phys. 146, 211101 (2017). DOI: 10.1063/1.4984777

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). DOI: 10.1021/acs.jpclett.7b00774

226. S. Hu, A. V. Soudackov, S. Hammes-Schiffer, and J. P. Klinman, “Enhanced rigidification within a double mutant of soybean lipoxygenase provides experimental support for vibronically nonadiabatic proton-coupled electron transfer models,” ACS Catal. 7, 3569-3574 (2017). DOI: 10.1021/acscatal.7b00688

225. Z. K. Goldsmith, A. K. Harshan, J. B. Gerken, M. Voros, G. Galli, S. S. Stahl, and S. Hammes-Schiffer, “Characterization of NiFe oxyhydroxide electrocatalysts by integrated electron structure calculations and spectroelectrochemistry,” Proc. Nat. Acad. Sci. USA 114, 3050-3055 (2017). DOI: 10.1073/pnas.1702081114

224. S. Hammes-Schiffer, “Catalysis by design: The power of theory,” Acc. Chem. Res. 50, 561-566 (2017). DOI: 10.1021/acs.accounts.6b00555

223. M. N. Ucisik and S. Hammes-Schiffer, “Effects of active site mutations on specificity of nucleobase binding in human DNA polymerase η,” J. Phys. Chem. B 121, 3667-3675 (2017). DOI: 10.1021/acs.jpcb.6b09973

222. J. L. Bingaman, S. Zhang, D. R. Stevens, N. H. Yennawar,  S. Hammes-Schiffer, and P. C. Bevilacqua, “GlcN6P cofactor serves multiple catalytic roles in the glmS ribozyme,” Nat. Chem. Biol. 13, 439-445 (2017). DOI: 10.1038%2Fnchembio.2300

221. P. Goyal and S. Hammes-Schiffer, “Role of active site conformational changes in photocycle activation of the AppA BLUF photoreceptor,” Proc. Nat. Acad. Sci. USA 114, 1480-1485 (2017). DOI: 10.1073/pnas.1621393114

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). DOI: 10.1021/acs.jpca.6b10124

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). DOI: 10.1021/jacs.6b11856

218. P. Goyal and S. Hammes-Schiffer, “Tuning the ultrafast dynamics of photoinduced proton-coupled electron transfer in energy conversion processes,” ACS Energy Lett. 2, 512-519 (2017). DOI: 10.1021/acsenergylett.6b00723

217. S. Hammes-Schiffer, “A conundrum for density functional theory,” Science 355, 28-29 (2017). Reprint

2016

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). DOI: 10.1039/C6FD00122J

215. M. T. Huynh, C. W. Anson, A. C. Cavell, S. S. Stahl, and S. Hammes-Schiffer, “Quinone 1 e and 2 e/2 H+ reduction potentials: Identification and analysis of deviations from systematic scaling relationships,” J. Am. Chem. Soc. 138, 15903-15910 (2016). DOI: 10.1021/jacs.6b05797

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). DOI: 10.1021/acs.jpclett.6b01854

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). DOI: 10.1021/acs.jpclett.6b01626

212. T. Culpitt, K. R. Brorsen, M. V. Pak, and S. Hammes-Schiffer, “Multicomponent density functional theory embedding formulation,” J. Chem. Phys. 145, 044106 (2016). DOI: 10.1063/1.4958952

211. O. A. Ulloa, M. T. Huynh, C. P. Richers, J. A. Bertke, M. J. Nilges, S. Hammes-Schiffer, and T. B. Rauchfuss, “Mechanism of H2 production by models for the [NiFe]-hydrogenases: Role of reduced hydrides,” J. Am. Chem. Soc. 138, 9234–9245 (2016). DOI: 10.1021/jacs.6b04579

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). DOI: 10.1021/acs.biochem.6b00203

209. D. Schilter, J. M. Camara, M. T. Huynh, S. Hammes-Schiffer, and T. B. Rauchfuss, “Hydrogenase enzymes and their synthetic models: The role of metal hydrides,” Chem. Rev. 116, 8693–8749 (2016). DOI: 10.1021/acs.chemrev.6b00180

208. S. Ghosh, A. V. Soudackov, and S. Hammes-Schiffer, “Electrochemical electron transfer and proton-coupled electron transfer: Effects of double layer and ionic environment on solvent reorganization energies,” J. Chem. Theory Comput. 12, 2917-2925 (2016). DOI: 10.1021/acs.jctc.6b00233

207. A. K. Harshan, B. H. Solis, J. R. Winkler, H. B. Gray, and S. Hammes-Schiffer, “Computational study of fluorinated diglyoxime-iron complexes: Tuning the electrocatalytic pathways for hydrogen evolution,” Inorg. Chem. 55, 2934–2940 (2016). DOI: 10.1021/acs.inorgchem.5b02857

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). DOI: 10.1021/jacs.6b00254

205. P. Goyal, C. A. Schwerdtfeger, A. V. Soudackov, and S. Hammes-Schiffer, “Proton quantization and vibrational relaxation in nonadiabatic dynamics of photoinduced proton-coupled electron transfer in a solvated phenol-amine complex,” J. Phys. Chem. B 120, 2407-2417 (2016). DOI: 10.1021/acs.jpcb.5b12015

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). DOI: 10.1021/acs.inorgchem.5b02035

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). DOI: 10.1021/acs.inorgchem.5b02262

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). DOI: 10.1073/pnas.1521834112

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). DOI: 10.1021/acs.inorgchem.5b01662

2015

200. A. V. Soudackov and S. Hammes-Schiffer, “Nonadiabatic rate constants for proton transfer and proton-coupled electron transfer reactions in solution: Effects of quadratic term in the vibronic coupling expansion,” J. Chem. Phys. 143, 194101 (2015). DOI: 10.1063/1.4935045

199. M. N. Ucisik and S. Hammes-Schiffer, “Comparative molecular dynamics studies of human DNA polymerase η,” J. Chem. Inf. Model. 55, 2672-2681 (2015). DOI: 10.1021/acs.jcim.5b00606

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). DOI: 10.1021/jacs.5b08451

197. A. K. Harshan, T. Yu, A. V. Soudackov, and S. Hammes-Schiffer, “Dependence of vibronic coupling on molecular geometry and environment: Bridging hydrogen atom transfer and electron-proton transfer,” J. Am. Chem. Soc. 137, 13545-13555 (2015). DOI: 10.1021/jacs.5b07327

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). DOI: 10.1063/1.4931667

195. P. Goyal and S. Hammes-Schiffer, “Role of solvent dynamics in photoinduced proton-coupled electron transfer in a phenol-amine complex in solution,” J. Phys. Chem. Lett. 6, 3515-3520 (2015). DOI: 10.1021/acs.jpclett.5b01475

194. S. Hammes-Schiffer, “Proton-coupled electron transfer: Moving together and charging forward,” J. Am. Chem. Soc. 137, 8860-8871 (2015). DOI: 10.1021/jacs.5b04087

193. K. R. Brorsen, A. Sirjoosingh, M. V. Pak, and S. Hammes-Schiffer, “Nuclear-electronic orbital reduced explicitly correlated Hartree-Fock approach: Restricted basis sets and open-shell systems,” J. Chem. Phys. 142, 214108 (2015). DOI: 10.1063/1.4921304

192. A. Sirjoosingh, M. V. Pak, K. R. Brorsen, and S. Hammes-Schiffer, “Quantum treatment or protons with the reduced explicitly correlated Hartree Fock approach,” J. Chem. Phys. 142, 214107 (2015). DOI: 10.1063/1.4921303

191. P. Thaplyal, A. Ganguly, S. Hammes-Schiffer, and P. C. Bevilacqua, “Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density,” Biochemistry 54, 2160-2175 (2015). DOI: 10.1021/acs.biochem.5b00190

190. P. Hanoian, C. T. Liu, S. Hammes-Schiffer, and S. J. Benkovic, “Perspectives on electrostatics and conformational motions in enzyme catalysis,” Acc. Chem. Res. 48, 482-489 (2015). DOI: 10.1021/ar500390e

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) . DOI: 10.1021/jp5126969

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). DOI: 10.1021/ja510387y

187. S. Ghosh and S. Hammes-Schiffer, “Calculation of electrochemical reorganization energies for redox molecules at self-assembled monolayer modified electrodes,” J. Phys. Chem. Lett. 6, 1-5 (2015). DOI: 10.1021/jz5023784

2014

186. B. H. Solis, A. G. Maher, T. Honda, D. C. Powers, D. G. Nocera, and S. Hammes-Schiffer, “Theoretical analysis of cobalt hangman prophyrins: Ligand dearomatization and mechanistic implications for hydrogen evolution,” ACS Catal. 4, 4516–4526 (2014). DOI: 10.1021/cs501454y

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). DOI: 10.1073/pnas.1415940111

184.  N. M. Tubman, I. Kylänpää, S. Hammes-Schiffer, and D. M. Ceperley, “Beyond the Born-Oppenheimer approximation with quantum Monte Carlo,” Phys. Rev. A 90, 042507 (2014). DOI: 10.1103/PhysRevA.90.042507

183. D. K. Bediako, B. H. Solis, D. K. Dogutan, M. M. Roubelakis, A. G. Maher, C. H. Lee, M. B. Chambers, S. Hammes-Schiffer, and D. G. Nocera, “Role of pendant proton relays and proton-coupled electron transfer on the hydrogen evolution reaction by nickel hangman porphyrins,” Proc. Natl. Acad. Sci. USA 111, 15001-15006 (2014). DOI: 10.1073/pnas.1414908111

182. A. V. Soudackov and S. Hammes-Schiffer, “Probing nonadiabaticity in the proton-coupled electron transfer reaction catalyzed by soybean lipoxygenase,” J. Phys. Chem. Lett. 5, 3274-3278 (2014). DOI: 10.1021/jz501655v

181. M. T. Huynh, W. Wang, T. B. Rauchfuss, and S. Hammes-Schiffer, “Computational investigation of [FeFe]-hydrogenase models: Characterization of singly and doubly protonated intermediates and mechanistic insights,” Inorg. Chem. 53, 10301-10311 (2014). DOI: 10.1021/ic5013523

180. M. T. Huynh, D. Schilter, S. Hammes-Schiffer, and T. B. Rauchfuss, “Protonation of nickel-iron hydrogenase models proceeds after isomerization at nickel,” J. Am. Chem. Soc. 136, 12385-12395 (2014). DOI: 10.1021/ja505783z

179. C. T. Liu, J. P. Layfield, R. J. Stewart III, J. B. French, P. Hanoian, J. B. Asbury, S. Hammes-Schiffer, and S. J. Benkovic, “Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase,” J. Am. Chem. Soc. 136, 10349-10360 (2014). DOI: 10.1021/ja5038947

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). DOI: 10.1021/ja502726s

177. B. H. Solis and S. Hammes-Schiffer, “Proton-coupled electron transfer in molecular electrocatalysis: Theoretical methods and design principles,” Inorg. Chem. 53, 6427-6443 (2014). DOI: 10.1021/ic5002896

176. S. Ghosh, S. Horvath, A. V. Soudackov, and S. Hammes-Schiffer, “Electrochemical solvent reorganization energies in the framework of the polarizable continuum model,” J. Chem. Theory Comput. 10, 2091-2102 (2014). DOI: 10.1021/ct500051e

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). DOI: 10.1021/bi401671t

174. C. A. Schwerdtfeger, A. V. Soudackov, and S. Hammes-Schiffer, “Nonadiabatic dynamics of electron transfer in solution: Explicit and implicit solvent treatments that include multiple relaxation time scales,” J. Chem. Phys. 140, 034113 (2014). DOI: 10.1063/1.4855295

173. A. Ganguly, P. Thaplyal, E. Rosta, P. C. Bevilacqua, and S. Hammes-Schiffer, “Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme,” J. Am. Chem. Soc. 136, 1483-1496 (2014). DOI: 10.1021/ja4104217

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). DOI: 10.1002/anie.201308431

171. J. P. Layfield and S. Hammes-Schiffer, “Hydrogen tunneling in enzymes and biomimetic models,” Chem. Rev. 114, 3466-3494 (2014). DOI: 10.1021/cr400400p

2013

170. P. Thaplyal, A. Ganguly, B. L. Golden, and S. Hammes-Schiffer, “Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme,” Biochemistry 52, 6499-6514 (2013). DOI: 10.1021/bi4000673

169. C. Ko and S. Hammes-Schiffer, “Charge-transfer excited states and proton transfer in model guanine-cytosine DNA duplexes in water,” J. Phys. Chem. Lett. 4, 2540-2545 (2013). DOI: 10.1021/jz401144c

168. A. Sirjoosingh, M. V. Pak, C. Swalina, and S. Hammes-Schiffer, “Reduced explicitly correlated Hartree-Fock approach within the nuclear-electronic orbital framework: Applications to positronic molecular systems,” J. Chem. Phys. 139, 034103 (2013). DOI: 10.1063/1.4812259

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). DOI: 10.1063/1.4812257

166. B. H. Solis, Y. Yu, and S. Hammes-Schiffer, “Effects of ligand modification and protonation on metal oxime hydrogen evolution electrocatalysts,” Inorg. Chem. 52, 6994-6999 (2013). DOI: 10.1021/ic400490y

165. C. T. Liu, P. Hanoian,, J. B. French, T. H. Pringle, S. Hammes-Schiffer, and S. J. Benkovic, “Functional significance of evolving protein sequence in dihydrofolate reductase from bacteria to humans,” Proc. Natl. Acad. Sci. USA 110, 10159-10164 (2013). DOI: 10.1073/pnas.1307130110

164. S. Horvath, L. E. Fernandez, A. M. Appel, and S. Hammes-Schiffer, “pH-dependent reduction potentials and proton-coupled electron transfer mechanisms in hydrogen-producing nickel molecular electrocatalysts,”Inorg. Chem. 52, 3643-3652 (2013). DOI: 10.1021/ic302056j

163. L. E. Fernandez, S. Horvath, and S. Hammes-Schiffer, “Theoretical design of molecular electrocatalysts with flexible pendant amines for hydrogen production and oxidation,” J. Phys. Chem. Lett. 4, 542-546 (2013). DOI: 10.1021/jz3020277

162. J. Chen, A. Ganguly, Z. Miswan, S. Hammes-Schiffer, P. C. Bevilacqua, and B. L. Golden, “Identification of the catalytic Mg2+ ion in the hepatitis delta virus ribozyme, ” Biochemistry 52, 557-567 (2013). DOI: 10.1021/bi3013092

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). DOI: 10.1021/bi301515j

159. J. P. Layfield and S. Hammes-Schiffer, “Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding,” J. Am. Chem. Soc. 135, 717-725 (2013). DOI: 10.1021/ja3084384

158. B. L. Golden, S. Hammes-Schiffer, P. R. Carey, P. C. Bevilacqua, “An Integrated Picture of HDV Ribozyme Catalysis,” pp. 135-167 in Biophysics of RNA Folding, ed. R. Russell (Springer, New York, 2013). DOI: 10.1007/978-1-4614-4954-6_8

2012

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). DOI: 10.1021/ja306857q

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). DOI: 10.1021/jp3031682

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). DOI: 10.1063/1.4709609

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). DOI: 10.1063/1.4704124

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). DOI: 10.1073/pnas.1118333109

152. S. Hammes-Schiffer, “Proton-coupled electron transfer: Classification scheme and guide to theoretical methods,” Energy and Environ. Sci. 5, 7696-7703 (2012). DOI: 10.1039/C2EE03361E

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). DOI: 10.1021/jp210690q

2011

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). DOI: 10.1021/jz2013215

149. G. G. Hammes, S. J. Benkovic, and S. Hammes-Schiffer, “Flexibility, diversity, and cooperativity: Pillars of enzyme catalysis” Biochemistry 50, 10422-10430 (2011). DOI: 10.1021/bi201486f

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). DOI: 10.1021/ja208091e

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). DOI: 10.1063/1.3651083

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). DOI: 10.1021/ic201842v

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). DOI: 10.1021/ct200473r

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). DOI: 10.1021/ct200356b

143. P. Hanoian, and S. Hammes-Schiffer, “Water in the active site of ketosteroid isomerase,” Biochemistry 50, 6689-6700 (2011). DOI: 10.1021/bi200703y

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). DOI: 10.1063/1.3611054

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). DOI: 10.1021/jp203202e

140. S. Hammes-Schiffer, “When electrons and protons get excited,” Proc. Natl. Acad. Sci. USA 108, 8531-8532 (2011). DOI: 10.1073/pnas.1105806108

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). DOI: 10.1021/ja201560v

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). DOI: 10.1021/jz200277p

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). DOI: 10.1021/bi2000164

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). DOI: 10.1021/jp111210c

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). DOI: 10.1021/jz101532g

2010

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). DOI: 10.1021/bi101428e

133. S. Hammes-Schiffer, “Introduction: Proton-coupled electron transfer,” Chem. Rev. 110, 6937-6938 (2010). DOI: 10.1021/cr100367q

132. S. Hammes-Schiffer and A. A. Stuchebrukhov, “Theory of coupled electron and proton transfer reactions,”Chem. Rev. 110, 6939-6960 (2010). DOI: 10.1021/cr1001436

131. V. C. Nashine, S. Hammes-Schiffer, and S. J. Benkovic, “Coupled motions in enzyme catalysis,” Curr. Op. Chem. Biol. 14, 644-651 (2010). DOI: 10.1016/j.cbpa.2010.07.020

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). DOI: 10.1021/jp1051547

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). DOI: 10.1016/j.jmb.2010.07.025

128. S. Hammes-Schiffer, “Theoretical Perspectives of DNA: Editorial,” J. Phys. Chem. Lett. 1, 1906 (2010). DOI: 10.1021/jz100657p

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). DOI: 10.1021/ja102714u

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). DOI: 10.1021/jp100133p

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). DOI: 10.1063/1.3332769

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). DOI: 10.1021/ja910277p

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). DOI: 10.1021/jp907193g

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). DOI: 10.1021/jp908798n

2009

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). DOI: 10.1021/bi901353v

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). DOI: 10.1021/jp907808t

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). DOI: 10.1063/1.3249964

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). DOI: 10.1063/1.3236844

117. L. Hammarström and S. Hammes-Schiffer, “Artificial photosynthesis and solar fuels: Guest editorial,” Acc. Chem. Res. 42, 1859-1860 (2009). DOI: 10.1021/ar900267k

116. S. Hammes-Schiffer, “Theory of proton-coupled electron transfer in energy conversion processes,” Acc. Chem. Res. 42, 1881-1889 (2009). DOI: 10.1021/ar9001284

115. I. Navrotskaya and S. Hammes-Schiffer, “Electrochemical proton-coupled electron transfer: Beyond the golden rule,” J. Chem. Phys. 131, 024112 (2009). DOI: 10.1063/1.3158828

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). DOI: 10.1021/ja9001184

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). DOI: 10.1021/jp810363k

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). DOI: 10.1021/jp810410y

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). DOI: 10.1063/1.3068526

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). DOI: 10.1021/jp809122y

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). DOI: 10.1039/9781847559975-00079

2008

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). DOI:  10.1063/1.2998312

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). DOI: 10.1021/ct8003386

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). DOI: 10.1021/jp805876e

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). DOI: 10.1103/PhysRevLett.101.153001

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). DOI: 10.1063/1.2940203

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). DOI: 10.1063/1.2943144

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). DOI: 10.1021/jp802171y

101. S. J. Benkovic, G. G. Hammes, and S. Hammes-Schiffer, “Free energy landscape of enzyme catalysis,”Biochemistry 47, 3317-3321 (2008). DOI: 10.1021/bi800049z

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). DOI: 10.1021/jp7098015

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). DOI: 10.1016/j.ccr.2007.07.019

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). DOI: 10.1021/jp0753474

2007

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). DOI: doi.org/10.1021/ja072708k

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). DOI: doi.org/10.1021/jp0704463

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). DOI: doi.org/10.1021/jp0682661

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). DOI: doi.org/10.1021/jp065569m

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). DOI: doi.org/10.1021/ja0667211

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). DOI: 10.1002/9783527611546.ch46

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).

2006

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). DOI: doi.org/10.1021/ja0656548

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). DOI: doi.org/10.1063/1.2362823

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). DOI: 10.1063/1.2354500

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). DOI: 10.1021/jp065034t

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). DOI: 10.1021/jp0634297

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). DOI: 10.1063/1.2206175

84. S. Hammes-Schiffer and J. B. Watney, “Hydride transfer catalyzed by Escherichia coli and Bacillus subtilisdihydrofolate reductase: Coupled motions and distal mutations,” Phil. Trans. R. Soc. B 361, 1365-1373 (2006). DOI: 10.1098/rstb.2006.1869

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). DOI: 10.1021/jp0605956

82. S. J. Benkovic and S. Hammes-Schiffer, “Enzyme motions inside and out,” Science 312, 208-209 (2006). DOI: 10.1126/science.1127654

81. S. Hammes-Schiffer and S. J. Benkovic, “Relating protein motion to catalysis,” Annu. Rev. Biochem. 75, 519-541 (2006). DOI: 10.1146/annurev.biochem.75.103004.142800

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). DOI: 10.1021/jp056939u

2005

79. S. Hammes-Schiffer, “Hydrogen tunneling and protein motion in enzyme reactions,” Acc. Chem. Res. 39, 93-100 (2006). DOI: 10.1021/ar040199a

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). DOI: 10.1016/j.cplett.2005.10.129

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). DOI: 10.1016/j.chemphys.2005.05.043

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). DOI: 10.1021/jp053552i

75. J. H. Skone, M. V. Pak, and S. Hammes-Schiffer, “Nuclear-electronic orbital nonorthogonal configuration interaction approach,” J. Chem. Phys. 123, 134108 (2005). DOI: 10.1063/1.2039727

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). DOI: 10.1021/jp052909f

73. A. Reyes, M. V. Pak, and S. Hammes-Schiffer, “Investigation of isotope effects with the nuclear-electronic orbital approach”, J. Chem. Phys. 123, 064104 (2005). DOI: 10.1063/1.1990116

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, 014303 (2005). DOI: 10.1063/1.1940634

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). DOI: 10.1073/pnas.0408343102

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). DOI: 10.1016/j.cplett.2005.01.115

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). DOI: 10.1063/1.1814635

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).

2004

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). DOI: 10.1021/jp048565v

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). DOI: 10.1016/j.chemphys.2004.06.009

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). DOI: 10.1021/jp037671e

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). DOI: 10.1021/ja039606o

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). DOI: 10.1016/j.sbi.2004.03.008

62. M. V. Pak and S. Hammes-Schiffer, “Electron-proton correlation for hydrogen tunneling systems,” Phys. Rev. Lett. 92, 103002 (2004). DOI: 10.1103/physrevlett.92.103002

61. S. Hammes-Schiffer and N. Iordanova, “Theoretical studies of proton-coupled electron transfer reactions,”Biochim. Biophys. Acta. 1655, 29-36 (2004). DOI: 10.1016/j.bbabio.2003.07.009

2003 

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). DOI: 10.1021/ja035588z

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). DOI: 10.1063/1.1592509

58. S. J. Benkovic and S. Hammes-Schiffer, “A perspective on enzyme catalysis,” Science 301, 1196-1202 (2003). DOI: 10.1126/science.1085515

57. T. Iordanov and S. Hammes-Schiffer, “Vibrational analysis for the nuclear-electronic orbital method,” J. Chem. Phys. 118, 9489-9496 (2003). DOI: 10.1063/1.1569913

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). DOI: 10.1021/ja028487u

2002

55. S. Hammes-Schiffer, “Impact of enzyme motion on activity,” Biochemistry 41, 13335-13343 (2002). DOI: 10.1021/bi0267137

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). DOI: 10.1063/1.1494980

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). DOI: 10.1021/jp0209392

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). DOI: 10.1021/ja017633d

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). DOI: 10.1021/jp020190v

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. Natl. Acad. Sci. USA 99, 2794-2799 (2002). DOI: 10.1073/pnas.052005999

49. S. Hammes-Schiffer, “Comparison of hydride, hydrogen atom, and proton-coupled electron transfer reactions,” Chem. Phys. Chem. 3, 33-42 (2002). DOI: 10.1002/1439-7641(20020118)3:1<33::AID-CPHC33>3.0.CO;2-6

2001

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). DOI: 10.1021/ja011384b

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). DOI: 10.1021/jp012102x

46. S. Hammes-Schiffer and S. R. Billeter, “Hybrid approach for the dynamical simulation of proton and hydride transfer in solution and proteins,” Int. Rev. Phys. Chem. 20, 591-616 (2001). DOI: 10.1080/01442350110067402

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). DOI: 10.1063/1.1376143

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). DOI: 10.1021/ja0100524

43. S. Hammes-Schiffer, “Theoretical perspectives on proton-coupled electron transfer reactions,” Acc. Chem. Res. 34, 273-281 (2001). DOI: 10.1021/ar9901117

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). DOI: 10.1016/S0009-2614(01)00298-6

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). DOI: 10.1063/1.1356441

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).

2000

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). DOI: doi.org/10.1021/jp001967s

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). DOI: doi.org/10.1063/1.1289528

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). DOI: doi.org/10.1021/jp001635n

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). DOI: 10.1021/jp000449e

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). DOI: 10.1063/1.482053

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). DOI: 10.1021/ja994456w

1999

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). DOI: 10.1021/ja992380y

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). DOI: 10.1021/jp991602b

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). DOI: 10.1002/ijch.199900045

30. A. Soudackov and S. Hammes-Schiffer, “Multistate continuum theory for multiple charge transfer reactions in solution,” J. Chem. Phys. 111, 4672-4687 (1999). DOI: 10.1063/1.479229

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). DOI: 10.1063/1.479058

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). DOI: 10.1021/jp984775u

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). DOI: 10.1016/S0009-2614(98)01347-5

1998

26. S. Hammes-Schiffer, “Mixed quantum/classical dynamics of hydrogen transfer reactions”, J. Phys. Chem. A 102, 10443-10454 (1998). DOI: 10.1021/jp983246n

25. S. Hammes-Schiffer, “Quantum dynamics of multiple modes for reactions in complex systems”, Faraday Discuss110, 391-406 (1998). DOI: 10.1039/A801120F

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 III 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). DOI: 10.1063/1.477388

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). DOI: 10.1063/1.476126

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). DOI: 10.1063/1.476095

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). DOI: 10.1002/bbpc.19981020337

1997

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). DOI: 10.1063/1.475185

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). DOI: 10.1063/1.474333

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). DOI: 10.1063/1.474397

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). DOI: 10.1021/jp970269d

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). DOI: 10.1063/1.473903

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). DOI: 10.1016/S0009-2614(97)00251-0

1996

13. S. Hammes-Schiffer, “Multiconfigurational molecular dynamics with quantum transitions: Multiple proton transfer reactions,” J. Chem. Phys. 105, 2236-2246 (1996). DOI: 10.1063/1.472093

1995

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). DOI: 10.1063/1.470162

11. S. Hammes-Schiffer and J. C. Tully, “Vibrationally enhanced proton transfer,” J. Phys. Chem. 99, 5793-5797 (1995). DOI: 10.1021/j100016a011

1994

10. S. Hammes-Schiffer and J. C. Tully, “Proton transfer in solution: molecular dynamics with quantum transitions,” J. Chem. Phys. 101, 4657-4667 (1994). DOI: 10.1063/1.467455

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). DOI: 10.1063/1.468145

1993

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). DOI: 10.1063/1.465776

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). DOI: 10.1063/1.465305

1991

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). DOI: 10.1021/j100159a024

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). DOI: 10.1016/S0006-3495(91)82029-X

1990

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). DOI: 10.1073/pnas.87.15.5682

1989

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). DOI: 10.1063/1.457458

1988

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). DOI: 10.1103/PhysRevA.38.2678

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). DOI: 10.1016/0022-2364(88)90044-3