QM/MM

Direct proton-coupled electron transfer between interfacial tyrosines in ribonucleotide reductase

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

QM/MM modeling of vibrational polariton induced energy transfer and chemical dynamics

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

Role of water in proton-coupled electron transfer between tyrosine and cysteine in ribonucleotide reductase

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

Environmental effects on guanine-thymine mispair tautomerization explored with quantum mechanical/molecular mechanical free energy simulations

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).

David’s paper on examining the mechanism of phosphite dehydrogenase with quantum mechanical/molecular mechanical free energy simulations is published in Biochemistry!

Examining the mechanism of phosphite dehydrogenase with quantum mechanical/molecular mechanical free energy simulations

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).

Early photocycle of Slr1694 blue-light using flavin photoreceptor unraveled through adiabatic excited state quantum mechanical/molecular mechanical dynamics

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).

Exploring the role of the third active site metal ion in DNA polymerase η with QM/MM free energy simulations

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).

Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: Quantum mechanical/molecular mechanical free energy simulations

188. S. Zhang, A. Ganguly, P. Goyal, J. Bingamin, 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).

Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme

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).