Methods for extended systems

The effect of solvent on electronic structure can be inlcuded via embedding techniques, ranging from QM/MM (electrostatic embedding using fixed charges from classical force fields) to EFP (polarizable embedding). EFP, which is a QM based potential, is a more sophisticated method than simple parameterized MM methods. EFP describes the interaction between the fragments as sum of Coulombic and polarization terms, as well as exchange-repulsion and dispersion. It has no fitted parameters. The EFP Hamiltonian is mostly pairwise, however, leading many-body effects are included through a self-consistent treatment of polarization. EFP is a computationally inexpensive alternative to high-level ab initio calculations.

Related Publications

305. R. Sarangi, K. Nanda, and A.I. Krylov
Two- and one-photon absorption spectra of aqueous thiocyanate anion highlight the role of symmetry in condensed phase
J. Comp. Chem.  45, 878 – 885 (2024) Abstract  PDF 

304. S. Dey, S. D. Folkestad, A. Paul, H. Koch, and A.I. Krylov
Core-ionization spectrum of liquid water
Phys. Chem. Chem. Phys.  26, 1845 – 1859 (2024) Abstract  PDF Supporting info

289. B.L. Grigorenko, I. Polyakov, G. Giudetti, S. Faraji, A.I. Krylov, and A.V. Nemukhin
QM/MM simulations of the covalent inhibition of the SARS-CoV-2 main protease: Four compounds and three reaction mechanisms
J. Am. Chem. Soc.  145, 13204 – 13214 (2023) Abstract  PDF 

287. R. Sarangi, K. Nanda, and A.I. Krylov
Charge-transfer-to-solvent states provide a sensitive spectroscopic probe of the local solvent structure around anions
Mol. Phys.  121, e2148582 (2023) Abstract  PDF 

280. G. Giudetti, I. Polyakov, B.L. Grigorenko, S. Faraji, A.V. Nemukhin, and A.I. Krylov
How reproducible are QM/MM simulations? Lessons from computational studies of the covalent inhibition of the SARS-CoV-2 main protease by carmofur
J. Chem. Theo. Comp.  18, 5056 – 5067 (2022) Abstract  PDF Supporting info

212. K. Nanda and A. I. Krylov
The effect of polarizable environment on two-photon absorption cross sections characterized by the equation-of-motion coupled-cluster singles and doubles method combined with the effective fragment potential approach
J. Chem. Phys.  149, 164109 (2018) Abstract  PDF Supporting info

171. P. Kumar, A. Acharya, D. Ghosh, D. Kosenkov, I. Kaliman, Y. Shao, A.I. Krylov, and L.V. Slipchenko
Extension of the effective fragment potential method to macromolecules
J. Phys. Chem. B 120, 6562 – 6574 (2016) Abstract  PDF Supporting info

130. D. Ghosh, D. Kosenkov, V. Vanovschi, J. Flick, I. Kaliman, Y. Shao, A.T.B. Gilbert, A.I. Krylov, and L.V. Slipchenko
Effective Fragment Potential method in Q-Chem: A guide for users and developers
J. Comp. Chem. 34, 1060 – 1070 (2013) Abstract  PDF Supporting info

121. D. Ghosh, A. Roy, R. Seidel, B. Winter, S.E. Bradforth, and A.I. Krylov
First-principle protocol for calculating ionization energies and redox potentials of solvated molecules and ions: Theory and application to aqueous phenol and phenolate
J. Phys. Chem. B 116, 7269 – 7280 (2012) Abstract  PDF Supporting info

103. D. Ghosh, O. Isayev, L.V. Slipchenko, and A.I. Krylov
The effect of solvation on vertical ionization energy of thymine: From microhydration to bulk
J. Phys. Chem. A 115, 6028 – 6038 (2011) Abstract  PDF Supporting info

100. D. Ghosh, D. Kosenkov, V. Vanovschi, C.F. Williams, J.M. Herbert, M.S. Gordon, M.W. Schmidt, L.V. Slipchenko, and A.I. Krylov
Non-covalent interactions in extended systems described by the Effective Fragment Potential method: Theory and application to nucleobase oligomers
J. Phys. Chem. A 114, 12739 – 12754 (2010) Abstract  PDF Supporting info