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Multiscale Modelling:Hybrid Quantum Mechanics/Molecular Mechanics as an Example and some Recent Developments


Affiliations
1 Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411 008, India
 

Most of the physical phenomena are multiscale in nature and therefore, to depict it properly one requires multiscale modelling techniques, i.e. physical models that are accurate over multiple length and time scales. The seminal work by Warshel and Levitt marks the beginning of hybrid quantum mechanics/molecular mechanics (QM/MM) method as a successful strategy towards the understanding of chemistry and physics in condensed phases and especially in biological systems. Recently, these methods have been extended to problems such as light-matter interaction, where the QM sub-system is excited from the ground to the excited states. The MM environment provides a field that changes the potential energy landscape of both the ground and excited states in a distinctly different way. In this review, we discuss the general strategy of multiscale modelling with emphasis on hybrid QM/MM and the recent developments in excited state QM/MM methods.

Keywords

Biological Systems, Hybrid Quantum Mechanics/Molecular Mechanics, Multiscale.
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  • Warshel, A. and Levitt, M., Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol., 1976, 103, 227–249.

  • Kadanoff, L. P., Scaling laws for ising models near high tc. Physics, 1966, 2, 263–272.

  • Wilson, K. G., The renormalization group: critical phenomena and the kondo problem. Rev. Mod. Phys., 1975, 47, 773–840.

  • White, S. R. and Noack, R. M., Real space quantum renormalization group. Phys. Rev. Lett., 1992, 68, 3487–3490.

  • Chan, G. K.-L. and Head-Gordon, M., Highly correlated calculations with a polynomial cost algorithm: a study of density matrix renormalization group. J. Chem. Phys., 2002, 116, 4462–4476.

  • Ghosh, D., Hachmann, J., Yanai, T. and Chan, G. K.-L., Orbital optimization in density matrix renormalization group, with applications to polyenes and -carotene. J. Chem. Phys., 2008, 128, 144117(1)–14417(14).

  • Tomasi, J., Mennucci, B. and Cances, E., The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level. J. Mol. Struct. Theochem., 1999, 464, 211–226.

  • Cossi, M., Barone, V., Mennucci, B. and Tomasi, J., Ab initio study of ionic solutions by a polarizable continuum dielectric model. Chem. Phys. Lett., 1998, 286, 253–260.

  • Cossi, M., Rega, N., Scalmani, G. and Barone, V., Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. J. Comput. Chem., 2003, 24, 669–681.

  • Cramer, C. J. and Truhlar, D. G., Implicit solvation models: equilibria, structure, spectra, and dynamics. Chem. Rev., 1999, 99, 2161.

  • Rudd, R. E. and Broughton, J. Q., Coarse-grained molecular dynamics and the atomic limit of finite elements. Phys. Rev. B, 1998, 58, 5893–5896.

  • Ensing, B., Nielsen, S. O., Moore, P. B. and Parrinello, M., Energy conservation in adaptive hybrid atomistic/coarse-grain molecular dynamics. J. Chem. Theory Comput., 2007, 3, 1100– 1105.

  • Marrink, S. J., Risselada, H. J., Yefimov, S., Tieleman, D. P. and de Vries, A. H., The martini force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B, 2007, 111, 7812– 7814.

  • Jorgensen, W. L., Maxwell, D. S. and Tirado-Rives, J., Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc., 1996, 118, 11225–11236.

  • Parr, R. G., Density functional theory of atoms and molecules. In Horizons of Quantum Chemistry, Springer, pp. 5–15.

  • Hohenberg, P. and Kohn, W., Inhomogeneous electron gas. Phys. Rev. Lett., 1964, 136, 864–871.

  • Kohn, W. and Sham, L. J., Self-consistent equations including exchange and correlation effects. Phys. Rev. Lett., 1965, 140, 1133–1138.

  • Lin, H. and Truhlar, D. G., QM/MM: what have we learned, where are we, and where do we go from here? Theor. Chem. Acc., 2007, 117, 185–199.

  • Senn, H. M. and Thiel, W., QM/MM methods for biological systems. Topics Curr. Chem., 2007, 268, 173–290.

  • Dapprich, S., Komaromi, I., Byun, K. S., Morokuma, K. and Frisch, M. J., A new oniom implementation in Gaussian. Part I. the calculation of energies, gradients, vibrational frequencies and electric field derivatives. J. Mol. Struct. Theochem., 1999, 461, 1–21.

  • Gordon, M. S., Freitag, M. A., Bandyopadhyay, P., Jensen, J. H., Kairys, V. and Stevens, W., The effective fragment potential method: a QM based MM approach to modelling environmental effects in chemistry. J. Phys. Chem. A, 2001, 105, 293–307.

  • Ghosh, D. et al., Non-covalent interactions in extended systems described by the effective fragment potential method: theory and application to nucleobase oligomers. J. Phys. Chem. A, 2010, 114, 12739–12754.

  • Ghosh, D. et al., Effective fragment potential method in Q-Chem: A guide for users and developers. J. Comput. Chem., 2013, 34, 1060–1070.

  • Sneskov, K., Schwabe, T., Kongsted, J. and Christiansen, O., The polarizable embedding coupled cluster method. J. Chem. Phys., 2011, 134, 104108(1)–104108(18).

  • Ferre, N. and Olivucci, M., The amide bond: pitfalls and drawbacks of the link atom scheme. J. Mol. Struc. Theochem., 2003, 632, 71–82.

  • Zhang, D. W. and Zhang, J. Z. H., Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein molecule interaction energy. J. Chem. Phys., 2003, 119, 3599– 3605.

  • Ghosh, D., Isayev, O., Slipchenko, L. V. and Krylov, A. I., The effect of solvation on vertical ionization energy of thymine: from microhydration to bulk. J. Phys. Chem. A, 2011, 115, 6028–6038.

  • Ghosh, D., Perturbative approximation to hybrid equation of motion coupled cluster/effective fragment potential method. J. Chem. Phys., 2014, 140, 094101(1)–094101(9).

  • Bose, S., and Ghosh, D., Effect of solvation on electron detachment and excitation energies of a green fluorescent protein chromophore variant. J. Phys. Chem. B, 2016, 120, 4410–4420.

  • Ghosh, D., Roy, A., Seidel, R., Winter, B., Bradforth, S. E. and Krylov, A. I., A 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, 2012, 116, 7269–7280.

  • Ghosh, D., Hybrid equation-of-motion coupled-cluster/effective fragment potential method: a route toward understanding photoprocesses in the condensed phase. J. Phys. Chem. A., 2017, 121(4), 741–752.

  • Sahu, N. and Gadre, S. R., Molecular tailoring approach: a route for ab initio treatment of large clusters. Acc. Chem. Res., 2014, 47, 2739–2747.

  • Fedorov, D. G. and Kitaura, K., Extending the power of quantum chemistry to large systems with the fragment molecular orbital method. J. Phys. Chem. A, 2007, 111, 6904–6914.

  • Mayhall, N. J. and Raghavachari, K., Molecules-in-molecules: an extrapolated fragment-based approach for accurate calculations on large molecules and materials. J. Chem. Theory Comput., 2011, 7, 1336–1343.

  • Gurunathan, P. et al., The extension of the effective fragment potential method to macromolecules. J. Phys. Chem. B, 2016, 120, 6562–6574.


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  • Multiscale Modelling:Hybrid Quantum Mechanics/Molecular Mechanics as an Example and some Recent Developments

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Authors

Debashree Ghosh
Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411 008, India

Abstract


Most of the physical phenomena are multiscale in nature and therefore, to depict it properly one requires multiscale modelling techniques, i.e. physical models that are accurate over multiple length and time scales. The seminal work by Warshel and Levitt marks the beginning of hybrid quantum mechanics/molecular mechanics (QM/MM) method as a successful strategy towards the understanding of chemistry and physics in condensed phases and especially in biological systems. Recently, these methods have been extended to problems such as light-matter interaction, where the QM sub-system is excited from the ground to the excited states. The MM environment provides a field that changes the potential energy landscape of both the ground and excited states in a distinctly different way. In this review, we discuss the general strategy of multiscale modelling with emphasis on hybrid QM/MM and the recent developments in excited state QM/MM methods.

Keywords


Biological Systems, Hybrid Quantum Mechanics/Molecular Mechanics, Multiscale.

References





DOI: https://doi.org/10.18520/cs%2Fv112%2Fi07%2F1455-1462