Abstract
We discuss quantum mechanical methods for the description of the potential energy surface and for the treatment of nuclear quantum effects in chemical and biological applications. Two novel electronic structure methods are described, including an electronic structure-based explicit polarization (X-Pol) force field and an effective Hamiltonian molecular orbital and valence bond (EH-MOVB) theory. In addition, we present two path integral techniques to treat nuclear quantum effects, which include an analytical pathintegral method based on Kleinert’s variational perturbation theory, and integrated pathintegral free-energy perturbation and umbrella sampling (PI-FEP/UM) simulation. Studies have shown that quantum mechanics can be applied to biocatalytic systems in a variety of ways and scales. We hope that the methods presented in this article can further expand the scope of quantum mechanical applications to biomolecular systems
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Gao J, Ma S, Major DT, Nam K, Pu J, Truhlar DG (2006) Mechanisms and free energies of enzymatic reactions. Chem Rev 106(8):3188–3209
Pu J, Gao J, Truhlar DG (2006) Multidimensional tunneling, recrossing, and the transmission coefficient for enzymatic reactions. Chem Rev 106(8):3140–3169
Garcia-Viloca M, Gao J, Karplus M, Truhlar DG (2004) How enzymes work: Analysis by modern rate theory and computer simulations. Science (Washington, DC) 303(5655):186–195
Gao J (1997) Toward a molecular orbital derived empirical potential for liquid simulations. J Phys Chem B 101(4):657–663
Gao J (1998) A molecular-orbital derived polarization potential for liquid water. J Chem Phys 109(6):2346–2354
Xie W, Gao J (2007) Design of a next generation force field: the X-POL potential. J Chem Theory Comput 3(6):1890–1900
Xie W, Song L, Truhlar DG, Gao J (2008) The variational explicit polarization potential and analytical first derivative of energy: towards a next generation force field. J Chem Phys 128(23):234108
Xie W, Song L, Truhlar DG, Gao J (2008) Incorporation of QM/MM buffer zone in the variational double self-consistent field method. J Phys Chem B 112(45):14124–14131
Mo Y, Gao J (2000) Ab initio QM/MM simulations with a molecular orbital-valence bond (MOVB) method: application to an SN2 reaction in water. J Comput Chem 21(16):1458–1469
Mo Y, Gao J, (2000) An ab initio molecular orbital-valence bond (MOVB) method for simulating chemical reactions in solution. J Phys Chem A 104(13):3012–3020
Song L, Gao J (2008) On the construction of diabatic and adiabatic potential energy surfaces based on ab initio valence bond theory. J Phys Chem A ASAP
Wong K-Y, Gao J (2007) An automated integration-free path-integral method based on Kleinert’s variational perturbation theory. J Chem Phys 127(21): 211103
Wong K-Y, Gao J (2008) Systematic approach for computing zero-point energy, quantum partition function, and tunneling effect based on Kleinert’s variational perturbation theory. J Chem Theory Comput 4(9):1409–1422
Jang S, Voth GA (2001) A relationship between centroid dynamics and path integral quantum transition state theory. J Chem Phys 112(8747–8757): Erratum: 114, 1944
Feynman RP, Hibbs AR (1965) Quantum Mechanics and Path Integrals. McGraw-Hill: New York, p xiv, 365 p. For the applications in quantum statistics, see chapters 10 and 11; Corrections to the errata in the book: http://www.oberlin.edu/physics/dstyer/FeynmanHibbs/ and http://www.physik.fu-berlin.de/kleinert/Feynman-Hibbs/
Bixon M, Lifson S (1967) Potential functions and conformations in cycloalkanes. Tetrahedron 23(2):769–784
Levitt M (2001) The birth of computational structural biology. Nat Struct Biol 8(5):392–393
Kohen A, Limbach H-H (2006) Isotope Effects in Chemistry and Biology. Taylor & Francis: Boca Raton, p xiv, 1074 p
Major DT, Gao J (2007) An integrated path integral and free-energy perturbation-umbrella sampling method for computing kinetic isotope effects of chemical reactions in solution and in enzymes. J Chem Theory Comput 3:949–960
Gao J, Wong K-Y, Major DT (2008) Combined QM/MM and path integral simulations of kinetic isotope effects in the proton transfer reaction between nitroethane and acetate ion in water. J Comput Chem 29:514–522
Kleinert H (2004) Path integrals in quantum mechanics, statistics, polymer physics, and financial markets. 3rd edition.; World Scientific: Singapore; River Edge, NJ, p xxvi, 1468 p. For the quantum mechanical integral equation, see Section 1.9; For the variational perturbation theory, see Chapters 3 and 5
Sprik M, Klein ML, Chandler D (1985) Phys. ReV. B: Condens. Matter Mater. Phys. 31:4234–4244
Hwang J-K, Warshel A (1996) J Am Chem Soc 118:11745–11751
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer Science+Business Media B.V.
About this chapter
Cite this chapter
Wong, KY. et al. (2009). Quantum Mechanical Methods for Biomolecular Simulations. In: York, D.M., Lee, TS. (eds) Multi-scale Quantum Models for Biocatalysis. Challenges and Advances in Computational Chemistry and Physics, vol 7. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-9956-4_4
Download citation
DOI: https://doi.org/10.1007/978-1-4020-9956-4_4
Publisher Name: Springer, Dordrecht
Print ISBN: 978-1-4020-9955-7
Online ISBN: 978-1-4020-9956-4
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)