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Quantum Mechanical Insights into Biological Processes at the Electronic Level

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Computational Modeling of Biological Systems

Part of the book series: Biological and Medical Physics, Biomedical Engineering ((BIOMEDICAL))

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Abstract

The realm of biology is always governed by underlying electronic effects. These effects are often treated implicitly and may go nearly unnoticed in classical biomolecular simulations, such as Monte Carlo or molecular dynamics. It is important to remember, however, that these classical methods always operate on the single, ground electronic potential energy surface (PES). Furthermore, classical methods assume the classical behavior of the atomic nuclei, and thus rely on the so-called Born–Oppenheimer approximation (BAO) heavily used in quantum mechanics, as discussed in detail below. Due to the BAO, the ground PES can be obtained by finding the optimal electronic solution for every position of stationary classical nuclei. The combined electronic and nuclear energy as a function of nuclear coordinates in the PES. The Born–Oppenheimer PES is usually very close to the chemical reality. Parameters of classical force fields are optimized to reproduce this ground PES, either calculated quantum mechanically or derived from the experiment. Thus, electronic structure is always an active player in classical simulations through the parameters of the force field in use. However, when it comes to the assessment of the mechanism of a biochemical reaction that involves breaking and forming of covalent bonds, quantum mechanics is an almost exclusive reliable approach, with a prominent classical exception being the empirical valence bond method. Furthermore, there is a large class of biological processes that simply cannot be assessed without explicit quantum mechanical treatment. An obvious example is electron transfer in enzymes or DNA that plays a pivotal role in every oxidation or reduction event in living cells.

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References

  1. Møller, C., Plesset, M.S.: Note on an approximation treatment for many-electron systems. Phys. Rev. 46, 0618–22 (1934)

    Article  ADS  Google Scholar 

  2. Cizek, J.: (1969) In: Hariharan P.C. (ed.) Advances in Chemical Physics, vol. 14, Wiley Interscience, New York. http://www.gaussian.com/g_tech/g_ur/refs.htm

  3. Purvis, I.I.I.G.D., Bartlett, R.J.: A full coupled-cluster singles and doubles model—the inclusion of disconnected triples. J. Chem. Phys. 76, 1910–18 (1982)

    Google Scholar 

  4. Pople, J.A., Head-Gordon, M., Raghavachari, K.: Quadratic configuration interaction — a general technique for determining electron correlation energies. J. Chem. Phys. 87, 5968–75 (1987)

    Article  ADS  Google Scholar 

  5. Foresman, J.B., Head-Gordon, M., Pople, J.A., Frisch, M.J.: Toward a systematic molecular orbital theory for excited states. J. Phys. Chem. 96, 135–49 (1992)

    Article  Google Scholar 

  6. Pople, J.A., Seeger, R., Krishnan, R.: Variational Configuration Interaction Methods and Comparison with Perturbation Theory. Int. J. Quantum. Chem. Suppl. Y-11, 149–63 (1977)

    Google Scholar 

  7. Hegarty, D., Robb, M.A.: Application of unitary group-methods to configuration-interaction calculations. Mol. Phys. 38, 1795–812 (1979)

    Article  MathSciNet  ADS  Google Scholar 

  8. Andersson, K., Malmqvist, P.A., Roos, B.O.: Second-order perturbation theory with a complete active space self-consistent field reference function. J. Chem. Phys. 96, 1218 (1992)

    Article  ADS  Google Scholar 

  9. Chen, H., Lai, W., Shaik, S.: Multireference and multiconfiguration ab initio methods in heme-related systems: what have we learned so far? J. Phys. Chem B. 115, 1727–1742 (2011)

    Article  Google Scholar 

  10. Knowles, P.J., Werner, H.J.: An efficient method for the evaluation of coupling coefficients in configuration interaction calculations. Chem. Phys. Lett. 145, 514–522 (1988)

    Article  ADS  Google Scholar 

  11. Werner, H.J., Knowles, P.J.: An efficient internally contracted multiconfiguration-reference configuration interaction method. J. Chem. Phys. 89, 5803 (1988)

    Article  ADS  Google Scholar 

  12. Evangelista, F.A., Allen, W.D., Schaefer, H.F.: High-order excitations in state-universal and statespecific multireference coupled cluster theories: model systems. J. Chem. Phys. 125, 154113 (2006)

    Article  ADS  Google Scholar 

  13. Evangelista, F.A., Allen, W.D., Schaefer, H.F.: Coupling term derivation and general implementation of state-specific multireference coupled cluster theories. J. Chem. Phys. 127, 024102 (2007)

    Article  ADS  Google Scholar 

  14. Parr, R.G., Yang, W.: Density-Functional Theory of Atoms and Molecules. New York, Oxford University Press (1989)

    Google Scholar 

  15. Tomasi, J., Mennucci, B., Cammi, R.: Quantum mechanical continuum solvation models. Chem. Rev. 105, 2999–3093 (2005)

    Article  Google Scholar 

  16. Suárez, D., Díaz, N., Merz, K.M. Jr: Ureases: quantum chemical calculations on cluster models. J. Am. Chem. Soc. 125, 15324–15337 (2003)

    Article  Google Scholar 

  17. Jensen, K.P., Bell, I.I.I.C.B., Clay, M.D., Solomon, E.I.: Peroxo-type intermediates in class i ribonucleotide reductase and related binuclear non-heme iron enzymes. J. Am. Chem. Soc. 131, 12155–12171 (2009)

    Google Scholar 

  18. Rothlisberger, D., Khersonsky, O., Wollacott, A.M., Jiang, L., Dechancie, J., Betker, J., Gallaher, J.L., Althoff, E., Zanghellini, A.A., Dym, O., Albeck, S., Houk, K.N., Tawfik, D.S., Baker, D.: Kemp elimination catalysts by computational enzyme design. Nature. 453, 109–195, (2008)

    Article  Google Scholar 

  19. Senn, H.M., Thiel, W.: QM/MM methods for biomolecular systems. Angew. Chem. Int. Ed. 48, 1198–1229 (2009)

    Article  Google Scholar 

  20. Warshel, A., Levitt, M.: Theoretical studies of enzymatic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103, 227–249 (1976)

    Article  Google Scholar 

  21. Froese, R.D.J., Morokuma, K.: (1998) Hybrid methods. In: P.V.R. Schleyer (ed.) Encyclopedia of Computational Chemistry, vol. 2 Wiley, Chichester

    Google Scholar 

  22. Jorgensen, W.L., Tirado-Rives, J.: Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. J. Comput. Chem. 26, 1689–1700 (2005)

    Article  Google Scholar 

  23. Chung, L.W., Li, X., Sugimoto, H., Shiro, Y., Morokuma, K.: ONIOM study on a missing piece in our understanding of heme chemistry: bacterial tryptophan 2,3-dioxygenase with dual oxidants. J. Am. Chem. Soc. 132, 11993–12005 (2010)

    Article  Google Scholar 

  24. Alexandrova, A.N., Rothlisberger, D., Baker, D., Jorgensen, W.L.: Catalytic mechanism and performance of computationally designed enzymes for kemp elimination. J. Am. Chem. Soc. 130, 15907–15915 (2008)

    Article  Google Scholar 

  25. Marques, M.A.L., Ullrich, C.A., Nogueira, F., Rubio, A., Burke, K., Gross, E.K.U.(eds.) Time-Dependent Density Functional Theory. Springer, Verlag (2006)

    MATH  Google Scholar 

  26. Wu, Q., Van Voorhis, T.: Direct optimization method to study constrained systems within dnsityfuncitonal theory. Phys. Rev. A. 72, 024502-1–024502-4 (2005)

    Google Scholar 

  27. Krylov, A.I.: Equation-of-motion coupled-cluster methods for open-shell and electronically excited species: the hitchhiker’s guide to fock space. Ann. Rev. Phys. Chem. 59, 433–462,  (2008)

    Article  ADS  Google Scholar 

  28. Slavíček, P., Winter, B., Faubel, M., Sbadforth, S.E., Jungwirth, P.: Ionization energies of aqueous nucleic acids: photoelectron spectroscopy of pyrimidine nucleosides and ab initio calculations. J. Am. Chem. Soc. 131, 6460–6467 (2009)

    Article  Google Scholar 

  29. Epifanovsky, E., Polyakov, I., Grigorenko, B., Nemukhin, A., Krylov, A.I.: The effect of oxidation on the electronic structure of the green fluorescent protein chromophore. J. Chem. Phys. 132, 115104 (2010)

    Article  ADS  Google Scholar 

  30. Fülscher, M.P., Serrano-Andrés, L., Roos, B.O.: A theoretical study of the electronic spectra of adenine and guanine. J. Am. Chem. Soc. 119, 6168–6176 (1997)

    Article  Google Scholar 

  31. Boggio-Pasqua, M., Groenhof, G., Schäfer, L.V., Grubmüller, H., Robb, M.A.: Ultrafast deactivation channel for thymine dimerization. J. Am. Chem. Soc. 129, 10996–10997 (2007)

    Article  Google Scholar 

  32. Yamazaki, S., Kato, S.: Solvent effect on conical intersections in excited-state 9H-adenine: radiationless decay mechanism in polar solvent. J. Am. Chem. Sos. 129, 2901–2909 (2007)

    Article  Google Scholar 

  33. Bunker, D.L.: Classical trajectory methods. Meth. Comp. Phys. 10, 287 (1971)

    Google Scholar 

  34. Raff, L.M., Thompson, D.L.: (1985) Advances in classical trajectory methods. In: Baer M (ed.) Theory of Chemical Reaction Dynamics, CRC, Boca Raton, FL

    Google Scholar 

  35. Car, R., Parrinello, M.: Unified approach for molecular-dynamics and density-functional theory. Phys. Rev. Lett. 55, 2471–74 (1985)

    Article  ADS  Google Scholar 

  36. Tully, J.C.: Molecular dynamics with electronic transitions. J. Chem. Phys. 93, 1061 (1990)

    Article  ADS  Google Scholar 

  37. Ben-Nun, M., Martínez, T.J.: Nonadiabatic molecular dynamics: validation of the multiple spawning method for a multidimensional problem. J. Chem. Phys. 108, 7244–7257 (1998)

    Article  ADS  Google Scholar 

  38. Ben-Nun, M.; Martínez, T.J.: Ab initio quantum molecular dynamics. Adv. Chem. Phys. 121, 439–512 (2002)

    Article  Google Scholar 

  39. Masson, M., Laino, T., Tavernelli, I., Rothlisberger, U., Hutter, J.: Computational study of thymine dimer radical anion splitting in the self-repair process of duplex DNA. J. Am. Chem. Soc. 130, 3443–3450, (2008)

    Article  Google Scholar 

  40. Groenhof, G., Schäfer, L.V., Boggio-Pasqua, M., Goette, M., Grubmüller, H., Robb, M.A.: Ultrafast deactivation of an excited cytosine-guanine base pair in DNA. J. Am. Chem. Soc. 129, 6812–6819 (2007)

    Article  Google Scholar 

  41. Hudock, H.R., Martínez, T.J.: Excited-state dynamics of cytosine reveal multiple intrinsic subpicosecond pathways. Chem. Phys. Chem. 9, 2486–2490 (2008)

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, 90095-1569, USA

    Anastassia N. Alexandrova

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  1. Anastassia N. Alexandrova
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Correspondence to Anastassia N. Alexandrova .

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  1. , Biochemistry and Biophysics, University of North Carolina at Chapel H, Mason Farm Rd 120, Chapel Hill, 27599-7260, North Carolina, USA

    Nikolay V Dokholyan

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Alexandrova, A.N. (2012). Quantum Mechanical Insights into Biological Processes at the Electronic Level. In: Dokholyan, N. (eds) Computational Modeling of Biological Systems. Biological and Medical Physics, Biomedical Engineering. Springer, Boston, MA. https://doi.org/10.1007/978-1-4614-2146-7_6

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  • DOI: https://doi.org/10.1007/978-1-4614-2146-7_6

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