Density-fragment Interaction Approach for Quantum-mechanical/molecular-mechanical Calculations with Application to the Excited States of a Mg(2+)-sensitive Dye

Overview

Journal J Chem Phys

Publisher American Institute of Physics

Specialties Biophysics
Chemistry

Date 2008 Aug 14

PMID 18698883

Citations 8

Authors

Kazuhiro Fujimoto

Weitao Yang

Affiliations

Soon will be listed here.

Abstract

A density-fragment interaction (DFI) approach for large-scale calculations is proposed. The DFI scheme describes electron density interaction between many quantum-mechanical (QM) fragments, which overcomes errors in electrostatic interactions with the fixed point-charge description in the conventional quantum-mechanical/molecular-mechanical (QM/MM) method. A self-consistent method, which is a mean-field treatment of the QM fragment interactions, was adopted to include equally the electron density interactions between the QM fragments. As a result, this method enables the evaluation of the polarization effects of the solvent and the protein surroundings. This method was combined with not only density functional theory (DFT) but also time-dependent DFT. In order to evaluate the solvent polarization effects in the DFI-QM/MM method, we have applied it to the excited states of the magnesium-sensitive dye, KMG-20. The DFI-QM/MM method succeeds in including solvent polarization effects and predicting accurately the spectral shift caused by Mg(2+) binding.

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References

Monard G, Bernal-Uruchurtu M, van der Vaart A, Merz Jr K, Ruiz-Lopez M . Simulation of liquid water using semiempirical Hamiltonians and the divide and conquer approach. J Phys Chem A. 2006; 109(15):3425-32. DOI: 10.1021/jp0459099. View

Fedorov D, Kitaura K . The importance of three-body terms in the fragment molecular orbital method. J Chem Phys. 2004; 120(15):6832-40. DOI: 10.1063/1.1687334. View

Hu H, Yang W . Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. Annu Rev Phys Chem. 2008; 59:573-601. PMC: 3727228. DOI: 10.1146/annurev.physchem.59.032607.093618. View

Lu Z, Nowak W, Lee G, Marszalek P, Yang W . Elastic properties of single amylose chains in water: a quantum mechanical and AFM study. J Am Chem Soc. 2004; 126(29):9033-41. DOI: 10.1021/ja031940x. View

Liu H, Elstner M, Kaxiras E, Frauenheim T, Hermans J, Yang W . Quantum mechanics simulation of protein dynamics on long timescale. Proteins. 2001; 44(4):484-9. DOI: 10.1002/prot.1114. View

Becke . Density-functional exchange-energy approximation with correct asymptotic behavior. Phys Rev A Gen Phys. 1988; 38(6):3098-3100. DOI: 10.1103/physreva.38.3098. View

Nakajima T, Hirao K . A dual-level approach to density-functional theory. J Chem Phys. 2006; 124(18):184108. DOI: 10.1063/1.2198529. View

Kobayashi M, Akama T, Nakai H . Second-order Møller-Plesset perturbation energy obtained from divide-and-conquer Hartree-Fock density matrix. J Chem Phys. 2006; 125(20):204106. DOI: 10.1063/1.2388261. View

Zheng X, Chen G, Li Z, Deng S, Xu N . Quantum-mechanical investigation of field-emission mechanism of a micrometer-long single-walled carbon nanotube. Phys Rev Lett. 2004; 92(10):106803. DOI: 10.1103/PhysRevLett.92.106803. View

10.

Warshel A, 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(2):227-49. DOI: 10.1016/0022-2836(76)90311-9. View

11.

Cohen A, Mori-Sanchez P, Yang W . Development of exchange-correlation functionals with minimal many-electron self-interaction error. J Chem Phys. 2007; 126(19):191109. DOI: 10.1063/1.2741248. View

12.

Lee , Yang , PARR . Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B Condens Matter. 1988; 37(2):785-789. DOI: 10.1103/physrevb.37.785. View

13.

Wang B, Brothers E, van der Vaart A, Merz Jr K . Fast semiempirical calculations for nuclear magnetic resonance chemical shifts: a divide-and-conquer approach. J Chem Phys. 2004; 120(24):11392-400. DOI: 10.1063/1.1752877. View

14.

Fedorov D, Kitaura K . Second order Møller-Plesset perturbation theory based upon the fragment molecular orbital method. J Chem Phys. 2004; 121(6):2483-90. DOI: 10.1063/1.1769362. View

15.

Suzuki Y, Komatsu H, Ikeda T, Saito N, Araki S, Citterio D . Design and synthesis of Mg2+-selective fluoroionophores based on a coumarin derivative and application for Mg2+ measurement in a living cell. Anal Chem. 2002; 74(6):1423-8. DOI: 10.1021/ac010914j. View

16.

Rocha G, Freire R, Simas A, Stewart J . RM1: a reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I. J Comput Chem. 2006; 27(10):1101-11. DOI: 10.1002/jcc.20425. View

17.

Hu H, Lu Z, Yang W . QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase. J Chem Theory Comput. 2008; 3(2):390-406. PMC: 2600730. DOI: 10.1021/ct600240y. View

18.

Nakatsuji H, Miyahara T, Fukuda R . Symmetry-adapted-cluster/symmetry-adapted-cluster configuration interaction methodology extended to giant molecular systems: ring molecular crystals. J Chem Phys. 2007; 126(8):084104. DOI: 10.1063/1.2464113. View

19.

Yang . Direct calculation of electron density in density-functional theory. Phys Rev Lett. 1991; 66(11):1438-1441. DOI: 10.1103/PhysRevLett.66.1438. View

20.

Hu H, Lu Z, Elstner M, Hermans J, Yang W . Simulating water with the self-consistent-charge density functional tight binding method: from molecular clusters to the liquid state. J Phys Chem A. 2007; 111(26):5685-91. PMC: 2518942. DOI: 10.1021/jp070308d. View