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602 related items for PubMed ID: 21815177

  • 1. Toward a new approach for determination of solute's charge distribution to analyze interatomic electrostatic interactions in quantum mechanical/molecular mechanical simulations.
    Yamada K, Koyano Y, Okamoto T, Asada T, Koga N, Nagaoka M.
    J Comput Chem; 2011 Nov 15; 32(14):3092-104. PubMed ID: 21815177
    [Abstract] [Full Text] [Related]

  • 2. Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations.
    Lu Z, Yang W.
    J Chem Phys; 2004 Jul 01; 121(1):89-100. PubMed ID: 15260525
    [Abstract] [Full Text] [Related]

  • 3. Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations.
    Lin H, Truhlar DG.
    J Phys Chem A; 2005 May 05; 109(17):3991-4004. PubMed ID: 16833721
    [Abstract] [Full Text] [Related]

  • 4. Geometry optimization using tuned and balanced redistributed charge schemes for combined quantum mechanical and molecular mechanical calculations.
    Wang B, Truhlar DG.
    Phys Chem Chem Phys; 2011 Jun 14; 13(22):10556-64. PubMed ID: 21403957
    [Abstract] [Full Text] [Related]

  • 5. Comparison of polarizable continuum model and quantum mechanics/molecular mechanics solute electronic polarization: study of the optical and magnetic properties of diazines in water.
    Manzoni V, Lyra ML, Coutinho K, Canuto S.
    J Chem Phys; 2011 Oct 14; 135(14):144103. PubMed ID: 22010694
    [Abstract] [Full Text] [Related]

  • 6. Computation of the free energy change associated with one-electron reduction of coenzyme immersed in water: a novel approach within the framework of the quantum mechanical/molecular mechanical method combined with the theory of energy representation.
    Takahashi H, Ohno H, Kishi R, Nakano M, Matubayasi N.
    J Chem Phys; 2008 Nov 28; 129(20):205103. PubMed ID: 19045881
    [Abstract] [Full Text] [Related]

  • 7. Conformational dependence of charges in protein simulations.
    Söderhjelm P, Ryde U.
    J Comput Chem; 2009 Apr 15; 30(5):750-60. PubMed ID: 18773405
    [Abstract] [Full Text] [Related]

  • 8. pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.
    Riccardi D, Schaefer P, Cui Q.
    J Phys Chem B; 2005 Sep 22; 109(37):17715-33. PubMed ID: 16853267
    [Abstract] [Full Text] [Related]

  • 9. The roles of electronic exchange and correlation in charge-transfer- to-solvent dynamics: Many-electron nonadiabatic mixed quantum/classical simulations of photoexcited sodium anions in the condensed phase.
    Glover WJ, Larsen RE, Schwartz BJ.
    J Chem Phys; 2008 Oct 28; 129(16):164505. PubMed ID: 19045282
    [Abstract] [Full Text] [Related]

  • 10. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.
    Monari A, Rivail JL, Assfeld X.
    Acc Chem Res; 2013 Feb 19; 46(2):596-603. PubMed ID: 23249409
    [Abstract] [Full Text] [Related]

  • 11. Polarization and charge-transfer effects in aqueous solution via ab initio QM/MM simulations.
    Mo Y, Gao J.
    J Phys Chem B; 2006 Feb 23; 110(7):2976-80. PubMed ID: 16494296
    [Abstract] [Full Text] [Related]

  • 12. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.
    Hu H, Lu Z, Parks JM, Burger SK, Yang W.
    J Chem Phys; 2008 Jan 21; 128(3):034105. PubMed ID: 18205486
    [Abstract] [Full Text] [Related]

  • 13. A quantum chemical approach to the free energy calculations in condensed systems: the QM/MM method combined with the theory of energy representation.
    Takahashi H, Matubayasi N, Nakahara M, Nitta T.
    J Chem Phys; 2004 Sep 01; 121(9):3989-99. PubMed ID: 15332945
    [Abstract] [Full Text] [Related]

  • 14. Tuned and Balanced Redistributed Charge Scheme for Combined Quantum Mechanical and Molecular Mechanical (QM/MM) Methods and Fragment Methods: Tuning Based on the CM5 Charge Model.
    Wang B, Truhlar DG.
    J Chem Theory Comput; 2013 Feb 12; 9(2):1036-42. PubMed ID: 26588746
    [Abstract] [Full Text] [Related]

  • 15. Long-range electrostatic interactions in hybrid quantum and molecular mechanical dynamics using a lattice summation approach.
    Dehez F, Martins-Costa MT, Rinaldi D, Millot C.
    J Chem Phys; 2005 Jun 15; 122(23):234503. PubMed ID: 16008458
    [Abstract] [Full Text] [Related]

  • 16. Hybrid density functional theory/molecular mechanics calculations of two-photon absorption of dimethylamino nitro stilbene in solution.
    Arul Murugan N, Kongsted J, Rinkevicius Z, Aidas K, Mikkelsen KV, Ågren H.
    Phys Chem Chem Phys; 2011 Jul 21; 13(27):12506-16. PubMed ID: 21660320
    [Abstract] [Full Text] [Related]

  • 17. CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model.
    Patel S, Mackerell AD, Brooks CL.
    J Comput Chem; 2004 Sep 21; 25(12):1504-14. PubMed ID: 15224394
    [Abstract] [Full Text] [Related]

  • 18. Performance assessment of semiempirical molecular orbital methods in describing halogen bonding: quantum mechanical and quantum mechanical/molecular mechanical-molecular dynamics study.
    Ibrahim MA.
    J Chem Inf Model; 2011 Oct 24; 51(10):2549-59. PubMed ID: 21942911
    [Abstract] [Full Text] [Related]

  • 19. Simple and exact approach to the electronic polarization effect on the solvation free energy: formulation for quantum-mechanical/molecular-mechanical system and its applications to aqueous solutions.
    Takahashi H, Omi A, Morita A, Matubayasi N.
    J Chem Phys; 2012 Jun 07; 136(21):214503. PubMed ID: 22697554
    [Abstract] [Full Text] [Related]

  • 20. Communication: Quantum polarized fluctuating charge model: a practical method to include ligand polarizability in biomolecular simulations.
    Kimura SR, Rajamani R, Langley DR.
    J Chem Phys; 2011 Dec 21; 135(23):231101. PubMed ID: 22191857
    [Abstract] [Full Text] [Related]

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