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Journal Abstract Search

254 related items for PubMed ID: 16706406

  • 1. Classical polarization in hybrid QM/MM methods.
    Illingworth CJ, Gooding SR, Winn PJ, Jones GA, Ferenczy GG, Reynolds CA.
    J Phys Chem A; 2006 May 25; 110(20):6487-97. PubMed ID: 16706406
    [Abstract] [Full Text] [Related]

  • 2. 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]

  • 3. Toward a consistent treatment of polarization in model QM/MM calculations.
    Illingworth CJ, Parkes KE, Snell CR, Ferenczy GG, Reynolds CA.
    J Phys Chem A; 2008 Nov 27; 112(47):12151-6. PubMed ID: 18986123
    [Abstract] [Full Text] [Related]

  • 4. Assessing the role of polarization in docking.
    Illingworth CJ, Morris GM, Parkes KE, Snell CR, Reynolds CA.
    J Phys Chem A; 2008 Nov 27; 112(47):12157-63. PubMed ID: 18986122
    [Abstract] [Full Text] [Related]

  • 5. 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]

  • 6. Applications and assessment of QM:QM electronic embedding using generalized asymmetric Mulliken atomic charges.
    Parandekar PV, Hratchian HP, Raghavachari K.
    J Chem Phys; 2008 Oct 14; 129(14):145101. PubMed ID: 19045166
    [Abstract] [Full Text] [Related]

  • 7. Prediction and rationalization of protein pKa values using QM and QM/MM methods.
    Jensen JH, Li H, Robertson AD, Molina PA.
    J Phys Chem A; 2005 Aug 04; 109(30):6634-43. PubMed ID: 16834015
    [Abstract] [Full Text] [Related]

  • 8. Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential.
    Freindorf M, Shao Y, Furlani TR, Kong J.
    J Comput Chem; 2005 Sep 04; 26(12):1270-8. PubMed ID: 15965971
    [Abstract] [Full Text] [Related]

  • 9. A combined effective fragment potential-fragment molecular orbital method. I. The energy expression and initial applications.
    Nagata T, Fedorov DG, Kitaura K, Gordon MS.
    J Chem Phys; 2009 Jul 14; 131(2):024101. PubMed ID: 19603964
    [Abstract] [Full Text] [Related]

  • 10. QM-MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians.
    Geerke DP, Thiel S, Thiel W, van Gunsteren WF.
    Phys Chem Chem Phys; 2008 Jan 14; 10(2):297-302. PubMed ID: 18213415
    [Abstract] [Full Text] [Related]

  • 11. Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping.
    Xiang Y, Warshel A.
    J Phys Chem B; 2008 Jan 24; 112(3):1007-15. PubMed ID: 18166038
    [Abstract] [Full Text] [Related]

  • 12. 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]

  • 13. Energy decomposition in molecular complexes: implications for the treatment of polarization in molecular simulations.
    Curutchet C, Bofill JM, Hernández B, Orozco M, Luque FJ.
    J Comput Chem; 2003 Jul 30; 24(10):1263-75. PubMed ID: 12820134
    [Abstract] [Full Text] [Related]

  • 14. The implementation of a fast and accurate QM/MM potential method in Amber.
    Walker RC, Crowley MF, Case DA.
    J Comput Chem; 2008 May 30; 29(7):1019-31. PubMed ID: 18072177
    [Abstract] [Full Text] [Related]

  • 15. Computational methods for the study of enzymic reaction mechanisms III: a perturbation plus QM/MM approach for calculating relative free energies of protonation.
    Cummins PL, Gready JE.
    J Comput Chem; 2005 Apr 30; 26(6):561-8. PubMed ID: 15726569
    [Abstract] [Full Text] [Related]

  • 16. 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]

  • 17. Polarization energy gradients in combined quantum mechanics, effective fragment potential, and polarizable continuum model calculations.
    Li H, Gordon MS.
    J Chem Phys; 2007 Mar 28; 126(12):124112. PubMed ID: 17411113
    [Abstract] [Full Text] [Related]

  • 18. Quantum capping potentials with point charges: a simple QM/MM approach for the calculation of large-molecule NMR shielding tensors.
    Moon S, Christiansen PA, DiLabio GA.
    J Chem Phys; 2004 May 15; 120(19):9080-6. PubMed ID: 15267843
    [Abstract] [Full Text] [Related]

  • 19. YinYang atom: a simple combined ab initio quantum mechanical molecular mechanical model.
    Shao Y, Kong J.
    J Phys Chem A; 2007 May 10; 111(18):3661-71. PubMed ID: 17429951
    [Abstract] [Full Text] [Related]

  • 20. QM:QM electronic embedding using Mulliken atomic charges: energies and analytic gradients in an ONIOM framework.
    Hratchian HP, Parandekar PV, Raghavachari K, Frisch MJ, Vreven T.
    J Chem Phys; 2008 Jan 21; 128(3):034107. PubMed ID: 18205488
    [Abstract] [Full Text] [Related]

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