Interfacing the Core-Shell or the Drude Polarizable Force Field With Car-Parrinello Molecular Dynamics for QM/MM Simulations

被引:18
作者
Sahoo, Sudhir K. [1 ,2 ]
Nair, Nisanth N. [1 ]
机构
[1] Indian Inst Technol Kanpur, Dept Chem, Kanpur, Uttar Pradesh, India
[2] Univ Paderborn, Dept Chem, Paderborn, Germany
来源
FRONTIERS IN CHEMISTRY | 2018年 / 6卷
关键词
QMMM simulations; MD; POLARIZED MM; catalysis; CPMD-GULP; AB-INITIO; HYDROGEN-EXCHANGE; PROTON-EXCHANGE; ALPHA-QUARTZ; ALKANE; MODEL; ACTIVATION; CHARMM; OSCILLATORS; TEMPERATURE;
D O I
10.3389/fchem.2018.00275
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
We report a quantum mechanics/polarizable-molecular mechanics (QM/p-MM) potential based molecular dynamics (MD) technique where the core-shell (or the Drude) type polarizable MM force field is interfaced with the plane-wave density functional theory based QM force field which allows Car-Parrinello MD for the QM subsystem. In the QM/p-MM Lagrangian proposed here, the shell (or the Drude) MM variables are treated as extended degrees of freedom along with the Kohn-Sham (KS) orbitals describing the QM wavefunction. The shell and the KS orbital degrees of freedom are then adiabatically decoupled from the nuclear degrees of freedom. In this respect, we also present here the Nose-Hoover Chain thermostat implementation for the dynamical subsystems. Our approach is then used to investigate the effect of MM polarization on the QM/MM results. Especially, the consequence of MM polarization on reaction free energy barriers, defect formation energy, and structural and dynamical properties are investigated. A low point charge polarizable potential (p-MZHB) for pure siliceous systems is also reported here.
引用
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页数:10
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共 52 条
  • [11] THEORY OF THE DIELECTRIC CONSTANTS OF ALKALI HALIDE CRYSTALS
    DICK, BG
    OVERHAUSER, AW
    [J]. PHYSICAL REVIEW, 1958, 112 (01): : 90 - 103
  • [12] DOWNS RT, 1994, AM MINERAL, V79, P9
  • [13] Hydrogen HID Exchange and Activation of C1-n-C4 Alkanes on Ga-Modified Zeolite BEA Studied with 1H Magic Angle Spinning Nuclear Magnetic Resonance in Situ
    Gabrienko, Anton A.
    Arzumanov, Sergei S.
    Toktarev, Alexander V.
    Freude, Dieter
    Haase, Juergen
    Stepanov, Alexander G.
    [J]. JOURNAL OF PHYSICAL CHEMISTRY C, 2011, 115 (28) : 13877 - 13886
  • [14] GULP: A computer program for the symmetry-adapted simulation of solids
    Gale, JD
    [J]. JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS, 1997, 93 (04): : 629 - 637
  • [15] Combined QM/MM molecular dynamics study on a condensed-phase SN2 reaction at nitrogen:: The effect of explicitly including solvent polarization
    Geerke, Daan P.
    Thiel, Stephan
    Thiel, Walter
    van Gunsteren, Wilfred F.
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2007, 3 (04) : 1499 - 1509
  • [16] Semiempirical GGA-type density functional constructed with a long-range dispersion correction
    Grimme, Stefan
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2006, 27 (15) : 1787 - 1799
  • [17] Classical polarization in hybrid QM/MM methods
    Illingworth, Christopher J. R.
    Gooding, Stuart R.
    Winn, Peter J.
    Jones, Garth A.
    Ferenczy, Gyorgy G.
    Reynolds, Christopher A.
    [J]. JOURNAL OF PHYSICAL CHEMISTRY A, 2006, 110 (20) : 6487 - 6497
  • [18] COMPRESSION MECHANISMS IN ALPHA-QUARTZ STRUCTURES-SIO2 AND GEO2
    JORGENSEN, JD
    [J]. JOURNAL OF APPLIED PHYSICS, 1978, 49 (11) : 5473 - 5478
  • [19] Escaping free-energy minima
    Laio, A
    Parrinello, M
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (20) : 12562 - 12566
  • [20] A Hamiltonian electrostatic coupling scheme for hybrid Car-Parrinello molecular dynamics simulations
    Laio, A
    VandeVondele, J
    Rothlisberger, U
    [J]. JOURNAL OF CHEMICAL PHYSICS, 2002, 116 (16) : 6941 - 6947