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
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
收藏
页数:10
相关论文
共 52 条
[1]   Methane Activation on In-Modified ZSM-5 Zeolite. H/D Hydrogen Exchange of the Alkane with Bronsted Acid Sites [J].
Arzumanov, Sergei S. ;
Moroz, Ilya B. ;
Freude, Dieter ;
Haase, Juergen ;
Stepanov, Alexander G. .
JOURNAL OF PHYSICAL CHEMISTRY C, 2014, 118 (26) :14427-14432
[2]   Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling [J].
Awasthi, Shalini ;
Nair, Nisanth N. .
JOURNAL OF CHEMICAL PHYSICS, 2017, 146 (09)
[3]  
Bakowies D, 1996, J PHYS CHEM-US, V100, P10580, DOI 10.1021/jp9536514
[4]   Toward QM/MM Simulation of Enzymatic Reactions with the Drude Oscillator Polarizable Force Field [J].
Boulanger, Eliot ;
Thiel, Walter .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2014, 10 (04) :1795-1809
[5]   Solvent Boundary Potentials for Hybrid QM/MM Computations Using Classical Drude Oscillators: A Fully Polarizable Model [J].
Boulanger, Eliot ;
Thiel, Walter .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2012, 8 (11) :4527-4538
[6]   Proton exchange of small hydrocarbons over acidic chabazite:: Ab initio study of entropic effects [J].
Bucko, Tomas ;
Benco, Lubomir ;
Hafner, Juergen ;
Angyan, Janos G. .
JOURNAL OF CATALYSIS, 2007, 250 (01) :171-183
[7]   UNIFIED APPROACH FOR MOLECULAR-DYNAMICS AND DENSITY-FUNCTIONAL THEORY [J].
CAR, R ;
PARRINELLO, M .
PHYSICAL REVIEW LETTERS, 1985, 55 (22) :2471-2474
[8]   Mechanism of alkane H/D exchange over zeolite H-ZSM-5 at low temperature: a combined computational and experimental study [J].
Chu, Yueying ;
Xue, Nianhua ;
Xu, Bolian ;
Ding, Qian ;
Feng, Zhaochi ;
Zheng, Anmin ;
Deng, Feng .
CATALYSIS SCIENCE & TECHNOLOGY, 2016, 6 (14) :5350-5363
[9]  
CPMD (v 13. 2), 1990, CPMD PROGR PACK
[10]   Molecular-dynamics simulation of MgO surfaces in liquid water using a shell-model potential for water [J].
de Leeuw, NH ;
Parker, SC .
PHYSICAL REVIEW B, 1998, 58 (20) :13901-13908