Fragment molecular orbital calculations under periodic boundary condition

Abstract The periodic boundary condition (PBC) is incorporated in the fragment molecular orbital (FMO) method to appropriately describe systems with aqueous solutions. We present benchmark calculations for ( H 2 O ) 64 and show that this PBC-FMO method can eliminate artificial surface effects. An application to molecular dynamics simulation for liquid water is also shown, and calculated radial distribution functions are in reasonable agreement with those obtained from experiments. It is thus confirmed that the present PBC-FMO method is useful for ab initio simulations in aqueous solution.

[1]  Calculation of packing structure of methanol solid using ab initio lattice energy at the MP2 level , 2003 .

[2]  Masami Uebayasi,et al.  Pair interaction molecular orbital method: an approximate computational method for molecular interactions , 1999 .

[3]  T. Nakano,et al.  Fragment interaction analysis based on local MP2 , 2007 .

[4]  Masami Uebayasi,et al.  The fragment molecular orbital method for geometry optimizations of polypeptides and proteins. , 2007, The journal of physical chemistry. A.

[5]  K. Kitaura,et al.  Fragment molecular orbital method: an approximate computational method for large molecules , 1999 .

[6]  Kazuo Kitaura,et al.  The three-body fragment molecular orbital method for accurate calculations of large systems , 2006 .

[7]  U. Nagashima,et al.  Development of an ab initio MO-MD program based on fragment MO method – an attempt to analyze the fluctuation of protein , 2004 .

[8]  Makoto Taiji,et al.  Fast and accurate molecular dynamics simulation of a protein using a special‐purpose computer , 1997 .

[9]  T. Nakano,et al.  Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Zn(II) ion , 2010 .

[10]  Kazuo Kitaura,et al.  Importance of the hybrid orbital operator derivative term for the energy gradient in the fragment molecular orbital method , 2010 .

[11]  Kazuo Kitaura,et al.  The importance of three-body terms in the fragment molecular orbital method. , 2004, The Journal of chemical physics.

[12]  Makoto Haraguchi,et al.  Parallel molecular dynamics simulation of a protein , 2001, Parallel Comput..

[13]  B. Berne,et al.  Quantum effects in liquid water: Path-integral simulations of a flexible and polarizable ab initio model , 2001 .

[14]  K. Kitaura,et al.  Excited state geometry optimizations by time-dependent density functional theory based on the fragment molecular orbital method , 2009 .

[15]  Hiroaki Tokiwa,et al.  Theoretical study of intramolecular interaction energies during dynamics simulations of oligopeptides by the fragment molecular orbital-Hamiltonian algorithm method. , 2005, The Journal of chemical physics.

[16]  Yuichi Inadomi,et al.  Fragment molecular orbital method: application to molecular dynamics simulation, ‘ab initio FMO-MD’ , 2003 .

[17]  Kazuo Kitaura,et al.  Extending the power of quantum chemistry to large systems with the fragment molecular orbital method. , 2007, The journal of physical chemistry. A.

[18]  Yuji Mochizuki,et al.  Large scale MP2 calculations with fragment molecular orbital scheme , 2004 .

[19]  A. Seitsonen,et al.  Importance of van der Waals interactions in liquid water. , 2009, The journal of physical chemistry. B.

[20]  Sotiris S. Xantheas,et al.  Ab initio studies of cyclic water clusters (H2O)n, n=1–6. I. Optimal structures and vibrational spectra , 1993 .

[21]  Kaori Fukuzawa,et al.  Large scale FMO-MP2 calculations on a massively parallel-vector computer , 2008 .

[22]  K. Kitaura,et al.  Ab initio MO based lattice energy for molecular crystals: packing structure of electron donor–acceptor (EDA) complex H3N–BF3 , 2003 .

[23]  Takeshi Ishikawa,et al.  Fragment Molecular Orbital method‐based Molecular Dynamics (FMO‐MD) as a simulator for chemical reactions in explicit solvation , 2009, J. Comput. Chem..

[24]  Takeshi Ishikawa,et al.  Partial energy gradient based on the fragment molecular orbital method: Application to geometry optimization , 2010 .

[25]  Yutaka Akiyama,et al.  Fragment molecular orbital method: application to polypeptides , 2000 .

[26]  S. Hirata Fast electron-correlation methods for molecular crystals: an application to the alpha, beta(1), and beta(2) modifications of solid formic acid. , 2008, The Journal of chemical physics.

[27]  Kazuo Kitaura,et al.  The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems , 2009 .

[28]  Kaori Fukuzawa,et al.  Accuracy of fragmentation in ab initio calculations of hydrated sodium cation , 2009 .

[29]  Yuto Komeiji,et al.  Fragment molecular orbital-based molecular dynamics (FMO-MD) method with MP2 gradient , 2011 .

[30]  G. Schenter,et al.  A quantitative account of quantum effects in liquid water. , 2006, The Journal of chemical physics.

[31]  Yuto Komeiji,et al.  Fragment molecular orbital method: analytical energy gradients , 2001 .

[32]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[33]  Greg L. Hura,et al.  A high-quality x-ray scattering experiment on liquid water at ambient conditions , 2000 .

[34]  Kaori Fukuzawa,et al.  Fragment molecular orbital method: use of approximate electrostatic potential , 2002 .

[35]  Yuichi Inadomi,et al.  PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules. , 2004, Computational biology and chemistry.

[36]  A. Soper,et al.  Joint structure refinement of x-ray and neutron diffraction data on disordered materials: application to liquid water , 2007, Journal of physics. Condensed matter : an Institute of Physics journal.

[37]  Umpei Nagashima,et al.  Ab Initio MO-MD Simulation Based on the Fragment MO Method. A Case of (−)-Epicatechin Gallate with STO-3G Basis Set , 2008 .

[38]  Takeshi Ishikawa,et al.  A fully quantum mechanical simulation study on the lowest n-π* state of hydrated formaldehyde , 2007 .

[39]  Umpei Nagashima,et al.  A parallelized integral-direct second-order Møller–Plesset perturbation theory method with a fragment molecular orbital scheme , 2004 .

[40]  T. Nakano,et al.  Does amination of formaldehyde proceed through a zwitterionic intermediate in water? Fragment molecular orbital molecular dynamics simulations by using constraint dynamics. , 2010, Chemistry.

[41]  Yuto Komeiji,et al.  Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD)☆ , 2010 .

[42]  Shigenori Tanaka,et al.  Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method , 2009 .

[43]  Takeshi Ishikawa,et al.  How does an S(N)2 reaction take place in solution? Full ab initio MD simulations for the hydrolysis of the methyl diazonium ion. , 2008, Journal of the American Chemical Society.

[44]  Kazuo Kitaura,et al.  Derivatives of the approximated electrostatic potentials in the fragment molecular orbital method , 2009 .

[45]  Alan K. Soper,et al.  The radial distribution functions of water and ice from 220 to 673 K and at pressures up to 400 MPa , 2000 .

[46]  Kazuya Ishimura,et al.  Accuracy of the three‐body fragment molecular orbital method applied to Møller–Plesset perturbation theory , 2007, J. Comput. Chem..

[47]  Yuto Komeiji,et al.  Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum simulation tool for large molecular systems , 2009 .

[48]  Jay W. Ponder,et al.  Accurate modeling of the intramolecular electrostatic energy of proteins , 1995, J. Comput. Chem..