Geometry optimizations with the incremental molecular fragmentation method

被引:7
|
作者
Meitei, Oinam Romesh [1 ]
Hesselmann, Andreas [1 ]
机构
[1] Friedrich Alexander Univ Erlangen Nurnberg, Dept Chem & Pharm, Lehrstuhl Theoret Chem, Egerlandstr 3, D-91058 Erlangen, Germany
来源
关键词
Molecular fragmentation; geometry optimization; polypeptide; QUANTUM-MECHANICAL CALCULATION; BASIS-SET CONVERGENCE; MANY-BODY EXPANSION; CORRELATED CALCULATIONS; ACCURATE CALCULATIONS; CONJUGATE CAPS; ENERGY; EFFICIENT; IMPLEMENTATION; ELECTRON;
D O I
10.1142/S0219633618500372
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Nuclear energy gradients for the incremental molecular fragmentation (IMF) method presented in our previous work [Meitei OR, HeBelmann A, Molecular energies from an incremental fragmentation method, J Chem Phys 144(8):084109, 2016] have been derived. Using the secondorder Moller-Plesset perturbation theory method to describe the bonded and nonbonded energy and gradient contributions and the uncorrelated Hartree-Fock method to describe the correction increment, it is shown that the IMF gradient can be easily computed by a sum of the underlying individual derivatives of the energy contributions. The performance of the method has been compared against the supermolecular method by optimizing the structures of a range of polyglycine molecules with up to 36 glycine residues in the chain. It is shown that with a sensible set of parameters used in the fragmentation the supermolecular structures can be fairly well reproduced. In a few cases the optimization with the IMF method leads to structures that differ from the supermolecular ones. It was found, however, that these are more stable geometries also on the supermolecular potential energy surface.
引用
收藏
页数:39
相关论文
共 50 条
  • [1] Molecular energies from an incremental fragmentation method
    Meitei, Oinam Romesh
    Hesselmann, Andreas
    JOURNAL OF CHEMICAL PHYSICS, 2016, 144 (08):
  • [2] The fragment molecular orbital method for geometry optimizations of polypeptides and proteins
    Fedorov, Dmitri G.
    Ishida, Toyokazu
    Uebayasi, Masami
    Kitaura, Kazuo
    JOURNAL OF PHYSICAL CHEMISTRY A, 2007, 111 (14): : 2722 - 2732
  • [3] Geometry Optimizations of Open-Shell Systems with the Fragment Molecular Orbital Method
    Pruitt, Spencer R.
    Fedorov, Dmitri G.
    Gordon, Mark S.
    JOURNAL OF PHYSICAL CHEMISTRY A, 2012, 116 (20): : 4965 - 4974
  • [4] The effect of numerical error on the reproducibility of molecular geometry optimizations
    Christopher I. Williams
    Miklos Feher
    Journal of Computer-Aided Molecular Design, 2008, 22 : 39 - 51
  • [5] The effect of numerical error on the reproducibility of molecular geometry optimizations
    Williams, Christopher I.
    Feher, Miklos
    JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 2008, 22 (01) : 39 - 51
  • [6] Hybrid RHF/MP2 Geometry Optimizations with the Effective Fragment Molecular Orbital Method
    Christensen, Anders S.
    Steinmann, Casper
    Fedorov, Dmitri G.
    Jensen, Jan H.
    PLOS ONE, 2014, 9 (02):
  • [7] ON THE USE OF A HESSIAN MODEL FUNCTION IN MOLECULAR-GEOMETRY OPTIMIZATIONS
    LINDH, R
    BERNHARDSSON, A
    KARLSTROM, G
    MALMQVIST, PA
    CHEMICAL PHYSICS LETTERS, 1995, 241 (04) : 423 - 428
  • [8] Incremental Verification of Compiler Optimizations
    Fedyukovich, Grigory
    Gurfinkel, Arie
    Sharygina, Natasha
    NASA FORMAL METHODS, NFM 2014, 2014, 8430 : 300 - 306
  • [9] A new implementation of population based incremental learning method for optimizations in electromagnetics
    Yang, S. Y.
    Ho, S. L.
    Ni, G. Z.
    Machado, Jose Marcio
    Wong, K. F.
    IEEE TRANSACTIONS ON MAGNETICS, 2007, 43 (04) : 1601 - 1604
  • [10] 3RD-ORDER METHODS FOR MOLECULAR-GEOMETRY OPTIMIZATIONS
    VOGEL, S
    FISCHER, TH
    HUTTER, J
    LUTHI, HP
    INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 1993, 45 (06) : 679 - 688