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Volumn 3, Issue 3, 2012, Pages 375-379

RI-MP2 gradient calculation of large molecules using the fragment molecular orbital method

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL ADVANTAGES; COMPUTATIONAL EFFORT; CORRELATION EFFECT; FRAGMENT MOLECULAR ORBITAL METHODS; GRADIENT CALCULATIONS; HARTREE-FOCK; HUMAN IMMUNODEFICIENCY VIRUS TYPE-1; IDENTITY APPROXIMATION; ILLUSTRATIVE EXAMPLES; PERTURBATION THEORY; PRION PROTEIN; SECOND ORDERS;

EID: 84856610786     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz201697x     Document Type: Article
Times cited : (44)

References (34)
  • 1
    • 36849099978 scopus 로고
    • Coulombic Potential Energy Integrals and Approximations
    • Whitten, J. L. Coulombic Potential Energy Integrals and Approximations J. Chem. Phys. 1973, 58, 4496-4501
    • (1973) J. Chem. Phys. , vol.58 , pp. 4496-4501
    • Whitten, J.L.1
  • 2
    • 36749106524 scopus 로고
    • On Some Approximations in Applications of X α Theory
    • Dunlap, B. I.; Connolly, J. W. D.; Sabin, J. R. On Some Approximations in Applications of X α Theory J. Chem. Phys. 1979, 71, 3396-4402
    • (1979) J. Chem. Phys. , vol.71 , pp. 3396-4402
    • Dunlap, B.I.1    Connolly, J.W.D.2    Sabin, J.R.3
  • 3
    • 20344365516 scopus 로고
    • Integral Approximations for LCAO-SCF Calculations
    • Vahtras, O.; Almlöf, J.; Feyereisen, M. W. Integral Approximations for LCAO-SCF Calculations Chem. Phys. Lett. 1993, 213, 514-518
    • (1993) Chem. Phys. Lett. , vol.213 , pp. 514-518
    • Vahtras, O.1    Almlöf, J.2    Feyereisen, M.W.3
  • 5
    • 20344381993 scopus 로고
    • Use of Approximate Integrals in Ab Initio Theory. An Application in MP2 Energy Calculations
    • Feyereisen, M.; Fitzgerald, G.; Komornicki, A. Use of Approximate Integrals in Ab Initio Theory. An Application in MP2 Energy Calculations Chem. Phys. Lett. 1993, 208, 359-363
    • (1993) Chem. Phys. Lett. , vol.208 , pp. 359-363
    • Feyereisen, M.1    Fitzgerald, G.2    Komornicki, A.3
  • 6
    • 0031285839 scopus 로고    scopus 로고
    • RI-MP2: First Derivatives and Global Consistency
    • Weigend, F.; Häser, M. RI-MP2: First Derivatives and Global Consistency Theor. Chem. Acc. 1997, 97, 331-340
    • (1997) Theor. Chem. Acc. , vol.97 , pp. 331-340
    • Weigend, F.1    Häser, M.2
  • 7
    • 33745727718 scopus 로고    scopus 로고
    • Analytical Gradient of Restricted Second-Order Møller-Plesset Correlation Energy with the Resolution of the Identity Approximation, Applied to the TCNE Dimer Anion Complex
    • Rhee, Y. M.; DiStasio, R. A., Jr.; Lochan, R. C.; Head-Gordon, M. Analytical Gradient of Restricted Second-Order Møller-Plesset Correlation Energy with the Resolution of the Identity Approximation, Applied to the TCNE Dimer Anion Complex Chem. Phys. Lett. 2006, 426, 197-203
    • (2006) Chem. Phys. Lett. , vol.426 , pp. 197-203
    • Rhee, Y.M.1    Distasio Jr., R.A.2    Lochan, R.C.3    Head-Gordon, M.4
  • 8
    • 33644810669 scopus 로고    scopus 로고
    • Distributed Memory Parallel Implementation of Energies and Gradients for Second-Order Møller-Plesset Perturbation Theory with the Resolution-of-the-Identity Approximation
    • Hättig, C.; Hellweg, A.; Löhn, A. Distributed Memory Parallel Implementation of Energies and Gradients for Second-Order Møller-Plesset Perturbation Theory with the Resolution-of-the-Identity Approximation Phys. Chem. Chem. Phys. 2006, 8, 1159-1169
    • (2006) Phys. Chem. Chem. Phys. , vol.8 , pp. 1159-1169
    • Hättig, C.1    Hellweg, A.2    Löhn, A.3
  • 9
    • 0001188539 scopus 로고
    • Coupled-Cluster Theory Employing Approximate Integrals: An Approach to Avoid the Input/Output and Storage Bottlenecks
    • Rendell, A. P.; Lee, T. J. Coupled-Cluster Theory Employing Approximate Integrals: An Approach to Avoid the Input/Output and Storage Bottlenecks J. Chem. Phys. 1994, 101, 400-408
    • (1994) J. Chem. Phys. , vol.101 , pp. 400-408
    • Rendell, A.P.1    Lee, T.J.2
  • 10
    • 0000170061 scopus 로고    scopus 로고
    • Pair interaction molecular orbital method: An approximate computational method for molecular interactions
    • PII S0009261499009379
    • Kitaura, K.; Ikeo, E.; Asada, T.; Nakano, T.; Uebayasi, M. Pair Interaction Molecular Orbital Method: An Approximate Computational Method for Molecular Interactions Chem. Phys. Lett. 1999, 312, 319-324 (Pubitemid 129556608)
    • (1999) Chemical Physics Letters , vol.312 , Issue.2-4 , pp. 319-324
    • Kitaura, K.1    Sawai, T.2    Asada, T.3    Nakano, T.4    Uebayasi, M.5
  • 11
    • 0000721543 scopus 로고    scopus 로고
    • Fragment molecular orbital method: An approximate computational method for large molecules
    • PII S000926149900874X
    • Kitaura, K.; Ikeo, E.; Asada, T.; Nakano, T.; Uebayasi, M. Fragment Molecular Orbital Method: An Approximate Computational Method for Large Molecules Chem. Phys. Lett. 1999, 313, 701-706 (Pubitemid 129556715)
    • (1999) Chemical Physics Letters , vol.313 , Issue.3-4 , pp. 701-706
    • Kitaura, K.1    Ikeo, E.2    Asada, T.3    Nakano, T.4    Uebayasi, M.5
  • 12
    • 34248164602 scopus 로고    scopus 로고
    • The fragment molecular orbital method for geometry optimizations of polypeptides and proteins
    • DOI 10.1021/jp0671042
    • Fedorov, D. G.; Ishida, T.; Uebayasi, M.; Kitaura, K. The Fragment Molecular Orbital Method for Geometry Optimizations of Polypeptides and Proteins J. Phys. Chem. A 2007, 111, 2722-2732 (Pubitemid 46713283)
    • (2007) Journal of Physical Chemistry A , vol.111 , Issue.14 , pp. 2722-2732
    • Fedorov, D.G.1    Ishida, T.2    Uebayasi, M.3    Kitaura, K.4
  • 13
    • 78649933706 scopus 로고    scopus 로고
    • Partial Energy Gradient Based on the Fragment Molecular Orbital Method: Application to Geometry Optimization
    • Ishikawa, T.; Yamamoto, N.; Kuwata, K. Partial Energy Gradient Based on the Fragment Molecular Orbital Method: Application to Geometry Optimization Chem. Phys. Lett. 2010, 500, 149-154
    • (2010) Chem. Phys. Lett. , vol.500 , pp. 149-154
    • Ishikawa, T.1    Yamamoto, N.2    Kuwata, K.3
  • 14
    • 79951909482 scopus 로고    scopus 로고
    • Geometry Optimization of the Active Site of a Large System with the Fragment Molecular Orbital Method
    • Fedorov, D. G.; Alexeev, Y.; Kitaura, K. Geometry Optimization of the Active Site of a Large System with the Fragment Molecular Orbital Method J. Phys. Chem. Lett. 2011, 2, 282-288
    • (2011) J. Phys. Chem. Lett. , vol.2 , pp. 282-288
    • Fedorov, D.G.1    Alexeev, Y.2    Kitaura, K.3
  • 15
    • 33847253334 scopus 로고    scopus 로고
    • * state of hydrated formaldehyde
    • DOI 10.1016/j.cplett.2007.02.016, PII S0009261407001820
    • Mochizuki, Y.; Komeiji, Y.; Ishikawa, T.; Nakano, T.; Yamataka, H. A Fully Quantum Mechanical Simulation Study on the Lowest n-π* State of Hydrated Formaldehyde Chem. Phys. Lett. 2007, 437, 66-72 (Pubitemid 46331064)
    • (2007) Chemical Physics Letters , vol.437 , Issue.1-3 , pp. 66-72
    • Mochizuki, Y.1    Komeiji, Y.2    Ishikawa, T.3    Nakano, T.4    Yamataka, H.5
  • 17
    • 58149241004 scopus 로고    scopus 로고
    • Fragment Molecular Orbital Method-Based Molecular Dynamics (FMO-MD) as a Simulator for Chemical Reactions in Explicit Salvation
    • Komeiji, Y.; Ishikawa, T.; Mochizuki, Y.; Yamataka, H.; Nakano, T. Fragment Molecular Orbital Method-Based Molecular Dynamics (FMO-MD) as a Simulator for Chemical Reactions in Explicit Salvation J. Comput. Chem. 2009, 30, 40-50
    • (2009) J. Comput. Chem. , vol.30 , pp. 40-50
    • Komeiji, Y.1    Ishikawa, T.2    Mochizuki, Y.3    Yamataka, H.4    Nakano, T.5
  • 18
    • 60749099088 scopus 로고    scopus 로고
    • Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD), A Quantum Simulation Tool for Large Molecular Systems
    • Komeiji, Y.; Mochizuki, Y.; Nakano, T.; Fedorov, D. G. Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD), A Quantum Simulation Tool for Large Molecular Systems J. Mol. Struct. 2009, 898, 2-7
    • (2009) J. Mol. Struct. , vol.898 , pp. 2-7
    • Komeiji, Y.1    Mochizuki, Y.2    Nakano, T.3    Fedorov, D.G.4
  • 20
    • 79961060567 scopus 로고    scopus 로고
    • Analytic Energy Gradient for Second-Order Møller-Plesset Perturbation Theory Based on the Fragment Molecular Orbital Method
    • Nagata, T.; Fedorov, D. G.; Ishimura, K.; Kitaura, K. Analytic Energy Gradient for Second-Order Møller-Plesset Perturbation Theory Based on the Fragment Molecular Orbital Method J. Chem. Phys. 2011, 135, 044110
    • (2011) J. Chem. Phys. , vol.135 , pp. 044110
    • Nagata, T.1    Fedorov, D.G.2    Ishimura, K.3    Kitaura, K.4
  • 21
    • 65549157902 scopus 로고    scopus 로고
    • Fragment Molecular Orbital Calculation with RI-MP2 Method
    • Ishikawa, T.; Kuwata, K. Fragment Molecular Orbital Calculation with RI-MP2 Method Chem. Phys. Lett. 2009, 474, 195-198
    • (2009) Chem. Phys. Lett. , vol.474 , pp. 195-198
    • Ishikawa, T.1    Kuwata, K.2
  • 22
    • 77950296671 scopus 로고    scopus 로고
    • Acceleration of Fragment Molecular Orbital Calculations with Cholesky Decomposition Approach
    • Okiyama, Y.; Nakano, T.; Yamashita, K.; Mochizuki, Y.; Taguchi, N.; Tanaka, S. Acceleration of Fragment Molecular Orbital Calculations with Cholesky Decomposition Approach Chem. Phys. Lett. 2010, 490, 84-89
    • (2010) Chem. Phys. Lett. , vol.490 , pp. 84-89
    • Okiyama, Y.1    Nakano, T.2    Yamashita, K.3    Mochizuki, Y.4    Taguchi, N.5    Tanaka, S.6
  • 23
    • 81555208182 scopus 로고    scopus 로고
    • Application of Resolution of Identity Approximation of Second-Order Møller-Plesset Perturbation Theory to Three-Body Fragment Molecular Orbital Method
    • Katouda, M. Application of Resolution of Identity Approximation of Second-Order Møller-Plesset Perturbation Theory to Three-Body Fragment Molecular Orbital Method Theor. Chem. Acc. 2011, 130, 449-453
    • (2011) Theor. Chem. Acc. , vol.130 , pp. 449-453
    • Katouda, M.1
  • 25
    • 66349090423 scopus 로고    scopus 로고
    • Derivatives of the Approximated Electrostatic Potentials in the Fragment Molecular Orbital Method
    • Nagata, T.; Fedorov, D. G.; Kitaura, K. Derivatives of the Approximated Electrostatic Potentials in the Fragment Molecular Orbital Method Chem. Phys. Lett. 2009, 475, 124-131
    • (2009) Chem. Phys. Lett. , vol.475 , pp. 124-131
    • Nagata, T.1    Fedorov, D.G.2    Kitaura, K.3
  • 26
    • 11944271156 scopus 로고    scopus 로고
    • A parallelized integral-direct second-order Møller-Plesset perturbation theory method with a fragment molecular orbital scheme
    • DOI 10.1007/s00214-004-0602-3
    • Mochizuki, Y.; Nakano, T.; Koikegami, S.; Tanimori, S.; Abe, Y.; Nagashima, U.; Kitaura, K. A Parallelized Integral-Direct Second-Order Møller-Plesset Perturbation Theory Method with a Fragment Molecular Orbital Scheme Theor. Chem. Acc. 2004, 112, 442-452 (Pubitemid 40100848)
    • (2004) Theoretical Chemistry Accounts , vol.112 , Issue.5-6 , pp. 442-452
    • Mochizuki, Y.1    Nakano, T.2    Koikegami, S.3    Tanimori, S.4    Abe, Y.5    Nagashima, U.6    Kitaura, K.7
  • 27
    • 4344708244 scopus 로고    scopus 로고
    • Second Order Møller-Plesset Perturbation Theory Based upon the Fragment Molecular Orbital Method
    • Fedorov, D. G.; Kitaura, K. Second Order Møller-Plesset Perturbation Theory Based upon the Fragment Molecular Orbital Method J. Chem. Phys. 2004, 121, 2483-2490
    • (2004) J. Chem. Phys. , vol.121 , pp. 2483-2490
    • Fedorov, D.G.1    Kitaura, K.2
  • 28
    • 36549092414 scopus 로고
    • On the Evaluation of Analytic Energy Derivatives for Correlated Wave Functions
    • Handy, N. C.; Schaefer, H. F., III On the Evaluation of Analytic Energy Derivatives for Correlated Wave Functions J. Chem. Phys. 1984, 81, 5031-5033
    • (1984) J. Chem. Phys. , vol.81 , pp. 5031-5033
    • Handy, N.C.1    Schaefer Iii, H.F.2
  • 29
    • 84986524957 scopus 로고
    • Convergence Acceleration of Iterative Sequences. The Case of SCF Iteration
    • Pulay, P. Convergence Acceleration of Iterative Sequences. The Case of SCF Iteration Chem. Phys. Lett. 1980, 73, 393-398
    • (1980) Chem. Phys. Lett. , vol.73 , pp. 393-398
    • Pulay, P.1
  • 30
    • 70349898416 scopus 로고    scopus 로고
    • Theoretical Study of the Prion Protein Based on the Fragment Molecular Orbital Method
    • Ishikawa, T.; Ishikura, T.; Kuwata, K. Theoretical Study of the Prion Protein Based on the Fragment Molecular Orbital Method J. Comput. Chem. 2009, 30, 2594-2601
    • (2009) J. Comput. Chem. , vol.30 , pp. 2594-2601
    • Ishikawa, T.1    Ishikura, T.2    Kuwata, K.3
  • 31
    • 33746614482 scopus 로고
    • Gaussian Basis Sets for Use in Correlated Molecular Calculations. I. The Atoms Boron Through Neon and Hydrogen
    • Dunning, T. H. Gaussian Basis Sets for Use in Correlated Molecular Calculations. I. The Atoms Boron Through Neon and Hydrogen J. Chem. Phys. 1989, 90, 1007-1023
    • (1989) J. Chem. Phys. , vol.90 , pp. 1007-1023
    • Dunning, T.H.1
  • 32
    • 0037154597 scopus 로고    scopus 로고
    • Efficient use of the correlation consistent basis sets in resolution of the identity MP2 calculations
    • DOI 10.1063/1.1445115
    • Weigend, F.; Köhn, A.; Hättig, C. Efficient Use of the Correlation Consistent Basis Sets in Resolution of the Identity MP2 Calculations J. Chem. Phys. 2002, 116, 3175-3183 (Pubitemid 34221281)
    • (2002) Journal of Chemical Physics , vol.116 , Issue.8 , pp. 3175-3183
    • Weigend, F.1    Kohn, A.2    Hattig, C.3


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