메뉴 건너뛰기




Volumn 45, Issue 4, 2012, Pages 663-672

Calculations on noncovalent interactions and databases of benchmark interaction energies

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; FACTUAL DATABASE; QUALITY CONTROL; QUANTUM THEORY; THERMODYNAMICS;

EID: 84859917592     PISSN: 00014842     EISSN: 15204898     Source Type: Journal    
DOI: 10.1021/ar200255p     Document Type: Article
Times cited : (182)

References (30)
  • 2
    • 77955003137 scopus 로고    scopus 로고
    • Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories
    • Riley, K. E.; Pitonak, M.; Jurecka, P.; Hobza, P. Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories Chem. Rev. 2010, 110, 5023
    • (2010) Chem. Rev. , vol.110 , pp. 5023
    • Riley, K.E.1    Pitonak, M.2    Jurecka, P.3    Hobza, P.4
  • 4
    • 33744470857 scopus 로고    scopus 로고
    • Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
    • Jurecka, P.; Sponer, J.; Cerny, J.; Hobza, P. Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs Phys. Chem. Chem. Phys. 2006, 8, 1985-1993
    • (2006) Phys. Chem. Chem. Phys. , vol.8 , pp. 1985-1993
    • Jurecka, P.1    Sponer, J.2    Cerny, J.3    Hobza, P.4
  • 5
    • 77951119829 scopus 로고    scopus 로고
    • Basis set consistent revision of the S22 test set of noncovalent interaction energies
    • Takatani, T.; Hohenstein, E. G.; Malagoli, M.; Marshall, M. S.; Sherrill, C. D. Basis set consistent revision of the S22 test set of noncovalent interaction energies J. Chem. Phys. 2010, 132, 144104
    • (2010) J. Chem. Phys. , vol.132 , pp. 144104
    • Takatani, T.1    Hohenstein, E.G.2    Malagoli, M.3    Marshall, M.S.4    Sherrill, C.D.5
  • 6
    • 77955949129 scopus 로고    scopus 로고
    • Improved interaction energy benchmarks for dimers of biological relevance
    • Podeszwa, R.; Patkowski, K.; Szalewicz, K. Improved interaction energy benchmarks for dimers of biological relevance Phys. Chem. Chem. Phys. 2010, 12, 5974-5979
    • (2010) Phys. Chem. Chem. Phys. , vol.12 , pp. 5974-5979
    • Podeszwa, R.1    Patkowski, K.2    Szalewicz, K.3
  • 7
    • 69149091172 scopus 로고    scopus 로고
    • Further analysis and comparative study of intermolecular interactions using dimers from the S22 database
    • Molnar, L. F.; He, X.; Wang, B.; Merz, K. M., Jr. Further analysis and comparative study of intermolecular interactions using dimers from the S22 database J. Chem. Phys. 2009, 131, 065102
    • (2009) J. Chem. Phys. , vol.131 , pp. 065102
    • Molnar, L.F.1    He, X.2    Wang, B.3    Merz Jr., K.M.4
  • 8
    • 77955578570 scopus 로고    scopus 로고
    • Comparative study of selected wave function and density functional methods for noncovalent interaction energy calculations using the extended S22 data set
    • Grafova, L.; Pitonak, M.; Rezac, J.; Hobza, P. Comparative study of selected wave function and density functional methods for noncovalent interaction energy calculations using the extended S22 data set J. Chem. Theory Comput. 2010, 6, 2365-2376
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 2365-2376
    • Grafova, L.1    Pitonak, M.2    Rezac, J.3    Hobza, P.4
  • 9
    • 80051662513 scopus 로고    scopus 로고
    • S66: A well balanced database of benchmark interaction energies relevant to biomolecular structures
    • Rezac, J.; Riley, K. E.; Hobza, P. S66: A well balanced database of benchmark interaction energies relevant to biomolecular structures J. Chem. Theory Comput. 2011, 7, 2427-2438
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2427-2438
    • Rezac, J.1    Riley, K.E.2    Hobza, P.3
  • 10
    • 80755150198 scopus 로고    scopus 로고
    • Extensions of the S66 data set: More accurate interaction energies and angular-displaced nonequilibrium geometries
    • 3470
    • Rezac, J.; Riley, K. E.; Hobza, P. Extensions of the S66 data set: more accurate interaction energies and angular-displaced nonequilibrium geometries. J. Chem. Theory Comput. 2011, 7, 3466 - 3470.
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 3466
    • Rezac, J.1    Riley, K.E.2    Hobza, P.3
  • 11
    • 2442420030 scopus 로고    scopus 로고
    • CCSDT and CCSD(T) calculations on model H-bonded and stacked complexes
    • Pittner, J.; Hobza, P. CCSDT and CCSD(T) calculations on model H-bonded and stacked complexes Chem. Phys. Lett. 2004, 390, 496-499
    • (2004) Chem. Phys. Lett. , vol.390 , pp. 496-499
    • Pittner, J.1    Hobza, P.2
  • 13
    • 20844449600 scopus 로고    scopus 로고
    • On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level
    • Dabkowska, I.; Jurecka, P.; Hobza, P. On geometries of stacked and H-bonded nucleic acid base pairs determined at various DFT, MP2, and CCSD(T) levels up to the CCSD(T)/complete basis set limit level J. Chem. Phys. 2005, 122, 204322
    • (2005) J. Chem. Phys. , vol.122 , pp. 204322
    • Dabkowska, I.1    Jurecka, P.2    Hobza, P.3
  • 14
    • 42149175886 scopus 로고    scopus 로고
    • Improved supermolecular second order Moller-Plesset intermolecular interaction energies using time-dependent density functional response theory
    • Hesselmann, A. Improved supermolecular second order Moller-Plesset intermolecular interaction energies using time-dependent density functional response theory J. Chem. Phys. 2008, 128, 144112
    • (2008) J. Chem. Phys. , vol.128 , pp. 144112
    • Hesselmann, A.1
  • 15
    • 0038617502 scopus 로고    scopus 로고
    • Improved second-order Moller-Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies
    • Grimme, S. Improved second-order Moller-Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies J. Chem. Phys. 2003, 118, 9095
    • (2003) J. Chem. Phys. , vol.118 , pp. 9095
    • Grimme, S.1
  • 16
    • 34250306276 scopus 로고    scopus 로고
    • Optimized spin-component scaled second-order Mller-Plesset perturbation theory for intermolecular interaction energies
    • DOI 10.1080/00268970701283781, PII 779449801
    • Distasio, R. A.; Head-Gordon, M. Optimized spin-component scaled second-order Moller-Plesset perturbation theory for intermolecular interaction energies Mol. Phys. 2007, 105, 1073-1083 (Pubitemid 46911864)
    • (2007) Molecular Physics , vol.105 , Issue.8 , pp. 1073-1083
    • Distasio Jr., R.A.1    Head-Gordon, M.2
  • 17
    • 58149499025 scopus 로고    scopus 로고
    • Scaled MP3 non-covalent interaction energies agree closely with accurate CCSD(T) benchmark data
    • Pitonak, M.; Neogrady, P.; Cerny, J.; Grimme, S.; Hobza, P. Scaled MP3 non-covalent interaction energies agree closely with accurate CCSD(T) benchmark data ChemPhysChem 2009, 10, 282-289
    • (2009) ChemPhysChem , vol.10 , pp. 282-289
    • Pitonak, M.1    Neogrady, P.2    Cerny, J.3    Grimme, S.4    Hobza, P.5
  • 18
    • 41549128916 scopus 로고    scopus 로고
    • Improvement of the coupled-cluster singles and doubles method via scaling same- and opposite-spin components of the double excitation correlation energy
    • Takatani, T.; Hohenstein, E. G.; Sherrill, C. D. Improvement of the coupled-cluster singles and doubles method via scaling same- and opposite-spin components of the double excitation correlation energy J. Chem. Phys. 2008, 128, 124111
    • (2008) J. Chem. Phys. , vol.128 , pp. 124111
    • Takatani, T.1    Hohenstein, E.G.2    Sherrill, C.D.3
  • 19
    • 77955915542 scopus 로고    scopus 로고
    • Spin-component scaled coupled-clusters singles and doubles optimized towards calculation of noncovalent interactions
    • Pitonak, M.; Rezac, J.; Hobza, P. Spin-component scaled coupled-clusters singles and doubles optimized towards calculation of noncovalent interactions Phys. Chem. Chem. Phys. 2010, 12, 9611-9614
    • (2010) Phys. Chem. Chem. Phys. , vol.12 , pp. 9611-9614
    • Pitonak, M.1    Rezac, J.2    Hobza, P.3
  • 20
    • 84871705949 scopus 로고    scopus 로고
    • MP2.X: A generalized MP2.5 method that produces improved binding energies with smaller basis sets
    • in press
    • Riley, K. E.; Rezac, J.; Hobza, P. MP2.X: A generalized MP2.5 method that produces improved binding energies with smaller basis sets. Phys. Chem. Chem. Phys., in press.
    • Phys. Chem. Chem. Phys.
    • Riley, K.E.1    Rezac, J.2    Hobza, P.3
  • 21
    • 0000965687 scopus 로고    scopus 로고
    • Structure, Energetics, and Dynamics of the Nucleic Acid Base Pairs: Nonempirical Ab Initio Calculations
    • Hobza, P.; Sponer, J. Structure, energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations Chem. Rev. 1999, 99, 3247-3276 (Pubitemid 129583053)
    • (1999) Chemical Reviews , vol.99 , Issue.11 , pp. 3247-3276
    • Hobza, P.1    Sponer, J.2
  • 22
    • 35448937584 scopus 로고    scopus 로고
    • Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements
    • DOI 10.1007/s00894-007-0233-4
    • Stewart, J. J. P. Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements J. Mol. Model. 2007, 13, 1173-1213 (Pubitemid 47629446)
    • (2007) Journal of Molecular Modeling , vol.13 , Issue.12 , pp. 1173-1213
    • Stewart, J.J.P.1
  • 23
    • 0035871701 scopus 로고    scopus 로고
    • Description of peptide and protein secondary structures employing semiempirical methods
    • DOI 10.1002/1096-987X(20010415)22:5<509::AID-JCC1022>3.0.CO;2-K
    • Möhle, K.; Hofmann, H.-J.; Thiel, W. Description of peptide and protein secondary structures employing semiempirical methods J. Comput. Chem. 2001, 22, 509-520 (Pubitemid 32291687)
    • (2001) Journal of Computational Chemistry , vol.22 , Issue.5 , pp. 509-520
    • Mohle, K.1    Hofmann, H.-J.2    Thiel, W.3
  • 24
    • 0035932162 scopus 로고    scopus 로고
    • Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment
    • Elstner, M.; Hobza, P.; Frauenheim, T.; Suhai, S.; Kaziras, E. Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment J. Chem. Phys. 2001, 114, 5149
    • (2001) J. Chem. Phys. , vol.114 , pp. 5149
    • Elstner, M.1    Hobza, P.2    Frauenheim, T.3    Suhai, S.4    Kaziras, E.5
  • 25
    • 67849101722 scopus 로고    scopus 로고
    • Semiempirical quantum chemical PM6 method augmented by dispersion and H-bonding correction terms reliably describes various types of noncovalent complexes
    • Rezac, J.; Fanfrlik, J.; Salahub, D. R.; Hobza, P. Semiempirical quantum chemical PM6 method augmented by dispersion and H-bonding correction terms reliably describes various types of noncovalent complexes J. Chem. Theory Comput. 2009, 5, 1749-1760
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 1749-1760
    • Rezac, J.1    Fanfrlik, J.2    Salahub, D.R.3    Hobza, P.4
  • 26
    • 77950139248 scopus 로고    scopus 로고
    • A transferable H-bonding correction for semiempirical quantum-chemical methods
    • Korth, M.; Pitonak, M.; Rezac, J.; Hobza, P. A transferable H-bonding correction for semiempirical quantum-chemical methods J. Chem. Theory Comput. 2010, 6, 344-352
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 344-352
    • Korth, M.1    Pitonak, M.2    Rezac, J.3    Hobza, P.4
  • 27
    • 79959921557 scopus 로고    scopus 로고
    • Semiempirical quantum mechanical method PM6-DH2X describes the geometry and energetics of CK2-Inhibitor complexes involving halogen bonds well, while the empirical potential fails
    • Dobes, P.; Rezac, J.; Fanfrlik, J.; Hobza, P. Semiempirical quantum mechanical method PM6-DH2X describes the geometry and energetics of CK2-Inhibitor complexes involving halogen bonds well, while the empirical potential fails J. Phys. Chem. B 2011, 115, 8581-8589
    • (2011) J. Phys. Chem. B , vol.115 , pp. 8581-8589
    • Dobes, P.1    Rezac, J.2    Fanfrlik, J.3    Hobza, P.4
  • 28
    • 79955395664 scopus 로고    scopus 로고
    • Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors
    • Dobes, P.; Rezac, J.; Fanfrlik, J.; Otyepka, M.; Hobza, P. Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors J. Comput.-Aided Mol. Des. 2011, 25, 223-235
    • (2011) J. Comput.-Aided Mol. Des. , vol.25 , pp. 223-235
    • Dobes, P.1    Rezac, J.2    Fanfrlik, J.3    Otyepka, M.4    Hobza, P.5
  • 29
    • 77957291978 scopus 로고    scopus 로고
    • A reliable docking/scoring scheme based on the semiempirical quantum mechanical PM6-DH2 method accurately covering dispersion and H-bonding: HIV-1 protease with 22 ligands
    • Fanfrlik, J.; Bronowska, A. K.; Rezac, J.; Prenosil, O.; Konvalinka, J.; Hobza, P. A reliable docking/scoring scheme based on the semiempirical quantum mechanical PM6-DH2 method accurately covering dispersion and H-bonding: HIV-1 protease with 22 ligands J. Phys. Chem. B 2010, 114, 12666-12678
    • (2010) J. Phys. Chem. B , vol.114 , pp. 12666-12678
    • Fanfrlik, J.1    Bronowska, A.K.2    Rezac, J.3    Prenosil, O.4    Konvalinka, J.5    Hobza, P.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.