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Volumn 118, Issue 50, 2014, Pages 14612-14626

Recommending Hartree-Fock theory with London-dispersion and basis-set-superposition corrections for the optimization or quantum refinement of protein structures

Author keywords

[No Author keywords available]

Indexed keywords

DENSITY FUNCTIONAL THEORY; DISPERSIONS; ERRORS; MOLECULAR PHYSICS; PHASE EQUILIBRIA; PROTEINS; QUANTUM CHEMISTRY; STRUCTURAL OPTIMIZATION;

EID: 84918826463     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp510148h     Document Type: Article
Times cited : (54)

References (150)
  • 1
    • 33846797895 scopus 로고    scopus 로고
    • Accurate Metal-Site Structures in Proteins Obtained by Combining Experimental Data and Quantum Chemistry
    • Ryde, U. Accurate Metal-Site Structures in Proteins Obtained by Combining Experimental Data and Quantum Chemistry. Dalton Trans. 2007, 607-625.
    • (2007) Dalton Trans , pp. 607-625
    • Ryde, U.1
  • 2
    • 0345227309 scopus 로고    scopus 로고
    • Quantum Refinement - A Combination of Quantum Chemistry and Protein Crystallography
    • Ryde, U.; Nilsson, K. Quantum Refinement - A Combination of Quantum Chemistry and Protein Crystallography. J. Mol. Struct. (THEOCHEM) 2003, 632, 259-275.
    • (2003) J. Mol. Struct. (Theochem) , vol.632 , pp. 259-275
    • Ryde, U.1    Nilsson, K.2
  • 3
    • 78149440040 scopus 로고    scopus 로고
    • A Comparison of Different Initialization Protocols to Obtain Statistically Independent Molecular Dynamics Simulations
    • Genheden, S.; Ryde, U. A Comparison of Different Initialization Protocols to Obtain Statistically Independent Molecular Dynamics Simulations. J. Comput. Chem. 2011, 32, 187-195.
    • (2011) J. Comput. Chem. , vol.32 , pp. 187-195
    • Genheden, S.1    Ryde, U.2
  • 4
    • 0344012221 scopus 로고    scopus 로고
    • Quantum Chemistry Can Locally Improve Protein Crystal Structures
    • Ryde, U.; Nilsson, K. Quantum Chemistry Can Locally Improve Protein Crystal Structures. J. Am. Chem. Soc. 2003, 125, 14232-14233.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 14232-14233
    • Ryde, U.1    Nilsson, K.2
  • 5
    • 13844270250 scopus 로고    scopus 로고
    • The Protonation Status of Compound II in Myoglobin, Studied by a Combination of Experimental Data and Quantum Chemical Calculations: Quantum Refinement
    • Nilsson, K.; Hersleth, H. P.; Rod, T. H.; Andersson, K. K.; Ryde, U. The Protonation Status of Compound II in Myoglobin, Studied by a Combination of Experimental Data and Quantum Chemical Calculations: Quantum Refinement. Biophys. J. 2004, 87, 3437-3447.
    • (2004) Biophys. J. , vol.87 , pp. 3437-3447
    • Nilsson, K.1    Hersleth, H.P.2    Rod, T.H.3    Andersson, K.K.4    Ryde, U.5
  • 7
    • 33745727307 scopus 로고    scopus 로고
    • Structure of Reduced and Oxidized Manganese Superoxide Dismutase: A Combined Computational and Experimental Approach
    • Rulisek, L.; Ryde, U. Structure of Reduced and Oxidized Manganese Superoxide Dismutase: A Combined Computational and Experimental Approach. J. Phys. Chem. B 2006, 110, 11511-11518.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 11511-11518
    • Rulisek, L.1    Ryde, U.2
  • 8
    • 0036667496 scopus 로고    scopus 로고
    • Quantum Chemical Geometry Optimizations in Proteins Using Crystallographic Raw Data
    • Ryde, U.; Olsen, L.; Nilsson, K. Quantum Chemical Geometry Optimizations in Proteins Using Crystallographic Raw Data. J. Comput. Chem. 2002, 23, 1058-1070.
    • (2002) J. Comput. Chem. , vol.23 , pp. 1058-1070
    • Ryde, U.1    Olsen, L.2    Nilsson, K.3
  • 9
    • 78649588488 scopus 로고    scopus 로고
    • Quantum Refinement of Protein Structures: Implementation and Application to the Red Fluorescent Protein Dsred.M1
    • Hsiao, Y.-W.; Sanchez-Garcia, E.; Doerr, M.; Thiel, W. Quantum Refinement of Protein Structures: Implementation and Application to the Red Fluorescent Protein Dsred.M1. J. Phys. Chem. B 2010, 114, 15413-15423.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 15413-15423
    • Hsiao, Y.-W.1    Sanchez-Garcia, E.2    Doerr, M.3    Thiel, W.4
  • 10
    • 79952267690 scopus 로고    scopus 로고
    • 2 Intermediate of the Photoactive Yellow Protein: Structure and Excitation Energies
    • 2 Intermediate of the Photoactive Yellow Protein: Structure and Excitation Energies. J. Phys. Chem. B 2011, 115, 2097-2106.
    • (2011) J. Phys. Chem. B , vol.115 , pp. 2097-2106
    • Hsiao, Y.-W.1    Thiel, W.2
  • 11
    • 84884197748 scopus 로고    scopus 로고
    • Amine Oxidation Mediated by Lysine-Specific Demethylase 1: Quantum Mechanics/Molecular Mechanics Insights into Mechanism and Role of Lysine 661
    • Karasulu, B.; Patil, M.; Thiel, W. Amine Oxidation Mediated by Lysine-Specific Demethylase 1: Quantum Mechanics/Molecular Mechanics Insights into Mechanism and Role of Lysine 661. J. Am. Chem. Soc. 2013, 135, 13400-13413.
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 13400-13413
    • Karasulu, B.1    Patil, M.2    Thiel, W.3
  • 12
    • 84884185644 scopus 로고    scopus 로고
    • Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins
    • Sumner, S.; Söderhjelm, P.; Ryde, U. Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins. J. Chem. Theory Comput. 2013, 9, 4205-4214.
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 4205-4214
    • Sumner, S.1    Söderhjelm, P.2    Ryde, U.3
  • 13
    • 84882302136 scopus 로고    scopus 로고
    • Convergence of QM/MM and Cluster Models for the Spectroscopic Properties of the Oxygen-Evolving Complex in Photosystem II
    • Retegan, M.; Neese, F.; Pantazis, D. A. Convergence of QM/MM and Cluster Models for the Spectroscopic Properties of the Oxygen-Evolving Complex in Photosystem II. J. Chem. Theory Comput. 2013, 9, 3832-3842.
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3832-3842
    • Retegan, M.1    Neese, F.2    Pantazis, D.A.3
  • 14
    • 84873476820 scopus 로고    scopus 로고
    • Determinants of Regioselectivity and Chemoselectivity in Fosfomycin Resistance Protein Fosa from QM/MM Calculations
    • Liao, R.-Z.; Thiel, W. Determinants of Regioselectivity and Chemoselectivity in Fosfomycin Resistance Protein Fosa from QM/MM Calculations. J. Phys. Chem. B 2013, 117, 1326-1336.
    • (2013) J. Phys. Chem. B , vol.117 , pp. 1326-1336
    • Liao, R.-Z.1    Thiel, W.2
  • 15
    • 84898075763 scopus 로고    scopus 로고
    • Computational and Experimental Study of O-Glycosylation. Catalysis by Human UDP-GalNAc Polypeptide:Gal-NAc Transferase-T2
    • Gomez, H.; Rojas, R.; Patel, D.; Tabak, L. A.; Lluch, J. M.; Masgrau, L. A Computational and Experimental Study of O-Glycosylation. Catalysis by Human UDP-GalNAc Polypeptide:Gal-NAc Transferase-T2. Org. Biomol. Chem. 2014, 12, 2645-2655.
    • (2014) Org. Biomol. Chem. , vol.12 , pp. 2645-2655
    • Gomez, H.1    Rojas, R.2    Patel, D.3    Tabak, L.A.4    Lluch, J.M.5    Masgrau, L.A.6
  • 16
    • 84897008464 scopus 로고    scopus 로고
    • How Important Is the Synclinal Conformation of Sulfonylureas to Explain the Inhibition of AHAS: A Theoretical Study
    • Jaña, G. A.; Delgado, E. J.; Medina, F. E. How Important Is the Synclinal Conformation of Sulfonylureas to Explain the Inhibition of AHAS: A Theoretical Study. J. Chem. Inf. Model. 2014, 54, 926-932.
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 926-932
    • Jaña, G.A.1    Delgado, E.J.2    Medina, F.E.3
  • 18
    • 84902664425 scopus 로고    scopus 로고
    • A DFT and ONIOM Study of C-H Hydroxylation Catalyzed by Nitrobenzene 1,2-Dioxygenase
    • Geronimo, I.; Paneth, P. A DFT and ONIOM Study of C-H Hydroxylation Catalyzed by Nitrobenzene 1,2-Dioxygenase. Phys. Chem. Chem. Phys. 2014, 16, 13889-13899.
    • (2014) Phys. Chem. Chem. Phys. , vol.16 , pp. 13889-13899
    • Geronimo, I.1    Paneth, P.2
  • 19
    • 84902962855 scopus 로고    scopus 로고
    • Understanding Bacterial Bioluminescence: A Theoretical Study of the Entire Process, from Reduced Flavin to Light Emission
    • Hou, C.; Liu, Y.-J.; Ferré, N.; Fang, W.-H. Understanding Bacterial Bioluminescence: A Theoretical Study of the Entire Process, from Reduced Flavin to Light Emission. Chem.-Eur. J. 2014, 20, 7979-7986.
    • (2014) Chem.-Eur. J. , vol.20 , pp. 7979-7986
    • Hou, C.1    Liu, Y.-J.2    Ferré, N.3    Fang, W.-H.4
  • 20
    • 84899814949 scopus 로고    scopus 로고
    • The Mechanism of Citryl-Coenzyme A Formation Catalyzed by Citrate Synthase
    • Aleksandrov, A.; Zvereva, E.; Field, M. The Mechanism of Citryl-Coenzyme A Formation Catalyzed by Citrate Synthase. J. Phys. Chem. B 2014, 118, 4505-4513.
    • (2014) J. Phys. Chem. B , vol.118 , pp. 4505-4513
    • Aleksandrov, A.1    Zvereva, E.2    Field, M.3
  • 21
    • 84901616657 scopus 로고    scopus 로고
    • Can Molecular Dynamics and QM/MM Solve the Penicillin Binding Protein Protonation Puzzle?
    • Hargis, J. C.; White, J. K.; Chen, Y.; Woodcock, H. L. Can Molecular Dynamics and QM/MM Solve the Penicillin Binding Protein Protonation Puzzle? J. Chem. Inf. Model. 2014, 54, 1412-1424.
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 1412-1424
    • Hargis, J.C.1    White, J.K.2    Chen, Y.3    Woodcock, H.L.4
  • 23
    • 84896882744 scopus 로고    scopus 로고
    • Effect of Protein Environment within Cytochrome P450cam Evaluated Using a Polarizable-Embedding QM/MM Method
    • Thellamurege, N. M.; Hirao, H. Effect of Protein Environment within Cytochrome P450cam Evaluated Using a Polarizable-Embedding QM/MM Method. J. Phys. Chem. B 2014, 118, 2084-2092.
    • (2014) J. Phys. Chem. B , vol.118 , pp. 2084-2092
    • Thellamurege, N.M.1    Hirao, H.2
  • 24
    • 84894110313 scopus 로고    scopus 로고
    • Identification and Characterization of Noncovalent Interactions That Drive Binding and Specificity in DD-Peptidases and β-Lactamases
    • Hargis, J. C.; Vankayala, S. L.; White, J. K.; Woodcock, H. L. Identification and Characterization of Noncovalent Interactions That Drive Binding and Specificity in DD-Peptidases and β-Lactamases. J. Chem. Theory Comput. 2014, 10, 855-864.
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 855-864
    • Hargis, J.C.1    Vankayala, S.L.2    White, J.K.3    Woodcock, H.L.4
  • 25
    • 84883174012 scopus 로고    scopus 로고
    • Photophysics of Structurally Modified Flavin Derivatives in the Blue-Light Photoreceptor YtvA: A Combined Experimental and Theoretical Study
    • Silva-Junior, M. R.; Mansurova, M.; Gärtner, W.; Thiel, W. Photophysics of Structurally Modified Flavin Derivatives in the Blue-Light Photoreceptor YtvA: A Combined Experimental and Theoretical Study. ChemBioChem 2013, 14, 1648-1661.
    • (2013) ChemBioChem , vol.14 , pp. 1648-1661
    • Silva-Junior, M.R.1    Mansurova, M.2    Gärtner, W.3    Thiel, W.4
  • 26
    • 84881124786 scopus 로고    scopus 로고
    • QM/MM Structural and Spectroscopic Analysis of the Di-iron(II) and Di-iron(III) Ferroxidase Site in M Ferritin
    • Harris, T. V.; Morokuma, K. QM/MM Structural and Spectroscopic Analysis of the Di-iron(II) and Di-iron(III) Ferroxidase Site in M Ferritin. Inorg. Chem. 2013, 52, 8551-8563.
    • (2013) Inorg. Chem. , vol.52 , pp. 8551-8563
    • Harris, T.V.1    Morokuma, K.2
  • 27
    • 84884907008 scopus 로고    scopus 로고
    • Convergence in the QM-Only and QM/MM Modeling of Enzymatic Reactions: A Case Study for Acetylene Hydratase
    • Liao, R.-Z.; Thiel, W. Convergence in the QM-Only and QM/MM Modeling of Enzymatic Reactions: A Case Study for Acetylene Hydratase. J. Comput. Chem. 2013, 34, 2389-2397.
    • (2013) J. Comput. Chem. , vol.34 , pp. 2389-2397
    • Liao, R.-Z.1    Thiel, W.2
  • 28
    • 67651230413 scopus 로고    scopus 로고
    • Protein NMR Chemical Shift Calculations Based on the Automated Fragmentation QM/MM Approach
    • He, X.; Wang, B.; Merz, K. M. Protein NMR Chemical Shift Calculations Based on the Automated Fragmentation QM/MM Approach. J. Phys. Chem. B 2009, 113, 10380-10388.
    • (2009) J. Phys. Chem. B , vol.113 , pp. 10380-10388
    • He, X.1    Wang, B.2    Merz, K.M.3
  • 29
    • 80052398418 scopus 로고    scopus 로고
    • Pairwise Additivity of Energy Components in Protein-Ligand Binding: The HIV II Protease-Indinavir Case
    • Ucisik, M. N.; Dashti, D. S.; Faver, J. C.; Merz, K. M. Pairwise Additivity of Energy Components in Protein-Ligand Binding: The HIV II Protease-Indinavir Case. J. Chem. Phys. 2011, 135, 085101.
    • (2011) J. Chem. Phys. , vol.135 , pp. 085101
    • Ucisik, M.N.1    Dashti, D.S.2    Faver, J.C.3    Merz, K.M.4
  • 30
    • 84887045057 scopus 로고    scopus 로고
    • Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method
    • Ionescu, C.-M.; Geidl, S.; Svobodová Vařeková, R.; Koča, J. Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. J. Chem. Inf. Model. 2013, 53, 2548-2558.
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 2548-2558
    • Ionescu, C.-M.1    Geidl, S.2    Svobodová Vařeková, R.3    Koča, J.4
  • 31
    • 0000218385 scopus 로고    scopus 로고
    • A Hybrid QM-MM Potential Employing Hartree-Fock or Density Functional Methods in the Quantum Region
    • Lyne, P. D.; Hodoscek, M.; Karplus, M. A Hybrid QM-MM Potential Employing Hartree-Fock or Density Functional Methods in the Quantum Region. J. Phys. Chem. A 1999, 103, 3462-3471.
    • (1999) J. Phys. Chem. A , vol.103 , pp. 3462-3471
    • Lyne, P.D.1    Hodoscek, M.2    Karplus, M.3
  • 32
    • 84890110473 scopus 로고    scopus 로고
    • Quantum Mechanics/Molecular Mechanics Restrained Electrostatic Potential Fitting
    • Burger, S. K.; Schofield, J.; Ayers, P. W. Quantum Mechanics/Molecular Mechanics Restrained Electrostatic Potential Fitting. J. Phys. Chem. B 2013, 117, 14960-14966.
    • (2013) J. Phys. Chem. B , vol.117 , pp. 14960-14966
    • Burger, S.K.1    Schofield, J.2    Ayers, P.W.3
  • 33
    • 84884549753 scopus 로고    scopus 로고
    • Exploring the Desumoylation Process of SENP1: A Study Combined MD Simulations with QM/MM Calculations on SENP1-SUMO1-RanGAP1
    • Shi, T.; Han, Y.; Li, W.; Zhao, Y.; Liu, Y.; Huang, Z.; Lu, S.; Zhang, J. Exploring the Desumoylation Process of SENP1: A Study Combined MD Simulations with QM/MM Calculations on SENP1-SUMO1-RanGAP1. J. Chem. Inf. Model. 2013, 53, 2360-2368.
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 2360-2368
    • Shi, T.1    Han, Y.2    Li, W.3    Zhao, Y.4    Liu, Y.5    Huang, Z.6    Lu, S.7    Zhang, J.8
  • 35
    • 4143104515 scopus 로고    scopus 로고
    • Semiempirical Molecular Orbital Calculations with Linear System Size Scaling
    • Dixon, S. L.; Merz, K. M. Semiempirical Molecular Orbital Calculations with Linear System Size Scaling. J. Chem. Phys. 1996, 104, 6643-6649.
    • (1996) J. Chem. Phys. , vol.104 , pp. 6643-6649
    • Dixon, S.L.1    Merz, K.M.2
  • 36
    • 0346506503 scopus 로고    scopus 로고
    • Fast, Accurate Semiempirical Molecular Orbital Calculations for Macromolecules
    • Dixon, S. L.; Merz, K. M. Fast, Accurate Semiempirical Molecular Orbital Calculations for Macromolecules. J. Chem. Phys. 1997, 107, 879-893.
    • (1997) J. Chem. Phys. , vol.107 , pp. 879-893
    • Dixon, S.L.1    Merz, K.M.2
  • 37
    • 67349218843 scopus 로고    scopus 로고
    • Application of the PM6 Method to Modeling Proteins
    • Stewart, J. J. P. Application of the PM6 Method to Modeling Proteins. J. Mol. Model. 2009, 15, 765-805.
    • (2009) J. Mol. Model. , vol.15 , pp. 765-805
    • Stewart, J.J.P.1
  • 38
    • 33748341319 scopus 로고    scopus 로고
    • Density-Functional Geometry Optimization of the 150,000-Atom Photosystem-I Trimer
    • Canfield, P.; Dahlbom, M. G.; Hush, N. S.; Reimers, J. R. Density-Functional Geometry Optimization of the 150,000-Atom Photosystem-I Trimer. J. Chem. Phys. 2006, 124, 024301.
    • (2006) J. Chem. Phys. , vol.124 , pp. 024301
    • Canfield, P.1    Dahlbom, M.G.2    Hush, N.S.3    Reimers, J.R.4
  • 39
    • 34548557196 scopus 로고    scopus 로고
    • y Absorption Spectrum of Photosystem-I from Thermosynechococcus elongatus Based on CAMB3LYP Calculations at the PW91-Optimized Protein Structure
    • y Absorption Spectrum of Photosystem-I from Thermosynechococcus elongatus Based on CAMB3LYP Calculations at the PW91-Optimized Protein Structure. J. Phys. Chem. B 2007, 111, 9923-9930.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 9923-9930
    • Yin, S.1    Dahlbom, M.G.2    Canfield, P.J.3    Hush, N.S.4    Kobayashi, R.5    Reimers, J.R.6
  • 40
    • 84874882127 scopus 로고    scopus 로고
    • Protein Effects on the Optical Spectrum of the Fenna-Matthews-Olson Complex from Fully Quantum Chemical Calculations
    • König, C.; Neugebauer, J. Protein Effects on the Optical Spectrum of the Fenna-Matthews-Olson Complex from Fully Quantum Chemical Calculations. J. Chem. Theory Comput. 2013, 9, 1808-1820.
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 1808-1820
    • König, C.1    Neugebauer, J.2
  • 41
    • 84862566881 scopus 로고    scopus 로고
    • Fully ab Initio Protein-Ligand Interaction Energies with Dispersion Corrected Density Functional Theory
    • Antony, J.; Grimme, S. Fully ab Initio Protein-Ligand Interaction Energies with Dispersion Corrected Density Functional Theory. J. Comput. Chem. 2012, 33, 1730-1739.
    • (2012) J. Comput. Chem. , vol.33 , pp. 1730-1739
    • Antony, J.1    Grimme, S.2
  • 42
    • 84860116357 scopus 로고    scopus 로고
    • A Geometrical Correction for the Interand Intra-Molecular Basis Set Superposition Error in Hartree-Fock and Density Functional Theory Calculations for Large Systems
    • Kruse, H.; Grimme, S. A Geometrical Correction for the Interand Intra-Molecular Basis Set Superposition Error in Hartree-Fock and Density Functional Theory Calculations for Large Systems. J. Chem. Phys. 2012, 136, 154101.
    • (2012) J. Chem. Phys. , vol.136 , pp. 154101
    • Kruse, H.1    Grimme, S.2
  • 43
    • 84879214573 scopus 로고    scopus 로고
    • Corrected Small Basis Set Hartree-Fock Method for Large Systems
    • Sure, R.; Grimme, S. Corrected Small Basis Set Hartree-Fock Method for Large Systems. J. Comput. Chem. 2013, 34, 1672-1685.
    • (2013) J. Comput. Chem. , vol.34 , pp. 1672-1685
    • Sure, R.1    Grimme, S.2
  • 44
    • 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
  • 45
    • 34548243709 scopus 로고    scopus 로고
    • Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method
    • Fedorov, D. G.; Kitaura, K. Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method. J. Phys. Chem. A 2007, 111, 6904-6914.
    • (2007) J. Phys. Chem. A , vol.111 , pp. 6904-6914
    • Fedorov, D.G.1    Kitaura, K.2
  • 46
    • 34248164602 scopus 로고    scopus 로고
    • The Fragment Molecular Orbital Method for Geometry Optimizations of Polypeptides and Proteins
    • 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.
    • (2007) J. Phys. Chem. A , vol.111 , pp. 2722-2732
    • Fedorov, D.G.1    Ishida, T.2    Uebayasi, M.3    Kitaura, K.4
  • 47
    • 79953324148 scopus 로고    scopus 로고
    • Fully Analytic Energy Gradient in the Fragment Molecular Orbital Method
    • Nagata, T.; Brorsen, K.; Fedorov, D. G.; Kitaura, K.; Gordon, M. S. Fully Analytic Energy Gradient in the Fragment Molecular Orbital Method. J. Chem. Phys. 2011, 134, 124115.
    • (2011) J. Chem. Phys. , vol.134 , pp. 124115
    • Nagata, T.1    Brorsen, K.2    Fedorov, D.G.3    Kitaura, K.4    Gordon, M.S.5
  • 48
    • 79551619581 scopus 로고    scopus 로고
    • A Combined Effective Fragment Potential-Fragment Molecular Orbital Method. II. Analytic Gradient and Application to the Geometry Optimization of Solvated Tetraglycine and Chignolin
    • Nagata, T.; Fedorov, D. G.; Sawada, T.; Kitaura, K.; Gordon, M. S. A Combined Effective Fragment Potential-Fragment Molecular Orbital Method. II. Analytic Gradient and Application to the Geometry Optimization of Solvated Tetraglycine and Chignolin. J. Chem. Phys. 2011, 134, 034110.
    • (2011) J. Chem. Phys. , vol.134 , pp. 034110
    • Nagata, T.1    Fedorov, D.G.2    Sawada, T.3    Kitaura, K.4    Gordon, M.S.5
  • 50
    • 0000990502 scopus 로고    scopus 로고
    • Linear-Scaling Quantum Mechanical Calculations of Biological Molecules: The Divide-and-Conquer Approach
    • Lee, T. S.; Lewis, J. P.; Yang, W. T. Linear-Scaling Quantum Mechanical Calculations of Biological Molecules: The Divide-and-Conquer Approach. Comput. Mater. Sci. 1998, 12, 259-277.
    • (1998) Comput. Mater. Sci. , vol.12 , pp. 259-277
    • Lee, T.S.1    Lewis, J.P.2    Yang, W.T.3
  • 51
    • 0043144732 scopus 로고
    • A Density-Matrix Divide-and-Conquer Approach for Electronic Structure Calculations of Large Molecules
    • Yang, W.; Lee, T. S. A Density-Matrix Divide-and-Conquer Approach for Electronic Structure Calculations of Large Molecules. J. Chem. Phys. 1995, 103, 5674-5678.
    • (1995) J. Chem. Phys. , vol.103 , pp. 5674-5678
    • Yang, W.1    Lee, T.S.2
  • 52
    • 0034301415 scopus 로고    scopus 로고
    • Quantum Mechanical/Quantum Mechanical Methods. I. A Divide and Conquer Strategy for Solving the Schrödinger Equation for Large Molecular Systems Using a Composite Density Functional-Semiempirical Hamiltonian
    • Gogonea, V.; Westerhoff, L. M.; Merz, K. M. Quantum Mechanical/Quantum Mechanical Methods. I. A Divide and Conquer Strategy for Solving the Schrödinger Equation for Large Molecular Systems Using a Composite Density Functional-Semiempirical Hamiltonian. J. Chem. Phys. 2000, 113, 5604-5613.
    • (2000) J. Chem. Phys. , vol.113 , pp. 5604-5613
    • Gogonea, V.1    Westerhoff, L.M.2    Merz, K.M.3
  • 53
    • 47249166012 scopus 로고    scopus 로고
    • First Principles Calculations Using Density Matrix Divide-and-Conquer within the Siesta Methodology
    • Cankurtaran, B. O.; Gale, J. D.; Ford, M. J. First Principles Calculations Using Density Matrix Divide-and-Conquer within the Siesta Methodology. J. Phys.: Condens. Matter 2008, 20, 294208.
    • (2008) J. Phys.: Condens. Matter , vol.20 , pp. 294208
    • Cankurtaran, B.O.1    Gale, J.D.2    Ford, M.J.3
  • 54
    • 77950172747 scopus 로고    scopus 로고
    • Divide and Conquer Hartree-Fock Calculations on Proteins
    • He, X.; Merz, K. M. Divide and Conquer Hartree-Fock Calculations on Proteins. J. Chem. Theory Comput. 2010, 6, 405-411.
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 405-411
    • He, X.1    Merz, K.M.2
  • 55
    • 0030567425 scopus 로고    scopus 로고
    • Linear Scaling Density Functional Calculations via the Continuous Fast Multipole Method
    • White, C. A.; Johnson, B. G.; Gill, P. M. W.; Head-Gordon, M. Linear Scaling Density Functional Calculations via the Continuous Fast Multipole Method. Chem. Phys. Lett. 1996, 253, 268-278.
    • (1996) Chem. Phys. Lett. , vol.253 , pp. 268-278
    • White, C.A.1    Johnson, B.G.2    Gill, P.M.W.3    Head-Gordon, M.4
  • 56
    • 12344294827 scopus 로고    scopus 로고
    • A Quantum Chemical Method for Rapid Optimization of Protein Structures
    • Wada, M.; Sakurai, M. A Quantum Chemical Method for Rapid Optimization of Protein Structures. J. Comput. Chem. 2005, 26, 160-168.
    • (2005) J. Comput. Chem. , vol.26 , pp. 160-168
    • Wada, M.1    Sakurai, M.2
  • 57
    • 79955926989 scopus 로고    scopus 로고
    • Molecules-in-Molecules: An Extrapolated Fragment-Based Approach for Accurate Calculations on Large Molecules and Materials
    • Mayhall, N. J.; Raghavachari, K. Molecules-in-Molecules: An Extrapolated Fragment-Based Approach for Accurate Calculations on Large Molecules and Materials. J. Chem. Theory Comput. 2011, 7, 1336-1343.
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 1336-1343
    • Mayhall, N.J.1    Raghavachari, K.2
  • 59
    • 0037028243 scopus 로고    scopus 로고
    • Ab Initio-Quality Electrostatic Potentials for Proteins: An Application of the ADMA Approach
    • Exner, T. E.; Mezey, P. G. Ab Initio-Quality Electrostatic Potentials for Proteins: An Application of the ADMA Approach. J. Phys. Chem. A 2002, 106, 11791-11800.
    • (2002) J. Phys. Chem. A , vol.106 , pp. 11791-11800
    • Exner, T.E.1    Mezey, P.G.2
  • 60
    • 22944470256 scopus 로고    scopus 로고
    • A New Method for Direct Calculation of Total Energy of Protein
    • He, X.; Zhang, J. Z. H. A New Method for Direct Calculation of Total Energy of Protein. J. Chem. Phys. 2005, 122, 031103.
    • (2005) J. Chem. Phys. , vol.122 , pp. 031103
    • He, X.1    Zhang, J.Z.H.2
  • 61
    • 79551669207 scopus 로고    scopus 로고
    • Kohn-Sham Density Functional Theory Electronic Structure Calculations with Linearly Scaling Computational Time and Memory Usage
    • Rudberg, E.; Rubensson, E. H.; Sałek, P. Kohn-Sham Density Functional Theory Electronic Structure Calculations with Linearly Scaling Computational Time and Memory Usage. J. Chem. Theory Comput. 2010, 7, 340-350.
    • (2010) J. Chem. Theory Comput. , vol.7 , pp. 340-350
    • Rudberg, E.1    Rubensson, E.H.2    Sałek, P.3
  • 62
    • 0001131626 scopus 로고    scopus 로고
    • Application of Localized Molecular Orbitals to the Solution of Semiempirical Self-Consistent Field Equations
    • Stewart, J. J. P. Application of Localized Molecular Orbitals to the Solution of Semiempirical Self-Consistent Field Equations. Int. J. Quantum Chem. 1996, 58, 133-146.
    • (1996) Int. J. Quantum Chem. , vol.58 , pp. 133-146
    • Stewart, J.J.P.1
  • 64
    • 84873640615 scopus 로고    scopus 로고
    • Acceleration of Electron Repulsion Integral Evaluation on Graphics Processing Units via Use of Recurrence Relations
    • Miao, Y.; Merz, K. M. Acceleration of Electron Repulsion Integral Evaluation on Graphics Processing Units via Use of Recurrence Relations. J. Chem. Theory Comput. 2013, 9, 965-976.
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 965-976
    • Miao, Y.1    Merz, K.M.2
  • 65
    • 84885401667 scopus 로고    scopus 로고
    • Real-Space Density Functional Theory on Graphical Processing Units: Computational Approach and Comparison to Gaussian Basis Set Methods
    • Andrade, X.; Aspuru-Guzik, A. Real-Space Density Functional Theory on Graphical Processing Units: Computational Approach and Comparison to Gaussian Basis Set Methods. J. Chem. Theory Comput. 2013, 9, 4360-4373.
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 4360-4373
    • Andrade, X.1    Aspuru-Guzik, A.2
  • 66
    • 84934442784 scopus 로고    scopus 로고
    • QM and QM/MM Simulations of Proteins
    • Monticelli, L., Salonen, E., Eds.; Humana Press: New York
    • Steinbrecher, T.; Elstner, M. QM and QM/MM Simulations of Proteins. In Biomolecular Simulations; Monticelli, L., Salonen, E., Eds.; Humana Press: New York, 2013; Vol. 924, pp 91-124.
    • (2013) Biomolecular Simulations , vol.924 , pp. 91-124
    • Steinbrecher, T.1    Elstner, M.2
  • 69
    • 84855491863 scopus 로고    scopus 로고
    • Toward ab Initio Refinement of Protein X-ray Crystal Structures: Interpreting and Correlating Structural Fluctuations
    • Falklöf, O.; Collyer, C. A.; Reimers, J. R. Toward ab Initio Refinement of Protein X-ray Crystal Structures: Interpreting and Correlating Structural Fluctuations. Theor. Chem. Acc. 2012, 131, 1076.
    • (2012) Theor. Chem. Acc. , vol.131 , pp. 1076
    • Falklöf, O.1    Collyer, C.A.2    Reimers, J.R.3
  • 71
    • 0026597444 scopus 로고
    • Free R Value: A Novel Statistical Quantity for Assessing the Accuracy of Crystal Structures
    • Brunger, A. T. Free R Value: A Novel Statistical Quantity for Assessing the Accuracy of Crystal Structures. Nature 1992, 355, 472-475.
    • (1992) Nature , vol.355 , pp. 472-475
    • Brunger, A.T.1
  • 72
    • 10644250257 scopus 로고
    • Inhomogeneous Electron Gas
    • Hohenberg, P.; Kohn, W. Inhomogeneous Electron Gas. Phys. Rev. B 1964, 136, B864.
    • (1964) Phys. Rev. B , vol.136 , pp. B864
    • Hohenberg, P.1    Kohn, W.2
  • 73
    • 0042113153 scopus 로고
    • Self-Consistent Equations Including Exchange and Correlation Effects
    • Kohn, W.; Sham, L. J. Self-Consistent Equations Including Exchange and Correlation Effects. Phys. Rev. 1965, 140, A1133-A1138.
    • (1965) Phys. Rev. , vol.140 , pp. A1133-A1138
    • Kohn, W.1    Sham, L.J.2
  • 74
    • 4243553426 scopus 로고
    • Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior
    • Becke, A. D. Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior. Phys. Rev. A 1988, 38, 3098-3100.
    • (1988) Phys. Rev. A , vol.38 , pp. 3098-3100
    • Becke, A.D.1
  • 75
    • 18144378706 scopus 로고
    • Accurate and Simple Density Functional for the Electronic Exchange Energy: Generalized Gradient Approximation
    • Perdew, J. P.; Yue, W. Accurate and Simple Density Functional for the Electronic Exchange Energy: Generalized Gradient Approximation. Phys. Rev. B 1986, 33, 8800-8802.
    • (1986) Phys. Rev. B , vol.33 , pp. 8800-8802
    • Perdew, J.P.1    Yue, W.2
  • 76
    • 0000189651 scopus 로고
    • Density-Functional Thermochemistry. III. The Role of Exact Exchange
    • Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange. J. Chem. Phys. 1993, 98, 5648-5652.
    • (1993) J. Chem. Phys. , vol.98 , pp. 5648-5652
    • Becke, A.D.1
  • 77
    • 33751157732 scopus 로고
    • Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
    • Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields. J. Phys. Chem. 1994, 98, 11623-11627.
    • (1994) J. Phys. Chem. , vol.98 , pp. 11623-11627
    • Stephens, P.J.1    Devlin, F.J.2    Chabalowski, C.F.3    Frisch, M.J.4
  • 78
    • 0347170005 scopus 로고
    • Self-Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian-Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules
    • Hehre, W. J.; Ditchfield, R.; Pople, J. A. Self-Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian-Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules. J. Chem. Phys. 1972, 56, 2257-2261.
    • (1972) J. Chem. Phys. , vol.56 , pp. 2257-2261
    • Hehre, W.J.1    Ditchfield, R.2    Pople, J.A.3
  • 79
    • 26344435738 scopus 로고
    • Fully Optimized Contracted Gaussian-Basis Sets for Atoms Li to Kr
    • Schäfer, A.; Horn, H.; Ahlrichs, R. Fully Optimized Contracted Gaussian-Basis Sets for Atoms Li to Kr. J. Chem. Phys. 1992, 97, 2571-2577.
    • (1992) J. Chem. Phys. , vol.97 , pp. 2571-2577
    • Schäfer, A.1    Horn, H.2    Ahlrichs, R.3
  • 80
    • 26244461462 scopus 로고    scopus 로고
    • Balanced Basis Sets of Split Valence, Triple Zeta Valence and Quadruple Zeta Valence Quality for H to Rn: Design and Assessment of Accuracy
    • Weigend, F.; Ahlrichs, R. Balanced Basis Sets of Split Valence, Triple Zeta Valence and Quadruple Zeta Valence Quality for H to Rn: Design and Assessment of Accuracy. Phys. Chem. Chem. Phys. 2005, 7, 3297-3305.
    • (2005) Phys. Chem. Chem. Phys. , vol.7 , pp. 3297-3305
    • Weigend, F.1    Ahlrichs, R.2
  • 81
    • 4243476736 scopus 로고
    • A Density-Functional Study of van der Waals Forces: Rare Gas Diatomics
    • Pérez-Jordá, J. M.; Becke, A. D. A Density-Functional Study of van der Waals Forces: Rare Gas Diatomics. Chem. Phys. Lett. 1995, 233, 134-137.
    • (1995) Chem. Phys. Lett. , vol.233 , pp. 134-137
    • Pérez-Jordá, J.M.1    Becke, A.D.2
  • 82
    • 37549004997 scopus 로고
    • Can (Semi)Local Density-Functional Theory Account for the London Dispersion Forces?
    • Kristyan, S.; Pulay, P. Can (Semi)Local Density-Functional Theory Account for the London Dispersion Forces? Chem. Phys. Lett. 1994, 229, 175-180.
    • (1994) Chem. Phys. Lett. , vol.229 , pp. 175-180
    • Kristyan, S.1    Pulay, P.2
  • 83
    • 84986461296 scopus 로고
    • Density-Functional Theory and Molecular Clusters
    • Hobza, P.; Sponer, J.; Reschel, T. Density-Functional Theory and Molecular Clusters. J. Comput. Chem. 1995, 16, 1315-1325.
    • (1995) J. Comput. Chem. , vol.16 , pp. 1315-1325
    • Hobza, P.1    Sponer, J.2    Reschel, T.3
  • 84
    • 0001225025 scopus 로고    scopus 로고
    • Base Stacking in Cytosine Dimer. A Comparison of Correlated ab Initio Calculations with Three Empirical Potential Models and Density Functional Theory Calculations
    • Sponer, J.; Leszczynski, J.; Hobza, P. Base Stacking in Cytosine Dimer. A Comparison of Correlated ab Initio Calculations with Three Empirical Potential Models and Density Functional Theory Calculations. J. Comput. Chem. 1996, 17, 841-850.
    • (1996) J. Comput. Chem. , vol.17 , pp. 841-850
    • Sponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 86
    • 68749098493 scopus 로고    scopus 로고
    • Nonlocal van der Waals Density Functional Made Simple
    • Vydrov, O. A.; Van Voorhis, T. Nonlocal van der Waals Density Functional Made Simple. Phys. Rev. Lett. 2009, 103, 063004.
    • (2009) Phys. Rev. Lett. , vol.103 , pp. 063004
    • Vydrov, O.A.1    Van Voorhis, T.2
  • 88
    • 78650908745 scopus 로고    scopus 로고
    • Nonlocal van der Waals Density Functional: The Simpler the Better
    • Vydrov, O. A.; Van Voorhis, T. Nonlocal van der Waals Density Functional: The Simpler the Better. J. Chem. Phys. 2010, 133, 244103.
    • (2010) J. Chem. Phys. , vol.133 , pp. 244103
    • Vydrov, O.A.1    Van Voorhis, T.2
  • 89
    • 83455260606 scopus 로고    scopus 로고
    • Performance of the van der Waals Density Functional VV10 and (Hybrid)GGA Variants for Thermochemistry and Noncovalent Interactions
    • Hujo, W.; Grimme, S. Performance of the van der Waals Density Functional VV10 and (Hybrid)GGA Variants for Thermochemistry and Noncovalent Interactions. J. Chem. Theory Comput. 2011, 7, 3866-3871.
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 3866-3871
    • Hujo, W.1    Grimme, S.2
  • 90
    • 4043164887 scopus 로고    scopus 로고
    • Accurate Description of van der Waals Complexes by Density Functional Theory Including Empirical Corrections
    • Grimme, S. Accurate Description of van der Waals Complexes by Density Functional Theory Including Empirical Corrections. J. Comput. Chem. 2004, 25, 1463-1473.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1463-1473
    • Grimme, S.1
  • 91
    • 33750559983 scopus 로고    scopus 로고
    • Semiempirical GGA-Type Density Functional Constructed with a Long-Range Dispersion Correction
    • Grimme, S. Semiempirical GGA-Type Density Functional Constructed with a Long-Range Dispersion Correction. J. Comput. Chem. 2006, 27, 1787-1799.
    • (2006) J. Comput. Chem. , vol.27 , pp. 1787-1799
    • Grimme, S.1
  • 92
    • 19644400832 scopus 로고    scopus 로고
    • Optimization of Effective Atom Centered Potentials for London Dispersion Forces in Density Functional Theory
    • von Lilienfeld, O. A.; Tavernelli, I.; Rothlisberger, U.; Sebastiani, D. Optimization of Effective Atom Centered Potentials for London Dispersion Forces in Density Functional Theory. Phys. Rev. Lett. 2004, 93, 153004.
    • (2004) Phys. Rev. Lett. , vol.93 , pp. 153004
    • Von Lilienfeld, O.A.1    Tavernelli, I.2    Rothlisberger, U.3    Sebastiani, D.4
  • 93
    • 43049141516 scopus 로고    scopus 로고
    • The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals
    • Zhao, Y.; Truhlar, D. G. The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals. Theor. Chem. Acc. 2008, 120, 215-241.
    • (2008) Theor. Chem. Acc. , vol.120 , pp. 215-241
    • Zhao, Y.1    Truhlar, D.G.2
  • 94
    • 20844452831 scopus 로고    scopus 로고
    • Exchange-Hole Dipole Moment and the Dispersion Interaction
    • Becke, A. D.; Johnson, E. R. Exchange-Hole Dipole Moment and the Dispersion Interaction. J. Chem. Phys. 2005, 122, 154104.
    • (2005) J. Chem. Phys. , vol.122 , pp. 154104
    • Becke, A.D.1    Johnson, E.R.2
  • 95
    • 80755185211 scopus 로고    scopus 로고
    • Comprehensive Bench-marking of a Density-Dependent Dispersion Correction
    • Steinmann, S. N.; Corminboeuf, C. Comprehensive Bench-marking of a Density-Dependent Dispersion Correction. J. Chem. Theory Comput. 2011, 7, 3567-3577.
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 3567-3577
    • Steinmann, S.N.1    Corminboeuf, C.2
  • 96
    • 61349180195 scopus 로고    scopus 로고
    • Accurate Molecular van der Waals Interactions from Ground-State Electron Density and Free-Atom Reference Data
    • Tkatchenko, A.; Scheffler, M. Accurate Molecular van der Waals Interactions from Ground-State Electron Density and Free-Atom Reference Data. Phys. Rev. Lett. 2009, 102, 073005.
    • (2009) Phys. Rev. Lett. , vol.102 , pp. 073005
    • Tkatchenko, A.1    Scheffler, M.2
  • 97
    • 84863609102 scopus 로고    scopus 로고
    • A (Nearly) Universally Applicable Method for Modeling Noncovalent Interactions Using B3LYP
    • Torres, E.; DiLabio, G. A. A (Nearly) Universally Applicable Method for Modeling Noncovalent Interactions Using B3LYP. J. Phys. Chem. Lett. 2012, 3, 1738-1744.
    • (2012) J. Phys. Chem. Lett. , vol.3 , pp. 1738-1744
    • Torres, E.1    DiLabio, G.A.2
  • 98
    • 77951680464 scopus 로고    scopus 로고
    • Consistent and Accurate ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu
    • Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A Consistent and Accurate ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu. J. Chem. Phys. 2010, 132, 154104.
    • (2010) J. Chem. Phys. , vol.132 , pp. 154104
    • Grimme, S.1    Antony, J.2    Ehrlich, S.3    Krieg, H.A.4
  • 99
    • 79952943559 scopus 로고    scopus 로고
    • Effect of the Damping Function in Dispersion Corrected Density Functional Theory
    • Grimme, S.; Ehrlich, S.; Goerigk, L. Effect of the Damping Function in Dispersion Corrected Density Functional Theory. J. Comput. Chem. 2011, 32, 1456-1465.
    • (2011) J. Comput. Chem. , vol.32 , pp. 1456-1465
    • Grimme, S.1    Ehrlich, S.2    Goerigk, L.3
  • 100
    • 84875674943 scopus 로고    scopus 로고
    • Density Functional Theory with London Dispersion Corrections
    • Grimme, S. Density Functional Theory with London Dispersion Corrections. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 211-228.
    • (2011) Wiley Interdiscip. Rev.: Comput. Mol. Sci. , vol.1 , pp. 211-228
    • Grimme, S.1
  • 101
    • 84866983386 scopus 로고    scopus 로고
    • Perspective: Advances and Challenges in Treating van der Waals Dispersion Forces in Density Functional Theory
    • Klimes, J.; Michaelides, A. Perspective: Advances and Challenges in Treating van der Waals Dispersion Forces in Density Functional Theory. J. Chem. Phys. 2012, 137, 120901.
    • (2012) J. Chem. Phys. , vol.137 , pp. 120901
    • Klimes, J.1    Michaelides, A.2
  • 102
    • 84896308676 scopus 로고    scopus 로고
    • How Do DFT-DCP, DFT-NL, and DFT-D3 Compare for the Description of London-Dispersion Effects in Conformers and General Thermochemistry?
    • Goerigk, L. How Do DFT-DCP, DFT-NL, and DFT-D3 Compare for the Description of London-Dispersion Effects in Conformers and General Thermochemistry? J. Chem. Theory Comput. 2014, 10, 968-980.
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 968-980
    • Goerigk, L.1
  • 103
    • 82955229521 scopus 로고    scopus 로고
    • Benchmarking Density Functional Methods against the S66 and S66x8 Datasets for Non-Covalent Interactions
    • Goerigk, L.; Kruse, H.; Grimme, S. Benchmarking Density Functional Methods against the S66 and S66x8 Datasets for Non-Covalent Interactions. ChemPhysChem 2011, 12, 3421-3433.
    • (2011) ChemPhysChem , vol.12 , pp. 3421-3433
    • Goerigk, L.1    Kruse, H.2    Grimme, S.3
  • 104
    • 84876268668 scopus 로고    scopus 로고
    • Dispersion-Corrected Density Functional Theory for Aromatic Interactions in Complex Systems
    • Ehrlich, S.; Moellmann, J.; Grimme, S. Dispersion-Corrected Density Functional Theory for Aromatic Interactions in Complex Systems. Acc. Chem. Res. 2013, 46, 916-926.
    • (2013) Acc. Chem. Res. , vol.46 , pp. 916-926
    • Ehrlich, S.1    Moellmann, J.2    Grimme, S.3
  • 105
    • 84874817224 scopus 로고    scopus 로고
    • Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes
    • Risthaus, T.; Grimme, S. Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes. J. Chem. Theory Comput. 2013, 9, 1580-1591.
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 1580-1591
    • Risthaus, T.1    Grimme, S.2
  • 106
    • 84875170778 scopus 로고    scopus 로고
    • Accurate Quantum Chemical Energies for Tetrapeptide Conformations: Why MP2 Data with an Insufficient Basis Set Should Be Handled with Caution
    • Goerigk, L.; Karton, A.; Martin, J. M. L.; Radom, L. Accurate Quantum Chemical Energies for Tetrapeptide Conformations: Why MP2 Data with an Insufficient Basis Set Should Be Handled with Caution. Phys. Chem. Chem. Phys. 2013, 15, 7028-7031.
    • Phys. Chem. Chem. Phys. , vol.2013 , Issue.15 , pp. 7028-7031
    • Goerigk, L.1    Karton, A.2    Martin, J.M.L.3    Radom, L.4
  • 107
    • 84884142444 scopus 로고    scopus 로고
    • Effects of London Dispersion Correction in Density Functional Theory on the Structures of Organic Molecules in the Gas Phase
    • Grimme, S.; Steinmetz, M. Effects of London Dispersion Correction in Density Functional Theory on the Structures of Organic Molecules in the Gas Phase. Phys. Chem. Chem. Phys. 2013, 15, 16031-16042.
    • (2013) Phys. Chem. Chem. Phys. , vol.15 , pp. 16031-16042
    • Grimme, S.1    Steinmetz, M.2
  • 108
    • 79952981826 scopus 로고    scopus 로고
    • A Thorough Benchmark of Density Functional Methods for General Main Group Thermochemistry, Kinetics, and Noncovalent Interactions
    • Goerigk, L.; Grimme, S. A Thorough Benchmark of Density Functional Methods for General Main Group Thermochemistry, Kinetics, and Noncovalent Interactions. Phys. Chem. Chem. Phys. 2011, 13, 6670-6688.
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 6670-6688
    • Goerigk, L.1    Grimme, S.2
  • 109
    • 79955662781 scopus 로고    scopus 로고
    • On the Importance of the Dispersion Energy for the Thermodynamic Stability of Molecules
    • Grimme, S.; Huenerbein, R.; Ehrlich, S. On the Importance of the Dispersion Energy for the Thermodynamic Stability of Molecules. ChemPhysChem 2011, 12, 1258-1261.
    • (2011) ChemPhysChem , vol.12 , pp. 1258-1261
    • Grimme, S.1    Huenerbein, R.2    Ehrlich, S.3
  • 110
    • 84918827333 scopus 로고    scopus 로고
    • First Steps Towards Quantum Refinement of Protein X-ray Structures
    • Zeng, J., Zhang, R. Q., Treutlein, H. R., Eds.; Springer: Dordrecht, The Netherlands
    • Goerigk, L.; Falklöf, O.; Collyer, C. A.; Reimers, J. R. First Steps Towards Quantum Refinement of Protein X-ray Structures. In Quantum Simulations of Materials and Biological Systems; Zeng, J., Zhang, R. Q., Treutlein, H. R., Eds.; Springer: Dordrecht, The Netherlands, 2012; pp 87-120.
    • (2012) Quantum Simulations of Materials and Biological Systems , pp. 87-120
    • Goerigk, L.1    Falklöf, O.2    Collyer, C.A.3    Reimers, J.R.4
  • 111
    • 0000657451 scopus 로고
    • A Simple but Reliable Method for the Prediction of Intermolecular Potentials
    • Hepburn, J.; Scoles, G.; Penco, R. A Simple but Reliable Method for the Prediction of Intermolecular Potentials. Chem. Phys. Lett. 1975, 36, 451-456.
    • (1975) Chem. Phys. Lett. , vol.36 , pp. 451-456
    • Hepburn, J.1    Scoles, G.2    Penco, R.3
  • 112
    • 0001373611 scopus 로고
    • Intermolecular Forces in Simple Systems
    • Ahlrichs, R. Intermolecular Forces in Simple Systems. Chem. Phys. 1977, 19, 119-130.
    • (1977) Chem. Phys. , vol.19 , pp. 119-130
    • Ahlrichs, R.1
  • 113
    • 84882449698 scopus 로고    scopus 로고
    • Diffusion Energy Profiles in Silica Mesoporous Molecular Sieves Modelled with the Fragment Molecular Orbital Method
    • Roskop, L.; Fedorov, D. G.; Gordon, M. S. Diffusion Energy Profiles in Silica Mesoporous Molecular Sieves Modelled with the Fragment Molecular Orbital Method. Mol. Phys. 2013, 111, 1622-1629.
    • (2013) Mol. Phys. , vol.111 , pp. 1622-1629
    • Roskop, L.1    Fedorov, D.G.2    Gordon, M.S.3
  • 114
    • 84906230648 scopus 로고    scopus 로고
    • Dispersion Corrected Hartree-Fock and Density Functional Theory for Organic Crystal Structure Prediction
    • Brandenburg, J. G.; Grimme, S. Dispersion Corrected Hartree-Fock and Density Functional Theory for Organic Crystal Structure Prediction. Top. Curr. Chem. 2014, 345, 1-23.
    • (2014) Top. Curr. Chem. , vol.345 , pp. 1-23
    • Brandenburg, J.G.1    Grimme, S.2
  • 115
    • 84890021933 scopus 로고
    • Calculation of Small Molecular Interactions by Differences of Separate Total Energies. Some Procedures with Reduced Errors
    • Boys, S. F.; Bernardi, F. Calculation of Small Molecular Interactions by Differences of Separate Total Energies. Some Procedures with Reduced Errors. Mol. Phys. 1970, 19, 553-566.
    • (1970) Mol. Phys. , vol.19 , pp. 553-566
    • Boys, S.F.1    Bernardi, F.2
  • 116
    • 84892580461 scopus 로고    scopus 로고
    • Can the Counterpoise Correction for Basis Set Superposition Effect Be Justified?
    • Mentel, Ł. M.; Baerends, E. J. Can the Counterpoise Correction for Basis Set Superposition Effect Be Justified? J. Chem. Theory Comput. 2013, 10, 252-267.
    • (2013) J. Chem. Theory Comput. , vol.10 , pp. 252-267
    • Mentel, Ł.M.1    Baerends, E.J.2
  • 117
    • 41649106123 scopus 로고    scopus 로고
    • Evaluation of the Intramolecular Basis Set Superposition Error in the Calculations of Larger Molecules: [n]Helicenes and Phe-Gly-Phe Tripeptide
    • Valdes, H.; Klusak, V.; Pitonak, M.; Exner, O.; Stary, I.; Hobza, P.; Rulisek, L. Evaluation of the Intramolecular Basis Set Superposition Error in the Calculations of Larger Molecules: [n]Helicenes and Phe-Gly-Phe Tripeptide. J. Comput. Chem. 2008, 29, 861-870.
    • (2008) J. Comput. Chem. , vol.29 , pp. 861-870
    • Valdes, H.1    Klusak, V.2    Pitonak, M.3    Exner, O.4    Stary, I.5    Hobza, P.6    Rulisek, L.7
  • 119
    • 84921060746 scopus 로고    scopus 로고
    • The Structure of the Gas-Phase Tyrosine-Glycine Dipeptide
    • Toroz, D.; Van Mourik, T. The Structure of the Gas-Phase Tyrosine-Glycine Dipeptide. Mol. Phys. 2006, 104, 559-570.
    • (2006) Mol. Phys. , vol.104 , pp. 559-570
    • Toroz, D.1    Van Mourik, T.2
  • 120
    • 31144461637 scopus 로고    scopus 로고
    • Molecular Conformations and Relative Stabilities Can Be as Demanding of the Electronic Structure Method as Intermolecular Calculations
    • van Mourik, T.; Karamertzanis, P. G.; Price, S. L. Molecular Conformations and Relative Stabilities Can Be as Demanding of the Electronic Structure Method as Intermolecular Calculations. J. Phys. Chem. A 2006, 110, 8-12.
    • (2006) J. Phys. Chem. A , vol.110 , pp. 8-12
    • Van Mourik, T.1    Karamertzanis, P.G.2    Price, S.L.3
  • 121
    • 34250641957 scopus 로고    scopus 로고
    • Insufficient Description of Dispersion in B3LYP and Large Basis Set Superposition Errors in MP2 Calculations Can Hide Peptide Conformers
    • Holroyd, L. F.; van Mourik, T. Insufficient Description of Dispersion in B3LYP and Large Basis Set Superposition Errors in MP2 Calculations Can Hide Peptide Conformers. Chem. Phys. Lett. 2007, 442, 42-46.
    • (2007) Chem. Phys. Lett. , vol.442 , pp. 42-46
    • Holroyd, L.F.1    Van Mourik, T.2
  • 122
    • 42149135944 scopus 로고    scopus 로고
    • Intramolecular Basis Set Superposition Error Effects on the Planarity of Benzene and Other Aromatic Molecules: A Solution to the Problem
    • Asturiol, D.; Duran, M.; Salvador, P. Intramolecular Basis Set Superposition Error Effects on the Planarity of Benzene and Other Aromatic Molecules: A Solution to the Problem. J. Chem. Phys. 2008, 128, 144108.
    • (2008) J. Chem. Phys. , vol.128 , pp. 144108
    • Asturiol, D.1    Duran, M.2    Salvador, P.3
  • 123
    • 77950114691 scopus 로고    scopus 로고
    • An Atomic Counterpoise Method for Estimating Inter- and Intramolecular Basis Set Superposition Errors
    • Jensen, F. An Atomic Counterpoise Method for Estimating Inter- and Intramolecular Basis Set Superposition Errors. J. Chem. Theory Comput. 2010, 6, 100-106.
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 100-106
    • Jensen, F.1
  • 124
    • 84870865284 scopus 로고    scopus 로고
    • Why the Standard B3LYP/6-31G∗ Model Chemistry Should Not Be Used in DFT Calculations of Molecular Thermochemistry: Understanding and Correcting the Problem
    • Kruse, H.; Goerigk, L.; Grimme, S. Why the Standard B3LYP/6-31G∗ Model Chemistry Should Not Be Used in DFT Calculations of Molecular Thermochemistry: Understanding and Correcting the Problem. J. Org. Chem. 2012, 77, 10824-10834.
    • (2012) J. Org. Chem. , vol.77 , pp. 10824-10834
    • Kruse, H.1    Goerigk, L.2    Grimme, S.3
  • 125
    • 84884948006 scopus 로고    scopus 로고
    • Geometrical Correction for the Inter- and Intramolecular Basis Set Superposition Error in Periodic Density Functional Theory Calculations
    • Brandenburg, J. G.; Alessio, M.; Civalleri, B.; Peintinger, M. F.; Bredow, T.; Grimme, S. Geometrical Correction for the Inter- and Intramolecular Basis Set Superposition Error in Periodic Density Functional Theory Calculations. J. Phys. Chem. A 2013, 117, 9282-9292.
    • (2013) J. Phys. Chem. A , vol.117 , pp. 9282-9292
    • Brandenburg, J.G.1    Alessio, M.2    Civalleri, B.3    Peintinger, M.F.4    Bredow, T.5    Grimme, S.6
  • 126
    • 84880028699 scopus 로고    scopus 로고
    • Efficient Methods for the Quantum Chemical Treatment of Protein Structures: The Effects of London-Dispersion and Basis-Set Incompleteness on Peptide and Water-Cluster Geometries
    • Goerigk, L.; Reimers, J. R. Efficient Methods for the Quantum Chemical Treatment of Protein Structures: The Effects of London-Dispersion and Basis-Set Incompleteness on Peptide and Water-Cluster Geometries. J. Chem. Theory Comput. 2013, 9, 3240-3251.
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 3240-3251
    • Goerigk, L.1    Reimers, J.R.2
  • 127
    • 22744441344 scopus 로고    scopus 로고
    • Design of Density Functionals That Are Broadly Accurate for Thermochemistry, Thermochemical Kinetics, and Nonbonded Interactions
    • Zhao, Y.; Truhlar, D. G. Design of Density Functionals That Are Broadly Accurate for Thermochemistry, Thermochemical Kinetics, and Nonbonded Interactions. J. Phys. Chem. A 2005, 109, 5656-5667.
    • (2005) J. Phys. Chem. A , vol.109 , pp. 5656-5667
    • Zhao, Y.1    Truhlar, D.G.2
  • 128
    • 0000646464 scopus 로고
    • On a Remarkable Bacteriolytic Element Found in Tissues and Secretions
    • Fleming, A. On a Remarkable Bacteriolytic Element Found in Tissues and Secretions. Proc. R. Soc. London B: Biol. 1922, 93, 306-317.
    • (1922) Proc. R. Soc. London B: Biol. , vol.93 , pp. 306-317
    • Fleming, A.1
  • 129
    • 37049058324 scopus 로고
    • A Fourier Map of Electron Density at 6 A˚ Resolution Obtained by X-ray Diffraction
    • Blake, C. C. F.; Poljak, R. J.; Fenn, R. H.; North, A. C. T.; Phillips, D. C. A Fourier Map of Electron Density at 6 A˚ Resolution Obtained by X-ray Diffraction. Nature 1962, 196, 1173-1176.
    • (1962) Nature , vol.196 , pp. 1173-1176
    • Blake, C.C.F.1    Poljak, R.J.2    Fenn, R.H.3    North, A.C.T.4    Phillips, D.C.5
  • 130
    • 23244460838 scopus 로고
    • Atoms, Molecules, Solids, and Surfaces: Applications of the Generalized Gradient Approximation for Exchange and Correlation
    • Perdew, J. P.; Chevary, J. A.; Vosko, S. H.; Jackson, K. A.; Pederson, M. R.; Singh, D. J.; Fiolhais, C. Atoms, Molecules, Solids, and Surfaces: Applications of the Generalized Gradient Approximation for Exchange and Correlation. Phys. Rev. B 1992, 46, 6671-6687.
    • (1992) Phys. Rev. B , vol.46 , pp. 6671-6687
    • Perdew, J.P.1    Chevary, J.A.2    Vosko, S.H.3    Jackson, K.A.4    Pederson, M.R.5    Singh, D.J.6    Fiolhais, C.7
  • 131
    • 0033515394 scopus 로고    scopus 로고
    • A New ONIOM Implementation in Gaussian 98. Part I. The Calculation of Energies, Gradients, Vibrational Frequencies and Electric Field Derivatives
    • Dapprich, S.; Komaromi, I.; Byun, K. S.; Morokuma, K.; Frisch, M. J. A New ONIOM Implementation in Gaussian 98. Part I. The Calculation of Energies, Gradients, Vibrational Frequencies and Electric Field Derivatives. J. Mol. Struct. (THEOCHEM) 1999, 461, 1-21.
    • (1999) J. Mol. Struct. (Theochem) , vol.461 , pp. 1-21
    • Dapprich, S.1    Komaromi, I.2    Byun, K.S.3    Morokuma, K.4    Frisch, M.J.5
  • 133
    • 4243539377 scopus 로고
    • Electronic Structure Calculations on Workstation Computers: The Program System TURBOMOLE
    • Ahlrichs, R.; Bar, M.; Haser, M.; Horn, H.; Kolmel, C. Electronic Structure Calculations on Workstation Computers: The Program System TURBOMOLE. Chem. Phys. Lett. 1989, 162, 165-169.
    • (1989) Chem. Phys. Lett. , vol.162 , pp. 165-169
    • Ahlrichs, R.1    Bar, M.2    Haser, M.3    Horn, H.4    Kolmel, C.5
  • 137
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron-Density
    • Lee, C. T.; Yang, W. T.; Parr, R. G. Development of the Colle-Salvetti Correlation-Energy Formula into a Functional of the Electron-Density. Phys. Rev. B 1988, 37, 785-789.
    • (1988) Phys. Rev. B , vol.37 , pp. 785-789
    • Lee, C.T.1    Yang, W.T.2    Parr, R.G.3
  • 138
    • 4243943295 scopus 로고    scopus 로고
    • Generalized Gradient Approximation Made Simple
    • Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple. Phys. Rev. Lett. 1996, 77, 3865-3868.
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 3865-3868
    • Perdew, J.P.1    Burke, K.2    Ernzerhof, M.3
  • 139
    • 0242593713 scopus 로고    scopus 로고
    • Climbing the Density Functional Ladder: Nonempirical Meta-Generalized Gradient Approximation Designed for Molecules and Solids
    • Tao, J. M.; Perdew, J. P.; Staroverov, V. N.; Scuseria, G. E. Climbing the Density Functional Ladder: Nonempirical Meta-Generalized Gradient Approximation Designed for Molecules and Solids. Phys. Rev. Lett. 2003, 91, 146401.
    • (2003) Phys. Rev. Lett. , vol.91 , pp. 146401
    • Tao, J.M.1    Perdew, J.P.2    Staroverov, V.N.3    Scuseria, G.E.4
  • 141
    • 0031285825 scopus 로고    scopus 로고
    • Auxiliary Basis Sets for Main Row Atoms and Transition Metals and Their Use to Approximate Coulomb Potentials
    • Eichkorn, K.; Weigend, F.; Treutler, O.; Ahlrichs, R. Auxiliary Basis Sets for Main Row Atoms and Transition Metals and Their Use to Approximate Coulomb Potentials. Theor. Chem. Acc. 1997, 97, 119-124.
    • (1997) Theor. Chem. Acc. , vol.97 , pp. 119-124
    • Eichkorn, K.1    Weigend, F.2    Treutler, O.3    Ahlrichs, R.4
  • 142
    • 84856845711 scopus 로고    scopus 로고
    • Difficulties in Applying Pure Kohn-Sham Density Functional Theory Electronic Structure Methods to Protein Molecules
    • Rudberg, E. Difficulties in Applying Pure Kohn-Sham Density Functional Theory Electronic Structure Methods to Protein Molecules. J. Phys.: Condens. Matter 2012, 24, 072202.
    • (2012) J. Phys.: Condens. Matter , vol.24 , pp. 072202
    • Rudberg, E.1
  • 143
    • 84961980743 scopus 로고
    • COSMO: A New Approach to Dielectric Screening in Solvents with Explicit Expressions for the Screening Energy and Its Gradient
    • Klamt, A.; Schuurmann, G. COSMO: A New Approach to Dielectric Screening in Solvents with Explicit Expressions for the Screening Energy and Its Gradient. J. Chem. Soc., Perkin Trans. 2 1993, 799-805.
    • (1993) J. Chem. Soc., Perkin Trans. , vol.2 , pp. 799-805
    • Klamt, A.1    Schuurmann, G.2
  • 144
    • 84894230573 scopus 로고    scopus 로고
    • Self-Consistent Field Convergence for Proteins: A Comparison of Full and Localized-Molecular-Orbital Schemes
    • Wick, C.; Hennemann, M.; Stewart, J. P.; Clark, T. Self-Consistent Field Convergence for Proteins: A Comparison of Full and Localized-Molecular-Orbital Schemes. J. Mol. Model. 2014, 20, 2159.
    • (2014) J. Mol. Model. , vol.20 , pp. 2159
    • Wick, C.1    Hennemann, M.2    Stewart, J.P.3    Clark, T.4
  • 145
    • 84861425552 scopus 로고    scopus 로고
    • Linking Crystallographic Model and Data Quality
    • Karplus, P. A.; Diederichs, K. Linking Crystallographic Model and Data Quality. Science 2012, 336, 1030-1033.
    • (2012) Science , vol.336 , pp. 1030-1033
    • Karplus, P.A.1    Diederichs, K.2
  • 148
    • 0036385792 scopus 로고    scopus 로고
    • A Fully Direct RI-HF Algorithm: Implementation, Optimised Auxiliary Basis Sets, Demonstration of Accuracy and Efficiency
    • Weigend, F. A Fully Direct RI-HF Algorithm: Implementation, Optimised Auxiliary Basis Sets, Demonstration of Accuracy and Efficiency. Phys. Chem. Chem. Phys. 2002, 4, 4285-4291.
    • (2002) Phys. Chem. Chem. Phys. , vol.4 , pp. 4285-4291
    • Weigend, F.1
  • 149
    • 59349105675 scopus 로고    scopus 로고
    • Efficient, Approximate and Parallel Hartree-Fock and Hybrid DFT Calculations. A 'Chain-of-Spheres' Algorithm for the Hartree-Fock Exchange
    • Neese, F.; Wennmohs, F.; Hansen, A.; Becker, U. Efficient, Approximate and Parallel Hartree-Fock and Hybrid DFT Calculations. A 'Chain-of-Spheres' Algorithm for the Hartree-Fock Exchange. Chem. Phys. 2009, 356, 98-109.
    • (2009) Chem. Phys. , vol.356 , pp. 98-109
    • Neese, F.1    Wennmohs, F.2    Hansen, A.3    Becker, U.4


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