Calculation of weakly polar interaction energies in polypeptides using density functional and local Møller‐Plesset perturbation theory
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József Csontos | Nicholas Y. Palermo | Richard F. Murphy | Sándor Lovas | R. Murphy | S. Lovas | J. Csontos
[1] Qin Wu,et al. Empirical correction to density functional theory for van der Waals interactions , 2002 .
[2] Donald G Truhlar,et al. Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions. , 2006, Journal of chemical theory and computation.
[3] Vincenzo Barone,et al. Toward reliable adiabatic connection models free from adjustable parameters , 1997 .
[4] Gautam R. Desiraju,et al. The Weak Hydrogen Bond , 2001 .
[5] Stefan Grimme,et al. Accurate description of van der Waals complexes by density functional theory including empirical corrections , 2004, J. Comput. Chem..
[6] M. Frisch,et al. Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields , 1994 .
[7] Noriyuki Kurita,et al. Adjustment of Perdew-Wang exchange functional for describing van der Waals and DNA base-stacking interactions , 2003 .
[8] Miquel Solà,et al. Parametrization of the Becke3‐LYP hybrid functional for a series of small molecules using quantum molecular similarity techniques , 2001, J. Comput. Chem..
[9] P. Balaram,et al. Tryptophan-containing peptide helices: interactions involving the indole side chain. , 2005, The journal of peptide research : official journal of the American Peptide Society.
[10] José M. Pérez-Jordá,et al. A density-functional study of van der Waals forces: rare gas diatomics. , 1995 .
[11] Vincenzo Barone,et al. Exchange functionals with improved long-range behavior and adiabatic connection methods without adjustable parameters: The mPW and mPW1PW models , 1998 .
[12] Donald G Truhlar,et al. Design of density functionals that are broadly accurate for thermochemistry, thermochemical kinetics, and nonbonded interactions. , 2005, The journal of physical chemistry. A.
[13] Richard A Friesner,et al. Pseudospectral Local Second-Order Møller-Plesset Methods for Computation of Hydrogen Bonding Energies of Molecular Pairs. , 2005, Journal of chemical theory and computation.
[14] Serguei Patchkovskii,et al. An Efficient a Posteriori Treatment for Dispersion Interaction in Density-Functional-Based Tight Binding. , 2005, Journal of chemical theory and computation.
[15] P Pulay,et al. Local Treatment of Electron Correlation , 1993 .
[16] Richard A. Friesner,et al. Pseudospectral localized Mo/ller–Plesset methods: Theory and calculation of conformational energies , 1995 .
[17] A. Becke. Density-functional thermochemistry. V. Systematic optimization of exchange-correlation functionals , 1997 .
[18] G A Petsko,et al. Aromatic-aromatic interaction: a mechanism of protein structure stabilization. , 1985, Science.
[19] J. W. Neidigh,et al. Designing a 20-residue protein , 2002, Nature Structural Biology.
[20] Peter Pulay,et al. CAN (SEMI) LOCAL DENSITY FUNCTIONAL THEORY ACCOUNT FOR THE LONDON DISPERSION FORCES , 1994 .
[21] Christopher A. Hunter,et al. The nature of .pi.-.pi. interactions , 1990 .
[22] Petros Koumoutsakos,et al. Dispersion corrections to density functionals for water aromatic interactions. , 2004, The Journal of chemical physics.
[23] Fred A. Hamprecht,et al. Development and assessment of new exchange-correlation functionals , 1998 .
[24] Stephen K. Burley,et al. Dimerization energetics of benzene and aromatic amino acid side chains , 1986 .
[25] R A Friesner,et al. New methods for electronic structure calculations on large molecules. , 1991, Annual review of physical chemistry.
[26] Robert M. Hughes,et al. Effects of Lysine Acetylation in a β-Hairpin Peptide: Comparison of an Amide−π and a Cation−π Interaction , 2006 .
[27] Saroj K. Nayak,et al. Towards extending the applicability of density functional theory to weakly bound systems , 2001 .
[28] Peter Pulay,et al. Efficient elimination of basis set superposition errors by the local correlation method: Accurate ab initio studies of the water dimer , 1993 .
[29] J. V. Lenthe,et al. State of the Art in Counterpoise Theory , 1994 .
[30] Yixiang Cao,et al. Correlated ab Initio Electronic Structure Calculations for Large Molecules , 1999 .
[31] Parr,et al. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.
[32] G. Scuseria,et al. Comparative assessment of a new nonempirical density functional: Molecules and hydrogen-bonded complexes , 2003 .
[33] Martin Head-Gordon,et al. A Resolution-Of-The-Identity Implementation of the Local Triatomics-In-Molecules Model for Second-Order Møller-Plesset Perturbation Theory with Application to Alanine Tetrapeptide Conformational Energies. , 2005, Journal of chemical theory and computation.
[34] M. Szczęśniak,et al. Origins of Structure and Energetics of van der Waals Clusters from ab Initio Calculations , 1994 .
[35] Xin Xu,et al. The extended Perdew-Burke-Ernzerhof functional with improved accuracy for thermodynamic and electronic properties of molecular systems. , 2004, The Journal of chemical physics.
[36] James A Platts,et al. Spin-Component Scaling Methods for Weak and Stacking Interactions. , 2007, Journal of chemical theory and computation.
[37] G. Tóth,et al. Investigation of aromatic-backbone amide interactions in the model peptide acetyl-Phe-Gly-Gly-N-methyl amide using molecular dynamics simulations and protein database search. , 2001, Journal of the American Chemical Society.
[38] A. Becke. A New Mixing of Hartree-Fock and Local Density-Functional Theories , 1993 .
[39] Marcey L. Waters,et al. Comparison of C−H···π and Hydrophobic Interactions in a β-Hairpin Peptide: Impact on Stability and Specificity , 2004 .
[40] C. R. Watts,et al. Significance of aromatic‐backbone amide interactions in protein structure , 2001, Proteins.
[41] Emily A. Carter,et al. Pseudospectral Møller-Plesset perturbation theory through third order , 1994 .
[42] Martin W. Feyereisen,et al. Use of approximate integrals in ab initio theory. An application in MP2 energy calculations , 1993 .
[43] Henry Margenau,et al. Theory of intermolecular forces , 1969 .
[44] Alberto Vela,et al. Charge-Transfer Complexes: Stringent Tests for Widely Used Density Functionals , 1996 .
[45] Donald G Truhlar,et al. How well can new-generation density functional methods describe stacking interactions in biological systems? , 2005, Physical chemistry chemical physics : PCCP.
[46] Kieron Burke,et al. The adiabatic connection method: a non-empirical hybrid , 1997 .
[47] Martin Head-Gordon,et al. Closely approximating second-order Mo/ller–Plesset perturbation theory with a local triatomics in molecules model , 2000 .
[48] Gergely Tóth,et al. Aromatic - Backbone interactions in α-helices , 2004 .
[49] G. Tóth,et al. Stabilization of local structures by pi-CH and aromatic-backbone amide interactions involving prolyl and aromatic residues. , 2001, Protein engineering.
[50] Donald G. Truhlar,et al. Hybrid Meta Density Functional Theory Methods for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions: The MPW1B95 and MPWB1K Models and Comparative Assessments for Hydrogen Bonding and van der Waals Interactions , 2004 .
[51] N. Handy,et al. Left-right correlation energy , 2001 .
[52] Hans Peter Lüthi,et al. Interaction energies of van der Waals and hydrogen bonded systems calculated using density functional theory: Assessing the PW91 model , 2001 .
[53] Jonathan D. Hirst,et al. Influence of Tyrosine on the Electronic Circular Dichroism of Helical Peptides , 2003 .
[54] Thomas Frauenheim,et al. Hydrogen bonding and stacking interactions of nucleic acid base pairs: A density-functional-theory based treatment , 2001 .
[55] Peter Pulay,et al. A low-scaling method for second order Møller–Plesset calculations , 2001 .
[56] Philippe Y. Ayala,et al. Linear scaling second-order Moller–Plesset theory in the atomic orbital basis for large molecular systems , 1999 .
[57] Pavel Hobza,et al. Density functional theory and molecular clusters , 1995, J. Comput. Chem..
[58] Donald G. Truhlar,et al. Development and Assessment of a New Hybrid Density Functional Model for Thermochemical Kinetics , 2004 .
[59] Michael C. Owen,et al. Aromatic‐backbone interactions in model α‐helical peptides , 2007, J. Comput. Chem..
[60] Donald G. Truhlar,et al. Adiabatic connection for kinetics , 2000 .
[61] S. Fomine,et al. How important is the dispersion interaction for cyclobis(paraquat-p-phenylene)-based molecular , 2005 .
[62] P Hobza,et al. Noncovalent interactions: a challenge for experiment and theory. , 2000, Chemical reviews.
[63] B. Charloteaux,et al. Aromatic side‐chain interactions in proteins. I. Main structural features , 2002, Proteins.
[64] Pavel Hobza,et al. Unexpectedly strong energy stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues: correlated ab initio quantum chemical calculations. , 2005 .
[65] James A. Platts,et al. Hybrid density functional theory for π‐stacking interactions: Application to benzenes, pyridines, and DNA bases , 2006, J. Comput. Chem..
[66] Axel D. Becke,et al. Density‐functional thermochemistry. IV. A new dynamical correlation functional and implications for exact‐exchange mixing , 1996 .
[67] Trygve Helgaker,et al. Basis-set convergence in correlated calculations on Ne, N2, and H2O , 1998 .
[68] Frederick R. Manby,et al. Fast linear scaling second-order Møller-Plesset perturbation theory (MP2) using local and density fitting approximations , 2003 .
[69] T. Steiner,et al. Hydrogen bonds with pi-acceptors in proteins: frequencies and role in stabilizing local 3D structures. , 2001, Journal of molecular biology.
[70] Jackson,et al. Atoms, molecules, solids, and surfaces: Applications of the generalized gradient approximation for exchange and correlation. , 1992, Physical review. B, Condensed matter.
[71] G. M. Smith,et al. Electronic distributions within protein phenylalanine aromatic rings are reflected by the three-dimensional oxygen atom environments. , 1982, Proceedings of the National Academy of Sciences of the United States of America.
[72] T. Walsh,et al. Exact exchange and Wilson-Levy correlation: a pragmatic device for studying complex weakly-bonded systems. , 2005, Physical chemistry chemical physics : PCCP.
[73] Jirí Cerný,et al. 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. , 2006, Physical chemistry chemical physics : PCCP.
[74] Angela K. Wilson,et al. The Effect of Basis Set Superposition Error (BSSE) on the Convergence of Molecular Properties Calculated with the Correlation Consistent Basis Sets , 1998 .
[75] C. Hunter,et al. Sequence-dependent DNA structure. The role of base stacking interactions. , 1993, Journal of molecular biology.
[76] Donald F. Weaver,et al. Data mining, Ab initio, and molecular mechanics study on conformation of phenylalanine and its interaction with neighboring backbone amide groups in proteins , 2002 .
[77] Donald G. Truhlar,et al. Effectiveness of Diffuse Basis Functions for Calculating Relative Energies by Density Functional Theory , 2003 .
[78] Jirí Cerný,et al. The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking. , 2005, Physical chemistry chemical physics : PCCP.
[79] G. Petsko,et al. Weakly polar interactions in proteins. , 1988, Advances in protein chemistry.
[80] Donald G Truhlar,et al. Improved density functionals for water. , 2005, The journal of physical chemistry. B.
[81] Xin Xu,et al. From The Cover: The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties. , 2004, Proceedings of the National Academy of Sciences of the United States of America.