Water interactions with hydrophobic groups: assessment and recalibration of semiempirical molecular orbital methods.
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Antoine Marion | Francesca Ingrosso | G. Monard | M. Ruiz‐López | A. Marion | Gérald Monard | Manuel F Ruiz-López | Francesca Ingrosso
[1] Arshad Khan,et al. Theoretical studies of CH4(H2O)20, (H2O)21, (H2O)20, and fused dodecahedral and tetrakaidecahedral structures: How do natural gas hydrates form? , 1999 .
[2] Walter Thiel,et al. Semiempirical quantum-chemical methods in computational chemistry , 2005 .
[3] Martin Korth,et al. Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields , 2010 .
[4] E. Coitiño,et al. AM1 study of hydrogen bonded complexes of water , 1989 .
[5] G. Monard,et al. Importance of Polarization and Charge Transfer Effects to Model the Infrared Spectra of Peptides in Solution. , 2011, Journal of chemical theory and computation.
[6] M. Ruiz‐López,et al. An improved semiempirical method for hydrated systems , 2004 .
[7] Jonathan Tennyson,et al. A database of water transitions from experiment and theory (IUPAC Technical Report) , 2014 .
[8] Manuel F. Ruiz-López,et al. Calibration of the Quantum/Classical Hamiltonian in Semiempirical QM/MM AM1 and PM3 Methods , 2000 .
[9] Jirí Cerný,et al. Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations , 2007, J. Comput. Chem..
[10] Martin Head-Gordon,et al. Quadratic configuration interaction. A general technique for determining electron correlation energies , 1987 .
[11] Manuel F. Ruiz-López,et al. Basic ideas for the correction of semiempirical methods describing H-bonded systems , 2000 .
[12] Pavel Hobza,et al. On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions , 2013 .
[13] M. Ruiz‐López,et al. Can semi-empirical models describe HCl dissociation in water? , 2007 .
[14] T. Dunning,et al. Electron affinities of the first‐row atoms revisited. Systematic basis sets and wave functions , 1992 .
[15] W. Thiel,et al. Extension of the MNDO formalism tod orbitals: Integral approximations and preliminary numerical results , 1992 .
[16] Hong Wang,et al. Towards a quantum mechanical force field for carbohydrates: a reparametrized semi-empirical MO approach. , 2004 .
[17] M. Dewar,et al. Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters , 1977 .
[18] J. Stewart. Optimization of parameters for semiempirical methods I. Method , 1989 .
[19] Pavel Hobza,et al. 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. , 2010, The journal of physical chemistry. B.
[20] Joost VandeVondele,et al. Linear Scaling Self-Consistent Field Calculations with Millions of Atoms in the Condensed Phase. , 2012, Journal of chemical theory and computation.
[21] J. Max,et al. Isotope effects in liquid water by infrared spectroscopy. III. H2O and D2O spectra from 6000 to 0 cm(-1). , 2009, The Journal of chemical physics.
[22] János G. Ángyán,et al. The origin of the problems with the PM3 core repulsion function , 1997 .
[23] J. Pople,et al. Self‐consistent molecular orbital methods. XX. A basis set for correlated wave functions , 1980 .
[24] G. Monard,et al. Combining a genetic algorithm with a linear scaling semiempirical method for protein–ligand docking , 2009 .
[25] A. Schäfer,et al. Fully optimized contracted Gaussian basis sets of triple zeta valence quality for atoms Li to Kr , 1994 .
[26] K. Merz,et al. Simulation of liquid water using semiempirical Hamiltonians and the divide and conquer approach. , 2005, The journal of physical chemistry. A.
[27] Julio Daniel Carvalho Maia,et al. GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations. , 2012, Journal of chemical theory and computation.
[28] J. Stewart. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements , 2007, Journal of molecular modeling.
[29] E. Dartois,et al. Methane clathrate hydrate FTIR spectrum - Implications for its cometary and planetary detection , 2008 .
[30] Claude Millot,et al. Improving description of hydrogen bonds at the semiempirical level: water–water interactions as test case , 2000 .
[31] D. York,et al. Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions: H, O, and P Atoms. , 2007, Journal of chemical theory and computation.
[32] I. Csizmadia,et al. Ab initio and density functional study of the conformational space of 1C4 α‐L‐fucose , 1997 .
[33] William L. Jorgensen,et al. Ab Initio Study Of Hydrogen-Bonded Complexes Of Small Organic Molecules With Water , 1998 .
[35] James J. P. Stewart,et al. Application of the PM6 method to modeling proteins , 2009, Journal of molecular modeling.
[36] Stefan Grimme,et al. Accurate description of van der Waals complexes by density functional theory including empirical corrections , 2004, J. Comput. Chem..
[37] Pavel Hobza,et al. Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. , 2010, Chemical reviews.
[38] Pavel Hobza,et al. A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods. , 2010, Journal of chemical theory and computation.
[39] Pavel Hobza,et al. Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods. , 2012, Journal of chemical theory and computation.
[40] J. Pople,et al. Approximate Self-Consistent Molecular Orbital Theory. I. Invariant Procedures , 1965 .
[41] Gábor I. Csonka,et al. Analysis of the core‐repulsion functions used in AM1 and PM3 semiempirical calculations: Conformational analysis of ring systems , 1993, J. Comput. Chem..
[42] G. Corongiu,et al. Van der Waals Interaction Energies of Helium, Neon, and Argon with Naphthalene , 2001 .
[43] Stefan Grimme,et al. Semiempirical GGA‐type density functional constructed with a long‐range dispersion correction , 2006, J. Comput. Chem..
[44] B. Militzer,et al. Hydrogen storage in molecular clathrates. , 2007, Chemical reviews.
[45] J. Dannenberg. Hydrogen bonds: a comparison of semiempirical and ab initio treatments , 1997 .
[46] Giacinto Scoles,et al. Intermolecular forces in simple systems , 1977 .
[47] Eamonn F. Healy,et al. Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model , 1985 .
[48] Michael J. Frisch,et al. MP2 energy evaluation by direct methods , 1988 .
[49] Alfredo Mayall Simas,et al. RM1: A reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I , 2006, J. Comput. Chem..
[50] S. Grimme,et al. Density functional theory with dispersion corrections for supramolecular structures, aggregates, and complexes of (bio)organic molecules. , 2007, Organic & biomolecular chemistry.
[51] William L. Jorgensen,et al. PDDG/PM3 and PDDG/MNDO: Improved semiempirical methods , 2002, J. Comput. Chem..
[52] Xin Wu,et al. Semiempirical Quantum Chemical Calculations Accelerated on a Hybrid Multicore CPU-GPU Computing Platform. , 2012, Journal of chemical theory and computation.
[53] C. Koh,et al. Towards a fundamental understanding of natural gas hydrates. , 2002, Chemical Society reviews.
[54] Pavel Hobza,et al. A halogen-bonding correction for the semiempirical PM6 method , 2011 .
[55] Walter Thiel,et al. OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application. , 2008, Physical chemistry chemical physics : PCCP.
[56] Bodo Martin,et al. Dispersion treatment for NDDO‐based semiempirical MO techniques , 2006 .
[57] Walter Thiel,et al. Extension of MNDO to d Orbitals: Parameters and Results for the Second-Row Elements and for the Zinc Group , 1996 .
[58] I. H. Hillier,et al. Semi-empirical molecular orbital methods including dispersion corrections for the accurate prediction of the full range of intermolecular interactions in biomolecules. , 2007, Physical chemistry chemical physics : PCCP.
[59] James J. P. Stewart,et al. Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters , 2012, Journal of Molecular Modeling.
[60] Teodoro Laino,et al. Semiempirical self-consistent polarization description of bulk water, the liquid-vapor interface, and cubic ice. , 2011, The journal of physical chemistry. A.
[61] B. C. Garrett,et al. Self-consistent polarization neglect of diatomic differential overlap: application to water clusters. , 2008, The Journal of chemical physics.
[62] Walter Thiel,et al. Specific Reaction Path Hamiltonian for Proton Transfer in Water: Reparameterized Semiempirical Models. , 2013, Journal of chemical theory and computation.