Comparison of different computational methods for water structure optimisation

Azam SS, Zaheer-Il-Haq Fatmi MQ. Classical and QM/MM MD simulations of sodium(I) and potassium(I) ions in aqueous solution. J Mol Liq 2010;153:95-100.10.1016/j.molliq.2010.01.005Search in Google Scholar

Bandad M, Alavi S, Nafaji B, et al. A new expression for radial distribution function and infinite shear modulus of Lennard-Jones fluids. Chem Phys. 2006;325:554-562.10.1016/j.chemphys.2006.02.001Search in Google Scholar

Campo MG. Structural and dynamic properties of SPC/E water. Papers Phys. 2010;2:1-7.10.4279/pip.020001Search in Google Scholar

Cordeiro MAM, Santana WP, Cusinato R, et al. Monte carlo investigations of intermolecular interactions in water-amide mixtures. J Mol Struct: THEOCHEM. 2006;759:159-164.10.1016/j.theochem.2005.11.016Search in Google Scholar

Cornell WD, Cieplack P, Bayly CI, et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J Am Chem Soc. 1995;117:5179-1597.10.1021/ja00124a002Search in Google Scholar

Dewar MJS, Thiel W. Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model. J Am Chem. Soc. 1977;99:4899-4907.Search in Google Scholar

Dewar MJS, Zoebisch EG, Healy EF, et al. Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model. J Am Chem Soc. 1985;107: 3902-3909.10.1021/ja00299a024Search in Google Scholar

Fan XF, Bing D, Zhang JY, et al. Predicting the hydrogen bond ordered structures of ice Ih, II, III, VI and ice VII: DFT methods with localized based set. Comput Mater Sci. 2010;49:S170-S175.10.1016/j.commatsci.2010.04.004Search in Google Scholar

Garrido NM, Queimada AJ, Jorge M, et al. Molecular simulation of absolute hydration Gibbs energies of polar compounds. Fluid Phase Equil. 2010;296:110-115.10.1016/j.fluid.2010.02.041Search in Google Scholar

Guillot B. A reappraisal of what we have learnt during three decades of computer simulations on water. J Mol Liq. 2002;101:219-260.10.1016/S0167-7322(02)00094-6Search in Google Scholar

Hao H, Elstner M, Hermans J. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution. Proteins: Structure, Function and Genetics 2003;50:451-463.10.1002/prot.1027912557187Search in Google Scholar

Head-Gordon T. Water Structure from Scattering Experiments and Simulation. Chem Rev. 2002;102:2651-2670.10.1021/cr0006831Search in Google Scholar

Hohenb erg P, Kohn W. Inhomogeneous Electron Gas Phys Rev. 1964;136: B864-B873.10.1103/PhysRev.136.B864Search in Google Scholar

Hugosson HW, Laio A, Maurer P, et al. A comparative theoretical study of dipeptide solvation in water. J Comput Chem. 2006;27:672-684.10.1002/jcc.20360Search in Google Scholar

Hura G, Sorenson J M, Glaesert RM, et al. High-quality X-ray scattering experiment on liquid water at ambient conditions. J Chem Phys. 2000;113:9140-9148.10.1063/1.1319614Search in Google Scholar

HyperChem (TM) Professional 7.51, Hypercube, Inc., 1115 NW 4th Street, Gainesville, Florida 32601, USASearch in Google Scholar

Intharathep P, Tongraar A, Sagarik K. Ab initio QM/MM dynamics of H3O+ in water. J Comput Chem. 2006;27:1723-1732.10.1002/jcc.20503Search in Google Scholar

Kohn W, Sham L. Quantum Density Oscillations in an Inhomogeneous Electron Gas. J Phys Rev. 1965;137:A1697-A1705.10.1103/PhysRev.137.A1697Search in Google Scholar

Korth M, Pitonak M, Rezac J, et al. A Transferable H-Bonding Correction for Semiempirical Quantum-Chemical Methods. J Chem Theory Comput. 2010;6:344-352.10.1021/ct900541nSearch in Google Scholar

Korth M. Third-Generation Hydrogen-Bonding Corrections for Semiempirical QM Methods and Force Fields. J Chem Theory Comput. 2010;6:3808-3816.10.1021/ct100408bSearch in Google Scholar

Kuhne TD, Krack M, Parrinello M. Static and Dynamical Properties of Liquid Water from First Principles by a Novel Car? Parrinello-like Approach. J Chem Theory Comput. 2009;5:235-241.10.1021/ct800417qSearch in Google Scholar

Madan B, Sharp K. Changes in water structure induced by a hydrophobic solute probed by simulation of the water hydrogen bond angle and radial distribution functions. Biophys Chem. 1999;78:33-41.10.1016/S0301-4622(98)00227-0Search in Google Scholar

James J. P. Stewart, Stewart Computational Chemistry, Version 10.153W Accesed at http://OpenMOPAC.netSearch in Google Scholar

Murugan NA. Modeling Solvatochromism of a Quinolinium Betaine Dye in Water Solvent Using Sequential Hybrid QM/MM and Semicontinuum Approach. J Phys Chem. B 2011;115:1056-1061.10.1021/jp1049342Search in Google Scholar

Ordejon P, Artacho E, Soler JM. SIESTA code written. Phys Rev B. 1996;53:10441-10444.Search in Google Scholar

Perdev JP, Burke K, Ernzerhof M. Generalized Gradient Approximation Made Simple. Phys Rev Lett. 1996;77:3865-3868.10.1103/PhysRevLett.77.3865Search in Google Scholar

Perez A, Marchan I, Svozil D, et al. Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of a/g Conformers. Biophys J. 2007;92:3817-3829.10.1529/biophysj.106.097782Search in Google Scholar

Ponder JW, Case DA. Force Fields for Protein Simulations. Adv. Protein Chem. 2003; 66:27-85.Search in Google Scholar

Pople JA, Beveridge DL, Dobosh PA. Approximate self-consistent molecular-orbital theory. V. Intermediate neglect of differential overlap. J Chem Phys. 1967;47:2026-2033.10.1063/1.1712233Search in Google Scholar

Pople JA, Santry DP, Segal GA, Approximate self-consistent molecular orbital theory. I. Invariant procedures. J Chem Phys. 1965;43:S129-S135.10.1063/1.1701475Search in Google Scholar

Ramachandra KI, Deepa G, Namboori K. Computational Chemistry and Molecular Modeling, Springer-Verlag, Inc. Berlin, 2008.Search in Google Scholar

Sakata T, Kawashima Y, Nakano H, Solvent effect on the absorption spectra of coumarin 120 in water: A combined quantum mechanical and molecular mechanical study. J Chem Phys. 2011;134:14501-14502.10.1063/1.3506616Search in Google Scholar

SIESTA. Accessed at http://www.icmab.es/siesta/Search in Google Scholar

Soper AK. The radial distribution functions of water and ice from 220 to 673 K and at pressures up to 400 MPa. Chem Phys. 2000;258:121-137.10.1016/S0301-0104(00)00179-8Search in Google Scholar

Sorenson JM, Hura G, Glaeser RM, et al. What can x-ray scattering tell us about the radial distribution functions of water? J Chem Phys. 2000;113:9149-9162.10.1063/1.1319615Search in Google Scholar

Stewart JJP. Optimization of parameters for semiempirical methods I. Method. J Comput Chem. 1989;10:209-220.10.1002/jcc.540100208Search in Google Scholar

Stewart JJP. Optimization of parameters for semiempirical methods V Modification of NDDO approximations and application to 70 elements. J Mol Model. 2007;13:1173-1213.10.1007/s00894-007-0233-4203987117828561Search in Google Scholar

Tunon I, Martins-Costa MTC, Millot C, et al. A coupled density functional-molecular mechanics Monte Carlo simulation method: The water molecule in liquid water. J Comput Chem. 1996;17:19-29.10.1002/(SICI)1096-987X(19960115)17:1<19::AID-JCC2>3.0.CO;2-3Search in Google Scholar

Urquidi J, Cho CH, Singh S, et al. Temperature and pressure effects on the structure of liquid water. J Mol Struct. 1999;485-486:363-371.10.1016/S0022-2860(99)00052-6Search in Google Scholar

Vega C, McBride C, Sanz E, et al. Radial distribution functions and densities for the SPC/E, TIP4P and TIP5P models for liquid water and ices Ih, Ic, II, III, IV, V, VI, VII, VIII, IX, XI and XII. Phys Chem. 2005;7:1450-1456.10.1039/b418934eSearch in Google Scholar

Woods RJ, Tessier MB. Computational glycoscience: characterizing the spatial and temporal properties of glycans and glycan-protein complexes. Curr Opin Struct Biol. 2010;20:575-583.10.1016/j.sbi.2010.07.005Search in Google Scholar

Zhang S, Baker J, Pulay P. A Reliable and Efficient First Principles-Based Method for Predicting pKa Values, 1. Methodology. J. Phys. Chem. 2010;114:425-431.Search in Google Scholar