Hydrogen bonds in molecular mechanics force fields.

This chapter reviews formulation and parametrization of molecular mechanics force fields with special attention to technical and inherent problems. Most striking among the shortcomings is the inadequacy of the simple point charge description as a means to describe energy and forces of interactions between polar molecules and between polar groups in macromolecules, including hydrogen bonds. The current state of efforts to improve the description of polar interactions is discussed.

[1]  P. Procacci,et al.  Comparing polarizable force fields to ab initio calculations reveals nonclassical effects in condensed phases. , 2005, The Journal of chemical physics.

[2]  J. Hermans,et al.  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 , 2003, Proteins.

[3]  S. Lifson,et al.  Consistent Force Field Studies of Intermolecular Forces in Hydrogen-Bonded Crystals. 3. The C=O-*H-O Hydrogen Bond and the Analysis of the Energetics and Packing of Carboxylic Acids , 1979 .

[4]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[5]  J. Hermans,et al.  Nonbonded Interatomic Potential Functions and Crystal Structure: Non Hydrogen-Bonded Organic Molecules , 1970 .

[6]  D. Baker,et al.  Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[7]  S. Lifson,et al.  Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 1. Carboxylic acids, amides, and the C:O.cntdot..cntdot..cntdot.H- hydrogen bonds , 1979 .

[8]  F. Stillinger,et al.  Improved simulation of liquid water by molecular dynamics , 1974 .

[9]  M Elstner,et al.  Quantum mechanics simulation of protein dynamics on long timescale , 2001, Proteins.

[10]  Efthimios Kaxiras,et al.  A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method , 2001 .

[11]  Sándor Suhai,et al.  Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties , 1998 .

[12]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[13]  Tanja Kortemme,et al.  Potential functions for hydrogen bonds in protein structure prediction and design. , 2005, Advances in protein chemistry.

[14]  D. Baker,et al.  An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. , 2003, Journal of molecular biology.

[15]  Efthimios Kaxiras,et al.  A Self-Consistent Charge Density-Functional Based Tight-Binding Scheme for Large Biomolecules , 2000 .

[16]  Alexander D. MacKerell,et al.  Improved treatment of the protein backbone in empirical force fields. , 2004, Journal of the American Chemical Society.

[17]  A. T. Hagler,et al.  Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 3. The C:O.cntdot..cntdot..cntdot.H-O hydrogen bond and the analysis of the energetics and packing of carboxylic acids , 1979 .

[18]  A. T. Hagler,et al.  Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 2. A benchmark for the objective comparison of alternative force fields , 1979 .

[19]  P. Schleyer.  Encyclopedia of computational chemistry , 1998 .

[20]  Julian Tirado-Rives,et al.  Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[21]  P. Wernet,et al.  The Structure of the First Coordination Shell in Liquid Water , 2004, Science.

[22]  R. Friesner,et al.  Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† , 2001 .

[23]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[24]  W. L. Jorgensen.  OPLS Force Fields , 2002 .

[25]  Donald E. Williams.  Nonbonded Potential Parameters Derived from Crystalline Hydrocarbons , 1967 .

[26]  H. Berendsen,et al.  A consistent empirical potential for water–protein interactions , 1984 .

[27]  Richard A Friesner,et al.  Modeling Polarization in Proteins and Protein-ligand Complexes: Methods and Preliminary Results. , 2005, Advances in protein chemistry.

[28]  Harold A. Scheraga,et al.  Calculations of Conformations of Polypeptides , 1968 .

[29]  Michael W. Mahoney,et al.  A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions , 2000 .

[30]  Ming-Jing Hwang,et al.  Derivation of class II force fields: V. Quantum force field for amides, peptides, and related compounds , 1998, J. Comput. Chem..

[31]  H. Berendsen,et al.  Interaction Models for Water in Relation to Protein Hydration , 1981 .

[32]  F. Weinhold,et al.  Resonance Character of Hydrogen-bonding Interactions in Water and Other H-bonded Species. , 2005, Advances in protein chemistry.