Hydrogen bonding computational modeling

Ken Jordan received his Ph.D. in physical chemistry in 1974 under the direction of Bob Silbey at MIT. He then joined the Department of Engineering and Applied Science, Yale University, as a J.W. Gibbs Instructor, being promoted to Assistant Professor in 1976. In 1978 Professor Jordan moved to the Chemistry Department at the University of Pittsburgh where he is now Professor and Director of the Center for Molecular and Materials Simulations. His interest in the application of computers to chemical problems stems from his graduate student days. Professor Jordan s recent research has focused on the properties of hydrogen-bonded clusters, modeling chemical reactions on surfaces, electron-induced chemistry and the development of new methods for Monte Carlo simulations. 

Fig. 22 A hydrogen bonding network model derived from kinetic and computational stuides...

Various equations of state have been developed to treat association ia supercritical fluids. Two of the most often used are the statistical association fluid theory (SAET) (60,61) and the lattice fluid hydrogen bonding model (LEHB) (62). These models iaclude parameters that describe the enthalpy and entropy of association. The most detailed description of association ia supercritical water has been obtained usiag molecular dynamics and Monte Carlo computer simulations (63), but this requires much larger amounts of computer time (64—66). 

Raevsky OA, Skvortsov VS (2002) 3D hydrogen bond thermodynamics (HYBOT) potentials in molecular modelling. J Comput Aided Mol Des 16(1) 1-10... 

Fig. 12.9. Structure and relative energies of four modes of hydrogen bonding in transition structures for epoxidation of 2-propen-l-ol by peroxyformic acid. Relative energies are from B3I.YP/6-311G -level computations with a solvation model for CH2C12, e = 8.9. Reproduced from / Org. Chem., 64, 3853 (1999), by permission of the American Chemical Society.

A computer-built model, having an axial rise per disaccharide of 0.84 nm and possible stabilization by an 0-3-H 0-5, intramolecular hydrogen-bond from a hexosamine to a uronic acid residue, is a rather extended, two-fold helix (see Fig. 8),346 with each fold approximately corresponding341,346 to the disaccharide repeat in Fig. 7a. A substantially similar model was obtained by use of calculations also taking into consid-... 

Fig. 2.6 Comparison of the calculated structures for glycine in the gas-phase and in water (COSMO solvation model). Note that the central bond angle in the zwitterionic form 1 is distorted by the hydrogen bond length of 1.96A computed for this structure in the gas phase. When solvation effects are included in the calculation using COSMO, the electrostatic interaction is reduced in magnitude due to charge screening by water, and the bond angle distortion is no longer present.

Cieplak, P., Caldwell, J. W., Kollman, P. A., Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation aqueous solution free energies of methanol and IV-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases, J. Comput. Chem. 2001, 22, 1048-1057... 

---