Hydrogen bond

About: Hydrogen bond is a research topic. Over the lifetime, 57701 publications have been published within this topic receiving 1306326 citations.

New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure.

Abstract: An empirical energy function designed to calculate the interaction energy of a chemical probe group, such as a carbonyl oxygen or an amine nitrogen atom, with a target molecule has been developed. This function is used to determine the sites where ligands, such as drugs, may bind to a chosen target molecule which may be a protein, a nucleic acid, a polysaccharide, or a small organic molecule. The energy function is composed of a Lennard-Jones, an electrostatic and a hydrogen-bonding term. The latter is dependent on the length and orientation of the hydrogen bond and also on the chemical nature of the hydrogen-bonding atoms. These terms have been formulated by fitting to experimental observations of hydrogen bonds in crystal structures. In the calculations, thermal motion of the hydrogen-bonding hydrogen atoms and lone-pair electrons may be taken into account. For example, in a alcoholic hydroxyl group, the hydrogen may rotate around the C-O bond at the observed tetrahedral angle. In a histidine residue, a hydrogen atom may be bonded to either of the two imidazole nitrogens and movement of this hydrogen will cause a redistribution of charge which is dependent on the nature of the probe group and the surrounding environment. The shape of some of the energy functions is demonstrated on molecules of pharmacological interest.

The Nature of the Hydrogen Bond in DNA Base Pairs: The Role of Charge Transfer and Resonance Assistance

Abstract: The view that the hydrogen bonds in Watson - Crick adenine - thy- mine (AT) and guanine - cytosine (GC) base pairs are in essence electrostatic interactions with substantial resonance assistance from the p electrons is ques- tioned. Our investigation is based on a state-of-the-art density functional theo- retical (DFT) approach (BP86/TZ2P) that has been shown to properly repro- duce experimental data. Through a quantitative decomposition of the hy- drogen bond energy into its various physical terms, we demonstrate that, contrary to the widespread belief, do- nor - acceptor orbital interactions (i.e., charge transfer) in s symmetry between N or O lone pairs on one base and NH s*-acceptor orbitals on the other base do provide a substantial bonding contri- bution which is, in fact, of the same order of magnitude as the electrostatic interaction term. The overall orbital interactions are reinforced by a small p component which stems from polariza- tion in the p-electron system of the individual bases. This p component is, however, one order of magnitude small- er than the s term. Furthermore, we have investigated the synergism in a base pair between charge transfer from one base to the other through one hydrogen bond and in the opposite direction through another hydrogen bond, as well as the cooperative effect between the donor - acceptor interac- tions in the s- and polarization in the p- electron system. The possibility of CH ··· O hydrogen bonding in AT is also examined. In the course of these analyses, we introduce an extension of the Voronoi deformation density (VDD) method which monitors the redistribution of the s- and p-electron densities individually out of (DQ> 0) or into (DQ< 0) the Voronoi cell of an atom upon formation of the base pair from the separate bases.

Hydrogen Bond Dynamics in Water and Ultrafast Infrared Spectroscopy

Abstract: Molecular dynamics simulations are used to examine two key aspects of recent ultrafast infrared experiments on liquid water dynamics. It is found that the relation between the OH stretch frequency and the length of the hydrogen bond in which the OH is involved, currently assumed to be one-to-one, is instead characterized by considerable dispersion and that the time scale currently interpreted in terms of a stochastic modulation by the surrounding solvent of a highly frictionally damped hydrogen bond system is shown to be governed by hydrogen bond-breaking and -making dynamics, whereas the motion of an intact hydrogen-bonded complex is underdamped in character.

Directing macromolecular conformation through halogen bonds

Abstract: The halogen bond, a noncovalent interaction involving polarizable chlorine, bromine, or iodine molecular substituents, is now being exploited to control the assembly of small molecules in the design of supramolecular complexes and new materials. We demonstrate that a halogen bond formed between a brominated uracil and phosphate oxygen can be engineered to direct the conformation of a biological molecule, in this case to define the conformational isomer of a four-stranded DNA junction when placed in direct competition against a classic hydrogen bond. As a result, this bromine interaction is estimated to be ≈2–5 kcal/mol stronger than the analogous hydrogen bond in this environment, depending on the geometry of the halogen bond. This study helps to establish halogen bonding as a potential tool for the rational design and construction of molecular materials with DNA and other biological macromolecules.