Hydrogen bond

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

Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds

Abstract: The directional properties of hydrogen bonds play a major role in determining the specificity of intermolecular interactions. An energy function which takes explicit account of these properties has been developed for use in the determination of energetically favorable ligand binding sites on molecules of known structure by the GRID method (Goodford, P.J.J. Med. Chem. 1985, 28, 849. Boobbyer, D.N.A.; Goodford, P.J.; McWhinnie, P.M.; Wade, R.C.J. Med. Chem. 1989, 32, 1083). In this method, the interaction energy between a target molecule and a small chemical group (a probe), which may be part of a larger ligand, was calculated using an energy function consisting of Lennard-Jones, electrostatic, and hydrogen bond terms. The latter term was a function of the length of the hydrogen bond, its orientation at the hydrogen-bonding atoms, and their chemical nature. We now describe hydrogen bond energy functions which take account of the spatial distribution of the hydrogen bonds made by probes with the ability to form two hydrogen bonds. These functions were designed so as to model the experimentally observed angular dependence of the hydrogen bonds. We also describe the procedure to locate the position and orientation of the probe at which the interaction energy is optimized. The use of this procedure is demonstrated by examples of biological and pharmacological interest which show that it can produce results that are consistent with other theoretical approaches and with experimental observations.

A Hydrogen Bond Surrogate Approach for Stabilization of Short Peptide Sequences in α-Helical Conformation

Abstract: α-Helices constitute the largest class of protein secondary structures and play a major role in mediating protein−protein interactions. Development of stable mimics of short α-helices would be invaluable for inhibition of protein−protein interactions. This Account describes our efforts in developing a general approach for constraining short peptides in α-helical conformations by a main-chain hydrogen bond surrogate (HBS) strategy. The HBS α-helices feature a carbon−carbon bond derived from a ring-closing metathesis reaction in place of an N-terminal intramolecular hydrogen bond between the peptide i and i + 4 residues. Our approach is centered on the helix−coil transition theory in peptides, which suggests that the energetically demanding organization of three consecutive amino acids into the helical orientation inherently limits the stability of short α-helices. The HBS method affords preorganized α-turns to overcome this intrinsic nucleation barrier and initiate helix formation. The HBS approach is an a...

An empirical correlation between stretching vibration redshift and hydrogen bond length

Abstract: A correlation is found between the magnitude of the redshift (Δν=20 to 2500 cm−1 relative to the free molecule) of the stretching mode of H-bonded A–H groups in an A–H···B complex, and the length of the H-bond (rH···B=0.28 to 0.12 nm). The correlation is based on both new spectral data for narrow decoupled H-bands in cold isotopically diluted carbohydrate crystals with known H-bond distances and on literature spectral and structural data from a total of 36 systems. Once established, additional data for H-bonded crystals (hydrates, acid salts of carboxylic acids) and for gas phase dimer systems also fit this correlation quite well. Hydrogen bond enthalpies in the range of −ΔH=10–80 kJ mol−1 correlate with the inverse third power of the H-bond length. Literature experimental data on −ΔH and rH···B of ten gas phase dimers confirm this relationship.

Role of Intramolecular and Intermolecular Hydrogen Bonding in Both Singlet and Triplet Excited States of Aminofluorenones on Internal Conversion, Intersystem Crossing, and Twisted Intramolecular Charge Transfer†

Abstract: Time-dependent density functional theory method was performed to investigate the intramolecular and intermolecular hydrogen bonding in both the singlet and triplet electronic excited states of aminofluorenones AF, MAF, and DMAF in alcoholic solutions as well as their important roles on the excited-state photophysical processes of these aminofluorenones, such as internal conversion, intersystem crossing (ISC), twisted intramolecular charge transfer (TICT), and so forth. The intramolecular hydrogen bond C═O···H−N can be formed between the carbonyl group and amino group for the isolated AF and MAF. However, no intramolecular hydrogen bond for DMAF can be formed. At the same time, the most stable conformation of DMAF is out-of-plane structure, where the two dihedral angles formed between dimethyl groups and fluorenone plane are 163.1° and 41.74°, respectively. The formation of intramolecular hydrogen bond for AF and MAF is tightly associated with the intersystem crossing of these aminofluorenones. Furthermore...