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Hydrogen bond

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


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Journal ArticleDOI
16 Nov 1995-Nature
TL;DR: Observations of the femtosecond dynamics of tautomerization in model base pairs (7-azaindole dimers) containing two hydrogen bonds establish the molecular basis of the dynamics and the role of quantum tunnelling.
Abstract: Hydrogen bonds commonly lend robustness and directionality to molecular recognition processes and supramolecular structures. In particular, the two or three hydrogen bonds in Watson–Crick base pairs bind the double-stranded DNA helix and determine the complementarity of the pairing. Watson and Crick pointed out, however, that the possible tautomers of base pairs, in which hydrogen atoms become attached to the donor atom of the hydrogen bond, might disturb the genetic code, as the tautomer is capable of pairing with different partners. But the dynamics of hydrogen bonds in general, and of this tautomerization process in particular, are not well understood. Here we report observations of the femtosecond dynamics of tautomerization in model base pairs (7-azaindole dimers) containing two hydrogen bonds. Because of the femtosecond resolution of proton motions, we are able to examine the cooperativity of formation of the tautomer (in which the protons on each base are shifted sequentially to the other base), and to determine the characteristic timescales of the motions in a solvent-free environment. We find that the first step occurs on a timescale of a few hundred femtoseconds, whereas the second step, to form the full tautomer, is much slower, taking place within several picoseconds; the timescales are changed significantly by replacing hydrogen with deuterium. These results establish the molecular basis of the dynamics and the role of quantum tunnelling.

452 citations

Journal ArticleDOI
TL;DR: A new empirical scoring function is presented that estimates the free energy of binding for a protein–ligand complex of known 3D structure and is suitable for the application in a 3D database search or de novo ligand design program such as LUDI.
Abstract: A dataset of 82 protein–ligand complexes of known 3D structure and binding constant Ki was analysed to elucidate the important factors that determine the strength of protein–ligand interactions. The following parameters were investigated: the number and geometry of hydrogen bonds and ionic interactions between the protein and the ligand, the size of the lipophilic contact surface, the flexibility of the ligand, the electrostatic potential in the binding site, water molecules in the binding site, cavities along the protein–ligand interface and specific interactions between aromatic rings. Based on these parameters, a new empirical scoring function is presented that estimates the free energy of binding for a protein–ligand complex of known 3D structure. The function distinguishes between buried and solvent accessible hydrogen bonds. It tolerates deviations in the hydrogen bond geometry of up to 0.25 A in the length and up to 30 °Cs in the hydrogen bond angle without penalizing the score. The new energy function reproduces the binding constants (ranging from 3.7 × 10-2 M to 1 × 10-14 M, corresponding to binding energies between -8 and -80 kJ/mol) of the dataset with a standard deviation of 7.3 kJ/mol corresponding to 1.3 orders of magnitude in binding affinity. The function can be evaluated very fast and is therefore also suitable for the application in a 3D database search or de novo ligand design program such as LUDI. The physical significance of the individual contributions is discussed.

452 citations

Journal ArticleDOI
TL;DR: The results from absorption spectral titration and circular dichroism (CD), thermal denaturation and viscosity experiments indicate that the qdppZ and hqdppz complexes bind more avidly than the ip, pip and hpip complexes, and the ammonia co-ligands of the complexes are possibly involved in hydrogen bonding with the intrastrand nucleobases to favour intercalation of the extended aromatic ligands.

451 citations

Journal ArticleDOI
TL;DR: In this article, a density functional theory study of water adsorption on metal surfaces is presented, where the water-surface interaction is dominated by the lone pair-d band coupling through the surface states and a simultaneous enhancement of hydrogen bonding is generally observed in many adsorbed structures.
Abstract: We present a density functional theory study of water adsorption on metal surfaces. Prototype water structures including monomers, clusters, one-dimensional chains, and overlayers have been investigated in detail on a model system-a Pt(111) surface. The structure, energetics, and vibrational spectra are all obtained and compared with available experimental data. This study is further extended to other metal surfaces including Ru(0001), Rh(111), Pd(111), and Au(111), where adsorption of monomers and bilayers has been investigated. From these studies, a general picture has emerged regarding the water-surface interaction, the interwater hydrogen bonding, and the wetting order of the metal surfaces. The water-surface interaction is dominated by the lone pair-d band coupling through the surface states. It is rather localized in the contacting layer. A simultaneous enhancement of hydrogen bonding is generally observed in many adsorbed structures. Some special issues such as the partial dissociation of water on Ru(0001) and in the RT39 bilayer phase, the H-up and H-down conversion, and the quantum-mechanical motions of H atoms are also discussed.

449 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20232,352
20224,647
20211,701
20201,599
20191,598
20181,668