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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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TL;DR: In most cases it seems that the interactions are not guided simply by the presence of a required atom in a specific position in the groove, but that the identity of the base possessing this atom is crucial, which may have important implications in molecular design experiments.

211 citations

Journal ArticleDOI
TL;DR: The combined potentials improve performance in a variety of scientific benchmarks including decoy discrimination, side chain prediction, and native sequence recovery in protein design simulations and establishes a new standard energy function for Rosetta.
Abstract: Interactions between polar atoms are challenging to model because at very short ranges they form hydrogen bonds (H-bonds) that are partially covalent in character and exhibit strong orientation preferences; at longer ranges the orientation preferences are lost, but significant electrostatic interactions between charged and partially charged atoms remain. To simultaneously model these two types of behavior, we refined an orientation dependent model of hydrogen bonds [Kortemme et al. J. Mol. Biol. 2003, 326, 1239] used by the molecular modeling program Rosetta and then combined it with a distance-dependent Coulomb model of electrostatics. The functional form of the H-bond potential is physically motivated and parameters are fit so that H-bond geometries that Rosetta generates closely resemble H-bond geometries in high-resolution crystal structures. The combined potentials improve performance in a variety of scientific benchmarks including decoy discrimination, side chain prediction, and native sequence reco...

211 citations

Journal ArticleDOI
TL;DR: Ligand tuning led to the development of a method that allows for installation of an aryl group on a range of acyclic and cyclic amides containing β-methylene C(sp(3))-H bonds.
Abstract: Pd(II) insertion into β-methylene C(sp3)–H bonds was enabled by a mutually repulsive and electron-rich quinoline ligand. Ligand tuning led to the development of a method that allows for installation of an aryl group on a range of acyclic and cyclic amides containing β-methylene C(sp3)–H bonds.

211 citations

Journal Article
TL;DR: Density functional theory calculations showed that the transfer of hydrogen from surface hydroxyls to the molecule and its interaction with surface hydoxyls substantially lowered the activation barrier for rotational motion across the surface.
Abstract: Stop or Go on Oxide Surfaces Direct studies of surface diffusion with instruments such as the scanning tunneling microscope (STM) have often focused on species on metal surfaces, but surface diffusion can play an important role for reactions on metal oxide surfaces. Li et al. (p. 882) used STM and density functional theory calculations to study how catechol (a benzene ring bearing two −OH groups) diffuses on the surface of the rutile phase of titanium dioxide. Both mobile and immobile species were observed on the time scale of minutes while making repeated STM scans. Hydrogen atom transfers between surface OH groups and the molecule changed the interaction energy between the molecule and the surface, and hence the barrier for diffusion. The diffusion barrier for an organic molecule on a hydroxylated metal oxide surface depends on hydrogen bond formation. Direct studies of how organic molecules diffuse on metal oxide surfaces can provide insights into catalysis and molecular assembly processes. We studied individual catechol molecules, C6H4(OH)2, on a rutile TiO2(110) surface with scanning tunneling microscopy. Surface hydroxyls enhanced the diffusivity of adsorbed catecholates. The capture and release of a proton caused individual molecules to switch between mobile and immobile states within a measurement period of minutes. Density functional theory calculations showed that the transfer of hydrogen from surface hydroxyls to the molecule and its interaction with surface hydroxyls substantially lowered the activation barrier for rotational motion across the surface. Hydrogen bonding can play an essential role in the initial stages of the dynamics of molecular assembly.

211 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