Herein we present, an exhaustive docking analysis considering the case of autotaxin (ATX). HA155, a small molecule inhibitor of ATX, is co-crystallized. In order to further extract conclusions on the nature of the bond formed between the ligands and the amino acid residues of the active site, density functional theory (DFT) calculations were undertaken. However, docking does not provide reprodu...

Bonding in the recently synthesized NaBH3− cluster is investigated using high level Valence Bond BOVB method. Contrary to earlier conclusions, Na−B bond found be neither a genuine dative bond, nor standard polar-covalent at equilibrium. It rather revealed as split and polarized weakly coupled electron-pair, which allows this more effectively stabilized by combination of (major) dipole-dipole el...

The synthesis of a linear beryllium bis(diazaborolyl) compound featuring the first non-cluster bond between boron and beryllium has been achieved through the reaction of Yamashita's lithium diazaborolide and BeCl2. In accord with the established chemistry of beryllium, the bonding is polar covalent in character, as determined by structural and spectroscopic analysis, as well as reactivity studies.

In this work, based on the experimental electron density, we present the approximate spatial distributions of the Pauli potential, one of the key quantities in the orbital-free density functional, for three crystalline systems: diamond, cubic boron nitride, and magnesium diboride. Our aim is to reveal a link between the Pauli potential and the orbital-free picture of chemical bond. We also expa...

Here we describe the updated MolProbity rotamer-library distributions derived from an order-of-magnitude larger and more stringently quality-filtered dataset of about 8000 (vs. 500) protein chains, and we explain the resulting changes and improvements to model validation as seen by users. To include only side-chains with satisfactory justification for their given conformation, we added residue-...

We report a facile synthetic strategy to prepare UBL-AMP electrophilic probes that form a covalent bond with the catalytic cysteine of cognate E1s, mimicking the tetrahedral intermediate of the E1-UBL-AMP complex. These probes enable the structural and biochemical study of both canonical- and non-canonical E1s.

The nature of chemical bonds on dynamic paths was investigated using the complete active space valence-bond (CASVB) method and the Born-Oppenheimer dynamics. To extract the chemical bond picture during reactions, a scheme to collect contributions from several VB (resonance) structures into a small numbers of indices was introduced. In this scheme, a tree diagram for the VB structures is constru...

The dinuclear title compound, [Pb(2)(C(6)H(8)O(4))(NO(3))(2)(C(19)H(13)N(5))(2)], lies with the mid-point of the butyl chain of the bridging adipate unit on a center of inversion. The Pb(II) ion is covalently bonded to the nitrate anion and is bonded to a carboxyl-ate group of the adipate unit by another covalent bond. The N-heterocycle functions in a chelating tridentate mode. The metal atom e...

Biological catalysis frequently causes changes in noncovalent bonding. By building on Pauling's assertion that any long-lived, chemically distinct interaction is a chemical bond, this article redefines enzyme catalysis as the facilitated making and/or breaking of chemical bonds, not just of covalent bonds. It is also argued that nearly every ATPase or GTPase is misnamed as a hydrolase and actua...

We have employed ab initio molecular dynamics to investigate the equilibrium geometries, energetics, and the nature of bonding in mixed Li-Sn clusters. Our studies reveal that a small percentage of Sn in Li-rich clusters introduces significant changes in the equilibrium geometries. It is also seen that the geometries of Sn-rich clusters are influenced by the Sn10 motif. Analysis of the nature o...