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...

A novel [3]rotaxane composed of two 25-membered crownophanes and one axle molecule having two anthryl end groups was successfully synthesized via covalent bond formation followed by aminolysis, and can incorporate caesium ion into the space between the two macrocycles as a 1 : 1 sandwich-type complex, whereas it makes a 1 : 2 complex with lithium ion.

Modeling indicates the presence of a region of low electronic density (a "σ-hole") on group 14 elements, and this offers an explanation for the ability of these elements to act as electrophilic sites and to form attractive interactions with nucleophiles. While many papers have described theoretical investigations of interactions involving carbon and silicon, such investigations of the heavier g...

We report novel molecular compound formation from silane-hydrogen mixtures with intermolecular interactions unprecedented for hydrogen-rich solids. A complex H_{2} vibron spectrum with anticorrelated pressure-frequency dependencies and a striking H-D exchange below 10 GPa reveal strong and unusual attractive interactions between SiH_{4} and H_{2} and molecular bond destabilization at remarkably...

An improved density matrix functional [correction to Buijse and Baerends functional (BBC)] is proposed, in which a hierarchy of physically motivated repulsive corrections is employed to the strongly overbinding functional of Buijse and Baerends (BB). The first correction C1 restores the repulsive exchange-correlation (xc) interaction between electrons in weakly occupied natural orbitals (NOs) a...

To understand the structural basis of biology, it is necessary to understand the transformations of macromolecules during functional cycles. These changes can involve large-scale conformational transformations, changes in the state of ligation or association, changes in dynamics, or alterations in covalent bond structure. X-ray crystallography and NMR spectroscopy have been invaluable for the d...