QM/MM calculations of electronic excitations with diffuse basis sets often have large errors due to spill-out of electrons from the quantum subsystem. The Pauli repulsion of the electrons by the environment has to be included to avoid this. We propose transferable atomic all-electron pseudopotentials that can readily be combined with most MM force fields to avoid electron spill-out. QM/MM excitation ...

DFT calculations with the well-tested OLYP and B3LYP* exchange-correlation functionals (along with D3 dispersion corrections and all-electron ZORA STO-TZ2P basis sets) and careful use of group theory have led to significant insights into the question of metal- versus ligand-centered redox in Co and Ni B,C-tetradehydrocorrin complexes. For the cationic complexes, both metals occur in their low-spin ...

DNA ligases, the enzymes responsible for joining breaks in the phosphodiester backbone of DNA during replication and repair, vary considerably in size and structure. The smallest members of this enzyme class carry out their functions with pared-down protein scaffolds comprising only the core catalytic domains. Here we use sequence similarity network analysis of minimal DNA ligases from all biological ...

The interpretation of the ultrafast photophysics of transition metal complexes following photo-absorption is quite involved as the heavy metal center leads to a complicated and entangled singlet–triplet manifold. This opens up multiple pathways for deactivation, often with competitive rates. As a result, intersystem crossing (ISC) and phosphorescence are commonly observed in transition metal complexes. ...

We investigate the performance of CC2 and TDDFT/CAM-B3LYP for the calculation of two-photon absorption (TPA) strengths and cross sections and contrast our results to a recent coupled cluster equation-of-motion (EOM-EE-CCSD) benchmark study [K. D. Nanda and A. I. Krylov, J. Chem. Phys., 2015, 142, 064118]. In particular, we investigate whether CC2 TPA strengths are significantly overestimated compared ...

Background Cellulases play a key role in the enzymatic conversion of plant cell-wall polysaccharides into simple and economically relevant sugars. Thus, the discovery of novel cellulases from exotic biological niches is of great interest as they may present properties that are valuable in the biorefning of lignocellulosic biomass. Results We have characterized a glycoside hydrolase 5 (GH5) domain ...

Iron is an essential nutrient for bacteria, however its propensity to form toxic hydroxyl radicals at high intracellular concentrations, requires its acquisition to be tightly regulated. Ferric uptake regulator (Fur) is a metal-dependent DNA-binding protein that acts as a transcriptional regulator in maintaining iron metabolism in bacteria and is a highly interesting target in the design of new ...

Natural products obtained from marine organisms continue to be a rich source of novel structural architecture and of importance in drug discovery, medicine, and health. However, the success of such endeavors depends on the exact structural elucidation and access to sufficient material, often by stereoselective total synthesis, of the isolated natural product of interest. (−)-Mucosin (1), a fatty ...

Multipartite bacteria have one chromosome and one or more chromid. Chromids are believed to have properties that enhance genomic flexibility, making them a favored integration site for new genes. However, the mechanism by which chromosomes and chromids jointly contribute to this flexibility is not clear. To shed light on this, we analyzed the openness of chromosomes and chromids of the two bacteria, ...

In recent years, considerable progress has been made in the conversion of biomass into renewable chemicals, yet the range of value-added products that can be formed from biomass remains relatively small. Herein, we demonstrate that molecules available from biomass serve as viable starting materials for the synthesis of phosphine ligands, which can be used in homogeneous catalysis. Specifically, ...