Reddy et al. performed calculations of equilibrium geometries, binding energies, ionization potentials, and magnetic

CRISPR-Cas9 is a genome editing technology with major impact in life sciences. In this system, the endonuclease Cas9 generates double strand breaks in DNA upon RNA-guided recognition of a complementary DNA sequence, which strictly requires the presence of a protospacer adjacent motif (PAM) next to the target site. Although PAM recognition is essential for cleavage, it is unknown whether and how PAM binding activates Cas9 for DNA cleavage at spatially distant sites. Here, we find evidence of a PAM-induced allosteric mechanism revealed by microsecond molecular dynamics simulations. PAM acts as an allosteric effector and triggers the interdependent conformational dynamics of the Cas9 catalytic domains (HNH and RuvC), responsible for concerted cleavage of the two DNA strands. Targeting such an allosteric mechanism should enable control of CRISPR-Cas9 functionality.

Ligand exchange reactions are important to functionalize and modify the optical and electronic properties of thiolate-protected gold nanoparticles. A theoretical investigation of the kinetics of the ligand exchange process was performed for the Au 25 (SH) 18 − nanocluster with CH 3 SH as the incoming thiol ligand. Three possible ligand exchange sites were investigated: between the core gold atom and the terminal −SH unit, between the staple gold atom and the terminal −SH unit, and between a staple gold atom and the central −SH unit. We found that the most favorable ligand exchange takes place between terminal −SH units and staple gold atoms.

Hybrid density functional theory calculations have been employed to investigate the water oxidation reaction on model cobalt oxide dimer and cubane complexes. Electronic structure and energetics of these model compounds were thoroughly investigated. The thermodynamically lowest energy pathway on the dimer catalyst proceeds through a nucleophilic attack of a solvent water molecule to Co(V)-O radical moiety. The lowest energy pathway on the cubane catalyst involves a geminal coupling of Co(V)-O radical oxo group with bridging oxo sites. Model systems were found to be very sensitive to the positions of ligands and to the hydrogen-bonding environment leading to different isomer energies.

Predicting the solution viscosity of monoclonal antibody (mAb) drug products remains as one of the main challenges in antibody drug design, manufacturing, and delivery. In this work, the concentration-dependent solution viscosity of 27 FDA-approved mAbs was measured at pH 6.0 in 10 mM histidine-HCl. Six mAbs exhibited high viscosity (>30 cP) in solutions at 150 mg/mL mAb concentration. Combining molecular modeling and machine learning feature selection, we found that the net charge in the mAbs and the amino acid composition in the Fv region are key features which govern the viscosity behavior. For mAbs whose behavior was not dominated by charge effects, we observed that high viscosity is correlated with more hydrophilic and fewer hydrophobic residues in the Fv region. A predictive model based on the net charges of mAbs and a high viscosity index is presented as a fast screening tool for classifying low-and highviscosity mAbs.