Energy decomposition analysis of the metal–oxime bond in [M{RC(NOH)C(NO)R}2] (M = Ni(II), Pd(II), Pt(II), R = CH3, H, F, Cl, Br, Ph, CF3)

Synthesis, Characterisation and Theoretical and Antibacterial Studies of Hg(II), Cd(II) and Ag(I) Complexes with a New Monodentate Phosphorus Ylide

Reaction of a new phosphorus ylide ( p-tolyl)3P=CHC(O)C6H4( m-OCH3) (Y) with mercury(II) halides in equimolar ratios using methanol as solvent yielded binuclear complexes of the type [Y. HgX2]2 (X = Cl, Br, I). The ylide reacts with Hg(NO3)2.H2O and Cd(NO3)2.4H2O in the same solvent with equimolar ratios to give polynuclear complexes [M(Y)(NO3)(μ-NO3)]n (M = Hg, Cd) and with AgNO3 and AgOTf in 1:2 molar ratio to give mononuclear complexes [AgY2]Z [Z = NO3 or OTf]. A theoretical study of structure and bonding in [Y. HgX2]2 (X = Cl, Br, I) at the BP86/def2-SVP level of theory is reported and the synthesised compounds were screened for their antibacterial activity against six Gram negative and Gram positive bacteria.

Metal-interacted histidine dimer: an ETS-NOCV and XANES study

We have analyzed the metal coordination in a histidine dimer, hydrated with a water molecule, based on the extended transition state scheme with the theory of natural orbitals for chemical valence (ETS-NOCV).

New Pd(ii) complexes of sulfur ylides; synthesis, X-ray characterization, a theoretical study and catalytic activity toward the Mizoroki–Heck reaction

The reaction of sulfur ylides SMe₂C(H)C(O)R (R = 4-nitrophenyl, phenyl, and 3-nitrophenyl) with [PdCl₂(cod)] gives the new Pd(ii) complexes of type cis- and trans-[PdCl₂(SMe₂C(H)C(O)R)₂] (R = phenyl (1), 3-nitrophenyl (2), and 4-nitrophenyl (3)).

Energy decomposition analysis approaches and their evaluation on prototypical protein–drug interaction patterns

The partitioning of the interaction energy into chemical components such as electrostatics, polarization, and charge transfer is possible with energy decomposition analysis approaches. We review and evaluate these for biomolecular applications.

The stabilization effect of dielectric constant and acidic amino acids on arginine-arginine (Arg-Arg) pairings: database survey and computational studies

Database survey in this study revealed that about one-third of the protein structures deposited in the Protein Data Bank (PDB) contain arginine-arginine (Arg-Arg) pairing with a carbon···carbon (CZ···CZ) interaction distance less than 5 Å. All the Arg-Arg pairings were found to bury in a polar environment composed of acidic residues, water molecules, and strong polarizable or negatively charged moieties from binding site or bound ligand. Most of the Arg-Arg pairings are solvent exposed and 68.3% Arg-Arg pairings are stabilized by acidic residues, forming Arg-Arg-Asp/Glu clusters. Density functional theory (DFT) was then employed to study the effect of environment on the pairing structures. It was revealed that Arg-Arg pairings become thermodynamically stable (about -1 kcal/mol) as the dielectric constant increases to 46.8 (DMSO), in good agreement with the results of the PDB survey. DFT calculations also demonstrated that perpendicular Arg-Arg pairing structures are favorable in low dielectric constant environment, while in high dielectric constant environment parallel structures are favorable. Additionally, the acidic residues can stabilize the Arg-Arg pairing structures to a large degree. Energy decomposition analysis of Arg-Arg pairings and Arg-Arg-Asp/Glu clusters showed that both solvation and electrostatic energies contribute significantly to their stability. The results reported herein should be very helpful for understanding Arg-Arg pairing and its application in drug design.