Towards a system for the systematic structural study of intermolecular interactions in crystals of transition metal complexes

Pseudo-macrocyclic complexes of copper(II), and in one instance nickel(II), incorporating the bidentate ligands methyl N-(4-oxo-5,5-diphenyl-4,5-dihydro-1H-imidazol-2-yl)imidocarbamate and N,N-dimethyl-N'-(4-oxo-5,5-diphenyl-4,5-dihydro-1H-imidazol-2-yl)guanidine are reported and their X-ray structures compared with those previously reported for related complexes of two N-(4-oxo- 5,5-diphenyl-4,5-dihydro-1H-imidazol-2-yl)alkanimidamides. A feature of these complexes is that they are capable of forming hydrogen bonded chains or chains in which adjacent complexes are linked by phenyl 'embraces'. Changes in supramolecular structure arising from small changes in ligand structure or on crystallisation from different solvents are also discussed.     

Molecular orbital energy levels for the sulfate Ion

A series of semiempirical molecular orbital calculations for the SO₄ ^2? ion is described. These calculations show the effect on the order of the molecular orbital energy levels of a) using the Wolfsberg-Helmholz approximation, b) using the Cusachs approximation, c) variation of the proportionality constant, F, in the Wolfsberg-Helmholz approximation, d) inclusion of d-orbitals in the basis set, and e) variation of ζ_d when d-orbitals are included. It is found that the highest filled level is t ₁ for all the Wolfsberg-Helmholz calculations when d-orbitals are included and is 3t ₂ for all the other calculations.     

Relative raman line intensities for H2 and for D2. Correction factors for molecular non-rigidity

Ab initio calculations are presented for H₂ and D₂ relative Raman intensities originating from common rotational levels for both vibrational-rotational and pure rotational transitions. Factors f(J) required to correct measured intensities for molecular non-rigidity (e.g. in temperature measurements) are tabulated. The calculations are compared with literature perturbation-theory equations (significant differences at large J in vibration-rotation) and with experiment.     

Modified AutoDock for accurate docking of protein kinase inhibitors

Protein kinases are an important class of enzymes controlling virtually all cellular signaling pathways. Consequently, selective inhibitors of protein kinases have attracted significant interest as potential new drugs for many diseases. Computational methods, including molecular docking, have increasingly been used in the inhibitor design process [1]. We have considered several docking packages in order to strengthen our kinase inhibitor work with computational capabilities. In our experience, AutoDock offered a reasonable combination of accuracy and speed, as opposed to methods that specialize either in fast database searches or detailed and computationally intensive calculations.However, AutoDock did not perform well in cases where extensive hydrophobic contacts were involved, such as docking of SB203580 to its target protein kinase p38. Another shortcoming was a hydrogen bonding energy function, which underestimated the attraction component and, thus, did not allow for sufficiently accurate modeling of the key hydrogen bonds in the kinase-inhibitor complexes.We have modified the parameter set used to model hydrogen bonds, which increased the accuracy of AutoDock and appeared to be generally applicable to many kinase-inhibitor pairs without customization. Binding to largely hydrophobic sites, such as the active site of p38, was significantly improved by introducing a correction factor selectively affecting only carbon and hydrogen energy grids, thus, providing an effective, although approximate, treatment of solvation.