Molecular modeling for Cu(II)-aminopolycarboxylate complexes: Structures, conformational energies, and ligand binding affinities

Liquid-assisted mechanochemical synthesis, crystallographic, theoretical and molecular docking study on HIV instasome of novel copper complexes: (µ-acetato)-bis(2,2'-bipyridine)-copper and bromidotetrakis(2-methyl-1H-imidazole)-copper bromide

In the present work the two new Cu(II) complexes, (µ-acetato)-bis(2,2'-bipyridine)-copper [Cu(bpy)2(CH3CO2)] and bromidotetrakis(2-methyl-1H-imidazole)-copper bromide [Cu(2-methylimid)4Br]Br have been synthesized by liquid assisted mechanochemical method. The [Cu(bpy)2(CH3CO2)] complex (1) and [Cu(2-methylimid)4Br]Br complex (2) characterised by IR and UV-visible spectroscopy and the structure are confirmed by XRD diffraction studies. Complex (1) crystallized in the Monoclinic with the space group of C2/c where a = 24.312(5) Å, b = 8.5892(18) Å, c = 14.559(3) Å, α = 90°, β = 106.177(7)° and γ = 90° and Complex (2) crystallized in the Tetragonal with the space group of P4nc, a = 9.9259(2) Å, b = 9.9259(2) Å, c = 10.9357(2) Å, α = 90°, β = 90° and γ = 90°. The complex (1) has distorted octahedral geometry where the acetate ligand showed bidentate bridging with the central metal ion and complex (2) has slightly deformed square pyramidal geometry. The HOMO-LUMO energy gap value and the low chemical potential showed that the complex (2) is stable and difficult to polarize compare to complex (1). The molecular docking study of complexes with the HIV instasome nucleoprotein showed the binding energy values - 7.1 and - 5.3 kcal/mol for complex (1) and complex (2) respectively. The negative binding energy values showed the complexes have affinity to bind with HIV instasome nucleoproteins. The in-silico pharmacokinetic study of the complex (1) and complex (2) showed non AMES toxicity, non-carcinogens and low honey Bee toxicity but weakly inhibit Human Ether-a-go-go-related gene.

Theoretical study of copper binding to GHK peptide

We report ligand field molecular mechanics, density functional theory and semi-empirical studies on the binding of Cu(II) to GlyHisLys (GHK) peptide. Following exhaustive conformational searching using molecular mechanics, we show that relative energy and geometry of conformations are in good agreement between GFN2-xTB semi-empirical and B3LYP-D DFT levels. Conventional molecular dynamics simulation of Cu-GHK shows the stability of the copper-peptide binding over 100 ps trajectory. Four equatorial bonds in 3N1O coordination remain stable throughout simulation, while a fifth in apical position from C-terminal carboxylate is more fluxional. We also show that the automated conformer and rotamer search algorithm CREST is able to correctly predict the metal binding position from a starting point consisting of separated peptide, copper and water.

Molecular modeling of zinc paddlewheel molecular complexes and the pores of a flexible metal organic framework

A new all-atom first-principles force field (FF) is constructed for the bimetallic, four-bladed zinc paddlewheel (ZPW) motif. Zinc-ligand interactions are described via Morse functions and the angular geometry at the metal centers is modeled with a pure ligand-ligand repulsion term. The ZPW-FF is principally based on 15 DFT-optimized model systems of general formula ZnPR.nL, where ZnP is the base Zn2(O2CR)4 unit, R = H, CH3 or CF3, L = NH3 or pyridine, and n = 0, 1 or 2. It correctly generates the distorted tetrahedral coordination of the uncapped [Zn2(O2CR)4] species in their ground states as well as giving reasonable structures and energies for the higher symmetry D4h transition state conformations. The zinc-ligand Morse function reference distance, r 0 , is further refined against 30 complexes located in the Cambridge Structural Database and this FF is applied to pore models of the flexible metal-organic framework (MOF) [Zn(bdc)2(dabco)]n (bdc = 1,4-benzendicarboxylate; dabco = 1,4-diazabicyclo(2.2.2)octane). A single pore model reproduces the unit cell of the evacuated MOF system while a 3×3 grid model is necessary to provide good agreement with the observed pronounced structural changes upon adsorption of either dimethylformamide or benzene.