conformations and electronic properties of a series of imidazobenzodiazepines are investigated by am1 semi-empirical quantum mechanics method. it is shown that substitution of cl in position 7 instead of 8, changes the geometry of the seven membered lactam ring; this may put the n5 nitrogen in a better positon to act as a hydrogen bond acceptor, and the phenyl ring in position 6 is probably mor...

As a commonly used structure-based approach for virtual screening, molecular design and lead optimization, molecular docking can search the preferred orientation and conformation of a ligand for its optimal binding to a receptor or enzyme active site. In doing so, selecting an appropriate method to calculate the electrostatic potentials is critical. In the current report, nine different semi-em...

Semi-empirical calculations including an empirical dispersive correction are used to calculate intermolecular interaction energies and structures for a large database containing 156 biologically relevant molecules (hydrogen-bonded DNA base pairs, interstrand base pairs, stacked base pairs and amino acid base pairs) for which MP2 and CCSD(T) complete basis set (CBS) limit estimates of the intera...

Phosphate transfer reactions are ubiquitous in nature and play fundamental roles in ATP hydrolysis and protein phosphorylation processes. The mechanisms of these reactions involve a pentacoordinated phosphorus atom that can be an intermediate or a transition state. These structures are very sensitive to both internal and external electrostatic effects and their description with quantum mechanic...

In maize the am1-1 mutant allele results in both the male and female meiocytes undergoing mitosis in place of the meiotic divisions. A second mutant allele am1-praI enables both the male and female meiocytes to proceed to the early zygotene stage of meiotic prophase I before being blocked. Here we report on three new alleles that allow all male meiocytes to undergo mitosis but in female meiocyt...

the results of mndo, am1 and pm3 semi-empirical calculations and hf/6-31g*, mp/6-31g*, mp2/6-311+g**, and b3lyp/6-311g** and qcisd/6-31g* ab initio methods for angle strain and conjugation effects in twist-boat, boat, and half-chair geometries of (z,z,z)-cycloocta-1,3,5-triene indicate that all methods, except pm3, predict wrong ordering of the conformations.

13C NMR spectra of molecules containing one or two benzene rings linked with CH=CH2, CH=CH (transor cis-), C C and CH=N groups revealed the existence of long range deuterium isotope effects on 13C chemical shifts. It was found that deuterium isotope effects over six bonds (6D) are related to the conformation of investigated molecules. Molecular torsional angles were calculated by ab initio HF/6...

Thermostable glycoprotein amyloid bioemulsifier BE-AM1 was reported from Solibacillus silvestris AM1. S. could produce better in 1% inoculum size and 18h age. The production by AM1 has been seen to be unaffected amending the growth medium (Zobel Marine medium) with Carbon Nitrogen sources. effects of 16 nutrient factors (from ZM were analyzed statistically one factor at a time, Plackett-Burman ...

L-phenylalanine (Phe), an essential amino acid, is necessary for the synthesis of proteins such as catecholamine and melanin, also precursor acid L-tyrosine (Tyr). In this paper, optimized structures Phe, were calculated by using semi-empirical models AM1, PM3 MNDO; Density Functional (DFT) at B3LYP Hartreefock methods (HF) with 6-311++G (d,p) level. The energies geometric parameters Kaempferol...