Accurate force fields are essential for describing biological systems in a molecular dynamics simulation. To analyze the docking of the small redox protein cytochrome c (cyt c) requires simulation parameters for the heme in both the reduced and oxidized states. This work presents parameters for the partial charges and geometries for the heme in both redox states with ligands appropriate to cyt ...

The study of the minimum Born–Oppenheimer structures of the protonated water clusters, H2O nH, is performed for n=20 and 21. The structures belonging to four basic morphologies are optimized at the Hartree–Fock, second-order many-body perturbation theory and coupled cluster level, with the 6–31G, 6-31G , and 6-311G basis sets, using the parallel ACES III program. The lowest energy structure for...

A reliable computational method for the prediction of organoselenium geometries and bond dissociation energies (BDEs) has been determined on the basis of the performance of density functional theory (DFT: B3LYP and B3PW91) and ab initio molecular orbital procedures (Hartree-Fock (HF)) in conjunction with various Pople basis sets including (but not limited to) the 6-31G(d), 6-31G(d,p), 6-311G(d)...

The results of ab initio molecular orbital calculations of excited states and electronic couplings (for energy transfer) between the B800 and B850 bacteriochlorophyll a (Bchl) chromophores in the peripheral lightharvesting complex (LH2) of the purple photosynthetic bacterium Rhodopseudomonas acidophila are reported. Electronic couplings are estimated from “supermolecule” calculations of Bchl di...

Analytic gradients of dual-basis Hartree-Fock and density functional theory energies have been derived and implemented, which provide the opportunity for capturing large basis-set gradient effects at reduced cost. Suggested pairings for gradient calculations are 6-31G/6-31G**, dual[-f,-d]/cc-pVTZ, and 6-311G*/6-311 + +G(3df,3pd). Equilibrium geometries are produced within 0.0005 A of large-basi...

The reaction paths for formation and isomerization of a set of silica SimOn (m = 2,3, n = 1-5) nanoclusters have been investigated using second-order perturbation theory (MP2) with the 6-31G(d) basis set. The MP2/6-31G(d) calculations have predicted singlet ground states for all clusters excluding Si3O2. The total energies of the most important points on the potential energy surfaces (PES) have...

8-chloro-3-((3-chlorobenzyl)thio)-[1,2,4]triazolo[4,3-a]pyridine was synthesized and recrystallized from EtOH. The compound was characterized by 1H NMR, 13C NMR, FTIR, MS, elemental analysis and X-ray diffraction. The compound was crystallized in the monoclinic space group P2(1)/c with a = 8.1992(5), b = 21.7731(12), c = 7.8454(6) Å, α = 90, β = 108.421(7), γ = 90°, V = 1328.81 (15)Å3, Z = 4 an...

2, 3-Dichloro-5,8-dimethoxy-1,4-naphthoquinone (DDNQ) is a synthetic naphthaquinone which has shown reduced chemotoxicity and enhanced chemotherapeutic activity in in vitro studies. The ability of DDNQ to serve as a chemical dopant of graphene resulting improved performance of graphene by tuning its band gap is also being explored. In this report surface enhanced Raman scattering (SERS) spectro...

Several triterpenic derivatives, with the A-ring functionalized, were semisynthesized from oleanolic and maslinic acids. The reactivities of sulfites, sulfate, and epoxides in these triterpene compounds were investigated under different reaction conditions. Moreover, contracted A-ring triterpenes (five-membered rings) were obtained, by different treatments of the sulfate 7. From the epoxide 8, ...

The FT-IR and FT-Raman vibrational spectra of selegiline were recorded. The optimized geometry and wavenumbers in the ground state were calculated using density functional (B3LYP) method with standard 6-31G(d,p) basis set. The computed B3LYP/6-31G(d,p) results show the best agreement with the experimental values over the other methods. Natural bond orbital analysis of selegiline is also carried...