Intramolecular interactions of L‐phenylalanine: Valence ionization spectra and orbital momentum distributions of its fragment molecules

Intramolecular interactions between fragments of L ‐phenylalanine, i.e., phenyl and alaninyl, have been investigated using dual space analysis (DSA) quantum mechanically. Valence space photoelectron spectra (PES), orbital energy topology and correlation diagram, as well as orbital momentum distributions (MDs) of L ‐phenylalanine, benzene and L ‐alanine are studied using density functional theory methods. While fully resolved experimental PES of L ‐phenylalanine is not yet available, our simulated PES reproduces major features of the experimental measurement. For benzene, the simulated orbital MDs for 1e_1g and 1a_2u orbitals also agree well with those measured using electron momentum spectra. Our theoretical models are then applied to reveal intramolecular interactions of the species on an orbital base, using DSA. Valence orbitals of L ‐phenylalanine can be essentially deduced into contributions from its fragments such as phenyl and alaninyl as well as their interactions. The fragment orbitals inherit properties of their parent species in energy and shape (ie., MDs). Phenylalanine orbitals show strong bonding in the energy range of 14‐20 eV, rather than outside of this region. This study presents a competent orbital based fragments‐in‐molecules picture in the valence space, which supports the fragment molecular orbital picture and building block principle in valence space. The optimized structures of the molecules are represented using the recently developed interactive 3D‐PDF technique. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the particle mesh Ewald method (PME) for solution of Poisson's Equation for the electrostatic potential under periodic boundary conditions. We discuss elements of our implementation of the PME algorithm on GPUs as well as pertinent performance issues. We proceed to show results of simulations of extended lipid bilayer systems using our program, FEN ZI. We performed simulations of DMPC bilayer systems consisting of 17,004, 68,484, and 273,936 atoms in explicit solvent. We present bilayer structural properties (atomic number densities, electron density profiles), deuterium order parameters (S(CD)), electrostatic properties (dipole potential, water dipole moments), and orientational properties of water. Predicted properties demonstrate excellent agreement with experiment and previous all-atom molecular dynamics simulations. We observe no statistically significant differences in calculated structural or electrostatic properties for different system sizes, suggesting the small bilayer simulations (less than 100 lipid molecules) provide equivalent representation of structural and electrostatic properties associated with significantly larger systems (over 1000 lipid molecules). We stress that the three system size representations will have differences in other properties such as surface capillary wave dynamics or surface tension related effects that are not probed in the current study. The latter properties are inherently dependent on system size. This contribution suggests the suitability of applying emerging GPU technologies to studies of an important class of biological environments, that of lipid bilayers and their associated integral membrane proteins. We envision that this technology will push the boundaries of fully atomic-resolution modeling of these biological systems, thus enabling unprecedented exploration of meso-scale phenomena (mechanisms, kinetics, energetics) with atomic detail at commodity hardware prices.     

Protective Effect of Withania somnifera and Cardiospermum halicacabum Extracts Against Collagenolytic Degradation of Collagen

The irreversible destruction of extracellular matrix (ECM) such as cartilage, tendon, and bone that comprise synovial joints is the hallmark of both rheumatoid arthritis and osteoarthritis by over-expression of matrix metalloproteinase (MMP)-collagenases. We report herein the detailed study on the inhibitory effects of Withania somnifera extract (WSE) and Cardiospermum halicacabum extract (CHE) on Clostridium histolyticum collagenase (ChC) activity against the degradation of the ECM component of bovine Achilles tendon type I collagen by hydroxyproline assay method. Interaction of WSE and CHE with ChC exhibited 71% and 88% inhibition, respectively, to the collagenolytic activity of ChC against collagen degradation, and the inhibition was found to be concentration-dependent. The inhibition kinetics of ChC by both the extracts has been deduced from the extent of hydrolysis of N-[3-(2-furyl) acryloyl]-Leu-Gly-Pro-Ala. Both WSE and CHE are provided competitive and mixed type inhibition on ChC activity, respectively. Circular dichroism studies of ChC on treatment with WSE and CHE revealed changes in the secondary structure of collagenase. These results suggest that the WSE and CHE facilitated collagen stabilization through collagenase inhibition.     

Mean field theory of charged dendrimer molecules

Using self-consistent field theory (SCFT), we study the conformational properties of polyelectrolyte dendrimers. We compare results for three different models of charge distributions on the polyelectrolytes: (1) a smeared, quenched charge distribution characteristic of strong polyelectrolytes; (2) a smeared, annealed charge distribution characteristic of weak polyelectrolytes; and (3) an implicit counterion model with Debye-Huckel interactions between the charged groups. Our results indicate that an explicit treatment of counterions is crucial for the accurate characterization of the conformations of polyelectrolyte dendrimers. In comparing the quenched and annealed models of charge distributions, annealed dendrimers were observed to modulate their charges in response to the density of polymer monomers, counterions, and salt ions. Such phenomena is not accommodated within the quenched model of dendrimers and is shown to lead to significant differences between the predictions of quenched and annealed model of dendrimers. In this regard, our results indicate that the average dissociated charge α inside the dendrimer serves as a useful parameter to map the effects of different parametric conditions and models onto each other. We also present comparisons to the scaling results proposed to explain the behavior of polyelectrolyte dendrimers. Inspired by the trends indicated by our results, we develop a strong segregation theory model whose predictions are shown to be in very good agreement with the numerical SCFT calculations.     

A novel acid-catalyzed C5-alkylation of oxindoles using alcohols

A novel C5-alkylation of oxindoles using alcohols as alkylating agents under acid catalysis is described for the first time. The reactions of various benzylic, allylic and propargylic alcohols are studied to obtain the corresponding 5-substituted oxindoles in good yields.     

Effect of terminal N-substitution in 2-oxo-1,2-dihydroquinoline-3-carbaldehyde thiosemicarbazones on the mode of coordination, structure, interaction with protein, radical scavenging and cytotoxic activity of copper(II) complexes

Four 2-oxo-1,2-dihydroquinoline-3-carbaldehyde N-substituted thiosemicarbazone ligands (H(2)-OQtsc-R, where R = H, Me, Et or Ph) and their corresponding new copper(II) complexes [CuCl(2)(H(2)-OQtsc-H)]·2H(2)O (1), [CuCl(2)(H(2)-OQtsc-Me)]·2H(2)O (2), [CuCl(2)(H(2)-OQtsc-Et)(CH(3)OH)]Cl (3) and [CuCl(H-OQtsc-Ph)]·CH(3)OH (4) have been synthesized in order to correlate the effect of terminal N-substitution on coordination behaviour, structure and biological activity. Single crystal X-ray diffraction studies revealed that the complexes 1, 2 and 3 have square pyramidal geometry around the central metal ion. In the complexes 1 and 2, the copper ion is coordinated by the ligand with ONS donor atoms, one chloride ion in apical position and the other chloride in the basal plane. Complex 3 consists of [CuCl(2)(H(2)-OQtsc-Et)(CH(3)OH)](+) cation and a chloride as counter ion. The copper ion is coordinated by the ligand with ONS donor atoms and by one chloride ion in the basal plane. One methanol molecule is bonded through its neutral oxygen in the apical position. Complex 4 is square planar with the ligand coordinating through uni-negative tridentate ONS(-) and by one chloride ion in the basal plane. The binding of complexes with lysozyme protein was carried out by fluorescence spectroscopy. Investigations of antioxidation properties showed that all the copper(II) complexes have strong radical scavenging properties. The cytotoxicity of the complexes 3 and 4 against NIH 3T3 and HeLa cell lines showed that synergy between the metal and ligands results in a significant enhancement in the cell death with IC(50) of ~10-40 μM. A size dependence of substitution at terminal N in the thiosemicarbazones on the biological activities of the complexes has been observed.     

Total synthesis and stereochemical assignment of burkholdac B, a depsipeptide HDAC inhibitor

Three diastereomers of burkholdac B were prepared by total synthesis, enabling the full stereochemical assignment of the natural product. It is proposed that burkholdac B is identical to thailandepsin A independently isolated by Cheng from the same strain of Burkholderia thailandensis . Burkholdac B is the most potent among depsipeptide histone deacetylase inhibitors in growth inhibition of the MCF7 breast cancer cell line with an IC(50) of 60 pM.     

An easily accessible Re-based catalyst for the selective conversion of methanol: evidence for an unprecedented active site structure through combined operando techniques

Heterogeneous Re/SiO(2) catalysts prepared using a one pot sol-gel synthesis were found to display high activity in the direct, selective methanol conversion to methylal, which is correlated to an unprecedented rhenium oxide structure.     

MHD effects on free convective flow over moving semi-infinite vertical cylinder with temperature oscillation

Numerical solutions of magnetodynamics(MHD) effects on the free convective flow of an incompressible viscous fluid past a moving semi-infinite vertical cylinder with temperature oscillation are presented.The dimensionless,unsteady,non-linear,and coupled governing partial differential equations are solved by using an implicit finite difference method of the Crank-Nicolson type.The velocity,temperature,and concentration profiles are studied for various parameters.The local skin-friction,the average skin-fr...     

Studies on the growth,structural, optical,SHG and thermal properties of γ-glycine single crystal: An organic nonlinear optical crystal

Single crystals of the organic nonlinear optical material γ-glycine have been grown in the presence of Zinc sulphate by slow evaporation technique at ambient temperature for the first time. Bulk growth of γ-glycine single crystals was grown by Top-seeded solution growth method. The γ-phase of glycine was confirmed by powder X-ray diffraction and the FTIR analysis. Elemental analysis CHN was performed to confirm the non-inclusion of zinc sulphate species into the solution. Inductively coupled plasma optical emission spectrometry study (ICP-OES) was employed to quantify the concentration of Zinc element in the grown γ-glycine single crystals. The optical transmission was ascertained from UV–Vis–NIR spectrum. The optical band gap was estimated for γ-glycine single crystal using UV–Vis–NIR study. Differential scanning calorimetry analysis was employed to explore information about thermal stability, phase transition and melting point of the grown crystal. The second harmonic generation relative efficiency was measured by Kurtz and Perry powder technique.