On the utility of momentum space in the density functional theory description of the steric effect

This paper assesses the utility of momentum space in the density-based quantification of the steric effect proposed by Liu [J. Chem. Phys. 126, 244103 (2007)], which is based on a new energy partition scheme where the total electronic energy is decomposed into contributions from three independent effects: steric, electrostatic, and the fermionic quantum. The steric energy defined in this way is repulsive, exclusive, and extensive and intrinsically linked to Bader's quantum theory of atoms in molecules. In this work, the plausibility of defining and computing steric energies using momentum densities according to this scheme is confirmed from numerical tests. Moreover, we found that the correlation between the experimental scales of the steric energies and theoretical values computed from momentum densities is even better than the same correlation with theoretical estimations obtained from position densities.     

A Comprehensive Computational Investigation into the Conserved Virulent Proteins of Shigella species Unveils Potential Small-Interfering RNA Candidates as a New Therapeutic Strategy against Shigellosis

Shigella species account for the second-leading cause of deaths due to diarrheal diseases among children of less than 5 years of age. The emergence of multi-drug-resistant Shigella isolates and the lack of availability of Shigella vaccines have led to the pertinence in the efforts made for the development of new therapeutic strategies against shigellosis. Consequently, designing small-interfering RNA (siRNA) candidates against such infectious agents represents a novel approach to propose new therapeutic candidates to curb the rampant rise of anti-microbial resistance in such pathogens. In this study, we analyzed 264 conserved sequences from 15 different conserved virulence genes of Shigella sp., through extensive rational validation using a plethora of first-generation and second-generation computational algorithms for siRNA designing. Fifty-eight siRNA candidates were obtained by using the first-generation algorithms, out of which only 38 siRNA candidates complied with the second-generation rules of siRNA designing. Further computational validation showed that 16 siRNA candidates were found to have a substantial functional efficiency, out of which 11 siRNA candidates were found to be non-immunogenic. Finally, three siRNA candidates exhibited a sterically feasible three-dimensional structure as exhibited by parameters of nucleic acid geometry such as: the probability of wrong sugar puckers, bad backbone confirmations, bad bonds, and bad angles being within the accepted threshold for stable tertiary structure. Although the findings of our study require further wet-lab validation and optimization for therapeutic use in the treatment of shigellosis, the computationally validated siRNA candidates are expected to suppress the expression of the virulence genes, namely: IpgD (siRNA 9) and OspB (siRNA 15 and siRNA 17) and thus act as a prospective tool in the RNA interference (RNAi) pathway. However, the findings of our study require further wet-lab validation and optimization for regular therapeutic use for treatment of shigellosis.     

Opening of substituted oxetanes with H(2)O(2) and alkyl hydroperoxides: stereoselective approach to 3-peroxyalcohols and 1,2,4-trioxepanes

[reaction: see text] Lewis acid-catalyzed opening of oxetanes by hydrogen peroxide proceeds regioselectively and with good to moderate stereoselectivity to furnish enantiomerically enriched 3-hydroperoxyalkanols. The corresponding opening using alkyl hydroperoxides furnishes 3-peroxyalkanols. The hydroperoxyalkanols are easily converted into enantiomerically enriched 1,2,4-trioxepanes, building blocks for antimalarials.     

Balancing conformational and oxidative kinetic traps during the folding of bovine pancreatic trypsin inhibitor (BPTI) with glutathione and glutathione disulfide

The oxidative folding of bovine pancreatic trypsin inhibitor (BPTI) has served as a paradigm for the folding of disulfide-containing proteins from their reduced form, as well as for protein folding in general. Many extracellular proteins and most pharmaceutically important proteins contain disulfide bonds. Under traditional conditions, 0.125 mM glutathione disulfide (GSSG) and no glutathione (GSH), the folding pathway of BPTI proceeds through a nonproductive route via N* (a two disulfide intermediate), or a productive route via N' (and other two disulfide intermediates which are in rapid equilibrium with N'). Both routes have the rearrangement of disulfide bonds as their rate-determining steps. However, the effects of the composition of the redox buffer, GSSG and GSH, on folding has not been extensively investigated. Interestingly, BPTI folds more efficiently in the presence of 5 mM GSSG and 5 mM GSH than it does under traditional conditions. These conditions, which are similar to those found in vivo, result in a doubly mixed disulfide between N' and glutathione, which acts as an oxidative kinetic trap as it has no free thiols. However, with 5 mM GSSG and 5 mM GSH the formation of the double mixed disulfide is compensated for by N* being less kinetically stable and the more rapid conversion of the singly mixed disulfides between N' and glutathione to native protein (N). Thus a major rate-determining step becomes the direct conversion of a singly mixed disulfide to N, a growth-type pathway. Balancing the formation of N* and its stability versus the formation of the doubly mixed disulfide and its stability results in more efficient folding. Such balancing acts may prove to be general for other disulfide-containing proteins.     

A new natural product and insecticidal amides from seeds of Piper nigrum Linn

Studies on the petroleum ether soluble and insoluble fraction of ethanol extract of dried ground seeds of Piper nigrum resulted in the isolation and structure elucidation of 1 new and 11 known compounds which include 3 hitherto unreported constituents, namely, cinnamylideneacetone, 3,4-methylenedioxyphenylpropiophenone and 2-hydroxy-4,5-methylenedioxypropiophenone from this plant.     

Insecticidal amides from fruits of Piper nigrum Linn

The petroleum ether and ethyl acetate fractions of dried ground seeds of Piper nigrum Linn. afforded sixteen compounds (1-16) including one new insecticidal amide, pipwaqarine (1) and six constituents (3,4,6,7,11,15) previously unreported from this plant. The structure of (1) has been elucidated through extensive 1D-, 2D-NMR spectral studies as, 1-[13-(3',4'-methylenedioxyphenyl)-2E,4E,12E-tridecatrienoyl]-N-isopentylamide, while those of known constituents through comparison of spectral data. 1 exhibited toxicity of 30ppm against fourth instar larvae of Aedes aegypti Liston determined by WHO method. A portion of petroleum ether fraction was also subjected to GC and GC-MS analysis resulting in the identification of three compounds (17-19) using the NIST Mass spectral search program 1998 and Kovat's retention indices. Two of these compounds, 17 and 18, are reported for the first time from this plant.     

Gamma Radiation Induced Biodegradable Shellac Films Treated by Acrylic Monomer and Ethylene Glycol

In this study the mechanical properties of shellac films, prepared by solution casting, were evaluated with varying amounts of Ethylene Glycol (EG) and 2-Ethyl-2-(hydroxymethyl)-1,3-propandiol-trimethacrylate (EHMPTMA). Mechanical properties such as tensile strength (TS) and elongation at break (Eb) of the raw shellac film were found to be 1.86 MPa and 4%, respectively. A series of formulations was prepared using shellac and varying percentages of EG and EHMPTMA in methanol. The films were prepared and irradiated under gamma (Co-60) radiation at different doses (50–500 krad). Grafting of EHMPTMA showed better results compared to raw shellac and EG treated films. Thermal properties, degradation tests in water and soil of the films were also evaluated.     

A promising dehydrogenase-based bioanode for a glucose biosensor and glucose/O2 biofuel cell

A new type of dehydrogenase-based amperometric glucose biosensor was constructed using glucose dehydrogenase (GDH) which was immobilized on the edge-plane pyrolytic graphite (EPPG) electrode modified with poly(phenosafranin)-functionalized single-walled carbon nanotubes (PPS-SWCNTs). The PPS-SWCNT-modified EPPG electrode was prepared by electropolymerization of phenosafranin on the EPPG electrode which had been previously coated with SWCNTs. The performance of the GDH/PPS-SWCNT/EPPG bioanode was evaluated using cyclic voltammetry and amperometry in the presence of glucose. The GDH/PPS-SWCNT/EPPG electrode possesses promising characteristics as a glucose sensor: a wide linear dynamic range of 50 to 700 μM, low detection limit of 0.3 μM, fast response time (1-2 s), high sensitivity (96.5 μA cm(-2) mM(-1)), and anti-interference and anti-fouling abilities. Moreover, the performance of the GDH/PPS-SWCNT/EPPG bioanode was tested in a glucose/O(2) biofuel cell. The maximum power density delivered by the assembled glucose/O(2) biofuel cell could reach 64.0 μW cm(-2) at a cell voltage of 0.3 V with 40 mM glucose.