MolBridge: a program for identifying nonbonded interactions in small molecules and biomolecular structures

Identification and analysis of nonbonded interactions within a molecule and with the surrounding molecules are an essential part of structural studies, given the importance of these interactions in defining the structure and function of any supramolecular entity. MolBridge is an easy to use algorithm based purely on geometric criteria that can identify all possible nonbonded interactions, such as hydrogen bond, halogen bond, cation-pi, pi-pi and van der Waals, in small molecules as well as biomolecules. The user can either upload three-dimensional coordinate files or enter the molecular ID corresponding to the relevant database. The program is available in a standalone form and as an interactive web server with Jmol and JME incorporated into it. The program is freely downloadable and the web server version is also available at http://nucleix.mbu.iisc.ernet.in/molbridge/index.php.

Long range emission enhancement and anisotropy in coupled quantum dots induced by aligned gold nanoantenna

Quantum dot arrays have been projected as the material of choice for next generation displays and photodetectors. Extensive ongoing research aims at improving optical and electrical efficiencies of such devices. We report experimental results on non-local long range emission intensity enhancement and anisotropy in quantum dot assemblies induced by isolated and partially aligned gold nanoantennas. Spatially resolved photoluminescence clearly demonstrate that the effect is maximum, when the longitudinal surface plasmon resonance of the nanoantenna is resonant with the emission maxima of the quantum dots. We estimated the decay length of this enhancement to be similar to 2.6 mu m, which is considerably larger than the range of near field interaction of metal nanoantenna. Numerical simulations qualitatively capture the near field behavior of the nanorods but fail to match the experimentally observed non-local effects. We have suggested how strong interactions of quantum dots in the close packed assemblies, mediated by the nanoantennas, could lead to such observed behavior. (C) 2014 AIP Publishing LLC.

Gold Catalyzed Plasma Assisted Growth of Germanium Nanoneedles

A systematic study of Gold catalyzed growth of Ge nanoneedles by PECVD at low temperatures (<400 degrees C) is presented. Morphology, growth rate and aspect ratio of the needles are studied as a function of power, gas flow rate and chamber pressure. Nanoneedles were grown at pre-defined positions with catalytic particles obtained by e-Beam Lithography and lift off. This opens up the possibility of using Ge Nano needles in photovoltaic, nanoelectronics and nanosensor device applications.

A Gold Sensors Array for Imaging The Real Tissue Phantom in Electrical Impedance Tomography

Surface electrodes in Electrical Impedance Tomography (EIT) phantoms usually reduce the SNR of the boundary potential data due to their design and development errors. A novel gold sensors array with high geometric precision is developed for EIT phantoms to improve the resistivity image quality. Gold thin films are deposited on a flexible FR4 sheet using electro-deposition process to make a sixteen electrode array with electrodes of identical geometry. A real tissue gold electrode phantom is developed with chicken tissue paste and the fat cylinders as the inhomogeneity. Boundary data are collected using a USB based high speed data acquisition system in a LabVIEW platform for different inhomogeneity positions. Resistivity images are reconstructed using EIDORS and compared with identical stainless steel electrode systems. Image contrast parameters are calculated from the resistivity matrix and the reconstructed images are evaluated for both the phantoms. Image contrast and image resolution of resistivity images are improved with gold electrode array.

Suppression of protein aggregation by gold nanoparticles: a new way to store and transport proteins

Suppression of the aggregation of proteins has tremendous implications in biology and medicine. In the pharmaceuticals industry, aggregation of therapeutically important proteins and peptides while stored, reduces the efficacy and promptness of action leading to, in many instances, intoxication of the patient by the aggregate. Here we report the effect of gold nanoparticles (Au-NPs) in preventing the thermal and chemical aggregation of two unrelated proteins of different size, alcohol dehydrogenase (ADH, 84 kDa) and insulin (6 kDa), respectively, in physiological pH. Our principal observation is that there is a significant reduction (up to 95%) in the extent of aggregation of ADH and insulin in the presence of gold nanoparticles (Au-NPs). Aggregation of these proteins at micromolar concentration is prevented using nanomolar or less amounts of gold nanoparticles which is remarkable since chaperones which prevent such aggregation in vivo are required in micromolar quantity. The prevention of aggregation of these two different proteins under two different denaturing environments has established the role of Au-NPs as a protein aggregation prevention agent. The extent of prevention increases rapidly with the increase in the size of the gold nanoparticles. Protein molecules get physisorbed on the gold nanoparticle surface and thus become inaccessible by the denaturing agent in solution. This adsorption of proteins on AuNPs has been established by a variety of techniques and assays.

Theoretical Insights to Niobium-Doped Monolayer MoS2-Gold Contact

We report a first principles study of the electronic properties for a contact formed between Nb-doped monolayer MoS2 and gold for different doping concentrations. We first focus on the shift of energy levels in band structure and the density of states with respect to the Fermi level for a geometrically optimized 5 x 5 MoS2 supercell for both pristine and Nb-doped structures. The doping is achieved by substituting Mo atoms with Nb atoms at random positions. It is observed that for an experimentally reported sheet hole doping concentration of (rho(2D)) 1.8 x 10(14) cm(-2), the pristine MoS2 converts to degenerate p-type semiconductor. Next, we interface this supercell with six layers of < 111 > cleaved surface of gold to investigate the contact nature of MoS2-Au system. By careful examination of projected band structure, projected density of states, effective potential and charge density difference, we demonstrate that the Schottky barrier nature observed for pure MoS2-Au contact can be converted from n-type to p-type by efficient Nb doping.

Cytotoxicity of Ultrasmall Gold Nanoparticles on Planktonic and Biofilm Encapsulated Gram-Positive Staphylococci

The emergence of multidrug resistant bacteria, especially biofilm-associated Staphylococci, urgently requires novel antimicrobial agents. The antibacterial activity of ultrasmall gold nanoparticles (AuNPs) is tested against two gram positive: S. aureus and S. epidermidis and two gram negative: Escherichia coli and Pseudomonas aeruginosa strains. Ultrasmall AuNPs with core diameters of 0.8 and 1.4 nm and a triphenylphosphine-monosulfonate shell (Au0.8MS and Au1.4MS) both have minimum inhibitory concentration (MIC) and minimum bactericidal concentration of 25 x 10(-6)m Au]. Disc agar diffusion test demonstrates greater bactericidal activity of the Au0.8MS nanoparticles over Au1.4MS. In contrast, thiol-stabilized AuNPs with a diameter of 1.9 nm (AuroVist) cause no significant toxicity in any of the bacterial strains. Ultrasmall AuNPs cause a near 5 log bacterial growth reduction in the first 5 h of exposure, and incomplete recovery after 21 h. Bacteria show marked membrane blebbing and lysis in biofilm-associated bacteria treated with ultrasmall AuNP. Importantly, a twofold MIC dosage of Au0.8MS and Au1.4MS each cause around 80%-90% reduction in the viability of Staphylococci enveloped in biofilms. Altogether, this study demonstrates potential therapeutic activity of ultrasmall AuNPs as an effective treatment option against staphylococcal infections.

Effect of ultra-fast mixing in a microchannel due to a soft wall on the room temperature synthesis of gold nanoparticles

The room-temperature synthesis of mono-dispersed gold nanoparticles, by the reduction of chlorauric acid (HAuCl4) with tannic acid as the reducing and stabilizing agent, is carried out in a microchannel. The microchannel is fabricated with one soft wall, so that there is a spontaneous transition to turbulence, and thereby enhanced mixing, when the flow Reynolds number increases beyond a critical value. The objective of the study is to examine whether the nanoparticle size and polydispersity can be modified by enhancing the mixing in the microchannel device. The flow rates are varied in order to study nanoparticle formation both in laminar flow and in the chaotic flow after transition, and the molar ratio of the chlorauric acid to tannic acid is also varied to study the effect of molar ratio on nanoparticle size. The formation of gold nanoparticles is examined by UV-visual spectroscopy and the size distribution is determined using scanning electron microscopy. The synthesized nanoparticles size decreases from a parts per thousand yen6 nm to a parts per thousand currency sign4 nm when the molar ratio of chlorauric acid to tannic acid is increased from 1 to 20. It is found that there is no systematic variation of nanoparticle size with flow velocity, and the nanoparticle size is not altered when the flow changes from laminar to turbulent. However, the standard deviation of the size distribution decreases by about 30% after transition, indicating that the enhanced mixing results in uniformity of particle size.

SUB1 Plays a Negative Role during Starvation Induced Sporulation Program in Saccharomyces cerevisiae

Saccharomyces cerevisiae Sub1 is involved in several cellular processes such as, transcription initiation, elongation, mRNA processing and DNA repair. It has also been reported to provide cellular resistance during conditions of oxidative DNA damage and osmotic stress. Here, we report a novel role of SUB1 during starvation stress-induced sporulation, which leads to meiosis and spore formation in diploid yeast cells. Deletion of SUB1 gene significantly increased sporulation efficiency as compared to the wild-type cells in S288c genetic background. Whereas, the sporulation functions of the sub1(Y66A) missense mutant were similar to Sub1. SUB1 transcript and protein levels are downregulated during sporulation, in highly synchronized and sporulation proficient wild-type SK1 cells. The changes in Sub1 levels during sporulation cascade correlate with the induction of middle sporulation gene expression. Deletion of SUB1 increased middle sporulation gene transcript levels with no effect on their induction kinetics. In wild-type cells, Sub1 associates with chromatin at these loci in a temporal pattern that correlates with their enhanced gene expression seen in sub1. cells. We show that SUB1 genetically interacts with HOS2, which led us to speculate that Sub1 might function with Set3 repressor complex during sporulation. Positive Cofactor 4, human homolog of Sub1, complemented the sub1. sporulation phenotype, suggesting conservation of function. Taken together, our results suggest that SUB1 acts as a negative regulator of sporulation.

Directed Assembly of Ultrathin Gold Nanowires over Large Area by Dielectrophoresis

Ultrathin Au nanowires (similar to 2 nm diameter) are interesting from a fundamental point of view to study structure and electronic transport and also hold promise in the field of nanoelectronics, particularly for sensing applications. Device fabrication by direct growth on various substrates has been useful in demonstrating some of the potential applications. However, the realization of practical devices requires device fabrication strategies that are fast, inexpensive, and efficient. Herein, we demonstrate directed assembly of ultrathin Au nanowires over large areas across electrodes using ac dielectrophoresis with a mechanistic understanding of the process. On the basis of the voltage and frequency, the wires either align in between or across the contact pads. We exploit this assembly to produce an array of contacting wires for statistical estimation of electrical transport with important implications for future nanoelectronic/sensor applications.

Self-assembled gold nanofilms as a simple, recoverable and recyclable catalyst for nitro-reduction

Hexaazamacrocycle (L) stabilized gold nanoparticles (AuNPs) were prepared by combining L with HAuCl4 center dot 3H(2)O in a variety of alcohol-water (1 : 1) mixtures. The dual roles of L as a reducing and stabilizing agent were exploited for the synthesis of AuNPs under the optimized ratio of L to Au3+ (2 : 1). Self-assembled gold nanofilms (AuNFs) were constructed at liquid-liquid interfaces by adding equal volumes of hexane to the dispersions of AuNPs in the alcohol-water systems. The nanofilms were formed spontaneously by shaking the two-phase mixture for a minute followed by standing. The alcohols explored for the self-assembly phenomenon were methanol, ethanol, i-propanol and t-butanol. The systems containing methanol or t-butanol resulted in AuNFs at the interfaces, whereas the other two alcohols were found not suitable and the AuNPs remained dispersed in the corresponding alcohol-water medium. The AuNFs prepared under suitable conditions were coated on a variety of surfaces by the dip and lift-off method/solvent removal approach. The AuNFs were characterized by UV-vis, SEM, TEM, AFM and contact angle measurement techniques. A coated glass-vial or cuvette was used as a catalytic reservoir for nitro-reduction reactions under ambient and aqueous conditions using NaBH4 as the reducing agent. The reduced products (amines) were extracted by aqueous work-up using ethyl acetate followed by evaporation of the organic layer; the isolated products required no further purification. The catalyst was recovered by simply decanting the reaction mixture whereupon the isolated catalyst remained coated inside the vessel. The recovered catalyst was found to be equally efficient for further catalytic cycles.

Prediction and validation of gold nanoparticles (GNPs) on plant growth promoting rhizobacteria (PGPR): a step toward development of nano-biofertilizers

Several soil microbes are present in the rhizosphere zone, especially plant growth promoting rhizobacteria (PGPR), which are best known for their plant growth promoting activities. The present study reflects the effect of gold nanoparticles (GNPs) at various concentrations on the growth of PGPR. GNPs were synthesized chemically, by reduction of HAuCl 4, and further characterized by UV-Vis spectroscopy, X-ray diffraction technique (XRD), and transmission electron microscopy (TEM), etc. The impact of GNPs on PGPR was investigated by Clinical Laboratory Standards Institute (CLSI) recommended Broth-Microdilution technique against four selected PGPR viz., Pseudomonas fluorescens, Bacillus subtilis, Paenibacillus elgii, and Pseudomonas putida. Neither accelerating nor reducing impact was observed in P. putida due to GNPs. On the contrary, significant increase was observed in the case of P. fluorescens, P. elgii, and B. subtilis, and hence, GNPs can be exploited as nano-biofertilizers.

Hydrogelation of bile acid-peptide conjugates and in situ synthesis of silver and gold nanoparticles in the hydrogel matrix

Fabricating supramolecular hydrogels with embedded metal nanostructures is important for the design of novel hybrid nanocomposite materials for diverse applications such as biosensing and chemosensing platforms, catalytic and antibacterial functional materials etc. Supramolecular self-assembly of bile acid-dipeptide conjugates has led to the formation of new supramolecular hydrogels. Gelation of these molecules depends strongly on the hydrophobic character of the bile acids. The possibility of in situ fabrication of Ag and Au NPs in these supramolecular hydrogels by incorporating Ag+ and Au3+ salts was investigated via photoreduction. Chemical reductions of Ag+ and Au3+ salts in the hydrogels were performed without adding any external stabilizing agents. In this report we have shown that the color, size and shape of silver nanoparticles formed by photoreduction depend on the amino acid residue of the side chain.

Gold catalyzed intramolecular hydroalkoxylation assisted ring opening of furans to the corresponding saturated gamma-keto esters

A facile ring opening of furans in furyl propargyl alcohols to the corresponding saturated gamma-keto esters is observed in the gold(III) chloride catalyzed reaction with MeOH. It is found that the ring opening of furan is driven by the intramolecular hydroalkoxylation. Mitigating the intramolecular hydroalkoxylation led to the expected conjugated enyne resulting from the dehydration. (C) 2015 Elsevier Ltd. All rights reserved.