Application of spectroscopic techniques for monitoring microbial diversity and bioremediation

Microbes are the most fascinating group, with huge diversity devising myriad functional applications in the field of medicine, pharmaceuticals, environmental remediation, and industries. Quantitative and qualitative determination of biomolecules and microbial assisted phenomena by spectroscopy is a pioneer approach. It facilitates the study of atomic and molecular geometries, energy levels, chemical bonds, and interactions between molecules and microbes. It produces fingerprints of the microbial species serving to characterize, differentiate, and identify microorganisms, in both the environment and at single-cell level. Spectroscopy-based bioremediation techniques like Fourier transform infrared spectroscopy, mass spectroscopy, force spectroscopy, Raman spectroscopy, photoemission spectroscopy, and laser-induced breakdown spectroscopy have been very well represented and linked with the microbial applications. This review summarizes the traditional spectroscopic techniques used for the study of microbes and microbial-assisted products as well as illustrates its application in the field of microbial diversity and remediation. This will provide an outlook for the intricate characterization and dimension of microbes to be used for effective application in bioremediation.     

Current gain and external quantum efficiency modeling of GeSn based direct bandgap multiple quantum well heterojunction phototransistor

This paper aims to provide the performance characteristics of proposed, strain balanced direct band gap multiple quantum wells (MQWs) hetero phototransistor (HPT) made of SiGeSn/GeSn alloys grown on Si substrate which is compatible with recent CMOS fabrication technology. This also presents a comprehensive comparison of this proposed structure with the existing HPT structure made of indirect gap Ge/SiGe MQWs. Alloys of Ge and Sn grown on Si platform shows about tenfold increase in absorption over Ge at C and L-bands due to direct nature of band gap in GeSn. Initial work begins the solution of continuity equation to solve the different terminal current densities and optical gain of the multiple quantum well structure. Main analysis was concentrated on finding the external quantum efficiency depending on the doping variations of emitter and base, base width etc. Finally the photocurrent density variations are estimated for the structure and compared with existing indirect band gap HPT. The calculated values for direct band gap GeSn HPT device are found to be comparable with those for indirect band gap SiGe device to flourish as a potential candidate of photo detectors for the present day telecommunication network.     

On dynamics of velocity vector potential in incompressible fluids

An elegant quaternionic formulation is given for the Lagrangian advection equation for velocity vector potential in fluid dynamics. At first we study the topological significance of a restricted conserved quantity viz., stream-helicity and later more realistic configuration of open streamlines is figured out. Also, using Clebsch parameterisation of the velocity vector potential yet another physical significance for the stream-helicity is provided. Finally we give a Nambu-Poisson formalism of the Lagrangian advection equation for velocity vector potential.     

Effect of unfolding on the thickness of the hydration layer of a protein

Properties of water in the hydration layer around a protein is intimately correlated with its function. A knowledge of the thickness of the hydration layer is important to understand its role in guiding the folding-unfolding of the protein. We have performed atomistic molecular dynamics simulations of the folded native and a partially unfolded molten globule structure of the villin headpiece subdomain or HP-36 in aqueous solution to estimate the effect of unfolding on the thickness of hydration layer around different segments of the protein. In particular, several dynamic properties of water around different segments of the folded native and the unfolded structure have been calculated by varying the thickness of the hydration layers. It is found that unfolding of a segment of the protein is correlated with the dynamics of water around it, i.e., within the first hydration layer. The effect of unfolding on water properties has been found to diminish when water molecules present beyond the first hydration layer were included in the calculations.      

Stabilization of β-hairpin structures via inter-strand π-π and hydrogen bond interactions in α-, β-, γ-hybrid peptides

Synthesis and conformational studies of α-, β-, γ-hybrid peptides containing a pyrrole amino acid (Paa, 1) and a furan amino acid (Faa, 2), namely Boc-β-Phe-Faa-d-Pro-Gly-Paa-β-HGly-Faa-OMe (3) and Boc-Paa-β-Phe-Faa-d-Pro-Gly-Paa-β-HGly-Faa-OMe (4), were carried out and they adopt β-hairpin structures stabilized via inter-strand π-π and hydrogen bonding interactions.     

Kinetic study of uranium speciation in model solutions and in natural waters using Competitive Ligand Exchange Method

Kinetic speciation of uranium in model solutions containing uranium and humic acid (HA) and in natural waters has been investigated by Competitive Ligand Exchange Method (CLEM). In alkaline freshwaters, most of uranium species were uranium-carbonate species, which were labile in the CLEM experiment. The uranium speciation of every sample was characterized either as “labile” or “non-labile” uranium complexes depending on the dissociation rate coefficients of the complexes. The results showed that as the U(VI)/HA ratio was decreased, the dissociation rate coefficients decreased and the labile fraction decreased as well. When the U(VI)/HA ratio was 0.1, the labile fraction of the U(VI)-HA increased with increasing pH; however, there was no pH effect on the dissociation of U(VI)-HA complexes at lower U(VI)/HA ratios. Chelex-100 had some limitations in its use for the study of dissociation of U(VI)-HA complex at very low U(VI)/HA ratios. By developing an analytical method and procedure for quantitative determination of kinetic parameters for the dissociation of uranium-HA complexes in model solutions and natural waters, this work has made a substantial contribution to analytical chemistry.     

Syndiotactic Polystyrene / Fullerene Composites: Elucidation of Structural Aspect

Summary: Syndiotactic polystyrene (sPS), an attractive polymer due to its wide range of application, forms polymer-solvent intercalates with a large variety of solvent molecules ranging from liquids to solids. Recently, it has been realized that sPS intercalate prepared from SPS/naphthalene gel is more promising of making mesoporous materials. Here, the composite of sPS/fullerene have been prepared by taking advantage of sublimation of naphthalene. The different techniques as like XRD, SEM, HRTEM, FT-IR, DSC, TGA etc have been employed to characterized sPS/fullerene composite. XRD investigation shows the presence of δ form sPS in the composite. SEM and HRTEM reveal the fibrillar network with fringe like structure in presence of fullerene only and the average diameter of fibril has increased as compared to pure sPS fibrils. The conductivities of these fibrils have been increased with increasing amount of fullerene.     

Chemomechanics of surface stresses induced by DNA hybridization

When biomolecular reactions occur on one surface of a microcantilever beam, changes in intermolecular forces create surface stresses that bend the cantilever. While this phenomenon has been exploited to create label-free biosensors and biomolecular actuators, the mechanisms through which chemical free energy is transduced to mechanical work in such hybrid systems are not fully understood. To gain insight into these mechanisms, we use DNA hybridization as a model reaction system. We first show that the surface grafting density of single-stranded probe DNA (sspDNA) on a surface is strongly correlated to its radius of gyration in solution, which in turn depends on its persistence length and the DNA chain length. Since the persistence length depends on ionic strength, the grafting density of sspDNA can be controlled by changing a solution's ionic strength. The surface stresses produced by the reaction of complementary single-stranded target DNA (sstDNA) to sspDNA depend on the length of DNA, the grafting density, and the hybridization efficiency. We, however, observe a remarkable trend: regardless of the length and grafting density of sspDNA, the surface stress follows an exponential scaling relation with the density of hybridized sspDNA.     

Oxo- and oxoperoxo-molybdenum(VI) complexes with aryl hydroxamates: synthesis, structure, and catalytic uses in highly efficient, selective, and ecologically benign peroxidic epoxidation of olefins

A solution obtained by dissolving MoO3 in H2O2 reacts separately with secondary hydroxamic acids (viz., N-benzoyl N-phenyl hydroxamic acid (BPHAH), N-benzoyl N-ortho-, -meta-, -para-tolyl hydroxamic acids, (BOTHAH, BMTHAH, and BPTHAH, respectively), and N-cinnamoyl N-phenyl hydroxamic acid (CPHAH) affording [MoO(O2)(BPHA)2] (1), [MoO(O2)(BOTHA)2] (2), [MoO(O2)(BMTHA)2] (3), [MoO(O2)(BPTHA)2] (4), and [Mo(O)2(CPHA)2](5), respectively. The O and O2 are situated cis to each other in 2-4, but in each case, they are disordered and distributed over four sites. This disorder does not exist in the 6-coordinate cis dioxo complex 5, to which crude MoO(O2)(CPHA)2 (5') was converted during recrystallization. An aqueous molybdate solution readily reacts with all those hydroxamic acids producing [Mo(O)2(hydroxamate)2] (6). While 2, 3, and 4 possess a very distorted pentagonal bipyramidal structure, 5 has a distorted octahedral geometry. In the solid state, as well as in solution, 5 exists as two apparently enantiomerically related molecules differing in the orientation of the pendant phenyl rings. To emphasize that the formation and structural uniqueness of 5 compared to 1-4 is caused by the influence of the cinnamoyl residue, one compound of the 6 series, namely, [Mo(O)2(BPHA)2] (6A), was structurally characterized to prove directly that the special stereochemical properties of 5 rely on the special electronic structure of CPHA- ligand. Complexes 1-5, as well as 6, show high potential and selectivity as catalysts in the epoxidation of olefins at room temperature in the presence of NaHCO3 as a promoter and H2O2 as a terminal oxidant. A comparative epoxidation study has been performed to determine the relative efficiency of the catalysts. To make the epoxidation method cost effective, a study to optimize the use of H2O2 has also been performed. To obtain evidence in favor of our suggested mechanism to this homogeneous olefin --> epoxide conversion, it was necessary to synthesize a peroxo-rich compound, namely, [MoO(O2)2BMTHA]- (7), but the attempted synthesis culminated in the isolation of [MoO(O2)2(C6H5COO)]- (8), obviously, via the hydrolysis of coordinated BMTHA.     

Conformational analysis of some C2-symmetric cyclic peptides containing tetrahydrofuran amino acids

Cyclic oligomers of tetrahydrofuran amino acids, cyclo-(Taa1-Leu-Val)2 (left), cyclo-(Taa2-Leu-Val)2 (middle), and cyclo-(Taa2-Phe-Leu)2 (right), displayed well-defined intramolecularly hydrogen-bonded structures with distorted "beta-beta corner" motifs similar to the tennis ball seam.