Enhancement of Fe(III), Co(III), and Cr(VI) reduction at elevated temperatures and by a thermophilic bacterium

Applied Biochemistry and Biotechnology - An unusual thermophilic bacterium has been isolated from deep subsurface sediments and tested for its ability to enhance Fe(III), Co(III), and Cr(VI)...     

Quality factors and effective-average modal gain or loss ininhomogeneous spherical resonators: application to two-photon absorption

A method is presented for calculating the quality factors (Q's) and the effective-average gain and loss coefficients for the modes of a dielectric sphere which has a spatial perturbation of the imaginary part of the refractive index. The method is applicable to gain calculations in spherical lasers, to spatial hole burning and to stimulated Raman scattering in spheres. A time-independent perturbation method is also used to compute the Q's of the resonances. Results computed using both methods are compared with analytical results for layered spheres. The methods are used to compute the near-resonance backscattering by a sphere having an intensity-dependent (two-photon absorption) loss     

Positron-hydrogen-like-ion scattering

Scattering of positrons by hydrogen-like-ions (He⁺, Li²⁺, Be³⁺ and B⁴⁺) has been studied using two variants of the polarized orbital method. The positronium formation channel has not been included in the calculations,s-wave phase shifts obtained using the two variants differ appreciably from each other. Moreover, the polarized orbitals-wave phase shifts fore ⁺-B⁴⁺ scattering differ from the corresponding variational results qualitatively in the low energy region. The differential cross sections are reported.     

Computational study of ketosteroid isomerase: insights from molecular dynamics simulation of enzyme bound substrate and intermediate

Delta(5)-3-Ketosteroid Isomerase (KSI) catalyzes the isomerization of 5,6-unsaturated ketosteroids to their 4,5-unsaturated isomers at a rate approaching the diffusion limit. The isomerization reaction follows a two-step general acid-base mechanism starting with Asp38-CO(2)(-) mediated proton abstraction from a sp(3)-hybridized carbon atom, alpha to carbonyl group, providing a dienolate intermediate. In the second step, Asp38-CO(2)H protonates the C6 of the intermediate providing a 4,5-unsaturated ketosteroid. The details of the mechanism have been highly controversial despite several experimental and computational studies of this enzyme. The general acid-base catalysis has been proposed to involve either a catalytic diad or a cooperative hydrogen bond mechanism. In this paper, we report our results from the 1.5 nanosecond molecular dynamics (MD) simulation of enzyme bound natural substrate (E.S) and enzyme bound intermediate (E.In) solvated in a TIP3P water box. The final coordinates from our MD simulation strongly support the cooperative hydrogen bond mechanism. The MD simulation of E.S and E.In shows that both Tyr14 and Asp99 are hydrogen bonded to the O3 of the substrate or intermediate. The average hydrogen bonding distance between Tyr14-OH and O3 becomes shorter and exhibits less fluctuation on E.S --> E.In. We also observe dynamic motions of water moving in and out of the active site in the E.S structures. This free movement of water disappears in the E.In structures. The active site is shielded by hydrophobic residues, which come together and squeeze out the waters from the active site in the E.In complex.     

Computer simulations of trypanosomal nucleoside hydrolase: determination of the protonation state of the bound transition-state analogue

Inosine-uridine nucleoside hydrolase (IU-NH) catalyzes the hydrolysis of nucleosides into base and ribose moieties via a ribooxocarbenium ion transition state, which has been characterized using kinetic isotope effects. Protozoan parasites lack de novo purine and pyrimidine biosynthesis and depend on the purine salvage from the host. Vern Schramm and co-workers characterized p-aminophenyliminoribitol (pAPIR) to be a potent inhibitor of IU-NH from Crithidia fasciculata with K(d) of 30 nM. The cyclic amine function of the iminoribitol ring can be either protonated (pAPIRH(+)) or unprotonated (pAPIR). pAPIRH(+) resembles the charge and geometry of the ribooxocarbenium ion transition state and can be looked upon as a transition-state analogue inhibitor; however, it is known that the pAPIR species is initially bound to the enzyme. We have characterized the pAPIRH(+) species as resident of the active site using ab initio calculations and molecular dynamics simulations. This is a novel use of molecular dynamics to investigate the protonation state of the bound ligand to the active site. Nanosecond molecular dynamics simulations reveal a short hydrogen-bonding network between pAPIRH(+)-O2'-Asp14-His241 triad, which is not seen in the crystal structure. Other features discussed are: hydrogen bonding between pAPIRH(+) and Asn168, unusual geometry of the iminoribitol ring, and hydrophobic interactions.     

Bleaching-resistant,Near-continuous Single-molecule Fluorescence and FRET Based on Fluorogenic and Transient DNA Binding

Photobleaching of fluorescent probes limits the observation span of typical single-molecule fluorescence measurements and hinders observation of dynamics at long timescales. Here, we present a general strategy to circumvent photobleaching by replenishing fluorescent probes via transient binding of fluorogenic DNAs to complementary DNA strands attached to a target molecule. Our strategy allows observation of near-continuous single-molecule fluorescence for more than an hour, a timescale two orders of magnitude longer than the typical photobleaching time of single fluorophores under our conditions. Using two orthogonal sequences, we show that our method is adaptable to Förster Resonance Energy Transfer (FRET) and that can be used to study the conformational dynamics of dynamic structures, such as DNA Holliday junctions, for extended periods. By adjusting the temporal resolution and observation span, our approach enables capturing the conformational dynamics of proteins and nucleic acids over a wide range of timescales.     

Beryllium bonding with noble gas atoms

Quantum chemical calculations were carried out to investigate the nature of the bonding between a neutral Be₃ ring and noble gas atom. Electronic structure calculation for these complexes was carried out at different computational levels in association with natural bond orbital, quantum theory of atoms in molecules, electron localization function, symmetry adapted perturbation theory, and molecular electrostatic potential surface analysis of Be₃ complexes. The Be atoms in the Be₃ moiety are chemically bonded to one another, with the Be Be bond dissociation energy being ~125 kJ mol⁻¹. The Be₃ ring interacts with the noble gases through non-covalent interactions. The binding energies of the noble gas atoms with the Be₃ ring increases with increase in their atomic number. The non-covalent interaction index, density overlap region indicator and independent gradient model analyses reveal the presence of non-covalent inter-fragment interactions in the complexes. Energy decomposition analysis reveals that dispersion plays the major role towards stabilizing these systems.     

Photoquantum Hall Effect and Light‐Induced Charge Transfer at the Interface of Graphene/InSe Heterostructures

The transfer of electronic charge across the interface of two van der Waals crystals can underpin the operation of a new class of functional devices. Among van der Waals semiconductors, an exciting and rapidly growing development involves the “post‐transition” metal chalcogenide InSe. Here, field effect phototransistors are reported where single layer graphene is capped with n‐type InSe. These device structures combine the photosensitivity of InSe with the unique electrical properties of graphene. It is shown that the light‐induced transfer of charge between InSe and graphene offers an effective method to increase or decrease the carrier density in graphene, causing a change in its resistance that is gate‐controllable and only weakly dependent on temperature. The charge transfer at the InSe/graphene interface is probed by Hall effect and photoconductivity measurmentes and it is demonstrated that light can induce a sign reversal of the quantum Hall voltage and photovoltaic effects in the graphene layer. These findings demonstrate the potential of light‐induced charge transfer in gate‐tunable InSe/graphene phototransistors for optoelectronics and quantum metrology.     

The Mechanisms of Rectification in Au|Molecule|Au Devices Based on Langmuir–Blodgett Monolayers of Iron(III) and Copper(II) Surfactants

Langmuir–Blodgett films of metallosurfactants were used in Au|molecule|Au devices to investigate the mechanisms of current rectification.