A New Improved Procedure for the Synthesis of 4-Formylcarane - Precursor to Sandatrile, a Novel Perfumery Chemical

Stereospecific synthesis of 4-formylcarane (2) has been achieved through hydroboration-carbonylation of DELTA-3-carene. Both the reactions are optimised using sodium borohydride. The method is utilised for the synthesis of sandatrile (3), a novel perfumery chemical.

The potential of microbial ecological indicators to guide ecosophisticated management of hydrocarbon-contaminated soils

Soil is an unrenewable natural resource under increasing anthropogenic pressure. One of the main threats to soils, compromising their ability to provide us with the goods and ecosystem services we expect, is pollution. Oil hydrocarbons are the most common soil contaminants, and they disturb not just the biota but also the physicochemical properties of soils. Indigenous soil micro-organisms respond rapidly to changes in the soil ecosystem, and are chronically in direct contact with the hydrophobic pollutants on the soil surfaces. Soil microbial variables could thus serve as an intrinsically relevant indicator of soil quality, to be used in the ecological risk assessment of contaminated and remediated soils. Two contrasting studies were designed to investigate soil microbial ecological responses to hydrocarbons, together with parallel changes in soil physicochemical and ecotoxicological properties. The aim was to identify quantitative or qualitative microbiological variables that would be practicable and broadly applicable for the assessment of the quality and restoration of oil-polluted soil. Soil bacteria commonly react on hydrocarbons as a beneficial substrate, which lead to a positive response in the classical microbiological soil quality indicators; negative impacts were accurately reflected only after severe contamination. Hydrocarbon contaminants become less bioavailable due to weathering processes, and their potentially toxic effects decrease faster than the total concentration. Indigenous hydrocarbon degrader bacteria, naturally present in any terrestrial environment, use specific mechanisms to improve access to the hydrocarbon molecules adsorbed on soil surfaces. Thus when contaminants are unavailable even to the specialised degraders, they should pose no hazard to other biota either. Change in the ratio of hydrocarbon degrader numbers to total microbes was detected to predictably indicate pollutant effects and bioavailability. Also bacterial diversity, a qualitative community characteristic, decreased as a response to hydrocarbons. Stabilisation of community evenness, and community structure that reflected clean reference soil, indicated community recovery. If long-term temporal monitoring is difficult and appropriate clean reference soil unavailable, such comparison could possibly be based on DNA-based community analysis, reflecting past+present, and RNA-based community analysis, showing exclusively present conditions. Microbial ecological indicators cannot replace chemical oil analyses, but they are theoretically relevant and operationally practicable additional tools for ecological risk assessment. As such, they can guide ecologically informed and sustainable ecosophisticated management of oil-contaminated lands.

Dynamic coupling between the LID and NMP domain motions in the catalytic conversion of ATP and AMP to ADP by adenylate kinase

The catalytic conversion of adenosine triphosphate (ATP) and adenosine monophosphate (AMP) to adenosine diphosphate (ADP) by adenylate kinase (ADK) involves large amplitude, ligand induced domain motions, involving the opening and the closing of ATP binding domain (LID) and AMP binding domain (NMP) domains, during the repeated catalytic cycle. We discover and analyze an interesting dynamical coupling between the motion of the two domains during the opening, using large scale atomistic molecular dynamics trajectory analysis, covariance analysis, and multidimensional free energy calculations with explicit water. Initially, the LID domain must open by a certain amount before the NMP domain can begin to open. Dynamical correlation map shows interesting cross-peak between LID and NMP domain which suggests the presence of correlated motion between them. This is also reflected in our calculated two-dimensional free energy surface contour diagram which has an interesting elliptic shape, revealing a strong correlation between the opening of the LID domain and that of the NMP domain. Our free energy surface of the LID domain motion is rugged due to interaction with water and the signature of ruggedness is evident in the observed root mean square deviation variation and its fluctuation time correlation functions. We develop a correlated dynamical disorder-type theoretical model to explain the observed dynamic coupling between the motion of the two domains in ADK. Our model correctly reproduces several features of the cross-correlation observed in simulations. (C) 2011 American Institute of Physics. doi:10.1063/1.3516588]

Surface Chemistry of Thiobacillus ferrooxidans Relevant to Adhesion on Mineral Surfaces

Thiobacillus ferrooxidans cells grown on sulfur, pyrite, and chalcopyrite exhibit greater hydrophobicity than ferrous ion-grown cells. The isoelectric points of sulfur-, pyrite-, and chalcopyrite-grown cells were observed to be at a pH higher than that for ferrous ion-grown cells. Microbe-mineral interactions result in change in the surface chemistry of the organism as well as that of the minerals with which it has interacted. Sulfur, pyrite, and chalcopyrite after interaction with T. ferrooxidans exhibited a significant shift in their isoelectric points from the initial values exhibited by uninteracted minerals. With antibodies raised against sulfur-grown T. ferrooxidans, pyrite- and chalcopyrite-grown cells showed immunoreactivity, whereas ferrous ion-grown cells failed to do so. Fourier transform infrared spectroscopy of sulfur-grown cells suggested that a proteinaceous new cell surface appendage synthesized in mineral-grown cells brings about adhesion to the solid mineral substrates. Such an appendage was found to be absent in ferrous ion-grown cells as it is not required during growth in liquid substrates.

Thermomechanical behaviour of pin joints subjected to sheet loads

An important problem regarding pin joints in a thermal environment is addressed. The motivation emerges from structural safety requirements in nuclear and aerospace engineering. A two-dimensional model of a smooth, rigid misfit pin in a large isotropic sheet is considered as an abstraction. The sheet is subjected to a biaxial stress system and far-field unidirectional heat flow. The thermoelastic analysis is complex due to non-linear load-dependent contact and separation conditions at the pin-hole interface and the absence of existence and uniqueness theorems for the class of frictionless thermoelastic contact problems. Identification of relevant parameters and appropriate synthesis of thermal and mechanical variables enables the thermomechanical generalization of pin-joint behaviour. This paper then proceeds to explore the possibility of multiple solutions in such problems, especially interface contact configuration.

Characterization of substrate UpA binding to RNase A--computer modelling and energetics approach.

In the past two decades RNase A has been the focus of diverse investigations in order to understand the nature of substrate binding and to know the mechanism of enzyme action. Although this system is reasonably well characterized from the view point of some of the binding sites, the details of interactions in the second base binding (B2) site is insufficient. Further, the nature of ligand-protein interaction is elucidated generally by studies on RNase A-substrate analog complexes (mainly with the help of X-ray crystallography). Hence, the details of interactions at atomic level arising due to substrates are inferred indirectly. In the present paper, the dinucleotide substrate UpA is fitted into the active site of RNase A Several possible substrate conformations are investigated and the binding modes have been selected based on Contact Criteria. Thus identified RNase A-UpA complexes are energy minimized in coordinate space and are analysed in terms of conformations, energetics and interactions. The best possible ligand conformations for binding to RNase A are identified by experimentally known interactions and by the energetics. Upon binding of UpA to RNase A the changes associated,with protein back bone, Side chains in general and at the binding sites in particular are described. Further, the detailed interactions between UpA and RNase A are characterized in terms of hydrogen bonds and energetics. An extensive study has helped in interpreting the diverse results obtained from a number of experiments and also in evaluating the extent of changes the protein and the substrate undergo in order to maximize their interactions.

The mechanical response of tetragonal zirconia polycrystal to conical indentation

Blocks of 3Y-TZP were indented with conical diamond indenters. indentation caused tetragonal to monoclinic phase transformation in a subsurface. Of the cracks generated in the subsurface, radial and lateral cracks can be accounted for by a continuum model of the indented subsurface, built using a combination of the Boussinesq and blister stress fields. Additional ring, median and cone cracks were also observed. It is hypothesized that the latter are motivated by the reduction in blister strength or residual energy brought about by the material damage caused by the phase transformation. This damage reduces the load bearing capacity of the material progressively with increasing normal load.

Application of scaled particle theory to alkyl-aryl surfactants: a two zone model of micellar core

Scaled Particle Theory (SPT) has been applied to predict the total free energies of micellization of ionic as well as nonionic micellar systems containing an aryl ring. A modification of the previously developed model has been made, proposing a two-zone model of micellar core which corroborates with the structural information available for such systems. The results are in good agreement with experimental data and also confirm the dictating role of cavity forming free energies for such systems

Breakage of a drop of inviscid fluid due to a pressure fluctuation at its surface

In this work, an attempt is made to gain a better understanding of the breakage of low-viscosity drops in turbulent flows by determining the dynamics of deformation of an inviscid drop in response to a pressure variation acting on the drop surface. Known scaling relationships between wavenumbers and frequencies, and between pressure fluctuations and velocity fluctuations in the inertial subrange are used in characterizing the pressure fluctuation. The existence of a maximum stable drop diameter d(max) follows once scaling laws of turbulent flow are used to correlate the magnitude of the disruptive forces with the duration for which they act. Two undetermined dimensionless quantities, both of order unity, appear in the equations of continuity, motion, and the boundary conditions in terms of pressure fluctuations applied on the surface. One is a constant of proportionality relating root-mean-square values of pressure and velocity differences between two points separated by a distance l. The other is a Weber number based on turbulent stresses acting on the drop and the resisting stresses in the drop due to interfacial tension. The former is set equal to 1, and the latter is determined by studying the interaction of a drop of diameter equal to d(max) with a pressure fluctuation of length scale equal to the drop diameter. The model is then used to study the breakage of drops of diameter greater than d(max) and those with densities different from that of the suspending fluid. It is found that, at least during breakage of a drop of diameter greater than d(max) by interaction with a fluctuation of equal length scale, a satellite drop is always formed between two larger drops. When very large drops are broken by smaller-length-scale fluctuations, highly deformed shapes are produced suggesting the possibility of further fragmentation due to instabilities. The model predicts that as the dispersed-phase density increases, d(max) decreases.

Novel geodesic splitting on paraboloid of revolution with applications to ray-theoretic analysis

Computer simulations have shown a novel geodesic splitting on the paraboloid of revolution leading to a multiplicity of surface ray paths. Such a phenomenon would have wide ramifications for wave propagation problems in general, besides applications in target-detection problems and the computational requirements of ray-theoretic formulations such as the UTD, in computing the antenna characteristics in the high-frequency domain.

Production of Dirac particles due to riccion coupling

It has been noted that at high energy the Ricci scalar is manifested in two different ways, as a matter field as well as a geometrical field (which is its usual nature even at low energy). Here, using the material aspect of the Ricci scalar, its interaction with Dirac spinors is considered in four-dimensional curved spacetime. We find that a large number of fermion-antifermion pairs can be produced by the exponential expansion of the early universe.

Stabilisation of unusual simultaneous binding of four cytosine nucleobases to copper(II) by a novel network of bifurcated hydrogen bonding

The crystal structure of tetrakis(cytosine)copper(II) perchlorate dihydrate has been determined. All the hydrogen atoms were obtained from Fourier-difference synthesis. The geometry around. copper is a bicapped octahedron (4 + 2 + 2*). The adjacent cytosine rings are oriented head-to-tail with respect to each other and are roughly at right angles to the co-ordination plane. The exocyclic oxo groups form an interligand, intracomplex hydrogen-bonding network above and below the co-ordination plane with the exocyclic amino groups of alternate cytosine bases. The EPR and electronic spectra are consistent with the retention of the solid-state structure in solution. The steric effect of the C(2)=O group of cytosine is offset by the presence of the intracomplex hydrogen-bonding network. The trend in Ei values of Cu-II-Cu-I couples for 1.4 complexes of cytosine, cytodine, pyridine, 2-methylpyridine and N-methylimidazole suggests that both steric effects and pi-delocalization in imidazole and pyridine ligands and the steric effect of C(2)=O in pyrimidine ligands are important in stabilising Cu-I relative to Cu-II.

Responsiveness of human male volunteers to immunization with ovine follicle stimulating hormone vaccine: Results of a pilot study

A study of 140 days duration was performed to examine if human male volunteers (n = 5) respond to ovine follicle stimulating hormone (oFSH) immunization (administered adsorbed on Alugel on days 1, 20, 40 and 70) by producing antibodies capable of both binding and neutralizing bioactivity of human FSH. The kinetics of antibody production for both the immunogen (oFSH) and the cross-reactive antigen (hFSH) were essentially similar, The volunteers responded only to the first two immunizations, The boosters given on days 40 and 70 were ineffective, probably because of the presence of substantial amounts of circulating antibody to oFSH. Of the antibodies generated to oFSH, 25-45% bound hFSH with a mean binding affinity of 0.65 x 10(9) +/- 0.53 M(-1). The binding capacities at the time of high (30-80 days of immunization) and low (>110 days) titres were 346 +/- 185 and 10.5 +/- 5.8 ng hFSH/ml respectively, During the period of high titre, free serum FSH (value in normal males 1-5 ng/ml) was not monitorable, A 50 mu l aliquot of the antiserum obtained from different volunteers between days 30 and 80 and on day 140 blocked binding of I-125-labelled hFSH to its receptor by 82 +/- 9.7 and 53 +/- 12.2% respectively, The antibody produced was specific for FSH, and no significant change in the values of related glycoprotein hormones (luteinizing hormone/testosterone and thyroid stimulating hormone/thyroxine) were recorded, Seminal plasma transferrin, a marker of Sertoli cell as well as of seminiferous tubular function, showed marked reduction (30-90%) following immunization with oFSH. Considering that endogenous FSH remained neutralized for approximately one sperm cycle only (65 days), the reduction in sperm counts (30-74%) exhibited by some volunteers is encouraging, Immunization with oFSH did not result in any significant changes in haematology, serum biochemistry or hormonal profiles, There was no production of antibodies capable of interacting with non-specific tissues, It is concluded that it should be possible to obtain a sustained long-term blockade of endogenous FSH action in men by using oFSH as an immunogen, This is a prerequisite for obtaining significant reduction in the quality and quantity of spermatozoa produced, thus leading to infertility.

Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions

In this article, we present a novel application of a quantum clustering (QC) technique to objectively cluster the conformations, sampled by molecular dynamics simulations performed on different ligand bound structures of the protein. We further portray each conformational population in terms of dynamically stable network parameters which beautifully capture the ligand induced variations in the ensemble in atomistic detail. The conformational populations thus identified by the QC method and verified by network parameters are evaluated for different ligand bound states of the protein pyrrolysyl-tRNA synthetase (DhPylRS) from D. hafniense. The ligand/environment induced re-distribution of protein conformational ensembles forms the basis for understanding several important biological phenomena such as allostery and enzyme catalysis. The atomistic level characterization of each population in the conformational ensemble in terms of the re-orchestrated networks of amino acids is a challenging problem, especially when the changes are minimal at the backbone level. Here we demonstrate that the QC method is sensitive to such subtle changes and is able to cluster MD snapshots which are similar at the side-chain interaction level. Although we have applied these methods on simulation trajectories of a modest time scale (20 ns each), we emphasize that our methodology provides a general approach towards an objective clustering of large-scale MD simulation data and may be applied to probe multistate equilibria at higher time scales, and to problems related to protein folding for any protein or protein-protein/RNA/DNA complex of interest with a known structure.