Singular value decomposition of torsional angles of analogs of the dopamine reuptake inhibitor GBR 12909

Analysis of large, flexible molecules, such as the dopamine reuptake inhibitor GBR 12909 (1), is complicated by the fact that they can take on a wide range of closely related conformations. The first step in the analysis is to classify the conformers into groups. Here, Singular Value Decomposition (SVD) was used to group conformations of GBR 12909 analogs by the similarity of their nonring torsional angles. The significance of the present work, the first application of SVD to the analysis of very flexible molecules, lies in the development of a novel scaling technique for circular data and in the grouping of molecular conformations using a technique that is independent of molecular alignment. Over 700 conformers each of a piperazine (2) and piperidine (3) analog of 1 were studied. Analysis of the score and loading plots showed that the conformers of 2 separate into three large groups due to torsional angles on the naphthalene side of the molecule, whereas those of 3 separate into nine groups due to torsional angles on the bisphenyl side of the molecule. These differences are due to nitrogen inversion at the unprotonated piperazinyl nitrogen of 2, which results in a different ensemble of conformers than those of 3, where no inversion is possible at the corresponding piperidinyl carbon.     

Estimation of intramolecular hydrogen bond energy via molecular tailoring approach

A novel method, based on the molecular tailoring approach for estimating intramolecular hydrogen bond energies, is proposed. Here, as a case study, the O-H...O bond energy is directly estimated by addition/subtraction of the single point individual fragment energies. This method is tested on polyhydroxy molecules at MP2 and B3LYP levels of theory. It is seen to be able to distinguish between weak ( approximately 1 kcal mol(-1)) and moderately strong ( approximately 5 kcal mol(-1)) hydrogen bonds in polyhydroxy molecules.     

A Highly Thermostable Alkaline Cellulase-Free Xylanase from Thermoalkalophilic <Emphasis Type="Italic">Bacillus</Emphasis> sp. JB 99 Suitable for Paper and Pulp Industry: Purification and Characterization

A highly thermostable alkaline xylanase was purified to homogeneity from culture supernatant of Bacillus sp. JB 99 using DEAE-Sepharose and Sephadex G-100 gel filtration with 25.7-fold increase in activity and 43.5% recovery. The molecular weight of the purified xylanase was found to be 20 kDA by SDS-PAGE and zymogram analysis. The enzyme was optimally active at 70 °C, pH 8.0 and stable over pH range of 6.0–10.0.The relative activity at 9.0 and 10.0 were 90% and 85% of that of pH 8.0, respectively. The enzyme showed high thermal stability at 60 °C with 95% of its activity after 5 h. The K _m and V _max of enzyme for oat spelt xylan were 4.8 mg/ml and 218.6 μM min⁻¹ mg⁻¹, respectively. Analysis of N-terminal amino acid sequence revealed that the xylanase belongs to glycosyl hydrolase family 11 from thermoalkalophilic Bacillus sp. with basic pI. Substrate specificity showed a high activity on xylan-containing substrate and cellulase-free nature. The hydrolyzed product pattern of oat spelt xylan on thin-layer chromatography suggested xylanase as an endoxylanase. Due to these properties, xylanase from Bacillus sp. JB 99 was found to be highly compatible for paper and pulp industry.     

Molecular interpretation of water structuring and destructuring effects: hydration of alkanediols

Molecular electrostatic potential (MESP) guidelines are employed for understanding the reactivity and hydration patterns in alkanediol molecules. The deeper oxygen lone pair MESP minima indicate stronger basicity of 1,n-diols and 2,4-pentanediol (2,4-PeD) as compared to that of vicinal diols. The existence and strength of the intramolecular hydrogen bond in diols are gauged in terms of the electron density at the bond saddle points. A model named electrostatic potential for intermolecular complexation (EPIC) is used for generating the structures of hydrated complexes, which are subsequently subjected to ab initio calculations at M?ller-Plesset second-order perturbation level of theory. Further, the nature of water...water as well as diol...water interactions is appraised employing many-body energy decomposition analysis. It is seen that water...water interactions are more favorable in vicinal diol...6H(2)O than those in 1,n-diol...6H(2)O (n=3, 4, 5,...) complexes. Exactly opposite trends are shown by diol...water interaction energies. Thus vicinal diols, being more effective at strengthening water...water network, are expected to act as water structuring agents, whereas the non-vicinal diols are expected to be water destructuring agents.     

Complex Permittivity Spectra of Binary Pyridine–Amide Mixtures Using Time–Domain Reflectometry

Frequency spectra of the complex permittivity for pyridine–amide binary mixtures have been determined over the frequency range 10 MHz to 10 GHz, at 5, 15, 25, and 40°C, using the time–domain reflectometry method, for 11 compositions of each pyridine–amide system, e.g., formamide, N-methylformamide, and N,N-dimethylformamide. The relaxation in these systems can be described by a single relaxation time using the Debye model. The static dielectric constant, relaxation time, the corresponding excess dielectric properties, Kirkwood correlation factor, and molar activation energy of the mixtures have been determined. The excess permittivity is found to be positive in the amide-rich region and negative in the pyridine-rich region. The excess inverse relaxation time is negative, except in the pyridine-rich region. The static dielectric constants for the mixtures have been fitted with the modified Bruggeman model. The temperature-dependent relaxation times show the expected Arrhenius behavior.     

Asphaltene aggregation in organic solvents

Asphaltenic solids formed in the Rangely field in the course of a carbon dioxide flood and heptane insolubles in the oil from the same field were used in this study. Four different solvents were used to dissolve the asphaltenes. Near-infrared (NIR) spectroscopy was used to determine the onset of asphaltene precipitation by heptane titration. When the onset values were plotted versus asphaltene concentrations, distinct break points (called critical aggregation concentrations (CAC) in this paper) were observed. CACs for the field asphaltenes dissolved in toluene, trichloroethylene, tetrahydrofuran, and pyridine occurred at concentrations of 3.0, 3.7, 5.0, and 8.2 g/l, respectively. CACs are observed at similar concentrations as critical micelle concentrations (CMC) for the asphaltenes in the solvents employed and can be interpreted to be the points at which rates of asphaltene aggregations change. CMC values of asphaltenes determined from surface tension measurements (in pyridine and TCE) were slightly higher than the CAC values measured by NIR onset measurements. The CAC for heptane-insoluble asphaltenes in toluene was 3.1 g/l. Thermal gravimetric analysis (TGA) and elemental compositions of the two asphaltenes showed that the H/C ratio of the heptane-insoluble asphaltenes was higher and molecular weight (measured by vapor pressure osmometry) was lower.     

Synthesis of poly(thio-1,4-phenylene) by oxidative coupling reaction of diphenyl disulfide with potassium persulfate in strongly acidic solutions

The synthesis of poly(thio- 1,4-phenylene) (PPS) at room temperature by the reaction of diphenyl disulfide with potassium persulfate (K₂S₂O₈) in non-basic solvents, in the presence of trifluoromethanesulfonic acid, is reported. The reaction in chlorinated solvents, such as dichloromethane and tetrachloroethane, resulted in partial oxidation of sulfide to sulfoxide and sulfone. On the other hand, the polymerization proceeded well in nitrobenzene and the PPS formed was free of branches, crosslinks and thianthrene units. The molecular weight of the polymers formed in different solvents were in the range 2000–8000. The reaction proceeded under identical conditions with bis(2,6-dimethylphenyl) disulfide as well, but the polymer yield was lower.     

IBX/TEAB-mediated oxidative dimerization of thioamides: synthesis of 3,5-disubstituted 1,2,4-thiadiazoles

Thioamides undergo oxidative dimerization on treatment with hypervalent iodine(V)-containing reagents, particularly o-iodoxybenzoic acid (IBX), in the presence of tetraethylammonium bromide (TEAB) to generate 3,5-disubstituted 1,2,4-thiadiazoles in excellent yield.     

Health risk assessment for nanoparticles: A case for using expert judgment

Uncertainties in conventional quantitative risk assessment typically relate to values of parameters in risk models. For many environmental contaminants, there is a lack of sufficient information about multiple components of the risk assessment framework. In such cases, the use of default assumptions and extrapolations to fill in the data gaps is a common practice. Nanoparticle risks, however, pose a new form of risk assessment challenge. Besides a lack of data, there is deep scientific uncertainty regarding every aspect of the risk assessment framework: (a) particle characteristics that may affect toxicity; (b) their fate and transport through the environment; (c) the routes of exposure and the metrics by which exposure ought to be measured; (d) the mechanisms of translocation to different parts of the body; and (e) the mechanisms of toxicity and disease. In each of these areas, there are multiple and competing models and hypotheses. These are not merely parametric uncertainties but uncertainties about the choice of the causal mechanisms themselves and the proper model variables to be used, i.e., structural uncertainties. While these uncertainties exist for PM2.5 as well, risk assessment for PM2.5 has avoided dealing with these issues because of a plethora of epidemiological studies. However, such studies don’t exist for the case of nanoparticles. Even if such studies are done in the future, they will be very specific to a particular type of engineered nanoparticle and not generalizable to other nanoparticles. Therefore, risk assessment for nanoparticles will have to deal with the various uncertainties that were avoided in the case of PM2.5. Consequently, uncertainties in estimating risks due to nanoparticle exposures may be characterized as ‘extreme’. This paper proposes a methodology by which risk analysts can cope with such extreme uncertainty. One way to make these problems analytically tractable is to use expert judgment approaches to study the degree of consensus and/or disagreement between experts on different parts of the exposure–response paradigm. This can be done by eliciting judgments from a wide range of experts on different parts of the risk causal chain. We also use examples to illustrate how studying expert consensus/disagreement helps in research prioritization and budget allocation exercises. The expert elicitation can be repeated over the course of several years, over which time, the state of scientific knowledge will also improve and uncertainties may possibly reduce. Results from expert the elicitation exercise can be used by risk managers or managers of funding agencies as a tool for research prioritization.     

Unstable flux flow due to heated electrons in superconducting films

A flux instability occurs in superconductors at low temperatures, where e-e scattering is more rapid than e-ph, whereby the dissipation significantly elevates the electronic temperature while maintaining a thermal-like distribution function. The reduction in condensate and rise in resistivity produce a nonmonotonic current-voltage response. In contrast to the Larkin-Ovchinnikov instability where the vortex shrinks, in this scenario the vortex expands and the quasiparticle population rises. Measurements in Y(1)Ba(2)Cu(3)O(7-delta) agree quantitatively with the distinct predictions of this mechanism.