Stereoselectivity in the addition of hydrogen chloride to cyclohex-1-enecarbonitrile: Possible role of chlorine lone pair-nitrile π-orbital pseudoallylic A1, 3 interaction

The (overall trans) addition of hydrogen chloride to cyclohex-1- enecarbonitrile in anhydrous alcoholic media proceeds to give cis-2-chlorocyclohexanecarboxylate (together with some cis-2- chlorocyclohexanecarboxamide): no corresponding products with the trans-configuration are detectable. In anhydrous ether the addition proceeds to give a single isomer, presumably cis-, of 2-chlorocyclohexanecarbonitrile, indicating that the configuration of the products may not be equilibrium-controlled in alcoholic media. An examination of the steric factors indicates that the transition state for protonation of the presumed intermediate, 2-chlorocyclohexylidenemethylideneimine, leading to cis-product is favoured if interaction between the lateral π-orbital of the C-N double bond and the lone-pairs on the chlorine atom at the 2-position is large. Consideration of interactions in the transition states meets Zimmerman's criticism that invoking A1, 3 interaction existing in ground states to explain product configuration takes insufficient account of the Curtin-Hammett principle.

Asymtotic solution of the Frieman and Book equation for the pair-correlation function

Using Thomé's procedure, the asymptotic solutions of the Frieman and Book equation for the two-particle correlation in a plasma have been obtained in a complete form. The solution is interpreted in terms of the Lorentz distance. The exact expressions for the internal energy and pressure are evaluated and they are found to be a generalization of the result obtained earlier by others.

Quinone Studies—II : Reduction potentials of some 3-substituted phenanthrene quinones

Polarographic reduction potentials of seven 3-substituted phenanthrenequinones have been determined in aqueous dioxan and aqueous ethanol under different pH conditions. The substituent effects on the reduction potentials could be correlated with the Hammett σ- constants (correlation coefficients> 0·995). The possibility of using reduction potentials as an accurate measure of resonance energy has been pointed out.

Chemical potentials of oxygen for fayalite-quartz-lron and fayalite-quartz-magnetite equilibria

The oxygen potentials corresponding to fayalite-quartz-iron (FQI) and fayalite-quartz-magnetite (FQM) equilibria have been determined using solid-state galvanic cells: Pt,Fe + Fe2SiO4 + SiO2/(Y2O3)ZrO2/Fe + \r"FeO,\l"Pt and Pt, Fe3O4 + Fe2SiO4 + SiO2/(Y2O3)ZrO2/Ni + NiO, Pt in the temperature ranges 900 to 1400 K and 1080 to 1340 K, respectively. The cells are written such that the right-hand electrodes are positive. Silica used in this study had the quartz structure. The emf of both cells was found to be reversible and to vary linearly with temperature. From the emf, Gibbs energy changes were deduced for the reactions: 0.106Fe (s) + 2Fe0.947O (r.s.) + SiO2 (qz) → Fe2SiO4 (ol) δG‡= -39,140+ 15.59T(± 150) J mol-1 and 3Fe2SiO4 (ol) + O2 (g) → 2Fe3O4 (sp) + 3SiO2 (qz) δG‡ = -471,750 + 160.06 T±} 1100) J mol-1 The “third-law≓ analysis of fayalite-quartz-wustite and fayalite-quartz-magnetite equilibria gives value for δH‡298 as -35.22 (±0.1) and -528.10 (±0.1) kJ mol-1, respectively, independent of temperature. The Gibbs energy of formation of the spinel form of Fe2SiO4 is derived by com-bining the present results on FQI equilibrium with the high-pressure data on olivine to spinel transformation of Fe2SiO4.

Bond length distortions associated with torsion potentials; ab-initio studies on methanedio

The 4-31G basis set is used to study the bond length variations as functions of dihedral angels in methanediol. This study is compared with O---C---O bond angle optimization studies by Gorenstein and Kar and the possible reason for bond length shorteing in the trans---trans configuration is analysed.

Nonadiabatic charge pumping by oscillating potentials in one dimension: Results for infinite system and finite ring

We study charge pumping when a combination of static potentials and potentials oscillating with a time period T is applied in a one-dimensional system of noninteracting electrons. We consider both an infinite system using the Dirac equation in the continuum approximation and a periodic ring with a finite number of sites using the tight-binding model. The infinite system is taken to be coupled to reservoirs on the two sides which are at the same chemical potential and temperature. We consider a model in which oscillating potentials help the electrons to access a transmission resonance produced by the static potentials and show that nonadiabatic pumping violates the simple sin phi rule which is obeyed by adiabatic two-site pumping. For the ring, we do not introduce any reservoirs, and we present a method for calculating the current averaged over an infinite time using the time evolution operator U(T) assuming a purely Hamiltonian evolution. We analytically show that the averaged current is zero if the Hamiltonian is real and time-reversal invariant. Numerical studies indicate another interesting result, namely, that the integrated current is zero for any time dependence of the potential if it is applied to only one site. Finally we study the effects of pumping at two sites on a ring at resonant and nonresonant frequencies, and show that the pumped current has different dependences on the pumping amplitude in the two cases.

An algorithm to find distant repeats in a pair of protein sequences

Distant repeats between a pair of protein sequences can be exploited to study the various aspects of proteins such as structure-function relationship, disorders due to protein malfunction, evolutionary analysis, etc. An in-depth analysis of the distant repeats would facilitate to establish a stable evolutionary relation of the repeats with respect to their three-dimensional structure. To this effect, an algorithm has been devised to identify the distant repeats in a pair of protein sequences by essentially using the scores of PAM (Percent Accepted Mutation) matrices. The proposed algorithm will be of much use to researchers involved in the comparative study of various organisms based on the amino-acid repeats in protein sequences. (C) 2010 Elsevier B.V. All rights reserved.

Enhanced Pair Hydrophobicity in the Water-Dimethylsulfoxide (DMSO) Binary Mixture at Low DMSO Concentrations

We observe a surprisingly sharp increase in the pair hydrophobicity in the water climethylsulfoxide (DMSO) binary mixture at small DMSO concentrations, with the mole fraction of DMSO (x(D)) in the range 0.12-0.16. The increase in pair hydrophobicity is measured by an increase in the depth of the first minimum in the potential of mean force (PMF) between two methane molecules. However, this enhanced hydrophobicity again weakens at higher DMSO concentrations. We find markedly unusual behavior of the pure binary mixture (in the same composition range) in the diffusion coefficient of DMSO and in the local composition fluctuation of water, We find that, in the said composition range, the average coordination number of the methyl groups (of distinct DMSO) varies between 2.4 and 2.6, indicating the onset of the formation of a chain-like extended connectivity in an otherwise stable tetrahedral network comprising of water and DMSO molecules. We propose that the enhanced pair hydrophobicity of the binary mixture at low DMSO concentrations is due to the participation of the two methane molecules in the local structural order and the emerging molecular associations in the water-DMSO mixture.

Empirical torsional potential functions from protein structure data. Phi- and psi-potentials for non-glycyl amino acid residues.

The torsional potential functions Vt(phi) and Vt(psi) around single bonds N--C alpha and C alpha--C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (phi, psi)-plane with the value of Vtot(phi, psi), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in L-configuration, are Vt(phi) = 1.0 cos (phi + 60 degrees); Vt(psi) = 0.5 cos (psi + 60 degrees) - 1.0 cos (2 psi + 30 degrees) - 0.5 cos (3 psi + 30 degrees). The dipeptide energy maps Vtot(phi, psi) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line psi = 0 degrees. These functions derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.

DNA polymorphism and local variation in base-pair orientation: a theoretical rationale

Basepair stacking calculations have been carried out to understand the conformational polymorphism of DNA and its sequence dependence. The recently developed self-consistent parameter set, which is specially suitable for describing irregular DNA structures, has been used to describe the geometry of a basepair doublet. While for basepairs without any propeller, the favourable stacking patterns do not appear to have very strong features, much more noticeable sequence dependent stacking patterns emerge once a propeller is applied to the basepairs. The absolute minima for most sequences occurs for a doublet geometry close to the B-DNA fibre models. Hence in the B-DNA region, no strong sequence dependent features are found, but the range of doublet geometries observed in the crystal structures generally lie within the low energy contours, obtained from stacking energy calculations. The doublet geometry corresponding to the A-DNA fibre model is not energetically favourable for the purine-pyrimidine sequences, which prefer small roll angle values when the slide has a large negative value as in A-DNA. However positive roll with large negative slide is allowed for GG, GA, AG and the pyrimidine-purine steps. This is consistent with the observed geometries of various steps in A-DNA crystals. Thus the general features of the basepair doublets predicted from these theoretical studies agree very well with the results from crystal structure analysis. However, since most sequences show an overall preference for B-type doublet geometry, the B --> A transition for random sequence DNA cannot be explained on the basis of basepair stacking interactions.

Geometries of the antiproton-nucleus optical potentials at 180 MeV

The moments of the real and the absorptive parts of the antiproton optical potentials are evaluated for the first time to study the geometries of the potentials at 180 MeV. Interesting features are revealed which are found to be comparable to the proton case in general despite the presence of strong annihilation. A few interesting deviations, however, are also found compared to the proton case.

Potentiodynamic behaviour of β-lead dioxide in neutral media at positive potentials

The behaviour of the PbO2 electrode in NaNO3, Na2SO4 NaClO4 and NaCl in the pH range 3.0–10.5 has been studied by cyclic voltammetry. When the electrode is cycled between 0.30 and 1.90 V, a large cathodic current peak appears in the negative scan; in the subsequent cycle, two anodic peaks appear. The addition of H2O2 at low concentrations to the electrolyte also results in two anodic peaks at the same potentials. A number of possible explanations for the appearance of the cathodic peak, and a mechanism for the oxidation of PbO to PbO2 through Pb3O4 corresponding to the two anodic peaks, are proposed.

The influence of lone-pair repulsions on C–C bond lengths: a critical evaluation of the experimental and theoretical evidence

X-Ray structural data, as well as semiempirical and ab initio molecular orbital calculations, reveal no systematic and substantial difference between the C–C bond lengths of cis and trans 1,2-diketones. Additional results on various conformations of 1,2-diimines and 1,2-dithiones follow the same pattern. Therefore, lone-pair repulsions cannot be implicated in the observed lengthening of C–C bonds in isatin and several related molecules. Conjugation in these systems occurs peripherally avoiding the participation of the central C–C bond. Negative hyperconjugative interaction between the oxygen lone pairs and the adjacent C–C σ* orbital is suggested to be the principal reason for the relatively long C–C bond in diketones. This effect is found in both the cis and trans conformations.

Empirical torsional potential functions from protiesn structure DATA Phi- and Psi-Potentials for Non-glycyl Amino Acid Residues

The torsional potential functions Vt(φ) and Vt(ψ) around single bonds N–Cα and Cα-C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (φ, ψ)-plane with the value of Vtot(φ, ψ), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in l-configuration, are Vt(φ) = – 1.0 cos (φ + 60°); Vt(ψ) = – 0.5 cos (ψ + 60°) – 1.0 cos (2ψ + 30°) – 0.5 cos (3ψ + 30°). The dipeptide energy maps Vtot(φ, ψ) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left-handed alpha helix and the C7 conformation, and the relatively high density of points near the line ψ = 0°. These functions, derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.