An ab-initio study of the proton affinity of conjugated schiff-base and related nitrogen compounds: an analysis of the triggering site of bacteriorhodopsin

The chemical groups which take part in the proton transfer reaction in bacteriorhodopsin have been studied by ab initio quantum chemical methods. The various factors such as conjugation with a linear system, electron delocalization of the guanidine type, cis-trans isomerism, geometry distortion and hydrogen bonding with charged groups can influence the properties of a given chemical group. Several systems are studied at 4-31G and STO-3G levels. Some of the Schiff-base analogues and guanidine type molecules are characterized by their molecular orbital diagrams, energy levels and the nature of charge distribution. Also, the effects of the above-mentioned factors on proton affinity are studied. It is hoped that the values thus obtained can be helpful in evaluating various structural models for proton transfer.

Ab initio studies on the tri- and diphosphate fragments of adenosine triphosphate

Pyrophosphate prototypes such as methyl triphosphate and methyl diphosphate molecules in their different protonation states have been investigated at high levels of quantum chemical calculations. The optimized geometries, the thermochemistry of the hydrolysis and the molecular orbitals contributing to the high energy of these compounds have been analyzed. These investigations provide insights into the "high energy" character of ATP molecule. Further, the dependence of vibrational frequencies on the number of phosphate groups and the charged states has also been presented. These results can aid the interpretation of spectra obtained by experiments on complexes containing pyrophosphate prototypes.

Studies on a nanocomposite solid polymer electrolyte with hydrotalcite as a filler

We have prepared a new nanocomposite polymer electrolyte using nanoparticles of hydrotalcite, an anionic clay, as the filler. Hydrotalcite has the chemical composition [M-1-x(2+) M-x(3+) (OH)(2)](x+) [A(x/n)(n-)center dot mH(2)O] where M2+ is a divalent cation (e.g. Mg2+, Ni2+, Co2+,etc.) and M3+ is a trivalent cation (e.g. Al3+, Fe3+, Cr3+, etc.). A(n-) is an anion intercalated between the positively charged double hydroxide layers. The nanoparticles of [Mg0.67Al0.33 (OH)(2)] [(CO3)(0.17)center dot mH(2)O] were prepared by the co-precipitation method (average particle size as observed by TEM similar to 50 nm) and were doped into poly(ethylene glycol) PEG (m.w.2000) complexed with LiCIO4. Samples with different wt.% of hydrotalcite were prepared and characterized using XRD, DSC, TGA, impedance spectroscopy and NMR. Ionic conductivity for the pristine sample, similar to 7.3 x 10(-7) S cm(-1), was enhanced to a maximum of = 1.1 x 10(-5) S cm(-1) for 3.6 wt.% nanoparticle doped sample. We propose that the enhancement of ionic conductivity is caused by percolation effects of the high conductivity paths provided by interfaces between the nanoparticles and the polymer electrolyte. (C) 2010 Elsevier B.V. All rights reserved.

Synergistic use of thermogravimetric and electrochemical techniques for thermodynamic study of TiOx (1.67 <= x <= 2.0) at 1573 K

A thermodynamic study of the Ti-O system at 1573 K has been conducted using a combination of thermogravimetric and emf techniques. The results indicate that the variation of oxygen potential with the nonstoichiometric parameter delta in stability domain of TiO2-delta with rutile structure can be represented by the relation, Delta mu o(2) = -6RT In delta - 711970(+/-1600) J/mol. The corresponding relation between non-stoichiometric parameter delta and partial pressure of oxygen across the whole stability range of TiO2-delta at 1573 K is delta proportional to P-O2(-1/6). It is therefore evident that the oxygen deficient behavior of nonstoichiometric TiO2-delta is dominated by the presence of doubly charged oxygen vacancies and free electrons. The high-precision measurements enabled the resolution of oxygen potential steps corresponding to the different Magneli phases (Ti-n O2n-1) up to n = 15. Beyond this value of n, the oxygen potential steps were too small to be resolved. Based on composition of the Magneli phase in equilibrium with TiO2-delta, the maximum value of n is estimated to be 28. The chemical potential of titanium was derived as a function of composition using the Gibbs-Duhem relation. Gibbs energies of formation of the Magneli phases were derived from the chemical potentials of oxygen and titanium. The values of -2441.8(+/-5.8) kJ/mol for Ti4O7 and -1775.4(+/-4.3) kJ/mol for Ti3O5 Obtained in this study refine values of -2436.2(+/-26.1) kJ/mol and-1771.3(+/-6.9) kJ/mol, respectively, given in the JANAF thermochemical tables.

Interaction of synthetic analogs of distamycin and netropsin with nucleic acids. Does curvature of ligand play a role in distamycin-DNA interactions?

Distamycin and netropsin, a class of minor groove binding nonintercalating agents, are characterized by their B-DNA and A-T basespecific interactions. To understand the CQI I ~OIT~ ~ I ~ ~aOnMd ~c hemical basis of the above specificities, the DNA-binding characteristics of a novel synthetic analogue of distamycin have been studied. The analogue, mPD derivative, has the requisite charged end groups and a number of potential hydrogen-bonding loci equal to those of distamycin. The difference in the backbone curvatures of the ligands, distamycin, the mPD derivative, and NSC 101327 (another structurally analogous compound),is a major difference between these ligands. UV and CD spectrosoopic studies reported here show the following salient features: The mPD derivative recognizes only B-DNA, to which it binds via the minor groove. On the other hand, unlike distamycin, it binds with comparable affinities to A-T and G-C base pairs in a natural DNA. These DNA-binding properties are compared with those reported earlier for distamycin and NSC 101327 [Zimmer, Ch., & Wahnert, U. (1986) Prog. Biophys. Mol. Biol. 47, 31-1121. The backbone structures of these three ligands were compared to show the progressive decrease in curvatures in the order distamycin, mPD derivative, and NSC 101327. The plausible significance of the backbone curvature vis-&vis the characteristic B-DNA and AT-specific binding of distamycin is discussed. To our knowledge, this is the first attempt (with a model synthetic analogue) to probe the possible influence of backbone curvature upon the specificity of interactions of the distamycin class of groove-binding ligands with DNA.

Ab initio studies on the tri- and diphosphate fragments of adenosine triphosphate

Pyrophosphate prototypes such as methyl triphosphate and methyl diphosphate molecules in their different protonation states have been investigated at high levels of quantum chemical calculations. The optimized geometries, the thermochemistry of the hydrolysis and the molecular orbitals contributing to the high energy of these compounds have been analyzed. These investigations provide insights into the ``high energy'' character of ATP molecule. Further, the dependence of vibrational frequencies on the number of phosphate groups and the charged states has also been presented. These results can aid the interpretation of spectra obtained by experiments on complexes containing pyrophosphate prototypes. (c) 2005 Elsevier B.V. All rights reserved.

Effect of electric field on ammonium perchlorate decomposition

A novel method of detecting the charge-carrying species in inorganic decomposable salts is described. In ammonium perchlorate it is observed that the charge-carrying species at temperatures 150 and 230°C are oppositely charged; i.e., they are negatively charged (ClO−4 ions) at 230°C and positively charged (H+ or NH+4) at 150°C.

A kinetic Ising model study of dynamical correlations in confined fluids: Emergence of both fast and slow time scales

Experiments and computer simulation studies have revealed existence of rich dynamics in the orientational relaxation of molecules in confined systems such as water in reverse micelles, cyclodextrin cavities, and nanotubes. Here we introduce a novel finite length one dimensional Ising model to investigate the propagation and the annihilation of dynamical correlations in finite systems and to understand the intriguing shortening of the orientational relaxation time that has been reported for small sized reverse micelles. In our finite sized model, the two spins at the two end cells are oriented in the opposite directions to mimic the effects of surface that in real system fixes water orientation in the opposite directions. This produces opposite polarizations to propagate inside from the surface and to produce bulklike condition at the center. This model can be solved analytically for short chains. For long chains, we solve the model numerically with Glauber spin flip dynamics (and also with Metropolis single-spin flip Monte Carlo algorithm). We show that model nicely reproduces many of the features observed in experiments. Due to the destructive interference among correlations that propagate from the surface to the core, one of the rotational relaxation time components decays faster than the bulk. In general, the relaxation of spins is nonexponential due to the interplay between various interactions. In the limit of strong coupling between the spins or in the limit of low temperature, the nature of relaxation of the spins undergoes a qualitative change with the emergence of a homogeneous dynamics where decay is predominantly exponential, again in agreement with experiments. (C) 2010 American Institute of Physics. doi: 10.1063/1.3474948]

Identifying N60D mutation in omega subunit of Escherichia coli RNA polymerase by bottom-up proteomic approach

Escherichia coli RNA polymerase is a multi-subunit enzyme containing alpha(2)beta beta'omega sigma, which transcribes DNA template to intermediate RNA product in a sequence specific manner. Although most of the subunits are essential for its function, the smallest subunit omega (average molecular mass similar to 10,105 Da) can be deleted without affecting bacterial growth. Creating a mutant of the omega subunit can aid in improving the understanding of its role. Sequencing of rpoZ gene that codes for omega subunit from a mutant variant suggested a substitution mutation at position 60 of the protein: asparagine (N) -> aspartic acid (D). This mutation was verified at the protein level by following a typical mass spectrometry (MS) based bottom-up proteomic approach. Characterization of in-gel trypsin digested samples by reverse phase liquid chromatography (LC) coupled to electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) enabled in ascertaining this mutation. Electron transfer dissociation (ETD) of triply charged (M + 3H)(3+)] tryptic peptides (residues 53-67]), EIEEGLINNQILDVR from wild-type and EIEEGLIDNQILDVR from mutant, facilitated in unambiguously determining the site of mutation at residue 60.

Effect of electric field on ammonium perchlorate decomposition

A novel method of detecting the charge-carrying species in inorganic decomposable salts is described. In ammonium perchlorate it is observed that the charge-carrying species at temperatures 150 and 230°C are oppositely charged; i.e., they are negatively charged (ClO−4 ions) at 230°C and positively charged (H+ or NH+4) at 150°C.

Computer modelling studies on the mechanism of action of ribonuclease T1

The mechanism of action of ribonuclease (RNase) T1 is still a matter of considerable debate as the results of x-ray, 2-D nmr and site-directed mutagenesis studies disagree regarding the role of the catalytically important residues. Hence computer modelling studies were carried out by energy minimisation of the complexes of RNase T1 and some of its mutants (His40Ala, His40Lys, and Glu58Ala) with the substrate guanyl cytosine (GpC), and of native RNase T1 with the reaction intermediate guanosine 2',3'-cyclic phosphate (G greater than p). The puckering of the guanosine ribose moiety in the minimum energy conformer of the RNase T1-GpC (substrate) complex was found to be O4'-endo and not C3'-endo as in the RNase T1-3'-guanylic acid (inhibitor/product) complex. A possible scheme for the mechanism of action of RNase T1 has been proposed on the basis of the arrangement of the catalytically important amino acid residues His40, Glu58, Arg77, and His92 around the guanosine ribose and the phosphate moiety in the RNase T1-GpC and RNase T1-G greater than p complexes. In this scheme, Glu58 serves as the general base group and His92 as the general acid group in the transphosphorylation step. His40 may be essential for stabilising the negatively charged phosphate moiety in the enzyme-transition state complex.

Synthesis of graphene oxide-intercalated alpha-hydroxides by metathesis and their decomposition to graphene/metal oxide composites

Graphene oxide-intercalated alpha-metal hydroxides were prepared using layers from the delaminated colloidal dispersions of cetyltrimethylammonium-intercalated graphene oxide and dodecylsulfate-intercalated alpha-hydroxide of nickel/cobalt as precursors. The reaction of the two dispersions leads to de-intercalation of the interlayer ions from both the layered solids and the intercalation of the negatively charged graphene oxide sheets between the positively charged layers of the alpha-hydroxide. Thermal decomposition of the intercalated solids yields graphene/nanocrystalline metal oxide composites. Electron microscopy analysis of the composites indicates that the nanoparticles are intercalated between graphene layers. (C) 2010 Elsevier Ltd. All rights reserved.

Inertial effects in solvation dynamics

The dynamics of solvation of newly created charged species in dense dipolar liquids can proceed at a high speed with time constants often in the subpicosecond domain. The motion of the solvent molecules can be in the inertial limit at such short times. In this paper we present a microscopic study of the effects of inertial motion of solvent molecules on the solvation dynamics of a newly created ion in a model dipolar liquid. Interesting dynamical behavior emerges when the relative contribution of the translational modes in the wave-vector-dependent longitudinal relaxation time is significant. Especially, the theory predicts that the time correlation function of the solvation energy can become oscillatory in some limiting situations. In general, the dynamics becomes faster in the presence of the inertial contribution. We discuss the experimental situations where the inertial effects can be noticeable.

Isolation and characterization of a naturally occurring inhibitor from mung bean (Vigna radiata) seedlings for serine hydroxymethyltransferase

A naturally occurring inhibitor of serine hydroxymethyltransferase (EC2.1.2.1) in mung bean seedlings extracts was purified by ammonium sulphate precipitation, phenyl-Sepharose chromatography followed by heating to release the inhibitor bound to the protein. The inhibitor had an absorption maximum at 200 nm, was not precipitated by trichloroacetic acid, was dialysable and resistant to inactivation by heating at 98-degrees-C for 4 hr, protease and ribonuclease digestion; but was acid labile. The chromatographically pure preparation inhibited both mung bean and sheep liver SHMT. Qualitative and quantitative analyses indicated that it contained a carbohydrate moiety, an O-amino and vicinal diol groups. Paper electrophoresis at pH 4.3 suggested that the inhibitor was positively charged.

Solitons of Coupled Scalar Field Theories in Two Dimensions

This work offers a method for finding some exact soliton solutions to coupled relativistic scalar field theories in 1+1 dimensions. The method can yield static solutions as well as quasistatic "charged" solutions for a variety of Lagrangians. Explicit solutions are derived as examples. A particularly interesting class of solutions is nontopological without being either charged or time dependent.