Thermodynamic investigation of the state of water adsorbed by carbonaceous adsorbents

The state of water adsorbed on active carbons and canal soot was studied using the “chemical potential—entropy—temperature” diagram. In the range of the relative pressures from 0.174 to 1, the state of adsorbed water is similar to the state of a stretched liquid. The molar volume, heat of evaporation, and surface tension of stretched water were calculated at different relative pressures. Near the spinodal, the molar volume of stretched water is 25% higher, and the surface tension is considerably lower compared to water. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 3, pp. 464–468, March, 1997.     

Conformational analysis of [Met5]-enkephalin: Solvation and ionization considerations

[Met5]-Enkephalin has the sequence Tyr-Gly-Gly-Phe-Met. Only the extended conformation of the peptide has been observed by X-ray crystallography. Nuclear magnetic resonance spectroscopy supports the presence of a turn at Gly 3 and Phe 4 in dimethyl sulfoxide. In this study, the peptide conformational states and thermodynamic properties are understood in terms of ionization state and solvent environment. In the calculation, final conformations obtained from multiple independent Monte Carlo simulated annealing conformational searches are starting points for molecular dynamics simulations. In an aqueous environment given by the use of solvation free energy and the zwitterionic state, dominant structural motifs computed are G-P Type II bend, G-G Type II bend, and G-G Type I bend motifs, in order of increasing free energy. In the calculation of the peptide with neutral N- and C-termini and solvation free energy, the extended conformer dominates (by at least a factor of 2.5), and the conformation of another low free energy conformer superimposes well on the pharmacophoric groups of morphine. Neutralization of charge and solvation induce and stabilize the extended conformation, respectively. A mechanism of inter-conversion between the extended conformer and three bent conformers is supported by /-scatter plots, and by the conformer relative free energies. An estimate of the entropy change of receptor unbinding is 8.3 cal K-1 mol-1, which gives rise to a -2.5 kcal/mol entropy contribution to the free energy of unbinding at 25 °C. The conformational analysis methodology described here should be useful in studies on short peptides and flexible protein surface loops that have important biological implications.     

One site fits both: A model for the ternary complex of folate + NADPH in R67 dihydrofolate reductase, a D2 symmetric enzyme

R67 dihydrofolate reductase (DHFR) is a novel enzyme that confers resistance to the antibiotic trimethoprim. The crystal structure of R67 DHFR displays a toroidal structure with a central active-site pore. This homotetrameric protein exhibits 222 symmetry, with only a few residues from each chain contributing to the active site, so related sites must be used to bind both substrate (dihydrofolate) and cofactor (NADPH) in the productive R67 DHFR?NADPH?dihydrofolate complex. Whereas the site of folate binding has been partially resolved crystallographically, an interesting question remains: how can the highly symmetrical active site also bind and orient NADPH for catalysis? To model this ternary complex, we employed DOCK and SLIDE, two methods for docking flexible ligands into proteins using quite different algorithms. The bound pteridine ring of folate (Fol I) from the crystal structure of R67 DHFR was used as the basis for docking the nicotinamide-ribose-P_i (NMN) moiety of NADPH. NMN was positioned by both DOCK and SLIDE on the opposite side of the pore from Fol I, where it interacts with Fol I at the pore's center. Numerous residues serve dual roles in binding. For example, Gln 67 from both the B and D subunits has several contacts with the pteridine ring, while the same residue from the A and C subunits has several contacts with the nicotinamide ring. The residues involved in dual roles are generally amphipathic, allowing them to make both hydrophobic and hydrophilic contacts with the ligands. The result is a `hot spot' binding surface allowing the same residues to co-optimize the binding of two ligands, and orient them for catalysis.     

Ionization of five aqueous fluorobenzoic acids: Conductance and thermodynamics

The three monofluorobenzoic acids together with 2,4-difluoro and 2,6-difluorobenzoic acids in aqueous solution are the subject of precision conductance measurements. The experimental data are analyzed to give ionization constants and limiting conductances at temperatures from 0 to 100°C. Walden products for the acid anions are derived from the limiting conductances while the ionization consatants are fitted by statistical methods to the function pK _a (m)=A+B/T+ C logT+DT. Only the 2,6- acid requires the fourth term of the function to fit the data to a precision of better than 0.03%. Mathematical analysis of the pK function gives the standard changes in enthalpy, entropy, and heat capacity. All the acids studied are more acidic than the parent, benzoic acid, as well as more acidic than the isoelectronic methylbenzoic acids. In general the increased acidity is tied to decreases in enthalpy while entropy changes on ionization differn little from those found for the parent acid.     

Net information measures for modified Yukawa and Hulthén potentials

The dimensional analyses of the position and momentum variances‐based quantum mechanical Heisenberg uncertainty measure, as well as the entropic information measures given by the Shannon information entropy sum and the product of Fisher information measures are carried out for two widely used nonrelativistic isotropic exponential‐cosine screened Coulomb potentials generated by multiplying the superpositions of (i) Yukawa‐like, ?Z(e^?μr/r), and (ii) Hulthén‐like, ?Zμ(1/(e^μr ? 1)), potentials by cos(bμr) followed by addition of the term a/r², where a and b ≥ 0, μ are the screening parameters and Z, in case of atoms, denotes the nuclear charge. Under the spherical symmetry, all the information measures considered are shown to be independent of the scaling of the set [μ, Z] at a fixed value of μ/Z, a, and b and the other parameters defining the superpositions of the potentials. Numerical results are presented, which support the validity of the scaling properties. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Quantitative Correlations for the Estimation of Thermodynamic and Molecular Properties of Pyridines and 2,2′-Bipyridyines

Standard heats of formation, entropies, ionization potentials, and molecular dipole moments of a series of pyridines have been calculated by MNDO, AM1 and PM3 methods. Linear relationship have been established which permit a priori estimation of thermodynamic and molecular characteristics of pyridines. Correlation have been found between the values of pK_a for 2,2′-bipyridines for aqueous solutions and their gas phase proton affinities.__________Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, 391–402, March, 2005.     

Some results on the behavior and estimation of the fractal dimensions of distributions on attractors

The strong interest in recent years in analyzing chaotic dynamical systems according to their asymptotic behavior has led to various definitions of fractal dimension and corresponding methods of statistical estimation. In this paper we first provide a rigorous mathematical framework for the study of dimension, focusing on pointwise dimension(x) and the generalized Renyi dimensionsD(q), and give a rigorous proof of inequalities first derived by Grassberger and Procaccia and Hentschel and Procaccia. We then specialize to the problem of statistical estimation of the correlation dimension and information dimension. It has been recognized for some time that the error estimates accompanying the usual procedures (which generally involve least squares methods and nearest neighbor calculations) grossly underestimate the true statistical error involved. In least squares analyses of and we identify sources of error not previously discussed in the literature and address the problem of obtaining accurate error estimates. We then develop an estimation procedure for which corrects for an important bias term (the local measure density) and provides confidence intervals for. The general applicability of this method is illustrated with various numerical examples.     

A simple optimization strategy based on Rs-minimum and information theory of chromatography

Summary A simple optimization method based on the well-known Rs-minimum method and on the information theory of FUMI Φ is proposed. Resolution (Rs), peak area and height (or width) are the only parameters necessary for the calculation of the information Φ and information flow ϑ. The most precise analysis can be selected as the chromatogram having maximal ϑ. Mobile phase composition, column length, flow rate, detection wavelength, amount of internal standard, etc. can be optimized by this method.     

Conductance Study of Binding of Some Rb+ and Cs+ Ions by Macrocyclic Polyethers in Acetonitrile Solution

A conductance study of the interaction between Rb+ and Cs+ ions and18-crown-6 (18C6), dicyclohexyl-18-crown-6 (DC18C6), dibenzo-18-crown-6 (DB18C6),dibenzo-24-crown-8 (DB24C8), and dibenzo-30-crown-10 (DB30C10) inacetonitrile solution has been carried out at various temperatures. The formationconstants of the resulting 1:1 complexes were determined from the molarconductance-mole ratio data and found to vary in the orderDC18C6 > 18C6 > DB30C10 > DB18C6 DB24C8for Rb+ ion andDC18C6 > 18C6 > DB30C10 DB24C8 > DB18C6for Cs+ ion. The enthalpy and entropy of complexation were determined fromthe temperature dependence of the formation constants. The complexes with the18-crowns are both enthalpy and entropy stabilized while, in the case of largecrown ethers, the corresponding complexes are enthalpy stabilized but entropydestabilized.     

Time-resolved fluorescence analysis of the mobile flavin cofactor in p -hydroxybenzoate hydroxylase

Conformational heterogeneity of the FAD cofactor in p-hydroxybenzoate hydroxylase (PHBH) was investigated with time-resolved polarized flavin fluorescence. For binary enzyme/substrate (analogue) complexes of wild-type PHBH and Tyr222 mutants, crystallographic studies have revealed two distinct flavin conformations; the ‘in’ conformation with the isoalloxazine ring located in the active site, and the ‘out’ conformation with the isoalloxazine ring disposed towards the protein surface. Fluorescence-lifetime analysis of these complexes revealed similar lifetime distributions for the ‘in’ and ‘out’ conformations. The reason for this is twofold. First, the active site of PHBH contains various potential fluorescence-quenching sites close to the flavin. Fluorescence analysis of uncomplexed PHBH Y222V and Y222A showed that Tyr222 is responsible for picosecond fluorescence quenching free enzyme. In addition, other potential quenching sites, including a tryptophan and two tyrosines involved in substrate binding, are located nearby. Since the shortest distance between these quenching sites and the isoalloxazine ring differs only little on average, these aromatic residues are likely to contribute to fluorescence quenching. Second, the effect of flavin conformation on the fluorescence lifetime distribution is blurred by binding of the aromatic substrates: saturation with aromatic substrates induces highly efficient fluorescence quenching. The flavin conformation is therefore only reflected in the small relative contributions of the longer lifetimes.