New theoretical insight into the interactions and properties of formic acid: development of a quantum-based pair potential for formic acid

We performed ab initio quantum-chemical studies for the development of intra- and intermolecular interaction potentials for formic acid for use in molecular-dynamics simulations of formic acid molecular crystal. The formic acid structures considered in the ab initio studies include both the cis and trans monomers which are the conformers that have been postulated as part of chains constituting liquid and crystal phases under extreme conditions. Although the cis to trans transformation is not energetically favored, the trans isomer was found as a component of stable gas-phase species. Our decomposition scheme for the interaction energy indicates that the hydrogen-bonded complexes are dominated by the Hartree-Fock forces while parallel clusters are stabilized by the electron correlation energy. The calculated three-body and higher interactions are found to be negligible, thus rationalizing the development of an atom-atom pair potential for formic acid based on high-level ab initio calculations of small formic acid clusters. Here we present an atom-atom pair potential that includes both intra- and inter molecular degrees of freedom for formic acid. The newly developed pair potential is used to examine formic acid in the condensed phase via molecular-dynamics simulations. The isothermal compression under hydrostatic pressure obtained from molecular-dynamics simulations is in good agreement with experiment. Further, the calculated equilibrium melting temperature is found to be in good agreement with experiment.     

A theoretical investigation of the preferred conformations of glutathione and its constituent amino acid residues

The preferred conformations of the tripeptide glutathione have been investigated by performing quantum mechanical calculations using the PCILO method. A series of model compounds representing fragments of the tripeptide has been studied as well as the complete molecule. The results are compared with the available experimental data.     

Dimerization of some substituted benzoic acids in aqueous solution from conductance measurements

Precision molar conductances of benzoic, o-toluic, 2,6-dimethylbenzoic, 2,3,6-trimethylbenzoic, and, o-fluorobenzoic acids have been determined in aqueous solution as a function of temperature and of concentration up to near saturation (<0.035 M). At the higher concentrations molar conductances are found to be less than anticipated for the simple dissociation of a 1-1 electrolyte. Although the deviations are only 1% or less they have been interpreted to show that these acids are dimerized in solution. The interpretation includes an assumption that the dimer ionizes to produce a triple ion. Increasing numbers of methyl groups lead to increasing dimerization. For those acids with two ortho groups the dimerization increases with increasing temperature while the other three show decreasing dimerization with increasing temperature. Temperature functions have been determined for the dimerization constants and from these functions standard changes in enthalpy, entropy, and heat capacity have been determined. Comparisons are made with dimerization studies in non-aqueous solvents. From these as well as the behavior of benzene in water it is concluded that a major factor driving the dimerization is hydrophobic interaction. To provide a limiting conductance of the triple ion needed in the dimerization calculations a conductance study was also made for o-Phenylbenzoic acid on the assumption that its anion provides an approximate model of the triple ion.     

The search for a new model structure of β-Factor XIIa

We present the search for a new model of -factor XIIa, a blood coagulation enzyme, with an unknown experimental 3D-structure. We decided to build not one but three different models using different homologous proteins as well as different techniques and different modellers. Additional studies, including extensive molecular dynamics simulations on the solvated state, allowed us to draw several conclusions concerning homology modelling, in general, and -factor XIIa, in particular.     

Compositional Profiles in Silica-Based Sol-Gel Films Doped with Erbium and Silver, by RBS and ERDA

Photosensitive organic-titania hybrid materials have been prepared from metal alkoxides and various organic ester compounds with double bonds. The refractive index of the film increases with the decrease of the concentration of the organic ester compound, and the highest refractive index of 1.62 is obtained when 2-hydroxymethyl acrylate (HOA) is used as the organic ester and the molar ratio of HOA to Ti is 0.5. The material with the highest refractive index is exposed to femtosecond pulse using the multi-beam laser interference technique. After laser irradiation, the irradiated parts of the material are photopolymerized and periodic structures can be obtained by development of the unirradiated parts. In the case of laser irradiation of 120 J total energy for 5 min, the periodic structure obtained corresponds to 2D photonic crystal structure which is composed of two parts; the material with the highest refractive index and the air.     

Environmental UV‐A and UV‐B Threshold Doses for Apoptosis and Necrosis in Humans Fibroblasts¶

Apoptosis involves a highly organized and programmed series of events aimed at maintaining genomic stability by eliminating defective host cells. The purpose of this study was to determine the threshold doses and environmental UV‐A and UV‐B exposure times necessary to produce apoptosis and necrosis in the normal cells of a human fibroblast cell line. Enviromental UV‐A and UV‐B doses were measured over a 6 year period with a four‐channel UV radiometer. The fibroblasts were irradiated once using an Oriel UV Solar Simulator with six doses of environmentally‐based UV. Doses corresponded to 0,11,19,23 and 45 min of average environmental UV‐A and UV‐B radiation at solar noon in Puerto Rico. The Annexin‐V binding method was used to differentiate between normal fibroblasts and apoptotic or necrotic fibroblasts. The threshold dose from apoptosis to necrosis was found between 24–28 kJ/m², which corresponded to 19 and 23 min of environmental UV‐A and UV‐B exposure. This study provides the first data that specify the environmental threshold doses of UV‐A and UV‐B at which human fibroblasts undergo apoptosis and necrosis. These results may provide valuable dose‐response thresholds for apoptosis and necrosis for future mechanistic studies and baseline data for skin cancer prevention programs.     

Theoretical study of ribonucleotide reductase mechanism-based inhibition by 2'-azido-2'-deoxyribonucleoside 5'-diphosphates

2'-azido-2'-deoxyribonucleoside 5'-diphosphates are mechanism-based inhibitors of Ribonucleotide Reductase. Considerable effort has been made to elucidate their mechanism of inhibition, which is still controversial and not fully understood. Previous studies have detected the formation of a radical intermediate when the inhibitors interact with the enzyme, and several authors have proposed possible structures for this radical. We have conducted a theoretical study of the possible reactions involved, which allowed us to identify the structure of the new radical among the several proposals. A new reactional path is also proposed that is the most kinetically favored to yield this radical and ultimately inactivate the enzyme. The energetic involved in this mechanism, both for radical formation and radical decay, as well as the calculated Hyperfine Coupling Constants for the radical intermediate, are in agreement with the correspondent experimental values. This mechanistic alternative is fully coherent with remaining experimental data.     

Solution-phase, triangular ag nanotriangles fabricated by nanosphere lithography

A novel method to produce solution-phase triangular silver nanoparticles is presented. Ag nanoparticles are prepared by nanosphere lithography and are subsequently released into solution. The resulting nanoparticles are asymmetrically functionalized to produce either single isolated nanoparticles or dimer pairs. The structural and optical properties of Ag nanoparticles have been characterized. Mie theory and the Discrete Dipole Approximation method (DDA) have been used to model and interpret the optical properties of the released Ag nanoparticles.