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Equilibrium Structure (equilibrium + structure)
Selected AbstractsChemInform Abstract: Equilibrium Structure and Torsional Barrier of BH3NH3.CHEMINFORM, Issue 33 2008Jean Demaison Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Equilibrium Structure and Ti-Catalyzed H2 Desorption in NaAlH4 Nanoparticles from Density Functional Theory.CHEMINFORM, Issue 2 2007Tejs Vegge Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source] ChemInform Abstract: High-Resolution Infrared Spectroscopy of trans- and cis-H18ON18O: Equilibrium Structures of the Nitrous Acid Isomers.CHEMINFORM, Issue 5 2009V. Sironneau J. Orphal Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] MULTILOCUS GENETICS AND THE COEVOLUTION OF QUANTITATIVE TRAITSEVOLUTION, Issue 7 2006Michael Kopp Abstract We develop and analyze an explicit multilocus genetic model of coevolution. We assume that interactions between two species (mutualists, competitors, or victim and exploiter) are mediated by a pair of additive quantitative traits that are also subject to direct stabilizing selection toward intermediate optima. Using a weak-selection approximation, we derive analytical results for a symmetric case with equal locus effects and no mutation, and we complement these results by numerical simulations of more general cases. We show that mutualistic and competitive interactions always result in coevolution toward a stable equilibrium with no more than one polymorphic locus per species. Victimexploiter interactions can lead to different dynamic regimes including evolution toward stable equilibria, cycles, and chaos. At equilibrium, the victim is often characterized by a very large genetic variance, whereas the exploiter is polymorphic in no more than one locus. Compared to related one-locus or quantitative genetic models, the multilocus model exhibits two major new properties. First, the equilibrium structure is considerably more complex. We derive detailed conditions for the existence and stability of various classes of equilibria and demonstrate the possibility of multiple simultaneously stable states. Second, the genetic variances change dynamically, which in turn significantly affects the dynamics of the mean trait values. In particular, the dynamics tend to be destabilized by an increase in the number of loci. [source] On the performance of eleven DFT functionals in the description of the vibrational properties of aluminosilicatesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 2 2010Raffaella Demichelis Abstract The performance of eleven DFT functionals in describing the equilibrium structure and the vibrational spectra at the , point of pyrope (Mg3Al2Si3O12), forsterite (,-Mg2SiO4), ,-quartz (,-SiO2) and corundum (,-Al2O3) is discussed. The four systems, for which accurate experimental data are available, are here used as a representative sample of the large aluminosilicates family. Calculations were performed with the periodic ab initio CRYSTAL code by using all-electron Gaussian-type basis sets. All the functionals here considered provide reasonable structural predictions, the hybrid PBE0 giving the least deviation from the experimental unit cell volumes (from ,0.3% to +0.6%). At the other extreme, SVWN and SPWLSD (,,3%) and PBE and PW91 (, +3%) provide the largest volume under- and over-estimation, respectively. Vibrational frequencies are more accurate when computed with hybrid functionals, with the best performance provided by B3LYP and WC1LYP (mean absolute differences with respect to experiments evaluated on a set of 134 vibrational frequencies, ||t , 5.5 cm,1). The three recently proposed GGA functionals, PBEsol, SOGGA-PBE and WC-PBE, provide a good description of the vibrational spectra, of the same quality as the one provided by PBE0 and B1WC (||t , 10 cm,1), whereas poorer results are obtained with PBE (||t , 17 cm,1). © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Simulation of the N -terminus of HIV-1 glycoprotein 41000 fusion peptide in micellesJOURNAL OF PEPTIDE SCIENCE, Issue 4 2005Allison Langham Abstract In this paper, the N -terminus of glycoprotein-41, the HIV-1 fusion peptide, was studied by molecular dynamics simulations in an explicit sodium dodecyl sulfate micelle. The simulation provides a detailed picture of the equilibrium structure and peptide stability as it interacts with the micelle. The equilibrium location of the peptide shows the peptide at the surface of the micelle with hydrophobic residues interacting with the micelle's core. At equilibrium, the peptide adopts an ,-helical structure from residues 5,16 and a type-1 ,-turn from 17,20 with the other residues exhibiting more flexible conformations. The primary hydrophobic interactions with the micelle are from the leucine and phenylalanine residues (Leu-7, Phe-8, Leu-9, Phe-11, Leu-12) while the alanine and glycine residues (Ala-1, Gly-3, Gly-5, Ala-6, Gly-10, Gly-13, Ala-14, Ala-15, Gly-16, Gly-10, Ala-21) interact favorably with water molecules. The results suggest that Phe-8, part of the highly conserved FLG motif of the fusion peptide, plays a key role in the interaction of the peptide with membranes. Our simulations corroborate experimental investigations of the fusion peptide in SDS micelles, providing a high-resolution picture that explains the experimental findings. Copyright © 2004 European Peptide Society and John Wiley & Sons, Ltd. [source] A broad transition zone between an inner Baltic hybrid swarm and a pure North Sea subspecies of Macoma balthica (Mollusca, Bivalvia)MOLECULAR ECOLOGY, Issue 6 2008RAISA NIKULA Abstract The populations of the bivalve clam Macoma balthica in the low-salinity Northern Baltic Sea represent an admixture of two strongly diverged genomic origins, the Pacific Macoma balthica balthica (approx. 60% genomic contribution) and Atlantic Macoma balthica rubra (40%). Using allozyme and mtDNA characters, we describe the broad transition from this hybrid swarm to the pure M. b. rubra in the saline North Sea waters, spanning hundreds of kilometre distance. The zone is centred in the strong salinity gradient of the narrow Öresund strait and in the adjacent Western Baltic. Yet the multilocus clines show no simple and smoothly monotonic gradation: they involve local reversals and strong differences between neighbouring populations. The transitions in different characters are not strictly coincident, and the extent of introgression varies among loci. The Atlantic influence extends further into the Baltic in samples from the southern and eastern Baltic coasts than on the western coast, and further in deeper bottoms than at shallow (< 1 m) sites. This fits with the counterclockwise net circulation pattern and with a presumably weaker salinity barrier for invading Atlantic type larvae in saline deeper water, and corresponding facilitation of outwards drift of Baltic larvae in diluted surface waters. Genotypic disequilibria were strong particularly in the shallow-water samples of the steepest transition zone. This suggests larval mixing from different sources and limited interbreeding in that area, which makes a stark contrast to the evidence of thorough amalgamation of the distinct genomic origins in the inner Baltic hybrid swarm of equilibrium structure. [source] Does Sutton apply to supermarkets?THE RAND JOURNAL OF ECONOMICS, Issue 1 2007Paul B. Ellickson I present empirical evidence that endogenous fixed costs play a central role in determining the equilibrium structure of the supermarket industry. Using the framework developed in Sutton (1991), I construct a model of supermarket competition where escalating investment infirm-level distribution systems is driven by the incentive to produce a greater variety of products in every store. Employing a store-level census and 51 distinct geographic markets, I demonstrate that the supermarket industry is a natural oligopoly in which a small number of firms (between four and six)capture the majority of sales, regardless of market size. [source] Time-dependent and time-independent approaches for the computation of absorption spectra of Uracil derivatives in solutionINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2010Roberto Improta Abstract In this contribution we discuss the most significant benefits and drawbacks of the alternative time-independent (TI) and time-dependent (TD) approaches to the calculation of absorption spectra of molecules in solutions. Eigenstate-free TD methods are in principle the most suitable route to face with the calculation of optical spectra in nonadiabatic systems, most of all in presence of conical intersections easily accessible from the Franck,Condon region. However, here we show that, in selected cases, a combined strategy that adopts TD methods to assess the impact of nonadiabatic couplings on the spectrum and subsequently applies TI methods to include all the degrees of freedom can reveal very convenient. Such a combined TD/TI strategy has been applied to the calculation of the spectrum of Uracil and 5Fluoro-Uracil in acetonitrile. TD studies on reduced dimensionality diabatic models indicate that nonadiabatic effects are moderate and are not the main origin of the diffuse spectral shapes observed in experiments. Subsequent full-coordinate TI calculations allow assigning this feature to intrinsic characteristics of a ,,* excitation of a small molecular ring structure. This latter introduces remarkable deformation in all the ring structure thus inducing a FC activity in many molecular normal modes both due to displacements of the equilibrium structures and to Duschinsky mixings of the normal coordinates. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Intra and intermolecular hydrogen bonding in formohydroxamic acid,INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2008Damanjit Kaur Abstract The presence of hydrogen bonding interactions in several tautomeric forms of formohydroxamic acid (FHA) and 1:1 association among the tautomeric forms and water-coordinated tautomeric forms of FHA is explored theoretically. Out of the seven equilibrium structures, four tautomeric forms have been selected for aggregation with single water molecule and dimer formation. Fifteen aggregates of FHA with H2O have been optimized at MP2/AUG-cc-PVDZ level and analyzed for intramolecular and intermolecular H-bond interactions. Twenty-seven dimers of the four tautomeric forms have been obtained at MP2/6-31+G* level. The stabilization energies associated with dimerization and adduct formation with water are the result of H-bond interactions and range from very weak to medium. The atomic charges and NBO analysis indicate that the electrostatic and the charge transfer are the important components favoring H-bond formation. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: Application to alanine tetrapeptide conformational analysisJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2007Robert A. Distasio JR. Abstract We present a new algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory (RI-MP2) and thoroughly assess its computational performance and chemical accuracy. This algorithm addresses the potential I/O bottlenecks associated with disk-based storage and access of the RI-MP2 t -amplitudes by utilizing a semi-direct batching approach and yields computational speed-ups of approximately 2,3 over the best conventional MP2 analytical gradient algorithms. In addition, we attempt to provide a straightforward guide to performing reliable and cost-efficient geometry optimizations at the RI-MP2 level of theory. By computing relative atomization energies for the G3/99 set and optimizing a test set of 136 equilibrium molecular structures, we demonstrate that satisfactory relative accuracy and significant computational savings can be obtained using Pople-style atomic orbital basis sets with the existing auxiliary basis expansions for RI-MP2 computations. We also show that RI-MP2 geometry optimizations reproduce molecular equilibrium structures with no significant deviations (>0.1 pm) from the predictions of conventional MP2 theory. As a chemical application, we computed the extended-globular conformational energy gap in alanine tetrapeptide at the extrapolated RI-MP2/cc-pV(TQ)Z level as 2.884, 4.414, and 4.994 kcal/mol for structures optimized using the HF, DFT (B3LYP), and RI-MP2 methodologies and the cc-pVTZ basis set, respectively. These marked energetic discrepancies originate from differential intramolecular hydrogen bonding present in the globular conformation optimized at these levels of theory and clearly demonstrate the importance of long-range correlation effects in polypeptide conformational analysis. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Ionization-Induced Proton Transfer in Model DNA Base Pairs: A Theoretical Study of the Radical Ions of the 7-Azaindole DimerCHEMPHYSCHEM, Issue 12 2004Hsing-Yin Chen Dr. Abstract Proton-transfer reactions of the radical anion and cation of the 7-Azaindole (7AI) dimer were investigated by means of density functional theory (DFT). The calculated results for the dimer anion and cation were very similar. Three equilibrium structures, which correspond to the non-proton-transferred (normal), the single-proton-transferred (SPT) and the double-proton-transferred (tautomeric) forms, were found. The transition states for proton-transfer reactions were also located. The calculations showed that the first proton-transfer reaction (normal,SPT) is exothermic and almost barrier-free; therefore, it should occur spontaneously in the period of a vibration. In contrast, the second proton-transfer reaction (SPT,tautomer) was found to be far less-probable in terms of reaction energy and barrier. Hence, it was concluded that both (7AI)2and (7AI)2exist in the SPT form. The conclusion was further confirmed by the calculated electron vertical detachment energy (VDE) of the SPT form of (7AI)2, 1.33 eV, which is very close to the experimental measurement of 1.35 eV. The calculated VDEs of the normal and tautomeric (7AI)2forms were too small compared to the experimental value. The proton transfer process was found to be multidimensional in nature involving not only proton motion but also intermolecular rocking motion. In addition, IR spectra were calculated and reported. The spectra of the three structures showed very different features and, therefore, can be considered as fingerprints for future experimental identifications. The implications of these results to biology and spectroscopy are also briefly discussed. [source] | |||||||||||||