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Molecular Configuration (molecular + configuration)
Selected AbstractsOn the flow-phase diagram for nematic liquid crystalline polymer under magnetic fieldJOURNAL OF APPLIED POLYMER SCIENCE, Issue 3 2009Shufang Fu Abstract The effect of magnetic fields on molecular configuration of liquid crystalline polymers under shear flows are numerically analyzed using the extended Doi theory in which a molecular shape parameter is admitted. The evolution equation for the probability density function of the LCP molecules is directly solved without any closure approximations. One case is considered that the magnetic field makes 45° with respect to the flow direction. We can find that the magnetic fields strongly affect on the transition among flow-orientation modes, such as tumbling, wagging, and aligning modes. And a new aligning flow-orientation mode emerges at low shear rate, which is macroscopically same as the ordinary aligning mode, but is microscopically quite different from the ordinary one. © 2009 Wiley Periodicals, Inc. J Appl Polym Sci, 2009 [source] Heavy atom motions and tunneling in hydrogen transfer reactions: the importance of the pre-tunneling stateJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 7 2010Hans-Heinrich Limbach Abstract Arrhenius curves of selected hydrogen transfer reactions in organic molecules and enzymes are reviewed with the focus on systems exhibiting temperature-independent kinetic isotope effects. The latter can be rationalized in terms of a ,pre-tunneling state' which is formed from the reactants by heavy atom motions and which represents a suitable molecular configuration for tunneling to occur. Within the Bell,Limbach tunneling model, formation of the pre-tunneling state dominates the Arrhenius curves of the H and the D transfer even at higher temperatures if a large energy Em is required to reach the pre-tunneling state. Tunneling from higher vibrational levels and the over-barrier reaction via the transition state which lead to temperature-dependent kinetic isotope effects dominate the Arrhenius curves only if Em is small compared to the energy of the transition state. Using published data on several hydrogen transfer systems, the type of motions leading to the pre-tunneling state is explored. Among the phenomena which lead to large energies of the pre-tunneling state are (i) cleavage of hydrogen bonds or coordination bonds of the donor or acceptor atoms to molecules or molecular groups in order to allow the formation of the pre-tunneling state, (ii) the occurrence of an energetic intermediate on the reaction pathway within which tunneling takes place, and (iii) major reorganization of a molecular skeleton, requiring the excitation of specific vibrations in order to reach the pre-tunneling state. This model suggests a solution to the puzzle of Kwart's findings of temperature-independent kinetic isotope effects for hydrogen transfer in small organic molecules. Copyright © 2010 John Wiley & Sons, Ltd. [source] Defect contributions to conductivity in poly(3-hexylthiophene)?PHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 6 2006A. N. Caruso Abstract We find evidence for a gradual change in the electronic properties of spin coated poly(3-hexylthiophene) thin films with temperature. The conduction properties appears to be mediated by hopping conduction dominated by a low density of defects states within the highest occupied molecular orbital to lowest unoccupied molecular orbital gap, not by a change in band gap. The photoemission and transport measurements indicate a loss of charge mobility or carrier concentration occurs with decreasing temperature, while the molecular configuration (through chain conjugation) also changes with temperature. The defects states identified by photoemission (,1.7 eV) as well as others contributing to the transport properties are believed to be very heterogeneous along the polymer backbone. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Experimental Study on the Molecular Dimension and Configuration of Polymer and Its Flow Characteristics from Electrolyte EffectCHINESE JOURNAL OF CHEMISTRY, Issue 4 2009Xiangguo LU Abstract Molecular clew dimension and configuration of polymer, and flow characteristics of polymer solution were studied from electrolyte effect, by making use of dynamic light scattering (DLS), scanning electron microscopy (SEM), apparent viscosity method and core flow experiment. It can be observed that with the electrolyte concentration increasing, there exists a variation trend of "decreasing, increasing and decreasing again" to the molecular clew dimension of the polymer. The compression action of Ca2+ or Mg2+ to the double electrode layer of polymer molecules is more powerful by comparison against Na+, which results in that Ca2+ and Mg2+ have a more extensive effect on the viscosity of polymer solution, and clew dimensions and their distribution. With the electrolyte concentration increasing, the polymer molecular configuration of multi-layer stereoscopic random reticulation transformed into a dendritic one. During the succeeding water flooding, the variation degree of injection pressure of core was mainly determined by the swelling extent of molecular clew of retained polymer and the produced amount of polymer. And the bigger the molecular weight of polymer is, the stronger the compression or swelling action of electrolyte to the molecule clews is, and the greater the increasing degree of injection pressure during succeeding water flooding is. The greater difference of electrolyte concentrations in used water between polymer flooding and succeeding water flooding can result in greater increasing degree of injection pressure during the succeeding water flooding. So, an advisable increasing in difference of electrolyte concentrations in used water between the polymer flooding and succeeding water flooding was proposed when designing the polymer flooding performance in oilfields, which has promising result for improving effect of polymer flooding. [source] Basic ingredients of free energy calculations: A reviewJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2010Clara D. Christ Abstract Methods to compute free energy differences between different states of a molecular system are reviewed with the aim of identifying their basic ingredients and their utility when applied in practice to biomolecular systems. A free energy calculation is comprised of three basic components: (i) a suitable model or Hamiltonian, (ii) a sampling protocol with which one can generate a representative ensemble of molecular configurations, and (iii) an estimator of the free energy difference itself. Alternative sampling protocols can be distinguished according to whether one or more states are to be sampled. In cases where only a single state is considered, six alternative techniques could be distinguished: (i) changing the dynamics, (ii) deforming the energy surface, (iii) extending the dimensionality, (iv) perturbing the forces, (v) reducing the number of degrees of freedom, and (vi) multi-copy approaches. In cases where multiple states are to be sampled, the three primary techniques are staging, importance sampling, and adiabatic decoupling. Estimators of the free energy can be classified as global methods that either count the number of times a given state is sampled or use energy differences. Or, they can be classified as local methods that either make use of the force or are based on transition probabilities. Finally, this overview of the available techniques and how they can be best used in a practical context is aimed at helping the reader choose the most appropriate combination of approaches for the biomolecular system, Hamiltonian and free energy difference of interest. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A reviewJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2008Markus Christen Abstract Methods to search for low-energy conformations, to generate a Boltzmann-weighted ensemble of configurations, or to generate classical-dynamical trajectories for molecular systems in the condensed liquid phase are briefly reviewed with an eye to application to biomolecular systems. After having chosen the degrees of freedom and method to generate molecular configurations, the efficiency of the search or sampling can be enhanced in various ways: (i) efficient calculation of the energy function and forces, (ii) application of a plethora of search enhancement techniques, (iii) use of a biasing potential energy term, and (iv) guiding the sampling using a reaction or transition pathway. The overview of the available methods should help the reader to choose the combination that is most suitable for the biomolecular system, degrees of freedom, interaction function, and molecular or thermodynamic properties of interest. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] | ||||||||||