Search results for "Networks"
showing 10 items of 3260 documents
Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates
2013
Conformational changes are known to be able to drive an enzyme through its catalytic cycle, allowing, for example, substrate binding or product release. However, the influence of protein motions on the chemical step is a controversial issue. One proposal is that the simple equilibrium fluctuations incorporated into transition-state theory are insufficient to account for the catalytic effect of enzymes and that protein motions should be treated dynamically. Here, we propose the use of free-energy surfaces, obtained as a function of both a chemical coordinate and an environmental coordinate, as an efficient way to elucidate the role of protein structure and motions during the reaction. We sho…
Solid state halogen bonded networks vs. dynamic assemblies in solution: explaining N⋯X interactions of multivalent building blocks
2015
Tetrapyridine functionalized resorcinarene macrocycles were used as multivalent building blocks for the construction of halogen bonded networks with aryl halide linkers. In the solid state, resorcinarene macrocycles and aryl halide linker molecules assembled into interpenetrated, multidimensional halogen bonded networks with porous structure caused by the 3D block scaffold of the resorcinarenes. 19F NMR spectroscopy proved halogen bond formation also in solution, as either upfield or downfield shifts were observed depending on the bivalent or monovalent halogen bond binding mode. The binding mode in solution was explained by density functional theory computations. peerReviewed
Tryptophan catabolism via kynurenine production in Streptomyces coelicolor: identification of three genes coding for the enzymes of tryptophan to ant…
2011
Most enzymes involved in tryptophan catabolism via kynurenine formation are highly conserved in Prokaryotes and Eukaryotes. In humans, alterations of this pathway have been related to different pathologies mainly involving the central nervous system. In Bacteria, tryptophan and some of its derivates are important antibiotic precursors. Tryptophan degradation via kynurenine formation involves two different pathways: the eukaryotic kynurenine pathway, also recently found in some bacteria, and the tryptophan-to-anthranilate pathway, which is widespread in microorganisms. The latter produces anthranilate using three enzymes also involved in the kynurenine pathway: tryptophan 2,3-dioxygenase (TD…
Polymer Films in the Normal-Liquid and Supercooled State: A Review of Recent Monte Carlo Simulation Results
2000
This paper reviews recent Monte Carlo simulation studies of the glassy behavior in thin polymer films. The simulations employ a version of the bond-fluctuation lattice model, in which the glass transition is driven by the competition between a stiffening of the polymers and their dense packing in the melt. The melt is geometrically confined between two impenetrable walls separated by distances ranging from once to about fifteen times the bulk radius of gyration. The confinement influences static and dynamic properties of the films: Chains close to the wall preferentially orient parallel to it. This orientation tendency propagates through the film and leads to a layer structure at low temper…
Disorder Classification of the Vibrational Spectra of Modern Glasses
2021
Using the coherent-potential approximation in heterogeneous-elasticity theory with a log-normal distribution of elastic constants for the description of the Raman spectrum and the temperature dependence of the specifi?c heat, we are able to reconstruct the vibrational density of states and characteristic descriptors of the elastic heterogeneity of a wide range of glassy materials. These descriptors are the non-affi?ne contribution to the shear modulus, the mean-square fluctuation of the local elasticity, and its correlation length. They enable a physical classification scheme for disorder in modern, industrially relevant glass materials. We apply our procedure to a broad range of real-world…
Effect of physical aging on the low-frequency vibrational density of states of a glassy polymer
2003
The effects of the physical aging on the vibrational density of states (VDOS) of a polymeric glass is studied. The VDOS of a poly(methyl methacrylate) glass at low-energy (<15 meV), was determined from inelastic neutron scattering at low-temperature for two different physical thermodynamical states. One sample was annealed during a long time at temperature lower than Tg, and another was quenched from a temperature higher than Tg. It was found that the VDOS around the boson peak, relatively to the one at higher energy, decreases with the annealing at lower temperature than Tg, i.e., with the physical aging.
Supramolecular isomerism in spin crossover networks with aurophilic interactions
2004
Assembly of FeII, 3-cyanopyridine and [Au(CN)2]– affords, in one-pot reaction, three coordination polymers that represent a genuine example of supramolecular isomerism with strong influence in the spin crossover regime of the FeII ions. Real Cabezos, Jose Antonio, Jose.A.Real@uv.es
Re-entrant glass transition in a colloid-polymer mixture with depletion attractions.
2002
Performing light scattering experiments we show that introducing short-ranged attraction to a colloidal suspension of nearly hard spheres by addition of free polymer produces new glass transition phenomena. We observe a dramatic acceleration of the density fluctuations amounting to the melting of a colloidal glass. Increasing the strength of the attractions the system freezes into another nonergodic state sharing some qualitative features with gel states occurring at lower colloid packing fractions. This reentrant glass transition is in qualitative agreement with recent theoretical predictions.
Monte Carlo and molecular dynamics simulation of the glass transition of polymers
1998
Two coarse-grained models for polymer chains in dense glass-forming polymer melts are studied by computer simulation: the bond-fluctuation model on a simple cubic lattice, where a bond-length potential favors long bonds, is treated by dynamic Monte Carlo methods, and a bead-spring model in the continuum with a Lennard-Jones potential between the beads is treated by Molecular Dynamics. While the dynamics of both models differ for short length scales and associated time scales, on mesoscopic spatial and temporal scales both models behave similarly. In particular, the mode coupling theory of the glass transition can be used to interpret the slowing down of the undercooled polymer melt. For the…
Interfacial properties of glassy polymer melts: A Monte Carlo study
1996
The properties of the interface between a polymer melt and a solid wall are studied over a wide range of temperatures by dynamic Monte Carlo simulations. It is shown that in the supercooled state near the glass transition of the melt an “interphase” forms, the structure of which is influenced by the wall. The thickness of this interphase is determined from the monomer density profile near the surface and is strongly temperature dependent. At low glass-like temperatures it is larger than the bulk radius of gyration of the chains.