Conformation And C-N Rotational Barrier Of Dithiocarbamate Esters Nmr And Molecular-Orbital Studies

The variable temperature proton and ambient temperature carbon-13 NMR spectra of S-methyl dithiocarbamate esters have been recorded. The results of the theoretical energy calculations (CNDO/2 and EHT types) together with the experimental data have been interpreted in terms of the molecular conformations. The barrier heights for the rotation about the thioamide C—N bond are calculated using the CNDO/2 method and the results are discussed in terms of the computed charge densities and bond orders.

A model for the interaction of trifluoroethanol with peptides and proteins

The structural stabilizing property of 2,2,2-trifluoroethanol (TFE) in peptides has been widely demonstrated, More recently, TFE has been shown to enhance secondary structure content in globular proteins, and to influence quaternary interactions in protein multimers. The molecular mechanisms by which TFE exerts its Influence on peptide and protein structures remain poorly understood. The present analysis integrates the known physical properties of TFE with a variety of experimental observations on the interaction of TFE with peptides and proteins and on the properties of fluorocarbons. Two features of TFE, namely the hydrophobicity of the trifluoromethyl group and the hydrogen bonding character (strong donor and poor acceptor), emerge as the most important factors for rationalising the observed effects of TFE. A model is proposed for TFE interaction with peptides which involves an initial replacement of the hydration shell by fluoroalcohol molecules, a process driven by apolar interactions and favourable entropy of dehydration. Subsequent bifurcated hydrogen-bond formation with peptide carbonyl groups, which leave intramolecular interactions unaffected, promotes secondary structure formation.

Molecular assemblies for solar energy conversion - Biomimetic approach

Excitation energy migration followed by electron transfer forms the main components of natural photosynthesis. An understanding of these aspects is essential to reenact the primary processes in laboratory under conditions that are precisely repeatable. Here we describe the state of understanding of the natural process and several model systems designed to harvest solar energy and conversion to useful form of chemical energy. The molecular assemblies constituting the model systems offer a great advantage in terms of better comprehension of the mechanistic aspects and yield valuable information on the design of molecular photonic devices.

Lattice model for rapidly folding protein-like heteropolymers

Protein folding is a relatively fast process considering the astronomical number of conformations in which a protein could find itself. Within the framework of a lattice model, we show that one can design rapidly folding sequences by assigning the strongest attractive couplings to the contacts present in a target native state, Our protein design can be extended to situations with both attractive and repulsive contacts. Frustration is minimized by ensuring that all the native contacts are again strongly attractive. Strikingly, this ensures the inevitability of folding and accelerates the folding process by an order of magnitude, The evolutionary implications of our findings are discussed.

Protein Model Discrimination Using Mutational Sensitivity Derived from Deep Sequencing

A major bottleneck in protein structure prediction is the selection of correct models from a pool of decoys. Relative activities of similar to 1,200 individual single-site mutants in a saturation library of the bacterial toxin CcdB were estimated by determining their relative populations using deep sequencing. This phenotypic information was used to define an empirical score for each residue (Rank Score), which correlated with the residue depth, and identify active-site residues. Using these correlations, similar to 98% of correct models of CcdB (RMSD <= 4 angstrom) were identified from a large set of decoys. The model-discrimination methodology was further validated on eleven different monomeric proteins using simulated RankScore values. The methodology is also a rapid, accurate way to obtain relative activities of each mutant in a large pool and derive sequence-structure-function relationships without protein isolation or characterization. It can be applied to any system in which mutational effects can be monitored by a phenotypic readout.

Modeling the effect of transmission errors on TCP controlled transfers over infrastructure 802.11 wireless LANs

There have been several studies on the performance of TCP controlled transfers over an infrastructure IEEE 802.11 WLAN, assuming perfect channel conditions. In this paper, we develop an analytical model for the throughput of TCP controlled file transfers over the IEEE 802.11 DCF with different packet error probabilities for the stations, accounting for the effect of packet drops on the TCP window. Our analysis proceeds by combining two models: one is an extension of the usual TCP-over-DCF model for an infrastructure WLAN, where the throughput of a station depends on the probability that the head-of-the-line packet at the Access Point belongs to that station; the second is a model for the TCP window process for connections with different drop probabilities. Iterative calculations between these models yields the head-of-the-line probabilities, and then, performance measures such as the throughputs and packet failure probabilities can be derived. We find that, due to MAC layer retransmissions, packet losses are rare even with high channel error probabilities and the stations obtain fair throughputs even when some of them have packet error probabilities as high as 0.1 or 0.2. For some restricted settings we are also able to model tail-drop loss at the AP. Although involving many approximations, the model captures the system behavior quite accurately, as compared with simulations.

Carrier mobility in polycrystalline semiconductors

This letter presents a modified version of the grain boundary barrier model for polycrystalline semiconductors which takes into account the carrier transport in the bulk of the grain and the dynamic process of capture and release of free carriers by the grain boundary traps.

Ions in water: Role of attractive interactions in size dependent diffusivity maximum

A molecular dynamics study of model ions in water is reported. The van der Waals diameter of both the cations and anions is varied. We have carried out two sets of simulations-with and without dispersion interaction-between the ion and water. Self-diffusivity of the ions exhibits an anomalous maximum as a function of the van der Waals diameter for both these sets. This existence of a maximum in self-diffusivity when there is no dispersion interaction between the ion and the water is attributed to the attractive term from electrostatic interactions. Detailed analysis of this effect shows that the solvent shell is more strongly defined in the presence of dispersion interactions. A smaller ion exhibits biexponential decay while a single exponential decay is seen for the ion with maximum diffusivity in the self-part of the intermediate scattering function. The solvent structure around the ion appears to determine much of the dynamics of the ion. Interesting trends are seen in the activation energies and these can be understood in terms of the levitation effect. (C) 2010 American Institute of Physics. doi:10.1063/1.3481656]

Dynamic growth of tensile cracks by ductile and brittle fracture mechanisms in a viscoplastic material

In this paper, a finite element analysis of steady-state dynamic crack growth under Mode I, plane strain, small-scale yielding conditions is performed in a rate dependent plastic material characterized by the over-stress model. The main objective of the paper is to obtain theoretically the dependence of dynamic fracture toughness on crack speed. Crack propagation due to a ductile (micro-void) mechanism or a brittle (cleavage) mechanism, as well as transition from one mode to another are considered. The conversion from ductile to brittle has been observed experimentally but has received very little attention using analytical methods. Local fracture criteria based on strains and stresses are used to describe ductile and brittle fracture mechanisms. The results obtained in this paper are in general agreement with micro-structural observations of mode conversion during fracture initiation. Finally, the particular roles played by material rate sensitivity and inertia are examined in some detail.

Levitation Effect: Role of Symmetry and Dependence of Diffusivity on the Bond Length of Homonuclear and Heteronuclear Diatomic Species

Molecular dynamics investigation of model diatomic species confined to the alpha-cages of zeolite NaY is reported. The dependence of self-diffusivity on the bond length of the diatomic species has been investigated. Three different sets of runs have been carried out. In the first set, the two atoms of the diatomic molecule interact with the zeolite atoms with equal strength (example, O-2, the symmetric case). In the second and third sets which correspond to asymmetric cases, the two atoms of the diatomic molecule interact with unequal strengths (example, CO). The result for the symmetric case exhibits a well-defined maximum in self-diffusivity for an intermediate bond length. In contrast to this, the intermediate asymmetry leads to a less pronounced maximum. For the large asymmetric case, the maximum is completely absent. These findings are analyzed by computing a number of related properties. These results provide a direct confirmation at the microscopic level of the suggestion by Derouane that the supermobility observed experimentally by Kemball has its origin in the mutual cancellation of forces. The maximum in diffusivity from molecular dynamics is seen at the value predicted by the levitation effect. Further, these findings suggest a role for symmetry in the existence of a diffusivity maximum as a function of diameter of the diffusant often referred to as the levitation effect. The nature of the required symmetry for the existence of anomalous diffusivity is interaction symmetry which is different from that normally encountered in crystallography.

Double Gaussian distribution of barrier height observed in densely packed GaN nanorods over Si (111) heterostructures

GaN nanorods were grown by plasma assisted molecular beam epitaxy on intrinsic Si (111) substrates which were characterized by powder X-ray diffraction, field emission scanning electron microscopy, and photoluminescence. The current-voltage characteristics of the GaN nanorods on Si (111) heterojunction were obtained from 138 to 493K which showed the inverted rectification behavior. The I-V characteristics were analyzed in terms of thermionic emission model. The temperature variation of the apparent barrier height and ideality factor along with the non-linearity of the activation energy plot indicated the presence of lateral inhomogeneities in the barrier height. The observed two temperature regimes in Richardson's plot could be well explained by assuming two separate Gaussian distribution of the barrier heights. (C) 2014 AIP Publishing LLC.

Solid-solid collapse transition in a two dimensional model molecular system

Solid-solid collapse transition in open framework structures is ubiquitous in nature. The real difficulty in understanding detailed microscopic aspects of such transitions in molecular systems arises from the interplay between different energy and length scales involved in molecular systems, often mediated through a solvent. In this work we employ Monte-Carlo simulation to study the collapse transition in a model molecular system interacting via both isotropic as well as anisotropic interactions having different length and energy scales. The model we use is known as Mercedes-Benz (MB), which, for a specific set of parameters, sustains two solid phases: honeycomb and oblique. In order to study the temperature induced collapse transition, we start with a metastable honeycomb solid and induce transition by increasing temperature. High density oblique solid so formed has two characteristic length scales corresponding to isotropic and anisotropic parts of interaction potential. Contrary to the common belief and classical nucleation theory, interestingly, we find linear strip-like nucleating clusters having significantly different order and average coordination number than the bulk stable phase. In the early stage of growth, the cluster grows as a linear strip, followed by branched and ring-like strips. The geometry of growing cluster is a consequence of the delicate balance between two types of interactions, which enables the dominance of stabilizing energy over destabilizing surface energy. The nucleus of stable oblique phase is wetted by intermediate order particles, which minimizes the surface free energy. In the case of pressure induced transition at low temperature the collapsed state is a disordered solid. The disordered solid phase has diverse local quasi-stable structures along with oblique-solid like domains. (C) 2013 AIP Publishing LLC.

Gel-coated ion-exchange resin: A new kinetic model

Regenerable 'gel-coated' cationic resins with fast sorption kinetics and high sorption capacity have application potential for removal of trace metal ions even in large-scale operations. Poly(acrylic acid) has been gel-coated on high-surface area silica (pre-coated with ethylene-vinyl acetate copolymer providing a thin barrier layer) and insolubilized by crosslinking with a low-molecular-weight diepoxide (epoxy equivalent 180 g) in the presence of benzyl dimethylamine catalyst at 70 degrees C, In experiments performed for Ca2+ sorption from dilute aqueous solutions of Ca(NO,),, the gel-coated acrylic resin is found to have nearly 40% higher sorption capacity than the bead-form commercial methacrylic resin Amberlite IRC-50 and also several limes higher rate of sorption. The sorption on the gel-coated sorbent under vigorous agitation has the characteristics of particle diffusion control with homogeneous (gel) diffusion in resin phase. A new mathematical model is proposed for such sorption on gel-coated ion-exchange resin in finite bath and solved by applying operator-theoretic methods. The analytical solution so obtained shows goad agreement with experimental sorption kinetics at relatively low levels (< 70%) of resin conversion.

A molecular dynamics investigation of the structure of PbO---PbF2 glasses*1

The structure of PbO---PbF2 glasses has been studied using molecular dynamics (MD). The existence of [OPb4] structural units is observed over the entire glass-forming range, in conformity with a model proposed earlier based on various structural investigations of this system. Various other features of the structural model are also supported by the MD calculations.

Coarse-Grained Molecular Dynamics Simulation of the Aggregation Properties of Multiheaded Cationic Surfactants in Water

The aggregation property of multiheaded surfactants has been investigated by constant pressure molecular dynamics (MD) simulation in aqueous medium. The model multiheaded surfactants contain more than one headgroup (x = 2, 3, and 4) for a single tail group. This increases the hydrophilic charge progressively over the hydrophobic tail which has dramatic consequences in the aggregation behavior. In particular, we have looked at the change in the aggregation property such as critical micellar concentration (cmc), aggregation number, and size of the micelles for the multiheaded surfactants in water. We find with increasing number of headgroups of the Multiheaded surfactants that the cmc values increase and the aggregation numbers as well as the size of the micelles decrease. These trends are in agreement with the experimental findings as reported earlier with x = 1, 2, and 3. We also predict the aggregation properties of multiheaded surfactant With four headgroups (x = 4) for which no experimental studies exist yet.