DMC: A multifunctional hybrid dynamics/Monte Carlo simulation algorithm for the evaluation of conformational space

A hybrid conformational search algorithm (DMC) is described that combines a modified form of molecular dynamics with Metropolis Monte Carlo sampling, using the COSMIC(90) force field. Trial configurations are generated by short bursts of high-temperature dynamics in which the initial kinetic energy is focused into single bond rotations or alternatively into “corner-flapping” motions in ring systems. Constant temperature and simulated annealing search protocols have been applied to the conformational analysis of several model hydrocarbons (cyclopentane, cyclohexane, cycloheptane, cyclooctane, cycloheptadecane, decane, and tetradecane), and the performance compared with conventional molecular dynamics and Monte Carlo sampling methods. Optimum Metropolis sampling temperatures have been determined and range from 1000–2000 K for acyclic molecules to 3000 K for cyclic systems. Simulated annealing runs are most successful at locating the global minimum when cooling slowing from these optimum temperatures.     

Electron spin echo as a tool for investigation of surface structure of finely dispersed fractal solids

The ESE method was successfully used for investigating the texture of the adsorbents and catalysts. Equations were obtained for the kinetics of ESE signal decay due to dipole-dipole interaction between motionless paramagnetic centers distributed uniformly on the fractal surface of solid.

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Water-Soluble imide-amide copolymers. II. Preparation and characterization of poly (acrylamide-co-p-maleimidobenzoic acid)

The comonomer required, p-maleimidobenzoic acid (MBA) was first prepared in good yield by refinements of published methods. p-Carboxysuccinanilic acid (CSA), and p-succinimidobenzoic acid (SBA), were also prepared to provide models useful for IR and NMR for spectroscopic assignments of the new copolymers. Polymerization of MBA with acrylamide in glacial acetic acid at 60°C gave copolymers with estimated viscosity average molecular weights of 60,000 to 90,000. Yields and viscosity average molecular weights decreased as the MBA to acrylamide monomer feed ratio was increased. The rate of incorporation of MBA into the copolymer rose from 7 to 23% when the mole ratio in the feed was raised from 5 to 20%. Decreasing the initiator concentration increased molecular weights by less than predicted and reduced the yield of copolymer for any given feed ratio of MBA to acrylamide. In all cases about 30–40% of the MBA units in the purified copolymers were hydrolyzed. A change to dimethyl sulfoxide solvent gave good, and poor yields of copolymer at 5 and 10 mol % MBA, respectively, and no copolymer at 20 mol % MBA. Viscosity average molecular weights of the copolymer products prepared in DMSO were somewhat lower than obtained for the copolymers prepared in acetic acid. Polymerization in a DMSO-water mixture gave a negligible yield of polymeric product. Instead, only hydrolysates of MBA precipitated when the coloured polymerization solutions were added to methanol.     

Preparation de membranes echangeuses de cations par photogreffage d'ethers allyliques du poly (alcool vinylique). Etude de certaines de leurs proprietes—II: Photogreffage des poly (alcools vinyliques) allyles

Poly(vinyl alcohols) partially allylated have been grafted with sulphonic acid. The influence of experimental parameters (vinyl sulphonic acid concentration, swelling before grafting, photoinitiator concentration, grafting temperature and duration of the irradiation) have been studied in detail.     

Identification of inhibitors for UDP-galactopyranose mutase

The flavoenzyme uridine 5'-diphosphate (UDP)-galactopyranose mutase (UGM) plays a key role in the cell wall biosynthesis of many pathogens, including Mycobacterium tuberculosis. Using a synthetic fluorescent ligand, we screened 16 000 compounds in a fluorescence polarization assay. Effective inhibitors of UGM were identified.     

Computational modeling of amorphous silica. 4. Modeling the initial structures. Aerogel

A qualitative classification algorithm for constructing large clusters of aerogel model structures is used. According to this algorithm, aerogel is classified with polysilicas characterized by a packing of long chains of silicon-oxygen tetrahedra. A model of the aerogel structure is suggested, according to which aerogel is described as a set of cross-linked chains forming double or more complex ribbons. This model is in agreement with the conclusions drawn from analysis of the vibration spectra of its components. Institute of Surface Chemistry, Ukrainian Academy of Sciences. Russian University of Peoples' Friendship. Translated fromZhurnal Strukturnoi Khimii, Vol. 35, No. 3, pp. 35–38, May–June, 1994. Translated by O. Kharlamova     

Biomimetic dyes as affinity chromatography tools in enzyme purification

Affinity adsorbents based on immobilized triazine dyes offer important advantages circumventing many of the problems associated with biological ligands. The main drawback of dyes is their moderate selectivity for proteins. Rational attempts to tackle this problem are realized through the biomimetic dye concept according to which new dyes, the biomimetic dyes, are designed to mimic natural ligands. Biomimetic dyes are expected to exhibit increased affinity and purifying ability for the targeted proteins. Biocomputing offers a powerful approach to biomimetic ligand design. The successful exploitation of contemporary computational techniques in molecular design requires the knowledge of the three-dimensional structure of the target protein, or at least, the amino acid sequence of the target protein and the three-dimensional structure of a highly homologous protein. From such information one can then design, on a graphics workstation, the model of the protein and also a number of suitable synthetic ligands which mimic natural biological ligands of the protein. There are several examples of enzyme purifications (trypsin, urokinase, kallikrein, alkaline phosphatase, malate dehydrogenase, formate dehydrogenase, oxaloacetate decarboxylase and lactate dehydrogenase) where synthetic biomimetic dyes have been used successfully as affinity chromatography tools.     

Determination of low levels of an antioxidant in polyolefins by large-volume injection temperature-programmed packed capillary liquid chromatography

Sub-ambient column temperatures, promoting strong interactions between the analyte and the stationary phase material, were utilized to focus large volumes of the polyolefin antioxidant Irganox 1076 [benzenepropanoic acid, 3.5-bis(1,1-dimethylethyl)-4-hydroxy-, octadecyl ester] on the column inlet, using pure acetonitrile as sample solvent and mobile phase. Injection volumes up to 100 microl were successfully employed on a 50 cm x 320 microm I.D. capillary column packed with 5 microm Kromasil 100 ODS particles. Irganox 1076 was eluted after completed injection by temperature programming, using a temperature program from 7 to 90 degrees C, in 3 degrees C min(-1). UV detection, using a low-dispersion "U"-shaped flowcell, was performed at 280 nm. The method was applied for the determination of Irganox 1076 that was extracted from low-density polyethylene (0.6 ppm, w/w). Both Soxhlet and microwave-aided solvent extractions were performed, using chloroform and acetonitrile as solvents, respectively. The microwave-aided extraction with acetonitrile was found to give approximately the same yield as the standard Soxhlet reference method. Consequently, small volumes of acetonitrile could be used both as extraction solvent, sample solvent and mobile phase, simplifying the analysis process. The mass limit of detection of the method was found to be 3.3 ng, corresponding to a concentration limit of detection of 33 ng ml(-1), utilizing an injection volume of 100 microl. The within and between day precision of retention times displayed relative standard deviations below 1.2%.     

Rheology of PVC plastisol--VI: criteria for yielding and fracture of an immobilized layer

PVC plastisol exhibits pseudo-plastic flow in steady shear; that is, viscosity decreases with the increasing shear rate. At higher shear rates viscosity reaches a minimum and then increases, i.e., dilatant behavior. Previously, pseudo-plastic behavior was explained by a mechanism in which the suspended particles partition into an immobilized layer and a mobile phase. The development of the immobilized layer with the increase in shear rate was shown to quantitatively account for pseudo-plastic behavior. In higher shear rates dilatation of the immobilized layer was shown to be the cause of dilatacy. At even higher shear rates the immobilized layer fractures. In this paper the viscosity minimum was interpreted as the yielding of the immobilized layer. Subsequently, data in the literature were analyzed to find criteria for the yielding and fracture of the immobilized layer. Yielding was found to obey Coulomb's criterion, from which the coefficient of friction and the cohesive strength of the immobilized layer were evaluated. These properties were controlled by the nature of particle assembly in the immobilized layer and the plasticizer type had only a minor effect. The value of the coefficient of friction was on the lower side and within the range of values found in the literature for other materials. There were two modes of fracture of the immobilized layer, one with low strength, low strain to break, and the other with high strength, high strain to break. The former is analogous to the brittle fracture of solids and the latter ductile failure. The strength of brittle fracture was somewhat higher than cohesive strength, which was evaluated from yielding data. This is akin to Griffith's criterion for brittle fracture of a solid. Ductile failure occurred when the shear stress exceeded normal stress.