Adsorption of organic substances on broken clay surfaces: a quantum chemical study

Hydrogen-bonded interactions between local defect structures on broken clay surfaces modeled as molecular clusters and the organic molecules acetic acid, acetate, and N-methylacetamide (NMA) have been investigated. Density functional theory and polarized basis sets have been used for the computation of optimized interaction complexes and formation energies. The activity of the defect structures has been characterized as physical or chemical in terms of the strength of the hydrogen bonds formed. Chemical defects lead to significantly enhanced interactions with stronger hydrogen bonds and larger elongation of OH bonds in comparison to the physical defects. The type of interaction with the defect structure significantly influences the planarity of the model peptide bond in NMA. Both cases, enhancement of the planarity by increase of the CN double bond character and strong deviations from planarity, are observed.     

The computer program LUDI: A new method for the de novo design of enzyme inhibitors

Summary A new computer program is described, which positions small molecules into clefts of protein structures (e.g. an active site of an enzyme) in such a way that hydrogen bonds can be formed with the enzyme and hydrophobic pockets are filled with hydrophobic groups. The program works in three steps. First it calculates interaction sites, which are discrete positions in space suitable to form hydrogen bonds or to fill a hydrophobic pocket. The interaction sites are derived from distributions of nonbonded contacts generated by a search through the Cambridge Structural Database. An alternative route to generate the interaction sites is the use of rules. The second step is the fit of molecular fragments onto the interaction sites. Currently we use a library of 600 fragments for the fitting. The final step in the present program is the connection of some or all of the fitted fragments to a single molecule. This is done by bridge fragments. Applications are presented for the crystal packing of benzoic acid and the enzymes dihydrofolate reductase and trypsin.     

interaction of nitro compounds with radicals: a quantum chemical study

Photoreduction of nitro compounds is accompanied by formation of various radical products that can react with the starting nitro compound, thus causing deviation of the decomposition kinetics from the first-order kinetics with respect to the nitro compound. The results of quantum chemical modeling of the reactions of nitro compounds with radicals and the pathways of further transformations of radical adducts formed in the reactions are presented. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 2, pp. 202–206, February, 2006.     

Parameter identification of thermophilic anaerobic degradation of valerate

The considered mathematical model of the decomposition of valerate presents three unknown kinetic parameters, two unknown stoichiometric coefficients, and three unknown initial concentrations for biomass. Applying a structural identifiability study, we concluded that it is necessary to perform simultaneous batch experiments with differenitial conditions for estimating these parameters. Four simultaneous batch experiments were conducted at 55°C, characterized by four different initial acetate concentrations. Product inhibition of valerate degradation by acetate was considered. Practical identification was done optimizing the sum of the multiple determination coefficients for all measured state viariables and for all experiments simultaneously. The estimated values of kinetic parameters and stoichiometric coefficients were characterized by the parameter correlation matrix, the confidence interval, and the student's t-test at 9% significance level with positive results except for the saturation constant, for which more eperiments for improving its identifiability should be conducted. In this article, we discussekinetic parameter estimation methods.     

Solution conformation by NMR and molecular modeling of three sulfide-free somatostatin octapeptide analogs compared to angiopeptin

Summary The conformation in dimethylsulfoxide of the somatostatin derivative angiopeptin and of three disulfide-free analogs was estimated by two-dimensional nuclear magnetic resonance spectroscopy at room temperature. The resulting 3D molecular graphics were compared and shown to reflect the observed differences in the inhibition of restenosis after rat aorta balloon injury by these octapeptide inhibitors. Angiopeptin and its active analog 2 displayed a relatively rigid conformation of the cyclic hexapeptide backbone due to the presence of two well-defined hydrogen bonds, further stabilized by a third hydrogen bond outside the ring. No such constraints were detected for the two biologically inactive analogs, which, compared to 2, had a two-atom longer or shorter hexapeptide ring. The well-defined structure of compound 2 may serve as an improved pharmacophore for this new class of drugs.     

Three-Dimensional Modeling of the Turbulent Plasma Jet Impinging upon a Flat Plate and with Transverse Particle and Carrier-Gas Injection

Modeling results are presented concerning the turbulent thermal plasma jet impinging normally on a substrate and with transverse injection of feedstock particles and their carrier gas from a single injection tube. The k- two-equation model is employed to model the turbulence, and particle dispersion is studied considering the interaction between the moving particles and turbulent eddies and considering the effect on particle trajectories of the random variation of the turbulent fluctuating velocities in their magnitude and direction. A well-validated three-dimensional (3-D) computer code is used in the modeling. The 3-D effects due to the carrier gas injection on the jet flow field and thus on the particle trajectories and heating histories are shown to be appreciable. The radial location of the injection tube with respect to the plasma jet is shown to be a critical parameter for the study of 3-D effects, besides the carrier-gas/plasma stream mass flux ratio. Particle dispersion considerably widens the distribution of the particle trajectories and heating histories. In addition, although pertinent swirl number is often rather small, swirling may also affect the modeling results.     

A pseudoreceptor docking study of 4,5-α-epoxymorphinans with a range of dielectric constants

Summary Thirteen 4,5-epoxymorphinan agonists with established analgesic action were docked into an Asp-Lys-His-Phe pseudoreceptor complex under a range of distance-dependent dielectric conditions. The number of compounds with potential energies of the docked complexes that agreed in rank order with corresponding analgesic potencies was determined for each condition. Two dielectric conditions, n-decane (1.991) and ethanol (24.3), enabled the greatest number of compounds to relate to their pseudoreceptors with each having 9 and 8 successes respectively. Both of these conditions demonstrated unique influences on the types of structures that were successfully docked. For example, the morphine stereoisomer -isomorphine, the geometric isomer B/C trans-morphine, and the 8-position-substituted -isomorphine were successes in the n-decane condition, whereas the ethanol condition produced the substituted codeine derivatives dihydroco-deinone and dihydroxycodeinone. These findings emphasize the importance of dielectric influence when developing force-field modeled quantitative structure-activity relationships for a closely related homologous series.     

Solid-liquid equilibrium diagrams of common ion binary salt hydrate mixtures involving nitrates and chlorides of magnesium, cobalt, nickel, manganese, and iron(III)

The solid-liquid equilibrium diagrams of binary mixtures involving magnesium nitrate hexahydrate with cobalt nitrate hexahydrate, nickel nitrate hexahydrate (partly), manganese nitrate tetrahydrate, and iron(III) nitrate nonahydrate and of magnesium chloride hexahydrate with cobalt and nickel chlorides hexahydrates and manganese chloride tetrahydrate, and the of two manganese salts were determined. Those diagrams that showed a simple eutectic were fitted by the Ott equation and where the required BET parameters were available, the magnesium salt rich parts of the liquidus were modeled by means of this method.     

可生物降解聚合物药物释放数学模拟研究进展

由于可降解的聚合物作为药物载体可以使得药物释放具有较高的靶向性、药物释放更加平缓 ,特别是可以使一些不稳定、半衰期短的药物在人体内达到可控制释放的效果 ,因此将可降解聚合物应用于药物释放体系中作为药物载体得到了较深入的研究。随着研究的深入 ,通过数学方法模拟或预测聚合物载体的降解过程以及聚合物降解过程中药物的释放行为是控释体系设计与应用的一个重要发展方向。由于影响因素较多 ,将所有因素逐一考虑将使得数学模型过于庞杂而失去实际意义 ,所以一个数学模型通常只考虑最主要几个的影响因素 ,并对药物释放系统进行相应的假设。目前文献中报道的降解 (溶蚀 )控制药物释放体系的数学模型大致可以分为两类 :假设药物释放按照零级过程 (zeroorderprocess)进行的经验模型和考虑影响药物释放的多种物理化学过程(如局部传质、化学反应 )的理论模型。本文综述了这些理论模型及其研究进展     

ansa-Zirconocenium catalysis of syndiospecific polymerization of propylene: Theory and experiment

The syndiospecific propylene polymerizations catalyzed by isopropylidene(cyclopentadienyl)(fluorenyl)- and (2,2-dimethylpropylidene)(cyclopentadienyl)(fluorenyl)-zirconocenium ( 1 ⁺ and 2 ⁺) have been investigated theoretically and compared with experimental observations. With the ab initio calculated structures for the transition state (TS) of 1 ⁺(M)P and 2 ⁺(M)P (M = propylene, P = 2-methylpentyl), their steric energies (E°) have been computed using MM2 force-field. The difference between steric energies E°(m) and E°(r) for the meso and racemic enchainment of propylene, respectively, is defined as the stereocontrol energy [δE°(m ? r)] for syndiotactic propagation. The δE°(m ? r) for the TS of 1 ⁺ (M)P is about 2.1 kcal/mol, the value is 1 kcal/mol greater for 2 ⁺(M)P. The observed steric pentad distributions of the syndiotactic poly(propylene) obtained by these catalysts are consistent with smaller effective stereocontrol energy, which is about two-third as large as δE°(m ? r) values calculated for the MM2 optimized structure. Syndiotactic enchainment is favored over isotactic enchainment for all combinations of site configurations in the catalyst. α-Agostic interaction seems to enhance syndioselectivity, whereas γ-agostic interaction changes the stereoselectivity to meso enchainment. The mirror plane symmetry of the syndiotactic propagating species renders the stereoselectivity of the polymerization insensitive to reaction conditions. These catalysts are also highly regiospecific. © 1995 John Wiley & Sons, Inc.