CHARGE ACCUMULATION IN THE REACTION CENTER OF PHOTOSYSTEM 2

Abstract— The significance of the accumulation of positive charge in the reaction center of the oxygen-evolving system of photosynthesis is discussed. Many experiments on delayed and prompt fluorescence are explained by the electric field caused by positive charges on the various components at the oxidizing side of the photosystem 2 reaction center. A molecular model for this reaction center is proposed.     

The molecular electrostatic potential of some simple molecules

The calculation of the molecular electrostatic potential from simplified models of the electron density is considered. Results are shown for water, hydrogen fluoride and ammonia. Little loss of accuracy is evident when the density is represented by a linear sum of well-chosen Gaussians. When these are further simplified into sets of point charges the inner parts of the molecule are poorly represented. More elaborate point moments make the representation worse. On the other hand a mixed representation with point charges and one diffuse Gaussian gives all the essential features of the potential of these molecules.     

Prediction of protein structural class using novel evolutionary collocation-based sequence representation

Knowledge of structural classes is useful in understanding of folding patterns in proteins. Although existing structural class prediction methods applied virtually all state-of-the-art classifiers, many of them use a relatively simple protein sequence representation that often includes amino acid (AA) composition. To this end, we propose a novel sequence representation that incorporates evolutionary information encoded using PSI-BLAST profile-based collocation of AA pairs. We used six benchmark datasets and five representative classifiers to quantify and compare the quality of the structural class prediction with the proposed representation. The best, classifier support vector machine achieved 61-96% accuracy on the six datasets. These predictions were comprehensively compared with a wide range of recently proposed methods for prediction of structural classes. Our comprehensive comparison shows superiority of the proposed representation, which results in error rate reductions that range between 14% and 26% when compared with predictions of the best-performing, previously published classifiers on the considered datasets. The study also shows that, for the benchmark dataset that includes sequences characterized by low identity (i.e., 25%, 30%, and 40%), the prediction accuracies are 20-35% lower than for the other three datasets that include sequences with a higher degree of similarity. In conclusion, the proposed representation is shown to substantially improve the accuracy of the structural class prediction. A web server that implements the presented prediction method is freely available at http://biomine.ece.ualberta.ca/Structural_Class/SCEC.html.     

Experimental and theoretical assessment of the mechanism involved in the reaction of steroidal ketone semicarbazone with hydrogen peroxide

3β-Acetoxy-5α-cholestan-6-one semicarbazone 1 on reaction with hydrogen peroxide affords selectively 3β-acetoxy-5α-cholestan-6-spiro-1',2',4'-triazolidine-3'-one 2. The structural assignment of the product was confirmed by spectral data and elemental analysis. A free radical mechanism of the present reaction was described successfully by calculating theoretical models of 1, A, B and 2, using DFT with B3LYP/6-31G* basis set. It was found that the reaction undergoes through the formation of two radical intermediates and the only one isomer of the product in which -NH-CO- group is cis with respect C5α-H, was selectively obtained. Frontier molecular orbital, spin electronic density, electrostatic potential and atomic charges were discussed.     

Chemical markup,XML, and the World Wide Web. 4. CML schema

A revision to Chemical Markup Language (CML) is presented as a XML Schema compliant form, modularized into nonchemical and chemical components. STMML contains generic concepts for numeric data and scientific units, while CMLCore retains most of the chemical functionality of the original CML 1.0 and extends it by adding handlers for chemical substances, extended bonding models and names. We propose extension via new namespaced components for chemical queries, reactions, spectra, and computational chemistry. The conformance with XML schemas allows much greater control over datatyping, document validation, and structure.     

Potential energy surfaces for small alcohol dimers I: methanol and ethanol

Potential energy landscapes for homogeneous dimers of methanol and ethanol were calculated using counterpoise (CP) corrected energies at the MP26-311+G(2df,2pd) level. The landscapes were sampled at approximately 15 dimer separation distances for different relative monomer geometries, or routes, given in terms of a relative monomer yaw, pitch, and roll and the spherical angles between the monomer centers (taken as the C atom attached to the O). The 19 different routes studied for methanol and the 22 routes examined for ethanol include 607 CP corrected energies. Both landscapes can be adequately represented by site-site, pairwise-additive models, suitable for use in molecular simulations. A modified Morse potential is used for the individual pair interactions either with or without point charges to represent the monomer charge distribution. A slightly better representation of the methanol landscape is obtained using point charges, while the potential energy landscape of ethanol is slightly better without point charges. This latter representation may be computationally advantageous for molecular simulations because it avoids difficulties associated with long-range effects of point-charge-type models.     

Rapid gel-like latex film formation through controlled ionic coacervation of latex polymer particles containing strong cationic and protonated weak acid functionalities

We introduce a controlled ionic coacervation (CIC) process that rapidly forms uniform, gel-like latex films with significant mechanical integrity without loss of water from the film. This process uses latex particles that contain both strong cationic charges and weak protonated acid groups. An increase in pH ionizes the weak acid and triggers the rapid setting of the latex films. The necessary increase in pH can be achieved by coating the latex onto an alkaline surface (such as concrete) or by controlled release of a fugitive acid (such as carbon dioxide). We explore the effect of latex composition and concentration on this process. We show that the CIC process does not require a water-soluble polymer to obtain the rapid-set film properties. Our proposed mechanism for CIC process is consistent with models for rapid, irreversible, particle-particle aggregation.     

Class IV charge models: A new semiempirical approach in quantum chemistry

Summary We propose a new criterion for defining partial charges on atoms in molecules, namely that physical observables calculated from those partial charges should be as accurate as possible. We also propose a method to obtain such charges based on a mapping from approximate electronic wave functions. The method is illustrated by parameterizing two new charge models called AM1-CM1A and PM3-CM1P, based on experimental dipole moments and, respectively, on AM1 and PM3 semiempirical electronic wave functions. These charge models yield rms errors of 0.30 and 0.26 D, respectively, in the dipole moments of a set of 195 neutral molecules consisting of 103 molecules containing H, C, N and O, covering variations of multiple common organic functional groups, 68 fluorides, chlorides, bromides and iodides, 15 compounds containing H, C, Si or S, and 9 compounds containing C-S-O or C-N-O linkages. In addition, partial charges computed with this method agree extremely well with high-level ab initio calculations for both neutral compounds and ions. The CM1 charge models provide a more accurate point charge representation of the dipole moment than provided by most previously available partial charges, and they are far less expensive to compute.     

Free energy of charge transfer and intraprotein electric field: method of calculation depends on the charge state of protein at a given structure.

Free energy of charge transfer presents a basic characteristic of reactions such as protonation, oxido-reduction and similar. Evaluation of this quantity requires calculation of charging energy. Proteins are structured dielectrics, and a consistent incorporation of their structure into calculation of intraprotein electric field results in expression for charging energy of an active group in protein, which is essentially different from that for a simple dielectric. An algorithm for semi-continuum calculation of relevant free energies is described. First of the two components of charging energy in protein, energy of the medium response to charge redistribution in reactants, should be always calculated as the charging energy by the charge redistribution using the static dielectric constant of protein. The second term is interaction energy of the charge redistribution with the 'frozen' electric field of the system before reaction. Charges of protein groups, at which the protein structure has been determined, are often different from those before reaction of charge transfer, so is the corresponding intraprotein field. The field is expressed through either both the optical and static dielectric constants of protein or only optical one depending on whether the charges of protein groups before reaction and upon structural analysis are the same or not. Proper allowance for difference in charges of reacting groups before reaction and upon structural analysis of protein is thermodynamically necessary and quantitatively important. The expression for activation free energy for charge transfer in proteins is derived in the form presenting explicitly an invariant contribution of protein structure.     

A catalytic reaction of alkynes via multiple-site functionalization

The first multiple-site activation of alkynes with amine/halogen functionalities has been established. The reaction was performed by treating alkyne with N,N-dichlorobenzenesulfonamide at 80 degrees C in the presence of palladium acetate catalyst. A new mechanism was proposed which involves the novel formation of beta-halovinyl palladium and pi-allylpalladium species. Excellent regio- and stereoselectivities were achieved with the absolute structure determined by X-ray structural analysis.     

Hepatitis C virus contact map prediction based on binary encoding strategy

Inter-residue contact map is an important two-dimensional representation of protein spatial structure, and has much potential application in the area of understanding protein fold mechanism. In the present note, a 19-bit binary input encoding strategy, integrating with residue pair conformational features (possible residue pairwise, residue classification, secondary structure, sequence length, and sequence separation information), is proposed for the purpose of capturing mapping relationship of protein sequence. Simulation results on a set of 61 hepatitis C virus (HCV) retrieved from the protein data bank (PDB) demonstrate that the proposed encoding scheme could precisely capture conformational patterns within HCV protein sequence. This promising result could provide some useful insights into the nature of HCV protein fold mechanism.     

Theoretical study of the interaction between selected adhesives and oxide surfaces

We investigate the competition of the various organic components of two representative adhesive systems for reactive defect sites at model surfaces of both SiO2 and Al2O3. The reaction energies of resin monomers, curing agents, and in some cases also of additional adhesion promoters with the defects are calculated. We applied a density-functional based tight-binding method including a self-consistent correction of the Mulliken charges, which has already proven to be a useful tool for computational materials science, delivering reliable structural and energetic information.     

渣油加氢脱残炭的动力学模型研究

以渣油为原料在200 mL反应装置上进行加氢脱残炭试验，同时依据渣油残炭的结构组成以及加氢脱残炭的反应历程，对试验结果进行了分析，在此基础上提出渣油加氢脱残炭的三集总反应动力学模型，并与一集总和二集总加氢脱残炭反应动力学模型进行比较。结果表明，一集总动力学模型不能用来描述渣油加氢脱残炭过程，从二、三集总动力学模型的预测数据与试验值误差来分析，将沥青质与胶质做为一个集总或渣油原料的沥青质含量较少时所建立的动力学模型，两者误差精度相当。用三集总的一级反应动力学模型预测渣油加氢脱残炭过程时，与试验值相比，加氢脱残炭转化率的平均绝对误差为0.005 6，加氢渣油残炭值的平均相对误差为1.01％。     

Modeling Strategies for the Propagation of Terminal Double Bonds During the Polymerization of N‐Vinylpyrrolidone and Experimental Validation

Based on a recently suggested reaction mechanism, which involves the production and propagation of terminal double bonds (TDBs), kinetic models for the polymerization of N‐vinylpyrrolidone in aqueous solution are developed. Two modeling strategies, the classes and the pseudodistribution approach, are applied to handle the multidimensional property distributions that result from this reaction mechanism and to get detailed structural property information, e.g., on the chain length distribution and the distribution of TDBs. The structural property information is then used to develop reduced models with significantly lower computational effort, which can be used for process design, on‐line applications or coupled to computational fluid dynamic simulations. To validate the derivations, the models are first compared against each other and finally to experimental results from a continuous stirred tank reactor. The evolution of monomer conversion and molecular weight average data as well as molecular weight distributions can be represented very well by the models that are derived in this article. These results support the correctness of the reaction mechanism predicted by quantum mechanical simulations.     

The effect of external and internal diffusion on the sorption of radioactive ions by reactive cloth filter: Part I

In this study, a new mathematical model was suggested to account for the effect of internal and external diffusion on fluid–solid noncatalytic reactions. The special features of this model are the combination of the transport processes and the chemical reaction kinetics with the added factor due to the structural properties of the solid reactant. The model was examined theoretically and experimentally. A reactive cloth filter that separates radionuclides from radioactive waste solutions is used as a practical application for the model. Analyses of the respective rate data in accordance with another two theoretical models showed that process is controlled by the rate of the diffusion step. The external and internal mass transfer constants across the liquid film and the resin matrix were determined from the graphical representation of the proposed model. The practical validation with the theoretical results offered satisfactory agreement at most of the process stages.     

One-pot synthesis of novel fused pentacyclic chromenopyrimidobenzimidazolones and benzimidazolyl-chromenyl-substituted thiazolidinones

The ultrasound promoted synthesis of a number of novel fused pentacyclic chromenopyrimido[1,2-α]benzimidazolones by the one-pot reaction of 3-formylchromones with 2-aminobenzimidazole is described. Moreover, the isolated pentacyclic chromone derivatives upon microwave irradiation with 2-mercaptocarboxylic acids afforded benzimidazolyl-chromenylthiazolidinones incorporating three pharmacophoric heterocycles; the same thiazolidinones were also formed through a multicomponent reaction under microwave irradiation involving 3-formylchromones, aminobenzimidazole and 2-mercaptocarboxylic acids. The structural elucidation of the products was accomplished by 1D and 2D NMR experiments and for thiazolidinones was also confirmed by X-ray crystallographic analysis. Full assignment of all ¹H and ¹³C NMR chemical shifts has been unambiguously achieved. The proposed reaction mechanism is also discussed.     

硝酸根接枝诱导组装金红石相TiO2纳米束以增强光催化产氢（英文）

化石燃料的快速消耗加速了全球能源危机和环境污染等问题.光催化产氢直接利用清洁和可持续的太阳能实现向化学燃料的转化,因而成为一种有前景的技术.众多半导体光催化剂中,二氧化钛因其高光催化活性、稳定的化学性质、低成本和无毒等优势而被广泛用作分解水产氢的光催化剂.最近,金红石相TiO2纳米晶体在某些情况下被证明具有光催化的潜力,然而其光生电子-空穴对的快速复合显著抑制了光催化效率.表面修饰、构建异质结和负载助催化剂等策略被用来提高光生载流子的分离效率以减少复合损失,从而提升光催化活性.由于光催化反应通常发生在光催化剂的表面活性位点上,因此通过改善表面性质改变电荷转移途径对光催化活性具有重要影响.磷酸、硫酸、硼酸和盐酸等无机酸的修饰可以改变光催化剂的表面基团,分别通过促进表面羟基的形成和氧气的吸附以及改变表面电荷性质更有效地捕获空穴,实现光生电子和空穴的分离,有助于光催化降解有机污染物.然而,这种影响机制显然不适用于光催化产氢体系,目前对无机酸修饰用于分解水产氢的研究鲜有报道.因此,通过酸改性策略制备高效产氢的光催化剂仍然是一个相当大的挑战.本文利用硝酸诱导策略合成纺锤状金红石相二氧化钛纳米束(R-TiO2).首先,制备层状质子化钛酸盐(LPT)作为TiO2的前体,随后,加入浓硝酸以诱导向金红石相TiO2的转变,并组装形成纺锤状纳米束.对照实验显示,硝酸的酸化可以诱导LPT向金红石相TiO2的转变,而相同条件下浓硝酸后处理不会引起晶相的转变.纺锤形纳米束的形成源于,硝酸诱导R-TiO2沿(110)方向生长并彼此粘附,硝酸诱导组装过程成功在TiO2表面修饰上硝酸根,同时扩大了光吸收范围,有效减少了电荷复合损失.光催化产氢测试证明了R-TiO2光催化剂具有高效的产氢性能,产氢速率为402.4μmol h-1,是Degussa P25的3.1倍,并且显著高于未经浓硝酸处理的锐钛矿(52.0μmol h^-1)或金红石相(110.8μmol h^-1)光催化剂.为了说明表面硝酸根的影响,分别从晶体和化学结构、形态以及表面电荷性质方面比较了光催化反应前后的变化,结果表明,R-TiO2增强的光催化效率可归因于硝酸根基团的负场效应,有利于在表面上捕获带正电的质子以促进载流子分离,提高光催化产氢的效率.总之,本工作不仅对于发展表面修饰策略制备高效产氢光催化剂的研究具有重要意义,而且提出了一种不同于文献报道的无机酸影响机制.     

碳化硼及掺硅系列的量子化学计算研究

应用离散变分Xα 量子化学分子轨道计算方法 ,根据 5类共 2 8个不同的结构模型 ,研究了碳化硼及掺硅系列组成 ,结构 ,化学键及热电性能之间的关系。不掺硅时碳化硼的典型结构是〔C -B -B(C)〕δ - 〔B1 1 C〕δ + 。C -B -B链连接B1 1 C二十面体的模型趋于更稳定地存在 ,它们的二十面体上的电荷最低 ,更有利于极化子的形成 ;符合碳含量为 13 .3 %时 ,碳化硼的电导率有极大值的实验结果。碳化硼掺硅后的典型结构是〔C -B -Si〕ε + 〔B1 1 C〕ε - 。由于掺硅后多种结构形式的形成 ,极化反应所需的能量降低 ,为极化子的跃迁提供更多的途径 ,导致电导率增大。同时 ,碳化硼掺硅后共价键减弱 ,热导率减小。因此 ,碳化硼掺硅后 ,其热电性能得到改善     

Analysis of nonlinear reactions in modulated molecular beam surface experiments

An approximate method of analyzing nonlinear reaction models in modulated molecular beam surface kinetic studies is developed. The exact method for treating nonlinear surface mechanisms is tedious and almost always requires computer analysis. The proposed approximate method is a simple extension of the Fourier expansion technique valid for linear surface reactions; it quickly provides analytical expressions for the phase lag and amplitude of the reaction product for any type of nonlinear surface mechanism, which greatly facilitates comparison of theory and experiment. The approximate and exact methods are compared for a number of prototypical adsorption–desorption reactions which include coverage-dependent adsorption and desorption kinetics of order greater than unity. Except for certain extreme forms of coverage-dependent adsorption, the approximate method provides a good representation of the exact solution. The errors increase as the nonlinearities become stronger. Fortunately, when the discrepancy between the two methods is substantial, the reaction product signal is so highly demodulated that reliable experimental data usually cannot be obtained in these regions anyway.     

Self-assembly of Polyaniline: Mechanism Study

Anisotropic polyaniline (PAni) plates decorated with self-aligned nanofiber arrays were synthesized under the hydrothermal conditions. The formation mechanism of the self-assembled structures was investigated by studying the effect on PAni micro-structure with additive electrolyte in reaction system, and numerical simulation for dependence of systematic electrostatic energy on cross angles of self-assembled nanofiber arrays in grid textured PAni plates. It is proposed that the electrostatic interaction based on ionic doping charges plays an important role in the formation of the self-assembled PAni structures.