Evaluation of the protein solvent-accessible surface using reduced representations in terms of critical points of the electron density

The aim of our study is the development of a method for calculating the interface of dimerization of protein-protein complexes based on simplified medium-resolution structures. In particular, we wished to evaluate if the existing concepts for the computation of the Solvent-Accessible Surface Area (SASA) of macromolecules could be applied to medium-resolution models. Therefore, we selected a set of 140 protein chains and computed their reduced representations by topological analysis of their electron density maps at 2.85 A crystallographic resolution. This procedure leads to a limited number of critical points (CPs) that can be identified and associated to backbone and side-chain parts. To evaluate the SASA and interfaces of dimerization of the reduced representations, we chose and modified two existing programs that calculate the SASA of atomic representations, and tested (1) several radii tables of amino acids, (2) the influence of the backbone and side-chain points, and (3) the radius of the solvent molecule, which rolls over the surface. The results are shown in terms of relative error compared to the values calculated on the corresponding atomic representations of the proteins.     

Critical Points in a Crystal and Procrystal

The critical points in the model electron density distributions of LiF, NaF, NaCl, and MgO crystals, constructed from accurate X-ray diffraction data, are determined. For LiF and MgO they are compared with those obtained from a Hartree–Fock electron density calculation. Both experiment and theory show the same type of critical points on the bond lines. The topological features in areas between structural units, where the electron density is low and near-uniform, turn out to be model dependent and cannot be established well with the data available. Topological analysis of procrystals (hypothetical systems consisting of spherical atoms or ions placed on the same sites as atoms in real crystal) show that (3, –1) critical points, usually connected with bonding interaction, are observed on interatomic lines in these nonbonded systems as well.     

The practice for eight-year operation of the cobalt-60 irradiation facility at Beijing Radiation Application Research Center

The radiation facility was made by Sulzer Company in Switzerland. The designed capacity is 3.7 × 10¹⁶Bq( 1MCi) and 12.21 × 10¹⁵Bq(330kCi)of Cobalt -60 source was loaded at the first phase. Current cobalt -60 source-loading is 2.4 × 10¹⁶Bq(650kCi). The equipment assembling and installation regulating and testing were completed at the end of 1988. The facility was put into commissioning in 1989. It operates 7000–8000 hours per year. The facility has been utilized to carry out many research work and irradiate many kinds of items. Lots of economical benefits have been gained since then. Now it is becoming a radiation processing model base in China. This paper summarized the strong and weak points of the design of the facility through in eight years' practice and analysed the economical benefits.     

Properties of Ionic Liquid Confined in Porous Silica Matrix

Porous silica matrices of different pore sizes with confined ionic liquid (1‐butyl‐3‐methylimidazolium hexafluorophosphate) [BMIM] [PF₆] were prepared by sol‐gel technique using a tetraethyl orthosilicate (TEOS) precursor with an aim to study the changes in physico‐chemical properties of ionic liquid on confinement. It is found that on confinement 1) melting point decreases, 2) fluorescence spectra shows a red shift and 3) the vibrational bands are affected particularly those of imadazolium ring, which interacts more with the walls of the silica matrix. Preliminary theoretical calculations suggest that SiO₂ matrix interact more with the heterocyclic group of [BMIM] cation than the tail alkyl chain end group resulting in significant changes in the aromatic vibrations.     

衍生气相色谱-质谱法测定水中氯代酸性除草剂

采用H2SO4加入法改变了酸性除草剂在水中的存在状态,对碱性活化点的存在与消除进行了分析,同时对不同试剂的萃取效率进行了对比,建立了衍生气相色谱-质谱法测定水中10种氯代酸性除草剂的方法。化合物检出限均低于10.0 ng/L,回收率范围为60%～120%。     

Do intramolecular halogen bonds exist? Ab initio calculations and crystal structures’ evidences

Cl···O intramolecular contacts are analysed here. Hence the Cambridge Structural Database (CSD) search was performed to find five-membered Cl–C=C–C=O pseudo-rings closed through Cl···O intramolecular contacts. Such rings were analysed and it was found that some of Cl···O distances are smaller than the corresponding sum of van der Waals radii. Additionally ab initio MP2/6-311++G(d,p) calculations and AIM analyses were carried out here on 3-chloropropenal and its fluoro derivatives to deepen the nature of intramolecular Cl···O interactions, some of findings may indicate that they are attractive and stabilizing ones. This paper is dedicated to Prof. T. M. Krygowski on the occasion of his 70th birthday     

Mutual solubilities of hydrocarbons and water with the CPA EoS

The knowledge of hydrocarbon/water phase equilibria is important in the design and operation of equipment for petroleum transport and refining and petrochemical plants. The presence of water in a hydrocarbon mixture can affect the product quality and damage the operation equipment due to corrosion and formation of gas hydrates. Tracing the concentration of hydrocarbons in aqueous media is also important for technical purposes like preventing oil spills and for ecological concerns such as predicting the fate of these organic pollutants in the environment.     

Freezing temperatures of aqueous solutions of methyl formate and ethyl acetate with a variety of nonelectrolytes. Gibbs energy of interaction of the ester group with other functional groups

Freezing temperatures of dilute aqueous solutions of ethyl acetate and mixtures with myo-inositol, D-mannitol, formamide, 1,3,5-trioxane, 1,4-dioxane, acetamide, hexamethylenetetramine, and methyl formate have been measured. In addition, freezing temperatures of dilute aqueous solutions of methyl formate and mixtures with the above solutes have been measured. From these data, the pairwise molecular Gibbs energies of interaction between the molecules were calculated. Using the additivity principle, the pairwise functional group Gibbs energies of interaction were calculated for ester group interactions with a variety of other functional groups.     

Thermodynamics of saturated lanthanide nitrate-water systems

The thermodynamic properties of saturated aqueous lanthanide nitrate solutions were determined using recently published critically evaluated solubility and activity data. The variation of the thermodynamic functions and congruent melting points as a function of atomic number are interpreted in terms of changes in inner sphere coordination number in both the solid hexahydrates and in the aquo ions, and in terms of the double-double effect.Inconsistencies in experimental solubility data are generally caused by uncertainties in solid phase composition which is shown to be due to the very small Gibbs energies accompanying transitions from stable to metastable systems differing in the number of hydrating water molecules.Presentation to First International Symposium on Solubility Phenomena, University of Western Ontario, London, Ontario, August 21–23, 1984.     

A reduced-restricted-quasi-Newton–Raphson method for locating and optimizing energy crossing points between two potential energy surfaces

We present a method for the location and optimization of an intersection energy point between two potential energy surfaces. The procedure directly optimizes the excited state energy using a quasi-Newton–Raphson method coupled with a restricted step algorithm. A linear transformation is also used for the solution of the quasi-Newton–Raphson equations. The efficiency of the algorithm is analyzed and demonstrated in some examples. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 :992–1003, 1997