A comparative study of various computational approaches in calculating the structure of pyridoxal 5'-phosphate (PLP)-dependent beta-lyase protein. The importance of protein environment

Various computational approaches, using molecular mechanics (Amber), semiempirical (AM1), density functional (B3LYP), and various ONIOM methods, have been comparatively investigated for the structure of Escherichia coli NifS CsdB protein. The structure of the entire monomer containing 407 amino acid residues and 579 surrounding water molecules has been optimized. The full geometry optimization in the "active site-only" approach (including only active site atoms) has been found to give the largest root-mean-square (RMS) deviation from the X-ray structure; a much better agreement has been achieved by keeping the atoms leading to the backbones of some amino acids frozen in their positions in the X-ray structure. The best agreement has been attained by including the surrounding protein in the calculations using the two-layer ONIOM (B3LYP:Amber) approach. The results presented in this study conclusively demonstrate the importance of the protein/active-site interaction on the active-site structure of the enzyme. The present theoretical study represents the largest system studied at the ONIOM level to date, containing 7992 atoms, including 84 atoms in the QM region and rest in the MM region.     

Weak dihydrogen bond interactions in organic crystals

Database analysis on H ? H interactions of the type CH₂ ? H₂C and N-H ? H-N in organic crystals substantiate the occurrence of dihydrogen bonds in the absence of metal atoms.     

Enthalpic interaction coefficients of formamides dissolved in N,N-dimethylformamide

Enthalpies of dilution of formamide, N-methylformamide, N-ethylformamide, N-propylformamide, N-butylformamide, N-pentylformamide, N,N-diethyl-formamide, N,N-dipropylformamide, N,N-dibutylformamide, and N,N-dipentyl-formamide dissolved in N,N-dimethylformamide as solvent have been measured calorimetrically at 25°C. The results are interpreted in terms of the McMillan-Mayer theory. Enthalpic interaction parameters are obtained for pairs, triplets, and in some cases, quadruplets of solute molecules. In general, the enthalpic pair interaction coefficients are negative, whereas the triplet coefficients are positive. The interaction enthalpies are positive only for N-methylformamide and formamide. The magnitudes of the enthalpic pair and triplet interaction coefficients increase with increasing number of C atoms in the N-alkyl groups. The results for the formamides presented in this paper are compared with those for corresponding acetamides published earlier. Although the trends are comparable, distinct differences are observed. The contribution of the -CH₃ group at the CO side of the dialkylacetamides to the enthalpic interaction coefficients appears to be negligible. The same is true for -CH₂ groups at the NH side of a number of amides and related compounds. The enthalpic pair interaction coefficients of the mono-N-alkylsubstituted formamides show a shift of about 100 J-kg-mol^–2 as compared with isomeric N-alkylacetamides. This is discussed in terms of the difference in proton donating and accepting ability of several types of amide molecules. It is concluded that substitution effects should be incorporated in additivity models for these type of systems.     

Thermodynamics of mixed electrolyte solutions. XI. An isopiestic study of the quaternary system NaCl−KCl−CaCl2−H2O at 25°C

Osmotic and activity coefficients in the aqueous quaternary system sodium chloride-potassium chloride-calcium chloride were derived from isopiestic measurements at 25°C. The isopiestic data were treated by the various procedures of Scatchard, Friedman, and Reilly, Wood, and Robinson. The results obtained showed good agreement with those obtained by pseudo-ternary transforms. Interaction parameters obtained indicated the preponderance of pairwise interactions. Excess Gibbs free energies of mixing were calculated.     

Correlated intermolecular interaction components from asymptotically corrected Kohn-Sham orbitals

In these years there was considerable interest inunderstanding of intermolecular forces in energetic(explosive) systems[1—3]. The supermolecular approach(SM) is widely adopted for calculating ab initio in-termolecular interactions. Nevertheless, it is unable toprovide physically meaningful interaction contribu-tions such as electrostatic, induction, repulsion anddispersion energies. In contrast, the symmetry-adaptedperturbation theory (SAPT)[4—8] has the ability to de-rive these correlated…     

Microcalorimetry, energetics and binding studies of DNA-dimethyltin dichloride complexes

The interaction of dimethyltin dichloride (Me₂SnCl₂) with calf thymus DNA was studied at 27 °C, pH 7.6 using various techniques including isothermal titration calorimetry (ITC) and UV-Vis, fluorescence and IR spectrophotometries. The binding isotherm and enthalpy curve for Me₂SnCl₂-DNA interaction was a biphasic transition process. This was determined by the analysis of the binding data with the Hill equation. The first phase of the enthalpy curve (exothermic process) was consistent with the first set of binding site, the second phase (endothermic process, less exothermicity) was consistent with second set of binding site from the cited interactions. Our results showed that the first set of binding sites is occupied by one mole of ligand bound per near 1 base pair of DNA. The DNA-ethidium bromide (EB) complex, in the presence of Me₂SnCl₂, caused the quenching of the fluorescence emission. The Scatchard plots illustrated a non-intercalating manner for such quenching. The DNA-EB complex results indicated that the binding of Me₂SnCl₂ is with the phosphate groups of DNA at low ligand concentrations (<9 mM). This was confirmed with the IR spectrophotometric spectra. However, the binding at higher ligand concentrations (>9 mM) was with the base groups of DNA. Therefore, these results suggest that the Me₂SnCl₂ binding to DNA at low concentrations occurs through an outside interaction by an exothermic process. However, the partial unfolding of the DNA caused at higher concentrations of Me₂SnCl₂ is through an endothermic process involving interactions with the base groups.     

四溴代邻苯二甲酸根桥联的双核钴（Ⅱ）配合物的合成和表征

合成和表征了４种以四溴代邻苯二甲酸根阴离子（４Ｂｒ－ＰＨＴＨ）桥联、以１，１０－菲咯啉（ｐｈｅｎ），５－硝基－１，１０－菲咯啉（ＮＯ_２－ｐｈｅｎ），２，２′－联吡啶（ｂｐｙ）和４，４′－二甲基－２，２′－联吡啶（Ｍｅ_２ｂｐｙ）端接的双核钴（Ⅱ）配合物［Ｃｏ_２（４Ｂｒ－ＰＨＴＨ）（Ｌ）_４］（ＣｌＯ_４）（Ｌ＝ｐｈｅｎ（ｌ），ＮＯ_２－ｐｈｅｎ（２），ｂｐｙ（３），Ｍｅ_２ｂｐｙ（４））。基于ＩＲ光谱、元素分析、电导测量等方法推定配合物具有四溴代邻苯二甲酸根桥联结构和Ｃｏ（Ⅱ）离子具有畸变的八面体配位环境。进行了配合物变温磁化率（７５～３００Ｋ）的测定，其数据已用从自旋哈密顿符导出的磁方程拟合，求得交换参数Ｊ＝－０．８７ｃｍ~（－１）（１），－０．８４ｃｍ~（－１）（２），－０．８２ｃｍ~（－１）（３），－０．８５ｃｍ~（－１）（４），表明金属离子间有弱的反铁磁性自旋交换相互作用。     

Synthesis of new peptidic glycoclusters derived from β-alanine

The synthesis of an asymmetric glycocluster 1 has been achieved by coupling of a sugar unit with the β-alanine polypeptide, the principal chain, and combining a carbohydrate chain with the side chain causing it to branch from the N terminal. The synthesis of this side chain multivalent ligands is based on the scaffolding of some ω-amino acid (glycine, β-alanine, and GABA) derivatives. This method facilitated the synthesis of the cluster, of which the length of each unit differs.     

静电和疏水效应对TGEV主蛋白酶二聚体稳定性的影响

从TGEV 3CL蛋白酶二聚体结构出发,研究了TGEV 3CL蛋白酶二聚体单体之间的静电和疏水相互作用.蛋白质的静电相互作用通过有限差分方法求解Poisson-Boltzmann方程得到,疏水相互作用通过分析溶剂可及性表面模型得到.考察了不同pH值对TGEV 3CL蛋白酶二聚体静电和疏水相互作用的影响,在pH值为5.5～8.5时,二聚体静电相互作用能、静电去溶剂化能和疏水自由能都较小,表明在该条件下静电和疏水相互作用有利于二聚体的稳定存在,这符合实验结晶所需条件.pH值对静电去溶剂化能的影响大于疏水自由能,表明静电作用是造成强酸或强碱条件下二聚体不能稳定存在的主要原因.     

稀土化合物Ho2Co14Fe3的磁性分析

在分析稀土磁性常用的哈密顿中，引入了自旋－自旋偶极作用，用参数拟合的方法对Ｈｏ２Ｃｏ１４Ｆｅ３的磁化曲线进行了分析，计算结果与实验数据符合得很好，并且提示了Ｈｏ２Ｃｏ１４Ｆｅ３磁矩的突变现象。