Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

Summary An extensive crystal survey of the Cambridge Structural Database has been carried out to provide hydrogen-bond data for use in drug-design strategies. Previous crystal surveys have generated 1D frequency distributions of hydrogen-bond distances and angles, which are not sufficient to model the hydrogen bond as a ligand-receptor interaction. For each hydrogen-bonding group of interest to the drug designer, geometric hydrogen-bond criteria have been derived. The 3D distribution of complementary atoms about each hydrogen-bonding group has been ascertained by dividing the space about each group into bins of equal volume and counting the number of observed hydrogen-bonding contacts in each bin. Finally, the propensity of each group to form a hydrogen bond has been calculated. Together, these data can be used to predict the potential site points with which a ligand could interact and there-fore could be used in molecular-similarity studies, pharmacophore query searching of databases, or de novo design algorithms.     

Syntheses, crystal structures and magnetic properties of a new nitronyl nitroxide NIT2-bithph and its manganese(II) compound [Mn(hfac)2(IMHBithph)]2·(NIT2-bithph)(C6H14)

A new nitronyl nitroxide NIT2-bithph (1) and its manganese(II) compound [Mn(hfac)₂(IMHBithph)]₂·(NIT2-bithph)(C₆H₁₄) (2) (hfac = hexafluoroacetylacetonate; NIT2-bithph = 4,4,5,5-tetramethyl-2-(bithiophenal-2-yl)imidazoline-1-oxyl-3-oxide; IMHBithph = 1-hydroxy-2-bithiophenal-4,4,5,5-tetramethyl-4,5-dihydro- 1H-imidazole) have been synthesized and structurally characterized by X-ray diffraction methods. The units of compound 1 were connected as one-dimensional chain by the intermolecular hydrogen bonds which afford an intermolecular antiferromagnetic interaction between nitronyl nitroxide radicals within the chain (J = −1.89 cm⁻¹). Compound 2 resulting from the reaction of Mn(hfac)₂·2H₂O and NIT2-bithph is dinuclear and includes the reduced amidino-oxide form of NIT2-bithph, it is made up of three parts: a [Mn(hfac)₂(IMHBithph)]₂ dimer unit, an uncoordinated NIT2-bithph radical and a noncoordinated solvent molecule of hexane, the molecule of radical is hydrogen bonded to its reduced form. Two reduced IMHBithph ligands bridge the two manganese(II) ions through their amidino-oxide oxygen atoms resulting in a small intramolecular antiferromagnetic interaction between the manganese ions (J = −1.55 cm⁻¹).     

The predictive accuracy for estimating infinite dilution activity coefficients by γ∞-based UNIFAC

The predictive accuracy for estimating infinite dilution activity coefficients by a modification of the UNIFAC method wherein the group interaction parameters were based on only data (referred to as -based UNIFAC) has been studied. Estimates and measured values were compared for six prototypical solutes in a series of homologous n-alkanes, l-alcohols and alkanenitrile solvents. Despite the fact that the interaction parameters were derived using only data, this approach still gave serious errors due to several inherent problems in the original UNIFAC model. Its performance is sometimes even poorer than that of the original UNIFAC method. For example for nitromethane in alcohols and p-dioxane in nitriles values predicted by the -based UNIFAC are essentially zero. The large errors for these systems are most likely due to inaccurate interaction parameters in the -based UNIFAC method.     

Interactions between gelatin and sodium dodecyl sulphate: binding isotherm and solution properties

The interaction between sodium dodecyl sulphate (SDS) and gelatin was studied at pH 4.5 and 6.5 where the gelatin is positively charged (i.e.p. 8). At pH 4.5 a SDS/gelatin concentration range was found where gelatin precipitates. At pH 6.5 the SDS-gelatin complex remains soluble although three SDS concentration domains were distinguished where the SDS-gelatin complex had very different affinities for the solvent. Below C₁ the complex was highly surface active but other measurements (viscosity, potentiometry, protons uptake) did not reveal any particular consequence of binding. Between C₁ and C₂ the molecular size decreased (viscosity lowering) upon charge neutralization and collapse about small SDS aggregates (17 SDS molecules per gelatin molecule). Above C₂ a cooperative binding mechanism lead to the formation of SDS aggregates; the complex stretched out and turned strongly hydrophilic (the viscosity increases, low surface activity). At saturation one gelatin molecule bound about 200 SDS molecules. Above the overlap concentration (about 3 wt%) SDS aggregates formed between several gelatin molecules, the viscosity increased continuously with SDS concentration and the binding ratio was lower than in dilute gelatin solutions. A very good correspondence was found between the different analytical data including turbidity, viscosity, surface tension, protons uptake and direct potentiometric SDS binding measurements.     

Structural Studies of Transition Metal Compounds

A historical overview will be given on the structural studies on transition metal compounds and their interaction with other fields of coordination chemistry. About three decades have passed away since the structure and absolute configuration of tris(ethylenediamine)cobalt(III) complex ion were determined. At present accumulation of the structural data for isomers has enabled us to understand structural principles of chelate complexes in considerable detail. The energy minimization calculations can predict the detailed geometries of the complexes. Differences in thermodynamic properties between different conformers are well reproduced. Aspherical distribution of 3d electrons in transition metal complexes was detected for the first time in crystals of [Co(NH3)₆][Co(CN)₆] in 1973. Such an accurate electron density study provides important information on the d electrons placed in a ligand field. The high-spin and low-spin states can be distinguished unequivocally. In spite of a very small valence/total electron ratio, the asphericity of 4d and 5d electrons in a ligand field can be detected. The crystal structures of a series of dimeric copper(II) carboxylate adducts of the general formula [Cu(RCOO)₂L]₂ have been determined or redetermined as accurately as possible. The temperature dependent magnetic susceptibility of these crystals indicated that the isolated pairs of Cu(II) ions interact strongly through exchange forces. Molecular orbital calculations revealed that the electron population in the carbon atom of the bridging OCO group plays an important role in determining the strength of the spin superexchange interaction. In the crystals of some cobaloxime complexes, racemization of chiral groups bonded to Co proceeds on X-ray exposure without degradation of crystallinity. Several intermediate stages could be determined by X-ray analysis. Various reaction pathways were recognized and the reaction rate could be correlated with the atomic arrangement in the crystal.     

Emissive Annular Digold(I) Compounds Containing Diphosphine and Dithiolate Ligands

Molecular structures of three emissive annular digold compounds [Au₂(dmpm)(dtc)]Cl (dmpm = Me₂PCH₂PMe_2,dtc = S₂CNEt₂), 1 , [Au₂(dppm)(dtc)]PF₆, (dppm = Ph₂PCH₂PPh₂),₂,and [Au₂(dppe)(dtc)]-(PF₂) (dppe = Ph₂P(CH₂)₂PPh₂), 3, were determined. All three compounds are dimetallacycles having two gold atoms bridged by a dithiolate ligand and a diphosphine ligand, the geometry around each gold atom being almost linear. All the dimetal lacy die rings are slightly distorted from planarity with intramolecular Au-Au distances shorter than 3.0 Å. Compound 1 forms a polymeric chain through intermolecular Au-Au contacts (3.061 ? 3.135 Å). Compound 2 forms a tetramer through intermolecular Au-Au interactions (Au-Au distances ranging from 3.086 to 3.222 ). Compound 3 is monomeric. All of the compounds luminesce at 77 K in the solid state. Emissions originating from ³LMCT from dtc ligand to Au excited states are assigned. The emission maxima of 1 ? 3 are at 541,535 and 520 nm respectively and are blue shifted as the number of Au-Au interactions is decreased.     

A novel separation technique of diastereomeric esters of pyridylethanols by extraction: formal total synthesis of PNU-142721, HIV-1 reverse transcriptase inhibitor

The separation of diastereomeric esters derived from (±)-pyridylethanols and 3β-acetoxyetienic acid were achieved by an extraction technique using diethyl ether and aqueous hydrochloric acid. A formal total synthesis of PNU-142721 was effectively carried out to prepare the chiral, non-racemic synthon 1-furo[2,3-c]pyridin-5-yl-ethanol (1) by means of this technique. The structure optimized using MOPAC calculations on each diastereomer suggested the presence of intramolecular CH/π interaction in only the (S)-isomer of the diastereomers.     

蛋白质-蛋白质相互作用界面统计分析

以作者开发的从蛋白质结合部位推导出其界面所具有的疏水性质和氢键性质的计算程序PP_SITE为基础,利用蛋白质结构数据库(PDB),对蛋白质-蛋白质相互作用界面进行了统计分析.从PDB中挑出非冗余的链间相互作用对,计算出这个数据集中所有链间界面的疏水和氢键相互作用特征.对得到的界面特征进行统计分析,寻找能够明显聚类的界面特征.结果表明，界面大小、氢键和疏水相互作用在界面所占比例以及疏水相互作用的集中程度可以作为分类的依据.     

使用疏水作用色谱研究蛋白质的构象变化

研究了高效疏水作用液相色谱中(HIC)色谱条件改变对蛋白质构象的影响。发现固定相配体的疏水性、温度及流动相中盐的阴离子、阳离子和pH值都影响蛋白质的构象。     

Enthalpies of dilution of l-cystine in aqueous solutions of sodium hydroxide, potassium hydroxide and hydrochloric acid

The enthalpies of dilution of l-cystine in solutions of two strong alkalis and one strong acid have been determined by isothermal flow-mix calorimetry at the temperatures 298.15 K, 303.15 K, 308.15 K, 313.15 K and 318.15 K. Equations of apparent enthalpies of dilution have been obtained from the experimental data in terms of the improved McMillan-Mayer theory. Enthalpic interaction coefficients, h₂, h₃, and h₄, are obtained and the values of pair-wise enthalpic interaction coefficient, h₂, discussed in the light of solute-solute and solute-solvent interactions.