CombiDOCK: Structure-based combinatorial docking and library design

We have developed a strategy for efficiently docking a large combinatorial library into a target receptor. For each scaffold orientation, all potential fragments are attached to the scaffold, their interactions with the receptor are individually scored and factorial combinations of fragments are constructed. To test its effectiveness, this approach is compared to two simple control algorithms. Our method is more efficient than the controls at selecting best scoring molecules and at selecting fragments for the construction of an exhaustive combinatorial library. We also carried out a retrospective analysis of the experimental results of a 10×10×10 exhaustive combinatorial library. An enrichment factor of approximately 4 was found for identifying the compounds in the library that are active at 330 nM.     

Three-dimensional quantum dynamics study of vibrational predissociation of HeI_2 van der Waals molecule for low vibrational excitation using the time-dependent wave packet method

Three-dimensional quantum mechanical calculations for vibrational predissociation of HeI2(B) van der Waals molecules are presented using the time-dependent wave packet technique within the golden rule approxima tion.The total and partial decay widths,lifetimes,rates and their dependence on initial vibrational states were obtained for HeI2 at low initial vibrational excited levels.Our calculations show that the calculated tota decay widths,lifetimes and rates agree well with those extrapolated from experimental data available The predicted total decay widths as a function of initial vibrational states exhibit highly nonlinear behavior.The very short propagation time (less.than 1 ps) required in the golden rule wave packet calculation is determined by the duration time of the final state inter-action between the fragments on the vibrationally deexcited adiabatic potential surface.The final state interaction between the fragments is shown to play an important role in determining the final rotational distri     

Crystal structures of phenyl-substituted cyclopropanes. IV. the crystal structure (at 21‡C and −100‡C) and the phenyl ring conformation in 4-cyclopropylacetanilide

The crystal structure of 4-cyclopropylacetanilide was investigated at room temperature (21C) and at –100C in order to determine the orientation of the phenyl ring with respect to the cyclopropane moiety and the effect of this substituent on the stereochemistry of the three-membered ring. The compound was chosen because it is one of the few species containing a simple phenyl ring as the sole cyclopropane ring substituent and whose crystals are suitable for X-ray diffraction at room temperature. The substance crystallizes in space groupP2_l/c at either temperature (no phase transitions) with cell constants: (at 21C)a=9.725(2),b=10.934(3), andc=9.636(2) å,=106.13(1);V=984.21 å³ andd(calc;z=4)=1.182 g cm^–3. The relevant parameters for the –100C structure area=9.557(4),b=10.980(2), andc=9.641(2) å,=106.34(3);V=970.76 å³ and d(calc;z=4)=1.199 g cm^–3. Final values wereR(F)=0.042, R_w=0.035, using unit weights, and its nonhydrogen atoms were used to phase the low-temperature data, whose final discrepancy indices wereR(F)=0.051,R _w =0.061. The phenyl substituent is almost exactly in the bisecting conformation with respect to the C-C-C angle at the point of attachment to cyclopropane and conjugative effects are clearly evident in the lengths of the cyclopropane ring [1.494(3), 1.498(3), and 1.474(4) å, the later being the distal bond]. If one omits the terminal methylene fragments at C10 and C11, the atoms comprising the acetanilide fragment and the substituted carbon of the cyclopropane ring lie in a nearly perfect plane. Molecular mechanics as well as semiempirical (AM1) calculations were carried out in order to determine the structure of the energy-minimized configurations in the two computational environments. The molecular conformations thus obtained are close to that experimentally observed from the X-ray diffraction experiment. In both theoretical models, the lowest energy conformation is that in which the plane of the phenyl ring bisects the cyclopropane C-C-C angle as was experimentally observed. Finally, the shape of the conformational barrier as a function of the orientation of the plane of the phenyl ring was computed, giving a maximum barrier to rotation of 2.2 kcal/mol. Similar calculations were carried out for two other aryl cyclopropanes, whose rings (naphthalene and anthracene) cannot adopt the bisecting position. Comparisons of experimental geometrical parameters as well as of the barriers to rotation are presented.on leave at the University of Houston, 1995–1996.     

激光产生的钒硫簇离子的统计分布与结构探讨

以脉冲激光在高真空中溅射钒粉和硫粉的混合物，产生了一系列钒硫原子簇正负离子。根据对其实验记录的激光等离子体质谱进行分析，发现钒硫原子簇的化学键基本上是共价型的，对应于相同钒原子数目的正负离子的相对丰度分别符合于不同形式的对数正态分布。正离子的相对丰度随硫原子数的增加呈对数衰减，由此可以确定各种大小簇合物的簇骼与几何构型；负离子的相对丰度则基本上呈正常的正态分布，说明在簇骼上结合了不同数量硫原子的负离子之结构稳定性大致相近。在实验中还观察到一类硫原子含量较高的簇离子，其中的部分硫原子可能在本身成键形成环状的硫集团后，又与原来的簇骼结合，因而在硫原子数较多时它们的相对丰度符合另一条对数正态分布曲线。     

Metal ion distribution and solubility of Mn1−xCux(HCOO)2 · 2 H2O Mixed Crystals [1–5]

The metal ion distribution on the two metal sites of monoclinic Mn_1?xCu_x(HCOO)₂ · 2(H,D)₂O mixed crystals are studied by infrared and Raman spectroscopic methods. The spectral regions 3 200–3 400 cm^?1 (v_OH), 2 875–2 990 cm^?1 (v_CH), 2 330–2 500 cm^?1 (v_OD of matrix isolated HDO molecules), 1 350–1 400 cm^?1 (symmetric CO₂ stretching modes), 570–950 cm^?1 (H₂O librations), and 490 cm^?1 (M? O lattice modes) are mostly sensitive to the metal ions present. The frequency shifts of these bands with increasing content of copper show that Cu²⁺ prefers the M(1) site, coordinated by HCOO^? only. The strengths of the hydrogen bonds increase on going from manganese to copper formate, due to the increased synergetic effect of Cu²⁺. Solubility and X-ray data of the mixed crystals are included. Irrespective of the same crystal structure, two series of mixed crystals are formed: eutonic area at 0.65 ≥ x ≥ 0.5.     

Particle-size distribution of polycyclic aromatic hydrocarbons in urban air in southern Spain

The size distribution of polycyclic aromatic hydrocarbons (PAH) was determined for airborne particles from a large city with high vehicular traffic. The analytical method was optimised and validated using NIST standard reference material (SRM 1649a Urban Dust). The 16 priority PAH listed in the US-EPA were Soxhlet-extracted from filtered particulate matter and then fractionated using on-column chromatography. The aromatic fraction was quantified by gas chromatography-mass spectrometry. Real samples of particles collected in Seville (Spain) were analysed using the validated method. Values for the total concentration of PAH in the air, as well as the concentrations of each PAH in six particle-size ranges were obtained. Values of the PAH in TSP, PM₁₀, PM_2.5 and PM₁ were assessed.     

Controllable donor-acceptor neutral [2]rotaxanes

In pursuit of a neutral bistable [2]rotaxane made up of two tetraarylmethane stoppers--both carrying one isopropyl and two tert-butyl groups located at the para positions on each of three of the four aryl rings--known to permit the slippage of the pi-electron-donating 1,5-dinaphtho[38]crown-10 (1/5DNP38C10) at the thermodynamic instigation of pi-electron-accepting recognition sites, in this case, pyromellitic diimide (PmI) and 1,4,5,8-naphthalenetetracarboxylate diimide (NpI) units separated from each other along the rod section of the rotaxane's dumbbell component, and from the para positions of the fourth aryl group of the two stoppers by pentamethylene chains, a modular approach was employed in the synthesis of the dumbbell-shaped compound NpPmD, as well as of its two degenerate counterparts, one (PmPmD) which contains two PmI units and the other (NpNpD) which contains two NpI units. The bistable [2]rotaxane NpPmR, as well as its two degenerate analogues PmPmR and NpNpR, were obtained from the corresponding dumbbell-shaped compounds NpPmD, PmPmD, and NpNpD and 1/5DNP38C10 by slippage. Dynamic 1H NMR spectroscopy in CD2Cl2 revealed that shuttling of the 1/5DNP38C10 ring occurs in NpNpR and PmPmR, with activation barriers of 277 K of 14.0 and 10.9 kcal mol(-1), respectively, reflecting a much more pronounced donor-acceptor stabilizing interaction involving the NpI units over the PmI ones. The photophysical and electrochemical properties of the three neutral [2]rotaxanes and their dumbbell-shaped precursors have also been investigated in CH2Cl2. Interactions between 1/5DNP38C10 and PmI and NpI units located within the rod section of the dumbbell components of the [2]rotaxane give rise to the appearance of charge-transfer bands, the energies of which correlate with the electron-accepting properties of the two diimide moieties. Comparison between the positions of the visible absorption bands in the three [2]rotaxanes shows that, in NpPmR, the major translational isomer is the one in which 1/5DNP38C10 encircles the NpI unit. Correlations of the reduction potentials for all the compounds studied confirm that, in this non-degenerate [2]rotaxane, one of the translational isomers predominates. Furthermore, after deactivation of the NpI unit by one-electron reduction, the 1/5DNP38C10 macrocycle moves to the PmI unit. Li+ ions have been found to strengthen the interaction between the electron-donating crown ether and the electron-accepting diimide units, particularly the PmI one. Titration experiments show that two Li+ ions are involved in the strengthening of the donor-acceptor interaction. Addition of Li+ ions to NpPmR induces the 1/5DNP38C10 macrocycle to move from the NpI to the PmI unit. The Li+-ion-promoted switching of NpPmR in a 4:1 mixture of CD2Cl2 and CD3COCD3 has also been shown by 1H NMR spectroscopy to involve the mechanical movement of the 1/5DNP38C10 macrocycle from the NpI to the PmI unit, a process that can be reversed by adding an excess of [12]crown-4 to sequester the Li+ ions.     

Λ-、△-[Rh（bpy）2chrysi]^3＋对含C：T错配的DNA序列识别作用的分子模拟研究

通过分子模拟方法研究了手性金属配合物[Rh（bpy）2Chrysi]^3＋（bpy=2，2’-bipyridineChrysi=5，6-chrysenequinonediimine）对包含C：T错配碱基对的B-DNA序列的识别作用．结合类似的针对含G：A错配的和正常的B-DNA序列的识别作用研究，发现配合物I-Rh（bpy）zChrysi]^3＋可以对错配B-DNA序列进行序列特异性的识别．能量对比计算结果表明，该经典插入识别作用倾向于在错配碱基对附近进行，其中△-[Rh（bpy）2chrysi]^3＋比其手性异构体更占优势．这同Barton教授工作组的实验结果是一致的．另外插入作用倾向于在错配序列中的正常双碱基对C3A4／G3T4（错配碱基对附近）中从小沟进行．与该配合物对含G：A错配的和正常的B-DNA序列的识别作用不同的是，对包含C：T错配碱基对的B-DNA序列的识别作用倾向于从小沟进行．这一点可能源于C：T碱基对结构的不同．     

ADSORPTION OF 2,4-D ON MODIFIED HYPERCROSSLINKED POLYSTYRENE （NDA-99） AND XAD-4 RESIN

The adsorption behavior of pesticide 2,4-dichlorophenoxyacetic acid (2,4-D) in aqueous solution has been investigated using a hypercrosslinked polystyrene adsorbent (NDA-99) modified by dimethylamine group as well as a nonionic macroporous adsorbent (XAD-4). The Langmuir and Freundlich isotherm models were employed to fit the experimental data to describe adsorption mechanism. It shows that NDA-99 resin exhibits an adsorption affinity for 2,4-D higher than XAD-4 resin owing to its exceptional micropore structure and the amine group of the hypercrosslinked matrix.Further studies indicate that the hydrogen bonding interaction and the stronger π-π conjugation play a significant role in the course of the adsorption of 2,4-D on NDA-99 resin, which is in agreement with the IR spectroscopic results and the △E values of HOMO (the highest occupied molecular orbit) of adsorbent and LUMO (the lowest unoccupied molecular orbit) of adsorbate calculated from the MINDO/3 model.     

Oxidation of mandelic acid derivatives catalysed by Bi(0)/O2 systems: mechanistic considerations

Mandelic acid and some aryl substituted derivatives were oxidised under molecular oxygen and a catalytic amount of Bi(0). The corresponding aldehydes and/or the carboxylic acids were obtained selectively depending on the nature of the substituent. Aldehydes and α-keto acids were oxidised under the same Bi(0)/O₂ system and α-keto acids were proposed as intermediates in the formation of benzoic acid derivatives.