Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.

Macrocyclic polyamine-modified poly(glycidyl methacrylate-co-ethylene dimethacrylate) monolith for capillary electrochromatography

1,4,10,13,16-Pentaazatricycloheneicosane-9,17-dione (macrocyclic polyamine)-modified polymer-based monolithic column for CEC was prepared by ring opening reaction of epoxide groups from poly(glycidyl methacrylate-co-ethylene dimethacrylate) (GMA-co-EDMA) monolith with macrocyclic polyamine. Conditions such as reaction time and concentration of macrocyclic polyamine for the modification reaction were optimized to generate substantial EOF and enough chromatographic interactions. Anodic EOF was observed in the pH range of 2.0-8.0 studied due to the protonation of macrcyclic polyamine at the surface of the monolith. Morphology of the monolithic column was examined by SEM and the incorporation of macrocyclic polyamine to the poly(GMA-co-EDMA) monolith was characterized by infrared (IR) spectra. Successful separation of inorganic anions, isomeric benzenediols, and benzoic acid derivatives on the monolithic column was achieved for CEC. In addition to hydrophobic interaction, hydrogen bonding and electrostatic interaction played a significant role in the separation process.

Study of microstructure of high stability hydrogenated amorphous silicon films by Raman scattering and infrared absorption spectroscopy

The microstructure, hydrogen bonding configurations and hydrogen content of high quality and stable hydrogenated amorphous silicon (a-Si:H) films prepared by a simple ''uninterrupted growth/annealing" plasma enhanced chemical vapor deposition technique have been investigated by Raman scattering and infrared absorption spectroscopy. The high stability a-Si:H films contain small amounts of a microcrystalline phase and not less hydrogen (10-16 at. %), particularly, the clustered phase hydrogen, Besides, the hydrogen distribution is very inhomogeneous. Some of these results are substantially distinct from those of conventional device-quality n-Si:H film or stable cr-Si:H films prepared by the other techniques examined to date. The stability of n-Si:H films appears to have no direct correlation with the hydrogen content or the clustered phase hydrogen concentration. The ideal n-Si:H network with high stability and low defect density is perhaps not homogeneous. (C) 1998 American Institute of Physics.

硫手性有机小分子催化剂的设计、合成及其在不对称亚胺氢转移还原中的应用

过去十多年，世界手性药物市场需求迅速增长，手性制药工业的发展壮大，已经引起了各国政府、学术界，特别是企业界的高度重视。手性药物中含有大量的手性胺单元，因此研究高效构建手性胺结构单元的方法具有重要的意义和实用价值，而亚胺的不对称还原是合成手性胺最便捷的方法。 手性有机小分子路易斯碱催化三氯氢硅不对称还原亚胺是最近几年才发展起来的一类新的亚胺不对称还原方法。尽管在对映选择性和底物适用范围等方面已经获得了突破性的进展，但是，高性能的路易斯碱催化剂仅局限于N-甲酰氨基酸酰胺一种类型，而且其底物适用范围和催化活性仍不够理想。因此，发展新型催化剂很有必要。 手性硫氧化物作为手性诱导剂的应用已经有数十年的时间，广泛应用在不对称合成及天然产物的全合成中。理论上，硫氧结构单元也可以作为路易斯碱，对硅烷类试剂进行活化，而且硫氧键还有碳氧键难以比拟的先天优势，硫原子自带手性特征，在反应过程中，手性中心离反应位点更近，因此，从手性硫氧化合物出发，极有可能开发出新的高效手性路易斯碱催化剂。最近，Kobayashi和Khiar在亚胺的不对称烯丙基化反应中用手性亚砜活化烯丙基三氯硅烷，获得了较好的ee值，但反应中手性亚砜的用量都需要化学计量以上，因此还不能算做真正意义上的催化剂，进一步的文献调研也未见真正意义上的硫手性有机小分子催化剂。 本文首次成功将硫手性亚磺酰胺衍生物应用于催化三氯氢硅对亚胺的不对称还原，在经过对亚磺酰胺衍生物的多次结构优化，开发出了合成容易，催化活性和立体选择性都很优良，并且有着前所未有的底物普适性的新型手性路易斯碱催化剂。 我们首先尝试将商品化的20mol%叔丁基亚磺酰胺和对甲基亚磺酰胺直接用作催化剂催化三氯氢硅对亚胺的不对称还原，尽管仅获得中等的收率和很低的对映选择性，但证明我们的设计思路是可行的。在此基础上，我们以叔丁基亚磺酰胺为原料和基本骨架，设计合成了一系列的亚磺酰胺类催化剂，通过对催化剂的结构改造，发现当催化剂中存在较强酸性的酚羟基时，催化效果得到大幅提高。随着对催化剂的进一步结构优化，我们找到了一个结构简单，催化效果还不错的催化剂，经过反应条件优化以后，催化反应的收率最高能达到98%，对映选择性最高达93%，并且这个催化剂的底物适应范围比之前报道的催化剂都要广泛。针对酚羟基在催化剂中的重要作用，我们进行了仔细的机理研究后发现，在催化反应中，催化剂极有可能是通过双分子机理去活化三氯氢硅从而实现不对称催化的，而酚羟基的作用就是通过分子间氢键促进双分子催化剂与三氯氢硅的络合。受此启发，我们设计了一系列具有双齿结构的催化剂，通过对双齿催化剂的结构优化，最终筛选出了一个结构更加简单，但催化效果更好的双齿催化剂。10mol%该催化剂催化亚胺还原最高获得95%的收率和96%的ee值。这一结果也进一步验证了我们先前对催化剂机理的推测。 随后，我们还尝试将这些催化剂用于二级胺和芳香酮的直接还原胺化反应中，虽然能获得不错的收率，但对映选择性却很差，我们对反应条件进行了仔细的摸索，仍然没有获得突破。但这些实验为进一步研究二级胺和酮的不对称直接还原胺化反应奠定了良好的基础。 In the past decade, the rapid growth of the global chiral drug market and the significant development of the chiral pharmaceutical industry have attracted a great deal of attention from government, academia and enterprises. Chiral amine is an important structural motif of chiral drugs. Therefore, development of methods for the construction of this motif is of great importance. Catalytic enantioselective reduction of imines represents one of the most straightforward and efficient methods for the preparation of chiral amines. The chiral Lewis base organocatalysts promoted asymmetric reduction of imines by HSiCl3 has recently achieved significant advancements. Although big breakthroughs have been made in terms of substrate generality and enantioselectivity, the highly effective catalysts are limited to N-formyl amino acid amides, of which the efficiency and substrate scope remain unsatisfactory. Therefore, development of novel organocatalysts for this transformation is in great demand. Chiral sulfoxides have been well established as efficient and versatile stereocontrollers and have been extensively used in asymmetric synthesis and total synthesis of natural products. The S=O structural motif of sulfoxide could also behave as Lewis base activator for cholorsilane reagents, which, moreover, could be even better than caboxamide considering that the sulfur atom is chiral and thus the chirality center is closer to the reaction center. There exist great potentials that highly effective novel Lewis base organocatalysts could be developed starting from S-chiral sulfoxides. Recently, several S-chiral sulfoxides were reported by Kobayashi and Khiar to be used as Lewis base catalyst to activate allyltrichlorosilanes in asymmetric allylations and good enantioselectivities were obtained. However, these S-chiral sulfoxides were all used at a more than stoichiometric amount and were thus not authentically catalytic. A careful literature survey further revealed that there has been so far no S-chiral organocatalyst available. In this study, we, for the first time, successfully used S-chiral sulfinamides as Lewis base organocatalysts for the asymmetric reduction of ketimines by HSiCl3. After several rounds of structural optimization, we developed the first example of highly effective S-chiral organocatalysts, which promoted the asymmetric reduction of ketimines with trichlorosilane in high yield and excellent enantioselectivity with unprecedented substrate spectrum. In our initial practice, we examined 20mol% of the commercially available (R)-tert-butanesulfinamide and (S)-toluenesulfinamide as the catalyst in the hydrosilylation of ketimine. Although the product was only furnished in moderate yield and low ee, these results demonstrated that our strategy of catalyst design is on the right way. Next, starting from chiral tert-butanesulfinamide, we prepared a series of tert-butanesulfinamide derivatives via simple reductive amination and examined their catalytic efficiencies in the reduction of ketimine. We found that the catalyst bearing a phenolic hydroxyl group exhibited good reactivity and enantioselectivity. On the basis of which, we obtained a structurally simple and highly effective novel organocatalyst, affording the product in 98% yield and 93% ee under optimal reaction conditions. After careful exploration on the role of phenolic hydroxyl group in the catalyst, we speculated that two molecules of the catalyst be involved in the course of reaction, of which the assembly around the silicon center is facilitated by the intermolecular hydrogen bonding through the phenolic hydroxyl groups. Thus, we incorporated two units of sulfonamide into one molecular and prepared a new type of bissulfinamides organocatalysts and examined their catalytic efficiencies in the reduction of ketimine. After optimizing the structure of these catalysts, we finally obtained a novel organocatalyst which has even simpler molecular structure but showed better efficacies, 10mol% of which afforded up to 97% yield and 96% ee under optimal reaction conditions. These results further proved our speculation about the catalytic mechanism. We also examined the newly developed S-chiral organocatalysts in direct asymmetric reductive amination of secondary amines with aromatic ketone. The product was furnished in good yield but in low ee. No better results could be obtained despite our intense opimization efforts. Nevertheless, these experiments laid excellent foundations for eventual success.

Molecularly imprinted solid-phase extraction sorbent for removal of nicotine from tobacco smoke

A sorbent showing specific affinity for nicotine was prepared by molecular imprinting technique, using nicotine as the template, methacrylic acid (MAA) as the functional monomer, ethyleneglycol dimethacrylate (EDMA) as the crosslinker and chloroform as the porogen. UV spectroscopic analysis in the molecular imprinting prepolymerization stage confirmed that nicotine could complex with the functional monomer by electrostatic interaction (ionic interaction and hydrogen bonding). The affinity and the binding properties of the imprinted polymer towards nicotine were investigated by equilibrium rebinding experiments. The results indicated the presence of nicotine-specific binding sites in the imprinted polymer, and that the imprinted polymer had a good capacity (90 mumol/g polymer) for nicotine. The elution conditions were optimized on the column packed with the imprinted polymer to elute nicotine quantitatively. The imprinted polymer was used as a solid-phase extraction (SPE) material for the removal of nicotine from tobacco smoke. The results obtained showed that the imprinted polymer was superior in terms of removing nicotine in tobacco smoke, compared with the commercial filter tip.

Molecularly imprinted monolithic stationary phases for liquid chromatographic separation of enantiomers and diastereomers

The method for preparation of molecularly imprinted monolithic stationary phase has been improved to achieve liquid chromatographic separation of enantiomers and diastereomers. By adopting low polar porogenic solvents of toluene and dodecanol and optimal polymerization conditions, the molecularly imprinted monolithic stationary phases with good flow-through properties and high resolution were prepared. Enantiomers of amino acid derivatives and diastereomers of cinchona alkaloids were completely resolved using the monolithic stationary phases. The influence of porogenic composition, monomer-template ratio and polymerization conditions on the chromatographic performance was investigated. Some chromatographic conditions such as the composition of the mobile phase and the temperature were characterized. Scanning electron microscopy showed that the molecularly imprinted monolithic stationary phase has a large through-pore structure to allow the mobile phase to flow through the column at very low backpressure. Accelerated separations of enantiomers and diastereomers were therefore achieved at elevated flow rates. Finally, the chiral recognition performance of the prepared stationary phase in aqueous media was investigated. Hydrophobic interaction, and ionic and/or hydrogen bonding interactions were proposed to be responsible for the recognition mechanism. (C) 2002 Elsevier Science B.V. All rights reserved.

Proton transfer reactions within the pyridazine-methanol cluster ion

The multiphoton ionization of the hydrogen-bonding cluster pyridazine-methanol (C4H4N2-CH3OH) was studied using a time-of-flight mass spectrometer at the wavelengths of 355 and 532 nm. At both wavelengths, a series of protonated C4H4N2-(CH3OH)(n)-H+ cluster ions were obtained. Relevant ab initio calculations were performed with HF and B3LYP methods. Equilibrium geometries of both neutral and ionic C4H4N2-CH3OH clusters, and dissociation channels and dissociation energies of ionic clusters, are presented. The results show that when C4H4N2-CH3OH is vertically ionized, C4H4N2H+ and CH3O are the dominant products via proton transfer reaction. A high energy barrier makes another channel corresponding to the production of C4H4N2H+ and CH2OH disfavored. (C) 2002 Elsevier Science B.V. All rights reserved.

Enantiomeric Recognition by Molecularly Imprinted Polymers Using Hydrophobic Interactions

Molecularly imprinted polymers prepared using acrylamide as the hydrogen bonding functional monomer exhibited good enantiomeric recognition properties in aqueous solutions. Our results indicate that the recognition improved with increased mobile phase water percentage and ionic strength, and was also very much pH dependent upon the ionisation properties of the sample molecules. The results can be interpreted in terms of specific hydrophobic interactions between the enantiomeric species and the recognition sites of imprinted polymers. A study of substrate selectivity showed differences between a pure organic system and a water/organic system as the mobile phases. The hydrophobicity of the test compounds was found to be an important parameter in determining the selectivity.

Effects of pH on the Interactions and Conformation of Bovine Serum Albumin: Comparison between Chemical Force Microscopy and Small-Angle Neutron Scattering

The conformation of bovine serum albumin (BSA), as well as its interactions with negatively charged mica surfaces in saline solutions of different pH values, have been studied by small-angle neutron scattering (SANS) and chemical force microscopy (CFM), respectively. A new approach to extract the contribution of elementary interactions from the statistically averaged force-extension curves through self-consistent fitting was proposed and used to understand the effects of pH on the interactions and conformation of BSA in saline solutions. When pH increases, the SANS results reveal that the sizes of BSA molecules increase slightly, while the statistical analysis of the CFM results shows that the averaged pull-off force for the elongation monotonously decreases. The decrease of pull-off force with the increase of pH results from the decrease in the strength of hydrogen bonding and the number of interaction pairs, as well as the slight increase of the strength of van der Waals interaction. When pH approaches the isoelectric point (pI) of BSA, results from both SANS and CFM suggest a loss of long-range interactions in BSA molecules. Our results also suggest that the force-extension curve is mainly contributed by the van der Waals interaction. The combination of SANS and CFM provides new insight to understand the interactions and conformation of BSA molecules

(Z)-2-(2-chloro-3,3,3-trifluoroprop-1enyl)-6-methoxyphenyl acetate

The crystal structure of the title compound, C12H10ClF3O3, was determined in order to establish the configuration of the C double bond. The compound was found to be the Z isomer. The crystal structure is dominated by Cl center dot center dot center dot O halogen bonds [Cl center dot center dot center dot O = 3.111 (3) angstrom], as well as C-H center dot center dot center dot O and C-H center dot center dot center dot F hydrogen-bonding interactions, that connect neighboring molecules into a three-dimensional supramolecular network.

Self-assembly of p-sulfonatocalix[4]arene and a Ag-hmt coordination polymer into a porous structure

A novel porous material constructed from p-sulfonatocalix[4]arene molecules and a Ag-I coordination polymer has been structurally characterized. The porous supramolecular complex features a bilayer arrangement of p-sulfonatocalix[4]arene molecules linked by a Ag-I-hmt (hmt: hexamethylene- tetramine) coordination polymer through metal-ligand bonding, hydrogen bonding and host-guest interactions.

A copper/p-sulfonatocalix[6]arene/phenanthroline supramolecular compound with 1D [Cu-2-calixarene](n) coordination chains

A supramolecular complex [Cu(phen)(2)H2O]{[Cu(phen)(H2O)](2)[C6AS]}center dot 2.5H(2)O (phen = 1,10'-phenanthroline and C6AS = p-sulfonatocalix[6]arene) has been synthesized under hydrothermal condition, and characterized by IR spectroscopy, TG analysis and single crystal X-ray diffraction. In the structure, unprecedented 1D ({[Cu(phen)(H2O)](2)[C(6)AS]}(2-))(n) coordination chains (exactly being belts) are stacked into some 2D layers by the pi center dot center dot center dot pi stacking interactions, which are further interconnected into a 3D extended structure by hydrogen bonding.

Assembly of supramolecular compounds with water-soluble calix[4]arenes

Three new copper compounds, Cu-2[C12H8N2](2)[C28H2OS4O16][H2O](11.9) (1), Cu-2[C12H8N2](3)[C28H20S4O16][H2O](5) (2), and Cu-2[C12H8N2](4)[C24H12S8O16][H2O](10.5) (3), were hydrothermally synthesized and structurally determined by X-ray diffraction and TG-DTA analyses. Interestingly, Compounds 1 and 2 were synthesized in a one-pot reaction. Complexes 1 and 3 contain capsule units, which are further assembled into three-dimensional (3-D) architectures with a-Po-related topology by pi-pi stacking and/or hydrogen-bonding interactions.

Molecular Nanocluster with a [Sn4Ga4Zn2Se20](8-) T3 Supertetrahedral Core

A multinary molecular nanocluster, in which a T3 supertetrahedral [Sn4Ga4Zn2Se20](8-) core was neutralized and covalently terminated by four [(TEPA)Mn](2+) (TEPA = tetraethylenepentamine) metal complexes, was synthesized and characterized. The cluster is assembled into, through hydrogen bonding and van de Waals forces, a superlattice that is chemically stable and free of strong covalent coupling. The four different cations were distributed within the cluster in such a manner that both the local charge balance and global charge compensation by the metal complex could be satisfied.