DETERMINATION OF THREE-DIMENSIONAL STRUCTURE OF CODEINE BY NMR MOLECULAR GRAPHICS TECHNIQUES

In this paper, we describe a method for calculating the three-dimensional structure ofantagonist drug codeine by means of one- and two-dimensional NMR and computer tech-niques. The calculation of molecular mechanics is based on NMR data, so we call it NMRmolecular graphics (NMRMG). With codeine as a demonstration. we find that the molecularstructure data from NMRMG are in quite good agreement with those by X-ray diffractionmeasurement. NMRMG can be utilized to study configuration and conformation of naturalproducts, especially rigid structure compounds in solution.     

Artificial intelligence systems for molecular spectral analysis

A brief survey is given of the most recent publications on development of artificial-intelligence systems for molecular spectral analysis. A new approach to solution of the problems of qualitative molecular spectral analysis is based on an applied logical calculus developed by the authors for fuzzy predicates. It is suggested that spectral-structural knowledge should be specified in the language of fuzzy predicates, and mechanical theorem-proving procedures used for solving qualitative problems of spectral analysis, the initial information being considered as a set of axioms. System-oriented matters are given consideration. The formalism suggested is a basis for the development of an artificial-intelligence dialogue system capable of solving various problems in molecular spectral analysis while maintaining a dialogue with a research worker using a professionally-restricted natural language.     

Understanding sterol-membrane interactions part I: Hartree-Fock versus DFT calculations of 13C and 1H NMR isotropic chemical shifts of sterols in solution and analysis of hydrogen-bonding effects

1H and 13C NMR chemical shifts are exquisitely sensitive probes of the local environment of the corresponding nuclei. Ultimately, direct determination of the chemical shifts of sterols in their membrane environment has the potential to reveal their molecular interactions and dynamics, in particular concerning the hydrogen-bonding partners of their OH groups. However, this strategy requires an accurate and efficient means to quantify the influence of the various interactions on chemical shielding. Herein the validity of Hartree-Fock and DFT calculations of the 13C and 1H NMR chemical shifts of cholesterol and ergosterol are compared with one another and with experimental chemical shifts measured in solution at 500 MHz. A computational strategy (definition of basis set, simpler molecular models for the sterols themselves and their molecular complexes) is proposed and compared with experimental data in solution. It is shown in particular that the effects of hydrogen bonding with various functional groups (water as a hydrogen-bond donor and acceptor, acetone) on NMR chemical shifts in CDCl3 solution can be accurately reproduced with this computational approach.     

Raman Spectroscopic Signature of Ectoine Conformations in Bulk Solution and Crystalline State

Recent crystallographic results revealed conformational changes of zwitterionic ectoine upon hydration. By means of confocal Raman spectroscopy and density functional theory calculations, we present a detailed study of this transformation process as part of a Fermi resonance analysis. The corresponding findings highlight that all resonant couplings are lifted upon exposure to water vapor as a consequence of molecular binding processes. The importance of the involved molecular groups for water binding and conformational changes upon hydration is discussed. Our approach further shows that the underlying rapid process can be reversed by carbon dioxide saturated atmospheres. For the first time, we also confirm that the conformational state of ectoine in aqueous bulk solution coincides with crystalline ectoine in its dihydrate state, thereby highlighting the important role of a few bound water molecules.     

Aqueous molecular clusters isolated as liquid fragments by adiabatic expansion of liquid jets

A new approach to solution chemistry and cluster physics has been developed by combining molecular beam mass-spectrometry with liquid jet expansion method. Many features characteristic of molecular association in aqueous solution were observed in the cluster mass spectra and some of them showed good agreement with reported values of enthalpy changes and entropy changes for molecular association-dissociation equilibria in liquid phase. Although it lacks persuadable theoretical analysis at this stage, several new findings obtained by this technique are introduced to appeal its potentialities of physical analysis of solution systems at molecular levels.     

Synthesis and functionalization of heteroatom-bridged bicyclocalixaromatics, large molecular triangular prisms with electron-rich and -deficient aromatic interiors

The synthesis and functionalization of oxygen and nitrogen atom bridged bicyclocalixaromatics of triangular prism structures are reported. By means of a fragment coupling approach, molecular triangular prisms of electron-rich and electron-deficient aromatic interiors were prepared using 1,3,5-tri(p-hydroxyphenyl)benzene and 2,4,6-tri(p-aminophenyl)triazine as base units and chlorotriazines as pillars. Aromatic nucleophilic substitution reaction of chlorotriazine moieties with functionalized amines led to triangular prisms with functionalizations on the peripheral edge positions, while functionalized triangular prisms on the vertex nitrogen positions were obtained using 2,4,6-tri[(p-allylamino)phenyl]triazine derivative as a starting material. Symmetrical and distorted molecular triangular prisms in the solid state were revealed by X-ray crystallography. As evidenced by NMR spectroscopic data, however, all cage molecules synthesized most probably adopted highly symmetric triangular prism structures in solution phase. The functionalized shape-persistent triangular prism structures might find applications in molecular recognition and in the construction of higher and more sophisticated molecular architectures in supramolecular chemistry.     

Quantitative Structure–Activity Relationships of Natural-Product-Inspired,Aminoalkyl-Substituted 1-Benzopyrans as Novel Antiplasmodial Agents

On the basis of the finding that various aminoalkyl-substituted chromene and chromane derivatives possess strong and highly selective in vitro bioactivity against Plasmodium falciparum, the pathogen responsible for tropical malaria, we performed a structure–activity relationship study for such compounds. With structures and activity data of 52 congeneric compounds from our recent studies, we performed a three-dimensional quantitative structure–activity relationship (3D-QSAR) study using the comparative molecular field analysis (CoMFA) approach as implemented in the Open3DQSAR software. The resulting model displayed excellent internal and good external predictive power as well as good robustness. Besides insights into the molecular interactions and structural features influencing the antiplasmodial activity, this model now provides the possibility to predict the activity of further untested compounds to guide our further synthetic efforts to develop even more potent antiplasmodial chromenes/chromanes.     

基于MCM-41硬模板的镍铁磁性纳米管的合成及其磁性研究

以Si-MCM-41为硬模板,利用介孔材料的吸附作用,将Fe3+和Ni 2+按一定比例定量吸附组装到介孔材料的孔壁上;然后通过程序升温在900℃条件下高温焙烧,并经氢氟酸处理,得到直径大约为3.0nm的中空铁氧体纳米管.分别利用傅立叶变换红外光谱仪、扫描电镜、透射电镜、X射线衍射仪分析了合成材料的结构、组成、形貌;采用振动样品磁强计测定了其磁性能.结果表明,合成的镍铁氧体纳米管具有良好的管状形貌,其结构与分子筛MCM-41的结构相似,并具有良好的磁学性能.这说明MCM-41分子筛孔道结构具有可复制性,本研究可望为制备具有适当长径比的一维纳米磁性材料打下良好基础.     

When is a molecule properly solvated by a continuum model or in a cluster ansatz? A first-principles simulation of alanine hydration

In order to test the validity of the cluster ansatz approach as well as of the continuum model approach and to learn about the solvation shell, we carried out first-principles molecular dynamics simulations of the alanine hydration. Our calculations contained one alanine molecule dissolved in 60 water molecules. Dipole moments of individual molecules were derived by means of maximally localized Wannier functions. We observed an average dipole moment of about 16.0 D for alanine and of about 3.3 D for water. In particular, the average water dipole moment in proximity of alanine's COO(-) group decayed continously with increasing distance, while, surprisingly, close to the CH3 and NH3+ group, the dipole moment first rose before its value dropped. In a cluster ansatz approach, we considered snapshots of alanine surrounded by different water molecule shells. The dipole moments from the cluster approaches utilizing both maximally localized Wannier functions as well as natural population analysis served to approximate the dipole moments of the total trajectory. Sufficient convergence of the cluster ansatz approach is found for either of the two solvent shells around the polar groups and one solvent shell around the apolar groups or two solvent shells around the polar groups surrounded by a dieletric continuum.     

负载金属催化剂Ir(γ-Al2O3)对阿维菌素选择加氢反应研究

分别采用氢气、NaBH₄、醇水混合溶剂还原, PVP(聚乙烯吡咯烷酮)保护和微乳液法制备了γ-Al₂O₃负载的Ir金属催化剂, 通过XPS、XRD、TEM对催化剂的结构进行了表征, 考察了催化剂对阿维菌素选择加氢制备伊维菌素的性能, 探讨了催化剂制备方法对催化剂活性和选择性的影响. 实验结果表明, 在不同金属催化剂Ru/γ-Al₂O₃、Pd/γ-Al₂O₃、Pt/γ-Al₂O₃、Ir/γ-Al₂O₃中, Ir/γ-Al₂O₃的活性和选择性最好. 用PVP保护的Ir/γ-Al₂O₃, 其催化活性和选择性比没有PVP保护的催化剂有显著提高; 采用微乳液法制备的Ir/γ-Al₂O₃催化剂显示出最好的活性, 但反应选择性比PVP保护的催化剂差.     

Adsorption of Sodium Dodecyl Sulfate to Colloidal Titanium Dioxide: An Electrophoretic Fingerprinting Investigation

The adsorption of sodium dodecyl sulfate to colloidal titanium dioxide was investigated using the electrophoretic fingerprinting approach. An electrophoretic fingerprint is a contour diagram of the observed electrophoretic mobility as a function of the bulk solution pH and plambda, the log of the bulk solution conductivity. Surfactant adsorption was observed to be strong under acidic conditions, as illustrated in the dramatic changes in the electrophoretic fingerprints. Electrokinetic data were compared with adsorption isotherm data obtained by a depletion method and good qualitative agreement was found. The observed pH changes associated with surfactant adsorption suggested ligand exchange as a possible mechanism of adsorption. Electrophoretic fingerprinting was shown to be a powerful means of examining surfactant adsorption to colloidal particles. Copyright 2000 Academic Press.     

Thermal and optical control of electronic states in a single layer of switchable paramagnetic molecules

The control of the charge distribution in a monolayer of switchable cobalt–dioxolene complexes undergoing Valence Tautomerism (VT) has been achieved by means of thermal and optical stimuli. Thiol-derivatised VT molecules have been grafted on polycrystalline gold surface as monolayers from solution. X-ray photoelectron spectroscopy and time-of-flight secondary ions mass spectrometry evidenced the formation of a covalent bond between intact VT molecules and the surface and excluded the presence of physisorbed molecules. X-ray absorption spectroscopy revealed that the temperature- and light-induced conversion profiles of the monolayer closely reproduce the ones found for the crystalline phase. This study demonstrates that a wet chemistry based approach allows to transfer switchable paramagnetic molecules at the nanoscale, widening the playground to develop new hybrid molecular based architectures for novel technologies.     

Zinc bis-Schiff base complexes: Synthesis,structure, and application in ring-opening polymerization of rac-lactide

A series of bis-ligated zinc complexes supported by Schiff base ligands were successfully synthesized and characterized by ¹H,¹³C NMR,elemental analysis,and X-ray crystallography.These zinc complexes can be used as catalysts for the polymerization of rac-lactide in solution as well as in molten lactide.The results show that all catalysts exhibited high catalytic activity and obtained moderate heterotactic PLAs with the expected molecular weight.Complex 1 can catalyze the polymerization of rac-lactide under controllable conditions with living and immortal character in toluene solution.In addition,the steric hindrance and electronic effects has a great influence on the catalytic activity and selectivity of catalysts.     

Towards the understanding of the activity of G9a inhibitors: an activity landscape and molecular modeling approach

In this work, we analyze the structure–activity relationships (SAR) of epigenetic inhibitors (lysine mimetics) against lysine methyltransferase (G9a or EHMT2) using a combined activity landscape, molecular docking and molecular dynamics approach. The study was based on a set of 251 G9a inhibitors with reported experimental activity. The activity landscape analysis rapidly led to the identification of activity cliffs, scaffolds hops and other active an inactive molecules with distinct SAR. Structure-based analysis of activity cliffs, scaffold hops and other selected active and inactive G9a inhibitors by means of docking followed by molecular dynamics simulations led to the identification of interactions with key residues involved in activity against G9a, for instance with ASP 1083, LEU 1086, ASP 1088, TYR 1154 and PHE 1158. The outcome of this work is expected to further advance the development of G9a inhibitors.

     

Advantages of time-resolved difference X-ray solution scattering curves in analyzing solute molecular structure

Time-resolved X-ray solution scattering provides a powerful method for investigating reaction dynamics in the solution phase. Since X-rays scatter from all atoms in the solution sample, the scattering intensity is contributed from not only the solute but also the solvent and the solute–solvent cross terms. For a typical concentration the solvent molecules outnumber the solute molecules and thus the relative sensitivity of the scattering intensity to the solute structure is extremely low. To increase the structural sensitivity to the solute and to extract only the signal from structural changes, time-resolved difference scattering signal is obtained by subtracting the original raw scattering curve at a negative reference time delay from that at a positive time delay. Here we show and emphasize that time-resolved difference X-ray scattering curves generally exhibit higher structural sensitivity to the solute molecular structure and lower influence from experimental background and imperfection of theory than original raw scattering curves. These characteristics justify the validity of fitting models to difference curves to obtain transient structural information even when the magnitude of the time-resolved difference curves is smaller than the discrepancy between the theory and experiment for the original scattering curve. We considered small molecules and proteins in solution probed by time-resolved X-ray solution scattering.     

Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: from protein structure to nanodisk assemblies

Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on the basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.     

微波法研制碱土金属氧化物负载型MCM-48碱性介孔材料

以立方相介孔分子筛MCM-48为载体,用微波辐射分散MgO或CaO和醋酸镁溶液浸渍等方法研制碱性介孔材料。MCM-48能经受微波辐射,负载碱性客体之后也保持介相结构。异丙醇分解探针反应表明:载体本身没有碱催化活性,而碱性MCM-48介孔材料的活性随温度升高而提高。本文还对介孔材料在微波分散和碱性催化方面的特点进行分析。     

Solid-phase synthesis and biological screening of N-alpha-mercaptoamide template-based matrix metalloprotease inhibitors

A series of N-alpha-mercaptoacetyl containing dipeptides have been prepared on solid-phase supports as putative matrix metalloprotease (MMP) inhibitors. Inhibitor design was based on a positional scanning approach of the amino acids present within a template molecule, previously shown to be an MMP inhibitor with good pharmacological characteristics. This study is the first step in a unique programme, designed to expand the repertoire of molecular templates which can be chosen as starting points for the development of more focused parallel and/or combinatorial libraries of MMP inhibitors as a means to accelerate the lead discovery process. This paper reports the success of such an approach in the development of agents with activity against a number of pathologically important MMPs. After screening of these positional scanning libraries, we have obtained important SAR information, in particular, pharmacophores with the ability to impart selectivity for particular MMP species.