Navigating chemical space for biology and medicine

Despite over a century of applying organic synthesis to the search for drugs, we are still far from even a cursory examination of the vast number of possible small molecules that could be created. Indeed, a thorough examination of all 'chemical space' is practically impossible. Given this, what are the best strategies for identifying small molecules that modulate biological targets? And how might such strategies differ, depending on whether the primary goal is to understand biological systems or to develop potential drugs?     

Chemical space and biology

Chemical space--which encompasses all possible small organic molecules, including those present in biological systems--is vast. So vast, in fact, that so far only a tiny fraction of it has been explored. Nevertheless, these explorations have greatly enhanced our understanding of biology, and have led to the development of many of today's drugs. The discovery of new bioactive molecules, facilitated by a deeper understanding of the nature of the regions of chemical space that are relevant to biology, will advance our knowledge of biological processes and lead to new strategies to treat disease.     

Efficient organic photovoltaic diodes based on doped pentacene

Recent work on solar cells based on interpenetrating polymer networks and solid-state dye-sensitized devices shows that efficient solar-energy conversion is possible using organic materials. Further, it has been demonstrated that the performance of photovoltaic devices based on small molecules can be effectively enhanced by doping the organic material with electron-accepting molecules. But as inorganic solar cells show much higher efficiencies, well above 15 per cent, the practical utility of organic-based cells will require their fabrication by lower-cost techniques, ideally on flexible substrates. Here we demonstrate efficiency enhancement by molecular doping in Schottky-type photovoltaic diodes based on pentacene--an organic semiconductor that has received much attention as a promising material for organic thin-film transistors, but relatively little attention for use in photovoltaic devices. The incorporation of the dopant improves the internal quantum efficiency by more than five orders of magnitude and yields an external energy conversion efficiency as high as 2.4 per cent for a standard solar spectrum. Thin-film devices based on doped pentacene therefore appear promising for the production of efficient 'plastic' solar cells.     

A combustion-free methodology for synthesizing zeolites and zeolite-like materials

Zeolites are mainly used for the adsorption and separation of ions and small molecules, and as heterogeneous catalysts. More recently, these materials are receiving attention in other applications, such as medical diagnosis and as components in electronic devices. Modern synthetic methodologies for preparing zeolites and zeolite-like materials typically involve the use of organic molecules that direct the assembly pathway and ultimately fill the pore space. Removal of these enclathrated species normally requires high temperature combustion that destroys this high cost component, and the associated energy release in combination with the formed water can be extremely detrimental to the inorganic structure. Here we report a synthetic methodology that avoids these difficulties by creating organic structure-directing agents (SDAs) that can be disassembled within the zeolite pore space to allow removal of their fragments for possible use again by reassembly. The methodology is shown for the synthesis of zeolite ZSM-5 using a SDA that contains a cyclic ketal group that is removed from the SDA while it is inside the zeolite without destruction of the inorganic framework. This approach should be applicable to the synthesis of a wide variety of inorganic and organometallic structures.     

A.Flavus Mediated Biotransformations for the Syntheses of Active A-oxyfunctionalized Compounds

1 Results Biotransformations are enzyme- and whole cell-catalysed conversions of non-natural substrates to products.They are important tools in organic synthesis,especially for the syntheses of chiral molecules,where the reactions catalysed may be asymmetric syntheses or the resolution of racemates.The main advantages associated with the use of single enantiomer compounds are increased specificity and the avoidance of adverse side effects[1].Whole cell reactions are advantegous over enzyme-catalyzed rea...     

A small-molecule screen in C. elegans yields a new calcium channel antagonist

Small-molecule inhibitors of protein function are powerful tools for biological analysis and can lead to the development of new drugs. However, a major bottleneck in generating useful small-molecule tools is target identification. Here we show that Caenorhabditis elegans can provide a platform for both the discovery of new bioactive compounds and target identification. We screened 14,100 small molecules for bioactivity in wild-type worms and identified 308 compounds that induce a variety of phenotypes. One compound that we named nemadipine-A induces marked defects in morphology and egg-laying. Nemadipine-A resembles a class of widely prescribed anti-hypertension drugs called the 1,4-dihydropyridines (DHPs) that antagonize the alpha1-subunit of L-type calcium channels. Through a genetic suppressor screen, we identified egl-19 as the sole candidate target of nemadipine-A, a conclusion that is supported by several additional lines of evidence. egl-19 encodes the only L-type calcium channel alpha1-subunit in the C. elegans genome. We show that nemadipine-A can also antagonize vertebrate L-type calcium channels, demonstrating that worms and vertebrates share the orthologous protein target. Conversely, FDA-approved DHPs fail to elicit robust phenotypes, making nemadipine-A a unique tool to screen for genetic interactions with this important class of drugs. Finally, we demonstrate the utility of nemadipine-A by using it to reveal redundancy among three calcium channels in the egg-laying circuit. Our study demonstrates that C. elegans enables rapid identification of new small-molecule tools and their targets.     

塔里木盆地煤层坍塌机理研究

利用化学分析和力学研究 ,探讨了塔里木盆地依奇克里克区块侏罗系和三叠系煤层的坍塌机理。这两种煤样的煤化程度较低 ,密度、强度低。煤样比表面积大 ,并含有较多亲水基团 ,相对吸水量和比吸水量都很高。由于水削弱了煤中大分子之间的氢键和范德华力 ,因而煤岩膨胀 ,致使煤岩抗压强度和抗拉强度降低 ,这是煤层坍塌的重要因素。此外 ,煤本身为有机质 ,有较强的亲油性 ,煤岩吸油后造成大分子间交联键和有机小分子的溶解 ,破坏了煤的骨架结构 ,使其强度下降     

Single crystals of an ionic anthracene aggregate with a triplet ground state

Crystalline supramolecular aggregates consisting of charged organic molecules, held together through metal-cluster-mediated Coulomb interactions, have attracted interest owing to their unusual structural, chemical and electronic properties. Aggregates containing metal cation clusters 'wrapped' by lipophilic molecular anions have, for example, been shown to be kinetically stable and soluble in nonpolar liquids such as saturated hydrocarbons. The formation of supramolecular aggregates can even be exploited to generate aromatic hydrocarbons that carry four negative charges and crystallize in the form of organic poly(metal cation) clusters or helical polymers. Here we report the anaerobic crystallization of an ionic organic aggregate--a contact ion septuple consisting of a fourfold negatively charged 'tripledecker' of three anthracene molecules bridged by four solvated potassium cations. Its electronic ground state is shown experimentally, using temperature-dependent electron paramagnetic resonance spectroscopy, to be a triplet. Although the spins in this biradical ionic solid are separated by a considerable distance, density functional theory calculations indicate that the triplet ground state is 84 kJ mol(-1) more stable than the first excited singlet state. We expect that the successful crystallization of the ionic solid we report here, and that of a covalent organic compound with a triplet ground state at room temperature, will stimulate further attempts to develop new triplet-ground-state materials for practical use.     

平衡透析法用于有机小分子和蛋白质相互作用研究进展

生物大分子是近年来生命科学研究的热点和难点之一,有关蛋白质的各类研究也是人们比较感兴趣的课题.平衡透析法是定量研究蛋白质与有机小分子相互作用的经典方法.通过平衡透析法的研究我们可以讨论蛋白质与有机小分子的结合数目、结合平衡常数及作用力情况等.近年来,国内外学者在此方面做了大量的工作,提出了各种各样的结合模型.本文就此方面的研究进行综述.     

Measurement of the conductance of single conjugated molecules

Electrical conduction through molecules depends critically on the delocalization of the molecular electronic orbitals and their connection to the metallic contacts. Thiolated (- SH) conjugated organic molecules are therefore considered good candidates for molecular conductors: in such molecules, the orbitals are delocalized throughout the molecular backbone, with substantial weight on the sulphur-metal bonds. However, their relatively small size, typically approximately 1 nm, calls for innovative approaches to realize a functioning single-molecule device. Here we report an approach for contacting a single molecule, and use it to study the effect of localizing groups within a conjugated molecule on the electrical conduction. Our method is based on synthesizing a dimer structure, consisting of two colloidal gold particles connected by a dithiolated short organic molecule, and electrostatically trapping it between two metal electrodes. We study the electrical conduction through three short organic molecules: 4,4'-biphenyldithiol (BPD), a fully conjugated molecule; bis-(4-mercaptophenyl)-ether (BPE), in which the conjugation is broken at the centre by an oxygen atom; and 1,4-benzenedimethanethiol (BDMT), in which the conjugation is broken near the contacts by a methylene group. We find that the oxygen in BPE and the methylene groups in BDMT both suppress the electrical conduction relative to that in BPD.     

有机小分子及金属有机配合物电子传输材料的研究进展

概述了有机小分子及金属有机配合物电子传输材料的研究进展,对由小分子电子传输材料构成的有机电致发光器件的发光性能、发光效率等方面进行了比较,并对小分子材料的研究前景进行了展望.     

Enantioselective silyl protection of alcohols catalysed by an amino-acid-based small molecule

Reliable, selective and environmentally friendly chemical transformations are crucial to the development of new therapeutics and the design of novel materials. Chiral catalysts that can be easily prepared and used to obtain organic molecules of high enantiomeric purity are critical to modern chemical synthesis. The development of protecting groups that shield reactive functionalities has also proved indispensable in the preparation of complex biologically active molecules. Here we present a chiral catalyst that promotes the enantioselective protection of a secondary alcohol as one of the most commonly used protected forms of an alcohol: a silyl ether. The catalyst is a small, simple molecule that can be prepared in three steps from commercial materials without the need for rigorously controlled conditions. Enantioselective silylations are performed with commercial silyl chlorides and produce yields of up to 96 per cent at an enantiomeric ratio of up to 98:2. Chiral catalysts for selective formation of commonly used protecting groups such as silyl ethers should significantly enhance the ability of chemical synthesis to deliver, in a more practical and efficient manner, important organic molecules.     

Hexagonal nanoporous germanium through surfactant-driven self-assembly of Zintl clusters

Surfactant templating is a method that has successfully been used to produce nanoporous inorganic structures from a wide range of oxide-based material. Co-assembly of inorganic precursor molecules with amphiphilic organic molecules is followed first by inorganic condensation to produce rigid amorphous frameworks and then, by template removal, to produce mesoporous solids. A range of periodic surfactant/semiconductor and surfactant/metal composites have also been produced by similar methods, but for virtually all the non-oxide semiconducting phases, the surfactant unfortunately cannot be removed to generate porous materials. Here we show that it is possible to use surfactant-driven self-organization of soluble Zintl clusters to produce periodic, nanoporous versions of classic semiconductors such as amorphous Ge or Ge/Si alloys. Specifically, we use derivatives of the anionic Ge9(4-) cluster, a compound whose use in the synthesis of nanoscale materials is established. Moreover, because of the small size, high surface area, and flexible chemistry of these materials, we can tune optical properties in these nanoporous semiconductors through quantum confinement, by adsorption of surface species, or by altering the elemental composition of the inorganic framework. Because the semiconductor surface is exposed and accessible in these materials, they have the potential to interact with a range of species in ways that could eventually lead to new types of sensors or other novel nanostructured devices.     

Supramolecular self-assembled molecules as organic directing agent for synthesis of zeolites

Solid materials with uniform micropores, such as zeolites, can act as selective catalysts and adsorbents for molecular mixtures by separating those molecules small enough to enter their pores while leaving the larger molecules behind. Zeolite A is a microporous material with a high void volume. Despite its widespread industrial use in, for example, molecular separations and in detergency, its capability as a petroleum-refining material is limited owing to its poor acid-catalytic activity and hydrothermal stability, and its low hydrophobicity. These characteristics are ultimately a consequence of the low framework Si/Al ratio (normally around one) and the resulting high cationic fraction within the pores and cavities. Researchers have modified the properties of type-A zeolites by increasing the Si/Al compositions up to a ratio of three. Here we describe the synthesis of zeolite A structures exhibiting high Si/Al ratios up to infinity (pure silica). We synthesize these materials, named ITQ-29, using a supramolecular organic structure-directing agent obtained by the self-assembly, through pi-pi type interactions, of two identical organic cationic moieties. The highly hydrophobic pure-silica zeolite A can be used for hydrocarbon separations that avoid oligomerization reactions, whereas materials with high Si/Al ratios give excellent shape-selective cracking additives for increasing propylene yield in fluid catalytic cracking operations. We have also extended the use of our supramolecular structure-directing agents to the synthesis of a range of other zeolites.     

电子结构计算方法研究进展

电子结构方法是化学物理研究中的一个重要的研究领域。电子结构方法普遍被用来计算分子和固体材料的各种物理和化学性质,并在理解各种化学反应机理方面有着重要的基础地位。改进现有方法、发展新的电子结构方法一直是该领域的研究热点。分析和讨论了电子结构计算方法特别是基于波函数的低标度电子结构方法研究的最新进展;报告了最近在定域关联方法的发展及其在有机光电材料理论研究的应用方面所作的工作,结果表明,定域关联方法可以在大幅度降低计算代价的同时保证计算精度,是一种很有前途的实现低标度电子结构方法的途径。     

Highly controlled acetylene accommodation in a metal-organic microporous material

Metal-organic microporous materials (MOMs) have attracted wide scientific attention owing to their unusual structure and properties, as well as commercial interest due to their potential applications in storage, separation and heterogeneous catalysis. One of the advantages of MOMs compared to other microporous materials, such as activated carbons, is their ability to exhibit a variety of pore surface properties such as hydrophilicity and chirality, as a result of the controlled incorporation of organic functional groups into the pore walls. This capability means that the pore surfaces of MOMs could be designed to adsorb specific molecules; but few design strategies for the adsorption of small molecules have been established so far. Here we report high levels of selective sorption of acetylene molecules as compared to a very similar molecule, carbon dioxide, onto the functionalized surface of a MOM. The acetylene molecules are held at a periodic distance from one another by hydrogen bonding between two non-coordinated oxygen atoms in the nanoscale pore wall of the MOM and the two hydrogen atoms of the acetylene molecule. This permits the stable storage of acetylene at a density 200 times the safe compression limit of free acetylene at room temperature.     

Molecular control over Au/GaAs diodes

The use of molecules to control electron transport is an interesting possibility, not least because of the anticipated role of molecules in future electronic devices. But physical implementations using discrete molecules are neither conceptually simple nor technically straightforward (difficulties arise in connecting the molecules to the macroscopic environment). But the use of molecules in electronic devices is not limited to single molecules, molecular wires or bulk material. Here we demonstrate that molecules can control the electrical characteristics of conventional metal-semiconductor junctions, apparently without the need for electrons to be transferred onto and through the molecules. We modify diodes by adsorbing small molecules onto single crystals of n-type GaAs semiconductor. Gold contacts were deposited onto the modified surface, using a 'soft' method to avoid damaging the molecules. By using a series of multifunctional molecules whose dipole is varied systematically, we produce diodes with an effective barrier height that is tuned by the molecule's dipole moment. These barrier heights correlate well with the change in work function of the GaAs surface after molecular modification. This behaviour is consistent with that of unmodified metal-semiconductor diodes, in which the barrier height can depend on the metal's work function.     

The advent and development of organocatalysis

The use of small organic molecules as catalysts has been known for more than a century. But only in the past decade has organocatalysis become a thriving area of general concepts and widely applicable asymmetric reactions. Here I present my opinion on why the field of organocatalysis has blossomed so dramatically over the past decade.     

芘类有机半导体材料研究进展

由于芘具有大环共轭和易于修饰的特性,近年来,芘类共轭衍生物成为有机半导体的重要组成部分.最主要的文献报道为芘类电致发光材料,它们从化学结构上可分为四类材料：小分子、寡聚物、树枝状大分子和聚合物.其中小分子芘衍生物又可分为单取代衍生物、双取代衍生物和四取代衍生物.同时,近年来也有部分文献开始报道芘类材料在场效应晶体管、太阳能电池和其他方面的应用.文中按以上内容,分别进行了比较分析,最后提出了该类材料的未来发展方向.     

杯芳烃对有机小分子识别作用的研究进展

简要综述了近年来杯芳烃识别有机小分子的研究进展，主要涉及以非共价键作用发生的包结及作用方式。