SiOM(M=Li,Be,B,Na,Mg,Al)分子结构的DFT研究

利用Gaussian-94计算程序,B3LYP方法,6-311+G(2d)6d基组,对SiOM(M=Li,Be,B,Na,Mg,Al)诸体系的几何结构进行优化.结果表明,M既可与SiO中的Si键合,也可与O键合.第一和第二主族的SiOM体系以折线形构型为最稳定构型,而第三主族则以近直线形或直线形构型为最稳定构型.从Si-O间键长R_SiO、力常数f_SiO及自然键轨道分析可知,第一主族的SiOLi和SiONa的最稳定构型中SiO-M间的离子键成分较大,可近似看作离子键;而对SiOLi,SiOBe,SiOB和SiOMg体系的以Si为中心的构型,M-SiO间的离子键成分很小,不能看作离子键,可认为M与SiO之间存在着弱相互作用     

Amaryllidaceae,sceletium, imidazole,oxazole, thiazole,peptide and miscellaneous alkaloids

This review covers alkaloids classified in the plant families Amaryallidaceae and Sceletium. In addition alkaloids possessing imidazole, oxazole and thiazole structures are listed followed by alkaloids possessing peptide linkages. Finally miscellaneous alkaloids include those compounds found naturally which cannot be classified into known groups; a relative Pandora's box. A total of 620 structures has been reviewed from 218 references found in the literature for the period July 1999 to June 2000.     

Theoretical Study on the Structure and Stability of Si4X（X=Li, Be, B, C, N, O, F） Clusters

1 INTRODUCTION Silicon is an important kind of semiconductormaterial having been used to produce many sorts ofapparatus, digital and linear integrated circuit andLarge Scale Integrated circuit (LSI), and its clustershave drawn many scientists’ atten…     

Structures, energetics, and spectra of hydrated hydroxide anion clusters

The structures, energetics, electronic properties, and spectra of hydrated hydroxide anions are studied using density functional and high level ab initio calculations. The overall structures and binding energies are similar to the hydrated anion clusters, in particular, to the hydrated fluoride anion clusters except for the tetrahydrated clusters and hexahydrated clusters. In tetrahydrated system, tricoordinated structures and tetracoordinated structures are compatible, while in pentahydrated systems and hexahydrated systems, tetracoordinated structures are stable. The hexahydrated system is similar in structure to the hydrated chloride cluster. The thermodynamic quantities (enthalpies and free energies) of the clusters are in good agreement with the experimental values. The electronic properties induced by hydration are similar to hydrated chloride anions. The charge-transfer-to-solvent energies of these hydrated-hydroxide anions are discussed, and the predicted ir spectra are used to explain the experimental data in terms of the cluster structures. The low-energy barriers between the conformations along potential energy surfaces are reported.     

Effect of meso-hexestrol, a synthetic estrogen, on S-tubulin

We have reported that meso-hexestrol, a synthetic estrogen, inhibits microtubule assembly and induces microtubule proteins into twisted ribbon structures. On the other hand, Serrano et al. proved that S-tubulin, which lacks the C-terminal moiety of tubulin subunits, assembles into sheet structures in the absence of microtubule-associated proteins (MAPs). In the present investigation, we attempted to clarify whether meso-hexestrol could induce the ribbon structure from S-tubulin. meso-Hexestrol delayed the initiation of polymerization of S-tubulin into sheet structures in a dose-dependent manner below 50 microM. But the effect of meso-hexestrol on S-tubulin was reduced in the presence of either tau or microtubule-associated protein 2 (MAP2) in a MAPs-concentration-dependent manner. At concentrations higher than 100 microM, meso-hexestrol inhibited the polymerization of S-tubulin into sheet structures, without forming ribbon structures. The present results may indicate that moso-hexestrol interacts with S-tubulin, and its interaction is affected by MAPs.     

Isomeric structures, isomerization and decomposition of silylenoids H2SiMX(MX=KF,KCl LiBr,NaBr and KBr)

The isomeric structures,isomerization and decomposition of silylenoids H2SiMX (MX= KF,KCI,LiBr,NaBr and KBr) have been investigated by 06 initio molecular orbital theory.These silylenoids have four kinds of very similar equilibrium structures.The three-membered ring and p-complex structures should be stable and experimentally detectable.The lifetime of o-complex and tetrahedral structures would be very short and experimentally undetectable.     

Density functional studies of molecular structures of N-methyl formamide, N,N-dimethyl formamide, and N,N-dimethyl acetamide

Density functional theory was applied to the calculation of molecular structures of N-methyl formamide (NMF), N,N-dimethyl formamide (DMF), and N,N-dimethyl acetamide (DMA). DFT calculations on NMF, DMF, and DMA were performed using a combination of the local functional of Vosko, Wilk, and Nusair (VWN) with the nonlocal exchange functional of Becke and the nonlocal correlational functional of Lee, Yang, and Parr (BLYP). The adiabatic connection method (ACM) of Becke has also been used, for the first time, for the calculation of molecular structures of NMF, DMF, and DMA. The calculated molecular structures are in excellent agreement with the experimental geometries of NMF and DMA derived from gas-phase electron-diffraction studies. Sparse experimental data on the gas-phase geometry of DMF reported in the literature compares well with the DFT results on DMF. DFT emerges as a powerful method to calculate molecular structures.     

Strictly Biphasic Soft and Hard Janus Structures: Synthesis,Properties, and Applications

Janus structures, named after the ancient two‐faced Roman god Janus, comprise two hemistructures (e.g. hemispheres) with different compositions and functionalities. Much research has been carried out over the past few years on Janus structures because of the intriguing properties and promising potential applications of these unusually shaped materials. This Review discusses recent progress made in the synthesis, properties, and applications of strictly biphasic Janus structures possessing symmetrical structures but made of disparate materials. Depending on the chemical compositions, such biphasic structures can be categorized into soft, hard, and hybrid soft/hard Janus structures of different architectures, including spheres, rodlike, disclike, or any other shape. The main synthetic routes to soft, hard, and hybrid soft/hard Janus structures are summarized and their unique properties and applications are introduced. The perspectives for future research and development are also described.     

聚合物纳米杂化材料的控制合成、自组装及功能化

聚合物纳米杂化材料的制备及功能化是当前国际前沿研究课题之一.特殊结构的聚合物可以通过分子间特殊相互作用,在纳米尺度上自发地组装成具有特殊结构和形态的集合体,这类材料在新材料、电子以及生物医学等领域具有广泛的应用前景.本文介绍国内外,特别是厦门大学在双亲性分子及嵌段共聚物的模板自组装、基于POSS单体纳米构筑单元以及POSS嵌段聚合物自组装的有机/无机纳米杂化材料、模板控制导电高分子材料纳米形态构筑等领域材料的可控合成和组装,与此同时对相关材料的性能及功能化应用进行了简要的讨论.     

Novel structural motifs in clusters of dipolar spheres: knots, links, and coils

We present the structures of putative global potential energy minima for clusters bound by the Stockmayer (Lennard-Jones plus point dipole) potential. A rich variety of structures is revealed as the cluster size and dipole strength are varied. Most remarkable are groups of closed-loop structures with the topology of knots and links. Despite the large number of possibilities, energetically optimal structures exhibit only a few such topologies.     

The oxygen-rich carboxide series: COn (n = 3, 4, 5, 6, 7, or 8)

The lowest-energy isomers of the high-order carboxide series, COn (n = 3-8), have been elucidated via ab initio quantum chemical calculations. The structures of the lowest order of these (3 and 4) are in close agreement with previous calculations and with experimental data. The structures of the higher-order species are elucidated and correlated to the previous structures, showing similarities in structure and reactivity pathways. The reaction energies of the formation of all products are shown to be related. Exothermic pathways of formation often involve a C2v form of CO2, which was shown to be metastable. The newly identified species could be intermediates in atmospheric reactions. The calculated vibrational frequencies and IR intensities may be used to identify these metastable species.     

Characterization,mechanical, and antibacterial properties of nanofibers derived from olive leaf,fumitory, and terebinth extracts

In this study, nanofiber structures were obtained with convenient polymers (PVA [polyvinyl alcohol] and PCL [poly ^o-caprolactone]) derived from the herbal extracts of olive leaves, fumitory, and terebinth plants. Optimum nanofiber structures were identified by measuring viscosity and conductivity values and performing morphological analysis, characterization, and mechanical tests of the prepared solutions. The potential use for wound healing at the most efficient level was determined as a result of antibacterial analysis of the structures obtained. APT (PVA/terebinth) and BFO (PCL/fumitory) nanofibers had the thinnest diameter range and the highest strength values. In terms of the determination of antibacterial effects, nanofiber structures of all 3 plant species proved to be effective against bacteria. The greatest effect was observed against Escherichia coli in the nanofiber structure containing olive leaves, with a zone diameter of 32 mm. In addition, APT and BFO nanofibers had the highest values of thinness and strength. In these 2 samples, using BFO against Staphylococcus aureus and APT against Candida albicans increased their areas of activity. In the literature review, no study was available about obtaining nanofibers, especially from fumitory and terebinth plants. This study aimed to increase knowledge on obtaining nanofiber structures, including various polymers derived from olive leaves, fumitory, and terebinth plants.     

Symmetries, vibrational instabilities, and routes to stable structures of clusters of Al, Sn, and As

We investigate the stability of small clusters using density functional theory to compute the total energy, forces, and vibrational frequencies using linear response. We exhibit an efficient and computationally low-cost route to finding stable structures, by starting with high-symmetry structures and distorting them according to their unstable modes. We illustrate this by application to 4-, 6-, and 13-atom clusters of Al, Sn, and As. This technique also naturally elucidates the origins of stability of the lower symmetry structures, which is variously due to the linear or pseudo Jahn-Teller effect, combined with a lowering of various contributions to the total energy. We show that the situation is more complex than has generally been appreciated.     

Ab initio study of hydrated sodium halides NaX(H2O)(1-6) (X=F, Cl, Br, and I)

We have studied the dissociation phenomena of sodium halides by water molecules. The structures, binding energies, electronic properties, and IR spectroscopic features have been investigated by using the density-functional theory, second-order Moller-Plesset perturbation theory, and coupled clusters theory with single, double, and perturbative triplet excitations. In the case that the sodium halides are hydrated by three water molecules, the most stable structures show the partial (or half) dissociation feature. The dissociated structures are first found for NaX(H2O)(n=5) for X=BrI, though these structures are slightly higher in energy than the global minimum-energy structure. In the case of hexahydrated sodium halides the global minimum-energy structures (which are different from the structures reported in any previous work) are found to be dissociated (X=F/I) or partially/half dissociated (X=Cl/Br), while other nearly isoenergetic structures are undissociated, and the dissociated cubical structures are higher in energy than the corresponding global minimum-energy structure.     

Studies in hydrogen bonding: simulation of the crystalline solids of ice, ammonia, and ammonia hydrate

The crystal structures of ice, ammonia and ammonia hydrate have been simulated with rigid molecules using the interatomic potential function EPEN/2 and the computer program WMIN. Structural parameters were adjusted to give structures with minimum energy. The hydrogen bonding in the simulated structures is compared with that in the experimental structures.     

CH_2=CH(XM)(X=S,Se,Te;M=H,Li,Na,K,Rb,Cs,-)的从头算研究

应用相对论有效势在ＭＰ２水平上对ＣＨ２ＣＨ（ＸＭ）（Ｘ＝Ｓ，Ｓｅ，Ｔｅ；Ｍ＝Ｈ，Ｌｉ，Ｎａ，Ｋ，Ｒｂ，Ｃｓ，－）进行了从头计算研究．结果表明，所研究的化合物都有平面式和非平面桥式两种构型．分析了碱金属离子对两可亲核底物ＣＨ２ＣＨＸ－（Ｘ＝Ｓ，Ｓｅ，Ｔｅ）离域化的影响，并用自然布局分析方法（ＮＰＡ）研究了电荷分布的变化，得出了有价值的结论．     

Global reaction route mapping on potential energy surfaces of formaldehyde, formic acid, and their metal-substituted analogues

Global reaction route mapping of equilibrium structures, transition structures, and their connections on potential energy surface (PES) has been done for MCHO (M = H, Li, Na, Al, Cu) and HCO2M (M = H, Li). A one-after-another technique based on the scaled hypersphere search method has been successfully applied to exploring unknown chemical structures, transition structures, and reaction pathways for organometallic systems. Upon metal substitution, considerable changes of stable structures, reaction pathways, and relative heights of transition structures have been discovered, though some features are similar among the analogues. Al and Cu atoms were found to behave as very strong scissors to cut the CO double bond in MCHO. Energy profiles of the CO insertion into Li-H and Li-CH3 bonds were found to be very similar, especially around the structures where the Li atom is not directly connected with the methyl group, which indicates little effects of alkyl substitution on the reaction route topology.     

Chiolite,a case study for combining NMR crystallography,diffraction and structural simulation

Chiolite has been selected as a test case for developing a general approach to solve inorganic structures from powders by combining NMR, modeling, and X-ray diffraction. The different steps of the strategy are successfully performed, building the candidate integrant units using NMR, simulating candidate crystal structures using the computational AASBU method, and checking the consistency of the candidate structures against the diffraction data analyzed with FOX computer program.     

Amine-templated open-framework zinc arsenates of varying dimensionalities: synthesis, structure, polymorphism, and transformation reactions

Eight new open-framework zinc arsenates, encompassing the entire hierarchy of open-framework structures, have been prepared hydrothermally. The structures include zero-dimensional, one-dimensional chains, two-dimensional layers, and three-dimensional structures formed through the transformation of the molecular zinc arsenates. The structure of [C6N4H21][Zn(HAsO4)2(H2AsO4)], I, is composed of ZnO4 and H2AsO4 units connected through the vertices forming four-membered rings with HAsO4 units hanging from the Zn center. The four-membered rings are connected through the corners forming the one-dimensional chain structures in [C4N2H12][Zn(HAsO4)2] x H2O, II, and [C5N2H14][Zn(HAsO4)2] x H2O, III. ZnO4 and AsO4 units form a fully four-connected two-dimensional structure in [C4N2H12][Zn(AsO4)]2, IV. One-dimensional zigzag ladders are connected through HAsO4 units forming two-dimensional layers in [C4N2H12]1.5[Zn2(AsO4)(HAsO4)2] x H2O, V, while the similar building units form a layer with hanging HAsO4 units in the layered arsenate [C6N4H21]6[Zn12(HAsO4)21], VI. Hanging HAsO4 units are also observed in the polymorphic structures of [C6N3H20][Zn2(AsO4)(HAsO4)2] x 2H2O, VII and VIII. Formation of zero-dimensional monomer, I, a fully four-connected layer, IV, and the polymorphic structures, VII and VIII, are important and noteworthy. The transformation reactions of I indicate that the monomer is reactive and gives rise to structures of higher dimensionalities, indicating a possible Aufbau-type building-up process in these structures.     

Size, shape, and flexibility of RNA structures

Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of RNA in the Protein Data Bank we find that the size of the folded RNA structures, measured using the radius of gyration R(G), follows the Flory scaling law, namely, R(G)=5.5N(1/3) A, where N is the number of nucleotides. The shape of RNA molecules is characterized by the asphericity Delta and the shape S parameters that are computed using the eigenvalues of the moment of inertia tensor. From the distribution of Delta, we find that a large fraction of folded RNA structures are aspherical and the distribution of S values shows that RNA molecules are prolate (S>0). The flexibility of folded structures is characterized by the persistence length l(p). By fitting the distance distribution function P(r), that is computed using the coordinates of the folded RNA, to the wormlike chain model we extracted the persistence length l(p). We find that l(p) approximately 1.5N(0.33) A which might reflect the large separation between the free energies that stabilize secondary and tertiary structures. The dependence of l(p) on N implies that the average length of helices should increase as the size of RNA grows. We also analyze packing in the structures of ribosomes (30S, 50S, and 70S) in terms of R(G), Delta, S, and l(p). The 70S and the 50S subunits are more spherical compared to most RNA molecules. The globularity in 50S is due to the presence of an unusually large number (compared to 30S subunit) of small helices that are stitched together by bulges and loops. Comparison of the shapes of the intact 70S ribosome and the constituent particles suggests that folding of the individual molecules might occur prior to assembly.