Protein three-dimensional structural databases: Domains, structurally aligned homologues and superfamilies

This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homologous families. This database has been derived by identifying the presence of structural domains in proteins on the basis of inter-secondary structural distances using the program DIAL [Sowdhamini & Blundell (1995), Protein Sci. 4, 506-520]. The alignment of proteins in superfamilies has been performed on the basis of the structural features and relationships of individual residues using the program COMPARER [Sali & Blundell (1990), J. Mol. Biol. 212, 403-428]. The alignment databases contain information on the conserved structural features in homologous proteins and those belonging to superfamilies. Available data include the sequence alignments in structure-annotated formats and the provision for viewing superposed structures of proteins using a graphical interface. Such information, which is freely accessible on the WWW, should be of value to crystallographers in the comparison of newly determined protein structures with previously identified protein domains or existing families.

Comparison of quantum chemistry calculation methods of nucleic acid base-quartets

Nine base-quartets were calculated by six semi-empirical methods and ab initio Hartree-Fork method using STO-3G basis set. The results showed that PM3 method can be use to calculate base quartets, the results of PM3 calculations are close to the ab initio

4-Benzyl-5-ethyl-2-(2-furylcarbonylmethylsulfanyl) pyrimidin-6(1H)-one

The title compound, C19H18N2O3S, shows favourable activity against HIV-1. The phenyl ring is twisted with respect to the pyrimidine ring by 61.56 (9)degrees. Intermolecular N-H center dot center dot center dot O and C-H center dot center dot center dot O

Tensile and compressive mechanical behavior of twinned silicon carbide nanowires

Molecular dynamics simulations with the Tersoff potential were used to study the response of twinned SiC nanowires under tensile and compressive strain. The critical strain of the twinned nanowires can be enhanced by twin stacking faults, and their critical strains are larger than those of perfect nanowires with the same diameters. Under axial tensile strain, the bonds of the nanowires are stretched just before failure. The failure behavior is found to depend on the twin segment thickness and the diameter of the nanowires. An atomic chain is observed for thin nanowires with small twin segment thickness under tension strain. Under axial compressive strain, the collapse of twinned SiC nanowires exhibits two different failure modes, depending on the length and diameter of the nanowires, i.e., shell buckling for short nanowires and columnar buckling for longer nanowires.

Effect of trimethylgallium flow on the structural and optical properties of InGaN/GaN multiple quantum wells

InGaN/GaN multiple quantum wells (MQWs) are grown by metal-organic chemical vapour deposition on (0001) sapphire substrates. Triple-axis X-ray diffraction (TXRD) and photoluminescence (PL) spectra are used to assess the influence of trimethylgallium (TMGa) flow on structural defects, such as dislocations and interface roughness, and the optical properties of the MQWs. In this paper, a method, involving an ! scan of every satellite peak of TXRD, is presented to measure the mean dislocation density of InGaN/GaN MQWs. The experimental results show that under certain conditions which keep the trimethlyindium flow constant, dislocation density and interface roughness decrease with the increase of TMGa flow, which will improve the PL properties. It can be concluded that dislocations, especially edge dislocations, act as nonradiative recombination centres in InGaN/GaN MQWs. Also noticed is that changing the TMGa flow has more influence on edge dislocations than screw dislocations.

Synthesis and application on parallel image storage of bisfurylfulgide

A bisfurylfulgide, E, E-3,4-bis[1-(2,5-dimethyl-3-furyl)ethylidene]-3,4-dihydrofuran-2,5-dione, is synthesized by Stobbe condensation reaction. The molecular structure of target compound is confirmed by single crystal X-ray crystallography analysis. It shows that the distances between two possible reaction sites of molecule are 0.3394 and 0.3406 nm respectively, which is favorable to photocyclization. The photochromic properties of this compound in different solvents are investigated, and the result shows that the compound exhibits excellent photochromic behavior. The primary result of applied research on parallel image storage is also presented.

丁香和升麻的化学成分研究

本论文由三部分共四章组成。第一部分介绍丁香化学成分的研究成果，第二部分为升麻的化学成分研究，第三部分综述了环菠萝蜜烷三萜结构和活性关系的研究现状。 第一部分包括第一和第二章。第一章介绍了丁香（Eugenia caryophyllataThunb.）花蕾的化学成分和结构鉴定。采用正、反相硅胶柱层析等各种分离方法，从其乙醇提取物的乙酸乙酯萃取物和正丁醇萃取物中共分离出34 个化合物，它们的结构类型分属黄酮、三萜、鞣质等。其中1 个为新的酚苷类化合物，其结构经波谱分析鉴定为2-O-(6'-O-没食子酰基)-b-D-葡萄糖基苯甲酸甲酯（24），另外还有12 个化合物为首次从该植物中分离得到。第二章介绍了丁香挥发油的气相色谱- 质谱联用（ GC-MS ）和正丁醇萃取物的高效液相色谱- 质谱联用（HPLC-MS/MS）分析，尝试简单快速地检测丁香挥发油及极性部分的主要化学成分的方法。 第二部分为第三章。本章介绍了传统中药升麻（Cimicifuga foetida L.）根部乙醇提取物化学成分的分离纯化和结构鉴定。通过正、反相硅胶柱层析等分离纯化方法和MS、NMR 等波谱解析技术，共分离鉴定了20 个化合物，主要为环菠萝蜜烷三萜，其中5 个新三萜化合物分别鉴定为cimicidol-3-one（38）、3'-O-乙酰基升麻苷H-1（41）、2'-O-乙酰基升麻苷H-1（42）、(3b,12b,16b)-12-乙酰氧-16,23-环氧-9,19-环羊毛甾烷-22-烯-24-酮3-O-b-D-吡喃木糖苷（44）和升麻碱（54）。新化合物54 为结构新颖的环菠萝蜜烷三萜皂苷生物碱，这是首个发现的具有环菠萝蜜烷三萜骨架的生物碱，也是从升麻属植物中发现的第一个三萜生物碱，它的结构通过多种波谱解析，特别是2D-NMR 的充分应用，并结合化学降解和反应得到证实。此外，还介绍了分离得到的一种具有明显抑制破骨细胞活性的化合物(QS29)的体外活性研究。 第三部分即第四章，综述了升麻属植物中环菠萝蜜烷三萜与其生物活性的构效关系研究现状。 This dissertation consists of three parts. In the first and the second parts, thechemical constituents from the flower buds of Eugenia caryophyllata and therhizomes of Cimicifuga foetida were reported. The third part is a review on astructure-activity relationship of the cycloartane triterpenoid from Cimicifuga species. The first part is composed of two chapters. The chapter 1 is about the isolationand identification of the chemical constituents from the flower buds of E.caryophyllata. A new phenolic glucoside gallate, methyl 2-O-(6’-O-galloyl)-b-D-glucopyranosylbenzoate (24), together with thirty-three known compounds has beenisolated from the ethanol extract of the flower buds of E. caryophyllata throughrepeated column chromatography on normal and reversed phase silica gel. Thestructure of the new compound was elucidated on the basis of spectral and chemicalevidence. Those kno wn compounds were belonged to flavone, triterpenoid, tannin andsome simple compounds. Among them, 12 compounds were isolated from the titleplant for the first time. The second chapter describes the capillary GC-MS analysis ofthe volatile components and the HPLC-MS/MS analysis of the polar constituents fromthe flower buds of E. caryophyllata, in order to detect the main constituents in thecrude extract rapidly and precisely. The third chapter is about the chemical constituents of the rhizomes C. foetida, atraditional Chinese medicine which was used as anti-inflammatory, analgesic andantipyretic agents. Our investigation of the bioactivities constituents of the rhizomesof C. foetida led to the isolation of five new cycloartane triterpenoids, which werecharacterized as cimicidol-3-one (38), 3'-O-acetyl cimicifugoside H-1 (41),2'-O-acetyl cimicifugoside H-1 (42), (3b,12b,16b)-12-acetoxy-16,23-epoxy-9,19-cyclolanost-22-ene-24-one 3-O-b-D-xylopyranoside (44) and cimicifugadine (54),along with fifteen known compounds through repeated column chromatography onnormal and reversed phase silica gel. Among them, 54 is a novel cycloartanealkaloid and first discovered as a new type alkaoid from nature. The structures ofthese compounds were elucidated on the basis of spectral and chemical evidence, andcimicidol-3-one was confirmed by X-ray crystallography analysis. Moreover, onecompound exhibited strong anti-osteoporosis activity in vitro experiment. The fourth part is a review on a structure-activity relationship analysis of thecycloartane triterpenoid from Cimicifuga species.

双花千里光、川芎及宽叶羌活的化学成分研究

本论文由四章组成。第一、二和三章分别报道了双花千里光、川芎和宽叶羌活的化学成分研究。从三种药用植物中共分离和鉴定了40 个化学成分，其中8个为新化合物。第四章概述了藳本属植物及日本川芎的化学成分研究进展。 第一章包括三个部分。第一部分报道双花千里光（Senecio dianthus Franch.）地上部分乙醇提取物的化学成分。采用正、反相硅胶柱层析等各种分离方法，从中共分离出8 个艾里莫酚型倍半萜内酯，其中5 个是新化合物，并且有1 个为首次发现的连接了含氮原子取代基的艾里莫酚型倍半萜内酯。它们的结构经MS、IR、NMR及X-单晶衍射等解析方法确定为2b-angeloyloxy-10b-hydroxyeremophil-7(11)-en-8a,12-olide (1)、6b-angeloyloxy-10b-hydroxyeremophil-7(11)-en-8a,12-olide (2)、2b-angeloyloxy-8b,10b- dihydroxyeremophil-7(11)-en-8a,12-olide (3)、2b-angeloyloxy-8a-hydroxyeremophil-7(11),9(10)-dien-8b,12-olide (4)和8b-amino-10b- hydroxyleremophil-7(11)-en-8a,12-olide (5)。这8 个倍半萜内酯经体外生物活性测试表明均具有通过抑制巨噬细胞增殖抵制破骨细胞增生的活性。第二部分对艾里莫酚型倍半萜内酯的质谱裂解规律进行了初步探讨。第三部分报道双花千里光茎、和叶花的挥发油成分分析。采用传统水蒸气蒸馏法分别提取了双花千里光茎、叶和花的挥发油，用气相色谱－质谱联用（GC-MS）技术分别分离鉴定了其化学成分，从茎、叶和花挥发油中各分离和鉴定出70、80 和73 种化学成分，分别占挥发油总量的91.2％、85.7％及93.4％。 第二章包括两个部分。第一部分报道川芎（Ligusticum chuanxiong Hort.）根茎乙醇提取物的化学成分。通过正、反相硅胶柱层析等分离纯化和MS、NMR及X-单晶衍射等解析方法，共分离鉴定了21 个化合物，结构类型分属于苯酞、二聚苯酞、香豆素和脂肪酸类。其中2 个为结构比较新颖的二聚苯酞类化合物：chuanxiongnolide A (19)和chuanxiongnolide B (20)，化合物19 的结构经X-单晶衍射得到确证。第二部分报道川芎挥发油的化学成分。采用不同的提取方法（溶剂萃取法、水蒸气蒸馏法、CO2 超临界流体萃取法）提取川芎挥发油，同时采集不同产地（四川彭县、四川郫县、云南鹤庆）及不同品质（川芎、奶芎、苓子）的川芎产品，利用GC-MS 技术分离鉴定其挥发油的化学成分，计算各成分的相对含量，并对比分析其中的异同。 第三章报道宽叶羌活（Notopterygium forbesii Boiss.）根茎化学成分的分离纯化和结构鉴定。通过正、反相硅胶柱层析等分离纯化和MS、NMR 等解析方法，共分离鉴定了13 个化合物，结构类型分属于香豆素、二氢异香豆素、甾体和羧酸类。其中1 个新二氢异香豆素类成分鉴定为6-methoxy-hydrangenol (37)。 第四章概述了藳本属植物及日本川芎化学成分的研究进展。 This dissertation consisted of four chapters. The former three chaptersrespectively elaborated the phytochemical investigation of three herbal medicines:Senecio dianthus Franch., Ligusticum chuanxiong Hort. and Notopterygium forbesiiBoiss.. Forty compounds, including eight new ones, were isolated and identified byspectral and chemical evidence. The fourth chapter elaborated the study progress ofchemical constituents of Ligusticum genus and Cnidium offcinale. The first chapter consisted of three parts. The first part is about the chemicalconstituents of ethanol extraction and essential oils from the aerial parts of S. dianthu.Eight eremophilenolides were isolated and identified. Among them, five ones are newcompounds and one of them is a novel eremophilenolide attched with an amino group.The structures of the new compounds were identified as 2b-angeloyloxy-10b-hydroxyeremophil-7(11)-en-8a,12-olide (1)，6b-angeloyloxy-10b-hydroxyeremophil-7(11)-en-8a,12-olide (2)，2b-angeloyloxy-8b,10b-dihydroxyeremophil-7(11)-en-8a,12-olide (3)，2b-angeloyloxy-8a-hydroxyeremophil-7(11),9(10)-dien-8b,12-olide (4) and8b-amino-10b-hydroxyeremophil-7(11)-en-8a,12-olide (5) by spectral evidence andX-ray crystallography analysis. All the compounds were evaluated for theiranti-osteoclstogenesis activity using a proliferation inhibit assay with microphagecells. The second part elementarily discussed the characteristic fragmentation oferemophilenolides isolated from S. dianthus in ESI-MS.The latter part is about thechemical constituents of essential oil extracted from stems, leaves and flowers of S.dianthus with steam distillation. By the GC-MS analysis, 70, 80 and 73 compoundswere respectively isolated and identified which accounted for more than 91.2％, 85.7％ and 93.4％ of total essential oil. The second chapter, including two parts, is about the the chemical constituents ofethanol extraction and essential oils from rhizomes of L. chuanxion. In the first part, twenty-one compounds were isolated and iedntified. Two ones are novel dimericphthalides and the structures were suggested as chuanxiongnolide A (19) andchuanxiongnolide B (20) by spectral evidence and confirmed by X-raycrystallography analysis. In the second part, the samples were collected from differentextract techniques (solvent extraction, steam distillation and supercriticalfluid extraction), different habitats (Peng and Pi counties, Sichuan province; Heqing,Yunnan province) and different qualities (Chuanxiong, Naixiong and Lingzi). Thechemical constituents of essential oil from L. chuanxiong were analyzed by GC-MS and were compared each other. The third chapter is about the chemical constituents of rhizomas of N. forbesii,which belongs to a endemic genus of China. Thirteen compounds were isolated andidentified. One of them is a new dihydroisocoumarin and the structure was identifiedas 6-methoxy-hydrangenol (37) by spectral evidence. The fourth chapter is a review on study progress of chemical constituents ofLigusticum species and Cnidium offcinale.

钩藤和蹄叶橐吾的化学成分研究

本论文由三章组成。第一、二章分别报道钩藤、蹄叶橐吾的化学成分研究工作。从两种药用植物中共分离和鉴定了37 个化合物，其中有1 组6 个新的骨架相似的鞘糖脂类同系物及5 个新的倍半萜类化合物。第三章概述了艾里莫芬烷内酯类化合物的研究进展。 第一章报道钩藤(Uncaria rhynchophylla)带钩茎枝乙醇提取物的化学成分。采用正、反相硅胶柱层析等分离方法，运用NMR、MS 等波谱技术共分离鉴定得到22 个化合物，分属于五环三萜类化合物、鞘糖脂类化合物等，其中有1 组6个新的鞘糖脂类化合物同系物，另外有7 个化合物首次从该植物中分离得到。 第二章报道蹄叶橐吾(Ligularia fischeri)根部乙醇提取物化学成分的分离纯化和结构鉴定。通过正、反相硅胶柱层析等分离纯化和MS、NMR 等波谱解析，共分离鉴定得到18 个化合物，其中5 个是新化合物。它们的结构分别确定为3β-acetyl-6β, 8α, 10β-trihydroxyeremophila-7(11)-en-8, 12-olide (23), 3β-acetyl-8β,10β-dihydroxy-6β-(2-methylbutyryloxy)-eremophilenolide (24), 3β-acetyl-6β, 10β-dihydroxyeremophila-7(11), 8(9)-dien-8, 12-olide (25), 3β-acetyl-6β, 10β-dihydroxyeremophila- 7(11), 8(9)-dien-8, 12-olide (26), (3aR, 4R, 5S, 7aS)-2-acetyl-7ahydroxy-3a, 4, 5, 6, 7, 7a-hexahydro-1H-inden-5-yl acetate (27)。这5 个化合物经体外生物活性测试，结果表明化合物23 具有抑制酪氨酸磷酸酯酶的活性, 其IC50 值为1.30 μg/ml。 第三章概述了近二十年来艾里莫芬烷内酯类化合物的研究进展，包括其结构及药理活性两个方面，列举了从23 种植物中分到的114 个艾里莫芬烷内酯类化合物，同时也对其主要生物活性进行了总结。 This dissertation consists of three chapters. The first and second chapters elaborate the phytochemical investigation of Uncaria rhynchophylla and Ligularia fischeri. Thirty-seven compounds, including six new ones, were isolated and identified by spectroscopic methods and X-ray diffraction experiments. The third chapter is a review on the study progress of Eremophilanolides. The first chapter focus on the isolation and identification of chemical constituents from Uncaria rhynchophylla. Twenty-two compounds were isolated from the roots of U. rhynchophylla by repeat column chromatography over normal and reversed phase silica gel. Those compounds mainly belonged pentacyclic triterpenoids and sphingolipids. Among them, a series homologues of six sphingolipids were new compounds and seven compounds were firstly reported in this plant. The second chapter is about the phytochemical investigation of L. fischeri. Eighteen compounds were isolated and identified. Among them, four new erem-ophilanolides and a new dinoreremophilane derivative were characterized as 3β-acetyl-6β, 8α, 10β-trihydroxyeremophila-7(11)-en-8, 12-olide (23), 3β-acetyl-8β, 10β-dihydroxy-6β-(2-methylbutyryloxy)-eremophilenolide (24), 3β-acetyl-6β, 10β-dihydroxyeremophila-7(11), 8(9)-dien-8,12-olide (25), 3β-acetyl-6β, 10α-dihydroxyeremophila- 7(11), 8(9)-dien-8,12-olide (26), (3aR,4R,5S,7aS)-2-acetyl-7a-hydroxy-3a, 4, 5, 6,7, 7a-hexahydro-1H-inden-5-yl acetate (27) by spectroscopic analysis and confirmed by X-ray crystallography analysis. It was revealed that compound 23 has the ability to inhabit the PTP1B in vivo. And its IC50 is 1.30 μg/ml. The third part is a review on the study progress of Eremophilanolides.

Synthesis and identification of Heterocyclic derivatives of fullerene C-60: Unexpected reaction of anionic C-60 with benzonitrile

During the reaction of reduced C-60 with benzyl bromide in benzonitrile, a novel cis-1 C-60 adduct, 1,4-dibenzyl-2,3-cyclic phenylimidate C-60 (1), Was obtained rather than the expected product of 1,4-dibenzyl C-60. The structure of compound 1 was analyzed by X-ray single-crystal diffraction, identifying the presence of a five-membered heterocycle at a [5,6] bond of C-60. One of the heteroatoms is assigned as a nitrogen atom; however, the identity of the other heteroatom cannot be determined unambiguously by crystallography due to similarity between the nitrogen and oxygen atoms.

Selective Synthesis of Single-Crystalline Rhombic Dodecahedral, Octahedral, and Cubic Gold Nanocrystals

This paper reports a versatile seed-mediated growth method for selectively synthesizing single-crystalline rhombic dodecahedral, octahedral, and cubic gold nanocrystals. In the seed-mediated growth method, cetylpyridinium chloride (CPC) and CPC-capped single-crystalline gold nanocrystals 41.3 nm in size are used as the surfactant and seeds, respectively. The CPC-capped gold seeds can avoid twinning during the growth process, which enables us to study the correlations between the growth conditions and the shapes of the gold nanocrystals. Surface-energy and kinetic considerations are taken into account to understand the formation mechanisms of the single-crystalline gold nanocrystals with varying shapes.

Synthesis, crystal structures and spectroscopic properties of copper(I) complexes containing beta-dialdiminato supporting ligands

Two mononuclear neutral copper(I) complexes, Cu(L-1)PPh3 (1), Cu(L-2)(PPh3)(2) (2) ([L-1](-) = [{N((C6H3Pr2)-Pr-i-2,6)C(H)}(2)CPh](-); [L-2](-) = [{N(C6H5)C(H)}(2)CPh](-)) have been synthesized and structurally characterized by X-ray crystallography. In complex 1, the copper(I) atom is in a distorted three-coordinate trigonal planar environment, whereas in complex 2 with the less sterically hindered beta-dialdiminato ligand, the copper(I) atom is the centre of a four-coordinate distorted tetrahedron. At room temperature complexes 1 and 2 in a film of PMMA exhibit green emission at 543 and 549 nm with lifetimes of 5.28 and 5.32 ns, respectively.

Synthesis, photophysical and electrophosphorescent properties of mononuclear Pt(II) complexes with arylamine functionalized cyclometalating ligands

Four cyclometalated Pt(II) complexes, i.e., [(L-2)PtCl] (1b), [(L-3)PtCl] (1c), [(L-2)PtC CC6H5] (2b) and [(L-3)PtC CC6H5] (2c) (HL2 = 4-[p-(N-butyl-N-phenyl)anilino]-6-phenyl-2,2'-bipyridine and HL3 = 4-[p(-N,N'-dibutyl-N'-phenyl)phenylene-diamino]-phenyl-6-phenyl-2,2'-bipyridine), have been synthesized and verified by H-1 NMR, C-13 NMR and X-ray crystallography. Unlike previously reported complexes [(L-1)PtCl] (1a) and [(L-1)PtC CC6H5] (2a) (HL1 = 4,6-diphenyl-2,2'-bipyridine), intense and continuous absorption bands in the region of 300-500 nm with strong metal-to-ligand charge transfer ((MLCT)-M-1) (d pi(Pt) -> pi*(L)) transitions (epsilon similar to 2 x 10(4) dm(3) mol (1) cm (1)) at 449-467 nm were observed in the UV-Vis absorption spectra of complexes 1b, 1c, 2b and 2c.

Synthesis, characterization, photophysics and electrophosphorescent applications of phosphorescent platinum cyclometalated complexes with 9-arylcarbazole moieties

A series of cyclometalating platinum(II) complexes with substituted 9-arylcarbazolyl chromophores have been synthesized and characterized. These complexes are thermally stable and most of them have been characterized by X-ray crystallography. The phosphorescence emissions of the complexes are dominated by (MLCT)-M-3 excited states. The excited state properties of these complexes can be modulated by varying the electronic characteristics of the cyclometalating ligands via substituent effects, thus allowing the emission to be tuned from bright green to yellow, orange and red light. The correlation between the functional properties of these metallophosphors and the results of density functional theory calculations was made. Because of the propensity of the electron-rich carbazolyl group to facilitate hole injection/transport, the presence of such moiety can increase the highest occupied molecular orbital levels and improve the charge balance in the resulting complexes relative to the parent platinum(II) phosphor with 2-phenylpyridine ligand.