A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

Generating artificial homologous proteins according to the representative family character in molecular mechanics properties - an attempt in validating an underlying rule of protein evolution

The molecular mechanics property is the foundation of many characters of proteins. Based on intramolecular hydrophobic force network, the representative family character underlying a protein’s mechanics property is described by a simple two-letter scheme. The tendency of a sequence to become a member of a protein family is scored according to this mathematical representation. Remote homologs of the WW-domain family could be easily designed using such a mechanistic signature of protein homology. Experimental validation showed that nearly all artificial homologs have the representative folding and bioactivity of their assigned family. Since the molecular mechanics property is the only consideration in this study, the results indicate its possible role in the generation of new members of a protein family during evolution.

Enhancement of three-photon absorption cross-sections in a novel class of symmetrical charge transfer fluorene-based molecules

The three-photon absorption effect (3PA) of two novel symmetrical charge transfer fluorene-based molecules (abbreviated as BASF and BMOSF) has been determined by using a Q-switched Nd:YAG laser pumped with 38 ps pulses at 1064 nm in DMF. The measured 3PA cross-sections are 84 x 10(-78) and 114 x 10(-78) cm(6) s(2), respectively. The geometries and electronic excitations of these two molecules are systematically studied by PM3 and ZINDO/S methods. The relationships between 3PA cross-sections and intramolecular charge transfer are discussed micromechanically. The experimental and theoretical results have shown that the larger intramolecular charge transfer, which was characterized by the charge density difference between the ground state (SO) and the first excited state (S-I), the greater enhancement of the 3PA cross-sections. (c) 2005 Elsevier B.V. All rights reserved.

α-异噁唑偶氮基-β-二酮类衍生物及其互变异构体的光谱

研究了5种新型的具有不同结构的aα-异噁唑偶氮基-β-二酮类衍生物的红外光谱和紫外光谱，讨论了它们的酮式-烯醇式以及偶氮式．腙式之间的互变异构化现象。结果表明，所有化合物无论以固体形式或在溶液中均以腙式二酮体和偶氮式烯醇体的混合形式存在。各化合物的紫外吸收谱均呈双峰状，峰值分别处于246～262nm和326～339nm之间，其中，高波长吸收峰的强度明显高于低波长吸收峰强度，说明了各化合物中偶氮式烯醇体形式均多于腙式二酮体形式，其原因是由于各化合物中偶氮式烯醇体的异构体较多，且易以分子内氢键形式形成六元环，

A novel antimicrobial peptide from amphibian skin secretions of Odorrana grahami

A novel antimicrobial peptide named odorranain-NR was identified from skin secretions of the diskless odorous frog, Odorrana grahami. It is composed of 23 amino acids with an amino acid sequence of GLLSGILGAGKHIVCGLTGCAKA. Odorranain-NR was classified into a novel family of antimicrobial peptide although it shared similarity with amphibian antimicrobial peptide family of nigrocin. Odorranain-NR has an unusual intramolecular disulfide-bridged hexapeptide segment that is different from the intramolecular disulfide-bridged heptapeptide segment at the C-terminal end of nigrocins. Furthermore, the -AKA fragment at the C-terminal of odorranain-NR is also different from nigrocins. Three different cDNAs encoding two odorranain-NR precursors and only one mature odorranain-NR was cloned from the cDNA library of the skin of O. grahami. This peptide showed antimicrobial activities against tested microorganisms except Escherichia coli (ATCC25922). Its antimicrobial mechanisms were investigated by transmission electron microcopy. odorranain-NR exerted its antimicrobial functions by various means depending on different microorganisms. (C) 2008 Elsevier Inc. All rights reserved.

茚基含氮、氧侧链分子内配位稀土有机化合的合成和性质

稀土有机碳σ-键配合物和氢化物不仅可以催化许多有机反应,而且还可以催化极性单体与非极性单体的聚合.作为稀土有机碳σ-键配合物与氢化物的前体,双配稀土氯化物(C<,9>H<,7>)<,2>LnCl一直是稀土有机化学中研究的热点.1.合成了一系列双配(四氢糠基茚基)稀土氯化物(C<,4>H<,7>OCH<,2>C<,9>H<,6>)<,2>LnCl(Ln=La,Pr,Nd,Sm,Gd,Dy,Y,Ho,Er,Yb,Lu).除了Pr以外,所有化合物的晶体结构都被X-射线衍射表征.2.合成并用X-衍射表征了3-(2-吡啶甲基)茚基锂(C<,5>H<,4>NCH<,2>C<,9>H<,6>)Li(THF)<,2>的晶体结构.3.合成了双配[3-(2-吡啶甲基)茚基]稀土氯化物(C<,5>H<,4>NCH<,2>C<,9>H<,6>)<,2>LnCl(Ln=Sm,Nd),并得到了配合物Nd的晶体结构.4.用二碘化钐(镱)与3-(2-吡啶甲基)茚基锂反应合成了二价双配[3-(2-吡啶甲基)茚基]稀土配合物(C<,5>H<,4>NCH<,2>C<,9>H<,6>)<,2>Ln(Ⅱ)(THF)(Ln=Sm,Yb).5.在用无水氯化稀土YbCl<,3>与3-(2-吡啶甲基)茚基锂反应合成双配[3-(2-吡啶甲基)茚基]稀土氯化物时,由于发生了还原反应,得到了二价双配[3-(2-吡啶甲基)茚基]镱化物(C<,5>H<,4>NCH<,2>C<,9>H<,6>)<,2>Yb(Ⅱ)(THF).6.二价双配[3-(2-吡啶甲基)茚基]稀土配合物(C<,5>H<,4>NCH<,2>C<,9>H<,6>)<,2>Ln(Ⅱ)(THF)(Ln=Sm,Yb)对已内酯具有很好的催化聚合活性.聚合反应可控,并具有活性聚合的特征.

具有环氧化酶-2选择性抑制活性的多取代蒽醌的合成

1-甲基-2-甲氧羰基-3, 6, 8-三羟基-7-甲氧基蒽醌是从唐菖蒲干球茎中分离到的具有环氧化酶-2选择性抑制活性的多取代蒽醌类化合物。本文试图合成该化合物，实现了其类似物的合成，同时发现了几个未见报道的反应。 1．通过Diels-Alder 反应合成了关键中间体——3-甲基-5-羟基-1, 2, 4-苯三甲酸三甲酯，1-COOMe选择性水解产物与1, 2, 3-三甲氧基苯进行分子间Friedel-Crafts反应的产物再进行分子内Friedel-Crafts反应得到了目标产物的类似物1-甲基-2-甲氧羰基-3-羟基-6，7，8-三甲氧基蒽醌（路线1）。目标产物及其它类似物的合成正在进行中。 2．以乙酰乙酸甲酯和巴豆醛为原料，经过Michael加成、分子内的Aldol反应、芳香化、选择性甲酰化和还原反应，得到关键中间体2-甲基-3-羟甲基-6-甲氧基苯甲酸甲酯及其衍生物。通过该化合物与3，4，5-三甲氧基苯甲酸甲酯进行Friedel-Crafts烷基化反应得到了多取代的二苯基甲烷衍生物，拟进一步关环合成目标化合物（路线2）。 3．发现邻甲氧基苯甲酸甲酯中酯甲基可以被正丁基锂和仲丁基锂中烷基交换生成相应的酯，反应的机理不明确。当使用叔丁基锂时，得到的是邻甲氧基苯基叔丁酮，这个方法可以用来合成芳基叔丁酮类化合物。 4．以2-苄氧基-6-甲基苯甲酸甲酯为原料进行氯甲基化反应时，以苯和二氯乙烷作溶剂，发生了苄基的迁移和芳环的偶联，分别得到2，2'-二甲基-3，3'-二甲氧羰基-4，4'-二羟基联苯和2，2'-二甲基-3，3'-二甲氧羰基-4，4'-二羟基-5，5'-二苄基联苯。这是对称联苯合成的新方法。 5．水杨酸羟基邻对位的选择性甲酰化可以分别通过水杨酸和水杨酸甲酯用HMTA/CF3COOH来实现。 6．Lewis酸催化3，4，5-三甲氧基苄醇环化成1, 2, 3, 6, 7, 8, 11, 12, 13-nonamethoxyl-10,15-dihydro-5H-trbibenzo [a, d, g] cyclononene (NDTC)，产率(54%)高于已有方法（12%）。 Methyl 3,6,8-trihydroxy-7-methoxy-1-methylanthraquinone-2-carboxylate is a new COX-2 selective inhibitor isolated from Gladiolus gandavensis. Two strategies were investigated to synthesis this compound, in which some important reactions were discovered. 1. The key intermediate 5-hydroxy-3-methylbenzene-1,2,4-tricarboxylic acid 2,4-dimethyl ester was prepared via Diels-Alder reaction followed by selective hydrolysis of 1-COOMe. This compound was coupled with 1,2,3-trimethoxybenzene and the product undergo intramolecular Friedel-Crafts reaction to give methyl 3-hydroxy-5,6,7-trimethoxy-1-methylanthraquinone-2-carboxylate (1st route). The target compound and other analogues are being prepared with the same procedure. 2. The key intermediates methyl 3-hydroxymethyl-6-methoxy-2-methylbenzoate and its derivatives were prepared starting from crotonaldehyde and methyl acetoacetate via Michael addition, intramolecular aldol reaction, aromatization, formylation and reduction. The intermediates were coupled respectively with derivatives of gallic acid to give polysubstituted diphenylmethane. However, attempts to cyclize these compounds to the target compounds and analogues were not successful (2nd route). 3. In the process for ortho-lithiation of methyl 2-methoxybenzoate, the substrate converted respectively to n-butyl 2-methoxybenzoate and sec-butyl 2-methoxybenzoate when n-BuLi and sec-BuLi were used. However, tert-BuLi reacted with methyl 2-methoxybenzoate afford 2-methoxyphenyl tert-butyl ketone, which could be used to synthesize aryl tert-butyl ketones. 4. The transformtion of methyl 2-benzoxy-6-methylbenzoate to dimethyl 4,4'-dihydroxy-2,2'-dimethylbiphenyl-3,3'-dicarboxylate in benzene, and dimethyl 5,5'-dibenzyl-4,4'-dihydroxy-2,2'-dimethylbiphenyl-3,3'-dicarboxylate in 1,2-dichloroethane in the presence of ZnCl2 provides a new method for the synthesis of symmetric biphenyl. 5. The formylation of salicylic acid at C-5 and methyl 2-hydroxybenzoate at C-3 could be regioselectively realized by using HMTA/CF3COOH. 6. Racemic 1, 2, 3, 6, 7, 8, 11, 12, 13-nonamethoxyl-10, 15-dihydro-5H-trbibenzo [a, d, g] cyclononene was prepared via Lewis acids catalyzed trimerization of 3, 4, 5-trimethoxylbenzyl alcohol with yield (54%) higher than the reported procesure (12%).

N-烷基氮杂糖及其衍生物的合成

多羟基哌啶类化合物通常称为氮杂糖，由于与糖结构的相似性，亚胺基环醇表现出强的糖苷酶和糖基转移酶抑制活性，可调控在生物识别及酶结构控制中起到重要作用的糖蛋白的生物合成与水解。因此这类抑制剂有望成为与糖代谢紊乱有关的疾病的治疗药物，如：抗糖尿病、抗肿瘤、抗溶酶体贮积症及抗病毒感染（包括艾滋病）等药物。正是由于氮杂糖的重要生物活性及诱人的药用开发前景，近年来，有关氮杂糖及其衍生物的合成、生物活性及应用研究备受关注。 本论文探索了一系列的作为潜在的迈克加成中间体1-C-乙酰甲基/甲氧羰基甲基-5-N-取代呋喃核糖碳苷衍生物在碱的作用下先发生β-消除反应，接着发生分子内的迈克加成反应生成1-C-乙酰甲基-N-取代氮杂吡喃糖碳苷衍生物及1-C-甲氧羰基甲基-N-取代氮杂吡喃糖碳苷衍生物的方法，该转变过程为先通过β-消除得到非环状的α/β不饱和共轭酮或酯的中间体，接着5-N-取代氨基与分子内的α/β不饱和共轭酮或酯发生分子内的1,4-亲核加成，其中，2'-酯的环加成立体选择性的得到β型1-C-乙酰甲基-N-取代氮杂吡喃糖碳苷衍生物，而2'-酮的环加成得到立体异构体1-C-乙酰甲基-N-取代氮杂吡喃糖碳苷衍生物。此外，该类N-取代氮杂吡喃糖碳苷衍生物进一步脱除保护基，得到了一系列新的N-取代氮杂吡喃糖衍生物，拓展了氮杂吡喃糖碳苷分子库。 中间体1-C-(2'-oxoalkyl)-5-N-alkylated glycoribofuranoside的合成是由核糖为原料，通过对其结构修饰，在C-5氮原子上先引入不同的取代基，在C-1上引入乙酰甲基或甲氧羰基甲基。C-5取代氨基的引入通过两种方法：(a) 5-取代链状脂肪氨基可由链状的伯胺直接与5-甲磺酰基发生SN2亲核取代得到；(b) 5-取代芳香氨基可通过芳香醛与C-5氨基缩合再由硼氢化钠还原得到。2'-酰基的引入通过烯丙基氧化得到：2'-酮羰基由醋酸汞和琼斯试剂氧化得到；2'-酯基由高锰酸钾氧化再碘甲烷的作用下得到。 The polyhydroxylated piperidines, commonly be called azasugars. Iminocyclitols and their derivatives have exhibited remarkable biological activity to inhibit glycosidase-processing enzymes, with resulting potential chemotherapeutic applications against diabetes, cancer, lysosomal storage disorders and viral infections including AIDS. Recently, because of the important biological activity and excellent foreground on pharmaceutical application, great attention has been attracted to the synthesis of the new derivatives and analogues. In this dissertation, 1-C-(2'-oxoalkyl)-5-N-substituted-glycoribofuranosides, which used as latent substrates for intramolecular hetero-Michael addition, were converted to 2-ester and 2-ketone aza-C-glycopyranosides by base treatment. The transformation was achieved through β-elimination to an acyclic α/β-conjugated ketone or ester, followed by an intramolecular hetero-Michael addition by the 5-N-alkylated amino group. The 2-ester cycloaddition was highly stereoselective in favor of an equatorial 1-C-substitution while the 2-ketone cycloaddition was produced a pair of stereoisomers of 2′-ketonyl aza-C-glycoside. Additionally, the resultant different N-alkylated aza-C-glycopyranosides could be further prepared for various azasugar library constructions by removal of protecting groups. Synthesis of the key intermediate 1-C-(2'-oxoalkyl)-5-N-alkylated glycoribo- furanoside involved the introduction of 5-substituted amino and 1-C-2′-oxoalkyl groups from D-ribose. The 5-alkylated amino was introduced through two methods: (a) the 5-aliphatic series amino synthesized by the nucleophilic substitution of 5-mesylate using neat ethylamine, propylamine, butylamine, and hexylamine, (b) the 5-aromatic series amino synthesized by various aromatic aldehydes with C-5 amino under NaBH4 reduction. The 1-C-2′-oxoalkyl groups were introduced through oxidation of the ally group: the 1-C-allyl group was oxidized with Hg(OAc)2 and Jones reagent to the 2-ketonyl C-glycoside; the 1-C-allyl group was oxidized with KMnO4 and CH3I/NaHCO3 to 1-C-methyl acetate glycoside.

Ultrafast dynamics of dye molecules in solution as a function of temperature

Femtosecond time-resolved studies using fluorescence depletion spectroscopy were performed on Rhodamine 700 in acetone solution and on Oxazine 750 in acetone and formamide solutions at different temperatures. The experimental curves that include both fast and slow processes have been fitted using a biexponential function. Time constants of the fast process, which corresponds to the intramolecular vibrational redistribution (IVR) of solute molecules, range from 300 to 420 fs and increase linearly as the temperature of the environment decreases. The difference of the average vibrational energy of solute molecules in the ground state at different temperatures is a possible reason that induces this IVR time-constant temperature dependence. However, the time constants of the slow process, which corresponds to the energy transfer from vibrational hot solute molecules to the surroundings occurred on a time scale of 1-50 ps, changed dramatically at lower temperature, nonlinearly increasing with the decrease of temperature. Because of the C-H...O hydrogen-bond between acetone molecules, it is more reasonable that acetone molecules start to be associated, which can influence the energy transfer between dye molecules and acetone molecules efficiently, even at temperatures far over the freezing point.

Ultrafast vibrational and thermal relaxation of dye molecules in solutions

Intra- and intermolecular relaxations of dye molecules are studied after the excitation to the high-lying excited states by a femtosecond laser pulse, using femtosecond time-resolved stimulated emission pumping fluorescence depletion spectroscopy (FS TR SEP FD). The biexponential decays indicate a rapid intramolecular vibrational redistribution (IVR) depopulation followed by a slower process, which was contributed by the energy transfer to the solvents and the solvation of the excited solutes. The time constants of IVR in both oxazine 750 and rhodamine 700 are at the 290-360 fs range, which are insensitive to the characters of solvents. The solvation of the excited solutes and the cooling of the hot solute molecules by collisional energy transfer to the surrounding takes place in the several picoseconds that strongly depend on the properties of solvents. The difference of Lewis basicity and states density of solvents is a possible reason to explain this solvent dependence. The more basic the solvent is, which means the more interaction between the solute and the neighboring solvent shell, the more rapid the intermolecular vibrational excess energy transfer from the solute to the surroundings and the solvation of the solutes are. The higher the states density of the solvent is, the more favorable the energy transfer between the solute and solvent molecules is.

Molecular imprinting of nitrophenol and hydroxybenzoic acid isomers: effect of molecular structure and acidity on imprinting

Three nitrophenol isomer-imprinted polymers were prepared under the same conditions using 4-vinylpyridine as a functional monomer. Different recognition capacities for template molecules were observed for the three polymers. Another imprinting system with stronger acidity than nitrophenol isomers, 2-hydroxybenzoic acid (salicylic acid) and 4-hydroxybenzoic acid, was imprinted using 4-vinylpyridine or acrylamide as functional monomer respectively. Both 4-hydroxybenzoic acid-imprinted polymers using the two monomers showed recognition ability for the template molecule. However, when acrylamide was chosen as functional monomer, the salicylic acid-imprinted polymer showed very weak recognition for the template molecule, whereas strong recognition ability of the resultant polymer for salicylic acid was observed with 4-vinylpyridine as functional monomer. It seems that the structure and acidity of template molecules is responsible for the difference in recognition, by influencing the formation and strength of interaction between template molecule and functional monomer during the imprinting process. An understanding of the mechanism of molecular imprinting and molecular recognition of MIPs will help to predict the selectivity of MIPs on the basis of template molecule properties. Copyright (C) 2003 John Wiley Sons, Ltd.

Collisional quantum interference effect on rotational energy transfer in an atom-diatom system

The theoretical model of collisional quantum interference (CQI) in intramolecular rotational energy transfer is described in an atom-diatom system, based on the first Born approximation of time-dependent perturbation theory and considering a long-range interaction potential. The relation between differential and integral interference angles is obtained. For the CO A(1)Pi (v = 0)/e(3)Sigma (-)(v = 1)-He collision system, the calculated integral interference angles are consistent with the experimental values. The physical significance of interference angle and the essential factors it depends on as well as the influence of the short-range interaction on CQI are discussed. (C) 2001 Elsevier Science B.V. All rights reserved.

Efficient One-Pot Synthesis of Highly Substituted Thiophene Library from 1,3-Dicarbonyl Compounds

A faccile and efficient one-pot synthesis of highly substituted thiophenes has been developed and employed for the preparation of a small focused library. Treatment of 1,3-dicarbonyl compounds 1 with CS2 in the presence of K2CO3 in DMF at room temperature, followed by stepwise addition of alkyl bromides 2 and methylene active bromides 3, provided via intramolecular cyclization 2,3,4,5-tetrasubstituted thiophenes 4 in yields of 77-94%. This protocol, combining construction and modification of the thiophene ring, increases the structural diversity of final products from readily available materials. A mechanism for the one-pot synthesis of thiophenes of type 4 has been proposed. A small focused library of thiophenes is prepared using the sequential addition of reagents to achieve unique substitution in the 2 and 5 position of the thiophene ring

A Facile and Efficient Synthesis of Polyfunctionalized Pyridin-2(1H)-ones from β-Oxo Amides under Vilsmeier Conditions

A facile and efficient one-pot synthesis of polysubstituted pyridin-2(1H)-ones from a variety of beta-oxo amides under Vilsmeier conditions is described, and a mechanism involving sequential halogenation, formylation and intramolecular nucleophilic cyclization is proposed

Efficient and Divergent Synthesis of Fully Substituted 1H-Pyrazoles and

Efficient and divergent one-pot synthesis of fully substituted 1H-pyrazoles and isoxazoles from cyclopropyl oximes based on reaction conditions selection is reported. Under Vilsmeier conditions (POCl3/DMF), substituted 1H-pyrazoles were synthesized from 1-carbamoyl, 1-oximyl cyclopropanes via sequential ring-opening, chlorovinylation, and intramolecular aza-cyclization. In the presence of POCl3/CH2Cl2, substituted isoxazoles were obtained from the cyclopropyl oximes via ring-opening and intramolecular nucleophilic vinylic substitution (SNV) reactions