A quantum chemical investigation of the electronic structure of thionine

We have examined the electronic and molecular structure of 3,7-diaminophenothiazin-5-ium dye (thionine) in the electronic ground state and in the lowest excited states. The electronic structure was calculated using a combination of density functional theory and multi-reference configuration interaction (DFT/MRCI). Equilibrium geometries were optimized employing (time-dependent) density functional theory (B3LYP functional) combined with the TZVP basis set. Solvent effects were estimated using the COSMO model and micro-hydration with up to five explicit water molecules. Our calculated electronic energies are in good agreement with experimental data. We find the lowest excited singlet and triplet states at the ground state geometry to be of π→π* (S(1), S(2), T(1), T(2)) and n→π* (S(3), T(3)) character. This order changes when the molecular structure in the electronically excited states is relaxed. Geometry relaxation has almost no effect on the energy of the S(1) and T(1) states (~0.02 eV). The relaxation effects on the energies of S(2) and T(2) are moderate (0.14-0.20 eV). The very small emission energy results in a very low fluorescence rate. While we were not able to locate the energetic minimum of the S(3) state, we found a non-planar minimum for the T(3) state with an energy which is very close to the energy of the S(1) minimum in the gas phase (0.04 eV above). When hydration effects are taken into account, the n→π* states S(3) and T(3) are strongly blueshifted (0.33 and 0.46 eV), while the π→π* states are only slightly affected (<0.06 eV).     

Absolute configuration of labdanes and ent-clerodanes from Chromolaena pulchella by vibrational circular dichroism

The aerial parts of Chromolaena pulchella biosynthesize two groups of diterpenes belonging to opposite enantiomeric series, specifically, the furanoid ent-clerodanes (5R,8R,9S,10R)-(-)-hardwikiic acid (1), methyl (5R,8R,9S,10R)-(-)-hardwikiate (2), (5S,8R,9S,10R)-(-)-hautriwaic acid lactone (3), methyl (5R,8R,9S,10R)-(-)-nidoresedate (4) and methyl (8R,9R)-(-)-strictate (5), as well as the labdanes (5S,8R,9R,10S)-(+)-(13E)-labd-13-ene-8,15-diol (6) and (5S,8R,9R,10S)-(+)-isoabienol (7). The absolute configuration of the two groups of diterpenes was unambiguously assigned by comparison of the vibrational circular dichroism spectra of 3 for ent-clerodanes, and of 7 for labdanes with their theoretical spectra obtained by density functional theory calculations. The results support a biogenetic proposal to diterpenes found in the studied botanical species.     

肋果茶中的萜类化学成分研究

从肋果茶(Sladenia celastrifolia)95％乙醇提取物的乙酸乙酯部位中分离得到15个萜类化合物,经波谱学方法分别鉴定为sladeniafolin A(1),grasshopper ketone (2),(3S,5R,6S,7E,9R) -7-megastigmene-3,6,9-triol (3),hedytriol (4),(3S,5R,6R,7E,9R) -3,5,6,9-tetrahydroxy-7-megastigmene(5),1′S*,4′R*-8-(4′-hydroxy-2′,6′,6′-trimethylcyclohex-2-enyl)-6-methyloct-3E,5E,7E-trien -2-one (6),2α,3α,19α,23-tetrahydroxyurs-12-en-28-oic acid (7),2α,3β,19α,23-tetrahydroxyurs-12-en-28-oic acid(8),pomolic acid(9),3-O-acetyl pomolic acid(10),ursaldehyde (11),camarolide (12),3β-hydroxyurs-11-en-13β(28) -olide (13),3β-hydroxy -11α,12α-epoxy-urs-13β,28-olide (14)和28-0-β-D-glucopyranosyl euscaphic acid (15).以上化合物均首次从该植物中分离得到,其中1为新的C9裂环烯醚萜.     

南海柳珊瑚鳞海底柏化学成分的研究

本文对南海柳珊瑚鳞海底柏Melitodes squarnata Nutting进行了化学成分的研究.通过用工业乙醇:二氯甲烷(2∶1)进行了提取,采用硅胶柱色谱、Sephadex LH-20凝胶色谱、高效液相半制备色谱和薄层制备等方法对鳞海底柏的化学成分进行了分离,并利用波谱分析技术和文献对照鉴定其结构.从鳞海底柏中分离得到了17个化合物,分别鉴定为:malonganenone E(1),malonganenone D(2),nuttingin A(3),腺嘌呤核苷(4),1,3,7-三甲基黄嘌呤(5),2'-脱氧胸腺嘧啶核苷(6),3-甲基-6-次黄嘌呤(7),2'-脱氧尿苷(8),(22E,24R)-ergosta-8 (14),22-dien-3β,5α,6β,7α-tetrol(9),(22E)-胆甾-5,22-二烯-3β-醇(10),胆甾醇(11),(2S,3S,4R)-N-hexadecanoyl-2-amino-1,3,4-eicosanetriol( 12),(2S,2'R,3R,4E,8E)-N-2'- Hydroxytetradecanoyl-2-amino-9-methyl-4,8-octadecaa-diene-1,3-diol(13),鲨肝醇(14),十六烷基甘油醚(15),三油酸甘油酯(16)和4-hydroxy-2,3-dimetlhy1-2-nonen-4-olide(17).     

羊角拗茎的化学成分及其抗炎活性研究

探讨羊角拗茎的化学成分及其抗炎活性,采用硅胶、Sephadex LH-20等色谱分离技术分离纯化羊角拗茎乙醇提取物的乙酸乙酯萃取物中的化合物,通过质谱和核磁共振等波谱技术对其结构进行鉴定,确定出了13个化合物,包括常春藤皂苷元(1)、(-)-loliolide(2)、(3S,5R,6S,7E)-3,5,6-trihydroxy-7-megastigmen-9-one(3)、(3R,6R,7E)-3-hydroxy-4,7-megastigmadien-9-one(4)、松脂素(5)、表松脂素(6)、4,4′-dihydroxy-3,3′-dimethoxybenzophenone(7)、6-羟基柚皮素(8)、东莨菪素(9)、6-羟基-7,8-二甲氧基香豆素(10)、吲唑(11)、香草酸(12)、对羟基苯甲酸(13)。其中化合物1～4和6～13为首次从羊角拗中分离得到。采用LPS诱导小鼠单核巨噬细胞RAW 264.7体外细胞炎症模型测试结果表明,化合物5能显著抑制NO的产生,IC₅₀值为18.09±1.09μM。     

三种毒菌的化学成分研究

本文对三种毒菌的化学成分进行了研究。从光盖伞(Psilocybe spp)分离鉴定了4个化合物,经波谱分析鉴定为:(22E,24R)-麦角甾-7,22-二烯-3β-十八烷酸酯(1)、β-胡萝卜苷(2)、(22E,24R)-5α,6α-环氧麦角甾-8,22-二烯-3β,7α-二醇(3)、色氨酸(4);从假褐云斑鹅膏(Amanita pseudoporphyria)分离鉴定了4个化合物:(22E,24R)-3β-羟基-5α,8α-过氧化麦角甾-6,22-二烯(5)、(22E,24R)-麦角甾-7,22-二烯-3β,5α,6β-三醇(6)、1-O-β-D-吡喃葡萄糖基-(2S,3R,4E,8E,2′R)-2-N-(2′-羟基棕榈酰)-9-甲基-4,8-脱氢鞘氨醇(7)、1-O-β-D-吡喃葡萄糖基-(2S,3R,4E,8E,2′R)-2-N-(2′-羟基十八烷酰)-9-甲基-4,8-脱氢鞘氨醇(8);大青褶伞(Chlorophyllum molybdites)发酵菌丝体分离鉴定了4个化合物:5、6、(22E,24R)-5α,6α-环氧麦角甾-8(14),22-二烯-3β,7α-二醇(9)、(22E,24R)-麦角甾-7,22-二烯-3β-醇(10)。除化合物9外其它化合物均为首次从以上相应毒菌中分离得到。     

Synthesis of the diastereomers of thymidine glycol, determination of concentrations and rates of interconversion of their cis-trans epimers at equilibrium and demonstration of differential alkali lability within DNA.

5,6-dihydroxy-5,6-dihydrothymidine (thymidine glycol) is a major product of the reaction of thymidine with reactive oxygen species, including those generated by ionizing radiation. Thymidine glycol exists as 2 diastereomeric pairs by virtue of the chirality of the C(5) and C(6) atoms. A simple procedure is described for synthesizing and purifying each of the diastereomeric pairs separately. After brominating thymidine, the two trans 5-bromo-6-hydroxy-5,6-dihydrothymidine (thymidine bromohydrin) C(5) diastereomers were easily separated by High Performance Liquid Chromatography. Each thymidine bromohydrin was quantitatively converted to the corresponding diastereomeric thymidine glycol pair by reflux in aqueous solution. The concentrations at equilibrium of the cis (5S,6R),(5R,6S) and trans (5S,6S),(5R,6R) forms of the thymidine glycol diastereomers were determined and were 80% cis and 20% trans for the 5S pair and 87% cis and 13% trans for the 5R pair. At equilibrium, the rate of cis-trans epimerization of the two sets of diastereomers was essentially identical. The 5S diastereomeric pair was significantly more alkali labile than the 5R pair due to the higher concentration of the 5S trans epimer at equilibrium. This differential alkali lability was also manifest when the thymine glycol moiety was present in chemically oxidized poly(dA-dT).poly(dA-dT) indicating that the chemical differences between the diastereomeric pairs are preserved in DNA. These chemical differences may affect the biological properties of this important oxidative derivative of thymine in DNA.     

黄河三角洲耐盐真菌Penicillium chrysogenum HK14-01的次生代谢产物

【目的】从黄河三角洲耐盐微生物的代谢产物中寻找具有抗菌和抗肿瘤活性的化合物。【方法】应用化学与生物活性相集成的筛选方法,从耐盐微生物中筛选获得代谢产物丰富并具有生物活性的目标菌株;通过高盐胁迫目标菌株,利用硅胶柱色谱、凝胶柱色谱和高效液相色谱等方法对发酵产物进行分离、纯化,运用波谱解析、钼靶X-射线单晶衍射分析、圆二色散谱(CD)和密度泛函数(DFT)-ECD的计算鉴定化合物的结构。【结果】从采自黄河三角洲的泥土样品中得到一株耐盐真菌HK14-01,鉴定为产黄青霉Penicilliumchrysogenum;从其发酵产物中分离鉴定了8个化合物:(2S,3R)-oxaline(1,主产物)、(3R,4R)-3,4,8-trihydroxy-3,4-dihydronaphthalen-1(2H)-one(2)、(Z)-N-(4-hydroxystyryl)formamide(3)、(E)-N-(4-hydroxystyryl)formamide(4)、emodin(5)、4-(2-hydroxyethyl)benzene-1,2-diol(6)、methyl 2-(4-hydroxyphenyl)acetate(7)和2-(4-hydroxy phenyl)acetonitrile(8);化合物1、3和4对大肠杆菌以及化合物1和5对金黄色葡萄球菌表现出抑菌活性,化合物5对P388细胞表现出微弱的细胞增殖抑制活性。【结论】首次确定了化合物2的绝对构型、首次报道了化合物1和2的CD数据;从黄河三角洲的耐盐微生物的次生代谢产物中可以得到活性化合物,这一区域的耐盐微生物资源值得深入研究。     

苋科植物的丛枝菌根

有些种子植物如莎草科、十字花科、灯心草科、藜科、石竹科等20余科,以往曾被认为不能或不易形成丛枝菌根(郭秀珍等,1989;刘润进等,2000).随着对菌根的深入研究,曾被认为是不易与菌根菌组合的湿地生植物、寄生性植物、或一年生植物都被发现是可以形成内生菌根的(Trappe等,1992).此外,Allen等(1989)研究证实,Salsola kali,Atriplex roseum等生长于沙漠、海滨的藜科植物,进行接种处理后,也能形成丛枝菌根.我们在西双版纳调查热带雨林植物的丛枝菌根状况时,偶然发现刺苋(Amaranthus spinosus Linn.)的根系受到了丛枝菌根真菌的侵染,因此,对苋科植物作了扩大采样调查.本文主要报道从热带采集的5属6种苋科植物的根受丛枝菌根真菌感染形成丛枝菌根(arbuscular mycorrhiza,AM)和这些植物根际士壤中的丛枝菌根真菌(arbuscular mycorrhizal fungi,AMF)的状况.     

陆地革菌的化学成分研究

从陆地革菌(Thelephora terrestris)子实体中分离得到9个已知化合物,经波谱学分析鉴定为:(22E,24R)-麦角甾-7,22-二烯-3β -醇 (1),(22E, 24R)-麦角甾-7, 22-二烯-3β ,5α,6β -三醇 (2),(22E,24R)-麦角甾-4,6,8(14),22-四烯-3-酮 (3),24-亚甲基羊毛甾-8-烯-3β -醇 (4),熊果酸 (5),木栓酮 (6),cerebroside B (7),(2S,3S,4R,2'R)-2-(2'-羟基二十二碳酰氨基)-十八碳烷-1,3,4-三醇 (8),(2S,3S,4R,2'R)-2-(2'-羟基二十三碳酰氨基)-十八碳烷-1,3,4-三醇 (9)。     

黄瓜藤的化学成分研究

从丽江产黄瓜藤甲醇提取物的氯仿部位分离得到9个化合物,经理化和波谱分析鉴定为α-菠甾醇(1)、α-菠甾醇-3-O-β-D-葡萄糖苷(2)、β-谷甾醇(β-sitosterol,3)、豆甾-7-烯-3-O-β-D-葡萄糖苷(4)、22-亚甲基-9,19-环羊毛甾烷-3β-醇(5)、(2S,3S,4R,10E)-2-(2′,3′-二羟基二十四烷酰氨基)-10-十八烯-1,3,4-三醇(6)、(2S,3S,4R,10E)-2-[(2′R)-2-羟基二十四烷酰氨基]-10-十八烯-1,3,4-三醇(7)、(2S,3S,4R,10E)-1-(β-D-葡萄糖苷)-2-[(2′R)-2-羟基二十四烷酰氨基]-10-十八烯-1,3,4-三醇(8)、大豆脑苷(9),除化合物3外,其它化合物均为首次从该植物中分离得到.     

Excited state intermolecular hydrogen bond’s effect on the luminescent behaviour of the 2D covalent organic framework (PPy-COF): A TDDFT insight

The theoretical investigation of electronically excited stated intermolecular hydrogen bonding dynamics of the 2D luminescent polypyrene covalent organic framework and methanol molecule (PPy-COF-MeOH) was performed using the density functional theory (DFT) and time-dependent (TD-DFT) method. The strengthening of Hydrogen bonds C-H---O-H and B-O---H-O upon photoexcitation was confirmed via comparison of geometric structures, electronic transition energies, ¹H-NMR, binding energies, UV-Vis and infrared spectra in S0 and S1 states. Frontier molecular orbitals (MOs) analysis, electronic configuration, Mulliken charge analysis; and the charge density variation in hydrogen bonding proximity demonstrated that the strengthened hydrogen bonds facilitate the nonradiative path which may consequently proceed the luminescence quenching. Hence, the molecular material property prediction package (MOMAP) programme verified the fluorescence quenching because PPy-COF-MeOH complex showed a lower fluorescent rate constant compared to isolated PPy-COF fragment. The S1-T1 energy gap analysis also revealed the possibility of the Intersystem crossing (ISC). Above results significantly highlighted the role of the hydrogen bonding dynamics on luminescence property of the PPy-COF.     

First-principles simulations of the chemical functionalization of (5,5) boron nitride nanotubes

We perform density functional theory studies to investigate structural and electronic properties of the (5,5) boron nitride nanotubes (BNNTs) with surfaces and ends functionalized by thiol (SH) and hydroxyl (OH) groups. The exchange-correlation energies are treated according to the functional of Hamprecht-Cohen-Tozer-Handy within the generalized gradient approximation (HCTH-GGA). We use the base function with double polarization DNP. To determine the (5,5) BNNT-SH and (5,5) BNNT-OH relaxed structures the minimum energy criterion is applied considering six different geometries depending upon the SH and OH functional groups orientation: (C1) The adsorbed functional group is oriented toward the N atom, (C2) the functional group is oriented toward the B atom, (C3) the functional group is at the central hexagon of the BNNT surface. The (C4) fourth and (C5) fifth configurations are formed by allowing bonds (of S or O) with B or N atoms at one end of the nanotube. (C6) The sixth geometry is obtained by placing the functional group at the center of one end of the BNNT. The (5,5) BNNT-SH system, in vacuum, suffers a semiconductor to metal transition while the (5,5) BNNT-OH system retains the semiconductor behavior. When structures are solvated in water these systems behave as semiconductors. The polarity increases as a consequence of the functional group-nanotube interactions no matter if they are in vacuum or in solvation situation, which indicates the possible solubility and dispersion. According to the work function the best option to construct a device is with the BNNT-OH system.     

On the aggregation of bilirubinoids in solution as evidenced by VCD and ECD spectroscopy and DFT calculations

Vibrational and electronic circular dichroism (VCD and ECD) spectra of 3 optically active bilirubin analogs with propionic acid groups replaced by (1) 1‐(S)‐methylpropyl groups, (2) 3‐acetoxy‐1‐(S)‐methylpropyl groups, and (3) 1‐(S)‐2‐(R)‐dimethyl‐2‐(methoxycarbonyl)ethyl groups have been recorded at different concentrations in chloroform. The aliphatic chains attached to C‐8 and C‐12 of the 3 chosen mesobilirubins were modified so as to possess no OH group. The variation of the VCD spectra with concentration is consistent with the formation of dimers at high concentration. Density functional theory and time‐dependent density functional theory calculations on monomeric and dimeric forms support such a conclusion. Comparing with previous VCD (ECD) and IR (UV) studies of other mesobilirubin molecules, it is concluded that here, the key feature for aggregation is the missing OH groups on the propionic acid chains. The latter, in synergy with the polar groups of lactam moieties, appear to be involved in intramolecular phenomena and thus favor monomeric forms. Investigation of ECD and UV spectra of the same compounds in mixed DMSO/chloroform solutions provide further clues to the proposed picture.     

B3LYP/6-311++G** study of alpha- and beta-D-glucopyranose and 1,5-anhydro-D-glucitol: 4C1 and 1C4 chairs, (3,O)B and B(3,O) boats, and skew-boat conformations

Geometry optimization, at the B3LYP/6-311++G** level of theory, was carried out on 4C1 and 1C4 chairs, (3,O)B and B(3,O) boats, and skew-boat conformations of alpha- and beta-D-glucopyranose. Similar calculations on 1,5-anhydro-D-glucitol allowed examination of the effect of removal of the 1-hydroxy group on the energy preference of the hydroxymethyl rotamers. Stable minimum energy boat conformers of glucose were found, as were stable skew boats, all having energies ranging from approximately 4-15 kcal/mol above the global energy 4C1 chair conformation. The 1C4 chair electronic energies were approximately 5-10 kcal/mol higher than the 4C1 chair, with the 1C4 alpha-anomers being lower in energy than the beta-anomers. Zero-point energy, enthalpy, entropy, and relative Gibbs free energies are reported at the harmonic level of theory. The alpha-anomer 4C1 chair conformations were found to be approximately 1 kcal/mol lower in electronic energy than the beta-anomers. The hydroxymethyl gt conformation was of lowest electronic energy for both the alpha- and beta-anomers. The glucose alpha/beta anomer ratio calculated from the relative free energies is 63/37%. From a numerical Hessian calculation, the tg conformations were found to be approximately 0.4-0.7 kcal/mol higher in relative free energy than the gg or gt conformers. Transition-state barriers to rotation about the C-5-C-6 bond were calculated for each glucose anomer with resulting barriers to rotation of approximately 3.7-5.8 kcal/mol. No energy barrier was found for the path between the alpha-gt and alpha-gg B(3,O) boat forms and the equivalent 4C1 chair conformations. The alpha-tg conformation has an energy minimum in the 1S3 twist form. Other boat and skew-boat forms are described. The beta-anomer boats retained their starting conformations, with the exception of the beta-tg-(3,O)B boat that moved to a skew form upon optimization.     

高等真菌黑虎掌子实体的化学成分

黑虎掌 (Ｓａｒｃｏｄｏｎａｓｐｒａｔｕｍ (Ｂｅｒｋ .)Ｓ .Ｉｔｏ) ,又名香茸 ,是一种美味食用菌。近年来发现该属Ｓ .ｓｃａｂｒｏ ｓｕｓ (Ｆｒ.)Ｐ .Ｋａｒｓｔ.中含有对神经生长因子 (ＮＧＦ)的合成具有诱导作用的生物活性二萜 (Ｏｈｔ等 ,1998)。作为“高等真菌生物活性代谢产物研究”的一部分 ,我们对采自云南武定的样品进行了化学分析。从黑虎掌的新鲜子实体中分得 15个化合物。它们分别为ｃｅｒｅｂｒｏｓｉｄｅＢ (1) (12 0ｍｇ) ,阿洛酮糖腺苷(2 ) (12ｍｇ) ,三磷酸尿苷 (3) (7ｍｇ) ,尿嘧啶 (4 ) (12ｍｇ) ,腺嘌呤 (5 ) (8ｍ…     

Potato micro-tuber inducing hydroxylasiodiplodins from Lasiodiplodia theobromae

Three hydroxylasiodiplodins were isolated from the mycelium extracts of Lasiodiplodia theobromae IFO 31059; and their structures were identified as (3R),(4S)-4-hydroxylasiodiplodin, (3R),(6R)-6-hydroxy-de-O-methyllasiodiplodin and (3R),(5R)-5-hydroxy-de-O-methyllasiodiplodin. All showed potato micro-tuber inducing activity.     

石菖蒲的化学成分研究

运用色谱法从石菖蒲根茎提取物中分离得到18个化合物,经波谱学分析鉴定为:(7S,8R)-4,9’-di-hydroxyl-3,3’-dimethoxyl-7,8-dihydrobenzofuran-1’-propylneolignan(1),(7S,8R)-4,9’-dihydroxyl-3,3’-dimethoxyl-7,8-dihydrobenzofuran-1’-propylneoligan-9-O-β-D-glucopyranoside(2),7’-hydroxylariciresinol-9-acetate(3),5-羟基-3,7,4’-三甲氧基黄酮(4),野漆树苷(5),紫云英苷(6),松属素-3-O-芸香糖苷(7),山奈酚-3-O-芸香糖苷(8),德钦红景天苷(9),isoschaftoside(10),5-羟甲基糠醛(11),反式桂皮酸(12),3,7-dihydroxy-11,15,23-trioxo-lanost-8,16-dien-26-oicacid(13),3,7-dihydroxy-11,15,23-trioxo-lanost-8,16-dien-26-oic acid methyl ester(14),环阿屯醇(15),胡萝卜苷(16),羽扇豆醇(17),(22E,24R)-ergosta-5,7,22-trien-3β-ol(18)。除化合物4、11和16外,其余15个化合物均为首次从该植物中分离得到。     

Oxidation of diiron and triiron sulfurdithiolato complexes: mimics for the active site of [FeFe]-hydrogenase

The oxidation of the hexacarbonyl(1,3-dithiolato-S,S')diiron complexes 4a-4c with varying amounts of dimethyldioxirane (DMD) was systematically studied. The chemoselectivity of the oxidation products depended upon the substituent R (R=H, Me, 1/2 (CH2)(5)). For R=H, four oxidation products, 6a-6d, have been obtained. In the case of R=Me, three products, 7a-7c, were formed, and for R=1/2 (CH2)(5), only complex 8 was observed. These observations are due to steric and electronic effects caused by the substituent R. Additionally, oxidation of the triiron complex 5 with DMD was performed to yield the products 9a and 9b. X-Ray diffraction analyses were performed for 6a-6d, 7a, and 7c, as well as for 9a and 9b. The electronic properties were determined by density-functional theory (DFT) calculations.     

Absolute configuration of eremophilanoids by vibrational circular dichroism

The absolute configurations (AC) of natural occurring 6-hydroxyeuryopsin (1), of its acetyl derivative 2, and of eremophilanolide 8 were confirmed by comparison of the experimental vibrational circular dichroism (VCD) spectra with theoretical curves generated from density functional theory (DFT) calculations. Initial analyses were carried out using a Monte Carlo searching with the MMFF94 molecular mechanics force field. All MMFF94 conformers were further optimized using DFT at the B3LYP/6-31G(d) level of theory, followed by calculations of their vibrational frequencies at the B3LYP/6-31G(d,p); the VCD spectra of 2 and 8 were also calculated at the B3PW91/DGDZVP level of theory. Good agreement between theoretical and experimental VCD curves unambiguously verified the 4S,5R,6S absolute configuration for 1 and 2, and the 1S,4S,5R,6S,8S,10S configuration for 8.