Theoretical Studies on the Structure and Intramolecular Interactions of Fagopyrins—Natural Photosensitizers of Fagopyrum

Simple SummaryThe study determines the spatial structure and intramolecular interactions of fagopyrins—natural photosensitizers of Fagopyrum species. In silico calculations show many fagopyrin conformers characterized by the formation of strong intramolecular interactions.AbstractCompounds characterized by a double-anthrone moiety are found in many plant species. One of them are fagopyrins—naturally occurring photosensitizers of Fagopyrum. The photosensitizing properties of fagopyrins are related to the selective absorption of light, which is a direct result of their spatial and electronic structure and many intramolecular interactions. The nature of the interactions varies in different parts of the molecule. The aim of this study is to determine the structure and intramolecular interactions of fagopyrin molecules. For this purpose, in silico calculations were used to perform geometry optimization in the gas phase. QTAIM and NCI analysis suggest the formation of the possible conformers in the fagopyrin molecules. The presence of a strong OHO hydrogen bond was shown in the anthrone moiety of fagopyrin. The minimum energy difference for selected conformers of fagopyrins was 1.1 kcal∙mol⁻¹, which suggested that the fagopyrin structure may exist in a different conformation in plant material. Similar interactions were observed in previously studied structures of hypericin and sennidin; however, only fagopyrin showed the possibility of brake the strong OHO hydrogen bond in favor of forming a new OHN hydrogen bond.     

Halogen Interactions in Halogenated Oxindoles: Crystallographic and Computational Investigations of Intermolecular Interactions

X-ray structural determinations and computational studies were used to investigate halogen interactions in two halogenated oxindoles. Comparative analyses of the interaction energy and the interaction properties were carried out for Br···Br, C-H···Br, C-H···O and N-H···O interactions. Employing Møller–Plesset second-order perturbation theory (MP2) and density functional theory (DFT), the basis set superposition error (BSSE) corrected interaction energy (E_int(BSSE)) was determined using a supramolecular approach. The E_int(BSSE) results were compared with interaction energies obtained by Quantum Theory of Atoms in Molecules (QTAIM)-based methods. Reduced Density Gradient (RDG), QTAIM and Natural bond orbital (NBO) calculations provided insight into possible pathways for the intermolecular interactions examined. Comparative analysis employing the electron density at the bond critical points (BCP) and molecular electrostatic potential (MEP) showed that the interaction energies and the relative orientations of the monomers in the dimers may in part be understood in light of charge redistribution in these two compounds.     

铀酰配合物单晶的合成与结构

铀作为重要的核材料,是核燃料循环中最受关注的元素之一。在铀的开采、纯化以及应用等过程中,不可避免地会产生铀的释放。环境中的无机酸根及土壤有机质的羧酸根可与铀形成配合物,从而可能影响其迁移与吸附行为。通过研究铀酰配合物晶体的结构可以为吸附或迁移模型以及从分子水平探讨吸附机理提供结构参数。本文综述了国际上铀酰固体化学领域的研究进展,阐述了铀酰配合物的结构特点,铀酰无机含氧酸、过氧及草酸配合物的合成与晶体结构。在对国内外主要开展铀酰配合物晶体研究的课题组之研究工作进行归纳和分析的基础上,提出铀酰配合物研究的思路和建议,以期为国内锕系元素固体化学研究工作的开展提供参考。     

Dissecting Bonding Interactions in Cysteine Dimers

Neutral (n) and zwitterionic (z) forms of cysteine monomers are combined in this work to extensively explore the potential energy surfaces for the formation of cysteine dimers in aqueous environments represented by a continuum. A simulated annealing search followed by optimization and characterization of the candidate structures afforded a total of 746 structurally different dimers held together via 80 different types of intermolecular contacts in 2894 individual non-covalent interactions as concluded from Natural Bond Orbitals (NBO), Quantum Theory of Atoms in Molecules (QTAIM) and Non-Covalent Interactions (NCI) analyses. This large pool of interaction possibilities includes the traditional primary hydrogen bonds and salt bridges which actually dictate the structures of the dimers, as well as the less common secondary hydrogen bonds, exotic X⋯Y (X = C, N, O, S) contacts, and H⋯H dihydrogen bonds. These interactions are not homogeneous but have rather complex distributions of strengths, interfragment distances and overall stabilities. Judging by their Gibbs bonding energies, most of the structures located here are suitable for experimental detection at room conditions.     

2-氨基苯并噻唑配合物的晶体结构及抑菌活性

合成了2-氨基苯并噻唑与钴和锌的两种金属配合物,利用红外光谱、元素分析、X射线单晶衍射和热重分析等对其结构进行了表征;并研究了两种金属配合物对金黄色葡萄球菌、大肠杆菌、酵母菌的抑菌活性.结果表明,Zn(Ⅱ)和Co(Ⅱ)分别与2个O原子和2个N原子通过4配位形成扭曲的四面体构型;两种配合物对三种菌种均有较强的选择性抑制作用.     

Novel Lanthanide (III) Complexes Derived from an Imidazole–Biphenyl–Carboxylate Ligand: Synthesis,Structure and Luminescence Properties

A series of neutral mononuclear lanthanide complexes [Ln(HL)₂(NO₃)₃] (Ln = La, Ce, Nd, Eu, Gd, Dy, Ho) with rigid bidentate ligand, HL (4′-(1H-imidazol-1-yl)biphenyl-4-carboxylic acid) were synthesized under solvothermal conditions. The coordination compounds have been characterized by infrared spectroscopy, thermogravimetry, powder X-ray diffraction and elemental analysis. According to X-ray diffraction, all the complexes are a series of isostructural compounds crystallized in the P2/n monoclinic space group. Additionally, solid-state luminescence measurements of all complexes show that [Eu(HL)₂(NO₃)₃] complex displays the characteristic emission peaks of Eu(III) ion at 593, 597, 615, and 651 nm.     

两个由异烟酰胺构筑的钴、镍配合物的合成及晶体结构

采用溶液培养法,在室温下合成了2个新的过渡金属配合物[Co(inta)2(H2O)4][Co(H2O)6](tdc)2.2H2O(1)和[Ni(inta)2(H2O)4](tdc).2H2O(2)(inta=异烟酰胺,H2tdc=2,5-噻吩二甲酸)。并对其进行了元素分析、红外光谱、紫外光谱、热重和X-射线单晶衍射测定。这两个配合物通过氢键和π-π相互作用形成了三维超分子网状结构。     

Synthesis and Crystal Structure of the Novel Chiral o—Hydroxyphenyloxazoline Metal Complexes

1 INTRODUCTION Optically active oxazolines have been extensi- vely used as valuable chiral ligands for transition metals in asymmetric catalysis[1]. The design and syntheses of new chiral oxazoline ligands have inspired many scientists to work with great efforts during the recent years. Our interest has been focus- ed on the studies of enantioselective transition- metal catalysis of heterocyclic ligands. In the pre- sent work, we choose o-hydroxyphenyloxazoline ligand for it has a rigi…     

单核锇配合物的合成、晶体结构及其与DNA的作用

使用溶剂热合成法,以p-bitmb配体(1,4-二(1-咪唑基-亚甲基)-2,3,5,6-四甲基苯)与[(η6-cymene)Os(μ-Cl)Cl]2或[(η6-bip)Os(μ-Cl)Cl]2为原料,合成了2种单核芳基锇配合物,并利用核磁、质谱、元素分析和X射线单晶衍射等手段对配合物进行了表征。配合物1属于单斜晶系,P21/c空间群,为一个单核锇的结构。中心锇原子与2个配体p-bitmb上的氮原子以及氯原子进行配位,2个配体的另一个咪唑基团通过一个亚甲基碳原子进行连接形成咪唑嗡离子,形成一个类似"碗"状的结构。一个氯离子通过氢键装载在结构的空腔内。利用核磁共振氢谱研究了结构中亚甲基的来源,并研究了配合物在缓冲溶液中的稳定性。用紫外吸收光谱、圆二色谱以及粘度法研究了配合物与DNA的相互作用,结果表明,配合物中的亚甲基来自于溶剂二氯甲烷。配合物以嵌入的方式与CT-DNA相互作用,结合常数分别为3.222×10~4 L·mol-1 (1)和1.53×10~4 L·mol-1 (2),同时配合物会减弱DNA的碱基堆积作用并可以使DNA发生解旋。     

Anion–Anion Interactions in Aerogen-Bonded Complexes. Influence of Solvent Environment

Ab initio calculations are applied to the question as to whether a AeX₅⁻ anion (Ae = Kr, Xe) can engage in a stable complex with another anion: F⁻, Cl⁻, or CN⁻. The latter approaches the central Ae atom from above the molecular plane, along its C₅ axis. While the electrostatic repulsion between the two anions prevents their association in the gas phase, immersion of the system in a polar medium allows dimerization to proceed. The aerogen bond is a weak one, with binding energies less than 2 kcal/mol, even in highly polar aqueous solvent. The complexes are metastable in the less polar solvents THF and DMF, with dissociation opposed by a small energy barrier.     

配合物[Ln(CH3COO)2(NO3)(bipy)]2的合成与晶体结构

合成了５种新型镧系四元混合阴离子配合物,用Ｘ射线四圆衍射仪测定了［Ｐｒ（ＣＨ３ＣＯＯ）２（ＮＯ３）（ｂｉｐｙ）］２的晶体结构,四个醋酸根呈两种配位方式,测定了铕和钆配合物的荧光和ＥＳＲ谱．     

稀土-NTO配合物晶体结构的多样性研究

用３硝基１，２，４三唑５酮（ＮＴＯ）的锂盐与稀土硝酸盐反应，制备ＮＴＯ镨、铕、镝、镱、钇五种配合物单晶。Ｘ射线衍射方法测定配合物的晶体结构。研究表明ＮＴＯ作为配体与稀土形成配合物时，表现出ＮＴＯ环上的羰基氧原子与稀土金属形成配位键的共性；配合物的空间结构随中心稀土离子半径的变化而变化，随着稀土离子半径的变小，较大体积配体ＮＴＯ－的配位数目逐渐变小。     

基于二茂铁羧酸配体的镉配合物的合成及结构研究

以二茂铁甲酸根FcCOO^-(Fc=(η⁵-C₅H₅)Fe(η⁵-C₅H₄))为主要配体，合成了3个新的配合物[Na₂Cd( μ₃-η²-FcCOO^-)₂(μ₂-η²-FcCOO^-)₂(CH₃OH)₂]_n (1)、[Cd(phen)(FcCOO^-)(η²-FcCOO)(H₂O)](phen=邻菲咯啉) (2)、[Cd(Det)(η²-FcCOO^-)(FcCOO^-)](H₂O)₂(Det=二乙撑三胺) (3)。测定了配合物的晶体结构。配合物1为单斜晶系，C2/c空间群，二茂铁甲酸根采用μ₃-η²-FcCOO^-和μ₂-η²-FcCOO^-的配位方式将Cd²⁺和Na⁺连接成一维无限链状结构。配合物2和3均为单核结构，单斜晶系，P2₁/c空间群，二茂铁甲酸根都采用 FcCOO^-和η²-FcCOO^-的方式配位。2中phen以双齿螯合形式配位，水分子参与配位，中心镉离子配位数为6。3中Det以三齿螯合形式配位，中心镉离子配位数也为6，但水分子未参与配位。     

配体分子结构对Pd(Ⅱ)-Phen-PCA体系堆积作用的影响

用pH电位滴定法测定了含l，10-邻菲咯啉(Phen)和羧酸(CA)配体的三元混配配合物Pd(Phen)(CA)体系的稳定常数，比较和讨论了各种三元混配配合物之间的稳定性差异．实验结果表明，在三元混配配合物Pd(Phen)(PCA)中(PCA为苯基羧酸)存在分子内芳环堆积作用，堆积程度依赖于苯基和配位的羧酸根之间的亚甲基数目，其中以2-苯乙酸和3-苯丙酸与邻菲咯啉为最佳堆积．     

呋喃酰腙及其镍、锰配合物的合成与晶体结构及抑菌活性

通过2-呋喃甲醛与4-甲氧基苯甲酰肼缩合,得到一种新型的希夫碱配体2-呋喃甲醛缩-4-甲氧基苯甲酰腙(HL),将HL与Ni(NO₃)₂·6H₂O、MnCl₂·4H₂O分别在乙醇与丙酮的混合溶剂中反应,采用溶剂挥发获得配体单晶、不同构型的新型配合物NiL₂和Mn(HL)₂Cl₂单晶。采用元素分析、红外光谱、核磁共振、X-射线单晶衍射对HL、NiL₂和Mn(HL)₂Cl₂进行表征,结构分析表明HL属于三方晶系,空间群R3,晶胞参数a=2.442(2)nm,b=2.442(2)nm,c=1.1354(10)nm,γ=120°,Z=18。NiL₂和Mn(HL)₂Cl₂均属于单斜晶系,空间群P2₁/n和P2₁/c。NiL₂属于近似平面四方构型,晶胞参数a=1.2067(8)nm,b=0.5774(4)nm,c=1.8418(13)nm,β=107.122(11)°,Z=2;Mn(HL)₂Cl₂属于扭曲八面体构型,晶胞参数a=0.9155(4)nm,b=0.7217(4)nm,c=2.0336(9)nm,β=96.047(9)°,Z=2。用琼脂扩散法测定了配体和配合物对大肠杆菌、金黄色葡萄球菌、绿脓杆菌的抑制活性,结果显示NiL₂对金色葡萄球菌有显著的抑制作用。     

呋喃酰腙及其镍、锰配合物的合成与晶体结构及抑菌活性

通过2-呋喃甲醛与4-甲氧基苯甲酰肼缩合,得到一种新型的希夫碱配体2-呋喃甲醛缩-4-甲氧基苯甲酰腙(HL),将HL与Ni(NO3)2·6H2O、MnCl2·4H2O分别在乙醇与丙酮的混合溶剂中反应,采用溶剂挥发获得配体单晶、不同构型的新型配合物NiL2和Mn(HL)2Cl2单晶。采用元素分析、红外光谱、核磁共振、X-射线单晶衍射对HL、NiL2和Mn(HL)2Cl2进行表征,结构分析表明HL属于三方晶系,空间群R3,晶胞参数a=2.442(2)nm,b=2.442(2)nm,c=1.135 4(10)nm,γ=120°,Z=18。NiL2和Mn(HL)2Cl2均属于单斜晶系,空间群P21/n和P21/c。NiL2属于近似平面四方构型,晶胞参数a=1.206 7(8)nm,b=0.577 4(4)nm,c=1.841 8(13)nm,β=107.122(11)°,Z=2;Mn(HL)2Cl2属于扭曲八面体构型,晶胞参数a=0.915 5(4)nm,b=0.721 7(4)nm,c=2.033 6(9)nm,β=96.047(9)°,Z=2。用琼脂扩散法测定了配体和配合物对大肠杆菌、金黄色葡萄球菌、绿脓杆菌的抑制活性,结果显示NiL2对金色葡萄球菌有显著的抑制作用。     

Intermolecular Interactions of 3,5-Di-tert-butyl-4-hydroxybenzyl Acetate in Crystal and in Solutions

The molecular and crystal structure of 3,5-di-tert-butyl-4-hydroxybenzyl acetate was studied by single-crystal X-ray diffraction. The molecules form infinite chains in the crystals via hydrogen bonds between the hydroxy and carbonyl groups. The interchain bonding is provided by CH- interactions. In carbon tetrachloride, the molecules of the title compound form weak associates via hydrogen bonds between the hydroxy and carbonyl groups.     

氮杂环卡宾羰基氯钌配合物的合成、晶体结构及催化性质

合成了2个N-杂环卡宾钌配合物[RuCl₂（L1）（CO）]（1）,L1=（2,6-二（甲基咪唑-2-鎓盐）吡啶）和[RuCl₂（L2）（CO）]（2）,L2=（2,6-二（正丁基-2-鎓盐）吡啶）,并通过元素分析、红外光谱、核磁共振氢谱和核磁共振碳谱对它们的结构进行了表征,X-射线单晶衍射测定了配合物2的分子结构,结果表明配合物2属单斜晶系,C2/c空间群,a=1.8148（4）nm,b=1.1292（3）nm,c=1.1196（2）nm,β=108.862（3）°,且中心Ru（Ⅱ）离子是六配位,同时研究了配合物1和2在Suzuki-Miyaura偶联反应中的催化性质。