Molecular Recognition in Anion Coordination Chemistry. Structure,Binding Constants and Receptor-Substrate Complementarity of a Series of Anion Cryptates of a Macrobicyclic Receptor Molecule

The crystal structures of four anion cryptates [X^? ? BT -6H⁺] formed by the protonated macrobicyclic receptor BT -6H⁺ with F^?, Cl^?, Br^? and N have been determined. They provide a homogeneous series of anion coordination patterns with the same ligand. The small F^?-ion is tetracoordinated, while Cl^? and Br^? are bound in an octahedron of H-bonds. The non-complementarity between these spherical anions and the ellipsoïdal cavity of BT -6H⁺ is reflected in ligand distortions. Structural complementarity is achieved for the linear triatomic substrate N, which is bound by two pyramidal arrays of three H-bonds, each interacting with a terminal N-atom of N. The formation constants of the complexes formed by BT -6H⁺ with a variety of anions (halides, N, NO, carboxylates, SO, HPO, AMP^2?, ADP^3?, ATP^4?, P₂O) have been determined. Very strong complexations are found, as well as marked electrostatic and structural effects on stability and selectivity; in particular the binding of F^?, Cl^?, Br^?, and N may be analyzed in terms of the crystal structure data. The cryptand BT -6H⁺ is a molecular receptor containing an ellipsoïdal recognition site for linear triatomic substrates of size compatible with the size of the molecular cacity. Further developments of various aspects of anion coordination chemistry are considered.     

波浪形一维链状镉配合物的合成、结构及分子识别性能

以四水合硝酸镉(Cd(NO_3)_2·4H_2O)与2-(邻溴)苯基-4,5-咪唑二羧酸(o-BrPhH_3IDC)和草酸铵通过水热反应,合成了一个波浪形一维链状配合物{[Cd(o-BrPhH_2IDC)_2(H_2O)]·H_2O}_n(1)。并通过元素分析、傅里叶变换红外光谱、热重分析和单晶X射线衍射等技术手段对配合物1进行了表征。结果表明,配合物1为正交晶系,Pbca空间群。配合物1在316 nm波长激发下,在356 nm处有最大的荧光发射峰。配合物1对小分子具有识别性能,乙腈使配合物荧光强度明显增强,甲醇、乙醇使配合物荧光强度明显减弱,而吡啶处理后的样品在356 nm附近的发射峰消失,显示对吡啶有识别作用。     

Determination of Complex Small‐Molecule Structures Using Molecular Alignment Simulation

Correct structural assignment of small molecules and natural products is critical for drug discovery and organic chemistry. Anisotropy‐based NMR spectroscopy is a powerful tool for the structural assignment of organic molecules, but it relies on the utilization of a medium that disrupts the isotropic motion of molecules in organic solvents. Here, we establish a quantitative correlation between the atomic structure of the alignment medium, the molecular structure of the small molecule, and molecule‐specific anisotropic NMR parameters. The quantitative correlation uses an accurate three‐dimensional molecular alignment model that predicts residual dipolar couplings of small molecules aligned by poly(γ‐benzyl‐l ‐glutamate). The technique facilitates reliable determination of the correct stereoisomer and enables unequivocal, rapid determination of complex molecular structures from extremely sparse NMR data.     

NMR and MO Studies on the Molecular Structure of a Fluoranthene-Benzene Complex

Summary. Fluoranthene (FA) forms a 1:1 van der Waals complex with benzene in cyclohexane. The ¹H NMR spectrum of this complex shows that the FA moiety in the complex state has five kinds of hydrogen atoms and that the ¹H NMR peaks assigned to the protons attached to the naphthalene skeleton are largely shifted to higher magnetic field on complex formation with benzene. These observations indicate that the complex takes the structure of C_S symmetry, in which the benzene molecule mainly interacts with the electronic system localized on the naphthalene moiety of FA. The present ab initio calculations reproduce well the ¹H NMR spectral shifts mentioned above and the experimentally predicted C_S structure of the complex. According to the PPP calculations for the electronic absorption spectral changes on the complex formation, the FA-benzene complex is considered to take a sandwich type structure.     

NMR and MO Studies on the Molecular Structure of a Fluoranthene-Benzene Complex

Fluoranthene (FA) forms a 1:1 van der Waals complex with benzene in cyclohexane. The ¹H NMR spectrum of this complex shows that the FA moiety in the complex state has five kinds of hydrogen atoms and that the ¹H NMR peaks assigned to the protons attached to the naphthalene skeleton are largely shifted to higher magnetic field on complex formation with benzene. These observations indicate that the complex takes the structure of C_S symmetry, in which the benzene molecule mainly interacts with the electronic system localized on the naphthalene moiety of FA. The present ab initio calculations reproduce well the ¹H NMR spectral shifts mentioned above and the experimentally predicted C_S structure of the complex. According to the PPP calculations for the electronic absorption spectral changes on the complex formation, the FA-benzene complex is considered to take a sandwich type structure.     

外电场下氮化铝分子结构和光谱研究

以6-311＋G(2DF)为基函数, 采用密度泛函B3P86的方法研究了外电场作用下氮化铝(AlN)基态分子的几何结构、HOMO能级、LUMO能级、能隙及谐振频率. 结果表明, 外电场的大小和方向对AlN分子基态的这些性质有明显影响. 在所加的电场范围内, 随着外电场的增大分子键长减小, 谐振频率增大, 总能量升高, 在F＝0.02 a.u.时能量达到最大, 为－297.4217 a.u., 此后继续增大电场强度, 系统总能量则开始降低; EH 和EL 随着电场的增加均逐渐增大, 在 F＝0.01 a.u.时, EH 和EL均取得最大值, 分别为－0.2776和－0.0828 a.u., 随着电场的继续增大, 能级EH和EL均逐渐减小, 而能隙在外电场增大的过程中始终处于减小趋势.     

靶向Toll样受体4的小分子调节剂

Toll样受体(Toll-like receptors,TLRs)是进化保守的天然免疫模式识别受体,能够识别外源的病原菌相关分子模式(Pathogen-associated molecular patterns,PAMPs)、内源的损害相关分子模式(Damage-associated molecular patterns,DAMPs)和异源物相关分子模式(Xenobiotic-associated molecular patterns),诱导炎症免疫反应。 其中,TLR4(Toll-like receptor 4)是目前研究最为广泛的Toll样受体之一,TLR4是脂多糖(lipopoiysaccharide,LPS)的主要受体,LPS激活的TLR4信号通路在炎症信号的传递中发挥着重要作用,而此信号转导需要通过LPS与TLR4及其附属蛋白髓样分化因子2(myeloid differentiation factor 2,MD-2)的相互作用来实现。 因此,TLR4/MD-2成为炎症反应和免疫调控最重要的研究热点。 本文综述靶向TLR4/MD-2的小分子激动剂和抑制剂的研究进展,以进一步理解TLR4小分子调节剂与其相互作用的复杂性,帮助靶向TLR4/MD-2的免疫调节剂药物发现。     

基态UC2分子的结构和势能函数

采用密度泛函理论(DFT)的B3LYP方法和相对论有效原子实势理论模型(RECP),对UC2分子可能的结构进行优化计算,得到UC2分子稳定构型为角形C-U-C(C2v);由微观可逆性原理,判断了UC2分子的离解极限;并且导出了基态UC2分子(X 5B1)的多体项展式势能函数,其势能面等值图展现了C-U-C(C2v)稳定结构;根据势能面等值图,讨论了C+UC(X 3П)反应和U+C2(X 1∑+g)反应的势能面静态特征.     

Single‐Molecule Electroluminescence of a Phosphorescent Organometallic Complex

Lighting one by one: The electroluminescence (EL) from single molecules of a red phosphorescent iridium complex dispersed in a hole‐transporting polymer matrix is studied. The single‐molecule EL dynamics is determined by local structural inhomogeneities in the matrix polymer (see picture).

     

Molecular Recognition of Anionic Substrates. Crystal Structures of the Supramolecular Inclusion Complexes of Terephthalate and Isophthalate Dianions with a Bis-intercaland Receptor Molecule

Molecular recognition of flat substrates requires the design of receptor molecules containing complementary flat units. If two such units are incorporated into a macrocyclic framework, a face to face inclusion of a planar substrate may take place, leading to an intercalative supramolecular structure. The water-soluble macrocyclic bis-intercaland receptor 1.4H+, containing two naphthalene subunits, linked by two positively charged oxy-bis- ethylamine binding sites, is able to bind strongly flat organic anions. The crystal structures of the terephthalate 2 and isophthalate 3 inclusion complexes are reported here. Complex 2, triclinic, P-1(N°), a = 7.717(3), b = 10.625(6), c = 16.238(9) Å, = 99.00(7), = 99.70(6), = 109.46(4)°, Z = 1. Complex 3, triclinic, P1 (N°1), a = 7.513(10), b = 10.640(9), c = 16.164(10) Å, = 98.81(5), = 99.77(10), = 109.36(12)°, Z = 1. Comparison of the environment (water molecules, anions and macrocycle) in the two X-ray structures highlights the formation of a similar organized assembly with the two different substrates.     

Crystal Structure of the Molecular Complex of Silicon Tetrafluoride with 4-Phenylpyridine

Russian Journal of General Chemistry - The crystal structure of the silicon tetrafluoride molecular complex with 4-phenylpyridine SiF4·2ppy has been determined by X-ray diffraction analysis....     

Towards Unveiling the Exact Molecular Structure of Amorphous Red Phosphorus by Single‐Molecule Studies

Since the discovery of amorphous red phosphorus (a‐red P) in 1847, many possible structures have been proposed. However, the exact molecular structure has not yet been determined because of its amorphous nature. Herein several methods are used to investigate basic properties of a‐red P. Data from scanning tunneling microscopy (STM) and gel permeation chromatography (GPC) confirm that a‐red P is a linear inorganic polymer with a broad molecular weight distribution. The theoretical single‐molecule elasticities of the possible a‐red P structures are obtained by quantum mechanical (QM) calculations. The experimental single‐molecule elasticity of a‐red P measured by single‐molecule AFM matches with the theoretical result of the zig‐zag ladder structure, indicating that a‐red P may adopt this structure. Although this conclusion needs further validation, this fundamental study represents progress towards solving the structure of a‐red P. It is expected that the strategy utilized in this work can be applied to study other inorganic polymers.     

Molecular Structure of 1-Germatrahol and its Complex With Chloroform

The crystal structures of anhydrous 1-germatranol and its complex with HCCl₃ are centrosymmetrical dimers because of their intermolecular hydrogen bonds. In the germatranol crystal, the axial and equatorial oxygen atoms of its two molecules are hydrogen bonded into an eight-membered coordination cycle. In the complex with HCCl₃, the two molecules of germatranol are likewise linked in dimers, and both axial oxygen atoms are H bonded with HCCl₃. In the investigated structures, the axial Ge—O bond is shorter than the equatorial ones. Depending on the number and strength of the hydrogen bonds, the interatomic Ge—O and Ge ← N distances change markedly. The quantitative estimates of the H bond energy are obtained from quantum chemical calculations of the model systems containing 1-germatranol and HCCl₃ molecules.     

Molecular Modeling of Cyclodextrin-Guest Molecule Interactions

Abstract

Inclusion complexes formed with substituted aromatic compounds and ß-cyclodextrin were studied using molecular modeling techniques. Energies of the MM2 optimized structures were correlated with HPLC retention times. A direct correlation between the inclusion complex stability and the HPLC retention times for the bonded ß-cyclodextrin was found within a series of disubstituted aromatic compounds. Evidence for a secondary mechanism of separation was found.