原子团簇

原子团簇与无机纳米材料一样,可以看作是纳米尺度的无机物质形态,但是具有确定的结构和组成,因此可以成为认识和研究纳米乃至大块固体表面结构的分子模型。由原子团簇组装的材料,有可能兼具纳米材料和分子材料的特性。     

取代型钒氧簇合物

钒氧簇是多金属氧簇的一个重要分支.由于钒氧簇具有多样的结构、优良的物理特性,使得其在催化、磁性及光学材料等方面具有广阔的应用前景,引起了人们的日益关注.将主族的金属或非金属元素引入到钒氧簇体系,可以形成结构新颖的取代型钒氧簇.新颖构型及其拓展结构取代型钒氧簇合物的合成,极大地丰富了钒氧簇的结构类型,推动了钒氧簇合成化学...     

多金属氧簇与倍半硅氧烷簇构筑的簇-簇杂化分子的合成及自组装结构

以Wells-Dawson型多金属氧簇(POM)与T₈型倍半硅氧烷簇(POSS)为构筑单元,通过点击化学反应制备了一种由共价键连接形成的、新型的纳米簇-簇杂化分子(POM-2POSS),并采用核磁共振(NMR)、质谱(MS)和红外光谱(IR)对产物化学结构进行了表征. 由于两个POSS簇连接在POM簇的同一侧,分子呈现“V”形. 同时,利用X射线衍射(XRD)及透射电子显微镜(TEM)表征了簇-簇杂化分子在本体中通过自组装过程形成的超分子结构,结果表明该簇-簇杂化分子形成了有序的层状结构,周期仅为5.1 nm. 本研究获得结果对以这类纳米簇为构筑单元构筑新型杂化分子以及通过自组装过程形成的、有序超分子结构的新型杂化材料的设计及制备提供了一个新的思路.     

水分子簇的研究进展

水分子簇结构与功能的探索已引起科学界的广泛关注并逐渐成为簇科学研究领域中的一个热点。本文综述了近年来水分子簇间作用力研究的进展、内容和方法并加以比较, 重点介绍了远红外振转隧道光谱法, 简述了超冷水的分子结构特征, 并对该领域的研究前景作了展望。     

原子团簇P6同分异构体的可能性

使用分子图形学方法设计出 2 3种可能的同分异构体 ,并对其进行了分子力学、PM3半经验量子化学和 ADF密度泛函优化。在 P6原子团簇模型设计中 ,磷原子采用一、二、三或四配位。从各异构体的比较可得知 ,由正四面体 P4派生出的结构在能量方面具有优势。椅式结构、船式结构和平面结构的能量依次增大     

小分子硫原子团簇的结构稳定性

用分子图形软件设计出68种硫原子团簇S_3～S_(13)的结构,使用B3LYP密度泛函进行几何构型优化和振动频率计算,排除了振动频率为负值的非局域极小点的结构,根据分子的总能量得出最稳定的同分异构体。在硫原子团簇中,除了部分原子采用一、三配位之外,大部分原子为二配位成键,带三配位的硫原子团簇的总能量较高,硫原子团簇难以生成高配位的笼状结构。从S_5开始链状结构能量高于环状,中性大分子硫原子团簇多呈链状结构。     

分子团簇的量子化学研究

采用Hartree-Fock方法、密度泛函(DFT)方法(BLYP、B3LYP)和MP2方法对Se4分子团簇的各种可能构型进行了结构优化和频率分析, 结果表明有5种构型是势能面上的稳定驻点, 同时对上述4种量子化学方法计算结果的差异进行了分析。并对这5种构型的结构稳定性、几何构型、前线分子轨道、Mulliken布局分析和偶极矩进行了分析, 根据分析结果对Se4分子的某些物理和化学性质进行了预测。     

团簇研究中的原子间势函数

原子间势函数在团簇结构和性质的理论研究中十分重要.本文将模拟团簇原子间相互作用的势函数划分成三类,对各类势函数的发展状况进行了综述;并对原子间势函数与最优化方法和分子动力学相结合,在团簇结构和性能研究中的应用和发展方向进行了讨论.     

碳团簇的结构及其演进

碳团簇是一种新型的碳材料,自20世纪80年代被发现以来,就以其独特的结构和优越的性能而在科学界掀起了研究狂潮。碳团簇的范畴非常广泛,小到气相中的单个碳原子,大到富勒烯、碳纳米管、碳纳米锥、石墨烯等都可以看作是碳团簇的存在形式。研究碳团簇的结构及其演进,解开碳团簇形成机理之谜,对开拓新型碳团簇材料的结构和应用都具有重要意义。本文对碳团簇的结构及其演进过程进行了回顾,并概述了目前碳团簇的合成方法、碳团簇结构的表征手段以及碳团簇演进的研究现状。     

过渡金属羰基簇的成键规则

原子簇化合物在性质、结构和成键方式等方面的特殊性,引起了合成化学、结构化学、催化化学及理论化学界的浓厚兴趣,且具有日益广阔的应用前景。对于其成键规律的研究,继Wade等提出的多面体骨架电子对理论之后,已有不少工作。本文系统研究了过渡金属羰基型原子簇化合物的结构特点,提出了确定9N-μ规则中μ值的四项条款,并用以解释了许多种过渡金属羰基簇化合物。讨论了它们的电子结构、反应性、成键特点等性质。由此还可     

Electronic Structure and Circular Dichroism of Natural Alboatisins Isolated from Aerial Parts of Isodon Albopilosus: DFT and TDDFT Study

The stable conformations of a series of bioactive molecules, (?)-alboatisins A?C, are identified via Monte Carlo searching with the MMFF94 molecular mechanics force field. Then, the optical rotation (OR) values, vibrational circular dichroism (VCD), and electronic circular dichroism (ECD) spectra were calculated using the gradient-corrected density functional theory method. The vibrational and transition modes of molecular chirality were explored in terms of their microscopic origin. The calculated specific rotations are in agreement with the experimental values. From the OR analysis, it was concluded that optical rotation values areregulated by hydroxyl substitution. Vibrations occurring on the chiral skeleton may cause strong absorption in VCD spectra; VCD spectra are thus the spectral response to deformation vibrations on the chiral carbon skeleton. The lowest-energy negative Cotton effect is caused by σ→π^* transition. Frontier molecular orbital analysis showed that strong ECD absorptions are produced when the dominant transition on the chiral skeleton is asymmetric; ECD spectra show the result of transitions lacking asymmetry on the chiral skeleton.     

六羟基化合物为骨架的高分子固-固相变材料的合成与性能

分别使用三种含6个羟基的化合物(山梨醇、双季戊四醇和肌醇)作为分子骨架,聚乙二醇(PEG)作为相变功能链,4,4'-二苯基甲烷二异氰酸酯(MDI)为交联剂,合成了3种具有不同交联结构的新型固-固相变储能材料。通过傅里叶变换红外光谱(FT IR)、X-射线衍射(XRD)、偏光显微镜(POM)、示差扫描量热法(DSC)和热重量分析法(TG)分别对合成材料的分子结构、结晶性能、相变行为和热稳定性进行了研究。结果显示,所制备的材料在30~70℃温度范围内具有典型的固-固相变特性,其升温和冷却过程的相变焓最高可达107.5J/g和102.9J/g。此外,通过热重分析发现所合成材料具有较好的可重复使用性和热稳定性。因此,合成的新型固-固相变材料在热能储存和控温领域具有巨大的应用潜力。     

过渡金属杂硼烷结构规则的量子化学计算

用EHMO量子化学计算方法,计算了过渡金属杂硼烷骨架Fe_{nB6-n(n=0,1,…,6),验证和讨论了过渡金属杂硼烷的价成键和价非键轨道数BMO+NBMO=4n1+9n2-F。其中n1、n2和F都只与骨架的几何性质有关。}     

Similarity metrics for ligands reflecting the similarity of the target proteins

In this study we evaluate how far the scope of similarity searching can be extended to identify not only ligands binding to the same target as the reference ligand(s) but also ligands of other homologous targets without initially known ligands. This "homology-based similarity searching" requires molecular representations reflecting the ability of a molecule to interact with target proteins. The Similog keys, which are introduced here as a new molecular representation, were designed to fulfill such requirements. They are based only on the molecular constitution and are counts of atom triplets. Each triplet is characterized by the graph distances and the types of its atoms. The atom-typing scheme classifies each atom by its function as H-bond donor or acceptor and by its electronegativity and bulkiness. In this study the Similog keys are investigated in retrospective in silico screening experiments and compared with other conformation independent molecular representations. Studied were molecules of the MDDR database for which the activity data was augmented by standardized target classification information from public protein classification databases. The MDDR molecule set was split randomly into two halves. The first half formed the candidate set. Ligands of four targets (dopamine D2 receptor, opioid delta-receptor, factor Xa serine protease, and progesterone receptor) were taken from the second half to form the respective reference sets. Different similarity calculation methods are used to rank the molecules of the candidate set by their similarity to each of the four reference sets. The accumulated counts of molecules binding to the reference target and groups of targets with decreasing homology to it were examined as a function of the similarity rank for each reference set and similarity method. In summary, similarity searching based on Unity 2D-fingerprints or Similog keys are found to be equally effective in the identification of molecules binding to the same target as the reference set. However, the application of the Similog keys is more effective in comparison with the other investigated methods in the identification of ligands binding to any target belonging to the same family as the reference target. We attribute this superiority to the fact that the Similog keys provide a generalization of the chemical elements and that the keys are counted instead of merely noting their presence or absence in a binary form. The second most effective molecular representation are the occurrence counts of the public ISIS key fragments, which like the Similog method, incorporates key counting as well as a generalization of the chemical elements. The results obtained suggest that ligands for a new target can be identified by the following three-step procedure: 1. Select at least one target with known ligands which is homologous to the new target. 2. Combine the known ligands of the selected target(s) to a reference set. 3. Search candidate ligands for the new targets by their similarity to the reference set using the Similog method. This clearly enlarges the scope of similarity searching from the classical application for a single target to the identification of candidate ligands for whole target families and is expected to be of key utility for further systematic chemogenomics exploration of previously well explored target families.     

以主族元素为桥的梯形化合物的光电性质

梯形化合物具有大的平面π共轭结构, 不会产生构象扭曲, 可以有效增加π共轭长度, 因而表现出非常好的光电性质. 将主族元素引入到梯形化合物骨架中作为桥接单元不仅可以固定其结构而且由于主族元素和π共轭骨架之间的轨道相互作用, 可以实现对这类化合物光电性质的调节. 采用密度泛函理论对一系列主族元素桥的梯形化合物的结构和光电性质进行了理论研究, 从而可更好地理解和预测这类化合物的性质. 研究发现, 这类化合物的电子结构可以通过引入主族元素进行调节. 由于具有更大的π共轭程度, 四主族元素桥化合物的吸收与双主族元素桥化合物相比有明显的红移, 而且荧光寿命较短. 另外, 通过计算离子化势(IPs)、电子亲和能(EAs)和重组能(λ)考察了这类化合物的电子和空穴注入及传输性质. 研究发现, 四主族元素桥化合物表现出更强的电子和空穴注入能力.     

Putting molecular similarity into context: asymmetric indices for field-based similarity measures

Some of the most widely used indices in molecular similarity searching are intrinsically symmetric in nature, meaning that each molecule under comparison contributes equally to the similarity index. For example, the Carbó and the Hodgkin–Richards similarity indices are respectively, related to the geometric and arithmetic averages of the molecular self-similarities. This work introduces the asymmetric forms of an entire family of field-based molecular similarity indices. By incorporating a weighted contribution of each molecule into the similarity index, the newly obtained asymmetric forms allow for measuring and modulating the similarity of one molecule in the context of another and thus have the potential of alleviating the size dependency often observed in chemical similarity searching     

Enumeration of substitutional isomers with restrictive mutual positions of ligands: I. Overall counts

We address systematics for the enumeration of substitutional isomers when there is constrained positioning of ligands on a molecular skeleton. One constraint involves ‘restrictive ligands’ where two of the same kind are forbidden to occupy adjacent sites in a molecular skeleton. This may arise because of steric hindrance, or because of groups which in neighbor proximity react to eliminate one. For instance, no pair of –OH groups attach to the same C atom in a molecular skeleton. In another case, malonic acid residues decarboxylate leaving no more than one decarboxylation in each residue. The enumeration with such restrictive ligands may be addressed via a Polya-theoretic cycle index hybridized with the graph-theoretic independence polynomial (when there is just a single such neighbor-excluding ligand and another which is not), while more generally a hybridization with the chromatic polynomial is needed. Another substitional-isomer constraint involves bidentate ligands, with each ligand-part occupying adjacent sites, and possibly also with additional separate unidentate ligands. Here, the set of all pure & mixed such ligand placements is analytically represented by a ‘symmetry-reduced’ matching polynomial (which is a hybrid now of the matching polynomial and Polya’s cycle index). This result gives the generating function for isomer enumeration, taking into account every possible so-restricted assortment of the employed ligands. Here we make such novel hybridizations (for these and other graphtheoretic polynomials) to deal with such oft-encountered chemical problems, which nevertheless transcend typical earlier unconstrained formulizations. Further subsymmetry classification & enumerations, along with examples are considered in a further article.     

Theoretical studies on the heats of formation and the interactions among the difluoroamino groups in polydifluoroaminocubanes

The heats of formation (HOFs) were calculated for a series of polydifluoroaminocubanes by using density functional theory (DFT), Hartree-Fock, and MP2 method with 6-31G basis set as well as semiempirical methods. The cubane skeleton was not broken in the process of designing isodesmic reactions; i.e., the cubane skeleton was chosen for a reference compound. The contribution of difluoroamino group to the heat of formation deviates from group additivity. The semiempirical MO (MNDO, AM1, and PM3) methods did not produce accurate and reliable results for the HOFs of the title compounds. The relationship between HOFs and molecular structures was discussed. It was found that the HOFs decreased dramatically initially and then gradually with each difluoroamino group attached to the cubane skeleton. The distance between difluoroamino groups influences the values of HOFs. The interacting energies of polydifluoroaminocubanes are in the range 14-20 kJ/mol. The interaction of neighbor difluoroamino groups discords with the group additivity. The average interaction energy between the nearest-neighbor NF(2) group in the most stable conformer of octadifluoroaminocubane is 13.94 kJ/mol at the B3LYP/6-31G level. The NF(2) group can rotate freely around the C-N bond. The relative stability of the title compounds was accessed on the basis of the calculated HOFs, the energy gaps between the frontier orbitals, and the bond order of C-NF(2). These results provide basic information for the molecular design of novel high energetic density materials.     

New Carbonyl Compounds in the High-Boiling Fraction of Lavender Oil. 1st Communication

A series of new carbonyl compounds with santalane ( 3–9 ) as well as cadinane skeleton ( 10–13 ) have been identified for the first time in lavender oil. Most of the structures established by spectra interpretation are corroborated by partial synthesis starting from well-defined natural products.