Evaluation of the relationship between spectral and structural similarity in IR spectroscopy

Representation of a structural formula of a compound as a complete set of nonisomorphic k-vertex (2 ≤k≤7) connected fragments is used to evaluate the structural similarity of compounds. The spectra and structures of spectrally or structurally alike compounds are compared statistically using a database containing 32,000 IR spectra and structures. This study reveals some tendencies typical for both full IR spectra and their abbreviated versions represented by sets of most characteristic peaks. Applicability of IR databases to spectrum simulation for compounds with a specified structure is justified statistically. A method is proposed for evaluating the efficiency of a search algorithm selecting structural analogs of the compound from an IR database according to the query spectrum. Translated fromZhurnal Strukturnoi Khimii, Vol. 41, No. 2, pp. 379–390, March–April, 2000.     

Efficient enumeration of stereoisomers of outerplanar chemical graphs using dynamic programming

Exhaustive and nonredundant generation of stereoisomers of a chemical compound with a specified constitution is an important tool for molecular structure elucidation and molecular design. It is known that many chemical compounds have outerplanar graph structures. In this paper we deal with chemical compounds composed of carbon, hydrogen, oxygen, and nitrogen atoms whose graphical structures are outerplanar and consider stereoisomers caused only by asymmetry around carbon atoms. Based on dynamic programming, we propose an algorithm of generating all stereoisomers without duplication. We treat a given outerplanar graph as a graph rooted at its structural center. Our algorithm first recursively computes the number of stereoisomers of the subgraph induced by the descendants of each vertex and then constructs each stereoisomer by backtracking the process of computing the numbers of stereoisomers. Our algorithm correctly counts the number of stereoisomers in O(n) time and space and correctly enumerates all of the stereoisomers in O(n3) time per stereoisomer on average and in O(n) space, where n is the number of atoms in a given structure.     

Algorithm of choice of the structural module and modular design of crystals

The principle of modular structure of crystals has been formulated and the possibility of the tailor-made choice of a specified structure type of compounds for subsequent modular design has been discussed. For some structure types based on cubic close packing, the modular characteristics—the fundamental and basic modules and the module that allows to obtain a certain variety of modular structures related to the initial “parent” type—have been described. The algorithm of choice of such a module has been reported. Comparative analysis of the theoretically derived module with the modules of experimentally determined modular structures has been performed for spinelloids, compounds with spinel-like structures.     

Identification of unknown compounds using data bases and computer simulation of mass spectra

The possibility of identification based on the comparison of experimental electron-ionization mass spectrum of an unknown (in our case, model) compound with the mass spectra of the candidate compounds generated by the Mass Frontier software has been demonstrated by the example of three model compounds. The structural isomers of the identified substances found in the ChemExper database have been used as the candidate compounds. The candidate substances have been ranged by the degree of similarity between their simulated mass spectra and the experimental mass spectrum of the unknown compound. The mass spectra have been compared on the basis of the algorithm used in the NIST MS Search standard search system. In all three cases, the sought-after structure has been indicated as the most probable one of all the candidate structures.     

What can calorimetry tell us about changes of three-dimensional aggregate structures of phospholipids and glycolipids?

It is reported on the structural polymorphism of the main amphiphilic cell membrane compounds, phospholipids and glycolipids, with special regard to calorimetric analyses. These lipids may form a large variety of aggregate structures in dependence on their chemical primary structure, on temperature, water content, and concentrations of cations. The entity of aggregate structures is usually called the phase diagram of the respective lipids. This should, however, not to be confused with the gel and liquid crystalline phases of the hydrocarbon chains of lipids, which differ in the fluidity of the acyl chains, and between which a first order transition can be observed. Thus, in this contribution, exemplary results are presented on the structural behaviour of biologically important lipids including their phase behaviour and structural preferences under different ambient conditions, and how phase and structural transitions are connected with enthalpy changes.     

药效团检索设计新的HIV-1蛋白酶抑制剂

通过对自建的未开发化合物三维结构库进行药效团检索,得到了4个对HIV-1蛋白酶抑制活化的化合物,通过构象分析发现包含药效团的构象处于优势构象,而且4个结构都含有带两个邻位羟基的苯环和一个间位羰基的药效团以及公共子结构。通过计算发现它们的疏水参数都很小。在考虑满足包含药效团的结构特征和有适中的疏水参数两个因素的前提下,设计出了新的具有潜在抑制HIV-1蛋白酶活性的化合物。它们的结构都比检索得到的四个化合物更为简单,因此易于合成。     

A computer search system for chemical structure elucidation based on low-resolution mass spectra

A computerized search system which employs the data on the masses and relative abundances of spectral peaks and primary neutral losses is designed for computer elucidation of chemical structures. Recognition of structural fragments is based on analysis of the structures of reference compounds selected as best matches to the mass spectrum of the compound under investigation. Tests of the system on 67 “unknowns” show that the probability of recognizing a large structural fragment lies in the interval 60–80%, depending on the fragment size (100–50% of molecular weight), and that the reliability of the corresponding structural conclusion is 98%. An approach to automatic selection of the substructure common to all or several of the selected compounds is discussed.     

Pesticide residue determination in fruit and vegetables by liquid chromatography-mass spectrometry

An overview is given of pesticide residue determination in fruit and vegetables by liquid chromatography-mass spectrometry (LC-MS). Emphasis is placed on the thermospray, particle beam and atmospheric pressure ionization interfaces including advantages and drawbacks and typical detection limits. The capacity of each interface to provide useful data for identification/confirmation of analytes and the possibility of obtaining structural information for the identification of target and non-target compounds is discussed. Finally, sample preparation techniques are dealt with in relation to their influence on further LC-MS determination.     

Crystal engineering of hydroxy group hydrogen bonding: design and synthesis of new diol lattice inclusion hosts

The diols 7-11 have been synthesized, and their X-ray crystal structures determined, to learn how to influence and control lattice hydroxy group hydrogen bonding using crystal engineering ideas. To obtain new lattice inclusion hosts precise structural rules can be defined which enable the necessary supramolecular interactions to be duplicated. In this manner the helical tubuland 10 and ellipsoidal clathrate 11 hosts were obtained for the first time and their chloroform inclusion compounds characterized. New synthetic routes were utilized to obtain the bicyclo[3.3.2]decane and 9-thiatricyclo[4.3.1.1(3,8)]undecane frameworks present in these compounds. The solid-state conformations of bicyclo[3.3.2]decane derivatives 9 and 10 are compared with prior predictions and studies made on this uncommon ring system.     

Efficient enumeration of stereoisomers of tree structured molecules using dynamic programming

Nonredundant and exhaustive generation of stereoisomers of a chemical compound with a specified constitution is one of the important tools for molecular structure elucidation and molecular design. In this paper, we deal with chemical compounds composed of carbon, hydrogen, oxygen and nitrogen atoms whose graphical structures are tree-like graphs because these compounds are most fundamental, and consider stereoisomers that can be generated by asymmetric carbon atoms and double bonds between two adjacent carbon atoms. Based on dynamic programming, we propose an algorithm of generating all stereoisomers without duplication. We treat a given tree-like graph as a tree rooted at its structural center. Our algorithm first computes recursively the numbers of stereoisomers of the subgraphs induced by the descendants of each vertex, and then constructs each stereoisomer by backtracking the process of computing the numbers of stereoisomers. Our algorithm correctly counts the number of stereoisomers in O(n) time and space, and correctly enumerates all the stereoisomers in O(n) space and in O(n) time per stereoisomer, where n is the number of atoms in a given structure. The source code of the program implementing the proposed algorithm is freely available for academic use upon request.     

On the relationship between the structure of CaFe2O4 and hollandite

The relationship between the structure of CaFe₂O₄ and those of rutile and hollandite is shown. CaFe₂O₄ may be regarded as a glide reflection twin derivative of a distorted hollandite-type structure. On the basis of this structural relationship the possibility of the existence of compounds with intermediate structures is suggested.     

Algebraic characterization of bridged polycyclic compounds

An approach based on the topological distance matrix is used for algebraic characterization of bridged polycyclic compounds. The classical bridged structures which have external bridges between cycles were examined together with the more complicated three-dimensional polycyclic systems regarded as containing internal bridges. Thirteen rules are given for characterizing the main types of structural rearrangements in these compounds. The important topological characteristic of (poly)cyclic systems, the molecular cyclicity, is examined in the polycyclic condensed, spiro- and bridged structures, respectively.     

Identification of Compounds that Selectively Stabilize Specific G‐Quadruplex Structures by Using a Thioflavin T‐Displacement Assay as a Tool

Small molecules are used in the G‐quadruplex (G4) research field in vivo and in vitro, and there are increasing demands for ligands that selectively stabilize different G4 structures. Thioflavin T (ThT) emits an enhanced fluorescence signal when binding to G4 structures. Herein, we show that ThT can be competitively displaced by the binding of small molecules to G4 structures and develop a ThT‐displacement high‐throughput screening assay to find novel and selective G4‐binding compounds. We screened approximately 28 000 compounds by using three different G4 structures and identified eight novel G4 binders. Analysis of the structural conformation and stability of the G4 structures in presence of these compounds demonstrated that the four compounds enhance the thermal stabilization of the structures without affecting their structural conformation. In addition, all four compounds also increased the G4‐structure block of DNA synthesis by Taq DNA polymerase. Also, two of these compounds showed selectivity between certain Schizosaccharomyces pombe G4 structures, thus suggesting that these compounds or their analogues can be used as selective tools for G4 DNA studies.     

STRUCTURAL RULES OF TRANSITIONMETAL CARBONYL COMPOUNDS

In this article we have proposed two topological rules to account for the electronic structures of transition-metal carbonyl compounds. The second rule is applied to those which have polyhedral metalhc skeletons with triangular faces and their derivates, while the first rule is applied to all the others We have used these two rules to analyze 261 structure-known compounds with the number of metal atoms from 2 to 12, and the results show that the two rules are in good agreement with the experimental facts. Furthermore, we have also derived from the second rule a formula which can be used to account for the electronic structures of closedpacking carbonyl compounds and which is the same as that given by Ciani and his coworkers.     

Nutmeg as a narcotic. A contribution to the chemistry and pharmacology of nutmeg (Myristica fragrans)

The abuse of nutmeg for narcotic purposes has led to renewed chemical and pharmacological interest in this drug. Several allylbenzene derivatives whose biological transformation products have structures resembling mescaline and amphetamine have been identified as psychotropic constituents. It is suggested that the intensity of the hallucinogenic action of these compounds is due to the possibility of simulation of LSD-like structural elements.     

Synthesis and supramolecular characterization of a novel class of glycopyranosyl-containing amphiphiles

A novel class of glycopeptidolipids is described, which potentially can be used as a novel antigen-delivery system. The compounds have been prepared by a combination of solid-supported and solution-based methods. The use of the orthogonally protected FmocLysDde derivative provided an opportunity to incorporate two different types lipids. It was found that the model compound 1 forms aggregates in aqueous media which can be described as rod or tubelike structures. The aggregates can be stabilized by topotactic photopolymerization. Studies on the structural analogues 2-5 revealed the effect of the carbohydrate, peptide, and lipid moiety on the aggregation properties. It is concluded that none of the structure elements can lay claim to be exclusively important for the formation of highly organized aggregates such as tubes, fibers, or helical ribbons from 1, but the presence of all of these structural elements afforded the most uniformly shaped extended structures.