Taxonomy of Structures Selected from the IR Spectroscopy Database

This paper reports on taxonomy of the structural formulas of organic compounds selected from an IR spectroscopy database (DB) based on the similarity between the query spectrum and DB spectra. Two molecular graph models are compared: connectivity matrix and vector representation (exhaustive set of nonisomorphic connected k-vertex fragments). In both cases, taxonomy according to the shortest distance framework of the distance graph gives a classification of structural analogs into groups (taxons). An analysis of IR spectra and common subgraphs in the respective groups of graphs reveals large structural fragments of the compounds.     

Methods and algorithms for predicting the properties of chemical compounds by common fragments of molecular graphs

Methods and algorithms for predicting the properties of chemical compounds by common fragments of their molecular graphs are described. The prediction algorithms are based on determination of a measure of structural proximity (distance) between molecular graphs, which depends on the size of their common fragment. The prediction procedure involves the following steps: partitioning the property classes of the training sample compounds into subclasses of structurally similar compounds; seeking structurally typical compounds and their fragments in each subclass; classifying control compounds according to their distances from the training sample compounds or fragments of classes; forming a set of essential fragments of samples potentially responsible for the properties exhibited by the compounds. The algorithms were successfully tested in the BACC system for analyzing and classifying biologically active compounds designed at the Institute of Mathematics, Siberian Branch, Russian Academy of Sciences. S. L. Sobolev Institute of Mathematics, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 39, No. 1, pp. 113–125, January–February, 1998.     

The hydrogen perturbation in molecular connectivity computations

A new algorithm for the delta(v) number, the basic parameter of molecular connectivity indices, is proposed. The new algorithm, which is centered on graph concepts like complete graphs and general graphs, encodes the information of the bonded hydrogen on different atoms through a perturbation parameter that makes use of no new graph concepts. The model quality of the new algorithm is tested with 13 properties of seven different classes of compounds, as well as with composite classes of compounds with the same property and with composite properties of the same class of compounds. Chosen properties and classes of compounds display different percentage of bonded hydrogen atoms, which allow a checking of the importance of this parameter. A comparison is drawn with previous results with zero contribution for the hydrogen perturbation as well as among results obtained by changing the number of compounds of a property but keeping constant the percentage of hydrogen atoms. Results underline the importance of the property as well as the importance of the number of compounds in determining the level of the hydrogen perturbation. Molecular connectivity terms are in some cases more critical than the combination of indices in detecting the perturbation introduced by the hydrogen atoms.     

Spectral moments of phenylenes

In a series of publications Estrada (Estrada, E. J. Chem. Inf. Comput. Sci. 1996, 36, 844-849; 1997 37, 320-328; 1998, 38, 23-27) employed spectral moments of line graphs in QSPR and QSAR relationship studies of various classes of compounds. A recent paper (Markovi?, S.; Gutman, I. J. Chem. Inf Comput. Sci. 1999, 39, 289-293) reported that in QSPR and QSAR investigations of benzenoid hydrocarbons based on linear combination of spectral moments, it made no difference whether one used spectral moments of the molecular graph or those of the line graph. In the present work spectral moments of molecular graphs (Mk) and line graphs (muk) of phenylenes are considered. The first few Mk's and muk'S of phenylenes are dependent on identical structural parameters. It is proved that the two sets of moments of phenylenes are linearly dependent. It is also shown that in the case of the heat of formation of phenylenes there is no advantage in using lower spectral moments of line graphs instead of lower spectral moments of molecular graphs. In this way the redundancy observed in the case of benzenoid hydrocarbons is also shown to exist in the class of phenylenes.     

Spherical polyunsaturated organosilicon and organogermanium first generation dendrimers of regular structure

Synthesis of the mononuclear organosilicon tri-and tetradendrones of the first generation with the repeating CΞC groups as well as the synthones for their construction is carried out. The tetrabranched polyunsaturated dendrimers G1 having regular structure of containing silicon and germanium atoms simultameously are synthesized. The IR and NMR spectra of all the compounds obtained are studied, and molecular masses of the compounds are calculated and evaluated experimentally. Key parameters and chemical graphs of new dendrimers are presented.     

The possibility of using femtosecond IR spectroscopy to determine the composition of molecules in the gas phase

The possibility of using one method of femtosecond laser spectroscopy, IR pump-probe, is considered for analyzing the molecular composition of gas. The measured intramolecular relaxation time of the vibrational energy is proposed as an individual characteristic of molecules. A number of compounds of different classes having the molecular chromophore group C=O are investigated. It is shown that the characteristic relaxation times of the corresponding analytical signals in the resonant exciting of C=O vibrations are significantly different for different molecules (ten or more), making it possible to identify molecules in mixtures by means of temporal selection. The linear dependence of the analytical signal on the vapor pressure of the investigated compounds and the energy fluence of the exciting radiation is revealed. It is shown that the analytical signal is not dependent on the pressure of the buffer gas (nitrogen) up to 1 atm.     

Establishment of correlations between the structure and reactivity of molecules in the gas phase based on information theory

A general approach to revealing correlations between the structure of molecules and their reactivity in fragmentation processes under electron impact conditions based on the use of generalized structural and mass spectral characteristics is suggested. The characteristics were obtained using information theory, molecular graphs, and absolute reaction rates. Information topological indices of molecular graphs were used as generalized structural characteristics of molecules. They are a quantitative measure of the structural complexity of molecules and are expressed in information units. The gas-phase process of fragmentation of molecules under electron impact was used as a general reaction series for all volatiles. In terms of information theory, the mass spectrum represents the distribution of probabilities of the formation of ions of each type, and the information entropy of this distribution appears to be an integral characteristic of the reactivity of a molecule during fragmentation under electron impact in the gas phase. Using organic and organometallic compounds of several classes (ferrocene derivatives, arylsilanes, aromatic azo compounds,etc.) as examples, linear correlations between the information indices of the mass spectra and the information topological indices of the appropriate molecular graphs or electronic parameters of molecules have been found, which testifies that the approach suggested is adequate.Translated fromIzvestiya Akodemii Nouk. Seriya Khimicheskaya, No. 11, pp. 2683–2688, November, 1996.     

Core electrons and hydrogen atoms in chemical graph theory

General and complete graphs have recently been used to free chemical graph theory, and especially molecular connectivity theory, from spurious concepts, which belonged to quantum chemistry with no direct counterpart in graph theory. Both types of graph concepts allow the encoding of multiple bonds, non-bonding electrons, and core electrons. Furthermore, they allow the encoding of the bonded hydrogen atoms, which are normally suppressed in chemical graphs. This suppression could sometimes have nasty consequences, like the impossibility to differentiate between compounds, whose hydrogen-suppressed chemical graphs are completely equivalent, like for the CH₂F₂ and BHF₂ compounds. At the computational level the new graph concepts do not introduce any dramatic changes relatively to previous QSPR/QSAR studies. These concepts can nevertheless help in encoding the many electronic features of a molecule, achieving, as a bonus, an improved quality of the modeled properties, as it is here exemplified with a set of properties of different classes of compounds.     

Designing sedative/hypnotic compounds from a novel substructural graph-theoretical approach

A novel approach to computer-aided molecular design is illustrated. This approach is based on the calculation of the spectral moments of the bond adjacency matrix of graphs representing molecular structures. Spectral moments are then expressed as linear combinations of the different sub-structures present in molecules. Two series of compounds, one containing sedative/hypnotic and the other containing different classes of drugs were used to find a discriminant function with the present approach. Several compounds from the Merck Index were identified by the model as sedative/hypnotic, five of them were found in the recent literature as possessing this activity. The critical fragments, actives and inactive ones, were detected.     

Equilibrium properties in the liquid state from interactions of walks

Abstract

When molecules of chemical compounds are represented by graphs, thermodynamic properties may be connected with numbers of certain classes of walks on graphs. The basic proposition of summing up contributions resulting from interactions of walks is related to fluid distribution functions. The principle of corresponding volumes and structural schemes are discussed. Exemplary calculations for normal alkanes and their binary mixtures give in many cases values within limits of the experimental accuracy     

SIRS-SS: a system for simulating IR/Raman spectra. 1. Substructure/subspectrum correlation

An IR/RAMAN spectra simulation system is reported. The development of this software was based on the substructure/subspectrum relationships established for four different structural classes: small molecules, special fragments, atom-centered FRELs, and bond-centered FRELs (FREL: Fragment centered on an Environment which is Limited). Four corresponding knowledge-bases (now, at a pilot stage) are constructed from usual correlation charts or data analyses of large populations of compounds using data mining techniques.     

Similarity searching using reduced graphs

Reduced graphs provide summary representations of chemical structures. In this work, the effectiveness of reduced graphs for similarity searching is investigated. Different types of reduced graphs are introduced that aim to summarize features of structures that have the potential to form interactions with receptors while retaining the topology between the features. Similarity searches have been carried out across a variety of different activity classes. The effectiveness of the reduced graphs at retrieving compounds with the same activity as known target compounds is compared with searching using Daylight fingerprints. The reduced graphs are shown to be effective for similarity searching and to retrieve more diverse active compounds than those found using Daylight fingerprints; they thus represent a complementary similarity searching tool.     

Complete graph conjecture for inner-core electrons: homogeneous index case

The complete graph conjecture that encodes the inner-core electrons of atoms with principal quantum number n >or= 2 with complete graphs, and especially with odd complete graphs, is discussed. This conjecture is used to derive new values for the molecular connectivity and pseudoconnectivity basis indices of hydrogen-suppressed chemical pseudographs. For atoms with n = 2 the new values derived with this conjecture are coincident with the old ones. The modeling ability of the new homogeneous basis indices, and of the higher-order terms, is tested and compared with previous modeling studies, which are centered on basis indices that are either based on quantum concepts or partially based on this new conjecture for the inner-core electrons. Two similar algorithms have been proposed with this conjecture, and they parallel the two "quantum" algorithms put forward by molecular connectivity for atoms with n > 2. Nine properties of five classes of compounds have been tested: the molecular polarizabilities of a class of organic compounds, the dipole moment, molar refraction, boiling points, ionization energies, and parachor of a series of halomethanes, the lattice enthalpy of metal halides, the rates of hydrogen abstraction of chlorofluorocarbons, and the pED(50) of phenylalkylamines. The two tested algorithms based on the odd complete graph conjecture give rise to a highly interesting model of the nine properties, and three of them can even be modeled by the same set of basis indices. Interesting is the role of some basis indices all along the model.     

An existence theorem for molecular graphs determined by a sequence of valence states

Vertices of molecular graphs (multigraphs with restricted vertex valences and edge multiplicities) are described by the so-called valence states — an ordered triple of non-negative integers that are equal to the number of edges with a given multiplicity that are incident with the vertex. For molecular graphs, which correspond to standard organic-chemistry compounds composed of H, C, N, and O atoms, there may appear only ten eligible valence states. In order to construct exhaustively all graphs assigned to a given sequence of valence states, it is advantageous to know under what condition the sequence is graphical. An existence theorem for sequences composed of eligible valence states to be graphical is proved.     

Synthesis and molecular structures of nitrosoarene metalloporphyrin complexes of ruthenium

Several new ruthenium porphyrins containing nitrosoarene ligands have been synthesized and characterized by IR and (1)H NMR spectroscopy, and by single-crystal X-ray crystallography. Bis-nitrosoarene complexes of the form (por)Ru(ArNO)(2)(Ar = aryl group; por = TPP, TTP; TPP = tetraphenylporphyrinato dianion, TTP = tetratolylporphyrinato dianion) were prepared in good yields from the reaction of the nitrosoarenes with (por)Ru(CO). The IR spectra of the complexes (as KBr pellets) display new bands in the 1346-1350 cm(-1) region due to nu(NO). Reactions of the (por)Ru(ArNO)(2) complexes with excess pyridine and 1-methylimidazole produce the mono-nitrosoarene complexes (por)Ru(ArNO)(py) and (por)Ru(ArNO)(1-MeIm), respectively. The IR spectra of these mono-nitrosoarene complexes reveal a lowering of nu(NO) by 14-44 cm(-1), a feature consistent with the replacement of one of the pi-acid ArNO ligands with the more basic pyridine and 1-MeIm ligands. The solid-state molecular structures of two members of each of the three classes of compounds, namely (por)Ru(ArNO)(2), (por)Ru(ArNO)(py) and (por)Ru(ArNO)(1-MeIm) were determined by single-crystal X-ray diffraction, and reveal the N-binding mode of the ArNO ligands.     

Classification of topologically chiral molecules

Graphs are partitioned into six classes from the perspective of chirality, depending on whether they are topologically achiral, whether there is at least one topologically achiral embedding, whether there is at least one rigidly achiral embedding, and whether there is at least one rigidly achiral presentation. Three of these classes are well represented by a variety of chemical structures: topologically chiral molecular graphs with no topologically achiral embeddings, topologically chiral molecular graphs with at least one rigidly achiral embedding, and topologically achiral molecular graphs with at least one rigidly achiral presentation. Known representatives of these three classes are described. Various meanings associated with the concepts molecular graph and intrinsic chirality are critically discussed. Previous arrangements of molecular graphs and molecules in a hierarchical order, ranging from the most to the least chiral, are interpreted in terms of the graph's and molecule's chiral persistence.