Sol–gel derived organic–inorganic hybrid materials: synthesis,characterizations and applications

Organic/inorganic hybrid materials prepared by the sol–gel approach have rapidly become a fascinating new field of research in materials science. The explosion of activity in this area in the past decade has made tremendous progress in both the fundamental understanding of the sol–gel process and the development and applications of new organic/inorganic hybrid materials. Polymer-inorganic nanocomposite present an interesting approach to improve the separation properties of polymer material because they possess properties of both organic and inorganic such as good permeability, selectivity, mechanical strength, and thermal and chemical stability. Composite material derived by combining the sol–gel approach and organic polymers synthesis of hybrid material were the focus area of review It has also been demonstrated in this review that a more complete understanding of their structure–property behavior can be gained by employing many of the standard tools that are utilized for developing similar structure–property relationships of organic polymers. This review article is introductory in nature and gives introduction to composite materials/nanocomposite, their applications and the methods commonly employed for their synthesis and characterization. A brief literature survey on the polysaccharide templated and polysaccharide/protein dual templated synthesis of silica composite materials is also presented in this review article.     

Enumeration of internal rotation reactions and their reaction graphs

Threefold and twofold internal rotation reactions and their reaction graphs are enumerated using the generalized wreath product method developed by the author in an earlier paper. The correspondence between reaction directed graphs (digraphs) and finite topologies on isomers is established. It is shown that the reaction digraphs can be represented by Borel fields. Atropisomerism in polyphenyl compounds is discussed. Applications to spontaneous generation of optical activity and NMR spectroscopy are considered. Borel fields are enumerated by bumping squares of the upper rows of Young diagrams starting from the Young diagram containing just one row.     

Calculating physical properties of organic compounds for environmental modeling from molecular structure

Mathematical models for predicting the transport and fate of pollutants in the environment require reactivity parameter values – that is the value of the physical and chemical constants that govern reactivity. Although empirical structure–activity relationships have been developed that allow estimation of some constants, such relationships are generally valid only within limited families of chemicals. The computer program, SPARC, uses computational algorithms based on fundamental chemical structure theory to estimate a large number of chemical reactivity parameters and physical properties for a wide range of organic molecules strictly from molecular structure. Resonance models were developed and calibrated using measured light absorption spectra, whereas electrostatic interaction models were developed using measured ionization pK_as in water. Solvation models (i.e., dispersion, induction, H-bonding, etc.) have been developed using various measured physical properties data. At the present time, SPARC’s physical property models can predict vapor pressure and heat of vaporization (as a function of temperature), boiling point (as a function of pressure), diffusion coefficient (as a function of pressure and temperature), activity coefficient, solubility, partition coefficient and chromatographic retention time as a function of solvent and temperature. This prediction capability crosses chemical family boundaries to cover a broad range of organic compounds.     

On Harary index

We report lower and upper bounds for the Harary index of a connected (molecular) graph, and, in particular, upper bounds of triangle- and quadrangle-free graphs. We also give the Nordhaus–Gaddum-type result for the Harary index. Dedicated to the memory of Professor Frank Harary (1921–2005), the late grandmaster of both graph theory and chemical graph theory.     

Chemoinformatics: a new field with a long tradition

Chemoinformatics is the application of informatics methods to solve chemical problems. Although this term was introduced only a few years ago, this field has a long history with its roots going back more than 40 years. Work on chemical structure representation and searching, quantitative structure–activity relationships, chemometrics, molecular modeling as well as computer-assisted structure elucidation and synthesis design was initiated in the 1960s. These different origins have now merged into a discipline of its own that is in full bloom. All areas of chemistry from analytical chemistry to drug design can benefit from chemoinformatics methods. And there are still many challenging chemical problems waiting for solutions through the further development of chemoinformatics.     

Fourier transform infrared spectroscopy as a tool to study structural properties of cytochromes P450 (CYPs)

Cytochrome P450 proteins (CYPs) are a big class of heme proteins which are involved in various metabolic processes of living organisms. CYPs are the terminal catalytically active components of monooxygenase systems where the substrate binds and is hydroxylated. In order to be functionally competent, the protein structures of CYPs possess specific properties that must be explored in order to understand structure–function relationships and mechanistic aspects. Fourier transform infrared spectroscopy (FTIR) is one tool that is used to study these structural properties. The application of FTIR spectroscopy to the secondary structures of CYP proteins, protein unfolding, protein–protein interactions and the structure and dynamics of the CYP heme pocket is reviewed. A comparison with other thiolate heme proteins (nitric oxide synthase and chloroperoxidase) is also included. Figure The protein secondary structure, protein unfolding, redox-partner protein–protein interaction, structural changes induced by the reduction of the heme iron, and the structure and dynamics of the active site of cytochromes P450 (CYP) can be studied using Fourier transform infrared spectroscopy (FTIR). FTIR spectroscopy is a good approach for gaining a deeper insight into structure–function relationships in CYPs. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Characterizations for Some Types of DNA Graphs

Vertex induced subgraphs of directed de Bruijn graphs with labels of fixed length k and over α letter alphabet are (α,k)-labelled. DNA graphs are (4,k)-labelled graphs. Pendavingh et al. proved that it is NP-hard to determine the smallest value α _k (D) for which a directed graph D can be (α _k (D),k)-labelled for any fixed . In this paper, we obtain the following formulas: and for cycle C _n and path P _n . Accordingly, we show that both cycles and paths are DNA graphs. Next we prove that rooted trees and self-adjoint digraphs admit a (Δ,k)-labelling for some positive integer k and they are DNA graphs if and only if Δ ≤ 4, where Δ is the maximum number in all out-degrees and in-degrees of such digraphs.     

How to confirm identified toxicants in effect-directed analysis

Due to the production and use of a multitude of chemicals in modern society, waters, sediments, soils and biota may be contaminated with numerous known and unknown chemicals that may cause adverse effects on ecosystems and human health. Effect-directed analysis (EDA), combining biotesting, fractionation and chemical analysis, helps to identify hazardous compounds in complex environmental mixtures. Confirmation of tentatively identified toxicants will help to avoid artefacts and to establish reliable cause–effect relationships. A tiered approach to confirmation is suggested in the present paper. The first tier focuses on the analytical confirmation of tentatively identified structures. If straightforward confirmation with neat standards for GC–MS or LC–MS is not available, it is suggested that a lines-of-evidence approach is used that combines spectral library information with computer-based structure generation and prediction of retention behaviour in different chromatographic systems using quantitative structure–retention relationships (QSRR). In the second tier, the identified toxicants need to be confirmed as being the cause of the measured effects. Candidate components of toxic fractions may be selected based, for example, on structural alerts. Quantitative effect confirmation is based on joint effect models. Joint effect prediction on the basis of full concentration–response plots and careful selection of the appropriate model are suggested as a means to improve confirmation quality. Confirmation according to the Toxicity Identification Evaluation (TIE) concept of the US EPA and novel tools of hazard identification help to confirm the relevance of identified compounds to populations and communities under realistic exposure conditions. Promising tools include bioavailability-directed extraction and dosing techniques, biomarker approaches and the concept of pollution-induced community tolerance (PICT). Figure Toxicity confirmation in EDA as a tiered approach     

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.     

Laser-induced breakdown spectroscopy for polymer identification

This study aims at differentiating several organic materials, particularly polymers, by laser induced breakdown spectroscopy. The goal is to apply this technique to the fields of polymer recycling and cultural heritage conservation. We worked with some usual polymers families: polyethylene (PE), polypropylene (PP), polyoxymethylene, (POM), poly(vinyl chloride), polytetrafluoroethylene, polyoxyethylene (POE), and polyamide for the aliphatic ones, and poly(butylene terephthalate), acrylonitrile–butadiene–styrene, polystyrene, and polycarbonate for the aromatic ones. The fourth harmonic of a Nd:YAG laser (266 nm) in ambient air at atmospheric pressure was used. A careful analysis of the C₂ Swan system (0,0) band in polymers containing no C–C (POM), few C–C (POE), or aromatic C–C linkages led us to the conclusion that the C₂ signal might be native, i.e., the result of direct ablation from the sample. With use of these results, aliphatic and aromatic polymers could be differentiated. Further data treatments, such as properly chosen line ratios, principal component analysis, and partial least squares regression, were evaluated. It was shown that many polymers could be separated, including PE and PP, despite their similar chemical structures.     

Zhang–Zhang polynomials of cyclo-polyphenacenes

The Zhang–Zhang polynomial (i.e., Clar covering polynomial) of hexagonal systems is introduced by H. Zhang and F. Zhang, which can be used to calculate many important invariants such as the Clar number, the number of Kekulé structures and the first Herndon number, etc. In this paper, we give out an explicit recurrence expression for the Zhang–Zhang polynomials of the cyclo-polyphenacenes, and determine their Clar numbers, numbers of Kekulé structures and their first Herndon numbers.     

Quantum chemical reaction networks,reaction graphs and the structure of potential energy hypersurfaces

Global properties of the Born-Oppenheimer energy expectation value functional, defined over the nuclear configuration space R, are analyzed. Quantum chemical reaction graphs and reaction networks are defined in terms of intersection graphs of connected sets of nuclear geometries, representing various chemical structures. The set of all possible reaction mechanisms on the given energy hypersurface and the associated activation energy conditions are analyzed using reachability matrices defined over digraphs D ^s() and D ^s(, E).     

Mass spectrometry as test bench for medicinal chemistry studies

This review describes how mass spectrometry can be used as a powerful test bench to obtain information on the biological activity of target compounds. Considering that mass spectrometry is based on the chemical reactivity of the analytes, it is possible to investigate the stability of the active compounds, to predict their behaviour in the environment of interest, and to obtain structure–reactivity relationships for new molecules of pharmacological interest. Electron ionization and metastable ion studies give evidence of the correlation between the mutagenic properties of a series of aryl and heteroaryl triazenes and mass spectrometric data. A linear relationship between the energetics of C(O)–O bond cleavage of some carbamic acid O-aryl esters and their FAAH inhibition activity has been proved by electrospray-ionization ion-trap mass spectrometry. An inverse correlation between the stability and cytotoxic activity of some copper complexes has been clearly established by electrospray-ionization mass spectrometry. Moreover, because of the sensitivity and specificity of mass spectrometry, it has been possible to determine and characterize impurities that in some cases can be the real bioactive compound.     

Global versus local QSPR models for persistent organic pollutants: balancing between predictivity and economy

Experimentally determined data on the key physicochemical parameters for halogenated congeners of persistent organic pollutants (POPs) are available only for a limited number of compounds. In the absence of experimental data, a range of computational methods can be applied to characterize those species for which experimental data is not available. One of the techniques widely used in this context is quantitative structure–property relationships (QSPR) approach. There are two ways to develop the QSPR models: using a more complex global model or fitting a simple local model that covers a specific class of chemically related compounds. The essence of the study was to investigate, if local models have significantly better explanatory and predictive ability than global models with wider applicability domains. Based on the obtained results, we concluded that whenever global models fulfill all quality recommendations by OECD, they would be applied in practice as more efficient ones in state of more time consuming procedure of modeling the particular groups of POPs one-by-one. On the contrary, local models are applicable to solve specific problems (i.e., related to only one group of POPs), when high-quality experimental data are available for a sufficient number of training and validation compounds.     

Application of the electronegativity indices of organic molecules to tasks of chemical informatics

An efficient structure filtration method for the operation with chemical databases containing information on the structures and properties of organic molecules was proposed. The technique involves the use of electronegativity indices for generation of identification keys and for isomorphism tests of the molecular graphs corresponding to the structural formulas. The test set for the method proposed included a total of 95,000,000 molecules containing up to sixty carbon atoms. Tests revealed a high discriminating capability of the electronegativity indices and high efficiency of the method for solving both general problems (recognition of chemical structures, chemical database management systems) and specific tasks (generation of molecular graphs, etc.) in chemical informatics. Dedicated to Academician N. S. Zefirov on the occasion of his 70th birthday. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 2166–2176, September, 2005.     

The methods of synthesis,modification, and biological activity of 4-quinolones (review)

Data on methods for the construction of the 4-quinolone skeleton and modification of the substituents around it are reviewed. The “structure–activity” relationships of 4-quinolones are examined with respect to antibacterial and antitumor activity.     

Synthesis, structure, and solvatochromic properties of pharmacologically active 5-substituted 5-phenylhydantoins

Abstract  

A series of 5-substituted 5-phenylhydantoins was synthesized and their UV absorption spectra were recorded in the region 200–400 nm in selected solvents of different polarity. The effects of solvent dipolarity/polarizability and solvent–solute hydrogen-bonding interactions were analyzed by means of the linear solvation energy relationship concept proposed by Kamlet and Taft. The lipophilicities of the investigated hydantoins were estimated by calculation of their log P values. The quantitative relationship between the ratio of the contributions of specific solvent interactions and the corresponding lipophilicity parameter is discussed. The correlation equations were combined with the corresponding ED₅₀ values and different physicochemical parameters to generate new equations that demonstrate the reasonable relationships between solute–solvent interactions and the structure–activity parameters. In order to determine a spectroscopic assignment of the absorption bands in different solvents, quantum chemical calculations were done.     

Cyclical Edge-Connectivity of Fullerene Graphs and (k, 6)-Cages

It is shown that every fullerene graph G is cyclically 5-edge-connected, i.e., that G cannot be separated into two components, each containing a cycle, by deletion of fewer than five edges. The result is then generalized to the case of (k,6)-cages, i.e., polyhedral cubic graphs whose faces are only k-gons and hexagons. Certain linear and exponential lower bounds on the number of perfect matchings in such graphs are also established.     

Structural covariance of graphs

Algebraic structures including multiple rank tensors, linear and non-linear operators are related to and represented with various types of graphs. Special emphasis is placed on linear operators e.g. on the Hibert space. A different graph represents the same operator depending on the basis frame used, in general non-orthonormal. All such graphs are shown to belong in one equivalence class and are termed structurally covariant. Crucial indices related to eigenvalues but invariant under any basis frame changes including non-orthonormal ones provide one way to characterize each class. A set of rules are given that allow one to find the graphs structurally covarinat with a given one and/or to deduce the class indices directly by simple pictorial manipulations on a graph. Applications in various fields including the quantum theory of molecules and reactions are indicated.