Topology chemical structure

These indices are based on sound chemical, structural (topologic and geometrical), and mathematical grounds. 

An association coefficient that is widely used for calculating the similarity between pairs of chemical structures. Topological torsion... 

Another approach applies graph theory. The analogy between a structure diagram and a topological graph is the basis for the development of graph theoretical algorithms to process chemical structure information [33-35]. 

A molecule editor can draw a chemical structure and save it, for example as a Molfile. Although it is possible to include stereochemical properties in the drawing as wedges and hashed bonds, or even to assign a stereocenter/stereogroup with its identifiers R/S or E/Z), the connection table of the Molfile only represents the constitution (topology) of the molecule. 

To code the configuration of a molecule various methods are described in Section 2.8. In particular, the use of wedge symbols clearly demonstrates the value added if stereodescriptors are included in the chemical structure information. The inclusion of stereochemical information gives a more realistic view of the actual spatial arrangement of the atoms of the molecule imder consideration, and can therefore be regarded as between the 2D (topological) and the 3D representation of a chemical structure. 

Structure databases are databases that contain information on chemical structures and compounds. The compounds or structure diagrams are not stored as graphics but are represented as connection tables (see Section 2.4). The information about the structure includes the topological arrangement of atoms and the connection between these atoms. This strategy of storage is different from text files and allows one to search chemical structures in several ways. 

A substructure search algorithm is usually the first step in the implementation of other important topological procedures for the analysis of chemical structures such as identification of equivalent atoms, determination of maximal common substructure, ring detection, calculation of topological indices, etc. 

B and W J Howe 1991. Computer Design of Bioactive Molecules - A Method for Receptor-Based Novo Ligand Design. Proteins Structure, Function and Genetics 11 314-328. i H L 1965. The Generation of a Unique Machine Description for Chemical Structures - A hnique Developed at Chemical Abstracts Service. Journal of Chemical Documentation 5 107-113. J 1995. Computer-aided Estimation of Symthetic Accessibility. PhD thesis. University of Leeds, itan R, N Bauman, J S Dixon and R Venkataraghavan 1987. Topological Torsion A New )lecular Descriptor for SAR Applications. Comparison with Other Descriptors. Journal of emical Information and Computer Science 27 82-85. 

Ivanduc, O., Balahan, A. T. The graph description of chemical structures. In Topological Indices and Related Descriptors in QSAR and QSPR, Devillers,). 

The importance of methods to predict log P from chemical structure was described in Chapter 14, which is focused on fragment- and atom-based approaches. In this chapter property-based approaches are reviewed, which comprise two main categories (i) methods that use three-dimensional (3D) structure representation and (ii) methods that are based on topological descriptors. 

The presence of an (applied) potential at the aqueous/metal interface can, in addition, result in significant differences in the reaction thermodynamics, mechanisms, and structural topologies compared with those found in the absence of a potential. Modeling the potential has been a challenge, since most of today s ab initio methods treat chemical systems in a canonical form whereby the number of electrons are held constant, rather than in the grand canonical form whereby the potential is held constant. Recent advances have been made by mimicking the electrochemical model... 

In addition to looking for data trends in physical property space using PCA and PLS, trends in chemical structure space can be delineated by viewing nonlinear maps (NLM) of two-dimensional structure descriptors such as Unity Fingerprints or topological atom pairs using tools such as Benchware DataMiner [42]. Two-dimensional NLM plots provide an overview of chemical structure space and biological activity/molecular properties are mapped in a 3rd and/or 4th dimension to look for trends in the dataset. 

In conclusion, the electrochemical data offer a fingerprint of the chemical and topological structure of these dendrimers. Furthermore, the knowledge of the electrochemical properties of the mononuclear components and the synthetic control of the supramolecular structure allow the design of dendrimers with predetermined redox patterns. 

We have investigated the static and dynamic mechanical properties of networks of different chemical and topological structures ( 19,20). In a previous paper, we reported results obtained on networks with crosslink functionality four (21). In the present study, we investigated the effect of the structure of junctions on the mechanical behaviour of PDMS. Rather uncommon networks with comb-like crosslinks were employed, intending that these would be most challenging to theoretical predictions. 

The second virial coefficient is not a universal quantity but depends on the primary chemical structure and the resulting topology of their architecture. It also depends on the conformation of the macromolecules in solution. However, once these individual (i.e., non-universal) characteristics are known, the data can be used as scaling parameters for the description of semidilute solutions. Such scaling has been very successful in the past with flexible linear chains [4, 18]. It also leads for branched macromolecules to a number of universality classes which are related to the various topological classes [9-11,19]. These conclusions will be outlined in the section on semidilute solutions. 

There is no systematic nomenclature developed for molecular sieve materials. The discoverer of a synthehc species based on a characteristic X-ray powder diffraction pattern and chemical composihon typicaUy assigns trivial symbols. The early syn-thehc materials discovered by Milton, Breck and coworkers at Uruon Carbide used the modem Lahn alphabet, for example, zeoHtes A, B, X, Y, L. The use of the Greek alphabet was inihated by Mobil and Union Carbide with the zeoHtes alpha, beta, omega. Many of the synthetic zeoHtes which have the structural topology of mineral zeoHte species were assigned the name of the mineral, for example, syn-thehc mordenite, chabazite, erionite and offretite.The molecular sieve Hterature is replete with acronyms ZSM-5, -11, ZK-4 (Mobil), EU-1, FU-1, NU-1 (ICI), LZ-210, AlPO, SAPO, MeAPO, etc. (Union Carbide, UOP) and ECR-1 (Exxon). The one pubHcaHon on nomenclature by lUPAC in 1979 is Hmited to the then-known zeoHte-type materials [3]. 

To overcome this weakness, we are developing a quantitative structure-activity strategy that is conceptually applicable to all chemicals. To be applicable, at least three criteria are necessary. First, we must be able to calculate the descriptors or Independent variables directly from the chemical structure and, presumably, at a reasonable cost. Second, the ability to calculate the variables should be possible for any chemical. Finally, and most importantly, the variables must be related to a parameter of Interest so that the variables can be used to predict or classify the activity or behavior of the chemical (j ) One important area of research is the development of new variables or descriptors that quantitatively describe the structure of a chemical. The development of these indices has progressed into the mathematical areas of graph theory and topology and a large number of potentially valuable molecular descriptors have been described (7-9). Our objective is not concerned with the development of new descriptors, but alternatively to explore the potential applications of a group of descriptors known as molecular connectivity indices (10). 

The study of chemical reactions requires the definition of simple concepts associated with the properties ofthe system. Topological approaches of bonding, based on the analysis of the gradient field of well-defined local functions, evaluated from any quantum mechanical method are close to chemists intuition and experience and provide method-independent techniques [4-7]. In this work, we have used the concepts developed in the Bonding Evolution Theory [8] (BET, see Appendix B), applied to the Electron Localization Function (ELF, see Appendix A) [9]. This method has been applied successfully to proton transfer mechanism [10,11] as well as isomerization reaction [12]. The latter approach focuses on the evolution of chemical properties by assuming an isomorphism between chemical structures and the molecular graph defined in Appendix C. 

These dendrimers are therefore optimal candidates as charge storing devices because of the made-to-order synthetic control of the reversible exchange (storage and release) of a controlled number of electrons at a certain potential. It is worth noting that the electrochemical data offer also a fingerprint of the chemical and topological structure of the dendrimers. 

Graph theory is largely applied to the characterization of chemical structures, as well as to structure-property and structure-activity correlations, by means of so-called topological indices. These are numerical quantities based on various invariants or characteristics of molecular graphs. 

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