Browsing by Author "Pérez-Giménez, Facundo"

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    Discrete Derivatives for Atom-Pairs as a Novel Graph Theoretical Invariant for Generating New Molecular Descriptors: Orthogonality, Interpretation and QSARs/ QSPRs on Benchmark Databases
    (Molecular Informatics, 2014) Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J.; Torrens, Francisco; Pérez-Giménez, Facundo
    This report presents a new mathematical method based on the concept of the derivative of a molecular graph (G) with respect to a given event (S) to codify chemical structure information. The derivate over each pair of atoms in the molecule is defined as ∂G/∂S(vi , vj)=(fi−2fij+fj)/fij, where fi (or fj) and fij are the individual frequency of atom i (or j) and the reciprocal frequency of the atoms i and j, respectively. These frequencies characterize the participation intensity of atom pairs in S. Here, the event space is composed of molecular sub-graphs which participate in the formation of the G skeleton that could be complete (representing all possible connected sub-graphs) or comprised of sub-graphs of certain orders or types or combinations of these. The atom level graph derivative index, Δi, is expressed as a linear combination of all atom pair derivatives that include the atomic nuclei i. Global [total or local (group or atom-type)] indices are obtained by applying the so called invariants over a vector of Δi values. The novel MDs are validated using a data set of 28 alkyl-alcohols and other benchmark data sets proposed by the International Academy of Mathematical Chemistry. Also, the boiling point for the alcohols, the adrenergic blocking activity of N,N-dimethyl-2-halo-phenethylamines and physicochemical properties of polychlorinated biphenyls and octanes are modeled. These models exhibit satisfactory predictive power compared with other 0–3D indices implemented successfully by other researchers. In addition, tendencies of the proposed indices are investigated using examples of various types of molecular structures, including chain-lengthening, branching, heteroatoms-content, and multiple bonds. On the other hand, the relation of atom-based derivative indices with 17O NMR of a series of ethers and carbonyls reflects that the new MDs encode electronic, topological and steric information. Linear independence between the graph derivative indices and other 0-3D MDs is demonstrated by using principal component analysis on a dataset of 41 heterogeneous molecules. It is concluded that the graph derivative indices are independent indices containing important structural information to be used in QSPR/QSAR and drug design studies, and permit obtaining easier, more interpretable and robust mathematical models than the majority of those reported in the literature.
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    Extended GT-STAF Information Indices based on Markov Approximation Models
    (Chemical Physics Letters, 2013) Barigye, Stephen J.; Marrero-Ponce, Yovani; Alfonso-Reguera, Vitalio; Pérez-Giménez, Facundo
    A series of novel information theory-based molecular parameters derived from the insight of a molecular structure as a chemical communication system were recently presented and usefully employed in QSAR/QSPRs (J. Comp. Chem, 2013, 34, 259; SAR and QSAR in Environ. Res. 2013, 24). This approach permitted the application of Shannon’s source and channel coding entropic measures to a chemical information source comprised of molecular ‘fragments’, using the zero-order Markov approximation model (atom-based approach). This report covers the theoretical aspects of the extensions of this approach to higher-order models, introducing the first, second and generalized-order Markov approximation models.
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    Structural and Physicochemical Interpretation of GT-STAF Information Theory-Based Indices
    (Bulletin of the Chemical Society of Japan, 2015) Barigye, Stephen J.; Marrero-Ponce, Yovani; Zupan, Jure; Pérez-Giménez, Facundo
    The underlying structural and physicochemical interpretation of the recently defined information indices (denominated as GT-STAF indices) is examined, with the aim of gaining greater insight on the codified chemical information. It is found that these indices are related with molecular symmetry in the context of the defined molecular “fragment” model. Moreover, these indices are sensitive to structural differences, demonstrating gradual changes consistent with modifications in the molecular structure. A principal component analysis reveals that the GT-STAF indices generally codify conformational, physicochemical, and thermodynamic properties of amino acids. A study with aniline derivatives demonstrates that the GT-STAF indices do not directly correlate with the ionization constant (pKa); but rather require multivariate contributions to yield correlations comparable with univariate models for quantum chemical parameters, suggesting that the former codify some other form of electronic information orthogonal to the latter. Finally, an evaluation of atomic contributions to the molecular hydrophobicity in furylethylenes demonstrates that the GT-STAF approach generally approximates to chemical properties quite well.
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    Trends in Information Theory-based Chemical Structure Codification
    (Molecular diversity, 2014) Barigye, Stephen J.; Marrero-Ponce, Yovani; Pérez-Giménez, Facundo; Bonchev, Danail
    This report offers a chronological review of the most relevant applications of information theory in the codification of chemical structure information, through the so-called information indices. Basically, these are derived from the analysis of the statistical patterns of molecular structure representations, which include primitive global chemical formulae, chemical graphs, or matrix representations. Finally, new approaches that attempt to go “back to the roots” of information theory, in order to integrate other information-theoretic measures in chemical structure coding are discussed.