Search results for "Molecular graph"
showing 7 items of 7 documents
Generalized Molecular Descriptors Derived From Event-Based Discrete Derivative.
2016
In the present study, a generalized approach for molecular structure characterization is introduced, based on the relation frequency matrix (F) representation of the molecular graph and the subsequent calculation of the corresponding discrete derivative (finite difference) over a pair of elements (atoms). In earlier publications (22- 24), an unique event, named connected subgraphs, (based on the Kier-Hall's subgraphs) was systematically employed for the computation of the matrix F. The present report is a generalization of this notion, in which eleven additional events are introduced, classified in three categories, namely, topological (terminal paths, vertex path incidence, quantum subgrap…
Dynamic Molecular Graphs: “Hopping” Structures
2013
This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscen…
Discrete Derivatives for Atom-Pairs as a Novel Graph-Theoretical Invariant for Generating New Molecular Descriptors: Orthogonality, Interpretation an…
2013
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 comp…
O-Doped Nanographenes: A Pyrano/Pyrylium Route Towards Semiconducting Cationic Mixed-Valence Complexes
2020
Herein we report an efficient synthesis to prepare O‐doped nanographenes, which derive from the longitudinally and latitudinally p‐extension of pyrene. The derivatives are highly fluorescent and feature low‐oxidation potentials. Exploiting electrooxidation, crystals of cationic mixed valence (MV) complexes were grown in which the organic salts organize into face‐to‐face p‐ p stacks, a favorable solid‐state arrangement for organic electronics. Variable‐temperature EPR measurements and relaxation studies suggest a strong electron delocalization along the longitudinal axis of the columnar p‐stacking architectures. Electric measurements of single crystals of the MV salts exhibited a semiconduct…
Improved AMYR program: an algorithm for the theoretical simulation of molecular associations, including geometrical and topological characterization …
1991
Program AMYR, originally written by S. Fraga (University of Alberta, Canada), allows for the calculation of molecular associations using a pair-wise atom-atom potential. The interaction energy is evaluated through a 1/R expansion. Our improved version includes a dispersion energy term in the potential corrected by damping functions, the possibility of carrying out energy minimizations through variable metric methods, as well as the optional calculation of geometrical and topological indices. Program AMYR has been adapted also for high-performance computing and vectorization. An interactive version of the program carries out real-time molecular graphics showing simultaneously the energy prof…
Bond-extended stochastic and nonstochastic bilinear indices. I. QSPR/QSAR applications to the description of properties/activities of small-medium si…
2010
Bond-extended stochastic and nonstochastic bilinear indices are introduced in this article as novel bond-level molecular descriptors (MDs). These novel totals (whole-molecule) MDs are based on bilinear maps (forms) similar to use defined in linear algebra. The proposed nonstochastic indices try to match molecular structure provided by the molecular topology by using the kth Edge(Bond)-Adjacency Matrix (Ek, designed here as a nonstochastic E matrix). The stochastic parameters are computed by using the kth stochastic edge-adjacency matrix, ESk, as matrix operators of bilinear transformations. This new edge (bond)-adjacency relationship can be obtained directly from Ek and can be considered li…
Relations frequency hypermatrices in mutual, conditional and joint entropy-based information indices.
2012
Graph-theoretic matrix representations constitute the most popular and significant source of topological molecular descriptors (MDs). Recently, we have introduced a novel matrix representation, named the duplex relations frequency matrix, F, derived from the generalization of an incidence matrix whose row entries are connected subgraphs of a given molecular graph G. Using this matrix, a series of information indices (IFIs) were proposed. In this report, an extension of F is presented, introducing for the first time the concept of a hypermatrix in graph-theoretic chemistry. The hypermatrix representation explores the n-tuple participation frequencies of vertices in a set of connected subgrap…