Molecular Graph Theory: From Adjacency Information to Colored Topology by Chemical Reactivity

Tudoran, Marina A.; Putz, Mihai V.

doi:10.2174/1385272819666141216232941

Cited by 13 publications

(5 citation statements)

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“…The Kier and Hall [ 31 , 32 ] molecular connectivity indices have been recently studied by Estrada in terms of the Relative Bond Accessibility Area (RBA), C ij , which is expressed in square Randics ( R 2 ) [ 33 , 34 ]. The reactivity of an atom is related with its accessibility, and the accessibility can by quantified from topological features of the molecular structure that contains this atom [ 35 , 36 ].…”

Section: Structural and Physicochemical Interpretation Of Gdismentioning

confidence: 99%

Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

Martínez-Santiago

Marrero-Ponce

Barigye

et al. 2016

IJMS

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This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms.

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Section: Structural and Physicochemical Interpretation Of Gdismentioning

confidence: 99%

Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

Martínez-Santiago

Marrero-Ponce

Barigye

et al. 2016

IJMS

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“…While one group considered that the topology should be, strictly speaking, enrolled in the field of the mathematical application domain (e.g., analysis of functions in the Cartesian space or momentum, construction of Hamiltonians that use only atomic connectivity's as input (Huckel-like), others stated that it could be constituted as an autonomous field that might provide new theoretical basis for future development of chemistry [72][73][74]. Nevertheless, it is notable to note that many of them mentioned the field of drug design as one of the most interesting for future applications.…”

Section: New Trends In Qsar: Novel Topological Descriptorsmentioning

confidence: 99%

“…The models showed a good predictive power as compared with other 0 --3D indexes used by other researchers on the same properties and data sets. About the physicochemical meaning of the novel indices, it was investigated by predicting NMR parameters of a series of ethers and carbonyls, thereby deducing that the new descriptors encode electronic, topological and steric information [73]. As a fundamental conclusion, it can be established that the novel indices encode important structural information so that more interpretable and robust mathematical models can be constructed and used in QSAR and drug design studies.…”

Section: New Trends In Qsar: Novel Topological Descriptorsmentioning

confidence: 99%

Latest advances in molecular topology applications for drug discovery

Zanni

Gálvez-Llompart

García-Domènech

et al. 2015

Expert Opinion on Drug Discovery

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Recent years have witnessed a remarkable rise in QSAR methods based on MT and its application to drug design. New methodologies have been introduced in the area such as QSAR multi-target, Markov networks or perturbation methods. Moreover, novel topological indices, such as Bourgas' descriptors and other new concepts as the derivative of a graph or cliques capable to distinguish between conformers, have also been introduced. New drugs have also been discovered, including anticonvulsants, anineoplastics, antimalarials or antiallergics, just to name a few. In the authors' opinion, MT and QSAR have moved from an attractive possibility to representing a foundation stone in the process of drug discovery.

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“…It is extensively used in the structural analysis of chemical compounds, where vertices represent atoms and edges represent chemical bonds, allowing chemists to predict molecular properties and behaviors [1,2]. Additionally, graph theory aids in understanding and predicting chemical reaction pathways by modeling reaction networks and studying kinetics and mechanisms [3,4]. It also plays a crucial role in Piotr Wawrzyniak and Piotr Formanowicz have contributed equally to this work.…”

Section: Introductionmentioning

confidence: 99%

Graph realization of sets of integers

Wawrzyniak,

Formanowicz

2024

J Math Chem

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Graph theory is used in many areas of chemical sciences, especially in molecular chemistry. It is particularly useful in the structural analysis of chemical compounds and in modeling chemical reactions. One of its applications concerns determining the structural formula of a chemical compound. This can be modeled as a variant of the well-known graph realization problem. In the classical version of the problem, a sequence of natural numbers is given, and the question is whether there exists a graph in which the vertices have degrees equal to the given numbers. In the variant considered in this paper, instead of a sequence of natural numbers, a sequence of sets of natural numbers is given, and the question is whether there exists a multigraph such that each of its vertices has a degree equal to a number from one of the sets. This variant of the graph realization problem matches the nature of the problem of determining the structural formula of a chemical compound better than other variants considered in the literature. We propose a polynomial time exact algorithm solving this variant of the problem.

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Molecular Graph Theory: From Adjacency Information to Colored Topology by Chemical Reactivity

Cited by 13 publications

References 0 publications

Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

Latest advances in molecular topology applications for drug discovery

Graph realization of sets of integers

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