Graph Theoretical Similarity Approach To Compare Molecular Electrostatic Potentials

Characterization of chemical libraries is an essential task in everyday chemoinformatics practice. This study describes some potential uses of network visualization and analysis methods to identify distinguished members of compound libraries. Molecules were ordered into networks by their structural similarity defined by molecular fingerprints. Various properties of such networks were examined. It was shown, that the correlation methods used to calculate the similarity between two structures radically determined the topology of networks. From the same set of molecules, the Russel-Rao and the Baroni-Urbani methods created sparser and denser networks, respectively, than using the Tanimoto method. Central nodes, corresponding to central compounds in the libraries, were determined for some example data sets. It was shown by the case of adenosine A1, A2, and dual antagonists that the methods used to identify central nodes could be divided into two groups: (1) centrality methods, exemplified by the centroid centrality, which could pick up structures that were the most similar to the largest number of other molecules and (2) group, exemplified by betweenness centrality, that could identify molecules that had intermediate structures between some homogeneous subsets of the library. The latter method gave significantly higher ranks to dual adenosine antagonists, hinting the suitability of this measure to identify molecules with multiple activities. Some practical applications of the method for clustering of and sample selection from chemical libraries are presented. In the frame of the study, a Jchem plug-in has been developed to the Cytoscape network visualization software, which makes the visual observation of molecular networks more convenient. The plug-in is included in the Supporting Information of the article for free usage.

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“…33,34 In the current study however, we applied similar fingerprints as the introduced work; thus, we think their findings are relevant.…”

Section: Effect Of Correlation Coefficients On the Topology Of Molecumentioning

confidence: 93%

Finding Key Members in Compound Libraries by Analyzing Networks of Molecules Assembled by Structural Similarity

Lepp

Huang

Okada

2009

J. Chem. Inf. Model.

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“…It is known that MEP and molecular electric field reveal features of electron density distribution as sensitive properties and can be used to predict chemical reactivity qualitatively [43][44][45][46][47][48][49]. Chemical hardness (η), defined as LUMO energy minus HOMO energy [50], was calculated for all the PAHs studied here.…”

Section: Methods Of Calculationsmentioning

confidence: 99%

Lowest Π–Π* electronic transitions in linear and two-dimensional polycyclic aromatic hydrocarbons: enhanced electron density edge effect

Yadav¹,

Mishra²

2013

Molecular Physics

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Polycyclic aromatic hydrocarbons (PAHs) form an important class of molecules as they are ubiquitous, pollute air and cause severe health problems. Lowest vertical π -π * singlet-singlet or triplet-triplet excitation energies and corresponding oscillator strengths were studied for several linear and two-dimensional PAHs employing time-dependent density functional theory. Excited-state electron density, molecular electrostatic potential (MEP) and spin density distributions in the PAHs, along with ground-state chemical hardness, were also studied. It has been found that, generally, excitation energies and oscillator strengths decrease with increase in PAH size, and excitation energies and chemical hardness are strongly linearly correlated. Enhanced electron density edge effect, which was found to occur in the ground states of the molecules, continues to hold in their excited states also. A strong similarity between the ground and π -π * excited-state MEP maps suggests that σ electrons are the main contributors to the enhanced electron density at the edges. Due to their strong electronic absorption transitions in the visible and infrared regions, the PAHs can be used for harnessing solar energy efficiently.

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“…The electrostatic potential is a powerful tool that has provided insights into molecular properties of small molecules and intermolecular association as well as action of drug molecules and their analogs (Murray et al, 1991;Politzer et al, 1985;Weiner et al, 1982;Marin et al, 2008).…”

Section: Molecular Electrostatic Potential Analysismentioning

confidence: 99%

Synthesis, X-ray structure and antiproliferative activity of 3-benzylthio-4-propargylselenoquinoline

et al. 2009

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Synthesis, antiproliferative activity and the X-ray single-crystal structure of the 3-benzylthio-4-propargylselenoquinoline are described. The title compound belongs to the group of the acetylenic derivatives of thioquinolines, which have been intensively investigated as a source of new anticancer agents. The comparative study regarding the X-ray structure, the molecular electrostatic potential analysis, and structure-activity relationship for the title compound and the 3-methylthio-4-propargylthioquinoline and 3-methylthio-4-propargylselenoquinoline are presented.

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Graph Theoretical Similarity Approach To Compare Molecular Electrostatic Potentials

Cited by 34 publications

References 71 publications

Finding Key Members in Compound Libraries by Analyzing Networks of Molecules Assembled by Structural Similarity

Finding Key Members in Compound Libraries by Analyzing Networks of Molecules Assembled by Structural Similarity

Lowest Π–Π* electronic transitions in linear and two-dimensional polycyclic aromatic hydrocarbons: enhanced electron density edge effect

Synthesis, X-ray structure and antiproliferative activity of 3-benzylthio-4-propargylselenoquinoline

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