A graph theory method for determining the basis of homodesmic reactions for acyclic chemical compounds

Хурсан, С. Л.; Ismagilova, A. S.; Спивак, С. И.

doi:10.1134/s0012501617060033

Cited by 15 publications

(8 citation statements)

References 3 publications

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“…The molecular energetics of the substituted cyclopropanes was investigated using our original methodology based on the construction of the complete set of homodesmotic reactions for the compounds under study. The complete set of HDRs was constructed within the framework of the graph theory approach described in ref . It implies the approximation of the structure with a graph.…”

Section: Theoretical Methodssupporting

confidence: 61%

“…The use of complete sets of homodesmotic reactions has a number of indisputable advantages in the analysis of the molecular energetics of organic compounds. As previously noted, 12,13 diversified assessment of the thermochemical parameters of compounds increases the accuracy of calculating the enthalpies of formation, bond strengths, strain energies, etc. and allows identifying and filtering out unreliable data for reference compounds.…”

Section: ■ Conclusionmentioning

confidence: 98%

“…Their total number, disregarding the symmetry of the molecule, is 2 n − 1, where n is the number of decomposition operations with the adjacency matrix. We developed this concept as it demonstrated the effectiveness in the theoretical determination of the enthalpies of formation for the representative set of acyclic compounds 12 and the ring strain energies of 71 C-, N-, and O-containing cyclic structures. 13 In the latter case, we found that the primary thermochemical information (heat effects of the complete set of HDRs) is sufficient for efficiently separating RSE and SSE with the use of simple correlations.…”

Section: ■ Introductionmentioning

confidence: 99%

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Interplay of the Ring and Steric Strains in the Highly Substituted Cyclopropanes

Хурсан

Akhmetshina

2021

J. Phys. Chem. A

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Using the concept of a complete set of homodesmotic reactions for the analysis of molecular energetics of polysubstituted methyl- and fluorocyclopropanes allows assessing the strain energy SE of cyclopropanes, free from interfering effects, in full accordance with the IUPAC definition (“relative to a reference ... hypothetical ‘strainless’ structure”). The correct SE calculation requires quantifying nonvalence interactions in the products of formal homodesmotic reactions (HDRs) using a routine multiregression analysis. The complete HDR set provides the information necessary for the analysis, namely, the heat effects of HDRs calculated by the G4 composite method and the wide set of reference compounds with various combinations of nonvalence effects. We have found that the SE value for methylcyclopropanes lies in the range from 117.0 (1.1-dimethylcyclopropane) to 146.1 kJ/mol (hexamethylcyclopropane). It is the sum of the ring strain energy RSE = 117.9 ± 0.3 kJ mol, which does not depend on the number of methyl substituents, and the Pitzer strain energy of 4.4±0.1 kJ/mol per one contact (the standard deviation is shown as an error of determination). In the series of fluorocyclopropanes, SE varies from 137.9 (monosubstituted cyclopropane) to 260.0 kJ/mol (hexafluorocyclopropane) and well correlates with the ∑DBCP parameter deduced from the QTAIM analysis of the electron density of the compound, representing the total deviation of bond critical points from geometrical C–C bond lines of CC bonds. The ∑DBCP parameter characterizes the curvature of banana-like bonds in cyclopropanes.

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Section: Theoretical Methodssupporting

confidence: 61%

Section: ■ Conclusionmentioning

confidence: 98%

Section: ■ Introductionmentioning

confidence: 99%

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Interplay of the Ring and Steric Strains in the Highly Substituted Cyclopropanes

Хурсан

Akhmetshina

2021

J. Phys. Chem. A

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“…It may provide few illustrative examples of recent publications using the homodesmotic method for calculating the enthalpy characteristics of organic molecules and radicals [8][9][10][11][12][13][14][15][16], quantitative description of aromaticity [17][18][19], determination of strain energies in cyclic structures and compounds of a complex structure [20][21][22][23][24][25][26][27]. As with additive approaches, the homodesmotic method Molecules 2022, 27, 7814 2 of 15 is convenient for the algorithmization and application of computational technologies in thermochemical analysis [28][29][30][31][32][33].…”

Section: Introductionmentioning

confidence: 99%

Heat Capacity Estimation Using a Complete Set of Homodesmotic Reactions for Organic Compounds

Khursan

2022

Molecules

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Reliable information about isobaric heat capacities CP is necessary to determine the energies of organic compounds and chemical processes at an arbitrary temperature. In this work, the possibility of theoretical estimation of CP by the homodesmotic method is analyzed. Three cases of CP calculation applying the methodology of the complete set of homodesmotic reactions (CS HDRs) are considered: the gas- and liquid-phase CP of organic compounds of various classes at 298 K (the mean absolute value of reaction heat capacity, MA ΔCP = 1.44 and 2.83 J/mol·K for the gas and liquid phase, correspondingly); and the gas-phase CP of n-alkanes C2–C10 in the temperature range of 200–1500 K with an average error in calculating the heat capacity of 0.93 J/mol·K. In the latter case, the coefficients of the Shomate equation are determined for all n-alkanes that satisfy the homodesmoticity condition. New values of gas- and liquid-phase heat capacities are obtained for 41 compounds. The CS HDRs-based approach for estimating the CP of organic compounds is characterized by high accuracy, which is not inferior to that of the best CP-additive schemes and allows us to analyze the reproducibility of the calculation results and eliminate unreliable reference data.

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“…There is a great resemblance between a graph and structural formula, as depicted in Figure 1, in which a direct correlation among vertices and atoms, as well as edges and chemical bonds, is clearly perceived. Unfortunately, a critical drawback precludes a more generalized use of the graph theory in chemistry-the incapability to distinguish atoms or bonds [11][12][13][14][15][16][17][18][19][20][21][22]. The quantification of specific interactions among substructural fragments is crucial to infer any molecular property and, to do so, it is crucial to differentiate atoms and chemical bonds, as stated previously.…”

Section: Introductionmentioning

confidence: 99%

Chemical Graph Theory for Property Modeling in QSAR and QSPR—Charming QSAR & QSPR

et al. 2020

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Quantitative structure-activity relationship (QSAR) and Quantitative structure-property relationship (QSPR) are mathematical models for the prediction of the chemical, physical or biological properties of chemical compounds. Usually, they are based on structural (grounded on fragment contribution) or calculated (centered on QSAR three-dimensional (QSAR-3D) or chemical descriptors) parameters. Hereby, we describe a Graph Theory approach for generating and mining molecular fragments to be used in QSAR or QSPR modeling based exclusively on fragment contributions. Merging of Molecular Graph Theory, Simplified Molecular Input Line Entry Specification (SMILES) notation, and the connection table data allows a precise way to differentiate and count the molecular fragments. Machine learning strategies generated models with outstanding root mean square error (RMSE) and R2 values. We also present the software Charming QSAR & QSPR, written in Python, for the property prediction of chemical compounds while using this approach.

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A graph theory method for determining the basis of homodesmic reactions for acyclic chemical compounds

Cited by 15 publications

References 3 publications

Interplay of the Ring and Steric Strains in the Highly Substituted Cyclopropanes

Interplay of the Ring and Steric Strains in the Highly Substituted Cyclopropanes

Heat Capacity Estimation Using a Complete Set of Homodesmotic Reactions for Organic Compounds

Chemical Graph Theory for Property Modeling in QSAR and QSPR—Charming QSAR & QSPR

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