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Chemical Descriptors (chemical + descriptor)

Distribution by Scientific Domains
Chemistry100%

Selected Abstracts

Disproving a Silicon Analog of an Alkyne with the Aid of Topological Analyses of the Electronic Structure and Ab Initio Molecular Dynamics Calculations

CHEMPHYSCHEM, Issue 9 2005
Carlo A. Pignedoli Dr.
Abstract A silicon compound has recently been synthesized that was claimed to exhibit the first realization of a silicon,silicon triple bond. We debate this classification on the basis of a thorough investigation of the nature of the chemical bond, using the rigorous topological analysis of the electron density as developed in Bader's atoms-in-molecules theory, that of the electron localization function and the related orbital-independent definitions of the bond order. Our results refer both to the ground-state geometry and to nonequilibrium configurations, which are accessed by the system in a room-temperature ab initio molecular dynamics simulation. We also use the reciprocal compliance force constant as an independent chemical descriptor. All the above procedures are in agreement and do not support the classification of the silicon,silicon central bond as triple. The characterization which consistently emerges from the present study is one in which two electron pairs participate in the bonding and the other pair belongs mainly to nonbonding regions. [source]

Estimation of Aqueous-Phase Reaction Rate Constants of Hydroxyl Radical with Phenols, Alkanes and Alcohols

MOLECULAR INFORMATICS, Issue 11-12 2009
Ya-nan Wang
Abstract A quantitative structure activity relationship (QSAR) model was developed for the aqueous-phase hydroxyl radical reaction rate constants (kOH) employing quantum chemical descriptors and multiple linear regressions (MLR). The QSAR development followed the OECD guidelines, with special attention to validation, applicability domain (AD) and mechanistic interpretation. The established model yielded satisfactory performance: the correlation coefficient square (R2) was 0.905, the root mean squared error (RMSE) was 0.139, the leave-many-out cross-validated QLMO2 was 0.806, and the external validated QEXT2 was 0.922 log units. The AD of the model covering compounds of phenols, alkanes and alcohols, was analyzed by Williams plot. The main molecular structural factors governing kOH are the energy of the highest occupied molecular orbital (EHOMO), average net atomic charges on hydrogen atoms (), molecular surface area (MSA) and dipole moment (,). It was concluded that kOH increased with increasing EHOMO and MSA, while decreased with increasing and ,. [source]

An Electrophilicity Based Analysis of Toxicity of Aromatic Compounds Towards Tetrahymena Pyriformis

MOLECULAR INFORMATICS, Issue 2 2006
R. Roy
Abstract Electrophilicity index is one of the important quantum chemical descriptors in describing toxicity or biological activities of the diverse classes of chemicals to bio-systems in the context of development of Quantitative Structure Activity Relationship (QSAR). In this study a large number of selected 174 aromatic compounds containing phenols, nitrobenzenes and benzonitriles are chosen as the training set to verify their toxic potency to Tetrahymena pyriformis in the light of electrophilicity. A systematic analysis has been made to find out the electron donation/acceptance nature of these model compounds by comparing their electronegativity values with those of the NA bases/DNA base pairs. The training sets are classified into two groups, viz., the electron donor group comprising 97 phenol derivatives and the electron acceptor group consisting of 77 nitrobenzenes and benzonitriles grouped together. Regression analysis in terms of correlation coefficient (), variance adjusted to degrees of freedom () and variance of leave-one-out cross-validation () has been made for both the electron donor and acceptor aromatic groups to predict the toxicity values of these model compounds to Tetrahymena pyriformis. It is heartening to note that the global and local electrophilicity indices along with the total Hartree-Fock energy can explain more than 80% of cross-validation variance of data of those aromatic molecules. [source]

Quantitative Structure-retention Relationship for Gas Chromatography of Polychlorinated Naphthalenes by Ab initio Quantummechanical Calculations and a Cl Substitution Position Method

MOLECULAR INFORMATICS, Issue 1 2006
Zhi-Cai Zhai
Abstract Three quantitative structure-retention relationship (QSRR) models have been developed for gas chromatographic relative retention indices (RIs) of polychlorinated naphthalene (PCN) congeners. With computation at HF/6-31G* and B3LYP/6-31G* levels in Gaussian98 program, the structural parameters of PCNs were obtained and used as chemical descriptors to correlate with their gas chromatographic RIs by multiple linear regression analysis, resulting in model,1 and model,2. The squared correlation coefficients (r2) of the first two models are 0.9814 and 0.9957, and the cross-validation correlation coefficients (q2) are 0.9771 and 0.9948, respectively. On the other hand, the third model, model,3, was developed using the relative position of chlorine substitution as molecular descriptor, and its multiple squared correlation coefficient is r2,=,0.9967 and q2,=,0.9959, suggesting model,3 is practical and especially has a optimum predictive power. [source]

Universal prediction of intramolecular hydrogen bonds in organic crystals

ACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2010
Peter T. A. Galek
A complete exploration of intramolecular hydrogen bonds (IHBs) has been undertaken using a combination of statistical analyses of the Cambridge Structural Database and computation of ab initio interaction energies for prototypical hydrogen-bonded fragments. Notable correlations have been revealed between computed energies, hydrogen-bond geometries, donor and acceptor chemistry, and frequencies of occurrence. Significantly, we find that 95% of all observed IHBs correspond to the five-, six- or seven-membered rings. Our method to predict a propensity for hydrogen-bond occurrence in a crystal has been adapted for such IHBs, applying topological and chemical descriptors derived from our findings. In contrast to intermolecular hydrogen bonding, it is found that IHBs can be predicted across the complete chemical landscape from a single optimized probability model, which is presented. Predictivity of 85% has been obtained for generic organic structures, which can exceed 90% for discrete classes of IHB. [source]

Molecular Structure and QSAR Study on Antispasmodic Activity of some Xanthoxyline Derivatives

ARCHIV DER PHARMAZIE, Issue 5 2006
Rodrigo dos Santos
Abstract Semi-empirical molecular orbital calculations at AM1 level were done with the aim to investigate the structure-activity relationships of antispasmodic activities of ten 2-(X-benzyloxy)-4,6-dimethoxyacetophenones with X = H, 4,-F, 4,-NO2, 4,-CH3, 4,-Cl, 3,,4,-(CH3)2, 4,-OCH3, 4,-Br, 4,-OCH2C6H5, and 4,-C(CH3)3, against acetylcholine-induced contraction of the guinea pig ileum. The most significant quantum chemical descriptors for this series of compounds were the net atomic charges, nucleophilic and electrophilic frontier electron density, HOMO and LUMO orbitals, and reactivity indices. While no significant correlations were found employing molecular parameters such as heat of formation, dipole moment, molecular polarizability, and so on, good correlations were obtained using the reactivity indices of HOMO and LUMO orbitals at specific atoms of the molecules. These results indicate that the spatial distribution of HOMO and LUMO orbitals over these specific atoms play an important role for an increase of biological activity. [source]