The role of electronic properties to the mutagenic activity of 1,6- and 3,6-dinitrobenzo[a]pyrene isomers

Combined 4D-QSAR and target-based approaches for the determination of bioactive Isatin derivatives

The hybrid method of the Electron-Conformational Genetic Algorithm (EC-GA) was used to determine the pharmacophore groups and to estimate anticancer activity in isatin derivatives using a robust 4D-QSAR software (EMRE). To build the model, each compound is represented by a set of conformers rather than a single conformation. The Electron Conformational Matrix of Congruity (ECMC) is composed via EMRE software. Electron Conformational Submatrix of Activity (ECSA) was calculated by the comparison of these matrices. Genetic algorithm was used to select important variables to predict theoretical activity. The model with the best seven parameters produced satisfactory results. The E statistics technique was applied to the generated EC-GA model to evaluate the individual contribution of each of the descriptors on biological activity. The r² and q² values of the training set compounds were found to be 0.95 and 0.93, respectively. Because no previous 4D-QSAR studies on isatin derivatives have been conducted, this study is important in the development of new isatin derivatives. In this study, 27 isatin derivatives whose activities were estimated using the hybrid EC-GA method were also investigated through molecular docking and molecular dynamics simulations for their BCL-2 inhibitory activity.

A novel hybrid method named electron conformational genetic algorithm as a 4D QSAR investigation to calculate the biological activity of the tetrahydrodibenzazosines

To understand the structure-activity correlation of a group of tetrahydrodibenzazocines as inhibitors of 17β-hydroxysteroid dehydrogenase type 3, we have performed a combined genetic algorithm (GA) and four-dimensional quantitative structure-activity relationship (4D-QSAR) modeling study. The computed electronic and geometry structure descriptors were regulated as a matrix and named as electron-conformational matrix of contiguity (ECMC). A chemical property-based pharmacophore model was developed for series of tetrahydrodibenzazocines by EMRE software package. GA was employed to choose an optimal combination of parameters. A model has been developed for estimating anticancer activity quantitatively. All QSAR models were established with 40 compounds (training set), then they were considered for selective capability with additional nine compounds (test set). A statistically valid 4D-QSAR ( R training 2 = 0.856 , R test 2 = 0.851 and q² = 0.650) with good external set prediction was obtained.

Theoretical study of nitrodibenzofurans: A possible relationship between molecular properties and mutagenic activity

In this study we present a theoretical investigation of the molecular properties of nitrodibenzofurans (NDFs) and dinitrodibenzofurans (DNDFs) and their relation to mutagenic activity. Equilibrium geometries, relative energies, vertical ionization potentials (IP), vertical electron activities (EA), electronic dipole polarizabilities, and dipole moments of all NDFs and three DNDFs calculated by Density Functional Theory (DFT) methods are reported. The Ziegler/Rauk Energy Decomposition Analysis (EDA) is employed for a direct estimate of the variations of the orbital interaction and steric repulsion terms corresponding to the nitro group and the oxygen of the central ring of NDFs. The results indicate differences among NDF isomers for the cleavage of the related bonds and steric effects in the active site. The results show a good linear relationship between polarizability (<α>), anisotropy of polarizability (Δα), the summation of IR intensities (ΣIIR) and the summation of Raman activities (ΣARaman) over all 3N-6 vibrational modes and experimental mutagenic activities of NDF isomers in Salmonella typhimurium TA98 strain. The polarizability changes with respect to the νsNO+CN vibrational mode are in correlation with the mutagenic activities of NDFs and suggest that intermolecular interactions are favoured along this coordinate.

Two nitro derivatives of azabenzo[a]pyrene N-oxide: electronic properties and their relation to mutagenic activity

The equilibrium geometries, relative energies, IR and Raman spectra, vertical ionization potentials (IP), vertical electron affinities (EA), dipole moments (μ), electronic dipole polarizabilities (α), and molecular electrostatic potentials (MEP) of two species that show very high mutagenicity, 1-nitro-6-azabenzo[a]pyrene N-oxide (1-N-6-ABPO) and 3-nitro-6-azabenzo[a]pyrene N-oxide (3-N-6-ABPO), are investigated by means of Density Functional Theory (DFT) using B3LYP functional with different basis sets. The 3-N-6-ABPO isomer was estimated to be much more mutagenic in Salmonella typhimurium tester strain TA98 (396,000 revertants/nmol) than 1-N-6-ABPO (36100 revertants/nmol) (Fukuhara et al., 1992). The results show that for both isomers the structural, energetic, and vibrational properties are similar. The orientation of the nitro group with respect to the plane of the aromatic system as well as the nitroreduction and oxidation reaction and polarizability seem not be important for the determination of different mutagenic behavior of these isomers. However, the dipole moment of 3-N-6-ABPO is about 3 times that of 1-N-6-ABPO. The larger dipole moment and the different electronic charge distribution of 3-N-6-ABPO compared to 1-N-6-ABPO imply stronger electrostatic and inductive molecular interactions so that the active site of the enzyme involved in the mutagenic activation can more effectively bind 3-N-6-ABPO compared to 1-N-6-ABPO.

Theoretical study of the molecular properties of dimethylanthracenes as properties for the prediction of their biodegradation and mutagenicity

There is little information available on methyl derivatives of anthracene and their interaction with the enzymes of bacterial consortia that could be found in petroleum sludge. In this study a theoretical investigation of all dimethylanthracenes (DMA) isomers and their relation to biodegradation are presented. Equilibrium geometries, ionization potentials (IP), electronic affinities (EA), dipole moments and electronic dipole polarizabilities of DMA isomers calculated by Density Functional Theory (DFT) methods are reported. The calculated IP and EA values vary little along the series of isomers. The polarizability values (〈α〉, Δα, and αyy) increase on passing from meso,meso- and α,meso- to β,β-DMA isomers. The computed polarizability values of DMAs can be used as predictors in determining differences in biodegradation rates of DMAs. The summation over Raman activity ∑ARaman over 3N-6 vibrational modes is sensitive to the position of the methyl substituent. The ∑ARaman values of 1-methylanthracene (MA), 2-MA, 2,9-DMA and 9,10-DMA are consistent with observed mutagenic activities in Salmonella Typhimurium strains TA98 and TA100.

Prediction of mutagenic activity of nitrophenanthrene and nitroanthracene isomers by simulated IR and Raman spectra

This paper expands upon our original work on nitroanthracenes in (Alparone, A., Librando, V., 2012. Spectrochim. Acta A 89, 129-136) on the series of nitrophenanthrene isomers. Geometries, electric properties, IR and Raman spectra of 1-, 2-, 3-, 4- and 9-nitrophenanthrene (1-NP, 2-NP, 3-NP, 4-NP and 9-NP) were obtained and analyzed using Density Functional Theory calculations. The balance between steric and π-conjugative interactions determines the order of stability 4-NP<1-NP~9-NP<2-NP∼3-NP. IR and Raman spectral zones between 1000 and 1600 cm(-1) show intense bands noticeably affected by the position of the substituent, being potentially useful to discriminate and monitor the investigated isomers. Dipole moments, summations of IR intensity (ΣI(IR)) and Raman activity (ΣA(Raman)) over the 3N-6 vibrational modes are sensitive to the structure, increasing steadily from the non-planar to the planar isomers. Good linear relationships between the ΣI(IR) (r=0.90) and ΣA(Raman) (r=0.99) against the Salmonella typhimurium strain TA98 mutagenic activity of nitrophenanthrenes and isomeric nitroanthracenes are found. On the basis of the structural and vibrational properties, 4-NP seems to have not mutagenic activity, while the unknown TA98 mutagenic potency of 1-nitroanthracene is predicted to be between that of 9-NP and 3-NP. Calculated ΣI(IR) and ΣA(Raman) values could be used as molecular descriptors for QSARs applications of series of isomers.

The electronic properties of trimethylnaphthalenes as properties for the prediction of biodegradation rates: ab initio and DFT study

There is little information on trimethylnaphthalenes (TMNs) which are constituents of diesel fuel and bitumen emissions. In this study, a theoretical investigation of the electronic properties of all trimethylnaphthalene (TMN) isomers and their relation to biodegradation are presented. Equilibrium geometries, ionization potentials (IPs), electron affinities (EAs), dipole moments and electronic dipole polarizabilities of TMN isomers calculated by ab initio and Density Functional Theory (DFT) methods are reported. Polarizability and dipole moment computations have been performed in gas and in water solution using the polarizable continuum model (PCM). The results obtained show that the IP value varies little along the series of isomers while averaged static dipole polarizabilities (<α>) increase on passing from α,α,α-TMN to β,β,β-TMN isomers. This indicates that the binding affinity between TMNs and active site of bacterial enzymes is mainly determined by dispersive and inductive effects. Therefore, the computed polarizability values of TMNs can be used as predictors of the rates of biodegradation of TMNs.

IR and Raman spectra of nitroanthracene isomers: substitional effects based on density functional theory study

Structure, IR and Raman spectra of 1-, 2- and 9-nitroanthracene isomers (1-NA, 2-NA and 9-NA) were calculated and analyzed through density functional theory computations using the B3LYP functional with the 6-311+G** basis set. Steric and π-conjugative effects determine the characteristic ONCC dihedral angles, which vary from 0° (2-NA) to 28-29° (1-NA) and 59° (9-NA), influencing the relative order of stability along the series 9-NA<1-NA<2-NA. The spectral regions at wavenumber values>3000 cm(-1) and <1000 cm(-1) little depend on the substituent position. The Raman and IR intensity values of the characteristic symmetric nitro group stretching transition, appearing between 1310 and 1345 cm(-1), are rather sensitive to the position of the substituent, decreasing regularly on passing from the planar to the NO2-rotated isomers (9-NA<1-NA<2-NA). In the medium-energy spectral region (1000-1700 cm(-1)), the number and the relative position of the strongest Raman bands are of potential utility to discriminate the NA isomers. Structural and spectroscopic results suggest that the unknown mutagenic activity of 1-NA is expected to be between that of 9-NA and 2-NA.

Contrastive analysis of the Raman spectra of polychlorinated benzene: hexachlorobenzene and benzene

Detection of persistent pollutants such as polychlorinated benzene in environment in trace amounts is challenging, but important. It is more difficult to distinguish homologues and isomers of organic pollutantd when present in trace amounts because of their similar physical and chemical properties. In this work we simulate the Raman spectra of hexachlorobenzene and benzene, and figure out the vibration mode of each main peak. The effect on the Raman spectrum of changing substituents from H to Cl is analyzed to reveal the relations between the Raman spectra of homologues and isomers of polychlorinated benzene, which should be helpful for distinguishing one kind of polychlorinated benzene from its homologues and isomers by surface enhanced Raman scattering.

Quantitative bioactivity prediction and pharmacophore identification for benzotriazine derivatives using the electron conformational-genetic algorithm in QSAR

The electron conformational-genetic algorithm (EC-GA), a sophisticated hybrid approach combining the GA and EC methods, has been employed for a 4D-QSAR procedure to identify the pharmacophore for benzotriazines as sarcoma inhibitors and for quantitative prediction of activity. The calculated geometry and electronic structure parameters of every atom and bond of each molecule are arranged in a matrix described as the electron-conformational matrix of contiguity (ECMC). By comparing the ECMC of one of the most active compounds with other ECMCs we were able to obtain the features of the pharmacophore responsible for the activity, as submatrices of the template known as electron conformational submatrices of activity. The GA was used to select the most important descriptors and to predict the theoretical activity of training and test sets. The predictivity of the model was internally validated. The best QSAR model was selected, having r² = 0.9008, standard error = 0.0510 and cross-validated squared correlation coefficient, q² = 0.8192.