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Omelchenko I.V.,Ukrainian Academy of Sciences | Shishkin O.V.,Ukrainian Academy of Sciences | Shishkin O.V.,University of Kharkiv | Gorb L.,Badger Technical Services LLC | And 3 more authors.
Structural Chemistry | Year: 2012

Geometrical parameters, aromaticity, and conformational flexibility of the set of polysubstituted benzenes with different number and position of nitro and amino groups were calculated at the MP2/cc-pvdz level of theory. The key factor for structural and energetic changes has been identified. This is related to the presence of nitro and amino groups in vicinal positions that forms strong intramolecular resonance-assisted hydrogen bonds with a binding energy of 7-14 kcal/mol. Increasing number of such bonds facilitates a cooperative effect, inducing notable changes in molecular geometry (particularly increasing bond alternation within H 2N-C-C-NO 2 fragment and planarization of amino group), drastic increasing of conformational flexibility and decreasing of aromaticity. In spite of well-known π-electron effects of nitro and amino substituents, influence of their push-pull interaction through aromatic moiety is negligible compared to the effect of the hydrogen bonding. That results in great difference of the ortho-isomers as compared to meta-and para-isomers. © 2012 Springer Science+Business Media, LLC. Source

Yang Y.,University of Southern Mississippi | Maxwell A.,University of Southern Mississippi | Zhang X.,Nanjing University | Wang N.,University of Southern Mississippi | And 3 more authors.
BMC Bioinformatics | Year: 2013

Background: Pathway alterations reflected as changes in gene expression regulation and gene interaction can result from cellular exposure to toxicants. Such information is often used to elucidate toxicological modes of action. From a risk assessment perspective, alterations in biological pathways are a rich resource for setting toxicant thresholds, which may be more sensitive and mechanism-informed than traditional toxicity endpoints. Here we developed a novel differential networks (DNs) approach to connect pathway perturbation with toxicity threshold setting. Methods: Our DNs approach consists of 6 steps: time-series gene expression data collection, identification of altered genes, gene interaction network reconstruction, differential edge inference, mapping of genes with differential edges to pathways, and establishment of causal relationships between chemical concentration and perturbed pathways. A one-sample Gaussian process model and a linear regression model were used to identify genes that exhibited significant profile changes across an entire time course and between treatments, respectively. Interaction networks of differentially expressed (DE) genes were reconstructed for different treatments using a state space model and then compared to infer differential edges/interactions. DE genes possessing differential edges were mapped to biological pathways in databases such as KEGG pathways. Results: Using the DNs approach, we analyzed a time-series Escherichia coli live cell gene expression dataset consisting of 4 treatments (control, 10, 100, 1000 mg/L naphthenic acids, NAs) and 18 time points. Through comparison of reconstructed networks and construction of differential networks, 80 genes were identified as DE genes with a significant number of differential edges, and 22 KEGG pathways were altered in a concentration-dependent manner. Some of these pathways were perturbed to a degree as high as 70% even at the lowest exposure concentration, implying a high sensitivity of our DNs approach. Conclusions: Findings from this proof-of-concept study suggest that our approach has a great potential in providing a novel and sensitive tool for threshold setting in chemical risk assessment. In future work, we plan to analyze more time-series datasets with a full spectrum of concentrations and sufficient replications per treatment. The pathway alteration-derived thresholds will also be compared with those derived from apical endpoints such as cell growth rate. © 2013 Yang et al; licensee BioMed Central Ltd. Source

Tsendra O.,Jackson State University | Tsendra O.,Ukrainian Academy of Sciences | Scott A.M.,U.S. Army | Gorb L.,Badger Technical Services LLC | And 6 more authors.
Journal of Physical Chemistry C | Year: 2014

A cluster approach extended to the ONIOM methodology has been applied using several density functionals and Møller-Plesset perturbation theory (MP2) to simulate the adsorption of selected nitrogen-containing compounds [NCCs, 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAN), and 3-nitro-1,2,4-triazole-5-one (NTO)] on the hydroxyated (100) surface of α-quartz. The structural properties were calculated using the M06-2X functional and 6-31G(d,p) basis set. The M06-2X-D3, PBE-D3, and MP2 methods were used to calculate the adsorption energies. Results have been compared with the data from other studies of adsorption of compounds of similar nature on silica. Effect of deformation of the silica surface and adsorbates on the binding energy values was also studied. The atoms in molecules (AIM) analysis was employed to characterize the adsorbate-adsorbent binding and to calculate the bond energies. The silica surface shows different sorption affinity toward the chemicals considered depending on their electronic structure. All target NCCs are physisorbed on the modeled silica surface. Adsorption occurs due to the formation of multiple hydrogen bonds between the functional groups of NCCs and surface silanol groups. Parallel orientation of NCCs interacting with the silica surface was found to be favorable when compared with perpendicularly oriented NCCs. NTO was found to be the most strongly adsorbed on the silica surface among all of the considered compounds. Dispersion correction was shown to play an important role in the DFT calculations of the adsorption energies of silica-NCC systems. © 2014 American Chemical Society. Source

Hill F.C.,U.S. Army | Sviatenko L.K.,Jackson State University | Sviatenko L.K.,Kirovohrad State Pedagogical University | Gorb L.,Badger Technical Services LLC | And 5 more authors.
Chemosphere | Year: 2012

The nitroaromatic compounds 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT) and 2,4-dinitroanisole (DNAN) are potential environmental contaminants and their transformations under a variety of environmental conditions are consequently of great interest. One possible method to safely degrade these nitrocompounds is alkaline hydrolysis. A mechanism of the initial stages of this reaction was investigated computationally. Simulations of UV-VIS and NMR spectra for this mechanism were also produced. The results obtained were compared to available experimental data on the alkaline hydrolysis of TNT and suggest that the formation of Meisenheimer complexes and an anion of TNT are potential first-step intermediates in the reaction path. As the reaction proceeds, computational results indicate that polynegative complexes dominate the degradation pathway, followed by cycles of carbon chain opening and breaking. A second possible pathway was identified that leads to polymeric products through Janovsky complex formation. Results from this study indicate that the order of increasing resistance to alkaline hydrolysis is TNT, DNT and DNAN. © 2012 Elsevier Ltd. Source

Scott A.M.,U.S. Army | Burns E.A.,Badger Technical Services LLC | Hill F.C.,U.S. Army
Journal of Molecular Modeling | Year: 2014

The adsorption of nitrogen-containing compounds (NCCs) including 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAN), and 3-nitro-1,2,4-triazol-5-one (NTO) on kaolinite surfaces was investigated. The M06-2X and M06-2X-D3 density functionals were applied with the cluster approximation. Several different positions of NCCs relative to the adsorption sites of kaolinite were examined, including NCCs in perpendicular and parallel orientation toward both surface models of kaolinite. The binding between the target molecules and kaolinite surfaces was analyzed and bond energies were calculated applying the atoms in molecules (AIM) method. All NCCs were found to prefer a parallel orientation toward both kaolinite surfaces, and were bound more strongly to the octahedral than to the tetrahedral site. TNT exhibited the strongest interaction with the octahedral surface and DNAN with the tetrahedral surface of kaolinite. Hydrogen bonding was shown to be the dominant non-covalent interaction for NCCs interacting with the octahedral surface of kaolinite with a small stabilizing effect of dispersion interactions. In the case of adsorption on the tetrahedral surface, kaolonite-NCC binding was shown to be governed by the balance between hydrogen bonds and dispersion forces. The presence of water as a solvent leads to a significant decrease in the adsorption strength for all studied NCCs interacting with both kaolinite surfaces. © Springer-Verlag 2014. Source

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