Search

The adsorption of Sarin (GB) and Soman (GD) on the edge tetrahedral fragments of clay minerals is studied at the B3LYP/6-31G(d) and MP2/6-31G(d) levels of theory. Several different orientations of Sarin and Soman on tetrahedral edge mineral surfaces are found to depend on the charge and a mineral cluster termination.

A study using the two level ONIOM (B3LLYP/6-31G(d,p):PM3) and ONIOM (B3LYP/6-31G(d,p):HF/3-21G) methodology together with cluster model approximation is conducted to determine the adsorption of sarin (GB) and soman (GD) on the octahedral surface of dicksite. It is reported that polarization occurs due to adsorption and changes in the geometric parameters of the adsorbed molecules and also forms an attractive contact between the GB, GD and the surface of the dickite.

The adsorption and decomposition of Sarin on the surface of magnesium oxide is studied theoretically using small and large models of the MgO cluster at the B3LYP/6-31G(d) and MP2/6-31G(d) levels of theory. The adsorption on the small fragment of MgO can lead to decomposition of Sarin so that the fluorine atom is removed from Sarin and transferred into the binding distance with the Mg atom of the surface.

Alkaline hydrolysis of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine), as one of the most promising methods for nitrocompound remediation, was investigated computationally at the PCM(Pauling)/M06-2X/6-311++G(d,p) level of theory. Computational simulation shows that RDX hydrolysis is a highly exothermic multistep process involving initial deprotonation and nitrite elimination, cycle cleavage, further transformation of cycle-opened intermediates to end products caused by a series of C–N bond ruptures, hydroxide attachments, and proton transfers. Computationally predicted products of RDX hydrolysis such as nitrite, nitrous oxide, formaldehyde, formate, and ammonia correspond to experimentally observed ones. Accounting of specific hydration of hydroxide is critical to create an accurate kinetic model for alkaline hydrolysis. Simulated kinetics of the hydrolysis are in good agreement with available experimental data. A period of one month is necessary for 99% RDX decomposition at pH 10. Computations predict significant increases of the reaction rate of hydrolysis at pH 11, pH 12, and pH 13. [ABSTRACT FROM AUTHOR]

Nitroaromatic compounds and the products of their degradation are toxic to bacteria, cells and animals. Various studies have been carried out to better understand the mechanism of toxicity of aromatic nitrocompounds and their relationship to humans and the environment. Recent data relate cytotoxicity of nitroaromatic compounds to their single- or two-electron enzymatic reduction. However, mechanisms of animal toxicity could be more complex. This work investigates the estimated reduction and oxidation potentials of 34 nitroaromatic compounds using quantum chemical approaches. All geometries were optimized with density functional theory (DFT) using the solvation model based on density (SMD) and polarizable continuum model (PCM) solvent model protocols. Quantitative structure–activity/property (QSAR/QSPR) models were developed using descriptors obtained from quantum chemical optimizations as well as the DRAGON software program. The QSAR/QSPR equations developed consist of two to four descriptors. Correlations have been identified between electron affinity (ELUMO) and hydrophobicity (logP). [ABSTRACT FROM PUBLISHER]

cis-2-Butene-1,4-dial represents a microsomal metabolite of furan, an industrially important chemical found in cigarette smoke, air pollution, and also in canned or jarred food. It is expected to be a human carcinogen. Aim. Investigation of an effect of cis-2-butene-1,4-dial on the 2'-deoxyguanosine which is a model of DNA site. Methods. Optimization of reaction species molecular structures, spectral parameters and Gibbs free energy calculations were performed using Gaussian09 program. Systems of differential equations for kinetics generation were solved using Mathcad15 program. Results. The predicted mechanism of the reaction of cis-2-butene-1,4- dial with 2'-deoxyguanosine consists of four-step process formation of four diastereomeric primary adducts and further base-mediated five-step transformation of the primary adducts to the secondary one. The reaction kinetics, which allows defining the concentration change of any reaction species was calculated. Conclusions. Under physiological conditions the interaction between cis-2-butene-1,4-dial and 2'-deoxyguanosine leads to the formation of a stable adduct which could be responsible for the furan genotoxicity. [ABSTRACT FROM AUTHOR]

The adsorption of benzene, polycyclic aromatic hydrocarbons(PAHs),and nitroaromatic compounds (NACs) on the carbonaceous surfaces fromthe gas phase and water solution was investigated. Several differentlevels of theory were applied, including DFT-, MP2-, and CCSD(T)-basedmethods, to find an approach that is computationally inexpensive andcan provide accurate thermodynamic parameters for studied adsorptionphenomena. The methods and techniques used (including cluster andperiodic approximations) were evaluated on the basis of comparisonwith available experimental data. The optimized structures of calculatedcomplexes are obtained, and the interaction energies and Gibbs freeenergies are predicted. Good agreement was revealed for the theoreticaland experimental adsorption energies of benzene and PAHs adsorbedon the carbon surfaces. The adsorption of benzene, PAHs, and NACson carbon is suggested to be effective from the gas phase for allstudied compounds and for PAHs and NACs also from water solution atroom temperature. [ABSTRACT FROM AUTHOR]

The Hierarchical Technology for Quantitative Structure-Activity Relationships (HiT QSAR) was applied to 95 diverse nitroaromatic compounds (including some widely known explosives) tested for their toxicity (50% inhibition growth concentration, IGC50) against the ciliate Tetrahymena pyriformis. The dataset was divided into subsets according to putative mechanisms of toxicity. The Classification and Regression Trees (CART) approach implemented within HiT QSAR has been used for prediction of mechanism of toxicity for new compounds. The resulting models were shown to have ∼80% accuracy for external datasets indicating that the mechanistic dataset division was sensible. The Partial Least Squares (PLS) statistical approach was then used to develop 2D QSAR models. Validated PLS models were explored to: (1) elucidate the effects of different substituents in nitroaromatic compounds on toxicity; (2) differentiate compounds by probable mechanisms of toxicity based on their structural descriptors; and (3) analyse the role of various physical-chemical factors responsible for compounds' toxicity. Models were interpreted in terms of molecular fragments promoting or interfering with toxicity. It was also shown that mutual influence of substituents in benzene ring plays the determining role in toxicity variation. Although chemical mechanism based models were statistically significant and externally predictive ( [image omitted] = 0.64 for the external set of 63 nitroaromatics identified after all calculations have been completed), they were also shown to have limited coverage (57% for modelling and 76% for external set). [ABSTRACT FROM AUTHOR]

The interactions between methyl tert-butyl ether (MTBE) and differently defected tetrahedral and octahedral fragments of clay minerals containing Si4+, Al3+, and Mg2+ central cations have been studied at the B3LYP and MP2 levels of theory in conjunction with the 6-31G(d) basis set. MTBE interacts with defect clay structures due to the formation of multiple C&bond;H...O and O&bond;H...O hydrogen bonds. Interactions of MTBE with systems containing different types of defected mineral fragments were found to vary. Systems containing the same type of defected mineral fragment with different central cation interact almost the same way with MTBE. The formation of hydrogen bonds leads to changes in the geometrical parameters and to the polarization of MTBE. The values of the interaction energies depend on the charge of the mineral fragment. They amount to 5 kcal/mol–35 kcal/mol. MTBE interacts more preferably with octahedral fragments than with tetrahedral fragments that contain an Al3+ central cation. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005 [ABSTRACT FROM AUTHOR]

The potential functions of internal rotation around the C $$_{sp^2 }$$ -S bond in the C6H5S(O)CH3 and C6H5S(O)CF3 molecules were obtained by ab initio MP2(full)/6-31+G* calculations. The stationary points were identified by solving the vibrational problems. The structures in which the plane of the C $$_{sp^2 }$$ -S-C $$_{sp^3 }$$ bonds is approximately perpendicular to the benzene ring plane correspond to the energy minimum. The barriers to rotation around the C $$_{sp^2 }$$ -S bond, corrected for the zero-point vibration energy, are 21.29 [C6H5S(O)CH3] and 28.98 [C6H5S(O)CF3] kJ mol−1. The bond angles (deg) are as follows: 95.7 (CSC), 107.1 ( C $$_{sp^2 }$$ SO), 106.3 ( C $$_{sp^3 }$$ SO) in C6H5S(O)CH3; 93.5 (CSC), 108.2 ( C $$_{sp^2 }$$ SO), 105.2 ( C $$_{sp^3 }$$ SO) in C6H5S(O)CF3. The bond lengths are as follows (Å): 1.520 (S=O), 1.804 ( C $$_{sp^2 }$$ -S), 1.810 ( C $$_{sp^3 }$$ -S) in C6H5S(O)CH3; 1.507 (S=O), 1.799 ( C $$_{sp^2 }$$ -S), 1.870 ( C $$_{sp^3 }$$ -S) in C6H5S(O)CF3. According to the results of NBO calculations, the formally double S=O bond consists of a strongly polarized covalent σ bond (S→O) and an almost ionic bond. An increase in the S=O bond multiplicity relative to a single bond is mainly due to hyperconjugation by the mechanism n(O)→σ*( C $$_{sp^2 }$$ -S) and n(O)→σ*( C $$_{sp^3 }$$ -S) and, to a lesser extent, by interaction of the oxygen lone electron pairs with the Rydberg orbitals of the S atoms, characterized by a large contribution of the d component. [ABSTRACT FROM AUTHOR]

The adsorption of methyl tert‐butyl ether (MTBE) on the substituted tetrahedral surface of dickite has been studied using the n‐layered integrated molecular orbital and molecular mechanics (ONIOM) approach and Becke's three‐parameter exchange functional and the gradient‐corrected functional of Lee, Yang, and Paar (B3LYP)/6‐31G(d):PM3 approximation. Two Si atoms of the tetrahedral side were substituted by Al atoms in three different mutual arrangements (1,2‐, 1,3‐, and 1,4‐substitution). The negative charge of the layer originating from the substitution was compensated by the exchangeable Mg2+ cation. Initially the Mg2+ cation was placed above the center of the six‐member ring with the tetrahedral structure of the mineral fragment. The Mg2+ cation plays a crucial role in the adsorption of MTBE on the substituted surface of dickite. Methyl tert‐butyl ether is adsorbed due to the formation of a chemical bond between the oxygen atom of MTBE and the Mg2+ cation and due to the formation of multiple weak C‐H…O hydrogen bonds between the C–H groups of MTBE and the surface oxygen atoms. The adsorption results in changes in the structural parameters of MTBE that are the most significant in the case of the 1,3‐substituted system. The interaction energies of MTBE adsorbed on the substituted surface of dickite corrected by basis set superposition error were predicted. The values of adsorption energies range from −42.8 kcal/mol (1,2‐substitution) to −45.9 kcal/mol (1,3‐substitution) to −47.2 kcal/mol (1,4‐substitution). © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004 [ABSTRACT FROM AUTHOR]

The MINDO/3 semiempirical approximation in SCF MO LCAO has been used to examine whether a cluster scheme can be used to calculate the electronic structures for aluminum oxides. Conditions are defined under which the hypervalent environment of the aluminum atom is stable under geometry optimization. A univalent pseudoatom model is compared with an uncharged ionic one to estimate the geometrical optimization. A univalent pseudoatom model is compared with an uncharged ionic one to estimate the geometrical and energy characteristics for clusters representing three-coordinated, four-coordinated, and six-coordinated Al. [ABSTRACT FROM AUTHOR]