Electronic structure and models of receptor of monooxygenase inductors from a number of polychlorinated polycyclic compounds. IV. MNDO calculations of halogen-substituted azobenzenes

The electron and geometric structures of the cis and trans isomers of 3,3,4,4-tetrachloroazobenzene (3,3,4,4-TCAB) and the trans isomers of 3,3,5,5-TCAB and 3,3-dichloro-4,4-difluoroazobenzene were calculated by the MNDO method. It was established that the trans isomer, which has a planar structure, is most stable for 3,3,4,4-TCAB. Change in the position of the Cl atoms in the azobenzene, i.e., the transition from 3,3,4,4-TCAB to 3,3,5,5-TCAB, does not lead to appreciable change in the formation energy, the position of the electronic levels, the nature of the frontier orbitals, or the charge distribution in the molecules. This gives reason to suggest that the biological activity of 3,3,4,4-TCAB is due to the metabolism products and not to the action of the substrates themselves.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1797–1801, August, 1990.     

Electronic structure and models of monooxygenase inductor receptor from a number of polychlorinated polycyclic compounds. 5. MNDO calculations of halogen derivatives of azoxybenzenes

The MNDO method has been used to calculate the electronic and geometric structure of 3,3,4,4-tetraehloroazoxybenzene (TCAOB), 3,3,4,4-tetrachloro-6-hydroxyazobenzene (TCHAB), and 2,3,7,8-tetrachlorodibenzofuran (TCDF). The TCAOB exists in the gas phase in the form of two configurations, one nonplanar and one nearly planar. The latter is approximately 4 kcal/mole less stable than the first. The oxidation of 3,3,4,4-tetrachloroazobenzene (TCAB) to TCAOB is endothermic only in the case of the acton of hydrogen peroxide, not molecular oxygen. The isomerization of TCAOB to TCHAB proceeds with a gain in energy (–62 kcal/mole); however, the reaction from the ground state of the TCAOB molecule is symmetry-forbidden and is possible only from an excited state of the TCAOB. The process of oxidation of TCAOB and TCHAB by molecular oxygen to form TCDF or 2,3,7,8-tetrachlorobenzo-p-dioxin is energy-favorable; this is important in judging the biological action of TCAOB.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 1, pp. 101–105, January, 1991.     

Electronic structure and models of receptor of monooxygenase inductors from a number of polychlorinated polycyclic compounds. 2. Calculation of substrate-receptor pairs in perturbation-theory approximation

A theoretical quantum-chemical analysis of the interaction of xenobiotics of the dioxin type with a model of their receptor in the ground state supports the possibility of forming rather stable substrate-receptor pairs, with not only oxidized but also reduced cytochrome P-450. General features have been identified in the interaction of the most dangerous xenobiotics of the dioxin type with the model of their receptor.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 11, pp. 2540–2544, November, 1989.     

Electronic structure and reactivity of organofluorine compounds. 5. Electronic structure of CF3-substituted fluoroethylenes from MNDO and STO-3G calculations

It was established by MNDO and STO-3G quantum-chemical calculations of higher perfluorinated olefins that substitution of the fluorine atoms in C₂F₄ by CF₃ groups leads to stabilization of the -MO and destabilization of the -MO of the molecule. The CF₃ group in perfluorinated olefins acts simultaneously as electron donor to the system and electron acceptor to the system. The effective charge on the CF₃ group acquires a small positive value, i.e., according to the sum of the and effects the allylic CF₃ group in perfluorinated olefins is an electron donor.A. N. Nesmeyanov Institute of Heteroorganic Compounds, Russian Academy of Sciences, 117813 Moscow. Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 6, pp. 1334–1340, June, 1992.     

Electron structure and reactivity of organofluorine compounds. 3. Mndo and ami calculations of the ground state of perfluoroalkyl chlorides,bromides, and iodides

The semiempirical quantum chemical MNDO and AMI methods were used to determine the equilibrium geometries and electron properties of molecules of perfluoroalkyl halides (R_FX): CF₃X, CF₃CF₂X, (CF₃)₂CFX, (CF₃)₃CX for X=Cl, Br, and I. It was determined that the effective charge on the Cl atom in R_FCl is negative, positive on the I atom in R_FI, and depends on R_F for the Br atom in R_FBr. The CF₃ group can act as either an electron acceptor or donor in various perfluoroalkyl halides. The strongest C–I bond in the perfluoroalkyl halides occurs with a tertiary RF group.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 5, pp. 1059–1063, May, 1990.     

Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models

Next-generation solvation models are devised to mimic the accuracy and generality of explicit solvation models at the speed of current popular implicit solvation models. One such method is the first-shell of hydration (FiSH) continuum model that was trained on hydration energetics from LIE calculations and molecular dynamics simulations in explicit solvent. Here we tested prospectively the FiSH model on the SAMPL-3 hydration data set that zooms in the effect of chlorination on solvation. We compare these FiSH predictions with those from retrospective LIE calculations. We find that neither FiSH nor LIE can reproduce well the absolute values and the trend of hydration free energies in the biphenyl and dioxin aromatic chlorination series. Some of the hypotheses behind this performance are discussed and tested. The LIE explicit-solvent model shows some improvement relative to the FiSH continuum model, and we correct a systematic deviation in the continuum van der Waals term of FiSH associated with aromatic Cl atom type.     

Electronic and spatial structure of five-membered oxygen-or sulfur-containing cyclic phosphorus and arsenic compounds based on quantum-chemical calculations

We have carried out nonempirical quantum-chemical calculations for five-membered heterocyclic molecules containing O or S atoms and also P or As atoms in the ring, using RHF/6-31G(d) and MP2/6-31G(d) methods with full optimization of their geometry. We have studied their electronic and spatial structure and the characteristics of the interaction between atoms in the molecules. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 4, pp. 629–634 April, 2006.     

Clustering a large number of compounds. 3. The limits of classification

Clustering is normally used to group items that are similar. In this application of obtaining a diverse sample from the 230,000 compounds in the National Cancer Institute Repository, we cluster to select compounds that are different from the rest, to optimize screening for new leads. With these constraints, our approach yielded many singleton clusters. We can interpret these results as evidence for a limit to classification, contrary to the customary view of chemistry as a study of classes of compounds.     

Electronic structure of pentatomic heterocyclic compounds containing N,O, S and Se. Gas-phase UV photoelectron spectra and quantum-mechanical calculations

The gas-phase UV photoelectron spectra of a series of pentatomic heterocyclic molecules having the hydantoin skeleton, i.e.

are discussed on the ground of comparison with the spectra of analogous molecules and with the results of HAM 3 and/or CNDO/S calculations. Evidence was found of the presence of significant interactions between the π orbitals of the chalcogen atoms when X and Y were sulfur and/or selenium. The π orbitals of the nitrogen atoms are on the contrary pretty much localised in the whole series, particularly when X=Y=O and in the monosubstituted derivatives.     

Extension of a temperature-dependent aqueous solvation model to compounds containing nitrogen, fluorine, chlorine, bromine, and sulfur

Most methods for predicting free energies of solvation have been developed or validated exclusively for room temperature. Recently, we developed a model called SM6T for predicting aqueous solvation free energies as a function of temperature for solutes composed of C, H, or O, and here we present solvation model 8 with temperature dependence (SM8T) for predicting the temperature dependence of aqueous free energies of solvation for compounds containing H, C, N, O, F, S, Cl, and Br in the range 273-373 K. We also describe the database of experimental aqueous free energies of solvation used to parametrize the model. SM8T partitions the temperature dependence of the free energy of solvation into two components: the temperature dependence of the bulk electrostatic contribution to the free energy of solvation, which is computed using the generalized Born equation, and the temperature dependence of first-solvation-shell effects, which is modeled by terms proportional to the solvent-exposed surface areas of atoms in functional groups determined entirely by geometry. SM8T predicts the temperature dependence of aqueous free energies of solvation with a mean unsigned error of 0.08 kcal/mol over a database of 4403 measurements on 348 compounds at various temperatures. We also discuss the accuracy of SM8T for predicting the temperature dependence of aqueous free energies of solvation for ions and present free energies of solvation as a function of temperature for two sample ions.     

Electronic and geometric structure of isomers of nitric acid. DFT quantum chemical calculations

Based on the B3LYP/6-311++G(3df,3pd) density functional method, quantum chemical calculations of the electronic structure, geometry, and thermodynamic parameters of eight isomers of nitric acid (three known isomers in the form of peroxynitrous acid ONOOH and five new isomers in the form of oxo-conformation OON(H)O) are presented in the work. The molecular structure of each isomer is characterized by a local minimum on the potential energy hypersurface of the HNO₃ molecular system and corresponds to one of its stationary states. A theoretical study of the reactivity of nitric acid oxo-isomers characterized for the first time can provide adequate explanation for experiments on the autocatalytic use of nitric acid vapors in binding molecular nitrogen. The results obtained can be a direction for developing principally new methods to bind atmospheric nitrogen and activate methane, which are fundamental problems in chemical science and technology.     

Analysis of industrial contaminants in indoor air: Part 1. Volatile organic compounds,carbonyl compounds,polycyclic aromatic hydrocarbons and polychlorinated biphenyls

This article reviews recent literature on the analysis of industrial contaminants in indoor air in the framework of the REACH project, which is mainly intended to improve protection of human health and the environment from the risks of more than 34 millions of chemical substances. Industrial pollutants that can be found in indoor air may be of very different types and origin, belonging to the volatile organic compounds (VOCs) and semivolatile organic compounds (SVOCs) categories. Several compounds have been classified into the priority organic pollutants (POPs) class such as polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins and furans (PCDD/PCDFs) and related polychlorinated compounds, and polycyclic aromatic hydrocarbons (PAHs). Many of these compounds are partially associated to the air gas phase, but also to the suspended particulate matter. Furthermore, settled dust can act as a concentrator for the less volatile pollutants and has become a matrix of great concern for indoors contamination. Main literature considered in this review are papers from the last 10 years reporting analytical developments and applications regarding VOCs, aldehydes and other carbonyls, PCBs, PCDDs, PCDFs, and PAHs in the indoor environment. Sample collection and pretreatment, analyte extraction, clean-up procedures, determination techniques, performance results, as well as compound concentrations in indoor samples, are summarized and discussed. Emergent contaminants and pesticides related to the industrial development that can be found in indoor air are reviewed in a second part in this volume.     

Electronic structure,magnetic properties,and mixed valence character of Ce2Ni3Si5 from first principles calculations

Cerium intermetallic compounds exhibit anomalous physical properties such as heavy fermion and Kondo behaviors. Here, an ab initio study of the electronic structure, magnetic properties, and mixed valence character of Ce₂Ni₃Si₅ using density functional theory (DFT) is presented. Two theoretical methods, including pure Perdew–Burke–Ernzerhof (PBE) and PBE + U , are used. In this study, Ce³⁺ and Ce⁴⁺ are considered as two different constituents in the unit cell. The formation energy calculations on the DFT level propose that Ce is in a stable mixed valence of 3.379 at 0 K. The calculated electronic structure shows that Ce₂Ni₃Si₅ is a metallic compound with a contribution at the Fermi level from Ce 4f and Ni 3d states. With the inclusion of the effective Hubbard parameter (U _eff), the five valence electrons of 5 Ce³⁺ ions are distributed only on Ce³⁺ 4f orbitals. Therefore, the occupied Ce³⁺ 4f band is located in the valence band (VB) while Ce⁴⁺ 4f orbitals are empty and Located at the Fermi level. The calculated magnetic moment in Ce₂Ni₃Si₅ is only due to cerium (Ce³⁺) in good agreement with the experimental results. The U _eff value of 5.4 eV provides a reasonable magnetic moment of 0.981 for the unpaired electron per Ce³⁺ ion. These results may serve as a guide for studying present mixed valence cerium‐based compounds. © 2017 Wiley Periodicals, Inc.     

Electronic structure of binuclear mixed valence copper azacryptates derived from integrated advanced EPR and DFT calculations

Binuclear, mixed valence copper complexes with a [Cu(+1)(.5), Cu(+1)(.5)] redox state and S = (1)/(2) can be stabilized with rigid azacryptand ligands. In this system the unpaired electron is delocalized equally over the two copper ions, and it is one of the very few synthetic models for the electron mediating Cu(A) site of nitrous oxide reductase and cytochrome c oxidase. The spatial and electronic structures of the copper complex in frozen solution were obtained from the magnetic interactions, namely the g-tensor and the (63,65)Cu, (14)N, (2)H, and (1)H hyperfine couplings, in combination with density functional theory (DFT) calculations. The magnetic interactions were determined from continuous wave (CW) electron paramagnetic resonance (EPR), pulsed electron nuclear double resonance (ENDOR), two-dimensional TRIPLE, and hyperfine sublevel correlation spectroscopy (HYSCORE) carried out at W-band or/and X-band frequencies. The DFT calculated g and Cu hyperfine values were in good agreement with the experimental values showing that the structure in solution is indeed close to that of the optimized structure. Then, the DFT calculated hyperfine parameters were used as guidelines and starting points in the simulations of the various experimental ENDOR spectra. A satisfactory agreement with the experimental results was obtained for the (14)N hyperfine and quadrupole interactions. For (1)H the DFT calculations gave good predictions for the hyperfine tensor orientations and signs, and they were also successful in reproducing trends in the magnitude of the various proton hyperfine couplings. These, in turn, were very useful for ENDOR signals assignments and served as constraints on the simulation parameters.