Structure-reactivity indices for the hydrolysis of diol epoxides of polycyclic aromatic hydrocarbons

Several different computational parameters have been used in an attempt to predict relative reactivity of carcinogenic bay-region diol epoxides. The correlation of experimentally observed hydrolytic reactivity with these parameters is described.     

Correlation of an electronic reactivity index with carcinogenicity in polycyclic aromatic hydrocarbons

Recent experimental studies indicate that one step in the transformation of polycyclic aromatic hydrocarbon precarcinogens to ultimate carcinogens involves oxidation of a dihydrodiol intermediate to a dihydrodiol epoxide. This step is examined for 25 compounds using a molecular orbital reactivity index, and a strong correlation with carcinogenic activity is found.     

Electrostatic potential mapping of polycyclic aromatic hydrocarbon diol epoxides using a dipole

Electrostatic potential maps of benz(a)anthracene diol epoxide, benzphenanthrene diol epoxide, chrysene diol epoxide, and tryphenylene diol epoxide, which are ultimate carcinogens derived from the corresponding polycyclic aromatic hydrocarbons, have been studied using a dipole of length 1 Å and strength 1 Debye. The net charge distributions in the molecules were obtained using the MNDO molecular orbital method. The maps were drawn for two closest distances of approach between the charged ends of the dipole and atoms of the molecules. Using the electric field directions and values of electrostatic potentials, reactive sites and relative reactivities of these molecules have been examined. Existence of a bay region appears to be important for the carcinogenic activity of a diol epoxide in this class of carcinogens.     

New aspects of quantum electrodynamics on electronic structure and dynamics

Application of Alpha-oscillator theory to quantum electrodynamics (QED) solves the mystery (Feynman) of the double-slit phenomenon involved in the foundation of quantum mechanics (QM). Even if with the same initial condition given, different spots on the screen can be predicted deterministically with no introduction of hidden variables. The interference pattern is similar to, but cannot be reproduced quantitatively by, that of the QM wave function, contrary to many-years-anticipation: a new prediction, awaiting experimental test over and above the Bohr–Einstein gedanken experiment. The general proof has already been published in Ref. [3a] and the concrete numerical algorithm of the extended normal mode technique for concrete trajectory of one electron in Ref. [3b]. In this article, (1) the new “interpretation” of the QED wave function is given in section “Interpretation of Wave Function in QED”: the QED wave function used in the extended normal mode technique gives probability density distribution function of the initial values of trajectories. Moreover, (2) for the sake of demonstration of this new interpretation, the time-independent stationary state QM wave function is substituted to the QED wave function in section “Internal Self-Stress of Energetic Particles”: the QED wave function is realized by internal self-stress revealed as energy density at the initial conditions. The renewed energy density is applied to study a unified scheme for generalized chemical reactivity. This is a new kind of chemical force acting in between electrons not in between nuclei. This paves a way for more advanced time-dependent simulation of electronic structure and dynamics in chemical reaction dynamics by tracing trajectories of many electrons. © 2018 Wiley Periodicals, Inc.     

A benchmark quantum chemical study of the stacking interaction between larger polycondensed aromatic hydrocarbons

Large-scale electronic structure calculations were performed for the interaction energy between coronene, C₂₄H₁₂ with circumcoronene, C₅₄H₁₈, and between two circumcoronene molecules, in order to get a picture of the interaction between larger graphene sheets. Most calculations were performed at the SCS-MP2 level but we have corrected them for higher-order correlation effects using a calculation on the coronene-circumcoronene system at the quadratic CI, QCISD(T) level. Our best estimate for the interaction energy between coronene and circumcoronene is 32.1?kcal/mol. We estimate the binding of coronene on a graphite surface to be 37.4 or 1.56?kcal/mol per carbon atom (67.5?meV/C atom). This is also our estimate for the exfoliation energy of graphite. It is higher than most previous theoretical estimates. The SCS-MP2 method which reproduces the CCSD(T) and QCISD(T) values very well for smaller aromatic hydrocarbons, e.g., for the benzene dimer, increasingly overestimates dispersion as the bandgap (the HOMO-LUMO separation) decreases. The barrier to the sliding motion of coronene on circumcoronene is 0.45?kcal/mol, and for two circumcoronene molecules 1.85?kcal/mol (0.018 and 0.034?kcal/mol per C atom, respectively). This means that larger graphenes cannot easily glide over each other.     

四苯硼阴离子电子结构的理论研究

分别应用半经验发子轨道理论的AM1方法和在HF／3－21G水平上的从头算分子轨道法,对四苯硼阴离子的电子结构进行了研究。采用解析梯度技术对四苯硼阴离子的平衡态几何构型进行了全优化,得到了分子轨道、电荷布居、静电势以及红外光谱和紫外光谱等参数,计算结果表明：四苯硼阴离子的静电势分布均匀,其前线轨道能级间隔为12．1398eV,利用组态相互作用法得到的紫外光谱跃迁吸收峰主要位于远紫外区,说明四苯硼离子比较稳定,从头算法得到的红外光谱吸收峰分布与实验结果一致,AM1法得到的红外吸收频率与实验值更接近。     

Electronic structure and reactivity of guanylthiourea: A quantum chemical study

Electronic structure analysis of guanylthiourea (GTU) and its isomers has been carried out using quantum chemical methods. Two major tautomeric classes (thione and thiol) have been identified on the potential energy (PE) surface. In both the cases conjugation of pi‐electrons and intramolecular H‐bonds have been found to play a stabilizing role. Various isomers of GTU on its PE surface have been analyzed in two different groups (thione and thiol). The interconversion from the most stable thione conformer ( GTU‐1 ) to the most stable thiol conformer ( GTU‐t1 ) was found to take place via bimolecular process which involves protonation at sulfur atom of GTU‐1 followed by subsequent C? N bond rotation and deprotonation. The detailed analysis of the protonation has been carried out in gas phase and aqueous phase (using CPMC model). Sulfur atom (S1) was found to be the preferred protonation site (over N4) in GTU‐1 in gas phase whereas N4 was found to be the preferred site of protonation in aqueous medium. The mechanism of S‐alkylation reaction in GTU has also been studied. The formation of alkylated analogs of thiol isomers (alkylated guanylthiourea) is believed to take place via bimolecular process which involves alkyl cation attack at S atom followed by C? N bond rotation and deprotonation. The reactive intermediate RS(NH₂)C? N? C(NH₂)₂⁺ belongs to the newly identified ^⊕N(←L)₂ class of species and provides the necessary dynamism for easy conversion of thione to thiol. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

A quantum chemical study of the electronic structure of substituted germocanes

The PRIRODA (riDFT method, BLYP functional, hf.bas basis set) and Gaussian 98 (HF method, 6-311G(d,p) basis set) programs are used to calculate the spatial and electronic structures of a number of molecules of substituted germocanes with a general formula of R,Rs’Ge(XCH₂CH₂)₂Y (where X = C, O, S, and Y = N, O, S). With the use of the AIM method the topological characteristics of Ge—Y donation bonds are calculated in these molecules. An analysis of the obtained data shows that up to the values of Ge—Y interatomic distances of ~2.7 Å these bonds can be considered as the intermediate type bonds. At Ge—Y distances of ~3.0 Å these bonds become ionic, therefore the Coulomb interaction between oppositely charged Ge and Y atoms mainly contributes to Ge—Y bonding.     

Understanding the reactivity of polycyclic aromatic hydrocarbons and related compounds

This perspective article summarizes recent applications of the combination of the activation strain model of reactivity and the energy decomposition analysis methods to the study of the reactivity of polycyclic aromatic hydrocarbons and related compounds such as cycloparaphenylenes, fullerenes and doped systems. To this end, we have selected representative examples to highlight the usefulness of this relatively novel computational approach to gain quantitative insight into the factors controlling the so far not fully understood reactivity of these species. Issues such as the influence of the size and curvature of the system on the reactivity are covered herein, which is crucial for the rational design of novel compounds with tuneable applications in different fields such as materials science or medicinal chemistry.

This perspective article summarizes recent applications of the combined activation strain model of reactivity and the energy decomposition analysis methods to the study of the reactivity of polycyclic aromatic hydrocarbons and related compounds.     

Experimental and quantum chemical studies of the electronic absorption spectra of pyrimidine derivatives

The electronic absorption spectra of different pyrimidine derivatives have been measured experimentally and calculated theoretically by the PPP and CNDO/S methods. These pyrimidine derivatives are: 4,6-dichloro-pyrimidine (I), 4,6-dichloro, 5-amino-pyrimidine (II), 2,4,6-trichloro-pyrimidine (III), 4,6-dihxdroxy-pyrimidine (IV), 4,6-dihxdroxy-5-nitro-pyrimidine (V), 2,4-diamino-pyrimidine (VI), 2,4-diamino-6-hydroxy-pyrimidine (VII), 2,4-dihydroxy-5-carboxy-pyrimidine (VIII), 2,4-dimethyl-6-hydroxy-pyrimidine (IX), 5-nitro-uracil (X), and orotic acid (XI). The observed electronic spectral shifts are quantitatively analyzed in relation to different solute–solvent interaction mechanisms. The effects of solvent polarity and hydrogen bonding on the spectra are discussed in the light of theoretical predictions. This comparative analysis provides a reasonable picture of the solvent effects on the absorption spectral properties of pyrimidine nucleobases.     

Topological aspects of chemical reactivity

The technique of the so-called More O'Ferrall diagrams was modified by incorporating the framework of recently introduced topological theory of chemical reactivity. On the basis of this modification, a new simple criterion was introduced, allowing the unequivocal classification of the mechanisms of pericyclic reactions from the point of view of concertedness and/or nonconcertedness.     

On the electronic properties of dehydrogenated polycyclic aromatic hydrocarbons

The electronic excited-state properties of a series of dehydrogenated polycyclic aromatic hydrocarbons from phenyl through to decacyl are reported. The radicals were investigated by use of time-dependent density functional theory in conjunction with the B3LYP functional. The pi and n orbitals were seen to converge in energy as the system increased in size, yet all radicals were found to have A' ground states. In addition to the study of the electronic state symmetries, the excited-state transitions and oscillator strengths were investigated with the resulting transitions found within the visible region of the spectrum, placing these radicals in the large group of candidate carriers of the diffuse interstellar bands.     

Interaction of oligopyrrole macrocycles with aromatic acids: spectroscopical, quantum chemical and chromatographic aspects

The study of the behavior of oligopyrrole macrocyclic compounds in solution and covalently bond on silica surface were carried out. For this purpose ultraviolet-visible titrations and chromatography measurements were employed. Interactions of porphyrin and sapphyrin with nitrobenzoic, aminobenzensulfonic, hydroxybenzoic and terephthalic acids were studied. The spectroscopic results were compared with quantum chemical calculations at semiempirical level and with the data obtained by HPLC measurements. Chromatographic data showed that interaction of the analytes with the metalled porphyrin and the sapphyrin core led to significant increase of retention factors of the aromatic acids and selectivity improvement of the separation.     

X-ray and quantum chemical study of the electronic structure of glycine and its metal complexes

OK_α spectra of glycine and some transition metal complexes with glycine ligands were obtained. The electronic structure of the glycine zwitterion is calculated by a quantum chemical method, and a theoretical X-ray spectrum of the glycine molecule is constructed. The nature of the metal-ligand bond in the compounds is discussed on the basis of experimental spectra and theoretical calculations. Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Moscow State Academy of Light Industry, Novosibirsk Branch. Moscow State Academy of Light Industry. Novosibirsk State University. Translated fromZhurnal Strukturnoi Khimii, Vol. 34, No. 4, pp. 112–116, July–August, 1994. Translated by L. Smolina     

Conformational effects on the electronic structure and chemical reactivity of lignin modelp-quinone methides and benzyl cations

The electronic structure and its dependence on the conformation in typical lignin model intermediates, β-arylethericp-quinone methide {2-methoxy-4-[2-(2-methoxyphenoxy)]propylidene-2,5-cyclohexadien-1-one} and related benzyl cation has been determined on the basis of semi-empirical quantum chemical calculations. Electrostatic but not frontier orbital characteristics of lignin intermediates were demonstrated to be dependent on the conformation. Conformationally induced electrostatic non-equivalence of two possible routes of nucleophile approach to the reaction center may be the main cause of stereoselectivity of the reactions of quinone methides (but not related cations) with nucleophiles. Quinone methides and related cations also differ in their intramolecular charge transfer properties.     

X-ray spectral and quantum chemical analyses of the electronic structure of poly(monofluorocarbon)

The electronic structure of poly(monofluorocarbon) has been studied by X-ray spectral and quantum chemical methods. Calculations were performed in terms of the MNDO method, with the fluorographite layer modeled by clusters of different sizes. The high-resolution CK_a and FK_a spectra have been obtained; the calculated spectra are consistent with the experimental ones. It has been shown that carbon and fluorine are bonded mainly through the σ bonds. The p orbitals of fluorine atoms that are perpendicular to the C-F bond are not involved in the chemical bond, while the transitions from the molecular orbitals consisting of these p orbitals are responsible for the main maximum in the FK_a spectrum. Deceased. Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 4, pp. 630–635, July–August, 1995. Translated by I. Izvekova     

Vibrational relaxtion in excited electronic states of aromatic hydrocarbons

Time-resolved experiments are reported Showing kinetic evidence for vibrational relaxation of electronically excited molecules in solution at room temperature. The experiments involve higher electronic states of 3,4,9,10-dibenzpyrene. Data are consistent with slow vibrational relaxation (≈ 15 ps), similar to that for ground state species.