Molecular mutagens and carcinogens are structures which carry chemical and electronic properties that disturb and interact with the genomic machinery. Principally, a rule of thumb for carcinogens is that carcinogens are expected to introduce covalent irreversible bonding to one or several types of DNA bases, causing errors in the reading frame for the polymerases. 8-methoxy-6-nitrophenanthro[3,4-d][1,3]dioxole-5-carboxylic acid, better known as Aristolochic acid (AA1) is a recognized carcinogen which causes urotherial cancer and is found in certain plants. Its structure is particularly interesting given that it is closely related to phenanthrene in its polycyclic arrangement, and has four functional groups, a carboxyl-, a nitro-, a methoxy- and a dioxolane group. In this work, the structure of AA1 has been resolved at the MPWPW91 density functional theory method in combination with Aug-cc-pVDZ basis sets. A geometry analysis shows that in AA1 the carboxyl group's torsion is caused by steric strain from the nitro group, which elevates the molecular plane of the first phenanthrene ring with 0.1Å. The wavefunction analysis of AA1 shows that the ring deformation enhances a double π-bond localization in the first ring, adjacent to the dioxalane group, and results in a decrease of ring aromaticity and induces a potentially frozen resonance. Intermolecular and intramolecular interactions were characterized by atoms in molecules and reduced density gradient analysis. This study brings novel information on the geometry and electronic structure of AA1, which are important for the further knowledge of its transformation in vivo and in situ. Copyright © 2013 John Wiley & Sons, Ltd.

We report computations of excitation energies, magnetizabilities, and current strengths for the dianion, tetraanion, and hexaanion of the previously introduced altan–corannulene, a molecule designed to hold a strong paratropic current. None of these ions has a fully diatropic or paratropic pattern: dianion and tetraanion both have a paratropic/diatropic/diatropic pattern, whereas the hexaanion has a diatropic/paratropic/diatropic pattern, which is the ‘mirror-image’ of that of the neutral species. The patterns have been interpreted according to the ipsocentric formulation of the current density. Magnetizability and excitation energy suggest that the hexaanion should be an aromatic molecule. The next homologue of altan-corannulene^6-, altan–altan–corannulene^6-, has also been studied. Its large diamagnetizability has been effectively used to model the magnetic response of C₈₀^6- cages. Copyright © 2013 John Wiley & Sons, Ltd.

The mechanism of sulfurization of substituted triphenylphosphines with 4-(3- and 4-substituted)-1,2,4-dithiazolidine-3,5-diones in acetonitrile, dichloromethane, tetrahydrofuran and toluene at 25 °C was studied. The reaction pathway involves rate-limiting initial nucleophilic attack of the phosphorus at sulfur followed by fast decomposition of the phosphonium intermediate to the corresponding phosphine sulfide, phenylisocyanate and carbonylsulfide. From the Hammett correlations and from the solvent dependency, it was concluded that the transition-state structure is very polar and resembles the zwitter-ionic intermediate. The extent of P–S bond formation and S–S bond cleavage is very similar in the solvents series, but the latter gradually decreases with the decreasing polarity of the solvent. Copyright © 2013 John Wiley & Sons, Ltd.

Through-conjugation for a wide range of 1,8-diamino-4,5-dinitronaphthalenes (N-acylated, N-alkylated, N,N′-bridged, N-heterocyclic, and N-deprotonated compounds) was for the first time quantified in solution by means of ultraviolet–visible and proton nuclear magnetic resonance spectroscopy and compared with that of the simpler naphthalene and benzene push-pull systems. Surprisingly, an extent of conjugation in 1,8-diamino-4-nitro- and 1,8-diamino-4,5-dinitronaphthalenes measured in dimethyl sulfoxide is commensurable. On the whole, the repulsive peri-interactions between the amino groups in systems with N-alkylated and N-deprotonated amino groups are more favorable for an effective D-π-A charge transfer than in N,N′-bridged compounds (perimidines, 2,3-dihydroperimidines and perimidin-2-ones). The best electron donors from peri-positions are pyrrolidin-1-yl and methylamido groups. The conclusions obtained from solution studies were deepened by solid- state X-ray experiments for a number of push–pull naphthalenes, including 6,7-dinitroperimidine N-anion and two representatives of 4,5-diaminonaphthalene-1,8-dicarbaldehydes. In particular, they helped to trace changes in the bond order redistribution and twisting of the naphthalene core. The latter reaches a record value of 27° for 4,5-dinitro-1,8-di(pyrrolidin-1-yl)naphthalene. Copyright © 2013 John Wiley & Sons, Ltd.

The mechanisms of the [2 + 2 + 2] cycloaddition reaction of three ethyne molecules were studied by ab initio molecular orbital and density functional methods. The transition states range from that of the concerted mechanism with D_3h symmetry to that of the stepwise mechanism with C₂ symmetry. The transition state structure and the activation energy depend on the basis set and computational method employed in the analysis. The activation energy barrier was determined to be in the range of 36–44 kcal/mol. The activation energy determined by various methods corresponds to the interaction energy, which is related to the electron correlation energy. The best estimation of the activation energy barrier is 41.6 kcal/mol, achieved from the relation between the interaction energy and the activation energy. Copyright © 2013 John Wiley & Sons, Ltd.

Pulse radiolysis with optical absorption detection has been used to study the reactions of hydroxyl radical (OH^•) with 4-thiouracil (4TU) in aqueous medium. The transient absorption spectrum for the reaction of OH^• with 4TU is characterized by λ_max 460 nm at pH 7. A second-order rate constant k_(4TU+OH) of 1.7 × 10¹⁰ M⁻¹ s⁻¹ is determined via competition kinetics method. The transient is envisaged as a dimer radical cation [4TU]₂^•+, formed via the reaction of an initially formed radical cation [4TU]^•+ with another 4TU. The formation constant of [4TU]₂^•+ is 1.8 × 10⁴ M⁻¹. The reactions of dibromine radical ion (Br₂^•−) at pH 7, dichlorine radical ion (Cl₂^•−) at pH 1, and azide radical (N₃^•) at pH 7 with 4TU have also produced transient with λ_max 460 nm. Density functional theory (DFT) studies at BHandHLYP/6–311 + G(d,p) level in aqueous phase showed that [4TU]₂^•+ is characterized by a two-centerthree electron (2c-3e) [−S∴S−] bond. The interaction energy of [−S∴S−] bond in [4TU]₂^•+ is −13.01 kcal mol⁻¹. The predicted λ_max 457 nm by using the time-dependent DFT method for [4TU]₂^•+ is in agreement with experimental λ_max. Theoretical calculations also predicted that compared with [4TU]₂^•+, 4-thiouridine dimer is more stable, whereas 4-thiothymine dimer is less stable. Copyright © 2013 John Wiley & Sons, Ltd.

Dihydrogen bond (DHB) and X–H…σ interaction are discussed and compared here. Both interactions possess numerous characteristics of the hydrogen bond (HB). The Natural Bond Orbitals method results show that σ → σ* is the most important interaction connected with the electron charge transfer from the Lewis base to the Lewis acid for the DHB as well as for the X–H…σ HB. However, there are distinct differences between these interactions, and this is evident from the analysis based on the Quantum Theory of Atoms in Molecules as well as from the decomposition of the energy of interaction. The X–H…π interaction is also discussed here since it possesses few characteristics typical for the X–H…σ interaction and not for the DHB. Copyright © 2013 John Wiley & Sons, Ltd.

We present a review of the methods most frequently used for the synthesis of fullerenes and the changes that these methods have experienced since 1985 when Kroto and co-workers discovered C₆₀. We also analyze the most important models that explain the mechanism of the formation of fullerenes in carbon soot, as well as the new methodologies that lead to the rational chemical synthesis of fullerenes and of fullerene fragments as precursors. Copyright © 2013 John Wiley & Sons, Ltd.

The kinetics and mechanism of the nucleophilic vinylic substitution of dialkyl (alkoxymethylidene)malonates (alkyl: methyl, ethyl) and (ethoxymethylidene)malononitrile with substituted hydrazines and anilines R¹–NH₂ (R¹: (CH₃)₂N, CH₃NH, NH₂, C₆H₅NH, CH₃CONH, 4-CH₃C₆H₄SO₂NH, 3- and 4-X-C₆H₄; X: H, 4-Br, 4-CH₃, 4-CH₃O, 3-Cl) were studied at 25 °C in methanol. It was found that the reactions with all hydrazines (the only exception was the reaction of (ethoxymethylidene)malononitrile with N,N-dimethylhydrazine) showed overall second-order kinetics and k_obs were linearly dependent on the hydrazine concentration which is consistent with the rate-limiting attack of the hydrazine on the double bond of the substrate. Corresponding Brønsted plots are linear (without deviating N-methyl and N,N-dimethylhydrazine), and their slopes (β_Nuc) gradually increase from 0.59 to 0.71 which reflects gradually increasing order of the C–N bond formed in the transition state. The deviation of both methylated hydrazines is probably caused by the different site of nucleophilicity/basicity in these compounds (tertiary/secondary vs. primary nitrogen). A somewhat different situation was observed with the anilines (and once with N,N-dimethylhydrazine) where parabolic dependences of the kinetics gradually changing to linear dependences as the concentration of nucleophile/base increases. The second-order term in the nucleophile indicates the presence of a steady-state intermediate - most probably T^±. Brønsted and Hammett plots gave β_Nuc = 1.08 and ρ = −3.7 which is consistent with a late transition state whose structure resembles T^±. Copyright © 2013 John Wiley & Sons, Ltd.

Preferential cross-coupling of differently N-substituted amides of 3-hydroxy-2-naphthoic acids 1 and 2 catalyzed by Cu(OH)Cl•TMEDA was observed. The reaction mechanism was investigated using mass spectrometry tools. It was shown that the complexation properties of the N-substituent significantly influence the properties of the corresponding copper complexes of the deprotonated compounds ([(1-H)Cu(TMEDA)]⁺ and [(2-H)Cu(TMEDA)]⁺). Analysis of the fragmentation patterns of the copper complexes revealed that while the former is prone to the one electron oxidation of (1-H)ˉ, the latter has a larger binding energy between (2-H)ˉ and copper(II). Interplay between the abundance of the copper complexes and their reactivities explains the preferential cross-coupling. The results are further supported by exploratory density functional theory calculations. Copyright © 2013 John Wiley & Sons, Ltd.

Gas-phase heats of formation (HOF), solid-phase HOF, detonation properties, electronic structure and thermal stability for a series of polynitro pyrazine derivatives containing three heterocycles have been investigated using density functional theory. It is found that the nitro group is an efficient tool to improve HOF of pyrazine derivatives. Furthermore, detonation velocities and detonation pressures of these compounds are evaluated using empirical Kamlet–Jacobs equations. As a result, it indicates that the nitro group is useful to enhance detonation properties. Detonation velocities of five compounds are 9.67, 9.20, 9.74, 9.76 and 9.87 km/s, respectively, which are significantly larger than that of HMX (9.10 km/s). Bond dissociation energy is also performed to investigate their thermal stability, showing that thermal stability of these compounds is little affected by nitro groups or the position of substituent groups. Considering solid-phase HOF, detonation properties and thermal stability, some of pyrazine derivatives can be potential high energy density materials. Copyright © 2013 John Wiley & Sons, Ltd.

Using Fourier Transform Ion Cyclotron Resonance Spectrometry, we have determined the gas-phase acidities (GA) of 1-phenylethanol, diphenylmethanol and triphenylmethanol. Combining these results with the available experimental data for other alcohols, we obtained three sets of experimental acidities for the families (CH₃)_nC–OH, (CF₃)_nC–OH and Ph_nC–OH (n = 1–3) as well for some other α-substituted alcohols combining these substituents. GA values for these alcohols were studied at the B3LYP/6-311 + G(d,p), MP2/6-311 + G(d,p), G3(MP2) and G3 levels. This allowed the prediction of a number of GA values for other alcohols. We also developed an empirical method for the estimation of these magnitudes and used it to predict the cases wherein simple additivity of substituent effects would break down. Copyright © 2013 John Wiley & Sons, Ltd.

For conventional organic substituents, an almost linear relationship can be established between the para Hammett constants in aqueous solutions and chemical shifts or natural population analysis charges (NPA charges). Based on these correlations, the Hammett constants of six synthesized ionic-pair substituents were estimated via the chemical shifts, which were well in agreement with the results calculated by NPA charges. The para Hammett constants of 89 different ionic-pair substituents (77 anion-cationic and 12 cation-anionic) were therefore calculated in the gas phase based on the density functional theory method. The results show that both the anion-cationic and cation-anionic substituents are electron-withdrawing groups and the different cation–anion combinations could tune the Hammett constants of the ionic-pair substituents in a range from 0.03 to 0.77. Copyright © 2013 John Wiley & Sons, Ltd.

Examining the structures presented by Loschmidt in 1861 shows that he portrayed organic structures in a visually appealing way, but the structures do not support several claims and accolades of Loschmidt's modern-day champions. There is serious doubt that Loschmidt viewed benzene as a planar cyclic array of six carbon atoms; he did not understand positional isomerism of benzene derivatives or the essence of geometric isomerism. He did not recognize that carbons of the C₆ nucleus could only be singly bonded to a substituent. Concerning his “prediction” of cyclopropane, Loschmidt may have been the first to consider a “circular” array of three atoms; this achievement must be viewed in the light of similar predictions for a cyclic dinitrogen oxide, tetracyclohexane, heptacyclononane, and a [1,1]-metacyclophane. His structures worked well for strings of sp²-hybridized carbons or for molecules with chains of tri-substituted carbons. Loschmidt did not differentiate between the bond lengths of double and triple bonds, as claimed. Copyright © 2013 John Wiley & Sons, Ltd.

The adducts of copper(II) chloride complexes with organic radicals may be intermediates in reactions of halohydrocarbons proceeding via radical mechanism and in catalyzed by chlorocuprates. In this paper, the structure and reactivity of chloroorganocuprates with general formula [CuCl_nCH₃]²⁻ⁿ (n = 0–4) were studied at density functional theory (DFT) level of theory. The comparison of geometric and electronic structures of chloroorganocuprates and corresponding copper(II) chloride complexes with the same number of chlorine atoms indicates the higher Cu oxidation state in [CuCl_nCH₃]²⁻ⁿ. The Natural Bonding Orbital analysis confirms the formation of covalent σ-Cu–C bond in these complexes. The analysis of the PES of the system CuCl₄²⁻–CH₃^• indentifies two local minima, corresponding to CuCH₃Cl₄²⁻ and weak complex CuCl₃²⁻···CH₃Cl, as well as transition state between them. The calculations evidence the spontaneous character of copper ion reduction with formation of halohydrocarbon by chlorine atom detachment from CuCl₄²⁻ with high energetic effect. Copyright © 2013 John Wiley & Sons, Ltd.

A set of N₊ nucleophilicity parameters (N₊″) are reported for amines, carbanions and various other nucleophiles in methanol at 20 °C. N₊″ = N″ +2.63, where N″ refers to logarithms of second-order rate constants for reactions of the dimethylamino- benzhydrylium cation (dma)₂CH⁺ with various nucleophiles in any solvent at 20 °C; as for other N₊ parameters, N₊″ = 4.75 for hydroxide in water. Logarithms of second-order rate constants (log k) are correlated by a hybrid of Swain-Scott and Ritchie (SSR) equations: log k = s_E × N₊″ + c, where s_E is the response of the electrophile to changes in N₊″ and c is a residual intercept term. Satisfactory results are obtained for some nucleophilic reactions at sp³ carbon, including S-methyldibenzothiophenium triflate (reference substrate for the N_T scale of solvent nucleophilicity), a methoxymethyl derivative and methyl p-nitrobenzenesulfonate. Less satisfactory results are obtained for acetyl chloride. The results extend the scope of the hybrid SSR equation to nucleophilic substitutions and provide additional insights into the factors influencing s_E. A previously published equation containing two response (s) parameters is shown to be less reliable, and an alternative is investigated. Copyright © 2012 John Wiley & Sons, Ltd.

We have calculated the complexes formed by guanidine/guanidinium and HCl/Cl⁻, HNO₃/NO₃⁻ and H₂SO₄/HSO₄⁻ both in the gas and aqueous Polarizable Continuum Model (PCM) phase to understand the effect that solvation has on their interaction energies. In the gas phase, the cation–anion complexes are much more stable than the rest; however, when PCM-water is considered, this energetic difference is not as large due to the extra stabilization that the ions suffer when in aqueous solution. All the complexes were analyzed in terms of their AIM and NBO properties. In all cases, water solvation seems to “dampen” those properties observed in the gas phase. The values of Nucleus Independent Chemical Shift (NICS)(1) and NICS(2) indicate a huge influence of the proximity of the carbon atom for short distances; thus, the 3D NICS values on the van der Waal isosurfaces have been used to evaluate the possible Y-aromaticity of the guanidinium system. The isosurface in this system is more similar to cyclohexane than to benzene as indication of poor aromaticity. Copyright © 2013 John Wiley & Sons, Ltd.

Phenanthrimidazoles as hole transport materials have been synthesized, characterized, and applied as nondoping emitters in organic light emitting devices. The synthesized molecules possess high fluorescent quantum yield and thermal properties and display film forming abilities. The highest occupied molecular orbital (HOMO) energies of these materials are shallower than the reported tris(8-hydroxyquinoline)aluminum (Alq₃), which enables the hole transport ability of these phenanthrimidazoles. Taking advantage of the thermal stability and hole transporting ability, these compounds can be used as a functional layer between NPB [4,4-bis(N-(1-naphthyl)-N-phenylamino)biphenyl] and Alq₃ layers and show that these phenanthrimidazoles can be alternatively used as novel hole transport materials and to improve the device performances. Geometrical, optical, electrical, and electroluminescent properties of these molecules have been probed. Further, natural bond orbital, nonlinear optical materials (NLO), molecular electrostatic potential, and HOMO–lowest unoccupied molecular orbital (LMO) energy analysis have been made by density functional theory (DFT) method to support the experimental results. Hyperpolarizability analysis reveals that the synthesized phenanthrimidazoles possess NLO behavior. The chemical potential, hardness, and electrophilicity index of phenanthrimidazoles have also been computed by DFT method. Photoinduced electron transfer explains the enhancement of fluorescence by nanoparticulate ZnO, and the apparent binding constant has been obtained. Adsorption of the fluorophore on ZnO nanoparticle lowers the HOMO and LUMO energy levels of the fluorophore. The strong adsorption of the phenanthrimidazoles on the surface of ZnO nanocrystals is likely due to the chemical affinity of the nitrogen atom of the organic molecule to Zn(II) on the surface of nanocrystal. Copyright © 2013 John Wiley & Sons, Ltd.

According to the quantum chemical calculations and Dynamic NMR experiments in the distally disubstituted classical and thiacalix[4]arenes (CCA and TCA) in addition to the C_2v symmetrical pinched cone (PC) conformation, the distorted cone (DC) form with an approximate C_s overall symmetry (with two OH groups bonded to one oxygen atom) also corresponds to the energy minimum. Moreover, in DC form, two different mutual orientations of O–R groups at a lower rim lead to two stable conformations: the first - with both these groups directed outward, the second - with both these groups pointing toward the same direction. In CCA, the PC is essentially favoured over the DC, while in TCA, energies of these forms are similar or the latter may be even preferable. Copyright © 2013 John Wiley & Sons, Ltd.

A series of cyclic esters of pentafluorophenylboronic acid have been obtained and their Lewis acidity evaluated experimentally by a modified Gutmann method. The results based on ³¹P NMR measurements were compared with those determined by quantum mechanical calculations at the DFT-VSXC/pcS-2 level of theory. The differences in Lewis acidity are discussed on the basis of electronic and geometric parameters. The calculations revealed that the complexes of investigated esters with Et₃PO have multiple conformers of a wide range of calculated ³¹P NMR shielding constants. Additionally, a correlation between the calculated O-B-O angle of esters and the experimental acceptor number was found. Copyright © 2013 John Wiley & Sons, Ltd.

A theoretical study on heavier group-14 substituting effect on the essential property of formamide, strong hydrogen bond with water and internal rotational barrier was performed within the framework of natural bond orbital (NBO) analysis and based on the density functional theory calculation. For heavier group-14 analogues of formamide (YHONH₂, Y = Si, Ge and Sn), the n_N–π_Y=O conjugation strength does not always reduce as Y becomes heavier, for example, silaformamide and germaformamide have similar strength of delocalization. Heavier formamides prefer being H-bond donors to form FYO–H₂O complexes to being H-bond acceptors to form FYH–H₂O complexes. The NEDA analysis indicates that H-bond energies of FYO–H₂O complexes increase as moving down group 14 due to concurrently stronger charge transfer (CT) and electrostatic attraction and for the FYH–H₂O complexes H-bond strengths are similar. The model of CTs from FYO to H₂O differs from that at FYH–H₂O complexes, which are contributed not only by aligning lone-pair orbital of O but also by another lone-pair orbital. At two lowest lying excited states (the triplet and S₁ excited states), formamide and its heavier analogues form double H-bonds with H₂O molecule at the same time. The barrier heights of internal rotation become gradually low from C to Sn, formamide (15.73 kcal/mol) > silaformamide (11.73 kcal/mol) > germaformamide (9.45 kcal/mol) > stannaformamide (7.50 kcal/mol) at the CCSD(T)/aug-cc-pVTZ//B3LYP/cc-pVTZ level. NBO analysis indicates that the barrier does not only come from the n_N→π*_YO conjugation, and for heavier analogues of formamide, the n_N→σ*_YO hyperconjugation effect and steric effect considerably contribute to the overall rotational barrier. Copyright © 2013 John Wiley & Sons, Ltd.

Cinnamic acid and its derivatives react with hydroxyl radical (HO^•), in neutral medium, to give hydroxylation products, whether on the benzene ring or on the exocyclic chain, and decarboxylation products. The latter compounds are also obtained after oxidation of the same substrates by the SO₄^•− radical anion. Evidence was provided for the protecting effects afforded by cinnamic acid and hydroxylated derivatives against oxidative reaction mediated by HO^•. By using adenine as a model compound, the results obtained suggest that the high protective effect is due to an antioxidising cascade process. Copyright © 2013 John Wiley & Sons, Ltd.

The thermal and light-induced O − O bond breaking of 2-ethyl-4-nitro-1(2H)-isoquinolinium hydroperoxide (IQOOH) were studied using ¹H NMR, steady-state UV/vis spectroscopy, femtosecond UV/vis transient absorption (fs TA) and time-dependent density functional theory (TD DFT) calculations. Thermal O − O bond breaking occurs at room temperature to generate water and the corresponding amide. The rate of this reaction, k = 5.4 · 10⁻⁶ s⁻¹, is higher than the analogous rates of simple alkyl and aryl hydroperoxides; however, the rate significantly decreases in the presence of small amounts of methanol. The calculated structure of the transition state suggests that the thermolysis is facilitated by a 1,2 proton shift. The photochemical process yields the same products, as confirmed using NMR and UV/vis spectroscopy. However, the quantum yield for the photolysis is low (Φ = 0.7%). Fs TA studies provide additional detail of the photochemical process and suggest that the S₁ state of IQOOH undergoes fast internal conversion to the ground state, and this process competes with the excited-state O − O bond breaking. This result was supported by the fact that the model compound IQOH exhibits similar excited-state decay lifetimes as IQOOH, which is assigned to the S₁ → S₀ internal conversion. Copyright © 2013 John Wiley & Sons, Ltd.