Aromaticities of azines relative to benzene; a theoretical approach through the dimethyldihydropyrene probe

The aromaticities of azines relative to benzene have been estimated by fusion with 15,16‐dimethyldihydropyrene. Chemical shift data for the azine‐fused dihydropyrenes (calculated at GIAO HF/6‐31G*//B3LYP/6‐31 + G*) were used to estimate the reduction in the dihydropyrene nucleus aromaticity. Choice of the saturated reference model was quite crucial in reliable estimation of aromaticity. Reference models with partial unsaturation at azine (21,23,25–32) gave better estimate of aromaticity than the parent dimethyldihydropyrene. Aromaticities of azines through chemical shift data and geometric parameter analysis were found to be 90–100% to that of benzene, highly consistent with the aromaticity estimation by nucleus independent chemical shift_(0)πzz calculations. Copyright © 2014 John Wiley & Sons, Ltd.     

Vibrational spectra and potential energy distributions for 1‐benzyl‐1H‐imidazole by normal coordinate analysis

The Fourier‐transform (FT) Raman and infrared (IR) spectra of the crystallized novel pharmaceutical molecule 1‐benzyl‐1H‐imidazole (BI) were recorded and analyzed. The geometry, intermolecular hydrogen bond, and harmonic vibrational wavenumbers of BI were investigated with the help of B3PW91 density functional theory (DFT) methods. The detailed interpretation of the vibrational spectra was carried out with the aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The aromaticities of the imidazole and phenyl rings were studied using the standard harmonic oscillator model of aromaticity (HOMA) index. Natural bond orbital (NBO) analysis on BI was carried out to demonstrate the various intramolecular interactions that are responsible for the stabilization of this molecule leading to its medicinal activity. The potential energy profile corresponding to the torsion around the bridge bonds connecting the two rings was drawn to explain the steric and/or electronic effects using potential energy surface (PES) scan studies. The pronounced double‐bond localization in the imidazole ring upon intermolecular H‐bonding appears to be the cause for its enhanced aromaticity. Copyright © 2008 John Wiley & Sons, Ltd.     

Structure prediction and aromaticity of acenes and phenylenes series. A combination method between asymmetric Kekulé structures

The combination method between asymmetric Kekulé structures (CMAK) was expanded to the structure prediction of a series of acenes and phenylenes. The structures predicted by the CMAK correspond to those calculated by the ab initio molecular orbital (MO) and B3LYP density functional methods. The CMAK can characterize the structures. The aromaticity for the whole ring and each ring in the treated compounds was estimated by the index of deviation from aromaticity (IDA). The estimated aromaticity corresponds fairly well to the characterization of the structure predicted by the CMAK. The predicted structures of linear acenes reveal the aromaticity of the central ring and also explain its reactivity. The side ring in [n]phenacene shows high aromaticity. The critical difference in the structure and aromaticity for the central six‐membered ring of the isomers benzo[1,2:4,5]dicyclobutene and benzo[1,2:5,6]dicyclobutene was explained. Copyright © 2012 John Wiley & Sons, Ltd.     

Theoretical prediction of size‐expansion effect on the C8‐site activity in the modified guanine‐cytosine analogs

Homo/hetero ring‐expanded DNA analogs have been shown to be rationally modified DNA motifs with improved physical or biological properties. In this work, using density functional theory, the stability of these artificial DNA base pairs was examined with regard to three aspects associated with DNA damage, namely deprotonation, H‐abstraction, and H‐radical addition. The effect of size expansion on C8 activity was investigated because C8‐oxidative guanine (G) is one of the most important products of DNA damage. Computational results indicate that the insertion of an aromatic spacer ring in G considerably decreases the electron density over the C8 site, leading to easier deprotonation or H‐abstraction from the C8 site and more difficult H ^. ‐radical attack on the C8 site. However, the opposite phenomenon is observed if the spacer ring is antiaromatic, because of the increased electron density over the C8 site. Moreover, these effects are more prominent the larger the aromaticity or antiaromaticity of the spacer ring. Further analyses, using natural bond orbitals (NBOs) and the nucleus‐independent chemical shift (NICS) index of aromaticity, indicate that the changes of the electron distribution over the C8 site arise because the aromatic spacer ring, involved in the conjugation structure, increases the electron delocalization from the electron‐rich imidazole ring to the diatropic six‐membered rings, while the antiaromatic spacer ring acts as an electron‐donating group, not only inhibiting the above electron delocalization, but also slightly increasing the electron density over the C8 site. The improved stability of these size‐expanded base pairs in different DNA‐damaged environments may encourage their use in practical applications. Copyright © 2009 John Wiley & Sons, Ltd.     

Synthesis,spectroscopic, and computational studies of charge‐transfer complexation between benzidine with 2,3‐dichloro‐5,6‐dicyano‐p‐benzoquinone and chloronil

The solid charge transfer (CT) complexes that have been formed from the reactions of donor benzidine (BZ) and the π‐acceptors such as 2,3‐dichloro‐5,6‐dicyano‐p‐benzoquinone (DDQ) and chloronil (CHL) have been studied and characterized experimentally and theoretically. The experimental work which includes the use of UV‐visible spectroscopy to identify the CT band of the CT‐complex. The composition of the complexes has been investigated successfully by using spectrophotometric titration and Job method of continuous variation to be 1:1. Furthermore, to calculate the formation constant and molar extinction coefficient, we have used the Benesi‐Hildebrand equation. Infrared and proton nuclear magnetic resonance spectral studies were used to characterize and confirm the formation of CT‐complex. The experimental studies were well supported by quantum chemical simulations by using density functional theory. The computational analysis of molecular geometry, Mulliken charges, and molecular electrostatic potential surfaces of reactants and complexes is very much helpful in assigning the CT route. The C═O bond length of DDQ and CHL increased upon complexation with BZ. We have also observed that the substantial amount of charge has been transferred from BZ to DDQ and CHL in the process of complexation. An excellent consistency has been achieved between experimental and theoretical results.     

Insights into unusual stability of 5‐membered‐ring endocyclic benzyl carbocations in aqueous solution

The acyclic o‐oxygen benzyl carbocation 1 , the 6‐membered‐ring endocyclic o‐oxygen benzyl carbocation 2 , and the 5‐membered‐ring endocyclic o‐oxygen benzyl carbocation 3 were used as model compounds to get insights into the general phenomenon for the unusual stability of the 5‐membered‐ring endocyclic benzyl carbocations in aqueous solution. The hydride‐ion affinities of 1 , 2 , and 3 in gas phase, acetonitrile, and DMSO were calculated and compared by the density functional theory method, and 3 isodesmic reactions were designed to confirm their thermodynamic stability. What we found is that the 5‐membered‐ring endocyclic o‐oxygen stabilizes the benzyl carbocation 3 less than the acyclic o‐oxygen stabilizes the benzyl carbocation 1 in gas phase because of ring strain and through‐bond induction. However, the high solvation energies of the 5‐membered‐ring endocyclic o‐oxygen benzyl carbocation 3 not only offset the destabilizing effects of ring strain and through‐bond induction but also make it even more stable than the acyclic o‐oxygen benzyl carbocation 1 in polar solvents like acetonitrile, DMSO, and water.     

Assessment of the aromaticity of borepin rings by spectroscopic,crystallographic and computational methods: a historical overview

This review presents a chronological discussion of the evolution of our conceptual and experimental understanding of aromaticity as pertaining to the borepin ring structure. Borepin is the boron‐containing charge‐neutral analogue of the carbocyclic tropylium ion, and many molecular variations involving the borepin motif have been synthesized over the past half century. The aromaticity of the borepin system has been probed with ultraviolet–visible (UV–vis), photoluminescence and infrared (IR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, X‐ray crystallography and computational analysis. Recently, the focus of borepin‐containing compounds has shifted to π‐electron materials, building on the foundation of a firm understanding of the physical organic properties of the borepin motif that will allow for electronic fine‐tuning toward desired applications. Copyright © 2015 John Wiley & Sons, Ltd.     

Ring strain energy in ether‐ and lactone‐containing spiro compounds

Ring strain energies (RSEs) have been calculated for oxygen‐containing spiro compounds using the group equivalent reaction (GER) formalism. The RSEs for all compounds studied were calculated from the energies of fully‐optimized structures at the MP2 + ZPE/cc‐pVDZ level and the more computationally costly G4(MP2) method. RSEs for selected compounds were also calculated with the CBS‐QB3 method, with less than 1 kcal/mol difference observed between G4(MP2) and CBS‐QB3. The difference between the less costly MP2 + ZPE and G4(MP2) methods was less than 1.5 kcal/mol. The highest RSEs were found for the compounds containing two three‐membered rings, and these compounds also exhibited the greatest excess strain energy (ESE) of about 12 kcal/mol. The RSEs of cyclic lactones vary with ring size differently than those of cyclic ethers. Cyclic ethers' RSEs decrease by a small amount from the three‐ to four‐membered rings then decrease drastically as the ring increases to 5 atoms, and approaches zero for the six‐membered ring, the same unexpected behavior as seen in cycloalkanes. Cyclic lactones' RSEs decrease linearly to almost zero from the three‐ to the five‐membered ring, then increase by 1–2 kcal/mol in the six‐membered ring. Lactone‐containing spiro compounds exhibit regularly diminishing ESE as the size of the lactone ring increases, down to about 3 kcal/mol in the δ‐lactone‐containing spiro compound. Substitution of methyl groups decreases RSE in these oxygen‐containing spiro compounds, while substitution of fluorine significantly increases RSE, as has been reported in other compounds. But RSE alone is shown to not correlate completely with chemical reactivity of these spiro compounds. Copyright © 2014 John Wiley & Sons, Ltd.     

Prototropy and π‐electron delocalization for purine and its radical ions – DFT studies

Complete tautomeric equilibria and π‐electron delocalization were studied at the B3LYP/6‐311+G** level for neutral purine ( P ) and its charged radicals ( P ^+? and P ^??). All possible nine tautomers (four NH and five CH forms) and all possible 36 tautomeric equilibria (six NⁱH → N^kH, twenty NH → CH, and ten CⁱH → C^kH conversions) were considered. The greatest variations of the tautomeric equilibrium constants (as pK_T) were observed for the NH → CH conversions when proceeding from neutral to reduced purine ( P + e → P ^??). These variations completely change the tautomeric preferences. One‐electron oxidation ( P ? e → P ^+?) has considerably smaller effect on the pK_T values and does not change the tautomeric preferences. π‐Electron delocalization depends on the position of the moving proton and on the type of the electron transfer. For individual tautomers, some linear relations between the relative stabilities and the HOMA (harmonic oscillator model of aromaticity) indices occur for neutral and oxidized purine. For reduced purine, a scatter plot is found. Copyright © 2010 John Wiley & Sons, Ltd.     

Microwave‐Assisted One‐Pot Synthesis of Metal‐Free Nitrogen and Phosphorus Dual‐Doped Nanocarbon for Electrocatalysis and Cell Imaging

Metal‐free nitrogen and phosphorus dual‐doped, electrocatlytically active, functionalized nanocarbon (FNC) and photoluminescent carbon nanodots (PCNDs) are simultaneously synthesized using a facile one‐pot microwave‐assisted process. The successful incorporation of phosphorus and nitrogen to oxygen rich PCNDs and FNC are confirmed using surface morphological and spectral studies. The characterization studies of FNC further reveals the presence of edge‐plane‐like sites/defects and remarkable electrocatalytical activity. In addition to the electroctalytical activity, FNC shows attractive properties as a metal‐free oxygen reduction catalyst and is resistant to methanol crossover effects in alkaline media. The 5–10 nm PCNDs, which exhibit blue fluorescence under UV exposure, are successfully used for bioimaging applications.     

First order molecular hyperpolarizabilities and intramolecular charge transfer from the vibrational spectra of NLO material: ethyl‐3‐(3, 4‐dihydroxyphenyl)‐2‐propenoate

As part of the efforts for the design of new organic nonlinear optical(NLO) materials with high efficiency for present day technological requirements, a comprehensive investigation on the intramolecular charge transfer(CT) of an efficient π‐conjugated potential push–pull NLO chromophore, ethyl‐3‐(3,4‐dihydroxyphenyl)‐2‐propenoate(EDP) to a strong electron‐acceptor group through the π‐conjugated bridge has been carried out from their vibrational spectra. The first hyperpolarizabilities of caffeic derivatives are investigated by ab initio method. The NLO efficiency is experimentally measured by powder efficiency experiment. The strongest vibrational modes contributing to the electro‐optic effect from the simultaneous infrared(IR) and Raman activities of the ring CC stretching modes, in‐plane deformation modes, and the umbrella mode of the methyl groups have been identified and analyzed unambiguously. The influence of electronic effects, hyperconjugation and backdonation, on the C H stretching vibrations of both methyl and methylene groups causing the decrease of stretching wavenumbers and IR intensities has been extensively investigated. Copyright © 2009 John Wiley & Sons, Ltd.     

Topological resonance energy,bond resonance energy,and circuit resonance energy

Circuit resonance energy (CRE) is a key quantity that links energetic and magnetic criteria of aromaticity for a polycyclic π‐system. Topological resonance energy (TRE) correlates well with the sum of CREs for an entire π‐system. We found that bond resonance energy (BRE), so far defined to estimate the degree of kinetic stability for a polycyclic π‐system, also correlates very well with the corresponding quantity defined with CREs. These findings justify the view that graph‐theoretical quantities, such as TRE and BRE, can be used safely even though they rely on unrealistic reference structures. Copyright © 2007 John Wiley & Sons, Ltd.     

Acid catalyzed intramolecular attack of β‐phenylthioureido group on amide function. Parallel formation of thiodihydrouracil and 4‐iminothiodihydrouracil. Different pathways in the Edman degradation reaction in the formation of six‐ versus five‐membered cyclic intermediates

Contrary to the cleavage of α‐phenylthioureido peptides 1 proceeding through intermediate 2‐anilinothiazolinone 2 , the b‐analog cis‐2‐(3‐phenylthioureido)cyclopentane‐carboxamide 5 forms transiently 4‐imino‐2‐thioxopyrimidine 6 . Monitoring amide cyclization and hydrolysis of iminopyrimidine 6 in acid by UV showed that an equilibrium between 5 and 6 was reached followed by slower conversion of both compounds into 2‐oxo‐4‐thioxopyrimidine 7 . Both processes were characterized by isosbestic points, the first due to parallel conversion of 5 into 6 and 7 (or 6 into 5 and 7 ) at a constant ratio while the second identical for both reactants – to conversion of equilibrated 5 and 6 into 7 . The special isosbestic points allowed the determination of the individual constants of Scheme 2. Further confirmation was obtained from NMR product analysis and following the cyclization of amide 5 in DMSO:DCl. Product 2‐oxo‐4‐ thioxopyrimidine 7 hydrolyzed reversibly to thioureido acid 8 . The cyclization rate of 8 allowed the participation of 6‐oxothiazine 10 formed by sulfur attack to be excluded. The absence of sulfur attack in the six‐membered case is explained by the longer C? S bond bringing about greater bond angle strain at the tetrahedral ring atoms due to the geometrical characteristics of five‐ and six‐membered rings with planar segments. The cyclizations of amide 5 to iminopyrimidine 6 and to thiodihydrouracil 7 are first order in [H⁺], while the reactions of protonated imine 6 H⁺ are zero order to amide and ?1 to thiodihydrouracil. The reaction orders can be reconciled by assuming a rate determining proton transfer from the tetrahedral intermediate in amide cyclization. Copyright © 2007 John Wiley & Sons, Ltd.     

An attempt to analyze the bark disease in Havea brasiliensis using X‐ray absorption near‐edge spectroscopy

The X‐ray absorption near‐edge spectroscopy (XANES) technique has been used to determine the chemical change of elements induced by bark diseases in Havea brasiliensis (rubber latex tree). The results show the good sensitivity of in situ XANES for characterizing the chemical structure of phosphorus, sulfur, potassium and calcium in healthy and diseased Havea brasiliensis. Important information for understanding the bark disease involved in the sulfur metabolism of plants was also obtained from XANES.     

Unexpected dimerization of 1,3‐dimethyl‐5‐methylenebarbituric acid revealed by a combined experimental and computational study

A comparison of experimental and calculated ¹³C‐nuclear magnetic resonance chemical shifts reveals the molecular structure of a dimer that was obtained by an unexpected dimerization of 1,3‐dimethyl‐5‐methylenebarbituric acid. Furthermore, the puckering angle of the cyclobutane unit linking the six‐membered rings is discussed in detail. The influence of substituents on 1,3‐position of the cyclobutane ring on the puckering angle is demonstrated based on 1,1,3,3‐tetramethylcyclobutane. Copyright © 2015 John Wiley & Sons, Ltd.     

Spectroscopic and stability studies on unsymmetrical 1,3‐dialkyl‐1,3‐diphosphacyclobutane‐2,4‐diyls

Air‐tolerant 2,4‐bis(2,4,6‐tri‐t‐butylphenyl)‐1,3‐diphosphacyclobutane‐2,4‐diyl singlet biradicals can be prepared by utilizing the unique reactivity of a kinetically stabilized P≡C triple bond compound. In this procedure, we studied the spectroscopic properties of a fundamental unsymmetrical P‐heterocyclic biradical containing both PEt and PMe moieties, and the effects of the PCH₂OMe group in relation to the stability of the P‐heterocyclic biradical skeleton. The experimentally observed nuclear magnetic resonance and photo‐absorption parameters of 1‐ethyl‐3‐methyl‐2,4‐bis(2,4,6‐tri‐t‐butylphenyl)‐1,3‐diphosphacyclobutane‐2,4‐diyl were discussed based on our previous findings and density functional theory calculations, suggesting particular structural characteristics of the P‐heterocyclic biradical skeleton and aromatic substituent effects on the sp²‐C atoms in the 4‐membered ring. Introduction of the methoxymethyl group in the P₂C₂ biradical moiety gave more stabilized 1,3‐diphosphacyclobutane‐2,4‐diyl derivatives. In comparison with considerably unstable biradicals bearing propargyl substituents, relatively higher lowest unoccupied molecular orbital energies suggest reluctant oxidation of the P‐heterocyclic skeleton. Copyright © 2011 John Wiley & Sons, Ltd.     

Self‐doping PPV oligomers – electrochemistry and structure of the self‐doped systems

A novel class of self‐doping conjugated oligomers, E,E‐2‐(sulfoalkoxy)‐5‐alkoxy‐1,4‐bis[2‐(2,4,6‐trimethoxyphenyl) ethenyl]benzenes, is presented. The synthesis and spectroscopic characterisation of five such oligomers are described, and an electrochemical analysis using cyclic voltammetry is performed to determine the anodic peak potentials. A structural study is performed on six self‐doping oligomers in which the structures and energies of the possible mono‐molecular forms of the electrically conducting doped material are described and evaluated using Hirshfeld charges and the Quantum Theory of Atoms In Molecules. Copyright © 2009 John Wiley & Sons, Ltd.     

Solvent effects on guanidinium‐anion interactions and the problem of guanidinium Y‐aromaticity

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.