Electrophilic and oxidative chemistry of pyrene and its non-alternant isomers: theoretical (DFT, GIAO-NMR, NICS) study of protonation carbocations and oxidation dications from pyrene, azupyrene (dicyclopenta[ef,kl]heptalene) and dicyclohepta[ed,gh]pentalene

Mono- and diprotonated carbocations and the two-electron oxidation dications derived from parent pyrene and its nonalternant isomers "azupyrene"(dicyclopenta[ef,kl]heptalene)(DCPH) and dicyclohepta[ed,gh]pentalene (DCHP) were studied by DFT at the B3LYP/6-31G(d) level. The most likely site(s) for mono- and diprotonation were determined based on relative arenium ion energies and the structures of the energetically most favored carbocations were determined by geometry optimization. The NMR chemical shifts for the protonated mono- and dications and the oxidation dications were computed by GIAO-NMR at the B3LYP/6-31G(d)//B3LYP/6-31G(d) level and their charge delocalization paths were deduced based on magnitude of the computed [capital Delta][small delta](13)C values and the NPA-derived changes in charges. Relative aromaticity/antiaromaticity in various rings in the energetically favored mono- and dications was estimated via NICS and [capital Delta]NICS. Calculated NMR chemical shift data for and were compared with the available experimental NMR values. The available data on chemical and physical properties of DCPH and DCHP are extremely limited and biological activity data are non-existent. The present study provides the first glance into their carbocations and oxidation dications, while augmenting and reinforcing the previous stable ion data on the pyrenium cations.     

Novel examples of three-dimensional aromaticity: 1,3-dehydro-silaadamantane dications. A theoretical (DFT,GIAO NMR,NICS) study

A DFT study of the hitherto elusive 1,3-dehydro-silaadamantane dications 2(2+)-5(2+) has been carried out. Computed nucleus independent chemical shift (NICS) values are strongly indicative of three-dimensional heteroaromaticity in the resulting caged dications (via 2-electron, 4-center homoconjugation). In the optimized structures, silicon is pyramidalized. Although charge calculations (NPA and MKS) indicate significant positive charge build-up at silicon(s), the (29)Si GIAO NMR chemical shifts are unusually shielded. The latter finding agrees with the recent DFT calculations on 7-silanobornadien-7-ylium monocation 10(+), suggesting that silicon shielding is a consequence of unusual bonding and homoconjugation in the dications. Both NICS values and silicon shielding decrease in going from 2(2+) to 5(2+). Natural bond orbital (NBO) analysis was utilized to shed light on the origin of the three-dimensional heteroaromaticity in these dications.     

Theoretical (DFT, GIAO-NMR, NICS) study of carbocations (M+H)+, dications (M2+) and dianions (M2-) from dihydro-dicyclopenta[ef,kl]heptalene (dihydro-azupyrene), dihydro-dicyclohepta[ed,gh]pentalene, and related bridged [14]annulenes

The annulenium ions of protonation, the two-electron oxidation dications, and the two-electron reduction dianions derived from dihydro- and dimethyldihydro derivatives (cis and trans) of dicyclopenta[ef,kl]heptalene (azupyrene) (1) and dicyclohepta[ed,gh]pentalene (2), which are the nonalternant isomers of pyrene, were studied by density functional theory (DFT) at the B3LYP/6-31G(d), 6-31+G(d,p), or 6-31++G(d,p) levels. Charge delocalization modes in the energetically most favored annulenium ions, as well as in the singlet and triplet dications and dianions, were assessed based on gauge-including atomic orbital (GIAO) Deltadelta](13)C values and via changes in natural population analysis (NPA) charges. Relative aromaticity/antiaromaticity in the annulenes were gauged via nucleus-independent chemical shift (NICS) and DeltaNICS. Annulenium ions of monoprotonation, the dications, and dianions derived from bismethano- and propanediylidene [14]annulenes were also studied by DFT for comparison with the cis-dihydro isomers derived from . Computed GIAO NMR data and the optimized geometries were compared with the experimental data when available, and the optimized geometries were compared with the X-ray data if known. A basis-set dependency study of the computed GIAO chemical shifts was also undertaken. The present DFT work represents the first detailed comparative theoretical study of charged annulenes derived from the dihydro derivatives of and .     

A theoretical (DFT, GIAO-NMR, NICS) study of the carbocations and oxidation dications from azulenes, homoazulene, benzazulenes, benzohomoazulenes, and the isomeric azulenoazulenes

Protonation of parent azulene (1), homoazulene (8), representative isomeric benzazulenes (9, 9A, and 9B), and benzohomoazulenes (10, 10A, and 10B) as well as the mono- and diprotonation of isomeric azulenoazulenes (11-16) were studied by DFT at the B3LYP/6-31G(d) level. The most likely carbocations were identified based on relative protonation energies. For comparison, complete experimental 13C NMR data were obtained for parent azulenium ion 1H+ and guaiazulenium ion 2H+ in TFA. The oxidation dications derived from benzazulenes (9, 9A, and 9B), benzohomoazulenes (10, 10A, and 10B) and azulenoazulenes (11, 16) were also investigated. For azulenoazulene dications the singlet and triplet states are both minima, but except for 11(2+) and 13(2+), the triplet states are higher in energy. Structural/geometrical changes in the carbocations were examined. GIAO-NMR, NPA charges (and changes in charges), and NICS (and delta NICS) were employed to compute the NMR chemical shifts (delta delta 13C values) in order to derive charge delocalization maps and to gauge relative aromaticitylantiaromaticity in the energetically most favored carbocations and oxidation dications. The emerging trends are discussed and compared. Creation of tropylium or homotropylium entities in the carbocations (monoprotonated) and carbodications (diprotonated) is identified as an important driving force governing the protonation outcomes. Consideration of the AM1-derived delta delta Hf values (and the DFT-derived delta delta G values) suggests that the two-electron oxidation of azulenoazulenes should be experimentally feasible. Given their antiaromatic (paratropic) character, azulenoazulene dications represent interesting targets for NMR study. GIAO-derived charge delocalization mapping allows the most likely sites for nucleophilic attack on the dications to be identified.     

Mechanisms of reactive oxygen species photogeneration by benzo[a]pyrene: A DFT study

Benzo[a]pyrene (BaP) possesses photosensitive activity and can photogenerate reactive oxygen species (ROS), which have been postulated to be involved in the BaP induced oxidative DNA damage. Therefore, in the present work, a thermodynamic analysis on the ROS-photogenerating mechanisms of BaP was performed on the basis of quantum chemical calculations. It was revealed that: (i) the ¹O₂-generating pathway involves direct energy transfer from triplet excited state BaP to ³O₂ both in benzene and water; (ii) BaP gives birth to O₂^? through two pathways in water, i.e., electron transfer from triplet excited state BaP or anion radical of BaP to ³O₂.     

Beta-silyl-substituted silaadamantyl,silabicyclo[2.2.2]octyl,silanorbornyl, and 1-silacyclohexyl cations. A theoretical (DFT and GIAO NMR) study

Parent 1-silaadamant-1-yl (1+) and a series of mono-beta-silyl-substituted- (2-Me+, 2-F+, 2-Cl+, 2-Br+), bis-beta-silyl-substituted- (3-Me+), and tris-beta-silyl-substituted (4-Me+)-1-silaadamant-1-yl cations were studied by the DFT method at the B3LYP/6-31G(d,p) level and by GIAO NMR at the B3LYP/ 6-31G(d,p)//B3LYP/6-31G(d,p) level. The geometries, relative energies, NMR chemical shifts, and charge distribution in the bridgehead silylium ions are discussed and compared. The magnitude of the beta-silyl effect (the Si-C-Si+ hyperconjugation) is gauged as a function of structure. Related model studies on the silabicyclo[2.2.2]octyl (5+, 6+, 5a+, and 6a+), silanorbornyl (7+ and 8+), and silacyclohexyl cations (9+ and 10+) were carried out in which the effect of beta-silyl substitution on geometry, stability, and NMR chemical shifts was probed. The acyclic model Me3Si-CH2-Si+(Me)2 (11+) was used to gauge the influence of the twist angle between the p-orbital at Si+ and the C-Si bond on relative stability and on the changes in the 29Si NMR chemical shifts. Finally, interaction of 1+ with H2O and MeOH and 2-Me+ with H2O was also examined. The resulting optimized structures (12+, 13+, and 14+) and the computed NMR chemical shifts are most compatible with the formation of silaoxonium ions.     

Measurement of benzo[a]pyrene,benzo[k]fluoranthene and benzo[g,h,i]perylene by ultraviolet spectroscopy

Microchimica Acta - The technique for determining benzo[a]pyrene, benzo[k]fhuoranthene, and benzo[g,h,i]perylene respectively inμg amounts by UV absorption measurements is described. The...     

DFT study on [4+2] and [2+2] cycloadditions to [60] fullerene

The functionalisation of C₆₀ fullerene with 2,3-dimethylene-1,4-dioxane (I) and 2,5-dioxabicyclo [4.2.0]octa-1(8),6-diene (II) was investigated by the use of density functional theory calculations in terms of its energetic, structural, field emission, and electronic properties. The functionalisation of C₆₀ with I was previously reported experimentally. The I and II molecules are preferentially attached to a C—C bond shared and located between two hexagons of C₆₀ via [4+2] and [2+2] cycloadditions bearing reaction energies of ?15.9 kcal mol^?1 and ?72.4 kcal mol^?1, respectively. The HOMO-LUMO energy gap and work function of C₆₀ are significantly reduced following completion of the reactions. The field electron emission current of the C₆₀ surface will increase after functionalisation of either the I or II molecule.     

Wavefunction and reactivity study of benzo[a]pyrene diol epoxide and its enantiomeric forms

Benzo[a]pyrene is a known carcinogen, which derives from fossil fuel combustion, cigarette smoke, and generic biomass combustion including traffic emissions. This potent carcinogen has a well-known mechanism of action, leading to the formation of adducts with the DNA, primarily at guanosine positions. The reactivity and chemistry of this notorious compound are, however, dependent on the electronic configuration of the biologically activated metabolite, the benzo[a]pyrene diol epoxide. The activated metabolite exists mainly as four isomers, which have particular chemical reactivities toward guanosine sites on the DNA. These isomers exert also a different carcinogenicity compared to one another, which is a feature that is conventionally attributed to their geometry. However, the reactivity and properties of the isomers are not fully defined, and a determination of these properties by wavefunction behavior is required. This study reports the electronic properties of the benzo[a]pyrene diol epoxide enantiomers, along with a detailed analysis of the energy landscape, geometry, and electronic configuration of the epoxide ring. The results show that the epoxide ring, the core of the reactivity, bears different properties at the level of wavefunction for each isomer. Each of the isomers has a distinct profile on the epoxide ring, in terms of hydrogen bonds and in terms of the non-covalent interaction between the diol groups and the epoxide. These profiles generate differential reactivities of epoxide group, which can be attributed to its local bond lengths, the electron localization function, and polarized bonds. Most interestingly, the quantum chemical calculations showed also that the epoxide ring is inclined more perpendicularly toward the angular ring plane for the more carcinogenic isomers, a feature which suggests a potential geometrical relationship between the inclination of the epoxide group and its interaction with the guanosine group upon adduct formation. Our results introduce novel and crucial information, which assist in understanding the mechanism of toxic potential of this known molecule, and display the strength and level of detail of applying quantum chemical methods to reveal the reactivity, energy properties, and electronic properties of a mutagen.     

Oxidized metabolites from benzo[a]pyrene, benzo[e]pyrene, and aza-benzo[a]pyrenes. A computational study of their carbocations formed by epoxide ring opening reactions

A DFT study aimed at understanding structure-reactivity relationships and fluorine substitution effects on carbocation stability in benzo[a]pyrene (BaP), benzo[e]pyrene (BeP), and aza-benzo[a]pyrene (aza-BaP) derivatives are reported. The relative energies of the resulting carbocations are examined and compared, taking into account the available biological activity data on these compounds. O-Protonation of the epoxides and diol epoxides leads to carbocation formation by barrierless processes. Charge delocalization modes in the resulting carbocations were deduced via NPA-derived changes in charges, and fluorine substitution effects were analyzed on the basis of charge density at different carbocation positions. Thus, fluorine substitution at sites bearing negative charge generated inductive destabilization of the carbocation, whereas a fluorine atom at a ring position which presented significant positive charge density produced a less pronounced destabilization due to fluorine p-pi back-bonding. Protonation reactions were also studied for the azaBaPs. In selected cases, the covalent adducts generated via bond formation with the exocyclic nitrogen of cytosine were computed and relative energies and geometries of the resulting adducts were examined.     

Second-derivative constant-wavelength synchronous scan spectrofluorimetry for determination of benzo[b]fluoranthene, benzo[a]pyrene and indeno[1,2,3-cd]pyrene in drinking water

The use of derivative constant-wavelength synchronous scan fluorimetry is reported for the determination of three polycyclic aromatic hydrocarbon pollutants in drinking water (linearity range 0.4-4 mug 1(-1)). The limits of detection (LD) and quantification (LQ) (mug 1(-1)) are 0.01 and 0.07 for benzo[b]fluoranthene, 0.03 and 0.12 for benzo[a]pyrene and 0.19 and 0.57 for indeno[1,2,3-cd]pyrene in the presence of three other pollutants, benzo[k]fluoranthene, benzo[ghi]perylene and fluoranthene. The precision (RSD /= 85%) were satisfactory.     

Thermodynamic study of (anthracene + benzo[a]pyrene) solid mixtures

To characterize better the thermodynamic behavior of a binary polycyclic aromatic hydrocarbon mixture, thermochemical and vapor pressure experiments were used to examine the phase behavior of the {anthracene (1) + benzo[a]pyrene (2)} system. A solid–liquid phase diagram was mapped for the mixture. A eutectic point occurs at x₁ = 0.26. The eutectic mixture is an amorphous solid that lacks organized crystal structure and melts between T = (414 and 420) K. For mixtures that contain 0.10 < x₁ < 0.90, the enthalpy of fusion is dominated by that of the eutectic. (Solid + vapor) equilibrium studies show that mixtures of anthracene and benzo[a]pyrene at x₁ < 0.10 sublime at the vapor pressure of pure benzo[a]pyrene. These results suggest that the (solid + vapor) equilibrium of benzo[a]pyrene is not significantly influenced by moderate levels of anthracene in the crystal structure.     

Persistent oxidation dications from twisted fluoranthenes, benzo[k]fluoranthene and dimethyldibenzo[j.l]fluoranthene: charge delocalization mode, tropicity, and formation of novel 8,8'-bifluoranthenyls. An NMR and theoretical study.

First examples of persistent oxidation dications from fluoranthene-PAHs namely 1,3,4,6,7,10-hexamethyl- 2 and 3,4-dichloro-1,6,7,10-tetramethylfluoranthene 3, benzo[k]fluoranthene 6, and 3,6-dimethyldibenzo[j,l]fluoranthene 9 are reported. Charge delocalization mode and tropicity in the resulting nonalternant dications are examined. Quenching of the superacid solutions of the dications resulted in the formation of novel 8,8'-bifluoranthenyls 2a-4a. AM1 was used as an initial guide for dication generation (DeltaDeltaH(f) degrees and ionization potentials) and for probing the structures of the crowded fluoranthene substrates and their bifluoranthenyls. In selected cases, the dications and their neutral precursors were calculated at the B3LYP/6-31G(d,p) level. Charge delocalization mode (difference in NPA charges) and DFT/GIAO-derived NMR chemical shifts were obtained for comparison with experiment; aromaticity was assessed via nucleus independent chemical shift (NICS) calculations.     

Distinctive unimolecular gas-phase reactivity of [M(en)2]2+ (M=Ni, Cu) dications and their inclusion complexes with the macrocyclic cavitand Cucurbit[8]uril

Electrospray ionization mass spectrometry makes it possible to generate gas-phase bis-ethylenediamine nickel and copper dications, [M(en)(2)](2+) (M = Ni, 1; M = Cu, 2), as well as their {[M(en)(2)]@cuc[8]}(2+) inclusion complexes with the macrocyclic cavitand cucurbit[8]uril (cuc[8]). The unimolecular gas-phase reactivity of these species has been investigated by electrospray ionization tandem mass spectrometry with a quadrupole-time-of-flight configuration. Distinctive fragmentation pathways have been observed for the free and encapsulated [M(en)(2)](2+) (M = Ni, Cu) dications under collision-induced dissociation (CID) conditions. The dications [M(en)(2)](2+) (M = Ni, Cu) dissociate according to several competitive pathways that involve intra-complex hydrogen or electron-transfer processes. Most of these channels are suppressed after encapsulation inside the cucurbit[8]uril macrocycle and, as a consequence, a simplification of the {[M(en)(2)]@cuc[8]}(2+) fragmentation pattern is observed. The results obtained demonstrate that the encapsulation of a coordination complex inside a host molecule can be used to alter the nature of the product ions generated under CID conditions.     

Synthesis and NMR characterization of a dioxa-analog of benzo[a]pyrene: The 1-benzopyrano[6,5,4-mna]-xanthene (1,6-dioxabenzo[a]pyrene)

1,6-Dioxabenzo[a]pyrene, the first dioxa-analog of benzo[a]pyrene, was synthesized from 5-methoxy-1-naphthol in an eight-step reaction involving two peri-heterocyclizations.     

1H NMR spectra of benzo[b]furan,benzo[b]thiophene and benzo[b]selenophene oriented in a lyotropic mesophase

The proton nuclear magnetic resonance spectra of benzo[b]-furan, -thiophene and -selenophene oriented in a potassium laurate lyotropic liquid crystal have been analyzed. Geometrical information has been obtained and compared to previous thermotropic results and various hypothetical models.     

Neutron diffraction and theoretical DFT studies of two dimensional molecular-based magnet K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O

Exchange mechanisms and magnetic structure in the two-dimensional cyano-bridged molecule-based magnet K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O have been investigated by a combination of neutron diffraction studies on both single crystal and powder samples and theoretical DFT calculations. The experimental spin density has been deduced from a new refinement of previously obtained polarized neutron diffraction (PND) data which was collected in the ordered magnetic state at 4 K under a saturation field of 3 T performed in the C2/c space group, determined by an accurate re-evaluation of the X-ray structure. Positive spin populations were observed on the two manganese sites, and negative spin populations were observed on the molybdenum site, which provides evidence of antiferromagnetic Mo3+-Mn2+ exchange interactions through the cyano bridge. The experimental data have been compared to the results of DFT calculations. Moreover, theoretical studies reveal the predominance of the spin polarization mechanism in the Mo-C-N-Mn sequence, with the antiferromagnetic nature of the interaction being due to the overlap between the magnetic orbitals relative to manganese and molybdenum in the cyano bridging region. The magnetic structure of K2[Mn(H2O)2]3[Mo(CN)7]2.6H2O has been solved at low temperature in zero field by powder neutron diffraction measurements. The structure was found to be ferrimagnetic where the manganese and molybdenum spins are aligned along the axis in opposite directions.     

Ruthenium-catalyzed [2+2] cycloadditions between substituted alkynes and norbornadiene: a theoretical study

Theoretical predictions have been made using density functional theory for the reaction paths of a series of substituted alkynes undergoing a ruthenium-catalyzed cycloaddition with norbornadiene. Substituents on the alkynes have been varied in order to probe electronic and steric effects and the role of an intramolecular hydrogen bond. Strong electron-withdrawing groups activate the alkyne and decrease the reaction barrier leading to an increased rate. Bulkier substituents are predicted to lead to higher barriers and slower rates. The hydroxyl group on the alkyne hydrogen bonds to the chlorine stabilizes the transition state and increases the reaction rate. Generally good agreement is found with the trends in recently reported experimental relative rates of reaction of substituted alkynes with norbornadiene.     

Development of single-chain variable fragment (scFv) antibodies against hapten benzo[a]pyrene: a binding study

Due to its highly carcinogenic and mutagenic effect on humans, a maximum tolerable limit of 10 ng/L of benzo[a]pyrene (B[a]P) in drinking water was set by the European Commission (Council Directive 98/83/EC). Although several polyclonal and monoclonal antibodies (mAb) for the detection of B[a]P and other polycyclic aromatic hydrocarbons (PAH) have been developed by others, a traditional enzyme-linked immunosorbent assay (ELISA) with a limit of quantification of 10 ng/L for monitoring B[a]P has not been developed. With this in mind, several single-chain variable fragment (scFv) antibodies were created using existing mAbs against the extremely hydrophobic hapten B[a]P, and their heavy and light chains recombined to make unique variable light (V_L) and heavy (V_H) chain combinations. Their binding behaviour was investigated using microtiter plate ELISA and surface plasmon resonance techniques. Specifically, the coding sequences for V_L and V_H chains of 10 murine anti-B[a]P antibody producing hybridoma cell lines were isolated by degenerate oligonucleotide primer sets, cloned in phagemid pIT2 and transferred into Escherichia coli HB2151. To systematically investigate the interaction of the V_L and V_H domains, three high-affinity B[a]P-specific and one nonspecific clone were selected and recombined to build a set of 16 different V_L and V_H combinations. On the basis of our data, it was shown that the V_H plays the major role for specific binding of B[a]P, whilst the V_L can, in some cases, increase the final sensitivity of the assay by one order of magnitude. Furthermore, the sequence analysis of scFvs indicates that the complementarity determining region H3 plays a major role in affinity, whilst cross-reactivity to seven other PAHs demonstrates the importance of the V_L in providing cross-reactivity.     

Construction of dsDNA biosensor based on dendritic SiO2 nanoparticle and investigation on its interaction with benzo[a]pyrene

In this work, a new dsDNA biosensor was constructed to monitor the interaction of DNA and benzo[a]pyrene (BaP). Firstly, dendritic SiO₂ nanoparticles were synthesized by silanization of SiO₂ nanoparticles with (??-(methacryloyloxy)propyl) trimethoxysilane and polymerization with acrylic acid. Then, due to the rich carboxyl groups of these nanoparticles, they were associated with the amino groups of a self-assembly membrane formed on the gold electrode by a sulfur-containing compound, 5-amino-3-mercapto-1,2,4-triazole. Finally, dsDNA was immobilized on the electrode surface by static adsorption with the aid of metallic ion. The whole immobilization steps were characterized by cyclic voltammogram and electrochemical impedance spectrum. After that, using methylene blue as a probe, the interaction of BaP with dsDNA was investigated. A linear relationship between the percentages of current decrease with the logarithm of BaP concentrations was found in the range from 0.33 to 133???M.