Molecular calculations with the nonempirical ab initioMODPOT,VRDDO, and MODPOT/VRDDO procedures. XII. Carcinogenic 3-methylcholanthrene and its metabolites using a MERGE technique

Ab initio MODPOT/VRDDO/MERGE calculations were carried out on carcinogenic 3-methylcholanthrene (3-MCA) and its metabolites. The results for 3-MCA were compared to our earlier similar calculations for carcinogenic benzo(a)pyrene (BP). Both compounds 3-MCA and BP are carcinogenic and are metabolically activated by similar mechanisms but in different positions. Both the calculated wave functions for 3-MCA and BP and the electrostatic molecular potential contour maps generated from these wave functions correctly reflect the similarity of mechanisms of metabolic activation and the differences in position. Our calculated results both for BP and for 3-MCA reflect accurately their experimentally observed behavior. Thus this combination of theoretical techniques can be used with confidence to describe the behavior of the polycyclic aromatic hydrocarbons (PAH's) and their metabolites. The ab initio MODPOT/VRDDO method incorporates two very desirable options into our fast ab initio Gaussian programs: MODPOT –ab initio effective core model potentials—and a charge-conserving integral prescreening approximation which we named VRDDO (variable retention of diatomic differential overlap). For orbital energies and population analysis the MODPOT/VRDDO results agree to essentially three decimal places with completely ab initio calculations using the same valence atomic basis set. For this series of very closely related congeners our recent MERGE technique which allows reuse of integrals from a common skeletal fragment was used. The ab initio MODPOT/VRDDO/MERGE calculations were carried out for 3-MCA, 3-MCA oxides, 3-MCA dihydrodiols, and 3-MCA dihydrodiolepoxides. The metabolites investigated were 3-MCA 9,10-oxide; 3-MCA 7,8-oxide; 3-MCA 9,10-dihydrodiol [trans(axial, axial); trans(equatorial, equatorial); cis(axial, equatorial); cis(equatorial, axial)]; and 3-MCA 9,10-dihydrodiol–7,8-epoxide [for both conformations A and B of the dihydrodiol and for all stereoisomers of the dihydrodiolepoxides relative to below and above the plane: ααα, and ααβ αβα αββ βαα βαβ ββα and βββ (most stable)]. Calculations were also carried out for opening of the C₇? O? C₈ epoxide ring both towards C₇ and C₈ for the most stable isomer Aβββ (above the ring). Opening the epoxide ring between C₇ and O leads to a more stable intermediate than opening the epoxide ring between C₈ and O. Again, however, as with opening the epoxide ring in BP 7,8-dihydrodiol–9,10-epoxide there is no buildup of positive charge on C₇ in the 3-MCA metabolites as postulated by some cancer researchers, but rather the C₇ becomes slightly more negative. Nor is there a buildup of negative charge on the O atom, but rather it becomes slightly more positive. As the epoxide ring is opened further than 90° for the O? C₇? C₈ or O? C₈? C₇ angles, there appears to be a possible mixing of configurations that is being investigated further.     

Molecular calculations with the nonempirical ab initioMODPOT,VRDDO, and MODPOT/VRDDO procedures. IX. Carcinogenic benzo(a)pyrene and its metabolites using a MERGE technique

Ab initio MODPOT /VRDDO calculations have been carried out on carcinogenic benzo(a)pyrene and its metabolites. The MODPOT /VRDDO method incorporates two very desirable options into our fast ab initio Gaussian programs: MODPOT —ab initio effective core model potentials—and a charge-conserving integral prescreening approximation which we named VRDDO (variable retention of diatomic differential overlap). For orbital energies and population analyses the MODPOT /VRDDO results agree to essentially three decimal places with completely ab initio calculations using the same valence atomic basis set. For this series of very closely related congeners a new MERGE technique was implemented that allows reuse of integrals of a common skeletal fragment. Since our program computes integrals efficiently by blocks, reusing information common to the block, it was more difficult to implement a MERGE technique than for integral programs which calculate the integrals one-byone. The MODPOT /VRDDO calculations were performed for benzo(a)pyrene (BP), BP oxides, BP dihydrodiols, and BP dihydrodiol epoxides. The metabolites investigated were BP-7,8-oxide, BP-4,5-oxide, BP-7,8-dihydrodiol [cis(e, a), cis(a, e), trans(e, e), and trans(a, a)], and BP-7,8-dihydrodiol-9,10-epoxide [β,β,β (the most stable), β,β,α; α,α,β, and α,α,α all derived from cis-BP-7,8-dihydrodiol and β,α,β; α,β,β and α,β,β derived from trans-BP-7,8-dihydrodiol]. Several different conformations were calculated for each of the BP dihydrodiols and BP dihydrodiol epoxides. Calculations were carried out for the opening of the C₉—O—C₁₀ epoxide ring both toward C₉ and C₁₀ for the, most stable β,β,β isomer of BP-7,8-dihydrodiol-9,10-epoxide. Opening the epoxide ring between C₁₀ and O leads to a more stable intermediate than opening the epoxide ring between C₉ and C₁₀. However, there is no buildup of positive charge in C₁₀ as has been postulated by some cancer researchers, but rather the C₁₀ becomes slightly more negative. Nor is there a buildup of negative charge on the O atom. rather it becomes slightly less negative. As the epoxide ring is opened further than 90° for the O—C₉—C₁₀ or O—C₁₀—C₉ angles, there appears to be a possible mixing of configurations that is being investigated further.     

Ab initioMODPOT/VRDDO/MERGE calculations on energetic compounds. IV. Nitrocubanes: Mononitro to octanitro quantum chemical calculations and electrostatic molecular potential contour maps

Ab initio MODPOT /VRDDO /MERGE calculations have been carried out for all the different position isomers of nitrocubane from mononitrocubane through octanitrocubane for a perfect symmetrical cubic cubane skeleton and for mononitrocubane through septanitrocubane for the almost cubic experimentally determined cubane skeleton. These calculations were carried out with our own rapid efficient ab initio programs which also incorporate a number of desirable computational strategies for calculations on large molecules. The skeletal total overlap population of the cubane skeleton (a theoretical index we showed years ago to be sensitive and predictive of stability of energetic molecular frameworks) indicates that successive nitration seems to increase the stability of the cubane skeleton. Successive nitration also seems to increase the total overlap population of the C? NO₂ bond. There are subtle differences depending on the exact positional isomer for a constant number of nitro groups—but the overall trend is definite. We have also generated electrostatic molecular potential contour (EMPC ) maps around these nitrocubanes. These maps are indicative of preferred positions of electrophilic and nucleophilic attack as a function of the number of nitro groups or their positions. These EMPC maps can also indicate, to a first approximation, a limit on how close these molecules may be able to approach each other in a crystal.     

Catalytic mechanism of limonene epoxide hydrolase, a theoretical study

The catalytic mechanism of limonene epoxide hydrolase (LEH) was investigated theoretically using the density functional theory method B3LYP. LEH is part of a novel limonene degradation pathway found in Rhodococcus erythropolis DCL14, where it catalyzes the hydrolysis of limonene-1,2-epoxide to give limonene-1,2-diol. The recent crystal structure of LEH was used to build a model of the LEH active site composed of five amino acids and a crystallographically observed water molecule. With this model, hydrolysis of different substrates was investigated. It is concluded that LEH employs a concerted general acid/general base-catalyzed reaction mechanism involving protonation of the substrate by Asp101, nucleophilic attack by water on the epoxide, and abstraction of a proton from water by Asp132. Furthermore, we provide an explanation for the experimentally observed regioselective hydrolysis of the four stereoisomers of limonene-1,2-epoxide.     

1-Methyl-2-(1′-methyl-2′-pyrrolyl)-1H-phenanthro[9,10-d]-imidazole. Synthesis and electrophilic substitution reactions

2-(1′-Methyl-2′-pyrrolyl)-1H-phenanthro[9,10-d]imidazole was synthesized by heating 9,10-phenanthrenequinone and 1-methyl-2-pyrrolecarboxaldehyde in glacial acetic acid in the presence of ammonium acetate. The reactions of electrophilic substitution (nitration, bromination, sulfonation, formylation, acylation) were studied for the product of its N-methylation in the KOH-DMSO medium. The electrophilic attack was found to affect exclusively the pyrrole ring.     

On the use of isovalued surfaces to determine molecule shape and reaction pathways

Summary Novel insights into local molecule structure and reactivity can be gained from viewing isovalued surfaces of the molecular electron density, electrostatic potential and molecular orbitals rendered as colored, 3-D objects. For example, drawing positive and negative electrostatic isopotential surfaces partitions the molecule into regions subject to nucleophilic or electrophilic attack. Similarly, coloring isodensity surfaces to indicate the magnitude of the gradient of the electron density maps the molecule surface into regions of high and low electronegativity.A basic understanding of reaction mechanisms can also come from viewing and manipulating isovalued surfaces. A theory of molecular interactions, based upon second-order perturbation theory, provides for the decomposition of the intermolecular interaction energy into steric, electrostatic and orbital interactions. Color figures illustrate the docking of reactant molecular densities, electrostatic potentials and orbitals on low-energy pathways. The figures are used to visualize the steric, electrostatic and orbital contributions to molecular interaction energy. The visualization not only identifies low-energy reaction pathways, but it frequently reveals local interactions which determine the magnitude of the total interaction energy. Similar insight is not easily obtained by simple evaluation of the total interaction energy. Approximate transition states, built from structures along low-energy approach pathways, are excellent starting points for transition state searches.CAChe^TM Technical Report No. 1, Tektronix Inc., Beaverton, OR.     

Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9,10-oxide

Glutathione S-transferases (GSTs) play an important role in the detoxification of xenobiotics in mammals. They catalyze the conjugation of glutathione to a wide range of electrophilic compounds. Phenanthrene 9,10-oxide is a model substrate for GSTs, representing an important group of epoxide substrates. In the present study, combined quantum mechanical/molecular mechanical (QM/MM) simulations of the conjugation of glutathione to phenanthrene 9,10-oxide, catalyzed by the M1-1 isoenzyme from rat, have been carried out to obtain insight into details of the reaction mechanism and the role of solvent present in the highly solvent accessible active site. Reaction-specific AM1 parameters for sulfur have been developed to obtain an accurate modeling of the reaction, and QM/MM solvent interactions in the model have been calibrated. Free energy profiles for the formation of two diastereomeric products were obtained from molecular dynamics simulations of the enzyme, using umbrella sampling and weighted histogram analysis techniques. The barriers (20 kcal/mol) are in good agreement with the overall experimental rate constant and with the formation of equal amounts of the two diastereomeric products, as experimentally observed. Along the reaction pathway, desolvation of the thiolate sulfur of glutathione is observed, in agreement with solvent isotope experiments, as well as increased solvation of the epoxide oxygen of phenanthrene 9,10-oxide, illustrating an important stabilizing role for active site solvent molecules. Important active site interactions have been identified and analyzed. The catalytic effect of Tyr115 through a direct hydrogen bond with the epoxide oxygen of the substrate, which was proposed on the basis of the crystal structure of the (9S,10S) product complex, is supported by the simulations. The indirect interaction through a mediating water molecule, observed in the crystal structure of the (9R,10R) product complex, cannot be confirmed to play a role in the conjugation step. A selection of mutations is modeled. The Asn8Asp mutation, representing one of the differences between the M1-1 and M2-2 isoenzymes, is identified as a possible factor contributing to the difference in the ratio of product formation by these two isoenzymes. The QM/MM reaction pathway simulations provide new and detailed insight into the reaction mechanism of this important class of detoxifying enzymes and illustrate the potential of QM/MM modeling to complement experimental data on enzyme reaction mechanisms.     

Nature of Noncovalent Carbon‐Bonding Interactions Derived from Experimental Charge‐Density Analysis

In an effort to better understand the nature of noncovalent carbon‐bonding interactions, we undertook accurate high‐resolution X‐ray diffraction analysis of single crystals of 1,1,2,2‐tetracyanocyclopropane. We selected this compound to study the fundamental characteristics of carbon‐bonding interactions, because it provides accessible σ holes. The study required extremely accurate experimental diffraction data, because the interaction of interest is weak. The electron‐density distribution around the carbon nuclei, as shown by the experimental maps of the electrophilic bowl defined by a (CN)₂C?C(CN)₂ unit, was assigned as the origin of the interaction. This fact was also evidenced by plotting the Δ²ρ(r) distribution. Taken together, the obtained results clearly indicate that noncovalent carbon bonding can be explained as an interaction between confronted oppositely polarized regions. The interaction is, thus electrophilic–nucleophilic (electrostatic) in nature and unambiguously considered as attractive.     

Activation of leinamycin by thiols: a theoretical study

Reaction of thiols with the 1,2-dithiolan-3-one 1-oxide heterocycle found in leinamycin (1) results in the conversion of this antitumor antibiotic to a DNA-alkylating episulfonium ion (5). While the products formed in this reaction have been rationalized by a mechanism involving initial attack of thiol on the central sulfenyl sulfur (S2') of the 1,2-dithiolan-3-one 1-oxide ring, the carbonyl carbon (C3') and the sulfinyl sulfur (S1') of this heterocycle are also expected to be electrophilic. Therefore, it is important to consider whether nucleophilic attack of thiol at these sites might contribute either to destruction of the antibiotic or conversion to its episulfonium ion form. To address this question, we have used computational methods to examine the attack of methyl thiolate on each of the three electrophilic centers in a simple analogue of the 1,2-dithiolan-3-one 1-oxide heterocycle found in leinamycin. Calculations were performed at the MP2/6-311+G(3df,p)//B3LYP/6-31G level of theory with inclusion of solvent effects. The results indicate that the most reasonable mechanism for thiol-mediated activation of leinamycin involves initial attack of thiolate at the S2'-position of the antibiotic's 1,2-dithiolan-3-one 1-oxide heterocycle, followed by conversion to the 1,2-oxathiolan-5-one intermediate (3).     

A computational analysis of ortho-lithiation in aromatic systems

We have analyzed the ability of a tertiary amide group to activate an ortho position on aromatic system toward an electrophilic attack using an ab initio SCF molecular orbital method. The molecular electrostatic potential was used to analyze the electronic nature of the ortho-lithiated intermediate complex and possible sites for electrophilic attack.     

Quantification of benzo[a]pyrene diol epoxide DNA-adducts by stable isotope dilution liquid chromatography/tandem mass spectrometry

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants found in car exhausts, charbroiled food, and tobacco smoke. Three pathways for the metabolic activation of B[a]P to ultimate carcinogens have been proposed. The most widely accepted pathway involves cytochrome-P450 (CYP) 1A1- and/or 1B1-mediated formation of B[a]P-7,8-oxide, which undergoes epoxide hydrolase-mediated metabolism to the proximate carcinogen B[a]P-7,8-dihydro-7,8-diol. Further CYP1A1- and/or CYP1B1-mediated activation of the dihydrodiol results in the formation of 7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (B[a]PDE), the ultimate carcinogen. In previous studies, it was demonstrated that (+)-anti-B[a]PDE was the most potent tumorigen of the CYP-derived B[a]PDE diastereomers. We have developed a stable isotope dilution, liquid chromatography multiple reaction monitoring/mass spectrometry (LC-MRM/MS) assay for all eight (+/-)-anti-B[a]PDE-derived dGuo and dAdo DNA-adducts. The LC-MRM/MS assay was rigorously validated and used to show that (+)-anti-trans-B[a]PDE-dGuo was the major adduct formed when naked DNA and human bronchoalveolar adenocarcinoma H358 cells were treated with (+/-)-anti-B[a]PDE. The preference for DNA-adducts derived from (+)-anti-B[a]PDE was even more apparent in cellular DNA. Thus, the increased potency of (+)-anti-B[a]PDE as a tumorigen is most likely due its ability to preferentially form DNA-adducts when compared with (-)-anti-B[a]PDE. Also, the adduct profile suggests that this occurs by binding of (+)-anti-B[a]PDE to DNA in a manner that facilitates covalent binding to dGuo rather than dAdo residues.     

Synthesis and properties of phosphorus-containing epoxy resins by novel method

Novel phosphorus-containing epoxy resins (1–3% phosphorus content) were synthesized by the reaction of 9,10-dihydro-9-oxa-10-phosphaphenanthrene 10-oxide (DOPO) and the diglycidyl ether of bisphenol A and then cured with 4,4′-diaminodiphenyl sulfone or phenol novolac. Differential scanning calorimetry, high performance liquid chromatography, and epoxide equivalent weight titration were used to trace the reaction between the DOPO and the epoxy. The thermal stability and flame retardancy were checked by thermal gravimetric analysis, the limiting oxygen index, and the UL-94 vertical test. The glass transitions were measured by dynamic mechanical analysis. The relation between these properties (thermal stability, flame retardancy, and glass transition) and the DOPO contents (phosphorus content) were discussed. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 3903–3909, 1999     

Influence of calculation level and effect of methylation on axial/equatorial equilibria in piperidines

A detailed conformational analysis was performed on the chair forms of piperidine, N-methylpiperidine, and some methylated derivatives using Hartree–Fock (HF) and MP2 ab initio methods with several basis sets (from 3–21G to 6–311++G**), and the most widely used semiempirical approaches (MNDO, AM1, and PM3). It was found that the use of polarized basis sets at the HF level is adequate enough for the prediction of conformational preferences in the axial/equatorial equilibrium of the N-R group in piperidines. On the other hand, the inclusion of electron correlation becomes necessary for predicting the axial/equatorial energy differences of the equilibria of the methyl group. Semiempirical methods are not recommended, because AM1 and PM3 predict opposite stabilities to those obtained experimentally and MNDO ring geometries are systematically too flat. The origin of the conformational stabilities was interpreted in terms of the natural bond orbital analysis of the HF/6–31G** wave functions. The equatorial preferences in the N-H equilibria is mainly due to lower Lewis energies, although delocalization of the nitrogen lone pair is favored in N-H axial forms. N-Methylation increases the equatorial M-Me preferences, because the Lewis energy of axial N-Me forms increases due to larger 1,3-diaxial interactions. Geometrical trends associated with the delocalization of the nitrogen lone pair and with interactions between the introduced N-R and C-Me groups were discussed and related to the degree of planarity of the six-membered ring by means of the puckering coordinates defined by Pople and Cremer. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 961–976, 1998     

Stable ion study of benzo[a]pyrene (BaP) derivatives: 7,8-dihydro-BaP, 9,10-dihydro-BaP and its 6-halo derivatives, 1- and 3-methoxy-9,10-dihydro-BaP-7(8H)-one,as well as the proximate carcinogen BaP 7,8-dihydrodiol and its dibenzoate,combined with a comparative DNA binding study of regioisomeric (1-, 4-, 2-) pyrenylcarbinols

A stable ion study of a series of BaP derivatives is reported. 7,8-Dihydro-BaP 1 gives a persistent bay-region benzyliclike carbocation which shows extensive charge delocalization into the pyrene moiety. In contrast, a "benzylic" carbocation can not be generated from 9,10-dihydro-BaP 2. Introduction of bulky substituents at peri C-6 of 9,10-dihydro-BaP (as in 4 and 5) prevents side reactions (dimerization) to the extent that the initially formed carbocation undergoes rearrangement to generate the corresponding bay-region "benzylic" carbocation as a persistent species. Introduction of methoxy substituents into the 1- or 3-positions of 9,10-dihydro-BaP-7(8H)-one (6,7) increases its electrophilic reactivity to the extent that stable carboxonium-arenium dications are produced in FSO3H-SO2ClF. A detailed NMR study (at 500 MHz) of the resulting mono- and dications is reported, and charge delocalization mode (as well as conformational aspects) are addressed. Other oxidized derivatives of BaP such as the 7,8-dihydrodiol 9 and the 7,8-dihydrodibenzoate 8 are not suitable models for stable ion study because of competing O-protonation (and elimination). Energies for various possible arenium ions and regioisomeric "benzylic" cations were computed by the DFT method at the B3LYP/6-31G(d)//B3LYP/6-31G(d) level or by AM1 for comparison with the experimental results. These findings provide further evidence in support of the stability sequence: 1-pyrenyl > 4-pyrenyl > 2-pyrenyl in alpha-pyrene-substituted carbocations as models for the intermediates arising from BaP-epoxide ring opening. In an effort to provide a parallel, a series of alpha-pyrenylcarbinols were subjected to a DNA binding study using human MCF-7 cells. The results/trends are discussed and compared with the stable ion data.     

Exploring the substrate selectivity of human sEH and M. tuberculosis EHB using QM/MM

The mechanisms of human soluble epoxide hydrolase (sEH) and the corresponding epoxide hydrolase enzyme from Mycobacterium tuberculosis (EHB) are studied computationally, using the quantum mechanics/molecular mechanics (QM/MM) method. To do this, we modeled the alkylation and the hydrolysis steps of three substrates: trans-1,3-diphenylpropene oxide, trans-stilbene oxide and cis-stilbene oxide. Studying the regioselectivity for trans-1,3-diphenylpropene oxide, we determined that both enzymes prefer ring opening via attack on the benzylic carbon. In agreement with experimental studies, our computations show that the rate-limiting step is hydrolysis of the ester intermediate, with reaction barriers of approximately 13 to 18 kcal/mol. Using the barrier energies of this rate-limiting step, the three epoxides were ranked in order of reactivity. Though the reactivity order was correctly predicted for sEH, the predicted order for EHB did not correspond to experimental observations. Next, the electrostatic contributions of individual residues on the barrier height of the rate-limiting step were also studied. This revealed several residues important for catalysis. The secondary tritium kinetic isotope effect for the alkylation step was determined using a cluster model for the active site of sEH. The calculated value was 1.27, suggesting a late transition state for the rate-limiting step. Finally, we analyzed the reactivity trends using reactivity indicators from conceptual density functional theory, allowing us to identify ease of electron transfer as the primary driving force for the reaction.

     

Conformational Analysis of C‐Trehaloses Using Molecular Mechanics Calculations

Relaxed‐residue energy maps based on the MM3 force field were computed for the three C‐linked (1‐1) d‐glucosyl disaccharides, C‐trehaloses: the axial–axial linked α,α‐trehalose, the axial–equatorial α,β‐trehalose and the equatorial–equatorial linked β,β‐trehalose. Optimized structures were calculated on a 20°‐grid spacing of the torsional angles about the C‐glycosidic bonds. Boltzman weighted ³J coupling constants were calculated and compared to the experimental values; they are satisfactory. The general shape of the energy maps indicates that α,α‐trehalose is a quite rigid molecule adopting only one conformation around the C‐glycosidic linkage, whereas the other two isomers are rather flexible. Compared to the corresponding O‐disaccharides α,β‐ and β,β‐trehaloses exhibit a larger number of low energy conformers and a larger area of the map energy < 8 kcal/mol. The preferred conformations of the axial C‐glycosidic bond are in agreement with the exo‐anomeric effect. Equatorial C‐ glycosidic bonds are rather flexible, influenced by the polarity of the milieu and the formation of interresidue hydrogen bonds.     

Transition-state effects in acid-catalyzed aryl epoxide hydrolyses

The hydronium ion-catalyzed hydrolyses of 5-methoxyindene 1,2-oxide and of 6-methoxy-1,2,3,4-tetrohydronaphthalene-1,2-epoxide were each found to yield 75-80% of cis diol and only 20-25% of trans diol as hydrolysis products. The relative stabilities of the cis and trans diols in each system were determined by treating either cis or trans diols with perchloric acid in water solutions and following the approach to an equilibrium cis/trans mixture as a function of time. These studies establish that the trans diol in each system is more stable than the corresponding cis diol. Thus, acid-catalyzed hydrolysis of each epoxide, which proceeds via a carbocation intermediate, yields the less stable cis diol as the major product. Transition-state effects, presumably of a hydrogen-bonding nature, selectively stabilize the transition state for attack of water on the intermediate 2-hydroxy-1-indanyl carbocation leading to the less stable cis diol in this system. Transition-state effects must also be responsible for formation of the less stable cis diol as the major product in the acid-catalyzed hydrolysis of 5-methoxy-1,2,3,4-tetrahydronaphthalene 1,2-epoxide. However, in this system steric effects at the transition state may be more important than hydrogen bonding in determining the cis/trans diol product ratio. The synthesis of 5-methoxyindene 1,2-oxide and a study of its rate of reaction as a function of pH in water and dioxane-water solutions are reported. Both an acid-catalyzed reaction leading to only diol products and a pH-independent reaction yielding 71% of 5-methoxy-2-indanone and 29% of diols are observed; the half-life of its pH-independent reaction in water is only 2.4 s.     

Computational studies of stable hexanuclear CulAgmAun (l + m + n = 6; l,m, n > 0) clusters

A DFT study was carried out on the ground state structures of ternary Cu_lAg_mAu_n (l + m + n = 6) clusters, with the aim of investigating changes of thermal and kinetic stabilities as an effect of composition, as well as the composition dependence of the electrostatic potential, of stable planar structures. DFT optimizations were performed using the PBE functional and the SDD basis set. All the optimized structures adopt planar geometries with bent triangular structures. Calculated binding energy values are in the range 1.5–1.9 eV/atom, which shows their thermal stability. The predicted HOMO‐LUMO energy gap values are in the semiconductor region, providing a qualitative indication of a moderate kinetic stability. NBO analyses indicate the existence of two mechanisms promoting planar structural stability, one due to bonding‐antibonding orbital interaction, and the other one due to the well‐known spd hybridization. Wiberg indices were obtained showing interatomic bonding. Electrostatic potential calculations show the existence of nucleophilic attack regions preferentially around silver and copper atoms located at the vertices while electrophilic attack regions are found in the vicinity of gold atoms over the cluster plane. Apparently, charge transfer occurs toward gold from silver and copper atoms when the concentration is favorable in the proximity of gold atoms. In particular, if the small ternary clusters discussed here contain only one gold atom, then a high electron density is observed at the site of this gold atom. © 2016 Wiley Periodicals, Inc.     

Influence of oxygen/sulfur-termination on electronic structure and surface electrostatic potential of (6,0) carbon nanotube: a DFT study

A density functional theory study was carried out to investigate the electronic and structural properties of oxygen- and sulfur-terminated models of zigzag (6,0) carbon nanotube (CNT). In general, the C–C bond lengths are significantly changed upon O/S-termination in the considered models. Our calculations indicate that due to the O/S-doping at the tip(s) of pristine CNT, the evaluated electron density tends to increase slightly at the axial C–C bond critical points. In order to characterize and provide valuable information of the origin of noncovalent interactions, electrostatic potentials are computed on the surface of the CNTs. Our results reveal that the characteristic surface patterns are considerably influenced by O/S-termination and the dopant atoms tend to activate the surface toward electrophilic/radical attack.     

Identification and quantification of urinary benzo[a]pyrene and its metabolites from asphalt fume exposed mice by microflow LC coupled to hybrid quadrupole time-of-flight mass spectrometry

Prolonged, extensive exposure to asphalt fume has been associated with several adverse health effects. Inhaled polycyclic aromatic hydrocarbons (PAHs) from asphalt fume exposure have been suspected of inducing such effects. In this study, a bioanalytical method was proposed and evaluated to identify and quantify benzo[a]pyrene and its hydroxy-metabolites. This method is based on coupling a microflow liquid chromatography (LC) to a hybrid quadrupole orthogonal acceleration time-of-flight mass spectrometry (Q-TOFMS). In the experiment, thirty-two B6C3FI mice were exposed to asphalt fume in a whole body inhalation chamber for 10 days (4 h day(-1)) and twelve other mice were used as controls. The asphalt fume was generated at 180 degrees C and the concentrations in the animal exposure chamber ranged 175-182 mg m(-3). Benzo[a]pyrene and its metabolites of 3-hydroxybenzo[a]pyrene, benzo[a]pyrene-7,8-dihydrodiol(+/-), benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide(+/-), and benzo[a]pyrene-7,8,9,10-tetrahydrotetrol(+/-) in the urine of asphalt fume exposed mice were identified and found at 3.18 ng 100 mL(-1), 31.36 ng 100 mL(-1), 11.56 ng 100 mL(-1), 54.92 ng 100 mL(-1), and 45.23 ng 100 mL(-1) respectively. The results revealed that the urinary benzo[a]pyrene and its hydroxy-metabolites from exposed mice were at significantly higher levels (p < 0.001) than those from the control groups. Compared with several other technologies such as HPLC-UV and HPLC-fluorescence, the new method is more sensitive and selective, and it can also provide additional useful information on the structures of the metabolites. Hence, this method can be used to perform the assessment and to study the mechanisms of the adverse health effects. The fragmentation patterns established in this study can also be used to identify and quantify PAH metabolites in other biological fluids.