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

Origin of metabolites diversity and selectivity of P450 catalyzed benzo[a]pyrene metabolic activation

Polycyclic Aromatic Hydrocarbon (PAHs) presents one of the most abundant class of environmental pollutants. Recent study shows a lab-synthesized PAHs derivative, helicenium, can selectively kill cancer cells rather than normal cells, calling for the in-depth understanding of the metabolic process. However, the origin of metabolites diversity and selectivity of P450 catalyzed PAHs metabolic activation is still unclear to a great extent. Here we systematically investigated P450 enzymes catalyzed activation mechanism of a representative PAHs, benzo[a]pyrene (BaP), and found the corresponding activation process mainly involves two elementary steps: electrophilic addition and epoxidation. Electrophilic addition step is evidenced to be rate determining step. Two representative binding modes of BaP with P450 were found, which enables the electrophilic addition of Heme (FeO) to almost all the carbons of BaP. This electrophilic addition was proposed to be accelerated by the P450 enzyme environment when compared with the gas phase and water solvent. To dig deeper on the origin of metabolites diversity, we built several linear regression models to explore the structural-energy relationships. The selectivity was eventually attributed to the integrated effects of structural (e.g. O-C distance and O-C-Fe angle) and electrostatic parameters (e.g. charge of C and O) from both BaP and P450.

Endocrine-disrupting metabolic activation of 2-nitrofluorene catalyzed by human cytochrome P450 1A1: A QM/MM approach

Nitropolycyclic aromatic hydrocarbons (NPAHs) present one of the most important airborne pollutants. Recent studies have shown that one of the most abundant NPAHs, 2-Nitrofluorene (NF), was supposed to be converted to endocrine-disrupting metabolites by cytochrome P450 1A1 (CYP1A1) in human cells. However, the mechanism is still largely unexplored. Here the metabolic activation and transformation mechanism of NF catalyzed by CYP1A1 were systematically studied with the aid of Molecular Dynamics, Density Functional Theory and Quantum Mechanics/Molecular Mechanics techniques. We evidence that CYP1A1 can activate NF through two elementary processes: (i) electrophilic addition (12.4 kcal·mol-1) or hydrogen abstraction (38.2 kcal·mol-1) and (ii) epoxidation (5.9 and 8.7 kcal·mol-1) or NIH shift (12.5 and 14.9 kcal·mol-1) or proton shuttle (12.1 kcal·mol-1). Electrophilic addition was found to be the rate-determining step while epoxidation rather than NIH shift or proton shuttle is the more feasible pathway after electrophilic addition. Metabolites 6,7-epoxide-2-nitrofluorene and 7,8-epoxide-2-nitrofluorene were identified as the major epoxidation products. Epoxides are unstable and easy to react with hydrated hydrogen ions and hydroxyls to produce endocrine disrupter 7-hydroxy-2-nitrofluorene. Toxic analysis shows that some of the metabolites are more toxic to model aquatic organisms (e.g. Green algea) than NF. Binding affinity analysis to human sex hormone binding globulin reveals that NF metabolites all have endocrine-disrupting potential. This study provides a comprehensive understanding on the biotransformation process of NF and may aid future studies on various NPAHs activation catalyzed by human P450 enzyme.

Computational study on the detoxifying mechanism of DDT metabolized by cytochrome P450 enzymes

Predicting the detoxifying mechanism and potential toxic derivatives of xenobiotic substances is significant for risk assessment. The present study delineated the detoxifying mechanism of 1-chloro-4-[2,2,2-trichloro-1-(4-chlorophenyl)ethyl]benzene (DDT) metabolized by human P450 enzymes using a combination of molecular dynamic (MD), quantum mechanics/molecular mechanics (QM/MM) and density functional theory (DFT). This study highlights that DDT can be metabolized by P450 enzymes through the hydrogen abstraction and electrophilic addition mechanism, and the main derivatives are epoxides (2,3-oxide-DDT and 3,4-oxide-DDT), DDE and dicofol. The epoxides are unstable and the C-O bond cleavage easily occurs by the reaction with hydronium ion or hydroxyl radicals, yielding endocrine disruptor hydroxylated DDT. The eco-toxicity evaluation indicates that the derivatives of DDT are less toxic than DDT, and the solubility increase of the derivatives can accelerate their excretion from the body. The study can provide an understanding of the biotransformation of DDT by the P450 enzymes in human livers.

Visible-Light-Mediated [2+2+1] Carbocyclization Reactions of 1,7-Enynes with Bromofluoroacetate to Form Fused Monofluorinated Cyclopenta[c]quinolin-4-ones

Herein, we describe a new protocol for photoinduced radical [2+2+1] carbocyclization reactions of 1,7-enynes with bromofluoroacetate. These reactions, which proceed via a cascade involving fluoroalkylation, 6-exo-dig and 5-endo-trig cyclizations, H-transfer step, and oxidative dehydrogenation, provide an efficient and general route to a variety of fused monofluorinated cyclopenta[c]quinolin-4-one derivatives.

Transformation potential of cannabinoids during their passage through engineered water treatment systems: A perspective

Cannabinoids are incipient contaminants with limited literature in the context of water treatment. With increasing positive public opinion toward legalization and their increasing use as a pharmaceutical, cannabinoids are expected to become a critical class of pollutant that requires attention in the water treatment industry. The destructive removal of cannabinoids via chlorination and other oxidation processes used in drinking water and wastewater treatment requires careful investigation, because the oxidation and disinfection byproducts (DBPs) may pose significant risks for public health and the environment. Understanding transformation of cannabinoids is the first step toward the development of management strategies for this emerging class of contaminant in natural and engineered aquatic systems. This perspective reviews the current understanding of cannabinoid occurrence in water and its potential transformation pathways during the passage through drinking water and wastewater treatment systems with chlorination process. The article also aims to identify research gaps on this topic, which demand attention from the environmental science and engineering community.

To freeze, or not to freeze: the impact of subzero temperature on quantifying organic contaminants in ocean sediments

Assessing the extent of ocean bed contamination by anthropogenic organic chemicals requires collecting and preserving the native state of sediments. The latter is particularly important since most sediment analyses are performed away from the sites of samples collection. Preservation, however, is presumptuous since commonly used sediment handling practices such as freezing are structurally disruptive, the impacts of which are not well understood. In this study, the impact of freezing on quantifying the total organic carbon (TOC) contents and the extent of PAH, DDT and PCB contamination in 17 split-paired sediment samples was investigated. The samples were collected from the Santa Monica Bay, California (USA). One-half of each split-pair was frozen at -20 °C and the other half was refrigerated at 4 °C for up to 11 days. The results suggest that no significant differences exist between the frozen and the refrigerated datasets for PCBs (F1,28 = 4.01, p > 0.05), DDTs (n = 16, t-Stat < t-Critical, p > 0.05) or TOC (n = 16, t-Stat < t-Critical, p > 0.05). The results however show that less PAHs were detected in the frozen sediments (F1,24 = 8.18, p < 0.05) than in the refrigerated sediments; the larger PAHs were affected the most. Interestingly, while benzo[a]pyrene, a large PAH molecule, was affected by this apparent temperature-induced difference, its structural isomer, benzo[e]pyrene, was not. Even more interesting was the finding that while non-coplanar PCBs were affected similarly, the coplanar PCBs were not. Overall, sediment freezing within this study's timeframe appears to offer little contextual advantage over sediment refrigeration.

Carcinogenic Metabolic Activation Process of Naphthalene by the Cytochrome P450 Enzyme 1B1: A Computational Study

The metabolic activation and transformation of naphthalene by the cytochrome P450 enzyme (CYP 1B1) plays an important role in its potential carcinogenicity. The process has been explored by a quantum mechanics/molecular mechanics (QM/MM) computational method. Molecular dynamic simulations were performed to explore the interaction between naphthalene and CYP 1B1. Naphthalene involves α- and β-carbon, the electrophilic addition of which would result in different reaction pathways. Our computational results show that both additions on α- and β-carbon can generate naphthalene 1,2-oxide. The activation barrier for the addition on β-carbon is higher than that for the α-carbon by 2.6 kcal·mol^-1, which is possibly caused by the proximity between β-carbon and the iron-oxo group of Cpd I in the system. We also found that naphthalene 1,2-oxide is unstable and the O-C bond cleavage easily occurs via cellular hydronium ion, hydroxyl radical/anion; then it will convert to the potential ultimate carcinogen 1,2-naphthoquinone. The results demonstrate and inform a detailed process of generating naphthalene 1,2-oxide and new predictions for its conversion.

Effect of epoxy monomer structure on the curing process and thermo-mechanical characteristics of tri-functional epoxy/amine systems: a methodology combining atomistic molecular simulation with experimental analyses

A methodology, which combined molecular simulation with experimental research, was established to expound the performance of a tri-functional epoxy/amine system.

Copper-catalyzed aerobic oxidative cleavage of C–C bonds in epoxides leading to aryl nitriles and aryl aldehydes

Novel copper-catalyzed aerobic synthesis of aryl nitriles and aldehydes from epoxides via C–C single bond cleavage has been discovered.

Computational toxicological investigation on the mechanism and pathways of xenobiotics metabolized by cytochrome P450: a case of BDE-47

Understanding the transformation mechanism and products of xenobiotics catalyzed by cytochrome P450 enzymes (CYPs) is vital to risk assessment. By density functional theory computation with the B3LYP functional, we simulated the reaction of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) catalyzed by the active species of CYPs (Compound I). The enzymatic and aqueous environments were simulated by the polarizable continuum model. The results reveal that the addition of Compound I to BDE-47 is the rate-determining step. The addition of Compound I to the ipso and nonsubstituted C atoms forms tetrahedral σ-adducts that further transform into epoxides. Hydroxylation of the epoxides leads to hydroxylated polybrominated diphenyl ethers and 2,4-dibromophenol. The addition to the Br-substituted C2 and C4 atoms has a higher barrier than addition to the nonsubstituted C atoms, forming phenoxide and cyclohexadienone which subsequently undergo debromination/hydroxylation. A novel mechanism was identified in which the approach of Compound I to C2 led to formation of a phenoxide and an expelled Br(-) ion. The predicted products were consistent with the metabolites identified by others. As a first attempt to simulate the enzymatic transformation of a polycyclic compound, this study may enlighten a computational method to predict the biotransformation of xenobiotics catalyzed by CYPs.

Mechanism of epoxide hydrolysis in microsolvated nucleotide bases adenine, guanine and cytosine: a DFT study

Six water molecules have been used for microsolvation to outline a hydrogen bonded network around complexes of ethylene epoxide with nucleotide bases adenine (EAw), guanine (EGw) and cytosine (ECw). These models have been developed with the MPWB1K-PCM/6-311++G(3df,2p)//MPWB1K/6-31+G(d,p) level of DFT method and calculated S(N)2 type ring opening of the epoxide due to amino group of the nucleotide bases, viz. the N6 position of adenine, N2 position of guanine and N4 position of cytosine. Activation energy (E(act)) for the ring opening was found to be 28.06, 28.64, and 28.37 kcal mol(-1) respectively for EAw, EGw and ECw. If water molecules were not used, the reactions occurred at considerably high value of E(act), viz. 53.51 kcal mol(-1) for EA, 55.76 kcal mol(-1) for EG and 56.93 kcal mol(-1) for EC. The ring opening led to accumulation of negative charge on the developing alkoxide moiety and the water molecules around the charge localized regions showed strong hydrogen bond interactions to provide stability to the intermediate systems EAw-1, EGw-1 and ECw-1. This led to an easy migration of a proton from an activated water molecule to the alkoxide moiety to generate a hydroxide. Almost simultaneously, a proton transfer chain reaction occurred through the hydrogen bonded network of water molecules and resulted in the rupture of one of the N-H bonds of the quaternized amino group. The highest value of E(act) for the proton transfer step of the reaction was 2.17 kcal mol(-1) for EAw, 2.93 kcal mol(-1) for EGw and 0.02 kcal mol(-1) for ECw. Further, the overall reaction was exothermic by 17.99, 22.49 and 13.18 kcal mol(-1) for EAw, EGw and ECw, respectively, suggesting that the reaction is irreversible. Based on geometric features of the epoxide-nucleotide base complexes and the energetics, the highest reactivity is assigned for adenine followed by cytosine and guanine. Epoxide-mediated damage of DNA is reported in the literature and the present results suggest that hydrated DNA bases become highly S(N)2 active on epoxide systems and the occurrence of such reactions can inflict permanent damage to the DNA.

Atmospheric Heterogeneous Reactions of Benzo(a)pyrene

This experimental study deals with heterogeneous reactions of benzo(a)pyrene (BaP) with ozone, nitrogen dioxide and hydroxyl radicals. BaP was adsorbed on silica particles chosen here as a model of mineral atmospheric particles. Compound extractions were assisted by focused microwave and analyses were performed by gas chromatography coupled with mass spectroscopy in single ion monitoring mode. Pseudo-first order rate constants were obtained from the fit of experimental decays of particulate-BaP concentration versus reaction time. Second order rate constants were determined considering the different oxidant gaseous concentrations except for the case of hydroxyl radicals where only a pseudo-first order rate constant was proposed. Values obtained at room temperature are (2.1±0.5)×10−15 cm3 molecule−1 s−1 for (BaP + ozone), (5.8±1.4)×10−16 cm3 molecule−1 s−1 for (BaP + nitrogen dioxide) and (3.4±0.8)×10−2 s−1 for (BaP + OH) reactions. Products have only been investigated for the NO2 and the OH (in the presence of NOx) reactions. 1-, 3- and 6-nitrobenzo(a)pyrenes were detected as degradation products and quantified. Reaction rate constants for product formation are (3.7±0.9)×10−16 cm3 molecule−1 s−1 for 6-NBaP, (2.2±0.6)×10−17 cm3 molecule−1 s−1 for 1-NBaP and (5.3±1.3)×10−17 cm3 molecule−1 s−1 for 3-NBaP. 1-, 3- and 6-nitroBaP account respectively for approximately 5%, 12% and 83% of total nitrated species. If in the presence of only nitrogen dioxide, BaP was totally degraded within few minutes, only 20 to 25 % of the initial BaP led to nitrated compounds when reacting with OH (in the presence of NOx).