Xiangli Shi

Computational Evidence for the Detoxifying Mechanism of Epsilon Class Glutathione Transferase Toward the Insecticide DDT

A combined quantum mechanics/molecular mechanics (QM/MM) computation of the detoxifying mechanism of an epsilon class glutathione transferases (GSTs) toward organochlorine insecticide DDT, 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane, has been carried out. The exponential average barrier of the proton transfer mechanism is 15.2 kcal/mol, which is 27.6 kcal/mol lower than that of the GS-DDT conjugant mechanism. It suggests that the detoxifying reaction proceeds via a proton transfer mechanism where GSH acts as a cofactor rather than a conjugate. The study reveals that the protein environment has a strong effect on the reaction barrier. The experimentally proposed residues Arg112, Glu116 and Phe120 were found to have a strong influence on the detoxifying reaction. The influence of residues Pro13, Cys15, His53, Ile55, Glu67, Ser68, Phe115, and Leu119 was detected as well. It is worth noticing that Ile55 facilitates the detoxifying reaction most. On the basis of the structure of DDT, structure 2, (BrC6H4)2CHCCl3, is the best candidate among all the tested structures in resisting the detoxification of enzyme agGSTe2.

Mechanism and kinetic properties for the OH-initiated atmospheric oxidation degradation of 9,10-Dichlorophenanthrene.

Chlorinated polycyclic aromatic hydrocarbons (ClPAHs) have become a serious environmental concern due to their widespread occurrence and dioxin-like toxicities. In this work, the mechanism of the OH-initiated atmospheric oxidation degradation of 9,10-dichlorophenanthrene (9,10-Cl₂Phe) was investigated by using high-accuracy quantum chemistry calculations. The rate constants of the crucial elementary reactions were determined by the Rice-Ramsperger-Kassel-Marcus (RRKM) theory. The theoretical results were compared with the available experimental data. The main oxidation products are a group of ring-retaining and ring-opening compounds including chlorophenanthrols, 9,10-dichlorophenanthrene-3,4-dione, dialdehydes, chlorophenanthrenequinones, nitro-9,10-Cl₂Phe and epoxides et al. The overall rate constant of the OH addition reaction is 2.35 × 10(-12)cm(3) molecule(-1)s(-1) at 298 K and 1 atm. The atmospheric lifetime of 9,10-Cl₂Phe determined by OH radicals is about 5.05 days. This study provides a comprehensive investigation of the OH-initiated oxidation degradation of 9,10-Cl₂Phe and should contribute to clarifying its atmospheric fate.

Mechanistic and kinetic studies on OH-initiated atmospheric oxidation degradation of benzo[α]pyrene in the presence of O2 and NOx

The degradation of polycyclic aromatic hydrocarbons (PAHs) in the atmosphere can lead to toxic derivatives which contribute to the carcinogenic potential of particulate organic matter. This paper aimed to investigate the mechanism of the OH-initiated oxidation degradation of benzo[α]pyrene (BaP), a cancer risk indicator. High-accuracy molecular orbital calculations were carried out, and all of the possible degradation pathways were discussed. The theoretical results were compared with the available experimental observation. The possible secondary reactions were also investigated. The rate constants of the crucial elementary steps were evaluated by using the Rice-Ramsperger-Kassel-Marcus (RRKM) theory. The dominant degradation products involve benzo[α]pyren-ol, nitro-benzo[α]pyrene, benzo[α]pyrene-7,10-dione as well as several ring-opened products such as alkyl substituted benzanthraldehyde et al. In particular, water plays an important role in the degradation pathways leading to the formation of nitro-benzo[α]pyrene. This work provides a comprehensive investigation of the OH-initiated degradation of BaP and should help to clarify its potential risk.

PBCDD/F formation from radical/radical cross-condensation of 2-Chlorophenoxy with 2-Bromophenoxy, 2,4-Dichlorophenoxy with 2,4-Dibromophenoxy, and 2,4,6-Trichlorophenoxy with 2,4,6-Tribromophenoxy.

Quantum chemical calculations were carried out to investigate the homogeneous gas-phase formation of mixed polybrominated/chlorinated dibenzo-p-dioxins/benzofurans (PBCDD/Fs) from the cross-condensation of 2-chlorophenoxy radical (2-CPR) with 2-bromophenoxy radical (2-BPR), 2,4-dichlorophenoxy radical (2,4-DCPR) with 2,4-dibromophenoxy radical (2,4-DBPR), and 2,4,6-trichlorophenoxy radical (2,4,6-TCPR) with 2,4,6-tribromophenoxy radical (2,4,6-TBPR). The geometrical parameters and vibrational frequencies were calculated at the MPWB1K/6-31+G(d,p) level, and single-point energy calculations were performed at the MPWB1K/6-311+G(3df,2p) level of theory. The rate constants of the crucial elementary reactions were evaluated by the canonical variational transition-state (CVT) theory with the small curvature tunneling (SCT) correction over a wide temperature range of 600-1200K. Studies show that the substitution pattern of halogenated phenols not only determines the substitution pattern of the resulting PBCDD/Fs, but also has a significant influence on the formation mechanism of PBCDD/Fs, especially on the coupling of the halogenated phenoxy radicals.

Influence of water on the homogeneous gas-phase formation mechanism of polyhalogenated dioxins/furans from chlorinated/brominated phenols as precursors.

Water is of great chemical importance due to its ability to form hydrogen bond. Polyhalogenated dibenzo-p-dioxin/benzofurans (PHDD/Fs) are notorious due to their persistence, bioaccumulation and extremely high toxicity. Water is ubiquitous, and a deep knowledge of its influence on the formation mechanism of PHDD/Fs is necessary. This work investigated the influence of water on the homogeneous gas-phase formation of PHDD/Fs from halogenated phenols (HPs) as precursors by using quantum chemical calculations with the aid of the MPWB1K theoretical approach in connection with the 6-31+G(d,p) and 6-311+G(3df,2p) basis sets. The schematic energy profile in the presence of water was constructed and compared with the situation without water. This study reveals for the first time that the introduction of water promotes the formation of halogenated phenoxy radicals (HPRs) from the H abstraction reactions of HPs with atomic H and OH radicals by lowering the reaction energy barriers and opening new low-energy pathways. Another intriguing finding of this work is that the inclusion of a water molecule produces a catalytic effect on the H-shift step involved in the formation of PHDFs and thus their formation potential is enhanced.

Mechanistic and kinetic studies on the OH-initiated atmospheric oxidation of fluoranthene.

The atmospheric oxidation of polycyclic aromatic hydrocarbons (PAHs) can generate toxic derivatives which contribute to the carcinogenic potential of particulate organic matter. In this work, the mechanism of the OH-initiated atmospheric oxidation of fluoranthene (Flu) was investigated by using high-accuracy molecular orbital calculations. All of the possible oxidation pathways were discussed, and the theoretical results were compared with the available experimental observation. The rate constants of the crucial elementary reactions were evaluated by the Rice-Ramsperger-Kassel-Marcus (RRKM) theory. The main oxidation products are a range of ring-retaining and ring-opening chemicals containing fluoranthols, fluoranthones, fluoranthenequinones, nitro-fluoranthenes, dialdehydes and epoxides. The overall rate constant of the OH addition reaction is 1.72×10(-11) cm(3) molecule(-1) s(-1) at 298 K and 1 atm. The atmospheric lifetime of Flu determined by OH radicals is about 0.69 days. This work provides a comprehensive investigation of the OH-initiated oxidation of Flu and should help to clarify its atmospheric conversion.

Mechanism for the growth of polycyclic aromatic hydrocarbons from the reactions of naphthalene with cyclopentadienyl and indenyl

Polycyclic aromatic hydrocarbons (PAHs) are globally concerned atmospheric particle-bound pollutants due to their toxicities. A mechanistic understanding of their formation from other environmental sources is of crucial importance for successful prevention of PAH. In the present work, the formation and growth mechanism of PAHs from the reactions of naphthalene with the cyclopentadienyl and indenyl radicals was investigated by using the hybrid density functional theory (DFT) at the MPWB1K/6-311+G(3df,2p)//MPWB1K/6-31+G(d,p) level. The rate constants for the crucial elementary steps were deduced with the aid of the canonical variational transition-state (CVT) theory with the small curvature tunneling (SCT) contribution. The formation of PAHs was involved in six elementary processes including: the addition reaction, ring closure, intramolecular H-shift, C-C cleavage, intramolecular H-shift and unimolecular elimination of CH3 or H. The C-C cleavage steps were revealed as the rate determining steps due to the extremely high barrier. At high temperature conditions like the combustion and pyrolysis of many hydrocarbons, the main products are phenanthrene, 4-methyl-phenanthrene and 1-methyl-phenanthrene from the reactions of naphthalene and cyclopentadienyl, and benzo(a)anthracene, 12-methyl-phenanthrene and 7-methyl-phenanthrene from the reactions of naphthalene and indenyl radicals. The reaction of naphthalene with indenyl radical is slightly more difficult than the reaction of naphthalene with cyclopentadienyl radical because of the bigger HOMO-LUMO orbital energy difference of naphthalene with indenyl relative to that of naphthalene with cyclopentadienyl.

Mechanism and thermal rate constant for the gas-phase ozonolysis of acenaphthylene in the atmosphere

Due to its prevalent presence, it is critical to clarify the atmospheric fate of acenaphthylene (Ary). In this paper, the reaction mechanism of the gas-phase ozonolysis of Ary was investigated by using quantum chemistry methods. Possible reaction pathways were discussed, and the theoretical results were compared with the available experimental data. The rate constants of the crucial elementary reactions were determined by the Rice-Ramsperger-Kassel-Marcus (RRKM) theory. The main products include secondary ozonide, naphthalene-1,8-dicarbaldehyde, 1,8-naphthalic anhydride, oxaacenaphthylene-2-one, 1-naphthaldehyde, 2-hydroxy-1-naphthaldehyde, and α-hydroxyhydroperoxide. The reaction of the unsaturated cyclo-pentafused ring with O₃ is the dominant pathway. The overall rate constant of the O₃ addition reaction is 5.31×10(-16)cm(3)molecule(-1)s(-1) at 298 K and 1 atm. The atmospheric lifetime of Ary determined by O₃ is about 0.75 h. This work provides a comprehensive investigation of the ozonolysis of Ary and should help to understand its atmospheric fate.

Insights into the mechanism and kinetics of the gas-phase atmospheric reaction of 9-chloroanthracene with NO3 radical in the presence of NOx

9-Chloroanthracene (9-ClAnt), an important member of the chlorinated polycyclic aromatic hydrocarbons (ClPAHs), has been demonstrated to show strong direct mutagenic effects. To elucidate the chemical transformations, degradation products and the capacity to undergo long-range transport of 9-ClAnt in the atmosphere, we conducted a theoretical investigation into the oxidation mechanism and kinetics of the NO3-initiated atmospheric transformation of 9-ClAnt by using a quantum chemistry method. The rate constants for the crucial elementary reactions were also estimated. The main oxidation products for the gas-phase reactions of 9-ClAnt with NO3 radicals include 9-chloroanthracen-yl nitrates, 9-chloroanthracenesdiones, epoxides, dialdehydes, 9-chloroanthracene-1,4-dione, anthracene-9,10-dione, 9-chloroanthracen-1-one, 10-chloroanthracen-1-one, 10-chloroanthracen-9-ol and 10-chloro-1-nitroanthracene etc. The overall rate constant of the NO3 addition reactions is 9.11 × 10−13 cm3 molecule−1 s−1 at 298 K and 1 atm. The atmospheric lifetime of 9-ClAnt determined by using NO3 radicals is about 0.61 h. This comprehensive investigation is the first report for the NO3-initiated oxidation of ClPAHs in the atmosphere. It should be conducive to clarifying their atmospheric fates and developing a full understanding of their toxic potential.

Mechanistic and Kinetic Studies on the Homogeneous Gas-Phase Formation of PCTA/DTs from 2,4-Dichlorothiophenol and 2,4,6-Trichlorothiophenol

Polychlorinated thianthrene/dibenzothiophenes (PCTA/DTs) are sulfur analogues compounds to polychlorinated dibenzo-p-dioxin/dibenzofurans (PCDD/Fs). Chlorothiophenols (CTPs) are key precursors to form PCTA/DTs. 2,4-DCTP has the minimum number of Cl atoms to form 2,4,6,8-tetrachlorinated dibenzothiophenes (2,4,6,8-TeCDT), which is the most important and widely detected of the PCDTs. In this paper, quantum chemical calculations were carried out to investigate the homogeneous gas-phase formation of PCTA/DTs from 2,4-DCTP and 2,4,6-TCTP precursors at the MPWB1K/6-311+G(3df,2p)//MPWB1K/6-31+G(d,p) level. Several energetically feasible pathways were revealed to compare the formation potential of PCTA/DT products. The rate constants of the crucial elementary reactions were evaluated by the canonical variational transition-state (CVT) theory with the small curvature tunneling (SCT) correction over a wide temperature range of 600–1200 K. This study shows that pathways that ended with elimination of Cl step were dominant over pathways ended with elimination of the H step. The water molecule has a negative catalytic effect on the H-shift step and hinders the formation of PCDTs from 2,4-DCTP. This study, together with works already published from our group, clearly illustrates an increased propensity for the dioxin formation from CTPs over the analogous CPs.