Computational evidence for the detoxifying mechanism of epsilon class glutathione transferase toward the insecticide DDT

Environmental biotransformation mechanisms by flavin-dependent monooxygenase: A computational study

The enzyme-catalyzed metabolic biotransformation of xenobiotics plays a significant role in toxicology evolution and subsequently environmental health risk assessment. Recent studies noted that the phase I human flavin-dependent monooxygenase (e.g., FMO3) can catalyze xenobiotics into more toxic metabolites. However, details of the metabolic mechanisms are insufficient. To fill the mechanism in the gaps, the systemic density functional theory calculations were performed to elucidate diverse FMO-catalyzed oxidation reactions toward environmental pollutants, including denitrification (e.g., nitrophenol), N-oxidation (e.g., nicotine), desulfurization (e.g., fonofos), and dehalogenation (e.g., pentachlorophenol). Similar to the active center compound 0 of cytochrome P450, FMO mainly catalyzed reactions with the structure of the tricyclic isoalloxazine C-4a-hydroperoxide (FADHOOH). As will be shown, FMO-catalyzed pathways are more favorable with a concerted than stepwise mechanism; Deprotonation is necessary to initiate the oxidation reactions for phenolic substrates; The regioselectivity of nicotine by FMO prefers the N-oxidation other than N-demethylation pathway; Formation of the P-S-O triangle ring is the key step for desulfurization of fonofos by FMO. We envision that these fundamental mechanisms catalyzed by FMO with a computational method can be extended to other xenobiotics of similar structures, which may aid the high-throughput screening and provide theoretical predictions in the future.

Potential Application of Machine-Learning-Based Quantum Chemical Methods in Environmental Chemistry

It is an important topic in environmental sciences to understand the behavior and toxicology of chemical pollutants. Quantum chemical methodologies have served as useful tools for probing behavior and toxicology of chemical pollutants in recent decades. In recent years, machine learning (ML) techniques have brought revolutionary developments to the field of quantum chemistry, which may be beneficial for investigating environmental behavior and toxicology of chemical pollutants. However, the ML-based quantum chemical methods (ML-QCMs) have only scarcely been used in environmental chemical studies so far. To promote applications of the promising methods, this Perspective summarizes recent progress in the ML-QCMs and focuses on their potential applications in environmental chemical studies that could hardly be achieved by the conventional quantum chemical methods. Potential applications and challenges of the ML-QCMs in predicting degradation networks of chemical pollutants, searching global minima for atmospheric nanoclusters, discovering heterogeneous or photochemical transformation pathways of pollutants, as well as predicting environmentally relevant end points with wave functions as descriptors are introduced and discussed.

Gold Nanoparticle as a Lewis Catalyst for Water Elimination of Tyrosine-•OH Adducts: A Radiation and Quantum Chemical Study

The role of gold nanoparticles (AuNPs) in the degradation of tyrosine intermediates formed during the radiation-induced ^•OH reaction with tyrosine at pH 6.5 is investigated by measuring the radiolytic yields, G, of tyrosine (-Tyr), dityrosine (DT), and 3,4 dihydroxyphenylalanine (DOPA). The G(DT) is doubled, whereas G(-Tyr) calculated is halved in the presence of 6.0 × 10^-10 mol dm^-3 AuNPs. Pulse radiolysis studies are carried out to elucidate the mechanism and nature of the transient formed in the reaction of ^•OH and ^•N₃ with tyrosine. The formation of tyrosyl radical in the presence of AuNPs is found to be a major pathway through the decay of tyrosine-^•OH adducts via the water elimination reaction, which is found to be 3× faster in the presence of AuNPs. Quantum chemical calculations on the system showed favorable formation of the tyrosine-AuNP complex. A new plausible mechanism of tyrosine-AuNP complex acting as a Lewis type catalyst in the decay of tyrosine-^•OH adducts leading to reduced DOPA formation is proposed. The proposed mechanism is also complemented by the electronic spectra and energetics of the reaction of ^•OH with tyrosine using density functional theory calculations. Significantly, the H-shift reaction of ortho-tyrosine-^•OH adducts is also found to be energetically viable. The investigation provides a new physical insight into the effect of AuNPs on the decay of free-radical transient species and demonstrates the potential of radiation chemical techniques and quantum chemical calculations as a tool for understanding the impact of metal nanoparticles in free-radical oxidation of amino acids, which is important in the use of metal nanoparticles for biomedical applications.

Development of quantitative structure-property relationship model for predicting the field sampling rate (Rs) of Chemcatcher passive sampler

Passive sampling technology has been considered as a promising tool to measure the concentration of environmental contaminants. With this technology, sampling rate (R_s) is an important parameter. However, as experimental methods employed to obtain the R_s value of a given compound were time-consuming, laborious, and expensive. A cost-effective method for deriving R_s is urgent. In addition, considering the great dependence of R_s value on water matrix properties, the laboratory measured R_s may not be a good alternative for field R_s. Thus, obtaining the field R_s is very necessary. In this study, a multiparameter quantitative structure-property relationship (QSPR) model was constructed for predicting the field R_s of 91 polar to semi-polar organic compounds. The determination coefficient (R²_Train), leave-one-out cross-validated coefficient (Q²_LOO), bootstrap coefficient (Q²_BOOT), and root mean square error (RMSE_Train) of the training set were 0.772, 0.706, 0.769, and 0.230, respectively, while the external validation coefficient (Q²_EXT) and RMSE_EXT of the validation set were 0.641 and 0.253, respectively. According to the acceptable criteria (Q² > 0.600, R² > 0.700), the model had good robustness, goodness-of-fit, and predictive performances. Therefore, we could use the model to fill the data gap for substances within the applicability domain on their missing R_s value.

Degradation mechanism for Zearalenone ring-cleavage by Zearalenone hydrolase RmZHD: A QM/MM study

The danger of zearalenone (ZEN) as an endocrine disruptor to humans and the environment has aroused increasing attention. In this study, we implemented the quantum mechanics/molecular mechanics (QM/MM) method to investigate the degradation mechanism of ZEN hydrolase (RmZHD) toward ZEN at the atomic level. The degradation process involves two concerted reaction pathways, where the active site contains a Ser-His-Glu triplet as a proton donor. With the Boltzmann-weighted average potential barriers of 18.1 and 21.5 kcal/mol, the process undergoes proton transfer and nucleophilic-substituted ring opening to form a hydroxyl product. Non-covalent interaction analyses elucidated hydrogen bonding between key amino acids with ZEN. The electrostatic influence analysis of 16 amino acids proposes residues Asp34 and His128 as the possible mutation target for future mutation design of enzyme RmZHD. An in-depth investigation of the protein environment of RmZHD can improve the bioremediation efficiency of endocrine disrupting chemicals.

Computational Biotransformation Profile of Emerging Phenolic Pollutants by Cytochromes P450: Phenol-Coupling Mechanism

Phenols are ubiquitous environmental pollutants, whose biotransformation involving phenol coupling catalyzed by cytochromes P450 may produce more lipophilic and toxic metabolites. Density functional theory (DFT) computations were performed to explore the debated phenol-coupling mechanisms, taking triclosan as a model substrate. We find that a diradical pathway facilitated by compound I and protonated compound II of P450 is favored vs alternative radical addition or electron-transfer mechanisms. The identified diradical coupling resembles a "two-state reactivity" from compound I characterized by significantly high rebound barriers of the phenoxy radicals, which can be formulated into three equations for calculating the ratio [coupling]/[hydroxylation]. A higher barrier for rebound than for H-abstraction in high-spin triclosan can facilitate the phenoxy radical dissociation and thus enable phenol coupling, while H-abstraction/radical rebound causing phenol hydroxylation via minor rebound barriers mostly occurs via the low-spin state. Therefore, oxidation of triclosan by P450 fits the first equation with a ratio [coupling]/[hydroxylation] of 1:4, consistent with experimental data indicating different extents of triclosan coupling (6-40%). The high rebound barrier of phenoxy radicals, as a key for the mechanistic identification of phenol coupling vs hydroxylation, originates from their weak electron donor ability due to spin aromatic delocalization. We envision that the revealed mechanism can be extended to the cross-coupling reactions between different phenolic pollutants, and the coupling reactions of several other aromatic pollutants, to infer unknown metabolites.

Binding interactions of halo-benzoic acids, halo-benzenesulfonic acids and halo-phenylboronic acids with human transthyretin

The anionic form-dependent binding interaction of halo-phenolic substances with human transthyretin (hTTR) has been observed previously. This indicates that ionizable compounds should be the primary focus in screening potential hTTR disruptors. Here, the potential binding potency of halo-benzoic acids, halo-benzenesulfonic acids/sulfates and halo-phenylboronic acids with hTTR was determined and analyzed by competitive fluorescence displacement assay integrated with computational methods. The laboratorial results indicated that the three test groups of model compounds exhibited a distinct binding affinity to hTTR. All the tested halo-phenylboronic acids, some of the tested halo-benzoic acids and halo-benzenesulfonic acids/sulfates were shown to be inactive with hTTR. Other halo-benzoic acids and halo-benzenesulfonic acids/sulfates were moderate and/or weak hTTR binders. The binding affinity of halo-benzoic acids and halo-benzenesulfonic acids/sulfates with hTTR was similar. The low distribution ability of the model compounds from water to hTTR may be the reason why they exhibited the binding potency observed with hTTR. By introducing other highly hydrophobic compounds, we observed that the binding affinity between compounds and hTTR increased with increasing molecular hydrophobicity. Those results indicated that the highly hydrophobic halo-benzoic acids and halo-benzenesulfonic acids/sulfates may be high-priority hTTR disruptors. Finally, a binary classification model was constructed employing three predictive variables. The sensitivity (S_n), specificity (S_p), predictive accuracy (Q) values of the training set and validation set were >0.83, indicating that the model had good classification performance. Thus, the binary classification model developed here could be used to distinguish whether a given ionizable compound is a potential hTTR binder or not.

Biodegradation mechanism of polyesters by hydrolase from Rhodopseudomonas palustris: An in silico approach

Massively used plastics have caused worldwide environmental concerns. Polyesters like polylactic acid (PLA) are one of the mostly used plastics due to its excellent physical and chemical properties and low-cost advantages. It is critical to develop the elimination and recycle techniques for polyesters. Experimental studies have shown that a hydrolase RPA1511 isolated from Rhodopseudomonas palustris can efficiently depolymerize polylactic acid (PLA) into oligomers and monomers. It was also active against emulsified aliphatic polymers as well as multipurpose soluble ester monomers (α-naphthyl ester and p-nitrophenyl ester). In the present study, molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area method were applied to screen all amino acids from hydrolase RPA1511 and identify the most important amino acids during substrate binding. Seven substrates were considered: PLA (dimer and tetramer), polycaprolactone, butylene succinate, 1-naphthyl acetate, 2-naphthyl formate, p-nitrophenyl acetate. The results highlighted the importance of amino acids like Tyr139, Tyr213, Arg259, Thr46. Subsequent quantum mechanics/molecular mechanics calculations were also performed to determine the detailed degradation mechanism of hydrolase RPA1511 toward PLA and explore the role of the active site residues during catalysis. The results demonstrated that degradation involves two elementary steps: enzyme acylation and PLA hydrolysis. The corresponding Boltzmann average barriers are 20.40 kcal/mol and 14.45 kcal/mol. The electrostatic influence analysis of 15 amino acids on the rate-determining step indicated that amino acids His114, Trp219 and Ala273 facilitate the reaction while the Arg244 suppresses the reaction which may serve as future mutation studies to enhance the enzymatic efficiency.

Mechanism insight of acetaminophen degradation by the UV/chlorine process: kinetics, intermediates, and toxicity assessment

The removal of acetaminophen (AAP) in aqueous solution by the UV/chlorine process was evaluated. The effect of chlorine dose, the initial AAP concentration, pH value, and UV intensity on the reaction were also investigated. The degradation mechanism and the ecological risk were further discussed. The results indicated that AAP degradation fitted pseudo-first-order kinetics. Compared with UV alone or dark chlorination, the combination of UV and chlorine significantly accelerated the degradation process. The AAP degradation was positively affected by chlorine dose and UV intensity, while negatively affected by the initial AAP concentration and ammonia nitrogen concentration during the UV/chlorine process. The frontier orbital theory analysis shows that the C5 position in the benzene ring of AAP is likely to be the first site attacked by HO• and Cl• radical to form the products. Twelve intermediates were identified by Q-TOF and GC-MS. The possible degradation pathways were also proposed. Luminescent bacteria experiment and ECOSAR prediction both revealed that acute toxicity of AAP degradation could only be partially reduced. Ecological risks during the UV/chlorine process need to be further evaluated.

Natural sunlight-driven aquatic toxicity enhancement of 2,6-di-tert-butylphenol toward Photobacterium phosphoreum

The tert-butylphenols (TBPs) are one group of alkylated phenolic compounds with wide applications in UV absorbers and antioxidants. They are becoming contaminants of emerging concern with residues frequently detected in natural surface water or drinking water. The direct sunlight may photolyze TBPs in waters and affect their aquatic toxicities; however, such data are very limited. In the present study, we investigate the photodegradation of 2,6-DTBP by direct sunlight in water and compare the aquatic toxicities of 2,6-DTBP with that of its product toward Photobacterium phosphoreum. 2,6-DTBP is photodegraded by 71.31 ± 2.64% under simulated sunlight following a pseudo-first-order kinetics with rate constant (k) of 0.061 h^-1. Density functional theory simulations at M06-2X/def2-SVP level reveal that the photodegradation occurred sequentially through oxidation, photo-isomerization and hydrogenation. The degradation product 2,5-DTBP is toxic to P. phosphoreum (EC₅₀ 3.389 × 10^-5 mol/L) whereas 2,6-DTBP is not harmful (EC₅₀ 3.917 × 10^-3 mol/L) as designated by the European Union Standard, indicating the enhanced toxicities driven by the direct sunlight photodegradation. We demonstrate the enhanced toxicities of 2,6-DTBP by natural sunlight, suggesting that negligence of photodegradation of TBPs-related contaminants will underestimate the comprehensive risk of these emerging contaminant in natural waters.

Application and Selection of Remediation Technology for OCPs-Contaminated Sites by Decision-Making Methods

The production and use of organochlorine pesticides (OCPs) for agricultural and industrial applications result in high levels of their residues, posing a significant risk to environmental and human health. At present, there are many techniques for OCP-contaminated soil remediation. However, the remediation of contaminated sites may suffer from a series of problems, such as a long recovery cycle, high costs, and secondary pollution, all of which could affect land redevelopment and reuse. Therefore, the selection of an appropriate technology is crucial for contaminated sites. In order to improve and support decision-making for the selection of remediation techniques, we provide a decision-making strategy for the screening of remediation techniques of OCP-contaminated sites. The screening procedure is proposed based on combining the analytic hierarchy process (AHP) and the technique for order preference by similarity to ideal solution (TOPSIS). The screening indexes include economic indicator, environmental indicator, and technical indicator. The assessment results show that co-processing in cement kiln obtained the highest overall score and was thus considered to be the most sustainable option. This suggested remediation technology was similar to the practical remediation project, indicating that the screening method could be applied for the selection of remediation technologies for sites contaminated with persistent organic pollutants.

Aedes aegypti Galectin Competes with Cry11Aa for Binding to ALP1 To Modulate Cry Toxicity

The key step for the toxicity of Bacillus thuringiensis subsp. israelensis (Bti) is the interaction between toxins and putative receptors; thus, many studies focus on identification of new toxin receptors and engineering of toxins with higher affinity/specificity for receptors. In the larvae of Aedes aegypti, galectin-14 was one of the genes upregulated by Bti treatment. RNAi knockdown expression of galectin-14 and feeding recombinant galectin-14-thioredoxin fusion protein significantly affected survival of Ae. aegypti larvae treated with Bti toxins. Recombinant galectin-14 protein bound to brush border membrane vesicles (BBMVs) of Ae. aegypti larvae, ALP1 and APN2, and galectin-14 and Cry11Aa bound to BBMVs with a similarly high affinity. Competitive binding results showed that galectin-14 competed with Cry11Aa for binding to BBMVs and ALP1 to prevent effective binding of toxin to receptors. These novel findings demonstrated that midgut proteins other than receptors play an important role in modulating the toxicity of Cry toxins.

Metabolic Mechanism of Aryl Phosphorus Flame Retardants by Cytochromes P450: A Combined Experimental and Computational Study on Triphenyl Phosphate

Understanding metabolic mechanisms is critical and remains a difficult task in the risk assessment of emerging pollutants. Triphenyl phosphate (TPHP), a widely used aryl phosphorus flame retardant (aryl-PFR), has been frequently detected in the environment, and its major metabolite was considered as diphenyl phosphate (DPHP). However, knowledge of the mechanism for TPHP leading to DPHP and other metabolites is lacking. Our in vitro study shows that TPHP is metabolized into its diester metabolite DPHP and mono- and dihydroxylated metabolites by cytochromes P450 (CYP) in human liver microsomes, while CYP1A2 and CYP2E1 isoforms are mainly involved in such processes. Molecular docking gives the conformation for TPHP binding with the active species Compound I (an iron IV-oxo heme cation radical) in specific CYP isoforms, showing that the aromatic ring of TPHP is likely to undergo metabolism. Quantum chemical calculations have shown that the dominant reaction channel is the O-addition of Compound I onto the aromatic ring of TPHP, followed by a hydrogen-shuttle mechanism leading to ortho-hydroxy-TPHP as the main monohydroxylated metabolite; the subsequent H-abstraction-OH-rebound reaction acting on ortho-hydroxy-TPHP yields the meta- and ipso-position quinol intermediates, while the former of which can be metabolized into dihydroxy-TPHP by fast protonation, and the latter species needs to go through type-I ipso-substitution and fast protonation to be evolved into DPHP. We envision that the identified mechanisms may give inspiration for studying the metabolism of several other aryl-PFRs by CYP.

Understanding the ozonated degradation of sulfadimethoxine, exploration of reaction site, and classification of degradation products

Ozonation has been demonstrated to be an efficient method of water treatment. In this study, the degradation of 20 mg/L of sulfadimethoxine (SDM) in different water matrices during ozonation was investigated. At pH 7.0, 100% removal of SDM was achieved by ozonation within 10 min. The degradation of SDM was more pronounced at acidic pH than under ambient environmental conditions, and was also dependent on different water matrices. Both direct and indirect oxidation of SDM by ozone were observed, and it was also shown that both ozone molecules and hydroxyl radicals were involved in the SDM degradation process, whereas it was found that the saturated ring of SDM made it O₃-recalcitrant. Seven transformation products (TPs) were identified during SDM ozonation, allowing three degradation pathways to be proposed. Additionally, the main reaction sites, including N (7) and C (2) on the aniline ring, and the ^__S^__N^__ bond, were confirmed both experimentally and theoretically. The toxicity evolution during the degradation process was investigated, and the results showed no toxic intermediate products obtained during ozonation.

Quantum chemical simulations revealed the toxicokinetic mechanisms of organic phosphorus flame retardants catalyzed by P450 enzymes

The metabolic fate and toxicokinetics of organic phosphorus flame retardants catalyzed by cytochrome P450 enzymes (CYPs) are here investigated by in silico simulations, leveraging an active center model to mimic the CYPs, triphenyl phosphate (TPHP), tris(2-butoxyethyl) phosphate and tris(1,3-dichloro-2-propyl) phosphate as substrates. Our calculations elucidated key main pathways and predicted products, which were corroborated by current in vitro data. Results showed that alkyl OPFRs are eliminated faster than aryl and halogenated alkyl-substituted OPFRs. In addition, we discovered a proton shuttle pathway for aryl hydroxylation of TPHP and P = O bond-assisted H-transfer mechanisms (rather than nonenzymatic hydrolysis) that lead to O-dealkylation/dearylation of phosphotriesters.

Transformation of naproxen during the chlorination process: Products identification and quantum chemistry validation

The by-products produced by pharmaceutically active compounds (PhACs) during chlorination are attracting wide concern. Thus, the transformation and toxicity of naproxen (NAP) during the chlorination process were assessed in this study. The transformation of NAP was found to follow pseudo-first-order kinetics, and the first-order rate constant was improved by increasing the NaOCl dose. High-resolution mass spectrometry (HRMS) was successfully applied to identify 14 chlorination products. This study represents the first elucidation and report of the exact structure of the primary chlorine substitution product ((2S)-2-(5-chloro-6-methoxy-2-naphthyl)propionic acid) based on HRMS and ¹H NMR. Chlorine will primarily substitute the hydrogen atom on the C7 position of the naphthalene ring to form the mono-chlorine substitution product, as further validated at the theoretical level by quantum chemical calculations. A series of HOCl-induced reactions, including substitution, demethylation, and dehydrogenation, led to the transformation of NAP during the chlorination process. ECOSAR program revealed that the potential aquatic toxicity of the transformation products is significantly higher than that of the parent NAP. Their introduction into the environment may still pose potential risks.

Insights into the catalytic mechanism of dehydrogenase BphB: A quantum mechanics/molecular mechanics study

The present study delineated the dehydrogenation mechanism of cis-2,3-dihydro-2,3-dihydroxybiphenyl (2,3-DDBPH) and cis-2,3-dihydro-2,3-dihydroxy-4,4'-dichlorobiphenyl (2,3-DD-4,4'-DBPH) by Pandoraea pnomenusa strain B-356 cis-2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase (BphB) in atomistic detail. The enzymatic process was investigated by a combined quantum mechanics/molecular mechanics (QM/MM) approach. Five different snapshots were extracted and calculated, which revealed that the Boltzmann-weighted average barriers of 2,3-DDBPH and 2,3-DD-4,4'-DBPH dehydrogenation processes are 10.7 and 11.5 kcal mol^-1, respectively. The established dehydrogenation mechanism provides new insight into the degradation processes of other chlorinated 2,3-DDBPH. In addition to Asn115, Ser142, and Lys149, the importance of Ile 89, Asn143, Pro184, Met 187, Thr189, and Lue 191 during the dehydrogenation process of 2,3-DDBPH and 2,3-DD-4,4'-DBPH were also highlighted to search for promising mutation targets for improving the catalytic efficiency of BphB.

Computational evidence for the degradation mechanism of haloalkane dehalogenase LinB and mutants of Leu248 to 1-chlorobutane

The catalytic degradation ability of the haloalkane dehalogenase LinB toward 1-chlorobutane (1-CB) was studied using a combined quantum mechanics/molecular mechanics (QM/MM) approach. Two major processes are involved in the LinB-catalyzed removal of halogens: dechlorination and hydrolyzation. The present study confirmed the experimentally proposed reaction path at the molecular level. Moreover, based on nucleophilic substitution mechanism (SN2 reaction), dechlorination was found to be the rate-determining step of the entire reaction process. In this study, the Boltzmann-weighted average barrier for dechlorination was determined to be 17.0 kcal mol-1, which is fairly close to the experimental value (17.4 kcal mol-1). The state of His107 and the influence of Leu248 on the dechlorination process were also explored. In addition, an intriguing phenomenon was discovered: the potential energy barrier decreased by 7.5 kcal mol-1 when the Leu248 residue was mutated into Phe248. This discovery might be of great help to design new mutant enzymes or novel biocatalysts.

Molecular Mechanism of Alternative P450-Catalyzed Metabolism of Environmental Phenolic Endocrine-Disrupting Chemicals

Understanding the bioactivation mechanisms to predict toxic metabolites is critical for risk assessment of phenolic endocrine-disrupting chemicals (EDCs). One mechanism involves ipso-substitution, which may contribute to the total turnover of phenolic EDCs, yet the detailed mechanism and its relationship with other mechanisms are unknown. We used density functional theory to investigate the P450-catalyzed ipso-substitution mechanism of the prominent xenoestrogen bisphenol A. The ipso-substitution proceeds via H-abstraction from bisphenol A by Compound I, followed by essentially barrierless OH-rebound onto the ipso-position forming a quinol, which can spontaneously decompose into the carbocation and hydroquinone. This carbocation can further evolve into the highly estrogenic hydroxylated and dimer-type metabolites. The H-abstraction/OH-rebound reaction mechanism has been verified as a general reaction mode for many other phenolic EDCs, such as bisphenol analogues, alkylphenols and chlorophenols. The identified mechanism enables us to effectively distinguish between type I (eliminating-substituent as anion) and type II (eliminating-substituent as cation) ipso-substitution in various phenolic EDCs. We envision that the identified pathways will be applicable for prediction of metabolites from phenolic EDCs whose fate are affected by this alternative type of P450 reactivity, and accordingly enable the screening of these metabolites for endocrine-disrupting activity.

Cry11Aa Interacts with the ATP-Binding Protein from Culex quinquefasciatus To Improve the Toxicity

Cry11Aa displays high toxicity to the larvae of several mosquito species, including Aedes, Culex, and Anopheles. To study its binding characterization against Culex quinquefasciatus, Cry11Aa was purified and western blot results showed that Cry11Aa could bind successfully to the brush border membrane vesicles. To identify Cry11Aa-binding proteins in C. quinquefasciatus, a biotin-based protein pull-down experiment was performed and seven Cry11Aa-binding proteins were isolated from the midgut of C. quinquefasciatus larvae. Analysis of liquid chromatography-tandem mass spectrometry showed that one of the Cry11Aa-binding proteins is the ATP-binding domain 1 family member B. To investigate its binding property and effect on the toxicity of Cry11Aa, western blot, far-western blot, enzyme-linked immunosorbent assay, and bioassays of Cry11Aa in the presence and absence of the recombinant ATP-binding protein were performed. Our results showed that the ATP-binding protein interacted with Cry11Aa and increased the toxicity of Cry11Aa against C. quinquefasciatus. Our study suggests that midgut proteins other than the toxin receptors may modulate the toxicity of Cry toxins against mosquitoes.

Adsorption of Insecticidal Crystal Protein Cry11Aa onto Nano-Mg(OH)2: Effects on Bioactivity and Anti-Ultraviolet Ability

The traditional Bacillus thuringiensis (Bt) formulations for field applications are not resistant to harsh environmental conditions. Hence, the active ingredients of the Bt bioinsecticides could degrade quickly and has low anti-ultraviolet ability in the field, which significantly limits its practical application. In the present study, we developed an efficient and stable delivery system for Bt Cry11Aa toxins. We coated Cry11Aa proteins with Mg(OH)₂ nanoparticles (MHNPs), and then assessed the effects of MHNPs on bioactivity and anti-ultraviolet ability of the Cry11Aa proteins. Our results indicated that MHNPs, like "coating clothes", could effectively protect the Cry protein and enhance the insecticidal bioactivity after UV radiation (the degradation rate was decreased from 64.29% to 16.67%). In addtion, MHNPs could improve the proteolysis of Cry11Aa in the midgut and aggravate the damage of the Cry protein to the gut epithelial cells, leading to increased insecticidal activity against Culex quinquefasciatus. Our results revealed that MHNPs, as an excellent nanocarrier, could substantially improve the insecticidal bioactivity and anti-ultraviolet ability of Cry11Aa.

Theoretical study on the hydrolytic step in the biotransformation of β-hexachlorocyclohexane degraded by haloalkane dehalogenase LinB

The hydrolytic process of LinB-catalyzed biotransformation of a notorious contaminant β-HCH was investigated in atomistic detail with a combined quantum mechanics/molecular mechanics approach. The Boltzmann-weighted averaging method amended by disproportionate effect analysis was showed to capture the fluctuation of a single molecule enzyme reaction. With the potential barriers of 18.7 and 2.6 kcal/mol, two elementary steps that refer to formation and decomposition of a tetrahedral intermediate are involved in the hydrolytic reaction, respectively. Polarized by Glu132, His272 serves as a proton carrier along the whole hydrolysis reaction. The electrostatic influence analysis highlighted residue Leu248 as a possible mutation target for rational design of LinB in enzyme modification. Further spatial location analysis provided explanation for the opposite effect of Asn38 toward the two elementary steps. Getting insight into the catalytic details and the structure and function of LinB can enrich the knowledge of it and promote its application in bioremediation of chlorinated hydrocarbon pollutants.

Enantioselectivity of haloalkane dehalogenase LinB on the degradation of 1,2-dichloropropane: A QM/MM study

The hydrolysis dechlorination mechanism of a chiral organochlorinepollutant, 1,2-dichloropropane (DCP), catalyzed by haloalkane dehalogenase LinB has been investigated by using a combined quantum mechanics/molecular mechanics method. LinB was confirmed to be enantioselective towards the catabolism of the racemic mixture. Based on the S_N2 nucleophilic substitution mechanism, the dechlorination process was identified as the rate-determining step in LinB-catalyzed degradation of 1,2-dichloropropane, the Boltzmann-weighted average potential barrier of which is 18.8kcal/mol for the (R)-isomer and 24.0kcal/mol for the (S)-isomer. A particular water molecule near (S)-DCP in the reaction system can strongly disturb the dechlorination process, which can account for the enantioselectivity of LinB. Further electrostatic influence analysis indicates that proper mutation of Gly37 may improve the catalytic efficiency of LinB towards DCP.

In silico environmental chemical science: properties and processes from statistical and computational modelling

Quantitative structure-activity relationships (QSARs) have long been used in the environmental sciences. More recently, molecular modeling and chemoinformatic methods have become widespread. These methods have the potential to expand and accelerate advances in environmental chemistry because they complement observational and experimental data with "in silico" results and analysis. The opportunities and challenges that arise at the intersection between statistical and theoretical in silico methods are most apparent in the context of properties that determine the environmental fate and effects of chemical contaminants (degradation rate constants, partition coefficients, toxicities, etc.). The main example of this is the calibration of QSARs using descriptor variable data calculated from molecular modeling, which can make QSARs more useful for predicting property data that are unavailable, but also can make them more powerful tools for diagnosis of fate determining pathways and mechanisms. Emerging opportunities for "in silico environmental chemical science" are to move beyond the calculation of specific chemical properties using statistical models and toward more fully in silico models, prediction of transformation pathways and products, incorporation of environmental factors into model predictions, integration of databases and predictive models into more comprehensive and efficient tools for exposure assessment, and extending the applicability of all the above from chemicals to biologicals and materials.

DFT study of the formation mechanism of anthraquinone from the reaction of NO2 and anthracene on NaCl clusters: the role of NaNO3

Polycyclic aromatic hydrocarbons (PAHs) and oxygenated-PAHs are globally worrisome air pollutants because of their highly direct-acting mutagenicity and carcinogenicity. The formation of oxygenated-PAHs is of crucial importance for the prevention of their atmospheric pollution successfully. In this paper, the formation mechanism of oxygenated-PAHs from the heterogeneous reaction of NO₂ with anthracene on the surface of NaCl was studied by density functional theory (DFT) calculations. At first, the various adsorption configurations of NO₂ and N₂O₄ on NaCl were investigated. The chemical conversion mechanisms among these configurations were also investigated. It is found that these structures can easily interconvert due to their low energy barriers. NaNO₃ was found to be the main product of the reaction of NO₂/N₂O₄ on NaCl. Then the oxidation mechanism of anthracene by NO₂ on the NaCl surface showed that NaNO₃ is able to oxidize anthracene and plays a catalytic role in the reaction process. This means that the formation of NaNO₃ is very important to promote the formation of 9,10-anthraquinone from the heterogeneous reaction of NO₂ with anthracene. Our calculations also showed that the introduction of water can greatly accelerate this reaction process.

QSAR Study for Carcinogenic Potency of Aromatic Amines Based on GEP and MLPs

A new analysis strategy was used to classify the carcinogenicity of aromatic amines. The physical-chemical parameters are closely related to the carcinogenicity of compounds. Quantitative structure activity relationship (QSAR) is a method of predicting the carcinogenicity of aromatic amine, which can reveal the relationship between carcinogenicity and physical-chemical parameters. This study accessed gene expression programming by APS software, the multilayer perceptrons by Weka software to predict the carcinogenicity of aromatic amines, respectively. All these methods relied on molecular descriptors calculated by CODESSA software and eight molecular descriptors were selected to build function equations. As a remarkable result, the accuracy of gene expression programming in training and test sets are 0.92 and 0.82, the accuracy of multilayer perceptrons in training and test sets are 0.84 and 0.74 respectively. The precision of the gene expression programming is obviously superior to multilayer perceptrons both in training set and test set. The QSAR application in the identification of carcinogenic compounds is a high efficiency method.

An On-the-Fly Surface-Hopping Program JADE for Nonadiabatic Molecular Dynamics of Polyatomic Systems: Implementation and Applications

Nonadiabatic dynamics simulations have rapidly become an indispensable tool for understanding ultrafast photochemical processes in complex systems. Here, we present our recently developed on-the-fly nonadiabatic dynamics package, JADE, which allows researchers to perform nonadiabatic excited-state dynamics simulations of polyatomic systems at an all-atomic level. The nonadiabatic dynamics is based on Tully's surface-hopping approach. Currently, several electronic structure methods (CIS, TDHF, TDDFT(RPA/TDA), and ADC(2)) are supported, especially TDDFT, aiming at performing nonadiabatic dynamics on medium- to large-sized molecules. The JADE package has been interfaced with several quantum chemistry codes, including Turbomole, Gaussian, and Gamess (US). To consider environmental effects, the Langevin dynamics was introduced as an easy-to-use scheme into the standard surface-hopping dynamics. The JADE package is mainly written in Fortran for greater numerical performance and Python for flexible interface construction, with the intent of providing open-source, easy-to-use, well-modularized, and intuitive software in the field of simulations of photochemical and photophysical processes. To illustrate the possible applications of the JADE package, we present a few applications of excited-state dynamics for various polyatomic systems, such as the methaniminium cation, fullerene (C20), p-dimethylaminobenzonitrile (DMABN) and its primary amino derivative aminobenzonitrile (ABN), and 10-hydroxybenzo[h]quinoline (10-HBQ).

How Many Conformations of Enzymes Should Be Sampled for DFT/MM Calculations? A Case Study of Fluoroacetate Dehalogenase

The quantum mechanics/molecular mechanics (QM/MM) method (e.g., density functional theory (DFT)/MM) is important in elucidating enzymatic mechanisms. It is indispensable to study "multiple" conformations of enzymes to get unbiased energetic and structural results. One challenging problem, however, is to determine the minimum number of conformations for DFT/MM calculations. Here, we propose two convergence criteria, namely the Boltzmann-weighted average barrier and the disproportionate effect, to tentatively address this issue. The criteria were tested by defluorination reaction catalyzed by fluoroacetate dehalogenase. The results suggest that at least 20 conformations of enzymatic residues are required for convergence using DFT/MM calculations. We also tested the correlation of energy barriers between small QM regions and big QM regions. A roughly positive correlation was found. This kind of correlation has not been reported in the literature. The correlation inspires us to propose a protocol for more efficient sampling. This saves 50% of the computational cost in our current case.

Catalytic mechanism of C–F bond cleavage: insights from QM/MM analysis of fluoroacetate dehalogenase

The catalytic mechanisms of fluoroacetate dehalogenase (FAcD) toward substrates fluoroacetate and chloroacetate were studied by a combined quantum mechanics/molecular mechanics (QM/MM) method.

Dehydrochlorination mechanism of γ-hexachlorocyclohexane degraded by dehydrochlorinase LinA from Sphingomonas paucimobilis UT26

The biotransformation pathway from γ-HCH to 1,3,4,6-TCDN catabolized by dehydrochlorinase LinA contains two discontinuous dehydrochlorination reactions and a conformational transition for the product of the first dehydrochlorination reaction.

Rapid Removal of Tetrabromobisphenol A by Ozonation in Water: Oxidation Products, Reaction Pathways and Toxicity Assessment

Tetrabromobisphenol A (TBBPA) is one of the most widely used brominated flame retardants and has attracted more and more attention. In this work, the parent TBBPA with an initial concentration of 100 mg/L was completely removed after 6 min of ozonation at pH 8.0, and alkaline conditions favored a more rapid removal than acidic and neutral conditions. The presence of typical anions and humic acid did not significantly affect the degradation of TBBPA. The quenching test using isopropanol indicated that direct ozone oxidation played a dominant role during this process. Seventeen reaction intermediates and products were identified using an electrospray time-of-flight mass spectrometer. Notably, the generation of 2,4,6-tribromophenol was first observed in the degradation process of TBBPA. The evolution of reaction products showed that ozonation is an efficient treatment for removal of both TBBPA and intermediates. Sequential transformation of organic bromine to bromide and bromate was confirmed by ion chromatography analysis. Two primary reaction pathways that involve cleavage of central carbon atom and benzene ring cleavage concomitant with debromination were thus proposed and further justified by calculations of frontier electron densities. Furthermore, the total organic carbon data suggested a low mineralization rate, even after the complete removal of TBBPA. Meanwhile, the acute aqueous toxicity of reaction solutions to Photobacterium Phosphoreum and Daphnia magna was rapidly decreased during ozonation. In addition, no obvious difference in the attenuation of TBBPA was found by ozone oxidation using different water matrices, and the effectiveness in natural waters further demonstrates that ozonation can be adopted as a promising technique to treat TBBPA-contaminated waters.

DDT Vertical Migration and Formation of Accumulation Layer in Pesticide-Producing Sites

Soil samples were collected at various depths (0.5-21.5 m) from ten boreholes that were drilled with a SH-30 Model Rig, four of which were at a dicofol production site while six were at a dichlorodiphenyltrichloroethane (DDT) production site. In industrial sites, the shallow soils at depths of 0-2 m were mostly backfill soils, which cannot represent the contamination situation of the sites. The contaminated levels in the deep original soil can represent the situation in contaminated sites. All the soil samples investigated at the DDT and dicofol production sites were found to be seriously polluted. The contents of both DDT (0.6-6071 mg/kg) and dicofol (0.5-1440 mg/kg) were much higher at the dicofol production site than at the DDT production site (DDTs, 0.01-664.6 mg/kg; dicofol, <0.1 mg/kg), even in the deep soil. DDTs had a different distribution in the soil of the pesticide production site from that in the soil outside the sites and that in agricultural soils. The results of the investigation revealed that DDTs were easily enriched in cohesive soil and in the bottom zone of aquifers, where the concentration was higher than in above the layers. DDTs were found to be hard to degrade, and their degradation speed was slower than their vertical migration, despite the fact that hydrophobic DDTs did not migrate easily in soils. In the dicofol production site, the value of DDE/DDD cannot indicate the degradation condition of DDTs, nor can the value of (DDE + DDD)/DDT identify how long DDTs have remained in the soil. It is debatable that the half-life of DDT inputted to soils is about 20-30 years, maybe longer than the generally recognized time.

Transformation pathways of MeO-PBDEs catalyzed by active center of P450 enzymes: a DFT investigation employing 6-MeO-BDE-47 as a case

Recent in vivo and in vitro experiments indicated that methoxylated polybrominated diphenyl ethers (MeO-PBDEs) can be biotransformed into hydroxylated PBDEs (HO-PBDEs) that are more toxic than PBDEs and MeO-PBDEs. Nevertheless, the enzymatic transformation mechanism is not clear. We hypothesized that cytochrome P450 enzymes (CYPs) play a key role in the transformation and employed the density functional theory calculations to unveil the mechanism. The transformation of a model compound, 6-MeO-BDE-47, catalyzed by the active center of CYPs (Compound I), was computed. For the first time, our results show that the energy barriers for the addition of Compound I to the C atoms on the phenyl of 6-MeO-BDE-47 are much higher than that for hydroxylation of the methoxyl, indicating that O-demethylation is a dominating metabolic pathway. This is in line with experimental observations performed by others. The pathways for the transformation of 6-MeO-BDE-47 catalyzed by Compound I were clarified. A C-H bond of the methoxyl is activated by Compound I, followed by radical rebound to form carbinol intermediates, then the carbinols decompose to form 6-HO-BDE-47 with the assistance of water molecules. The computational method can be potentially employed to develop models that predict biotransformation of xenobiotics catalyzed by CYPs.

Insight into the catalytic mechanism of meta-cleavage product hydrolase BphD: a quantum mechanics/molecular mechanics study

The catalytic mechanism of BphD (the fourth enzyme of the biphenyl catabolic pathway) toward its natural substrate 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) was investigated in atomistic detail by QM/MM approach.

Insights into the catalytic mechanism of chlorophenol 4-monooxygenase: a quantum mechanics/molecular mechanics study

The degradation mechanism of chlorophenol 4-monooxygenase toward pollutants 2,4,5-trichlorophenol, 2,4,6-trichlorophenol, and 2,5-dichloro-p-hydroquinone was studied by QM/MM investigations.