Free Energies for Degradation Reactions of 1,2,3-Trichloropropane from ab Initio Electronic Structure Theory

Role of Nitrogenous Functional Group Identity in Accelerating 1,2,3-Trichloropropane Degradation by Pyrogenic Carbonaceous Matter (PCM) and Sulfide Using PCM-like Polymers

Groundwater contamination by 1,2,3-trichloropropane (TCP) poses a unique challenge due to its human toxicity and recalcitrance to degradation. Previous work suggests that nitrogenous functional groups of pyrogenic carbonaceous matter (PCM), such as biochar, are important in accelerating contaminant dechlorination by sulfide. However, the reaction mechanism is unclear due, in part, to PCM's structural complexity. Herein, PCM-like polymers (PLPs) with controlled placement of nitrogenous functional groups [i.e., quaternary ammonium (QA), pyridine, and pyridinium cations (py+)] were employed as model systems to investigate PCM-enhanced TCP degradation by sulfide. Our results suggest that both PLP-QA and PLP-py+ were highly effective in facilitating TCP dechlorination by sulfide with half-lives of 16.91 ± 1.17 and 0.98 ± 0.15 days, respectively, and the reactivity increased with surface nitrogenous group density. A two-step process was proposed for TCP dechlorination, which is initiated by reductive ß-elimination, followed by nucleophilic substitution by surface-bound sulfur nucleophiles. The TCP degradation kinetics were not significantly affected by cocontaminants (i.e., 1,1,1-trichloroethane or trichloroethylene), but were slowed by natural organic matter. Our results show that PLPs containing certain nitrogen functional groups can facilitate the rapid and complete degradation of TCP by sulfide, suggesting that similarly functionalized PCM might form the basis for a novel process for the remediation of TCP-contaminated groundwater.

Abiotic natural attenuation of 1,2,3-trichloropropane by natural magnetite under O2 perturbation

1,2,3-Trichloropropane (TCP) is an emerging groundwater pollutant, but there is a lack of reported studies on the abiotic natural attenuation of TCP by iron minerals. Furthermore, perturbation by O2 is common in the shallow subsurface by both natural and artificial processes. In this study, natural magnetite was selected as the reactive iron mineral to investigate its role in the degradation of TCP under O2 perturbation. The results indicated that the mineral structural Fe(II) on magnetite reacted with dissolved oxygen to generate O2-· and HO·. Both O2-· and HO· contributed to TCP degradation, with O2-· playing a more important role. After 56 days of reaction, 66.7% of TCP was completely dechlorinated. This study revealed that higher magnetite concentrations, smaller magnetite particle sizes, and lower initial TCP concentrations favored TCP degradation. The presence of <10 mg/L natural organic matter (NOM) did not affect TCP degradation. These findings significantly advance our understanding of the abiotic natural attenuation mechanisms facilitated by iron minerals under O2 perturbation, providing crucial insights for the study of natural attenuation.

Perspectives of genetically engineered microbes for groundwater bioremediation

Biodegradation is the main process for the removal of organic compounds from the environment, but proceeds slowly for many synthetic chemicals of environmental concern. Research on microbial biodegradation pathways revealed that recalcitrance is - among other factors - caused by biochemical blockages resulting in dysfunctional catabolic routes. This has raised interest in the possibility to construct microorganisms with improved catabolic activities by genetic engineering. Although this goal has been pursued for decades, no full-scale applications have emerged. This perspective explores the lagging implementation of genetically engineered microorganisms in practical bioremediation. The major technical and scientific issues are illustrated by comparing two examples, that of 1,2-dichloroethane where successful full-scale application of pump-and-treat biotreatment processes has been achieved, and 1,2,3-trichloropropane, for which protein and genetic engineering yielded effective bacterial cultures that still await application.

Reduction of 1,2,3-trichloropropane (TCP): pathways and mechanisms from computational chemistry calculations

The characteristic pathway for degradation of halogenated aliphatic compounds in groundwater or other environments with relatively anoxic and/or reducing conditions is reductive dechlorination. For 1,2-dihalocarbons, reductive dechlorination can include hydrogenolysis and dehydrohalogenation, the relative significance of which depends on various structural and energetic factors. To better understand how these factors influence the degradation rates and products of the lesser halogenated hydrocarbons (in contrast to the widely studied per-halogenated hydrocarbons, like trichloroethylene and carbon tetrachloride), density functional theory calculations were performed to compare all of the possible pathways for reduction and elimination of 1,2,3-trichloropropane (TCP). The results showed that free energies of each species and reaction step are similar for all levels of theory, although B3LYP differed from the others. In all cases, the reaction coordinate diagrams suggest that β-elimination of TCP to allyl chloride followed by hydrogenolysis to propene is the thermodynamically favored pathway. This result is consistent with experimental results obtained using TCP, 1,2-dichloropropane, and 1,3-dichloropropane in batch experiments with zerovalent zinc (Zn⁰, ZVI) as a reductant.

Ion-Pair SN 2 Reaction of OH- and CH3 Cl: Activation Strain Analyses of Counterion and Solvent Effects

We have theoretically studied the non-identity S_N 2 reactions of M_n OH^(n-1) +CH₃ Cl (M⁺ =Li⁺ , Na⁺ , K⁺ , and MgCl⁺ ; n=0, 1) in the gas phase and in THF solution at the OLYP/6-31++G(d,p) level using polarizable continuum model (PCM) implicit solvation. We want to explore and understand the effect of the metal counterion M⁺ and solvation on the reaction profile and the stereoselectivity of these processes. To this end, we have explored the potential energy surfaces of the backside (S_N 2-b) and frontside (S_N 2-f) pathways. To explain the computed trends, we have carried out analyses with an extended activation strain model (ASM) of chemical reactivity that includes the treatment of solvation effects.

Hydrothermal carbonization of poly(vinyl chloride)

Poly(vinyl chloride) (PVC) was subjected to hydrothermal carbonization in subcritical water at 180-260 °C. Dehydrochlorination increased with increasing reaction temperature. The release of chlorine was almost quantitative above ∼235 °C. The fraction of organic carbon (OC) recovered in the hydrochar decreased with increasing operating temperature from 93% at 180 °C to 75% at 250 °C. A wide array of polycyclic aromatic hydrocarbons (PAHs) could be detected in the aqueous phase, but their combined concentration amounted to only ∼140 μg g(-1) PVC-substrate at 240 °C. A pathway for the formation of cyclic hydrocarbons and O-functionalized organics was proposed. Chlorinated hydrocarbons including chlorophenols could only be identified at trace levels (low ppb). Polychlorinated dibenzodioxins (PCDDs) and dibenzofurans (PCDFs) could not be detected. The sorption potential of the hydrochar turned out to be very low, in particular for polar organic pollutants. Our results provide strong evidence that hydrothermal carbonization of household organic wastes which can be tied to co-discarded PVC-plastic residues is environmentally sound regarding the formation of toxic organic products. Following these findings, hydrothermal treatment of PVC-waste beyond operating temperatures of ∼235 °C to allow complete release of organic chlorine should be further pursued.

A Pseudomonas putida strain genetically engineered for 1,2,3-trichloropropane bioremediation

1,2,3-Trichloropropane (TCP) is a toxic compound that is recalcitrant to biodegradation in the environment. Attempts to isolate TCP-degrading organisms using enrichment cultivation have failed. A potential biodegradation pathway starts with hydrolytic dehalogenation to 2,3-dichloro-1-propanol (DCP), followed by oxidative metabolism. To obtain a practically applicable TCP-degrading organism, we introduced an engineered haloalkane dehalogenase with improved TCP degradation activity into the DCP-degrading bacterium Pseudomonas putida MC4. For this purpose, the dehalogenase gene (dhaA31) was cloned behind the constitutive dhlA promoter and was introduced into the genome of strain MC4 using a transposon delivery system. The transposon-located antibiotic resistance marker was subsequently removed using a resolvase step. Growth of the resulting engineered bacterium, P. putida MC4-5222, on TCP was indeed observed, and all organic chlorine was released as chloride. A packed-bed reactor with immobilized cells of strain MC4-5222 degraded >95% of influent TCP (0.33 mM) under continuous-flow conditions, with stoichiometric release of inorganic chloride. The results demonstrate the successful use of a laboratory-evolved dehalogenase and genetic engineering to produce an effective, plasmid-free, and stable whole-cell biocatalyst for the aerobic bioremediation of a recalcitrant chlorinated hydrocarbon.

Computational electrochemistry: prediction of liquid-phase reduction potentials

This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.

Consistent estimation of Gibbs energy using component contributions

Standard Gibbs energies of reactions are increasingly being used in metabolic modeling for applying thermodynamic constraints on reaction rates, metabolite concentrations and kinetic parameters. The increasing scope and diversity of metabolic models has led scientists to look for genome-scale solutions that can estimate the standard Gibbs energy of all the reactions in metabolism. Group contribution methods greatly increase coverage, albeit at the price of decreased precision. We present here a way to combine the estimations of group contribution with the more accurate reactant contributions by decomposing each reaction into two parts and applying one of the methods on each of them. This method gives priority to the reactant contributions over group contributions while guaranteeing that all estimations will be consistent, i.e. will not violate the first law of thermodynamics. We show that there is a significant increase in the accuracy of our estimations compared to standard group contribution. Specifically, our cross-validation results show an 80% reduction in the median absolute residual for reactions that can be derived by reactant contributions only. We provide the full framework and source code for deriving estimates of standard reaction Gibbs energy, as well as confidence intervals, and believe this will facilitate the wide use of thermodynamic data for a better understanding of metabolism.

Effects of solution chemistry on the dechlorination of 1,2,3-trichloropropane by zero-valent zinc

The reactivity of zerovalent zinc (ZVZ) toward 1,2,3-trichloropropane (TCP) was evaluated under a variety of solution conditions, including deionized water, groundwater, and artificial groundwater, over a pH range of about 6.5-12. In deionized water, first-order rate constants for TCP disappearance (k(obs)) exhibit a broad minimum between pH 8 and 10, with increasing k(obs) observed at lower and higher pH. The similarity between this trend and zinc oxide (ZnO) solubility behavior suggests pH related changes to the ZnO surface layer strongly influence ZVZ reactivity. Values of k(obs) measured in acidic groundwater are similar to those measured in DI water, whereas values measured in alkaline groundwater are much smaller (>1 order of magnitude at pH values >10). Characterization of the surfaces of ZVZ exposed to deionized water, acidic groundwater, and alkaline groundwater suggests that the slower rates obtained in alkaline groundwater are related to the presence of a morphologically distinct surface film that passivates the ZVZ surface. TCP degradation rates in artificial groundwater containing individual solutes present in groundwater suggest that silicate anions contribute to the formation of this passivating film.