Bimolecular Reaction Rate Constants Research Articles

Development of a Five-Chemical-Probe Method to Determine Multiple Radicals Simultaneously in Hydroxyl and Sulfate Radical-Mediated Advanced Oxidation Processes.

Advanced oxidation processes (AOPs), such as hydroxyl radical (HO•)- and sulfate radical (SO4•-)-mediated oxidation, are attractive technologies used in water and wastewater treatments. To evaluate the treatment efficiencies of AOPs, monitoring the primary radicals (HO• and SO4•-) as well as the secondary radicals generated from the reaction of HO•/SO4•- with water matrices is necessary. Therefore, we developed a novel chemical probe method to examine five key radicals simultaneously, including HO•, SO4•-, Cl•, Cl2•-, and CO3•-. Five probes, including nitrobenzene, para-chlorobenzoic acid, benzoic acid, 2,4,6-trimethylbenzoic acid, and 2,4,6-trimethylphenol, were selected in this study. Their bimolecular reaction rate constants with diverse radicals were first calibrated under the same conditions to minimize systematic errors. Three typical AOPs (UV/H2O2, UV/S2O82-, and UV/HSO5-) were tested to obtain the radical steady-state concentrations. The effects of dissolved organic matter, Br-, and the probe concentration were inspected. Our results suggest that the five-probe method can accurately measure radicals in the HO•- and SO4•--mediated AOPs when the concentration of Br- and DOM are less than 4.0 μM and 15 mgC L-1, respectively. Overall, the five-probe method is a practical and easily accessible method to determine multiple radicals simultaneously.

Polyrate 2023: A computer program for the calculation of chemical reaction rates for polyatomics. New version announcement

Polyrate 2023: A computer program for the calculation of chemical reaction rates for polyatomics. New version announcement

Phototransformation of Lignin-related Compounds in Chromophoric Dissolved Organic Matter Solutions

Lignin is a major terrestrial source of chromophoric dissolved organic matter (CDOM), and studying the phototransformation of lignin monomers and their related compounds can enhance our understanding of CDOM intramolecular interactions. Coniferyl aldehyde (Coni) and sinapaldehyde (Sina) form ground-state complexes with CDOM, with equilibrium constants of 7,800 (± 1,800) and 20,000 (± 2,000) M−1, respectively. In comparison, vanillin (Van) exhibits minimal affinity for CDOM complexation. The bimolecular reaction rate constants between singlet oxygen (1O2) and these phenolic carbonyl compounds ranged from 0.46 (± 0.02) to 1.8 (± 0.1) × 107 M−1s−1, which is approximately one order of magnitude lower than their reaction rate constants (0.51 (± 0.02)–1.25 (± 0.02) × 108 M−1s−1) with the triplet excited state of CDOM (3CDOM*). In acidic CDOM solutions (pH 5.0), 1O2, H2O2, and organic peroxyl radicals had negligible impact on the transformation. Comparing the initial transformation rate in the presence and in the absence of NaN3 or furfuryl alcohol led to an overestimation of the contribution of 1O2 to the transformation of Van, Coni, or Sina. 3CDOM* scavengers could not fully inhibit the transformation of Coni or Sina. The remaining transformation is considered to arise from either the unquenched intra-CDOM phase 3CDOM* or a fraction of Coni⊂CDOM or Sina⊂CDOM complex, which underwent intramolecular photoinduced chemical reactions.

TUMME 2023: Tsinghua University Minnesota Master Equation program. New version announcement

This is an updated version of TUMME (Tsinghua University Minnesota Master Equation program), which is a computer program for setting up and solving master equations for chemical kinetics of unimolecular and bimolecular reactions. The master equation is discretized in terms of energy bins, and rate constants are calculated from chemically significant eigenmodes. TUMME has interfaces to Gaussian 16, Polyrate 2023, and MSTor 2023 output files that allow the master equation code to obtain the microcanonical flux coefficients needed for the kernel of the master equation as calculated by conventional transition state theory (TST), variational transition state theory (VTST) with various tunneling methods, or multi-structural or multi-path VTST (MS-VTST or MP-VTST) with various tunneling methods. The tunneling methods supported include zero-curvature tunneling (ZCT), small-curvature tunneling (SCT), large-curvature tunneling (LCT), and microcanonically optimized multidimensional tunneling (μOMT). For mechanisms involving only unimolecular isomerization (no bimolecular pairs), TUMME can set up and solve a conservative master equation for both rate constants and time-dependent energy-bin populations. For mechanisms involving bimolecular pairs, TUMME 2023 can set up and solve two kinds of master equation: (i) a nonconservative master equation for calculating rate constants of bimolecular reactions and (ii) a conservative master equation that includes bimolecular association in the transition matrix and that can be used for calculating the time evolution of the concentration of a pseudo-first-order bimolecular reactant. TUMME is written in double precision with Python 3; quadruple and octuple precision are also available for some subtasks in C++. The Python code can run in serial or parallel (MP or MPI), and C++ code can run on a single processor or on multiple processors with OpenMP. The program includes a manual and a tutorial. New version program summaryProgram Title: TUMME 2023CPC Library link to program files:https://doi.org/10.17632/whcnvm2mc9.2Developer's repository link:https://doi.org/10.5281/zenodo.7943283Licensing Provisions: Apache-2.0 for the program and CC-BY-4.0 for the manualProgramming languages: Python 3 and C++Does the new version supersede the previous version?: YesJournal reference of previous version: Comput. Phys. Commun. 270 (2022) 108140 [1]External libraries: Numpy, Scipy, Numba, mpi4py (optional), modified mpack (optional), qd (optional), omp (optional)Interfaces to other programs: Gaussian 16 [2], Polyrate 2023 [3], and/or MSTor 2023 [4]Nature of problem: Characterize and calculate rate constants for a temperature-dependent and pressure-dependent complex reaction systemSolution method: Solve the energy-grained master equation based on the chemically significant eigenmodes to get phenomenological rate constants and time evolutions of the populations [1,5–7].Reason for new version: The new version increases the functionality and accuracy, and it offers an easier way to run the program. In addition, some bugs have been corrected.Summary of revisions:1.Added an option (available in high precision) to treat pseudo-first-order bimolecular reactions to obtain the time evolution of the reactants and intermediates. [8]2.Added an inverse-Laplace-transform option in the REACTION block.3.Abandoned rounding the sizes of energy bins to an integer wavenumber (ESOT).4.Changed the way to run TUMME by providing an executable bash script.5.Slightly adjusted the strategy for eigenmode mergers to deal with some unexpected cases.6.Adjusted the output for the partition functions.7.Added options for large-curvature tunneling (LCT) and microcanonically optimized multidimensional tunneling (μOMT).8.Added the keyword pyrfile to support a Polyrate 2023 [3] file that ends with a suffix .fu100.9.Fixed some bugs.10.Updated the manual and added a tutorial to the program distribution, so the distribution now has both a manual and a tutorial.

Reactivity of tert‐butylperoxyl radical with some phenylthiazolidine derivatives and probucol

AbstractThe hybrid molecule phenylthiazolidine derivatives and probucol were kinetically examined as antioxidants (AOs) in scavenging tert‐butylperoxyl radical (t‐BuOO•) with comparable to the reference AO, butylated hydroxytoluene (BHT). The anti‐t‐BuOO• reactivity of phenylthiazolidine derivatives and probucol was established using the direct kinetic electron paramagnetic resonance (EPR) technique with pulse reactant injection. Absolute values of the bimolecular reaction rate constants and antiradical capacities of the studied compounds were measured from −63 to 0°C. The main antiperoxylradical sites of the compounds under study were revealed.High removal ability of t‐BuOO• by (2‐(4‐hydroxyphenyl)thiazolidine), 4‐[thiazolidin‐2‐yl]benzene‐1,2‐diol, 2‐(4‐hydroxyphenyl)thiazolidine‐4‐carboxylic acid and probucol was connected with the reaction of hydrogen atom abstraction from phenolic OH group.Weaker antiperoxylradical reactivity of 2‐phenylthiazolidine was connected with the slower reaction of hydrogen atom abstraction from benzylic C–H bond in reference to nitrogen and sulfur atoms compared with the phenolic OH group. It is found that sulfide groups had much weaker participation in antiperoxylradical reactivity of the studied compounds. It is concluded that removal of alkylperoxyl radicals by oxidizable phenylthiazolidine derivatives and probucol may partially account for biological activity of their compounds.

Kinetic and Mechanistic Considerations of the Photosensitized Transformation of Chlorine in Chromophoric Dissolved Organic Matter Solutions under Simulated Solar Irradiation.

Chlorination is one of the most common disinfection methods for water treatments. Although the direct photolysis of free available chlorine (FAC) induced by solar irradiation has been extensively investigated, the photosensitized transformation of FAC caused by chromophoric dissolved organic matter (CDOM) has not previously been examined. Our results suggest that the photosensitized transformation of FAC can occur in sunlit CDOM-enriched solutions. Interestingly, the photosensitized decay of FAC can be fitted using a combined zero- and first-order kinetic model. The photogenerated O2•- from CDOM contributes to the zero-order kinetic component. The reductive triplet CDOM (3CDOM*) contributes to the pseudo-first-order decay kinetic component. The bimolecular reaction rate constants of the model triplet (3-methoxyacetophenone) with HOCl and OCl- were (3.6 ± 0.2) × 109 and (2.7 ± 0.3) × 109 M-1 s-1, respectively. Under simulated solar irradiation, the quantum yield coefficient of the reductive 3CDOM* toward FAC attenuation (fFAC = 840 ± 40 M-1) was 13 times greater than that of the oxidative 3CDOM* toward trimethylphenol (TMP) attenuation (fTMP = 64 ± 4 M-1). This study provides new insights into the photochemical transformation of FAC in sunlit surface waters, and the results are applicable when sunlight/FAC system is employed as an advanced oxidation process.

Photolysis of 3-Nitro-1,2,4-triazol-5-one: Mechanisms and Products.

Insensitive munitions formulations that include 3-nitro-1,2,4-triazol-5-one (NTO) are replacing traditional explosive compounds. While these new formulations have superior safety characteristics, the compounds have greater environmental mobility, raising concern over potential contamination and cleanup of training and manufacturing facilities. Here, we examine the mechanisms and products of NTO photolysis in simulated sunlight to further inform NTO degradation in sunlit surface waters. We demonstrate that NTO produces singlet oxygen and that dissolved oxygen increases the NTO photolysis rate in deionized water. The rate of NTO photolysis is independent of concentration and decreases slightly in the presence of Suwannee River Natural Organic Matter. The apparent quantum yield of NTO generally decreases as pH increases, ranging from 2.0 × 10-5 at pH 12 to 1.3 × 10-3 at pH 2. Bimolecular reaction rate constants for NTO with singlet oxygen and hydroxyl radical were measured to be (1.95 ± 0.15) × 106 and (3.28 ± 0.23) × 1010 M-1 s-1, respectively. Major photolysis reaction products were ammonium, nitrite, and nitrate, with nitrite produced in nearly stoichiometric yield upon the reaction of NTO with singlet oxygen. Environmental half-lives are predicted to span from 1.1 to 5.7 days. Taken together, these data enhance our understanding of NTO photolysis under environmentally relevant conditions.

Theoretical study on the formation of Criegee intermediates from ozonolysis of pentenal: An example of trans-2-pentenal.

In this study, we investigated the reaction mechanism and kinetics of ozone with trans-2-pentenal using density functional theory (DFT) and conventional transition state theory (CTST). At 298K and 1atm, the gas-phase reaction mechanisms and kinetic parameters were calculated at the level of CCSD(T)/6-311+G(d,p)//M06-2X/6-311+G(d,p). Both CC and CO bond cycloaddition as well as hydrogen abstraction were found. The calculations indicated that the main reaction path is 1,3-dipole cycloaddition reactions of ozone with CC bond with the relatively lower syn-energy-barrier of 3.35kcalmol-1 to form primary ozonide which decomposed to produce a carbonyl oxide called a Criegee intermediate (CI) and an aldehyde. The subsequent reactions of CIs were analysed in detail. It is found that the reaction pathways of the novelty CIs containing an aldehyde group are extremely similar with general CIs when they react with NO, NO2, SO2, H2O, CH2O and O2. The condensed Fukui function were calculated to identify the active site of the chosen molecules. At 298K and 1atm, the reaction rate coefficient was 9.13×10-18cm3 molecule-1 s-1 with atmospheric lifetime of 1.3 days. The calculated rate constant is in general agreement with the available experimental data. The branching ratios indicated that syn-addition pathways are prior to anti-addition. The atmospheric ratios for CIs formation and the bimolecular reaction rate constants for the Criegee intermediates with the variety of partners were calculated. Our theoretical results are of importance in atmospheric chemistry of unsaturated aldehyde oxidation by ozone.

Effect of disinfection on the photoreactivity of effluent organic matter and photodegradation of organic contaminants

Chlorine, UV254, and ozone are three typical processes commonly used for wastewater disinfection, which could change the photoreactivity of dissolved organic matter (DOM) in effluents of wastewater treatment plants (WWTPs). The photoinduced reactive species (RS) from DOM, primarily including the excited triplet state of DOM (3DOM*), singlet oxygen (1O2), and hydroxyl radical (•OH), play important roles in the attenuation of contaminants. However, the effect of disinfection processes on the photosensitized degradation of contaminants is poorly understood. This paper presents the first evidence that 3DOM*, 1O2, and •OH interaction with three typical contaminants (diphenhydramine, cimetidine, and N,N-diethyl-m-toluamide (DEET)) was largely impacted by DOM after disinfection. The results of electron spin resonance (ESR) spectrometry and laser flash photolysis (LFP) experiments demonstrated that the chlorination increased the formation rate of 3DOM* and 1O2, while UV254 irradiation and ozonation decreased the formation rate of these RS. All these three disinfection processes promoted the photoproduction of •OH and increased the photodegradation rate constants (kobs) of DEET by 26−361%. The kobs of diphenhydramine, cimetidine, and DEET correlated positively with the formation rate of 3DOM*, 1O2, and •OH, respectively. The bimolecular reaction rate constant of 3DOM* with diphenhydramine increased by ∼41% after chlorination. These findings suggest that disinfection processes altered the photogeneration of RS from DOM, which significantly impacts the fate of trace pollutants in aquatic environments.

Dissociation-induced depletion of high-energy reactant molecules as a mechanism for pressure-dependent rate constants for bimolecular reactions.

In 1922, Lindemann proposed the now-well-known mechanism for pressure-dependent rate constants for unimolecular reactions: reactant molecules with sufficiently high energies dissociate more quickly than collisions can reestablish the Boltzmann distribution of the internal energies of the molecule during its dissociation at low pressures - yielding pressure-dependent rate constants for unimolecular reactions due to the preferential depletion of the high energy states capable of dissociation. In the last century, incredible progress has been made in achieving a far greater understanding of and quantitative predictions for unimolecular and association reactions. In the modern era, pressure-dependent phenomenological rate constants are now nearly universally used to describe the rates of unimolecular and associative reactions in phenomenological kinetic modeling. However, there is a second, more indirect, implication of Lindemann's mechanism that relates to how these dissociation-induced non-equilibrium distributions impact bimolecular reactions, including non-associative bimolecular reactions - which are generally not considered to have pressure-dependent rate constants. Yet, as we show herein, the same high energy states depleted due to dissociation would otherwise react most rapidly in high-activation-energy bimolecular reactions - yielding a mechanism for pressure-dependent rate constants for bimolecular reactions (including non-associative reactions). Here, we present results from a case study for CH2O dissociation, isomerization, and bimolecular reaction with O2 to explore this question. Results from our master equation calculations indicate that the effect of dissociation-induced non-equilibrium distributions on bimolecular reactions can be substantial - even when chemical timescales are well separated from internal energy relaxational timescales (i.e. when the traditional rate constant description would be thought to apply). This effect is found to be more pronounced - and more complex - for bimolecular reactions involving molecular entities whose chemical timescales are merged with the internal energy relaxational timescales. Finally, we present some ideas for discussion regarding what should be considered as "chemical species" in phenomenological kinetic models.

Zn Coordination and the Identity of the Halide Ancillary Ligand Dramatically Influence the Excited-State Dynamics and Bimolecular Reactions of 2,3-Di(pyridin-2-yl)benzo[g]quinoxaline.

The optical properties of coordination complexes with ligands containing nitrogen heterocycles have been extensively studied for decades. One subclass of these materials, metal complexes utilizing substituted pyrazines and quinoxalines as ligands, has been employed in a variety of photochemical applications ranging from photodynamic therapy to organic light-emitting diodes. A vast majority of this work focuses on characterization of the metal-to-ligand charge-transfer states in these metal complexes; however, literature reports rarely investigate the photophysics of the parent pyrazine or quinoxaline ligand or perform control experiments utilizing metal complexes that lack low-lying charge-transfer (CT) states in order to determine how metal-atom coordination influences the photophysical properties of the ligand. With this in mind, we examined the steady-state and time-resolved photophysics of 2,3-di(pyridin-2-yl)benzo[g]quinoxaline (dpb) and explored how the coordination of ZnX2 (X = Cl-, Br-, I-) affects the photophysical properties of dpb. In dpb, we find that the dominant mode of deactivation from the singlet excited state is intersystem crossing (ISC). Coordination of ZnX2 perturbs the relative energies of the ππ* and nπ* excited states of dpb, leading to drastically different rates of ISC as well as radiative and nonradiative decay in the [Zn(dpb)X2] complexes compared to dpb. These differences in the rates change the dominant singlet-excited-state decay pathway from ISC in dpb to a mixture of ISC and fluorescence in [Zn(dpb)Cl2] and [Zn(dpb)Br2] and to nonradiative decay in [Zn(dpb)I2]. Coordination of ZnX2 and the choice of the halide ligand also have profound effects on the rate constants for excited-state bimolecular reactions, including triplet-triplet annihilation and oxygen quenching. These results demonstrate that metal coordination, even in complexes lacking low-lying CT states, and the choice of the ancillary ligand can dramatically alter the photophysical properties of chromophores containing nitrogen heterocycles.

Modeling Chemical Reactivity at the Interfaces of Emulsions: Effects of Partitioning and Temperature.

Bulk phase chemistry is hardly ever a reasonable approximation to interpret chemical reactivity in compartmentalized systems, because multiphasic systems may alter the course of chemical reactions by modifying the local concentrations and orientations of reactants and by modifying their physical properties (acid-base equilibria, redox potentials, etc.), making them—or inducing them—to react in a selective manner. Exploiting multiphasic systems as beneficial reaction media requires an understanding of their effects on chemical reactivity. Chemical reactions in multiphasic systems follow the same laws as in bulk solution, and the measured or observed rate constant of bimolecular reactions can be expressed, under dynamic equilibrium conditions, in terms of the product of the rate constant and of the concentrations of reactants. In emulsions, reactants distribute between the oil, water, and interfacial regions according to their polarity. However, determining the distributions of reactive components in intact emulsions is arduous because it is physically impossible to separate the interfacial region from the oil and aqueous ones without disrupting the existing equilibria and, therefore, need to be determined in the intact emulsions. The challenge is, thus, to develop models to correctly interpret chemical reactivity. Here, we will review the application of the pseudophase kinetic model to emulsions, which allows us to model chemical reactivity under a variety of experimental conditions and, by carrying out an appropriate kinetic analysis, will provide important kineticparameters.

An experimental and statistical modeling study of the reactivity of Co+(CH3Br)n (n = 0,1) with methyl bromide

The temperature- and pressure-dependent kinetics of Co+(CH3Br)n (n = 0,1) + CH3Br are measured from 300 to 600 K and from 0.2 to 0.5 Torr. Results are interpreted using density functional calculations and modeled with statistical theory. In the n = 0 case, the associative product Co+(CH3Br) dominates with a rate constant between 5 and 30% of the collisional value, while a minor channel yields CoBr+ + CH3 with a rate constant increasing with temperature. 0K bond dissociation energies (BDE) are determined for Co+-Br (2.8 ± 0.1 eV) and Co+-CH3Br (2.4 ± 0.25 eV). Ligation of Co+ (i.e. n = 1) significantly increases the bimolecular reaction rate constant. CoBr+(CH3Br) + CH3 is formed and the reaction has a positive temperature dependence. Interestingly, this rate constant decreases with increasing pressure due to competition of the association channel. Ligation increases the (CH3Br)Co+-Br BDE (3.0 ± 0.1 eV) relative to Co+-Br, but decreases the (CH3Br)Co+-CH3Br BDE (1.95 ± 0.25) relative to Co+-CH3Br. Both bimolecular reactions proceed by a metal-insertion mechanism with a significantly submerged transition state that does not affect the kinetics. Instead, the endothermicity of the reaction is rate-limiting. Discussion about how energy, impact parameter, and angular momentum affect specific rate constants for dissociation to reactants, reaction to products, and association are presented.

Chemical insights into the atmospheric oxidation of thiophene by hydroperoxyl radical

The reaction mechanisms and kinetics of thiophene oxidation reactions initiated by hydroperoxyl radical, and decomposition of the related intermediates and complexes, have been considered herein by using high-level DFT and ab initio calculations. The main energetic parameters of all stationary points of the suggested potential energy surfaces have been computed at the BD(T) and CCSD(T) methods, based on the geometries optimized at the B3LYP/6-311 + g(d,p) level of theory. Rate constants of bimolecular reactions (high-pressure limit rate constants) at temperatures from 300 to 3000 K for the first steps of the title reaction have been obtained through the conventional transition state theory (TST), while the pressure dependent rate constants and the rate constants of the second and other steps have been calculated employing the Rice–Ramsperger–Kassel–Marcus/Master equation (RRKM/ME). The results show that the rate constants of addition to α and β carbons have positive temperature dependence and negative pressure dependence. It is found that the additions of HO2 to the α and β carbons of thiophene in the initial steps of the title reaction are the most favored pathways. Also, the addition to the sulfur atom has a minor contribution. But, all efforts for simulating hydrogen abstraction reactions have been unsuccessful. In this complex oxidation reaction, about 12 different products are obtained, including important isomers such as thiophene-epoxide, thiophene-ol, thiophene-oxide, oxathiane, and thiophenone. The calculated total rate constants for generation of all minimum stationary points show that the addition reactions to the α and β carbons are the fastest among all at temperatures below 1000 K, while the proposed multi-step parallel reactions are more competitive at temperatures above 1200 K. Furthermore, important inter-and intra-molecular interactions for some species have been investigated by two well-known quantum chemistry method, the NBO and AIM analyses. Thermochemical properties such as free energy, enthalpy, internal energy, and entropy for thiophene and hydroperoxyl radical and related species in the simulated reactions have been predicted using a combination of the B3LYP and BD(T) methods.

Phototransformation of an emerging cyanotoxin (Aerucyclamide A) in simulated natural waters

Aerucyclamide A (ACA) is an emerging cyanopeptide toxin produced by cyanobacteria, and its transformation pathway has rarely been reported. In the present study, ACA was purified from cyanobacterial extracts, and photodegradation processes were investigated in dissolved organic matter (DOM) solutions. Under simulated solar irradiation, the photodegradation of ACA was dominated by •OH oxidation, accounting for ~72% of the indirect photodegradation. The bimolecular reaction rate constant of ACA with •OH was (6.4 ± 0.2) × 109M − 1s − 1. Our results indicated that the major reactive sites of ACA toward •OH are thiazoline and thiazole moieties. Product analysis via high-resolution mass spectrometry suggested that hydrogen abstraction and gradual hydroxylation are the main photodegradation pathways. The acute toxicity assessment indicate that the products generated in photolysis process did not show any measurable toxicity to Thamnocephalus platyurus. Photodegradation experiments with various DOM-phycocyanin mixtures demonstrated that the half-life of ACA is much longer than that of microcystin-LR.

Cross-validation strategies in QSPR modelling of chemical reactions

ABSTRACT In this article, we consider cross-validation of the quantitative structure-property relationship models for reactions and show that the conventional k-fold cross-validation (CV) procedure gives an ‘optimistically’ biased assessment of prediction performance. To address this issue, we suggest two strategies of model cross-validation, ‘transformation-out’ CV, and ‘solvent-out’ CV. Unlike the conventional k-fold cross-validation approach that does not consider the nature of objects, the proposed procedures provide an unbiased estimation of the predictive performance of the models for novel types of structural transformations in chemical reactions and reactions going under new conditions. Both the suggested strategies have been applied to predict the rate constants of bimolecular elimination and nucleophilic substitution reactions, and Diels-Alder cycloaddition. All suggested cross-validation methodologies and tutorial are implemented in the open-source software package CIMtools (https://github.com/cimm-kzn/CIMtools).

Photochemical origin of reactive radicals and halogenated organic substances in natural waters: A review

Halogenated organic compounds, also termed organohalogens, were initially regarded to be of almost exclusively anthropogenic origin. However, recent research has demonstrated that photochemical reactions are important abiotic sources of organohalogen compounds in sunlit surface waters. Halide ions (X−, X represents Cl, Br and I) are common anions in natural waters and might be oxidized by reactive species originated from photochemistry of dissolved organic matter (DOM) or inorganic photoactive species. The resulting reactive halogen species may react with organic substances with diverse bimolecular reaction rate constants, depending on the complexity and structure of organic substances. Therefore, the chemical mechanism of halogenation remains challenging to be fully elucidated. To better understand the trends in the existing data and to identify the knowledge gaps that may merit further investigation, this review gives an integrative summary on the sources of reactive oxygen species (ROS) and halogen radicals (X/X2−). Photochemical halogenation of phenolic compounds and formation of methyl halide and brominated organic pollutants are highlighted. By evaluating existing literature and identifying some uncertainties, this review emphasizes the environmental significance of sunlight-driven halogenation and proposes further research directions on mechanistic investigation and rational experimental design close to natural systems.

Pilgrim: A thermal rate constant calculator and a chemical kinetics simulator

Pilgrim is a program written in Python and designed to use direct dynamics in the calculation of thermal rate constants of chemical reactions by the variational transition state theory (VTST), based on electronic structure calculations for the potential energy surface. Pilgrim can also simulate reaction mechanisms using kinetic Monte Carlo (KMC).For reaction processes with many elementary steps, the rate constant of each of these steps can be calculated by means of conventional transition state theory (TST) or by using VTST. In the current version, Pilgrim can evaluate thermal rates using the canonical version of reaction-path VTST, which requires the calculation of the minimum energy path (MEP) associated with each elementary step or transition structure. Multi-dimensional quantum effects can be incorporated through the small-curvature tunneling (SCT) approximation. These methodologies are available both for reactions involving a single structure of the reactants and the transition state and also for reactions involving flexible molecules with multiple conformations of the reactant and/or of the transition state. For systems with many conformers, the program can evaluate each of the elementary reaction rate constants by multipath canonical VTST or multi-structural VTST. Moreover, the reactant can be unimolecular or bimolecular.Torsional anharmonicity can be incorporated through either the MSTor or the Q2DTor programs. Dual-level calculations are also available in Pilgrim: automatic high-level single-point energies can be used to correct the energy of reactants, transition states, products, and MEP points using the interpolated single-point energies (ISPE) algorithm.When the rate constants of all the chemical processes of interest are known, by means of their calculation using Pilgrim or alternatively through analytical fits to the rate constants as functions of temperature, it is possible to simulate a multistep mechanism under specified laboratory conditions using KMC. This algorithm allows performing a kinetic simulation to monitor the evolution of each chemical species with time and obtain the product yields. Program summaryProgram Title: PilgrimCPC Library link to program files:http://dx.doi.org/10.17632/24cj4dwxvg.1Developer’s repository link:https://github.com/cathedralpkg/pilgrim/releases; https://comp.chem.umn.edu/pilgrim; https://conservancy.umn.edu/handle/11299/166578Licensing provisions: MITProgramming language: Python 3Nature of problem: Calculation of thermal rate constants for bimolecular and unimolecular chemical reactions and simulation of reaction mechanismsSolution method: The program uses variational transition state theory to calculate thermal rate constants and kinetic Monte Carlo to simulate reaction mechanisms.Restrictions and unusual features: The program cannot treat reactions without saddle points. Unimolecular reactions are calculated only in the high-pressure limit. Direct dynamics calculations with Pilgrim require an electronic structure package to be supplied by the user; currently, Pilgrim supports the Gaussian [Frisch et al. (2003), Frisch et al. (2016a), Frisch et al. (2016b)] and Orca [Neese (2011)] electronic structure packages. Pilgrim has an especially powerful suite of options for handling torsional anharmonicity and multistructural effects.

Mechanistic investigation of humic substances assisted photodegradation of imipramine under simulated sunlight

Imipramine (IMI) is a frequently prescribed tricyclic antidepressant and widely detected in the natural waters, while the environmental fate of IMI is yet poorly understood. Here, we investigated the photodegradation of IMI under simulated sunlight in the presence of humic substances (HS), typically including humic acid (HA) and fulvic acid (FA). The direct and indirect IMI photodegradation was found to increase both with increasing pH and with deoxygenation of the reaction solutions. The excited triplet state of HS (3HS⁎) was mainly responsible for the photosensitized degradation of IMI according to the steady-state quenching and direct time-resolved experiments. The electron transfer interaction between 3HS⁎ and IMI was observed by laser flash photolysis (LFP) with bimolecular reaction rate constants of (4.9 ± 0.4) × 109 M−1 s−1. Evidence of electron transfer from IMI to 3HS⁎ was further demonstrated by the photoproduct analysis. The indirect photodegradation was triggered off in the side chain of IMI with the nonbonding nitrogen electron transferring to 3HS⁎, followed by hydroxylation, demethylation and cleavage of the side chain. Very important that HS photosystem does not lose its efficiency with decreasing of IMI concentration, meaning that the studied photosystem still be used at environmentally relevant concentrations of IMI. These results suggest that photodegradation could be an important attenuation pathway for IMI in HS-rich and anaerobic natural waters.

Hydroxyl radical oxidation of cyclic methylsiloxanes D4 ∼ D6 in aqueous phase.

Cyclic methylsiloxanes (CMS) were listed as candidates of substances of very high concerns in 2018 by the REACH. These compounds can enter environmental waters, and potentially cause harmful effects to aquatic organisms and human beings. Until now, reaction mechanisms of these pollutants with hydroxyl radicals (HO) in aqueous phase were unknown. In this study, reaction mechanisms of three typical CMS (D4 ∼ D6) with HO in aqueous phase were investigated by employing both UV/H2O2 experiments and density functional theoretical calculations. Bimolecular reaction rate constants (kHO·) of D4 ∼ D6 with HO were determined as kHO·(D4) = 8kHO·(D5) = 12kHO·(D6) = 6.6 × 108 L mol-1 s-1. Half-lives of HO oxiding D4 ∼ D6 ranged from 12 to 140 days at [HO] = 10-15 mol L-1 in sunlit surface water, and were comparable to (D4, D5) or much shorter (D6) than hydrolytic half-lives. The reactivity to HO decreased with the increasing size of siloxane ring in aqueous phase, in an order totally opposite to that in gaseous phase. Calculation results indicated that HO oxidation of the three CMS proceeded spontaneously through an exothermic H-abstraction process at the first step. Water molecules participated into H-abstraction of CMS and caused energy barrier of D5 higher than that of D4. Thus, H-bonds formed by water molecules were responsible for the reverse reactivity of CMS in aqueous phase. This work provided basic evidences suggesting environmental persistence of CMS in aqueous phase completely different from that in gaseous phase.