A Benchmark Study of Kinetic Isotope Effects and Barrier Heights for the Finkelstein Reaction

Herein, we present a combined (experimental and computational) study of the Finkelstein reaction in condensed phase, where bromine is substituted by iodine in 2-bromoethylbenzene, in the presence of either acetone or acetonitrile as a solvent. Performance of various density functional theory and ab initio methods were tested for reaction barrier heights as well as for bromine and carbon kinetic isotope effects (KIEs). Two different implicit solvation models were examined (PCM and SMD). Theoretically predicted KIEs were compared with experimental values, while reaction barrier heights were assessed using the CCSD­(T)-level and experimental energies as reference. In general, although the tested parameters (energies and KIEs) do not exhibit any substantial difference upon a change of the solvent, the different behavior of the theoretical methods was observed depending on the solvent. With respect to isotope effects, both PCM and SMD seem to perform very similarly, though results obtained with PCM are slightly closer to the experimental values. For predicting reaction barriers, utilization of either PCM or SMD solvation models yielded different results. Functionals from the ωB97 family: ωB97, ωB97X, and ωB97X-D provide the most accurate results for the studied system

Can Path Integral Molecular Dynamics Make a Good Approximation for Vapor Pressure Isotope Effects Prediction for Organic Solvents? A Comparison to ONIOM QM/MM and QM Cluster Calculation

Isotopic fractionation of volatile organic compounds (VOCs), which are under strict measures of control because of their potential harm to the environment and humans, has an important ecological aspect, as the isotopic composition of compounds may depend on the conditions in which such compounds are distributed in Nature. Therefore, detailed knowledge on isotopic fractionation, not only experimental but also based on theoretical models, is crucial to follow conditions and pathways within which these contaminants are spread throughout the ecosystems. In this work, we present carbon and, for the first time, bromine vapor pressure isotope effect (VPIE) on the evaporation process from pure-phase systemsdibromomethane and bromobenzene, the representatives of aliphatic and aromatic brominated VOCs. We combine isotope effects measurements with their theoretical prediction using three computational techniques, namely path integral molecular dynamics, QM cluster, and hybrid ONIOM models. While evaporation of both compounds resulted in normal bromine VPIEs, the difference in the direction of carbon isotopic fractionation is observed for the aliphatic and aromatic compounds, where VPIEs are inverse and normal, respectively. Even though theoretical models tested here turned out to be insufficient for quantitative agreement with the experimental values, cluster electronic structure calculations, as well as two-layer ONIOM computations, provided better reproduction of experimental trends

Dehydrochlorination of Hexachlorocyclohexanes Catalyzed by the LinA Dehydrohalogenase. A QM/MM Study

The elucidation of the catalytic role of LinA dehydrohalogenase in the degradation processes of hexachlorocyclohexane (HCH) isomers is extremely important to further studies on the bioremediation of HCH polluted areas. Herein, QM/MM free energy simulations are employed to provide the details of the dehydrochlorination reaction of two HCH isomers (γ and β). In particular, the role of the protonation state of one of the catalytic residuesHis73is explored. Based on our calculations, two distinct minimum free energy pathways (concerted and stepwise) were found for γ-HCH and β-HCH. The choice of the reaction channel for the dehydrochlorination reactions of γ- and β-HCH was shown to depend on the initial mutual orientations of the reacting species in the active site and the protonation form of His73. The sequential pathway comprises the transfer of the proton (H_δ1) between His73 and Asp25 and subsequently the H₁/Cl₂ pair elimination from the substrate molecule. Within a concerted mechanism, the dehydrochlorination reaction of γ-/β-HCH is initiated with neutral His73 and the H_δ1 proton is transferred upon final product formation. We found that the concerted pathway for β-HCH results in significantly higher free energy of activation than the stepwise route and therefore can be disregarded as not a feasible mechanism. On the other hand, the reaction that occurs with much lower energetic barrier requires a stronger base (i.e., anionic His73) to abstract the proton (H₁) from the substrate molecule. The presence of such transient form of His results in higher energy than the respective Michaelis complex and was observed only in the stepwise pathway for both isomers. Furthermore, we have concluded that both pathways (concerted and stepwise) are feasible for the dehydrochlorination reaction of γ-HCH. The activation free energies obtained from the M05-2<i>X</i>/6-31+G­(d,p) corrected path coordinate PMF profiles for the dehydrochlorination reactions of the γ-/β-HCH are in good agreement with the experimental values

Characteristic Isotope Fractionation Patterns in <i>s</i>‑Triazine Degradation Have Their Origin in Multiple Protonation Options in the <i>s</i>‑Triazine Hydrolase TrzN

<i>s</i>-Triazine herbicides (atrazine, ametryn) are groundwater contaminants which may undergo microbial hydrolysis. Previously, inverse nitrogen isotope effects in atrazine degradation by <i>Arthrobacter aurescens</i> TC1 (i) delivered highly characteristic (¹³C/¹²C, ¹⁵N/¹⁴N) fractionation trends for pathway identification and (ii) suggested that the <i>s</i>-triazine ring nitrogen was protonated in the enzyme <i>s</i>-triazine hydrolase (TrzN) where (iii) TrzN crystal structure and mutagenesis indicated H⁺-transfer from the residue E241. This study tested the general validity of these conclusions for atrazine and ametryn with purified TrzN and a TrzN-E241Q site-directed mutant. TrzN-E241Q lacked activity with ametryn; otherwise, degradation consistently showed <i>normal carbon isotope effects</i> (ε_carbon = −5.0‰ ± 0.2‰ (atrazine/TrzN), ε_carbon = −4.2‰ ± 0.5‰ (atrazine/TrzN-E241Q), ε_carbon = −2.4‰ ± 0.3‰ (ametryn/TrzN)) and <i>inverse nitrogen isotope effects</i> (ε_nitrogen = 2.5‰ ± 0.1‰ (atrazine/TrzN), ε_nitrogen = 2.1‰ ± 0.3‰ (atrazine/TrzN-E241Q), ε_nitrogen = 3.6‰ ± 0.4‰ (ametryn/TrzN)). Surprisingly, TrzN-E241Q therefore still activated substrates through protonation implicating another proton donor besides E241. Sulfur isotope effects were larger in enzymatic (ε_sulfur = −14.7‰ ± 1.0‰, ametryn/TrzN) than in acidic ametryn hydrolysis (ε_sulfur = −0.2‰ ± 0.0‰, pH 1.75), indicating rate-determining <i>C–S</i> bond cleavage in TrzN. Our results highlight a robust inverse ¹⁵N/¹⁴N fractionation pattern for identifying microbial <i>s</i>-triazine hydrolysis in the environment caused by multiple protonation options in TrzN

Reaction between Peroxynitrite and Triphenylphosphonium-Substituted Arylboronic Acid Isomers: Identification of Diagnostic Marker Products and Biological Implications

Aromatic boronic acids react rapidly with peroxynitrite (ONOO^–) to yield phenols as major products. This reaction was used to monitor ONOO^– formation in cellular systems. Previously, we proposed that the reaction between ONOO^– and arylboronates (PhB­(OH)₂) yields a phenolic product (major pathway) and a radical pair PhB­(OH)₂O^•–···^•NO₂ (minor pathway). [Sikora, A. et al. (2011) Chem. Res. Toxicol. 24, 687−697]. In this study, we investigated the influence of a bulky triphenylphosphonium (TPP) group on the reaction between ONOO^– and mitochondria-targeted arylboronate isomers (<i>o</i>-, <i>m</i>-, and <i>p</i>-MitoPhB­(OH)₂). Results from the electron paramagnetic resonance (EPR) spin-trapping experiments unequivocally showed the presence of a phenyl radical intermediate from <i>meta</i> and <i>para</i> isomers, and not from the <i>ortho</i> isomer. The yield of <i>o</i>-MitoPhNO₂ formed from the reaction between <i>o</i>-MitoPhB­(OH)₂ and ONOO^– was not diminished by phenyl radical scavengers, suggesting a rapid fragmentation of the <i>o</i>-MitoPhB­(OH)₂O^•– radical anion with subsequent reaction of the resulting phenyl radical with ^•NO₂ in the solvent cage. The DFT quantum mechanical calculations showed that the energy barrier for the dissociation of the <i>o</i>-MitoPhB­(OH)₂O^•– radical anion is significantly lower than that of <i>m</i>-MitoPhB­(OH)₂O^•– and <i>p</i>-MitoPhB­(OH)₂O^•– radical anions. The nitrated product, <i>o</i>-MitoPhNO₂, is not formed by the nitrogen dioxide radical generated by myeloperoxidase in the presence of the nitrite anion and hydrogen peroxide, indicating that this specific nitrated product may be used as a diagnostic marker product for ONOO^–. Incubation of <i>o-</i>MitoPhB­(OH)₂ with RAW 264.7 macrophages activated to produce ONOO^– yielded the corresponding phenol <i>o-</i>MitoPhOH as well as the diagnostic nitrated product, <i>o-</i>MitoPhNO₂. We conclude that the <i>ortho</i> isomer probe reported here is most suitable for specific detection of ONOO^– in biological systems