Kinetics and thermodynamics of the hydroxylation products in the photodegradation of the herbicide Metolachlor

Electronic structure calculations have been performed to determine the thermochemistry and kinetics of the reaction between OH and the radicals of the S enantiomer of the herbicide Metolachlor, 2-chloro-N-(2-methyl-6-ethylphenyl)-N(2-methoxy-1-methylethyl) acetamide (MC), produced by photoinduced breaking of the C–Cl bond. Both density functional and ab initio composite methods were employed to calculate the structure of reactants, intermediates, transition states and products, in gas phase and in aqueous solution. The expected relative abundance of each product was calculated and compared to the experimentally observed concentrations. It is shown that a combination of thermodynamic and kinetic characteristics interplay to produce the expected theoretical abundances, which turn out to be in agreement with the experimentally observed distribution of products

Accurate Quantum Chemical Spectroscopic Characterization of Glycolic Acid: A Route Toward its Astrophysical Detection

The first step to shed light on the abiotic synthesis of biochemical building blocks, and their further evolution toward biological systems, is the detection of the relevant species in astronomical environments, including earthlike planets. To this end, the species of interest need to be accurately characterized from structural, energetic, and spectroscopic viewpoints. This task is particularly challenging when dealing with flexible systems, whose spectroscopic signature is ruled by the interplay of small- and large-amplitude motions (SAMs and LAMs, respectively) and is further tuned by the conformational equilibrium. In such instances, quantum chemical (QC) calculations represent an invaluable tool for assisting the interpretation of laboratory measurements or even observations. In the present work, the role of QC results is illustrated with reference to glycolic acid (CH2OHCOOH), a molecule involved in photosynthesis and plant respiration and a precursor of oxalate in humans, which has been detected in the Murchison meteorite but not yet in the interstellar medium or in planetary atmospheres. In particular, the equilibrium structure of the lowest-energy conformer is derived by employing the so-called semiexperimental approach. Then, accurate yet cost-effective QC calculations relying on composite post-Hartree–Fock schemes and hybrid coupled-cluster/density functional theory approaches are used to predict the structural and ro-vibrational spectroscopic properties of the different conformers within the framework of the second-order vibrational perturbation theory. A purposely tailored discrete variable representation anharmonic approach is used to treat the LAMs related to internal rotations. The computed spectroscopic data, particularly those in the infrared region, complement the available experimental investigations, thus enhancing the possibility of an astronomical detection of this molecule

A reinvestigation of the deceptively simple reaction of toluene with OH, and the fate of the benzyl radical : a combined thermodynamic and kinetic study on the competition between OH-addition and H-abstraction reactions

This work reports density functional and composite model chemistry calculations performed on the reactions of toluene with the hydroxyl radical. Both the experimentally observed H-abstraction from the methyl group and possible OH additions to the phenyl ring were investigated. Reaction enthalpies and barrier heights suggest that H-abstraction is more favorable than OH-addition to the ring. The calculated reaction rates at room temperature and the radical intermediate product fractions support this view. At first sight, this might seem to disagree with the fact that, under most experimental conditions, cresols are observed in a larger concentration than benzaldehyde. Since the accepted mechanism for benzaldehyde formation involves H-abstraction, a contradiction arises that calls for a more elaborate explanation. In this first exploratory study, we provide evidence that support the preference of H-abstraction over OH addition and present an alternative mechanism which shows that cresols can be actually produced also through H-abstraction and not only from OH-addition, thus justifying the larger proportion of cresols than benzaldehyde among the products

Computational study of the nitroderivatives of methyl thiyl radical (CH3S): structural, spectroscopic and energetic properties and modelization of formation reactions in atmospheric chemistry

Global scale emissions and reactivity of dimethylsulfide (CH3SCH3, DMS) make it an integral component in the atmospheric sulfur cycle. DMS is rapidly oxidized in the atmosphere by a complex gas-phase mechanism involving many species and reactions. The first subject of the current thesis is the computational study of one of the most important reactions in the overall mechanism of atmospheric sulfur oxidation, the thermal decomposition of methylthiomethoxy radical CH3SCH2O in formaldehyde CH2O and methylthiyl radical CH3S. By using quantum-mechanical ab initio and density functional theory (DFT) methods, the molecular structures, vibrational frequencies, energetic and thermodynamical properties of the above chemical species are calculated, while a theoretical estimate of the rate constant of the reaction is being made with the use of “Transition State Theory” (TST). It has been experimentally shown that one of the most effective ways of removing CH3S in the atmosphere, is its reactions with Ο3/ΝΟ2. Therefore, with the use of the same computational methods, the overall mechanism of the CH3S+NO2 reaction is studied in detail, namely energy minima and transition states. The subject of the current thesis continues with the investigation of the peroxy radicals CH3S(O)nOO (n=0, 1, 2), and the isomeric sulfonyl radicals CH3S(O)nO (n=1, 2, 3), resulting from the reaction of CH3S with 3Ο2, and their isomerization reactions. Based on the energetic parameters of the above chemical species, the Bond Dissociation Energy (BDE) S-OO is calculated in kcal/mol and the following order of decreasing stability is established: CH3S(O)2OO>CH3SOO>CH3S(O)OO. Furthermore, all the possible peroxynitrate compounds CH3S(O)nOONO2, and their corresponding isomeric nitro compounds, CH3S(O)n+1ONO2, CH3S(O)n+2NO2 (n=0, 1, 2), that may result from the reaction of peroxy radicals with NO2, are examined. Based on the energetic parameters of the above chemical species, the Bond Dissociation Energy (BDE) S-OO is calculated in kcal/mol and we observe that the same decreasing order of stability is followed: CH3S(O)2OOΝΟ2 > CH3SOOΝΟ2 > CH3S(O)OOΝΟ2. Finally, with the use of the same computational methods the overall mechanism of the reaction of the methylsulfonyl radical CH3S with NO2 is studied in detail. It is confirmed that the main products are CH3S(O)3+NO, a result that strongly supports the reliability of the relevant assumption on which the only experimental evaluation of the rate constant of the reaction was based.Οι παγκοσμίου κλίμακας εκπομπές και δραστικότητα του Διμεθυλοσουλφιδίου (CH3SCH3, DMS) το καθιστούν ως ένα από τα πιο αναπόσπαστα συστατικά του κύκλου του θείου (S) στην Ατμόσφαιρα. Το DMS οξειδώνεται ταχέως μέσω ενός πολύπλοκου μηχανισμού στην αέρια φάση, ο οποίος αποτελείται από ένα μεγάλο αριθμό χημικών ειδών και πολλών αντίστοιχων αντιδράσεων. Το αντικείμενο μελέτης της παρούσας διδακτορικής διατριβής αρχίζει με την υπολογιστική μελέτη μιας από τις πιο σημαντικές αντιδράσεις στο συνολικό μηχανισμό οξείδωσης του θείου στην ατμόσφαιρα, τη θερμική αποσύνθεση της μεθυλθειομεθοξυλικής ρίζας CH3SCH2O σε φορμαλδεΰδη CH2O και μεθυλθειιλική ρίζα CH3S. Χρησιμοποιώντας κβαντομηχανικές ab initio μεθόδους και τεχνικές θεωρίας συναρτησιακής πυκνότητας (DFT), υπολογίζονται οι μοριακές δομές, δονητικές συχνότητες, ενεργειακές και θερμοδυναμικές ιδιότητες των ανωτέρω χημικών ειδών, ενώ πραγματοποιείται και μια εκτίμηση της σταθεράς ταχύτητας k της αντίδρασης, βάσει της «Θεωρίας Μεταβατικής Κατάστασης» (TST). Έχει αποδειχθεί πειραματικά ότι ένας από τους πιο αποτελεσματικούς τρόπους απομάκρυνσης της CH3S στην ατμόσφαιρα είναι οι αντιδράσεις της με Ο3/ΝΟ2. Ως εκ τούτου, με τη χρήση των ίδιων υπολογιστικών μεθόδων μελετάται αναλυτικά ο συνολικός μηχανισμός της αντίδρασης CH3S+NO2, ήτοι ενεργειακά ελάχιστα και μεταβατικές καταστάσεις. Το αντικείμενο μελέτης της παρούσας διδακτορικής διατριβής συνεχίζεται με τη διερεύνηση των παραγόμενων υπεροξυλικών ριζών CH3S(O)nOO (n=0, 1, 2), και των σουλφονικών ισομερών τους CH3S(O)nO (n=1, 2, 3), που προκύπτουν από την αντίδραση της CH3S με το 3Ο2, καθώς και της μεταξύ τους αντίδρασης ισομερισμού. Βάσει των ενεργειακών ιδιοτήτων των παραπάνω χημικών ειδών, υπολογίζονται οι Ενέργειες Διάσπασης Δεσμού (BDE) S-OO σε kcal/mol και διαμορφώνεται η ακόλουθη σειρά φθίνουσας σταθερότητας: CH3S(O)2OO>CH3SOO>CH3S(O)OO. Επιπρόσθετα, διερευνώνται όλες οι πιθανές υπεροξυνιτρικές ενώσεις CH3S(O)nOONO2, καθώς και οι αντίστοιχες ισομερείς νιτρικές ενώσεις, CH3S(O)n+1ONO2, CH3S(O)n+2NO2 (n=0, 1, 2), που θα προκύψουν από την αντίδραση των υπεροξυλικών ριζών με το NO2. Βάσει των ενεργειακών ιδιοτήτων των παραπάνω χημικών ειδών, υπολογίζονται οι Ενέργειες Διάσπασης Δεσμού (BDE) S-OO σε kcal/mol και παρατηρούμε ότι ακολουθείται η ίδια σειρά φθίνουσας σταθερότητας CH3S(O)2OOΝΟ2>CH3SOOΝΟ2>CH3S(O)OOΝΟ2. Τέλος, με τη χρήση των ίδιων υπολογιστικών μεθόδων μελετάται αναλυτικά ο συνολικός μηχανισμός της αντίδρασης της μεθυλσουλφονικής ρίζας CH3S(O)2 με το ΝΟ2. Επιβεβαιώνεται ότι τα κυριότερα προϊόντα που θα προκύψουν είναι τα CH3S(O)3+NO, κάτι που υποστηρίζει σθεναρά την αξιοπιστία της σχετικής υπόθεσης στην οποία βασίστηκε η μοναδική πειραματική αξιολόγηση της σταθεράς ταχύτητας της αντίδρασης

Kinetics and Thermodynamics of the Hydroxylation Products in the Photodegradation of the Herbicide Metolachlor

Electronic structure calculations have been performed to determine the thermochemistry and kinetics of the reaction between OH and the radicals of the S enantiomer of the herbicide Metolachlor, 2-chloro-N-(2-methyl-6-ethylphenyl)-N(2-methoxy-1-methylethyl) acetamide (MC), produced by photoinduced breaking of the C-Cl bond. Both density functional and ab initio composite methods were employed to calculate the structure of reactants, intermediates, transition states and products. The expected relative abundance of each product was calculated. and compared to the experimentally observed concentrations. It is shown that a combination of thermodynamic and kinetic characteristics interplay to produce the expected theoretical abundances, which turn out to be in agreement with the experimentally observed distribution of products.</p

Reliable Gas Phase Reaction Rates at Affordable Cost by Means of the Parameter-Free junChS-F12 Model Chemistry

A recently developed strategy for the computation at affordable cost of reliable barrier heights ruling reactions in the gas-phase (junChS, [Barone et al. J. Chem. Theory Comput. 2021, 17, 4913-4928]) has been extended to the employment of explicitly-correlated (F12) methods. A thorough benchmark based on a wide range of prototypical reactions shows that the new model (referred to as junChS-F12), which employs cost-effective revDSD-PBEP86-D3(BJ) reference geometries, has an improved performance with respect to its conventional counterpart and outperforms the most well-known model chemistries without the need of any empirical parameter and at an affordable computational cost. Several benchmarks show that revDSD-PBEP86- D3(BJ) structures and force fields provide zero point energies and thermal contributions, which can be confidently used, together with junChS-F12 electronic energies, for obtaining accurate reaction rates in the framework of the master equation approach based on the ab initio transition-state theory

Computational Evidence Suggests That 1-chloroethanol May Be an Intermediate in the Thermal Decomposition of 2-chloroethanol into Acetaldehyde and HCl

The dehalogenation of 2-chloroethanol (2ClEtOH) in gas phase with and without participation of catalytic water molecules has been investigated using methods rooted into the density functional theory. The well-known HCl elimination leading to vinyl alcohol (VA) was compared to the alternative elimination route towards oxirane and shown to be kinetically and thermodynamically more favorable. However, the isomerization of VA to acetaldehyde in the gas phase, in the absence of water, was shown to be kinetically and thermodynamically less favorable than the recombination of VA and HCl to form the isomeric 1-chloroethanol (1ClEtOH) species. This species is more stable than 2ClEtOH by about 6 kcal mol-1, and the reaction barrier is 22 kcal mol-1 vs 55 kcal mol-1 for the direct transformation of VA to acetaldehyde. In a successive step, 1ClEtOH can decompose directly to acetaldehyde and HCl with a lower barrier (29 kcal mol-1) than that of VA to the same products (55 kcal mol-1). The calculations were repeated using a single ancillary water molecule (W) in the complexes 2ClEtOH_W and 1ClEtOH_W. The latter adduct is now more stable than 2ClEtOH_W by about 8 kcal mol-1, implying that the water molecule increased the already higher stability of 1ClEtOH in the gas phase. However, this catalytic water molecule lowers dramatically the barrier for the interconversion of VA to acetaldehyde (from 55 to 6 kcal mol-1). This barrier is now smaller than the one for the conversion to 1ClEtOH (which also decreases, but not so much, from 22 to 12 kcal mol-1). Thus, it is concluded that while 1ClEtOH may be a plausible intermediate in the gas phase dehalogenation of 2ClEtOH, it is unlikely that it plays a major role in water complexes (or, by inference, aqueous solution). It is also shown that neither in the gas phase nor in the cluster with one water molecule, the oxirane path is competitive with the VA alcohol path.</p

Theoretical Study of the Microhydration of 1-Chloro and 2-Chloro Ethanol as a Clue for Their Relative Propensity Toward Dehalogenation

This work reports a computational analysis of hydrogen bonded clusters of mono-, di-, tri- and tetra hydrates of the chlorohydrins CH3CHClOH (1ClEtOH) and CH2ClCH2OH (2ClEtOH). The goal of the study is to assess the role of the water solvent into the facilitation of the initial step for dehalogenation of these compounds, a process of interest in several contexts. Molecular orbital methods (MP2), density functional methods (B3LYP, M06 and wB97X-D) and composite model chemistries (CBS-QB3, G4) were employed to investigate the structure, electronic distribution and hydrogen-bonded structure of 7 monohydrates, 6 dihydrates, 5 trihydrates and 5 tetrahydrates of both species. Standard reaction enthalpy and standard Gibbs free reaction energy were computed for all aggregates with respect to n independent water molecules and with respect to the dimer, trimer and tetramer of water, respectively, in order to evaluate stability and hydrogen bonding network. The influence of the water chains on the length and vibrational frequencies, especially of the C-Cl and O-H bonds, was evaluated.</p

In Vitro and In Silico Vibrational-Rotational Spectroscopic Characterization of the Next-Generation Refrigerant HFO-1123

Very short-lived substances have recently been proposed as replacements for hydrofluorocarbons (HFCs), in turn being used in place of ozone-depleting substances, in refrigerant applications. In this respect, hydro-fluoro-olefins (HFOs) are attracting particular interest because, due to their reduced global warming potential, they are supposed to be environmentally friendlier. Notwithstanding this feature, they represent a new class of compounds whose spectroscopic properties and reactivity need to be characterized to allow their atmospheric monitoring and to understand their environmental fate. In the present work, the structural, vibrational, and ro-vibrational properties of trifluorothene (HFO-1123, F2C = CHF) are studied by state-of-the-art quantum chemical calculations. The equilibrium molecular structure has an expected error within 2 mÅ and 0.2° for bond lengths and angles, respectively. This represents the first step toward the computation of highly accurate rotational constants for both the ground and first excited fundamental vibrational levels, which reproduce the available experimental data well within 0.1%. Centrifugal distortion parameters and vibrational−rotational coupling terms are computed as well and used to solve some conflicting experimental results. Simulation of the vibrational transition frequencies and intensities beyond the double harmonic approximation and up to three quanta of vibrational excitation provides insights into the couplings ruling the vibrational dynamics and guides the characterization of the gas-phase infrared spectrum experimentally recorded in the range of 200−5000 cm−1. The full characterization of the IR features is completed with the experimental determination of the absorption cross sections over the 400−5000 cm−1 region from which the radiative forcing and global warming potential of HFO-1123 are derive