Research paperUnraveling the role of additional OH-radicals in the H–Abstraction from Dimethyl sulfide using quantum chemical computations
Graphical abstract
Introduction
Even though gas-phase sulfur compounds represent only a small fraction of the earth’s atmospheric composition, accounting for less than 1 ppmv [1], these minor constituents have a significant impact on the atmosphere, hydrosphere and biosphere. The potential of a given sulfur compound to make an impact on the environment is dependent on a variety of factors including distribution of the emission source, photochemistry, physical processes and local environment (e.g. humidity and temperature, concentration and properties of pre-existing particulates, mixing ratios of oxidants and other reactive trace species) [2]. Upon careful consideration of these factors, it becomes apparent that in addition to being major sources of atmospheric acidity in remote regions, organosulfur compounds may represent an important component in the earth′s climate system by making an impact on the earth-atmosphere radiation budget. A thorough understanding of the atmospheric oxidation of organosulfur compounds is necessary to evaluate accurately their role in this budget and how it changes with the fluxes of these gases into the atmosphere.
Dimethyl sulfide (DMS) is a product of biological processes involving marine phytoplankton, and is present in the marine boundary layer (MBL) globally [3]. It is estimated to account for approximately 60% of the total natural sulfur gases released to the atmosphere and recent work has shown that DMS oxidation products could play a direct role in new particle formation and growth in the Arctic troposphere [4]. The oxidation of DMS consists of a complex sequence of reactions [5], [6], [7]. Depending on the time of the day or altitude, the overall process can follow a variety of pathways. In general, however, the oxidation proceeds via chains of radical reactions. The reaction of OH with DMS is known to follow two independent channels: abstraction (reaction R1) and addition (reaction R2) [8], [9].
Although the rate coefficients for the initiation reactions of DMS with the OH radical are now reasonably well established, the subsequent steps responsible for the observed products and their yields is complex, and many aspects of the mechanism are still unclear. The identity and yields of the final products depend on the oxidation steps of several intermediates for which a multitude of different possible reaction pathways may exist, whose importance can vary with the prevailing atmospheric conditions [10], [11], [12]. A relatively recent review and critical assessment of 20 different models and their uncertainties by Faloona [13] concluded that the standard OH and NO3 mechanisms of oxidation of DMS do not fully account for diurnal decay rates typically observed in the MBL. Moreover, Mardyukov and Schreiner [6] studied five different DMS oxidation mechanisms and compared them with nine different field measurements, concluding that no single mechanism reproduced the observations and predictions. This indicates that the mechanism of DMS oxidation is very complex and not completely understood and that the branching ratios are strongly dependent upon environmental conditions and presence of clouds.
The general conclusion that has been reached from experimental and theoretical studies is in agreement with the global reaction proceeding by hydrogen abstraction in the absence of oxygen (Eq. R1) to form the methyl thiomethyl radical (MTMr) [14], [15], [16], [17]. In the presence of air, the reaction proceeds at least partly by reaction of the addition product of OH on sulfur (Eq. R2) with O2. Therefore, due to the abundance of oxygen in the atmosphere, it is expected that addition and further reaction with O2 is the predominant process [11]. However, even though there have been several theoretical studies concerning the production of the MTMr radical [14], [15], [16], [17] and its reaction with O2 [18], [19], [20], to the best of our knowledge no study has been performed until now on the addition of another OH radical to this species. This process is significant especially in connection with experiments performed in reaction chambers, where both a low O2 partial pressure and a high OH concentration are employed. For example, Arsene et al. [21] modified both the O2 partial pressure and temperature in the absence of NOx, while hydroxyl radical concentrations were kept in excess over DMS (since they were generated from an excess of H2O2 using mercury lamps). Barnes et al. [22] reported also this kind of experiments, in particular considering the absence of oxygen (i.e. vanishing oxygen partial pressure, see Table 1 in their paper). Several other experiments have been performed at zero O2 partial pressure (see Ref. [11], Table 4). In a study by Ramírez-Anguita et al. [23] the viability of the DMS-OH + OH reaction was analyzed theoretically from a thermodynamic and kinetic point of view, even though experimental data are not available for this isolated process. However, these authors studied the reaction with the second hydroxyl radical starting from the addition intermediate radical (Eq. R2) and not from the MTMr species coming from abstraction.
It must be noticed that oxidation of DMS by hydroperoxides in aqueous medium, designed to simulate the processes in water clouds, has also been investigated [24]. It is well known that, in solution, the oxidation of DMS by hydroperoxides leads to DMSO and the presence of the latter in rain and snow has already been documented. In particular, the mechanisms of oxidation of organic sulfides by H2O2 in aqueous solution were studied theoretically [25] and the presence of hydrogen peroxide in the atmosphere is well documented [26].
All the above considerations prompted us to study the reaction of MTMr with a second hydroxyl radical, akin to the experimental setups of Arsene et al. [21], Barnes et al. [22] and Albu et al. [11], characterized by vanishing oxygen partial pressure and excess of OH radicals. Two interesting radical-coupling termination reactions are possible (besides dimerization), due to the attack of the OH oxygen to the sulfur or the carbon atom belonging to the SCH2 moiety. Both the products of these reactions have been characterized in the present work, namely S-methyl methanesulfenic acid (hereafter SMMSA) and methanesulfenyl methanol (hereafter MSMOH). Furthermore, the transition state governing the interconversion between these two species (via OH shift) has been studied.
The study of the bonding pattern in SMMSA and MSMOH molecules can shed light on the reaction with the oxygen molecule itself, since in some cases at least the latter can be observed in reactions when oxygen is present. Therefore, in this work we performed a structural, spectroscopic and energetic study of these molecular species as well as the transition state interconnecting them.
Section snippets
Materials and methods
Calculations of the structure and energetics of the studied compounds were performed using composite model chemistry methods, density functional theory (DFT), and CCSD(T) single-point calculations on the DFT optimized geometries.
In particular, four DFT models were employed, namely the M06 [27], M06-2X-D3 [27], [28], ωB97X-D [29] and the double hybrid B2PLYP-D3 [28], [30] methods, with a variety of basis sets. We chose Pople′s 6–31 + G(d,p) basis set as an example of relatively low-cost (i.e.
Methodology
Abstraction of a hydrogen from one of the methyl groups of DMS by the OH radical generates a complex of water and the MTMr radical, as seen in reaction R1. The second reaction of the initial MTMr radical with another OH species may follow different paths. Conceptually, one could think of at least three alternative mechanisms: (i) unimolecular dissociation of MTMr to CH3 + CH2S and addition of OH to the methyl radical; (ii) approach of a second OH radical to the methyl group in MTMr; (iii)
Concluding remarks
In the present work we have used quantum chemistry models (DFT, CCSD(T) and composite methods) to study the geometrical structure, vibrational spectra, thermochemistry and reaction mechanisms of the species most likely formed in the radical coupling reaction between the radical produced after hydrogen abstraction from DMS by a hydroxyl radical (MTMr) and a secondary OH. The resulting structures, SMMSA and MSMOH, arise from the interaction of the incoming hydroxyl radical with either the sulfur
Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Acknowledgments
This work has been supported by the Italian MIUR (PRIN 2017, project “Physico-chemical Heuristic Approaches: Nanoscale Theory Of Molecular Spectroscopy, PHANTOMS”, prot. 2017A4XRCA) and by Scuola Normale Superiore (grant number SNS18_B_TASINATO). The SMART@SNS Laboratory (http://smart.sns.it) is acknowledged for providing high-performance computer facilities.
One of the authors acknowledges the continuing financial support of ANII (Uruguay), CSIC (UdelaR) and Pedeciba (Uruguay) for this program
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