Peroxy radicals are key intermediates in many atmospheric processes. Reactions between such radicals are of particular interest as they can lead to accretion products capable of participating in new particle formation (NPF). These reactions proceed through a tetroxide intermediate, which then decomposes to a complex of two alkoxy radicals and O2, with spin conservation dictating that the complex must be formed in the triplet state. The alkoxy complex can follow different pathways e.g. hydrogen(H)-shift reactions, dissociation reactions etc., but the details of the full processes are not yet fully understood. This paper establishes the microscopic mechanisms of the H-shift and other associated pathways in the context of a self-reaction between methoxy radicals, with focus on the roles of the singlet and triplet states involved. Dynamics in time is explored by two methods: the multireference XMS-CASPT2 and very recently developed mixed reference spin-flip TDDFT (MRSF-TDDFT). The metadynamics method is used to compute energetics. The XMS-CASPT2 and the MRSF-TDDFT dynamics simulations yield similar results. This would be very encouraging for future simulations for large radicals, since MRSF-TDDFT simulations enjoy the advantages of linear response theory. Our calculations demonstrate that the reaction between methoxy radicals, though initiated on the triplet state, leads to products predominantly on the singlet surface, following efficient intersystem crossing (ISC). The computed branching ratio between H-shift and dissociation channels agrees well with experiment.

We study the influence of an applied electric field on the structure and stability of some common bimolecular clusters that are found in the atmosphere. These clusters play an important role in new particle formation (NPF). For low values of the electric field (i.e., |E| ≤ 0.01 V Å-1), we demonstrate that the field response of the clusters can be predicted from simply calculating the dipole moment of the cluster and the dipole moments of the constituent molecules and that the influence on the association energy of the cluster is minimal (i.e., <0.5 kcal mol-1). For higher field strengths |E| > 0.2 V Å-1, there can be more dramatic effects on both structure and energetics, as the induced dipole, charge transfer, and geometric distortion play a larger role. Although such large fields are not very relevant in the atmosphere, they do exist in some situations of experimental interest, such as near interfaces and in intense laser fields.

Molecular self-assembly provides the means for creating large supramolecular structures, extending beyond the capability of standard chemical synthesis. To harness the power of self-assembly, it is necessary to understand its driving forces. A potent method is to exploit self-complementary hydrogen bonding, where a molecule interacts with its own copy by suitable positions of hydrogen-bond donor (D) and acceptor (A) groups. With four hydrogen bonds, there are two possible self complementary patterns: the DDAA/AADD and the DADA/ADAD motifs. Of these, the DDAA pattern is usually more stable. The traditional explanation assumes that the secondary interactions between equal groups, that is, between donors (D⋯D) or acceptors (A⋯A), are repulsive. DDAA arrays would then have two, and DADA arrays six repulsive interactions. Here, using high-end quantum chemical analysis, we show that contrary to the traditional explanation, the secondary A⋯A interactions are, in fact, attractive. We revise the model of secondary interactions accordingly.

Simulated pre-reactive complex lifetime is proportional to experimental measurements of the reactivity of peroxy radicals. This extends to measurements over a range of temperatures.

Dimeric accretion products have been observed both in atmospheric aerosol particles and in the gas phase. With their low volatilities, they are key contributors to the formation of new aerosol particles, acting as seeds for more volatile organic vapors to partition onto. Many particle-phase accretion products have been identified as esters. Various gas- and particle-phase formation pathways have been suggested for them, yet evidence remains inconclusive. In contrast, peroxide accretion products have been shown to form via gas-phase peroxy radical (RO2) cross reactions. Here, we show that these reactions can also be a major source of esters and other types of accretion products. We studied α-pinene ozonolysis using state-of-the-art chemical ionization mass spectrometry together with different isotopic labeling approaches and quantum chemical calculations, finding strong evidence for fast radical isomerization before accretion. Specifically, this isomerization seems to happen within the intermediate complex of two alkoxy (RO) radicals, which generally determines the branching of all RO2-RO2 reactions. Accretion products are formed when the radicals in the complex recombine. We found that RO with suitable structures can undergo extremely rapid C-C β scissions before recombination, often resulting in ester products. We also found evidence of this previously overlooked RO2-RO2 reaction pathway forming alkyl accretion products and speculate that some earlier peroxide identifications may in fact be hemiacetals or ethers. Our findings help answer several outstanding questions on the sources of accretion products in organic aerosol and bridge our knowledge of the gas phase formation and particle phase detection of accretion products. As esters are inherently more stable than peroxides, this also impacts their further reactivity in the aerosol.

The oxidation of aromatics contributes significantly to the formation of atmospheric aerosol. Using toluene as an example, we demonstrate the existence of a molecular rearrangement channel in the oxidation mechanism. Based on both flow reactor experiments and quantum chemical calculations, we show that the bicyclic peroxy radicals (BPRs) formed in OH-initiated aromatic oxidation are much less stable than previously thought, and in the case of the toluene derived ipso-BPRs, lead to aerosol-forming low-volatility products with up to 9 oxygen atoms on sub-second timescales. Similar results are predicted for ipso-BPRs formed from many other aromatic compounds. This reaction class is likely a key route for atmospheric aerosol formation, and including the molecular rearrangement of BPRs may be vital for accurate chemical modeling of the atmosphere.

The lifetimes of pre-reactive complexes, although implicitly part of the equations used to model many gas-phase bimolecular reactions, have seldom been included in quantitative calculations of rate coefficients. Here, we demonstrate the application of empirical molecular dynamics simulations of collisions between peroxy radicals to model association lifetimes. With the exception of the methyl peroxy-acetyl peroxy system, measurements of the lifetimes based on a phenomenological model are shown to correlate well with available experimental data for recombination reactions of peroxy radicals in cases where the rate -limiting transition state lies below the reactants in energy. Further, we predict reaction rates for larger alpha-pinene-derived peroxy radicals, and we interpret our results in tandem with available experimental data on these systems, which are of great relevance to improve our understanding of atmospheric aerosol formation.

Abstract. Proton-transfer-reaction (PTR) is a commonly applied ionization technique for mass spectrometers, where hydronium ions (H3O+) transfer a proton to analytes with higher proton affinities than the water molecule. This method has most commonly been used to quantify volatile hydrocarbons, but later generation PTR-instruments have been designed for better throughput of less volatile species, allowing detection of more functionalized molecules as well. For example, the recently developed Vocus PTR time-of-flight mass spectrometer (PTR-TOF) has been shown to agree well with an iodide adduct based chemical ionization mass spectrometer (CIMS) for products with 3-5 O-atoms from oxidation of monoterpenes (C10H16). However, while several different types of CIMS instruments (including those using iodide) detect abundant signals also at “dimeric” species, believed to be primarily ROOR peroxides, no such signals have been observed in the Vocus PTR, even though these compounds fulfil the condition of having higher proton affinity than water. More traditional PTR instruments have been limited to volatile molecules as the inlets have not been designed for transmission of easily condensable species. Some newer instruments, like the Vocus PTR, have overcome this limitation, but are still not able to detect the full range of functionalized products, suggesting that other limitations need to be considered. One such limitation, well-documented in PTR literature, is the tendency of protonation to lead to fragmentation of some analytes. In this work, we evaluate the potential for PTR to detect dimers and the most oxygenated compounds, as these have been shown to be crucial for forming atmospheric aerosol particles. We studied the detection of dimers using a Vocus PTR-TOF in laboratory experiments as well as through quantum chemical calculations. Only noisy signals of potential dimers were observed during experiments on the ozonolysis of the monoterpene α-pinene, while a few small signals of dimeric compounds were detected during the ozonolysis of cyclohexene. During the latter experiments, we also tested varying the pressures and electric fields in the ionization region of the Vocus PTR-TOF, finding that only small improvements were possible in the relative dimer contributions. Calculations for model ROOR and ROOH systems showed that most of these peroxides should fragment partially following protonation. With inclusion of additional energy from the ion-molecule collisions driven by the electric fields in the ionization source, computational results suggest substantial or nearly complete fragmentation of dimers. Our study thus suggests that while the improved versions of PTR-based mass spectrometers are very powerful tools for measuring hydrocarbons and their moderately oxidized products, other types of CIMS are likely more suitable for the detection of ROOR and ROOH species.

In this paper we study collisions between polyatomic radicals - an important process in fields ranging from biology to combustion. Energy transfer, formation of intermediate complexes and recombination reactions are treated, with applications to peroxy radicals in atmospheric chemistry. Multi-reference perturbation theory, supplemented by coupled-cluster calculations, describes the potential energy surfaces with high accuracy, including the interaction of singlet and triplet spin states during radical recombination. Our multi-reference molecular dynamics (MD) trajectories on methyl peroxy radicals confirm the reaction mechanism postulated in earlier studies. Specifically, they show that if suitable pre-reactive complexes are formed, they will rapidly lead to the formation and subsequent decomposition of tetroxide intermediates. However, generating multi-reference MD trajectories is exceedingly computationally demanding, and we cannot adequately sample the whole conformational space. To answer this challenge, we promote the use of a novel simplified semi-empirical MD methodology. It assumes the collision is governed by two states, a singlet (S0) and a triplet (T1) state. The method predicts differences between collisions on S0 and T1 surfaces, and qualitatively includes not only pre-reactive complex formation, but also recombination processes such as tetroxide formation. Finally, classical MD simulations using force-fields for non-reactive collisions are employed to generate thousands of collision trajectories, to verify that the semi-empirical method is sampling collisions adequately, and to carry out preliminary investigations of larger systems. For systems with low activation energies, the experimental rate coefficient is surprisingly well reproduced by simply multiplying the gas-kinetic collision rate by the simulated probability for long-lived complex formation.

We propose to analyze molecular dynamics (MD) output via a supervised machine learning (ML) algorithm, the decision tree. The approach aims to identify the predominant geometric features which correlate with trajectories that transition between two arbitrarily defined states. The data-driven algorithm aims to identify these features without the bias of human "chemical intuition". We demonstrate the method by analyzing the proton exchange reactions in formic acid solvated in small water clusters. The simulations were performed with ab initio MD combined with a method to efficiently sample the rare event, path sampling. Our ML analysis identified relevant geometric variables involved in the proton transfer reaction and how they may change as the number of solvating water molecules changes.

Atmospheric reactions, hitherto studied computationally mainly with static computations in conjunction with transition state theories, can be further described via path sampling calculations. Here we report on an exploratory study of the formic acid catalysed hydrolysis of SO3 to produce H2SO4. We demonstrate that precise measurements of rate coefficients can be obtained in principle for such reactions with an acceptable expenditure of computational resources, and that new insights into the reaction can be obtained by the analysis of the path space explored via path sampling techniques.

We present the results of ab initio molecular dynamics simulations of the solution−air interface of aqueous lithium bromide (LiBr). We find that, in agreement with the experimental data and previous simulation results with empirical polarizable force field models, Br− anions prefer to accumulate just below the first molecular water layer near the interface, whereas Li cations remain deeply buried several molecular layers from the interface, even at very high concentration. The separation of ions has a profound effect on the average orientation of water molecules in the vicinity of the interface. We also find that the hydration number of Li cations in the center of the slab Nc,Li−H2O ≈ 4.7 ± 0.3, regardless of the salt concentration. This estimate is consistent with the recent experimental neutron scattering data, confirming that results from nonpolarizable empirical models, which consistently predict tetrahedral coordination of Li to four solvent molecules, are incorrect. Consequently, disruption of the hydrogen bond network caused by Li may be overestimated in nonpolarizable empirical models. Overall, our results suggest that empirical models, in particular nonpolarizable models, may not capture all of the properties of the solution−air interface necessary to fully understand the interfacial chemistry.

The deprotonation of formic acid is investigated using metadynamics in tandem with Born-Oppenheimer molecular dynamics simulations. We compare our findings for formic acid in pure water with previous studies before examining formic acid in aqueous solutions of lithium bromide. We carefully consider different definitions for the collective variable(s) used to drive the metadynamics, emphasizing that the variables used must include all of the possible reactive atoms in the system, in this case carboxylate oxygens and water hydrogens. This ensures that all the various possible proton exchange events can be accommodated and the collective variable(s) can distinguish the protonated and deprotonated states, even over rather long ab initio simulation runs (ca. 200-300 ps). Our findings show that the formic acid deprotonation barrier and the free energy of the deprotonated state are higher in concentrated lithium bromide, in agreement with the available experimental data for acids in salt solution. We show that the presence of Br- in proximity to the formic acid hydroxyl group effectively inhibits deprotonation. Our study extends previous work on acid deprotonation in pure water and at air-water interfaces to more complex multicomponent systems of importance in atmospheric and marine chemistry.

We present the results of ab initio molecular dynamics simulations of the solution–air interface of aqueous lithium bromide (LiBr). We find that, in agreement with the experimental data and previous simulation results with empirical polarizable force field models, Br– anions prefer to accumulate just below the first molecular water layer near the interface, whereas Li+ cations remain deeply buried several molecular layers from the interface, even at very high concentration. The separation of ions has a profound effect on the average orientation of water molecules in the vicinity of the interface. We also find that the hydration number of Li+ cations in the center of the slab Nc,Li+–H2O ≈ 4.7 ± 0.3, regardless of the salt concentration. This estimate is consistent with the recent experimental neutron scattering data, confirming that results from nonpolarizable empirical models, which consistently predict tetrahedral coordination of Li+ to four solvent molecules, are incorrect. Consequently, disruption of the hydrogen bond network caused by Li+ may be overestimated in nonpolarizable empirical models. Overall, our results suggest that empirical models, in particular nonpolarizable models, may not capture all of the properties of the solution–air interface necessary to fully understand the interfacial chemistry.

We study the pressure-driven flow of aqueous NaCl in amorphous silica nanotubes using nonequilibrium molecular dynamics simulations featuring both polarizable and non-polarizable molecular models. Different pressures, electrolyte concentrations and pore sizes are examined. Our results indicate a flow that deviates considerably from the predictions of Poiseuille fluid mechanics. Due to preferential adsorption of the different ionic species by surface SiO- or SiOH groups, we find that a significant electric current is generated, but with opposite polarities using polarizable vs. fixed charge models for water and ions, emphasizing the need for careful parameterization in such complex systems. We also examine the influence of partial deprotonation of the silica surface, and we find that much more current is generated in a dehydrogenated nanopore, even though the overall efficiency remains low. These findings indicate that different methods of nanopore preparation, which can produce a range of surface properties, should be examined more closely in the related experimental methods to generate electrokinetic current.

ABSTRACT We use non-equilibrium molecular dynamics simulations to study dipolar dumbbell fluids in a thermal gradient. We study the relative orientation of size asymmetric molecules with respect to the thermal gradient, and the sensitivity of the orientation to whether the Wolf method or Ewald summation is employed to compute the electrostatic interactions. For these systems, we find that the Wolf method overestimates the degree of molecular orientation. We also present new data on fluids with very small dipole moments which give novel insight into how the molecular asymmetry influences the polarisation response in the thermal gradient.

We investigate, using non-equilibrium molecular dynamics simulations and theory, the response of molecular fluids confined in slit pores under the influence of a thermal gradient and/or an applied force. The applied force which has the same functional form as a gravitational force induces an inhomogeneous density in the confined fluid, which results in a net orientation of the molecules with respect to the direction of the force. The orientation is qualitatively similar to that induced by a thermal gradient. We find that the average degree of orientation is proportional to the density gradient of the fluid in the confined region and that the orientation increases with the magnitude of the force. The concurrent application of the external force and the thermal gradient allows us to disentangle the different mechanisms leading to the thermal orientation of molecular fluids. One mechanism is connected to the density variation of the fluid, while the second mechanism can be readily observed in molecular fluids consisting of molecules with mass or size asymmetry, even in the absence of a density gradient, hence it is connected to the application of the thermal gradient only.

We use density functional theory to investigate the impact that strong electric fields have on the structure and energetics of small lithium ion-water clusters, Li(+)·nH2O, with n = 4 or 6. We find that electric field strengths of ∼0.5 V/Å are sufficient to break the symmetry of the n = 4 tetrahedral energy minimum structure, which undergoes a transformation to an asymmetric cluster consisting of three water molecules bound to lithium and one additional molecule in the second solvation shell. Interestingly, this cluster remains the global minimum configuration at field strengths ≳0.15 V/Å. The 6-coordinated cluster, Li(+)·6H2O, features a similar transition to 5- and 4-coordinated clusters at field strengths of ∼0.2 and ∼0.3 V/Å, respectively, with the tetra-coordinated structure being the global minimum even in the absence of the field. Our findings are relevant to understanding the behavior of the Li(+) ion in aqueous environments under strong electric fields and in interfacial regions where field gradients are significant.