Assessment of Density Functional Theory in Predicting Structures and Free Energies of Reaction of Atmospheric Prenucleation Clusters

The reaction mechanism of SO3 with the multifunctional compound ethanolamine and its atmospheric implications

SO3 is an important reactive species in sulfur cycle and sulfuric acid formation processes and its reactions with some functional group substances, such as H2O, NH3, CH3OH, and organic and inorganic acids, have been extensively studied. However, its loss mechanism with multifunctional species is still lacking in detail. Herein, the reaction mechanism between SO3 and monoethanolamide (MEA) was investigated in the gas phase and on water droplets. The quantum chemical calculations indicate that the gas-phase reactions of SO3 with the OH and NH2 moieties of MEA hardly occur as their reaction energy barriers are up to 21.9-29.4 kcal mol-1. When a single water molecule is added into the SO3 + MEA reaction, it not only decreases the reaction barrier by at least 15.0 kcal mol-1 and thus enhances the rate obviously, but can also lead to the main product changing from HOCH2CH2NHSO3H to NH2CH2CH2OSO3H. The Born Oppenheimer molecular dynamics simulations on a water droplet show that the routes of the NH2CH2CH2OSO3-⋯H3O+ ion pair, HSO4- and HOCH2CH2NH3+ ions and zwitterionic formations of HOCH2CH2NH2+-SO3- and SO3--OCH2CH2NH3+ occur through a loop-structure route or chain reaction process, and can be finished within several picoseconds. Interestingly, the nucleation simulations show that the products of HOCH2CH2NHSO3H and NH2CH2CH2OSO3H have a potential ability to participate in the formation of new particles as they can form larger clusters with H2SO4, NH3 and H2O molecules within 20 ns. Thus, the present study will not only give new insight into the reaction between SO3 and multifunctional compounds, but also provide a new potential formation mechanism for particles resulting from the loss of SO3.

PointGAT: A Quantum Chemical Property Prediction Model Integrating Graph Attention and 3D Geometry

Predicting quantum chemical properties is a fundamental challenge for computational chemistry. While the development of graph neural networks has advanced molecular representation learning and property prediction, their performance could be further enhanced by incorporating three-dimensional (3D) structural geometry into two-dimensional (2D) molecular graph representation. In this study, we introduce the PointGAT model for quantum molecular property prediction, which integrates 3D molecular coordinates with graph-attention modeling. Comparison with other current models in molecular prediction tasks showed that PointGAT could provide higher predictive accuracy in various benchmark data sets from MoleculeNet, including ESOL, FreeSolv, Lipop, HIV, and 6 out of 12 tasks of the QM9 data set. To further examine PointGAT prediction of quantum mechanical (QM) energies, we constructed a C10 data set comprising 11,841 charged and chiral carbocation intermediates with QM energies calculated at the DM21/6-31G*//B3LYP/6-31G* levels. Notably, PointGAT achieved an R2 value of 0.950 and an MAE of 1.616 kcal/mol, outperforming even the best-performing graph neural network model with a reduction of 0.216 kcal/mol in MAE and an improvement of 0.050 in R2. Additional ablation studies indicated that incorporating molecular geometry into the model resulted in markedly higher predictive accuracy, reducing the MAE value from 1.802 to 1.616 kcal/mol. Moreover, visualization of PointGAT atomic attention weights suggested its predictions were interpretable. Findings in this study support the application of PointGAT as a powerful and versatile tool for quantum chemical property prediction that can facilitate high-accuracy modeling for fundamental exploration of chemical space as well as drug design and molecular engineering.

Gas-Phase Oxidation of Atmospherically Relevant Unsaturated Hydrocarbons by Acyl Peroxy Radicals

This study assesses the atmospheric impact of reactions between unsaturated hydrocarbons such as isoprene and monoterpenes and peroxy radicals containing various functional groups. We find that reactions between alkenes and acyl peroxy radicals have reaction rates high enough to be feasible in the atmosphere and lead to high molar mass accretion products. Moreover, the reaction between unsaturated hydrocarbons and acyl peroxy radicals leads to an alkyl radical, to which molecular oxygen rapidly adds. This finding is confirmed by both theoretical calculations and experiments. The formed perester peroxy radical may either undergo further H-shift reactions or react bimolecularly. The multifunctional oxygenated compounds formed through acyl peroxy radical + alkene reactions are potentially important contributors to particle formation and growth. Thus, acyl peroxy radical-initiated oxidation chemistry may need to be included in atmospheric models.

Cost-effective approach for atmospheric accretion reactions: a case of peroxy radical addition to isoprene

We present an accurate and cost-effective method for investigating the accretion reactions between unsaturated hydrocarbons and oxidized organic radicals. We use accretion between isoprene and primary, secondary and tertiary alkyl peroxy radicals as model reactions. We show that a systematic semiempirical transition state search can lead to better transition state structures than relaxed scanning with density functional theory with a significant gain in computational efficiency. Additionally, we suggest accurate and effective quantum chemical methods to study accretion reactions between large unsaturated hydrocarbons and oxidized organic radicals. Furthermore, we examine the atmospheric relevance of these types of reactions by calculating the bimolecular reaction rate coefficients and formation rates under atmospheric conditions from the quantum chemical reaction energy barriers.

Computational Tools for Handling Molecular Clusters: Configurational Sampling, Storage, Analysis, and Machine Learning

Computational modeling of atmospheric molecular clusters requires a comprehensive understanding of their complex configurational spaces, interaction patterns, stabilities against fragmentation, and even dynamic behaviors. To address these needs, we introduce the Jammy Key framework, a collection of automated scripts that facilitate and streamline molecular cluster modeling workflows. Jammy Key handles file manipulations between varieties of integrated third-party programs. The framework is divided into three main functionalities: (1) Jammy Key for configurational sampling (JKCS) to perform systematic configurational sampling of molecular clusters, (2) Jammy Key for quantum chemistry (JKQC) to analyze commonly used quantum chemistry output files and facilitate database construction, handling, and analysis, and (3) Jammy Key for machine learning (JKML) to manage machine learning methods in optimizing molecular cluster modeling. This automation and machine learning utilization significantly reduces manual labor, greatly speeds up the search for molecular cluster configurations, and thus increases the number of systems that can be studied. Following the example of the Atmospheric Cluster Database (ACDB) of Elm (ACS Omega, 4, 10965-10984, 2019), the molecular clusters modeled in our group using the Jammy Key framework have been stored in an improved online GitHub repository named ACDB 2.0. In this work, we present the Jammy Key package alongside its assorted applications, which underline its versatility. Using several illustrative examples, we discuss how to choose appropriate combinations of methodologies for treating particular cluster types, including reactive, multicomponent, charged, or radical clusters, as well as clusters containing flexible or multiconformer monomers or heavy atoms. Finally, we present a detailed example of using the tools for atmospheric acid-base clusters.

Atmospheric Chemistry of NH2SO3H in Polluted Areas: An Unexpected Isomerization of NH2SO3H in Acid-Polluted Regions

NH2SO3H is an effective nucleation agent for the formation of atmospheric aerosols and cloud particles. So, the ammonolysis of SO3 to form NH2SO3H without and with neutral (H2O) and basic (NH3) trace gases has been extensively investigated. However, the acidic trace gas X (X = H2SO4 and CH3SO3H)-assisted ammonolysis of SO3 is still up for debate. In this work, a comprehensive theoretical investigation of X-assisted ammonolysis of SO3 and its reverse reaction (the isomerization of NH2SO3H to form SO3-···NH3+) was carried out in the gas phase and at the air-water interface. The gas-phase results show that X-assisted isomerization of NH2SO3H to form SO3-···NH3+ is more energetically and kinetically favorable than its reverse reaction and the isomerization of NH2SO3H in the presence of H2O and NH3. Such unexpected findings revealed that gas-phase NH2SO3H is highly reactive in the presence of acidic trace gas in contrast to the high stability of NH2SO3H in neutral and basic conditions. At the air-water interface, the X-assisted isomerization reaction of NH2SO3H involves multiple water molecules. The loop structure of the reaction center (X···NH2SO3H···3H2O) promotes the transfer of protons in the water molecules to form the SO3-···NH3+ ion pair, which can then interact with several interfacial water molecules to form ammonium bisulfate. These interfacial reaction channels follow a stepwise mechanism and proceed at the picosecond time-scale. The findings of this study will contribute to a better understanding of the atmospheric behavior of NH2SO3H in polluted acidic trace gases.

Roles of Amides on the Formation of Atmospheric HONO and the Nucleation of Nitric Acid Hydrates

Nitrous acid (HONO) is hazardous to the human respiratory system, and the hydrolysis of NO₂ is the source of HONO. Hence, the investigation on the removal and transformation of HONO is urgently established. The effects of amide on the mechanism and kinetics of the formation of HONO with acetamide, formamide, methylformamide, urea, and its clusters of the catalyst were studied theoretically. The results show that amide and its small clusters reduce the energy barrier, the substituent improves the catalytic efficiency, and the catalytic effect order is dimer > monohydrate > monomer. Meanwhile, the clusters composed of nitric acid (HNO₃), amides, and 1-6 water molecules were investigated in the amide-assisted nitrogen dioxide (NO₂) hydrolysis reaction after HONO decomposes by combining the system sampling technique and density functional theory. The study on thermodynamics, intermolecular forces, optics properties of the clusters, as well as the influence of humidity, temperature, atmospheric pressure, and altitude shows that amide molecules promote the clustering and enhance the optical properties. The substituent facilitates the clustering of amide and nitric acid hydrate and lowers the humidity sensitivity of the clusters. The findings will help to control the atmospheric aerosol particle and then reduce the harm of poisonous organic chemicals on human health.

Thermodynamic and optical properties of HCOOH(H2O)n and HCOOH(NH3)(H2O)(n-1) clusters at various temperatures and pressures: a computational study

Density functional theory has been used to compute the gas-phase geometries, binding energies, ZPE-corrected binding energies, BSSE-corrected binding energies, binding enthalpies, and binding free energies of HCOOH(H₂O)_n and HCOOH(NH₃)(H₂O)_(n-1) clusters with n = 1-8, 10, 12, 14, 16, 18, and 20. Enthalpies and free energies are calculated for a range of atmospherically relevant temperatures (T) and pressures (P) (from T = 298.15 K, P = 1013.25 hPa to T = 216.65 K, P = 226.32 hPa). The optical properties of those clusters have been studied at the CAM-B3LYP/aug-cc-pVDZ level of theory.

Clusteromics V: Organic Enhanced Atmospheric Cluster Formation

Formic acid (FA) is a prominent candidate for organic enhanced nucleation due to its high abundance and stabilizing effect on smaller clusters. Its role in new particle formation is studied through the use of state-of-the-art quantum chemical methods on the cluster systems (acid)_1-2(FA)₁(base)_1-2 with the acids being sulfuric acid (SA)/methanesulfonic acid (MSA) and the bases consisting of ammonia (A), methylamine (MA), dimethylamine (DMA), trimethylamine (TMA), and ethylenediamine (EDA). A funneling approach is used to determine the cluster structures with initial configurations generated through the ABCluster program, followed by semiempirical PM7 and ωB97X-D/6-31++G(d,p) calculations. The final binding free energy is calculated at the DLPNO-CCSD(T₀)/aug-cc-pVTZ//ωB97X-D/6-31++G(d,p) level of theory using the quasi-harmonic approximation. Cluster dynamics simulations show that FA has a minuscule or negligible effect on the MSA-FA-base systems as well as most of the SA-FA-base systems. The SA-FA-DMA cluster system shows the highest influence from FA with an enhancement of 21%, compared to its non-FA counterpart.

Massive Assessment of the Binding Energies of Atmospheric Molecular Clusters

Quantum chemical studies of the formation and growth of atmospheric molecular clusters are important for understanding aerosol particle formation. However, the search for the lowest free-energy cluster configuration is extremely time consuming. This makes high-level benchmark data sets extremely valuable in the quest for the global minimum as it allows the identification of cost-efficient computational methodologies, as well as the development of high-level machine learning (ML) models. Herein, we present a highly versatile quantum chemical data set comprising a total of 11 749 (acid)_1-2(base)_1-2 cluster configurations, containing up to 44 atoms. Utilizing the LUMI supercomputer, we calculated highly accurate PNO-CCSD(F12*)(T)/cc-pVDZ-F12 binding energies of the full set of cluster configurations leading to an unprecedented data set both in regard to sheer size and with respect to the level of theory. We employ the constructed benchmark set to assess the performance of various semiempirical and density functional theory methods. In particular, we find that the r²-SCAN-3c method shows excellent performance across the data set related to both accuracy and CPU time, making it a promising method to employ during cluster configurational sampling. Furthermore, applying the data sets, we construct ML models based on Δ-learning and provide recommendations for future application of ML in cluster configurational sampling.

Computational chemistry of cluster: Understanding the mechanism of atmospheric new particle formation at the molecular level

New particle formation (NPF), which exerts significant influence over human health and global climate, has been a hot topic and rapidly expands field of research in the environmental and atmospheric chemistry recent years. Generally, NPF contains two processes: formation of critical nucleus and further growth of the nucleus. However, due to the complexity of the atmospheric nucleation, which is a multicomponent process, formation of critical clusters as well as their growth is still connected to large uncertainties. Detection limits of instruments in measuring specific gaseous aerosol precursors and chemical compositions at the molecular level call for computational studies. Computational chemistry could effectively compensate the deficiency of laboratory experiments as well as observations and predict the nucleation mechanisms. We review the present theoretical literatures that discuss nucleation mechanism of atmospheric clusters. Focus of this review is on different nucleation systems involving sulfur-containing species, nitrogen-containing species and iodine-containing species. We hope this review will provide a deep insight for the molecular interaction of nucleation precursors and reveal nucleation mechanism at the molecular level.

The driving effects of common atmospheric molecules for formation of prenucleation clusters: the case of sulfuric acid, formic acid, nitric acid, ammonia, and dimethyl amine

How secondary aerosols form is critical as aerosols' impact on Earth's climate is one of the main sources of uncertainty for understanding global warming. The beginning stages for formation of prenucleation complexes, that lead to larger aerosols, are difficult to decipher experimentally. We present a computational chemistry study of the interactions between three different acid molecules and two different bases. By combining a comprehensive search routine covering many thousands of configurations at the semiempirical level with high level quantum chemical calculations of approximately 1000 clusters for every possible combination of clusters containing a sulfuric acid molecule, a formic acid molecule, a nitric acid molecule, an ammonia molecule, a dimethylamine molecule, and 0-5 water molecules, we have completed an exhaustive search of the DLPNO-CCSD(T)/CBS//ωB97X-D/6-31++G** Gibbs free energy surface for this system. We find that the detailed geometries of each minimum free energy cluster are often more important than traditional acid or base strength. Addition of a water molecule to a dry cluster can enhance stabilization, and we find that the (SA)(NA)(A)(DMA)(W) cluster has special stability. Equilibrium calculations of SA, FA, NA, A, DMA, and water using our quantum chemical ΔG° values for cluster formation and realistic estimates of the concentrations of these monomers in the atmosphere reveals that nitric acid can drive early stages of particle formation just as efficiently as sulfuric acid. Our results lead us to believe that particle formation in the atmosphere results from the combination of many different molecules that are able to form highly stable complexes with acid molecules such as SA, NA, and FA.

New Reactions for the Formation of Organic Nitrate in the Atmosphere

Organic nitrates make an important contribution to the formation of secondary organic aerosols, but the formation mechanisms of organic nitrates are not fully understood at the molecular level. In the present work, we explore a new route for the formation of organic nitrates in the reaction of formaldehyde (HCHO) with nitric acid (HNO₃) catalyzed by water (H₂O), ammonia (NH₃), and dimethylamine ((CH₃)₂NH) using theoretical methods. The present results using CCSD(T)-F12a/cc-pVTZ-F12//M06-2X/MG3S unravel that dimethylamine has a stronger catalytic ability in the reaction of HCHO with HNO₃, reducing the barrier by 21.97 kcal/mol, while water and ammonia only decrease the energy barrier by 7.35 and 13.56 kcal/mol, respectively. In addition, the calculated kinetics combined with the corresponding concentrations of these species show that the HCHO + HNO₃ + (CH₃)₂NH reaction can compete well with the naked HCHO + HNO₃ reaction at 200-240 K, which may make certain contributions to the formation of organic nitrates under some atmospheric conditions.

Hydration effect of selected atmospheric gases with finite water clusters: A quantum chemical investigation towards atmospheric implications

Water vapor in atmosphere is ubiquitous, and it varies according to geographical locations. Various toxic and non-toxic gases co-exist with water vapor/moisture in the atmosphere. This computational study addresses the fact that how those gases interact with water vapor. We have done quantum chemical density functional theory calculations to probe the interaction of certain gases with a finite number of water molecules in gas phase with various functionals/basis sets. An ensemble of 14 gas molecules comprising various diatomic, triatomic, and polyatomic gases have been chosen for the investigations. The intermolecular interactions are understood from the interaction energy, electrostatic potential, frontier molecular orbitals, energy gap, and natural bond orbital analyses. Furthermore, quantum molecular descriptors such as electronegativity, chemical potential, chemical hardness and electrophilicity index are calculated to have deep insight on chemical nature of the gas molecules. Additionally, we have done implicit solvent modelling using PCM, and the corresponding solvation energies have been calculated. Interestingly, all the calculations and analyses have projected the similar results that Cl₂, SO_2, and NH₃ have very high interaction with the water clusters. To mimic various altitudes (0 km, 5 km and 10 km) in the atmosphere, thermochemistry calculations have been carried out at different temperature and pressure values. The Gibbs free energies of formation suggest that the hydration of Cl₂ is higher followed by O₂, SO₂ and NH₃ at all altitudes. Remarkably, it is found that the formation of hydrated clusters of Cl₂ and O₂ with 4H₂O are thermodynamically favourable. On the other hand, SO₂ and NH₃ requires 5H₂O and 3H₂O to form thermodynamically favourable clusters. In summary, it is anticipated that this kind of extensive computational studies facilitate to understand the structural, electronic, chemical and thermochemical properties of hydrated atmospheric gases that leads to the formation of prenucleation clusters followed by atmospheric aerosols.

Interaction of Glutamic Acid/Protonated Glutamic Acid with Amide and Water Molecules: A Theoretical Study

Amino acids are important nitrogen-containing compounds and organic carbon components that exist widely in the atmosphere. The formation of atmospheric aerosols is affected by their interactions with amides. The dimers formed by glutamic acid (Glu) or protonated glutamic acid (Glu⁺) with three kinds of amide molecules (formamide FA, acetamide AA, urea U) and the hydrated clusters formed by Glu or Glu⁺, U molecules along with one to six water molecules were systematically studied at the M06-2X/6-311++G(3df,3pd) level. U is predicted to form a more stable structure with Glu/Glu⁺ than FA and AA by thermodynamics. If the concentration ratio of FA to U is less than 10⁴, U will play a critical role in NPF. The degree of hydration in Glu⁺-mU-nW is higher than that of Glu-mU-nW (m = 0, 1; n = 0-6) clusters. Notably, Glu contributes more to the Rayleigh scattering properties than glutaric acid and sulfuric acid, and thus may lead to the destruction of atmospheric visibility. This study is helpful to better understand the properties of organic aerosols containing amino acids or amides.

Sulfuric acid-dimethylamine particle formation enhanced by functional organic acids: an integrated experimental and theoretical study

Atmospheric new particle formation (NPF), which has been observed globally in clean and polluted environments, is an important source of boundary-layer aerosol particles and cloud condensation nuclei, but the fundamental mechanisms leading to multi-component aerosol formation have not been well understood. Here, we use experiments and quantum chemical calculations to better understand the involvement of carboxylic acids in initial NPF from gas phase mixtures of carboxylic acid, sulfuric acid (SA), dimethylamine, and water. A turbulent flow tube coupled to an ultrafine condensation particle counter with particle size magnifier has been set up to measure NPF. Experimental results show that pyruvic acid (PA), succinic acid (SUA), and malic acid (MA) can enhance sulfuric acid-dimethylamine nucleation in the order PA < SUA < MA with a greater enhancement observed at lower SA concentrations. Computational results indicate that the carboxylic and hydroxyl groups are related to the enhancement. This experiment-theory study shows the formation of multi-component aerosol particles and the role of the organic functional group, which may aid in understanding the role of organics in aerosol nucleation and growth in polluted areas, and help to choose organic molecules of specific structures for simulation.

The effect of (H2O)n (n = 1-3) clusters on the reaction of HONO with HCl: a mechanistic and kinetic study

The reaction between HONO and HCl is a possible pathway for the generation of ClNO, which is prone to photolyze, produce chlorine radicals, and accelerate the oxidation of tropospheric VOCs. Current experimental and theoretical studies have significant differences in rate constants under similar conditions. This study aims to examine the reasons for this difference. In this study, the effects of a single water molecule, water dimer, water trimer, excess HCl and excess HONO on the reaction mechanism of HONO + HCl were studied at the CCSD(T)/aug-cc-pVTZ//M06-2X/6-311+G(2df,2p) level and the rate constants of each reaction channel were calculated. Our results showed that the reaction potential barrier of HONO with HCl was the lowest only when the water dimer was present, and the reaction rate constants were close to the experimental results, and both the cis-HONO⋯(H₂O)₂ + HCl and the trans-HONO⋯(H₂O)₂ + HCl reaction paths are likely to occur. We think that the reason for the inconsistency between experimental and theoretical results is that the water dimer is involved in the reaction in experiments.

Possible atmospheric source of NH2SO3H: the hydrolysis of HNSO2 in the presence of neutral, basic, and acidic catalysts

NH₂SO₃H can directly participate in H₂SO₄-(CH₃)₂NH-based cluster formation, and thereby substantially enhance the cluster formation rate. Herein, the reaction mechanisms and kinetics for the formation of NH₂SO₃H from the hydrolysis of HNSO₂ without and with neutral (H₂O, (H₂O)₂, and (H₂O)₃), basic (NH₃ and CH₃NH₂), and acidic (HCOOH, H₂SO₄, H₂SO₄⋯H₂O, and (H₂SO₄)₂) catalysts were studied theoretically at the CCSD(T)-F12/cc-pVDZ-F12//M06-2X/6-311+G(2df,2pd) level. The calculated results showed that neutral, basic, and acidic catalysts decrease the energy barrier by over 18.1 kcal mol^-1; meanwhile, the product formation of NH₂SO₃H was more strongly bonded to neutral, basic, and acidic catalysts than to the reactants HNSO₂ and H₂O. This reveals that the reported neutral, basic, and acidic catalysts promote the formation of NH₂SO₃H from the hydrolysis of HNSO₂ both kinetically and thermodynamically. Kinetic calculations using the master equation showed that (H₂O)₂ (100% RH) dominate over the other catalysts within the range of 0-10 km altitudes and 230-320 K with its rate ratio larger by at least 2.98 times, whereas HCOOH (3.2 × 10⁹ molecules cm^-3) is the most favorable catalysts at 15 km altitude in the troposphere. Overall, the present results will provide a definitive example that neutral, basic, and acidic catalysts have important influences on atmospheric reactions.

A theoretical study on the formation mechanism of carboxylic sulfuric anhydride and its potential role in new particle formation

New particle formation (NPF) is the major source of atmospheric aerosol particles. However, the chemical species involved and the exact mechanism are still unclear. Cycloaddition reaction of SO₃ to carboxylic acids bas been identified as a possible formation mechanism of carboxylic sulfuric anhydrides which may be involved in NPF. Herein, energy profiles for forming diaterpenylic acetate sulfuric anhydride (DTASA) through cycloaddition of SO₃ to diaterpenylic acid acetate (DTAA) and the potential role of DTASA in NPF were studied through computational methods combined with atmospheric cluster dynamics code (ACDC). Gas phase reaction barriers for the two carboxyl groups of DTAA are 0.4 and 0.6 kcal mol⁻¹, respectively, illustrating a feasible formation mechanism for DTASA. According to thermodynamical analysis and dynamical simulations, atmospheric clusters containing DTASA and atmospheric nucleation precursors sulfuric acid (SA), ammonia (NH₃) and dimethylamine (DMA) possess both thermodynamically and dynamically higher stabilities than those of DTAA-contained clusters. Furthermore, DTASA–NH₃ and DTASA–DMA are more stable than SA–NH₃ and SA–DMA, enabling DTASA, even carboxylic sulfuric anhydrides, to become potential participants in the atmospheric NPF process which may hence promote a better understanding of NPF.

Organic acids could improve their nucleation ability through the cycloaddition reaction of SO₃ to generate corresponding carboxylic sulfuric anhydrides which may play a potential role in the atmospheric new particle formation.

Theoretical analysis of sulfuric acid–dimethylamine–oxalic acid–water clusters and implications for atmospheric cluster formation

In recent years, organic compounds potentially involved in atmospheric particle formation have received increased attention. However, the contributions of organic acids as precursors in nucleation remain ambiguous. In this study, the low-lying structures and thermodynamics of the sulfuric acid–dimethylamine–oxalic acid–water system are obtained at the M06-2X/6-311+G(2d,p) level, and the single point energy of the clusters has been calculated at the DF-LMP2-F12/VDZ-F12 level. The formations of the multicomponent clusters are predicted based on thermodynamics, involving proton transfer and hydrogen bonding interactions. Oxalic acid can synergistically promote the formation of the sulfuric acid–dimethylamine–oxalic acid–water system while inhibiting this with the addition of more sulfuric acid molecules. The results of hydrate distribution show that un-hydrate clusters play a dominant role during formation. Moreover, dimethylamine and oxalic acid have similar effects on Rayleigh scattering properties, and the clusters involving complex mixtures of compounds can have high optical activities.

The structure of SA₂.DMA.OA.W₄ cluster.

A computational study of the HO2 + SO3 → HOSO2 + 3O2 reaction catalyzed by water monomer, water dimer and small clusters of sulfuric acid: kinetics and atmospheric implications

Herein, the reaction mechanisms and kinetics for the HO2 + SO3 → HOSO2 + 3O2 reaction catalyzed by water monomer, water dimer and small clusters of sulfuric acid have been...

A pH dependent sulfate formation mechanism caused by hypochlorous acid in the marine atmosphere

Secondary sulfate plays a crucial role in forming marine aerosol, which in turn is an important source of natural aerosol at a global level. Recent experimental studies suggest that oxidation of S(IV) compounds, in practice dissolved sulfur dioxide, to sulfate (S(VI)) by hypochloric acid could be one of the most significant pathways for sulfate formation in marine areas. However, the exact mechanism responsible for this process remains unknown. Using high-level quantum chemical calculations, we studied the reaction between dissolved sulfur dioxide and hypochloric acid. We account for the dominant protonation states of reactants in the pH range 3.0-9.0. We also consider possible catalytic effects of species such as H₂O. Our results show that sulfate formation in HOCl+HOSO₂^- and HOCl+SO₃^2- reactions relevant to acidic and nearly neutral conditions can occur either through previously proposed Cl⁺ transfer or through a novel HO⁺ transfer mechanism. In alkaline conditions, where the dominant reactants are OCl^- and SO₃^2-, an O atom transfer mechanism proposed in previous experimental studies may be more important than Cl⁺ transfer. Catalysis by common cloud-water species is found to lower barriers of Cl⁺ transfer mechanisms substantially. Nevertheless, we find that the dominant S(IV) + HOCl reaction mechanism for the full studied pH range is HO⁺ transfer from HOCl to SO₃^2-, which leads directly to sulfate formation without ClSO₃^- intermediates. The rate-limiting barrier of this reaction is low, leading to an essentially diffusion-controlled reaction rate. S(IV) lifetimes due to this reaction decrease with increasing pH due to the increasing fractional population of SO₃^2-. Especially in neutral and alkaline conditions, depletion of HOCl by the reaction is so rapid that S(IV) oxidation will be controlled mainly by mass transfer of gas-phase HOCl to the liquid phase. The mechanism proposed here may help to explain marine sulfate sources missing from current atmospheric models.

Rapid sulfuric acid-dimethylamine nucleation enhanced by nitric acid in polluted regions

Recent research [Wang et al., Nature 581, 184-189 (2020)] indicates nitric acid (NA) can participate in sulfuric acid (SA)-ammonia (NH₃) nucleation in the clean and cold upper free troposphere, whereas NA exhibits no obvious effects at the boundary layer with relatively high temperatures. Herein, considering that an SA-dimethylamine (DMA) nucleation mechanism was detected in megacities [Yao et al., Science 361, 278-281 (2018)], the roles of NA in SA-DMA nucleation are investigated. Different from SA-NH₃ nucleation, we found that NA can enhance SA-DMA-based particle formation rates in the polluted atmospheric boundary layer, such as Beijing in winter, with the enhancement up to 80-fold. Moreover, we found that NA can promote the number concentrations of nucleation clusters (up to 27-fold) and contribute 76% of cluster formation pathways at 280 K. The enhancements on particle formation by NA are critical for particulate pollution in the polluted boundary layer with relatively high NA and DMA concentrations.

Catalytic sulfate formation mechanism influenced by important constituents of cloud water via the reaction of SO2 oxidized by hypobromic acid in marine areas

Comprehensive investigations of the possible formation pathways of sulfate, the main composition of atmospheric aerosol in marine areas, continue to challenge atmospheric chemists. As one of the most important oxidation routes of S(iv) contributing to sulfate formation, the reaction process of S(iv) oxidized by hypobromic acid, which is ubiquitous with the gas-phase mixing ratios of ∼310 ppt and has a well-known oxidative capacity, has attracted wide attention. However, little information is available about the detailed reaction mechanism. Especially, due to the abundant species in cloud water, the potential effect of these compositions on these reaction processes and the corresponding effect mechanism are also uncertain. Using high-level quantum chemical calculations, we theoretically elucidate the two-step mechanism of Br+ transfer proposed by experiment through the verification of the key BrSO3- intermediate formation and subsequent hydrolysis reaction or the uncovered reaction of BrSO3- intermediate with OH-. Further, the novel and more competitive mechanisms (OH+ or O atom transfer pathways) that have not been considered in previous studies, leading to sulfate formation directly, have been found. Furthermore, it should be mentioned that we revealed the effect mechanism of constituents catalyzed in cloud water, especially the important H2O-catalyzed mechanism. In addition, all the above pathways follow this catalytic mechanism. This finding indicates a linkage between the complex nature of the atmospheric constituents and related atmospheric reaction, as well as the enhanced occurrence of atmospheric secondary sulfate formation in the atmosphere. Hence, this exploration of sulfate formation related to hypobromic acid could provide a better understanding about the sources of sulfate in marine areas.

Synergistic effect of glutaric acid and ammonia/amine/amide on their hydrates in the clustering: A theoretical study

The formation of molecular clusters makes influence on the atmosphere. The clusters of glutaric acid (GA) and common ammonia (A), amine (methylamine MA, dimethylamine DMA) and representative amide (urea U) along with water molecule were systematically studied theoretically. GA-A-nW (n = 1, 2), GA-MA-nW (n = 1, 2), GA-DMA-1W and GA-U-nW (n = 1-6) are predicted to be feasible thermodynamically with the hydrogen bonds as interaction force. GA and urea promote the clustering synergistically, and ammonia, methylamine, dimethylamine promote the clustering of small GA hydrates (n = 1-2), while inhibit that of large GA hydrates (n = 3-6). The results of humidity show that un-hydrate or mono-hydrate is the main form of GA-mbase-nW (m = 0, 1; n = 1-6) under relative humidity of 20%, 50% and 80%. The global minima remain dominant over the temperature range of 220-320 K. GA contributes more to the Rayleigh scattering properties than sulfuric acid. More importantly, the local minima can undergo isomerization to form the global minima crossing a free energy barrier ranging from 6.66 to 11.78 kcal mol^-1. This study indicates that GA and base molecules play a synergistic role to promote the formation of clusters. We hope it can provide more insights on interesting clustering in theory.

Thermodynamic properties of forming methanol-water and ethanol-water clusters at various temperatures and pressures and implications for atmospheric chemistry: A DFT study

The gas-phase geometries, binding energies, enthalpies, and free energies of methanol-(water)_n and ethanol-(water)_n clusters containing n=1-10,20,30,40, and 50 water molecules have been calculated using density functional theory. The binding energies are calculated at 0 K. The enthalpies are calculated at a temperature of 298.15 K and pressure of 1013.25 hPa (1 atm). The free energies are calculated at a wide range of temperature (T) and pressure (P) (from T = 298.15 K, P = 1013.25 hPa to T = 216.65 K, P = 226.32 hPa). The results show that the free energy of the formation of a specific cluster from its free molecules is negative (i.e., favorable) only below some critical temperature and pressure, which depends on the cluster's size. One of the most common volatile organic compounds (VOCs) in the troposphere is methanol, ethanol, and atmospheric aerosols containing methanol and ethanol. The Rayleigh scattering properties of methanol-water and ethanol-water clusters have been investigated. The scattering intensities were computed at static (∞ nm) and different wavelengths (700, 600, 500, and 400 nm) of naturally polarized light. Rayleigh scattering intensities increase about 9%-10% at 400 nm compared to the static limit (∞ nm) for both methanol-water and ethanol-water clusters.

The potential mechanism of atmospheric new particle formation involving amino acids with multiple functional groups

Amino acids are recognized as significant components of atmospheric aerosols. However, their potential role in atmospheric new particle formation (NPF) is poorly understood, especially aspartic acid (ASP), one of the most abundant amino acids in the atmosphere. It has not only two advantageous carboxylic acid groups but also one amino group, both of which are both effective groups enhancing NPF. Herein, the participation mechanism of ASP in the formation of new particle involving sulfuric acid (SA)-ammonia (A)-based system has been studied using the Density Functional Theory (DFT) combined with the Atmospheric Clusters Dynamic Code (ACDC). The results show that the addition of ASP molecules in the SA-A-based clusters provides a promotion on the interaction between SA and A molecules. Moreover, ACDC simulations indicate that ASP could present an obvious enhancement effect on SA-A-based cluster formation rates. Meanwhile, the enhancement strength R presents a positive dependence on [ASP] and a negative dependence on [SA] and [A]. Besides, the enhancement effect of ASP is compared with that of malonic acid (MOA) with two carboxylic acid groups (Chemosphere, 2018, 203, 26-33), and ASP presents a more obvious enhancement effect than MOA. The mechanism of NPF indicates that ASP could contribute to cluster formation as a "participator" which is different from the "catalytic" role of MOA at 238 K. These new insights are helpful to understand the mechanism of NPF involving organic compounds with multiple functional groups, especially the abundant amino acids, such as the ASP, in the urban/suburban areas with intensive human activities and industrial productions and therefore the abundant sources of amino acids. Furthermore, the NPF of the SA-A-based system involving amino acid should be considered when assessing the environmental risk of amino acid.

A theoretical investigation on the atmospheric degradation of the radical: reactions with NO, NO2, and NO3

The radical is the key intermediate in the atmospheric oxidation of benzaldehyde, and its further chemistry contributes to local air pollution. The reaction mechanisms of the radical with NO, NO₂, and NO₃ were studied by quantum chemistry calculations at the CCSD(T)/CBS//M06-2X/def2-TZVP level of theory. The explicit potential energy curves were provided in order to reveal the atmospheric fate of the radical comprehensively. The main products of the reaction of with NO are predicted to be , CO₂ and NO₂. The reaction of with NO₂ is reversible, and its main product would be C₆H₅C(O)O₂NO₂ which was predicted to be more stable than PAN (peroxyacetyl nitrate) at room temperature. The decomposition of C₆H₅C(O)O₂NO₂ at different ambient temperatures would be a potential long-range transport source of NO_x in the atmosphere. The predominant products of the reaction are predicted to be C₆H₅C(O)O₂H, C₆H₅C(O)OH, O₂ and O₃, while HO˙ is of minor importance. So, the reaction of with would be an important source of ozone and carboxylic acids in the local atmosphere, and has less contribution to the regeneration of HO˙ radicals. The reaction of with NO₃ should mainly produce , CO₂, O₂ and NO₂, which might play an important role in atmospheric chemistry of peroxy radicals at night, but has less contribution to the night-time conversion of ( and RO˙) to ( and HO˙) in the local atmosphere. The results above are in good accordance with the reported experimental observations.

Role of glycine on sulfuric acid-ammonia clusters formation: Transporter or participator

Glycine (Gly) is ubiquitous in the atmosphere and plays a vital role in new particle formation (NPF). However, the potential mechanism of its on sulfuric acid (SA) - ammonia (A) clusters formation under various atmospheric conditions is still ambiguous. Herein, a (Gly)_x·(SA)_y·(A)_z (z ≤ x + y ≤ 3) multicomponent system was investigated by using density functional theory (DFT) combined with Atmospheric Cluster Dynamics Code (ACDC) at different temperatures and precursor concentrations. The results show that Gly, with one carboxyl (-COOH) and one amine (-NH₂) group, can interact strongly with SA and A in two directions through hydrogen bonds or proton transfer. Within the relevant range of atmospheric concentrations, Gly can enhance the formation rate of SA-A-based clusters, especially at low temperature, low [SA], and median [A]. The enhancement (R) of Gly on NPF can be up to 340 at T = 218.15 K, [SA] = 10⁴, [A] = 10⁹, and [Gly] = 10⁷ molecules/cm³. In addition, the main growth paths of clusters show that Gly molecules participate into cluster formation in the initial stage and eventually leave the cluster by evaporation in subsequent cluster growth at low [Gly], it acts as an important "transporter" to connect the smaller and larger cluster. With the increase of [Gly], it acts as a "participator" directly participating in NPF.

Can nitrous acid contribute to atmospheric new particle formation from nitric acid and water?

The properties of (HNO₃)(HONO)(H₂O)_n (n = 1–6) clusters are reported including thermodynamics, structures, temperature-dependence, intermolecular forces, optical properties, and evaporation rates.

Atmospheric implication of synergy in methanesulfonic acid–base trimers: a theoretical investigation

Synergy between molecules is ubiquitous in atmospheric clusters and significantly affects new particle formation (NPF). Herein, the effects of the synergy between base molecules on the stability and evaporation of MSA–X–Y (MSA = methanesulfonic acid; X, Y = ammonia (A), methylamine (M), or dimethylamine (D)) trimers were investigated via density functional theory (DFT) and the atmospheric clusters dynamic code (ACDC) method. The results show that proton transfer from MSA to X is exothermal and barrierless due to the synergy between X and Y molecules in MSA–X–Y trimers compared with MSA-X dimers. Cyclic hydrogen bonds are a typical characteristic of the stable trimers. Topological analysis using atoms in molecules (AIM) theory indicates that the electron density (ρ) and Laplacian of the electron density (∇²ρ) at the bond critical points (BCPs) in the trimers exceed the standard range of hydrogen bonds. The affinity for attaching a Y molecule to the MSA–X dimers and the substitution of Y₁ (Y = A and MA) by Y₂ (Y₂ = MA and DMA) in the MSA–X–Y trimers are thermodynamically spontaneous. In addition, the cyclic stabilization energy of the MSA–X–Y trimers increased as the alkalinities of X and Y increased. The total evaporation rate of the trimers decreased as the alkalinities of X and Y increased. Low temperature and high pressure significantly facilitate the formation of trimers. It is further confirmed that synergy plays an important role in atmospheric NPF events.

The effects of synergy of between X and Y on the stability of MSA–X–Y trimers were investigated via quantum chemical and kinetics simulation method.

Hydrolysis of Formyl Fluoride Catalyzed by Sulfuric Acid and Formic Acid in the Atmosphere

Formyl fluoride (HFCO) is an important atmospheric molecule, and its reaction with the OH radical is an important pathway when degradation of HFCO is considered in earth's troposphere. Here, we study the hydrolysis of formyl fluoride (HFCO + H₂O) with sulfuric acid (H₂SO₄) and formic acid (HCOOH) acting as catalysts by utilizing M06-2X, CCSD(T)-F12a, and conventional transitional state theory with Eckart tunneling to explore the atmospheric impact of the above-said hydrolysis reactions. Our calculated results show that H₂SO₄ has a remarkably catalytic role in the gas-phase hydrolysis of HFCO, as the energy barriers of the HFCO + H₂O reaction are reduced from 39.22 and 41.19 to 0.26 and -0.63 kcal/mol with respect to the separate reactants, respectively. In addition, we also find that H₂SO₄ can significantly accelerate the decomposition of FCH(OH)₂ into hydrogen fluoride (HF) and HCOOH. This is because while the barrier height for the unimolecular decomposition of FCH(OH)₂ into HF and HCOOH is 31.63 kcal/mol, the barrier height for the FCH(OH)₂ + H₂SO₄ reaction is predicted to be -5.99 kcal/mol with respect to separate reactants. Nevertheless, the comparative relative rate analysis shows that the reaction between HFCO and the OH radical is still the most dominant pathway when the tropospheric degradation of HFCO is taken into account and that the gas-phase hydrolysis of HFCO may only occur with the help of H₂SO₄ when the atmospheric concentration of OH is about 10¹ molecules cm^-3 or less. Having an understanding from the present study that the gas-phase hydrolysis of HFCO in the presence of H₂SO₄ has very limited role possibly in the absence of sunlight, we also prefer here to emphasize that the HFCO + H₂O + H₂SO₄ reaction may occur on the surface of secondary organic aerosols for the formation of HCOOH.

Atmospheric chemistry of the self-reaction of HO2 radicals: stepwise mechanism versus one-step process in the presence of (H2O)n (n = 1-3) clusters

The effects of water on radical-radical reactions are of great importance for the elucidation of the atmospheric oxidation process of free radicals. In the present work, the HO2 + HO2 reactions with (H2O)n (n = 1-3) have been investigated using quantum chemical methods and canonical variational transition state theory with small curvature tunneling. We have explored both one-step and stepwise mechanisms, in particular the stepwise mechanism initiated by ring enlargement. The calculated results have revealed that the stepwise mechanism is the dominant one in the HO2 + HO2 reaction that is catalyzed by one water molecule. This is because its pseudo-first-order rate constant (kRWM1') is 3 orders of magnitude larger than that of the corresponding one-step mechanism. Additionally, the value of kRWM1' at 298 K has been found to be 4.3 times larger than that of the rate constant of the HO2 + HO2 reaction (kR1) without catalysts, which is in good agreement with the experimental findings. The calculated results also showed that the stepwise mechanism is still dominant in the (H2O)2 catalyzed reaction due to its higher pseudo-first-order rate constant, which is 3 orders of magnitude larger than that of the corresponding one-step mechanism. On the other hand, the one-step process is much faster than the stepwise mechanism by a factor of 105-106 in the (H2O)3 catalyzed reaction. However, the pseudo-first-order rate constants for the (H2O)2 and (H2O)3-catalyzed reactions are lower than that of the H2O-catalyzed reaction by 3-4 orders of magnitude, which indicates that the water monomer is the most efficient one among all the catalysts of (H2O)n (n = 1-3). The present results have provided a definitive example that water and water clusters have important influences on atmospheric reactions.

A molecular understanding of the interaction of typical aromatic acids with common aerosol nucleation precursors and their atmospheric implications

Aromatic acids, which are generated from numerous anthropogenic emissions and secondary transformations, have been considered to play a crucial role in new particle formation. In this study, we performed theoretical calculations at the PW91PW91/6-311++G(3df,3pd) level to investigate the interaction between typical aromatic acids namely benzoic acid (BA), phenylacetic acid (PAA), phthalic acid (PA), isophthalic acid (mPA), and terephthalic acid (PTA) and common atmospheric nucleation precursors namely sulfuric acid (SA), water (H2O), ammonia (NH3), methylamine (MA), dimethylamine (DMA), and trimethylamine (TMA). The geometric analysis, Gibbs free energy analysis, OH/NH-stretching vibrational frequency calculation, and atoms in molecules (AIM) analysis were conducted to determine the interactions in the complexes. The heterodimers formed a six to eight membered ring through four types of hydrogen bond, and the bond strength could be ranked in descending order: SO-H⋯O > O-H⋯O/N > N-H⋯O. The BA/PAA/mPA/PTA-SA complexes had the lowest Gibbs free energy values. PA was more likely to interact with NH3 or amines rather than SA due to an intra-molecular hydrogen bond. Additionally, the aromatic acids have similar ability to interact with SA and NH3 as monocarboxylic/dicarboxylic acid. The formation potential of the heterodimers from aromatic acids with common nucleation precursors in ambient atmosphere was investigated.

Theoretical study of the cis-pinonic acid and its atmospheric hydrolysate participation in the atmospheric nucleation

cis-Pinonic acid (CPA), one of the major photooxidation products of α-pinene, is believed to contribute to the formation of aerosols formed over forested areas. In the current study, we implement quantum chemical calculation to investigate the interaction between sulfuric acid (SA) and CPA as well as the hydrolysate of CPA (HCPA) in the presence of water or ammonia in the atmosphere. The lowest free energy configurations, reactants, transition states, intermediates, and products were optimized at 298/278K and 1atm at the M06-2X/6-311+G(3df,3pd) level. Our results show that one CPA molecule might initially nucleate with SA molecules and subsequently participate in the formation and growth of the new particle in the form of HCPA. More than one HCPA molecule may be involved in the critical nuclei. Furthermore, the hydrolysis reaction of CPA can be effectively catalyzed by SA and nitric acid (NA) in presence of water, which significantly increases the HCPA content in the atmosphere and subsequently promotes the particle nucleation. Overall, the current study elucidates a new mechanism of atmospheric nucleation driven by CPA and its hydrolysate.

Configurational Sampling of Noncovalent (Atmospheric) Molecular Clusters: Sulfuric Acid and Guanidine

We studied the configurational sampling of noncovalently bonded molecular clusters relevant to the atmosphere. In this article, we discuss possible approaches to searching for optimal configurations and present one alternative based on systematic configurational sampling, which seems able to overcome the typical problems associated with searching for global minima on multidimensional potential energy surfaces. Since atmospheric molecular clusters are usually held together by intermolecular bonds, we also present a cost-effective strategy for treating hydrogen bonding and proton transferring by using rigid molecules and ions in different protonation states and illustrate its performance on clusters containing guanidine and sulfuric acid.

Enhancement of Atmospheric Nucleation by Highly Oxygenated Organic Molecules: A Density Functional Theory Study

New particle formation (NPF) by gas-particle conversion is the main source of atmospheric aerosols. Highly oxygenated organic molecules (HOMs) and sulfuric acid (SA) are important NPF participants. 2-Methylglyceric acid (MGA), a kind of HOMs, is a tracer of isoprene-derived secondary organic aerosols. The nucleation mechanisms of MGA with SA were studied using density functional theory and atmospheric cluster dynamics simulation in this study, along with that of MGA with methanesulfonic acid (MSA) as a comparison. Our theoretical works indicate that the (MGA)(SA) and (MGA)(MSA) clusters are the most stable ones in the (MGA) _i(SA) _j ( i = 1-2, j = 1-2) and (MGA) _i(MSA) _j ( i = 1-2, j = 1-2) clusters, respectively. Both the formation rates of (MGA)(SA) and (MGA)(MSA) clusters are quite large and could have significant contributions to NPF. The results imply that the homomolecular nucleation of MGA is unlikely to occur in the atmosphere, and MGA and SA can effectively contribute to heteromolecular nucleation mainly in the form of heterodimers. MSA exhibits properties similar to SA in its ability to form clusters with MGA but is slightly weaker than SA.

Effects of methylation in acceptors on the hydrogen bond complexes between 2,2,2-trifluoroethanol and cyclic ethers

In order to explore the effect of methylation on the stability and spectral shift of hydrogen bond complexes, the complexes of 2,2,2-trifluoroethanol (TFE) with propylene oxide (PO) and isobutylene oxide (IBO) were investigated by Fourier transform infrared (FTIR) spectroscopy and ab initio computations. The comparable OH-stretching red shifts were observed upon complexation, and an enhancement of the OH-stretching band is shown with the partial pressure of monomers increasing. The OH-stretching frequency of TFE is red shifted by 180 and 201 cm^-1 with PO and IBO, respectively. By using quantum chemical calculations, we predicted the geometric parameters, binding energies, and spectral shifts of TFEPO/IBO hydrogen bond complexes. The calculated and observed spectral shifts follow the same trends. Compared with the TFEethylene oxide (EO) complex, the strength of the hydrogen bond in complex increases with the addition of methyl group, which likely results from the increase in basicity of the hydrogen bond acceptor. By combining the experimental integrated absorbance and the calculated IR intensity of the OH-stretching vibrational transition, the equilibrium constant for the complex formation was determined. In addition, atoms-in-molecules (AIM) and natural bond orbital (NBO) analyses were carried out to explain the red shift and the nature of the interaction in these complexes.

Benchmarking sampling methodology for calculations of Rayleigh light scattering properties of atmospheric molecular clusters

We present four different computational methods for benchmarking the sampling and Rayleigh light scattering of hydrogen bonded atmospheric molecular clusters.