Microsolvation of Hydrogen Sulfide: Exploration of H2S·(H2O)n and SH-·H3O+·(H2O)n-1 (n = 5−7) Cluster Structures on Ab Initio Potential Energy Surfaces by the Scaled Hypersphere Search Method

Theoretical study of the hydration effects on alkylamine and alkanolamine clusters and the atmospheric implication

Amines are important atmospheric nucleation precursors in polluted areas. However, specific roles of various amines in enhancing the stability of pre-nucleation clusters are poorly understood. Herein, different roles of trimethylamine (TMA) and monoethanolamine (MEA) in the formation of sulfuric acid (SA)-based pre-nucleation clusters were investigated. The hydration effects of up to four water (W) molecules on the interaction of the acid-base pairs of (TMA)(SA) and (MEA)(SA) were computationally investigated at the M06-2X/6-311++G (3df, 3pd) level of theory. Results show that the formation thermodynamics of key intermediate clusters are different with amines. Besides, MEA-enhanced formation of pre-nucleation clusters plays an important role in environments with high humidity while TMA may be the dominant nucleation precursors in dry conditions. The concentration of dominant MEA-containing pre-nucleation cluster is at least three orders of magnitude higher than that of TMA and dimethylamine near emission sources at conditions of T = 298.15 K and RH = 60%, indicating that alkanolamine may play an important role in atmospheric nucleation. Furthermore, the hydration of MEA is easier than that of alkylamines. Our results put forward the need to distinguish the performance of different types of amine under specific conditions to better model the new particle formation events in highly polluted areas. Besides, this study indicates that alkanolamines such as MEA are important participator in new particle formation.

A molecular-scale study on the hydration of sulfuric acid-amide complexes and the atmospheric implication

Amides are ubiquitous in atmosphere. However, the role of amides in new particle formation (NPF) is poorly understood. Herein, the interaction of urea and formamide with sulfuric acid (SA) and up to four water (W) molecules has been studied at the M06-2X/6-311++G(3df,3pd) level of theory. The structures and properties of (Formamide)(SA)(W)_n (n = 0-4) and (Urea)(SA)(W)_n (n = 0-4) clusters were investigated. Results show that the interaction of SA with the CO group of amides plays a more important role in amide clusters compared with the NH₂ group. Proton transfer to water molecule become dominant in highly hydrated amide clusters at lower temperatures. There is no proton transfer to CO group in formamide clusters. The Rayleigh light scattering intensities of amide clusters are comparable to that of amine and oxalic acid clusters reported previously. Moreover, unhydrated (Amide)(SA) clusters have similar or even higher ability than hydrated SA clusters to participate in ion-induced nucleation. In comparison with formamide, urea has more interacting sites and its clusters have higher Rayleigh light scattering intensities, larger dipole moment, stronger interaction with SA and lower water affinity. The intermolecular interaction in (Formamide)(SA) is slightly weaker than that of SA dimer, which may be compensated by the high concentration of formamide, thus enabling formamide to participate in initial steps of NPF. This study may bring new insight into the role of amides in initial steps of NPF from molecular scale and could help better understand the properties of amide-containing organic aerosol.

Molecular understanding of the interaction of amino acids with sulfuric acid in the presence of water and the atmospheric implication

Amino acids are important components of atmospheric aerosols. Despite the diversity of amino acids structures, however, the role of amino acids with additional non-characteristic functional groups in new particle formation (NPF) has almost remained unexplored. Herein, the interaction of serine (Ser) and threonine (Thr), which feature a hydroxyl group and differ by a methyl-substitution, with sulfuric acid (SA) and up to three water (W) molecules has been investigated at the M06-2X/6-311++G (3df, 3pd) level of theory. The effects of structural differences of amino acids on the structure and properties of clusters were also pointed out. Results show that serine may play more important role in stabilizing sulfuric acid to promote NPF in initial steps compared with threonine, glycine and alanine. Meanwhile, threonine may participate in ion-induced nucleation due to the high dipole moment of (Thr) (SA) isomers. Moreover, the effects of structure differences of amino acids can be seen in several aspects. Firstly, methyl substitution and hydroxyl group of amino acids have great influence on the structure of clusters. Secondly, hydrated (Ser) (SA) and (Tur) (SA) clusters could retain water even at low relative humidity, which may due to the hydroxyl group in serine and threonine. In addition, the Rayleigh light scattering intensities of amino acid-containing clusters are higher than trimethylamine, monoethanolamine and oxalic acid-involved counterparts. The effect of carboxyl group and methyl substitution on optical properties of clusters is also discussed. This study may bring new insight into the role of amino acids with additional non-characteristic functional groups in initial steps of NPF.

Modeling of Structure-Property Relationships of Polymerizable Surfactants with Antimicrobial Activity

Polymerizable quaternary ammonium salts (PQASs) were synthesized in a previous work and some of them were used as surfactants in the antimicrobial coating of commercial membranes. Herein, the electrostatic charges, maximum length, and aspect ratio of these antibacterial surfactants were calculated with the aim of investigating the relationship between the properties, recognized to control the biocidal activity of these molecules, and the molecular structures. The effect of the water molecules was considered through a quantum and molecular mechanics approach. The correlation between the number of carbons in the main aliphatic chain of PQAS and the above properties was investigated, by finding that the net charge on the ammonium group does not increase as the number of carbons in the aliphatic chain increase. Thus, although this number influences the antibacterial activity of the surfactants, this influence is not correlated with an increase of the ammonium positive charge. Unlike the partial charges, a different trend was obtained for the surfactants’ maximum length and aspect ratio in agreement with the experimental behavior. As this modeling does not use empirical or adjustable parameters, it can assist the synthetic plan of new structures for surface functionalization, in order to improve the biofouling resistance of the membranes.

Structures of protonated hydrogen sulfide clusters, H+(H2S)n, highlighting the nature of sulfur-centered intermolecular interactions

Though H₂S has the same hydrogen bond coordination property as H₂O, intermolecular structures of H⁺(H₂S)_n are very different from those of H⁺(H₂O)_n, indicating the competition among hydrogen bond and other intermolecular interactions.

Study of Potential Energy Surfaces towards Global Reaction Route Mapping

The potential energy surface (PES) is just a theoretical construct based on the Born-Oppenheimer approximation, but it underlies various phenomena, including molecular vibrations, collisional ionizations, and chemical reactions. This account describes how a new idea for global reaction route mapping (GRRM), which had seemed to be impossible for chemical systems with more than three atoms, was born and has been developed during the course of the study of the PES. GRRM has pioneered new fields of chemistry. Furthermore, techniques for GRRM are still developing, and GRRM is further extending its application to various areas of chemistry and chemical physics.

The mechanism of tautomerisation and geometric isomerisation in thioformic acid and its water complexes: exploring chemical pathways for water migration

A systematic and automated search for chemical pathways of isomerisation between geometric and tautomeric forms of gas-phase thioformic acid (TFA) and its water complexes is performed using a global reaction route mapping (GRRM) method, and an uncovered pathway for cis-trans isomerisation in the thiol form of TFA has been explored through computations performed at CCSD(T)/6-311++G(2d,2p)//B3LYP/6-311++G(2d,2p) level of the coupled cluster and density functional theories. To explore the routes for water migration, a detailed analysis of complexes of TFA with a single-water molecule is presented. Notably, during the isomerisation process in TFA, a positive catalytic effect of water was observed that can arise either by the stabilization of the reactant and/or of the transition state through extensive hydrogen bonding. Interesting behavior of isomeric forms of TFA along the pathways analysed is revealed through the Gibbs free-energy change and its temperature-dependence. The cis form of TFA(thiol) in the complexes of TFA with a single-water molecule is found to be thermodynamically equally feasible as the trans form which though is known to be the most dominating among the isomeric forms of TFA. Besides these, various complexes of TFA with two-water molecules have also been explored to study the hydrogen-bonding interaction through natural bond-orbital (NBO) analysis. The complexes of TFA with two-water molecules have also been characterized using spectral features including vibrational frequency analysis, and the effect of complexation has been observed by noting frequency shift.

Exploring water catalysis in the reaction of thioformic acid with hydroxyl radical: a global reaction route mapping perspective

Hydrogen abstraction pathways, in the gas-phase reaction of tautomers of thioformic acid (TFA), TFA(thiol), and TFA(thione), with hydroxyl radical in the presence and absence of single water molecule acting as a catalyst, is investigated with high-level quantum mechanical calculations at CCSD(T)/6-311++G(2d,2p)//MP2/6-311++G(2d,2p), CCSD(T)/6-311++G(d,p)//DFT/BHandHLYP/6-311++G(d,p), and DFT/B3LYP/6-311++G(2df,2p) levels of the theory. A systematic and automated search of the potential energy surface (PES) for the reaction pathways is performed using the global reaction route mapping (GRRM) method that employs an uphill walking technique to search prereaction complexes and transition states. The computations reveal significant lowering of the PES and substantial reduction in the activation energy for the hydrogen abstraction pathway in the presence of water, thereby proving water as an efficient catalyst in the reaction of both the TFA tautomers with OH radical. The hydrogen-bonding interactions are observed to be responsible for the large catalytic effect of water. Notably, in the case of TFA(thiol), formyl hydrogen abstraction is observed to be kinetically more favorable, while acidic hydrogen abstraction is observed to be thermodynamically more feasible. Interestingly, in the case of TFA(thione), reaction pathways involving only formyl hydrogen abstraction were observed to be feasible. The water-catalyzed hydrogen abstraction reaction of TFA with hydroxyl radical, investigated in this work, can provide significant insights into the corresponding reaction in the biological systems.

Stochastic structure determination for conformationally flexible heterogenous molecular clusters: application to ionic liquids

We present a novel method that enables accurate and efficient computational determination of conformationally flexible clusters, "Kick(3)" This method uses stochastically generated structures in combination with fast quantum mechanical methods. We demonstrate the power of this method by elucidating the structure of ionic liquid (IL) ([xMIM(+)][NO3(-)])n clusters (x = E, B, D, n = 1-10,15). Dispersion-corrected, third-order self-consistent-charge density-functional tight-binding (DFTB3) is shown to be a computationally efficient, yet reliable approximation to density functional theory for predicting and understanding IL structure and stability. The presented approach, therefore, enables the accurate and efficient screening of ILs with high potential toward practical applications, without recourse to more expensive quantum chemical methods.

On the perturbation of the H-bonding interaction in ethylene glycol clusters upon hydration

Ab initio and density functional methods have been employed to study the structure, stability, and spectral properties of various ethylene glycol (EG(m)) and ethylene glycol-water (EG(m)W(n)) (m = 1-3, n = 1-4) clusters. The effective fragment potential (EFP) approach was used to explore various possible EG(m)W(n) clusters. Calculated interaction energies of EG(m)W(n) clusters confirm that the hydrogen-bonding interaction between EG molecules is perturbed by the presence of water molecules and vice versa. Further, energy decomposition analysis shows that both electrostatic and polarization interactions predominantly contribute to the stability of these clusters. It was found from the same analysis that ethylene glycol-water interaction is predominant over the ethylene glycol-ethylene glycol and water-water interactions. Overall, the results clearly illustrate that the presence of water disrupts the ethylene glycol-ethylene glycol hydrogen bonds.

Kick: constraining a stochastic search procedure with molecular fragments

An extension of the Kick program developed by Bera et al. (J Phys Chem A 2006, 110, 4287) is described in which chemically sensible molecular fragments are used in an automated stochastic search algorithm. This results in a vastly reduced region of the potential energy surface which can be explored very quickly. We present use of this modified algorithm to the search for low-lying isomers, and we present candidates for the global energy minimum, for a range of chemical systems. We highlight the usefulness of this procedure for exploring reactions of molecules with transition metal clusters and to the microsolvation of a small dipeptide.