Thermodynamics of Forming Water Clusters at Various Temperatures and Pressures by Gaussian-2, Gaussian-3, Complete Basis Set-QB3, and Complete Basis Set-APNO Model Chemistries; Implications for Atmospheric Chemistry

A computational study of H-bonded networks in cyclic water clusters, (H2O)n (n = 3-12)

CONTEXT

We have performed a detailed MM and DFT investigation of neutral water clusters (H2O)n (n = 3-12). Our results show the trend of interaction energies in these clusters as a function of the size of the cluster. They show that the H-bond strength increases with cluster size and that the model of water is better described if two different partial charges are used on the hydrogen, depending on whether hydrogen is H-bonded or not. The average binding enthalpy change due to the formation of H-bonds between water molecules is found to be - 25.9 kJ mol-1 at B3LYP/aug-cc-pVDZ level of theory. We observe the formation of cyclic H-bonded networks through the analysis of frontier orbitals and IR vibrational frequencies spectra. For the water cluster with n = 11, we observe an unusual reduction of the bandgap indicative of a cyclic H-bonded network.

METHODS

Calculations were performed with the MMFF94 force field and the B3LYP method using various large basis sets. Molecular orbital diagrams and population analysis were done using standard tools in Gaussian.

Prebiotic dimer and trimer peptide formation in gas-phase atmospheric nanoclusters of water

Insight into the origin of prebiotic molecules is key to our understanding of how living systems evolved into the complex network of biological processes on Earth. By modelling diglycine and triglycine peptide formation in the prebiotic atmosphere, we provide a plausible pathway for peptide growth. By examining different transition states (TSs), we conclude that the formation of diglycine and triglycine in atmospheric nanoclusters of water in the prebiotic atmosphere kinetically favors peptide growth by an N-to-C synthesis of glycines through a trans conformation. Addition of water stabilizes the TS structures and lowers the Gibbs free activation energies. At temperatures that model the prebiotic atmosphere, the free energies of activation with a six water nanocluster as part of the TS are predicted to be 16 kcal mol-1 relative to the prereactive complex. Examination of the trans vs. cis six water transition states reveals that a homodromic water network that maximizes the acceptor/donor nature of the six waters is responsible for enhanced kinetic favorability of the trans N-to-C pathway. Compared to the non-hydrated trans TS, the trans six-water TS accelerates the reaction of diglycine and glycine to form triglycine by 13 orders of magnitude at 217 K. Nature uses the trans N-to-C pathway to synthesize proteins in the ribosome, and we note the similarities in hydrogen bond stabilization between the transition state for peptide synthesis in the ribosome and the transition states formed in nanoclusters of water in the same pathway. These results support the hypothesis that small oligomers formed in the prebiotic atmosphere and rained onto earth's surface.

The influence of a single water molecule on the reaction of BrO + HO2

The influence of a single water molecule on the BrO + HO2 hydrogen extraction reaction has been explored by taking advantage of CCSD(T)/aug-cc-pVTZ//B3LYP/6-311 +  + G(d,p) method. The reaction in the absence of water have two distinct kinds of H-extraction channels to generate HOBr + O2 (1Δg) and HBr + O3, and the channel of generation of HOBr + O2 (1Δg) dominated the BrO + HO2 reaction. The rate coefficient of the most feasible channel for the BrO + HO2 reaction in the absence of water is estimated to be 1.44 × 10-11 cm3 molecule-1 s-1 at 298.15 K, which is consistent with the experiment. The introduction of water made the reaction more complex, but the products are unchanged. Four distinct channels, beginning with HO2…H2O with BrO, H2O…HO2 with BrO, BrO…H2O with HO2, H2O…BrO with HO2 are researched. The most feasible channels, stemming from H2O…HO2 with BrO, and BrO…H2O with HO2, are much slower than the reaction of BrO + HO2 without water, respectively. Thus, the existence of water molecule takes a negative catalytic role for BrO + HO2 reaction.

Implementation of the self-consistent phonons method with ab initio potentials (AI-SCP)

The self-consistent phonon (SCP) method allows one to include anharmonic effects when treating a many-body quantum system at thermal equilibrium. The system is then described by an effective temperature-dependent harmonic Hamiltonian, which can be used to estimate its various dynamic and static properties. In this paper, we combine SCP with ab initio (AI) potential energy evaluation in which case the numerical bottleneck of AI-SCP is the evaluation of Gaussian averages of the AI potential energy and its derivatives. These averages are computed efficiently by the quasi-Monte Carlo method utilizing low-discrepancy sequences leading to a fast convergence with respect to the number, S, of the AI energy evaluations. Moreover, a further substantial (an-order-of-magnitude) improvement in efficiency is achieved once a numerically cheap approximation of the AI potential is available. This is based on using a perturbation theory-like (the two-grid) approach in which it is the average of the difference between the AI and the approximate potential that is computed. The corresponding codes and scripts are provided.

Hydrogen Bond Thermodynamics in Aqueous Acid Solutions: A Combined DFT and Classical Force-Field Approach

The thermodynamics of hydrogen bonds in aqueous and acidic solutions significantly impacts the kinetics and thermodynamics of acid reaction chemistry. We utilize in this work a multiscale approach, combining density functional theory (DFT) with classical molecular dynamics (MD) to model hydrogen bond thermodynamics in an acidic solution. Using thermodynamic cycles, we split the solution phase free energy into its gas phase counterpart plus solvation free energies. We validate this DFT/MD approach by calculating the aqueous phase hydrogen bond free energy between two water molecules (H₂O-···-H₂O), the free energy to transform an H₃O⁺ cation into an H₅O₂⁺ cation, and the hydrogen bond free energy of protonated water clusters (H₃O⁺-···-H₂O and H₅O₂⁺-···-H₂O). The computed equilibrium hydrogen bond free energy of H₂O-···-H₂O is remarkably accurate, especially considering the large individual contributions to the thermodynamic cycle. Turning to cations, we find the ion to be more stable than H₃O⁺ by roughly 1-2 k_BT. This small free energy difference allows for thermal fluctuation between the two idealized motifs, consistent with spectroscopic and simulation studies. Lastly, hydrogen bonding free energies between either H⁺ cation and H₂O in solution were found to be stronger than between two H₂O, though much less so than in vacuum because of dielectric screening in solution. Altogether, our results suggest the DFT/MD approach is promising for application in modeling hydrogen bonding and proton transfer thermodynamics in condensed phases.

Probing the Free Energy of Small Water Clusters: Revisiting Classical Nucleation Theory

By addressing the defects in classical nucleation theory (CNT), we develop an approach for extracting the free energy of small water clusters from nucleation rate experiments without any assumptions about the form of the cluster free energy. For temperatures higher than ∼250 K, the extracted free energies from experimental data points indicate that their ratio to the free energies predicted by CNT exhibits nonmonotonic behavior as the cluster size changes. We show that this ratio increases from almost zero for monomers and passes through (at least) one maximum before approaching one for large clusters. For temperatures lower than ∼250 K, the behavior of the ratio between extracted energies and CNT's prediction changes; it increases with cluster size, but it remains below one for almost all of the experimental data points. We also applied a state-of-the-art quantum mechanics model to calculate free energies of water clusters (2-14 molecules); the results support the observed change in behavior based on temperature, albeit for temperatures above and below ∼298 K. We compared two different model chemistries, DLPNO-CCSD(T)/CBS//ωB97xD/6-31++G** and G3, against each other and the experimental value for formation of the water dimer.

Amino Acids Compete with Ammonia in Sulfuric Acid-Based Atmospheric Aerosol Prenucleation: The Case of Glycine and Serine

We present a computational investigation of the sulfuric acid, glycine, serine, ammonia, and water system to understand if this system can form prenucleation clusters, which are precursors to larger aerosols in the atmosphere. We have performed a comprehensive configurational search of all possible clusters in this system, starting with the four different monomers and zero to five waters. Accurate Gibbs free energies of formation have been calculated with the DLPNO-CCSD(T)/complete basis set (CBS) method on ωb97xd/6-31++G** geometries. For the dry dimers of sulfuric acid, the weakest base, serine, is found to form the most stable complex, which is a consequence of the strong di-ionic complex formed between the bisulfate ion and the protonated serine cation. For the dry dimers without sulfuric acid, the glycine-serine complex is more stable than the glycine-ammonia or serine-ammonia complexes, stemming from the detailed structure and not related to base strength. For the larger complexes, sulfuric acid deprotonates and the proton is shifted to glycine, serine, or ammonia. The two amino acids and ammonia are almost interchangeable and there is no easy way to predict which molecule will be protonated without the calculated results. Assuming reasonable starting concentrations and a closed system of sulfuric acid, glycine, serine, ammonia, and five waters, we predict the concentrations of all possible complexes at two temperatures spanning the troposphere. The most negative ΔG° values are a function of the detailed molecular interactions of these clusters. These details are more important than the base strength of ammonia, glycine, and serine.

Monomers of Glycine and Serine Have a Limited Ability to Hydrate in the Atmosphere

The role of atmospheric aerosols on climate change is one of the biggest uncertainties in most global climate models. Organic aerosols have been identified as potential cloud condensation nuclei (CCN), and amino acids are organic molecules that could serve as CCN. Amino acids make up a significant portion of the total organic material in the atmosphere, and herein we present a systematic study of hydration for two of the most common atmospheric amino acids, glycine and serine. We compute DLPNO/CCSD(T)//M08-HX/MG3S thermodynamic properties and atmospheric concentrations of Gly(H₂O)_n and Ser(H₂O)_n, where n = 1-5. We predict that serine-water clusters have higher concentrations at n = 1 and 5, while glycine-water clusters have higher concentrations at n = 2-4. However, both glycine and serine are inferred to exist primarily in their nonhydrated monomer forms in the absence of other species such as sulfuric acid.

The favorable routes for the hydrolysis of CH2OO with (H2O)n (n = 1-4) investigated by global minimum searching combined with quantum chemical methods

The hydrolysis reaction of CH₂OO with water and water clusters is believed to be a dominant sink for the CH₂OO intermediate in the atmosphere. However, the favorable route for the hydrolysis of CH₂OO with water clusters is still unclear. Here global minimum searching using the Tsinghua Global Minimum program has been introduced to find the most stable geometry of the CH₂OO(H₂O)_n (n = 1-4) complex firstly. Then, based on these stable complexes, favorable hydrolysis of CH₂OO with (H₂O)_n (n = 1-4) has been investigated using the quantum chemical method of CCSD(T)-F12a/cc-pVDZ-F12//B3LYP/6-311+G(2d,2p) and canonical variational transition state theory with small curvature tunneling. The calculated results have revealed that, although the contribution of CH₂OO + (H₂O)₂ is the most obvious in the hydrolysis of CH₂OO with (H₂O)_n (n = 1-4), the hydrolysis of CH₂OO with (H₂O)₃ is not negligible in atmospheric gas-phase chemistry as its rate is close to the rate of the CH₂OO + H₂O reaction. The calculated results also show that, in a clean atmosphere, the CH₂OO + (H₂O)_n (n = 1-2) reaction competes well with the CH₂OO + SO₂ reaction at 298 K when the concentrations of (H₂O)_n (n = 1-2) range from 20% relative humidity (RH) to 100% RH, and SO₂ is 2.46 × 10¹¹ molecules per cm³. Meanwhile, when the RH is higher than 40%, it is a new prediction that the CH₂OO + (H₂O)₃ reaction can also compete well with the CH₂OO + SO₂ reaction at 298 K. Besides, Born-Oppenheimer molecular dynamics simulation results show that all the favorable channels of the CH₂OO + (H₂O)_n (n = 1-3) reaction cannot react on a time scale of 100 ps in the NVT simulation. However, the NVE simulation results show that the CH₂OO + (H₂O)₃ reaction can be finished well at 8.5 ps, indicating that the gas phase reaction of CH₂OO + (H₂O)₃ is not negligible in the atmosphere. Overall, the present results have provided a definitive example of how the favorable hydrolysis of important atmospheric species with (H₂O)_n (n = 1-4) takes place, which will stimulate one to consider the favorable hydrolysis of water and water clusters with other Criegee intermediates and other important atmospheric species.

NO3·-Initiated Gas-Phase Formation of Nitrated Phenolic Compounds in Polluted Atmosphere

Organic nitrogen (ON) compounds are key contents of particulate matter in the megacities of Asia. As a series of important ON, nitrated phenolic compounds (NPs) are of high concentration in the atmosphere, although their formation mechanism and role in particulate nucleation and growth are not fully understood. Herein, using a high level of quantum mechanical calculations, we explore the formation paths of NPs initiated by NO₃· radicals, where some common atmospheric species, such as H₂O, (H₂O)₂, NH₃, and dimethylamine (DMA), can act as molecular catalysts. The kinetic study predicts that the formation rate of methyl nitrophenols with the assistance of DMA and (H₂O)₂ can reach ∼10³ molecules·cm^-3·s^-1 in a polluted and humid atmosphere. The volatilities obtained from the empirical model show the formed NPs mainly belong to the intermediate and semivolatile organic compounds, which can participate in the growth process of aerosols rather than the early stage of cluster nucleation. Moreover, some NPs can be salified with atmospheric bases to further increase their contributions to the particulate formation.

A possible unaccounted source of atmospheric sulfate formation: amine-promoted hydrolysis and non-radical oxidation of sulfur dioxide

Numerous field and laboratory studies have shown that amines, especially dimethylamine (DMA), are crucial to atmospheric particulate nucleation. However, the molecular mechanism by which amines lead to atmospheric particulate formation is still not fully understood. Herein, we show that DMA molecules can also promote the conversion of atmospheric SO2 to sulfate. Based on ab initio simulations, we find that in the presence of DMA, the originally endothermic and kinetically unfavourable hydrolysis reaction between gaseous SO2 and water vapour can become both exothermic and kinetically favourable. The resulting product, bisulfite NH2(CH3)2 +·HSO3 -, can be readily oxidized by ozone under ambient conditions. Kinetic analysis suggests that the hydrolysis rate of SO2 and DMA with water vapour becomes highly competitive with and comparable to the rate of the reaction between SO2 and OH·, especially under the conditions of heavily polluted air and high humidity. We also find that the oxidants NO2 and N2O5 (whose role in sulfate formation is still under debate) appear to play a much less significant role than ozone in the aqueous oxidation reaction of SO2. The newly identified oxidation mechanism of SO2 promoted by both DMA and O3 provides another important new source of sulfate formation in the atmosphere.

Reaction mechanism, energetics, and kinetics of the water-assisted thioformaldehyde + ˙OH reaction and the fate of its product radical under tropospheric conditions

The reaction of thioformaldehyde with OH radical assisted by a single water molecule in the atmosphere is negligible.

Thermally Induced Hydrogen-Bond Rearrangements in Small Water Clusters and the Persistent Water Tetramer

Small water clusters absorb heat and catalyze pivotal atmospheric reactions. Yet, experiments produced conflicting results on water cluster distribution under atmospheric conditions. Additionally, it is unclear which "phase transitions" such clusters exhibit, at what temperatures, and what are their underlying molecular mechanisms. We find that logarithmically small tails in the radial probability densities of (H₂O) _n clusters (n = 2 - 6) provide direct testimony for such transitions. Using the best available water potential (MB-pol), an advanced thermostating algorithm (g-BAOAB), and sufficiently long trajectories, we map the "bifurcation", "melting", and (hitherto unexplored) "vaporization" transitions, finding that both melting and vaporization proceed via a "monomer on a ring" conformer, exhibiting huge distance fluctuations at the vaporization temperatures (T _v). T _v may play a role in determining the atmospheric cluster size distribution such that the dimer and tetramer, with their exceptionally low/high T _v values, are under/over-represented in these distributions, as indeed observed in nondestructive mass spectrometric measurements.

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.

Temperature Dependence of Intramolecular Vibrational Bands in Small Water Clusters

Cyclic water clusters are pivotal for understanding atmospheric reactions as well as liquid water, yet the temperature (T) dependence of their dynamics and spectroscopy is poorly studied. The development of highly accurate water potentials, such as MB-pol, partly rectifies this. It remains to account for the quantum nuclear effects (NQE), because quantum nuclear dynamics become increasingly inaccurate at low temperatures. From a practical point of view, we find that NQE can be accounted for simply by subtracting a constant from the frequencies obtained from the velocity autocorrelation functions (VACF) of classical nuclear dynamics, resulting in unprecedented agreement with experiment, mostly within 5 cm^-1. We have performed classical simulations of (H₂O)_n clusters (n = 2-5) from 20 K and up to their melting temperature, calculating both all-atom and partial VACF, thus generating the temperature dependence of the vibrational frequencies (IR and Raman bands). Focusing on the hydrogen-bonded (HBed) OH stretch and HOH bend, we find opposing T dependencies. The HBed OH modes blue shift linearly with T, attributed to ring expansion rather than any specific conformational change. The lowest-frequency Raman concerted mode is predicted to show the largest such shift. In contrast, the HOH bend undergoes a red-shift, with the highest frequency concerted band undergoing the largest red-shift. These results can be explained by a coupled-oscillator model for n hydrogen atoms on a ring, constrained to move either tangentially (stretch) or perpendicularly (bend) to the ring. With increasing temperature and weakening of HBs, the intrinsic force constant increases (stretch) or remains constant (bend), while the nearest-neighbor coupling constant decreases, and this results in the interesting behavior revealed herein. T-dependent Raman studies are required for testing some of these predictions.

Role of (H2O) n (n = 1-2) in the Gas-Phase Reaction of Ethanol with Hydroxyl Radical: Mechanism, Kinetics, and Products

The effect of water on the hydrogen abstraction mechanism and product branching ratio of CH₃CH₂OH + ^•OH reaction has been investigated at the CCSD(T)/aug-cc-pVTZ//BH&HLYP/aug-cc-pVTZ level of theory, coupled with the reaction kinetics calculations, implying the harmonic transition-state theory. Depending on the hydrogen sites in CH₃CH₂OH, the bared reaction proceeds through three elementary paths, producing CH₂CH₂OH, CH₃CH₂O, and CH₃CHOH and releasing a water molecule. Thermodynamic and kinetic results indicate that the formation of CH₃CHOH is favored over the temperature range of 216.7-425.0 K. With the inclusion of water, the reaction becomes quite complex, yielding five paths initiated by three channels. The products do not change compared with the bared reaction, but the preference for forming CH₃CHOH drops by up to 2%. In the absence of water, the room temperature rate coefficients for the formation of CH₂CH₂OH, CH₃CH₂O, and CH₃CHOH are computed to be 5.2 × 10^-13, 8.6 × 10^-14, and 9.0 × 10^-11 cm³ molecule^-1 s^-1, respectively. The effective rate coefficients of corresponding monohydrated and dihydrated reactions are 3-5 and 6-8 orders of magnitude lower than those of the unhydrated reaction, indicating that water has a decelerating effect on the studied reaction. Overall, the characterized effects of water on the thermodynamics, kinetics, and products of the CH₃CH₂OH + ^•OH reaction will facilitate the understanding of the fate of ethanol and secondary pollutants derived from it.

Catalytic effect of (H2O)n (n = 1–3) clusters on the HO2 + SO2 → HOSO + 3O2 reaction under tropospheric conditions

The HO₂ + SO₂ → HOSO + ³O₂ reaction without and with (H₂O)n (n = 1–3) have been investigated using CCSD(T)/CBS//M06-2X/aug-cc-pVTZ methods, and canonical variational transition state theory with small curvature tunneling.

Catalytic effect of (H2O) n (n = 1-3) on the HO2 + NH2 → NH3 + 3O2 reaction under tropospheric conditions

The effects of (H2O) n (n = 1-3) clusters on the HO2 + NH2 → NH3 + 3O2 reaction have been investigated by employing high-level quantum chemical calculations with M06-2X and CCSD(T) theoretical methods, and canonical variational transition (CVT) state theory with small curvature tunneling (SCT) correction. The calculated results show that two kinds of reaction, HO2⋯(H2O) n (n = 1-3) + NH2 and H2N⋯(H2O) n (n = 1-3) + HO2, are involved in the (H2O) n (n = 1-3) catalyzed HO2 + NH2 → NH3 + 3O2 reaction. Due to the fact that HO2⋯(H2O) n (n = 1-3) complexes have much larger stabilization energies and much higher concentrations than the corresponding complexes of H2N⋯(H2O) n (n = 1-3), the atmospheric relevance of the former reaction is more obvious with its effective rate constant of about 1-11 orders of magnitude faster than the corresponding latter reaction at 298 K. Meanwhile, due to the effective rate constant of the H2O⋯HO2 + NH2 reaction being respectively larger by 5-6 and 6-7 orders of magnitude than the corresponding reactions of HO2⋯(H2O)2 + NH2 and HO2⋯(H2O)3 + NH2, the catalytic effect of (H2O) n (n = 1-3) is mainly taken from the contribution of the water monomer. In addition, the enhancement factor of the water monomer is 10.06-13.30% within the temperature range of 275-320 K, which shows that at whole calculated temperatures, a positive water effect is obvious under atmospheric conditions.

The Role of (H₂O)1-2 in the CH₂O + ClO Gas-Phase Reaction

Mechanism and kinetic studies have been carried out to investigate whether one and two water molecules could play a possible catalytic role on the CH₂O + ClO reaction. Density functional theory combined with the coupled cluster theory were employed to explore the potential energy surface and the thermodynamics of this radical-molecule reaction. The reaction proceeded through four different paths without water and eleven paths with water, producing H + HCO(O)Cl, Cl + HC(O)OH, HCOO + HCl, and HCO + HOCl. Results indicate that the formation of HCO + HOCl is predominant both in the water-free and water-involved cases. In the absence of water, all the reaction paths proceed through the formation of a transition state, while for some reactions in the presence of water, the products were directly formed via barrierless hydrogen transfer. The rate constant for the formation of HCO + HOCl without water is 2.6 × 10-16 cm³ molecule-1 s-1 at 298.15 K. This rate constant is decreased by 9-12 orders of magnitude in the presence of water. The current calculations hence demonstrate that the CH₂O + ClO reaction is impeded by water.

Mechanistic Study on Water Splitting Reactions by Small Silicon Clusters Si3X, X = Si, Be, Mg, Ca

Interaction, dissociation, and dehydrogenation reactions of water monomer and dimer with pure and mixed tetrameric silicon clusters Si₃X with X = Si, Be, Mg, Ca were investigated using high accuracy quantum chemical calculations. While geometries were optimized using the DFT/B3LYP functional with the aug-cc-pVTZ basis set, reaction energy profiles were constructed making use of the coupled-cluster theory with extrapolation to complete basis set, CCSD(T)/CBS. Cleavage of the O-H bond in water dimer is found to be more favored than that of water monomer in the reaction with Si₄. The water acceptor monomer in water dimer performs as an internal catalyst facilitating H atom transfer to form H₂. Adsorption of water dimer on Si₃X clusters mostly takes place upon interaction of the donor water molecule with Si cluster. Water dimer adsorbs more strongly on Si₃M than on Si₄. The most stable complexes obtained upon interaction of water dimer with Si₃M mainly arise from M-O interaction in preference over a Si-O connection. Substitution of a Si atom in Si₄ by an earth alkaline metal induces a substantial reduction of the energy barrier for the (rate-limiting) first O-H bond cleavage of water dimer. The most remarkable achievement upon doping is a disappearance of the overall energy barrier for the initial O-H bond cleavage in water dimer. Of the three binary Si₃M clusters considered, dehydrogenation of water dimer driven by Si₃Be is the most kinetically and thermodynamically favorable pathway. In comparison to another cluster such as Al₆ and nanoparticles Ru₅₅, energy barriers for water dimer dissociation on Si₃M are much lower. The mixed clusters Si₃M turn out to be as efficient alternative reagents for O-H dissociation and hydrogen production from water dimer. This study proposes further searches for other mixed silicon clusters as realistic gas phase reagents for crucial dehydrogenation processes in such a way they can be prepared and conducted in experiment.

Role of the (H2O)n (n = 1–3) cluster in the HO2 + HO → 3O2 + H2O reaction: mechanistic and kinetic studies

Upon incorporation of the catalyst (H₂O)_n (n = 1–3) into the reaction HO₂ + HO → H₂O + ³O₂, the catalytic effects of water, water dimer, and water trimer mainly arise from the contribution of a single molecule of water vapor.

Hydrogen bond docking site competition in methyl esters

The OH⋯O hydrogen bonds in the 2,2,2-trifluoroethanol (TFE)-methyl ester complexes in the gas phase have been investigated by FTIR spectroscopy and DFT calculations. Methyl formate (MF), methyl acetate (MA), and methyl trifluoroacetate (MTFA) were chosen as the hydrogen bond acceptors. A dominant inter-molecular hydrogen bond was formed between the OH group of TFE and different docking sites in the methyl esters (carbonyl oxygen or ester oxygen). The competition of the two docking sites decides the structure and spectral properties of the complexes. On the basis of the observed red shifts of the OH-stretching transition with respect to the TFE monomer, the order of the hydrogen bond strength can be sorted as TFE-MA (119cm^-1)>TFE-MF (93cm^-1)>TFE-MTFA (44cm^-1). Combining the experimental infrared spectra with the DFT calculations, the Gibbs free energies of formation were determined to be 1.5, 4.5 and 8.6kJmol^-1 for TFE-MA, TFE-MF and TFE-MTFA, respectively. The hydrogen bonding in the MTFA complex is much weaker than those of the TFE-MA and TFE-MF complexes due to the effect of the CF₃ substitution on MTFA, while the replacement of an H atom with a CH₃ group in methyl ester only slightly increases the hydrogen bond strength. Topological analysis and localized molecular orbital energy decomposition analysis was also applied to compare the interactions in the complexes.

A prion-like mechanism for the propagated misfolding of SOD1 from in silico modeling of solvated near-native conformers

A prion-like mechanism has been developed to explain the observed promotion of amyloid aggregation caused by conversion of structurally intact SOD1 to a misfolded form. Superoxide dismutase [Cu-Zn], or SOD1, is a homo-dimeric protein that functions as an antioxidant by scavenging for superoxide. The misfolding and aggregation of SOD1 is linked to inherited, or familial, amyotrophic lateral sclerosis (FALS), a progressive and fatal neurodegenerative disease. Aberrant SOD1 folding has also been strongly implicated in disease causation for sporadic ALS, or SALS, which accounts for ~90% of ALS cases. Studies have found that mutant, misfolded SOD1 can convert wtSOD1 in a prion-like fashion, and that misfolded wtSOD1 can be propagated by release and uptake of protein aggregates. Here it is demonstrated that enervating the SOD1 electrostatic loop can lead to an experimentally observed gain of interaction (GOI) responsible for the formation of SOD1 amyloid-like filaments. This enervation is caused in turn by the formation of transient, non-obligate oligomers between pathogenic SOD1 mutants and wt SOD1.

Contribution of methane sulfonic acid to new particle formation in the atmosphere

Methane sulfonic acid (MSA) is present in substantial concentrations in the gas phase over oceans and coastal regions. We present an investigation into the contribution of MSA to new particle formation with the common atmospheric aerosol nucleation precursors including MSA, methanol, formic acid, acetone, dimethylether, formaldehyde, methyl formate, by making use a quantum chemical approach. Density functional theory calculations indicate that these bimolecular complexes are characterized by the presence of strong inter-molecular hydrogen bonds (SOH⋯O) with large binding energies and thermodynamic equilibrium constants. Topological analysis employing quantum theory of atoms in molecules shows that the charge density of the SOH⋯O hydrogen bonds of the MSA complexes falls in the range of hydrogen bonding criteria, but the Laplacian at bond critical points exceeds the range, which is due to the strong hydrogen bonding interactions. In all the studied complexes, the electrostatic interactions are found to be the main attractive force by localized molecular orbital energy decomposition analysis. All these indicate the environmental fate of MSA could play the role of nucleation centers in new particle formation. The effect of the atmospheric heights (0-12 km) was also considered. The Gibbs free energy of formation decreases with the increase of the atmospheric height owing to the decrease of the atmospheric temperature and pressure. The calculated Gibbs free energies of formation within the atmospheric temperature and pressure range could help to understand the atmospheric pollution.

Hydrogen Bonding Interaction between Atmospheric Gaseous Amides and Methanol

Amides are important atmospheric organic–nitrogen compounds. Hydrogen bonded complexes of methanol (MeOH) with amides (formamide, N-methylformamide, N,N-dimethylformamide, acetamide, N-methylacetamide and N,N-dimethylacetamide) have been investigated. The carbonyl oxygen of the amides behaves as a hydrogen bond acceptor and the NH group of the amides acts as a hydrogen bond donor. The dominant hydrogen bonding interaction occurs between the carbonyl oxygen and the OH group of methanol as well as the interaction between the NH group of amides and the oxygen of methanol. However, the hydrogen bonds between the CH group and the carbonyl oxygen or the oxygen of methanol are also important for the overall stability of the complexes. Comparable red shifts of the C=O, NH- and OH-stretching transitions were found in these MeOH–amide complexes with considerable intensity enhancement. Topological analysis shows that the electron density at the bond critical points of the complexes fall in the range of hydrogen bonding criteria, and the Laplacian of charge density of the O–H∙∙∙O hydrogen bond slightly exceeds the upper value of the Laplacian criteria. The energy decomposition analysis further suggests that the hydrogen bonding interaction energies can be mainly attributed to the electrostatic, exchange and dispersion components.

An improved model of homogeneous nucleation for high supersaturation conditions: aluminum vapor

A novel model of stationary nucleation, treating the thermodynamic functions of small clusters, has been built. The model is validated against the experimental data on the nucleation rate of water vapor obtained in a broad range of supersaturation values (S = 10-120), and, at high supersaturation values, it reproduces the experimental data much better than the traditional classical nucleation model. A comprehensive analysis of the nucleation of aluminum vapor with the usage of developed stationary and non-stationary nucleation models has been performed. It has been shown that, at some value of supersaturation, there exists a double potential nucleation barrier. It has been revealed that the existence of this barrier notably delayed the establishment of a stationary distribution of subcritical clusters. It has also been demonstrated that the non-stationary model of the present work and the model of liquid-droplet approximation predict different values of nucleation delay time, τ_s. In doing so, the liquid-droplet model can underestimate notably (by more than an order of magnitude) the value of τ_s.

Infrared spectroscopic probing of dimethylamine clusters in an Ar matrix

Amines have many atmospheric sources and their clusters play an important role in aerosol nucleation processes. Clusters of a typical amine, dimethylamine (DMA), of different sizes were measured with matrix isolation IR (infrared) and NIR (near infrared) spectroscopy. The NIR vibrations are more separated and therefore it is easier to distinguish different sizes of clusters in this region. The DMA clusters, up to DMA tetramer, have been optimized using density functional methods, and the geometries, binding energies and thermodynamic properties of DMA clusters were obtained. The computed frequencies and intensities of NH-stretching vibrations in the DMA clusters were used to interpret the experimental spectra. We have identified the fundamental transitions of the bonded NH-stretching vibration and the first overtone transitions of the bonded and free NH-stretching vibration in the DMA clusters. Based on the changes in vibrational intensities during the annealing processes, the growth of clusters was clearly observed. The results of annealing processes indicate that DMA molecules tend to form larger clusters with lower energies under matrix temperatures, which is also supported by the calculated reaction energies of cluster formation.

Hydrogen bonding in cyclic complexes of carboxylic acid–sulfuric acid and their atmospheric implications

Carboxylic acids form cyclic ring structures with sulfuric acid and they could potentially be important in new particle formation.

The catalytic effect of water, water dimers and water trimers on H2S +3O2formation by the HO2+ HS reaction under tropospheric conditions

Catalyst X (X = H₂O, (H₂O)₂and (H₂O)₃) is incorporated into the channel of H₂S +³O₂formation and the catalytic effect of water, water dimers and water trimers is mainly taken from the contribution of a single water vapor molecule.