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Rare base-pairs consists of guanine (G) paired with rare bases, such as 5-methylcytosine (5-meCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-caCyt), and 5-formylcytosine (5-fCyt), have become the focus of epigenetic research because they can be used as markers to detect some chronic diseases and cancers. However, the correlation detection of these rare base-pairs is limited, which in turn limits the development of diagnostic tests and devices. Herein, the interaction of rare base-pairs adsorbed on pure and B/N-doped γ-graphyne (γ-GY) nanosheets was explored using the density functional theory. The calculated adsorption energy showed that the system of rare base-pairs on B-doped γ-GY is more stable than that on pure γ-GY or N-doped γ-GY. Translocation time values indicate that rare base-pairs can be successfully distinguished as the difference in their translocation times is very large for pure and B/N-doped γ-GY nanosheets. Meanwhile, sensing response values illustrated that pure and B-doped γ-GY are the best for G-5-hmCyt adsorption, while the N-doped γ-GY is the best for G-Cyt adsorption. The findings indicate that translocation times and sensing response can be used as detection indexes for pure and B/N doped γ-GY, which will provide a new way for experimental scientists to develop the biosensor components. [ABSTRACT FROM AUTHOR]

The products resulting from the reactions between atmospheric acids and SO3 have a catalytic effect on the formation of new particles in aerosols. However, the SO3 + HCl reaction in the gas-phase and at the air–water interface has not been considered. Herein, this reaction was explored exhaustively by using high-level quantum chemical calculations and Born Oppenheimer molecular dynamics (BOMD) simulations. The quantum calculations show that the gas-phase reaction of SO3 + HCl is highly unlikely to occur under atmospheric conditions with a high energy barrier of 22.6 kcal mol−1. H2O and (H2O)2 play obvious catalytic roles in reducing the energy barrier of the SO3 + HCl reaction by over 18.2 kcal mol−1. The atmospheric lifetimes of SO3 show that the (H2O)2-assisted reaction dominates over the H2O-assisted reaction within the altitude range of 0–5 km, whereas the H2O-assisted reaction is more favorable within an altitude range of 10–50 km. BOMD simulations show that H2O-induced formation of the ClSO3−⋯H3O+ ion pair and HCl-assisted formation of the HSO4−⋯H3O+ ion pair were identified at the air–water interface. These routes followed a stepwise reaction mechanism and proceeded at a picosecond time scale. Interestingly, the formed ClSO3H in the gas phase has a tendency to aggregate with sulfuric acids, ammonias, and water molecules to form stable clusters within 40 ns simulation time, while the interfacial ClSO3− and H3O+ can attract H2SO4, NH3, and HNO3 for particle formation from the gas phase to the water surface. Thus, this work will not only help in understanding the SO3 + HCl reaction driven by water molecules in the gas-phase and at the air–water interface, but it will also provide some potential routes of aerosol formation from the reaction between SO3 and inorganic acids. [ABSTRACT FROM AUTHOR]

Liu et al. (Proc. Natl. Acad. Sci. U. S. A, 2019, 116, 24966–24971) showed that at an altitude of 0 km, the reaction of SO3 with CH3OH to form CH3OSO3H reduces the amount of H2SO4 produced by the hydrolysis of SO3 in regions polluted with CH3OH. However, the influence of the water molecule has not been fully considered yet, which will limit the accuracy of calculating the loss of SO3 in regions polluted with CH3OH. Here, the influence of water molecules on the SO3 + CH3OH reaction in the gas phase and at the air–water interface was comprehensively explored by using high-level quantum chemical calculations and Born–Oppenheimer molecular dynamics (BOMD) simulations. Quantum chemical calculations show that both pathways for the formation of CH3OSO3H and H2SO4 with water molecules have greatly lowered energy barriers compared to the naked SO3 + CH3OH reaction. The effective rate coefficients reveal that H2O-catalyzed CH3OSO3H formation (a favorable route for CH3OSO3H formation) can be competitive with H2O-assisted H2SO4 formation (a favorable process for H2SO4 formation) at high altitudes up to 15 km. BOMD simulations found that H2O-induced formation of the CH3OSO3−⋯H3O+ ion pair and CH3OH-assisted formation of HSO4− and H3O+ ions were observed at the droplet surface. These interfacial routes followed a loop-structure or chain reaction mechanism and proceeded on a picosecond time scale. These results will contribute to better understanding of SO3 losses in the polluted areas of CH3OH. [ABSTRACT FROM AUTHOR]

Herein, the reaction mechanisms and kinetics for the HO2 + SO3 → HOSO2 + 3O2 reaction catalyzed by a water monomer, a water dimer and small clusters of sulfuric acid have been studied theoretically by quantum chemical methods and the Master Equation/Rice–Ramsperger–Kassel–Marcus (ME/RRKM) rate calculations. The calculated results show that when H2O is introduced into the HO2 + SO3 reaction, it not only enhances the stability of the reactant complexes by 9.0 kcal mol−1 but also reduces the energy of the transition state by 8.7 kcal mol−1. As compared with H2O, catalysts (H2O)2, H2SO4, H2SO4⋯H2O and (H2SO4)2 are more effective energetically, which not only results from a higher binding energy of 21.3–26.0 kcal mol−1 for the reactant complexes but also from a reduction of the energy of the transition states by 8.6–17.2 kcal mol−1. Effective rate constant calculations show that, as compared with H2O, catalysts (H2O)2, H2SO4, H2SO4⋯H2O and (H2SO4)2 can never become more efficient catalysts within the altitude range of 0–15 km due to their relatively lower concentrations. Besides, at 0 km altitude, the enhancement factor for the H2O and (k′WD1/ktot) (H2O)2-assisted HO2 + SO3 reaction within the temperature range of 280–320 K was respectively calculated to be 0.31%–0.34% and 0.16%–0.27%, while the corresponding enhancement factor of H2O and (H2O)2 at higher altitudes of 5–15 km was respectively found only 0.002%–0.12% and 0.00001%–0.022%, indicating that the contributions of H2O and (H2O)2 are not apparent in the gas-phase reaction of HO2 with SO3 especially at higher altitude. Overall, the present work will give a new insight into how a water monomer, a water dimer and small clusters of sulfuric acid catalyze the HO2 + SO3 → HOSO2 + 3O2 reaction. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The adsorption of O2 on the Cu2O(111) surface at different coverages has been studied by spin-polarized density functional theory (DFT+U) calculations and atomic thermodynamics. It has been found that the dissociative O2 prefers to adsorb on the reconstructed Cu2O(111) surface at low coverages (1/4 to 1 monolayer), while totally dissociative and mixed molecular and dissociative O2 prefers to adsorb on the reconstructed Cu2O(111) surface thermodynamically at higher coverages (5/4 to 7/4 monolayers). More interesting is that the CuO film can be automatically formed on the Cu2O(111) surface that was induced by the surface reconstruction of the Cu2O(111) surface and adsorption of four dissociative O2 molecules (1 monolayer), which agrees well with the recent experimental results. Along higher coverages of O2 adsorption (5/4 to 7/4 monolayers), much stronger surface reconstruction and relaxation was found. The probability distribution of different single-O2 adsorbed states on the Cu2O(111) surface as a function of temperature was analyzed using a Boltzmann model. The adsorption mechanism of O2 on the Cu2O(111) surface was analyzed using the phase diagram and compared with other metal oxides. [ABSTRACT FROM AUTHOR]

To study the catalytic effects of (H2O)n (n = 1–3), the mechanisms of the reaction HO2 + HO →3O2 + H2O without and with (H2O)n (n = 1–3) have been investigated theoretically at the CCSD(T)/aug-cc-pVTZ//M06-2X/aug-cc-pVTZ level of theory, coupled with rate constant calculations using the conventional transition state theory. Our results show that upon incorporation of (H2O)n (n = 1–3) into the channel of H2O + 3O2 formation, two different reactions, i.e. HO + HO2…(H2O)n (n = 1–3) and HO2 + HO…(H2O)n (n = 1–3), have been observed, and these two reactions are competitive with each other. The catalytic effects of (H2O)n (n = 1–3) mainly arise from the contribution of a single water vapor molecule; this is because the effective rate constants with water are respectively larger by 2–3 and 3–4 orders of magnitude than those of the reactions with (H2O)2 and (H2O)3. Furthermore, the catalytic effects of the water monomer mainly arise from the H2O…HO2 + HO reaction, and the enhancement factor of this reaction is obvious within the temperature range of 240.0–425.0 K, with the branching ratio (k′(RW)/ktot) of 17.27–80.77%. Overall, the present results provide a new example of how water and water clusters catalyze gas phase reactions under atmospheric conditions. [ABSTRACT FROM AUTHOR]

In this article, the reaction mechanisms of H2S + 3O2 formation by the HO2 + HS reaction without and with catalyst X (X = H2O, (H2O)2 and (H2O)3) have been investigated theoretically at the CCSD(T)/6-311++G(3df,2pd)//B3LYP/6-311+G(2df,2p) level of theory, coupled with rate constant calculations by using conventional transition state theory. Our results show that in the presence of catalyst X (X = H2O, (H2O)2 and (H2O)3) into the channel of H2S + 3O2 formation, the reactions between the SH radical and HO2…(H2O)n (n = 1–3) complexes are more favorable than the corresponding reactions of the HO2 radical with HS…(H2O)n (n = 1–3) complexes due to the lower barrier of the former reactions and the higher concentrations of HO2…(H2O)n (n = 1–3) complexes. Meanwhile, the catalytic effect of water, water dimers and water trimers is mainly taken from the contribution of a single water vapor molecule, since the total effective rate constant of HO2…H2O + HS and H2O…HO2 + HS reactions was, respectively, larger by 7–9 and 9–12 orders of magnitude than that of SH + HO2…(H2O)2 and SH + HO2…(H2O)3 reactions. Besides, the enhancement factor of water vapor is only 0.37% at 240 K, while at high temperatures, such as 425 K, the positive water vapor effect is enhanced up to 38.00%, indicating that at high temperatures the positive water effect is obvious under atmospheric conditions. Overall, these results show how water and water clusters catalyze the gas phase reactions under atmospheric conditions. [ABSTRACT FROM AUTHOR]

The effect of a single water molecule on the HO2 + NO2 hydrogen abstraction reaction has been investigated by employing B3LYP and CCSD(T) theoretical approaches with the aug-cc-pVTZ basis set. The reaction without water has three types of reaction channels on both singlet and triplet potential energy surfaces, depending on how the HO2 radical approaches NO2. These correspond to the formation of trans-HONO + O2, cis-HONO + O2 and HNO2 + O2. Our calculated results show that triplet reaction channels are favorable and their total rate constant, at 298 K, is 2.01 × 10−15 cm3 molecule−1 s−1, which is in good agreement with experimental values. A single water molecule affects each one of these triplet reaction channels in the three different reactions of H2O…HO2 + NO2, HO2…H2O + NO2 and NO2…H2O + HO2, depending on the way the water interacts. Interestingly, the water molecule in these reactions not only acts as a catalyst giving the same products as the naked reaction, but also as a reactant giving the product of HONO2 + H2O2. The total rate constant of the H2O…HO2 + NO2 reaction is estimated to be slower than the naked reaction by 6 orders of magnitude at 298 K. However, the total rate constants of the HO2…H2O + NO2 and NO2…H2O + HO2 reactions are faster than the naked reaction by 4 and 3 orders of magnitude at 298 K, respectively. Their total effective rate constant is predicted to be 1.2 times that of the corresponding total rate constant without water at 298 K, which is in agreement with the prediction reported by Li et al. (science, 2014, 344, 292–296). [ABSTRACT FROM AUTHOR]

The gas-phase hydrogen abstraction reactions of CH3O2and HO2with HO2in the presence and absence of a single water molecule have been studied at the CCSD(T)/6-311++G(3d,2p)//B3LYP/6-311G(2d,2p) level of theory. The calculated results show that the process for O3formation is much faster than that for 1O2and 3O2formation in the water-catalyzed CH3O2+ HO2reaction. This is different from the results for the non-catalytic reaction of CH3O2+ HO2, in which almost only the process for 3O2formation takes place. Unlike CH3O2+ HO2reaction in which the preferred process is different in the catalytic and non-catalytic conditions, the channel for 3O2formation is the dominant in both catalytic and non-catalytic HO2+ HO2reactions. Furthermore, the calculated total CVT/SCT rate constants for water-catalyzed and non-catalytic title reactions show that the water molecule doesn't contribute to the rate of CH3O2+ HO2reaction though the channel for O3formation in this water-catalyzed reaction is more kinetically favorable than its non-catalytic process. Meanwhile, the water molecule plays an important positive role in increasing the rate of HO2+ HO2reaction. These results are in good agreement with available experiments. [ABSTRACT FROM AUTHOR]

SO 3 is an important reactive species in sulfur cycle and sulfuric acid formation processes and its reactions with some functional group substances, such as H 2 O, NH 3 , CH 3 OH, 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 SO 3 and monoethanolamide (MEA) was investigated in the gas phase and on water droplets. The quantum chemical calculations indicate that the gas-phase reactions of SO 3 with the OH and NH 2 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 SO 3 + 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 HOCH 2 CH 2 NHSO 3 H to NH 2 CH 2 CH 2 OSO 3 H. The Born Oppenheimer molecular dynamics simulations on a water droplet show that the routes of the NH 2 CH 2 CH 2 OSO 3 - ⋯H 3 O + ion pair, HSO 4 - and HOCH 2 CH 2 NH 3 + ions and zwitterionic formations of HOCH 2 CH 2 NH 2 + -SO 3 - and SO 3 - -OCH 2 CH 2 NH 3 + 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 HOCH 2 CH 2 NHSO 3 H and NH 2 CH 2 CH 2 OSO 3 H have a potential ability to participate in the formation of new particles as they can form larger clusters with H 2 SO 4 , NH 3 and H 2 O molecules within 20 ns. Thus, the present study will not only give new insight into the reaction between SO 3 and multifunctional compounds, but also provide a new potential formation mechanism for particles resulting from the loss of SO 3 .

The products resulting from the reactions between atmospheric acids and SO 3 have a catalytic effect on the formation of new particles in aerosols. However, the SO 3 + HCl reaction in the gas-phase and at the air-water interface has not been considered. Herein, this reaction was explored exhaustively by using high-level quantum chemical calculations and Born Oppenheimer molecular dynamics (BOMD) simulations. The quantum calculations show that the gas-phase reaction of SO 3 + HCl is highly unlikely to occur under atmospheric conditions with a high energy barrier of 22.6 kcal mol -1 . H 2 O and (H 2 O) 2 play obvious catalytic roles in reducing the energy barrier of the SO 3 + HCl reaction by over 18.2 kcal mol -1 . The atmospheric lifetimes of SO 3 show that the (H 2 O) 2 -assisted reaction dominates over the H 2 O-assisted reaction within the altitude range of 0-5 km, whereas the H 2 O-assisted reaction is more favorable within an altitude range of 10-50 km. BOMD simulations show that H 2 O-induced formation of the ClSO 3 - ⋯H 3 O + ion pair and HCl-assisted formation of the HSO 4 - ⋯H 3 O + ion pair were identified at the air-water interface. These routes followed a stepwise reaction mechanism and proceeded at a picosecond time scale. Interestingly, the formed ClSO 3 H in the gas phase has a tendency to aggregate with sulfuric acids, ammonias, and water molecules to form stable clusters within 40 ns simulation time, while the interfacial ClSO 3 - and H 3 O + can attract H 2 SO 4 , NH 3 , and HNO 3 for particle formation from the gas phase to the water surface. Thus, this work will not only help in understanding the SO 3 + HCl reaction driven by water molecules in the gas-phase and at the air-water interface, but it will also provide some potential routes of aerosol formation from the reaction between SO 3 and inorganic acids.

Liu et al. ( Proc. Natl. Acad. Sci. U. S. A , 2019, 116 , 24966-24971) showed that at an altitude of 0 km, the reaction of SO 3 with CH 3 OH to form CH 3 OSO 3 H reduces the amount of H 2 SO 4 produced by the hydrolysis of SO 3 in regions polluted with CH 3 OH. However, the influence of the water molecule has not been fully considered yet, which will limit the accuracy of calculating the loss of SO 3 in regions polluted with CH 3 OH. Here, the influence of water molecules on the SO 3 + CH 3 OH reaction in the gas phase and at the air-water interface was comprehensively explored by using high-level quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations. Quantum chemical calculations show that both pathways for the formation of CH 3 OSO 3 H and H 2 SO 4 with water molecules have greatly lowered energy barriers compared to the naked SO 3 + CH 3 OH reaction. The effective rate coefficients reveal that H 2 O-catalyzed CH 3 OSO 3 H formation (a favorable route for CH 3 OSO 3 H formation) can be competitive with H 2 O-assisted H 2 SO 4 formation (a favorable process for H 2 SO 4 formation) at high altitudes up to 15 km. BOMD simulations found that H 2 O-induced formation of the CH 3 OSO 3 - ⋯H 3 O + ion pair and CH 3 OH-assisted formation of HSO 4 - and H 3 O + ions were observed at the droplet surface. These interfacial routes followed a loop-structure or chain reaction mechanism and proceeded on a picosecond time scale. These results will contribute to better understanding of SO 3 losses in the polluted areas of CH 3 OH.

Herein, the reaction mechanisms and kinetics for the HO 2 + SO 3 → HOSO 2 + 3 O 2 reaction catalyzed by a water monomer, a water dimer and small clusters of sulfuric acid have been studied theoretically by quantum chemical methods and the Master Equation/Rice-Ramsperger-Kassel-Marcus (ME/RRKM) rate calculations. The calculated results show that when H 2 O is introduced into the HO 2 + SO 3 reaction, it not only enhances the stability of the reactant complexes by 9.0 kcal mol -1 but also reduces the energy of the transition state by 8.7 kcal mol -1 . As compared with H 2 O, catalysts (H 2 O) 2 , H 2 SO 4 , H 2 SO 4 ⋯H 2 O and (H 2 SO 4 ) 2 are more effective energetically, which not only results from a higher binding energy of 21.3-26.0 kcal mol -1 for the reactant complexes but also from a reduction of the energy of the transition states by 8.6-17.2 kcal mol -1 . Effective rate constant calculations show that, as compared with H 2 O, catalysts (H 2 O) 2 , H 2 SO 4 , H 2 SO 4 ⋯H 2 O and (H 2 SO 4 ) 2 can never become more efficient catalysts within the altitude range of 0-15 km due to their relatively lower concentrations. Besides, at 0 km altitude, the enhancement factor for the H 2 O and ( k ' WD1 / k tot ) (H 2 O) 2 -assisted HO 2 + SO 3 reaction within the temperature range of 280-320 K was respectively calculated to be 0.31%-0.34% and 0.16%-0.27%, while the corresponding enhancement factor of H 2 O and (H 2 O) 2 at higher altitudes of 5-15 km was respectively found only 0.002%-0.12% and 0.00001%-0.022%, indicating that the contributions of H 2 O and (H 2 O) 2 are not apparent in the gas-phase reaction of HO 2 with SO 3 especially at higher altitude. Overall, the present work will give a new insight into how a water monomer, a water dimer and small clusters of sulfuric acid catalyze the HO 2 + SO 3 → HOSO 2 + 3 O 2 reaction.

NH 2 SO 3 H can directly participate in H 2 SO 4 -(CH 3 ) 2 NH-based cluster formation, and thereby substantially enhance the cluster formation rate. Herein, the reaction mechanisms and kinetics for the formation of NH 2 SO 3 H from the hydrolysis of HNSO 2 without and with neutral (H 2 O, (H 2 O) 2 , and (H 2 O) 3 ), basic (NH 3 and CH 3 NH 2 ), and acidic (HCOOH, H 2 SO 4 , H 2 SO 4 ⋯H 2 O, and (H 2 SO 4 ) 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 NH 2 SO 3 H was more strongly bonded to neutral, basic, and acidic catalysts than to the reactants HNSO 2 and H 2 O. This reveals that the reported neutral, basic, and acidic catalysts promote the formation of NH 2 SO 3 H from the hydrolysis of HNSO 2 both kinetically and thermodynamically. Kinetic calculations using the master equation showed that (H 2 O) 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 × 10 9 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.

The hydrolysis reaction of CH 2 OO with water and water clusters is believed to be a dominant sink for the CH 2 OO intermediate in the atmosphere. However, the favorable route for the hydrolysis of CH 2 OO 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 CH 2 OO(H 2 O) n (n = 1-4) complex firstly. Then, based on these stable complexes, favorable hydrolysis of CH 2 OO with (H 2 O) 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 CH 2 OO + (H 2 O) 2 is the most obvious in the hydrolysis of CH 2 OO with (H 2 O) n (n = 1-4), the hydrolysis of CH 2 OO with (H 2 O) 3 is not negligible in atmospheric gas-phase chemistry as its rate is close to the rate of the CH 2 OO + H 2 O reaction. The calculated results also show that, in a clean atmosphere, the CH 2 OO + (H 2 O) n (n = 1-2) reaction competes well with the CH 2 OO + SO 2 reaction at 298 K when the concentrations of (H 2 O) n (n = 1-2) range from 20% relative humidity (RH) to 100% RH, and SO 2 is 2.46 × 10 11 molecules per cm 3 . Meanwhile, when the RH is higher than 40%, it is a new prediction that the CH 2 OO + (H 2 O) 3 reaction can also compete well with the CH 2 OO + SO 2 reaction at 298 K. Besides, Born-Oppenheimer molecular dynamics simulation results show that all the favorable channels of the CH 2 OO + (H 2 O) 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 CH 2 OO + (H 2 O) 3 reaction can be finished well at 8.5 ps, indicating that the gas phase reaction of CH 2 OO + (H 2 O) 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 (H 2 O) 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.

The H 2 O 2 + HO → HO 2 + H 2 O reaction is an important reservoir for both radicals of HO and HO 2 catalyzing the destruction of O 3 . Here, this reaction assisted by NH 3 and HCOOH catalysts was explored using the CCSD(T)-F12a/cc-pVDZ-F12//M06-2X/aug-cc-pVTZ method and canonical variational transition state theory with small curvature tunneling. Two possible sets of mechanisms, (i) one-step routes and (ii) stepwise processes, are possible. Our results show that in the presence of both NH 3 and HCOOH catalysts under relevant atmospheric temperature, mechanism (i) is favored both energetically and kinetically than the corresponding mechanism (ii). At 298 K, the relative rate for mechanism (i) in the presence of NH 3 (10, 2900 ppbv) and HCOOH (10 ppbv) is respectively 3-5 and 2-4 orders of magnitude lower than that of the water-catalyzed reaction. This is due to a comparatively lower concentration of NH 3 and HCOOH than H 2 O which indicates the positive water effect under atmospheric conditions. Although NH 3 and HCOOH catalysts play a negligible role in the reservoir for both radicals of HO and HO 2 catalyzing the destruction of O 3 , the current study provides a comprehensive example of how acidic and basic catalysts assisted the gas-phase reactions., Competing Interests: The authors declare no competing financial interest., (This journal is © The Royal Society of Chemistry.)

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.

Quantum chemical calculations at M06-2X and CCSD(T) levels of theory have been performed to investigate the effects of H 2 O, NH 3 , and HCOOH on the HO 2 + Cl → HCl + O 2 reaction. The results show that catalyzed reactions with three catalysts could proceed through two different mechanisms, namely a stepwise route and one elementary step, where the former reaction is more favorable than the latter. Meanwhile, for the stepwise route, a single hydrogen atom transfer pathway in the presence of all catalysts has more advantages than the respective double hydrogen atom transfer pathway. Then, the relative impacts of catalysts under tropospheric conditions were investigated by considering the temperature dependence of the rate constants and the altitude dependence of catalyst concentrations. The calculated results show that at 0 km altitude, the HO 2 + Cl → HCl + O 2 reaction with catalysts, such as H 2 O, NH 3 , or HCOOH, cannot compete with the reaction without a catalyst, as the effective rate constant with a catalyst is smaller by 2-6 orders of magnitude than the naked reaction within the temperature range 280-320 K. The calculated results also show that at altitudes of 5, 10 and 15 km, the effective rate constant of the HCOOH-catalyzed reaction increases obviously with an increase in altitude. At 15 km altitude, its value is up to 9.63 × 10 -11 cm 3 per molecule per s, which is close to the corresponding value of the reaction without a catalyst, showing that the contribution of HCOOH to the HO 2 + Cl → HCl + O 2 reaction cannot be neglected at high altitudes. The new findings in this investigation are not only of great necessity and importance for elucidating the gas-phase reaction of HO 2 with Cl in the presence of acidic, neutral and basic catalysts, but are also of great interest for understanding the importance of other types of hydrogen abstraction in the atmosphere., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

The effects of (H 2 O) n ( n = 1-3) clusters on the HO 2 + NH 2 → NH 3 + 3 O 2 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, HO 2 ⋯(H 2 O) n ( n = 1-3) + NH 2 and H 2 N⋯(H 2 O) n ( n = 1-3) + HO 2 , are involved in the (H 2 O) n ( n = 1-3) catalyzed HO 2 + NH 2 → NH 3 + 3 O 2 reaction. Due to the fact that HO 2 ⋯(H 2 O) n ( n = 1-3) complexes have much larger stabilization energies and much higher concentrations than the corresponding complexes of H 2 N⋯(H 2 O) 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 H 2 O⋯HO 2 + NH 2 reaction being respectively larger by 5-6 and 6-7 orders of magnitude than the corresponding reactions of HO 2 ⋯(H 2 O) 2 + NH 2 and HO 2 ⋯(H 2 O) 3 + NH 2 , the catalytic effect of (H 2 O) 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., Competing Interests: The authors declare no conflicts of interest., (This journal is © The Royal Society of Chemistry.)

The adsorption of O2 on the Cu2O(111) surface at different coverages has been studied by spin-polarized density functional theory (DFT+U) calculations and atomic thermodynamics. It has been found that the dissociative O2 prefers to adsorb on the reconstructed Cu2O(111) surface at low coverages (1/4 to 1 monolayer), while totally dissociative and mixed molecular and dissociative O2 prefers to adsorb on the reconstructed Cu2O(111) surface thermodynamically at higher coverages (5/4 to 7/4 monolayers). More interesting is that the CuO film can be automatically formed on the Cu2O(111) surface that was induced by the surface reconstruction of the Cu2O(111) surface and adsorption of four dissociative O2 molecules (1 monolayer), which agrees well with the recent experimental results. Along higher coverages of O2 adsorption (5/4 to 7/4 monolayers), much stronger surface reconstruction and relaxation was found. The probability distribution of different single-O2 adsorbed states on the Cu2O(111) surface as a function of temperature was analyzed using a Boltzmann model. The adsorption mechanism of O2 on the Cu2O(111) surface was analyzed using the phase diagram and compared with other metal oxides.

To study the catalytic effects of (H 2 O) n (n = 1-3), the mechanisms of the reaction HO 2 + HO → 3 O 2 + H 2 O without and with (H 2 O) n (n = 1-3) have been investigated theoretically at the CCSD(T)/aug-cc-pVTZ//M06-2X/aug-cc-pVTZ level of theory, coupled with rate constant calculations using the conventional transition state theory. Our results show that upon incorporation of (H 2 O) n (n = 1-3) into the channel of H 2 O + 3 O 2 formation, two different reactions, i.e. HO + HO 2 (H 2 O) n (n = 1-3) and HO 2 + HO(H 2 O) n (n = 1-3), have been observed, and these two reactions are competitive with each other. The catalytic effects of (H 2 O) n (n = 1-3) mainly arise from the contribution of a single water vapor molecule; this is because the effective rate constants with water are respectively larger by 2-3 and 3-4 orders of magnitude than those of the reactions with (H 2 O) 2 and (H 2 O) 3 . Furthermore, the catalytic effects of the water monomer mainly arise from the H 2 OHO 2 + HO reaction, and the enhancement factor of this reaction is obvious within the temperature range of 240.0-425.0 K, with the branching ratio (k'(RW)/k tot ) of 17.27-80.77%. Overall, the present results provide a new example of how water and water clusters catalyze gas phase reactions under atmospheric conditions.

Alcohol-induced liver injury (ALD) shows obvious metabolic disorders, categorized by a wide range of metabolite abnormalities. High-throughput metabolomics technology appears to be an appropriate solution. In this study, a urine metabolic profile was assessed using a UPLC-Q-TOF/HDMS (liquid chromatography coupled to high resolution mass spectrometry) approach to investigate the underlying molecular mechanisms of ALD and the therapeutic effect of geniposide. The endogenous low-molecular-weight metabolites in the mouse model of ALD were observed and 48 specific biomarkers were identified. Geniposide was found to have a regulatory effect on 32 of them. Furthermore, targeted analysis of biomarkers showed clear separation between the model and geniposide treatment group. Fifteen biomarkers with high contribution to group differentiation were screened out. Also, a comprehensive analysis of a significant disturbance of multiple metabolic pathways indicated that geniposide could modify abnormal metabolism due to ethanol exposure, during which disorders relating to amino acid metabolism and the oxidative stress state could be alleviated. At the same time, accessory examinations, including plasma biochemical indicators and liver tissue pathological analysis, showed similar results. It was suggested that geniposide was effective as a hepatoprotective agent against ethanol-induced liver damage by re-balancing a wide range of metabolic disorders.

In this article, the reaction mechanisms of H2S + (3)O2 formation by the HO2 + HS reaction without and with catalyst X (X = H2O, (H2O)2 and (H2O)3) have been investigated theoretically at the CCSD(T)/6-311++G(3df,2pd)//B3LYP/6-311+G(2df,2p) level of theory, coupled with rate constant calculations by using conventional transition state theory. Our results show that in the presence of catalyst X (X = H2O, (H2O)2 and (H2O)3) into the channel of H2S + (3)O2 formation, the reactions between the SH radical and HO2(H2O)n (n = 1-3) complexes are more favorable than the corresponding reactions of the HO2 radical with HS(H2O)n (n = 1-3) complexes due to the lower barrier of the former reactions and the higher concentrations of HO2(H2O)n (n = 1-3) complexes. Meanwhile, the catalytic effect of water, water dimers and water trimers is mainly taken from the contribution of a single water vapor molecule, since the total effective rate constant of HO2H2O + HS and H2OHO2 + HS reactions was, respectively, larger by 7-9 and 9-12 orders of magnitude than that of SH + HO2(H2O)2 and SH + HO2(H2O)3 reactions. Besides, the enhancement factor of water vapor is only 0.37% at 240 K, while at high temperatures, such as 425 K, the positive water vapor effect is enhanced up to 38.00%, indicating that at high temperatures the positive water effect is obvious under atmospheric conditions. Overall, these results show how water and water clusters catalyze the gas phase reactions under atmospheric conditions.

The effect of a single water molecule on the HO2 + NO2 hydrogen abstraction reaction has been investigated by employing B3LYP and CCSD(T) theoretical approaches with the aug-cc-pVTZ basis set. The reaction without water has three types of reaction channels on both singlet and triplet potential energy surfaces, depending on how the HO2 radical approaches NO2. These correspond to the formation of trans-HONO + O2, cis-HONO + O2 and HNO2 + O2. Our calculated results show that triplet reaction channels are favorable and their total rate constant, at 298 K, is 2.01 × 10(-15) cm(3) molecule(-1) s(-1), which is in good agreement with experimental values. A single water molecule affects each one of these triplet reaction channels in the three different reactions of H2O···HO2 + NO2, HO2···H2O + NO2 and NO2···H2O + HO2, depending on the way the water interacts. Interestingly, the water molecule in these reactions not only acts as a catalyst giving the same products as the naked reaction, but also as a reactant giving the product of HONO2 + H2O2. The total rate constant of the H2O···HO2 + NO2 reaction is estimated to be slower than the naked reaction by 6 orders of magnitude at 298 K. However, the total rate constants of the HO2···H2O + NO2 and NO2···H2O + HO2 reactions are faster than the naked reaction by 4 and 3 orders of magnitude at 298 K, respectively. Their total effective rate constant is predicted to be 1.2 times that of the corresponding total rate constant without water at 298 K, which is in agreement with the prediction reported by Li et al. (science, 2014, 344, 292-296).

The gas-phase hydrogen abstraction reactions of CH(3)O(2) and HO(2) with HO(2) in the presence and absence of a single water molecule have been studied at the CCSD(T)/6-311++G(3d,2p)//B3LYP/6-311G(2d,2p) level of theory. The calculated results show that the process for O(3) formation is much faster than that for (1)O(2) and (3)O(2) formation in the water-catalyzed CH(3)O(2) + HO(2) reaction. This is different from the results for the non-catalytic reaction of CH(3)O(2) + HO(2), in which almost only the process for (3)O(2) formation takes place. Unlike CH(3)O(2) + HO(2) reaction in which the preferred process is different in the catalytic and non-catalytic conditions, the channel for (3)O(2) formation is the dominant in both catalytic and non-catalytic HO(2) + HO(2) reactions. Furthermore, the calculated total CVT/SCT rate constants for water-catalyzed and non-catalytic title reactions show that the water molecule doesn't contribute to the rate of CH(3)O(2) + HO(2) reaction though the channel for O(3) formation in this water-catalyzed reaction is more kinetically favorable than its non-catalytic process. Meanwhile, the water molecule plays an important positive role in increasing the rate of HO(2) + HO(2) reaction. These results are in good agreement with available experiments.