Pre-reactive Complex Research Articles

Low temperature gas phase reaction rate coefficient measurements: Toward modeling of stellar winds and the interstellar medium

AbstractStellar winds of Asymptotic Giant Branch (AGB) stars are responsible for the production of ∼85% of the gas molecules in the interstellar medium (ISM), and yet very few of the gas phase rate coefficients under the relevant conditions (10 – 3000 K) needed to model the rate of production and loss of these molecules in stellar winds have been experimentally measured. If measured at all, the value of the rate coefficient has often only been obtained at room temperature, with extrapolation to lower and higher temperatures using the Arrhenius equation. However, non-Arrhenius behavior has been observed often in the few measured rate coefficients at low temperatures. In previous reactions studied, theoretical simulations of the formation of long-lived pre-reaction complexes and quantum mechanical tunneling through the barrier to reaction have been utilized to fit these non-Arrhenius behaviours of rate coefficients.Reaction rate coefficients that were predicted to produce the largest change in the production/loss of Complex Organic Molecules (COMs) in stellar winds at low temperatures were selected from a sensitivity analysis. Here we present measurements of rate coefficients using a pulsed Laval nozzle apparatus with the Pump Laser Photolysis - Laser Induced Fluorescence (PLP-LIF) technique. Gas flow temperatures between 30 – 134 K have been produced by the University of Leeds apparatus through the controlled expansion of N2 or Ar gas through Laval nozzles of a range of Mach numbers between 2.49 and 4.25.Reactions of interest include those of OH, CN, and CH with volatile organic species, in particular formaldehyde, a molecule which has been detected in the ISM. Kinetics measurements of these reactions at low temperatures will be presented using the decay of the radical reagent. Since formaldehyde and the formal radical (HCO) are potential building blocks of COMs in the interstellar medium, low temperature reaction rate coefficients for their production and loss can help to predict the formation pathways of COMs observed in the interstellar medium.

Tropospheric degradation of propanethiol initiated by Cl radicals: Kinetics, mechanism and computational studies

Abstract The rate coefficient for the reaction of Cl radicals with n-propanethiol has been determined at 298 K and atmospheric pressure to be: (2.37 ± 0.66) × 10−10 cm3 molecule−1 s−1. Dipropyl disulfide, sulfur dioxide, and propionaldehyde, were observed as main reaction products. The yield of formation of dipropyl disulfide was quantified. Potential energy surfaces and thermodynamic data at 298 K were calculated for the gauche and trans conformers of n-propanethiol using the CBS-QB3, M06-D3/cc-pVTZ and M06-2X/cc-pVTZ levels of theory. We concluded that the formation of the prereactive complex in which chlorine is ‘bound’ to the sulfur atom is the decisive step in the reaction paths.

A theoretical study on the kinetics of multichannel Multiwell reaction of H2S(1A1) with HO2(2A′′)

The mechanism and kinetics of the reaction of hydrogen sulphide (H2S(1A1)) with hydroperoxyl radical (HO2(2A″)) on the lowest doublet potential energy surface have been theoretically studied. The potential energy surface for possible pathways has been investigated by employing Complete Basis Set (CBS), DFT, and CCSD(T) methods. Three possible pathways are suggested for the title reaction. The most probable entrance channel consists of formation of a hydrogen-bonded pre-reaction complex (vdw1) and two energised intermediates. Multichannel RRKM-Steady State Approximation and CVT calculations have been carried out to compute the rate constants over a broad range of temperature from 200 K to 3000 K to cover the atmospheric and combustion conditions and pressure from 0.1 to 2000 Torr. No sign of pressure dependence was observed for the title reaction over the stated range of pressure. We have shown that the major products of the title reaction are H2O2 and SH while at higher temperatures, formation of the other products such as H2O, HOS, HSOH and OH are feasible, too. Our calculated overall rate constant is in agreement with the reported experimental data in the literature.

Experimental and computational studies of Criegee intermediate reactions with NH3 and CH3NH2.

Ammonia and amines are emitted into the troposphere by various natural and anthropogenic sources, where they have a significant role in aerosol formation. Here, we explore the significance of their removal by reaction with Criegee intermediates, which are produced in the troposphere by ozonolysis of alkenes. Rate coefficients for the reactions of two representative Criegee intermediates, formaldehyde oxide (CH2OO) and acetone oxide ((CH3)2COO) with NH3 and CH3NH2 were measured using cavity ring-down spectroscopy. Temperature-dependent rate coefficients, k(CH2OO + NH3) = (3.1 ± 0.5) × 10-20T2 exp(1011 ± 48/T) cm3 s-1 and k(CH2OO + CH3NH2) = (5 ± 2) × 10-19T2 exp(1384 ± 96/T) cm3 s-1 were obtained in the 240 to 320 K range. Both the reactions of CH2OO were found to be independent of pressure in the 10 to 100 Torr (N2) range, and average rate coefficients k(CH2OO + NH3) = (8.4 ± 1.2) × 10-14 cm3 s-1 and k(CH2OO + CH3NH2) = (5.6 ± 0.4) × 10-12 cm3 s-1 were deduced at 293 K. An upper limit of ≤2.7 × 10-15 cm3 s-1 was estimated for the rate coefficient of the (CH3)2COO + NH3 reaction. Complementary measurements were performed with mass spectrometry using synchrotron radiation photoionization giving k(CH2OO + CH3NH2) = (4.3 ± 0.5) × 10-12 cm3 s-1 at 298 K and 4 Torr (He). Photoionization mass spectra indicated production of NH2CH2OOH and CH3N(H)CH2OOH functionalized organic hydroperoxide adducts from CH2OO + NH3 and CH2OO + CH3NH2 reactions, respectively. Ab initio calculations performed at the CCSD(T)(F12*)/cc-pVQZ-F12//CCSD(T)(F12*)/cc-pVDZ-F12 level of theory predicted pre-reactive complex formation, consistent with previous studies. Master equation simulations of the experimental data using the ab initio computed structures identified submerged barrier heights of -2.1 ± 0.1 kJ mol-1 and -22.4 ± 0.2 kJ mol-1 for the CH2OO + NH3 and CH2OO + CH3NH2 reactions, respectively. The reactions of NH3 and CH3NH2 with CH2OO are not expected to compete with its removal by reaction with (H2O)2 in the troposphere. Similarly, losses of NH3 and CH3NH2 by reaction with Criegee intermediates will be insignificant compared with reactions with OH radicals.

Computational kinetics of the hydrogen abstraction reactions of n-propanol and iso-propanol by OH radical.

Propanol (n-propanol or iso-propanol (i-propanol)) is a promising clean-burning oxygenated fuel component and fuel additive. Understanding its reactions with OH radical is of great significance in both combustion and atmospheric chemistry. In this work, we calculate the rate constants and branching ratios of the hydrogen abstraction reactions of n-propanol and i-propanol by OH radical in a broad temperature range of 63-2000 K using the competitive canonical unified statistical (CCUS) model. For both n-propanol and i-propanol, in both the high-pressure and low-pressure limits, the total reaction rate constants show a significant negative dependence on temperature in the low temperature regime and approach the capture rate for the formation of the pre-reactive complex when temperature is down to the ultracold regime. Several factors, tunneling, remarkable anharmonicity of high-frequency modes of transition states, and the presence of reaction channels with a negative free energy barrier, contribute to this phenomenon. We observe pressure-dependent branching fractions at T < ∼400 K for n-propanol or T < 200 K for i-propanol, and at higher temperatures, the branching fractions are independent of the pressure. The alpha-hydrogen (Hα) abstraction with a lower barrier is not always dominant as traditionally expected. The H-abstraction from the terminal carbon (Ht) of i-propanol, with a higher barrier, is dominant above 1000 K because of the remarkably larger effect of multi-structural and torsional (MS-T) anharmonicity. In the pressure-dependent ultra-low temperature regime and high-pressure limit, the beta-hydrogen (Hβ) abstraction and the hydrogen abstraction from the hydroxyl group (HO) become dominant for n-propanol and i-propanol, respectively, mainly due to the tunneling effect.

Photoelectron spectroscopic study of I-·ICF3: a frontside attack SN2 pre-reaction complex.

Photodetachment and 2D photoelectron spectra of the mass-selected I-·CF3I complex are presented together with electronic structure calculations. Calculations show that the I- is located at the iodine side of CF3I. Vertical and adiabatic detachment energies were measured at 4.03 and approximately 3.8 eV, respectively. The photoelectron spectra and molecular orbitals show a significant covalent bonding character in the cluster. The presence of electronic excited states is observed. Below threshold, iodide is generated which can be assigned to the photoexcitation of degenerate charge-transfer bands from the off-axis p-orbitals localised on iodide. Near the onset of two spin-orbit thresholds, bright excited states are seen in the experiment and calculations. Excitation of these leads to the formation of slow electrons. The spectroscopy of I-·CF3I is compared to the well-studied I-·CH3I cluster, a pre-reaction complex in the text-book I- + CH3I SN2 reaction. Despite the reversed stereodynamics (i.e. inversion of the CX3 between X = H and F) of the SN2 reaction, striking similarities are seen. Both complexes possess charge transfer excited states near their respective vertical detachment energies and exhibit vibrational structure in their photoelectron spectra. The strong binding is consistent with observations in crossed molecular beam studies and molecular dynamics simulations that suggest that iodine as a leaving group in an SN2 reaction affects the reaction dynamics.

Ab Initio, Transition State Theory, and Kinetic Modeling Study of the HO2-Assisted Keto-Enol Tautomerism Propen-2-ol + HO2 ⇔ Acetone + HO2 under Combustion, Atmospheric, and Interstellar Conditions.

Keto-enol tautomerisms are important reactions in gaseous and liquid systems with implications in different chemical environments, but their kinetics have not been widely investigated. These reactions can proceed via a unimolecular process or may be catalyzed by another molecule. This work presents a theoretical study of the HO2-catalyzed tautomerism that converts propen-2-ol into acetone at conditions relevant to combustion, atmospheric and interstellar chemistry. We performed CCSD(T)/aug-cc-pVTZ//M06-2X/cc-pVTZ ab initio and multistructural torsional variational transition state theory calculations to compute the forward and reverse rate constants. These rate constants have not been investigated previously, and modelers approximate the kinetics by comparison to analogue reactions. Two features of the potential energy surface of the studied tautomerism are highlighted. First, the HO2 radical exhibits a pronounced catalytic effect by inducing a double hydrogen atom transfer reaction with a much lower barrier than that of the unimolecular process. Second, a prereactive complex is formed with a strong OH···π hydrogen bond. The role of the studied reaction under combustion conditions has been assessed via chemical kinetic modeling of 2-butanol (a potential alternative fuel) oxidation. The HO2-assisted process was found to not be competitive with the unimolecular and HCOOH-assisted tautomerisms. The rate constants for the formation of the prereactive complex were calculated with the variable reaction coordinate transition state theory, and pressure effects were estimated with the system-specific quantum Rice-Ramsperger-Kassel theory; this allowed us to investigate the role of the complex by using the canonical unified statistical model. The formation and equilibration of the prereactive complex, which is also important at low pressures, enhances the reactivity by inducing a large tunneling effect that leads to a significant increase of the rate constants at cold and ultracold temperatures. These findings may help to understand and model the fate of complex organic molecules in the interstellar medium, and suggest an alternative route for the high energy barrier keto-enol tautomerism which otherwise is not kinetically favored at low temperatures.

Key mechanistic details of paraoxon decomposition by polyoxometalates: Critical role of para-nitro substitution

We report computational studies of (O,O-dimethyl)-(O-4-nitrophenyl)-phosphate (DMNP) and (O,O-dimethyl)-(O-phenyl)-phosphate (DMPP) decomposition by the Zr-substituted Polyoxometalate {α-PW11O39Zr(μ-OH)(H2O)}4−, which has been recently shown to be a catalytic active species in the reaction of (Et2NH2)8[{α-PW11O39Zr(μ-OH)(H2O)}2]·7H2O with nerve agents. We studied two possible mechanisms of this reaction described as “hydrolysis first” and “OH-transfer first”. Both reaction pathways are initiated from the same pre-reaction complex (H2O)-(OH)-POM-(nerve agent). The “hydrolysis first” pathway starts by the concerted dissociation of the adsorbed water molecule and nucleophilic addition of the resulting OH group to the nerve agent. Conversely, the “OH-transfer first” pathway starts by nucleophilic addition of the Zr-coordinated OH ligand to the phosphorus of the nerve agent simulant. Calculations show that the “OH-transfer first” pathway exhibits a lower energy barrier for the decomposition of DMPP by ZrPOM. Thus, the presence of a hydroxo ligand in the coordination sphere of Zr(IV) introduces a mechanism switch from “hydrolysis first” [which was recently reported for the Sarin (GB) decomposition mechanism by the hexaniobate POM Cs8Nb6O19] to “OH-transfer first”. These findings imply that the pH of the catalytic solution could play a critical role and potentially control the mechanism of nerve agent and simulant decomposition by polyoxometalates. We also predict and corroborate that the presence of a strong electron-withdrawing para-substituent in the substrate phenyl group accelerates this reaction: DMNP decomposition by ZrPOM occurs with a smaller rate-limiting energy barrier. The calculations reveal several factors of the DMNP decomposition by the Zr(IV)-substituted polyoxometalates that provide design elements of Zr-based materials (including MOFs and POMs) for catalytic CWA decomposition under ambient conditions.

Competition of F/OH-Induced SN2 and Proton-Transfer Reactions with Increased Solvation.

The potential energy profiles of F/OH-induced nucleophilic substitution (SN2) and proton-transfer (PT) channels evolving with solvation for reactions of F-(H2O) n=1-2 + CH3I were characterized using B3LYP/ECP/d method. The hydrogen-bonded F-(H2O) n---HCH2I prereaction complex at the entrance of potential energy surface (PES) has a significant role on the reaction dynamics for each channel. Among the above three channels, the F-SN2 channel is the most preferred and OH-SN2 could be competitive. In contrast, the PT channel will occur at much higher collision energy. Importantly, for each channel, the central barrier is gradually increased with the addition of water molecules. This phenomenon indicates that the reactivity will decrease with degrees of solvation and this has been confirmed by experiment and direct dynamics simulations. Moreover, compared with the previous trajectory simulations, a non-IRC behavior has been uncovered. The water delivering process from fluorine to iodine side as illustrated on PES is barely observed, and instead, the reaction tends to dehydrate before passing through the SN2 barrier and proceeds with the less hydrated pathway in order to weaken the steric effect. The work presented here shows the comprehensive potential energy surfaces and structures information on the F-SN2, PT, and OH-SN2 channels, and predict their competitive relationship, which would be helpful for better understanding the dynamics behavior of the title and analogous reactions.

Quantum chemical and master equation study of OH + CH2O → H2O + CHO reaction rates in supercritical CO2 environment

AbstractWe investigated the reaction rates of OH + CH2O → H2O + CHO at CO2 pressures of up to 1000 atm with and without CO2 molecule included in a reactive complex. Both mechanisms begin with formation of the hydrogen‐bonded prereactive complexes. Our ab initio calculations indicate a possibility of catalytic effect, predicting an activation barrier that one order of magnitude lower when the CO2 molecule is involved. To verify this effect, we use the Rice–Ramsperger–Kassel–Marcus theory and solve unimolecular master equations in the steady‐state approximation. We assume the equilibrium between prereactive complexes and reactants and compare the bimolecular reaction rates for the two mechanisms. The catalyzed reaction mechanism is found to be faster at higher CO2 pressures and lower temperatures, when prereactive complexes have nonnegligible concentration. Therefore, this catalytic effect may be important for this reactive process in room temperature supercritical CO2 solvent, but is unlikely to play a role during oxy‐combustion.

A quantum mechanical insight into SN2 reactions: Semiclassical initial value representation calculations of vibrational features of the Cl-⋯CH3Cl pre-reaction complex with the VENUS suite of codes.

The role of vibrational excitation of reactants in driving reactions involving polyatomic species has been often studied by means of classical or quasi-classical trajectory simulations. We propose a different approach based on investigation of vibrational features of the Cl-⋯CH3Cl pre-reaction complex for the Cl- + CH3Cl SN2 reaction. We present vibrational power spectra and frequency estimates for the title pre-reaction complex calculated at the level of classical, semiclassical, and second-order vibrational perturbation theory on a pre-existing analytical potential energy surface. The main goals of the paper are the study of anharmonic effects and understanding of vibrational couplings that permit energy transfer between the collisional kinetic energy and the internal vibrations of the reactants. We provide both classical and quantum pictures of intermode couplings and show that the SN2 mechanism is favored by the coupling of a C-Cl bend involving the Cl- projectile with the CH3 rocking motion of the target molecule. We also illustrate how the routines needed for semiclassical vibrational spectroscopy simulations can be interfaced in a user-friendly way to pre-existing molecular dynamics software. In particular, we present an implementation of semiclassical spectroscopy into the VENUS suite of codes, thus providing a useful computational tool for users who are not experts of semiclassical dynamics.

Rapid Acceleration of Hydrogen Atom Abstraction Reactions of OH at Very Low Temperatures through Weakly Bound Complexes and Tunneling.

A generally accepted principle of chemical kinetics is that a reaction will be very slow at low temperatures if there is an activation barrier on the potential energy surface to form products. However, this Account shows that the reverse is true for gas-phase hydrogen abstraction reactions of the hydroxyl radical, OH, with organic molecules with which it can form a weakly bound (5-30 kJ mol-1) hydrogen-bonded complex. For hydrogen atom abstraction reactions of OH with volatile organic compounds (VOCs) containing alcohol, ether, carbonyl, and ester functional groups, the reaction accelerates rapidly at very low temperatures, with rate coefficients, k, that can be up to a 1000 times faster than those at room temperature, despite the barrier to products. The OH radical is a crucial intermediate in Earth's atmosphere, combustion processes, and the chemistry of the interstellar medium, where temperatures can reach as low as 10 K, so this behavior has very important implications for gas-phase chemistry in space. The key point is that at low temperatures the lifetime of the OH-VOC complex against re-dissociation back to reactants becomes much longer, and hence the probability of quantum mechanical tunneling under the reaction barrier to form products becomes much higher. These observations were made possible by using Laval nozzles to generate uniform supersonic flows at extremely low temperatures so that condensation of the reagents at reactor walls is avoided. In this Account, the use of laser flash-photolysis combined with laser-induced fluorescence spectroscopy within Laval flows is described to study the unusual kinetics of this type of reaction at temperatures down to 21 K and demonstrate the rapid upturn in the rate coefficient. For the reaction of OH with CH3OH, further evidence for the precomplex and tunneling mechanism comes from observation of the CH3O reaction product at very low temperatures, despite it being formed over the higher barrier to reaction. The experimental observations are supported by theoretical calculations using the MESMER master equation package to calculate k( T) and product yields as a function of temperature and which make use of potential energy surfaces determined using ab initio methods. The CH3O product is formed over a narrower barrier with a larger imaginary frequency and is calculated to be the sole product at very low temperatures. The kinetics of the OH reaction with CH3OH were measured to be independent of pressure, consistent with a tunneling mechanism rather than any collisional stabilization of the prereactive complex. In this Account, we collate available kinetic data and show that this newly discovered mechanism for H atom transfer reactions appears to be generally applicable for reactions of OH with organic molecules containing oxygenated functional groups, which have been observed in space by radio-astronomy. Rather than being ignored for a range of interstellar environments, these OH reactions are now being included in chemical networks in space and have been shown to significantly influence the abundance of OH, the organic molecules themselves, and reaction products and provide novel routes to forming even more complex functional groups, for example, precursors to prebiotic molecules.

Mechanistic study of the reaction of methyl peroxy radical (CH3O2) with formaldehyde (CH2O)

ABSTRACTA direct dynamic study on the reactions of CH3O2 + CH2O was carried out over the temperature range of 300–1500 K. All stationary points were calculated with the M06-2X/6-311++G(d,p) level of theory and identified for local minimum. The energetic parameters were refined at QCISD (T)/cc-pVTZ and CCSD (T)/cc-pVTZ levels of theory. Three channels were explored and a reaction of hydrogen abstraction from CH2O by CH3O2 was identified as dominant channel which involves the formation of a prereactive complex in the entrance channel. The rate coefficient of the dominant channel was calculated with TST and TST/Eck and the Eckart tunnelling effect is only important over the lower temperature region. The calculated rate coefficient of the dominant channel has positive temperature dependence and agrees reasonably with the available literature data.

Catalytic Effect of Carbon Dioxide on Reaction OH + CO → H + CO2 in Supercritical Environment: Master Equation Study

We investigated the reaction rates of OH + CO → H + CO2 in supercritical CO2 environment with and without additional CO2 molecule included in reactive complex. Ab initio potential energy surfaces previously reported a lower activation barrier and hence a catalytic effect of additional CO2 molecule. Here we solve the steady-state unimolecular master equations based on the Rice-Ramsperger-Kassel-Marcus theory (RRKM) and compare the rates for the two mechanisms. We found that the alternative reaction mechanism becomes faster at high pressure and low temperature, when the concentration of prereactive complex with additional CO2 molecule becomes appreciable. Therefore, this catalytic effect may be important for the chemical processes in CO2 solvent but is unlikely to play a role during combustion.

Mechanism of Nucleophilic Fluorination Facilitated by a Pyrene‐tagged Ionic Liquids: Synergistic Effects of Pyrene–Metal Cation π‐Interactions

We examine the mechanism of SN2 fluorination promoted by a pyrene‐tagged ionic liquid (PIL). Comparison is made for contact ion‐pair (CIP) vs. solvent‐separated ion‐pair (SSIP) mechanism by calculating the Gibbs free energies of pre‐reaction complexes and Gibbs free energies of activation G‡ for both processes. We find that the CIP mechanism is preferred for [PIL + MF + C3H7OMs] (M = Cs, K) system. SN2 fluorination of the [1‐Butyl‐3‐methylimidazolium (bmim)‐CsF] system is also studied in order to estimate the efficacy of PIL vs. more conventional ionic liquid [bmim][OMs]. The better promotion of the reaction by PIL is attributed to π interactions between the metal cation and pyrene, giving G‡ that is smaller (by approximately 1.3 kcal/mol) than that for the [bmim‐CsF] system, in excellent agreement with experimental observations.

Transition State Structure and Mechanism of the Reaction of Hydroxybenzenes with N-Centered Radical in Non-Ionizing Media

Experimentaly and theoretically, using the method of density functional theory, the structure of 2,2'-diphenyl-1-picrylhydrazyl radical and the mechanism of its reaction with di- and trihydroxybenzenes in non-ionizing media have been investigated. It was established that in nonpolar solvents the elimination of hydrogen atom from hydroxybenzene by the radical occurs as a conjugate transfer of proton and electron, as confirmed by the existence of a deuterium isotope effect as well as characteristic geometrical and electronic parameters of pre-reaction complexes and transition states of the reaction.

Mechanistic Study of the Reactions of Methyl Peroxy Radical with Methanol or Hydroxyl Methyl Radical.

An ab initio and direct dynamic study of the reactions of CH3O2 + CH3OH and CH3O2 + CH2OH has been carried out over the temperature range of 300-1500 K. All stationary points were calculated at the MP2/aug-cc-pVTZ level of theory for CH3O2 + CH3OH or at the M06-2X/MG3S level of theory for CH3O2 + CH2OH and identified for the local minimum. The energetic parameters were refined at the QCISD(T)/cc-pVTZ and CCSD(T)/aug-cc-pVTZ levels of theory. For the reaction of CH3OO + CH3OH, two hydrogen abstraction channels producing CH3OOH + CH2OH (R1) and CH3OOH + CH3O (R2) were confirmed. These two channels consist of the same reversible first step involving the formation of a prereactive complex in the entrance channel. The rate constants of these two channels have been calculated by canonical transition station theory (TST) and canonical variational transition station theory (VTST) with Eckart tunneling correction and compared with the available literature data. The positive temperature dependence of the rate constants was observed. The tunneling effect is important at low temperature and decreases with an increase of the temperature. The contribution of R1 to the total rate constant is dominant, with branching ratios of 0.93 at 500 K and 0.67 at 1000 K, although the branching ratio for R2 increases dramatically with the increase of the temperature from 500 K. For the reaction of CH3OO + CH2OH, eight channels were explored on the lowest singlet and triplet surfaces, and an excited intermediate was found to be formed on the singlet surface. A channel proceeding through the formation of an excited intermediate followed by its impulsive dissociation was confirmed as the dominant channels with a branching ratio more than 0.99 in the temperature range of 300-1500 K, where products of CH3O and OCH2OH were given. The rate constant of the dominant channel calculated by multichannel RRKM-VTST is comparable with the available literature data.

Insight into Chemistry on Cloud/Aerosol Water Surfaces

Cloud/aerosol water surfaces exert significant influence over atmospheric chemical processes. Atmospheric processes at the water surface are observed to follow mechanisms that are quite different from those in the gas phase. This Account summarizes our recent findings of new reaction pathways on the water surface. We have studied these surface reactions using Born-Oppenheimer molecular dynamics simulations. These studies provide useful information on the reaction time scale, the underlying mechanism of surface reactions, and the dynamic behavior of the product formed on the aqueous surface. According to these studies, the aerosol water surfaces confine the atmospheric species into a specific orientation depending on the hydrophilicity of atmospheric species or the hydrogen-bonding interactions between atmospheric species and interfacial water. As a result, atmospheric species are activated toward a particular reaction on the aerosol water surface. For example, the simplest Criegee intermediate (CH2OO) exhibits high reactivity toward the interfacial water and hydrogen sulfide, with the reaction times being a few picoseconds, 2-3 orders of magnitude faster than that in the gas phase. The presence of interfacial water molecules induces proton-transfer-based stepwise pathways for these reactions, which are not possible in the gas phase. The strong hydrophobicity of methyl substituents in larger Criegee intermediates (>C1), such as CH3CHOO and (CH3)2COO, blocks the formation of the necessary prereaction complexes for the Criegee-water reaction to occur at the water droplet surface, which lowers their proton-transfer ability and hampers the reaction. The aerosol water surface provides a solvent medium for acids (e.g., HNO3 and HCOOH) to participate in reactions via mechanisms that are different from those in the gas and bulk aqueous phases. For example, the anti-CH3CHOO-HNO3 reaction in the gas phase follows a direct reaction between anti-CH3CHOO and HNO3, whereas on a water surface, the HNO3-mediated stepwise hydration of anti-CH3CHOO is dominantly observed. The high surface/volume ratio of interfacial water molecules at the aerosol water surface can significantly lower the energy barriers for the proton transfer reactions in the atmosphere. Such catalysis by the aerosol water surface is shown to cause the barrier-less formation of ammonium bisulfate from hydrated NH3 and SO3 molecules rather than from the reaction of H2SO4 with NH3. Finally, an aerosol water droplet is a polar solvent, which would favorably interact with high polarity substrates. This can accelerate interconversion of different conformers (e.g., anti and syn) of atmospheric species, such as glyoxal, depending on their polarity. The results discussed here enable an improved understanding of atmospheric processes on the aerosol water surface.

Cracking the DNA Code for V(D)J Recombination

To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have determined crystal and cryo-EM structures of RAG1/2 with DNA in the pre-reaction and hairpin-forming complexes up to 2.75Å resolution. Both protein and DNA exhibit structural plasticity and undergo dramatic conformational changes. Coding-flank DNAs extensively rotate, shift, and deform for nicking and hairpin formation. Two intertwined RAG1 subunits crisscross four times between the asymmetric pair of severely bent 12/23-RSS DNAs. Location-sensitive bending of 60° and 150° in 12- and 23-RSS spacers, respectively, must occur for RAG1/2 to capture the nonamers and pair the heptamers for symmetric double-strand breakage. DNA pairing is thus sequence-context dependent and structure specific, which partly explains the "beyond 12/23" restriction. Finally, catalysis in crystallo reveals the process of DNA hairpin formation and its stabilization by interleaved base stacking.

Comparison of atmospheric reactions of NH3 and NH2 with hydroxyl radical on the singlet, doublet and triplet potential energy surfaces, kinetic and mechanistic study

The NH2 + OH and NH3 + OH reactions on the singlet, doublet and triplet potential energy surfaces carry out using MP2, QCISD, G3MP2, M06-2X, B3LYP, and CCSD(T)//MP2 levels. Three pre-reactive complexes, 1C1, 3C1 and 3C2 were formed among amidogen and hydroxyl radicals. From variety of the 1C1, four types of products are obtained that 1HNO + H2 is thermodynamically stable and three others are being stable after relaxation to triplet state. On the triplet state, five types of adducts are obtained that four of them have enough thermodynamic stability. Two intersystem crossing are presented among triplet and singlet states of the NH2 + OH reaction. 3NH + H2O adduct is spontaneous and exothermic in standard condition. Results lead to different adducts which are playing significant role in the atmospheric and combustion chemistry. The rate constants of selected pathways are calculated at the 300–2500 K temperature range at M06-2X/aug-ccpvqz and CCSD(T)/6-311++G(3df, 3pd) levels of theory.