Adsorption of Atmospherically Relevant Gases at the Air/Water Interface: Free Energy Profiles of Aqueous Solvation of N2, O2, O3, OH, H2O, HO2, and H2O2

Modelling consortium for chemistry of indoor environments (MOCCIE): integrating chemical processes from molecular to room scales

We report on the development of a modelling consortium for chemistry in indoor environments that connects models over a range of spatial and temporal scales, from molecular to room scales and from sub-nanosecond to days, respectively. Our modeling approaches include molecular dynamics (MD) simulations, kinetic process modeling, gas-phase chemistry modeling, organic aerosol modeling, and computational fluid dynamics (CFD) simulations. These models are applied to investigate ozone reactions with skin and clothing, oxidation of volatile organic compounds and formation of secondary organic aerosols, and mass transport and partitioning of indoor species to surfaces. MD simulations provide molecular pictures of limonene adsorption on SiO2 and ozone interactions with the skin lipid squalene, providing kinetic parameters such as surface accommodation coefficient, desorption lifetime, and bulk diffusivity. These parameters then constrain kinetic process models, which resolve mass transport and chemical reactions in gas and condensed phases for analysis of experimental data. A detailed indoor chemical box model is applied to simulate α-pinene ozonolysis with improved representation of gas-particle partitioning. Application of 2D-volatility basis set reveals that OH-induced aging sometimes drives increases in indoor organic aerosol concentrations, due to organic mass functionalization and enhanced partitioning. CFD simulations show that concentrations of ozone and primary product change near the human surface rapidly, indicating non-uniform spatial distributions from the occupant surface to ambient air, while secondary ozone product is relatively well-mixed throughout the room. This development establishes a framework to integrate different modeling tools and experimental measurements, opening up an avenue for development of comprehensive and integrated models with representations of various chemistry in indoor environments.

Computational insight into hydrogen persulfide and a new additive model for chemical and biological simulations

S-Sulfhydration of cysteine to the Cys-SSH persulfide is an oxidative post-translational modification that plays an important regulatory role in many physiological systems. Though hydrogen persulfide (H2S2) has recently been established as a signaling and cellular sulfhydration reagent, the chemistry and chemical biology of persulfides remain poorly explored. We first report an extensive high-level ab initio quantum chemical investigation of (H2S2)n, (H2S2)m·H2O, and (H2O)m·H2S2 clusters (n = 1-3 and m = 1, 2) and of H2S2 complexes with 19 compounds that model the side chains of naturally-occurring amino acids. The high polarizability of S necessitates the use of large, very diffuse, basis sets for proper description of H2S2 and its complexes. H2S2 possesses a skewed equilibrium geometry, with nonpolar trans and more polar cis conformers 6 and 8 kcal mol-1 higher in energy, respectively; the skewed conformation is preserved in all neutral and cationic complexes while a cis geometry prevails in some anionic complexes. H2S2 is found to be a better H-bond donor and a poorer acceptor than H2S, and that in complexes with H2O, alcohols and amines, H2S2 is a better H-bond donor. Radical delocalization on both S atoms stabilizes the perthiyl (HSS˙) over the thiyl (HS˙) radical and results in a ∼20 kcal mol-1 lower S-H homolytic bond dissociation in H2S2, making it a potential antioxidant. A simple additive model is optimized for H2S2 and used together with the TIP3P model and the CHARMM36 all-atom force field (FF) to investigate the structure and thermodynamic properties of liquid H2S2 and the solubility of H2S2 in water, and to model H2S2-protein interactions (for which new FF parameters are further developed). Very weak H-bonding characterizes liquid H2S2 and it is found immiscible in liquid water with a trend in H-bonding strengths between H2S2 and H2O in the order O-HO ≫ S-HO > O-HS. This work does not only provide a thorough description of the structure and energetics of H2S2 and its various complexes, but also yields a reliable FF for investigating H2S2 in chemistry and biology.

Mass Transfer Thermodynamics through a Gas-Liquid Interface

Molecular level information about thermodynamic variations (enthalpy, entropy, and free energy) of a gas molecule as it crosses a gas-liquid interface is strongly lacking from an experimental perspective under equilibrium conditions. Herein, we perform in situ measurements of water interacting with the ionic liquid (IL) 1-butyl-3-methylimidazolium acetate, [C₄mim][Ace], using ambient pressure X-ray photoelectron spectroscopy in order to assess the interfacial uptake of water quantitatively as a function of temperature, pressure, and water mole fraction ( x_w). The surface spectroscopy results are compared to existing bulk water absorption experiments, showing that the amount of water in the interfacial region is consistently greater than that in the bulk. The enthalpy and entropy of water sorption vary significantly between the gas-liquid interface and the bulk as a function of x_w, with a crossover that occurs near x_w = 0.6 where the water-IL mixture converts from being homogeneous ( x_w < 0.6) to nanostructured ( x_w > 0.6). Free energy results reveal that water at the gas-IL interface is thermodynamically more favorable than that in the bulk, consistent with the enhanced water concentration in the interfacial region. The results herein show that the efficacy for an ionic liquid to absorb a gas phase molecule is not merely a function of bulk solvation parameters but also is significantly influenced by the thermodynamics occurring across the gas-IL interface during the mass transfer process.

In Situ Chemical Analysis of the Gas-Aerosol Particle Interface

The gas-aerosol particle interface is believed to contribute to the growth of secondary organic aerosols in the atmosphere. Despite its importance, the chemical composition of the interface has not been probed directly because of a lack of suitable interface-specific analytical techniques. The preliminary result in our early work has demonstrated direct observations of molecules at the gas-aerosol particle interface with the development of second harmonic scattering (SHS). However, the SHS technique is far away from being an analytical tool of chemical compositions at the gas-aerosol particle interface. In this work, we continued to develop the interface-specific SHS for in situ chemical analysis of molecules at the gas-aerosol particle interface. As an example, we demonstrated coherent SHS signal of a new SHS probe, crystal violet (CV), from interfaces of aerosol particles. The development of the SHS technique includes: (1) Optimization for a more efficient femtosecond laser system in the generation of SHS from aerosol particles. A near 5 MHz repetition rate of a femtosecond laser was found to be optimal for the generation of SHS; (2) exploration of a more effective detector for SHS of aerosol particles. We found that both a CCD detector and a single-photon counter produce similar signal-to-noise ratios of the interfacial SHS signals from aerosol particles. The CCD detector is a more effective option for the detection of SHS and could greatly reduce sampling time of the interfacial responses; (3) combination of the optimal laser system with the CCD detector, which has greatly improved the detection sensitivity of interfacial molecules by more than 2 orders of magnitude and could potentially detect interfacial SHS from a single aerosol particle. These experimental results not only provided a thorough analysis of the SHS technique but also built a solid foundation for further development of a new vibrational sum frequency scattering (SFS) technique for chemical structures at the gas-aerosol particle interface.

A Simple Additive Potential Model for Simulating Hydrogen Peroxide in Chemical and Biological Systems

Hydrogen peroxide (H₂O₂) has numerous industrial, environmental, medical, cosmetic, and biological applications. Given its importance, we provide a simple model as an alternative to experiment for studying the properties of pure liquid H₂O₂ and its concentrated aqueous solutions, which are hazardous, and for understanding the biological roles of H₂O₂ at the molecular level. A four-site additive model is calibrated for H₂O₂ based on the ab initio and experimental properties of the gaseous monomer and the density and heat of vaporization of liquid H₂O₂ at 0 °C. Our model together with the TIP3P water model reproduce the ab initio binding energies of (H₂O₂) _m, H₂O₂· nH₂O, and nH₂O₂·H₂O clusters ( m = 2, 3 and n = 1, 2) calculated at the MP2 level using the 6-311++G(d,p) or the 6-311++G(3df,3pd) basis set. It yields structure, the self-diffusion coefficient, heat capacity, and densities at temperatures up to 200 °C of the pure liquid in good agreement with experiment. The model correctly predicts the hydration free energy of H₂O₂ and reproduces the experimental density of aqueous H₂O₂ solutions at 0-96 °C. Investigation of the solvation of H₂O₂ and H₂O in aqueous H₂O₂ solutions reveals that, as in the gas phase, H₂O₂ is a better H-bond donor but poorer acceptor than H₂O and the bonding stability follows the order O_p-H_p···O_w > O_w-H_w···O_w ≥ O_p-H_p···O_p > O_w-H_w···O_p. Stronger H-bonding in H₂O/H₂O₂ mixtures than in the pure liquids is consistent with exothermic heats of mixing and explains why the observed density and vapor pressure of the aqueous solutions are higher and lower, respectively, than expected from ideal mixing. Results also show that H₂O₂ adopts a skewed equilibrium geometry in gas and liquid phases but more polar cis and nonpolar trans conformations also are accessible and will stabilize H₂O₂ in environments of different polarity. In sum, our simple model presents a reliable tool for simulating H₂O₂ in chemistry and biology.

Impacts of cloud water droplets on the OH production rate from peroxide photolysis

Understanding the difference between observed and modeled concentrations of HO_x radicals in the troposphere is a current major issue in atmospheric chemistry. It is widely believed that existing atmospheric models miss a source of such radicals and several potential new sources have been proposed. In recent years, interest has increased on the role played by cloud droplets and organic aerosols. Computer modeling of ozone photolysis, for instance, has shown that atmospheric aqueous interfaces accelerate the associated OH production rate by as much as 3-4 orders of magnitude. Since methylhydroperoxide is a main source and sink of HO_x radicals, especially at low NO_x concentrations, it is fundamental to assess what is the influence of clouds on its chemistry and photochemistry. In this study, computer simulations for the photolysis of methylhydroperoxide at the air-water interface have been carried out showing that the OH production rate is severely enhanced, reaching a comparable level to ozone photolysis.

Extensive H-atom abstraction from benzoate by OH-radicals at the air-water interface

Much is known about OH-radical chemistry in the gas-phase and bulk water. Important atmospheric and biological processes, however, involve little investigated OH-radical reactions at aqueous interfaces with hydrophobic media. Here, we report the online mass-specific identification of the products and intermediates generated on the surface of aqueous (H₂O, D₂O) benzoate-h5 and -d5 microjets by ∼8 ns ˙OH(g) pulses in air at 1 atm. Isotopic labeling lets us unambiguously identify the phenylperoxyl radicals that ensue H-abstraction from the aromatic ring and establish a lower bound (>26%) to this process as it takes place in the interfacial water nanolayers probed by our experiments. The significant extent of H-abstraction vs. its negligible contribution both in the gas-phase and bulk water underscores the unique properties of the air-water interface as a reaction medium. The enhancement of H-atom abstraction in interfacial water is ascribed, in part, to the relative destabilization of a more polar transition state for OH-radical addition vs. H-abstraction due to incomplete hydration at the low water densities prevalent therein.

N2O5at water surfaces: binding forces, charge separation, energy accommodation and atmospheric implications

Studying the interactions between N₂O₅and water in nano-sized clusters, in bulk and on the surface of water.

Energetic Analysis of Adsorption and Absorption of Small Molecule to Nanodroplet of Water

Adsorption and absorption were analyzed for nonpolar and polar solutes to a water droplet of nanometer size and to a planar slab. All-atom molecular dynamics simulation was performed, and the free energy change for bringing the solute to the water aggregate was computed over a wide range of temperature. It was seen in both the droplet and slab systems that the solute is preferably located at the surface, and the propensity of the nonpolar solute at the surface relative to the bulk was found to be larger in the droplet than in the slab. A molecular-sized curvature thus enhances the surface propensity of a nonpolar solute, whereas the curvature effect is weaker for polar one. The attractive and repulsive interactions of the solute with water were further analyzed, and the role of the repulsive interaction is discussed with respect to the stability of the surface-bound state.

Reaching multi-nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling

We report an enhanced sampling technique that allows to reach the multi-nanosecond timescale in quantum mechanics/molecular mechanics molecular dynamics simulations. The proposed technique, called horsetail sampling, is a specific type of multiple molecular dynamics approach exhibiting high parallel efficiency. It couples a main simulation with a large number of shorter trajectories launched on independent processors at periodic time intervals. The technique is applied to study hydrogen peroxide at the water liquid-vapor interface, a system of considerable atmospheric relevance. A total simulation time of a little more than 6 ns has been attained for a total CPU time of 5.1 years representing only about 20 days of wall-clock time. The discussion of the results highlights the strong influence of the solvation effects at the interface on the structure and the electronic properties of the solute. © 2017 Wiley Periodicals, Inc.

"Sizing" Heterogeneous Chemistry in the Conversion of Gaseous Dimethyl Sulfide to Atmospheric Particles

The oxidation of biogenic dimethyl sulfide (DMS) emissions is a global source of cloud condensation nuclei. The amounts of the nucleating H2SO4(g) species produced in such process, however, remain uncertain. Hydrophobic DMS is mostly oxidized in the gas phase into H2SO4(g) + DMSO(g) (dimethyl sulfoxide), whereas water-soluble DMSO is oxidized into H2SO4(g) in the gas phase and into SO4(2-) + MeSO3(-) (methanesulfonate) on water surfaces. R = MeSO3(-)/(non-sea-salt SO4(2-)) ratios would therefore gauge both the strength of DMS sources and the extent of DMSO heterogeneous oxidation if Rhet = MeSO3(-)/SO4(2-) for DMSO(aq) + ·OH(g) were known. Here, we report that Rhet = 2.7, a value obtained from online electrospray mass spectra of DMSO(aq) + ·OH(g) reaction products that quantifies the MeSO3(-) produced in DMSO heterogeneous oxidation on aqueous aerosols for the first time. On this basis, the inverse R dependence on particle radius in size-segregated aerosol collected over Syowa station and Southern oceans is shown to be consistent with the competition between DMSO gas-phase oxidation and its mass accommodation followed by oxidation on aqueous droplets. Geographical R variations are thus associated with variable contributions of the heterogeneous pathway to DMSO atmospheric oxidation, which increase with the specific surface area of local aerosols.

Effects of Temperature, Oxygen Level, Ionic Strength, and pH on the Reaction of Benzene with Hydroxyl Radicals at the Air-Water Interface in Comparison to the Bulk Aqueous Phase

Atmospheric aerosols (e.g., fog droplets) are complex, multiphase mediums. Depending on location, time of day, and/or air mass source, there can be considerable variability within these droplets, relating to temperature, pH, and ionic strength. Due to the droplets' inherently small size, the reactions that occur within these droplets are determined by bulk aqueous phase and air-water interfacial conditions. In this study, the reaction of benzene and hydroxyl radicals is examined kinetically in a thin-film flow-tube reactor. By varying the aqueous volume (e.g., film thickness) along the length of the reactor, both bulk and interfacial reaction rates are measured from a single system. Temperature, pH, and ionic strength are varied to model conditions typical of fog events. Oxygen-poor conditions are measured to study oxygen's overall effect on the reaction pathway. Initial rate activation energies and the bulk aqueous phase and interfacial contributions to the overall rate constant are also obtained.

Interconnection of reactive oxygen species chemistry across the interfaces of atmospheric, environmental, and biological processes

Oxidation reactions are ubiquitous and play key roles in the chemistry of the atmosphere, in water treatment processes, and in aerobic organisms. Ozone (O3), hydrogen peroxide (H2O2), hydrogen polyoxides (H2Ox, x > 2), associated hydroxyl and hydroperoxyl radicals (HOx = OH and HO2), and superoxide and ozonide anions (O2(-) and O3(-), respectively) are the primary oxidants in these systems. They are commonly classified as reactive oxygen species (ROS). Atmospheric chemistry is driven by a complex system of chain reactions of species, including nitrogen oxides, hydroxyl and hydroperoxide radicals, alkoxy and peroxy radicals, and ozone. HOx radicals contribute to keeping air clean, but in polluted areas, the ozone concentration increases and creates a negative impact on plants and animals. Indeed, ozone concentration is used to assess air quality worldwide. Clouds have a direct effect on the chemical composition of the atmosphere. On one hand, cloud droplets absorb many trace atmospheric gases, which can be scavenged by rain and fog. On the other hand, ionic species can form in this medium, which makes the chemistry of the atmosphere richer and more complex. Furthermore, recent studies have suggested that air-cloud interfaces might have a significant impact on the overall chemistry of the troposphere. Despite the large differences in molecular composition, concentration, and thermodynamic conditions among atmospheric, environmental, and biological systems, the underlying chemistry involving ROS has many similarities. In this Account, we examine ROS and discuss the chemical characteristics common to all of these systems. In water treatment, ROS are key components of an important subset of advanced oxidation processes. Ozonation, peroxone chemistry, and Fenton reactions play important roles in generating sufficient amounts of hydroxyl radicals to purify wastewater. Biochemical processes within living organisms also involve ROS. These species can come from pollutants in the environment, but they can also originate endogenously, initiated by electron reduction of molecular oxygen. These molecules have important biological signaling activities, but they cause oxidative stress when dysfunction within the antioxidant system occurs. Excess ROS in living organisms can lead to problems, such as protein oxidation-through either cleavage of the polypeptide chain or modification of amino acid side chains-and lipid oxidation.

Stepwise Oxidation of Aqueous Dicarboxylic Acids by Gas-Phase OH Radicals

A leading source of uncertainty in predicting the climate and health effects of secondary organic aerosol (SOA) is how its composition changes over their atmospheric lifetimes. Because dicarboxylic acid (DCA) homologues are widespread in SOA, their distribution provides an ideal probe of both aerosol age and the oxidative power of the atmosphere along its trajectory. Here we report, for the first time, on the oxidation of DCA(aq) by ·OH(g) at the air-water interface. We found that exposure of aqueous HOOC-Rn-COOH (Rn = C2H4, C3H6, C4H8, C5H10, and C6H12) microjets to ∼10 ns ·OH(g) pulses from the 266 nm laser photolysis of O3(g)/O2(g)/H2O(g) mixtures yields the corresponding (n-1) species O═C(H)-Rn-1-COO(-)/HOOC-Rn-1-COO(-), in addition to an array of closed-shell HOOC-Rn(-H)(OOH)-COO(-), HOOC-Rn(-2H)(═O)-COO(-), HOOC-Rn(-H)(OH)-COO(-), and radical HOOC-Rn(-H)(OO·)-COO(-) species. Oxalic and malonic acids, which are shown to be significantly less hydrophobic and reactive than their higher homologues, will predictably accumulate in SOA, in accordance with field observations.

Temperature dependence of local solubility of hydrophobic molecules in the liquid-vapor interface of water

One important aspect of the hydrophobic effect is that solubility of small, nonpolar molecules in liquid water decreases with increasing temperature. We investigate here how the characteristic temperature dependence in liquid water persists or changes in the vicinity of the liquid-vapor interface. From the molecular dynamics simulation and the test-particle insertion method, the local solubility Σ of methane in the liquid-vapor interface of water as well as Σ of nonpolar solutes in the interface of simple liquids are calculated as a function of the distance z from the interface. We then examine the temperature dependence of Σ under two conditions: variation of Σ at fixed position z and that at fixed local solvent density around the solute molecule. It is found that the temperature dependence of Σ at fixed z depends on the position z and the system, whereas Σ at fixed local density decreases with increasing temperature for all the model solutions at any fixed density between vapor and liquid phases. The monotonic decrease of Σ under the fixed-density condition in the liquid-vapor interface is in accord with what we know for the solubility of nonpolar molecules in bulk liquid water under the fixed-volume condition but it is much robust since the solvent density to be fixed can be anything between the coexisting vapor and liquid phases. A unique feature found in the water interface is that there is a minimum in the local solubility profile Σ(z) on the liquid side of the interface. We find that with decreasing temperature the minimum of Σ grows and at the same time the first peak in the oscillatory density profile of water develops. It is likely that the minimum of Σ is due to the layering structure of the free interface of water.

Spectroscopic signatures of ozone at the air-water interface and photochemistry implications

First-principles simulations suggest that additional OH formation in the troposphere can result from ozone interactions with the surface of cloud droplets. Ozone exhibits an affinity for the air-water interface, which modifies its UV and visible light spectroscopic signatures and photolytic rate constant in the troposphere. Ozone cross sections on the red side of the Hartley band (290- to 350-nm region) and in the Chappuis band (450-700 nm) are increased due to electronic ozone-water interactions. This effect, combined with the potential contribution of the O3 + hν → O((3)P) + O2(X(3)Σg(-)) photolytic channel at the interface, leads to an enhancement of the OH radical formation rate by four orders of magnitude. This finding suggests that clouds can influence the overall oxidizing capacity of the troposphere on a global scale by stimulating the production of OH radicals through ozone photolysis by UV and visible light at the air-water interface.

Fenton chemistry at aqueous interfaces

In a fundamental process throughout nature, reduced iron unleashes the oxidative power of hydrogen peroxide into reactive intermediates. However, notwithstanding much work, the mechanism by which Fe(2+) catalyzes H2O2 oxidations and the identity of the participating intermediates remain controversial. Here we report the prompt formation of O=Fe(IV)Cl3(-) and chloride-bridged di-iron O=Fe(IV) · Cl · Fe(II)Cl4(-) and O=Fe(IV) · Cl · Fe(III)Cl5(-) ferryl species, in addition to Fe(III)Cl4(-), on the surface of aqueous FeCl2 microjets exposed to gaseous H2O2 or O3 beams for <50 μs. The unambiguous identification of such species in situ via online electrospray mass spectrometry let us investigate their individual dependences on Fe(2+), H2O2, O3, and H(+) concentrations, and their responses to tert-butanol (an · OH scavenger) and DMSO (an O-atom acceptor) cosolutes. We found that (i) mass spectra are not affected by excess tert-butanol, i.e., the detected species are primary products whose formation does not involve · OH radicals, and (ii) the di-iron ferryls, but not O=Fe(IV)Cl3(-), can be fully quenched by DMSO under present conditions. We infer that interfacial Fe(H2O)n(2+) ions react with H2O2 and O3 >10(3) times faster than Fe(H2O)6(2+) in bulk water via a process that favors inner-sphere two-electron O-atom over outer-sphere one-electron transfers. The higher reactivity of di-iron ferryls vs. O=Fe(IV)Cl3(-) as O-atom donors implicates the electronic coupling of mixed-valence iron centers in the weakening of the Fe(IV)-O bond in poly-iron ferryl species.

Bubble bursting as an aerosol generation mechanism during an oil spill in the deep-sea environment: molecular dynamics simulations of oil alkanes and dispersants in atmospheric air/salt water interfaces

Potential of mean force (PMF) calculations and molecular dynamics (MD) simulations were performed to investigate the properties of oil n-alkanes [i.e., n-pentadecane (C15), n-icosane (C20) and n-triacontane (C30)], as well as several surfactant species [i.e., the standard anionic surfactant sodium dodecyl sulfate (SDS), and three model dispersants similar to the Tween and Span species present in Corexit 9500A] at air/salt water interfaces. This study was motivated by the 2010 Deepwater Horizon (DWH) oil spill, and our simulation results show that, from the thermodynamic point of view, the n-alkanes and the model dispersants have a strong preference to remain at the air/salt water interface, as indicated by the presence of deep free energy minima at these interfaces. The free energy minimum of these n-alkanes becomes deeper as their chain length increases, and as the concentration of surfactant species at the interface increases. The n-alkanes tend to adopt a flat orientation and form aggregates at the bare air/salt water interface. When this interface is coated with surfactants, the n-alkanes tend to adopt more tilted orientations with respect to the vector normal to the interface. These simulation results are consistent with the experimental findings reported in the accompanying paper [Ehrenhauser et al., Environ. Sci.: Processes Impacts 2013, in press, (DOI: 10.1039/c3em00390f)]. The fact that these long-chain n-alkanes show a strong thermodynamic preference to remain at the air/salt water interfaces, especially if these interfaces are coated with surfactants, makes these species very likely to adsorb at the surface of bubbles or droplets and be ejected to the atmosphere by sea surface processes such as whitecaps (breaking waves) and bubble bursting. Finally, the experimental finding that more oil hydrocarbons are ejected when Corexit 9500A is present in the system is consistent with the deeper free energy minima observed for the n-alkanes at the air/salt water interface at increasing concentrations of surfactant species.

Reactive oxygen species at phospholipid bilayers: distribution, mobility and permeation

Reactive oxygen species (ROS) are involved in biochemical processes such as redox signaling, aging, carcinogenesis and neurodegeneration. Although biomembranes are targets for reactive oxygen species attack, little is known about the role of their specific interactions. Here, molecular dynamics simulations were employed to determine the distribution, mobility and residence times of various reactive oxygen species at the membrane-water interface. Simulations showed that molecular oxygen (O2) accumulated at the membrane interior. The applicability of this result to singlet oxygen ((1)O2) was discussed. Conversely, superoxide (O2(-)) radicals and hydrogen peroxide (H2O2) remained at the aqueous phase. Both hydroxyl (HO) and hydroperoxyl (HO2) radicals were able to penetrate deep into the lipid headgroups region. Due to membrane fluidity and disorder, these radicals had access to potential peroxidation sites along the lipid hydrocarbon chains, without having to overcome the permeation free energy barrier. Strikingly, HO2 radicals were an order of magnitude more concentrated in the headgroups region than in water, implying a large shift in the acid-base equilibrium between HO2 and O2(-). In comparison with O2, both HO and HO2 radicals had lower lateral mobility at the membrane. Simulations revealed that there were intermittent interruptions in the H-bond network around the HO radicals at the headgroups region. This effect is expected to be unfavorable for the H-transfer mechanism involved in HO diffusion. The implications for lipid peroxidation and for the effectiveness of membrane antioxidants were evaluated.

Insight into the molecular mechanism of water evaporation via the finite temperature string method

The process of water's evaporation at its liquid/air interface has proven challenging to study experimentally and, because it constitutes a rare event on molecular time scales, presents a challenge for computer simulations as well. In this work, we simulated water's evaporation using the classical extended simple point charge model water model, and identified a minimum free energy path for this process in terms of 10 descriptive order parameters. The measured free energy change was 7.4 kcal/mol at 298 K, in reasonable agreement with the experimental value of 6.3 kcal/mol, and the mean first-passage time was 1375 ns for a single molecule, corresponding to an evaporation coefficient of 0.25. In the observed minimum free energy process, the water molecule diffuses to the surface, and tends to rotate so that its dipole and one O-H bond are oriented outward as it crosses the Gibbs dividing surface. As the water molecule moves further outward through the interfacial region, its local density is higher than the time-averaged density, indicating a local solvation shell that protrudes from the interface. The water molecule loses donor and acceptor hydrogen bonds, and then, with its dipole nearly normal to the interface, stops donating its remaining hydrogen bond. At that point, when the final, accepted hydrogen bond is broken, the water molecule is free. We also analyzed which order parameters are most important in the process and in reactive trajectories, and found that the relative orientation of water molecules near the evaporating molecule, and the number of accepted hydrogen bonds, were important variables in reactive trajectories and in kinetic descriptions of the process.

Glutathione--hydroxyl radical interaction: a theoretical study on radical recognition process

Non-reactive, comparative (2 × 1.2 μs) molecular dynamics simulations were carried out to characterize the interactions between glutathione (GSH, host molecule) and hydroxyl radical (OH(•), guest molecule). From this analysis, two distinct steps were identified in the recognition process of hydroxyl radical by glutathione: catching and steering, based on the interactions between the host-guest molecules. Over 78% of all interactions are related to the catching mechanism via complex formation between anionic carboxyl groups and the OH radical, hence both terminal residues of GSH serve as recognition sites. The glycine residue has an additional role in the recognition of OH radical, namely the steering. The flexibility of the Gly residue enables the formation of further interactions of other parts of glutathione (e.g. thiol, α- and β-carbons) with the lone electron pair of the hydroxyl radical. Moreover, quantum chemical calculations were carried out on selected GSH/OH(•) complexes and on appropriate GSH conformers to describe the energy profile of the recognition process. The relative enthalpy and the free energy changes of the radical recognition of the strongest complexes varied from -42.4 to -27.8 kJ/mol and from -21.3 to 9.8 kJ/mol, respectively. These complexes, containing two or more intermolecular interactions, would be the starting configurations for the hydrogen atom migration to quench the hydroxyl radical via different reaction channels.

Molecular modeling of the green leaf volatile methyl salicylate on atmospheric air/water interfaces

Methyl salicylate (MeSA) is a green leaf volatile (GLV) compound that is emitted in significant amounts by plants, especially when they are under stress conditions. GLVs can then undergo chemical reactions with atmospheric oxidants, yielding compounds that contribute to the formation of secondary organic aerosols (SOAs). We investigated the adsorption of MeSA on atmospheric air/water interfaces at 298 K using thermodynamic integration (TI), potential of mean force (PMF) calculations, and classical molecular dynamics (MD) simulations. Our molecular models can reproduce experimental results of the 1-octanol/water partition coefficient of MeSA. A deep free energy minimum was found for MeSA at the air/water interface, which is mainly driven by energetic interactions between MeSA and water. At the interface, the oxygenated groups in MeSA tend to point toward the water side of the interface, with the aromatic group of MeSA lying farther away from water. Increases in the concentrations of MeSA lead to reductions in the height of the peaks in the MeSA-MeSA g(r) functions, a slowing down of the dynamics of both MeSA and water at the interface, and a reduction in the interfacial surface tension. Our results indicate that MeSA has a strong thermodynamic preference to remain at the air/water interface, and thus chemical reactions with atmospheric oxidants are more likely to take place at this interface, rather than in the water phase of atmospheric water droplets or in the gas phase.

Tracking all-vapor instant gas-hydrate formation and guest molecule populations: a possible probe for molecules trapped in water nanodroplets

Quantitative Fourier-transform infrared spectra for low-temperature (160-200 K) aerosols of clathrate-hydrate nanoparticles that contain large-cage catalysts and small-cage nonpolar guests have been extended to a broad range of vapor compositions and sampling conditions. The data better reveal the stages by which room-temperature vapor mixtures, when cooled below ∼220 K, instantly generate aerosols with particles composed exclusively of the corresponding clathrate hydrates. In particular the quantitative data help relate the nature of the hydrates that form to the composition of the aqueous nanodroplets of the first stages of the rapid transition from the all-vapor mixture. The overall transition from an all-vapor mixture to "gas"-hydrate nanocrystals is a multistage one that has been characterized as homogeneous nucleation and growth of solution nanodroplets (∼240 K) followed by nucleation and growth of the gas-hydrate particles (∼220 K); all occurring within a subsecond that follows pulsing of the warm vapor into a sampling cold chamber. This may serve well as a general description of the instantaneous generation of the gas-hydrate aerosols, but closer consideration of the nature of the sampling method, in context with recent computation-based insights to (a) gas-hydrate nucleation stages∕rates and (b) the lifetimes of trapped small nonpolar molecules in cold aqueous nanodroplets, suggests a more complex multistage transition. The simulated lifetimes and extensive new quantitative infrared data significantly broaden the knowledge base in which the instantaneous transition from vapor to crystalline hydrate particles is viewed. The apparent need for a high occupancy of large-cage catalytic guest molecules currently limits the practical value of the all-vapor method. Only through greater clarity in the molecular-level description of the transition will the ultimate limits be defined.