Ab initio molecular dynamics simulation of the OH radical in liquid water

The Mechanism of Ozone Oxidation of Coal and the Revelation of Coal Macromolecular Structure by Oxidation Products

Ozone was injected into a coal-water suspension, and an HRTEM test was carried out on the separated oxidation products. The results show that from the perspective of visualization the macromolecular network structure of coal contains a large number of graphite-like structures. However, the chemical reaction mechanism between the coal surface and O3 is not clear, and the microscopic formation mechanism of oxygen-containing functional groups in carbon quantum dots has not been explained. As a result, the reaction process between O3 and methylene on the coal surface was studied by the DFT method. We found that OH• generated by O3 in water can oxidize two adjacent carbon atoms in methylene into double bonds (C=C), and finally, aldehydes and carboxylic acids were generated. By calculation of thermodynamic parameters ΔG and ΔH, it is found that all reactions are spontaneous exothermic processes. The above chemical reaction is based on the physical adsorption of OH• with Ar-(CH2)6-Ar and O3 with Ar-CH2-CH=CH-(CH2)3-Ar. The calculated adsorption energies of the two systems are -9.41 and -12.55 kcal/mol, respectively. Then, the charge transfer and atomic orbital interaction before and after adsorption are analyzed from the perspectives of Mulliken charge, density of states, deformation density, and total charge density. The results show that the electrostatic attraction is the main driving force of adsorption. The ether bond (C-O-C) in coal is finally oxidized to an ester group (RCOOR'), the hydroxyl group (CH2-CH-OH) on the aliphatic chain is oxidized to a carbonyl group (CH2-C=O), and the benzene with two OH• forms phenol hydroxyl and one molecule of water. Finally, the coal and the corresponding coal-based carbon quantum dots were investigated by infrared spectroscopy; the difference in functional groups before and after oxidation was clarified, and the result was in good agreement with the simulation.

The effects of the gas-liquid interface and gas phase on Cl/ClO radical interaction with water molecules

In the marine boundary layer (MBL), chlorine (Cl) and chlorine monoxide (ClO) are powerful oxidants with high concentrations. The gas-liquid interface is also ubiquitous in the MBL as a favorable site for atmospheric reactions. Understanding the role of water in Cl/ClO radical chemistry is essential for predicting their behavior in the atmosphere and developing effective strategies for mitigating their harmful effects. However, the research studies on the system of Cl/ClO radicals on the surface of water droplets are still insufficient. In previous studies, we have found unique results related to the hydroxyl radical at the interface using ab initio molecular dynamics (AIMD). In this work, we have used AIMD to investigate interactions between Cl/ClO radicals and water molecules at the gas-liquid interface. Radical mobility, radial distribution functions, coordination, and population analyses were conducted to investigate the surface preference, bonding pattern, and track Cl/ClO radicals in the water droplets. In addition, density functional theory (DFT) analysis was conducted to compare the results at the gas-liquid interface with those in the gas phase. We found that Cl/ClO radicals tend to remain near the gas-liquid interface in water droplet systems and outside of water clusters in gas phase systems. The ClO radical can form O*-H and Cl-O bonds with water molecules; however, neither the O*-O hemibond nor the Cl-H bond was detected in all systems. Different dominant structures were obtained for ClO in the interface and gas phase. The ClO radical can be bonded to one water molecule from its oxygen side, (H2O)0-Cl-O*-(H2O)1 at the interface, or to two water molecules from the chlorine and oxygen sides, (H2O)1-Cl-O*-(H2O)1 in the gas phase. Meanwhile, the Cl radical can only form a dominant structure like Cl*-(H2O)1 at the gas-liquid interface by making a Cl*-O hemibond. Providing a thorough explanation of the Cl/ClO radical behavior at the gas-liquid interface, this study will improve our understanding of the MBL's oxidizing capacity and pollution causes.

A Molecular Dynamic Study of the Effects of Surface Partitioning on the OH Radical Interactions with Solutes in Multicomponent Aqueous Aerosols

The surface-bulk partitioning of small saccharide and amide molecules in aqueous droplets was investigated using molecular dynamics. The air-particle interface was modeled using a 80 Å cubic water box containing a series of organic molecules and surrounded by gaseous OH radicals. The properties of the organic solutes within the interface and the water bulk were examined at a molecular level using density profiles and radial pair distribution functions. Molecules containing only polar functional groups such as urea and glucose are found predominantly in the water bulk, forming an exclusion layer near the water surface. Substitution of a single polar group by an alkyl group in sugars and amides leads to the migration of the molecule toward the interface. Within the first 2 nm from the water surface, surface-active solutes lose their rotational freedom and adopt a preferred orientation with the alkyl group pointing toward the surface. The different packing within the interface leads to different solvation shell structures and enhanced interaction between the organic molecules and absorbed OH radicals. The simulations provide quantitative information about the dimension, composition, and organization of the air-water interface as well as about the nonreactive interaction of the OH radicals with the organic solutes. It suggests that increased concentrations, preferred orientations, and decreased solvation near the air-water surface may lead to differences in reactivities between surface-active and surface-inactive molecules. The results are important to explain how heterogeneous oxidation mechanisms and kinetics within interfaces may differ from those of the bulk.

Hidden Hemibonding in the Aqueous Hydroxyl Radical

The existence of a two-center, three-electron hemibond in the first solvation shell of ^•OH(aq) has long been a matter of debate. The hemibond manifests in ab initio molecular dynamics simulations as a small-r feature in the oxygen radial distribution function (RDF) for H₂O···^•OH, but that feature disappears when semilocal density functionals are replaced with hybrids, suggesting a self-interaction artifact. Using periodic simulations at the PBE0+D3 level, we demonstrate that the hemibond is actually still present (as evidenced by delocalization of the spin density) but is obscured by the hydrogen-bonded feature in the RDF due to a slight elongation of the hemibond. Computed electronic spectra for ^•OH(aq) are in excellent agreement with experiment and confirm that hemibond-like configurations play an outsized role in the spectroscopy due to an intense charge-transfer transition that is strongly attenuated in hydrogen-bonded configurations. Apparently, 25% exact exchange (as in PBE0) is insufficient to eliminate delocalization of unpaired spins.

The mobility and solvation structure of a hydroxyl radical in a water nanodroplet: a Born-Oppenheimer molecular dynamics study

Hydroxyl radicals (OH*) play a crucial role in atmospheric chemistry and biological processes. In this study, Born-Oppenheimer molecular dynamics simulations are performed under ambient conditions for a hydroxyl radical in a water nanodroplet containing 191 water molecules. Density functional theory calculations are performed at the BLYP-D3 level with some test calculations at the B3LYP-D3 level. In two 150 ps trajectories, either with OH* initially located in the interior region or at the surface of the water nanodroplet, the OH* radical ends up in the subsurface layer of the nanodroplet, which is different from the "surface preference" predicted from previous empirical force field simulations. The solvation structure of OH* contains fluctuating hydrogen bonds, as well as a two-center three-electron hemibond in some cases. The mobility of OH* is enhanced by hydrogen transfer, which has a free energy barrier of ∼4.6 kcal mol-1. The results presented in this study deepen our understanding of the structure and dynamics of OH* in aqueous solutions, especially around the air-water interface.

Role of hemibonding in the structure and ultraviolet spectroscopy of the aqueous hydroxyl radical

The presence of a two-center, three-electron hemibond in the solvation structure of the aqueous hydroxl radical has long been debated, as its appearance can be sensitive to self-interaction error in density functional theory.

Ab initio molecular dynamics of the reactivity of vitamin C toward hydroxyl and HO₂/O⁻₂ radicals

Vitamin C is one of the most abundant exogenous antioxidants in the cell, and it is of the utmost importance to elucidate its mechanism of action against radicals. In this study, the reactivity of vitamin C toward OH and [Formula: see text] radicals in aqueous medium was analyzed by ab initio molecular dynamics using CPMD code. The simulations led to results similar to those of static studies or experiments for the pair of [Formula: see text] radicals but bring new insights for the reactivity with hydroxyl radical: the reaction takes place before the formation of an adduct and consists of two steps: first an electron is transferred to hydroxyl radical and then the ascorbyl radical loses a proton. Graphical Abstract Reactivity of vitamin C toward hydroxyl and [Formula: see text] radicals.

The hemibond as an alternative condensed phase structure for the hydroxyl radical

Despite the critical importance of the hydroxyl radical in major scientific fields, there are still open questions on the behavior of this species in the aqueous phase. In particular, there has been much debate on the existence of a hemibonded interaction between the hydroxyl radical and water molecules. While some reports indicate that the hemibonded radical might explain some experimental data, others have claimed that this interaction is simply a density functional theory (DFT) artifact. Here, we provide results from high level (basis set limit of coupled-cluster levels up to single, double, triple excitations (CCSD(T)) and beyond) ab initio calculations of different OH•(H2O)n clusters in the gas phase to accurately explore the existence of the hemibonded interaction and its energy difference with respect to other well-defined hydrogen bond interactions. Additional comparisons with second order perturbation theory (MP2) and DFT are also presented. Constrained molecular dynamics was applied to determine the free energy for the formation/disruption and ice systems. Overall, our findings confirm that the hemibond can be an alternative structure for the hydroxyl radical in the condensed phase when the formation of hydrogen bonds is impeded. These results will aid the understanding of theoretical and experimental data and help future experimental designs for the detection of this important species.

Mobility mechanism of hydroxyl radicals in aqueous solution via hydrogen transfer

The hydroxyl radical (OH*) is a highly reactive oxygen species that plays a salient role in aqueous solution. The influence of water molecules upon the mobility and reactivity of the OH* constitutes a crucial knowledge gap in our current understanding of many critical reactions that impact a broad range of scientific fields. Specifically, the relevant molecular mechanisms associated with OH* mobility and the possibility of diffusion in water via a H-transfer reaction remain open questions. Here we report insights into the local hydration and electronic structure of the OH* in aqueous solution from Car-Parrinello molecular dynamics and explore the mechanism of H-transfer between OH* and a water molecule. The relatively small free energy barrier observed (~4 kcal/mol) supports a conjecture that the H-transfer can be a very rapid process in water, in accord with very recent experimental results, and that this reaction can contribute significantly to OH* mobility in aqueous solution. Our findings reveal a novel H-transfer mechanism of hydrated OH*, resembling that of hydrated OH(-) and presenting hybrid characteristics of hydrogen-atom and electron-proton transfer processes, where local structural fluctuations play a pivotal role.

Study of electronic structure and dynamics of interacting free radicals influenced by water

We present a study of electronic structure, stability, and dynamics of interaction and recombination of free radicals such as HO(2) and OH influenced by water. As simple model calculations, we performed ab initio and density functional calculations for the interaction of HO(2) and OH in the presence of water cluster. Results indicate that a significant interaction, overcoming the repulsive Columbic barrier, occurs at a separation distance between the radicals of 5.7 A. This confirms early predictions of the minimum size of molecular dianions stable in the gas phase. It is well known that atomic dianions are unstable in the gas phase but molecular dianions are stable when the size of the molecule is larger than 5.7 A. Ab initio molecular dynamics calculations with Car-Parrinello scheme show that the reaction is very fast and occurs on a time scale of about 1.5 ps. The difference in stability and dynamics of the interacting free radicals on singlet and triplet potential energy surfaces is also discussed.

The electron attachment energy of the aqueous hydroxyl radical predicted from the detachment energy of the aqueous hydroxide anion

Combining photoemission and electrochemical data from the literature we argue that the difference between the vertical and adiabatic ionization energy of the aqueous hydroxide anion is 2.9 eV. We then use density functional theory based molecular dynamics to show that the solvent response to ionization is nonlinear. Adding this to the experimental data we predict a 4.1 eV difference between the energy for vertical attachment of an electron to the aqueous hydroxyl radical and the corresponding adiabatic electron affinity. This places the state accepting the electron only 2.2 eV below vacuum or 7.7 eV above the edge of the valence band of water.

Reaction intermediates in the photoreduction of oxygen molecules at the (101) TiO2 (anatase) surface

The structural, electronic, and vibrational properties of intermediates of the O(2) photoreduction at the (101) TiO(2) (anatase) surface have been investigated by performing ab initio density functional calculations. In detail, a recently proposed approach has been used where molecules on the surface are treated like surface defects. Thus, by applying theoretical methods generally used in the physics of semiconductors, we successfully estimate the location and donor/acceptor character of the electronic levels induced by an adsorbed molecule in the TiO(2) energy gap, both crucial for the surface-molecule charge-transfer processes, and investigate the formation and the properties of charged intermediates. The present approach permits a view of the O(2) photoreduction process through several facets, which elucidates the molecule-surface charge-transfer conditions and reveals the key role played by charged intermediates. A comparison of present results with those of a highly sensitive IR (infrared) spectroscopy study of intermediates of the O(2) photoreduction leads to a deeper understanding of this process and to revised vibrational-line assignments and reaction paths.

Computational observation of enhanced solvation of the hydroxyl radical with increased NaCl concentration

Classical molecular dynamics simulations with many-body potentials were carried out to quantitatively determine the effect of NaCl salt concentration on the aqueous solvation and surface concentration of hydroxyl radicals. The potential of mean force technique was used to track the incremental free energy of the hydroxyl radical from the vapor, crossing the air-water interface into the aqueous bulk. Results showed increased NaCl salt concentration significantly enhanced hydroxyl radical solvation, which should significantly increase its accommodation on water droplets. This has been experimentally observed for ozone aqueous accommodation with increased NaI concentration, but, to our knowledge, no experimental study has probed this for hydroxyl radicals. The origin for this effect was found to be very favorable hydroxyl radical-chloride ion interactions, being stronger than those for water-chloride.

The structures of ozone and HOx radicals in aqueous solution from combined quantum/classical molecular dynamics simulations

Ozone in aqueous solution decomposes through a complex mechanism that involves initial reaction with a hydroxide ion followed by formation of a variety of oxidizing species such as HO, HO(2), and HO(3) radicals. Though a number of hydrogen-bonded complexes have been described in the gas phase, both theoretically and experimentally, the structures of ozone and HO(x) in liquid water remain uncertain. In this work, combined quantum/classical computer simulations of aqueous solutions of these species have been reported. The results show that ozone undergoes noticeable electron polarization but it does not participate in hydrogen bonds with liquid water. The main contribution of the solvation energy comes from dispersion forces. In contrast, HO(x) radicals form strong hydrogen bonds. They are better proton donors but weaker proton acceptors than water. Their electronic and geometrical structures are significantly modified by the solvent, especially in the case of HO(3). In all cases, fluctuations in amplitudes of electronic properties are considerable, suggesting that solvent effects might play a crucial role on oxidation mechanisms initiated by ozone in liquid water. These mechanisms are important in a broad range of domains, such as atmospheric processes, plant response to ambient ozone, and medical and industrial applications.

Charge Localization in Stacked Radical Cation DNA Base Pairs and the Benzene Dimer Studied by Self-Interaction Corrected Density-Functional Theory

The incomplete cancellation of the electron self-interaction can be a serious shortcoming of density-functional theory especially when treating odd-electron systems. In this work, several popular and potentially viable correction schemes are applied in order to characterize the electronic structure of stacked molecular pairs, consisting of a neutral molecule and adjacent radical cation, as a function of separation distance. The unphysical sharing of the positive charge between adjacent molecules separated by 6-7 A is corrected for by applying a new empirical scheme proposed by VandeVondele and Sprik [Phys. Chem. Chem. Phys. 2005, 7, 1363] with a unique choice of parameters. This method is subsequently applied to characterize the electronic structure of two neighboring guanines excised from a canonical Arnott B-DNA structure and will be used in future investigations of certain model DNA fibers.

The OH radical-H2O molecular interaction potential

The OH radical is one of the most important oxidants in the atmosphere due to its high reactivity. The study of hydrogen-bonded complexes of OH with the water molecules is a topic of significant current interest. In this work, we present the development of a new analytical functional form for the interaction potential between the rigid OH radical and H(2)O molecules. To do this we fit a selected functional form to a set of high level ab initio data. Since there is a low-lying excited state for the H(2)O.OH complex, the impact of the excited state on the chemical behavior of the OH radical can be very important. We perform a potential energy surface scan using the CCSD(T)/aug-cc-pVTZ level of electronic structure theory for both excited and ground states. To model the physics of the unpaired electron in the OH radical, we develop a tensor polarizability generalization of the Thole-type all-atom polarizable rigid potential for the OH radical, which effectively describes the interaction of OH with H(2)O for both ground and excited states. The stationary points of (H(2)O)(n)OH clusters were identified as a benchmark of the potential.

Thermodynamic Analysis of the Temperature Dependence of OH Adsorption on Pt(111) and Pt(100) Electrodes in Acidic Media in the Absence of Specific Anion Adsorption

The effect of temperature on the voltammetric OH adsorption on Pt(111) and Pt(100) electrodes in perchloric acid media has been studied. From a thermodynamic analysis based on a generalized adsorption isotherm, DeltaG degrees , DeltaH degrees , and DeltaS degrees values for the adsorption of OH have been determined. On Pt(111), the adsorption enthalpy ranges between -265 and -235 kJ mol(-1), becoming less exothermic as the OH coverage increases. These values are in reasonable agreement with experimental data and calculated values for the same reaction in gas phase. The adsorption entropy for OH adsorption on Pt(111) ranges from -200 J mol(-1) K(-1) (low coverage) to -110 J mol(-1) K(-1) (high coverage). On the other hand, the enthalpy and entropy of hydroxyl adsorption on Pt(100) are less sensitive to coverage variations, with values ca. DeltaH degrees = -280 kJ mol(-1) and DeltaS degrees = -180 J mol(-1) K(-1). The different dependence of DeltaS degrees with coverage on both electrode surfaces stresses the important effect of the substrate symmetry on the mobility of adsorbed OH species within the water network directly attached to the metal surface.

Reactions associated with ionization in water: A directab initiodynamics study of ionization in (H2O)17

Quasiclassical ab initio simulations of the ionization dynamics in a (H(2)O)(17) cluster, the first water cluster that includes a fourfold coordinated (internally solvated) water molecule, have been carried out to obtain a detailed picture of the elementary processes and energy redistribution induced by ionization in a model of aqueous water. General features observable from the simulations are the following: (i) well within 100 fs following the ionization, one or more proton transfers are seen to take place from the "ionized molecule" to neighboring molecules and beyond, forming a hydronium ion and a hydroxyl radical; (ii) two water molecules close to the ionized water molecule play an important role in the reaction, in what we term a "reactive trimer." The reaction time is gated by the encounter of the ionized water molecule with these two neighboring molecules, and this occurs anytime between 10 and 50 fs after the ionization. The distances of approach between the ionized molecule and the neighboring molecules indeed display best the time characteristics of the transfer of a proton, and thus of the formation of a hydronium ion and a OH radical. These findings are consistent with those for smaller cyclic clusters, albeit the dynamics of the proton transfer displays more varieties in the larger cluster than in the small cyclic clusters. We used a partitioning scheme for the kinetic energy in the (H(2)O)(17) system that distinguishes between the reactive trimer and the surrounding "medium." The analysis of the simulations indicates that the kinetic energy of the surrounding medium increases markedly right after the event of ionization, a manifestation of the local heating of the medium. The increase in kinetic energy is consistent with a reorganization of the surrounding medium, electrostatically forced in a very short time by the water cation and in a longer time by the formation of the hydronium ion.

Density Functional Theory Study of Tetrathiafulvalene and Thianthrene in Acetonitrile: Structure, Dynamics, and Redox Properties†

The redox potentials of the organic compounds tetrathiafulvalene (TTF) and thianthrene (TH) in an explicit aprotic polar solvent, acetonitrile, have been computed using ab initio molecular dynamics simulation based on a Gaussian basis set methodology. The density functional description of the pure solvent yields a diffuse and mobile liquid, with structural and dynamical properties that are in good agreement with earlier classical models and experiment. Molecular dynamics simulation of both solute species in their neutral and radical cation states combined with free energy difference calculations result in estimates for the redox potentials of the reactions TH*+ + TTF --> TH + TTF*+ and TH2+ + TTF*+ --> TH*+ + TTF2+. The obtained values are 0.95 +/- 0.06 and 1.09 +/- 0.06 V, respectively, in excellent agreement with experimental data of 0.93 and 1.08 V. Our computational approach is based on Marcus theory, assuming quadratic free energy surfaces. We show that this approximation can still be accurate in systems, such as TH, that undergo a significant change in geometry upon oxidation. Furthermore, despite the different localization of the spin density in the radical cations, results based on self-interaction-corrected functionals and on standard generalized gradient approximations are identical to within 10 meV.

Modeling solvent effects on electron-spin-resonance hyperfine couplings by frozen-density embedding

In this study, we investigate the performance of the frozen-density embedding scheme within density-functional theory [J. Phys. Chem. 97, 8050 (1993)] to model the solvent effects on the electron-spin-resonance hyperfine coupling constants (hfcc's) of the H2NO molecule. The hfcc's for this molecule depend critically on the out-of-plane bending angle of the NO bond from the molecular plane. Therefore, solvent effects can have an influence on both the electronic structure for a given configuration of solute and solvent molecules and on the probability for different solute (plus solvent) structures compared to the gas phase. For an accurate modeling of dynamic effects in solution, we employ the Car-Parrinello molecular-dynamics (CPMD) approach. A first-principles-based Monte Carlo scheme is used for the gas-phase simulation, in order to avoid problems in the thermal equilibration for this small molecule. Calculations of small H2NO-water clusters show that microsolvation effects of water molecules due to hydrogen bonding can be reproduced by frozen-density embedding calculations. Even simple sum-of-molecular-densities approaches for the frozen density lead to good results. This allows us to include also bulk solvent effects by performing frozen-density calculations with many explicit water molecules for snapshots from the CPMD simulation. The electronic effect of the solvent at a given structure is reproduced by the frozen-density embedding. Dynamic structural effects in solution are found to be similar to the gas phase. But the small differences in the average structures still induce significant changes in the computed shifts due to the strong dependence of the hyperfine coupling constants on the out-of-plane bending angle.

Classical molecular-dynamics simulation of the hydroxyl radical in water

We have studied the hydration and diffusion of the hydroxyl radical OH0 in water using classical molecular dynamics. We report the atomic radial distribution functions, hydrogen-bond distributions, angular distribution functions, and lifetimes of the hydration structures. The most frequent hydration structure in the OH0 has one water molecule bound to the OH0 oxygen (57% of the time), and one water molecule bound to the OH0 hydrogen (88% of the time). In the hydrogen bonds between the OH0 and the water that surrounds it the OH0 acts mainly as proton donor. These hydrogen bonds take place in a low percentage, indicating little adaptability of the molecule to the structure of the solvent. All hydration structures of the OH0 have shorter lifetimes than those corresponding to the hydration structures of the water molecule. The value of the diffusion coefficient of the OH0 obtained from the simulation was 7.1x10(-9) m2 s(-1), which is higher than those of the water and the OH-.

Molecular Dynamics Simulations of Atmospheric Oxidants at the Air−Water Interface: Solvation and Accommodation of OH and O3

A comparative study of OH, O3, and H2O equilibrium aqueous solvation and gas-phase accommodation on liquid water at 300 K is performed using a combination of ab initio calculations and molecular dynamics simulations. Polarizable force fields are developed for the interaction potential of OH and O3 with water. The free energy profiles for transfer of OH and O3 from the gas phase to the bulk liquid exhibit a pronounced minimum at the surface, but no barrier to solvation in the bulk liquid. The calculated surface excess of each oxidant is comparable to calculated and experimental values for short chain, aliphatic alcohols. Driving forces for the surface activity are discussed in terms of the radial distribution functions and dipole orientation distributions for each molecule in the bulk liquid and at the surface. Simulations of OH, O3, and H2O impinging on liquid water with a thermal impact velocity are used to calculate thermal accommodation (S) and mass accommodation (alpha) coefficients. The values of S for OH, O3, and H2O are 0.95, 0.90, and 0.99, respectively. The approaching molecules are accelerated toward the liquid surface when they are approximately 5 angstroms above it. The molecules that reach thermal equilibrium with the surface do so within 2 ps of striking the surface, while those that do not scatter into the gas phase with excess translational kinetic energy in the direction perpendicular to the surface. The time constants for absorption and desorption range from approximately 35 to 140 ps, and the values of alpha for OH, O3, and H2O are 0.83, 0.047, and 0.99, respectively. The results are consistent with previous formulations of gas-phase accommodation from simulations, in which the process occurs by rapid thermal and structural equilibration followed by diffusion on the free energy profile. The implications of these results with respect to atmospheric chemistry are discussed.