Marilia T. C. Martins-Costa

A COUPLED DENSITY FUNCTIONAL-MOLECULAR MECHANICS MONTE CARLO SIMULATION METHOD : THE WATER MOLECULE IN LIQUID WATER

A theoretical model to investigate chemical processes in solution is described. It is based on the use of a coupled density functional/molecular mechanics Hamiltonian. The most interesting feature of the method is that it allows a detailed study of the solutes electronic distribution and of its fluctuations. We present the results for isothermal‐isobaric constant‐NPT Monte Carlo simulation of a water molecule in liquid water. The quantum subsystem is described using a double‐zeta quality basis set with polarization orbitals and nonlocal exchange‐correlation corrections. The classical system is constituted by 128 classical TIP3P or Simple Point Charge (SPC) water molecules. The atom‐atom radial distribution functions present a good agreement with the experimental curves. Differences with respect to the classical simulation are discussed. The instantaneous and the averaged polarization of the quantum molecule are also analyzed.

MOLECULAR DYNAMICS SIMULATIONS OF ELEMENTARY CHEMICAL PROCESSES IN LIQUID WATER USING COMBINED DENSITY FUNCTIONAL AND MOLECULAR MECHANICS POTENTIALS. I. PROTON TRANSFER IN STRONGLY H-BONDED COMPLEXES

The first molecular dynamics (MD) simulation of a chemical process in solution with an ab initio description of the reactant species and a classical representation of the solvent is presented. We study the dynamics of proton (deuterium) transfer in strongly hydrogen-bonded systems characterized by an energy surface presenting a double well separated by a low activation barrier. We have chosen the hydroxyl-water complex in liquid water to analyze the coupling between the reactive system and the environment. The proton is transferred from one well to the other with a frequency close to 1 ps−1 which is comparable to the low-frequency band associated to hindered translations, diffusional translation and reorientation of water molecules in water. The proton transfer takes place in 20–30 fs whereas the solvent response is delayed by about 50 fs. Therefore, the reaction occurs in an essentially frozen-solvent configuration. In principle, this would produce a barrier increase with respect to the equilibrium react...

Improving description of hydrogen bonds at the semiempirical level: water–water interactions as test case

Hydrogen bonding is not well described by available semiempirical theories. This is an important restriction because hydrogen bonds represent a key feature in many chemical and biochemical processes, besides being responsible for the singular properties of water. In this study, we describe a possible solution to this problem. The basic idea is to replace the nonphysical gaussian correction functions (GCF) appearing in the core–core repulsion terms of most MNDO‐based semiempirical methods by a simple function exhibiting the correct physical behavior in the whole range of intermolecular separation distances. The parameterized interaction function (PIF) is the sum of atom‐pair contributions, each one having five adjustable parameters. In this work, the approach is used to study water–water interactions. The parameters are optimized to reproduce a reference ab initio intermolecular energy surface for the water–water dimer obtained at the MP2/aug‐cc‐pVQZ level. OO, OH, and HH parameters are reported for the PM3 method. The results of PM3‐PIF calculations remarkably improve qualitatively and quantitatively those obtained at the standard PM3 level, both for water–dimer properties and for water clusters up to the hexamer. For example, the root‐mean‐square deviation of the PM3‐PIF interaction energies, with respect to ab initio values obtained using 700 points of the water dimer surface, is only 0.47 kcal/mol. This value is much smaller than that obtained using the standard PM3 method (4.2 kcal/mol). The PM3‐PIF water dimer energy minimum (−5.0 kcal/mol) is also much closer to ab initio data (−5.0±0.01 kcal/mol) than PM3 (−3.50 kcal/mol). The method is therefore promising for the development of new semiempirical approaches as well as for application of combined quantum mechanics and molecular mechanics techniques to investigate chemical processes in water.

Molecular dynamics simulations of elementary chemical processes in liquid water using combined density functional and molecular mechanics potentials. II. Charge separation processes

A new approach to carry out molecular dynamics simulations of chemical reactions in solution using combined density functional theory/molecular mechanics potentials is presented. We focus our attention on the analysis of reactive trajectories, dynamic solvent effects and transmission coefficient rather than on the evaluation of free energy which is another important topic that will be examined elsewhere. In a previous paper we have described the generalities of this hybrid molecular dynamics method and it has been employed to investigate low energy barrier proton transfer process in water. The study of processes with activation energies larger than a few kT requires the use of specific techniques adapted to “rare events” simulations. We describe here a method that consists in the simulation of short trajectories starting from an equilibrated transition state in solution, the structure of which has been approximately established. This calculation is particularly efficient when carried out with parallel computers since the study of a reactive process is decomposed in a set of short time trajectories that are completely independent. The procedure is close to that used by other authors in the context of classical molecular dynamics but present the advantage of describing the chemical system with rigorous quantum mechanical calculations. It is illustrated through the study of the first reaction step in electrophilic bromination of ethylene in water. This elementary process is representative of many charge separation reactions for which static and dynamic solvent effects play a fundamental role.

Coupled density functional/molecular mechanics Monte Carlo simulations of ions in water. The bromide ion

Abstract A recently developed NPT Monte Carlo method using density functional theory/molecular mechanics potentials is applied to study ion hydration. Test calculations for Na+ and Cl− are in agreement with experimental and classical simulation results. In the case of Br− the DFT/MM atom-atom radial distribution function is in better agreement with the experimental bromide-oxygen distance than that obtained in the classical simulation. Both models predict a preferred linear BrH0 arrangement. Fluctuations of the bromide ion electronic cloud are illustrated through the calculation of the instantaneous dipole moment of the ion.

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.

Reactivity of volatile organic compounds at the surface of a water droplet.

Knowledge of the role of water droplets and aerosols in atmospheric chemistry is crucial to significantly improve our understanding of global warming and air quality. Chemistry at the air/water interface, in particular, is still poorly understood. There is a great need to understand how clouds and aerosols process chemistry of organics prevalent in the atmosphere. We report in this study the first computer simulation of a volatile organic compound (formaldehyde) at the air/water interface with explicit description of its ground and excited states electronic properties. We use an elaborated technique that combines molecular dynamics simulations together with a quantum/classical description of the formaldehyde-water system. We show that in spite of a large affinity for water, formaldehyde exhibits a preference for the air/water interface with respect to the bulk, roughly by 1.5 kcal/mol. Another important finding in our simulations is that frontier orbitals HOMO and LUMO undergo substantial stabilization at the interface due to surface water reorientation, which induces a local positive electrostatic potential. Such a potential is significantly larger than the one estimated in bulk water suggesting that the reactivity of formaldehyde could change with respect to both gas phase and bulk water. The conclusions presented in this work are expected to help/guide future experiments studying the chemical reactivity of volatile organic compounds at the air/water interface.

Reactivity of Atmospherically Relevant Small Radicals at the Air–Water Interface†

Aerosols and clouds play important roles in atmospheric chemistry, but molecular details of the process are not yet completely understood, despite many investigations carried out in the last few years. On one hand, the uptake of a compound into an aerosol or a water droplet modifies its gas-phase concentration and chemical kinetics. On the other hand, the condensed phase allows for otherwise unfeasible processes to occur in the atmosphere, ionic reactions in aqueous environments being a prototypical example. Indeed, the chemistry of one of the most important atmospheric species, the hydroperoxyl radical HO2, is thought to be highly influenced by these type of reactions. HO2 is acidic (pKa 4.7) and can be efficiently scavenged by cloud droplets through the following processes:

Studies of solvent effects using density functional theory. Co-operative interactions in H3N...HBr proton transfer

Abstract A self-consistent reaction field model is used to study solvent co-operative effects in ammonia—hydrogen bromide intermolecular interactions. Computations are carried out in the framework of density functional theory using gradient corrected exchange—correlation potentials. The fundamental equations of this SCRF-DFT model are given. Full geometry optimization is performed. In non-polar as well as in polar media, only one energy minimum is found. In the last case, the optimized structure can be represented by an ion pair. The role played by electronic polarization is emphasized.

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

Significance Ozone is one of the most important atmospheric trace gases in Earths atmosphere. It can interact with water in the gas phase as well as with water in cloud droplet surfaces. This work identifies unique spectral signatures for ozone adsorbed at the surface of cloud water droplets in the UV and visible light domains. The adsorption process itself is thermodynamically spontaneous. With this information, it is found that the photochemistry of ozone at the air–water interface is a significant previously unidentified source of OH radicals generated at the surface of clouds. The broader implication is that the surface of cloud water droplets can be an active chemical reactor that contributes to the oxidizing capacity of the troposphere on a global scale. 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(3P) + O2(X3Σg−) 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.