Density functional theory based molecular dynamics study of solution composition effects on the solvation shell of metal ions

We present an ab initio molecular dynamics study of the alkali metal ions Li+, Na+, K+ and Cs+, and of the alkaline earth metal ions Mg2+ and Ca2+ in both pure water and electrolyte solutions containing the counterions Cl- and SO42-. Simulations were conducted using different density functional theory methods (PBE, BLYP and revPBE), with and without the inclusion of dispersion interactions (-D3). Analysis of the ion-water structure and interaction strength, water exchange between the first and second hydration shell, and hydrogen bond network and low-frequency reorientation dynamics around the metal ions have been used to characterise the influence of solution composition on the ionic solvation shell. Counterions affect the properties of the hydration shell not only when they are directly coordinated to the metal ion, but also when they are at the second coordination shell. Chloride ions reduce the sodium hydration shell and expand the calcium hydration shell by stabilizing under-coordinated hydrated Na(H2O)5+ complexes and over-coordinated Ca(H2O)72+. The same behaviour is observed in CaSO4(aq), where Ca2+ and SO42- form almost exclusively solvent-shared ion pairs. Water exchange between the first and second hydration shell around Ca2+ in CaSO4(aq) is drastically decelerated compared with the simulations of the hydrated metal ion (single Ca2+, no counterions). Velocity autocorrelation function analysis, used to probe the strength of the local ion-water interaction, shows a smoother decay of Mg2+ in MgCl2(aq), which is a clear indication of a looser inter-hexahedral vibration in the presence of chloride ions located in the second coordination shell of Mg2+. The hydrogen bond statistics and orientational dynamics in the ionic solvation shell show that the influence on the water-water network cannot only be ascribed to the specific cation-water interaction, but also to the subtle interplay between the level of hydration of the ions, and the interactions between ions, especially those of opposite charge. As many reactive processes involving solvated metal ions occur in environments that are far from pure water but rich in ions, this computational study shows how the solution composition can result in significant differences in behaviour and function of the ionic solvation shell

Beyond Continuum Solvent Models in Computational Homogeneous Catalysis

Altres ajuts: Acord transformatiu CRUE-CSICIn homogeneous catalysis solvent is an inherent part of the catalytic system. As such, it must be considered in the computational modeling. The most common approach to include solvent effects in quantum mechanical calculations is by means of continuum solvent models. When they are properly used, average solvent effects are efficiently captured, mainly those related with solvent polarity. However, neglecting atomistic description of solvent molecules has its limitations, and continuum solvent models all alone cannot be applied to whatever situation. In many cases, inclusion of explicit solvent molecules in the quantum mechanical description of the system is mandatory. The purpose of this article is to highlight through selected examples what are the reasons that urge to go beyond the continuum models to the employment of micro-solvated (cluster-continuum) of fully explicit solvent models, in this way setting the limits of continuum solvent models in computational homogeneous catalysis. These examples showcase that inclusion of solvent molecules in the calculation not only can improve the description of already known mechanisms but can yield new mechanistic views of a reaction. With the aim of systematizing the use of explicit solvent models, after discussing the success and limitations of continuum solvent models, issues related with solvent coordination and solvent dynamics, solvent effects in reactions involving small, charged species, as well as reactions in protic solvents and the role of solvent as reagent itself are successively considered

How Solvent Dynamics Controls the Schlenk Equilibrium of Grignard Reagents: A Computational Study of CH₃MgCl in Tetrahydrofuran

The Schlenk equilibrium is a complex reaction governing the presence of multiple chemical species in solution of Grignard reagents. The full characterization at the molecular level of the transformation of CH₃MgCl into MgCl₂ and Mg(CH₃)₂ in tetrahydrofuran (THF) by means of ab initio molecular dynamics simulations with enhanced-sampling metadynamics is presented. The reaction occurs via formation of dinuclear species bridged by chlorine atoms. At room temperature, the different chemical species involved in the reaction accept multiple solvation structures, with two to four THF molecules that can coordinate the Mg atoms. The energy difference between all dinuclear solvated structures is lower than 5 kcal mol⁻¹. The solvent is shown to be a direct key player driving the Schlenk mechanism. In particular, this study illustrates how the most stable symmetrically solvated dinuclear species, (THF)CH₃Mg(μ-Cl)₂MgCH₃(THF) and (THF)CH₃Mg(μ-Cl)(μ-CH₃)MgCl(THF), need to evolve to less stable asymmetrically solvated species, (THF)CH₃Mg(μ-Cl)₂MgCH₃(THF)₂ and (THF)CH₃Mg(μ-Cl)(μ-CH₃)MgCl(THF)₂, in order to yield ligand exchange or product dissociation. In addition, the transferred ligands are always departing from an axial position of a pentacoordinated Mg atom. Thus, solvent dynamics is key to successive Mg–Cl and Mg–CH₃ bond cleavages because bond breaking occurs at the most solvated Mg atom and the formation of bonds takes place at the least solvated one. The dynamics of the solvent also contributes to keep relatively flat the free energy profile of the Schlenk equilibrium. These results shed light on one of the most used organometallic reagents whose structure in solvent remains experimentally unresolved. These results may also help to develop a more efficient catalyst for reactions involving these species

Theoretical Investigation of Fundamental Cathode Processes in Metal-02 Batteries

In this thesis we theoretically explore the different fundamental phenomena associated with metal-air batteries (where the metal can be Li, Na or K) using first principles density functional theory. We start by investigating the adsorption of the starting reactants/primary intermediates i.e. metal superoxides and superoxide anion on Au(111) and Au(211). We elucidate the influence of electric fields and the importance of including explicit solvents on the adsorption energy of these intermediates. We show that these effects are considerable and should be included for future reaction modeling of these batteries. Following this we investigate the reaction of M+ and O2‑ in solution phase where the solvents considered are dimethyl sulfoxide (DMSO) and Acetonitrile (ACN), which are commonly used electrolytes in these batteries. We show the for Li-O2 pair the peroxide species is the most stable final product while for Na-O2 and K-O2 pairs the metal superoxide is the most stable species. We explore the possibility of dimerization and trimerization of the metal superoxide and peroxide in solvent and show that only Li2O2 tends form clusters in solution. Next we proceed to investigate the discharge product formed as a result of the metal assited oxygen reduction reaction (M-ORR). We only consider the discharge product for Li-O2 batteries where the primary discharge product is Li2O2. We show that doping the discharge product during the electrochemical growth phase with solvated dopant/metal cations could lead to microdomains of discharge product. We use evolutionary algorithm as implemented in the USPEX package in conjunction with DFT to probe the potential energy surface for novel configurations of composition Li15DO16 (stoichiometric composition) and Li14DO16 (composition representing a structure with vacancy). Where D is the dopant atom. We consider Ba, Co, Mg Na and Ni ions as dopants which are commonly found as solvated ions in batteries. We show thermodynamically that these structures can viably form as compared to the P63/mmc Föppl structure of Li2O2. Additionally, we show that novel doped structures improve on the electron mobility through the bulk aiding in reduction of overpotential

A Multi-Scale Computational Study on the Mechanism of Streptococcus pneumoniae Nicotinamidase (SpNic)

Nicotinamidase (Nic) is a key zinc-dependent enzyme in NAD metabolism that catalyzes the hydrolysis of nicotinamide to give nicotinic acid. A multi-scale computational approach has been used to investigate the catalytic mechanism, substrate binding and roles of active site residues of Nic from Streptococcus pneumoniae (SpNic). In particular, density functional theory (DFT), molecular dynamics (MD) and ONIOM quantum mechanics/molecular mechanics (QM/MM) methods have been employed. The overall mechanism occurs in two stages: (i) formation of a thioester enzyme-intermediate (IC2) and (ii) hydrolysis of the thioester bond to give the products. The polar protein environment has a significant effect in stabilizing reaction intermediates and in particular transition states. As a result, both stages effectively occur in one step with Stage 1, formation of IC2, being rate limiting barrier with a cost of 53.5 kJ•mol−1 with respect to the reactant complex, RC. The effects of dispersion interactions on the overall mechanism were also considered but were generally calculated to have less significant effects with the overall mechanism being unchanged. In addition, the active site lysyl (Lys103) is concluded to likely play a role in stabilizing the thiolate of Cys136 during the reaction