Full Solvation Research Articles

Assignment of a Physical Energy Scale for the Dimensionless Interaction Energies within the PRIME20 Peptide Model.

We present a calibration scheme to determine the conversion factors from a coarse-grained stochastic approximation Monte Carlo approach using the PRIME20 peptide interaction model to atomistic force-field interaction energies at full explicit aqueous solvation. The conversion from coarse-grained to atomistic structures was performed according to our previously established inverse coarse-graining protocol. We provide a physical energy scale for both the backbone hydrogen bonding interactions and the sidechain interactions by correlating the dimensionless energy descriptors of the PRIME20 model with the energies averaged over molecular dynamics simulations. The conversion factor for these interactions turns out to be around 2 kJ/mol for the backbone interactions, and zero for the sidechain interactions. We discuss these surprisingly small values in terms of their molecular interpretation.

In Situ Pore Formation in Graphite Through Solvent Co‐Intercalation: A New Model for The Formation of Ternary Graphite Intercalation Compounds Bridging Batteries and Supercapacitors

AbstractFor Li‐ion and Na‐ion batteries, the intercalation behavior of graphite anodes is quite different. While Li‐ions intercalate, Na‐ions only co‐intercalate with solvent molecules from the electrolyte solution leading to ternary graphite intercalation compound (t‐GIC) formation along with an expansion of the graphite interlayer spacing to 1.2 nm. This large interlayer spacing represents a micropore with parallel slit geometry. Little is known about t‐GIC formation, but it is commonly believed that throughout the reaction the ion is accompanied by either a full or partial solvation shell. Here, it is elucidated for the first time, using two independent methods – mass measurements and electrochemical impedance spectroscopy – supplemented by operando microscopy, entropymetry and simulations, that the storage mechanism is far more complex. A new model for the electrochemical solvent co‐intercalation process is proposed: As soon as solvated ions enter, the graphite structure is flooded with free solvents, which are subsequently replaced by solvated ions. Close to full sodiation, few free solvents remain and structural rearrangement take place to reach the full storage capacity. Thus, t‐GICs represent a unique case of switchable microporous systems and hence appear as a bridge between ion storage in the bulk phase and in micropores, i.e., between batteries and supercapacitors.

Concentration Dependence of Dynamics and Structure among Hydrated Magnesium Ions: An Ultrafast Infrared Study.

The dynamics of aqueous magnesium chloride solutions, from relatively dilute (0.5 m) to near saturated (4.2 m) concentrations, were investigated using ultrafast two dimensional infrared and polarization selective pump-probe spectroscopies. The experiments were performed on two spectrally distinct nitrile stretch frequencies of the selenocyanate vibrational probe, corresponding to the CN nitrogen lone pair being associated with water and with Mg2+. No chemical exchange of the two species was observed over the experimental time scale (∼100 ps), enabling straightforward analysis of their dynamics. The dynamics reported by the Mg2+-associated peak are slower than those of the water-associated peak, suggesting that the immediate environment of the hydrated Mg2+ is different from the rest of the solution. Notably, the Mg2+-associated peak displays three spectral diffusion time scales, the slowest being ∼30 ps, while the water-associated peak decays as a faster biexponential. From the complete orientational relaxation time and hydrodynamic theory, a magnesium hydration number of six was obtained, which is in good agreement with NMR and X-ray diffraction studies. This hydration number holds for all concentrations until near saturation, when the linewidths and the dynamics deviate from linear trends, indicative of Mg2+ solvation structure changes resulting from a shortage of water molecules needed for full solvation.

Entropic Effects on the Aqueous Microsolvation of Protonated Glycine and Protonated β-Alanine. Hybrid Density Functional Theory Born-Oppenheimer Molecular Dynamics Studies.

Recent low-temperature infrared-based experimental studies provided information about the effects of aqueous microsolvation on the intramolecular hydrogen bond of protonated glycine and β-alanine [J. Phys. Chem. A 2019, 123, 3355]. Here we address the temperature-dependent entropic effects on the aqueous microsolvation patterns of these protonated amino acids using the AAH+(H2O)n (n = 1-8) cluster model at 50 K and room temperature with Born-Oppenheimer molecular dynamics using a calibrated hybrid density functional. The CCOOH-Ow, N-Ow, and center-of-mass-Ow radial distribution functions provide accurate structural data and temperature-dependent water coordination numbers vs. solvation degree. The solvation patterns for protonated glycine at 50 K show structural features in agreement with previous static optimizations. However, entropic effects at room temperature play a crucial role in the evolution of the intramolecular HB strength vs. solvation degree for both protonated amino acids. With increasing hydration entropic effects favor the making of solvent hydrogen bond networks over full solvation of protonated glycine. At room temperature four water molecules are needed to build the first solvation shell for protonated glycine while five are required for protonated β-alanine. A new statistical Cumulative Percentage of Structures (CPS) scheme is proposed; when the CPS data are analyzed in light of the empirical formula of Rozenberg et al. [Phys. Chem. Chem. Phys. 2000, 2, 2699] and the hydrogen bond relative strength (HBRS) criteria of Jeffrey [An Introduction to Hydrogen Bonding; Oxford University: 1997] we can provide a detailed molecular mechanism for the weakening of the intramolecular hydrogen bond based on the average dynamical structures, which clearly reveals the temperature dependence of this process. The new CPS-HBRS scheme proposed here can be utilized using any type of molecular dynamics trajectory (classical, BOMD, CPMD, etc.).

Resolving the odd-even oscillation of water dissociation at rutile TiO2(110)-water interface by machine learning accelerated molecular dynamics.

Aqueous rutile TiO2(110) is the most widely studied water-oxide interface, and yet questions about water dissociation are still controversial. Theoretical studies have systematically investigated the influence of the slab thickness on water dissociation energy (Ediss) at 1 monolayer coverage using static density functional theory calculation and found that Ediss exhibits odd-even oscillation with respect to the TiO2 slab thickness. However, less studies have accounted for the full solvation of an aqueous phase using ab initio molecular dynamics due to high computational costs in which only three, four, and five trilayer models of rutile(110)-water interfaces have been simulated. Here, we report Machine Learning accelerated Molecular Dynamics (MLMD) simulations of defect-free rutile(110)-water interfaces, which allows for a systematic study of the slab thickness ranging from 3 to 17 trilayers with much lower costs while keeping ab initio accuracy. Our MLMD simulations show that the dissociation degree of surface water (α) oscillates with the slab thickness and converges to ∼2% as the TiO2 slab becomes thicker. Converting α into dissociation free energy (ΔAdiss) and comparing with dissociation total energy Ediss calculated with a single monolayer of water, we find that the full solvation of the interfaces suppresses surface water from dissociating. It is interesting to note that the machine learning potential trained from the dataset containing exclusively the five trilayer TiO2 model exhibits excellent transferability to other slab thicknesses and further captures the oscillating behavior of surface water dissociation. Detailed analyses indicate that the central plane in odd trilayer slabs modulates the interaction between double trilayers and, thus, the bonding strength between terminal Ti and water, which affects pKa of surface water and water dissociation degree.

Real-Time Observation of Solvation Dynamics of Electron in Actinide Extraction Binary Solutions of Water and n-Tributyl Phosphate.

The excess electron in solution is a highly reactive radical involved in various radiation-induced reactions. Its solvation state critically determines the subsequent pathway and rate of transfer. For instance, water plays a dominating role in the electron-induced dealkylation of n-tributyl phosphate in actinide extraction processing. However, the underlying electron solvation processes in such systems are lacking. Herein, we directly observed the solvation dynamics of electrons in H-bonded water and n-tributyl phosphate (TBP) binary solutions with a mole fraction of water (Xw) varying from 0.05 to 0.51 under ambient conditions. Following the evolution of the absorption spectrum of trapped electrons (not fully solvated) with picosecond resolution, we show that electrons statistically distributed would undergo preferential solvation within water molecules extracted in TBP. We determine the time scale of excess electron full solvation from the deconvoluted transient absorption-kinetical data. The process of solvent reorganization accelerates by increasing the water molar fraction, and the rate of this process is 2 orders of magnitude slower compared to bulk water. We assigned the solvation process to hydrogen network reorientation induced by a negative charge of the excess electron that strongly depends on the local water environment. Our findings suggest that water significantly stabilizes the electron in a deeper potential than the pure TBP case. In its new state, the electron is likely to inhibit the dealkylation of extractants in actinide separation.

Determining Partial Atomic Charges for Liquid Water: Assessing Electronic Structure and Charge Models.

Partial atomic charges provide an intuitive and efficient way to describe the charge distribution and the resulting intermolecular electrostatic interactions in liquid water. Many charge models exist and it is unclear which model provides the best assignment of partial atomic charges in response to the local molecular environment. In this work, we systematically scrutinize various electronic structure methods and charge models (Mulliken, natural population analysis, CHelpG, RESP, Hirshfeld, Iterative Hirshfeld, and Bader) by evaluating their performance in predicting the dipole moments of isolated water, water clusters, and liquid water as well as charge transfer in the water dimer and liquid water. Although none of the seven charge models is capable of fully capturing the dipole moment increase from isolated water (1.85 D) to liquid water (about 2.9 D), the Iterative Hirshfeld method performs best for liquid water, reproducing its experimental average molecular dipole moment, yielding a reasonable amount of intermolecular charge transfer, and showing modest sensitivity to the local water environment. The performance of the charge model is dependent on the choice of the density functional and the quantum treatment of the environment. The computed molecular dipole moment of water generally increases with the percentage of the exact Hartree-Fock exchange in the functional, whereas the amount of charge transfer between molecules decreases. For liquid water, including two full solvation shells of surrounding water molecules (within about 5.5 Å of the central water) in the quantum chemical calculation converges the charges of the central water molecule. Our final pragmatic quantum chemical charge-assigning protocol for liquid water is the Iterative Hirshfeld method with M06-HF/aug-cc-pVDZ and a quantum region cutoff radius of 5.5 Å.

The important role of non-covalent interactions for the vibrational circular dichroism of lactic acid in aqueous solution

We present a computational study of vibrational circular dichroism (VCD) in solutions of (S)-lactic acid, relying on ab initio molecular dynamics (AIMD) and full solvation with bulk water.

Understanding the precursor chemistry for one-step deposition of mixed cation perovskite solar cells by methylamine route

Upscaling perovskite solar cell fabrication is one of the key challenges in the pathway for commercialization. The slow evaporation of frequently used solvents (DMF or DMSO) limits the fast perovskite layer crystallization, hindering their implementation in large scale deposition methods. Alternatively, methylamine-based precursors have demonstrated rapid crystallization, leading to uniform and specular films. Nonetheless, their application has been limited to MAPbI3 perovskites with limited efficiency and stability. In this work, we report the requirements for stabilizing α-phase of mixed cation perovskites with high amount of formamidinium by using a methylamine-based precursor. We found that even though, there are many methods for incorporating the methylamine (MA) in precursors or films; the MA content determines stabilization of the α-phase and therefore the viscous-solution route is the only method to incorporate high amounts of MA. At low amounts of MA, perovskite tend to crystallize in 1D dimensional FA3(MA)PbI5 phases due to the incomplete solvation of the PbI6− clusters. In contrast, high MA ratio induces a full solvation of the clusters, leading to a rapid crystallization and a full stabilization of the active 3D α-phase. These results open a window in the development and understanding of new precursors for the fabrication of high efficient, stable and scalable perovskite devices.

Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology.

The catalytic properties of RNA have been a subject of fascination and intense research since their discovery over 30 years ago. Very recently, several classes of nucleolytic ribozymes have emerged and been characterized structurally. Among these, the twister ribozyme has been center-stage, and a topic of debate about its architecture and mechanism owing to conflicting interpretations of different crystal structures, and in some cases conflicting interpretations of the same functional data. In the present work, we attempt to clean up the mechanistic "debris" generated by twister ribozymes using a comprehensive computational RNA enzymology approach aimed to provide a unified interpretation of existing structural and functional data. Simulations in the crystalline environment and in solution provide insight into the origins of observed differences in crystal structures, and coalesce on a common active site architecture, and dynamical ensemble in solution. We use GPU-accelerated free energy methods with enhanced sampling to ascertain microscopic nucleobase pK a values of the implicated general acid and base, from which predicted activity-pH profiles can be compared directly with experiments. Next, ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with full dynamic solvation under periodic boundary conditions are used to determine mechanistic pathways through multi-dimensional free energy landscapes for the reaction. We then characterize the rate-controlling transition state, and make predictions about kinetic isotope effects and linear free energy relations. Computational mutagenesis is performed to explain the origin of rate effects caused by chemical modifications and make experimentally testable predictions. Finally, we provide evidence that helps to resolve conflicting issues related to the role of metal ions in catalysis. Throughout each stage, we highlight how a conserved L-platform structural motif, to- gether with a key L-anchor residue, forms the characteristic active site scaffold enabling each of the catalytic strategies to come together not only for the twister ribozyme, but the majority of the known small nucleolytic ribozyme classes.

Why are trace amounts of chloride so highly surface-active?

On many metals, small quantities of chloride are known to be adsorbed at potentials well below the potential of zero charge and to influence other electrochemical processes. In order to understand this behavior, we have investigated the adsorption of a single Cl− ion from aqueous solution by a combination of density functional theory and classical molecular dynamics, taking Au(111) as a model surface. While in the vacuum, Cl is adsorbed directly on the surface in the 3-fold hollow sites, whereas in aqueous solution, the optimal position lies a fraction of an Ångstrom towards the solution, where the ion is almost fully solvated and mobile in the direction parallel to the surface. As a result, the adsorption of a single ion is exothermic by about −0.6 eV, even at the potential of zero charge. This adsorption behavior is limited to low coverages because the adsorbates repel each other and because full solvation shells can only form at low coverage.

Ab Initio Molecular Dynamics Reveal Spectroscopic Siblings and Ion Pairing as New Challenges for Elucidating Prenucleation Aluminum Speciation.

The characterization of prenucleation species is essential to understand crystallization mechanisms across many chemical systems and often involves the use of vibrational spectroscopy. Nowhere is this more evident than in the development of "green" aluminum processing technologies, where detailed understanding of the speciation of aluminum and its polynuclear analogues in highly alkaline, low water solutions is elusive. The aluminate anion Al(OH)4- predominates in alkaline conditions, yet equilibrium with dimeric species, either μ-oxo Al2O(OH)62- or di-μ-hydroxo Al2(OH)82-, can be assumed. Using ab initio molecular dynamics with full solvation and the presence of counterions, this work reconciles previous contradictory studies that had concluded only a single species under relevant solution conditions. We reveal that the two dimers are energetically separated by 2 kcal/mol in pure water but that the stability of each can be reversed by ion pairing expected in saturated salt solutions. Simulated Raman and IR spectra for each species (accounting for anharmonicity and the fluctuating solvating environment) provide the first proof that the considered species are "spectroscopic siblings", whose multiple overlapping bands prevent definitive assertions in terms of speciation when compared to the experimental spectra. These observations are likely to hold in higher order aluminate oligomers and as such present a massive challenge toward understanding the crystallization mechanisms relevant to aluminum processing.

Analysis of Lithium Insertion/Desorption Reaction at Interfaces between Graphite Electrodes and Electrolyte Solution Using Density Functional + Implicit Solvation Theory

The charge transfer reaction at the electrode/solution interface is regarded as a major component that limits the current densities of Li-ion batteries. A combination of density functional theory for the electronic structure calculations of an electrode and a reacting component with implicit solvation theory for an electrolyte solution is used for the lithium insertion/desorption reaction (R). At the interfaces between tilted-graphite electrodes and a 1 M LiPF6 ethylene carbonate solution, the energy landscapes of reaction R are revealed under constant electron chemical potential conditions. Across the transition state where the Li forms a half solvation shell, the reacting Li inside the electrode changes to a full solvation structure in the solution accompanied by electron transfer. On graphite with two tilt angles, the activation energies at the equilibrium potentials of reaction R are approximately 0.6 eV, which is consistent with the electrochemical impedance spectroscopy measurements. However, opposi...

Exploring Solvation Effects in Ligand-Exchange Reactions via Static and Dynamic Methods.

We investigate ligand-exchange reactions of a biomimetic Co(II)-based heterocubane complex in aqueous solution by means of various approaches for consideration of solvent effects. Static calculations based on geometry optimizations carried out in vacuum, with solvent continuum models, or with several explicit solvent molecules have been carried out as well as density functional theory (DFT)-based molecular dynamics simulations. In addition, reaction pathways and barriers have been elucidated via nudged elastic band calculations and metadynamics. The results show that static approaches with approximate consideration of the solvent environment lead to reaction energies, which may change drastically depending on the method employed. A more sophisticated approach is DFT-molecular dynamics at ambient conditions with full solvation, i.e. enough solvent molecules to retain bulk water properties far from the solute, which, however, comes with a much higher computational cost. The investigated example of the exchange of an acetate ligand by a hydroxide demonstrates that entropic contributions can be vital and consideration of electronic energies alone may be a rather rough approximation.

Electrochemical behavior of platinum, gold and glassy carbon electrodes in water-in-salt electrolyte

Superconcentrated electrolytes, including water-in-salt solutions, are currently attracting major interest in the field of rechargeable batteries. These electrolytes could potentially find application in other electrochemical systems. Therefore, it is relevant to investigate the electrochemical behavior of common electrode materials such as platinum, gold and glassy carbon in these electrolytes. Preliminary cyclic voltammetry results revealed that the electrochemical stability window of the electrodes increased by about 0.5V for platinum and gold and 1V for glassy carbon when the lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) concentration is increased from 1 to 5M (mol/L). This increase is mainly due to the shift of the oxygen evolution potential to a more positive value in the more concentrated solution. In the latter, the H2O/Li+ molar ratio of 2.6 is insufficient for full solvation of Li+ cations. The positively charged electrode is therefore compensated mainly by TFSI− anions because the electrolyte contains a negligible amount of free water molecules, leading to an enhancement of the oxidative stability of the electrolyte.

Convergence of Excitation Energies in Mixed Quantum and Classical Solvent: Comparison of Continuum and Point Charge Models

Mixed quantum mechanical (QM)/classical methods provide a computationally efficient approach to modeling both ground and excited states in the condensed phase. To accurately model short-range interactions, some amount of the environment can be included in the QM region, whereas a classical model can treat long-range interactions to maintain computational affordability. The best computational protocol for these mixed QM/classical methods can be determined by examining convergence of molecular properties. Here, we compare molecular mechanical (MM) fixed point charges to a polarizable continuum model (PCM) for computing electronic excitations in solution. We computed the excitation energy of three pairs of neutral/anionic molecules in aqueous solvent, including up to 250 water molecules in the QM region. Interestingly, the convergence is similar for MM point charges and a PCM, with convergence achieved when at least one full solvation shell is treated with QM. Although the van der Waals (VDW) definition of the PCM cavity is adequate with small amounts of QM solvent, larger QM solvent layers had gaps in the VDW PCM cavity, leading to asymptotically incorrect excitation energies. Given that the VDW cavity leads to unphysical solute-solvent interactions, we advise using a solvent-excluded surface cavity for QM/PCM calculations that include QM solvent.

Adiabatic Approximation in Explicit Solvent Models of RedOx Chemistry.

We propose a calculation scheme that accelerates QM/MM simulations of solvated systems. This new approach is based on the adiabatic approximation whereby the solute degrees of freedom are separated from those of the solvent. More specifically, we assume that the solute electron density remains constant with respect to the relaxation of the solvent molecules. This allows us to achieve a dramatic speed-up of QM/MM calculations by discarding the slow self-consistent field cycle. We test this method by applying it to the calculation of the redox potential of aqueous transition metal ions. The root-mean-square deviation (RMSD) between the full solvation and adiabatic approximation is only 0.17 V. We find a RMSD from experimental values of 0.32 V for the adiabatic approximation as compared to 0.31 V for the full solvation model, so that the two methods are of essentially the same accuracy. Meanwhile, the adiabatic calculations are up to 10 times faster than the full solvation calculations, meaning that the method proposed here reduces the cost of QM/MM calculations while retaining the accuracy.

Parameter optimization in differential geometry based solvation models.

Differential geometry (DG) based solvation models are a new class of variational implicit solvent approaches that are able to avoid unphysical solvent-solute boundary definitions and associated geometric singularities, and dynamically couple polar and non-polar interactions in a self-consistent framework. Our earlier study indicates that DG based non-polar solvation model outperforms other methods in non-polar solvation energy predictions. However, the DG based full solvation model has not shown its superiority in solvation analysis, due to its difficulty in parametrization, which must ensure the stability of the solution of strongly coupled nonlinear Laplace-Beltrami and Poisson-Boltzmann equations. In this work, we introduce new parameter learning algorithms based on perturbation and convex optimization theories to stabilize the numerical solution and thus achieve an optimal parametrization of the DG based solvation models. An interesting feature of the present DG based solvation model is that it provides accurate solvation free energy predictions for both polar and non-polar molecules in a unified formulation. Extensive numerical experiment demonstrates that the present DG based solvation model delivers some of the most accurate predictions of the solvation free energies for a large number of molecules.

Gas-Phase Infrared and NMR Investigation of the Conformers of Diacetone Diperoxide (DADP).

Gas-phase infrared measurements of diacetone diperoxide (DADP) indicate a chair conformation with less than 5% of the predicted twist conformer. Vibrational frequencies are very similar to those previously measured in the solid state. Solution NMR measurements using 2D exchange spectroscopy (EXSY) also set a very low maximum limit on the equilibrium population of the twist conformer, with a room-temperature free-energy difference in excess of 14.5 kJ/mol. These experimental results are in accord with high-level quantum calculations incorporating full thermochemistry and solvation effects, which indicate a free-energy difference in the range of 14.7-17.5 kJ/mol in polar solvents.

Hydrogen Atom Transfer from Water or Alcohols Activated by Presolvated Electrons.

High-energy irradiation of protic solvents can transiently introduce excess electrons that are implicated in a diverse range of reductive processes. Here we report the evolution of electron solvation in water and in alcohols following photodetachment from aqueous hydroxide or the corresponding alkoxides studied by two- and three-pulse femtosecond spectroscopy and ab initio molecular dynamic simulations. The experiments reveal an ultrafast recombination channel of the excess electrons. Through the calculations this channel emerges as an H-atom transfer process to the hydroxyl or alkoxy radical species from neighboring solvent molecules, which are activated as the presolvated electron occupies their antibonding orbitals. The initially low activation barrier in the early stages of electron solvation was found to increase (from 12 to 44 kJ/mol in water) as full solvation proceeded.