A transferable classical force field to describe glyme based lithium solvate ionic liquids.

A non-polarizable force field for lithium (Li+) and bis(trifluoromethanesulfonyl)imide (TFSI-) ions solvated in diglyme at around 0.2 mol fraction salt concentration was developed based on ab initio molecular dynamics (AIMD) simulations and a modified polymer consistent force field model. A force-torque matching based scheme, in conjunction with a genetic algorithm, was used to determine the Lennard-Jones (LJ) parameters of the ion-ion and ion-solvent interactions. This force field includes a partial charge scaling factor and a scaling factor for the 1-4 interactions. The resulting force field successfully reproduces the radial distribution function of the AIMD simulations and shows better agreement compared to the unmodified force field. The new force field was then used to simulate salt solutions with glymes of increasing chain lengths and different salt concentrations. The comparison of the MD simulations, using the new force field, with experimental data at different salt concentrations and AIMD simulations on equimolar concentrations of the triglyme system demonstrates the transferability of the force field parameters to longer glymes and higher salt concentrations. Furthermore, the force field appears to reproduce the features of the experimental x-ray structure factors, suggesting accuracy beyond the first solvation shell, for equimolar salt solutions using both triglyme and tetraglyme as the solvent. Overall, the new force field was found to accurately reproduce the molecular descriptions of LiTFSI-glyme systems not only at various salt concentrations but also with glymes of different chain lengths. Thus, the new force field provides a useful and accurate tool to perform in silico studies of this family of systems at the atomistic level.

Effect of anion identity on ion association and dynamics of sodium ions in non-aqueous glyme based electrolytes-OTf vs TFSI.

Sodium-based rechargeable battery technologies are being pursued as an alternative to lithium, in part due to the relative abundance of sodium compared to lithium. Despite their low dielectric constant, glyme-based electrolytes are particularly attractive for these sodium-based batteries due to their ability to chelate with the sodium ion and their high electrochemical stability. While the glyme chain length is a parameter that can be tuned to modify solvation properties, charge transport behavior, reactivity, and ultimately battery performance, anion identity provides another tunable variable. Trifluoromethanesulfonate (triflate/OTf) and bis(trifluoromethane)sulfonamide (TFSI) are chemically similar anions, which are often used in battery electrolytes for lithium-based batteries. In this paper, molecular simulations are used to examine the differences in ion association and charge transport between sodium salts of these two anions at different salt concentrations in glymes with the increasing chain length. The use of the modified force field developed for NaOTf in glymes for the NaTFSI electrolytes was validated by comparing the TFSI-sodium ion radial distribution functions to the results from ab initio molecular dynamics simulations on 1.5 M NaTFSI in diglyme. While the ion association behavior as a function of salt concentration showed similar trends for both NaOTf and NaTFSI in tetraglyme and triglyme electrolytes, the dominant solvation structures for the two sets of electrolytes are distinctly different in the monoglyme and diglyme cases. The conductivity is impacted by both the ion association behavior in these electrolytes and the non-vehicular or hopping transport of the anions in these systems.

Heterogeneous assembly of water from the vapor phase-Physical experiments and simulations with binding trifunctional organosilanes at the vapor/solid interface.

A trace amount of interfacial water is required to initiate hydrosilation reactions of trifunctional organosilanes to form surface assemblies. In recent studies, we have learned that water also has a critical role in directing molecular placement on surfaces because water can react with silicon to provide oxygenated sites for surface binding. Consequently, the wettability nature of substrates influences the placement and density of organosilane films formed by vapor-phase reactions. Nanopatterning protocols were designed using vapor-phase organosilanes and colloidal lithography to compare the wettability differences of hydrophilic mica(0001) compared to relatively hydrophobic Si(100) as a strategy for tracking the location of water on surfaces. The competition between hydrophobic and hydrophilic domains for the adsorption and coalescence of water condensed from vapor can be mapped indirectly by mapping the organosilanes, which bind to water at the solid interface, using atomic force microscopy. Trifunctional octadecyltrichlorosilane (OTS) was used as a marker molecule to map out the areas of the surface where water was deposited. The effect of systematic changes in film thickness and surface coverage of OTS was evaluated at the vapor/solid interface by adding an incremental amount of water to sealed reaction vessels to wet the surface and assessing the outcome after reaction with vapor-phase trichlorosilane. Reactive molecular dynamics simulations of the silicon-water vapor interface combined with electronic structure calculations of oxygenated silicon clusters with methyltrichlorosilane provided insight of the mechanism for surface binding, toward understanding the nature of the interface and wettability factors, which influence the association and placement of silane molecules on surfaces.

Mechanistic Perspectives in the Regioselective Indole Addition to Unsymmetrical Silyloxyallyl Cations.

Our investigations on the reaction mechanism to account for regioselectivity on the addition of indoles to unsymmetrical silyloxyallyl cations are reported. Using both experimental and computational methods, we confirmed the significance of steric effects from the silyl ether group toward directing the inward approach of indoles, leading to nucleophilic attack at the less substituted electrophilic α'-carbon. The role of residual water toward accelerating the rate of reaction is established through stabilization of the participating silyloxyallyl cation.

Ion Pairing in HCl-Water Clusters: From Electronic Structure Investigations to Multiconfigurational Force-Field Development.

In the bulk, condensed-phase HCl exists as a dissociated Cl- ion and a proton that is delocalized over solvating water molecules. However, in the gas phase, HCl is covalent, and even on the introduction of hydrating water molecules, the HCl covalent state dominates small clusters and is relevant at larger clusters including 21 water molecules. Electronic structure calculations (at the MP2 level) and ab initio metadynamics simulations (at the DFT level) have been carried out on HCl-(H2O)n clusters with n = 2-22 to investigate distinct solvation environments in clusters from covalent HCl structure, to contact ion pairs and solvent-separated ion pairs. The data were further used to train and validate a multiconfigurational force-field for HCl-water clusters that incorporates covalent HCl states into the MS-EVB3.2 formalism. Additionally, the many-body interaction of the Cl- ion with water and the excess proton was modeled by the introduction of two geometric three-body terms that incorporates the dominant many-body interaction in an efficient noniterative manner.

Towards a coarse-grained model of the peptoid backbone: the case of N,N-dimethylacetamide.

In this study, a coarse-grained (CG) model for N,N-dimethylacetamide (DMA), which represents the polypeptoid backbone, is developed as a step towards establishing a CG model of the complex polypeptoid system. Polypeptoids or poly N-substituted glycines are a type of peptidomimetic polymers that are highly tunable, and hence an ideal model system to study self-assembly as a function of chemical groups in aqueous soft matter systems. The DMA CG model is parameterized to reproduce the structural properties of DMA liquid as well as a dilute aqueous solution of DMA using a reference all atom model, namely the OPLS-AA force-field. The intermolecular forces are represented by the Stillinger-Weber potential, that consists of both two- and three-body terms that are very short-ranged. The model is validated on thermodynamic properties of liquid and aqueous DMA, as well as the vapor-liquid interface of liquid DMA and the structure of a concentrated aqueous solution of DMA in water as well as a simple peptoid in water. Without long-ranged interactions and the absence of interaction sites on hydrogen atoms, the CG DMA model is an order of magnitude faster than the higher resolution all-atom (AA) model.

Enantioselective Functionalization of Enamides at the ß-Carbon Center with Indoles.

We report an enantioconvergent approach for the functionalization of enamides at the ß-carbon atom, which involves a chiral Brønsted acid induced tautomerization of 2-amidoallyl into 1-amidoallyl cations. These putative reactive intermediates were produced by ionization of racemic α-hydroxy enamides with a chiral Brønsted acid and captured with substituted indoles in a highly regio- and enantioselective manner.

Effect of chemical structure of S-nitrosothiols on nitric oxide release mediated by the copper sites of a metal organic framework based environment.

The effect of chemical structure of different biologically compatible S-nitrosothiols on the solvation environment at catalytic copper sites in a metal organic framework (MOF) suspended in a solution of ethanol is probed using computational methods. The use of a copper based MOF as a storage vehicle and catalyst (copper sites of the MOF) in the controlled and sustained release of chemically stored nitric oxide (NO) from S-nitrosocysteine has been shown to occur both experimentally and computationally [J. Am. Chem. Soc., 2012, 134, 3330-3333; Phys. Chem. Chem. Phys., 2015, 17, 23403]. Previous studies on a copper based MOF, namely HKUST-1, concluded that modifications in the R-group of s-nitrosothiols and/or organic linkers of MOFs led to a method capable of modulating NO release. In order to test the hypothesis that larger R-groups slow down NO release, four different RSNOs (R = cysteine, N-acetylcysteine, N-acetyl-d,l-penicillamine or glutathione) of varying size were investigated, which in turn required the use of a larger copper based MOF. Due to its desirable copper centers and more extensive framework, MOF-143, an analog of HKUST-1 was chosen to further explore both the effect of different RSNOs as well as MOF environments on NO release. Condensed phase classical molecular dynamics simulations are utilized to study the effect of the complex MOF environment as well as the chemical structure and size of the RSNO on the species on the catalytic reaction. The results indicate that in addition to the size of the RSNO species and the organic linkers within the MOF, the reaction rates can be modulated by the molecular structure of the RSNO and furthermore combining different RSNO species can also be used to tune the rate of NO release.

Aggregation of cyclic polypeptoids bearing zwitterionic end-groups with attractive dipole-dipole and solvophobic interactions: a study by small-angle neutron scattering and molecular dynamics simulation.

Aggregation behavior of cyclic polypeptoids bearing zwitterionic end-groups in methanol has been studied using a combination of experimental and simulation techniques. The data from SANS and cryo-TEM indicate that the solution contains small clusters of these cyclic polypeptoids, ranging from a single polypeptoid chain to small oligomers, while the linear counterpart shows no cluster formation. Atomistic molecular dynamics simulations reveal that the driving force for this clustering behavior is due to the interplay between the effective repulsion due to the solvation of the dipoles formed by the charged end-groups in each polypeptoid chain and the attractive forces due to dipole-dipole interactions and the solvophobic effect.

A Visible-Light-Promoted O-Glycosylation with a Thioglycoside Donor.

Visible-light irradiation of 4-p-methoxyphenyl-3-butenylthioglucoside donors in the presence of Umemoto's reagent and alcohol acceptors serves as a mild approach to O-glycosylation. Visible-light photocatalysts are not required for activation, and alkyl- and arylthioglycosides not bearing the p-methoxystyrene are inert to these conditions. Experimental and computational evidence for an intervening electron donor-acceptor complex, which is necessary for reactivity, is provided. Yields with primary, secondary, and tertiary alcohol acceptors range from moderate to high. Complete ß-selectivity can be attained through neighboring-group participation.

Propensity of Hydrated Excess Protons and Hydroxide Anions for the Air-Water Interface.

Significant effort has been undertaken to better understand the molecular details governing the propensity of ions for the air-water interface. Facilitated by computationally efficient reactive molecular dynamics simulations, new and statistically conclusive molecular-scale results on the affinity of the hydrated excess proton and hydroxide anion for the air-water interface are presented. These simulations capture the dynamic bond breaking and formation processes (charge defect delocalization) that are important for correctly describing the solvation and transport of these complex species. The excess proton is found to be attracted to the interface, which is correlated with a favorable enthalpic contribution and consistent with reducing the disruption in the hydrogen bond network caused by the ion complex. However, a recent refinement of the underlying reactive potential energy function for the hydrated excess proton shows the interfacial attraction to be weaker, albeit nonzero, a result that is consistent with the experimental surface tension measurements. The influence of a weak hydrogen bond donated from water to the protonated oxygen, recently found to play an important role in excess hydrated proton transport in bulk water, is seen to also be important for this study. In contrast, the hydroxide ion is found to be repelled from the air-water interface. This repulsion is characterized by a reduction of the energetically favorable ion-water interactions, which creates an enthalpic penalty as the ion approaches the interface. Finally, we find that the fluctuation in the coordination number around water sheds new light on the observed entropic trends for both ions.

A computational study of the effect of the metal organic framework environment on the release of chemically stored nitric oxide.

The use of copper based metal organic frameworks as a vehicle for the storage and delivery of chemically stored nitric oxide has been proposed based on recent experiments [J. Am. Chem. Soc., 2012, 134, 3330-3333]. In these experiments copper based metal organic frameworks (MOFs) suspended in ethanol catalytically convert chemically stored nitric oxide (in the S-nitrosothiol or RSNO form) to free nitric oxide at a slow and sustained rate, as compared to a quick release in a solution of ethanol containing free copper ions. In order to gain insight on the effect of the MOF environment on the catalytic activity, a combination of electronic structure calculations on representative clusters and classical simulations using a force-field (partly parameterized on the above calculations) is used to study a simple RSNO species, S-nitrosomethane (CH3SNO) as well as the biologically compatible S-nitrosocysteine, both in the MOF and free copper solution. The free energy profiles of bringing the RSNO species to the catalytic centers have been compared and related to the different solvation environments of the copper catalyst in the complex solvated MOF and in free copper solution. Surprisingly, in the case of the simple CH3SNO moiety as well as the S-nitrosocysteine case, the free energy profile of bringing the first RSNO from the center of one of the pores to the catalytic site in the pore is very similar to the free solution case. On the other hand, bringing a second RSNO molecule to the same catalytic site or to the adjacent catalytic copper site show relatively higher barriers. These studies help shed light on the sustained nitric oxide release in the MOF environment.

Role of excited state solvent fluctuations on time-dependent fluorescence Stokes shift.

We explore the connection between the solvation dynamics of a chromophore upon photon excitation and equilibrium fluctuations of the solvent. Using molecular dynamics simulations, fluorescence Stokes shift for the tryptophan in Staphylococcus nuclease was examined using both nonequilibrium calculations and linear response theory. When the perturbed and unperturbed surfaces exhibit different solvent equilibrium fluctuations, the linear response approach on the former surface shows agreement with the nonequilibrium process. This agreement is excellent when the perturbed surface exhibits Gaussian statistics and qualitative in the case of an isomerization induced non-Gaussian statistics. However, the linear response theory on the unperturbed surface breaks down even in the presence of Gaussian fluctuations. Experiments also provide evidence of the connection between the excited state solvent fluctuations and the total fluorescence shift. These observations indicate that the equilibrium statistics on the excited state surface characterize the relaxation dynamics of the fluorescence Stokes shift. Our studies specifically analyze the Gaussian fluctuations of the solvent in the complex protein environment and further confirm the role of solvent fluctuations on the excited state surface. The results are consistent with previous investigations, found in the literature, of solutes dissolved in liquids.

Hydrated proton and hydroxide charge transfer at the liquid/vapor interface of water.

The role of the solvated excess proton and hydroxide ions in interfacial properties is an interesting scientific question with applications in a variety of aqueous behaviors. The role that charge transfer (CT) plays in interfacial behavior is also an unsettled question. Quantum calculations are carried out on clusters of water with an excess proton or a missing proton (hydroxide) to determine their CT. The quantum results are applied to analysis of multi-state empirical valence bond trajectories. The polyatomic nature of the solvated excess proton and hydroxide ion results in directionally dependent CT, depending on whether a water molecule is a hydrogen bond donor or acceptor in relation to the ion. With polyatomic molecules, CT also depends on the intramolecular bond distances in addition to intermolecular distances. The hydrated proton and hydroxide affect water's liquid/vapor interface in a manner similar to monatomic ions, in that they induce a hydrogen-bonding imbalance at the surface, which results in charged surface waters. This hydrogen bond imbalance, and thus the charged waters at the surface, persists until the ion is at least 10 Å away from the interface.

Hydration and vibrational dynamics of betaine (N,N,N-trimethylglycine).

Zwitterions are naturally occurring molecules that have a positive and a negative charge group in its structure and are of great importance in many areas of science. Here, the vibrational and hydration dynamics of the zwitterionic system betaine (N,N,N-trimethylglycine) is reported. The linear infrared spectrum of aqueous betaine exhibits an asymmetric band in the 1550-1700 cm(-1) region of the spectrum. This band is attributed to the carboxylate asymmetric stretch of betaine. The potential of mean force computed from ab initio molecular dynamic simulations confirms that the two observed transitions of the linear spectrum are related to two different betaine conformers present in solution. A model of the experimental data using non-linear response theory agrees very well with a vibrational model comprising of two vibrational transitions. In addition, our modeling shows that spectral parameters such as the slope of the zeroth contour plot and central line slope are both sensitive to the presence of overlapping transitions. The vibrational dynamics of the system reveals an ultrafast decay of the vibrational population relaxation as well as the correlation of frequency-frequency correlation function (FFCF). A decay of ∼0.5 ps is observed for the FFCF correlation time and is attributed to the frequency fluctuations caused by the motions of water molecules in the solvation shell. The comparison of the experimental observations with simulations of the FFCF from ab initio molecular dynamics and a density functional theory frequency map shows a very good agreement corroborating the correct characterization and assignment of the derived parameters.

Solvent-responsive properties of octadecyltrichlorosiloxane nanostructures investigated using atomic force microscopy in liquid.

An emerging challenge for nanoscale measurements is to capture and quantify the magnitude of structural changes in response to environmental changes. Certain environmental parameters can affect the nanoscale morphology of samples, such as changing the pH, solvent polarity, ionic strength, and temperature. We prepared test platforms of n-octadecyltrichlorosilane ring nanostructures to study surface morphology changes at the nanoscale in selected liquid media compared to dry conditions in air. Particle lithography combined with organosilane vapor deposition was used to fabricate nanostructures of regular dimensions. Multilayer nanostructures of OTS were used as a test platform for scanning probe studies of solvent-responsive properties where the sides of designed ring structures expose a 3D interface for studying the interaction of solvents with molecular side groups. In dry, ambient conditions, nanostructures of OTS were first imaged using contact mode atomic force microscopy (AFM). Next, ethanol or buffer was introduced to the sample cell, and images were acquired using the same probe. We observed substantial changes in the lateral and vertical dimensions of the ring nanostructures in AFM topography frames; the sizes of the rings were observed to swell by tens of nanometers. Even after heat treatment of samples to promote cross-linking, the samples still evidenced swelling in liquid media. This research will have consequences for studies of the properties of nanomaterials, such as solvent-responsive organic films and polymers.

Non-linear infrared spectroscopy of the water bending mode: direct experimental evidence of hydration shell reorganization?

The structure and dynamics of liquid water are further studied by investigating the bend vibrational mode of HDO/D2O and pure H2O via two-dimensional infrared spectroscopy (2D-IR) and linear absorption. The experimental findings and theoretical calculations support a picture in which the HDO bend is localized and the H2O bend is delocalized. The HDO and H2O bends present a loss of the frequency-frequency correlation in subpicosecond time scale. While the loss of correlation for the H2O bend is likely to be associated with the vibrational dynamics of a delocalized transition, the loss of the correlation in the localized HDO bend appears to arise from the fluctuations/rearrangements of the local environment. Interestingly, analysis of the HDO 2D-IR spectra shows the presence of multiple overlapping inhomogeneous distributions of frequencies that interchange in a few picoseconds. Theoretical calculations allow us to propose an atomistic model of the observed vibrational dynamics in which the different inhomogeneous distributions and their interchange are assigned to water molecules with different hydrogen-bond states undergoing chemical exchange. The frequency shifts as well as the concentration of the water molecules with single and double hydrogen-bonds as donors derived from the theory are in good agreement with our experimental findings.

Empowering Capacitive Devices: Harnessing Transfer Learning for Enhanced Data-Driven Optimization.

Developing data-driven models has found successful applications in engineering tasks, such as material design, process modeling, and process monitoring. In capacitive devices like deionization and supercapacitors, there exists potential for applying this data-driven machine learning (ML) model in optimizing its potential use in energy-efficient separations or energy generation. However, these models are faced with limited datasets, and even in large quantities, the datasets are incomplete, limiting their potential use for successful data-driven modeling. Here, the success of transfer learning in resolving the challenges with limited datasets was exploited. A two-step data-driven ML modeling framework named ImputeNet involving training with ML-imputed datasets and then with clean datasets was explored. Through data imputation and transfer learning, it is possible to develop a data-driven model with acceptable metrics mirroring experimental measurements. By using the model, optimization studies using the genetic algorithm were implemented to analyze the solution under the Pareto optimality. This early insight can be used in the initial stage of experimental measurements to rapidly identify experimental conditions worthy of further investigation. Moreover, we expect that the insights from these results will drive accurate predictive modeling in other fields including healthcare, genomic data analysis, and environmental monitoring with incomplete datasets.

Probing the Electrode-Electrolyte Interface of Sodium/Glyme-Based Battery Electrolytes.

Sodium-ion batteries (NIBs) are promising systems for large-scale energy storage solutions; yet, further enhancements are required for their commercial viability. Improving the electrochemical performance of NIBs goes beyond the chemical description of the electrolyte and electrode materials as it requires a comprehensive understanding of the underlying mechanisms that govern the interface between electrodes and electrolytes. In particular, the decomposition reactions occurring at these interfaces lead to the formation of surface films. Previous work has revealed that the solvation structure of cations in the electrolyte has a significant influence on the formation and properties of these surface films. Here, an experimentally validated molecular dynamics study is performed on a 1 M NaTFSI salt in glymes of different lengths placed between two graphite electrodes having a constant bias potential. The focus of this study is on describing the solvation environment around the sodium ions at the electrode-electrolyte interface as a function of glyme chain length and applied potential. The results of the study show that the diglyme/TFSI system presents features at the interface that significantly differ from those of the triglyme/TFSI and tetraglyme/TFSI systems. These computational predictions are successfully corroborated by the experimentally measured capacitance of these systems. In addition, the dominant solvation structures at the interface explain the electrochemical stability of the system as they are consistent with cyclic voltammetry characterization.

Computational Investigations of the Water Structure at the α-Al2O3(0001)-Water Interface.

The α-Al2O3(0001)-water interface is investigated using ab initio molecular dynamics (AIMD) simulations. The spectral signatures of the vibrational sum frequency generation (vSFG) spectra of OH stretching mode for water molecules at the interface are related to the interfacial water orientation, hydrogen bond network, and water dissociation process at different water/alumina interfaces. Significant differences are found between alumina surfaces at different hydroxylation levels, namely, Al-terminated and O-terminated α-Al2O3(0001). By calculating the vibrational sum frequency generation spectrum and its imaginary component from AIMD results, the structure of interfacial waters as well as the termination of alumina slab are related to the spectral signatures of vSFG data.