Structure and intermolecular interactions in ionic liquid 1-ethyl-3-methylimidazolium bromide and its aqueous solutions investigated by vibrational spectroscopy and quantum chemical computations.

The recently developed efficient protocol to explicit quantum mechanical modeling of structure and IR spectra of liquids and solutions (S. A. Katsyuba, S. Spicher, T. P. Gerasimova, S. Grimme, J. Phys. Chem. B 2020, 124, 6664) is applied to ionic liquid (IL) 1-ethyl-3-methylimidazolium bromide (EmimBr), its C2-deuterated analog [Emim-d]Br and its aqueous solutions. It is shown that the solvation strongly modifies frequencies and IR intensities of the CH/CD stretching vibrations (νCH/νCD) of the imidazolium ring. The main vibrational spectroscopic features of the neat IL are reproduced by the simulations for a cluster (EmimBr)9, in which all three imidazolium CH moieties of the solvated cation form short contacts with three Br- anions, and another two Br- anions are located on top and bottom of imidazolium ring. Cluster models of aqueous solutions reproduce the experimental vibrational frequencies of actual solutions, provided that the Br- anion of solvated contact ion pair (CIP) is situated on top of imidazolium ring, and CH/CD moieties of the latter participate in short contacts with surrounding water molecules. Both structural and spectroscopic analysis allow to interpret the short contacts CH/CD⋯Br- and CH/CD⋯OH2 as hydrogen bonds of approximately equal strength. Enthalpies of bonding of these liquid-state H-bonds, estimated with the use of empirical correlations, amount to ca. 1.4 kcal⋅mol-1, while the analogous estimates obtained for the gas-phase charged species [Emim]2Br+ increase to 5.6 kcal⋅mol-1. It is shown that formation of solvent-shared ion pair (SIP) in aqueous solution, where the counterions of IL are separated by two water molecules H-bonded to a Br- anion, produces frequency shifts ΔνCH/CD, strongly different from the case of CIP formation. This difference can be used for IR/Raman spectroscopic differentiation of the type of solvated ion pairs of EmimBr or other related ILs.

Ab-initio molecular dynamics and hybrid explicit-implicit solvation model for aqueous and nonaqueous solvents: GFP chromophore in water and methanol solution as case study.

Solute-solvent interactions are proxies for understanding how the electronic density of a chromophore interacts with the environment in a more exhaustive way. The subtle balance between polarization, electrostatic, and non-bonded interactions need to be accurately described to obtain good agreement between simulations and experiments. First principles approaches providing accurate configurational sampling through molecular dynamics may be a suitable choice to describe solvent effects on solute chemical-physical properties and spectroscopic features, such as optical absorption of dyes. In this context, accurate energy potentials, obtained by hybrid implicit/explicit solvation methods along with employing nonperiodic boundary conditions, are required to represent bulk solvent around a large solute-solvent cluster. In this work, a novel strategy to simulate methanol solutions is proposed combining ab initio molecular dynamics, a hybrid implicit/explicit flexible solvent model, nonperiodic boundary conditions, and time dependent density functional theory. As case study, the robustness of the proposed protocol has been gauged by investigating the microsolvation and electronic absorption of the anionic green fluorescent protein chromophore in methanol and aqueous solution. Satisfactory results are obtained, reproducing the microsolvation layout of the chromophore and, as a consequence, the experimental trends shown by the optical absorption in different solvents.

Can Alkaline Hydrolysis of γ-HCH Serve as a Model Reaction to Study Its Aerobic Enzymatic Dehydrochlorination by LinA?

Hexachlorocyclohexane (HCH) isomers constitute a group of persistent organic pollutants. Their mass production and treatment have led to a global environmental problem that continues to this day. The characterization of modes of degradation of HCH by isotope fractionation is a current challenge. Multi isotope fractionation analysis provides a concept to characterize the nature of enzymatic and chemical transformation reactions. The understanding of the kinetic isotope effects (KIE) on bond cleavage reaction contributes to analyses of the mechanism of chemical and enzymatic reactions. Herein, carbon, chlorine, and hydrogen kinetic isotope effects are measured and predicted for the dehydrochlorination reaction of γ-HCH promoted by the hydroxyl ion in aqueous solution. Quantum mechanical (QM) microsolvation with an implicit solvation model and path integral formalism in combination with free-energy perturbation and umbrella sampling (PI-FEP/UM) and quantum mechanical/molecular mechanical QM/MM potentials for including solvent effects as well as calculating isotope effects are used and analyzed with respect to their performance in reproducing measured values. Reaction characterization is discussed based on the magnitudes of obtained isotope effects. The comparative analysis between the chemical dehydrochlorination of γ-HCH in aqueous media and catalyzed reaction by dehydrochlorinase, LinA is presented and discussed. Based on the values of isotope effects, these two processes seem to occur via the same net mechanism.

Implicit and explicit solvent models for modeling a bifunctional arene ruthenium hydrogen-storage catalyst: a classical and ab initio molecular simulation study.

Classical and ab initio, density functional theory- and semiempirical-based molecular simulation, including molecular dynamics, have been carried out to compare and contrast the effect of explicit and implicit solvation representation of tetrahydrofuran (THF) solvent on the structural, energetic, and dynamical properties of a novel bifunctional arene ruthenium catalyst embedded therein. Particular scrutiny was afforded to hydrogen-bonding and energetic interactions with the THF liquid. It was found that the presence of explicit THF solvent molecules is required to capture an accurate picture of the catalyst's structural properties, particularly in view of the importance of hydrogen bonding with the surrounding THF molecules. This has implications for accurate modeling of the reactivity of the catalyst.

Computationally assisted vibrational spectroscopy of nucleic acid bases. 2. Thymine.

As in the case of cytosine [Phys. Chem. Chem. Phys. 2023, 25, 24121-24128], Raman and infrared (IR) spectra of aqueous thymine and its N-deuterated derivative, thymine-d2 have been computationally reproduced and interpreted with the use of the recently developed efficient protocol to explicit quantum mechanical modeling of structure and IR spectra of liquids and solutions [J. Phys. Chem. B, 2020, 124, 6664-6670]. A cluster model of a solute surrounded by 30 water molecules is shown to be sufficient to reproduce experimental vibrational frequencies and relative Raman intensities with the use of B3LYP-D3/def2-TZVP or B3LYP-D3/aug-cc-pVDZ simulations. Analogous PBE-D3 computations provided a less good, but still reasonably accurate, modeling of Raman spectra. It is shown that strong changes of frequencies and relative intensities of the Raman bands of thymine, caused by its hydration, can be interpreted mainly as a result of hydrogen bonding with 6 nearest water molecules. Non-negligible improvement of the quality of simulations for larger clusters comprising water molecules that do not have direct contacts with the solute, suggests that spectroscopic effects of hydration should be ascribed to the joined action of solute-solvent and solvent-solvent interactions. Nevertheless, the moderate number of water molecules required for successful simulations of the Raman spectra of aqueous thymine, suggests that the vibrational modes and derivatives of the polarizability of the solute are mainly locally influenced, while the effect of bulk water is rather modest.

GFN-xTB-Based Computations Provide Comprehensive Insights into Emulsion Radiation-Induced Graft Polymerization.

In this article, a deep insight into emulsion radiation-induced graft polymerization (RIGP) was obtained by computing explicit solvation free energies, conformational entropy, monomer radius and dipole moments with the state-of-the-art Conformer-Rotamer Ensemble Sampling Tool (CREST) package primarily at semiempirical GFN-xTB level. By leveraging the robustness of the CREST package, above parameters provided dynamic nature of methacrylate monomers with the consideration of realistic emulsion conditions. With the chemical and physical importance of the above results, CREST-determined explanatory variables sufficiently led to the building of the prediction models for the RIGP of methacrylate monomers. The machine learning model building resulted in effective reactivity predictions and unveiled important factors for the radiation-induced graft polymerization in a chemically interpretable fashion.

Ab initiomodelling of interfacial electrochemical properties: beyond implicit solvation limitations.

First-principles calculations are an important tool to investigate the complex processes occurring at solid/liquid interfaces which are at the heart of modern technologies. Currently, capturing the whole electrochemical environment at an interface, including the applied potential and solvation, still remains challenging as it necessitates to couple different approaches whose interactions are not fully understood. In this work, a grand canonical density functional theory approach is coupled with solvation models to investigate the electrochemical interfaces under applied potential. We show that a parametrized polarizable continuum model (PCM) which represent solvation in a mean field approach by a continuous polarizable media, possesses catastrophic limitations for the modelling of ionic and charged interfaces. We reveal the origin of PCM instabilities under chemical or electrochemical strong oxidation to be the consequence of a phase transition in the surface Li electronic structure. Thus, PCM undergoes an unphysical response to this phase transition by penetrating within the atomic radius of surface Li atoms. To recover a physical response, an explicit first solvation shell has to be included in addition to the PCM in order to properly describe the electrochemistry of the interface. The Fukui functions show that the first solvation shell becomes involved in the redox process as solvent electron doublet is transferred to the acidic Li+. If another explicit solvent layer is added, the interface electrochemical properties become independent of the PCM parameters: in particular capacitance can then be computed from a parameter-free electrochemical approach. This is an important conclusion as the experimental electrochemical capacitance are not easily found and thus the parametrization of the PCM for electrochemical interface can be difficult. This approach can easily be applied to investigate electrochemical properties at the atomic scale and generalized to any electrochemical device for which interfaces play a crucial role.

Linear correlation models for the redox potential of organic molecules in aqueous solutions.

In this study, we use the molecular orbital energy approximation (MOEA) and the energy difference approximation (EDA) to build linear correlation models for the redox potentials of 53 organic compounds in aqueous solutions. The molecules evaluated include nitroxides, phenols, and amines. Both the MOEA and EDA methods yield similar correlation models, however, the MOEA method is less computationally expensive. Correlation coefficients (R2) below 0.3 and mean absolute errors above 0.25 V were found for correlation models built without solvent effects. When explicit water molecules and a continuum solvent model are added to the calculations, correlation coefficients close to 0.8 are reached, and mean absolute errors below 0.18 V are obtained. The incorporation of solvent effects is necessary for good correlation models, particularly for redox processes of charged molecules in aqueous solutions. A comparison of the correlation models from different methodologies is provided. Graphical abstract.

α- and ß-Lapachone Isomerization in Acidic Media: Insights from Experimental and Implicit/Explicit Solvation Approaches.

Combined experimental and mixed implicit/explicit solvation approaches were employed to gain insights into the origin of switchable regioselectivity of acid-catalyzed lapachol cyclization and α-/ß-lapachone isomerization. It was found that solvating species under distinct experimental conditions stabilized α- and ß-lapachone differently, thus altering the identity of the thermodynamic product. The energy profile for lapachol cyclization revealed that this process can occur with low free-energy barriers (lower than 8.0 kcal mol-1 ). For α/ß isomerization in a dilute medium, the computed enthalpic barriers are 15.1 kcal mol-1 (α→ß) and 14.2 kcal mol-1 (ß→α). These barriers are lowered in concentrated medium to 11.5 and 12.6 kcal mol-1 , respectively. Experimental determination of isomers ratio was quantified by HPLC and NMR measurements. These findings provide insights into the chemical behavior of lapachol and lapachone derivatives in more complex environments.

Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions.

Solvent molecules interact intimately with proteins and can profoundly regulate their structure and function. However, accurately and efficiently modeling protein solvation effects at the molecular level has been challenging. Here, we present a method that improves the atomic-level modeling of soluble and membrane protein structures and binding by efficiently predicting de novo protein-solvent molecule interactions. The method predicted with unprecedented accuracy buried water molecule positions, solvated protein conformations, and challenging mutational effects on protein binding. When applied to homology modeling, solvent-bound membrane protein structures, pockets, and cavities were recapitulated with near-atomic precision even from distant homologs. Blindly refined atomic-level structures of evolutionary distant G protein-coupled receptors imply strikingly different functional roles of buried solvent between receptor classes. The method should prove useful for refining low-resolution protein structures, accurately modeling drug-binding sites in structurally uncharacterized receptors, and designing solvent-mediated protein catalysis, recognition, ligand binding, and membrane protein signaling.

Microhydration effects on geometric properties and electronic absorption spectra of ortho-aminobenzoic acid.

TD-DFT and a combination of polarized continuum model (PCM) and microhydration methods helped to simulate the optical electronic absorption spectrum of ortho-aminobenzoic acid (o-Abz). The microhydration method involved the use of different numbers, from 1 to 5, of first solvation layer water molecules. We examined how implicit and explicit water affected the energies of the HOMO-LUMO transition in the o-Abz/water systems. Adding until five water molecules, the theoretical spectrum becomes closer to the experimental data. Microhydration combined with the PCM method leads to agreement between the theoretical result for five water molecules and the experimentally measured absorption bands.