Polarizable Molecular Dynamics Simulations Research Articles

Impact of an Ionic Liquid Solution on Horseradish Peroxidase Activity.

Horseradish peroxidase (HRP) is an enzyme that oxidizes pollutants from wastewater. A previous report indicated that peroxidases can have an enhancement in initial enzymatic activity in an aqueous solution of 0.26 M 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) at neutral pH. However, the atomistic details remain elusive. In the enzymatic landscape of HRP, compound II (Cpd II) plays a key role and involves a histidine (H42) residue. Cpd II exists as oxoferryl (2a) or hydroxoferryl (2b(FeIV)) forms, where 2a is the predominantly observed form in experimental studies. Intriguingly, the ferric 2b(FeIII) form seen in synthetic complexes has not been observed in HRP. Here, we have investigated the structure and dynamics of HRP in pure water and aqueous [EMIm][EtSO4] (0.26 M), as well as the reaction mechanism of 2a to 2b conversion using polarizable molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations. When HRP is solvated in aq [EMIm][EtSO4], the catalytic water displaces, and H42 directly orients over the ferryl moiety, allowing a direct proton transfer (PT) with a significant energy barrier reduction. Conversely, in neat water, the reaction of 2a to 2b follows the previously reported mechanism. We further investigated the deprotonated form of H42. Analysis of the electric fields at the active site indicates that the aq [EMIm][EtSO4] medium facilitates the reaction by providing a more favorable environment compared with the system solvated in neat water. Overall, the atomic level supports the previous experimental observations and underscores the importance of favorable electric fields in the active site to promote catalysis.

Updates to Protex for Simulating Proton Transfers in an Ionic Liquid.

The Python-based program Protex was initially developed for simulating proton transfers in a pure protic ionic liquid via polarizable molecular dynamics simulations. This method employs a single topology approach wherein deprotonated species retain a dummy atom, which is transformed into a real hydrogen atom during the protonation process. In this work, we extended Protex to include more intricate systems and to facilitate the simulation of the Grotthuss mechanism to enhance alignment with the empirical findings. The handling of proton transfer events within Protex was further refined for increased flexibility. In the original model, each deprotonated molecule contained a single dummy atom connected to the hydrogen acceptor atom. This model posed limitations for molecules with multiple atoms that could undergo protonation. To mitigate this issue, Protex was extended to execute a proton transfer when one of these potential atoms was within a suitable proximity for the transfer event. For the purpose of maintaining simplicity, Protex continues to utilize only a single dummy atom per deprotonated molecule. Another new feature pertains to the determination of the eligibility for a proton transfer event. A range of acceptable distances can now be defined within which the transfer probability is gradually turned off. These modifications allow for a more nuanced approach to simulating proton transfer events, offering greater accuracy and control of the modeling process.

How Do Deep Eutectic Solvents Form Porous Liquids? The Example of Methyltriphenylphosphonium Bromide: Glycerol and ZIF-8.

Porous liquids are new materials that provide permanent porosity in the liquid phase through the dispersion of nanoporous solid particles in a bulky solvent. Herein, we aim at understanding how new sustainable solvents such as deep eutectic solvent (DES) can be used to form porous stable suspensions for the capture of gases of interest for sustainable chemistry. The properties of an ionic DES, methyltriphenylphosphonium bromide/glycerol in a 1:3 molar composition, and its behavior at the interface with a metal-organic framework (MOF), ZIF-8, are here investigated by polarizable molecular dynamics simulations. The structural and dynamic properties of the DES are analyzed in the bulk liquid and in the interfacial regions with the MOF, namely, in the accessible cavities exposed at the surface. The porosity of the suspension is maintained, and it is caused not only by the Coulomb cohesive energy between cations and anions, which prevents the small anions from entering the pores, but also by the glycerol molecules not penetrating the small aperture of the ZIF-8 structure. This was further verified by simulating a system composed of glycerol and ZIF-8. Simulations with CO2 show its partition between the DES and the MOF, with higher concentrations registered in the MOF cavities.

Liquid Structure and Hydrogen Bonding in Aqueous Hydroxylammonium Nitrate.

Hydroxylammonium nitrate (HAN) has emerged as a promising component in ionic liquid-based spacecraft propellants. However, the physicochemical and structural properties of aqueous HAN have been largely overlooked. The purpose of this study is to investigate the hydrogen bonding in aqueous HAN and understand its implications on these properties and the proton transfer mechanism as a function of concentration. Classical polarizable molecular dynamics simulations have been employed with the APPLE&P force field to analyze the geometry of individual hydrogen bonds and the overall hydrogen-bonding network in various concentrations of aqueous HAN. Radial distribution functions (RDFs) and spatial distribution functions (SDFs) indicate the structural arrangement of the species and their hydrogen bonds. Projections of water density and the orientation of its electric dipole moment near the ions provide insight into the hydrogen-bonding network. The incorporation of water into the hydrogen-bonding network at high ion concentrations occurs via interstitial accommodation around the ions immediately outside the first solvation shell. While ion pairs are observed at all concentrations considered, the frequency of Ha···On hydrogen bonds increases substantially with the ion concentration. The findings contribute to a better fundamental understanding of HAN and the precursors of reactivity, crucial to the development of "green" spacecraft propellants.

Comparative analysis of dielectric spectra in protic ionic liquids: Experimental findings and computational molecular decomposition

Using a combination of experimental measurements and polarizable molecular dynamics simulations, we investigate the dielectric spectra of the protic ionic liquid 1-methylimidazolium acetate, shedding light on their dynamic behavior and intermolecular interactions when adding 1-methylimidazolium trifluoroacetate to increase the fraction of a strong Brønsted acid in the system. The comparison between experimental and computational results provides valuable insights into the accuracy of the simulation models (with and without explicit proton transfer) and the ability to capture the intricate dynamical features of the protic ionic liquid. The investigation revealed complete deprotonation of trifluoroacetate, inducing a shift in the ionic liquid towards a more pronounced ionic state. The computational decomposition of the dielectric spectra into molecular translational and rotational contributions unveiled a reduction in the dielectric constant. This reduction was primarily ascribed to a decrease in translational contributions. Additionally, a strong correlation of the mutual orientation of molecules was found. The observed rise in conductivity upon the addition of 1-methylimidazolium trifluoroacetate to the system was attributed to an increase in proton transport.

Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes.

The formation of G-quadruplexes (GQs) occurs in guanine-rich sequences of DNA and RNA, producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs play crucial roles in regulating transcription, translation, and replication and maintaining the genome, among others; thus, changes to their structures can lead to diseases such as cancer. Previous studies using polarizable molecular dynamics simulations have shown differences in ion binding properties between telomeric and telomeric repeat-containing RNA GQs despite architectural similarities. Here, we used volume-based metadynamics and repulsive potential simulations in conjunction with polarizable force fields to quantify the impact of ion binding on the GQ dynamics and ion binding free energies. Furthermore, we describe how GQs exert electric fields on their surroundings to link dynamics with variations in the electronic structure. Our findings provide new insights into the energetic, physical, and conformational properties of GQs and expose subtle but important differences between DNA and RNA GQs with the same fold.

Solvent dependency of catalyst-substrate aggregation through π-πstacking in photoredox catalysis.

Assemblies of photoredox catalysts and their target substrates prior to photoexcitation is a phenomenon na\"ively overlooked by the majority of synthetic chemists, but can have profound influences on reactivity and selectivity in photocatalytic reactions. In this study, we determine the aggregation states of triarylamine radical cationic photocatalysts with various target arene substrates in different solvents by specifically parameterized polarizable molecular dynamics simulations. A $\pi$-stacking interaction previously implicated by more expensive, less-representative quantum calculations is confirmed. Critically, this study presents new insights on: i) the ability of solvents (MeCN vs DMF) to make or break a photocatalytic reaction by promoting (MeCN) or demoting (DMF) its catalyst-substrate assemblies, which is a determining factor for reactivity, ii) the average "lifetimes" of assemblies in solution from a dynamic simulation. We find that both in the ground state and photoexcited cationic radical state, the lifetimes of these assemblies all molecules remain relatively in tact for relatively large time periods, often higher than 60 ps, making them ideal to undergo reactions upon photoexcitation. Such aspects have not addressed by previous studies on synthetic photocatalytic reactions involving non-covalent assemblies.

Exploring the Aggregation Behavior of Extractant Molecules in Ionic Liquids: A Coupled Polarizable Molecular Dynamics and SAXS Study.

This study presents a comprehensive investigation of the aggregation behavior of a malonamide extractant molecule (N,N'-dimethyl,N,N'-dioctylhexylethoxymalonamide (DMDOHEMA)) in three different solvents, including two piperidinium- and (trifluoromethylsulfonyl)imide-based ionic liquids (1-ethyl-1-butylpiperidinium bis(trifluoromethylsulfonyl)imide ([EBPip+][NTf2-]) and 1-ethyl-1-octylpiperidinium bis(trifluoromethylsulfonyl)imide ([EOPip+][NTf2-])) and n-dodecane. By combining polarizable molecular dynamics simulations and small-angle X-ray scattering experiments, we extensively investigated the arrangement of supramolecular assemblies of the extractant molecules. Our results showed that the insertion of the alkyl chains of the extractant molecules into the apolar domain of [EOPip+][NTf2-] has a significant impact on the aggregation behavior of the extractant molecules, leading to the formation of smaller aggregates having a higher dispersion compared to other solvents. These findings provide new insights into the physicochemical properties of this type of system and are crucial in designing more effective solvents for rare earth metal extraction.

Solvation Environments in Porous Ionic Liquids Determine Selectivity in CO2 Conversion to Cyclic Carbonates.

Porous ionic liquids, which are suspensions of nanoporous particles in ionic liquids that maintain permanent porosity, are effective and selective media for the conversion of styrene oxide into styrene carbonate, absorbing CO2 [Zhou et al. Chem. Commun. 2021, 57, 7922-7925]. Here we elucidate the mechanism of selectivity using polarizable molecular dynamics simulations, which provide a detailed view on the structure of the porous ionic liquid and on the local solvation environments of the reacting species. The porous ionic liquids studied are composed of tetradecyltrihexylphosphonium chloride, or [P66614]Cl, and the ZIF-8 zinc-methylimidazolate metal-organic framework (MOF). The CL&Pol polarizable force field was extended to represent epoxide and cyclic carbonate functional groups, allowing the ionic liquid, the reactants, and the MOF to be all represented by fully flexible, polarizable force fields, providing a detailed description of interactions. The presence of reactant and product molecules leads to changes in the structure of the ionic liquid, revealed by domain analysis. The structure of local solvation environments, namely, the arrangement of charged moieties and CO2 around the epoxide ring of the reactant molecules, clearly indicate ring-opening the reaction mechanism. The MOF acts as a reservoir of CO2 through its free volume. The solute molecules are found in the accessible outer cavities of the MOF, which promotes reaction of the epoxide with CO2 excluding other epoxide molecules, thereby preventing the formation of oligomers, which explains the selectivity toward conversion to cyclic carbonates.

Partitioning free energies and induced dipole response of small molecules across a POPC membrane using polarizable molecular dynamics.

The cell membrane is the semi-permeable barrier that regulates flux of materials in and out of the cell. The membrane has a characteristic dielectric gradient due to the amphiphilic nature of its constituent lipids, which have polar head groups and hydrophobic tails. This gradient plays governs many aspects of small-molecule partitioning and membrane protein folding and function. Atomistic details of small-molecule partitioning related to hydration and electronic polarization are still largely unknown. Here, we used polarizable molecular dynamics simulations to understand how the electronic environment influences the process of partitioning. We performed a series of unbiased and umbrella sampling (US) simulations using the Drude polarizable force field (FF) for six different amino-acid sidechain analogs in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. Using a polarizable FF such as Drude allows for the investigation of explicit dipole responses as a function of local electric fields along the membrane normal. We assessed molecular dipole moments, which vary as a function of localization within the membrane, and compared outcomes of the Drude FF simulations to those of the nonpolarizable CHARMM36 FF to investigate the differences in the free energy surfaces of partitioning for our different amino-acid analogs. In doing so, we sought to quantify the effects of using the fixed-charge convention of nonpolarizable FFs, which may average out the influence of the membrane dielectric gradient. We show how polarity of small molecules influences their partitioning and describe key differences in the free energy surfaces between polarizable and nonpolarizable systems in these contexts. This work serves as a foundation for future investigations into polarizable simulations of drug partitioning, as well as simulations of membrane proteins.

Force field refinement for reproducing experimental infrared spectra of ionic liquids.

We employ polarizable molecular dynamics simulations with the newly developed FFGenOpt parametrization tool to reproduce IR spectra of several ionic liquid cations and anions in the gas phase. Our results show that polarizable force fields in the bulk phase provide a reasonable compromise between computational effort and accuracy for investigating IR spectra when treating the transition from gas to liquid phase carefully. Although collectivity seems to play only a minor role, the liquid phase not only changes the electrostatic environment of the molecules but also introduces friction and intermolecular interactions altering the IR spectrum significantly. In addition to the classical force field approach, we also tested if the additional computational effort of machine learning potentials justifies their application in reproducing IR spectra. However, the main purpose of this work is to improve the quality of polarizable force fields concerning vibrations and not the prediction of IR spectra which can be better done with quantum-mechanical cluster approaches.

Characterizing Ion-Polymer Interactions in Aqueous Environment with Electric Fields.

Polymers make the basis of highly tunable materials that could be designed and optimized for metal recovery from aqueous environments. While experimental studies show that this approach has potential, it suffers from a limited knowledge of the detailed molecular interaction between polymers and target metal ions. Here, we propose to calculate intrinsic electric fields from polarizable force field molecular dynamics simulations to characterize the driving force behind Eu3+ motion in the presence of poly(ethylenimine methylenephosphonate), a specifically designed metal chelating polymer. Focusing on the metal chelation initiation step (i.e., before binding), we can rationalize the role of each molecule on ion dynamics by projecting these electric fields along the direction of ion motion. We find that the polymer functional groups act indirectly, and the polymer-metal ion interaction is actually mediated by water. This result is consistent with the experimental observation that metal sequestration by these polymers is entropically driven. This study suggests that electric field calculations can help the design of metal chelating polymers, for example, by seeking to optimize polymer-solvent interactions rather than polymer-ion interactions.

Theoretical Analysis of Physical and Chemical CO2 Absorption by Tri- and Tetraepoxidized Imidazolium Ionic Liquids.

The efficient capture of CO2 from flue gas or directly from the atmosphere is a key subject to mitigate global warming, with several chemical and physical absorption methods previously reported. Through polarizable molecular dynamics (MD) simulations and high-level quantum chemical (QC) calculations, the physical and chemical absorption of CO2 by ionic liquids based on imidazolium cations bearing oxirane groups was investigated. The ability of the imidazolium group to absorb CO2 was found to be prevalent in both the tri- and tetraepoxidized imidazolium ionic liquids (ILs) with coordination numbers over 2 for CO2 within the first solvation shell in both systems. Thermodynamic analysis of the addition of CO2 to convert epoxy groups to cyclic carbonates also indicated that the overall reaction is exergonic for all systems tested, allowing for chemical absorption of CO2 to also be favored. The rate-determining step of the chemical absorption involved the initial opening of the epoxy ring through addition of the chloride anion and was seen to vary greatly between the epoxy groups tested. Among the groups tested, the less sterically hindered monoepoxy side of the triepoxidized imidazolium was shown to be uniquely capable of undergoing intramolecular hydrogen bonding and thus lowering the barrier required for the intermediate structure to form during the reaction. Overall, this theoretical investigation highlights the potential for epoxidized imidazolium chloride ionic liquids for simultaneous chemical and physical absorption of CO2.

Strategies for Enhancing the Dielectric Constant of Organic Materials.

High dielectric constant organic semiconductors, often obtained by the use of ethylene glycol (EG) side chains, have gained attention in recent years in the efforts of improving the device performance for various applications. Dielectric constant enhancements due to EGs have been demonstrated extensively, but various effects, such as the choice of the particular molecule and the frequency and temperature regime, that determine the extent of this enhancement require further understanding. In this work, we study these effects by means of polarizable molecular dynamics simulations on a carefully selected set of fullerene derivatives with EG side chains. The selection allows studying the dielectric response in terms of both the number and length of EG chains and also the choice of the group connecting the fullerene to the EG chain. The computed time- and frequency-dependent dielectric responses reveal that the experimentally observed rise of the dielectric constant within the kilo/megahertz regime for some molecules is likely due to the highly stretched dielectric response of the EGs: the initial sharp increase over the first few nanoseconds is followed by a smaller but persistent increase in the range of microseconds. Additionally, our computational protocol allows the separation of different factors that contribute to the overall dielectric constant, providing insights to make several molecular design guides for future organic materials in order to enhance their dielectric constant further.

Redox Potentials in Ionic Liquids: Anomalous Behavior?

Characterizing redox potentials in ionic liquids us essential for expanding the use of these electrolytes for electrochemical application. In particular, solvation energies of the different redox species (e.g. radical ions) determine the observed solvent-dependent trends in redox activity. In this regard, ionic liquids are fundamentally distinct from dipolar, molecular liquids in that solvation proceeds by entirely different physical mechanisms. Recently, it has been suggested that the unique ion arrangement of ionic liquids leads to dramatic deviations from Born theory in ion solvation. This conclusion was made from the theoretical assumptions of linear and homogenous response with a monopole approximation. We explore these theoretical approximations through a comparison to free energy calculations from atomistic and explicitly polarizable molecular dynamics simulations of a model ion in the prototypical ionic liquid BMIM/BF4. We find that a sharp peak in the susceptibility around 1 Å-1 is heavily influenced by the atomistic modeling and does not translate to significant free energy anomalies sans the monopole approximation. Furthermore, we show that ionic liquids largely can be approximated through linear response theory with satisfactory accuracy, although the continuum approximation does not adequately describe the system. We also explore the kinetics through the reorganization energy and observe similar trends.

Effects of Familial Alzheimer's Disease Mutations on the Folding Free Energy and Dipole-Dipole Interactions of the Amyloid β-Peptide.

Familial Alzheimer's disease (FAD) mutations of the amyloid β-peptide (Aβ) are known to lead to early onset and more aggressive Alzheimer's disease. FAD mutations such as "Iowa" (D23N), "Arctic" (E22G), "Italian" (E22K), and "Dutch" (E22Q) have been shown to accelerate Aβ aggregation relative to the wild-type (WT). The mechanism by which these mutations facilitate increased aggregation is unknown, but each mutation results in a change in the net charge of the peptide. Previous studies have used nonpolarizable force fields to study Aβ, providing some insight into how this protein unfolds. However, nonpolarizable force fields have fixed charges that lack the ability to redistribute in response to changes in local electric fields. Here, we performed polarizable molecular dynamics simulations on the full-length Aβ42 of WT and FAD mutations and calculated folding free energies of the Aβ15-27 fragment via umbrella sampling. By studying both the full-length Aβ42 and a fragment containing mutations and the central hydrophobic cluster (residues 17-21), we were able to systematically study how these FAD mutations impact secondary and tertiary structure and the thermodynamics of folding. Electrostatic interactions, including those between permanent and induced dipoles, affected side-chain properties, salt bridges, and solvent interactions. The FAD mutations resulted in shifts in the electronic structure and solvent accessibility at the central hydrophobic cluster and the hydrophobic C-terminal region. Using umbrella sampling, we found that the folding of the WT and E22 mutants is enthalpically driven, whereas the D23N mutant is entropically driven, arising from a different unfolding pathway and peptide-bond dipole response. Together, the unbiased, full-length, and umbrella sampling simulations of fragments reveal that the FAD mutations perturb nearby residues and others in hydrophobic regions to potentially alter solubility. These results highlight the role electronic polarizability plays in amyloid misfolding and the role of heterogeneous microenvironments that arise as conformational change takes place.

Lithium Salt Effects on the Liquid Structure of Choline Chloride–Urea Deep Eutectic Solvent

Deep eutectic solvents (DESs) added with lithium salts are emerging as alternative electrolytes for lithium-ion batteries (LIBs). Yet, to design, optimize, and develop efficient DES-based electrolytes for LIBs, an in-depth understanding of the role played by the lithium cations in the intermolecular interactions between all species in the mixture is crucial. A joint approach of experimental NMR techniques and polarizable molecular dynamics (MD) simulations is used here to gather a comprehensive picture of the structure and dynamics of the prototypical system composed of the DES choline chloride:urea (ChCl:U, xChCl = 0.33) and the lithium salt containing the same anion, LiCl. Strong coordination of lithium cations by chloride anions, resulting in the formation of LiCl32– units, is revealed. Other species (especially, urea) are present in the second coordination shell of lithium, creating an extensive hydrogen-bond network. The effect of small quantities of water, typically absorbed by DES from air moisture, on the studied properties is discussed.

Long-Range Organization Study of Piperidinium-Based Ionic Liquids by Polarizable Molecular Dynamics Simulations.

The nanoscale organization of some classes of ionic liquids is responsible for their singular properties. In this paper, we use polarizable molecular dynamics simulations and small-angle X-ray scattering to probe the structure of two piperidinium- and (trifluoromethylsulfonyl)imide-based ionic liquids ([EBPip+][NTf2-] and [EOPip+][NTf2-]) that differ in the alkyl chain length of their cation. The X-ray scattering intensities calculated numerically, from the radial distribution functions, are in excellent agreement with the experimental data. The analysis of the different contributions of the X-ray scattering data allowed us to highlight the correlations responsible for the low q peak observed for the long-chain alkyl cations. New angular analyses showed that anions were more likely to align with alkyl chains as their size increased, inducing angular correlation between anions at larger distances. They also showed that the long alkyl chains of the cations aligned more with each other than the short ones. These more aligned alkyl chains induce a smaller volume of the apolar microdomains compared to the well-studied imidazolium-based ionic liquids, leading to the smaller correlation distance for piperidinium-based ionic liquids.

Data related to the article "Ion Correlation in Choline Chloride-Urea Deep Eutectic Solvent (Reline) from Polarizable Molecular Dynamics Simulations"

Data related to the article "Ion Correlation in Choline Chloride-Urea Deep Eutectic Solvent (Reline) from Polarizable Molecular Dynamics Simulations"

Free Energy Prediction of Ion-Induced Nucleation of Aqueous Aerosols

Ion-induced nucleation (IIN) is thought to be an important nucleation pathway of atmospheric aerosols. We present a combined polarizable molecular dynamics (MD) simulation and the classic ion-induced nucleation theory (IINT) approach to predict the free energy profiles of the ion-induced nucleation of aqueous aerosols in a qualitative or semiquantitative way. The dependence of both cluster structure and thermodynamic properties on cluster sizes and ion species is also systemically studied. It is confirmed the ions can significantly enhance the cluster stability, and thereby increase the nucleation rate. The ability of the common atmospheric ions to enhance the nucleation rate follows the order SO42- > H3O+ > NH4+ > NO3-, coinciding with the order of their solvation free energies. Therefore, the solvation energy can be employed as a rough index for evaluating the INN ability. Overall, the consistency between the present predictions and previous experimental and theoretical observations demonstrates the combination of MD simulation and the IINT appears to be a promising approach for exploring the IIN process and understanding the microscopic mechanism of atmospheric-related ions.