Ab Initio Molecular Dynamics Simulations of Aqueous LiTFSI Solutions─Structure, Hydrogen Bonding, and IR Spectra.

Simulations of Density Functional Theory-based ab initio molecular dynamics (AIMD) have been performed for a series of aqueous lithium bis(trifluoromethylsulfonyl)imide (LiTFSI) solutions with concentrations ranging from salt-in-water to water-in-salt systems. Analysis of the structure of electrolytes has revealed a preference of Li+ cations to interact with water molecules. In concentrated LiTFSI solutions, water molecules form small associates. The total number of hydrogen bonds (HBs) in the system decreases with salt concentrations, with bonds to water acceptors being only partially replaced by interactions with TFSI anions. Infrared (IR) spectra in the region of the O-H stretching frequency calculated from AIMD trajectories are in good agreement with experimental data. Statistics of oscillations of individual O-H bonds have shown correlations between vibrational frequencies and the structure of HBs formed by water. The changes in the IR spectrum have been related to the varying contributions of different local environments of the water molecules. The abundances of the three spectral components calculated from the simulations agree well with the decomposition of the experimental IR spectra reported in the literature.

In Vitro and In Silico Studies of Functionalized Polyurethane Surfaces toward Understanding Biologically Relevant Interactions.

The solid-aqueous boundary formed upon biomaterial implantation provides a playground for most biochemical reactions and physiological processes involved in implant-host interactions. Therefore, for biomaterial development, optimization, and application, it is essential to understand the biomaterial-water interface in depth. In this study, oxygen plasma-functionalized polyurethane surfaces that can be successfully utilized in contact with the tissue of the respiratory system were prepared and investigated. Through experiments, the influence of plasma treatment on the physicochemical properties of polyurethane was investigated by atomic force microscopy, attenuated total reflection infrared spectroscopy, differential thermal analysis, X-ray photoelectron spectroscopy, secondary ion mass spectrometry, and contact angle measurements, supplemented with biological tests using the A549 cell line and two bacteria strains (Staphylococcus aureus and Pseudomonas aeruginosa). The molecular interpretation of the experimental findings was achieved by molecular dynamics simulations employing newly developed, fully atomistic models of unmodified and plasma-functionalized polyurethane materials to characterize the polyurethane-water interfaces at the nanoscale in detail. The experimentally obtained polar and dispersive surface free energies were consistent with the calculated free energies, verifying the adequacy of the developed models. A 20% substitution of the polymeric chain termini by their oxidized variants was observed in the experimentally obtained plasma-modified polyurethane surface, indicating the surface saturation with oxygen-containing functional groups.

Hydrogen Bonding and Infrared Spectra of Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide/Water Mixtures: A View from Molecular Dynamics Simulations.

Simulations of ab initio molecular dynamics have been performed for mixtures of ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EMIM-TFSI) ionic liquid and water. Statistics of donors and acceptors of hydrogen bonds has revealed that with increasing water content, hydrogen bonds between EMIM cations and TFSI anions are replaced by bonds to water molecules. In the mixture of liquids, the total number of bonds (from EMIM cations or water molecules) formed by TFSI acceptors increases. IR spectra obtained from ab initio molecular dynamics trajectories are in good agreement with literature data for ionic liquid/water systems. Analysis of oscillations of individual C-H and O-H bonds has shown correlations between vibrational frequencies and hydrogen bonds formed by an EMIM cation or water molecule and has indicated that the changes in the IR spectrum result from the decreased number of water-water hydrogen bonds in the mixture. The tests of DFTB methodology with tailored parameterizations have yielded reasonably good description of the IR spectrum of bulk water, whereas available parameterizations have failed in satisfactory reproduction of the IR spectrum of EMIM-TFSI/water mixtures in the region above 3000 cm-1.

Explicit and Hybrid Solvent Models for Estimates of Parameters Relevant to the Reduction Potential of Ethylene Carbonate.

Using ethylene carbonate as a sample solvent, we investigated two molecular parameters used to estimate the reduction potential of the solvent: electron affinity, and the energy of the lowest unoccupied molecular orbital (LUMO). The results showed that the values of these parameters are inconsistent for a single ethylene carbonate molecule in vacuum calculations and in the continuous effective solvent. We performed a series of calculations employing explicit or hybrid (explicit/continuous) solvent models for aggregates of solvent molecules or solvated salt ions. In the hybrid solvent model, values of the two estimates extrapolated to an infinite system size converged to one common value, whereas the difference of 1 eV was calculated in the purely explicit solvent. The values of the gap between the highest occupied molecular orbital (HOMO) and the LUMO obtained in the hybrid model were significantly larger than those resulting from the explicit solvent calculations. We related these differences to the differences in frontier orbitals and changes of electron density obtained in the two solvent models. In the hybrid solvent model, the location of the additional electron in the reduced system usually corresponds to the LUMO orbital of the oxidized system. The presence of salt ions in the solvent affects the extrapolated values of the electron affinity and LUMO energy.

How Temperature, Pressure, and Salt Concentration Affect Correlations in LiTFSI/EMIM-TFSI Electrolytes: A Molecular Dynamics Study.

Classical polarizable molecular dynamics simulations have been performed for LiTFSI solutions in the EMIM-TFSI ionic liquid. Different temperature or pressure values and salt concentrations have been examined. The structure and dynamics of the solvation shell of Li+ cations, diffusion coefficients of ions, conductivities of the electrolytes, and correlations between motions of ions have been analyzed. The results indicated that regardless of the conditions, significant correlations are present in all systems. The degree of correlations depends mainly on the salt fraction in the electrolyte and is much less affected by temperature and pressure changes. A positive correlation between motions of Li+ cations and TFSI anions, leading to the occurrence of negative Li+ transference numbers, exists for all conditions, although temperature and pressure changes affect the speed of anion exchange in Li+ solvation shells.

NaFSI and NaTFSI Solutions in Ether Solvents from Monoglyme to Poly(ethylene oxide)-A Molecular Dynamics Study.

Classical molecular dynamics simulations have been performed for a series of electrolytes based on sodium bis(fluorosulfonyl)imide or sodium bis(trifluoromethylsulfonyl)imide salts and monoglyme, tetraglyme, and poly(ethylene oxide) as solvents. Structural properties have been assessed through the analysis of coordination numbers and binding patterns. Residence times for Na-O interactions have been used to investigate the stability of solvation shells. Diffusion coefficients of ions and electrical conductivity of the electrolytes have been estimated from molecular dynamics trajectories. Contributions to the total conductivity have been analyzed in order to investigate the role of ion-ion correlations. It has been found that the anion-cation interactions are more probable in the systems with NaTFSI salts. Accordingly, the degree of correlations between ion motions is larger in NaTFSI-based electrolytes.

MeTFSI (Me = Li, Na) Solvation in Ethylene Carbonate and Fluorinated Ethylene Carbonate: A Molecular Dynamics Study.

Classical and ab initio molecular dynamics (MD) simulations have been performed for electrolytes based on LiTFSI and NaTFSI solutions in ethylene carbonate and its mono- and difluoro derivatives. Differences between electrolytes with Li+ or Na+ ions and the effect of fluorination on the structure and transport properties have been analyzed. The observed differences are related to the strength of Me+-carbonate binding, which is weaker for the Na+ cation and/or fluorinated solvents. Infrared spectra have been computed from ab initio MD and density functional tight binding (DFTB) MD trajectories. The changes of vibrational frequencies have been related to the local structure of the electrolyte and to interactions between salt cations and solvent molecules. The frequency shifts obtained from the AIMD simulations agree with experimental data, whereas DFTB underestimates Na+-carbonate interactions.

Estimates of Electrical Conductivity from Molecular Dynamics Simulations: How to Invest the Computational Effort.

Although the electrical conductivity of an electrolyte can be estimated from the molecular dynamics trajectory, it is often a challenging task because of the need to obtain a substantial amount of data to ensure sufficient averaging. Here, we present an analysis on the convergence of results with the number of simulated trajectories. A series of molecular dynamics simulations have been performed for a model electrolyte (NaCl in water) and the Einstein relation has been used to calculate the electrical conductivity. The standard deviation of the conductivity estimates is relatively large compared to the mean value, and it has been shown that the off-diagonal contributions to the collective displacement of ions are responsible for large deviations between systems. It has been found that about 40 independent MD simulations may be required to reduce the errors. A procedure to improve the final estimate of the conductivity has been proposed.

Quantum-Chemical and Molecular Dynamics Investigations of Magnesium Chloride Complexes in Dimethoxyethane Solutions.

Quantum-chemical calculations and classical and ab initio molecular dynamics simulations have been performed to study the Mg2+-conducting electrolytes based on Mg(TFSI)2/MgCl2 solutions in dimethoxyethane. It has been shown that depending on the TFSI/Cl- ratio, the Mg2Cl2 2+ or Mg3Cl4 2+ complexes are preferred as stable ion aggregates. In the initial stages of the ion association process, MgCl+, MgCl2, and Mg2Cl3 + are formed as intermediate species. Calculations of harmonic frequencies and simulations of the IR spectrum of the electrolyte from the ab initio MD trajectories have been used to identify the spectral range of vibrations of ion aggregates found in the modeled electrolyte. The results have been discussed in the context of experimental data.

Molecular Dynamics Investigation of Correlations in Ion Transport in MeTFSI/EMIM-TFSI (Me = Li, Na) Electrolytes.

Classical molecular dynamics simulations have been performed in polarizable and nonpolarizable force fields for series of electrolytes based on MeTFSI (Me = Li, Na) salts dissolved in EMIM-TFSI ionic liquid. Structure and dynamics of the solvation shell of Me+ ions have been investigated. Contributions to the total conductivity of the electrolyte arising from motions of different ions and cross-correlations between them have been analyzed. The analysis has indicated that regardless of the type of Me+ cation, motions of Me+ ions and ionic liquid anions are positively correlated, contributing toward conductivity decrease and leading to negative transference numbers of metal ions. The results have confirmed experimental findings of negative transference numbers of Li+ and have suggested that the effect of Me-anion correlations in certain concentration range is a general feature of Me+ solutions in ionic liquids.

Understanding the Structure of the Hydrogen Bond Network and Its Influence on Vibrational Spectra in a Prototypical Aprotic Ionic Liquid.

Analysis of the hydrogen bond network in aprotic ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (EMIM-TFSI) has been performed based on structures obtained from ab initio or classical molecular dynamics simulations. Statistics of different donor and acceptor atoms and the amount of chelating or bifurcated bonds has been presented. Most of the hydrogen bonds in EMIM-TFSI are formed with oxygen atoms as hydrogen acceptors; and the most probable bifurcated bonds are those with a mixed pair of oxygen and nitrogen acceptors. Spectral graph analysis has shown that the cations may form hydrogen bonds with up to five different anions and the connectivity of the whole hydrogen bond network is supported mainly by H-O bonds. In the structures of the liquid simulated via force field-based dynamics, the number of hydrogen bonds is smaller and fluorine atoms are the most favored hydrogen acceptors. One-dimensional potential energy profiles for hydrogen atom displacements and corresponding vibrational frequencies have been calculated for selected C-H bonds. Individual C-H stretching frequencies vary by 200-300 cm-1, indicating differences in local environment of hydrogen atoms forming C-H···O hydrogen bonds.

Molecular Dynamics Simulations of Ionic Liquid Based Electrolytes for Na-Ion Batteries: Effects of Force Field.

Classical molecular dynamics simulations were performed for Na+ conducting electrolytes based on EMIM-TFSI ionic liquid and NaTFSI salt. Several parametrizations of force fields have been tested, including polarizable fields with dipole polarizabilities or Drude-type polarization. Trajectories up to 1 µs long have been used to estimate viscosities, diffusion coefficients, and conductivities of electrolytes with increasing amount of sodium salt. Results have been compared to available experimental data. In most cases the best agreement to measured values has been obtained in nonpolarizable simulations. Nevertheless, results have indicated the need for further development of polarizable parametrizations, preferably based on the Drude polarization model.

Alternative Route Toward Nitrones: Experimental and Theoretical Findings.

Nitrones are important building blocks for natural and biologically active compounds, used as spin-trap reagents and therapeutic agents. All this makes nitrones intriguing and valuable compounds for fundamental studies and as useful chemicals in various synthetic strategies. Therefore, nitrones are still of great interest and in the limelight of researches. With our initial goal to solve synthetic problems toward 5-phenyl-2,2'-bipyridine (Phbpy), we found that this reaction can proceed through the formation of 6-phenyl-3-(pyridin-2-yl)-1,2,4-triazin-4(3H)-ol (4-OH), which rapidly isomerizes to a 3,4-dihydro-1,2,4-triazine-based nitrone, namely 6-phenyl-3-pyridin-2-yl-2,3-dihydro-1,2,4-triazin-4-oxide (4'), This encouraged us to study condensation of hydrazonophenylacetaldehyde oxime (2), obtained from 2-isonitrosoacetophenone (1), with other aldehydes. The reaction with both salicylaldehyde and p-tolualdehyde leads to the open-chain isomers, namely (2-hydroxybenzylidene)hydrazono-2-phenylacetaldehyde oxime (5) and (4-methylbenzylidene)hydrazono-2-phenylacetaldehyde oxime (6), respectively. The latter product exists in solution in equilibrium with its cyclic isomer 6-phenyl-3-(4-methylphenyl)-2,3-dihydro-1,2,4-triazin-4-oxide (6'), while the former one exists in solution exclusively in the open-chain form. It was also found that 2 reacts with acetone with the formation of 3,3-dimethyl-6-phenyl-2,3-dihydro-1,2,4-triazin-4-oxide (7'), which also exists in solution in equilibrium with its open-chain isomer 2-phenyl-2-(propan-2-ylidenehydrazono)acetaldehyde oxime (7). The static DFT as well as ab initio molecular dynamics simulations have corroborated the experimental findings.

Explicit Solvent Modeling of IR and UV-Vis Spectra of 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide Ionic Liquid.

Explicit solvent modeling of absorption spectra of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide has been performed. Fourier transform of the autocorrelation function of the dipole moment calculated from ab initio molecular dynamics (AIMD) simulations has been used to obtain the IR spectrum of the bulk liquid. A sequential molecular dynamics (MD)/time-dependent density functional theory procedure has been applied to calculate the UV-vis spectrum. Description of both spectra is improved by an explicit solvent model with respect to gas-phase calculations or an implicit solvent model, with good agreement between computed spectra and experimental data. The major factor contributing to the improvement has been found to be the better description of structures of cation-anion pairs sampled from MD simulations. AIMD with Fourier transform has been demonstrated to be a powerful methodology for calculating bulk IR spectra of ionic liquids.

Influence of the Homopolar Dihydrogen Bonding C-H⋠⋠⋠H-C on Coordination Geometry: Experimental and Theoretical Studies.

The reaction of the N-thiophosphorylated thiourea (HOCH2 )(Me)2 CNHC(S)NHP(S)(OiPr)2 (HL), deprotonated by the thiophosphorylamide group, with NiCl2 leads to green needles of the pseudotetrahedral complex [Ni(L-1,5-S,S')2 ]⋅0.5 (n-C6 H14 ) or pale green blocks of the trans square-planar complex trans-[Ni(L-1,5-S,S')2 ]. The former complex is stabilized by homopolar dihydrogen C-H⋅⋅⋅H-C interactions formed by n-hexane solvent molecules with the [Ni(L-1,5-S,S')2 ] unit. Furthermore, the dispersion-dominated C-H⋅⋅⋅ H-C interactions are, together with other noncovalent interactions (C-H⋅⋅⋅N, C-H⋅⋅⋅Ni, C-H⋅⋅⋅S), responsible for pseudotetrahedral coordination around the Ni(II) center in [Ni(L-1,5-S,S')2 ]⋅0.5 (n-C6 H14 ).

Explicit Solvent Modeling of Solvatochromic Probes in Ionic Liquids: Implications of Solvation Shell Structure.

Calculations of absorption spectra have been performed for three solvatochromic dyes (para-nitroaniline, N,N-diethyl-para-nitroaniline, and Reichardt's dye) in four ionic liquids based on 1-ethyl-3-methylimidazolium cation. Different variants of explicit solvent model have been used: fully explicit representation of solvent ions, charge embedding method, and mixed approach. Electrostatic solute-solvent interactions have been shown to induce structuring of the solvation shell around dipolar solute, causing significant and nonmonotonic dependence of calculated transition energies on the number of ion pairs included in calculations. A mixed approach with few fully explicit solvent ions embedded in electrostatic field of point charges appears as a promising method of calculations of solvatochromic response, provided that sufficiently large system sizes are used in explicit solvent modeling.

Li(+)-Oligoglyme Association in the Presence of Ionic Liquid Studied by Molecular Dynamics and Explicit or Implicit Solvent Model.

Molecular dynamics simulations have been applied to study properties of ternary oligoglyme/ionic liquid/lithium salt electrolytes. Different types of lithium coordination and phase behavior have been observed depending on the liquid/salt anion: from full phase separation and Li(+) coordination exclusively to anions in systems with BF4(-) to rather homogeneous systems and prevailing Li(+)-hexaglyme coordination for FSI(-) or B(CN)4(-) anion. Observed structural properties have been successfully correlated to the binding energies of Li(+)-glyme complexes in solution calculated within an explicit solvent model. Conversely, an implicit solvent approach has failed to predict differences between electrolytes based on different ionic liquids.

An anion induced multisignaling probe for Hg(2+) and its application for fish kidney and liver tissue imaging studies.

3',6'-Bis(diethylamino)-2-(pyridin-2-ylmethyl)spiro[isoindoline-1,9'-xanthen]-3-one () was synthesized for the selective fluorescence and colorimetric recognition of Hg(2+) at pH 6.0. In addition, was useful for imaging Hg(2+) in fish kidney and liver tissues using a fluorescence microscope. Spirolactam ring opening of for Hg(2+) recognition is strongly influenced by the nature of the mercury salt and found to be NO3(-)-induced. Other mercury salts such as HgCl2, Hg(CH3COO)2 and Hg(ClO4)2 failed to induce fluorescence and colorimetric response of under the same experimental conditions. For instance, the former salt does not exhibit spirolactam ring opening but forms a new ionic compound (H3L)2[Hg6Cl18]·2H2O (), whose structure has been elucidated by single crystal X-ray diffraction. This might be explained by (1) the higher covalent nature of Hg(2+) and, hence, the lower acidity of the metal center and its inability to induce the ring opening reaction, and (2) the bulky anion, in the case of Hg(ClO4)2, which is also ionic, faces steric hindrance to accommodate within the N(Et)2 group upon spirolactam ring opening.

Ratiometric sensing of lysine through the formation of the pyrene excimer: experimental and computational studies.

Several pyrene based fluorescent probes undergo lysine assisted monomer to excimer conversion in a ratiometric manner. Intracellular lysine is detected using fluorescence microscopy.

Stability of ion triplets in ionic liquid/lithium salt solutions: insights from implicit and explicit solvent models and molecular dynamics simulations.

Binding energies of ion triplets formed in ionic liquids by Li(+) with two anions have been studied using quantum-chemical calculations with implicit and explicit solvent supplemented by molecular dynamics (MD) simulations. Explicit solvent approach confirms variation of solute-ionic liquid interactions at distances up to 2 nm, resulting from structure of solvation shells induced by electric field of the solute. Binding energies computed in explicit solvent and from the polarizable continuum model approach differ largely, even in sign, but relative values generally agree between these two models. Stabilities of ion triplets obtained in quantum-chemical calculations for some systems disagree with MD results; the discrepancy is attributed to the difference between static optimized geometries used in quantum chemical modeling and dynamic structures of triplets in MD simulations.