Babak Minofar

Structural heterogeneity and unique distorted hydrogen bonding in primary ammonium nitrate ionic liquids studied by high-energy X-ray diffraction experiments and MD simulations.

Liquid structure and the closest ion-ion interactions in a series of primary alkylammonium nitrate ionic liquids [C(n)Am(+)][NO(3)(-)] (n = 2, 3, and 4) were studied by means of high-energy X-ray diffraction (HEXRD) experiments with the aid of molecular dynamics (MD) simulations. Experimental density and X-ray structure factors are in good accordance with those evaluated with MD simulations. With regard to liquid structure, characteristic peaks appeared in the low Q (Q: a scattering vector) region of X-ray structure factors S(Q)s for all ionic liquids studied here, and they increased in intensity with a peak position shift toward the lower Q side by increasing the alkyl chain length. Experimentally evaluated S(Q(peak))(r(max)) functions, which represent the S(Q) intensity at a peak position of maximum intensity Q(peak) as a function of distance (actually a integration range r(max)), revealed that characteristic peaks in the low Q region are related to the intermolecular anion-anion correlation decrease in the r range of 10-12 Å. Appearance of the peak in the low Q region is probably related to the exclusion of the correlations among ions of the same sign in this r range by the alkyl chain aggregation. From MD simulations, we found unique and rather distorted NH···O hydrogen bonding between C(n)Am(+) (n = 2, 3, and 4) and NO(3)(-) in these ionic liquids regardless of the alkyl chain length. Subsequent ab initio calculations for both a molecular complex C(2)H(5)NH(2)···HONO(2) and an ion pair C(2)H(5)NH(3)(+)···ONO(2)(-) revealed that such distorted hydrogen bonding is specific in a liquid state of this family of ionic liquids, though the linear orientation is preferred for both the N···HO hydrogen bonding in a molecular complex and the NH···O one in an ion pair. Finally, we propose our interpretation of structural heterogeneity in PILs and also in APILs.

Liquid Structure of and Li + Ion Solvation in Bis(trifluoromethanesulfonyl)amide Based Ionic Liquids Composed of 1-Ethyl-3-methylimidazolium and N-Methyl-N-propylpyrrolidinium Cations

Liquid structures of the bis(trifluoromethanesulfonyl)amide based ionic liquids composed of 1-ethyl-3-methylimidazolium and N-methyl-N-propylpyrrolidinium ([C(2)mIm(+)][TFSA(-)] and [C(3)mPyrro(+)][TFSA(-)], respectively) and Li(+) ion solvation structure in their lithium salt solutions were studied by means of high-energy X-ray diffraction (HEXRD) technique with the aid of MD simulations. With regard to neat ionic liquids, a small but significant difference was found at around 3.5 Å in the intermolecular radial distribution functions G(inter)(r)s for these two ionic liquids; i.e., G(inter)(r) for [C(2)mIm(+)][TFSA(-)] was positioned at a slightly shorter region relative to that for [C(3)mPyrro(+)][TFSA(-)], which suggests that the nearest neighboring cation-anion interaction in the imidazolium ionic liquid is slightly greater than that in the other. With regard to Li(+) ion solvation structure, G(inter)(r)s for [C(2)mIm(+)][TFSA(-)] dissolving Li(+) ion exhibited additional small peak of about 1.9 Å attributable to the Li(+)-O (TFSA(-)) atom-atom correlation, though the corresponding peak was unclear in [C(3)mPyrro(+)][TFSA(-)] due to overlapping with the intramolecular atom-atom correlations in [C(3)mPyrro(+)]. In addition, the long-range density fluctuation observed in the neat ionic liquids diminished with the increase of Li(+) ion concentration for both ionic liquid solutions. These observations indicate that the large scale Li(+) ion solvated clusters are formed in the TFSA based ionic liquids, and well support the formation of [Li(TFSA)(2)](+) cluster clarified by previous Raman spectroscopic studies. MD simulations qualitatively agree with the experimental facts, by which the decrease in the long-range oscillation amplitude of r(2){G(r) - 1} for the Li(+) containing ionic liquids can be ascribed to the variation in the long-range anion-anion correlations caused by the formation of the Li(+) ion solvated clusters.

Free-energy and structural analysis of ion solvation and contact ion-pair formation of Li(+) with BF4(-) and PF6(-) in water and carbonate solvents.

Free energy of contact ion-pair (CIP) formation of lithium ion with BF(4)(-) and PF(6)(-) in water, propylene carbonate (PC), dimethyl carbonate (DMC) are quantitatively analyzed using MD simulations combined with the energy representation method. The relative stabilities of the mono-, bi-, and tridentate coordination structures are assessed with and without solvent, and water, PC, and DMC are found to favor the CIP-solvent contact. The monodentate structure is typically most stable in these solvents, whereas the configuration is multidentate in vacuum. The free energy of CIP formation is not simply governed by the solvent dielectric constant, and microscopic analyses of solute-solvent interaction at a molecular level are then performed from energetic and structural viewpoints. Vacant sites of Li(+) cation in CIP are solvated with three carbonyl oxygen atoms of PC and DMC solvent molecules, and the solvation is stronger for the monodentate CIP than for the multidentate. Energetically favorable solute-solvent configurations are shown to be spatially more restricted for the multidentate CIP, leading to the observation that the solvent favors the monodentate coordination structure.

Interfacial Molecular Organization at Aqueous Solution Surfaces of Atmospherically Relevant Dimethyl Sulfoxide and Methanesulfonic Acid Using Sum Frequency Spectroscopy and Molecular Dynamics Simulation

The molecular organization at the aqueous dimethyl sulfoxide (DMSO) and methanesulfonic acid (MSA) surfaces was investigated using vibrational sum frequency generation (VSFG) spectroscopy and molecular dynamics (MD) simulation. The molecular orientation of surface DMSO and MSA is deduced based on the VSFG spectra of both C-H stretch and S-O stretch regions. The S-O stretch region was studied for the first time and is shown to be critical in molecular orientation determination. On average, the CH(3) groups of DMSO and MSA are preferentially pointing outward into the air. However, the DMSO S═O group points slightly inward away from the surface, while the SO(3) vector of dissociated MSA points nearly straight down. In addition, MD simulations reveal that the orientation distribution of surface DMSO is relatively broad in contrast with a narrow distribution of surface MSA, which agrees with the experiment findings.

Internal structure, hygroscopic and reactive properties of mixed sodium methanesulfonate-sodium chloride particles

Internal structures, hygroscopic properties and heterogeneous reactivity of mixed CH(3)SO(3)Na/NaCl particles were investigated using a combination of computer modeling and experimental approaches. Surfactant properties of CH(3)SO(3)(-) ions and their surface accumulation in wet, deliquesced particles were assessed using molecular dynamics (MD) simulations and surface tension measurements. Internal structures of dry CH(3)SO(3)Na/NaCl particles were investigated using scanning electron microscopy (SEM) assisted with X-ray microanalysis mapping, and time-of-flight secondary ion mass spectrometry (TOF-SIMS). The combination of these techniques shows that dry CH(3)SO(3)Na/NaCl particles are composed of a NaCl core surrounded by a CH(3)SO(3)Na shell. Hygroscopic growth, deliquescence and efflorescence phase transitions of mixed CH(3)SO(3)Na/NaCl particles were determined and compared to those of pure NaCl particles. These results indicate that particles undergo a two step deliquescence transition: first at ∼69% relative humidity (RH) the CH(3)SO(3)Na shell takes up water, and then at ∼75% RH the NaCl core deliquesces. Reactive uptake coefficients for the particle-HNO(3) heterogeneous reaction were determined at different CH(3)SO(3)Na/NaCl mixing ratios and RH. The net reaction probability decreased notably with increasing CH(3)SO(3)Na and at lower RH.

The C-terminal basic residues contribute to the chemical- and voltage-dependent activation of TRPA1

The ankyrin transient receptor potential channel TRPA1 is a non-selective cationic channel that is expressed by sensory neurons, where it can be activated by pungent chemicals, such as AITC (allyl isothiocyanate), cinnamon or allicin, by deep cooling (<18 °C) or highly depolarizing voltages (>+100 mV). From the cytoplasmic side, this channel can be regulated by negatively charged ligands such as phosphoinositides or inorganic polyphosphates, most likely through an interaction with as yet unidentified positively charged domain(s). In the present study, we mutated 27 basic residues along the C-terminal tail of TRPA1, trying to explore their role in AITC- and voltage-dependent gating. In the proximal part of the C-terminus, the function-affecting mutations were at Lys969, Arg975, Lys988 and Lys989. A second significant region was found in the predicted helix, centred around Lys1048 and Lys1052, in which single alanine mutations completely abolished AITC- and voltage-dependent activation. In the distal portion of the C-terminus, the charge neutralizations K1092A and R1099A reduced the AITC sensitivity, and, in the latter mutant, increased the voltage-induced steady-state responses. Taken together, our findings identify basic residues in the C-terminus that are strongly involved in TRPA1 voltage and chemical sensitivity, and some of them may represent possible interaction sites for negatively charged molecules that are generally considered to modulate TRPA1.

Surface Residence and Uptake of Methyl Chloride and Methyl Alcohol at the Air/Water Interface Studied by Vibrational Sum Frequency Spectroscopy and Molecular Dynamics †

Vibrational sum frequency generation (VSFG) spectroscopy and molecular dynamics (MD) simulations are used to study the surface residence and organization of gas-phase methyl halide and methyl alcohol molecules adsorbed to the air/water interface, while Raman spectroscopy is used to detect the uptake of the gas-phase species into the bulk aqueous phase. Spectroscopy results reveal the presence of methyl alcohol in the bulk and at the surface. Methyl chloride is detected in the bulk, but not at the surface. This indicates that methyl alcohol adsorbs to the aqueous surface in a layer that is ordered, in agreement with previous studies, and is also readily taken up into the bulk aqueous phase, whereas methyl chloride adsorbs, but, while being taken up into the bulk liquid, has lower surface number density and/or forms a more disordered surface layer than methyl alcohol. MD simulations show that methyl halide molecules transition readily between the gas phase and interface, resulting in significantly shorter residence times at the surface for the methyl halides relative to methyl alcohol. Both the geometries that the methyl species adopt at the interface and the interactions between the methyl species and the interfacial water molecules differ for the halides and the alcohol. Complementary studies of butyl species show similar results: butyl alcohol adsorbs to the aqueous surface in a layer that exhibits a certain degree of order corresponding to the chains aligned along the surface normal, while a markedly more disordered surface layer and shorter residence times are observed in MD simulations for the butyl halides as compared to the alcohol. Desorption from the interface was found to be less frequent for the butyl halides than for the methyl halides by MD simulations. Although Raman studies show uptake of the butyl alcohol into the bulk phase, neither Raman studies nor MD simulations provide any evidence for uptake of the butyl halides into the bulk phase. The profound difference in preferred orientations between alkyl halides and alcohols at the aqueous surface, with the halogen atom of the alkyl halides being to a large degree exposed to the vapor phase, is likely to have consequences for chemistry of alkyl halides adsorbed on the surface of atmospheric aerosol particles.

Regulation of the transient receptor potential channel TRPA1 by its N-terminal ankyrin repeat domain

The transient receptor potential channel A1 (TRPA1) is unique among ion channels of higher vertebrates in that it harbors a large ankyrin repeat domain. The TRPA1 channel is expressed in the inner ear and in nociceptive neurons. It is involved in hearing as well as in the perception of pungent and irritant chemicals. The ankyrin repeat domain has special mechanical properties, which allows it to function as a soft spring that can be extended over a large range while maintaining structural integrity. A calcium-binding site has been experimentally identified within the ankyrin repeats. We built a model of the N-terminal 17 ankyrin repeat structure, including the calcium-binding EF-hand. In our simulations we find the calcium-bound state to be rigid as compared to the calcium-free state. While the end-to-end distance can change by almost 50% in the apo form, these fluctuations are strongly reduced by calcium binding. This increase in stiffness that constraints the end-to-end distance in the holo form is predicted to affect the force acting on the gate of the TRPA1 channel, thereby changing its open probability. Simulations of the transmembrane domain of TRPA1 show that residue N855, which has been associated with familial episodic pain syndrome, forms a strong link between the S4-S5 connecting helix and S1, thereby creating a direct force link between the N-terminus and the gate. The N855S mutation weakens this interaction, thereby reducing the communication between the N-terminus and the transmembrane part of TRPA1.

Interaction of organic solvents with protein structures at protein-solvent interface

The effect of non-denaturing concentrations of three different organic solvents, formamide, acetone and isopropanol, on the structure of haloalkane dehalogenases DhaA, LinB, and DbjA at the protein-solvent interface was studied using molecular dynamics simulations. Analysis of B-factors revealed that the presence of a given organic solvent mainly affects the dynamical behavior of the specificity-determining cap domain, with the exception of DbjA in acetone. Orientation of organic solvent molecules on the protein surface during the simulations was clearly dependent on their interaction with hydrophobic or hydrophilic surface patches, and the simulations suggest that the behavior of studied organic solvents in the vicinity of hyrophobic patches on the surface is similar to the air/water interface. DbjA was the only dimeric enzyme among studied haloalkane dehalogenases and provided an opportunity to explore effects of organic solvents on the quaternary structure. Penetration and trapping of organic solvents in the network of interactions between both monomers depends on the physico-chemical properties of the organic solvents. Consequently, both monomers of this enzyme oscillate differently in different organic solvents. With the exception of LinB in acetone, the structures of studied enzymes were stabilized in water-miscible organic solvents.

Surface Analysis of Ionic Liquids with and without Lithium Salt Using X‑ray Photoelectron Spectroscopy

X-ray photoelectron spectroscopy (XPS) was applied to a neat ionic liquid 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [EMI(+)][Tf(2)N(-)] and its lithium salt solution at room temperature to clarify the composition and structure of its near-surface region. Core level peaks were recorded for Li 1s, N 1s, C 1s, F 1s, O 1s, S 2s, and S 2p. Valence band XPS spectra (0-40 eV binding energy) were also studied. The XPS spectra were analyzed using DV-Xα calculations. Results show that the planar type isomer of the EMI(+) cation is dominant at the near-surface region of EMI-Tf(2)N. Results of XPS measurements show a spectrum of Li 1s in Li/EMI-Tf(2)N. The proposed models for the preferred orientation of the ions exhibit good agreement with results obtained from the DV-Xα calculations.