Molecular dynamics simulation of room-temperature ionic liquid mixture of [bmim][BF4] and acetonitrile by a refined force field

1-Butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF4]) is one of the promising room-temperature ionic liquids. To test the refined force field for [bmim][BF4] proposed in our previously work (J. Phys. Chem. B, 2004, 108, 12978-12989), thermodynamic properties of mixtures of [bmim][BF4](1)+ acetonitrile (2) are presented by using molecular dynamics over the whole concentration range. The calculated densities are in good agreement with the experimental data with deviations less than 2%, indicating the force field is applicable to the mixtures. In addition, the diffusion constants, viscosities, heats of vaporization, cohesive energy densities and excess properties of the mixtures are reported. The microscopic structures are discussed in detail, corresponding to the thermodynamic properties.     

Thermodynamical and structural properties of imidazolium based ionic liquids from molecular simulation

We have performed molecular dynamics simulations to determine the densities and heat of vaporization as well as structural information for the 1-alkyl-3-methyl-imidazolium based ionic liquids [amim][Cl] and [amim][BF(4)] in the temperature range from 298 to 363 K. In this simulation study, we used an united atom model of Liu et al. [Phys. Chem. Chem. Phys. 8, 1096 (2006)] for the [emim(+)] and [bmim(+)] cations, which we have extended for simulation in [hmim]-ILs and combined with parameters of Canongia Lopes et al. [J. Phys. Chem. B 108, 2038 (2004)] for the [Cl(-)] anion. Our simulation results prove that both the original united atoms approach by Liu et al. and our extension yield reasonable predictions for the ionic liquid with a considerably reduced computational expense than that required for all atoms models. Radial distribution functions and spatial distribution functions where employed to analyze the local structure of this ionic liquid, and in which way it is influenced by the type of the anion, the size of the cation, and the temperature. Our simulations give evidence for the occurrence of tail aggregations in these ionic liquids with increasing length of the side chain and also increasing temperature.     

Molecular dynamics simulations of PAMAM dendrimer-induced pore formation in DPPC bilayers with a coarse-grained model

We have performed 0.5-micros-long molecular dynamics (MD) simulations of 0%, 50%, and 100% acetylated third- (G3) and fifth-generation (G5) polyamidoamine (PAMAM) dendrimers in dipalmitoylphosphatidylcholine (DPPC) bilayers with explicit water using the coarse-grained (CG) model developed by Marrink et al. (J.Phys. Chem. B 2004, 108, 750-760), but with long-range electrostatic interactions included. Radii of gyration of the CG G5 dendrimers are 1.99-2.32 nm, close to those measured in the experiments by Prosa et al. (J. Polym. Sci. 1997, 35, 2913-2924) and atomistic simulations by Lee et al. (J. Phys. Chem. B 2006, 110, 4014-4019). Starting with the dendrimer initially positioned near the bilayer, we find that positively charged un-acetylated G3 and 50%-acetylated and un-acetylated G5 dendrimers insert themselves into the bilayer, and only un-acetylated G5 dendrimer induces hole formation at 310 K, but not at 277 K, which agrees qualitatively with experimental observations of Hong et al. (Bioconj. Chem. 2004, 15, 774-782) and Mecke et al. (Langmuir 2005, 21, 10348-10354). At higher salt concentration (approximately 500 mM NaCl), un-acetylated G5 dendrimer does not insert into the bilayer. The results suggest that with inclusion of long-range electrostatic interactions into coarse-grained models, realistic MD simulation of membrane-disrupting effects of nanoparticles at the microsecond time scale is now possible.     

Polarizable and flexible model for ethanol

A polarizable, flexible model for ethanol is obtained based on an extensive series of B3LYP/6-311++G(d,p) calculations and molecular dynamics simulations. The ethanol model includes electric-field dependence in both the atomic charges and the intramolecular degrees of freedom. Field-dependent intramolecular potentials have been attempted only once previously, for OH and HH stretches in water [P. Cicu et al., J. Chem. Phys. 112, 8267 (2000)]. The torsional potential involving the hydrogen-bonding hydrogen in ethanol is found to be particularly field sensitive. The methodology for developing field-dependent potentials can be readily generalized to other molecules and is discussed in detail. Molecular dynamics simulations of bulk ethanol are performed and the results are assessed based on comparisons with the self-diffusion coefficient [N. Karger et al., J. Chem. Phys. 93, 3437 (1990)], dielectric constant [J. T. Kindt and C. A. Schmuttenmaer, J. Phys. Chem. 100, 10373 (1996)], enthalpy of vaporization [R. C. Wilhoit and B. J. Zwolinski, J. Phys. Chem. Ref. Data, Suppl. 2, 2 (1973)], and experimental interatomic distributions [C. J. Benmore and Y. L. Loh, J. Chem. Phys. 112, 5877 (2000)]. The simultaneous variation of the atomic charges and the intramolecular potentials requires modified equations of motion and a multiple time step algorithm has been implemented to solve these equations. The article concludes with a discussion of the bulk structure and properties with an emphasis on the hydrogen bonding network.     

Phase diagram for a model of urate oxidase

Urate oxidase from Asperigillus flavus has been shown to be a model protein for studying the effects of polyethylene glycol (PEG) on the crystallization of large proteins. Extensive experimental studies based on small angle x-ray scattering [Vivares and Bonnete, J. Phys. Chem. B 108, 6498 (2004)] have determined the effects of salt, pH, temperature, and most importantly PEG on the crystallization of this protein. Recently, some aspects of the phase diagram have also been determined experimentally. In this paper, we use Monte Carlo techniques to predict the phase diagram for urate oxidase in solution with PEG, including the liquid-liquid and liquid-solid coexistence curves. The model used includes an electrostatic interaction, van der Waals attraction, and a polymer-induced depletion interaction [Vivares et al., Eur. Phys. J. E 9, 15 (2002)]. Results from the simulation are compared with experimental results.     

Dependency of the delocalized charge density and of the structural parameters on the pseudorotational parameter phi in 1,1-dicyanocyclopentane

Encouraged by the results we recently obtained from the exploration of the dependency of the structural parameters of 1,1-dichlorocyclopentane (J. Chem. Phys. A 2004, 108, 4658) on the pseudorotational parameter phi, we decided to reinvestigate the structure and the potential function governing the conformational equilibrium of 1,1-dicyanocyclopentane (DCCP) in the light of these novel results. The improved potential function we developed describes more adequately the dependency of the geometrical parameters on the pseudorotational phase angle phi. In the present work, we also incorporated additional terms into the equations we developed earlier (J. Chem. Phys. A 2004, 108, 4658; J. Mol. Struct. 2002, 612, 181) for describing the dependency of the distribution of the delocalized net charges throughout the ring on phi to account for the observed systematic deviations between the computed atomic distances and those provided by these equations. Although the overall fit of the electron diffraction was not significantly different from that which we presented previously, however, applying these extended equations has led to a better fit by refining a smaller number of parameters.     

Molecular dynamics simulation of the energetic room-temperature ionic liquid, 1-hydroxyethyl-4-amino-1,2,4-triazolium nitrate (HEATN)

Molecular dynamics (MD) simulations have been performed to investigate the structure and dynamics of an energetic ionic liquid, 1-hydroxyethyl-4-amino-1,2,4-triazolium nitrate (HEATN). The generalized amber force field (GAFF) was used, and an electronically polarizable model was further developed in the spirit of our previous work (Yan, T.; Burnham, C. J.; Del Popolo, M. G.; Voth, G. A. J. Phys. Chem. B 2004, 108, 11877). In the process of simulated annealing from a liquid state at 475 K down to a glassy state at 175 K, the MD simulations identify a glass-transition temperature region at around 250-275 K, in agreement with experiment. The self-intermediate scattering functions show vanishing boson peaks in the supercooled region, indicating that HEATN may be a fragile glass former. The coupling/decoupling of translational and reorientational ion motion is also discussed, and various other physical properties of the liquid state are intensively studied at 400 K. A complex hydrogen bond network was revealed with the calculation of partial radial distribution functions. When compared to the similarly sized 1-ethyl-4-methyl-1,4-imidazolium nitrate ionic liquid, EMIM+/NO3-, a hydrogen bond network directly resulting in the poorer packing efficiency of ions is observed, which is responsible for the lower melting/glass-transition point. The structural properties of the liquid/vacuum interface shows that there is vanishing layering at the interface, in accordance with the poor ion packing. The effects of electronic polarization on the self-diffusion, viscosity, and surface tension of HEATN are found to be significant, in agreement with an earlier study on EMIM+/NO3- (Yan, T.; Burnham, C. J.; Del Popolo, M. G.; Voth, G. A. J. Phys. Chem. B 2004, 108, 11877).     

The structure and binding energies of the van der Waals complexes of Ar and N2 with phenol and its cation, studied by high level ab initio and density functional theory calculations

We have investigated, using both ab initio and density functional theory methods, the minimum energy structures and corresponding binding energies of the van der Waals complexes between phenol and argon or the nitrogen molecule, and the corresponding complexes involving the phenol cation. Structures were obtained at the MP2 level using a large basis, and the corresponding energies were corrected for basis set superposition error (BSSE), higher order electron correlation effects, and for basis set size. The structures of the global minima were further refined for the effects of BSSE and the corresponding binding energies were evaluated. For each neutral species, we find only a single true minimum, pi bonded for argon and OH bonded for nitrogen. For both cationic species, we find that the OH-bonded complex is preferred over other minima which we have identified as having Ar or N(2) between exogeneous atoms. The ab initio calculations are generally in excellent agreement with experimental binding energies and rotational constants. We find that the B3LYP functional is particularly poor at describing these complexes, while a density functional theory (DFT) method with an empirical correction for dispersive interactions (DFT-D) is very successful, as are some of the new functionals proposed by Zhao and Truhlar [J. Phys. Chem. A 109, 5656 (2005); J. Chem. Theory Comput. 2, 1009 (2006); Phys. Chem. Chem. Phys. 7, 2701 (2005); J. Phys. Chem. A 108, 6908 (2004)]. Both the ab initio and DFT-D methods accurately predict the intermolecular vibrational modes.     

A new force field (ECEPP-05) for peptides, proteins, and organic molecules

Parametrization and testing of a new all-atom force field for organic molecules and peptides with fixed bond lengths and bond angles are described. The van der Waals parameters for both the organic molecules and the peptides were taken from J. Phys. Chem. B 2003, 107, 7143 and J. Phys. Chem. B 2004, 108, 12181. First, the values of the 1-4 nonbonded and electrostatic scale factors appropriate to the new force field were determined by computing the conformational energies of six model molecules, namely, ethanol, ethylamine, propanol, propylamine, 1,2-ethanediol, and 1,3-propanediol with different values of these factors. The partial atomic charges of these molecules were obtained by fitting to the electrostatic potentials calculated with the HF/6-31G quantum-mechanical method. Two different charge models (single- and multiple-conformation-derived) were also considered. We demonstrated that the charge model has a stronger effect on the conformational energies than the 1-4 scaling. The choice of a charge model affected the conformational energies of even the smallest molecules considered, whereas the effect of the 1-4 electrostatic or nonbonded scaling was apparent only for 1,3-propanediol. The best agreement with high-level ab initio data was obtained with the multiple-conformation-derived charges and with no scaling of the 1-4 nonbonded or electrostatic interactions (scale factors of 1.0). Next, the torsional parameters of a large number of neutral and charged organic molecules, assumed to be models of the side chains of the 20 naturally occurring amino acids, were computed by fitting to rotational energy profiles obtained from ab initio MP2/6-31G calculations. The quality of the fits was high with average errors for torsional profiles of less than 0.2 kcal/mol. To derive the torsional parameters for the peptide backbone, the partial atomic charges of the 20 neutral and charged amino acids were obtained by fitting to the electrostatic potentials of terminally blocked amino acids using the HF/6-31G quantum-mechanical method. Then, the phi-psi energy maps of Ac-Ala-NMe and Ac-Gly-NMe were computed using MP2/6-31G//HF/6-31G quantum-mechanical methods. The phi-psi energy map of Ac-Ala-NMe was used for refinement of the nonbonded parameters for the backbone nitrogen and hydrogen bonded to it. Subsequently, the main-chain torsional parameters were obtained by fitting the molecular mechanics energies to the phi-psi energy maps of Ac-Ala-NMe and Ac-Gly-NMe. The transferability of the entire force field was demonstrated by reproducing the main energy minima of terminally blocked Ala3 from the literature. The performance of the force field was also evaluated by simulating crystal structures of small peptides. By comparison of simulated and experimental data, examination of the torsional-angle and atom-positional root-mean-square deviations of the energy-minimized crystal structures from the corresponding X-ray model structures demonstrated high accuracy of the force field.     

On the effects of ion-wall chemical association on the electric double layer: a density functional approach for the restricted primitive model at a charged wall

We describe a density functional theory for the restricted primitive model of ionic fluid at a charged wall with active sites to which ions can bond. The theory is an extension of our recent approach [Pizio et al., J. Chem. Phys. 121, 11957 (2004)] and is focused in the effects of specific adsorption of ions on the wall, besides the electrostatic phenomena. In order to solve the problem, we use the first-order thermodynamic perturbation theory of chemical association developed by Wertheim [J. Chem. Phys. 87, 7323 (1987)]. The microscopic structure of the electric double layer and the amount of adsorbed charge are investigated. Also, the temperature dependence of capacitance is analyzed. The capacitance depends on the kind of ions that form associative bonds with the surface sites and is determined by a net charge acting on the diffuse layer. The shape of the temperature dependence of capacitance essentially depends on the association energy and the density of bonding sites.     

Dipolar solvation dynamics in room temperature ionic liquids: an effective medium calculation using dielectric relaxation data

Solvation dynamics in four imidazolium cation based room temperature ionic liquids (RTIL) have been calculated by using the recently measured dielectric relaxation data [ J. Phys. Chem. B 2008, 112, 4854 ] as an input in a molecular hydrodynamic theory developed earlier for studying solvation energy relaxation in polar solvents. Coumarin 153 (C153), 4-aminophthalimide (4-AP), and trans-4-dimethylamino-4'-cyanostilbene (DCS) have been used as probe molecules for this purpose. The medium response to a laser-excited probe molecule in an ionic liquid is approximated by that in an effective dipolar medium. The calculated decays of the solvent response function for these RTILs have been found to be biphasic and the decay time constants agree well with the available experimental and computer simulation results. Also, no probe dependence has been found for the average solvation times in these ionic liquids. In addition, dipolar solvation dynamics have been predicted for two other RTILs for which experimental results are not available yet. These predictions should be tested against experiments and/or simulation studies.     

Incidence of partial charges on ion selectivity in potassium channels

Potassium channels are membrane proteins known to select potassium over sodium ions at a high diffusion rate. We conducted ab initio calculations on a filter model of KcsA of about 300 atoms at the Hartree-Fock level of theory. Partial charges were derived from the quantum mechanically determined electrostatic potential either with Merz-Kollman or Hinsen-Roux schemes. Large polarization and/or charge transfer occur on potassium ions located in the filter, while the charges on sodium ions remain closer to unity. As a result, a weaker binding is obtained for K(+) ions. Using a simplified version of a permeation model based on the concerted-motion mechanism for ion translocation within the single-file ion channel [P. H. Nelson, J. Chem. Phys. 117, 11396 (2002)], we discuss how differences in polarization effects in the adducts with K(+) and Na(+) can play a role as for ionic selectivity and conductance.     

Pair-correlated speed distributions for the OH+CH4/CD4 reactions: Further remarks on their classical trajectory calculations in a quantum spirit

Ten years ago, Liu and co-workers measured pair-correlated speed distributions for OH+CH₄/CD₄ reactions by means of velocity map imaging (VMI) techniques at a collision energy of ∼10 kcal/mol [B. Zhang, W. Shiu, J. J. Lin and K. Liu, J. Chem. Phys 122, 131102 (2005); B. Zhang, W. Shiu and K. Liu, J. Phys. Chem. A 109, 8989 (2005)]. Recently, two of us could semi-quantitatively reproduce these measurements by performing full-dimensional quasi-classical trajectory calculations in a quantum spirit on an ab-initio potential energy surface of their own [J. Espinosa-Garcia and J. C. Corchado, Theor. Chem. Acc. (2015) 134: 6; J. Phys. Chem. B 120, 1446 (2016)]. The goal of the present work is to show that these results can be significantly improved by adding a few more constraints in order to better comply with the restrictions imposed by VMI. Overall, the level of agreement between theory and experiment is remarkable owing to the large dimensionality of the reactions under scrutiny. This is an encouraging result considering the computational challenges of quantum scattering calculations for such large processes.     

Dynamic solvation in imidazolium-based ionic liquids on short time scales

Steady-state and time-resolved Stokes shift data for the probe coumarin 153 in two imidazoles, six imidazolium-based ionic liquids, and several other solvents are presented. These results are consistent with our original suggestion (J. Phys. Chem. B 2004, 108, 10245-10255) that initial solvation is dominated by the organic moiety of the ionic liquid, and they show that for the imidazole-based liquids initial solvation is in all cases very rapid. Solvation by methylimidazole and butylimidazole is complete in 100 ps, and all of the imidazolium ionic liquids demonstrate similarly rapid initial solvation. Owing to the importance of determining the amount of initial solvation that is missed in a given experiment with finite time resolution, we discuss a method of estimating the intramolecular contribution to the reorganization energy. This method yields 2068 cm(-1) and is compared with an alternative method.     

Interfacial energy and the law of corresponding states 2: associated fluids

A mesoscopic model for the liquid/vapor interface previously developed for nonpolar fluids [J. Phys. Chem. A 2003, 107, 875; 2003, 107, 883] is extended to the case of polar associated compounds. The interfacial energy is factorized in two terms: one corresponding to association depending on the hydrogen bonds density, the other corresponding to the nonpolar contribution. This last term is treated in the framework of the corresponding states formalism similar to the one used in the case of nonpolar fluids [J. Phys. Chem. B 2004, 108, 5951]. The model yields a generalized behavior of the association factor as a function of the dielectric constant for the treated fluids. The calculated surface tension shows a mean error of about 1% for seven compounds having different multivalent H-bond characters.     

Experimental and theoretical investigations of solvation dynamics of ionic fluids: appropriateness of dielectric theory and the role of DC conductivity

An analysis is provided of the subnanosecond dynamic solvation of ionic liquids in particular and ionic solutions in general. It is our hypothesis that solvation relaxation in ionic fluids, in the nonglassy and nonsupercooled regimes, can be understood rather simply in terms of the dielectric spectra of the solvent. This idea is suggested by the comparison of imidazolium ionic liquids with their pure organic counterpart, butylimidazole (J. Phys. Chem. B 2004, 108, 10245-10255). It is borne out by a calculation of the solvation correlation time from frequency dependent dielectric data for the ionic liquid, ethylammonium nitrate, and for the electrolyte solution of methanol and sodium perchlorate. Very good agreement is obtained between these theoretically calculated solvation relaxation functions and those obtained from fluorescence upconversion spectroscopy. Our comparisons suggest that translational motion of ions may not be the predominant factor in short-time solvation of ionic fluids and that many tools and ideas about solvation dynamics in polar solvents can be adapted to ionic fluids.     

Distributions of ionic concentrations and electric field around the three-phase contact at high rates of Langmuir-Blodgett deposition

A mathematical problem is formulated and numerically solved for addressing the electric field and ionic concentration distributions developing around the three-phase contact line during the Langmuir-Blodgett deposition of charged monolayers. Compared to a previous paper dealing with the same effect (J. Phys. Chem. B 2004, 108, 13449), the present analysis is not restricted to the case of low deposition rates and small concentration changes. The obtained results show that, for sufficiently high deposition rates, the subphase composition substantially changes in the immediate vicinity of the three-phase contact line. It is shown that the predicted changes in the subphase composition can drastically affect the adhesion work and the dynamic contact angle. On this basis, the influence of the concentration polarization effect on meniscus behavior is discussed.