Main and papain-like proteases as prospective targets for pharmacological treatment of coronavirus SARS-CoV-2.

The pandemic caused by the coronavirus SARS-CoV-2 led to a global crisis in the world healthcare system. Despite some progress in the creation of antiviral vaccines and mass vaccination of the population, the number of patients continues to grow because of the spread of new SARS-CoV-2 mutations. There is an urgent need for direct-acting drugs capable of suppressing or stopping the main mechanisms of reproduction of the coronavirus SARS-CoV-2. Several studies have shown that the successful replication of the virus in the cell requires proteolytic cleavage of the protein structures of the virus. Two proteases are crucial in replicating SARS-CoV-2 and other coronaviruses: the main protease (Mpro) and the papain-like protease (PLpro). In this review, we summarize the essential viral proteins of SARS-CoV-2 required for its viral life cycle as targets for chemotherapy of coronavirus infection and provide a critical summary of the development of drugs against COVID-19 from the drug repurposing strategy up to the molecular design of novel covalent and non-covalent agents capable of inhibiting virus replication. We overview the main antiviral strategy and the choice of SARS-CoV-2 Mpro and PLpro proteases as promising targets for pharmacological impact on the coronavirus life cycle.

Insight to the Local Structure of Mixtures of Imidazolium-Based Ionic Liquids and Molecular Solvents from Molecular Dynamics Simulations and Voronoi Analysis.

While the physicochemical properties as well as the NMR and vibration spectroscopic data of the mixtures of ionic liquids (ILs) with molecular solvents undergo a drastic change around the IL mole fraction of 0.2, the local structure of the mixtures pertaining to this behavior remains unclear. In this work, the local structure of 12 mixtures of 1-butyl-3-methylimidazolium cation (C4mim+) combined with perfluorinated anions, such as tetrafluoroborate (BF4-), hexafluorophosphate (PF6-), trifluoromethylsulfonate (TFO-), and bis(trifluoromethanesulfonyl)imide, (TFSI-), and aprotic dipolar solvents, such as acetonitrile (AN), propylene carbonate (PC), and gamma butyrolactone (γ-BL) is studied by molecular dynamics simulations in the entire composition range, with an emphasis on the IL mole fractions around 0.2. Distributions of metric properties corresponding to the Voronoi polyhedra of the particles (volume assigned to the particles, local density, radius of spherical voids) are determined, using representative sites of the cations, anions, and the solvent molecules, to characterize the changes in the local structure of these mixtures. By analyzing the mole fraction dependence of the average value, fluctuation, and skewness parameter of these distributions, the present study reveals that, around the IL mole fraction of 0.2, the local structure of the mixture undergoes a transition between that determined by the interionic interactions and that determined by the interactions between the ions and solvent molecules. It should be noted that the strength of the interactions between the ions and the solvent molecules, modulated by the change in the composition of the mixture, plays an important role in the occurrence of this transition. The signature of the change in the local structure is traced back to the nonlinear change of the mean values, fluctuations, and skewness values of the metric Voronoi polyhedra distributions.

Voronoi Polyhedra as a Tool for the Characterization of Inhomogeneous Distribution in 1-Butyl-3-methylimidazolium Cation-Based Ionic Liquids.

The inhomogeneity distribution in four imidazolium-based ionic liquids (ILs) containing the 1-butyl-3-methylimidazolium (C4mim) cation, coupled with tetrafluoroborate (BF4), hexafluorophosphate (PF6), bis(trifluoromethanesulfonyl)amide (TFSA), and trifluoromethanesulfonate (TfO) anions, was characterized using Voronoi polyhedra. For this purpose, molecular dynamic simulations have been performed on the isothermal-isobaric (NpT) ensemble. We checked the ability of the potential models to reproduce the experimental density, heat of vaporization, and transport properties (diffusion and viscosity) of these ionic liquids. The inhomogeneity distribution of ions around the ring, methyl, and butyl chain terminal hydrogen atoms of the C4mim cation was investigated by means of Voronoi polyhedra analysis. For this purpose, the position of the C4mim cation was described successively by the ring, methyl, and butyl chain terminal hydrogen atoms, while that of the anions was described by their F or O atom. We calculated the Voronoi polyhedra distributions of the volume, the density, and the asphericity parameters as well as that of the radius of the spherical intermolecular voids. We carried out the analysis in two steps. In the first step, both ions were taken into account. The calculated distributions gave information on the neighboring ions around a reference one. In the second step, to distinguish between like and oppositely charged ions and then to get information on the inhomogeneity distribution of the like ions, we repeated the same calculations on the same sample configurations and removed one of the ions and considered only the other one. Detailed analysis of these distributions has revealed that the ring hydrogen atoms are mainly solvated by the anions, while the methyl and butyl terminal H atoms are surrounded by like atoms. The extent of this inhomogeneity was assessed by calculating the cluster size distribution that shows that the dimers are the most abundant ones.

Distance Angle Descriptors of the Interionic and Ion-Solvent Interactions in Imidazolium-Based Ionic Liquid Mixtures with Aprotic Solvents: A Molecular Dynamics Simulation Study.

The aim of this paper is to quantify the changes of the interionic and ion-solvent interactions in mixtures of imidazolium-based ionic liquids, having tetrafluoroborate (BmimBF4), hexafluorophosphate (BmimPF6), trifluoromethylsulfonate (BmimTFO), or bis(trifluoromethanesulfonyl)imide (BmimTFSI), anions, and polar aprotic molecular solvents, such as acetonitrile (AN), γ-butyrolactone (GBL), and propylene carbonate (PC). For this purpose, we calculate, using the nearest-neighbor approach, the average distance between the imidazolium ring H atom in positions 2, 4, and 5 (H2,4,5) and the nearest high-electronegativity atom of the solvent or anion (X) as distance descriptors, and the mean angle formed by the C2,4,5-H2,4,5 bond and the H2,4,5···X axis around the H2,4,5 atom as angular descriptors of the cation-anion and cation-solvent interactions around the ring C-H groups. The behavior of these descriptors as a function of the ionic liquid mole fraction is analyzed in detail. The obtained results show that the extent of the change of these descriptors with respect to their values in the neat ionic liquid depends both on the nature of the anion and on the mixture composition. Thus, in the case of the mixtures of the molecular solvents with BmimBF4 and BmimTFO, a small change of the distance and a drastic increase of the angular descriptor corresponding to the cation-anion interactions are observed with decreasing mole fraction of the ionic liquid, indicating that the anion moves from the above/below position (with respect to the imidazolium ring plane) to a position that is nearly linearly aligned with the C2-H2 bond and hinders the possible interaction between the C2-H2 group and the solvent molecules. On the other hand, in the case of mixtures of BmimTFSI and BmimPF6 with the molecular solvents, both the observed increase of the distance descriptor and the slight change of the angular descriptor with decreasing ionic liquid mole fraction are compatible with the direct interactions of the solvent with the C2-H2 group. The behavior of these descriptors is correlated with the experimentally observed 1H chemical shift of the C2-H2 group and the red shift of the C2-H2 vibrational mode, particularly at low ionic liquid mole fractions. The present results are thus of great help in interpreting these experimental observations.

The local structure in the BmimPF6/acetonitrile mixture: the charge distribution effect.

The changes of the local structure in the binary mixture of 1-butyl-3-methylimidazolium hexafluorophosphate (BmimPF6) ionic liquid and acetonitrile are investigated over the entire composition range. Two charge distribution models of the ions are considered: in the first one, the atomic fractional charges of the cations and anions are kept equal with those in the neat ionic liquid, and hence they are independent from the mole fraction of the ionic liquid, while in the second one the charge distribution is scaled up by a mole fraction dependent factor. The sum of these charges converge to +1e and -1e on the cation and anion, respectively, at infinite dilution. All the other interactions and geometry parameters of the ions (i.e., Lennard-Jones, bond stretching, angle bending and dihedral parameters) are identical in the two cases. The effect of the fractional charge distribution on the hydrogen bonding between the counterions themselves and between the ions and solvent molecules, as well as on the stacking interactions between the cations, is analyzed. To this end, two distances, characteristic of the hydrogen bond formed by the donor moiety and its nearest neighbor acceptor, as well as a coordinate system that defines unambiguously the orientation between a reference cation and its nearest neighbor, are introduced. It is shown that, with the variable charge model, the neighboring cation-anion pairs maintain their relative arrangement similar to the neat ionic liquid down to an ionic liquid mole fraction of xIL = 0.10, whereas in the case of the constant charge model such changes occur already at xIL = 0.20. Furthermore, the analysis of the first and the second nearest neighbor distance distributions of an anion around a reference cation indicates that, at this mole fraction range, there are two different preferred arrangements of the anions around the cations. In the first one, similarly to the local structure around a reference cation in the neat ionic liquid, the anion forms a distorted hydrogen bond with the cation, while in the second one the anion is located farther from the cation, forming no hydrogen bond with it. The relative population of these two types of preferred nearest neighbor cation-anion arrangements is found to be sensitive to further decrease of the ionic liquid mole fraction. These findings correlate with experimental results concerning the behavior of many physical chemical properties (e.g., excess volume, excess viscosity, chemical shift, infrared and Raman vibrational mode shifts, diffusion, etc.) that were found to undergo a drastic change in this mole fraction range. Our results show that in this composition range a transition occurs from the situation where the macroscopic physical chemical properties of the system are determined primarily by the cation-anion hydrogen bonding interactions to that where they are determined by the solvation of the cation and the anion by the molecular solvent.

Poly(vinyl alcohol) as a water protecting agent for silver nanoparticles: the role of polymer size and structure.

Chemical modification of silver nanoparticles (AgNPs) with a stabilizing agent, such as poly(vinyl alcohol) (PVA), plays an important role in shape-controlled seeded-growth and colloidal stability. However, theoretical aspects of the stabilizing mechanism of PVA are still poorly understood. To gain a better understanding of the role of PVA in water protecting effects for silver nanoparticles, we developed an atomistic model of a AgNP grafted with single-chain PVA of various lengths. Our model, designed for classical molecular dynamics (MD) simulations, approximates the AgNP as a quasi-spherical silver nanocrystal with 3.9 nm diameter and uses a united-atom representation for PVA with its polymer chain length varying from 220 up to 1540 repeating units. We found that PVA adsorbs onto the AgNP surface through multiple non-covalent interactions, among which non-covalent bonding of the hydroxyl groups plays a key role. The analysis of adsorption isotherms by using the Hill, Scatchard, and McGhee & von Hippel models exhibits evidence for positive binding cooperativity with the cooperativity parameter varying from 1.55 to 2.12. Our results indicate that the size of the PVA polymer rather than its structure plays a crucial role in providing water protecting effects for the AgNP core, varying from 40% up to 91%. The water-protecting efficiency was well approximated by the Langmuir-Freundlich equation, allowing us to predict that the saturated coverage of the nanoparticle of a given diameter of 3.9 nm should occur when the PVA molecular weight approaches 115 kDa, which corresponds to the number of vinyl alcohol monomers being equal to 3100 units.

Competition between Cation-Solvent and Cation-Anion Interactions in Imidazolium Ionic Liquids with Polar Aprotic Solvents.

The subtle interplay between ion solvation and association was analyzed in mixtures of imidazolium-based ionic liquids (ILs) with polar aprotic solvents. A site-specific pattern of cation-solvent and cation-anion interactions was disclosed by a careful analysis of the 1 H and 13 C NMR chemical shift dependence of the mixture composition. It was established that the less polar but more donating γ-butyrolactone is more prone to establish H-bonds with the imidazolium-ring hydrogen atoms of the IL cations than propylene carbonate, particularly at the H2 site and at high dilutions xIL <0.1. The H2 site was found to be more sensitive to intermolecular interactions compared to H4, 5 in the case of ILs with asymmetric anions like trifluoromethanesulfonate (TfO- ) or bis(trifluoromethylsulfonyl)amide (TFSA- ).

Local Structure in Terms of Nearest-Neighbor Approach in 1-Butyl-3-methylimidazolium-Based Ionic Liquids: MD Simulations.

Description of the local microscopic structure in ionic liquids (ILs) is a prerequisite to obtain a comprehensive understanding of the influence of the nature of ions on the properties of ILs. The local structure is mainly determined by the spatial arrangement of the nearest neighboring ions. Therefore, the main interaction patterns in ILs, such as cation-anion H-bond-like motifs, cation-cation alkyl tail aggregation, and ring stacking, were considered within the framework of the nearest-neighbor approach with respect to each particular interaction site. We employed classical molecular dynamics (MD) simulations to study in detail the spatial, radial, and orientational relative distribution of ions in a set of imidazolium-based ILs, in which the 1-butyl-3-methylimidazolium (C4mim(+)) cation is coupled with the acetate (OAc(-)), chloride (Cl(-)), tetrafluoroborate (BF4(-)), hexafluorophosphate (PF6(-)), trifluoromethanesulfonate (TfO(-)), or bis(trifluoromethanesulfonyl)amide (TFSA(-)) anion. It was established that several structural properties are strongly anion-specific, while some can be treated as universally applicable to ILs, regardless of the nature of the anion. Namely, strongly basic anions, such as OAc(-) and Cl(-), prefer to be located in the imidazolium ring plane next to the C-H(2/4-5) sites. By contrast, the other four bulky and weakly coordinating anions tend to occupy positions above/below the plane. Similarly, the H-bond-like interactions involving the H(2) site are found to be particularly enhanced in comparison with the ones at H(4-5) in the case of asymmetric and/or more basic anions (C4mimOAc, C4mimCl, C4mimTfO, and C4mimTFSA), in accordance with recent spectroscopic and theoretical findings. Other IL-specific details related to the multiple H-bond-like binding and cation stacking issues are also discussed in this paper. The secondary H-bonding of anions with the alkyl hydrogen atoms of cations as well as the cation-cation alkyl chain aggregation turned out to be poorly sensitive to the nature of the anion.

Probing structural patterns of ion association and solvation in mixtures of imidazolium ionic liquids with acetonitrile by means of relative (1)H and (13)C NMR chemical shifts.

Mixtures of ionic liquids (ILs) with polar aprotic solvents in different combinations and under different conditions (concentration, temperature etc.) are used widely in electrochemistry. However, little is known about the key intermolecular interactions in such mixtures depending on the nature of the constituents and mixture composition. In order to systematically address the intermolecular interactions, the chemical shift variation of (1)H and (13)C nuclei has been followed in mixtures of imidazolium ILs 1-n-butyl-3-methylimidazolium tetrafluoroborate (BmimBF4), 1-n-butyl-3-methylimidazolium hexafluorophosphate (BmimPF6), 1-n-butyl-3-methylimidazolium trifluoromethanesulfonate (BmimTfO) and 1-n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BmimTFSI) with molecular solvent acetonitrile (AN) over the entire composition range at 300 K. The concept of relative chemical shift variation is proposed to assess the observed effects on a unified and unbiased scale. We have found that hydrogen bonds between the imidazolium ring hydrogen atoms and electronegative atoms of anions are stronger in BmimBF4 and BmimTfO ILs than those in BmimTFSI and BmimPF6. Hydrogen atom at position 2 of the imidazolium ring is substantially more sensitive to interionic hydrogen bonding than those at positions 4-5 in the case of BmimTfO and BmimTFSI ILs. These hydrogen bonds are disrupted upon dilution in AN due to ion dissociation which is more pronounced at high dilutions. Specific solvation interactions between AN molecules and IL cations are poorly manifested.

Non-covalent interactions in ionic liquid ion pairs and ion pair dimers: a quantum chemical calculation analysis.

Ionic liquids (ILs) being composed of bulky multiatomic ions reveal a plethora of non-covalent interactions which determine their microscopic structure. In order to establish the main peculiarities of these interactions in an IL-environment, we have performed quantum chemical calculations for a set of representative model molecular clusters. These calculations were coupled with advanced methods of analysis of the electron density distribution, namely, the quantum theory of atoms in molecules (QTAIM) and the non-covalent interaction (NCI; J. Am. Chem. Soc., 2010, 132, 6499) approaches. The former allows for profound quantitative characterization of non-covalent interactions between atoms while the latter gives an overview of spatial extent, delocalization, and relative strength of such interactions. The studied systems consist of 1-butyl-3-methylimidazolium (Bmim(+)) cations and different perfluorinated anions: tetrafluoroborate (BF4(-)), hexafluorophosphate (PF6(-)), trifluoromethanesulfonate (TfO(-)), and bis(trifluoromethanesulfonyl)imide (TFSI(-)). IL ion pairs and ion pair dimers were considered as model structures for the neat ILs and large aggregates. Weak electrostatic hydrogen bonding was found between the anions and the imidazolium ring hydrogen atoms of cations. Weaker but still appreciable hydrogen bonding was also noted for hydrogen atoms adjacent to the imidazolium ring alkyl groups of Bmim(+). The relative strength of the hydrogen bonding is higher in BmimTfO and BmimBF4 ILs than in BmimPF6 and BmimTFSI, whereas BmimTfO and BmimTFSI reveal higher sensitivity of hydrogen bonding at the different hydrogen atoms of the imidazolium ring.

Complexation of Ni(ClO4)2 and Mg(ClO4)2 with 3-hydroxyflavone in acetonitrile medium: conductometric, spectroscopic, and quantum chemical investigation.

The complex formation of Ni(ClO4)2 and Mg(ClO4)2 with 3-hydroxyflavone (HL, flavonol) in acetonitrile was studied using conductometric and spectroscopic methods. It was found that interaction of nickel cation with HL leads to formation of the doubly charged [Ni(HL)](2+) complex, whereas in solutions of magnesium perchlorate the complex with anion [MgClO4(HL)](+) is formed. Using the extended Lee-Wheaton equation, the limiting equivalent conductivities of [Ni(HL)](2+) and [MgClO4(HL)](+) and thermodynamic constants of their formation were obtained at 288, 298, 308, 318, and 328 K. Calculated Stoke's radii indicate weak solvation of the formed complexes and low temperature stability of their solvation shells. On the basis of the quantum chemical calculations and noncovalent interactions analysis, it is found that in the solvated [Ni(HL)](2+) and [MgClO4(HL)](+) complexes interaction of the Ni(2+) and Mg(2+) cations with flavonol occurs via the carbonyl group of HL. Complexation with Ni(2+) does not change the internal structure of HL greatly: in the [Ni(HL)](2+) complex, flavonol shows an intramolecular H-bond between 3-hydroxyl and carbonyl groups. When a complex with [MgClO4](+) is formed, the OH group turns out of the plane of the chromone moiety that leads to rupture of an intramolecular H-bond in the ligand molecule. Moreover, in the [MgClO4(HL)](+) complex, perchlorate anion possesses a strong ability to interact with HL, forming an intracomplex H-bond between hydrogen of the 3-hydroxyl group and oxygen of ClO4(-). Its strength is more pronounced than in the intramolecular one in both [Ni(HL)](2+) and uncomplexed 3-hydroxyflavone.

Structure, solvation, and dynamics of Mg²âº, Ca²âº, Sr²âº, and Ba²âº complexes with 3-hydroxyflavone and perchlorate anion in acetonitrile medium: a molecular dynamics simulation study.

Molecular dynamics simulations of complexes of Mg(2+), Ca(2+), Sr(2+), and Ba(2+) with 3-hydroxyflavone (flavonol, 3HF) and ClO4⁻ in acetonitrile were performed. The united atoms force field model was proposed for the 3HF molecule using the results of DFT quantum chemical calculations. 3HF was interpreted as a rigid molecule with two internal degrees of freedom, i.e., rotation of the phenyl ring and of the OH group with respect to the chromone moiety. The interatomic radial distribution functions showed that interaction of the cations with flavonol occurs via the carbonyl group of 3HF and it is accompanied with substitution of one of the acetonitrile molecules in the cations' first solvation shells. Formation of the cation-3HF complexes does not have significant impact on the rotation of the phenyl ring with respect to the chromone moiety. However, the orientation of the flavonol's OH-group is more sensitive to the interaction with doubly charged cations. When complex with Mg(2+) is formed, the OH-group turns out of the plane of the chromone moiety that leads to rupture of intramolecular H-bond in the ligand molecule. Complexation of Ca(2+), Sr(2+), and BaClO4⁺ with 3HF produces two structures with different OH-positions, as in the free flavonol with the intramolecular H-bond and as in the complex with Mg(2+) with disrupted H-bonding. It was shown that additional stabilization of the [MgClO4(3HF)](+) and [BaClO4(3HF)](+) complexes is determined by strong affinity of perchlorate anion to interact with flavonol via intracomplex hydrogen bond between an oxygen atom of the anion and the hydrogen atom of the 3-hydroxyl group. Noticeable difference in the values of the self-diffusion coefficients for Kt(2+) from one side and ClO4⁻, 3HF, and AN in the cations' coordination shell from another side implies quite weak interaction between cation, anion, and ligands in the investigated complexes.

Translational diffusion in mixtures of imidazolium ILs with polar aprotic molecular solvents.

Self-diffusion coefficients of cations and solvent molecules were determined with (1)H NMR in mixtures of 1-n-butyl-3-methylimidazolium (Bmim(+)) tetrafluoroborate (BF4(-)), hexafluorophosphate (PF6(-)), trifluoromethanesulfonate (TfO(-)), and bis(trifluoromethylsulfonyl)imide (TFSI(-)) with acetonitrile (AN), γ-butyrolactone (γ-BL), and propylene carbonate (PC) over the entire composition range at 300 K. The relative diffusivities of solvent molecules to cations as a function of concentration were found to depend on the solvent but not on the anion (i.e., IL). In all cases the values exhibit a plateau at low IL content (x(IL) < 0.2) and then increase steeply (AN), moderately (γ-BL), or negligibly (PC) at higher IL concentrations. This behavior was related to the different solvation patterns in the employed solvents. In BmimPF6-based systems, anionic diffusivities were followed via (31)P nuclei and found to be higher than the corresponding cation values in IL-poor systems and lower in the IL-rich region. The inversion point of relative ionic diffusivities was found around equimolar composition and does not depend on the solvent. At this point, a distinct change in the ion-diffusion mechanism appears to take place.

Control of Carbon Nanotube Electronic Properties by Lithium Cation Intercalation.

We show that the electronic properties of single walled carbon nanotubes (SWCNTs) can be tuned continuously from semiconducting to metallic by varying the location of ions inside the tubes. Focusing on the Li(+) cation inside the (26,0) zigzag semiconducting and (15,15) armchair metallic SWCNTs, we found that the Li(+)-SWCNT interaction is attractive. The interaction is stronger for the metallic SWCNT, indicating in particular that metallic tubes can enhance performance of lithium-ion batteries. The electronic properties of the metallic SWCNT are virtually independent of the presence of ions: Li(+) creates an energy level in the valence band slightly below the Fermi energy. On the contrary, the semiconducting SWCNT can be made metallic by placing ions close to the tube axis: Li(+) generates a new bottom of the conduction band. Letting the ions approach SWCNT walls recovers the semiconducting behavior.

Acetonitrile boosts conductivity of imidazolium ionic liquids.

We apply a new methodology in the force field generation (Phys. Chem. Chem. Phys.2011, 13, 7910) to study binary mixtures of five imidazolium-based room-temperature ionic liquids (RTILs) with acetonitrile (ACN). Each RTIL is composed of tetrafluoroborate (BF(4)) anion and dialkylimidazolium (MMIM) cations. The first alkyl group of MIM is methyl, and the other group is ethyl (EMIM), butyl (BMIM), hexyl (HMIM), octyl (OMIM), and decyl (DMIM). Upon addition of ACN, the ionic conductivity of RTILs increases by more than 50 times. It significantly exceeds an impact of most known solvents. Unexpectedly, long-tailed imidazolium cations demonstrate the sharpest conductivity boost. This finding motivates us to revisit an application of RTIL/ACN binary systems as advanced electrolyte solutions. The conductivity correlates with a composition of ion aggregates simplifying its predictability. Addition of ACN exponentially increases diffusion and decreases viscosity of the RTIL/ACN mixtures. Large amounts of ACN stabilize ion pairs, although they ruin greater ion aggregates.

A new force field model for the simulation of transport properties of imidazolium-based ionic liquids.

A new, non-polarizable force field model (FFM) for imidazolium-based, room-temperature ionic liquids (RTILs), 1-ethyl-3-methyl-imidazolium tetrafluoroborate and 1-butyl-3-methyl-imidazolium tetrafluoroborate, has been developed. Modifying the FFM originally designed by Liu et al. (J. Phys. Chem. B, 2004, 108, 12978-12989), the electrostatic charges on interacting sites are refined according to partial charges calculated by explicit-ion density functional theory. The refined FFM reproduces experimental heats of vaporization, diffusion coefficients, ionic conductivities, and shear viscosities of RTILs, which is a significant improvement over the original model (Zh. Liu, Sh. Huang and W. Wang, J. Phys. Chem. B, 2004, 108, 12978-12989). The advantages of the proposed procedure include clarity, simplicity, and flexibility. Expanding the functionality of our FFM conveniently only requires modification of the electrostatic charges. Our FFM can be extended to other classes of RTILs as well as condensed matter systems in which the ionic interaction requires an account of polarization effects.

Vibrational energy transfer between carbon nanotubes and liquid water: a molecular dynamics study.

The rates and magnitudes of vibrational energy transfer between single-wall carbon nanotubes (CNTs) and water are investigated by classical molecular dynamics. The interactions between the CNT and solvent confined inside of the tube, the CNT and solvent surrounding the tube, as well as the solvent inside and outside of the tube are considered for the (11,11), (15,15), and (19,19) armchair CNTs. The vibrational energy transfer exhibits two time scales, subpicosecond and picosecond, of roughly equal importance. Solvent molecules confined within CNTs are more strongly coupled to the tubes than the outside molecules. The energy exchange is facilitated by slow collective motions, including CNT radial breathing modes (RBM). The transfer rate between CNTs and the inside solvent shows strong dependence on the CNT diameter. In smaller tubes, the transfer is faster and the solvent coupling to RBMs is stronger. The magnitude of the CNT-outside solvent interaction scales with the CNT surface area, while that of the CNT-inside solvent exhibits scaling that is intermediate between the CNT volume and surface. The Coulomb interaction between the solvent molecules inside and outside of the CNTs is much weaker than the CNT-solvent interactions. The results indicate that the excitation energy supplied to CNTs in chemical and biological applications is rapidly deposited to the active molecular agents and should remain localized sufficiently long in order to perform the desired function.

Ab initio study of phonon-induced dephasing of electronic excitations in narrow graphene nanoribbons.

Vibrational dephasing of the lowest energy electronic excitations in the perfect (16,16) graphene nanoribbon (GNR) and those with the C2-bond insertion and rotation defects is studied with ab initio molecular dynamics. Compared to single-walled carbon nanotubes (SWCNTs) of similar size, GNRs shows very different properties. The dephasing in the ideal GNR occurs twice faster than that in the SWCNTs. It is induced primarily by the 1300 cm (-1) disorder mode seen in bulk graphite rather than by the 1600 cm (-1) C-C stretching mode as in SWCNTs. In contrast to SWCNTs, defects exhibit weaker electron-phonon coupling compared to the ideal system. Therefore, defects should present much less of a practical problem in GNRs compared to SWCNTs. The predicted optical line widths can be tested experimentally.

Uniform diffusion of acetonitrile inside carbon nanotubes favors supercapacitor performance.

An unusual behavior of liquid acetonitrile (AN) confined inside carbon nanotubes (CNTs) is predicted by molecular dynamics simulation. In contrast to water, which shows inhomogeneous variation of both translational and rotational diffusion with CNT diameter [ Nano Lett. 2003, 3, 589; 2004, 4, 619], the diffusion coefficient of AN changes uniformly and can be described by a simple analytic model. At the same time, the reorientation dynamics of AN vary irregularly in smaller CNTs because of specific packing structures. The uniform translational diffusion of the nonaqueous solvent is critical for stable performance of the new generation of supercapacitors [ Nat. Mater. 2006, 5, 987].

Dynamics and structure of nickel chloride-methanol solutions: quasi-elastic neutron scattering and molecular dynamics simulations.

The high-resolution quasi-elastic neutron scattering (QENS) technique has been applied to study the translational diffusion of methanol protons in pure methanol (MeOH) at 223 and 297 K, and in 0.3 and 1.3 molal non-aqueous electrolyte solutions (NAESs) of NiCl2 in methanol at 297 K. Molecular dynamics (MD) simulations, in conjunction with the present QENS results and our previously published structural results obtained by neutron diffraction isotopic substitution (NDIS) experiments, have been carried out in the NVT ensemble to explore the particle dynamics and microscopic structures of the experimentally investigated systems. The simulated structure of the ∼1.35 molal NiCl2-MeOH NAES has been compared with the structures of Ni2+ and Cl- coordination shells in ∼1.4 molal NAES obtained earlier by the NDIS technique.