A detailed investigation of hydrogen bonding in the pure ionic liquids [C4C1im]Cl and [C2C1im]Cl has been carried out using primarily molecular dynamics techniques. Analyses of the individual atom-atom pair radial distribution functions, and in particular those for C···Cl(-), have revealed that hydrogen bonding to the first methylene or methyl units of the substituent groups is important. Multiple geometric criteria for defining a hydrogen bond have been applied, and in particular the choice of the cutoff angle has been carefully examined. The interpretation of hydrogen bonding within these ionic liquids is highly angle dependent, and justification is provided for why it may be appropriate to employ a wider angle criteria than the 30° used for water or alcohol systems. The different types of hydrogen bond formed are characterized, and "top" conformations where the Cl anion resides above (or below) the imidazolium ring are investigated. The number of hydrogen bonds undertaken by each hydrogen atom (and the chloride anion) is quantified, and the propensity to form zero, one, or two hydrogen bonds is established. The effects of an increase in temperature on the static hydrogen bonding are also briefly examined.

The effect of intermolecular interactions of different strength on the local density inhomogeneities in pure supercritical fluids (scfs), with different intramolecular structure, was investigated by employing molecular dynamics (MD) simulation techniques. The simulations were performed at state points along an isotherm close to the critical temperature of each system (T(r) = T/T(c) = 1.03). The molecular fluids under study have been chosen on the basis of the electrostatic character of their intermolecular interactions as follows: monatomic, dipolar and hydrogen bonding (HB), quadrupolar, and octupolar. In the case of dipolar scfs, their HB nature when present was systematically explored and related to the behavior of the created local density inhomogeneities at all densities. The results obtained reveal strong influence of the dipolar and HB interactions of the investigated systems upon the local density augmentation. We found that this effect is fairly larger in the case of the dipolar and HB fluids (H2O, CH3OH, and NH3) compared to those for the non-dipolar ones (Xe, CH4, CO2, and N2). In the case of sc CO2, the dependence of the local density augmentation on the bulk density is in agreement with available experimental data as also reported previously. The estimated average number of hydrogen bonds per molecule (nHB) in these HB fluids shows an analogue nonlinear trend compared to the behavior of the average coordination numbers Nco(rho) of a particle with bulk density. The local density dynamics of the first and second solvation shell of each fluid were further analyzed and related to our previously proposed [Skarmoutsos, I.; Samios, J. J. Chem. Phys. 2007, 126, 044503] different time-scale relaxation mechanisms. Finally, the effect of the different strength of the molecular interactions corresponding to these fluids upon the local density dynamics has also been revealed in the behavior of the predicted appropriate time correlation functions and their corresponding correlation times.

The supercritical mixture ethanol-carbon dioxide (EtOH-CO2) with mole fraction of ethanol X(EtOH) congruent with 0.1 was investigated at 348 K, by employing the molecular dynamics simulation technique in the canonical ensemble. The local intermolecular structure of the fluid was studied in terms of the calculated appropriate pair radial distribution functions. The estimated average local coordination numbers and mole fractions around the species in the mixture reveal the existence of local composition enhancement of ethanol around the ethanol molecules. This finding indicates the nonideal mixing behavior of the mixture due to the existence of aggregation between the ethanol molecules. Furthermore, the local environment redistribution dynamics have been explored by analyzing the time correlation functions (TCFs) of the total local coordination number (solvent, cosolvent) around the cosolvent molecules in appropriate parts. The analysis of these total TCFs in the auto-(solvent-solvent, cosolvent-cosolvent) and cross-(solvent-cosolvent, cosolvent-solvent) TCFs has shown that the time dependent redistribution process of the first solvation shell of ethanol is mainly determined by the redistribution of the CO2 solvent molecules. These results might be explained on the basis of the CO2-CO2 and EtOH-CO2 intermolecular forces, which are sufficiently weaker in comparison to the EtOH-EtOH hydrogen bonding interactions, creating in this way a significantly faster redistribution of the CO2 molecules in comparison with EtOH. Finally, the self-diffusion coefficients and the single reorientational dynamics of both the cosolvent and solvent species in the mixture have been predicted and discussed in relationship with the local environment around the species, which in the case of the EtOH molecules seem to be strongly affected.

microRNAs (miRNAs) are small non-coding RNAs that actively fine-tune gene expression. The accurate characterization of the mechanisms underlying miRNA transcription regulation will further expand our knowledge regarding their implication in homeostatic and pathobiological networks. Aim of DIANA-miRGen v3.0 (http://www.microrna.gr/mirgen) is to provide for the first time accurate cell-line-specific miRNA gene transcription start sites (TSSs), coupled with genome-wide maps of transcription factor (TF) binding sites in order to unveil the mechanisms of miRNA transcription regulation. To this end, more than 7.3 billion RNA-, ChIP- and DNase-Seq next generation sequencing reads were analyzed/assembled and combined with state-of-the-art miRNA TSS prediction and TF binding site identification algorithms. The new database schema and web interface facilitates user interaction, provides advanced queries and innate connection with other DIANA resources for miRNA target identification and pathway analysis. The database currently supports 276 miRNA TSSs that correspond to 428 precursors and >19M binding sites of 202 TFs on a genome-wide scale in nine cell-lines and six tissues of Homo sapiens and Mus musculus.

As a step toward deeper insight on the "hydrogen bonding" in supercritical ethanol (scEtOH), we carried out NVT molecular dynamics simulations of the fluid over a wide range of temperatures and pressures. The fluid was studied at SC conditions for which thermodynamic and spectroscopic (NMR, infrared, Raman, dielectric) data are available. The various site-site pair distribution functions (pdf's) were calculated, and their temperature and pressure dependence was obtained. It was found that over the thermodynamic conditions investigated here, scEtOH remains highly structured. Moreover, the characteristic behavior of the first peaks in H-H, O-O, and H-O pdf's reveals that hydrogen bonds still exist in scEtOH. The analysis focuses also on the reorientational dynamics of the bond unit vectors O-H, C-O, and of the permanent dipole moment of the molecules as well as the total dipole moment of the sample. The corresponding Legendre time correlation functions were discussed in connection to the "hydrogen bonding" in the fluid and in the context of experimental results. Specifically, the behavior of the O-H dynamics exhibits the well-known associative nature of the molecules in the system. A further analysis of the hydrogen bonds was carried out, and the degree of aggregation (average number of H-bonds per molecule) was obtained and compared with results from NMR chemical shift studies. Also the estimated monomer and free O-H groups in the fluid were compared with results from IR and Raman vibrational spectroscopy. The percentage analysis fi of the liquid and scEtOH molecules, with i = 0, 1, 2, 3, ... hydrogen bonds per molecule, has been obtained. The results show the existence of small, linear-chain oligomers formed mainly by two molecules, whereas the number of the three body oligomers, and specifically that of four body oligomers in the sample, is relatively small.

No abstract

The thermodynamics, structural and transport properties (density, melting point, heat capacity, thermal expansion coefficient, viscosity and electrical conductivity) of a ferro-aluminosilicate slag have been studied in the solid and liquid state (1273–2273 K) using molecular dynamics. The simulations were based on a Buckingham-type potential, which was extended here, to account for the presence of Cr and Cu. The potential was optimized by fitting pair distribution function partials to values determined by Reverse Monte Carlo modelling of X-ray and neutron diffraction experiments. The resulting short range order features and ring statistics were in tight agreement with experimental data and created consensus for the accurate prediction of transport properties. Accordingly, calculations yielded rational values both for the average heat capacity, equal to 1668.58 J/(kg·K), and for the viscosity, in the range of 4.09–87.64 cP. The potential was consistent in predicting accurate values for mass density (i.e. 2961.50 kg/m3 vs. an experimental value of 2940 kg/m3) and for electrical conductivity (5.3–233 S/m within a temperature range of 1273.15–2273.15 K).

Modeling nanoparticles is an essential first step to assess their capacity in different uses such as in energy storage or drug delivery. However, creating an initial starting conformation for modeling and simulation is tedious because every crystalline material grows with a different crystal habit. In this application note, we describe Nano-Crystal, a novel web-based crystallographic tool, which creates nanoparticle models from any crystal structure guided by their preferred equilibrium shape under standard conditions according to the Wulff morphology (crystal habit). Users can upload a cif file, define the Miller indices and their corresponding minimum surface energies according to the Wulff construction of a particular crystal, and specify the size of the nanocrystal. As a result, the nanoparticle is constructed and visualized, and the coordinates of the atoms are output to the user. Nano-Crystal can be accessed and used at http://nanocrystal.vi-seem.eu/. File list (9) download file view on ChemRxiv NanoCrystal_22.8.pdf (1.56 MiB) download file view on ChemRxiv Supporting Information_22.8.pdf (14.73 MiB) download file view on ChemRxiv manual.pdf (1.45 MiB) download file view on ChemRxiv Use case TiO2.zip (21.96 KiB) download file view on ChemRxiv Use case LiFePO4.zip (390.76 KiB) download file view on ChemRxiv Use case Fe3O4.zip (142.71 KiB) download file view on ChemRxiv Use case Au.zip (185.50 KiB) download file view on ChemRxiv Use case Au.zip (185.50 KiB) download file view on ChemRxiv video_example.mp4 (15.02 MiB)