Correlated/non-correlated ion dynamics of charge-neutral ion couples: the origin of ionicity in ionic liquids.

Proton/fluoride spin-lattice (T1) nuclear magnetic relaxation dispersion (NMRD) measurements of 1-butyl-3-methyl-1H-imidazolium hexafluorophosphate, [C4mim][PF6], have been carried out using high field spectrometers and a fast-field-cycling instrument at proton Larmor frequencies ranging from 10 kHz to 40 MHz, at different temperatures. The NMRD profiles are interpreted by means of a simple relaxation model based on the inter- and intra-ionic dipole-dipole relaxation mechanism. Using an atomic molecular-ion dynamic simulation at 323 K the relevant spin dipole-dipole (DD) correlation functions are calculated. The results indicate that the NMRD profiles can be rationalized using intra- and inter-ionic spin DD interactions, however, anions are mainly modulated by ionic reorientation because of temporary correlations with cations, where modulation by translational diffusion plays a minor role. Reorientational dynamics of charge-neutral ion couples (i.e. [C4mim][PF6]) and [C4mim]+ ions are in the nano-second (ns) time range whereas the reorientation of [PF6]- is characterized by a reorientational correlation time in the pico-second (ps) regime. Based on the NMRD profiles we conclude that the main relaxation mechanism for [PF6]- is due to fast internal reorientational motion, a partially averaged F-F intra- and F-H inter-ionic DD coupling as the anion resides in close proximity to its temporary oppositely charged cation partner. The F-T1-NMRD data display a ns dispersion which is interpreted as being due to correlated reorientational modulations resulting from the H-containing charge-neutral ion couple [C4mim][PF6]. The analysis of ionicity is based on the free anion fraction, f, and it increases with temperature with f → 1 at the highest temperatures investigated. The fraction is obtained from the H-F NMRD profiles as correlated-non-correlated dynamics of the ions. The analysis of T1 relaxation rates of C, H, F and P at high fields cannot generally give the fraction of ions but is consistent with the interpretation based on the NMRD profiles with relaxation contributions due to DD-intra and -inter, CSA-intra (and -inter for C), including spin rotation for P. The investigation has led to a description of the mechanics governing ion transport in the title ionic liquid via identification of transient correlated/non-correlated ion dynamics.

Understanding the thermal decomposition mechanism of a halogen-free chelated orthoborate-based ionic liquid: a combined computational and experimental study.

In the last few decades, ionic liquids (ILs) have gained significant attention as lubricants and lubricant additives due to their polar nature, low vapour pressure and tunable physicochemical properties. In this work, quantum chemistry calculations and atomistic Molecular Dynamics (MD) simulations were employed to predict thermal degradation mechanisms of a potential lubricating agent - the tributyloctylphosphonium bis(oxalato)borate ([P4,4,4,8][BOB]) IL. It was found that the onset of decomposition of the studied IL coincides with a cleavage of the B-O bonds in the [BOB](-) anion. Consequently, a series of chemical reactions of the [P4,4,4,8](+) cation with the [BOB](-) anion was triggered yielding alkylboranes, alkenes, trialkylphosphines, CO and CO2. Another ionic system, consisting of [P4,4,4,8][Cl], was also tested for a comparison. Thermogravimetric measurements have shown a higher thermal stability of [P4,4,4,8][BOB] compared to that of [P4,4,4,8][Cl] at least at the initial stage of decomposition, in accord with the presented calculations. Quantum chemical frequency calculations also agreed with the experimental Fourier Transform Infrared (FTIR) spectroscopy results.

Conformational characteristics of single flexible polyelectrolyte chain.

The behaviour of a flexible anionic chain of 150 univalent and negatively charged beads connected by a harmonic-like potential with each other in the presence of an equal number of positive and free counterions, is studied in molecular dynamics simulations with Langevin thermostat in a wide range of temperatures. Simulations were carried out for several values of the bending parameter, corresponding to fully flexible polyion, moderately and strongly stiff polyion as well as for the case when bend conformation is preferable to the straight one. We have found that in all cases three regimes can be distinguished, which can be characterized as "random coil", observed at high temperatures; "extended conformation" observed at moderate temperatures (of the order of 1 in reduced units), and compact "globular conformation" attained at low temperatures. While the transition between high-temperature random and extended conformations is gradual, the transition from the extended coil to the globular state, taking place at a temperature of about 0.2 in reduced units, is of abrupt character resembling a phase transition.

Increasing large scale windstorm damage in Western, Central and Northern European forests, 1951-2010.

Using reports of forest losses caused directly by large scale windstorms (or primary damage, PD) from the European forest institute database (comprising 276 PD reports from 1951-2010), total growing stock (TGS) statistics of European forests and the daily North Atlantic Oscillation (NAO) index, we identify a statistically significant change in storm intensity in Western, Central and Northern Europe (17 countries). Using the validated set of storms, we found that the year 1990 represents a change-point at which the average intensity of the most destructive storms indicated by PD/TGS > 0.08% increased by more than a factor of three. A likelihood ratio test provides strong evidence that the change-point represents a real shift in the statistical behaviour of the time series. All but one of the seven catastrophic storms (PD/TGS > 0.2%) occurred since 1990. Additionally, we detected a related decrease in September-November PD/TGS and an increase in December-February PD/TGS. Our analyses point to the possibility that the impact of climate change on the North Atlantic storms hitting Europe has started during the last two and half decades.

Spermine: an "invisible" component in the crystals of B-DNA. A grand canonical Monte Carlo and molecular dynamics simulation study.

The association of spermine(4+) (Spm(4+)), Mg(2+) and monovalent (M(+)) ions with DNA in crystal form, have been studied using grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) computer simulations. GCMC calculations were used to calculate the distribution of Spm(4+), Mg(2+), and M(+) between the equilibrating solvent and the DNA crystal under conditions mimicking the crystal-growing protocols reported in a number of recent X-ray diffraction studies of DNA oligomers. The GCMC simulations show that the composition of ions neutralizing the negative charge of DNA can vary in a broad range. The GCMC simulations were used to provide appropriate conditions for subsequent 6 ns constant pressure and temperature MD simulations of DNA in a typical crystalline environment consisting of three DNA double helix decamers in a periodic hexagonal cell, containing 1200 water molecules, eight Spm(4+), 32 Na(+) and four Cl(-) ions. Based on the simulation results, it seems possible to give an explanation why spermine molecules are usually not detected in X-ray studies in spite of their high concentration in the preparatory samples used as the crystallizing agent. It appears that this flexible polyamine molecule has several binding modes, interacting in fairly irregular manner with different sites on DNA and showing no regular ordering in the DNA crystals. Ions of Na(+) and Spm(4+) compete with each other and with water molecules in binding to bases in the minor groove and they influence the structure of the DNA hydration shell in different ways.

Autologous stem cell transplantation versus novel drugs or conventional chemotherapy for patients with relapsed multiple myeloma after previous ASCT.

High-dose therapy (HDT) followed by autologous stem cell transplantation (ASCT) is the most common first-line treatment for patients with multiple myeloma (MM) under 65 years of age. A second ASCT at first relapse is frequently used but is challenged by the use of novel drugs. We retrospectively studied the outcome of second-line treatment in MM patients from the Nordic countries with relapse after first-line HDT and ASCT. Patients that underwent a second ASCT (n=111) were compared with patients re-treated with conventional cytotoxic drugs only (n=91) or with regimens including novel drugs (proteasome inhibitors and/or immunomodulatory drugs) (n=362) without a second ASCT. For patients receiving a second ASCT median overall survival was 4.0 years compared with 3.3 years (P<0.001) for the group treated with novel drugs and 2.5 years (P<0.001) for those receiving conventional cytotoxic drugs only. A second ASCT also resulted in a significantly longer second time to progression and a significantly longer time to next treatment. We conclude that, irrespective of the addition of novel drugs, MM patients in first relapse after ASCT still appear to benefit from a second ASCT. A second ASCT should be considered for all physically fit patients.

Surfactant effects and an order-disorder transition in binary gas-liquid nucleation

Density-functional theory is applied to the interaction site model to study gas-liquid nucleation in a partially immiscible binary system consisting of spherical Lennard-Jones atoms (monomers) and dumbbell molecules of two Lennard-Jones atoms (dimers). Increased interaction anisotropy between the dimer sites and monomers is shown to result in mutual enhancement of nucleation. Critical nuclei with a lamellar structure are observed at high dimer activities.

Molecular dynamics simulations of alpha-D-Manp-(1-->3)-beta-D-Glcp-OMe in methanol and in dimethyl sulfoxide solutions.

Molecular dynamics simulations have been performed of the disaccharide alpha-D-Manp-(1-->3)-beta-D-Glcp-OMe in two different solvents, namely in methanol and in dimethyl sulfoxide. The conformation of the disaccharide is similar to that previously determined in water. The three-dimensional structure around the solute was investigated by geometric hydrogen bonding criteria, radial distribution functions, coordination number analysis, residence times for hydrogen bonds, and spatial distribution functions. Differences and similarities between methanol and the aprotic dimethyl sulfoxide as solvent are analyzed.

Visualization of solvation structures in liquid mixtures.

Spatial distribution functions of atomic densities. SDFs, have been proposed as a natural starting point for analysis of local molecular structure in liquids and solutions. The local structure in these systems is often complex and this is reflected in the fact that SDFs can be difficult to visualize. Among the different methods that can be used to visualize SDFs we discuss 3D isodensity surfaces, cross-sections, and 'comic book' animations. We also discuss the possibility of a simultaneous visualization of SDFs and other 3D fields, such as the electron density. These techniques are all intended to emphasize and bring out aspects of SDFs that promote a further understanding of the local molecular structure. OpenGL-based software has been used under X-Windows to implement these techniques, and we argue that high-quality molecular graphics need not be expensive. Data from a molecular dynamics simulation of an equimolar binary mixture of water and acetonitrile have been used to illustrate the discussion.

Hydration of cytidine, 2'-deoxycytidine and their phosphate salts in the aqueous solutions. A molecular dynamics computer simulation study.

To compare the hydration pattern of the cytidine (Cyd) and 2'-deoxycytidine (dCyd) in the aqueous solutions at the level of microscopic interactions. Molecular Dynamics (MD) computer simulations have been undertaken. The results indicate that the hydration of the heterocyclic base moiety in cytidine and 2'-deoxycytidine has a hydrophobic character. None of the three potential Watson-Crick base pair centres hydrogen bonds with the water molecules and the formation of something akin to a clathrate cage structure of water around base moieties of nucleosides in the aqueous solution is suggested. In contrast, the hydration of Cyd and dCyd sugar moieties shows a hydrophilic character and the three-dimensional networks of H-bonds involving all hydrophilic centres are formed differently around the ribose and 2'-deoxyribose. The sugar hydroxyl groups participate in the hydrogen bonding with water both as H-donor and as H-acceptor. Their donor-acceptor abilities have been evaluated and compared. The coordination numbers, the geometrical data of the first hydration shell, and the number of hydrogen bonds have been calculated. The changes in the pattern of hydration with the increased concentration of nucleosides and upon nucleoside protonation are discussed. The analysis of the pairwise interaction energies are also presented.

Molecular dynamics simulations of DNA in solutions with different counter-ions.

Molecular dynamics simulations of the [d(ATGCAGTCAG]2 fragment of DNA, in water and in the presence of three different counter-ions (Li+, Na+ and Cs+) are reported. Three-dimensional hydration structure and ion distribution have been calculated using spatial distribution functions for a detailed picture of local concentrations of ions and water molecules around DNA. According to the simulations, Cs+ ions bind directly to the bases in the minor groove, Na+ ions bind prevailing to the bases in the minor groove through one water molecule, whereas Li+ ions bind directly to the phosphate oxygens. The different behavior of the counter-ions is explained by specific hydration structures around the DNA and the ions. It is proposed how the observed differences in the ion binding to DNA may explain different conformational behavior of DNA. Calculated self-diffusion coefficients for the ions agree well with the available NMR data.

A molecular dynamics computer simulation study of nucleotide analogues. Comparison of the hydration pattern of dithymidine phosphate with those of the dithymidine methylphosphonate diastereomers.

The hydration pattern of thymidyl(3'->5') thymidine 1 and those of Rp and Sp diastereomers of the corresponding methylphosphonate analogue 2, have been studied using Molecular Dynamics (MD) computer simulation. It was found that the methylphosphonate modification leads to significant changes in the coordination of water molecules around the internucleotidic linkage and these, in turn, affect the hydration pattern of other parts of the molecule. The most notable differences between Rp and Sp diastereomers 2a and 2b were found to occur at the deoxyribose moieties of the nucleosid-5'-yl units.

Atomic charges in molecular mechanical force fields: a theoretical insight.

Based on quantum theory of the Coulombic interactions between a molecule and its surrounding molecules, a theoretical derivation is presented to obtain an atomic charge model. The charge model shows that the appropriate atomic charge, used for example in molecular mechanical force fields, is simply the average value of the electrostatic potential (ESP) derived charge for an isolated molecule and that obtained for the molecule in the interaction system. Computational scheme to calculate the ESP derived atomic charges of a molecule in the interaction system is presented. The method is applied to two common liquids with associated hydrogen bonds: water and methanol. The obtained theoretical atomic charges are similar to those found in the common interaction potential models, such as: SPC, TIP3P, OPLS, etc. However, for methanol they differ considerably from those obtained using the restrained ESP method.

Nucleation probability in binary heterogeneous nucleation of water-n-propanol vapor mixtures on insoluble and soluble nanoparticles.

Nucleation probabilities for binary heterogeneous nucleation have been measured quantitatively. Heterogeneous nucleation of binary n-propanol-water vapor mixtures on partially soluble 6.9-nm NaCl particles and on nonsoluble oxidized and nonoxidized 8-nm Ag particles at a constant nucleation temperature of 288 K (NaCl) or 285 K (Ag) has been investigated experimentally and theoretically. An expansion chamber was applied to generate supersaturated vapor mixtures. Number concentrations of particles activated to condensational growth were determined optically for various vapor phase activities at constant temperature. Nucleation probabilities have been measured as functions of the vapor phase activities for several n-propanol-water vapor mixing ratios. Beyond certain vapor phase activities a sharp onset of heterogeneous nucleation was observed both for NaCl and for Ag particles. For insoluble particle surfaces the theoretical slopes of the nucleation probability versus vapor phase activity curves were found to be somewhat steeper as compared to the experiment. On the other hand, for soluble particles the experimental slopes were found to be in satisfactory agreement with theory. The onset of the nucleation process is defined at an activity value where 50% of the particles were activated to condensational growth. Onset activities were obtained for various mixing ratios of the binary vapor mixtures. In the case of NaCl nuclei for n-propanol rich mixtures, the heterogeneous nucleation calculations based on a thermodynamically consistent version of Fletcher theory and an experimentally determined contact angle provide a reasonable approximation of the experimental data. However, it appears that the Fletcher theory is not applicable in the region of transition from n-propanol rich to water rich mixtures. Based on the Köhler theory of activation of soluble particles, a theory was formulated accounting for the presence of two condensable vapors and limited solubility of NaCl in water-propanol liquid mixtures. This approach provides a satisfactory description of the transition from activation of soluble particles to nucleation of vapors on insoluble particles. In the case of silver particles Fletcher theory with macroscopic experimental contact angles as well as with contact angle zero results in strong deviations from experimental data. A significant improvement was achieved by introducing fit contact angles, which are substantially lower than the macroscopic experimental values and may be considered as approximate values of the microscopic contact angles.

Carbohydrates Exhibit a Distinct Preferential Solvation Pattern in Binary Aqueous Solvent Mixtures.

Molecular dynamics simulations reveal the entire solvation shell around a model disaccharide dissolved in the binary 1:3 molar mixture of dimethyl sulfoxide and water becomes distinctly structured (see drawing). Such preferential solvation is due to the large number of hydroxyl groups and the rich network of hydrogen bonds of a disaccharide formed with the solvent.

Formation of the smectic-B crystal from a simple monatomic liquid.

We report a molecular dynamics simulation demonstrating that the smectic-B crystalline phase (Cry-B), commonly observed in mesogenic systems of anisotropic molecules, can be formed by a system of identical particles interacting via a spherically symmetric potential. The Cry-B phase forms as a result of a first-order transition from an isotropic liquid phase upon isochoric cooling at appropriate number density. Its structure, determined by the design of the pair potential, corresponds to the Cry-B structure formed by elongated particles with the aspect ratio 1.8. The diffraction pattern and the real-space structure inspection demonstrate dominance of the ABC-type of axial layer stacking. This result opens a general possibility of producing smectic phases using isotropic interparticle interaction both in simulations and in colloidal systems.