Volume 85, Issue 1

Complex biological systems are intimately linked to their environment, a very crowded and equally complex solution compartmentalized by fluid membranes. Modeling such systems remains challenging and requires a suitable representation of these solutions and their interfaces. Here, we focus on particle-based modeling at an atomistic level using molecular dynamics (MD) simulations. As an example, we discuss important steps in modeling the solution chemistry of an ion channel of the ligand-gated ion channel receptor family, a major target of many drugs including anesthetics and addiction treatments. The bacterial pentameric ligand-gated ion channel (pLGIC) called GLIC provides clues about the functional importance of solvation, in particular for mechanisms such as permeation and gating. We present some current challenges along with promising novel modeling approaches.

A short review of recent theoretical advances in studies of the interaction between highly charged systems is presented. Such a system could not be described by the mean field theory. More advanced methods have to be used in order to introduce the correlations between highly charged particles. In this work I focus on the system of highly charged surfaces, separated by a solution of molecules with spatially distributed charge. Two different representations of the molecular shape will be considered: rod-like and spherical. The system will be theoretically described by the density functional theory. For sufficiently long molecules and large surface charge densities, an attractive force between like-charged surfaces arises due to the spatially distributed charges within the molecules. The added salt has influence on the condition for the attractive force between like-charged surfaces. The theoretical results will be compared with Monte Carlo (MC) simulations. Recent measurements with multivalent rigid rod-like particles will be discussed.

We present a first-principles simulation study of vibrational spectral diffusion and hydrogen-bond dynamics in solution of a fluoride ion in deuterated water. The present calculations are based on ab initio molecular dynamics simulation for trajectory generation and wavelet analysis for calculations of frequency fluctuations. The O–D bonds of deuterated water in the anion hydration shell are found to have lower stretching frequency than the bulk water. The dynamical calculations of vibrational spectral diffusion for hydration shell water molecules reveal three time scales: a short-time relaxation (~100 fs) corresponding to the dynamics of intact ion-water hydrogen bonds, a slower relaxation (~7.5 ps) corresponding to the lifetimes of fluoride ion-water hydrogen bonds, and an even longer time scale (~26 ps) associated with the escape dynamics of water from the anion hydration shell. However, the slowest time scale is not observed when the vibrational spectral diffusion is calculated over O–D bonds of all water molecules, including those in the bulk.

The electrophoretic mobility of sulfate latex nanospheres (radius 300 ± 10 nm) was measured as a function of ionic strength for different salts. The results were obtained from two similar instruments (Malvern ZetaSizer 3000 HSa and Malvern ZetaSizer Nano) using the same dispersions, in the same conditions. The values predicted from the standard electrokinetic model for constant surface charge were in good agreement with the data over a large range of ionic strength. The influence of the protocol used to fill the cells appears to be of importance between 1–10 mM of added monovalent salt. There, the capillary wall properties seem to influence the electrophoretic measurements, even at fast field reversal (FFR), where electroosmosis should be absent. We found that during a series of measurements with monovalent salts, it was best to fill the cell starting from high ionic strength and decreasing the ionic strength during the series. The measurements with divalent salts were not sensitive to the filling procedure.

Static and time-resolved X-ray absorption spectroscopy (XAS) is used to probe the solvent shell structure around iodide and iodine. In particular, we characterize the changes observed upon electron abstraction of aqueous iodide, which reflects the transition from hydrophilic to hydrophobic solvation after impulsive electron abstraction from iodide. The static spectrum of aqueous iodide, which is analyzed using quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, indicates that the hydrogens of the closest water molecules point toward the iodide, as expected for hydrophilic solvation. In addition, these simulations demonstrate a small anisotropy in the solvent shell. Following electron abstraction, most of the water molecules move away from iodine, while one comes closer to form a complex with it that survives for 3–4 ps. This lifetime is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform a hydrogen bond network in the hydrophobic solvation shell.

Standard dissolution experiments are carried out in stirred liquid. Therefore, the measured dissolution rate contains also diffusive and convective contributions, besides the desired surface reaction contribution. We present here a methodology, based on the hydrodynamical analysis of classical dissolution experiments, enabling us to extract the pure dissolution rate constant from the set of the already measured dissolution rates. The application of this analysis to the case of gypsum shows that the removal of the mass transport contribution from the dissolution rates of this mineral found in the literature brings, despite their apparent inconsistency, a coherent description of its dissolution kinetics and a well-defined value of its rate constant.

Molten salts (MSs) such as fluoride or chloride salts at high temperature (400–800 °C) are solvents known for their high solvation power and electroactivity range. Rare earths, lanthanides, actinides, and refractory metals can be dissolved, treated, and purified in MSs. The properties of these solvents are particularly interesting for nuclear spent-fuel reprocessing. The pyrochemical separation and extraction of solutes can be performed using several methods taking into account the effects of redox and/or acidity. This paper is focused on the reductive extraction method performed by contacting a liquid metal (LM) containing reductive species and an MS. The analytical model developed to calculate the efficiency of such a method is detailed in this paper. To apply this model, one essential point is the establishment of a database related to the redox and solvation properties of solutes in MSs. The approach retained to propose a database based on the analysis of both thermochemical data of pure compounds and experimental measurements reported in the literature is described in this paper in the case of lanthanides in fluoride MSs. The use of the database to calculate efficiency as a function of process parameters is given in this paper as well as the comparison between two reducing agents considered.

At elevated temperature, several properties of water are strongly altered compared to what our daily experience tells us: the dielectric constant of water, for example, is reduced, so that water can more easily solubilize organic molecules. In addition, the self-dissociation constant of water is increased (by three orders of magnitude at 250 °C), thus favoring H + - and OH – -catalyzed reactions. Surprisingly, while room-temperature water and supercritical water (SCW) are well known for promoting organic reactions, the middle temperature range still remains largely unexplored. Therefore, this contribution aims at giving an overview of organic reactions that may be promoted by superheated water.

In his version of the theory of multicomponent systems, Friedman used the analogy which exists between the virial expansion for the osmotic pressure obtained from the McMillan–Mayer (MM) theory of solutions in the grand canonical ensemble and the virial expansion for the pressure of a real gas. For the calculation of the thermodynamic properties of the solution, Friedman proposed a definition for the “excess free energy” that is a reminder of the ancient idea for the “osmotic work”. However, the precise meaning to be attached to his free energy is, within other reasons, not well defined because in osmotic equilibrium the solution is not a closed system and for a given process the total amount of solvent in the solution varies. In this paper, an analysis based on thermodynamics is presented in order to obtain the exact and precise definition for Friedman’s excess free energy and its use in the comparison with the experimental data.

The scaled particle theory (SPT) is applied to describe thermodynamic properties of a hard sphere (HS) fluid in random porous media. To this purpose, we extended the SPT2 approach, which has been developed previously. The analytical expressions for the chemical potential of an HS fluid in HS and overlapping hard sphere (OPH) matrices, sponge matrix, and hard convex body (HCB) matrix are obtained and analyzed. A series of new approximations for SPT2 are proposed. The grand canonical Monte Carlo (GGMC) simulations are performed to verify an accuracy of the SPT2 approach combined with the new approximations. A possibility of mapping between thermodynamic properties of an HS fluid in random porous media of different types is discussed. It is shown that thermodynamic properties of a fluid in the different matrices tend to be equal if the probe particle porosities and the specific surface pore areas of considered matrices are identical. The obtained results for an HS fluid in random porous media as reference systems are used to extend the van der Waals equation of state to the case of a simple fluid in random porous media. It is observed that a decrease of matrix porosity leads to lowering of the critical temperature and the critical density of a confined fluid, while an increase of a size of matrix particles causes an increase of these critical parameters.

The unusual interactions in organic liquids such as methane derivatives, arenes, and alkanes by the infrared (IR) method were revealed. The transformations of molecular shapes, arising from nonclassical hydrogen and dihydrogen bonds, as well as water factor provide the existence of supramolecular structures in organic fluids. The interpretation of the obtained results in terms of the quantum-chemical calculations has been suggested.

Natural organic matter (NOM) is ubiquitous in soil and groundwater, and its aqueous complexation with various inorganic and organic species can strongly affect the speciation, solubility, and toxicity of many elements in the environment. Despite significant geochemical, environmental, and industrial interest, the molecular-scale mechanisms of the physical and chemical processes involving NOM are not yet fully understood. Recent molecular dynamics (MD) simulations using relatively simple models of NOM fragments are used here to illustrate the challenges and opportunities for the application of computational molecular modeling techniques to the structural, dynamic, and energetic characterization of metal–NOM complexation and colloidal aggregation in aqueous solutions. The predictions from large-scale MD simulations are in good qualitative agreement with available experimental observations, but also point out the need for simulations at much larger time- and length-scales with more complex NOM models in order to fully capture the diversity of molecular processes involving NOM.

Statistical–mechanical, 3D-RISM-KH molecular theory of solvation (3D reference interaction site model with the Kovalenko–Hirata closure) is promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. 3D-RISM-KH explains the molecular mechanisms of self-assembly and conformational stability of synthetic organic rosette nanotubes (RNTs), aggregation of prion proteins and β-sheet amyloid oligomers, protein-ligand binding, and function-related solvation properties of complexes as large as the Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) and GroEL/ES chaperone. Molecular mechanics/Poisson–Boltzmann (generalized Born) surface area [MM/PB(GB)SA] post-processing of molecular dynamics (MD) trajectories involving SA empirical nonpolar terms is replaced with MM/3D-RISM-KH statistical–mechanical evaluation of the solvation thermodynamics. 3D-RISM-KH has been coupled with multiple time-step (MTS) MD of the solute biomolecule driven by effective solvation forces, which are obtained analytically by converging the 3D-RISM-KH integral equations at outer time-steps and are calculated in between by using solvation force coordinate extrapolation (SFCE) in the subspace of previous solutions to 3D-RISM-KH. The procedure is stabilized by the optimized isokinetic Nosé–Hoover (OIN) chain thermostatting, which enables gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties. The multiscale OIN/SFCE/3D-RISM-KH algorithm is implemented in the Amber package and illustrated on a fully flexible model of alanine dipeptide in aqueous solution, exhibiting the computational rate of solvent sampling 20 times faster than standard MD with explicit solvent. Further substantial acceleration can be achieved with 3D-RISM-KH efficiently sampling essential events with rare statistics such as exchange and localization of solvent, ions, and ligands at binding sites and pockets of the biomolecule. 3D-RISM-KH was coupled with ab initio complete active space self-consistent field (CASSCF) and orbital-free embedding (OFE) Kohn–Sham (KS) density functional theory (DFT) quantum chemistry methods in an SCF description of electronic structure, optimized geometry, and chemical reactions in solution. The (OFE)KS-DFT/3D-RISM-KH multi-scale method is implemented in the Amsterdam Density Functional (ADF) package and extensively validated against experiment for solvation thermochemistry, photochemistry, conformational equilibria, and activation barriers of various nanosystems in solvents and ionic liquids (ILs). Finally, the replica RISM-KH-VM molecular theory for the solvation structure, thermodynamics, and electrochemistry of electrolyte solutions sorbed in nanoporous materials reveals the molecular mechanisms of sorption and supercapacitance in nanoporous carbon electrodes, which is drastically different from a planar electrical double layer.

In contrast to the common intuitive/speculative approach based on an analysis of thermodynamic or structural data of (nonpolar) fluids, the statistical mechanical approach is used to extend the excluded volume concept to all other types of fluids. The (extended) excluded volume incorporates, in addition to common nonelectrostatic interactions defining the shape and size of the molecules, also the short-range part of the repulsive interactions between the embedded Coulombic sites. In this study we show that the extended excluded volume concept correctly predicts the behavior of the partial molar volume (PMV) at infinite dilution in different solvents and, particularly, differences between nonpolar and associating solvents. The concept is then applied to estimate the PMV of methanol in water.

In this research, the adsorption of Au(III) ion on ionic imprinted amino-silica hybrid (Im-ASH) in aqueous solution has been studied. Im-ASH was synthesized via sol-gel technique using a solution of sodium silicate (Na 2 SiO 3 ) from rice hull ash (RHA) as the precursor and Au(III) ion as the template. Adsorption was carried out in a batch system with variation of pH, contact time, and Au(III) ion concentration. The selectivity of adsorbent toward Au(III) was examined in the presence of Cu(II) ion. The result of the kinetic study demonstrated that the adsorption of Au(III) ion followed pseudo-second order. The optimum adsorption of Au(III) on Im-ASH and non-Im-ASH was obtained at pH of 3.0. Im-ASH was twice as selective toward Au(III) ion than ASH was.

The (H 2 SO 4 ) 2 , H 2 SO 4 -DMF, and (H 2 SO 4 ) 2 -DMF complexes have been investigated, using the B3LYP functional with cc-pVQZ basis set. The characteristics of structure and energetics for binary complexes of sulfuric acid with dimethylformamide (DMF) have been obtained for the first time. The H-bond formation both between molecules of sulfuric acid as well as sulfuric acid-DMF were studied, on the basis of Weinhold’s natural bond orbital (NBO) analysis. It was shown that the H-bond formation between sulfuric acid and DMF molecules is stronger than ones for the acids dimer. The value of charge transfer from lone pair (LP) orbitals of DMF oxygen to the antibonding orbital of acid OH-bond significantly exceeds the criterion of H-bond existance (0.01 e ). As follows from energy, among the complexes under investigation the most preferable one was found to be (H 2 SO 4 ) 2 -DMF in which sulfuric acid molecules are linked with each other by three H-bonds.

By using polarizable molecular dynamics (MD) simulations of lanthanoid(III) and actinoid(III) ions in water, we obtained ionic diffusion coefficients and hydration enthalpies for both series. These values are in good agreement with experiments. Simulations thus allow us to relate them to microscopic structure. In particular, across the series the diffusion coefficients decrease, reflecting the increase of ion–water interaction. Hydration enthalpies also show that interactions increase from light to heavy ions in agreement with experiment. The apparent contradictory result of the decrease of the diffusion coefficient with decreasing ionic radius is tentatively explained in terms of dielectric friction predominance on Stokes’ diffusive regime.

Our research on employing the cellular automata methodology to corrosion and passivation phenomena is reviewed. Examples of a peculiar pit development are found and presented. The diffusion rate in the corroding medium is argued and shown in the simulation results to affect mainly the characteristic length scale for the corrosion process. New data for the pitting corrosion development on a planar interface are presented and discussed.

Molecular gastronomy is the scientific discipline that looks for mechanisms of phenomena occurring during dish preparation and consumption. Solutions are studied because most foods, being based on animal and plant tissues, are gels, with a liquid fraction and a continuous solid phase. This is why food can be studied in situ using liquid NMR spectroscopy in the frequency domain (isq NMR). Using such tools, processes of the kind F @ M  →  F ' @ M ' (where F stands for the food matrix, M for its environment, and @ for inclusion) were investigated for various processes as classified using the complex disperse system/non-periodical organization of space formalism (“disperse systems formalism”, DSF). As an application of these studies, “note by note cuisine” was promoted as a new paradigm for culinary activities.

The goal of this work is to consider some peculiarities of heterogeneous systems with chemical interactions. The main task is to analyze the features of liquid–liquid (LL) phase diagrams of the systems with equilibrium and nonequilibrium chemical reaction in solution. The consideration of topology of these phase diagrams should include additional elements, such as stoichiometric lines, chemical equilibrium (CE), and isoaffinity manifolds (i.e., curves, surfaces, or hypersurfaces of constant affinity). The thermodynamic conditions of mutual disposition of LL tie-lines, isoaffinity, and stoichiometric lines in ternary system are presented in the paper. Quaternary mixtures are discussed with the use of our experimental data on the solubility in the systems with ethyl acetate and n -propyl acetate synthesis reactions. The binodal and CE surfaces in these systems are presented. The opportunity of simultaneous LL and CE is discussed. The special aim is to consider the critical surfaces in these systems: the examples are presented on the basis of our experimental data.

Differential scanning calorimetry (DSC), X-ray diffraction (XRD), and quasi-elastic neutron scattering (QENS) measurements have been made at 200~330 K for capillary-condensed water confined in periodic mesoporous organosilica (PMO) materials with the phenyl groups embedded in silica matrix (Ph-PMO; pore diameter 30 Å). The DSC data showed that the capillary-condensed water in Ph-PMO freezes at 228 K. X-ray radial distribution functions (RDFs) showed that the tetrahedral-like hydrogen-bonded structure of water is distorted in Ph-PMO pores, compared with bulk water; however, with lowering temperature the tetrahedral moiety of water is gradually recovered in the pores. Below the freezing point, cubic ice I c was formed in the Ph-PMO pores. The QENS data showed that the translational diffusion constant and the residence time and the rotational relaxation time of water molecule in Ph-PMO are comparable with those in bulk. The corresponding activation energies suggested that the more hydrophobic the nature of the wall is, the smaller the activation energy of diffusion and rotation of a water molecule; this implies that water molecules confined in the hydrophobic pores are present in the core of the pores, whereas those in the hydrophilic pores strongly interact with the silanol groups.

With the goal of presenting information in the scientific literature clearly and unambiguously, a set of rules for the abbreviation of protecting groups has been developed. It is based on principles designed to be as descriptive and systematic as possible, but also sufficiently pragmatic and flexible so as to accommodate the most important current abbreviations.