Characterization of the TIP4P-Ew water model: vapor pressure and boiling point

The liquid-vapor-phase equilibrium properties of the previously developed TIP4P-Ew water model have been studied using thermodynamic integration free-energy simulation techniques in the temperature range of 274-400 K. We stress that free-energy results from simulations need to be corrected in order to be compared to the experiment. This is due to the fact that the thermodynamic end states accessible through simulations correspond to fictitious substances (classical rigid liquids and classical rigid ideal gases) while experiments operate on real substances (liquids and real gases, with quantum effects). After applying analytical corrections the vapor pressure curve obtained from simulated free-energy changes is in excellent agreement with the experimental vapor pressure curve. The boiling point of TIP4P-Ew water under ambient pressure is found to be at 370.3+/-1.9 K, about 7 K higher than the boiling point of TIP4P water (363.7+/-5.1 K; from simulations that employ finite range treatment of electrostatic and Lennard-Jones interactions). This is in contrast to the approximately +15 K by which the temperature of the density maximum and the melting temperature of TIP4P-Ew are shifted relative to TIP4P, indicating that the temperature range over which the liquid phase of TIP4P-Ew is stable is narrower than that of TIP4P and resembles more that of real water. The quality of the vapor pressure results highlights the success of TIP4P-Ew in describing the energetic and entropic aspects of intermolecular interactions in liquid water.     

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

A re-parameterization of the standard TIP4P water model for use with Ewald techniques is introduced, providing an overall global improvement in water properties relative to several popular nonpolarizable and polarizable water potentials. Using high precision simulations, and careful application of standard analytical corrections, we show that the new TIP4P-Ew potential has a density maximum at approximately 1 degrees C, and reproduces experimental bulk-densities and the enthalpy of vaporization, DeltaH(vap), from -37.5 to 127 degrees C at 1 atm with an absolute average error of less than 1%. Structural properties are in very good agreement with x-ray scattering intensities at temperatures between 0 and 77 degrees C and dynamical properties such as self-diffusion coefficient are in excellent agreement with experiment. The parameterization approach used can be easily generalized to rehabilitate any water force field using available experimental data over a range of thermodynamic points.     

Influence of water-protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models

We report extensive replica exchange molecular dynamics (REMD) simulations on the folding/unfolding equilibrium of Trp-cage miniprotein using the Amber ff99SB all atom forcefield and TIP3P and TIP4P-Ew explicit water solvent models. REMD simulation-lengths in the 500 ns to the microsecond regime per replica are required to adequately sample the folding/unfolding equilibrium. We observe that this equilibrium is significantly affected by the choice of the water model. Compared with experimental data, simulations using the TIP3P solvent describe the stability of the Trp-cage quite realistically, providing a melting point which is just a few Kelvins above the experimental transition temperature of 317 K. The TIP4P-Ew model shifts the equilibrium towards the unfolded state and lowers the free energy of unfolding by about 3 kJ mol(-1) at 280 K, demonstrating the need to fine-tune the protein-forcefield depending on the chosen water model. We report evidence that the main difference between the two water models is mostly due to the different solvation of polar groups of the peptide. The unfolded state of the Trp-cage is stabilized by an increasing number of hydrogen bonds, destabilizing the α-helical part of the molecule and opening the R-D salt bridge. By reweighting the strength of solvent-peptide hydrogen bonds by adding a hydrogen bond square well potential, we can fully recover the effect of the different water models and estimate the shift in population as due to a difference in hydrogen bond-strength of about 0.4 kJ mol(-1) per hydrogen bond.     

Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models

Water is one of the simplest molecules in existence, but also one of the most important in biological and engineered systems. However, understanding the structure and dynamics of liquid water remains a major scientific challenge. Molecular dynamics simulations of liquid water were performed using the water models TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP to calculate the radial distribution functions (RDFs), the relative angular distributions, and the excess enthalpies, entropies, and free energies. In addition, lower-order approximations to the entropy were considered, identifying the fourth-order approximation as an excellent estimate of the full entropy. The second-order and third-order approximations are ~20% larger and smaller than the true entropy, respectively. All four models perform very well in predicting the radial distribution functions, with the TIP5P-Ewald model providing the best match to the experimental data. The models also perform well in predicting the excess entropy, enthalpy, and free energy of liquid water. The TIP4P-2005 and SWM4-NDP models are more accurate than the TIP3P-Ewald and TIP5P-Ewald models in this respect. However, the relative angular distribution functions of the four water models reveal notable differences. The TIP5P-Ewald model demonstrates an increased preference for water molecules to act both as tetrahedral hydrogen bond donors and acceptors, whereas the SWM4-NDP model demonstrates an increased preference for water molecules to act as planar hydrogen bond acceptors. These differences are not uncovered by analysis of the RDFs or the commonly employed tetrahedral order parameter. However, they are expected to be very important when considering water molecules around solutes and are thus a key consideration in modelling solvent entropy.     

Solubility of low-molecular-mass compounds in copolymers

The solubility of some low-molecular-mass antioxidants in polyethylene-based copolymers was studied. It is shown that another copolymer has a complex effect on the solubility of low-molecular-mass compounds and the concentration of their saturated vapor over the copolymers.     

Alcohols,ethers, carbohydrates,and related compounds. I. The MM4 force field for simple compounds

Simple alcohols and ethers have been studied with the MM4 force field. The structures of 13 molecules have been well fit using the MM4 force field. Moments of inertia have been fit with rms percentage errors as indicated: 18 moments for ethers, 0.28%; 21 moments for alcohols, 0.22%. Rotational barriers and conformational equilibria have also been examined, and the experimental and ab initio results are reproduced substantially better with MM4 than they were with MM3. Much of the improvement comes from the use of additional interaction terms in the force constant matrix, of which the torsion-bend and torsion-torsion are particularly important. Induced dipoles are included in the calculation, and dipole moments are reasonably well fit. It has been possible for the first time to fit conformational energetic data for both open chain and cyclic alcohols (e.g., propanol and cyclohexanol) with the same parameter set. For vibrational spectra, over a total of 82 frequencies, the rms error is 27 cm(-1), as opposed to 38 cm(-1) with MM3. Both the alpha and beta bond shortening resulting from the presence of the electronegative oxygen atom in the molecule are well reproduced. The electronegativity of the oxygen is sufficient that one must also include not only the alpha and beta electronegativity effects on bond lengths, but also on angle distortions, if structures are to be well reproduced. The heats of formation of 32 alcohols and ethers were fit overall to within experimental error (weighted standard deviation error 0.26 kcal/mol).     

Solubility of pyrene in simple and mixed solvent systems

The solubility of pyrene was experimentally determined in simple and complex solvent systems (single, binary, ternary, quaternary and pentinary solvent systems) composed of benzene, ethylbenzene, hexane, hexanol and methylcyclohexane over a temperature range from 293 to 318 K. In addition, six models were used in this study to represent pyrene solubility in the different solvent systems. The interaction parameters for modified Wilson, NIBS/Redlich-Kister, UNIQUAC and NRTL models were estimated using the solubility data generated for pyrene in single, binary and ternary solvent systems. By re-adjusting the interaction parameters reported for Dortmund UNIFAC and ASOG models, a better representation of the solubility of pyrene was obtained compared to using reported values. Furthermore, a correction term is introduced for the ASOG model in this study to better improve pyrene solubility prediction in simple and mixed solvent systems. These estimated or re-adjusted interaction parameters for the different models, along with the reported parameters for Dortmund UNIFAC and ASOG models, were tested on complex solvent systems (quaternary and pentinary solvent mixtures), in order to check their validity and accuracy for such predictions.     

Dynamics of TIP5P and TIP4P/ice potentials

The dynamics of a thin film of ice Ih deposited on MgO (001) is studied through molecular dynamics simulations performed with two new potential models of ice. This system is chosen because it is possible to compare the results of the simulations to incoherent neutron quasielastic scattering experiments performed few years ago and to previous molecular dynamics simulations using the TIP4P potential model. The present simulations are performed to determine the evolution of the translational and orientational order parameters of the ice film upon temperature increase in the 250-280 K range. They are also used to calculate the translational and orientational diffusion coefficients of the water molecules in the supported film as a function of the temperature. When using the TIP5P potential, the present results show a better agreement with experimental data than those calculated with the TIP4P potential, especially regarding the temperature above which significant changes are obtained in the dynamics of the water film. Similar conclusions are obtained when using the TIP4P/ice potential, although this latter potential clearly underestimates the translational diffusion coefficients.     

Solubility Behaviour of TiCl4, ZrCl4, and HfCl4 in Chloroaluminate Ionic Liquids

The solubility of NbCl₅, TaCl₅, TiCl₄, ZrCl₄, and HfCl₄ in neutral [BMIM][AlCl₄] (BMIM = 1‐butyl‐3‐methylimidazolium) was determined. While TiCl₄ was immiscible with the neutral ionic liquid, 0.80 molar equivalents of ZrCl₄ and stoichiometric amounts of HfCl₄ dissolved in the melt at ambient temperature. The crystal structures and the unit cell parameters of [BMIM]₂[Ti₂Cl₁₀], [BMIM]₂[Zr₂Cl₁₀], and [PhNMe₃][Hf₂Cl₉] were determined. [BMIM]₂[Ti₂Cl₁₀], and [BMIM]₂[Zr₂Cl₁₀] were crystallised from basic chloroaluminate melts. With a trimethylanilinium cation, [PhNMe₃][Hf₂Cl₉] crystallised from an equimolar composition of PhNMe₃Cl, AlCl₃, and HfCl₄. Obviously, HfCl₄ abstracted a chloride ligand from [AlCl₄]^– to give highly Lewis acidic [Al₂Cl₇]^– anions.     

Clustering of nonpolar organic compounds in lipid media: evidence and implications

Semivolatile and nonpolar organic compounds, such as persistent organic pollutants, have a tendency to accumulate in organic matter phases from air and water. Once they enter living systems, they partition into lipids/waxes and can exert adverse toxicological effects. The current paradigm assumes that such chemicals are uniformly distributed in organic phases such as soil organic matter, plant waxes, and animal lipids and that partitioning and adsorption processes occur independently of intermolecular contaminant interactions. With use of a recently developed technique, two-photon excitation microscopy coupled with autofluorescence allowed us to directly visualize novel organic chemical behavior in living vegetation and other matrixes. Here, we show for the first time that polycyclic aromatic hydrocarbons, which were uniformly distributed in pure oils and waxes at the beginning of a study, form clusters over time. The number and diameter (typically 0.2-5 microm) of these clusters are dependent on the physical-chemical properties of the compound-media systems and time. This behavior is not accounted for in current models of phase partitioning of chemicals and may have important implications for understanding their environmental fate and their potential toxicological effects.     

Structural properties of water: comparison of the SPC, SPCE, TIP4P, and TIP5P models of water

Molecular-dynamics simulations were carried out for the SPC, SPCE, TIP4P, and TIP5P models of water at 298 K. From these results we determine the following quantities: the absolute entropy using the two-particle approximation, the mean lifetime of the hydrogen bond, the mean number of hydrogen bonds per molecule, and the mean energy of the hydrogen bond. From the entropy calculations we find that nearly all contributions to the total entropy originates from the orientation effects. Moreover, we determine the contributions to the total entropy which originate from the first, second, and higher solvation shells. It is interesting that the limits between solvation shells are clearly visible. The first solvation shell (0.22 < r < 0.36 nm) contributes approximately 43 J mol K to the total entropy; the second solvation shell (0.36 < r < 0.60 nm) contributes approximately 12 J mol K, while contributions from the third and other solvation shells are very small, approximately 2 J mol K in summary. This indicates that water molecules are strongly ordered up to 0.55-0.6 nm around the central water molecule, and beyond this limit the ordering diminishes. The results of calculations (entropy and hydrogen bonds) are compared with the experimental data for the choosing of the best water model. We find that the SPC and TIP4P models reproduce the best experimental values, and we recommend these models for computer simulations of the aqueous solution of biomolecules.     

Solubility and thermal stability of some amino-mellitate compounds

By reaction between the anion of mellitic acid (benzenehexacarboxylic acid) and some protonated linear polyamines (diethylenetriamine, triethylenetetramine, tetraethylene-pentamine, pentaethylenehexamine, spermidine, and spermine), fairly insoluble complexes have been obtained, with the general formula (amine)(x)(mellitate)H(6) (diethylenetriamine and spermidine, x=1; triethylenetetramine and spermine, x=0.75; tetraethylenepentamine, x=0.6 and 0.8; pentaethylenehexamine, x=0.5). K(s0) values for these complexes have been determined at I=0 mol dm(-3) and T=25 degrees C (logK(s0) ranges between -48.2 and -56.6). The solubility has been studied as a function of pH and of ionic strength. The thermal analysis, performed using air or argon flow, showed that all the solids behave in a similar way. In the range 20-120 degrees C the loss of hydration water occurs, and in the range 150-350 degrees C the first step of non oxidative decomposition takes place, with complete decomposition at 650 degrees C in air flow, whilst in argon flow the decomposition is still incomplete at 900 degrees C. Preliminary results of a parallel diffractometric study are also reported.     

Solubility of nonpolar gases in 2,2,2-trifluoroethanol at 25°C and 101.33 kPa partial pressure of gas

Solubility measurements of several nonpolar gases (He, Ne, Ar, Kr, Xe, H₂, N₂, CH₄, C₂H₄, C₂H₆, CF₄, SF₆, and CO₂) in 2,2,2-trifluoroethanol at 25°C and 101.33 kPa partial pressure of gas are reported. Gibbs energy for the solution process at 25°C is evaluated from the experimental values of the solubility of gases expressed as mole fraction. Lennard-Jones 6–12 pair potential parameters for 2,2,2-trifluoroethanol are estimated by using the scaled particle theory (SPT); and experimental solubilities are compared with those calculated from the values of these parameters through the SPT model.     

Solubility of nonpolar gases in tetrahydropyran at 0 to 30°C and 101.33 kPa partial pressure of gas

Solubility measurements of several nonpolar gases (He, Ne, Ar, Kr, Xe, H₂, D₂, N₂, CH₄, C₂H₄, C₂H₆, CF₄, and SF₆) in tetrahydropyran at the temperature range 0 to 30°C and 101.33 kPa partial pressure of gas are reported. Thermodynamic functions for the solution process (Gibbs energy, enthalpy, and entropies) at 25°C are evaluated from the experimental values of the solubility of gases as mole fraction and their variation with the temperature. Lennard-Jones 6–12 pair potential parameters for tetrahydropyran are estimated by using the scale particle theory (SPT); and experimental solubilities are compared with the calculated values using this model. Experimental solubilities of gases in tetrahydropyran and intermolecular potential parameters are compared with those obtained for the same gases in other cycloethers.