Microheterogeneous structure of 1-octanol in neat and water-saturated state

The conformational and dynamic properties of 1-octanol in neat and in water-saturated states have been investigated by 1H NMR. It has been proved that neat 1-octanol is microheterogeneous in nature comprising regions enriched in either hydrocarbons or hydroxyl groups. A reversed micelle-like cluster model was proposed, where the octanol cluster has an inner polar core of hydrogen-bonded octanol hydroxyls and an outer shell of nonpolar alkyl chains radiating outside. It was also observed that the cluster structure of octanol experiences minor changes with the presence of water. In water-saturated octanol, water molecules associate via hydrogen bonding and reside in the innermost center of the polar region with restricted motion, whereas the octanol cluster structure is modified by loosening the compact structure. Moreover, the preferential solvations of both systems were tested and compared. It not only gives some clues about the microheterogeneity of the alcohol system and the structure of the cluster but also helps in advancing our understanding on the behavior and properties of the amphiphilic molecules system such as phospholipids.     

Understanding the nitrate coordination to Eu3+ ions in solution by potential of mean force calculations

Coordination of nitrate anions with lanthanoid cations (Ln(3+)) in water, methanol and octanol-1 has been studied by means of molecular dynamics simulations with explicit polarization. Potential of mean force (PMF) profiles have been calculated for a mono-complex of lanthanoid nitrate (Ln(NO(3))(2+)) in these solvents using umbrella-sampling molecular dynamics. In pure water, no difference in the nitrato coordination to lanthanoids (Nd(3+), Eu(3+) and Dy(3+)) is observed, i.e. the nitrate anion prefers the monodentate coordination, which promotes the salt dissociation. Then, the influence of the nature of the solvating molecules on the nitrato coordination to Eu(3+) has been investigated. PMF profiles point out that both monodenate and bidentate coordinations are stable in neat methanol, while in neat octanol, only the bidentate one is. MD simulations of Eu(NO(3))(3) in water-octanol mixtures with different concentrations of water have been then performed and confirm the importance of the water molecules' presence on the nitrate ion's coordination mode.     

A transferable coarse-grained model for hydrogen-bonding liquids

We present here a recent development of a generalized coarse-grained model for use in molecular simulations. In this model, interactions between coarse-grained particles consist of both van der Waals and explicit electrostatic components. As a result, the coarse-grained model offers the transferability that is lacked by most current effective-potential based approaches. The previous center-of-mass framework (P. A. Golubkov and P. Ren, J. Chem. Phys., 2006, 125, 64103) is generalized here to include arbitrary off-center interaction sites for both Gay-Berne and multipoles. The new model has been applied to molecular dynamic simulations of neat methanol liquid. By placing a single point multipole at the oxygen atom rather than at the center of mass of methanol, there is a significant improvement in the ability to capture hydrogen-bonding. The critical issue of transferability of the coarse-grained model is verified on methanol-water mixtures, using parameters derived from neat liquids without any modification. The mixture density and internal energy from coarse-grained molecular dynamics simulations show good agreement with experimental measurements, on a par with what has been obtained from more detailed atomic models. By mapping the dynamics trajectory from the coarse-grained simulation into the all-atom counterpart, we are able to investigate atomic-level structure and interaction. Atomic radial distribution functions of neat methanol, neat water and mixtures compare favorably to experimental measurements. Furthermore, hydrogen-bonded 6- and 7-molecule chains of water and methanol observed in the mixture are in agreement with previous atomic simulations.     

Hydrogen Bonding and Vaporization Thermodynamics in Hexafluoroisopropanol-Acetone and -Methanol Mixtures. A Joined Cluster Analysis and Molecular Dynamic Study

Binary mixtures of hexafluoroisopropanol with either methanol or acetone are analyzed via classical molecular dynamics simulations and quantum cluster equilibrium calculations. In particular, their populations and thermodynamic properties are investigated with the binary quantum cluster equilibrium method, using our in-house code Peacemaker 2.8, upgraded with temperature-dependent parameters. A novel approach, where the final density from classical molecular dynamics, has been used to generate the necessary reference isobars. The hydrogen bond network in both type of mixtures at molar fraction of hexafluoroisopropanol of 0.2, 0.5, and 0.8 respectively is investigated via the molecular dynamics trajectories and the cluster results. In particular, the populations show that mixed clusters are preferred in both systems even at 0.2 molar fractions of hexafluoroisopropanol. Enthalpies and entropies of vaporization are calculated for the neat and mixed systems and found to be in good agreement with experimental values.     

Effect of temperature and concentration on the structure of sec-butyl alcohol and isobutyl alcohol/water mixtures: near-infrared spectroscopic study

The effect of temperature and concentration on the structure of sec-butyl alcohol and isobutyl alcohol/water binary mixtures in the alcohol-rich region (mole fraction of water X(H2O) < 0.3) has been studied using Fourier transform (FT) near-infrared (NIR) spectroscopy. The experimental data were analyzed by a two-dimensional (2D) correlation approach and chemometric methods. It was found that molecules of both alcohols in the mixture with water are in the same environment as those in the pure alcohols. Even at very low water content (X(H2O) = 0.001) we did not observe water free from any specific interactions. The molecules of water are attached to the end free OH groups in the open chain associates of alcohol. In this way the structure of neat alcohol remains intact by addition of water. The water-alcohol interactions in sec-butyl alcohol and isobutyl alcohol/water mixtures are stronger than those in bulk water. The results obtained at higher water content or elevated temperatures indicate the possibility of water-water interaction. In the alcohol-rich region the hydrophobic effects are of minor importance and the structure and properties of these systems are determined by hydrogen bonding through the hydroxyl groups. Both alcohols behave similarly on the temperature or water content variation; the minor difference results from a different degree of self-association for sec-butyl alcohol and isobutyl alcohol.     

Structural characterization of interfacial n-octanol and 3-octanol using molecular dynamic simulations

Structurally isomeric octanol interfacial systems, water/vapor, 3-octanol/vapor, n-octanol/vapor, 3-octanol/water, and n-octanol/water are investigated at 298 K using molecular dynamics simulation techniques. The present study is intended to investigate strongly associated liquid/liquid interfaces and probe the atomistic structure of these interfaces. The octanol and water molecules were initially placed randomly into a box and were equilibrated using constant pressure techniques to minimize bias within the initial conditions as well as to fully sample the structural conformations of the interface. An interface formed via phase separation during equilibration and resulted in a slab geometry with a molecularly sharp interface. However, some water molecules remained within the octanol phase with a mole fraction of 0.12 after equilibration. The resulting "wet" octanol interfaces were analyzed using density profiles and orientational order parameters. Our results support the hypothesis of an ordered interface only 1 or 2 molecular layers deep before bulk properties are reached for both the 3-octanol and water systems. However, in contrast to most other interfacial systems studied by molecular dynamics simulations, the n-octanol interface extends for several molecular layers. The octanol hydroxyl groups form a hydrogen-bonding network with water which orders the surface molecules toward a preferred direction and produces a hydrophilic/hydrophobic layering. The ordered n-octanol produces an oscillating low-high density of oxygen atoms out of phase with a high-low density of carbon atoms, consistent with an oscillating dielectric. In contrast, the isomeric 3-octanol has only a single carbon-rich layer directly proximal to the interface, which is a result of the different molecular topology. Both 3-octanol and n-octanol roughen the water interface with respect to the water/vapor interface. The "wet" octanol phases, in the octanol/water systems reach bulk properties in a shorter distance than the "dry" octanol/vapor interfaces.     

Solvation of propylene oxide in water: vibrational circular dichroism, optical rotation, and computer simulation studies

The solvation of propylene oxide (PO) in water has been studied using vibrational circular dichroism (VCD) spectroscopy, optical rotation dispersion (ORD) spectroscopy, molecular dynamics simulations, and ab initio calculations. VCD and ORD measurements were carried out for PO as neat liquid, in CCl4, and in water solutions. The classical molecular dynamics simulations were carried out for the PO + water binary mixtures at different concentrations, and the solvation information was derived from the radial distribution functions obtained in the simulations. The total number of water molecules within the closest vicinity of PO was predicted to be about 3. The geometry optimizations, vibrational frequencies, and VCD intensities were evaluated for the PO monomer and the PO-(H2O)n clusters with n = 1-3 , using density functional theory calculations at the B3LYP/aug-cc-pVTZ level of theory. The chirality transfer VCD feature, which is a direct result of the explicit H-bonding between water and the chiral PO solute, was detected experimentally at the water bending band region. This feature exhibits high sensitivity to the solvation structure around PO. Comparison of the calculated and experimental chirality transfer features leads to the conclusion that the PO-water binary complex is the dominating species in aqueous solution at room temperature and the anti conformation, where water is on the opposite side of the oxirane ring of the PO methyl group, is preferred over the syn one. This conclusion is also supported by the complementary ORD studies. Possible contributions from the ternary and quaternary PO-water complexes are also discussed.     

Quantum-classical simulation of electron localization in negatively charged methanol clusters

A series of quantum molecular dynamics simulations have been performed to investigate the energetic, structural, dynamic, and spectroscopic properties of methanol cluster anions, [(CH(3)OH)(n)](-), (n = 50-500). Consistent with the inference from photo-electron imaging experiments, we find two main localization modes of the excess electron in equilibrated methanol clusters at ～200 K. The two different localization patterns have strikingly different physical properties, consistent with experimental observations, and are manifest in comparable cluster sizes to those observed. Smaller clusters (n ≤ 128) tend to localize the electron in very weakly bound, diffuse electronic states on the surface of the cluster, while in larger ones the electron is stabilized in solvent cavities, in compact interior-bound states. The interior states exhibit properties that largely resemble and smoothly extrapolate to those simulated for a solvated electron in bulk methanol. The surface electronic states of methanol cluster anions are significantly more weakly bound than the surface states of the anionic water clusters. The key source of the difference is the lack of stabilizing free hydroxyl groups on a relaxed methanol cluster surface. We also provide a mechanistic picture that illustrates the essential role of the interactions of the excess electron with the hydroxyl groups in the dynamic process of the transition of the electron from surface-bound states to interior-bound states.     

Molecular dynamics study of hydration in ethanol-water mixtures using a polarizable force field

The abnormal physicochemical characteristics of ethanol solvation in water are commonly attributed to the phenomenon of hydrophobic hydration. To investigate the structural organization of hydrophobic hydration in water-ethanol mixtures, we use molecular dynamics simulations based on detailed atomic models. Induced polarization is incorporated into the potential function on the basis of the classical Drude oscillator model. Water-ethanol mixtures are simulated at 11 ethanol molar fractions, from 0.05 to 0.9. Although the water and ethanol models are parametrized separately to reproduce the vaporization enthalpy, static dielectric constant, and self-diffusion constant of neat liquids at ambient conditions, they also reproduce the energetic and dynamical properties of the mixtures accurately. Furthermore, the calculated dielectric constant for the various water-alcohol mixtures is in excellent agreement with experimental data. The simulations provide a detailed structural characterization of the mixtures. A depletion of water-water hydrogen bonding in the first hydration shell of ethanol is compensated by an enhancement in the second hydration shell. The structuring effect from the second solvation shell gives rise to a net positive hydrogen-bonding excess for ethanol molar fractions up to approximately 0.5. For larger molar fractions, the second hydration shell is not sufficiently populated to overcome the net H-bond depletion from the first shell.     

Interaction of water with the model ionic liquid [bmim][BF4]: molecular dynamics simulations and comparison with NMR data

We report on molecular dynamics simulations of the ionic liquid [bmim][BF 4] and its mixtures with water, from zero up to 0.5 mol fraction of water. All of the simulations are carried out with two published force fields. The results are compared with each other and with published as well as new NMR data on the same mixtures, whenever possible. We perform extensive analyses of structural quantities, such as pair correlation functions, nearest-neighbor analysis and size distribution of the water clusters formed at higher concentrations. We show that the water clusters are formed almost exclusively by linear chains of hydrogen-bonded molecules. There is a nanoscale structuring of the mixtures but no macroscopic phase separation among the components, in agreement with experiment. Roughly, we identify two solvation regimes. At low water content, the ions are selectively coordinated by individual water molecules, but their ionic network is largely unperturbed. At high water content, the ionic network is somewhat disrupted or swollen in a nonspecific way by the water clusters.     

X-ray structural studies on microscopic mixing in binary mixtures of dimethyl sulphoxide with acetonitrile and N,N-dimethylformamide

The liquid structures of binary acetonitrile (AN)–dimethyl sulphoxide (DMSO) and N,N-dimethylformamide (DMF)–DMSO mixtures were investigated by the X-ray scattering method. Comparison of the X-ray scattering data of AN–DMSO liquid mixtures with those of neat AN and DMSO revealed that the intermolecular AN–DMSO interactions are practically not detected; that is, the X-ray scattering data of the liquid mixtures are well reproduced by summing up those of neat AN and DMSO weighted by their mole fractions. The same applies for DMF–DMSO mixtures. Thus, each component solvent molecule independently forms self-assembled clusters in the liquid mixtures, the structures of which are the same as those in the neat liquids. The clusters are mixed to form macroscopically homogeneous liquid mixtures. The thermodynamic quantities on mixing process for the AN–DMSO, DMF–DMSO and AN–DMF systems in the literature are well elucidated on the basis of the microscopic structure of the liquid mixtures.     

A quantum mechanical strategy to investigate the structure of liquids: the cases of acetonitrile, formamide, and their mixture

A computational strategy based on quantum mechanical (QM) calculations and continuum solvation models is used to investigate the structure of liquids (either neat liquids or mixtures). The strategy is based on the comparison of calculated and experimental spectroscopic properties (IR-Raman vibrational frequencies and Raman intensities). In particular, neat formamide, neat acetonitrile, and their equimolar mixture are studied comparing isolated and solvated clusters of different nature and size. In all cases, the study seems to indicate that liquids, even when strongly associated, can be effectively modeled in terms of a shell-like system in which clusters of strongly interacting molecules (the microenvironments) are solvated by a polarizable macroenvironment represented by the rest of the molecules. Only taking into proper account both these effects can a correct picture of the liquid structure be achieved.     

Simulating the nucleation of water/ethanol and water/n-nonane mixtures: mutual enhancement and two-pathway mechanism

A combination of the aggregation-volume-bias and configurational-bias Monte Carlo algorithms and the umbrella sampling technique was applied to investigate two different binary vapor-liquid nucleation systems: water/ethanol and water/n-nonane. The simulations are able to reproduce the different nonideal nucleation behavior observed experimentally for these two systems, i.e., the mutual enhancement of nucleation rates for water/ethanol mixtures and the two-pathway nucleation for water/n-nonane mixtures. Structural analysis provides microscopic explanations for the observed nucleation behavior. In particular, the simulations show a large and size-dependent surface enrichment of ethanol in the water/ethanol droplets, which confirms the previous experimental interpretation for this system. The immiscibility observed even for small water/n-nonane clusters causes the two-pathway nucleation mechanism.     

Solvation structure of hydroxyl radical by Car-Parrinello molecular dynamics

Car-Parrinello molecular dynamics simulations of a hydroxyl radical in liquid water have been performed. Structural and dynamical properties of the solvated structure have been studied in details. The partial atom-atom radial distribution functions for the hydrated hydroxyl do not show drastic differences with the radial distribution functions for liquid water. The OH is found to be a more active hydrogen bond donor and acceptor than the water molecule, but the accepted hydrogen bonds are much weaker than for the hydroxide OH- ion. The first solvation shell of the OH is less structured than the water's one and contains a considerable fraction of water molecules that are not hydrogen bonded to the hydroxyl. Part of them are found to come closer to the solvated radical than the hydrogen bonded molecules do. The lifetime of the hydrogen bonds accepted by the hydroxyl is found to be shorter than the hydrogen bond lifetime in water. A hydrogen transfer between a water molecule and the OH radical has been observed, though it is a much rarer event than a proton transfer between water and an OH- ion. The velocity autocorrelation power spectrum of the hydroxyl hydrogen shows the properties both of the OH radical in clusters and of the OH- ion in liquid.     

Nuclear magnetic resonance and ab initio studies of small complexes formed between water and pyridine derivatives in solid and liquid phases

The structure and geometry of hydrogen-bonded complexes formed between heterocyclic bases, namely, pyridine and 2,4,6-trimethylpyridine (collidine), and water were experimentally studied by NMR spectroscopy in frozen phase and in highly polar aprotic liquefied freon mixtures and theoretically modeled for gas phase. Hydrogen-bonded species in frozen heterocycle-water mixtures were characterized experimentally using 15N NMR. When base was in excess, one water molecule was symmetrically bonded to two heterocyclic molecules. This complex was characterized by the rHN distances of 1.82 Angstrom for pyridine and 1.92 Angstrom for collidine. The proton-donating ability of water in such complexes was affected by an anticooperative interaction between the two coupled hydrogen bonds and exhibited an apparent pK(a) value of about 6.0. When water was in excess, it formed water clusters hydrogen bonded to base. Theoretical analysis of binding energies of small model heterocycle-water clusters indicated that water in such clusters was oriented as a chain. The NMR estimated rHN distances in these species were 1.69 Angstrom for pyridine and 1.64 Angstrom for collidine. Here, the proton-donating ability of the hydroxyl group bonded to the heterocycle was affected by a mutual cooperative interaction with other water molecules in the chain and became comparable to the proton-donating ability of a fictitious acid, exhibiting an apparent pK(a) value of about 4.9. This value seems to depend only slightly on the length of the water chain and on the presence of another base at the other end of the chain if more than two water molecules are involved. Thus, the proton-donating ability of the outer hydroxyl groups of biologically relevant water bridges should be comparable to the proton-donating ability of a fictitious acid exhibiting a pK(a) value of about 4.9 in water. Driven by the mixing entropy, monomeric water presented in the aprotic freonic mixtures above 170 K but completely precipitated upon further cooling. Traces of water could be suspended in the mixtures down to 130 K in the presence of about 20-fold excess of heterocyclic bases. The obtained experimental data indicated that at these conditions water trended to form the symmetric 2:1 heterocycle-water complexes, whose bridge protons resonated around 6.7 ppm.     

Excess volumes of propanol-water mixtures at 5, 15, and 25°C

This paper reports on equipment for the automatic measurement of the density of binary mixtures as a function of concentration. The equipment is applied to mixtures of 1-propanol and water at 5, 15, and 25°C. An equilibrium mixture model, in which an alcohol-water solution is regarded as an ideal associated mixture, is fitted to the experimental data. Thermodynamic parameters characterizing the association of water to nonpolar alkyl groups (hydrophobic solvation) and to polar hydroxyl groups (hydrophilic solvation) are estimated.     

Molecular-dynamics study of anomalous volumetric behavior of water-benzene mixtures in the vicinity of the critical region

Molecular-dynamics simulations of water-benzene mixtures at 573 K and pressures in the 85-140 bars range have been performed to examine local structure and dynamics of the mixtures, which exhibit anomalously large volume expansion on mixing as recently found by in situ near-infrared measurements. Fractional charges for a simple-point-charge-type potential of water were adjusted so as to reproduce liquid densities and the gas-to-liquid transition pressure of neat water at 573 K. A Lennard-Jones-type potential for benzene was used and the Lorentz-Berthelot combination rule was applied to the water-benzene interaction. Simulations with a N-P-T ensemble of 800-molecule system have been performed and the results reproduce well the anomalous volumetric behavior of the mixtures with the mole fraction of benzene in the 0.3-0.8 range. Pair distribution functions, coordination numbers, and self-diffusion coefficients for the mixtures are calculated, and it is suggested that the local structure around water molecules undergoes drastic change by dissolution of benzene in the vicinity of the critical region, but that around benzene molecules seems to be understood as that of ordinary liquid mixtures.     

Comparison of two simulation methods to compute solvation free energies and partition coefficients

The thermodynamic integration (TI) and expanded ensemble (EE) methods are used here to calculate the hydration free energy in water, the solvation free energy in 1‐octanol, and the octanol‐water partition coefficient for a six compounds of varying functionality using the optimized potentials for liquid simulations (OPLS) all‐atom (AA) force field parameters and atomic charges. Both methods use the molecular dynamics algorithm as a primary component of the simulation protocol, and both have found wide applications in fields such as the calculation of activity coefficients, phase behavior, and partition coefficients. Both methods result in solvation free energies and 1‐octanol/water partition coefficients with average absolute deviations (AAD) from experimental data to within 4 kJ/mol and 0.5 log units, respectively. Here, we find that in simulations the OPLS‐AA force field parameters (with fixed charges) can reproduce solvation free energies of solutes in 1‐octanol with AAD of about half that for the solute hydration free energies using a extended simple point charge (SPC/E) model of water. The computational efficiency of the two simulation methods are compared based on the time (in nanoseconds) required to obtain similar standard deviations in the solvation free energies and 1‐octanol/water partition coefficients. By this analysis, the EE method is found to be a factor of nine more efficient than the TI algorithm. For both methods, solvation free energy calculations in 1‐octanol consume roughly an order of magnitude more CPU hours than the hydration free energy calculations. © 2012 Wiley Periodicals, Inc.     

Solvation in octanol: parametrization of the continuum MST model

This study reports the parametrization of the HF/6‐31G(d) version of the MST continuum model for n‐octanol. Following our previous studies related to the MST parametrization for water, chloroform, and carbon tetrachloride, a detailed exploration of the definition of the solute/solvent interface has been performed. To this end, we have exploited the results obtained from free energy calculations coupled to Monte Carlo simulations, and those derived from the QM/MM analysis of solvent‐induced dipoles for selected solutes. The atomic hardness parameters have been determined by fitting to the experimental free energies of solvation in octanol. The final MST model is able to reproduce the experimental free energy of solvation for 62 compounds and the octanol/water partition coefficient (log P_ow) for 75 compounds with a root‐mean‐square deviation of 0.6 kcal/mol and 0.4 (in units of log P), respectively. The model has been further verified by calculating the octanol/water partition coefficient for a set of 27 drugs, which were not considered in the parametrization set. A good agreement is found between predicted and experimental values of log P_o/w, as noted in a root‐mean‐square deviation of 0.75 units of log P. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1180–1193, 2001     

Preferential solvation of phenol in binary solvent mixtures. A molecular dynamics study

Molecular dynamics computer simulations were carried out to study the preferential solvation of phenol in equimolar acetonitrile-water and ethanol-water binary mixtures. Two water models were used to investigate the model dependence of preferential solvation. The results are compared to recent intermolecular 1H NOESY experiments reported on the same systems. In the case of acetonitrile-water the local mole fraction obtained from simulations agrees quite well with experiments. In the case of ethanol-water there was a qualitative difference, which was observed for both water models. However, when comparing the degree of preferential solvation of the two cosolvents ethanol and acetonitrile with each of the two water models, the trend obtained from the simulations agrees with experimental data.