Solvation thermodynamics of xenon in n-alkanes, n-alcohols and water

Experimental thermodynamic data for the solvation of xenon in n-alkanes, water and n-alcohols, from different sources, are analysed by means of a general theory of solvation. The standard solvation Gibbs energy change is given by the sum of the work spent to create a cavity suitable to host xenon and the energy gained to turn on xenon-solvent attractive interactions. The latter contribution is larger in magnitude than the former in both n-alkanes and n-alcohols; the reverse holds in water. This finding is due to the fact that liquid water is characterized by the largest work of cavity creation, because of the smallness of its molecules. Since the two contributions to the solvation Gibbs energy change are both larger in magnitude in n-alcohols with respect to n-alkanes of the same number of heavy atoms, the xenon solubility is not so different between the two classes of solvents. The H-bonds play an indirect role, being important to determine the density of the liquid. It is also shown that there is no clear correlation between the cohesive energy density of the liquid and the solubility of xenon in the liquid itself. The present study confirms that the effective molecular size of solvent molecules is the principal factor in controlling the solvation Gibbs energy changes.     

Temperature dependence of the solubility of non-polar gases in water

An explanation is provided for the experimentally observed temperature dependence of the solubility and the solubility minimum of non-polar gases in water. The influence of solute size and solute-water attractive interactions on the solubility minimum temperature is investigated. The transfer of a non-polar solute from the ideal gas into water is divided into two steps: formation of a cavity in water with the size and shape of the solute and insertion of the solute in this cavity which is equivalent to 'turning on' solute-water attractive interactions. This two step process divides the excess chemical potential of the non-polar solute in water into repulsive and attractive contributions, respectively. The reversible work for cavity formation is modeled using an information theory model of hydrophobic hydration. Attractive contributions are calculated by modeling the water structure in the vicinity of non-polar solutes. These models make a direct connection between microscopic quantities and macroscopic observables. Moreover, they provide an understanding of the peculiar temperature dependences of the hydration thermodynamics from properties of pure water; specifically, bulk water density and the water oxygen-oxygen radial distribution function.     

Atomic-scale analysis of the solvation thermodynamics of hydrophobic hydration.

Molecular dynamics simulations are used to model the transfer thermodynamics of krypton from the gas phase into water. Extra long, nanosecond simulations are required to reduce the statistical uncertainty of the calculated "solvation" enthalpy to an acceptable level. Thermodynamic integration is used to calculate the "solvation" free energy, which together with the enthalpy is used to calculate the "solvation" entropy. A comparison series of simulations are conducted using a single Lennard-Jones sphere model of water to identify the contribution of hydrogen bonding to the thermodynamic quantities. In contrast to the classical "iceberg" model of hydrophobic hydration, the favorable enthalpy change for the transfer process at room temperature is found to be due primarily to the strong van der Waals interaction between the solute and solvent. Although some stabilization of hydrogen bonding does occur in the solvation shell, this is overshadowed by a destabilization due to packing constraints. Similarly, whereas some of the unfavorable change in entropy is attributed to the reduced rotational motion of the solvation shell waters, the major component is due to a decrease in the number of positional arrangements associated with the translational motions.     

Roles for Ordered and Bulk Solvent in Ligand Recognition and Docking in Two Related Cavities

A key challenge in structure-based discovery is accounting for modulation of protein-ligand interactions by ordered and bulk solvent. To investigate this, we compared ligand binding to a buried cavity in Cytochrome c Peroxidase (CcP), where affinity is dominated by a single ionic interaction, versus a cavity variant partly opened to solvent by loop deletion. This opening had unexpected effects on ligand orientation, affinity, and ordered water structure. Some ligands lost over ten-fold in affinity and reoriented in the cavity, while others retained their geometries, formed new interactions with water networks, and improved affinity. To test our ability to discover new ligands against this opened site prospectively, a 534,000 fragment library was docked against the open cavity using two models of ligand solvation. Using an older solvation model that prioritized many neutral molecules, three such uncharged docking hits were tested, none of which was observed to bind; these molecules were not highly ranked by the new, context-dependent solvation score. Using this new method, another 15 highly-ranked molecules were tested for binding. In contrast to the previous result, 14 of these bound detectably, with affinities ranging from 8 µM to 2 mM. In crystal structures, four of these new ligands superposed well with the docking predictions but two did not, reflecting unanticipated interactions with newly ordered waters molecules. Comparing recognition between this open cavity and its buried analog begins to isolate the roles of ordered solvent in a system that lends itself readily to prospective testing and that may be broadly useful to the community.     

Determination of kinetic and retention properties of cartridge and disk devices for solid-phase extraction

The kinetic properties of cartridge and disk solid-phase extraction devices are determined by forced-flow liquid chromatography. Typical cartridges provide about 5–15 theoretical plates per cm of bed height and particle-loaded membranes provide about 4–9 theoretical plates for a 0.5-mm-thick membrane. It is shown that cartridge devices fail to provide their maximum trapping performance because of inadequate packing density and that the required packing density could be easily achieved in practice with particles of a standard size. The retention properties of common sorbents for extraction from water and air are characterized with the solvation parameter model. For predominantly aqueous solutions a favorable cavity term results in increased retention while polar interactions tend to reduce retention. Retention on porous polymer sorbents is more complicated because of their capacity to absorp significant amounts of the sample processing solvent resulting in solvent-dependent changes in retention properties. For trapping organic volatiles from air cavity formation and dispersion interactions are important, and in the case of Tenax its capacity for induction interactions is also significant.     

On the properties of aqueous amide solutions through classical molecular dynamics simulations

The structure and dynamics of infinitely diluted aqueous amide solutions is studied for 13 compounds in the NVT ensemble using classical molecular dynamics simulations. The aim of this work is to provide valuable insights into the effect of amides on liquid water properties in order to understand the amides role in the kinetic inhibition of clathrate hydrate formation in natural gas mixtures. The OPLS-AA forcefield is used to describe the amides, with parameters obtained through fitting of computed B3LYP/6-311++g^{* *} data when not available in the literature, and the SPC-E model is applied for water molecules. Structural properties of the solutions are analyzed via calculated radial distribution functions and dynamic properties are studied with the computed mean square displacements and velocity autocorrelation functions. Most of the studied compounds show a remarkable structuring effect on the surrounding water with strong interactions resulting from hydrogen bonding between solute and solvent molecules. Hydrophobic and hydrophilic synergistic effects influence the amide–water interaction and the properties of the water solvation shells around amides.     

Solvation thermodynamics of biopolymers. I. Separation of the volume and surface interactions with estimates for proteins

The present paper is a systematic first approach to the problem of solvation thermodynamics of biomolecules. Most previous approaches have been only crude estimates of solvent contributions, and have simply assessed solvation free energy as proportional to surface areas. Here we estimate the various contributions and divide them into (a) hard-core interactions dependent upon the entire volume of solute and (b) the remainder of interactions manifested through surfaces, such as van der Waals, charge-charge, or hydrogen bonds. We have estimated the work to create a cavity with scaled-particle theory (SPT), the van der Waals interactions on the surface, and hydrogen bonds between the surface and the solvent. The conclusion here is that this latter term is the largest component of the solvation free energy of proteins. From estimates on nine diverse proteins, it is clear that the larger the protein, the more dominant is the hydrogen-bond term. In the next paper, we indicate that correlations between hydrogen-bonding groups on the surfaces could increase the magnitude of the hydrogen-bond contribution.     

Effect of organic solvents on oxygen mass transfer in multiphase systems: Application to bioreactors in environmental protection

The absorption of oxygen in aqueous–organic solvent emulsions was studied in a laboratory-scale bubble reactor at a constant gas flow rate. The organic and the gas phases were dispersed in the continuous aqueous phase. Volumetric mass transfer coefficients (k_La) of oxygen between air and water were measured experimentally using a dynamic method. It was assumed that the gas phase contacts preferentially the water phase. It was found that addition of silicone oils hinders oxygen mass transfer compared to air–water systems whereas the addition of decane, hexadecane and perfluorocarbon PFC40 has no significant influence. By and large, the results show that, for experimental conditions (organic liquid hold-up ≤10% and solubility ratio ≤10), the k_La values of oxygen determined in binary air–water systems can be used for multiphase (gas–liquid–liquid) reactor design with applications in environmental protection (water and air treatment processes).     

Thermodynamic and Ultrasonic Properties of Ascorbic Acid in Aqueous Protic Ionic Liquid Solutions

In this work, we report the thermodynamic and ultrasonic properties of ascorbic acid (vitamin C) in water and in presence of newly synthesized ammonium based protic ionic liquid (diethylethanolammonium propionate) as a function of concentration and temperature. Apparent molar volume and apparent molar isentropic compression, which characterize the solvation state of ascorbic acid (AA) in presence of protic ionic liquid (PIL) has been determined from precise density and speed of sound measurements at temperatures (293.15 to 328.15) K with 5 K interval. The strength of molecular interactions prevailing in ternary solutions has been discussed on the basis of infinite dilution partial molar volume and partial molar isentropic compression, corresponding volume of transfer and interaction coefficients. Result has been discussed in terms of solute-solute and solute-solvent interactions occurring between ascorbic acid and PIL in ternary solutions (AA + water + PIL).     

Heat Effects of Dehydration of Human Serum Albumin in Hydrophilic Organic Solvents

A thermochemical model for describing the transfer of water from the protein phase to the organic solvent liquid phase and for determining how the solvation ability of organic solvents affects this process was developed. Enthalpy changes on the interaction of dried and hydrated human serum albumin (HSA) with hydrophilic organic solvents (dimethyl sulfoxide, formamide, ethanol, methanol and acetic acid) and water were measured by isothermal calorimetry at 25 °C. The initial hydration level of human serum albumin was varied in the entire water content range from 0–30 % [g water/g HSA]. The dependence of the interaction enthalpies on the initial water content is complex. The interaction enthalpies of the dried HSA with organic solvents are exothermic. At low water contents (less than 0.1 g/g), there is a sharp increase in the interaction enthalpy values. At the highest water contents (more than 0.2 g/g), the interaction enthalpies are endothermic for acetic acid and formamide and exothermic for DMSO, methanol, and ethanol. These thermochemical data were analyzed in conjunction with the results for the water adsorption in organic solvents to calculate the molar enthalpies of dehydration of HSA in organic liquids. It was found that the dehydration enthalpy changes may be endothermic or exothermic depending on the initial water content and the water solvation enthalpy value. From the results obtained, it can be concluded that: (i) only the solvation of water by hydrophilic organic solvent determines the changes in the dehydration enthalpy values, and (ii) the data for the enthalpies of solvation of water by the solvent at infinite dilution reflect this effect.     

水/乙醇溶剂中阿奇霉素的热力学及多晶型研究

在278.2~308.2 K温度范围内,测定阿奇霉素在水/乙醇混合溶剂中的溶解度,根据固液平衡理论建立了该体系的溶解度修正模型。采用X线粉末衍射法和差示扫描量热法,对阿奇霉素在不同温度、不同体积比的水/乙醇混合溶剂中得到的晶体进行鉴别。同时利用溶解度数据估算了阿奇霉素在水/乙醇体系中的溶解热(-25.26~-16.11 k J/mol)、混合热(-9.94~-3.25 k J/mol)。通过溶液化学理论推导了阿奇霉素溶剂化平衡常数K与活度系数γ2的方程:γ2=1/(1+K),建立了溶剂化焓与温度、水/乙醇两者体积比(φ)之间的关系式,为ΔH=RTln(17.86exp(3.4φ)-1)。采用溶析结晶方法得到的6种阿奇霉素晶体,均属单斜晶系,但具有不同的晶胞参数且其密度和熔点也不同。同时发现温度越高,水/乙醇体积比越大,得到的晶体稳定性越差(晶体的熔点和密度降低)。在水/乙醇混合溶剂的溶析结晶体系中,产生阿齐霉素多晶型的现象与溶剂化作用的强弱有关。     

Development of a novel bioreactor system for treatment of gaseous benzene

A novel, continuous bioreactor system combining a bubble column (absorption section) and a two-phase bioreactor (degradation section) has been designed to treat a gas stream containing benzene. The bubble column contained hexadecane as an absorbent for benzene, and was systemically chosen considering physical, biological, environmental, operational, and economic factors. This solvent has infinite solubility for benzene and very low volatility. After absorbing benzene in the bubble column, the hexadecane served as the organic phase of the two-phase partitioning bioreactor, transferring benzene into the aqueous phase where it was degraded by Alcaligenes xylosoxidans Y234. The hexadecane was then continuously recirculated back to the absorber section for the removal of additional benzene. All mass transfer and biodegradation characteristics in this system were investigated prior to operation of the integrated unit, and these included: the mass transfer rate of benzene in the absorption column; the mass transfer rate of benzene from the organic phase into the aqueous phase in the two-phase bioreactor; the stripping rate of benzene out of the two-phase bioreactor, etc. All of these parameters were incorporated into model equations, which were used to investigate the effects of operating conditions on the performance of the system. Finally, two experiments were conducted to show the feasibility of this system. Based on an aqueous bioreactor volume of 1 L, when the inlet gas flow and gaseous benzene concentration were 120 L/h and 4.2 mg/L, respectively, the benzene removal efficiency was 75% at steady state. This process is believed to be very practical for the treatment of high concentrations of gaseous pollutants, and represents an alternative to the use of biofilters.     

The translocation kinetics of antibiotics through porin OmpC: Insights from structure‐based solvation mapping using WaterMap

Poor permeability of the lipopolysaccharide‐based outer membrane of Gram‐negative bacteria is compensated by the existence of protein channels (porins) that selectively admit low molecular weight substrates, including many antibiotics. Improved understanding of the translocation mechanisms of porin substrates could help guide the design of antibiotics capable of achieving high intracellular exposure. Energy barriers to channel entry and exit govern antibiotic fluxes through porins. We have previously reported a hypothesis that the costs of transferring protein solvation to and from bulk medium underlie the barriers to protein‐ligand association and dissociation, respectively, concomitant with the gain and loss of protein‐ligand interactions during those processes. We have now applied this hypothesis to explain the published rates of entry (association) and exit (dissociation) of six antibiotics to/from reconstituted E. coli porin OmpC. WaterMap was used to estimate the total water transfer energies resulting from transient occupation by each antibiotic. Our results suggest that solvation within the porin cavity is highly energetically favorable, and the observed moderately fast entry rates of the antibiotics are consistent with replacement of protein‐water H‐bonds. The observed ultrafast exit kinetics is consistent with the lack of intrachannel solvation sites that convey unfavorable resolvation during antibiotic dissociation. These results are aligned with known general relationships between antibiotic efficacy and physicochemical properties, namely unusually low logP, reflecting an abundance of H‐bond partners. We conclude that antibiotics figuratively “melt” their way through porin solvation at a rate determined by the cost of exchanging protein‐solvent for protein‐antibiotic H‐bonds. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Solvent reorganization contribution to the transfer thermodynamics of small nonpolar molecules.

The experimental thermodynamic data for the dissolution of five simple hydrocarbon molecules in water were combined with the solute-solvent interaction energy from a computer simulation study to yield data on the enthalpy change of solvent reorganization. Similar data were generated for dissolving these same solute molecules in their respective neat solvents using the equilibrium vapor pressure and the heat of vaporization data for the pure liquid. The enthalpy and the free energy changes upon cavity formation were also estimated using the temperature dependence of the solute-solvent interaction energy. Both the enthalpy and T delta S for cavity formation rapidly increase with temperature in both solvent types, and the free energy of cavity formation can be reproduced accurately by the scaled particle theory over the entire temperature range in all cases. These results indicate that the characteristic structure formation around an inert solute molecule in water produces compensating changes in enthalpy and entropy, and that the hydrophobicity arises mainly from the difference in the excluded volume effect.     

A theoretical study of glucose mutarotation in aqueous solution

In this work the mechanism of glucose mutarotation is investigated in aqueous solution considering the most likely pathways proposed from experimental work. Two mechanisms are studied. The first involves an intramolecular proton transfer as proposed by textbooks of organic chemistry, and the second uses one solvent water molecule to assist proton transfer. Both mechanisms are studied in the gas phase and in aqueous solution with the help of a polarizable continuum model, which is adopted to introduce the electrostatic nonspecific influence of bulk solvent. The structures are fully characterized through the calculation of the corresponding vibrational frequencies. The rate coefficients for each mechanism are calculated following transition-state theory in both the gas phase and in aqueous solution. Values computed for the water-assisted pathway in the continuum solvent agree best with the experimental results.     

Non-polar solutes in water and in aqueous solutions of protein denaturants. Modeling of solution and transfer processes

A simple molecular model for the thermodynamic behavior of non-polar solutes in water and in aqueous solutions of protein denaturants is presented. Three contributions are considered: (i) combinatorial arising from the mixing process, (ii) interactional characterizing the molecular interactions occurring in the mixture and (iii) a contribution originating from the structural changes occurring in the first shell of water molecules around the solute. The latter is modeled assuming that water molecules in contact with the solute are involved in a chemical equilibrium between two states. The model describes well the temperature and denaturant concentration dependences of the Gibbs energies of solution and transfer for benzene, toluene and alkanes in water and aqueous solutions of urea and guanidine hydrochloride. Model parameters are physically meaningful, allowing a discussion of the molecular interactions involved. A preferential solvation of the solute by the denaturant is found. However, the non-polar solute-denaturant interaction is not specific, i.e. leading to a distinct chemical entity. Urea and guanidine hydrochloride are non-polar solubilizing agents because their interactions with the solute are less unfavorable than those between water and the solute.     

Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models

Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical structure and receptor docking mechanism are still not well understood. The conformational dynamics of this neuron peptide in liquid water are studied here by using all-atom molecular dynamics (MD) and implicit water Langevin dynamics (LD) simulations with AMBER potential functions and the three-site transferable intermolecular potential (TIP3P) model for water. To achieve the same simulation length in physical time, the full MD simulations require 200 times as much CPU time as the implicit water LD simulations. The solvent hydrophobicity and dielectric behavior are treated in the implicit solvent LD simulations by using a macroscopic solvation potential, a single dielectric constant, and atomic friction coefficients computed using the accessible surface area method with the TIP3P model water viscosity as determined here from MD simulations for pure TIP3P water. Both the local and the global dynamics obtained from the implicit solvent LD simulations agree very well with those from the explicit solvent MD simulations. The simulations provide insights into the conformational restrictions that are associated with the bioactivity of the opiate peptide dermorphin for the delta-receptor.     

Simulation of DNA bases in water: Comparison of the Monte Carlo algorithm with molecular mechanics force fields

The interaction between the nucleic acid bases and solvent molecules has an important effect in various biochemical processes. We have calculated total energy and free energy of the solvation of DNA bases in water by Monte Carlo simulation. Adenine, guanine, cytosine, and thymine were first optimized in the gas phase and then placed in a cubic box of water. We have used the TIP3 model for water and OPLS for the nucleic acid bases. The canonical (T, V, N) ensemble at 25 degrees C and Metropolis sampling technique have been used. Good agreement with other available computational data was obtained. Radial distribution functions of water around each site of adenine, guanine, cytosine, and thymine have been computed and the results have shown the ability of the sites for hydrogen bonding and other interactions. The computations have shown that guanine has the highest value of solvation free energy and N7 and N6 in adenine and guanine, N3 in cytosine, and N3 and O4 in thymine have the largest radial distribution function. Monte Carlo simulation has also been performed using the CHARMM program under the same conditions, and the results of two procedures are compared.     

Simulation of DNA bases in water: Comparison of the Monte Carlo algorithm with molecular mechanics force fields

The interaction between the nucleic acid bases and solvent molecules has an important effect in various biochemical processes. We have calculated total energy and free energy of the solvation of DNA bases in water by Monte Carlo simulation. Adenine, guanine, cytosine, and thymine were first optimized in the gas phase and then placed in a cubic box of water. We have used the TIP3 model for water and OPLS for the nucleic acid bases. The canonical (T, V, N) ensemble at 25°C and Metropolis sampling technique have been used. Good agreement with other available computational data was obtained. Radial distribution functions of water around each site of adenine, guanine, cytosine, and thymine have been computed and the results have shown the ability of the sites for hydrogen bonding and other interactions. The computations have shown that guanine has the highest value of solvation free energy and N7 and N6 in adenine and guanine, N3 in cytosine, and N3 and O4 in thymine have the largest radial distribution function. Monte Carlo simulation has also been performed using the CHARMM program under the same conditions, and the results of two procedures are compared.     

Energetics of interactions of aromatic hydrocarbons with water

The thermodynamics of transfer of aromatic (benzene, toluene) and aliphatic (ethane, propane, butane) hydrocarbons from the gas phase into water in the temperature range 5–125°C have been analyzed in order to determine the net hydration effect of these compounds. In the case of the aromatic hydrocarbons the enthalpic contribution predominates over the entropic contribution to the Gibbs energy of hydration. This results in a negative value of the hydration Gibbs energy of aromatic hydrocarbons, in contrast to the positive Gibbs energy of hydration of aliphatic hydrocarbons. The different sign of the hydration Gibbs energies indicates that the mechanism causing hydrophobicity of aromatic hydrocarbons has different nature than that causing the hydrophobicity of aliphatic hydrocarbons. The comparison of hydration of aliphatic and aromatic hydrocarbons leads to the following thermodynamic parameters for these additional interactions between the benzene ring and water at 25°C: enthalpy −5.4 kJ/mol, entropy 26.8 J/K mol and Gibbs energy −13.4 kJ/mol. The large enthalpic contribution to the Gibbs energy of hydration of aromatic hydrocarbons probably comes from the ability of the aromatic ring to accept hydrogens from water, forming hydrogen bonds.