Cavity formation and preferential interactions in urea solutions: Dependence on urea aggregation

A novel chitosan-urea encapsulated material for persulfate slow-release to degrade organic pollutants

A novel eco-friendly material (CS-U@PS) for persulfate slow-release to effectively degrade organic pollutants (methyl orange and pyrene) was synthesized using chitosan and urea as the encapsulated framework materials via an emulsion cross-linking method for the first time. The obtained CS-U@PS exhibits spherical shapes with a uniform size of approximately 2-3 µm according to the particle-size distribution and SEM image results. The slow-release mechanism was proposed through a kinetics model study and the Ritger-Peppas model fit well (r² = 0.9699) to indicate that the slow-release process is non-Fickian diffusion. The influences of urea and PS dosages and oxidative conditions on methyl orange degradation were studied, and all the results suggested that urea played an important role in PS slow-release and can also catalyze the activation of PS by iron to further produce radicals and improve the removal efficiency of pollutants. A pyrene removal rate of 90.53% was achieved in aqueous solutions and an above 80% removal rate was obtained in weakly acidic or neutral soil environments by CS-U@PS activated by Fe²⁺ with citric acid as the chelating agent. Therefore, the fabricated slow-release oxidation materials exhibit application potential for the remediation of organic polluted groundwater and soil.

Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20

A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and proteins is presented. The force field relies heavily on the use of Kirkwood-Buff theory to provide a comparison of simulated and experimental Kirkwood-Buff integrals for solutes containing the functional groups common in proteins, thus ensuring intermolecular interactions that provide a good balance between the peptide-peptide, peptide-solvent, and solvent-solvent distributions observed in solution mixtures. In this way, it differs significantly from other biomolecular force fields. Further development and testing of the intermolecular potentials are presented here. Subsequently, rotational potentials for the ϕ/ψ and χ dihedral degrees of freedom are obtained by analysis of the Protein Data Bank, followed by small modifications to provide a reasonable balance between simulated and observed α and β percentages for small peptides. This, the first of two articles, describes in detail the philosophy and development behind KBFF20.

Hydration and self-aggregation of a neutral cosolute from dielectric relaxation spectroscopy and MD simulations: the case of 1,3-dimethylurea

1,3-Dimethylurea irrotationally binds 1–2H₂O molecules close to its carbonyl and impedes dynamics of ca. 40 H₂O molecules by methyl substituents.

Urea hydration from dielectric relaxation spectroscopy: old findings confirmed, new insights gained

We report results on urea hydration obtained by dielectric relaxation spectroscopy (DRS) in a broad range of concentrations and temperatures. In particular, the effective hydration number and dipole moment of urea have been determined. The observed changes with composition and temperature were found to be insignificant and mainly caused by the changing number density of urea. Similarly, solute reorientation scaled simply with viscosity. In contrast, we find that water reorientation undergoes substantial changes in the presence of urea, resulting in two water fractions. The first corresponds to water molecules strongly bound to urea. These solvent molecules follow the reorientational dynamics of the solute. The second fraction exhibits only a minor increase of its relaxation time (in comparison with pure water) which is not linked to solution viscosity. Its activation energy decreases significantly with urea concentration, indicating a marked decrease of the number of H-bonds among the H2O molecules belonging to this fraction. Noncovalent interactions (NCI) analysis, capable to estimate the strength of the interactions within a cluster, shows that bound water molecules are most probably double-hydrogen bonded to urea via the oxygen atom of the carbonyl group and a cis-hydrogen atom. Due to the increased H-bond strength compared to the water dimer and the rigid position in the formed complex the reorientation of these bound H2O molecules is strongly impeded.

Effects of monohydric alcohols and polyols on the thermal stability of a protein

The thermal stability of a protein is lowered by the addition of a monohydric alcohol, and this effect becomes larger as the size of hydrophobic group in an alcohol molecule increases. By contrast, it is enhanced by the addition of a polyol possessing two or more hydroxyl groups per molecule, and this effect becomes larger as the number of hydroxyl groups increases. Here, we show that all of these experimental observations can be reproduced even in a quantitative sense by rigid-body models focused on the entropic effect originating from the translational displacement of solvent molecules. The solvent is either pure water or water-cosolvent solution. Three monohydric alcohols and five polyols are considered as cosolvents. In the rigid-body models, a protein is a fused hard spheres accounting for the polyatomic structure in the atomic detail, and the solvent is formed by hard spheres or a binary mixture of hard spheres with different diameters. The effective diameter of cosolvent molecules and the packing fractions of water and cosolvent, which are crucially important parameters, are carefully estimated using the experimental data of properties such as the density of solid crystal of cosolvent, parameters in the pertinent cosolvent-cosolvent interaction potential, and density of water-cosolvent solution. We employ the morphometric approach combined with the integral equation theory, which is best suited to the physical interpretation of the calculation result. It is argued that the degree of solvent crowding in the bulk is the key factor. When it is made more serious by the cosolvent addition, the solvent-entropy gain upon protein folding is magnified, leading to the enhanced thermal stability. When it is made less serious, the opposite is true. The mechanism of the effects of monohydric alcohols and polyols is physically the same as that of sugars. However, when the rigid-body models are employed for the effect of urea, its addition is predicted to enhance the thermal stability, which conflicts with the experimental fact. We then propose, as two essential factors, not only the solvent-entropy gain but also the loss of protein-solvent interaction energy upon protein folding. The competition of changes in these two factors induced by the cosolvent addition determines the thermal-stability change.

Molecular Thermodynamics of Methane Solvation in tert-Butanol-Water Mixtures

We studied solvation structure and thermodynamics of methane in mixtures of tert-butanol and water using computer simulations. We show that for alcohol mole fractions below 20%, methane is preferentially solvated by hydrated alcohol clusters. Because methane expels water molecules from these clusters, a large endothermic solvent reorganization enthalpy occurs. This process is responsible for the experimentally observed maximum of the heat of methane solvation close to 5% alcohol in the mixture and contributes to a positive entropy change relative to solvation in pure water. Because the structural solvent reorganization enthalpy is enthalpy-entropy compensating, the methane solvation free energy is a smoothly varying function of the alcohol/water solution composition.

Interaction preferences between nucleobase mimetics and amino acids in aqueous solutions

Despite the paramount importance of protein-nucleic acid interactions in different cellular processes, our understanding of such interactions at the atomistic level remains incomplete. We have used molecular dynamics (MD) simulations and 15 μs of sampling time to study the behavior of amino acids and amino-acid sidechain analogs in aqueous solutions of different mimetics of naturally occurring nucleobases, including dimethylpyridine (DMP) and unsubstituted purine and pyrimidine rings. By using structural and energetic analysis, we have derived preference scales for the interaction of amino acids and their sidechain analogs with different nucleobase mimetics and have exhaustively compared them with each other. A close correspondence with a standard hydrophobicity measure in the case of the pyrimidine mimetic DMP and purines suggests that the hydrophobic effect is the main defining factor behind such interactions. We analyze our findings in the context of the origin of the genetic code and the recently proposed cognate mRNA-protein complementarity hypothesis. Most importantly, we show that unsubstituted purine and pyrimidine rings alone cannot differentiate between predominantly purine- and pyrimidine-coded amino acids, suggesting that for such specificity to exist, it must primarily reside in ring substituents.

Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation

In aqueous solutions with high concentrations of chemical denaturants such as urea and guanidinium chloride (GdmCl) proteins expand to populate heterogeneous conformational ensembles. These denaturing environments are thought to be good solvents for generic protein sequences because properties of conformational distributions align with those of canonical random coils. Previous studies showed that water is a poor solvent for polypeptide backbones, and therefore, backbones form collapsed globular structures in aqueous solvents. Here, we ask if polypeptide backbones can intrinsically undergo the requisite chain expansion in aqueous solutions with high concentrations of urea and GdmCl. We answer this question using a combination of molecular dynamics simulations and fluorescence correlation spectroscopy. We find that the degree of backbone expansion is minimal in aqueous solutions with high concentrations of denaturants. Instead, polypeptide backbones sample conformations that are denaturant-specific mixtures of coils and globules, with a persistent preference for globules. Therefore, typical denaturing environments cannot be classified as good solvents for polypeptide backbones. How then do generic protein sequences expand in denaturing environments? To answer this question, we investigated the effects of side chains using simulations of two archetypal sequences with amino acid compositions that are mixtures of charged, hydrophobic, and polar groups. We find that side chains lower the effective concentration of backbone amides in water leading to an intrinsic expansion of polypeptide backbones in the absence of denaturants. Additional dilution of the effective concentration of backbone amides is achieved through preferential interactions with denaturants. These effects lead to conformational statistics in denaturing environments that are congruent with those of canonical random coils. Our results highlight the role of side chain-mediated interactions as determinants of the conformational properties of unfolded states in water and in influencing chain expansion upon denaturation.

Molecular wire of urea in carbon nanotube: a molecular dynamics study

We perform molecular dynamics simulations of narrow single-walled carbon nanotubes (SWNTs) in aqueous urea to investigate the structure and dynamical behavior of urea molecules inside the SWNT. Even at low urea concentrations (e.g., 0.5 M), we have observed spontaneous and continuous filling of SWNT with a one-dimensional urea wire (leaving very few water molecules inside the SWNT). The urea wire is structurally ordered, both translationally and orientationally, with a contiguous hydrogen-bonded network and concerted urea's dipole orientations. Interestingly, despite the symmetric nature of the whole system, the potential energy profile of urea along the SWNT is asymmetric, arising from the ordering of asymmetric urea partial charge distribution (or dipole moment) in confined environment. Furthermore, we study the kinetics of confined urea and find that the permeation of urea molecules through the SWNT decreases significantly (by a factor of ∼20) compared to that of water molecules, due to the stronger dispersion interaction of urea with SWNT than water, and a maximum in urea permeation happens around a concentration of 5 M. These findings might shed some light on the better understanding of unique properties of molecular wires (particularly the wires formed by polar organic small molecules) confined within both artificial and biological nanochannels, and are expected to have practical applications such as the electronic devices for signal transduction and multiplication at the nanoscale.

A Kirkwood-Buff force field for the aromatic amino acids

In a continuation of our efforts to develop a united atom non-polarizable protein force field based upon the solution theory of Kirkwood and Buff i.e., the Kirkwood-Buff Force Field (KBFF) approach, we present KBFF models for the side chains of phenylalanine, tyrosine, tryptophan, and histidine, including both tautomers of neutral histidine and doubly-protonated histidine. The force fields were specifically designed to reproduce the thermodynamic properties of mixtures over the full composition range in an attempt to provide an improved description of intermolecular interactions. The models were developed by careful parameterization of the solution phase partial charges to reproduce the experimental Kirkwood-Buff integrals for mixtures of solutes representative of the amino acid sidechains in solution. The KBFF parameters and simulated thermodynamic and structural properties are presented for the following eleven binary mixtures: benzene + methanol, benzene + toluene, toluene + methanol, toluene + phenol, toluene + p-cresol, pyrrole + methanol, indole + methanol, pyridine + methanol, pyridine + water, histidine + water, and histidine hydrochloride + water. It is argued that the present approach and models provide a reasonable description of intermolecular interactions which ensures that the required balance between solute-solute, solute-solvent, and solvent-solvent distributions is obtained.

The effect of urea on the morphology of NaCl crystals: A combined theoretical and simulation study

It has been known for over a century that the presence of cosolvents such as urea and formamide can alter the morphology of NaCl crystals grown from solution. To help understand this effect we have been developing a theoretical approach based on the Kirkwood-Buff (KB) theory of solutions, and have combined this with computer simulations of the interation of urea with different crystal faces of NaCl. In this way one can predict the effect of urea on the thermodynamic stability of different NaCl faces, with atomic level detail provided by the simulations. We observe that urea is preferentially excluded from 100 and 111 crystal faces, but is less excluded from 111 faces which present chloride ions at the surface. The results indicate that the 111 face is stabilized in urea solutions and promotes the formation of octahedral over cubic NaCl crystals. The approach is totally general and can be applied to understand a variety of interfacial properties. Furthermore, we apply KB theory to study several other issues regarding the simulation of crystal growth.

Developing Force Fields from the Microscopic Structure of Solutions

We have been developing force fields designed for the eventual simulation of peptides and proteins using the Kirkwood-Buff (KB) theory of solutions as a guide. KB theory provides exact information on the relative distributions for each species present in solution. This information can also be obtained from computer simulations. Hence, one can use KB theory to help test and modify the parameters commonly used in biomolecular studies. A series of small molecule force fields representative of the fragments found in peptides and proteins have been developed. Since this approach is guided by the KB theory, our results provide a reasonable balance in the interactions between self-association of solutes and solute solvation. Here, we present our progress to date. In addition, our investigations have provided a wealth of data concerning the properties of solution mixtures, which is also summarized. Specific examples of the properties of aromatic (benzene, phenol, p-cresol) and sulfur compounds (methanethiol, dimethylsulfide, dimethyldisulfide) and their mixtures with methanol or toluene are provided as an illustration of this kind of approach.

Theory and computer simulation of solute effects on the surface tension of liquids

A complete description of the thermodynamics of planar mixed solute-solvent interfaces suitable for the analysis of computer simulation data is provided. The approach uses surface probability distributions to characterize the interface regions, coupled with radial distribution functions and the Kirkwood-Buff theory of solutions to characterize the bulk solution properties. The approach is then used to understand the relationship between changes in the surface tension, the degree of surface adsorption or depletion, and the bulk solution properties of two aqueous solute systems. The first, aqueous NaCl solutions, provides an example of a surface excluded solute. The second, aqueous methanol solutions, provides an example of a surface adsorbed solute. The numerical results support the theoretical relationships described here and provide a consistent picture of the thermodynamics of solution interfaces involving any number of components which can be applied to a wide variety of systems.

On the theory of solute solubility in mixed solvents

A series of equations are developed for the study of the effects of cosolvents on the solubility of a solute in mixed solutions where the solute displays a finite solubility. The equations differ depending on the scale used for the solute (and cosolvent) concentrations. The expressions use Kirkwood-Buff integrals to relate the changes in solubility to changes in the local solution composition around the solute and can be applied to study any type of ternary system including electrolyte cosolvents. The expressions provided here differ from previous approaches because of the use of a semi-open ensemble and the extension to finite solute solubilities.

Recent applications of Kirkwood-Buff theory to biological systems

The effect of cosolvents on biomolecular equilibria has traditionally been rationalized using simple binding models. More recently, a renewed interest in the use of Kirkwood-Buff (KB) theory to analyze solution mixtures has provided new information on the effects of osmolytes and denaturants and their interactions with biomolecules. Here we review the status of KB theory as applied to biological systems. In particular, the existing models of denaturation are analyzed in terms of KB theory, and the use of KB theory to interpret computer simulation data for these systems is discussed.

Molecular basis of the apparent near ideality of urea solutions

Activity coefficients of urea solutions are calculated to explore the mechanism of its solution properties, which form the basis for its well-known use as a strong protein denaturant. We perform free energy simulations of urea solutions in different urea concentrations using two urea models (OPLS and KBFF models) to calculate and decompose the activity coefficients. For the case of urea, we clarify the concept of the ideal solution in different concentration scales and standard states and its effect on our subsequent analysis. The analytical form of activity coefficients depends on the concentration units and standard states. For both models studied, urea displays a weak concentration dependence for excess chemical potential. However, for the OPLS force-field model, this results from contributions that are independent of concentration to the van der Waals and electrostatic components whereas for the KBFF model those components are nontrivial but oppose each other. The strong ideality of urea solutions in some concentration scales (incidentally implying a lack of water perturbation) is discussed in terms of recent data and ideas on the mechanism of urea denaturation of proteins.

A Kirkwood-Buff derived force field for amides

A force field for the computer simulation of aqueous solutions of amides is presented. The force field is designed to reproduce the experimentally observed density and Kirkwood-Buff integrals for N-methylacetamide (NMA), allowing for an accurate description of the NMA activity. Other properties such as the translational diffusion constant and heat of mixing are also well reproduced. The force field is then extended to include N,N'-dimethylacetamide and acetamide with good success. Analysis of the simulations of low concentrations of NMA in water indicates a high degree of solvation with only 15% of the NMA molecules involved in solute-solute hydrogen bonding. There is only a weak angular dependence of the solute-solute hydrogen bonding interaction with a minimum at an angle of 65 degrees for the N-H and C=O dipole vectors. The models presented here provide a basis for an accurate force field for peptides and proteins.

Aqueous urea solutions: structure, energetics, and urea aggregation

Urea is ubiquitously used as a protein denaturant. To study the structure and energetics of aqueous urea solutions, we have carried out molecular dynamics simulations for a wide range of urea concentrations and temperatures. The hydrogen bonds between urea and water were found to be significantly weaker than those between water molecules, which drives urea self-aggregation due to the hydrophobic effect. From the reduction of the water exposed urea surface area, urea was found to exhibit an aggregation degree of ca. 20% at concentrations commonly used for protein denaturation. Structurally, three distinct urea pair conformations were identified and their populations were analyzed by translational and orientational pair distribution functions. Furthermore, urea was found to strengthen water structure in terms of hydrogen bond energies and population of solvation shells. Our findings are consistent with a direct interaction between urea and the protein as the main driving force for protein denaturation. As an additional, more indirect effect, urea was found to enhance water structure, which would suggest a weakening of the hydrophobic effect.

Preferential solvation in urea solutions at different concentrations: properties from simulation studies

We performed molecular dynamics simulations of urea solutions at different concentrations with two urea models (OPLS and KBFF) to examine the structures responsible for the thermodynamic solution properties. Our simulation results showed that hydrogen-bonding properties such as the average number of hydrogen bonds and their lifetime distributions were nearly constant at all concentrations between infinite dilution and the solubility limit. This implies that the characterization of urea-water solutions in the molarity concentration scale as nearly ideal is a result of facile local hydrogen bonding rather than a global property. Thus, urea concentration does not influence the local propensity for hydrogen bonds, only how they are satisfied. By comparison, the KBFF model of urea donated fewer hydrogen bonds than OPLS. We found that the KBFF urea model in TIP3P water better reproduced the experimental density and diffusion constant data. Preferential solvation analysis showed that there were weak urea-urea and water-water associations in OPLS solution at short distances, but there were no strong associations. We divided urea molecules into large, medium, and small clusters to examine fluctuation properties and found that any particular urea molecule did not stay in the same cluster for a long time. We found neither persistent nor large clusters.

A Kirkwood-Buff derived force field for the simulation of aqueous guanidinium chloride solutions

A force field for the simulation of aqueous guanidinium chloride solutions is presented. The force field was parametrized to reproduce the experimental density and Kirkwood-Buff integrals as a function of composition. Consequently, a reasonable description of the salt activity is obtained. The model also performs well for other properties such as the relative permittivity and enthalpy of mixing.