Kirkwood–Buff Integrals for Aqueous Urea Solutions Based upon the Quantum Chemical Electrostatic Potential and Interaction Energies

Does Urea Preferentially Interact with Amide Moieties or Nonpolar Sidechains? A Question Answered Through a Judicious Selection of Model Systems

The transfer model suggests that urea unfolds proteins mainly by increasing the solubility of the amide backbone, probably through urea-induced increase in hydrogen bonding. Other studies suggest that urea addition increases the magnitude of solvent-solute van der Waals interactions, which increases the solubility of nonpolar sidechains. More recent analyses hypothesize that urea has a similar effect in increasing the solubility of backbone and sidechain groups. In this work, we compare the effects of urea addition on the solvation of amides and alkyl groups. At first, we study the effects of urea addition upon solvent hydrogen bonding acidity and basicity through the perturbation in the fluorescence spectrum of probes 1-AN and 1-DMAN. Our results demonstrate that the solvent's hydrogen bonding properties are minimally affected by urea addition. Subsequently, we show that urea addition does not perturb the intra-molecular hydrogen bonding in salicylic acid significantly. Finally, we investigate how urea preferentially interacts with amide and alkyl groups moieties in water by comparing the effects of urea addition upon the solubility of acetaminophen and 4-tertbutylphenol. We show that urea affects amide and t-butyl solubility (lowers the transfer free energy of both amide (backbone) and alkyl (sidechain) groups) in a similar fashion. In other words, preferential interaction of urea with both moieties contributes to protein denaturation.

Solvation shell thermodynamics of extended hydrophobic solutes in mixed solvents

The ability of various cosolutes and cosolvents to enhance or quench solvent density fluctuations at solute–water interfaces has crucial implications on the conformational equilibrium of macromolecules such as polymers and proteins. Herein, we use an extended hydrophobic solute as a model system to study the effect of urea and methanol on the density fluctuations in the solute’s solvation shell and the resulting thermodynamics. On strengthening the solute–water/cosolute repulsive interaction, we observe distinct trends in the mutual affinities between various species in, and the thermodynamic properties of, the solvation shell. These trends strongly follow the respective trends in the preferential adsorption of urea and methanol: solute–water/cosolute repulsion strengthens, urea accumulation decreases, and methanol accumulation increases. Preferential accumulation of urea is found to quench the density fluctuations around the extended solute, leading to a decrease in the compressibility of the solvation shell. In contrast, methanol accumulation enhances the density fluctuations, leading to an increase in the compressibility. The mode of action of urea and methanol seems to be strongly coupled to their hydration behavior. The observations from this simple model is discussed in relation to urea driven swelling and methanol induced collapse of some well-known thermo-responsive polymers.

Mass effects for thermodiffusion in dilute aqueous solutions

Thermodiffusion is the phenomenon by which molecules in a mixture present concentration gradients in response to an imposed temperature gradient. Despite decades of investigations, this effect remains poorly understood at a molecular level. A common, phenomenological approach is to individuate the molecular factors that influence the Soret coefficient, the parameter that quantifies the resulting concentration-gradient. Experimental studies, often performed on organic mixtures, as well as simulations of model particle systems have evidenced that the difference in masses between the mixture components has an important effect on the amplitude of the Soret coefficient. Here, we use molecular dynamics simulations of a thermophoretic setting to investigate the mass dependence of the Soret coefficient in dilute aqueous solutions. An advantage of simulation approaches is that they are not limited in the range of explored molecular masses, which is often limited to isotopic substitutions in the experiments. Our simulations reveal that the mass dependence of the Soret coefficient in these solutions is in agreement with previous experimental and simulation work on molecular-size systems. In particular, it is sensitive to the relative mass difference between the solute and the solvent, but not to their absolute mass. Adjusting the mass of the solvent and of the solute can turn a thermophobic solution into a thermophilic one, where solute accumulation is reversed. This demonstrates that the mass effect can indeed compensate for the other contributions to the Soret coefficient. Finally, we find that changing the molecular moments of inertia has a much more limited impact as compared to a change in the total molecular mass.

In silico all-atom approach to thermodiffusion in dilute aqueous solutions

Thermodiffusion (or thermophoresis) is the phenomenon by which the spatial distributions of constituents of liquid or gas phases become inhomogeneous in response to a temperature gradient. It has been evidenced in a variety of systems and has many practical applications as well as implications in the context of the origins of life. A complete molecular picture of thermophoresis is still missing, and phenomenological approaches are often employed to account for the experimental observations. In particular, the amplitude of the resulting concentration-gradients (quantified by the Soret coefficient) depends on many factors that are not straightforwardly rationalized. All-atom molecular dynamics simulations appear as an exquisite tool to shed light on the molecular origins for this phenomenon in molecular systems, but the practical implementation of thermophoretic settings in silico poses significant challenges. Here, we propose a robust approach to tackle thermophoresis in dilute realistic solutions at the molecular level. We rely on a recent enhanced heat-exchange algorithm to generate temperature-gradients. We carefully assess the convergence of thermophoretic simulations in dilute aqueous solutions. We show that simulations typically need to be propagated on long timescales (hundreds of nanoseconds). We find that the magnitude of the temperature gradient and the box sizes have little effect on the measured Soret coefficients. Practical guidelines are derived from such observations. Provided with this reliable setup, we discuss the results of thermophoretic simulations on several examples of molecular, neutral solutes, which we find in very good agreement with experimental measurements regarding the concentration-, mass-, and temperature-dependence of the Soret coefficient.

Force-field parametrization based on radial and energy distribution functions

We propose a novel force‐field‐parametrization procedure that fits the parameters of potential functions in a manner that the pair distribution function (DF) of molecules derived from candidate parameters can reproduce the given target DF. Conventionally, approaches to minimize the difference between the candidate and target DFs employ radial DFs (RDF). RDF itself has been reported to be insufficient for uniquely identifying the parameters of a molecule. To overcome the weakness, we introduce energy DF (EDF) as a target DF, which describes the distribution of the pairwise energy of molecules. We found that the EDF responds more sensitively to a small perturbation in the pairwise potential parameters and provides better fitting accuracy compared to that of RDF. These findings provide valuable insights into a wide range of coarse graining methods, which determine parameters using information obtained from a higher‐level calculation than that of the developed force field. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.

Energetic, Structural and Dynamic Properties of Nucleobase-Urea Interactions that Aid in Urea Assisted RNA Unfolding

Understanding the structure-function relationships of RNA has become increasingly important given the realization of its functional role in various cellular processes. Chemical denaturation of RNA by urea has been shown to be beneficial in investigating RNA stability and folding. Elucidation of the mechanism of unfolding of RNA by urea is important for understanding the folding pathways. In addition to studying denaturation of RNA in aqueous urea, it is important to understand the nature and strength of interactions of the building blocks of RNA. In this study, a systematic examination of the structural features and energetic factors involving interactions between nucleobases and urea is presented. Results from molecular dynamics (MD) simulations on each of the five DNA/RNA bases in water and eight different concentrations of aqueous urea, and free energy calculations using the thermodynamic integration method are presented. The interaction energies between all the nucleobases with the solvent environment and the transfer free energies become more favorable with respect to increase in the concentration of urea. Preferential interactions of urea versus water molecules with all model systems determined using Kirkwood-Buff integrals and two-domain models indicate preference of urea by nucleobases in comparison to water. The modes of interaction between urea and the nucleobases were analyzed in detail. In addition to the previously identified hydrogen bonding and stacking interactions between urea and nucleobases that stabilize the unfolded states of RNA in aqueous solution, NH-π interactions are proposed to be important. Dynamic properties of each of these three modes of interactions have been presented. The study provides fundamental insights into the nature of interaction of urea molecules with nucleobases and how it disrupts nucleic acids.

Size and shape dependence of finite-volume Kirkwood-Buff integrals

Analytic relations are derived for finite-volume integrals over the pair correlation function of a fluid, the so-called Kirkwood-Buff integrals. Closed-form expressions are obtained for cubes and cuboids, the system shapes commonly employed in molecular simulations. When finite-volume Kirkwood-Buff integrals are expanded over an inverse system size, the leading term depends on shape only through the surface area-to-volume ratio. This conjecture is proved for arbitrary shapes and a general expression for the leading term is derived. From this, an extrapolation to the infinite-volume limit is proposed, which converges much faster with system size than previous approximations and thus significantly simplifies the numerical computations.