The hydrophobic effect: is water afraid, or just not that interested?

Macromolecular crowding effects on protein dynamics

Macromolecular crowding experiments bridge the gap between in-vivo and in-vitro studies by mimicking some of the cellular complexities like high viscosity and limited space, while still manageable for experiments and analysis. Macromolecular crowding impacts all biological processes and is a focus of contemporary research. Recent reviews have highlighted the effect of crowding on various protein properties. One of the essential characteristics of protein is its dynamic nature; however, how protein dynamics get modulated in the crowded milieu has been largely ignored. This article discusses how protein translational, rotational, conformational, and solvation dynamics change under crowded conditions, summarizing key observations in the literature. We emphasize our research on microsecond conformational and water dynamics in crowded milieus and their impact on enzymatic activity and stability. Lastly, we provided our outlook on how this field might move forward in the future.

A van der Waals Model of Solvation Thermodynamics

Exploiting the van der Waals model of liquids, it is possible to derive analytical formulas for the thermodynamic functions governing solvation, the transfer of a solute molecule from a fixed position in the ideal gas phase to a fixed position in the liquid phase. The solvation Gibbs free energy change consists of two contributions: (a) the high number density of all liquids and the repulsive interactions due to the basic fact that each molecule has its own body leading to the need to spend free energy to produce an appropriate cavity to contain the solute molecule; (b) the ubiquitous intermolecular attractive interactions lead to a gain in free energy for switching-on attractions between the solute molecule and neighboring liquid molecules. Also the solvation entropy change consists of two contributions: (a) there is an entropy loss in all liquids because the cavity presence limits the space accessible to liquid molecules during their continuous translations; (b) there is an entropy gain in all liquids, at room temperature, due to the liquid structural reorganization as a response to the perturbation represented by solute addition. The latter entropy contribution is balanced by a corresponding enthalpy term. The scenario that emerged from the van der Waals model is in qualitative agreement with experimental results.

Structural Order in the Hydration Shell of Nonpolar Groups versus that in Bulk Water

The poor solubility of nonpolar compounds in water around room temperature is governed by a large and negative entropy change, whose molecular cause is still debated. Since the Frank and Evans original proposal in 1945, the large and negative entropy change is usually attributed to the formation of ordered structures in the hydration shell of nonpolar groups. However, the existence of such ordered structures has never been proven. The present study is aimed at providing available structural results and thermodynamic arguments disproving the existence of ordered structures in the hydration shell of nonpolar groups.

Molecular-Scale Liquid Density Fluctuations and Cavity Thermodynamics

Equilibrium density fluctuations at the molecular level produce cavities in a liquid and can be analyzed to shed light on the statistics of the number of molecules occupying observation volumes of increasing radius. An information theory approach led to the conclusion that these probabilities should follow a Gaussian distribution. Computer simulations confirmed this prediction across various liquid models if the size of the observation volume is not large. The reversible work required to create a cavity and the chance of finding no molecules in a fixed observation volume are directly correlated. The Gaussian formula for the latter probability is scrutinized to derive the changes in enthalpy and entropy, which arise from the cavity creation. The reversible work of cavity creation has a purely entropic origin as a consequence of the solvent-excluded volume effect produced by the inaccessibility of a region of the configurational space. The consequent structural reorganization leads to a perfect compensation of enthalpy and entropy changes. Such results are coherent with those obtained from Lee in his direct statistical mechanical study.

The temperature-dependence of host-guest binding thermodynamics: experimental and simulation studies

The thermodynamic parameters of host-guest binding can be used to describe, understand, and predict molecular recognition events in aqueous systems. However, interpreting binding thermodynamics remains challenging, even for these relatively simple molecules, as they are determined by both direct and solvent-mediated host-guest interactions. In this contribution, we focus on the contributions of water to binding by studying binding thermodynamics, both experimentally and computationally, for a series of nearly rigid, electrically neutral host-guest systems and report the temperature-dependent thermodynamic binding contributions ΔGb(T), ΔHb(T), ΔSb(T), and ΔCp,b. Combining isothermal titration calorimetry (ITC) measurements with molecular dynamics (MD) simulations, we provide insight into the binding forces at play for the macrocyclic hosts cucurbit[n]uril (CBn, n = 7-8) and β-cyclodextrin (β-CD) with a range of guest molecules. We find consistently negative changes in heat capacity on binding (ΔCp,b) for all systems studied herein - as well as for literature host-guest systems - indicating increased enthalpic driving forces for binding at higher temperatures. We ascribe these trends to solvation effects, as the solvent properties of water deteriorate as temperature rises. Unlike the entropic and enthalpic contributions to binding, with their differing signs and magnitudes for the classical and non-classical hydrophobic effect, heat capacity changes appear to be a unifying and more general feature of host-guest complex formation in water. This work has implications for understanding protein-ligand interactions and other complex systems in aqueous environments.

Computation of entropy values for non-electrolyte solute molecules in solution based on semi-empirical corrections to a polarized continuum model

A simple heuristic model was developed for estimating the entropy of a solute molecule in an ideal solution based on quantum mechanical calculations with polarizable continuum models (QM/PCMs). A translational term was incorporated that included free-volume compensation for the Sackur-Tetrode equation and a rotational term was modeled based on the restricted rotation of a dipole in an electrostatic field. The configuration term for the solute at a given concentration was calculated using a simple lattice model that considered the number of configurations of the solute within the lattice. The configurational entropy was ascertained from this number based on Boltzmann's principle. Standard entropy values were determined for 41 combinations of solutes and solvents at a set concentration of 1 mol dm^-3 using the proposed model, and the computational values were compared with experimental data. QM/PCM calculations were conducted at the ωB97X-D/6-311++G(d,p)/IEF-PCM level using universal force field van der Waals radii scaled by 1.2. The proposed model accurately reproduced the entropy values reported for solutes in non-aqueous solvents within a mean absolute deviation of 9.2 J mol^-1 K^-1 for 33 solutions. This performance represents a considerable improvement relative to that obtained using the method based on the ideal gas treatment that is widely utilized in commercially available computation packages. In contrast, computations for aqueous molecules overestimated the entropies because hydrophobic effects that decrease the entropy of aqueous solutions were not included in the present model.

Benefits of electrochemistry studies for the majority of students who will not become electrochemists

In teaching electrochemistry, it is of primary importance to make students always aware of the relations between electrochemistry and all the non-electrochemical topics, which are taught. The vast majority of students will not specialise in electrochemistry, but they all can very much benefit from the basics and concepts of electrochemistry. This paper is aimed to give suggestions how the teaching of electrochemistry can easily be interrelated to topics of inorganic, organic, analytical, environmental chemistry, biochemistry and biotechnology.

Anti-Alopecia Activity of Alkaloids Group from Noni Fruit against Dihydrotestosterone-Induced Male Rabbits and Its Molecular Mechanism: In Vivo and In Silico Studies

Androgenic alopecia (AA) is a condition that most commonly affects adult men and is caused by an increase in the hormone dihydrotestosterone (DHT) in the hair follicles. Anti-alopecia drugs should be discovered for hair follicles to enter the anagen growth phase. Therefore, this study evaluated the hair growth-promoting activity of Noni fruit’s water, ethyl acetate, n-hexane fractions, and sub-fractions from the active fraction in the alopecia male white rabbit model. The Matias method was modified by inducing rabbits using DHT for 17 days, followed by topical application of Noni fruit solution for 21 days. Meanwhile, hair growth was evaluated by histological observation of the follicular density and the anagen/telogen (A/T) ratio in skin tissue. In the first stage, five groups of male white rabbits were studied to obtain the active fraction; DHT+Minoxidil as standard, DHT+vehicle (NaCMC 1%), DHT+FW, DHT+FEA, and DHT+FH. The FEA as the active fraction was followed by open-column chromatography separation (DCM:Methanol) with a gradient of 10% to produce sub-fractions. In the second stage, the six main sub-fraction groups of male rabbits studied were DHT+FEA-1 to DHT+FEA-6. The follicular density of groups FEA-3 was 78.00 ± 1.52 compared with 31.55 ± 1.64 and 80.12 ± 1.02 in the Vehicle and Minoxidil groups. Additionally, group FEA-3 showed large numbers of anagen follicles with an A/T ratio of 1.64/1 compared to the vehicle group of 1/1.50 and 1.39/1 for Minoxidil control. Group FEA-3 was identified by LC-MS/MS-QTOF, followed by molecular docking to the androgen receptor (PDB: 4K7A), causing alopecia. The results showed that three alkaloid compounds with skeleton piperazine and piperidine, namely (compounds 2 (−4.99 Kcal/mol), 3 (−4.60 Kcal/mol), and 4 (−4.57 Kcal/mol)) had a binding affinity similar to Minoxidil, with also has alkaloid skeleton piperidine−pyrimidine (−4.83 Kcal/mol). The dynamic behavior showed the stability of all androgen receptor compounds with good RMSD, SMSF, and SASA values after being studied with 100 ns molecular dynamics (MD) simulations. This study produced a common thread in discovering a class of alkaloid compounds as inhibitors of androgen receptors that cause alopecia.

The epigenetic dimension of protein structure

Accurate prediction of protein structure is one of the most challenging goals of biology. The most recent achievement is AlphaFold, a machine learning method that has claimed to have solved the structure of almost all human proteins. This technological breakthrough has been compared to the sequencing of the human genome. However, this triumphal statement should be treated with caution, as we identified serious flaws in some AlphaFold models. Disordered regions are often represented by large loops that clash with the overall protein geometry, leading to unrealistic structures, especially for membrane proteins. In fact, AlphaFold comes up against the notion that protein folding is not solely determined by genomic information. We suggest that all parameters controlling the structure of a protein without being strictly encoded in its amino acid sequence should be coined "epigenetic dimension of protein structure." Such parameters include for instance protein solvation by membrane lipids, or the structuration of disordered proteins upon ligand binding, but exclude sequence-encoded sites of post-translational modifications such as glycosylation. In our view, this paradigm is necessary to reconcile two opposite properties of living systems: beyond rigorous biological coding, evolution has given way to a certain level of uncertainty and anarchy.

Solutions, in Particular Dilute Solutions of Nonelectrolytes: A Review

The liquid state is one of the three principal states of matter and arguably the most important one; and liquid mixtures represent a large research field of profound theoretical and practical interest. This topic is of importance in many areas of the applied sciences, such as in chemical engineering, geochemistry, the environmental sciences, biophysics and biomedical technology. First, I will concisely present a review of important concepts from classical thermodynamics of nonelectrolyte solutions; this will be followed by a survey of (semi-)empirical approaches to representing the composition and temperature dependence of selected thermodynamic mixture properties, and finally the focus will be on dilute binary nonelectrolyte solutions where one component, a supercritical solute, is present in much smaller quantity than the other component, called the solvent. Partial molar properties in the limit of infinite dilution (indicated by a superscript ∞) are of particular interest. For instance, activity coefficients (Lewis–Randall (LR) convention) are customarily used to characterize mixing behavior, and infinite-dilution values $$\gamma_{i}^{{{\text{LR,}}\infty }}$$ γ i LR, ∞ provide a convenient route for obtaining binary parameters for several popular solution models. When discussing solute (j)—solvent (i) interactions in solutions where the solute is supercritical, the Henry fugacity $$h_{j,i} \left( {T,P} \right)$$ h j , i T , P , also known as Henry’s law (HL) constant, is a measurable thermodynamic key quantity. Its temperature dependence yields information on the partial molar enthalpy change on solution $$\Delta H_{j}^{\infty } \left( {T,P} \right)$$ Δ H j ∞ T , P , while its pressure dependence yields information on the partial molar volume $$V_{j}^{{{\text{L,}}\infty }} \left( {T,P} \right)$$ V j L, ∞ T , P of solute j in the liquid phase (superscript L). I will clarify issues frequently overlooked, touch upon solubility data reduction and correlation, report a few recent high-precision experimental results on dilute aqueous solutions of supercritical nonelectrolytes, and show the equivalency of results for caloric quantities (e.g. $$\Delta H_{j}^{\infty }$$ Δ H j ∞ ) obtained via van ’t Hoff analysis of high-precision solubility data with directly measured calorimetric data.

On the size, shape and energetics of the hydration shell around alkanes

A large number of clathrate-like cages have been proposed as the very first hydration shell of alkanes. The cages include canonical structures commonly found in clathrate hydrates and many others, not previously reported, derived from the carbon fullerene cavities. These structures have a rich and variegated form, which can adapt to the shape and conformation of the solute. They avoid "wasting" hydrogen bonds, while minimizing the volume cage and maximizing the solute-solvent van der Waals interactions. DFT/M06-2X and MP2 ab initio calculations give comparable structural and energetic results although the latter predicts slightly larger cages for a given solute. It is shown that the van der Waals interactions are substantial and the large exoenergetic values found for isobutane and cyclopentane provide an explanation for the surprising high melting points of related hydrates at room pressure. The encaging enthalpy for various hydrocarbons is similar to the enthalpy of solution measured at a temperature just above the melting point of aqueous hydrocarbon solutions, thus indicating that water molecules should not deviate too much from the configuration with O-H bonds tangentially oriented with respect to the solute surface. The computed trend differs from the enthalpy of solution measured at room temperature, thus the very first hydration shell departs, up to a certain degree, from the clathrate-like structures.