The influence of charge ordering in the microscopic structure of monohydroxy alcohols.

While radiation scattering data provides insight inside the microstructure of liquids, the Debye relation relating the scattering intensityI(k) to the atom-atom structure factorsSab(k)shows that, ultimately, it is these individual structure correlation functions which contain the relevant information about the micro-structure. However, these quantities are not observables, except in few cases where one can invert the Debye relation to obtain the structure functions. In the majority of other cases, the need for model dependent computer simulations is unavoidable. The resulting calculations reveal that the scattering pre-peak is the result of cancellations between positive pre-peaks and negative anti-peaks contributions from the atom-atom structure factors. What of systems where this cancellation is such that it entirely suppresses the scattering pre-peak? One would be tempted to falsely conclude that there is no underlying micro-heterogeneity. Hence, the structure functions appear as hidden variables, and it is important to understand the relation between their features and the micro-structure of the system. Through the computer simulation study of various mono-ols, ranging from methanol to 1-nonanol, as well as the branched octanols, we show how the features of the atom-atom pair correlation functiongab(r)affect that of the structure factorsSab(k), and reveal that the micro-structure is ultimately the result of the charge ordering between different atoms in the system.

On the dual behaviour of water in octanol-rich aqueous n-octanol mixtures: an X-ray scattering and computer simulation study.

Aqueous n-octanol (n = 1, 2, 3, and 4) mixtures from the octanol rich side are studied by X-ray scattering and computer simulation, with a focus on structural changes, particularly in what concerns the hydration of the hydroxyl-group aggregated chain-like structures, under the influence of various branching of the alkyl tails. Previous studies have indicated that hydroxyl-group chain-cluster formation is hindered in proportion to the branching number. Here, water mole fractions up to x = 0.2 are examined, i.e. up to the miscibility limit. It is found that water molecules within the hydroxyl-chain domains participate in the chain formations in a different manner for 1-octanol and the branched octanols. The hydration of the octanol hydroxyl chains is confirmed by the shifting of the scattering pre-peak position kPP to smaller values, both from measured and simulated X-ray scattering intensities, which corresponds to an increased size of the clusters. Experimental pre-peak amplitudes are seen to increase with increasing water content for 1-octanol, while this trend is reversed in all branched octanols, with the amplitudes decreasing with the increase of the branching number. Conjecturing that the amplitudes of pre-peaks are related to the density of the corresponding aggregates, these results are interpreted as water breaking large OH hydroxyl chains in 1-octanol, hence increasing the density of aggregates, while enhancing hydroxyl aggregates in branched alcohols by inserting itself into the OH chains. The analysis of the cluster distributions from computer simulations provide more details on the role of water. For cluster sizes smaller than dc = 2π/kPP, water is found to always play the role of a structure enforcer for all n-octanols, while for clusters of size dc water is always a destructor. For cluster sizes larger than dc, the role of water differs from 1-octanol and the branched ones: it acts as a structure maker or breaker in inverse proportion to the hindering of OH hydroxyl chain structures arising from the topology of the alkyl tails (branched or not).

Reply to the 'Comment on "Universal features in the lifetime distribution of clusters in hydrogen-bonding liquids"' by J. Grelska, Phys. Chem. Chem. Phys., 2024, 26, https://doi.org/10.1039/D3CP05269A.

In this reply, we discuss some aspects of the comments in Phys. Chem. Chem. Phys., 2024, 26, https://doi.org/10.1039/D3CP05269A, by Grelska, about our work Phys. Chem. Chem. Phys., 2021, 23, 19537. In this latter work, we have shown for the first time that, at short times below the picosecond range, the uninterrupted hydrogen lifetime probability L(t) is composed of 3 peaks that are universal across many hydrogen bonding systems. By definition, L(t) concerns pairs (dimers) of hydrogen bonded atoms, typically oxygen atoms. The first peak concerns the lifetime of strictly dimers, the second concerns the influence of chain clusters on dimers and the third the influence of their topology. The comment by Grelska contains a confirmation of our findings through similar calculations for other hydrogen bonding liquids. However, this author claims that it is the (first) dimer peak which concerns the topology of clusters, instead of the 3rd as we reported. Our response is that the 3rd peak reflects topology in the sense of branching, hence the presence of trimer bonding in the cluster, while the first peak shows clear species dependence at long times.

Role of Charge Ordering in the Dynamics of Cluster Formation in Associated Liquids.

Liquids are archetypes of disordered systems, yet liquids of polar molecules are locally more ordered than nonpolar molecules, due to the Coulomb interaction based charge ordering phenomenon. Hydrogen bonded liquids, such as water or alcohols, for example, represent a special type of polar liquids, in that they form labile clustered local structures. For water, in particular, hydrogen bonding and the related local tetrahedrality, play an important role in the various attempts to understand this liquid. However, labile structures imply dynamics, and it is not clear how it affects the understanding of this type of liquids from purely static point of view. Herein, we propose to reconsider hydrogen bonding as a charge ordering process. This concept allows us to demonstrate the insufficiency of the analysis of the microscopic structure based solely on static pair correlation functions, and the need for dynamical correlation functions, both in real and reciprocal space. The subsequent analysis allows to recover several aspects of our understanding of hydrogen bonded liquids, but from the charge order perspective. For water, it confirms the jump rotation picture found recently, and it allows to rationalize the contradicting pictures that arise when following the interpretations based on hydrogen bonding. For alcohols, it allows to understand the dynamical origin of the scattering prepeak, which does not exist for water, despite the fact that both these liquids have very similar hydroxyl group chain clusters. The concept of charge ordering complemented by the analysis of dynamical correlation functions appear as a promising way to understand microheterogeneity in complex liquids and mixtures from kinetics point of view.

Lifetime distribution of clusters in binary mixtures involving hydrogen bonding liquids.

Hydrogen bonded liquids are associated liquids and tend to exhibit local inhomogeneity in the form of clusters and segregated sub-nano domains. It is an open question as to whether Hbonded clusters in pure water have common features with the water segregated pockets observed in various aqueous binary mixtures, such as water-alcohol mixtures, for example. In the present study, we demonstrate through classical molecular dynamics studies of the lifetime distributions of the hydrogen bonds in different types of binary mixtures, that these lifetimes exhibit the same universal features in the case of the pure liquids, independently of the species concentrations. The same types of three distinct lifetimes are observed, all of them in the sub picosecond regime. The primary lifetime concerns that of Hbonded dimers, and strongly depends on Hbonding criteria such as the bonding distance. The two others are independent of bonding criteria and appear as universal accross many liquids and mixtures. The secondary lifetime ([Formula: see text] fs) concerns Hbonded cluster lifetimes, while the tertiary lifetime ([Formula: see text] fs) concerns the topology of these clusters, such as chains or globules, for example. This surprizing separation in three distinct lifetimes suggests the existence of associated three distinct kinetic mechanisms in the very short sub-picosecond time scales, with, in addition, an appealing connection to the concepts of local energy and entropy.

Camel back shaped Kirkwood-Buff integrals.

Some binary mixtures, such as specific alcohol-alkane mixtures or even water-tbutanol, exhibit two humps "camel back" shaped Kirkwood-Buff integrals (KBIs). This is in sharp contrast with the usual KBIs of binary mixtures having a single extremum. This extremum is interpreted as the region of maximum concentration fluctuations, usually occurs in binary mixtures presenting appreciable micro-segregation, and corresponds to where the mixture exhibits a percolation of the two species domains. In this paper, it is shown that two extrema occur in binary mixtures when one species forms "meta-particle" aggregates, the latter acts as a meta-species, and they have their own concentration fluctuations, hence their own KBI extremum. This "meta-extremum" occurs at a low concentration of the aggregate-forming species (such as alcohol in alkane) and is independent of the other usual extremum observed at mid-volume fraction occupancy. These systems are a good illustration of the concept of the duality between concentration fluctuations and micro-segregation.

Isomeric effects in structure formation and dielectric dynamics of different octanols.

The understanding of the microstructure of associated liquids promoted by hydrogen-bonding and constrained by steric hindrance is highly relevant in chemistry, physics, biology and for many aspects of daily life. In this study we use a combination of X-ray diffraction, dielectric spectroscopy and molecular dynamics simulations to reveal temperature induced changes in the microstructure of different octanol isomers, i.e., linear 1-octanol and branched 2-, 3- and 4-octanol. In all octanols, the hydroxyl groups form the basis of chain-, cyclic- or loop-like bonded structures that are separated by outwardly directed alkyl chains. This clustering is analyzed through the scattering pre-peaks observed from X-ray scattering and simulations. The charge ordering which pilots OH aggregation can be linked to the strength of the Debye process observed in dielectric spectroscopy. Interestingly, all methods used here converge to the same interpretation: as one moves from 1-octanol to the branched octanols, the cluster structure evolves from loose large aggregates to a larger number of smaller, tighter aggregates. All alcohols exhibit a peculiar temperature dependence of both the pre-peak and Debye process, which can be understood as a change in microstructure promoted by chain association with increased chain length possibly assisted by ring-opening effects. All these results tend to support the intuitive picture of the entropic constraint provided by branching through the alkyl tails and highlight its capital entropic role in supramolecular assembly.

Universal features in the lifetime distribution of clusters in hydrogen-bonding liquids.

Hydrogen-bonding liquids, typically water and alcohols, are known to form labile structures (network, chains, etc.); hence, the lifetime of these structures is an important microscopic parameter, which can be calculated via computer simulations. Since these cluster entities are mostly statistical in nature, one would expect that, in the short-timescale regime, their lifetime distribution would be a broad Gaussian-like function of time, with a single maximum representing their mean lifetime, and be weakly dependent on criteria such as the bonding distance and angle, much similar to non-hydrogen-bonding simple liquids, while the long-timescale regime is known to have some power law dependence. Unexpectedly, all the hydrogen-bonding liquids studied herein, namely water and alcohols, display three highly hierarchical specific lifetimes, in the sub-picosecond range 0-0.5 ps. The dominant lifetime depends very strongly on the bonding-distance criterion and is related to hydrogen-bonded pairs. This mode is absent in non-H-bonding simple liquids. The secondary and tertiary mean lifetimes are related to clusters and are nearly independent of the bonding criterion. Of these two lifetimes, only the first one can be related to that of simple liquids, which poses the question of the nature of the third lifetime. The study of alcohols reveals that this third lifetime is related to the topology of the H-bonded clusters and that its distribution may also be affected by the alkyl tail surrounding the "bath". This study shows that hydrogen-bonding liquids have a universal hierarchy of hydrogen-bonding lifetimes with a timescale regularity across very different types, and which depend on the topology of the cluster structures.

Why Should Metformin Not Be Given in Advanced Kidney Disease? Potential Leads from Computer Simulations.

Metformin is considered as the go-to drug in the treatment of diabetes. However, it is either prescribed in lower doses or not prescribed at all to patients with kidney problems. To find a potential explanation for this practice, we employed atomistic-level computer simulations to simulate the transport of metformin through multidrug and toxin extrusion 1 (MATE1), a protein known to play a key role in the expulsion of metformin into urine. Herein, we examine the hydrogen bonding between MATE1 and one or more metformin molecules. The simulation results indicate that metformin continuously forms and breaks off hydrogen bonds with MATE1 residues. However, the mean hydrogen bond lifetimes increase for an order of magnitude when three metformin molecules are inserted instead of one. This new insight into the metformin transport process may provide the molecular foundation behind the clinical practice of not prescribing metformin to kidney disease patients.

Comparative analysis of ethanol dynamics in aqueous and non-aqueous solutions.

In this study, we compare the results for vibrational, reorientational and hydrogen bond dynamics of ethanol in water and in hexane across the whole concentration range. Water and hexane are both commonly used as solvents, but so far, it has been unclear to what extent they modify the solute dynamics. Ethanol is chosen as the solute because it is an aliphatic molecule that is miscibile with both solvents. It is known that ethanol forms micelle-like domains in water and cyclic clusters resembling loops in hexane. This structural micro-heterogeneity is well known both in experiments and in simulations. The main question we raise here is: is there a signature of micro-heterogeneity in the dynamical quantities of ethanol? We focus on quantities such as the vibrational spectra, the reorientational correlation functions, the self-diffusion coefficients, the ethanol-ethanol hydrogen bond correlation functions and the corresponding hydrogen bond histograms. For the first time ever, we compute the van Hove functions to reveal the dynamical variations of spatial correlations in these systems. All these results complement each other and provide a unifying dynamical description of ethanol in binary mixtures.

On the X-ray Scattering Pre-peak of Linear Mono-ols and the Related Microstructure from Computer Simulations.

The X-ray scattering intensities (I(k)) of linear alkanols OH(CH2)n-1CH3 obtained from experiments (methanol to 1-undecanol) and computer simulations (methanol to 1-nonanol) of different force field models are comparatively studied particularly in order to explain the origin and the properties of the scattering pre-peak in the k-vector range 0.3-1 Å-1. The experimental I(k) values show two apparent features: the pre-peak position kP decreases with increasing n, and more intriguingly, the amplitude AP goes through a maximum at 1-butanol (n = 4). The first feature is well reproduced by all force-field models, while the second shows strong model dependence. The simulations reveal various shapes of clusters of the hydroxyl head-group from n>2. kP is directly related to the size of the meta-objects corresponding to such clusters surrounded by their alkyl tails. The explanation of the AP turnover at n = 4 is more involved in terms of cancellations of atom-atom structure factor S(k) contributions related to domain ordering. The flexibility of the alkyl tails tends to reduce the cross contributions, thus revealing the crucial importance of this parameter in the models. Force fields with all-atom representation are less successful in reproducing the pre-peak features for smaller alkanols, n<6, possibly because they blur the charge ordering process since all atoms bear partial charges. The analysis clearly shows that it is not possible to obtain a model-free explanation of the features of I(k).

Thermodynamic, structural and dynamic properties of selected non-associative neat liquids.

Non-associative neat liquids benzene, acetone and carbon tetrachloride have been examined via molecular dynamics simulations. Several models of each neat liquid have been simulated, and selected thermodynamic and structural results are presented. However, the models have been compared mainly in terms of their dynamic quantities. Since models are rarely parametrized with the dynamic properties in mind, the principal goal of this work is to present quantities such as the power spectra, rotational correlation functions and relaxation times, diffusion coefficients and self and distinct parts of the van Hove functions in relation to available experimental data. The general trends of the calculated data provide a benchmark for the behavior of neat simple liquids which will be built upon in the cases of mixtures with associative liquids.

Microscopic origin of the scattering pre-peak in aqueous propylamine mixtures: X-ray and neutron experiments versus simulations.

The structure of aqueous propylamine mixtures is investigated through X-ray and neutron scattering experiments, and the scattered intensities compared with computer simulation data. Both sets of data show a prominent scattering pre-peak, which first appears at propylamine mole fraction x ≥ 0.1 around scattering vector k ≈ 0.2 Å-1, and evolves towards k ≈ 0.8 Å-1 for neat propylamine x = 1. The existence of a scattering pre-peak in this mixture is unexpected, specifically in view of its absence in aqueous 1-propanol or aqueous DMSO mixtures. The detailed analysis of the various atom-atom structure factors and snapshots indicates that significant micro-structures exist, which produces correlation pre-peaks in the atom-atom structure factors, positive for like species atom correlations and negative for cross species correlations. The scattering pre-peak depends on how these two contributions cancel out or not. The way the amine group bonds with water produces a pre-peak through an imbalance of the positive and negative scattering contributions, unlike 1-propanol and DMSO, where these 2 contributions compensate exactly. Hence molecular simulations demonstrate how chemical details influence the microscopic segregation in different types of molecular emulsions and can be detected or not by scattering experiments.

A Simple Two Dimensional Model of Methanol.

Methanol is the simplest alcohol and possible energy carrier because it is easier to store than hydrogen and burns cleaner than fossil fuels. It is a colorless liquid, completely miscible with water and organic solvents and is very hygroscopic. Here, simple two-dimensional models of methanol, based on Mercedes-Benz (MB) model of water, are examined by Monte Carlo simulations. Methanol particles are modeled as dimers formed by an apolar Lennard-Jones disk, mimicking the methyl group, and a sphere with two hydrogen bonding arms for the hydroxyl group. The used models are the one proposed by Hribar-Lee and Dill (Acta Chimica Slovenica, 53:257, 2006.) with the overlapping discs and a new model with tangentially fused dimers. The comparison was done between the models, in connection to the MB water, as well as with experimental results and with new simulations done for 3D models of methanol. Both 2D models show similar trends in structuring and thermodynamics. The difference is the most pronounced at lower temperatures, where the smaller model exhibits spontaneous crystallization, while the larger model shows metastable states. The 2D structural organization represents well the clustering tendency observed in 3D models, as well as in experiments. The models qualitatively agree with the bulk methanol thermodynamic properties like density and isothermal compressibility, however, heat capacity at the constant pressure shows trend more similar to the water behavior. This work on the smallest amphiphilic organic solute provides a simple testing ground to study the competition between polar and non-polar effects within the molecule and physical properties.

Lifshitz phase: the microscopic structure of aqueous and ethanol mixtures of 1,n-diols.

We study binary mixtures of ethylene glycol and 1,3-propandiol with water or ethanol using computer simulations. Despite strong hydrogen bonding tendencies between all these molecules, we find that these mixtures are surprisingly homogeneous, in contrast to the strong micro-heterogeneity found in aqueous ethanol mixtures. The aqueous diol mixtures are found to be close to ideal mixtures, with near-ideal Kirkwood-Buff integrals. Ethanol-diol mixtures show weak non-ideality. The origin of this unexpected randomness is due to the fact that the two hydrogen bonding hydroxyl groups of the 1,n-diol are bound by the neutral alkyl bond, which prevents the micro-segregation of the different types of hydroxyl groups. These findings suggest that random disorder can arise in the presence of strong interactions - in contrast to the usual picture of random disorder due to weak interactions between the components. They point to the important role of molecular topology in tuning concentration fluctuations in complex liquids. We propose and justify herein the name of Lifshitz phases to designate such types of disordered systems.

The microscopic structure of cold aqueous methanol mixtures.

The evolution of the micro-segregated structure of aqueous methanol mixtures, in the temperature range 300 K-120 K, is studied with computer simulations, from the static structural point of view. The structural heterogeneity of water is reinforced at lower temperatures, as witnessed by a pre-peak in the oxygen-oxygen structure factor. Water tends to form predominantly chain-like clusters at lower temperatures and smaller concentrations. Methanol domains have essentially the same chain-like cluster structure as the pure liquid at high concentrations and becomes monomeric at smaller ones. Concentration fluctuations decrease with temperature, leading to quasi-ideal Kirkwood-Buff integrals, despite the enhanced molecular interactions, which we interpret as the signature of non-interacting segregated water and methanol clusters. This study throws a new light on the nature of the micro-heterogeneous structure of this mixture: the domain segregation is essentially based on the appearance of linear water clusters, unlike other alcohol aqueous mixtures, such as with propanol or butanol, where the water domains are more bulky.

Micro-heterogeneity versus clustering in binary mixtures of ethanol with water or alkanes.

Ethanol is a hydrogen bonding liquid. When mixed in small concentrations with water or alkanes, it forms aggregate structures reminiscent of, respectively, the direct and inverse micellar aggregates found in emulsions, albeit at much smaller sizes. At higher concentrations, micro-heterogeneous mixing with segregated domains is found. We examine how different statistical methods, namely correlation function analysis, structure factor analysis and cluster distribution analysis, can describe efficiently these morphological changes in these mixtures. In particular, we explain how the neat alcohol pre-peak of the structure factor evolves into the domain pre-peak under mixing conditions, and how this evolution differs whether the co-solvent is water or alkane. This study clearly establishes the heuristic superiority of the correlation function/structure factor analysis to study the micro-heterogeneity, since cluster distribution analysis is insensitive to domain segregation. Correlation functions detect the domains, with a clear structure factor pre-peak signature, while the cluster techniques detect the cluster hierarchy within domains. The main conclusion is that, in micro-segregated mixtures, the domain structure is a more fundamental statistical entity than the underlying cluster structures. These findings could help better understand comparatively the radiation scattering experiments, which are sensitive to domains, versus the spectroscopy-NMR experiments, which are sensitive to clusters.

Simple and complex disorder in binary mixtures with benzene as a common solvent.

Substituting benzene for water in computer simulations of binary mixtures allows one to study the various forms of disorder, without the complications often encountered in aqueous mixtures. In particular, we study the relationship between the local order generated by different types of molecular interactions and the nature of the global disorder, by analyzing the relationship between the concentration fluctuations and the correlation functions and the associated structure factors. Alkane-benzene mixtures are very close to ideal mixtures, despite appreciable short range shape mismatch interactions, acetone-benzene mixtures appear as a good example of regular mixtures, and ethanol-benzene mixtures show large micro-segregation. In the latter case, we can unambiguously demonstrate, unlike in the case of water, the appearance of domain-domain correlations, both in the correlation functions and the structure factor calculated in computer simulations. This finding helps to confirm the existence of a pre-peak in the structure factor associated with the micro-heterogeneity, which was speculated from several of our previous simulations of aqueous-alcohol mixtures. The fact that benzene as a solvent allows us to solve some of the problems that could not be solved with water points towards some of the particularities of water as a solvent, which we discuss herein. The concept of molecular emulsion put forward in our earlier work is useful in formulating these differences between water and benzene through the analogy with direct and inverse micellar aggregates.