Search Results (57)

This article summarizes a series of seventeen publications by the authors devoted to molecular dynamics modeling of various indicator dyes (molecular probes) enclosed in surfactant micelles. These dyes serve as generally recognized tools for studying various types of organized solutions, among which surfactant micelles in water are the simplest and most explored. The modeling procedure involves altogether 50 to 95 surfactant molecules, 16 to 28 thousand water molecules, and a single dye molecule. The presentation of the simulation results was preceded by a brief review of the state of experimental studies. This article consists of three parts. First, despite numerous literature data devoted to modeling the micelles itself, we decided to revisit this issue. The structure and hydration of the surface of micelles of surfactants, first of all of sodium n-dodecylsulfate, SDS, and cetyltrimethylammonium bromide, CTAB, were studied. The values of the electrical potential, Ψ, were estimated as functions of the ionic strength and distance from the surface. The decrease in the Ψ value with distance is gradual. Attempts to consider both DS⁻ and CTA⁺ micelles in water without counterions result in a decay into two smaller aggregates. Obviously, the hydrophobic interaction (association) of the hydrocarbon tails balances the repulsion of the charged headgroups of these small “bare” micelles. The second part is devoted to the study of seven pyridinium N-phenolates, known as Reichardt’s dyes, in ionic micelles. These most powerful solvatochromic indicators are now used for examining various colloidal systems. The localization and orientation of both zwitterionic and (colorless) cationic forms are generally consistent with intuitive ideas about the hydrophobicity of substituents. Hydration has been quantitatively described for both the dye molecule as a whole and the oxygen atom. A number of markers, including the visible absorption spectra of Reichardt’s dyes, enable assuming a better hydration of the micellar surface of SDS than that of CTAB. However, our data show that it is more correct to speak about the more pronounced hydrogen-bonding ability of water molecules in anionic micelles than about better hydration of the SDS micelles as compared to CTAB ones. Finally, a set of acid–base indicators firmly fixed in the micellar pseudophase were studied by molecular dynamics. They are instruments for estimating electrostatic potentials of micelles and related aggregates as Ψ$=\hspace{0.17em}2.303RT{F}^{-1}\hspace{0.17em}\left(\mathrm{p}{K}_{\mathrm{a}}^{\mathrm{i}}\hspace{0.17em}-\hspace{0.17em}\mathrm{p}{K}_{\mathrm{a}}^{\mathrm{app}}\right)$, where $\mathrm{p}{K}_{\mathrm{a}}^{\mathrm{i}}$ and $\mathrm{p}{K}_{\mathrm{a}}^{\mathrm{app}}$ are indices of so-called intrinsic and apparent dissociation constants. In this case, in addition to the location, orientation, and hydration, the differences between values of $\mathrm{p}{K}_{\mathrm{a}}^{\mathrm{app}}$ and indices of the dissociation constants in water were estimated. Only a semi-quantitative agreement with the experimental data was obtained. However, the differences between $\mathrm{p}{K}_{\mathrm{a}}^{\mathrm{app}}$ of a given indicator in two micellar solutions do much better agree with the experimental data. Accordingly, the experimental Ψ values of ionic micelles, as determined using the $\mathrm{p}{K}_{\mathrm{a}}^{\mathrm{app}}$ in nonionic micelles as $\mathrm{p}{K}_{\mathrm{a}}^{\mathrm{i}}$, are reproduced with reasonable accuracy for the corresponding indicator. However, following the experimental data, a scatter of the Ψ values obtained with different indicators for given micelles is observed. This problem may be the subject of further research. Full article

The concept of “solvent polarity” is widely used to explain the effects of using different solvents in various scientific applications. However, a consensus regarding its definition and quantitative measure is still lacking, hindering progress in solvent-based research. This study hopes to add to the conversation by presenting the development of two linear regression models for solvent polarity, based on Reichardt’s E_T(30) solvent polarity scale, using Abraham solvent parameters and a transformer-based model for predicting solvent polarity directly from molecular structure. The first linear model incorporates the standard Abraham solvent descriptors s, a, b, and the extended model ionic descriptors j⁺ and j⁻, achieving impressive test-set statistics of R² = 0.940 (coefficient of determination), MAE = 0.037 (mean absolute error), and RMSE = 0.050 (Root-Mean-Square Error). The second model, covering a more extensive chemical space but only using the descriptors s, a, and b, achieves test-set statistics of R² = 0.842, MAE = 0.085, and RMSE = 0.104. The transformer-based model, applicable to any solvent with an associated SMILES string, achieves test-set statistics of R² = 0.824, MAE = 0.066, and RMSE = 0.095. Our findings highlight the significance of Abraham solvent parameters, especially the dipolarity/polarizability, hydrogen-bond acidity/basicity, and ionic descriptors, in predicting solvent polarity. These models offer valuable insights for researchers interested in Reichardt’s E_T(30) solvent polarity parameter and solvent polarity in general. Full article

The structure of electrolyte solutions under pressure at a molecular level is a crucial issue in the fundamental science of understanding the nature of ion solvation and association and application fields, such as geological processes on the Earth, pressure-induced protein denaturation, and supercritical water technology. We report the structure of an aqueous 2 m (=mol kg⁻¹) MgCl₂ solution at pressures from 0.1 MPa to 4 GPa and temperatures from 300 to 500 K revealed by X-ray- and neutron-scattering measurements. The scattering data are analyzed by empirical potential structure refinement (EPSR) modeling to derive the pair distribution functions, coordination number distributions, angle distributions, and spatial density functions (3D structure) as a function of pressure and temperature. Mg²⁺ forms rigid solvation shells extended to the third shell; the first solvation shell of six-fold octahedral coordination with about six water molecules at 0 GPa transforms into about five water molecules and one Cl⁻ due to the formation of the contact ion pairs in the GPa pressure range. The Cl⁻ solvation shows a substantial pressure dependence; the coordination number of a water oxygen atom around Cl⁻ increases from 8 at 0.1 MPa/300 K to 10 at 4 GPa/500 K. The solvent water transforms the tetrahedral network structure at 0.1 MPa/300 K to a densely packed structure in the GPa pressure range; the number of water oxygen atoms around a central water molecule gradually increases from 4.6 at 0.1 MPa/298 K to 8.4 at 4 GPa/500 K. Full article

The hydration of phosphate ions, an essential component of many biological molecules, is studied using all-atom molecular dynamics (MD) simulation and quantum chemical methods. MD simulations are carried out by employing a mean-field polarizable water model. A good linear correlation between the self-diffusion coefficient and phosphate anion concentration is ascertained from the computed mean-square displacement (MSD) profiles. The HB dynamics of the hydration of the phosphate anion is evaluated from the time-dependent autocorrelation function C_HB(t) and is determined to be slightly faster for the phosphate–anion system as compared to that of the water–water system at room temperature. The coordination number (CN) of the phosphate ion is found to be 15.9 at 298 K with 0.05 M phosphate ion concentration. The average CN is also calculated to be 15.6 for the same system by employing non-equilibrium MD simulation, namely, the well-tempered meta-dynamics method. A full geometry optimization of the PO₄³⁻·16H₂O cluster is investigated at the ωB97X-D/aug-cc-pVTZ level of theory, and the hydration of the phosphate anion is observed to have both singly and doubly bonded anion–water hydrogen bonds and inter-water hydrogen bonds in a range between 0.169–0.201 nm and 0.192–0.215 nm, respectively. Modified Stokes–Einstein relation is used to calculate the conductivity of the phosphate ion and is found to be in good agreement with the experimentally observed value. Full article

The current state of the study of different liquid crystalline (LC) systems doped with carbon nanotubes (CNTs) is discussed. An attempt is endeavored to outline the state-of-the-art technology that has emerged after two past decades. Systematization and analysis are presented for the integration of single- and multi-walled carbon nanotubes in thermotropic (nematic, smectic, cholesteric, ferroelectric, etc.) and lyotropic LCs. Special attention is paid to the effects of alignment and supramolecular organization resulting from orientational coupling between CNTs and the LC matrix. The effects of the specific inter-molecular and inter-particle interactions and intriguing microstructural, electromagnetic, percolation, optical, and electro-optical properties are also discussed. Full article

This work focuses on determining the dissociation constants (pK_a) of eight amines, namely, 3-(Diethylamino) propylamine, 1,3-Diaminopentane, 3-Butoxypropylamine, 2-(Methylamino) ethanol, Bis(2-methoxyethyl) amine, α-Methylbenzylamine, 2-Aminoheptane, and 3-Amino-1-phenylbutane, within temperatures ranging from 293.15 K to 323.15 K. The thermodynamic properties of the protonated reactions were regressed from the pK_a work. In addition, the protonated order of both 3-(Diethylamino) propylamine and 1,3-Diaminopentane were determined using computational chemistry methods owing to their unsymmetrical structures. In addition to the experimental methods, the dissociation constants at the standard temperature (298.15 K) were also estimated using group functional models (paper–pencil) and computational methods. The computational methods include COSMO-RS and computational chemistry calculations. An artificial neural network (ANN) method was employed to model the data by collecting and combining the experimental properties to estimate the missing pK_a values. Although the ANN models can provide acceptable results, they depend on the availability of the data. Instead of using the experimental properties, they were generated using software such as Aspen Plus or CosmothermX. The simulated ANN model can also provide very good fits to the experimental constant values. Full article

The dynamics of pure ionic liquids and solutions with acetonitrile have been investigated through quasielastic neutron scattering (QENS). The translational diffusive motion of the 1-butyl-3-methyl-imidazolium cation was revealed as a function of concentration and temperature. The diffusion coefficients obtained are in reasonably good agreement with molecular dynamics (MD) computer simulations based on a classical potential. The diffusive mobility of the cation dramatically increases when adding acetonitrile. This increase in diffusivity is directly related to a maximum in conductivity of these ionic liquid solutions and might pave the way for new design of electrolytes. The translational motions in pure ionic liquids are too slow to be resolved by our experiment. However, localized motion resembling rotation on a sphere of the measured proton signal could be identified in the pure ionic liquids. Full article

Vapor–liquid equilibrium (VLE) and density data for binary systems of branched alkanes + ethyl acetate are scarce in the literature. In this study, the binary mixtures 3-methylpentane + ethyl acetate and 2,3-dimethylbutane + ethyl acetate were investigated. Density measurements at atmospheric pressure were performed using a vibrating tube density meter at 293.15, 298.15 and 303.15 K. Large and positive excess molar volumes were calculated and correlated using a Redlich–Kister-type equation. Isobaric VLE data at 101.3 kPa were obtained using a Gillespie-type recirculation ebulliometer. Equilibrium compositions were determined indirectly from density measurements. The experimental data were checked for consistency by means of the Fredenslund test and the Wisniak (L-W) test and were then successfully correlated using the NRTL model. The newly studied binary systems display high deviations from ideality and minimum boiling azeotropes, the coordinates of which are reported in this work. Full article

Interactions between DNA and graphene are paramount for a wide range of applications, such as biosensing and nanoelectronics; nonetheless, the molecular details of such interactions remain largely unexplored. We employ atomically detailed molecular dynamics simulations with an enhanced sampling technique to investigate the adsorption and mobility of double-stranded DNA along the basal plane of graphene, in an electrolytic aqueous medium. The study focuses on physiologically relevant conditions, using a buffer of [NaCl] = 134 mM. DNA physisorption is shown to be fast and irreversible, leading to deformation and partial melting of the double helix as a result of π–π stacking between the terminal nucleobases and graphene. Denaturation occurs primarily at the termini, with ensemble averaged H-bond ratios of 47.8–62%; these can, however, reach a minimum of 15%. Transition between free-energy minima occurs via a thermodynamical pathway driving the nucleic acid from a radius of gyration of 1.5 nm to 1.35 nm. Mobility along the basal plane of graphene is dominant, accounting for ~90% of all centre-of-mass translation and revealing that the DNA’s apparent diffusivity is similar to diffusion along the endohedral volume of carbon nanotubes, but one order of magnitude faster than in other 2D materials, such as BC₃ and C₃N. Full article

Using the ASEC-FEG approach in combination with atomistic simulations, we performed geometry optimizations of a C_s conformer of the lithium decahydroborate (Li@B₁₀H₁₄) complex in chloroform and in water, which has been shown to be the most stable in the gas phase and calculated its first hyperpolarizability. At room temperature, ASEC-FEG calculations show that this conformer is stable only in chloroform. However, it is found that the nonlinear response of the C_s conformer in chloroform is mild, and the result for the hyperpolarizability is markedly decreased in comparison with the result of the C_2v conformer. Full article

The initial formation cycles are critical to the performance of a lithium-ion battery (LIB), particularly in the case of silicon anodes, where the high surface area and extreme volume expansion during cycling make silicon susceptible to detrimental side reactions with the electrolyte. The solid electrolyte interface (SEI) that is formed during these initial cycles serves to protect the surface of the anode from a continued reaction with the electrolyte, and its composition reflects the composition of the electrolyte. In this work, ReaxFF reactive force field simulations were used to investigate the interactions between ether-based electrolytes with high LiTFSI salt concentrations (up to 4 mol/L) and a silicon oxide surface. The simulation investigations were verified with galvanostatic testing and post-mortem X-ray photoelectron spectroscopy, revealing that highly concentrated electrolytes resulted in the faster formation and SEIs containing more inorganic and silicon species. This study emphasizes the importance of understanding the link between electrolyte composition and SEI formation. This ReaxFF approach demonstrates an accessible way to tune electrolyte compositions for optimized performance without costly, time-consuming experimentation. Full article

Abraham model solute descriptors are reported for the first time for 62 additional C₁₀ through C₁₃ methyl- and ethyl-branched alkanes. The numerical values were determined using published gas chromatographic retention Kováts retention indices for 157 alkane solutes eluted from a squalane stationary phase column. The 95 alkane solutes that have known descriptor values were used to construct the Abraham model KRI versus L-solute descriptor correlation needed in our calculations. The calculated solute descriptors can be used in conjunction with previously published Abraham model correlations to predict a wide range of important physico-chemical and biological properties. The predictive computations are illustrated by estimating the air-to-polydimethylsiloxane partition coefficient for each of the 157 alkane solutes. Full article

In this paper, we proceed to illustrate the consequences and implications of the Dual Model of Liquids (DML) by applying it to the heat propagation. Within the frame of the DML, propagation of thermal (elastic) energy in liquids is due to wave-packet propagation and to the wave-packets’ interaction with the material particles of the liquid, meant in the DML as aggregates of molecules swimming in an ocean of amorphous liquid. The liquid particles interact with the lattice particles, a population of elastic wave-packets, by means of an inertial force, exchanging energy and momentum with them. The hit particle relaxes at the end of the interaction, releasing the energy and momentum back to the system a step forward and a time lapse later, like in a tunnel effect. The tunnel effect and the duality of liquids are the new elements that suggest on a physical basis for the first time, using a hyperbolic equation to describe the propagation of energy associated to the dynamics of wave-packet interaction with liquid particles. Although quantitatively relevant only in the transient phase, the additional term characterizing the hyperbolic equation, usually named the “memory term”, is physically present also once the stationary state is attained; it is responsible for dissipation in liquids and provides a finite propagation velocity for wave-packet avalanches responsible in the DML for the heat conduction. The consequences of this physical interpretation of the “memory” term added to the Fourier law for the phononic contribution are discussed and compiled with numerical prediction for the value of the memory term and with the conclusions of other works on the same topic. Full article

There is a remarkable wealth of thermodynamic information in freely accessible databases, the LSER database being a classical example. The LSER, or Abraham solvation parameter model, is a very successful predictive tool in a variety of applications in the (bio)chemical and environmental sector. The model and the associated database are very rich in thermodynamic information and information on intermolecular interactions, which, if extracted properly, would be particularly useful in various thermodynamic developments for further applications. Partial Solvation Parameters (PSP), based on equation-of-state thermodynamics, are designed as a versatile tool that would facilitate this extraction of information. The present work explores the possibilities of such an LSER–PSP interconnection and the challenging issues this effort is faced with. The thermodynamic basis of the very linearity of the LSER model is examined, especially, with respect to the contribution of strong specific interactions in the solute/solvent system. This is done by combining the equation-of-state solvation thermodynamics with the statistical thermodynamics of hydrogen bonding. It is verified that there is, indeed, a thermodynamic basis of the LFER linearity. Besides the provenance of the sought linearity, an insight is gained on the thermodynamic character and content of coefficients and terms of the LSER linearity equations. The perspectives from this insight for the further development of LSER and related databases are discussed. The thermodynamic LSER–PSP interconnection is examined as a model for the exchange in information between QSPR-type databases and equation-of-state developments and the associated challenges are examined with representative calculations. Full article