A density functional theory study on interactions in water-bridged dimeric complexes of lignin.

Lignin is the main plant cell wall component responsible for recalcitrance in the process of lignocellulosic biomass conversion into biofuels. The recalcitrance and insolubility of lignin in different reaction media are due in part to the hydrogen bonds and π interactions that hold syringyl (S) and guaiacyl (G) units together and promote the formation of stable water-bridged dimeric complexes (WBDCs): S⋯G and S⋯S, in native lignin. The current understanding of how each type of interaction influences the stability of these complexes within lignin native cell walls is still limited. Here, we found by DFT calculations that hydrogen bonding is more dominant than π-stacking interaction between aromatic rings of WBDCs. Although there is a stronger interaction of hydrogen bonds between subunits and water and higher π-stacking interaction in the S⋯S complex compared to the S⋯G complex, the former complex is less thermodynamically stable than the latter due to the entropic contribution coming from the methoxy substituents in the S-unit. Our results demonstrate that the methoxylation degree of lignin units does not significantly influence the structural geometries of WBDCs; if anything, an enhanced dispersion interaction between ring aromatics results in quasi-sandwich geometries as found in "coiled" lignin structures in the xylem tissue of wood. In the same way as that with ionic liquids, polar solvents can dissolve S-lignin by favorable interactions with the aliphatic hydroxyl group in the α-position as the key site or the aromatic hydroxyl group as the secondary site.

Interaction Between Endocrine Disruptors and Polyethylene Nanoplastic by Molecular Dynamics Simulations.

Nanoplastics (NPs) can come into contact with humans through different means such as ingesting contaminated food or exposure to contaminated air. Recent research indicates that these NPs can act as vectors for other contaminants. Further research is still needed to determine the effects of these interactions and whether they are significant under environmental conditions. Bisphenol A (BPA) and benzophenone (BZP) are possible contaminants that could be cotransported with NPs. Even in low concentrations, BPA and BZP can act as endocrine disruptors and have been linked to several diseases. In this study, we used molecular dynamics simulations to obtain the potential of mean force (PMF) profile between a polyethylene NP and a BPA/BZP molecule. The PMF shows a minimum of -8.0 kJ mol-1 for the BPA, whereas it is -23.5 kJ mol-1 for the BZP, meaning BZP has a much greater attractive potential to polyethylene than BPA. We can infer that the higher quantity of BPA's hydrogen bonds with the water contributes to the difference between BZP and BPA. The results indicate the need to address the possibility of NPs playing a role in the cotransport and bioaccumulation of contaminants in aquatic ecosystems.

Revisiting the pseudo-supercritical path method: An improved formulation for the alchemical calculation of solid-liquid coexistence.

Alchemical free energy calculations via molecular dynamics have been applied to obtain thermodynamic properties related to solid-liquid equilibrium conditions, such as melting points. In recent years, the pseudo-supercritical path (PSCP) method has proved to be an important approach to melting point prediction due to its flexibility and applicability. In the present work, we propose improvements to the PSCP alchemical cycle to make it more compact and efficient through a concerted evaluation of different potential energies. The multistate Bennett acceptance ratio (MBAR) estimator was applied at all stages of the new cycle to provide greater accuracy and uniformity, which is essential concerning uncertainty calculations. In particular, for the multistate expansion stage from solid to liquid, we employed the MBAR estimator with a reduced energy function that allows affine transformations of coordinates. Free energy and mean derivative profiles were calculated at different cycle stages for argon, triazole, propenal, and the ionic liquid 1-ethyl-3-methyl-imidazolium hexafluorophosphate. Comparisons showed a better performance of the proposed method than the original PSCP cycle for systems with higher complexity, especially the ionic liquid. A detailed study of the expansion stage revealed that remapping the centers of mass of the molecules or ions is preferable to remapping the coordinates of each atom, yielding better overlap between adjacent states and improving the accuracy of the methodology.

Charge Inversion in 1:1 Electrolytes: Analyzing the Energetics.

The effects of bulk concentration, surface charge density, ionic diameter, and bulk dielectric constant on charge inversion in 1:1 electrolyte systems are investigated. The framework of the classical density functional theory is used to describe the mean electrostatic potential and the volume and electrostatic correlations, which combine to define the adsorption of ions at a positively charged surface. Our results show that a decrease in the dielectric constant, in particular, creates charge inversion for 1:1 electrolytes by amplifying both the electrostatic potential and the screening component (which is generally much larger than the excluded-volume component). Local electrical potential inversion can occur even for moderate concentrations and surface charges. These findings are especially significant for ionic liquids and systems with organic molecules as solvents, as these generally have a dielectric constant much smaller than water.

A New Formulation for the Concerted Alchemical Calculation of van der Waals and Coulomb Components of Solvation Free Energies.

Alchemical free energy calculations via molecular dynamics have been widely used to obtain thermodynamic properties related to protein-ligand binding and solute-solvent interactions. Although soft-core modeling is the most common approach, the linear basis function (LBF) methodology [Naden, L. N.; et al. J. Chem. Theory Comput.2014, 10 (3), 1128; 2015, 11 (6), 2536] has emerged as a suitable alternative. It overcomes the end-point singularity of the scaling method while maintaining essential advantages such as ease of implementation and high flexibility for postprocessing analysis. In the present work, we propose a simple LBF variant and formulate an efficient protocol for evaluating van der Waals and Coulomb components of an alchemical transformation in tandem, in contrast to the prevalent sequential evaluation mode. To validate our proposal, which results from a careful optimization study, we performed solvation free energy calculations and obtained octanol-water partition coefficients of small organic molecules. Comparisons with results obtained via the sequential mode using either another LBF approach or the soft-core model attest to the effectiveness and correctness of our method. In addition, we show that a reaction field model with an infinite dielectric constant can provide very accurate hydration free energies when used instead of a lattice-sum method to model solute-solvent electrostatics.

Real Electrolyte Solutions in the Functionalized Mean Spherical Approximation: A Density Functional Theory for Simple Electrolyte Solutions.

The equation of state based on the mean spherical approximation (MSA) can describe electrolyte solutions as a primitive model, where the ions are charged hard-sphere particles and the solvent is a continuum medium. In recent years, many propositions of the classical density functional theory (cDFT) for electrolyte solutions have been presented. One of these is the functionalized MSA (fMSA) which has proven to be a great functional approach of MSA to calculate the electric double layer structures. This work demonstrates how the fMSA theory can describe real electrolyte solutions (e.g., NaCl, KI, and LiBr) where hydration and solvent concentration effects are present. Experimental data of the mean activity coefficients of different simple salts were successfully reproduced. When the hydrated diameter and the electrolyte solution electric permittivity are used, the fMSA predicts a charge inversion on the electrostatic potential near a charged surface at high salt concentrations.

Are all-atom any better than united-atom force fields for the description of liquid properties of alkanes?

Alkanes are a fundamental part in empirical force fields (FF) not only due to their technological relevance, but also due to the prevalence of alkane moieties in organic molecules, e.g., compounds containing a saturated carbon chain. Therefore, a good description of alkane interactions is crucial for determining the quality of a FF. In this study, the performance of 12 empirical force fields (FF) was evaluated in the context of reproducing liquid properties of alkanes. More specifically, n-octane was chosen as a reference compound since it is a liquid in a broad temperature range and it has numerous experimental data for thermodynamic, transport, and structural properties, as well as for their temperature dependencies. A normalized root-mean-square deviation (NRMSD) analysis was used to rank the force fields in their ability to reproduce the experimental data. Five out of the six best force fields considered were united-atom models. The GROMOS force field showed the smallest deviation in terms of NRMSD, followed by TRAPPE-EH, NERD, CHARMM-UA, TRAPPE-UA, and OPLS-UA. This overall better performance of the united-atom force fields indicates that complexity does not always bring quality.

Development of an AMBER-compatible transferable force field for poly(ethylene glycol) ethers (glymes).

An all-atom force field consistent with the general AMBER force field (GAFF) format for poly(ethylene glycol) dimethyl ether (diglyme or G2) was developed by fitting to experimental liquid densities and dielectric constants. Not surprisingly, the new force field gives excellent agreement with experimental liquid phase densities and dielectric constants over a wide temperature range. Other dynamic and thermodynamic properties of liquid G2 such as its self-diffusion coefficient, shear viscosity, and vaporization enthalpy were also calculated and compared to experimental data. For all of the properties studied, the performance of the proposed new force field is better than that of the standard GAFF force field. The force field parameters were transferred to model two other poly(ethylene glycol) ethers: monoglyme (G1) and tetraglyme (G4). The predictive ability of the modified force field for G1 and G4 was significantly better than that of the original GAFF force field. The proposed force field provides an alternative option for the simulation of mixtures containing glymes using GAFF-compatible force fields, particularly for electrochemical applications. The accuracy of a previously published force field based on the OPLS-AA format and the accuracies of two modified versions of that force field were also examined for G1, G2, and G4. It was found that the original OPLS-AA force field is superior to the modified versions of it, and that it has a similar accuracy to the proposed new GAFF-compatible force field. Graphical abstract Transferability of an AMBER-compatible force field parameterized for G2 to other glymes.

The electrostatic behavior of the bacterial cell wall using a smoothing function to describe the charge-regulated volume charge density profile.

The Donnan potential can be observed in many biological systems due to the presence of polyelectrolytes as proteins and nucleic acids. The aim of this work was to present a useful tool to describe the fixed and charge-regulated volume charge density profile through the use of a smoothing function and to obtain the electrostatic potential profile as well as the Donnan potential of this system by solving Poisson-Boltzmann (PB) equation. When we use the smoothing function, the Donnan potential arises automatically from the solution of only one Poisson-Boltzmann equation and it is not necessary to impose this potential for treating charged system in the presence of a membrane. The electrostatic behavior across the Bacillus brevis wall considering the dependence on the ionization of the cell wall functional groups as a function of the solution pH was analyzed. An important issue was to show that potentiometric titration data could be used together with the Poisson-Boltzmann equation to predict the electrostatic behavior (e.g., zeta potential) of the bacterial cell surface.

Membrane potential and ion partitioning in an erythrocyte using the Poisson-Boltzmann equation.

In virtually all mammal cells, we can observe a much higher concentration of potassium ions inside the cell and vice versa for sodium ions. Classical theories ignore the specific ion effects and the difference in the thermodynamic reference states between intracellular and extracellular environments. Usually, this differential ion partitioning across a cell membrane is attributed exclusively to the active ion transport. Our aim is to investigate how much the dispersion forces contribute to active ion pumps in an erythrocyte (red blood cell) as well as the correction of chemical potential reference states between intracellular and extracellular environments. The ionic partition and the membrane potential in an erythrocyte are analyzed by the modified Poisson-Boltzmann equation, considering nonelectrostatic interactions between ions and macromolecules. Results show that the nonelectrostatic potential calculated by Lifshitz theory has only a small influence with respect to the high concentration of K(+) in the intracellular environment in comparison with Na(+).

Attractive double-layer forces between neutral hydrophobic and neutral hydrophilic surfaces.

The interaction between surface patches of proteins with different surface properties has a vital role to play driving conformational changes in proteins in different salt solutions. We demonstrate the existence of ion-specific attractive double-layer forces between neutral hydrophobic and hydrophilic surfaces in the presence of certain salt solutions. This is performed by solving a generalized Poisson-Boltzmann equation for two unequal surfaces. In the calculations, we utilize parametrized ion-surface potentials and dielectric-constant profiles deduced from recent non-primitive-model molecular dynamics simulations that partially account for molecular structure and hydration effects.

Ion-specific thermodynamical properties of aqueous proteins.

Ion-specific interactions between two colloidal particles are calculated using a modified Poisson-Boltzmann (PB) equation and Monte Carlo (MC)simulations. PB equations present good results of ionic concentration profiles around a macroion, especially for salt solutions containing monovalent ions. These equations include not only electrostatic interactions, but also dispersion potentials originated from polarizabilities of ions and proteins. This enables us to predict ion-specific properties of colloidal systems. We compared results obtained from the modified PB equation with those from MC simulations and integral equations. Phase diagrams and osmotic second virial coefficients are also presented for different salt solutions at different pH and ionic strengths, in agreement with the experimental results observed Hofmeister effects. In order to include the water structure and hydration effect, we have used an effective interaction obtained from molecular dynamics of each ion and a hydrophobic surface combined with PB equation. The method has been proved to be efficient and suitable for describing phenomena where the water structure close to the interface plays an essential role. Important thermodynamic properties related to protein aggregation, essential in biotechnology and pharmaceutical industries, can be obtained from the method shown here.

Ion-specific thermodynamical properties of aqueous proteins

Ion-specific interactions between two colloidal particles are calculated using a modified Poisson-Boltzmann (PB)equationandMonteCarlo(MC)simulations. PBequationspresentgoodresultsofionicconcentration profiles around a macroion, especially for salt solutions containing monovalent ions. These equations include not only electrostatic interactions, but also dispersion potentials originated from polarizabilities of ions and proteins. This enables us to predict ion-specific properties of colloidal systems. We compared results obtained from the modified PB equation with those from MC simulations and integral equations. Phase diagrams and osmotic second virial coefficients are also presented for different salt solutions at different pH and ionic strengths, in agreement with the experimental results observed Hofmeister effects. In order to include the water structure and hydration effect, we have used an effective interaction obtained from molecular dynamics of each ion and a hydrophobic surface combined with PB equation. The method has been proved to be efficient and suitable for describing phenomena where the water structure close to the interface plays an essential role. Important thermodynamic properties related to protein aggregation, essential in biotechnology and pharmaceutical industries, can be obtained from the method shown here.

Interações íon-específicas (dependentes do tipo de íon presente em solução) entre duas partículas coloidais são calculadas usando a equação de Poisson-Boltzmann (PB) modificada e simulações de Monte Carlo (MC). As equações de PB apresentam bons resultados de perfis de concentração nas proximidades de um macro-íon, principalmente para soluções salinas contendo íons monovalentes. Estas equações incluem não só interações eletrostáticas, mas também potenciais de dispersão, que têm origem nas polarizabilidades de íons e proteínas, permitindo a predição de propriedades íon-específicas de sistemas coloidais. Os resultados obtidos a partir da equação de PB modificada são comparados com outros obtidos por simulação de MC e por equações integrais. Diagramas de fase e o segundo coeficiente de virial são obtidos para diferentes sais e diferentes valores de pH e força iônica, em concordância com efeitos de Hofmeister observados experimentalmente. Interações efetivas obtidas por dinâmica molecular entre cada íon e uma superfície hidrofóbica foram incluídas na equação de PB, a fim de considerar a estrutura da água e efeitos de hidratação. O método mostrou-se eficiente e adequado para descrever fenômenos onde a estrutura da água nas proximidades da interface desempenha papel essencial. Propriedades termodinâmicas importantes, relacionadas com a agregação de proteínas, essenciais em biotecnologia e indústrias farmacêuticas, podem ser obtidas pelo método aqui apresentado.

Finite volume solution of the modified Poisson-Boltzmann equation for two colloidal particles.

The double layer forces between spherical colloidal particles, according to the Poisson-Boltzmann (PB) equation, have been accurately calculated in the literature. The classical PB equation takes into account only the electrostatic interactions, which play a significant role in colloid science. However, there are at, and above, biological salt concentrations other non-electrostatic ion specific forces acting that are ignored in such modelling. In this paper, the electrostatic potential profile and the concentration profile of co-ions and counterions near charged surfaces are calculated. These results are obtained by solving the classical PB equation and a modified PB equation in bispherical coordinates, taking into account the van der Waals dispersion interactions between the ions and both surfaces. Once the electrostatic potential is known we calculate the double layer force between two charged spheres. This is the first paper that solves the modified PB equation in bispherical coordinates. It is also the first time that the finite volume method is used to solve the PB equation in bispherical coordinates. This method divides the calculation domain into a certain number of sub-domains, where the physical law of conservation is valid, and can be readily implemented. The finite volume method is implemented for several geometries and when it is applied to solve PB equations presents low computational cost. The proposed method was validated by comparing the numerical results for the classical PB calculations with previous results reported in the literature. New numerical results using the modified PB equation successfully predicted the ion specificity commonly observed experimentally.

Effect of salt identity on the phase diagram for a globular protein in aqueous electrolyte solution.

Monte Carlo simulations are used to establish the potential of mean force between two globular proteins in an aqueous electrolyte solution. This potential includes nonelectrostatic contributions arising from dispersion forces first, between the globular proteins, and second, between ions in solution and between each ion and the globular protein. These latter contributions are missing from standard models. The potential of mean force, obtained from simulation, is fitted to an analytic equation. Using our analytic potential of mean force and Barker-Henderson perturbation theory, we obtain phase diagrams for lysozyme solutions that include stable and metastable fluid-fluid and solid-fluid phases when the electrolyte is 0.2 M NaSCN or NaI or NaCl. The nature of the electrolyte has a significant effect on the phase diagram.