Modeling alkane+perfluoroalkane interactions using all-atom potentials: Failure of the usual combining rules

Universal Pairwise Interatomic van der Waals Potentials Based on Quantum Drude Oscillators

Repulsive short-range and attractive long-range van der Waals (vdW) forces play an appreciable role in the behavior of extended molecular systems. When using empirical force fields, the most popular computational methods applied to such systems, vdW forces are typically described by Lennard-Jones-like potentials, which unfortunately have a limited predictive power. Here, we present a universal parameterization of a quantum-mechanical vdW potential, which requires only two free-atom properties─the static dipole polarizability α1 and the dipole-dipole C6 dispersion coefficient. This is achieved by deriving the functional form of the potential from the quantum Drude oscillator (QDO) model, employing scaling laws for the equilibrium distance and the binding energy, and applying the microscopic law of corresponding states. The vdW-QDO potential is shown to be accurate for vdW binding energy curves, as demonstrated by comparing to the ab initio binding curves of 21 noble-gas dimers. The functional form of the vdW-QDO potential has the correct asymptotic behavior at both zero and infinite distances. In addition, it is shown that the damped vdW-QDO potential can accurately describe vdW interactions in dimers consisting of group II elements. Finally, we demonstrate the applicability of the atom-in-molecule vdW-QDO model for predicting accurate dispersion energies for molecular systems. The present work makes an important step toward constructing universal vdW potentials, which could benefit (bio)molecular computational studies.

Development, Validation, and Applications of Nonbonded Interaction Parameters between Coarse-Grained Amino Acid and Water Models

Interactions between amino acids and water play an important role in determining the stability and folding/unfolding, in aqueous solution, of many biological macromolecules, which affects their function. Thus, understanding the molecular-level interactions between water and amino acids is crucial to tune their function in aqueous solutions. Herein, we have developed nonbonded interaction parameters between the coarse-grained (CG) models of 20 amino acids and the one-site CG water model. The nonbonded parameters, represented using the 12-6 Lennard Jones (LJ) potential form, have been optimized using an artificial neural network (ANN)-assisted particle swarm optimization (PSO) (ANN-assisted PSO) method. All-atom (AA) molecular dynamics (MD) simulations of dipeptides in TIP3P water molecules were performed to calculate the Gibbs hydration free energies. The nonbonded force-field (FF) parameters between CG amino acids and the one-site CG water model were developed to accurately reproduce these energies. Furthermore, to test the transferability of these newly developed parameters, we calculated the hydration free energies of the analogues of the amino acid side chains, which showed good agreement with reported experimental data. Additionally, we show the applicability of these models by performing self-assembly simulations of peptide amphiphiles. Overall, these models are transferable and can be used to study the self-assembly of various biomaterials and biomolecules to develop a mechanistic understanding of these processes.

Influence of the Lennard-Jones Combination Rules on the Simulated Properties of Organic Liquids at Optimal Force-Field Parametrization

We recently introduced the CombiFF scheme [Oliveira et al., J. Chem. Theory Comput. 2020, 16, 7525], an approach for the automated refinement of force-field parameters against experimental condensed-phase data for large compound families. Using this scheme, once the time-consuming task of target-data selection and curation has been performed, the force-field optimization itself is both straightforward and fast. As a result, CombiFF provides an ideal framework for evaluating the influence of functional-form decisions on the accuracy of a force field at an optimal level of parametrization. We already used this approach to assess the effect of using an all-atom representation compared to united-atom representations in the force field [Oliveira et al., J. Chem. Theory Comput. 2022, 18, 6757]. Here, CombiFF is applied to assess the effect of three Lennard-Jones combination rules, geometric-mean (GM), Lorentz-Berthelot (LB), or Waldman-Hagler (WH), on the simulated properties of organic liquids. The comparison is performed in terms of the experimental liquid density ρ_liq, vaporization enthalpy ΔH_vap, surface-tension coefficient γ, static relative dielectric permittivity ϵ, and self-diffusion coefficient D. The calibrations of the three force-field variants are carried out independently against 2044 experimental values for ρ_liq, and ΔH_vap concerning 1516 compounds. The resulting root-mean-square deviations from experiment are 30.0, 26.9, and 36.7 kg m^-3 for ρ_liq and 2.8, 2.8, and 2.9 kJ mol^-1 for ΔH_vap, when applying the GM, LB, and WH combination rules, respectively. In terms of these (and the other) properties, the three combination rules perform comparatively well, with the GM and LB results being more similar to each other and slightly more accurate compared to experiment. In contrast, the use of distinct combination rules for the parameter calibration and property calculation leads to much larger errors.

Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set

The level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example the model resolution, the charge-derivation procedure, the van der Waals combination rules, the cutoff distance, and the treatment of the long-range interactions. Ideally, assessing the effect of a given FFV on the intrinsic accuracy of the force-field representation requires that only the specific FFV is changed and that this change is performed at an optimal level of parametrization, a requirement that may prove extremely challenging to achieve in practice. Here, we present a first attempt at such a comparison for one specific FFV, namely the choice of a united-atom (UA) versus an all-atom (AA) resolution in a force field for saturated acyclic (halo)alkanes. Two force-field versions (UA vs AA) are optimized in an automated way using the CombiFF approach against 961 experimental values for the pure-liquid densities ρ_liq and vaporization enthalpies ΔH_vap of 591 compounds. For the AA force field, the torsional and third-neighbor Lennard-Jones parameters are also refined based on quantum-mechanical rotational-energy profiles. The comparison between the UA and AA resolutions is also extended to properties that have not been included as parameterization targets, namely the surface-tension coefficient γ, the isothermal compressibility κ_T, the isobaric thermal-expansion coefficient α_P, the isobaric heat capacity c_P, the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔG_wat, and the free energy of solvation ΔG_che in cyclohexane. For the target properties ρ_liq and ΔH_vap, the UA and AA resolutions reach very similar levels of accuracy after optimization. For the nine other properties, the AA representation leads to more accurate results in terms of η; comparably accurate results in terms of γ, κ_T, α_P, ϵ, D, and ΔG_che; and less accurate results in terms of c_P and ΔG_wat. This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution.

Vacuum Interfacial Structure and X-ray Reflectivity of Imidazolium-Based Ionic Liquids with Perfluorinated Anions from a Theory and Simulations Perspective

We report studies of the vacuum interfacial structure of a series of 1-methyl-3-alkylimidazolium bis(perfluoroalkanesulfonyl)imide ionic liquids (ILs) and predict and explain their Fresnel-normalized X-ray reflectivity. To better interpret the results, we use a theory we recently developed dubbed "the peaks and antipeaks analysis of reflectivity" which splits the overall signal into that of different pair subcomponents. Whereas the overall reflectivity signal is not very informative, the peak and trough intensities for the pair subcomponents provide rich information for analysis. When species containing cationic alkyl or anionic fluoroalkyl tails are present at the interface, a tail layer is found next to a vacuum, and this tail layer can be composed of both alkyl and fluoroalkyl moieties. To maintain the positive-negative alternation of charged groups, alkyl and fluoroalkyl tails must necessarily be nearby and cannot segregate. Charged groups are found in the subsequent layer just below the interface and arranged to achieve lateral charge neutrality. In general, fluctuations at and away from the interface are based on polarity (i.e., heads and tails) and not on charge; when there are no significant alkyl or fluoroalkyl moieties in the IL, atomic density fluctuations away from the interface are small and appear to exist for the purpose of achieving lateral charge balance. For all the systems reported here, the persistence length of density fluctuations does not go beyond ∼7 nm.

Critical Packing Density of Water-Mediated Nonstick Self-Assembled Monolayer Coatings

Nanoparticle-mineral surface interactions are relevant in many biological and geological applications. We have previously studied nanoparticle coatings based on closely packed bicomponent polyol-fluoroalkane self-assembled monolayers (SAMs) that can have tunable stickiness on calcite surfaces by changing the compositions of fluoroalkanes in SAMs, where the coatings show nonstick properties if fluoroalkanes can effectively perturb hydration layers on calcite surfaces. However, when applying coatings on nanoparticles, it can be challenging to predict the maximum achievable coating density. Here, we study how would water-mediated SAM-calcite interactions change with different SAM coating densities. Molecular dynamics simulations show that compositionally repulsive, closely packed polyol-fluoroalkane SAMs become adhesive to calcite surfaces with decreasing coating densities. Our modeling shows that this results from the collapsing of fluoroalkanes into the voids of SAMs, where fluoroalkanes can no longer perturb hydration layers on calcite surfaces. Interestingly, we find that the nonstick-stick transition occurs when the volume fractions of the voids on SAMs are greater than the volume fractions of hydrophilic coating molecules.

Controlling water-mediated interactions by designing self-assembled monolayer coatings

Engineered nanoparticles have been broadly used in biological and geological systems. Hydrophilic molecules such as polyols have been used as coatings on nanoparticle surfaces due to their good biocompatibility and solubility in saline water. However, polyol coatings can cause huge retention of nanoparticles when encountering mineral surfaces. Here, molecular dynamics simulations enlightened that the strong adhesion of hydrophilic coatings to mineral surfaces stemming from the partitioning of the hydroxy groups on the hydrophilic molecules to the well-defined bound hydration layers on the mineral surfaces. To mitigate the nanoparticle adhesion, we investigated introducing small percentages of omniphobic fluoroalkanes to form a bicomponent system of hydrophilic and fluoroalkanes, which greatly perturbed the hydration layers on mineral surfaces and resulted in nonstick surface coatings. Our results provide important insight for the design of tunable “stickiness” nanoparticle coatings in different mineralogies, such as applications in subsurface environments or targeted delivery in mineralized tissues.

From nano-emulsions to phase separation: evidence of nano-segregation in (alkane + perfluoroalkane) mixtures using 129Xe NMR Spectroscopy

In this work we demonstrate that mixtures of (hexane + perfluorohexane) above the upper critical solution temperature segregate by forming domains at the nanometric scale. 129Xe NMR spectra obtained for solutions of xenon in liquid mixtures of (hexane + perfluorohexane) as a function of temperature suggest the existence of domains richer in the hydrogenated component, in which xenon "prefers" to be solvated. The average local concentration within the xenon coordination sphere is at least 0.05 higher in hexane mole fraction than the nominal concentration of the mixture. Atomistic molecular dynamics simulations support this analysis in excellent agreement with the experimental data. Additionally, 129Xe NMR spectra in pure perfluoroalkanes allow a detailed analysis of the liquid structure, continuing that previously reported for the liquid alkanes. It should be emphasised that nano-segregation is here observed in fluids governed exclusively by dispersion interactions, in contrast to other examples in which hydrogen bonding and polarity play important roles. Given its simplicity, this case study is thus prone to have a general impact in understanding the early mechanisms of segregation, phase separation and self-assembly.

Alkane Coiling in Perfluoroalkane Solutions: A New Primitive Solvophobic Effect

In this work, we demonstrate that n-alkanes coil when mixed with perfluoroalkanes, changing their conformational equilibria to more globular states, with a higher number of gauche conformations. The new coiling effect is here observed in fluids governed exclusively by dispersion interactions, contrary to other examples in which hydrogen bonding and polarity play important roles. FTIR spectra of liquid mixtures of n-hexane and perfluorohexane unambiguously reveal that the population of n-hexane molecules in all-trans conformation reduces from 32% in the pure n-alkane to practically zero. The spectra of perfluorohexane remain unchanged, suggesting nanosegregation of the hydrogenated and fluorinated chains. Molecular dynamics simulations support this analysis. The new solvophobic effect is prone to have a major impact on the structure, organization, and therefore thermodynamic properties and phase equilibria of fluids involving mixed hydrogenated and fluorinated chains.

Physical Absorption of Green House Gases in Amines: The Influence of Functionality, Structure, and Cross-Interactions

Monte Carlo simulations were performed in the isothermal-isobaric ensemble (NPT) to calculate the Henry constants of methane (CH₄), nitrous oxide (N₂O), and carbon dioxide (CO₂) in pure H₂O, amines, and alkanolamines using the classical Lorentz-Berthelot combining rules (L-B). The Henry constants of N₂O and CO₂ in water are highly overestimated and motivated us to propose a new set of unlike interactions. Contrarily, the Henry constant of N₂O in MEA is underestimated by around 40%, and again, a new reoptimized cross unlike parameter is able to reproduce the constant to within 10%. An analysis is given of the relationship between the physical absorption of these gases and the chemical structure or functionality of 12 molecules including amines and alkanolamines using the anisotropic united atom intermolecular potential (AUA4). Finally, the solubility of N₂O in an aqueous solution of monoethanolamine (MEA) at 30% (wt) was also studied. A Henry constant within 7% of the experimental value was found by using the reoptimized parameters along with L-B to account for the MEA + H₂O unlike interactions. This very good agreement without additional adjustments for the MEA + H₂O system may be attributed to the good excess properties predictions found in previous works for the binary mixture (MEA + H₂O). However, further work, including additional alkanolamines in aqueous solutions at several concentrations, is required to verify this particular point.

Liquid Mixtures Involving Hydrogenated and Fluorinated Alcohols: Thermodynamics, Spectroscopy, and Simulation

This article reports a combined thermodynamic, spectroscopic, and computational study on the interactions and structure of binary mixtures of hydrogenated and fluorinated substances that simultaneously interact through strong hydrogen bonding. Four binary mixtures of hydrogenated and fluorinated alcohols have been studied, namely, (ethanol + 2,2,2-trifluoroethanol (TFE)), (ethanol + 2,2,3,3,4,4,4-heptafluoro-1-butanol), (1-butanol (BuOH) + TFE), and (BuOH + 2,2,3,3,4,4,4-heptafluoro-1-butanol). Excess molar volumes and vibrational spectra of all four binary mixtures have been measured as a function of composition at 298 K, and molecular dynamics simulations have been performed. The systems display a complex behavior when compared with mixtures of hydrogenated alcohols and mixtures of alkanes and perfluoroalkanes. The combined analysis of the results from different approaches indicates that this results from a balance between preferential hydrogen bonding between the hydrogenated and fluorinated alcohols and the unfavorable dispersion forces between the hydrogenated and fluorinated chains. As the chain length increases, the contribution of dispersion increases and overcomes the contribution of H-bonds. In terms of the liquid structure, the simulations suggest the possibility of segregation between the hydrogenated and fluorinated segments, a hypothesis corroborated by the spectroscopic results. Furthermore, a quantitative analysis of the infrared spectra reveals that the presence of fluorinated groups induces conformational changes in the hydrogenated chains from the usually preferred all-trans to more globular arrangements involving gauche conformations. Conformational rearrangements at the CCOH dihedral angle upon mixing are also disclosed by the spectra.

Water based on a molecular model behaves like a hard-sphere solvent for a nonpolar solute when the reference interaction site model and related theories are employed

For neutral hard-sphere solutes, we compare the reduced density profile of water around a solute g(r), solvation free energy μ, energy U, and entropy S under the isochoric condition predicted by the two theories: dielectrically consistent reference interaction site model (DRISM) and angle-dependent integral equation (ADIE) theories. A molecular model for water pertinent to each theory is adopted. The hypernetted-chain (HNC) closure is employed in the ADIE theory, and the HNC and Kovalenko-Hirata (K-H) closures are tested in the DRISM theory. We also calculate g(r), U, S, and μ of the same solute in a hard-sphere solvent whose molecular diameter and number density are set at those of water, in which case the radial-symmetric integral equation (RSIE) theory is employed. The dependences of μ, U, and S on the excluded volume and solvent-accessible surface area are analyzed using the morphometric approach (MA). The results from the ADIE theory are in by far better agreement with those from computer simulations available for g(r), U, and μ. For the DRISM theory, g(r) in the vicinity of the solute is quite high and becomes progressively higher as the solute diameter d U increases. By contrast, for the ADIE theory, it is much lower and becomes further lower as d U increases. Due to unphysically positive U and significantly larger |S|, μ from the DRISM theory becomes too high. It is interesting that μ, U, and S from the K-H closure are worse than those from the HNC closure. Overall, the results from the DRISM theory with a molecular model for water are quite similar to those from the RSIE theory with the hard-sphere solvent. Based on the results of the MA analysis, we comparatively discuss the different theoretical methods for cases where they are applied to studies on the solvation of a protein.

PFC and Triglyme for Li-Air Batteries: A Molecular Dynamics Study

In this work, we present an all-atom molecular dynamics (MD) study of triglyme and perfluorinated carbons (PFCs) using classical atomistic force fields. Triglyme is a typical solvent used in nonaqueous Li-air battery cells. PFCs were recently reported to increase oxygen availability in such cells. We show that O2 diffusion in two specific PFC molecules (C6F14 and C8F18) is significantly faster than in triglyme. Furthermore, by starting with two very different initial configurations for our MD simulation, we demonstrate that C8F18 and triglyme do not mix. The mutual solubility of these molecules is evaluated both theoretically and experimentally, and a qualitative agreement is found. Finally, we show that the solubility of O2 in C8F18 is considerably higher than in triglyme. The significance of these results to Li-air batteries is discussed.

Optimizing Noble Gas-Water Interactions via Monte Carlo Simulations

In this work we present optimized noble gas-water Lennard-Jones 6-12 pair potentials for each noble gas. Given the significantly different atomic nature of water and the noble gases, the standard Lorentz-Berthelot mixing rules produce inaccurate unlike molecular interactions between these two species. Consequently, we find simulated Henry's coefficients deviate significantly from their experimental counterparts for the investigated thermodynamic range (293-353 K at 1 and 10 atm), due to a poor unlike potential well term (εij). Where εij is too high or low, so too is the strength of the resultant noble gas-water interaction. This observed inadequacy in using the Lorentz-Berthelot mixing rules is countered in this work by scaling εij for helium, neon, argon, and krypton by factors of 0.91, 0.8, 1.1, and 1.05, respectively, to reach a much improved agreement with experimental Henry's coefficients. Due to the highly sensitive nature of the xenon εij term, coupled with the reasonable agreement of the initial values, no scaling factor is applied for this noble gas. These resulting optimized pair potentials also accurately predict partitioning within a CO2-H2O binary phase system as well as diffusion coefficients in ambient water. This further supports the quality of these interaction potentials. Consequently, they can now form a well-grounded basis for the future molecular modeling of multiphase geological systems.

Classical force field for hydrofluorocarbon molecular simulations. Application to the study of gas solubility in poly(vinylidene fluoride)

A classical all-atoms force field for molecular simulations of hydrofluorocarbons (HFCs) has been developed. Lennard-Jones force centers plus point charges are used to represent dispersion-repulsion and electrostatic interactions. Parametrization of this force field has been performed iteratively using three target properties of pentafluorobutane: the quantum energy of an isolated molecule, the dielectric constant in the liquid phase, and the compressed liquid density. The accuracy and transferability of this new force field has been demonstrated through the simulation of different thermophysical properties of several fluorinated compounds, showing significant improvements compared to existing models. This new force field has been applied to study solubilities of several gases in poly(vinylidene fluoride) (PVDF) above the melting temperature of this polymer. The solubility of CH4, CO2, H2S, H2, N2, O2, and H2O at infinite dilution has been computed using test particle insertions in the course of a NpT hybrid Monte Carlo simulation. For CH4, CO2, and their mixtures, some calculations beyond the Henry regime have also been performed using hybrid Monte Carlo simulations in the osmotic ensemble, allowing both swelling and solubility determination. An ideal mixing behavior is observed, with identical solubility coefficients in the mixtures and in pure gas systems.

Perfluoroalkane force field for lipid membrane environments

In this work, we present atomic parameters of perfluoroalkanes for use within the CHARMM force field. Perfluorinated alkanes represent a special class of molecules. On the one hand, they are considerably more hydrophobic than lipids, but on the other hand, they are not lipophilic either. Instead, they represent an independent class of philicity, enabling a whole portfolio of applications within both materials science and biochemistry. We performed a thorough parametrization of all bonded and nonbonded parameters with a particular focus on van der Waals parameters. Here, the general framework of the CHARMM and CGenFF force fields has been followed. The van der Waals parameters have been fitted to experimental densities over a wide range of temperatures and pressures. This newly parametrized class of molecules will open the gate for a variety of simulations of biologically relevant systems within the CHARMM force field. A particular perspective for the present work is the influence of polyphilic transmembrane molecules on membrane properties, aggregation phenomena, and transmembrane channels.

Parametrization of 2,2,2-trifluoroethanol based on the generalized AMBER force field provides realistic agreement between experimental and calculated properties of pure liquid as well as water-mixed solutions

We present a novel force field model of 2,2,2-trifluoroethanol (TFE) based on the generalized AMBER force field. The model was exhaustively parametrized to reproduce liquid-state properties of pure TFE, namely, density, enthalpy of vaporization, self-diffusion coefficient, and population of trans and gauche conformers. The model predicts excellently other liquid-state properties such as shear viscosity, thermal expansion coefficient, and isotropic compressibility. The resulting model describes unexpectedly well the state equation of the liquid region in the range of 100 K and 10 MPa. More importantly, the proposed TFE model was optimized for use in combination with the TIP4P/Ew and TIP4P/2005 water models. It does not manifest excessive aggregation, which is known for other models, and therefore, it is supposed to more realistically describe the behavior of TFE/water mixtures. This was demonstrated by means of the Kirkwood-Buff theory of solutions and reasonable agreement with experimental data. We explored a considerable part of the parameter space and systematically tested individual combinations of parameters for performance in combination with the TIP4P/Ew and TIP4P/2005 water models. We observed ambiguity in parameters describing pure liquid TFE; however, most of them failed for TFE/water mixtures. We clearly demonstrated the necessity for balanced TFE-TFE, TFE-water, and water-water interactions which can be acquired only by employing implicit polarization correction in the course of parametrization.

Atomistic potentials for trisiloxane, alkyl ethoxylate, and perfluoroalkane-based surfactants with TIP4P/2005 and application to simulations at the air-water interface

The mechanism of superspreading, the greatly enhanced spreading of water droplets facilitated by trisiloxane surfactants, is still under debate, largely because the role and behavior of the surfactants cannot be sufficiently resolved by experiments or continuum simulations. Previous molecular dynamics studies have been performed with simple model molecules or inaccurate models, strongly limiting their explanatory power. Here we present a force field dedicated to superspreading, extending existing quantum-chemistry-based models for the surfactant and the TIP4P/2005 water model ( Abascal et al. J. Chem. Phys. , 2005 , 123 , 234505 ). We apply the model to superspreading trisiloxane surfactants and nonsuperspreading alkyl ethoxylate and perfluoroalkane surfactants at various concentrations at the air-water interface. We show that the developed model accurately predicts surface tensions, which are typically assumed important for superspreading. Significant differences between superspreading and traditional surfactants are presented and their possible relation to superspreading discussed. Although the force field has been developed for superspreading problems, it should also perform well for other simulations involving polymers or copolymers with water.