An Improved Force Field for the Prediction of the Vapor−Liquid Equilibria for Carboxylic Acids

Quantifying the Uncertainty of Force Field Selection on Adsorption Predictions in MOFs

Comparisons between simulated and experimental adsorption isotherms in MOFs are fraught with challenges. On the experimental side, there is significant variation between isotherms measured on the same system, with a significant percentage (∼20%) of published data being considered outliers. On the simulation side, force fields are often chosen "off-the-shelf" with little or no validation. The effect of this choice on the reliability of simulated adsorption predictions has not yet been rigorously quantified. In this work, we fill this gap by systematically quantifying the uncertainty arising from force field selection on adsorption isotherm predictions. We choose methane adsorption, where electrostatic interactions are negligible, to independently study the effect of the framework Lennard-Jones parameters on a series of prototypical materials that represent the most widely studied MOF "families". Using this information, we compute an adsorption "consensus isotherm" from simulations, including a quantification of uncertainty, and compare it against a manually curated set of experimental data from the literature. By considering many experimental isotherms measured by different groups and eliminating outliers in the data using statistical analysis, we conduct a rigorous comparison that avoids the pitfalls of the standard approach of comparing simulation predictions to a single experimental data set. Our results show that (1) the uncertainty in simulated isotherms can be as large as 15% and (2) standard force fields can provide reliable predictions for some systems but can fail dramatically for others, highlighting systematic shortcomings in those models. Based on this, we offer recommendations for future simulation studies of adsorption, including high-throughput computational screening of MOFs.

Accelerated Diffusion Following Deprotection in Chemically Amplified Resists

Polymeric chemically amplified resists (CARs) are critical materials for high-throughput lithographic processes. A photoactivated acid-anion catalyst changes the polymer's solubility via a deprotection reaction, which enables pattern development through selective dissolution. To capture observed reaction kinetics, reaction-diffusion models employ a catalyst diffusivity that is accelerated by reaction. However, the microscopic origin and factors contributing to this phenomena remain unclear. Herein, we employ detailed atomistic molecular dynamics simulations to examine the impact of protecting group removal and material relaxation on catalyst mobility. We report data on polymer density, catalyst dispersion, excess free volume, and segmental dynamics with increasing time/extent of deprotection. We then propose simple kinetic Monte Carlo algorithms that can describe both molecular dynamics simulations of deprotection reactions and experimental data.

Determination of liquid-vapor equilibrium and critical properties of fatty acids for biodiesel production through molecular dynamics

In recent years, biodiesel production has emerged as an option for renewable and green fuel generation due to the constant reduction of fossil fuel reservoirs. Biofuels as biodiesel also show valuable attributes, environmentally speaking, due to their low environmental impact, contributing to the achievement of sustainability. However, costs are not allowable for large-scale production. Thereby, several novel processes have been proposed (e.g., reactive distillation) to solve this issue. An inconvenience for the development of these processes is the little information in the literature about the critical properties of fatty acids, which are precursors of biodiesel. Determination of critical properties for fatty acids through experimentation is difficult. The reason is that fatty acids tend to self-associate (to dimerize) due to carboxylic groups presence through hydrogen bonds, and consequently, have higher boiling points than other compounds of similar molecular mass (e.g., hydrocarbons, esters). Therefore, alternative methods for this determination are required. One choice is the group-contribution method, which is based on the structure of the molecule; however, results can significantly vary among different group-contribution approaches. Another alternative (and the focus of this research) for the determination of these properties is molecular simulation techniques. In this work, the liquid-vapor equilibrium as a function of temperature and the surface tension of three pure fatty acids of long chain (linoleic, oleic, and palmitic acid) have been calculated. Simulations have been performed by molecular dynamics using the method of direct determination of phase coexistence with the software GROMACS; in which the transferable potentials for phase equilibria united atom forcefield (TraPPE-UA) have been implemented for these specific molecules. Orthobaric densities and surface tension values have been reported at temperatures near the critical point (from 650 K to 800 K). Critical properties (temperature, pressure, density) have been extrapolated from trajectories obtained in these simulations using scaling law relations. Critical properties for these compounds are not available experimentally, therefore, group contribution calculations from the literature were used as a reference. In this comparison, the palmitic acid properties calculated in this work, show the best agreement among the three substances investigated.

Molecular dynamics of liquid-liquid equilibrium and interfacial properties of aqueous solutions of methyl esters

In this work, the liquid-liquid phase equilibria and interfacial properties of methyl ester + water binary mixtures are determined at atmospheric pressure and from 278 to 358 K combining the direct coexistence technique and molecular dynamics simulations. Methyl esters are modelled using new parametrizations based on the united atom TraPPE model force field proposed recently by us [E. Feria, J. Algaba, J. M. Míguez, A. Mejía, P. Gómez-Álvarez and F. J. Blas, Phys. Chem. Chem. Phys., 2019, 22, 4974-4983] that are able to predict the vapour-liquid interfacial properties of pure methyl esters with high accuracy. In the case of water, we consider the well-known TIP4P/2005 model, the most popular rigid and non-polarizable model to describe the interfacial properties of pure water. The simulations are performed using the direct coexistence technique in the isothermal-isobaric or NP_zT ensemble in combination with molecular dynamics. We obtain density profiles, temperature-densities and temperature-composition projections of the phase diagrams, and interfacial tensions. The liquid-liquid interfacial tension is calculated from the normal and tangential components of the pressure tensor according to the mechanical virial route. We pay attention particularly to the ability of the molecular models in predicting the experimental behavior of the systems. Simulation results are able to account for the liquid-liquid phase equilibria of these binary mixtures, in good agreement with the experimental data taken from the literature. Unfortunately, experimental values for interfacial tensions are substantially overestimated by predictions from computer simulations in all cases. To our knowledge, this is the first time that the liquid-liquid phase equilibrium and interfacial properties of methyl ester + water mixtures have been predicted from computer simulations.

Effect of axial molecules and linker length on CO2 adsorption and selectivity of CAU-8: a combined DFT and GCMC simulation study

Density Functional Theory (DFT) and Grand Canonical Monte Carlo (GCMC) calculations are performed to study the structures and carbon dioxide (CO₂) adsorption properties of the newly designed metal–organic framework based on the CAU-8 (CAU stands for Christian-Albrechts Universität) prototype. In the new MOFs, the 4,4′-benzophenonedicarboxylic acid (H₂BPDC) linker of CAU-8 is substituted by 4,4′-oxalylbis(azanediyl)dibenzoic acid (H₂ODA) and 4,4′-teraphthaloylbis(azanediyl)dibenzoic acid (H₂TDA) containing amide groups (–CO–NH- motif). Furthermore, MgO₆ octahedral chains where dimethyl sulfoxide (DMSO) decorating the axial position bridged two Mg²⁺ ions are considered. The formation energies indicate that modified CAU-8 is thermodynamically stable. The reaction mechanisms between the metal clusters and the linkers to form the materials are also proposed. GCMC calculations show that CO₂ adsorptions and selectivities of Al-based MOFs are better than those of Mg-based MOFs, which is due to DMSO. Amide groups made CO₂ molecules more intensively distributed besides organic linkers. CO₂ uptakes and selectivities of MOFs containing H₂TDA linkers are better in comparison with those of MOFs containing H₂BPDC linkers or H₂ODA linkers.

Density Functional Theory (DFT) and Grand Canonical Monte Carlo (GCMC) calculations are performed to study the structures and CO₂ adsorption properties of the newly designed metal–organic framework based on the CAU-8 prototype.

Vapour–liquid phase equilibria and interfacial properties of fatty acid methyl esters from molecular dynamics simulations

Vapour–liquid surface tension as a function of temperature for methyl esters. Filled symbols are experimental data taken from the literature and open symbols MD NVT simulations.

Effect of Carboxylic Acid on the Wetting Properties of a Model Water-Octane-Silica System

Monte Carlo simulations are employed to determine the effects of acetic acid on the wetting properties of a model water-octane-silica system. We first compute the bulk liquid-vapor saturation properties of pure acetic acid and subsequently explore the bulk liquid-liquid saturation properties of the ternary water-octane-acid system. We introduce an expanded ensemble approach to compute the coexistence properties of the ternary system. An interface potential approach is then used to capture the evolution of the wetting properties of the water-octane-silica system upon the addition of acetic acid. We track the change in the octane-water interfacial tension and the contact angle of water droplet on a silica substrate in a mother octane fluid over a range of acetic acid activities. The structure of the fluid, including the partitioning of acetic acid within the interfacial system, is also considered at several state points. We observe that acetic acid has a strong tendency to adsorb at the octane-water interface, resulting in a reduction in the octane-water interfacial tension. The response of the contact angle is more sensitive to the temperature and the hydrophilicity of the silica substrate.

Counterion Effects on Aggregate Structure of 12-Hydroxystearate Salts in Hexane: A Quantum Mechanical and Molecular Dynamics Simulation Study

Salts of 12-hydroxystearate are important organogelators and grease thickeners, but a structural rationale for their rheological properties remains elusive. We use quantum mechanical calculations and molecular dynamics (MD) simulations to analyze aggregate structures for (1) ( R)-12-hydroxystearic acid (( R)-12HSA), (2) lithium ( R)-12-hydroxystearate (( R)-Li12HS), and (3) sodium ( R)-12-hydroxystearate (( R)-Na12HS). First, quantum mechanical calculations were used to establish the structure and complexation energies of dimers of acetic acid, lithium acetate, and sodium acetate. The expected acetic acid dimer is predicted, and both the lithium acetate and sodium acetate dimer formed a C_{2 h}-symmetric structure. All dimers were sufficiently stable to allow modeling them as pseudocovalent complexes in all-atom, explicit solvent MD. After microsecond-long MD, all systems produced strong ringlike ordered nuclei. The C_{2 h} lithium salt molecules produced aggregates that had the most efficient packing at the head group and a higher frequency of hydroxyl hydrogen bonding compared to the sodium salt. This ordering propensity explains the high melting temperature of ( R)-Li12HS. Also, the higher frequency of hydrogen bonding leads to fewer solvent-exposed hydrogen bond partners. This explains why lithium is a common counterion in high-temperature and water-resistant greases.

Prediction of Thermodynamic Properties of Levulinic Acid via Molecular Simulation Techniques

Second-generation biofuels are a complex mixture of organic compounds that can be further processed to hydrocarbon fuels and other valuable chemicals. One such chemical is levulinic acid (IUPAC name: 4-oxo pentanoic acid), which is a highly versatile ketoacid obtained from cellulose present in agricultural byproducts. For oxygen-containing compounds that decompose at elevated temperatures and pressures, determining the vapor-liquid equilibria data at high temperatures via the experimental route may be challenging. The molecular simulation approach is a cost-effective tool to obtain the necessary data while also allowing us to understand the microscopic origins of macroscopic observable properties. We have employed the transferable potential for phase equilibria-united atom force field to describe the interactions in this system with the parameters for a torsional interaction that are not reported in the literature (levulinic acid is a ketoacid) being determined from density functional theory calculations. We have verified our parameterization via density computations in the isothermal-isobaric ensemble and by comparing our simulation results with the corresponding data from experiments reported in the literature. We have performed grand-canonical transition-matrix Monte Carlo simulations in the temperature range from 580 to 690 K to estimate the vapor-liquid coexistence curves in the temperature-density plane and the Clapeyron plots. From this data, the critical point (T C = 755 K, ρC = 285.4 kg/m3, and P C = 30.57 bar) has been estimated, and this may be used as input to the equations of state employed in process simulation software for design of industrial separation processes including those for "biorefining". As levulinic acid is a "ketoacid", hydrogen bonding occurs, and the liquid phase structure has also been studied using radial distribution functions.

Ultra-Coarse-Grained Liquid State Models with Implicit Hydrogen Bonding

Coarse-graining (CG) methodologies have been widely used to extend the time and length scales of computer simulations by averaging over the atomistic details beneath the resolution of the CG models. Despite the efficiency of CG models, important configurational information during a given process may be lost at the CG resolution. One example of this is the topology of the hydrogen bonding network in the liquid state. When the functional group that participates in hydrogen bonding (e.g., -OH in methanol) is coarse-grained into one CG site, the effective interactions of the resultant CG model are usually derived from an averaged overall trajectory and, thus, do not take into account the hydrogen bonding interactions and topologies that are present at the all-atom resolution. In order to overcome this challenge, the present study develops new ultra-coarse-grained (UCG) models that include internal states within the CG sites that participate in hydrogen bonding, where each state represents a specific configuration such as the hydrogen bonding donor or acceptor. Internal states of the UCG beads are modeled to remain in quasi-equilibrium, and the degree of mixing is controlled by utilizing the effective local density of the UCG sites. In particular, we consider two groups of UCG models with different types of hydrogen bonding motifs: chain-like and ring-like. Using five different liquid systems that contain the same fundamental functional groups as biomolecules, we demonstrate the ability of the UCG models to reproduce the structural properties that originate from the configurations beneath the resolution of the UCG model. This proposed approach can also be applied to other liquids with such specific and directional interactions, or even to complex biomolecular systems in which hydrogen bonding is critical.

Effects of Optical Purity and Finite System Size on Self-Assembly of 12-Hydroxystearic Acid in Hexane: Molecular Dynamics Simulations

12-Hydroxystearic acid (12HSA) and its derivatives are well-known organogelators, and they play critical roles in a variety of applications. The overall aggregate structure of 12HSA is sensitive to the chirality at the 12th carbon, but a fundamental understanding of this dependence is lacking. In this study, molecular dynamics simulations were conducted on microsecond long time scales for (1) (R)-12HSA, (2) (S)-12HSA, and (3) a 50/50 racemic mixture, each solvated at 12.5 wt % in explicit hexane. Self-assembly was accelerated by turning off alkyl chain dihedral gauche states and forcing the molecules to adopt an all-trans conformation. The stability of the resulting aggregates was tested by quenching them with access to gauche states restored. Ordered aggregates produced from optically pure (R)- and (S)-12HSA remained stable for at least 1 μs. The characteristic ordered structure observed is termed a "ring-of-rings" motif, and it contains two twisted six-membered ringlike bundles connected through acetic acid dimerization and surrounded by six satellite bundles. The chirality at the 12th carbon dictates the overall twist of the rings and thereby the handedness of the aggregates. Racemic mixtures did not produce stable ordered aggregates likely due to insufficient enantiomerically pure ring formation. The most prevalent finite-size effect observed was the stochastic formation of percolating aggregates, which were later avoided by using solvent-permeable, solute-impermeable, confining walls. The resulting ordered aggregates were in all important ways identical to those produced in unconfined systems. The combination of cycling off and on gauche states and the semipermeable walls may be an important new way to study the self-assembly underlying aggregation at industrially relevant concentrations of surfactants in organic solvents.

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed.

Ionic aggregate structure in ionomer melts: effect of molecular architecture on aggregates and the ionomer peak

We perform a comprehensive set of coarse-grained molecular dynamics simulations of ionomer melts with varying polymer architectures and compare the results to experiments in order to understand ionic aggregation on a molecular level. The model ionomers contain periodically or randomly spaced charged beads, placed either within or pendant to the polymer backbone, with the counterions treated explicitly. The ionic aggregate structure was determined as a function of the spacing of charged beads and also depends on whether the charged beads are in the polymer backbone or pendant to the backbone. The low wavevector ionomer peak in the counterion scattering is observed for all systems, and it is sharpest for ionomers with periodically spaced pendant charged beads with a large spacing between charged beads. Changing to a random or a shorter spacing moves the peak to lower wavevector. We present new experimental X-ray scattering data on Na(+)-neutralized poly(ethylene-co-acrylic acid) ionomers that show the same two trends in the ionomer peak, for similarly structured ionomers. The order within and between aggregates, and how this relates to various models used to fit the ionomer peak, is quantified and discussed.

Salt-mediated self-assembly of thioctic acid on gold nanoparticles

Self-assembled monolayer (SAM) modification is a widely used method to improve the functionality and stability of bulk and nanoscale materials. For instance, the chemical compatibility and utility of solution-phase nanoparticles are often improved using covalently bound SAMs. Herein, solution-phase gold nanoparticles are modified with thioctic acid SAMs in the presence and absence of salt. Molecular packing density on the nanoparticle surfaces is estimated using X-ray photoelectron spectroscopy and increases by ∼20% when molecular self-assembly occurs in the presence versus the absence of salt. We hypothesize that as the ionic strength of the solution increases, pinhole and collapsed-site defects in the SAM are more easily accessible as the electrostatic interaction energy between adjacent molecules decreases, thereby facilitating the subsequent assembly of additional thioctic acid molecules. Significantly, increased SAM packing densities increase the stability of functionalized gold nanoparticles by a factor of 2 relative to nanoparticles functionalized in the absence of salt. These results are expected to improve the reproducible functionalization of solution-phase nanomaterials for various applications.

Effect of polymer architecture and ionic aggregation on the scattering peak in model ionomers

We perform molecular dynamics simulations of coarse-grained ionomer melts with two different architectures. Regularly spaced charged beads are placed either in the polymer backbone (ionenes) or pendant to it. The ionic aggregate structure is quantified as a function of the dielectric constant. The low wave vector ionomer scattering peak is present in all cases, but is significantly more intense for pendant ions, which form compact, discrete aggregates with liquidlike interaggregate order. This is in qualitative contrast to the ionenes, which form extended aggregates.