Thermodynamic Perturbation Theory Research Articles

Thermodynamics of the gas-phase dimerization of formic acid: Fully anharmonic finite temperature calculations at the CCSD(T) and many DFT levels.

A proof-of-concept study is undertaken to demonstrate the utility of the machine learning combined with the thermodynamic perturbation theory (MLPT) to test the accuracy of electronic structure methods in finite-temperature thermodynamic calculations. As a test example, formic acid dimer is chosen, which is one of the systems included in the popular benchmark set S22 [Jurečka et al., Phys. Chem. Chem. Phys. 8, 1985-1993 (2006)]. Starting from the explicit molecular dynamics and thermodynamic integration performed at the PBE + D2 level, the MLPT is used to obtain fully anharmonic dimerization free and internal energies at the reference quality CCSD(T) level and 19 different density functional approximations, including GGA, meta-GGA, non-local, and hybrid functionals with and without dispersion corrections. Our finite-temperature results are shown to be both qualitatively and quantitatively different from those obtained using the conventional benchmarking strategy based on fixed structures. The hybrid functional HSE06 is identified as the best performing approximate method tested, with the errors in free and internal energies of dimerization being 36 and 41meV, respectively.

Generic low-density corrections to the equation of state of chain molecules with repulsive intermolecular forces.

Molecular-based equations of state for describing the thermodynamics of chain molecules are often based on mean-field like arguments that reduce the problem of describing the interactions between chains to a simpler one involving only nonbonded monomers. While for dense liquids such arguments are known to work well, at low density they are typically less appropriate due to an incomplete description of the effect of chain connectivity on the local environment of the chains' monomer segments. To address this issue, we develop three semi-empirical approaches that significantly improve the thermodynamic description of chain molecules at low density. The approaches are developed for chain molecules with repulsive intermolecular forces; therefore, they could be used as reference models for developing equations of the state of real fluids based on perturbation theory. All three approaches are extensions of Wertheim's first-order thermodynamic perturbation theory (TPT1) for polymerization. The first model, referred to as TPT1-v, incorporates a second-virial correction that is scaled to zero at liquid-like densities. The second model, referred to as TPT1-y, introduces a Helmholtz-energy contribution to account for correlations between next-nearest-neighbor segments within chain molecules. The third approach, called TPT-E, directly modifies TPT1 without utilizing an additional Helmholtz energy contribution. By employing TPT1 at the core of these approaches, we ensure an accurate description of mixtures and enable a seamless extension from chains of tangentially bonded hard-sphere segments of equal size to hetero-segmented chains, fused chains, and chains of soft repulsive segments (which are influenced by temperature). The low-density corrections implemented in TPT1 are designed to preserve these good characteristics, as confirmed through comparisons with novel molecular simulation results for the pressure of various chain fluids. TPT1-v exhibits excellent transferability across different chain types, but it relies on knowing the second virial coefficient of the chain molecules, which is non-trivial to obtain and determined here using Monte Carlo simulation. The TPT1-y model, on the other hand, achieves comparable accuracy to TPT1-v while being fully predictive, requiring no input besides the geometry of the chain molecules.

Computational Procedure for Predicting Excipient Effects on Protein-Protein Affinities.

Protein-protein interactions lie at the center of many biological processes and are a challenge in formulating biological drugs, such as antibodies. A key to mitigating protein association is to use small-molecule additives, i.e., excipients that can weaken protein-protein interactions. Here, we develop a computationally efficient model for predicting the viscosity-reducing effect of different excipient molecules by combining atomic-resolution MD simulations, binding polynomials, and a thermodynamic perturbation theory. In a proof of principle, this method successfully ranks the order of four types of excipients known to reduce the viscosity of solutions of a particular monoclonal antibody. This approach appears useful for predicting the effects of excipients on protein association and phase separation, as well as the effects of buffers on protein solutions.

Reference-Quality Free Energy Barriers in Catalysis from Machine Learning Thermodynamic Perturbation Theory.

For the first time, we report calculations of the free energies of activation of cracking and isomerization reactions of alkenes that combine several different electronic structure methods with molecular dynamics simulations. We demonstrate that the use of a high level of theory (here Random Phase Approximation-RPA) is necessary to bridge the gap between experimental and computed values. These transformations, catalyzed by zeolites and proceeding via cationic intermediates and transition states, are building blocks of many chemical transformations for valorization of long chain paraffins originating, e.g., from plastic waste, vegetable oils, Fischer-Tropsch waxes or crude oils. Compared with the free energy barriers computed at the PBE+D2 production level of theory via constrained ab initio molecular dynamics, the barriers computed at the RPA level by the application of Machine Learning thermodynamic Perturbation Theory (MLPT) show a significant decrease for isomerization reaction and an increase of a similar magnitude for cracking, yielding an unprecedented agreement with the results obtained by experiments and kinetic modeling.

Reference‐Quality Free Energy Barriers in Catalysis from Machine Learning Thermodynamic Perturbation Theory

AbstractFor the first time, we report calculations of the free energies of activation of cracking and isomerization reactions of alkenes that combine several different electronic structure methods with molecular dynamics simulations. We demonstrate that the use of a high level of theory (here Random Phase Approximation—RPA) is necessary to bridge the gap between experimental and computed values. These transformations, catalyzed by zeolites and proceeding via cationic intermediates and transition states, are building blocks of many chemical transformations for valorization of long chain paraffins originating, e.g., from plastic waste, vegetable oils, Fischer–Tropsch waxes or crude oils. Compared with the free energy barriers computed at the PBE+D2 production level of theory via constrained ab initio molecular dynamics, the barriers computed at the RPA level by the application of Machine Learning thermodynamic Perturbation Theory (MLPT) show a significant decrease for isomerization reaction and an increase of a similar magnitude for cracking, yielding an unprecedented agreement with the results obtained by experiments and kinetic modeling.

Thermodynamics perturbation theory for solvation of nonpolar solutes in rose model.

A simple model of water, called the rose model, is used in this work. The rose model is a very simple model that can provide insight into the anomalous properties of water. In the rose water model, the molecules are represented as two-dimensional Lennard-Jones disks with potentials for orientation-dependent pairwise interactions mimicking formations of hydrogen bonds. We have recently applied a Wertheim integral equationtheory (IET) and a thermodynamic perturbation theory (TPT) to the rose model in bulk. These analytical theories offer the advantage of being computationally less intensive than computer simulations by orders of magnitudes. Here we have applied the TPT to study the transfer of a nonpolar solute into rose water, the so-called hydrophobic effect. Similarly as in our previous work for bulk water, we have found that the theory reproduces the computer simulation results quite well at higher temperatures, while the theories predict the qualitative trends at low temperatures.

Crystal structure prediction at finite temperatures

Crystal structure prediction is a central problem of crystallography and materials science, which until mid-2000s was considered intractable. Several methods, based on either energy landscape exploration or, more commonly, global optimization, largely solved this problem and enabled fully non-empirical computational materials discovery. A major shortcoming is that, to avoid expensive calculations of the entropy, crystal structure prediction was done at zero Kelvin, reducing to the search for the global minimum of the enthalpy rather than the free energy. As a consequence, high-temperature phases (especially those which are not quenchable to zero temperature) could be missed. Here we develop an accurate and affordable solution, enabling crystal structure prediction at finite temperatures. Structure relaxation and fully anharmonic free energy calculations are done by molecular dynamics with a forcefield (which can be anything from a parametric forcefield for simpler cases to a trained on-the-fly machine learning interatomic potential), the errors of which are corrected using thermodynamic perturbation theory to yield accurate results with full ab initio accuracy. We illustrate this method by applications to metals (probing the P–T phase diagram of Al and Fe), a refractory covalent solid (WB), an Earth-forming silicate MgSiO3 (at pressures and temperatures of the Earth’s lower mantle), and ceramic oxide HfO2.

Second virial coefficient, Boyle temperature and equation of state of van Hove fluids with a downward concavity attractive parabolic-well

The second virial coefficient, the Boyle temperature and the equation of state of van Hove fluids with a relatively short ranged attractive parabolic-well of downward concavity are considered. The analytic second virial coefficient for this fluid is obtained explicitly and it is used to compute the Boyle temperature of the fluid as a function of the range of the potential. Further, an equation of state is derived using the second-order thermodynamic perturbation theory of Barker and Henderson in the macroscopic compressibility approximation, with the hard-sphere fluid being the reference fluid. For this latter we profit from the fully analytical expression of the radial distribution function, consistent with the Carnahan-Starling equation state, derived within the so-called rational function approximation method up to a range twice the size of the hard-core diameter. The results for the reduced pressure of the fluid as a function of the packing fraction and two values of the range of the potential well at different temperatures are compared with Monte Carlo simulation data. Estimates of the values of the critical temperature are also provided.

Two-dimensional ordering of bacteriorhodopsins in a lipid bilayer and effects caused by repulsive core between lipid molecules on lateral depletion interaction: A study based on a thermodynamic perturbation theory

Using binary hard disk mixture models, we studied the two-dimensional ordering of bacteriorhodopsins in a lipid bilayer. The phase diagrams were calculated using the thermodynamic perturbation theory. We examined two types of effective interactions to discuss the lateral depletion effects caused by repulsive core interaction between lipid molecules. The results indicate that the core repulsions drastically broaden the coexistence region for the fluid-ordered phase.

IMPROVEMENT OF THE MATHEMATICAL DESCRIPTION OF THERMOPHYSICAL PROPERTIES OF ALTERNATIVE MOTOR FUELS BASED ON THE MODIFIED THERMODYNAMIC THEORY OF DISTURBANCE. PART 2

In the study, the purpose of which was to improve the mathematical apparatus based on the modified thermodynamic perturbation theory for describing the thermophysical characteristics of alternative motor fuels with a spherical configuration of interacting structural elements and an arbitrary aggregate state, the formal scheme of the modified perturbation theory was consistently constructed, the main characteristics of the model system were described, the parameters of the interaction potentials of the alternative fuel components were described, the thermophysical properties of the alternative fuel components were obtained by calculation, the thermodynamic properties of the alternative fuel components were calculated, the results of the calculation of the thermodynamic characteristics of the alternative fuel were analyzed and illustrated in the form of isotherm of phase equilibrium diagrams and data tables. The object of the study is the thermophysical characteristics of traditional, alternative and mixed motor fuels in a liquid or gaseous aggregate state. The subject of the study is a mathematical apparatus based on the modified thermodynamic perturbation theory for describing the thermophysical characteristics of motor fuels. The scientific novelty of the study results lies in the fact that a mathematical apparatus based on a modified perturbation theory has been improved for a comprehensive description of all thermophysical characteristics of motor fuels of any genesis, i.e. traditional, alternative and mixed, which are in both liquid and gaseous aggregate states in terms of reducing the calculation time and reducing the error of obtaining thermophysical characteristics in comparison with reference and experimental data. The practical significance of the research results is that the improved mathematical apparatus is marketable for providing accurate information to the composition of the initial data set in research on the production, storage, transportation, distribution, use of motor fuels of any genesis, which are in different states, as well as forecasting the course and results of processes of atmospheric pollution by gaseous products of complete and incomplete combustion of fuel components in combustion chambers of various types of heat engines.

IMPROVEMENT OF THE MATHEMATICAL DESCRIPTION OF THERMOPHYSICAL PROPERTIES OF ALTERNATIVE MOTOR FUELS BASED ON THE MODIFIED THERMODYNAMIC THEORY OF DISTURBANCE

In the study, the purpose of which was to improve the mathematical apparatus based on the modified thermodynamic perturbation theory for describing the thermophysical characteristics of alternative motor fuels with a spherical configuration of interacting structural elements and an arbitrary aggregate state, the formal scheme of the modified perturbation theory was consistently constructed, the main characteristics of the model system were described, the parameters of the interaction potentials of the alternative fuel components were described, the thermophysical properties of the alternative fuel components were obtained by calculation, the thermodynamic properties of the alternative fuel components were calculated, the results of the calculation of the thermodynamic characteristics of the alternative fuel were analyzed and illustrated in the form of isotherm of phase equilibrium diagrams and data tables. The object of the study is the thermophysical characteristics of traditional, alternative and mixed motor fuels in a liquid or gaseous aggregate state. The subject of the study is a mathematical apparatus based on the modified thermodynamic perturbation theory for describing the thermophysical characteristics of motor fuels. The scientific novelty of the study results lies in the fact that a mathematical apparatus based on a modified perturbation theory has been improved for a comprehensive description of all thermophysical characteristics of motor fuels of any genesis, i.e. traditional, alternative and mixed, which are in both liquid and gaseous aggregate states in terms of reducing the calculation time and reducing the error of obtaining thermophysical characteristics in comparison with reference and experimental data. The practical significance of the research results is that the improved mathematical apparatus is marketable for providing accurate information to the composition of the initial data set in research on the production, storage, transportation, distribution, use of motor fuels of any genesis, which are in different states, as well as forecasting the course and results of processes of atmospheric pollution by gaseous products of complete and incomplete combustion of fuel components in combustion chambers of various types of heat engines.

Ben Naim's four-arm model with density anomaly: Theory and computer simulations.

Molecular dynamics, Wertheim's integral equationtheory (IET), and thermodynamics perturbation theory (TPT) were used to study the thermodynamics and structure of particles interacting through angle-dependent potential. The particles are modeled as two-dimensional Lennard-Jones disks with four hydrogen bonding arms arranged symmetrically. The model was introduced by Ben-Naim and we call it the BN4 model. The BN4 model exhibits density anomaly and other anomalous properties similar to those in water and in the Mercedes-Benz (MB) model. The IET is based on the orientationally averaged version of the Ornstein-Zernike equationand correctly predicts the pair correlation function of the model at high temperatures. Both TPT and IET are in semiquantitative agreement with the simulation values of the molar volume, isothermal compressibility, thermal expansion coefficient, and heat capacity.

Mean ionic activity coefficient of associative electrolyte solutions: A comparison study

The performance of four implicit solvent models for associative and two models for non-associative electrolyte solutions has been compared and analyzed for the mean ionic activity coefficient (MIAC) of electrolytes in the solution. Two of these models for associative electrolyte solutions are based on a chemical approach (Fisher-Levin-Guillot-Guissani (FLGG) and Ebeling-Grigo (EG)), and one of them is based on the reference cavity approximation (Zhou-Yeh-Stell (ZYS)). The last one is based on the thermodynamic perturbation theory (Binding mean spherical approximation, BiMSA). Models without ion-pairing also consist of hard sphere (HS) contribution in addition to the electrostatic contribution from the Debye-Hückel (HS + DH) and the mean spherical approximation (HS + MSA) theories. To this aim, the models’ predictions are compared with the numerical solution of the Poisson-Boltzmann equation, the Monte Carlo simulations, and the experimental data. We have shown that considering the ion pairing results in a better agreement of the predicted MIAC against both simulations and experimental data of 2:2 electrolytes. We have also adjusted the ionic diameter and the distance between ion pairs to the MIAC experimental data and validated the estimated fractions of free ions with the electrical conductivity measurements. We have shown that the FLGG model captures the physics of the system more accurately compared to other models.

Modeling of polymer-enzyme conjugates formation: Thermodynamic perturbation theory and computer simulations

A simple model for the formation of the polymer-enzyme conjugates has been proposed and described using corresponding modification of the Wertheim's first-order thermodynamic perturbation theory (TPT) for the system of associating chain molecules. A set of computer simulation data for the polymer chains containing various number of functional groups was generated and used to testify the accuracy of the theoretical results. Predictions of the present theoretical approach are more accurate than that of the conventional TPT and are in a very good agreement with the computer simulation data. In particular, the theory is able to account for the difference in the position of the polymer functional groups along its backbone.

Modelling the solid–liquid–vapour phase behaviour of n-alkanes in a TPT-1 framework

We study the global phase behaviour of n-alkanes applying Wertheim's first order thermodynamic perturbation theory (TPT1). The molecules are modelled as homonuclear chains comprised of m freely jointed spherical segments interacting via the Lennard-Jones potential. Vega et al. [J. Chem. Phys. 116, 17 (2002)] have shown that the TPT1 is suitable to treat solid phases as well as fluid phases when model chains are considered, but that the adoption of a fully flexible chain model leads to the under-prediction of triple point temperatures and overestimation of the fluid ranges in comparison to experiment. Here, we propose a model in which a different number of segments are used to treat the fluid and the solid phase. The number of segments used to model the molecules in the fluid phase , and the LJ monomer potential parameters σ and ε are taken from published soft-SAFT values, whereas in the case of the solid phase a reduced temperature-dependent effective chain length is determined through a minimisation between theoretical and experimental liquid-solid phase equilibrium data. We refer to this model as effective-solid TPT1 (es-TPT1). We use the model proposed to calculate the solid–liquid–vapour phase diagrams of several n-alkanes and compare with experimental data. In the approach proposed, the conformation of chains in the solid phase is decoupled from the fluid phase, and an excellent description of the melting properties, as well as accurate predictions of the triple point temperatures for the n-alkanes examined is obtained. This simple solution provides an avenue to model the solid–liquid–vapour phase behaviour of other real substances in a TPT1 framework, and hence within the SAFT family of equations.

Classical density functional theory for interfacial properties of hydrogen, helium, deuterium, neon, and their mixtures.

We present a classical density functional theory (DFT) for fluid mixtures that is based on a third-order thermodynamic perturbation theory of Feynman-Hibbs-corrected Mie potentials. The DFT is developed to study the interfacial properties of hydrogen, helium, neon, deuterium, and their mixtures, i.e., fluids that are strongly influenced by quantum effects at low temperatures. White Bear fundamental measure theory is used for the hard-sphere contribution of the Helmholtz energy functional, and a weighted density approximation is used for the dispersion contribution. For mixtures, a contribution is included to account for non-additivity in the Lorentz-Berthelot combination rule. Predictions of the radial distribution function from DFT are in excellent agreement with results from molecular simulations, both for pure components and mixtures. Above the normal boiling point and 5% below the critical temperature, the DFT yields surface tensions of neon, hydrogen, and deuterium with average deviations from experiments of 7.5%, 4.4%, and 1.8%, respectively. The surface tensions of hydrogen/deuterium, para-hydrogen/helium, deuterium/helium, and hydrogen/neon mixtures are reproduced with a mean absolute error of 5.4%, 8.1%, 1.3%, and 7.5%, respectively. The surface tensions are predicted with an excellent accuracy at temperatures above 20K. The poor accuracy below 20K is due to the inability of Feynman-Hibbs-corrected Mie potentials to represent the real fluid behavior at these conditions, motivating the development of new intermolecular potentials. This DFT can be leveraged in the future to study confined fluids and assess the performance of porous materials for hydrogen storage and transport.

Soft fundamental measure theory functional for the Weeks-Chandler-Andersen repulsive potential.

We introduce a soft fundamental measure theory functional for the purely repulsive Weeks-Chandler-Andersen (WCA) fluid. This classical density functional could serve as a reference fluid for functionals created using thermodynamic perturbation theory instead of the hard-sphere fluid. Our functional incorporates temperature-dependent parameters describing the length scale and effective softness of the particle interaction, and which reproduce the second virial coefficient of the WCA fluid. We find that this approach is comparable in accuracy to the Barker-Henderson approach combined with the White Bear density functional for the hard-sphere fluid.

Dynamics of equilibrium-linked colloidal networks

Colloids that attractively bond to only a few neighbors (e.g., patchy particles) can form equilibrium gels with distinctive dynamic properties that are stable in time. Here, we use a coarse-grained model to explore the dynamics of linked networks of patchy colloids whose average valence is macroscopically, rather than microscopically, constrained. Simulation results for the model show dynamic hallmarks of equilibrium gel formation and establish that the colloid-colloid bond persistence time controls the characteristic slow relaxation of the self-intermediate scattering function. The model features re-entrant network formation without phase separation as a function of linker concentration, centered at the stoichiometric ratio of linker ends to nanoparticle surface bonding sites. Departures from stoichiometry result in linker-starved or linker-saturated networks with reduced connectivity and shorter characteristic relaxation times with lower activation energies. Underlying the re-entrant trends, dynamic properties vary monotonically with the number of effective network bonds per colloid, a quantity that can be predicted using Wertheim's thermodynamic perturbation theory. These behaviors suggest macroscopic in situ strategies for tuning the dynamic response of colloidal networks.

Liquid-vapour coexistence line and percolation line of rose water model

Monte Carlo simulations and Wertheim’s thermodynamic perturbation theory (TPT) are used to predict the phase diagram and percolation curve for the simple two-dimensional rose model of water. In the rose model of water, the water molecules are modelled as two-dimensional Lennard-Jones disks, with additional rose potentials for orientation dependent pairwise interactions that mimic formation of hydrogen bonds. Modifying both the shape and range of a 3-petal rose function, it was constructed an efficient and dynamical mimic of the 2D Mercedes Benz (MB) water model and experimental water. The liquid part of the phase space is explored using grand canonical Monte Carlo simulations and two versions of Wertheim’s TPT for associative fluids. We find that the theory reproduces well the physical properties of hot water but is less successful at capturing the more structured hydrogen bonding that occurs in cold water. In addition to reporting the phase diagram and percolation curve of the model, it is shown that the improved TPT predicts the phase diagram rather well, while the standard one predicts a phase transition at lower temperatures. For the percolation line, both versions have problems predicting the correct position of the line at high temperatures.

Study of Versions of Thermodynamic Perturbation Theory for Simulation of the Properties of Binary Mixtures of Fluids in Wide Ranges of Pressures and Temperatures

Study of Versions of Thermodynamic Perturbation Theory for Simulation of the Properties of Binary Mixtures of Fluids in Wide Ranges of Pressures and Temperatures