Peacemaker 2: Making clusters talk about binary mixtures and neat liquids

Domaros, Michael von; Perlt, Eva; Ingenmey, Johannes; Marchelli, Gwydyon; Kirchner, Barbara

doi:10.1016/j.softx.2018.11.002

“…As a first step, to find clusters, we performed a global minimum structure search for each cluster size and composition by running the genetic optimization algorithm OGOLEM [50,51] at the force field level of theory, using the AMBER 2016 program package [52] and the GAFF force field [53] implemented therein. The AMBER/OGOLEM combination is optimized to screen a great number of individual clusters [27,32,38] . The number of individuals per generation was varied between 80 and 240 in accordance to the cluster size to adjust for the increasing complexity.…”

Section: Computational Detailsmentioning

confidence: 99%

“…Boltzmann and bQCE weighting were compared in the past by our group in the field of the computational calculation of vibrational circular dichroism spectra of bulk phase, showing the advantages of our method over Boltzmann weighting [29] . For this purpose we use our in‐house code Peacemaker 2.8, which has proven to be a valuable tool to investigate the thermodynamic properties of both neat and mixed systems [27,30–38] . The standard bQCE method involves optimization of two empirical parameters by fitting them to a set of experimental data such as boiling points or isobars; however, even for simple mixtures of organic solvents, these data are often unavailable in the literature.…”

Section: Introductionmentioning

confidence: 99%

Hydrogen Bonding and Vaporization Thermodynamics in Hexafluoroisopropanol‐Acetone and ‐Methanol Mixtures. A Joined Cluster Analysis and Molecular Dynamic Study

Marchelli

¹

,

Ingenmey

²

,

Hollóczki

³

et al. 2021

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Binary mixtures of hexafluoroisopropanol with either methanol or acetone are analyzed via classical molecular dynamics simulations and quantum cluster equilibrium calculations. In particular, their populations and thermodynamic properties are investigated with the binary quantum cluster equilibrium method, using our in-house code Peacemaker 2.8, upgraded with temperature-dependent parameters. A novel approach, where the final density from classical molecular dynamics, has been used to generate the necessary reference isobars. The hydrogen bond network in both type of mixtures at molar fraction of hexafluoroisopropanol of 0.2, 0.5, and 0.8 respectively is investigated via the molecular dynamics trajectories and the cluster results. In particular, the populations show that mixed clusters are preferred in both systems even at 0.2 molar fractions of hexafluoroisopropanol. Enthalpies and entropies of vaporization are calculated for the neat and mixed systems and found to be in good agreement with experimental values.

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“…Another result of this strong interaction is that potassium vapor is known to consist of about 5% dimers at the NBP. 39,40 However, exploring the impact of dimerization using the Quantum-Cluster Equilibrium (QCE) approach as implemented in the Peacemaker program 41,42 revealed that this has negligible influence on the free energy at 1000 K (< 1 meV). The reason is that the decrease in entropy just cancels the stabilizing effects on internal energy and volume (pV ).…”

Section: Detailed Considerations For Xe K and Bmentioning

confidence: 99%

Predicting Elemental Boiling Points from First Principles

Mewes¹

2020

Preprint

0

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<div>The normal boiling point (NBP) is a fundamental property of liquids and marks the intersection of the Gibb’s free energies of the liquid and the gas phase at ambient pressure. In this work, we present the first comprehensive demonstration of an approach to calculate the boiling point of atomic liquids from first-principles molecular-dynamics simulations. To this end, we combine thermodynamic integration (TDI) and perturbation theory (TPT) with a density-functional theory (DFT) Hamiltonian to deliver converged absolute liquid free energies and entropies. Linear extrapolation to the intersection with the gas phase provides NBPs, which are corrected for systematic over- or under-binding of the DFT Hamiltonian, thereby eliminating any strong dependency on the density functional. Through fine-tuning of the TDI, we reduced the walltime from weeks to about a day per element (10 − 20k core-hours), which enables extensive testing for B, Al, Na, K, Ca, Sr, Ba, Mn, Cu, Xe and Hg. This demonstrates the excellent performance and particular robustness of the approach. With a mean absolute deviation (MAD) of less than 2% from experimental references, and very similar accuracy for liquid entropies (MAD 2.3 J/(mol*K), 2% relative), the overall deviation is several times smaller than the variation between literature values for several elements.</div>

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“…Another result of this strong interaction is that potassium vapor is known to consist of about 5% dimers at the NBP. 39,40 However, exploring the impact of dimerization using the Quantum-Cluster Equilibrium (QCE) approach as implemented in the Peacemaker program 41,42 revealed that this has negligible influence on the Gibbs energy at 1000 K (< 1 meV). The reason is that the decrease in entropy just cancels the stabilizing effects on internal energy and volume (pV ).…”

Section: Detailed Considerations For Xe K and Bmentioning

confidence: 99%

Predicting Elemental Boiling Points from First Principles

Mewes¹,

Smits²

2020

Preprint

0

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<div>The normal boiling point (NBP) is a fundamental property of liquids and marks the intersection of the Gibb’s free energies of the liquid and the gas phase at ambient pressure. In this work, we present the first comprehensive demonstration of an approach to calculate the boiling point of atomic liquids from first-principles molecular-dynamics simulations. To this end, we combine thermodynamic integration (TDI) and perturbation theory (TPT) with a density-functional theory (DFT) Hamiltonian to deliver converged absolute liquid free energies and entropies. Linear extrapolation to the intersection with the gas phase provides NBPs, which are corrected for systematic over- or under-binding of the DFT Hamiltonian, thereby eliminating any strong dependency on the density functional. Through fine-tuning of the TDI, we reduced the walltime from weeks to about a day per element (10 − 20k core-hours), which enables extensive testing for B, Al, Na, K, Ca, Sr, Ba, Mn, Cu, Xe and Hg. This demonstrates the excellent performance and particular robustness of the approach. With a mean absolute deviation (MAD) of less than 2% from experimental references, and very similar accuracy for liquid entropies (MAD 2.3 J/(mol*K), 2% relative), the overall deviation is several times smaller than the variation between literature values for several elements.</div>

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Peacemaker 2: Making clusters talk about binary mixtures and neat liquids

Cited by 33 publications

References 20 publications

Hydrogen Bonding and Vaporization Thermodynamics in Hexafluoroisopropanol‐Acetone and ‐Methanol Mixtures. A Joined Cluster Analysis and Molecular Dynamic Study

Hydrogen Bonding and Vaporization Thermodynamics in Hexafluoroisopropanol‐Acetone and ‐Methanol Mixtures. A Joined Cluster Analysis and Molecular Dynamic Study

Predicting Elemental Boiling Points from First Principles

Predicting Elemental Boiling Points from First Principles

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