1
|
Scalfi L, Vitali D, Kiefer H, Netz RR. Frequency-dependent hydrodynamic finite size correction in molecular simulations reveals the long-time hydrodynamic tail. J Chem Phys 2023; 158:2890455. [PMID: 37184000 DOI: 10.1063/5.0151406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/07/2023] [Indexed: 05/16/2023] Open
Abstract
Finite-size effects are challenging in molecular dynamics simulations because they have significant effects on computed static and dynamic properties, in particular diffusion constants, friction coefficients, and time- or frequency-dependent response functions. We investigate the influence of periodic boundary conditions on the velocity autocorrelation function and the frequency-dependent friction of a particle in a fluid, and show that the long-time behavior (starting at the picosecond timescale) is significantly affected. We develop an analytical correction allowing us to subtract the periodic boundary condition effects. By this, we unmask the power-law long-time tails of the memory kernel and the velocity autocorrelation function in liquid water and a Lennard-Jones fluid from simulations with rather small box sizes.
Collapse
Affiliation(s)
- Laura Scalfi
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Domenico Vitali
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Henrik Kiefer
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Roland R Netz
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| |
Collapse
|
2
|
Tillotson MJ, Diamantonis NI, Buda C, Bolton LW, Müller EA. Molecular modelling of the thermophysical properties of fluids: expectations, limitations, gaps and opportunities. Phys Chem Chem Phys 2023; 25:12607-12628. [PMID: 37114325 DOI: 10.1039/d2cp05423j] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
This manuscript provides an overview of the current state of the art in terms of the molecular modelling of the thermophysical properties of fluids. It is intended to manage the expectations and serve as guidance to practising physical chemists, chemical physicists and engineers in terms of the scope and accuracy of the more commonly available intermolecular potentials along with the peculiarities of the software and methods employed in molecular simulations while providing insights on the gaps and opportunities available in this field. The discussion is focused around case studies which showcase both the precision and the limitations of frequently used workflows.
Collapse
Affiliation(s)
- Marcus J Tillotson
- Department of Chemical Engineering, Imperial College London, London, UK.
| | | | | | | | - Erich A Müller
- Department of Chemical Engineering, Imperial College London, London, UK.
| |
Collapse
|
3
|
Schmitt S, Fleckenstein F, Hasse H, Stephan S. Comparison of Force Fields for the Prediction of Thermophysical Properties of Long Linear and Branched Alkanes. J Phys Chem B 2023; 127:1789-1802. [PMID: 36802607 DOI: 10.1021/acs.jpcb.2c07997] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The prediction of thermophysical properties at extreme conditions is an important application of molecular simulations. The quality of these predictions primarily depends on the quality of the employed force field. In this work, a systematic comparison of classical transferable force fields for the prediction of different thermophysical properties of alkanes at extreme conditions, as they are encountered in tribological applications, was carried out using molecular dynamics simulations. Nine transferable force fields from three different classes were considered (all-atom, united-atom, and coarse-grained force fields). Three linear alkanes (n-decane, n-icosane, and n-triacontane) and two branched alkanes (1-decene trimer and squalane) were studied. Simulations were carried out in a pressure range between 0.1 and 400 MPa at 373.15 K. For each state point, density, viscosity, and self-diffusion coefficient were sampled, and the results were compared to experimental data. The Potoff force field yielded the best results.
Collapse
Affiliation(s)
- Sebastian Schmitt
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern 67663, Germany
| | - Florian Fleckenstein
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern 67663, Germany
| | - Hans Hasse
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern 67663, Germany
| | - Simon Stephan
- Laboratory of Engineering Thermodynamics (LTD), RPTU Kaiserslautern, Kaiserslautern 67663, Germany
| |
Collapse
|
4
|
Oliveira MP, Gonçalves YMH, Ol Gheta SK, Rieder SR, Horta BAC, Hünenberger PH. 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. J Chem Theory Comput 2022; 18:6757-6778. [PMID: 36190354 DOI: 10.1021/acs.jctc.2c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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 ρliq and vaporization enthalpies ΔHvap 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 κT, the isobaric thermal-expansion coefficient αP, the isobaric heat capacity cP, the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔGwat, and the free energy of solvation ΔGche in cyclohexane. For the target properties ρliq and ΔHvap, 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, κT, αP, ϵ, D, and ΔGche; and less accurate results in terms of cP and ΔGwat. This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution.
Collapse
Affiliation(s)
- Marina P Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Yan M H Gonçalves
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - S Kashef Ol Gheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A C Horta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| |
Collapse
|
5
|
Iwashita T, Nagao M, Yoshimori A, Terazima M, Akiyama R. Usefulness of higher-order system-size correction for macromolecule diffusion coefficients: A molecular dynamics study. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
6
|
Are all-atom any better than united-atom force fields for the description of liquid properties of alkanes? 2. A systematic study considering different chain lengths. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118829] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
7
|
Montes-Zavala I, Castrejón-González EO, Rico-Ramírez V, Pérez E, Santamaría-Razo DA, González-Calderón JA. Which is better? Experimental and simulation analyses of the chemical modification of carbon nanotubes to improve their dispersion in water. J DISPER SCI TECHNOL 2021. [DOI: 10.1080/01932691.2020.1763179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- I. Montes-Zavala
- Departamento de Ingeniería Química, Tecnológico Nacional de México en Celaya, Celaya, Guanajuato, México
| | - E. O. Castrejón-González
- Departamento de Ingeniería Química, Tecnológico Nacional de México en Celaya, Celaya, Guanajuato, México
| | - V. Rico-Ramírez
- Departamento de Ingeniería Química, Tecnológico Nacional de México en Celaya, Celaya, Guanajuato, México
| | - Elias Pérez
- Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | | | - J. A. González-Calderón
- Cátedras CONACYT-Instituto de Física, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| |
Collapse
|
8
|
Erdős M, Frangou M, Vlugt TJH, Moultos OA. Diffusivity of α-, β-, γ-cyclodextrin and the inclusion complex of β-cyclodextrin: Ibuprofen in aqueous solutions; A molecular dynamics simulation study. FLUID PHASE EQUILIBRIA 2021; 528:112842. [PMID: 33024350 PMCID: PMC7529625 DOI: 10.1016/j.fluid.2020.112842] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/03/2020] [Accepted: 09/18/2020] [Indexed: 05/28/2023]
Abstract
Cyclodextrins (CDs) are widely used in drug delivery, catalysis, food and separation processes. In this work, a comprehensive simulation study on the diffusion of the native α-, β- and γ-CDs in aqueous solutions is carried out using Molecular Dynamics simulations. The effect of the system size on the computed self-diffusivity is investigated and it is found that the required correction can be as much as 75% of the final value. The effect of the water force field is examined and it is shown that the q4md-CD/TIP4P/2005 force field combination predicts the experimentally measured self-diffusion coefficients of CDs very accurately. The self-diffusion coefficients of the three native CDs were also computed in aqueous-NaCl solutions using the Joung and Cheatham (JC) and the Madrid-2019 force fields. It is found that Na+ ions have higher affinity towards the CDs when the JC force field is used and for this reason the predicted diffusivity of CDs is lower compared to simulations using the Madrid-2019 force field. As a model system for drug delivery and waste-water treatment applications, the diffusion of the β-CD:Ibuprofen inclusion complex in water is studied. In agreement with experiments for similar components, it is shown that the inclusion complex and the free β-CD have almost equal self-diffusion coefficients. Our analysis revealed that this is most likely caused by the almost full inclusion of the ibuprofen in the cavity of the β-CD. Our findings show that Molecular Dynamics simulation can be used to provide reasonable diffusivity predictions, and to obtain molecular-level understanding useful for industrial applications of CDs.
Collapse
Affiliation(s)
- Máté Erdős
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, Delft 2628CB, The Netherlands
| | - Michalis Frangou
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, Delft 2628CB, The Netherlands
| | - Thijs J H Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, Delft 2628CB, The Netherlands
| | - Othonas A Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, Delft 2628CB, The Netherlands
| |
Collapse
|
9
|
Leverant CJ, Harvey JA, Alam TM. Machine Learning-Based Upscaling of Finite-Size Molecular Dynamics Diffusion Simulations for Binary Fluids. J Phys Chem Lett 2020; 11:10375-10381. [PMID: 33236915 DOI: 10.1021/acs.jpclett.0c03108] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Molecular diffusion coefficients calculated using molecular dynamics (MD) simulations suffer from finite-size (i.e., finite box size and finite particle number) effects. Results from finite-sized MD simulations can be upscaled to infinite simulation size by applying a correction factor. For self-diffusion of single-component fluids, this correction has been well-studied by many researchers including Yeh and Hummer (YH); for binary fluid mixtures, a modified YH correction was recently proposed for correcting MD-predicted Maxwell-Stephan (MS) diffusion rates. Here we use both empirical and machine learning methods to identify improvements to the finite-size correction factors for both self-diffusion and MS diffusion of binary Lennard-Jones (LJ) fluid mixtures. Using artificial neural networks (ANNs), the error in the corrected LJ fluid diffusion is reduced by an order of magnitude versus existing YH corrections, and the ANN models perform well for mixtures with large dissimilarities in size and interaction energies where the YH correction proves insufficient.
Collapse
Affiliation(s)
- Calen J Leverant
- Department of WMD Threats & Aerosol Science, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
- Department of Chemical Engineering, University of Florida, Gainesville, Florida 32611, United States
| | - Jacob A Harvey
- Department of Geochemistry, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Todd M Alam
- Department of Organic Materials Science, Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| |
Collapse
|
10
|
da Silva GCQ, Silva GM, Tavares FW, Fleming FP, Horta BAC. Are all-atom any better than united-atom force fields for the description of liquid properties of alkanes? J Mol Model 2020; 26:296. [PMID: 33026509 DOI: 10.1007/s00894-020-04548-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/14/2020] [Indexed: 11/28/2022]
Abstract
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.
Collapse
Affiliation(s)
- Guilherme C Q da Silva
- Instituto de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos 149, CT, Bl. A-622, Cid. Univ., Rio de Janeiro, RJ, 21941-909, Brazil
| | | | - Frederico W Tavares
- Escola de Química (EQ) and Programa de Eng. Química (PEQ-COPPE), Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos 149, CT, Bl. A-622, Cid. Univ., Rio de Janeiro, RJ, 21941-909, Brazil
| | | | - Bruno A C Horta
- Instituto de Química, Universidade Federal do Rio de Janeiro, Av. Athos da Silveira Ramos 149, CT, Bl. A-622, Cid. Univ., Rio de Janeiro, RJ, 21941-909, Brazil.
| |
Collapse
|
11
|
Celebi AT, Jamali SH, Bardow A, Vlugt TJH, Moultos OA. Finite-size effects of diffusion coefficients computed from molecular dynamics: a review of what we have learned so far. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1810685] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alper T. Celebi
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Seyed Hossein Jamali
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - André Bardow
- Energy & Process Systems Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Zürich, Switzerland
| | - Thijs J. H. Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Othonas A. Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| |
Collapse
|
12
|
Kondratyuk N, Lenev D, Pisarev V. Transport coefficients of model lubricants up to 400 MPa from molecular dynamics. J Chem Phys 2020; 152:191104. [PMID: 33687262 DOI: 10.1063/5.0008907] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this paper, the predictive power of molecular dynamics methods is demonstrated for the cases of model paraffinic and aromatic lubricant liquids at pressures up to 400 MPa. The shear viscosity and self-diffusion coefficients are calculated for 2,2,4-trimethylpentane (C8H18) at 298 K and 1,1-diphenylethane (C14H14) at 333 K. Three force fields with different levels of accuracy are compared by the ability to predict the experimental data. The Stokes-Einstein correlation between viscosity and self-diffusion is demonstrated for both compounds.
Collapse
Affiliation(s)
- N Kondratyuk
- Joint Institute for High Temperatures Russian Academy of Sciences, Moscow, Russia
| | - D Lenev
- Joint Institute for High Temperatures Russian Academy of Sciences, Moscow, Russia
| | - V Pisarev
- Joint Institute for High Temperatures Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|