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Domingues TS, Coifman R, Haji-Akbari A. Estimating Position-Dependent and Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories: Existing Methods and Future Outlook. J Chem Theory Comput 2024; 20:4427-4455. [PMID: 38815171 DOI: 10.1021/acs.jctc.4c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Confinement can substantially alter the physicochemical properties of materials by breaking translational isotropy and rendering all physical properties position-dependent. Molecular dynamics (MD) simulations have proven instrumental in characterizing such spatial heterogeneities and probing the impact of confinement on materials' properties. For static properties, this is a straightforward task and can be achieved via simple spatial binning. Such an approach, however, cannot be readily applied to transport coefficients due to lack of natural extensions of autocorrelations used for their calculation in the bulk. The prime example of this challenge is diffusivity, which, in the bulk, can be readily estimated from the particles' mobility statistics, which satisfy the Fokker-Planck equation. Under confinement, however, such statistics will follow the Smoluchowski equation, which lacks a closed-form analytical solution. This brief review explores the rich history of estimating profiles of the diffusivity tensor from MD simulations and discusses various approximate methods and algorithms developed for this purpose. Besides discussing heuristic extensions of bulk methods, we overview more rigorous algorithms, including kernel-based methods, Bayesian approaches, and operator discretization techniques. Additionally, we outline methods based on applying biasing potentials or imposing constraints on tracer particles. Finally, we discuss approaches that estimate diffusivity from mean first passage time or committor probability profiles, a conceptual framework originally developed in the context of collective variable spaces describing rare events in computational chemistry and biology. In summary, this paper offers a concise survey of diverse approaches for estimating diffusivity from MD trajectories, highlighting challenges and opportunities in this area.
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Affiliation(s)
- Tiago S Domingues
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Ronald Coifman
- Department of Mathematics, Yale University, New Haven, Connecticut 06520, United States
- Department of Computer Science, Yale University, New Haven, Connecticut 06520, United States
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
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Micoulaut M. Pockets, jumps and filaments: classifying ionic motion and determining the role of structure in electrochemical properties of 2Li 2S-GeS 2superionic glasses. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:195703. [PMID: 38316043 DOI: 10.1088/1361-648x/ad266d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/05/2024] [Indexed: 02/07/2024]
Abstract
The structural properties of a typical solid electrolyte system (2Li2S-GeS2) is investigated from First principles molecular dynamics simulations. Results reveal that depolymerization of the base GeS2network by alkali additives takes place but appears reduced with respect to the corresponding sodium analog glass. Experimental structure functions are reproduced and reveal that the network is dominated by GeS4/2tetrahedra that are connected by edges (four-membered rings) and corners and disrupted by the addition of lithium, albeit a non-negligible fraction of connecting tetrahedra (Q2units) are still present in the glass structure. Dynamic and electric properties are also studied and emphasize that the size of the migrating cation (Li) is essential for ensuring a good level of ionic conductivity as it displays increased values with respect to the parent Na-bearing system. On the atomic (picosecond) timescale, different typical Li trajectories are identified and their distribution calculated: reduced cage-like motion in pockets constrained by the surrounding (Ge,S) network, back and forth jump motions with short transition states and long-range filamentary motion.
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Affiliation(s)
- Matthieu Micoulaut
- Sorbonne Université, Laboratoire de Physique Théorique de la Matiére Condensée, CNRS UMR 7600, 4 Place Jussieu, 75252 Paris Cedex 05, France
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Kardasis P, Tzourtzouklis I, Nega AD, Sakellariou G, Steinhart M, Floudas G. Topology sorting: Separating linear/star polymer blend components by imbibition in nanopores. J Chem Phys 2024; 160:044912. [PMID: 38294315 DOI: 10.1063/5.0189661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/07/2024] [Indexed: 02/01/2024] Open
Abstract
We report the imbibition and adsorption kinetics of a series of symmetric linear/star cis-1,4-polyisoprene blends within the long channels of self-ordered nanoporous anodic aluminum oxide (abbreviated: AAO). Using in situ nanodielectric spectroscopy, we followed the evolution of the longest chain modes in the blends with a judicious selection of molar masses for the constituent components. We demonstrated differences in the imbibition kinetics of linear and star components based on the relative viscosities (e.g., polymers with lower zero-shear viscosity penetrated first the nanopores). Following the complete imbibition of the pores, the adsorption time, τads, of each component was evaluated from the reduction in the dielectric strength of the respective chain modes. In the majority of blends, both components exhibited slower adsorption kinetics with respect to the homopolymers. The only exception was the case of entangled stars mixed with shorter linear chains, the latter acting as a diluent for the star component. This gives rise to what is known as topology sorting, e.g., the separation of linear/star blend components in the absence of solvent. Moreover, a simple relation (τads ∼ 10 × tpeak; tpeak is the time needed for the complete filling of pores) was found for linear polymers and stars. This suggested that the characteristic timescale of imbibition (tpeak) governs the adsorption process of polymers. It further implied the possibility of predicting the adsorption times of high molar mass polymers of various architectures by the shorter imbibition times.
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Affiliation(s)
| | | | - Alkmini D Nega
- Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Georgios Sakellariou
- Department of Chemistry, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Martin Steinhart
- Institut für Chemie neuer Materialien, Universität Osnabrück, D-49069 Osnabrück, Germany
| | - George Floudas
- Department of Physics, University of Ioannina, 45110 Ioannina, Greece
- University Research Center of Ioannina (URCI) - Institute of Materials Science and Computing, 45110 Ioannina, Greece
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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Sørensen SS, Smedskjaer MM, Micoulaut M. Evidence for Complex Dynamics in Glassy Fast Ion Conductors: The Case of Sodium Thiosilicates. J Phys Chem B 2023; 127:10179-10188. [PMID: 37976414 DOI: 10.1021/acs.jpcb.3c02909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Classical molecular dynamics is used to study the dynamics of alkali ions in a promising fast ion conductor glass system, i.e., Na2S-SiS2. Diffusion in such thiosilicates is found to display various salient features of alkali silicates, i.e., channel-like diffusion with typical length scales emerging as the temperature is decreased to the glassy state, and Arrhenius behavior for both Na ion diffusivity and calculated conductivity. The dynamics appears, however, to be largely heterogeneous as manifested by fast and slow Na ion motion at intermediate times, both in the high-temperature liquid and in the glassy state. In the former, a diffusion-limited regime is found due to the increased motion of the network-forming species that limits the Na ion dynamics, whereas at low temperatures, the typical dynamical heterogeneities are recovered as observed close to the glass transition.
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Affiliation(s)
- S S Sørensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - M M Smedskjaer
- Department of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark
| | - M Micoulaut
- Laboratoire de Physique Théorique de la Matière Condensée, CNRS UMR 7600, Sorbonne Université, 4 Place Jussieu, Paris Cedex 05 75252, France
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Dong Y, Steinhart M, Butt HJ, Floudas G. Conductivity of Ionic Liquids In the Bulk and during Infiltration in Nanopores. J Phys Chem B 2023; 127:6958-6968. [PMID: 37499259 DOI: 10.1021/acs.jpcb.3c01216] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The conductivity of ionic liquids (ILs) in nanopores is essential when considering their application as materials for energy. However, no consensus has been reached about the influence of confinement on the mobility of the ions. A series of ILs bearing the same cation, 1-butyl-3-methylimidazolium ([BMIM]+), and six different anions ([Cl]-, [Br]-, [I]-, [BF4]-, [PF6]-, and [TFSI]-) with radii from 0.168 to 0.326 nm were investigated with respect to their self-assembly, the thermodynamics, and the ionic conductivity in the bulk, during flow and under confinement in cylindrical nanopores with sizes in the range from 400 to 25 nm. In the bulk, the [BMIM]+[X]- exhibits weak ordering as a result of cation-anion correlations (charge alteration peak), and nanophase separation of polar/apolar groups. Liquid-to-glass temperatures were found to differ by ∼50 K, their viscosities by a factor of ∼270, and their conductivities by a factor of 24 (all at a temperature of 303 K). Electrostatic interactions were largely responsible for variations in the glass temperature, the viscosity, and the conductivity. Confined ILs behave differently from the bulk. The majority of ILs in the bulk were prone to crystallization during heating but were unable to crystallize in the smaller pores. Changes in dc-conductivity were used as markers of the phase state. This allowed the construction of the effective phase diagrams under confinement. The ILs penetrate the pores with an effective viscosity of the order of their viscosity in their bulk state. However, within the pores the dc-conductivity was reduced relative to bulk, indicating the immobilization of ions at the pore walls. Hydrophobization of the pore walls by hexamethyldisilazane could partially restore the conductivity. ILs are model systems where the phase state and ion mobility can be controlled by confinement.
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Affiliation(s)
- Yun Dong
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Martin Steinhart
- Institut für Chemie neuer Materialien, Universität Osnabrück, D-49069 Osnabrück, Germany
| | - Hans-Jürgen Butt
- Department of Physics, University of Ioannina, 45110 Ioannina, Greece
| | - George Floudas
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
- Department of Physics, University of Ioannina, 45110 Ioannina, Greece
- Institute of Materials Science and Computing, University Research Center of Ioannina (URCI), 45110 Ioannina, Greece
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Tu CH, Steinhart M, Berger R, Kappl M, Butt HJ, Floudas G. When crystals flow. SCIENCE ADVANCES 2023; 9:eadg8865. [PMID: 37163585 PMCID: PMC10171800 DOI: 10.1126/sciadv.adg8865] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/05/2023] [Indexed: 05/12/2023]
Abstract
Semicrystalline polymers are solids that are supposed to flow only above their melting temperature. By using confinement within nanoscopic cylindrical pores, we show that a semicrystalline polymer can flow at temperatures below the melting point with a viscosity intermediate to the melt and crystal states. During this process, the capillary force is strong and drags the polymer chains in the pores without melting the crystal. The unexpected enhancement in flow, while preserving the polymer crystallites, is of importance in the design of polymer processing conditions applicable at low temperatures, e.g., cold drawn polymers such as polytetrafluoroethylene, self-healing, and in nanoconfined donor/acceptor polymers used in organic electronics.
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Affiliation(s)
- Chien-Hua Tu
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Martin Steinhart
- Institut für Chemie neuer Materialien, Universität Osnabrück, D-49069 Osnabrück, Germany
| | - Rüdiger Berger
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Michael Kappl
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | | | - George Floudas
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
- Department of Physics, University of Ioannina, 45110 Ioannina, Greece
- University Research Center of Ioannina (URCI) - Institute of Materials Science and Computing, 45110 Ioannina, Greece
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