Fast and efficient optimization of Molecular Dynamics force fields for microporous materials: Bonded interactions via force matching

Gabrieli, Andrea; Sant, Marco; Demontis, Pierfranco; Suffritti, Giuseppe Baldovino

doi:10.1016/j.micromeso.2014.06.023

Cited by 12 publications

(27 citation statements)

References 70 publications

(92 reference statements)

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“…The basis sets for each atom kind are triple-ζ with two sets of polarization functions (TZV2P), except for Zn (TZVP) in accordance to previous works. [97][98][99] The DFT-D3 method 100 is used to take into account dispersion interactions. The charge density cutoff is 700 Ry (for ITQ-29 only this value is risen to 1000 Ry).…”

Section: Methodsmentioning

confidence: 99%

Partial Charges in Periodic Systems: Improving Electrostatic Potential (ESP) Fitting via Total Dipole Fluctuations and Multiframe Approaches

Gabrieli

Sant

Demontis

et al. 2015

J. Chem. Theory Comput.

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Two major improvements to the state-of-the-art Repeating Electrostatic Potential Extracted Atomic (REPEAT) method, for generating accurate partial charges for molecular simulations of periodic structures, are here developed. The first, D-REPEAT, consists in the simultaneous fit of the electrostatic potential (ESP), together with the total dipole fluctuations (TDF) of the framework. The second, M-REPEAT, allows the fit of multiple ESP configurations at once. When both techniques are fused into one, DM-REPEAT method, the resulting charges become remarkably stable over a large set of fitting regions, giving a robust and physically sound solution to the buried atoms problem. The method capabilities are extensively studied in ZIF-8 framework, and subsequently applied to IRMOF-1 and ITQ-29 crystal structures. To our knowledge, this is the first time that this approach is proposed in the context of periodic systems.

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Section: Methodsmentioning

confidence: 99%

Partial Charges in Periodic Systems: Improving Electrostatic Potential (ESP) Fitting via Total Dipole Fluctuations and Multiframe Approaches

Gabrieli

Sant

Demontis

et al. 2015

J. Chem. Theory Comput.

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“…The parameters of the effective potentials are determined by fitting large sets of either experimental or higher-level computational data (see e.g. Gabrieli et al 2014;Gabrieli et al 2016). In the study of zeolite materials, the most popular methods are Monte Carlo (MC) and Molecular Dynamics (MD) (Allen and Tildesley 1987;Demontis and Suffritti 1991;Frenkel and Smit 1996).…”

Section: Computational Modelingmentioning

confidence: 99%

The effect of pressure on open-framework silicates: elastic behaviour and crystal–fluid interaction

2017

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The elastic behaviour and the structural evolution of microporous materials compressed hydrostatically in a pressure-transmitting fluid are drastically affected by the potential crystal-fluid interaction, with a penetration of new molecules through the zeolitic cavities in response to applied pressure. In this manuscript, the principal mechanisms that govern the P-behaviour of zeolites with and without crystal-fluid interaction are described, on the basis of previous experimental findings and computational modelling studies.When no crystal-fluid interaction occurs, the effects of pressure are mainly accommodated by tilting of (quasi-rigid) tetrahedra around O atoms that behave as hinges. Tilting of tetrahedra is the An overview of the intrusion phenomena of monoatomic species (e.g., He, Ar, Kr), small (e.g., H 2 O, CO ) and complex molecules, along with the P-induced polymerization phenomena, (e.g., C 2 H 2 , C 2 H 4 , C 2 H 6 O, C 2 H 6 O 2 , BNH 6 , electrolytic MgCl 2 ·21H 2 O solution) is provided, with a discussion of potential technological and geological implications of these experimental findings.

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“…Since then, the method has been applied to systems including transition metal complexes, 33,34 anions, 35 ionic liquids, 36 and microporous materials. 37 Recently, the force-matching technique has also been employed to develop FFs for water, 38,39 water on graphene surface, 40 and explicit three-body interactions for molten carbon. 41 In this work, we extend the adaptive force matching technique to rapidly parameterize FFs for complex conjugated systems.…”

Section: Introductionmentioning

confidence: 99%

Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene

Jiang

Rogers

Hirst

et al. 2020

J. Chem. Theory Comput.

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Utilising a force matching procedure, we parameterise new force fields systematically for large conjugated systems. We model both conjugated polymers and molecular crystals that contain diketopyrrolopyrrole, thiophene, and thieno[3,2-b]thiophene units. These systems have recently been found to have low band gaps, which exhibit high efficiency for photovoltaic devices. The equilibrium structures, forces and energies of the building block chromophores: diketopyrrolopyrrole thiophene, and thieno[3,2b]thiophene computed using our parameters are comparable to those computed using the reference electronic structure method. We assess the suitability of this new force field for electronic property calculations by comparing the electronic excitation properties computed along classical and ab initio molecular dynamics trajectories. For both trajectories, we find similar distributions of TDDFT calculated excitation energies and oscillator strengths for the building block chromophore diketopyrrolopyrrole-thieno[3,2b]thiophene. The structural, dynamical, and electronic properties of the macromolecular assemblies built upon these chromophores are characterised. For both polymers and molecular crystals, pronounced peaks around 0 o or 180 o are observed for the torsions between chromophores under ambient conditions. The high planarity in these systems can promote local ordering and π-π stacking, thereby potentially facilitating charge transport across these materials. For the model conducting polymers, we found that the fluctuations in the density of states per chain per monomer is neglegibly small and does not vary significantly with chains comprising 20 to 40 monomers. Analysis of the electron-hole distributions and the transition density matrices indicates that the delocalised length is approximately four to six monomers, which is in good agreement with other theoretical and experimental studies of different conducting polymers. For the molecular crystals, our investigation of the characteristic timescale of the fluctuation in the excitonic couplings shows that low frequency vibration below 10 cm −1 is observed for the nearest neighbors. These observations are in line with previous studies on other molecular crystals, in which low frequency vibrations are believed to be responsible for the large modulation of the excitonic coupling. Thus, our approach and the new force fields provide a direct route for studying the structure-property relations and the molecular level origins of the high-efficiency of these classes of materials.

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Fast and efficient optimization of Molecular Dynamics force fields for microporous materials: Bonded interactions via force matching

Cited by 12 publications

References 70 publications

Partial Charges in Periodic Systems: Improving Electrostatic Potential (ESP) Fitting via Total Dipole Fluctuations and Multiframe Approaches

Partial Charges in Periodic Systems: Improving Electrostatic Potential (ESP) Fitting via Total Dipole Fluctuations and Multiframe Approaches

The effect of pressure on open-framework silicates: elastic behaviour and crystal–fluid interaction

Force Fields for Macromolecular Assemblies Containing Diketopyrrolopyrrole and Thiophene

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