Recent Open Issues in Coarse Grained Force Fields

Souza, Felipe Rodrigues de; Souza, Lucas Miguel Pereira; Pimentel, André Silva

doi:10.1021/acs.jcim.0c01265

Cited by 8 publications

(7 citation statements)

References 38 publications

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“…The most common approach to choose pseudo-atoms is the Martini approach, where four non-hydrogen atoms are represented by a single pseudo atom ( Marrink et al, 2007 ). However, the Martini approach has several noted drawbacks ( Souza et al, 2020 ), especially when applied to MOF frameworks that contain highly symmetric or infinitely long chain structures as building units and possible disorder ( Cheetham et al, 2016 ), which prove it difficult to apply directly to framework structures. Nonetheless, Dürholt et al reported a proof of concept approach of a parameterised coarse grained model for a Cu paddlewheel based MOF, HKUST-1 ( Dürholt et al, 2016 ).…”

Section: Simulation Approaches To Treat the Effect Of Crystal Sizementioning

confidence: 99%

Perspectives on the Influence of Crystal Size and Morphology on the Properties of Porous Framework Materials

et al. 2021

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Miniaturization is a key aspect of materials science. Owing to the increase in quality experimental and computational tools available to researchers, it has become clear that the crystal size and morphology of porous framework materials, including metal-organic frameworks and covalent organic frameworks, play a vital role in defining the physicochemical behaviour of these materials. However, given the multiscale and multidisciplinary challenges associated with establishing how crystal size and morphology affect the structure and behaviour of a material–from local to global structural modifications and from static to dynamic effects–a comprehensive mechanistic understanding of size and morphology effects is missing. Herein, we provide our perspective on the current state-of-the-art of this topic, drawn from various complementary disciplines. From a fundamental point of view, we discuss how controlling the crystal size and morphology can alter the mechanical and adsorption properties of porous framework materials and how this can impact phase stability. Special attention is also given to the quest to develop new computational tools capable of modelling these multiscale effects. From a more applied point of view, given the recent progress in this research field, we highlight the importance of crystal size and morphology control in drug delivery. Moreover, we provide an outlook on how to advance each discussed field by size and morphology control, which would open new design opportunities for functional porous framework materials.

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Section: Simulation Approaches To Treat the Effect Of Crystal Sizementioning

confidence: 99%

Perspectives on the Influence of Crystal Size and Morphology on the Properties of Porous Framework Materials

et al. 2021

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“…Multibody terms need to be introduced for structure modeling. Moreover, the site–site interaction potentials of most coarse-grained force fields are usually too “sticky”, this resulting in too compact modeled structures [ 71 , 72 , 73 , 74 , 75 ]. The “stickiness” arises from interaction imbalance, which can be caused by the absence of specific cross Lennard–Jones parameters for pairs of particles of different size or overly weak bond force constants [ 76 ].…”

Section: Theory and Methodologymentioning

confidence: 99%

“…The procedure has been summarized and illustrated with examples in our recent review article [ 26 ]. This feature solves part of the problem of force field “stickiness” pointed out in [ 75 ], because the force field contains explicit terms that couple the backbone-local and backbone-electrostatic conformational states, which prevent overly compact local chain fragments [ 80 ]. Another way of including the multibody terms is to introduce expressions derived based on structural regularities in crystal structures [ 60 , 81 ] or on a heuristic basis [ 82 , 83 ].…”

Section: Theory and Methodologymentioning

confidence: 99%

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

et al. 2021

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Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and the potential of mean force is the physical basis of the coarse-grained force fields. Moreover, the choice of coarse-grained variables and the fact that coarse-grained sites often do not have spherical symmetry implies a non-diagonal inertia tensor. We describe selected coarse-grained models used in molecular dynamics simulations, including the most popular MARTINI model developed by Marrink’s group and the UNICORN model of biological macromolecules developed in our laboratory. We conclude by discussing examples of the application of coarse-grained molecular dynamics to study biologically important processes.

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“… 83 However, molecular simulations also have limitations, just like any experiment or analytical procedure. 84 Considering the situation of lipid monolayers, there are issues with the computation of water surface tension and phospholipid monolayer surface pressure. 85 The phase separation of phospholipids monolayer from the experiment cannot be seen from simulation.…”

Section: Limitationsmentioning

confidence: 99%

The concentration-dependent effect of hydrocortisone on the structure of model lung surfactant monolayer by using an in silico approach

et al. 2022

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Recent Open Issues in Coarse Grained Force Fields

Cited by 8 publications

References 38 publications

Perspectives on the Influence of Crystal Size and Morphology on the Properties of Porous Framework Materials

Perspectives on the Influence of Crystal Size and Morphology on the Properties of Porous Framework Materials

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

The concentration-dependent effect of hydrocortisone on the structure of model lung surfactant monolayer by using an in silico approach

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