Coarse-Grained Models for Automated Fragmentation and Parametrization of Molecular Databases

Fraaije, J. G. E. M.; Male, Jan van; Becherer, Paul; Gracià, Rubèn Serral

doi:10.1021/acs.jcim.6b00003

Cited by 27 publications

(26 citation statements)

References 91 publications

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“…We should also remark that whilst the present approach is presented as a case study in DPD parametrization, it offers a route to calculate de novo log P values. As such it may not be competitive in terms of speed compared to the rapid empirical methods listed in the introduction, but it does appear to be competitive in terms of accuracy [34].…”

Section: Discussionmentioning

confidence: 99%

Dissipative particle dynamics: Systematic parametrization using water-octanol partition coefficients

Anderson

Bray

Ferrante³

et al. 2017

The Journal of Chemical Physics

223

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We present a systematic, top-down, thermodynamic parametrization scheme for dissipative particle dynamics (DPD) using water-octanol partition coefficients, supplemented by water-octanol phase equilibria and pure liquid phase density data. We demonstrate the feasibility of computing the required partition coefficients in DPD using brute-force simulation, within an adaptive semi-automatic staged optimization scheme. We test the methodology by fitting to experimental partition coefficient data for twenty one small molecules in five classes comprising alcohols and poly-alcohols, amines, ethers and simple aromatics, and alkanes (i.e., hexane). Finally, we illustrate the transferability of a subset of the determined parameters by calculating the critical micelle concentrations and mean aggregation numbers of selected alkyl ethoxylate surfactants, in good agreement with reported experimental values.

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Section: Discussionmentioning

confidence: 99%

Dissipative particle dynamics: Systematic parametrization using water-octanol partition coefficients

Anderson

Bray

Ferrante³

et al. 2017

The Journal of Chemical Physics

223

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“…The AFP method is extensively documented. 1 Molecules are fragmented according to a scoring function, through a simulated annealing function that cuts through bonds. The optimal bond scission pattern is preserved, and the fragments are stored.…”

Section: Methodsmentioning

confidence: 99%

“…The returning question has been, to what extent can coarse-grained interactions mimic the thermodynamics of real systems? In a recent work, we introduced the automated-fragmentation-parametrization protocol (AFP), 1 which aims to automate the cumbersome process of finding proper coarse-grained interaction parameters for a given set of arbitrary (organic) molecules. In short, AFP combines two steps: (i) the rule-based cutting of molecules into smaller pieces (referred to as fragments or beads) and (ii) the subsequent calibration of interactions through comparison with thermodynamic data.…”

Section: Introductionmentioning

confidence: 99%

Calculation of Diffusion Coefficients through Coarse-Grained Simulations Using the Automated-Fragmentation-Parametrization Method and the Recovery of Wilke–Chang Statistical Correlation

Fraaije

Male

Becherer

et al. 2018

J. Chem. Theory Comput.

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We introduce a model for the calculation of diffusion coefficients using dissipative particle dynamics coarse-grained molecular simulations. We validate the model on experimental diffusion data of small organics and drug-like molecules in water. The new model relies on our automated-fragmentation-parametrization protocol for cutting molecules into fragments, which are calibrated using the COSMO-RS thermodynamic model (10.1021/acs.jcim.6b0000327806564J. Chem. Inf. Model.20165623612377). By simulations over the entire CULGI database of more than 11000 molecules, we recover the decades-old empirical Wilke–Chang correlation between diffusion coefficient and molar volume. We believe this is the first demonstration of the correlation by simulation or theory. From a comparison of simulated and experimental diffusion coefficients, we find that one full time unit of coarse-grained simulation equals 64 ± 13 ps real time.

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“…The automated fragmentation and parametrization (AFP) protocol [36] is used to map the atomistic rendition of PPE to the coarse-grained molecules. The AFP protocol is briefly explained below.…”

Section: Step 1a-atomistic To Coarse-grained Mappingmentioning

confidence: 99%

A Multiscale Approach for Estimating Permeability Properties of Polymers with Complex Aromatic Backbones: A Case Study on Diffusivity of Small Gas Molecules in Polyphenylene Ether

Sweere

Patham²,

Sugur³

et al. 2020

Macro Theory & Simulations

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State‐of‐the‐art multiscale computational chemistry simulations is employed to predict diffusivity of small gaseous molecules in a generic polyphenylene ether (PPE). The diffusivities are obtained from trajectory analysis of gaseous molecules in molecular dynamics simulations using coarse‐grained dissipative particle dynamics (DPD) simulations to design the amorphous starting structure. Required intra‐ and intermolecular parameters of the DPD simulations are automatically generated using the automated fragmentation and parametrization protocol. A comparison of calculated diffusion coefficients with experimental data for five gaseous molecules in PPE shows adequate accuracy of computational‐chemistry‐based approaches in the prediction of diffusion coefficients. These estimates, validated against measurements reported in the literature, serve as proof of concept for applicability of these new multiscale modeling strategies for complex polymers with aromatic backbones.

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Coarse-Grained Models for Automated Fragmentation and Parametrization of Molecular Databases

Cited by 27 publications

References 91 publications

Dissipative particle dynamics: Systematic parametrization using water-octanol partition coefficients

Dissipative particle dynamics: Systematic parametrization using water-octanol partition coefficients

Calculation of Diffusion Coefficients through Coarse-Grained Simulations Using the Automated-Fragmentation-Parametrization Method and the Recovery of Wilke–Chang Statistical Correlation

A Multiscale Approach for Estimating Permeability Properties of Polymers with Complex Aromatic Backbones: A Case Study on Diffusivity of Small Gas Molecules in Polyphenylene Ether

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