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

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

doi:10.1021/acs.jctc.7b01093

Cited by 19 publications

(19 citation statements)

References 27 publications

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“…For partially soluble pairs where reliable solubility data are not available, the predictive method such as COSMOtherm can be used to obtain the corresponding iDACs. Different top-down approaches to obtain DPD parameters using COSMOtherm are introduced recently. − Conceptually, the surface charge density distribution of a molecule is first determined using quantum chemical calculations using the Turbomole program at the COSMO-BP-TZVP optimized basis set. ,, The obtained charge-density probability distributions are then used to predict the thermodynamic properties between molecules based on a conductor-like solvation model for real solvent (COSMO-RS) theory. − Here, the iDACs of the reference molecules (in Table ) for acid–tail and head–tail pairs are obtained by BIOVIA COSMOtherm software followed by a rescaling based on eq . ln(γ TW ∞ ) is the average value of the logarithmic iDACs for hexane and water, and ln(γ TW ∞ ) is that for carboxyl acid and hexane.…”

Section: Methodsmentioning

confidence: 99%

“…Groot and Warren linked the parameters to the Flory–Huggins parameters, making DPD suitable for modeling polymeric systems . Recent advances in parameterization include finer coarse-grained-based algorithms to improve the accuracy of the model, ,, and the linking to the quantum-chemical-based method such as COSMOtherm for handling the interactions between uncommon chemical fragments. − It is suggested that the nonbonded interaction parameters should be determined concurrently with the bonded parameters. , One approach is to obtain the bonded parameters by reproducing the molecular configurations of the chain molecules from MD simulations and to obtain nonbonded parameters by linking to infinite dilution activity coefficients (iDAC) obtained by COSMOtherm or experimental data. − The method has been proven applicable to modeling self-assembly of amphiphiles, including surfactants − and polymer electrolytes. − …”

Section: Introductionmentioning

confidence: 99%

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Micellization of Rhamnolipid Biosurfactants and Their Applications in Oil Recovery: Insights from Mesoscale Simulations

Lee

2021

J. Phys. Chem. B

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The dissipative particle dynamics (DPD) mesoscopic method is used to investigate the self-assembly of rhamnolipid congeners and their aggregation behaviors with paraffins including nonane and pentadecane. The coarse-grained force field is parameterized by combining molecular dynamics (MD) simulations, COSMOtherm calculations, and available experimental data. This model reproduces the vesicular formation of α-L-rhamnopyranosylβ-hydroxydecanoyl-β-hydroxydecanoate (Rha-C10-C10) reported by all-atom MD simulations. The vesicle composed of Rha-C10-C10 is found to be most stable at a surfactant concentration of 100−146 mM based on asphericity analysis. The architecture of rhamnolipid congeners affects the morphology of their aggregates. Di-rhamno-di-lipidic dRha-C16-C16 forms vesicles with a thicker unilamellar layer of 3.2 nm. Rha-C16-C16 forms vesicles at a lower concentration of 70 mM, but the enclosed water space collapses when the surfactant concentration increases. dRha-C10-C10 forms wormlike micelles, which agglomerate into a torus and interconnected network at higher concentrations. In the presence of alkane molecules, dRha-C10-C10 maintains its wormlike micellar morphology with alkane molecules wrapped inside the aggregates. For Rha-C10-C10, Rha-C16-C16, and dRha-C16-C16, nonane molecules are distributed in the hydrophobic subdomain formed by rhamnolipid molecules. Spherical vesicles are formed at a surfactant concentration of 50 mM and then develop into ellipsoidal vesicles when the concentration increases to 125 mM. When mixed with pentadecane, the alkane molecules are aggregated and surrounded by surfactants forming a core−shell structure at a low surfactant concentration of 20 mM. At higher alkane and surfactant concentrations, the morphologies develop into disk micelles, wormlike micelles, and vesicles, with pentadecane molecules being distributed and packed with rhamnolipids. The obtained simulation results suggest that these biosurfactants have potential as environmental remediation agents.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Micellization of Rhamnolipid Biosurfactants and Their Applications in Oil Recovery: Insights from Mesoscale Simulations

Lee

2021

J. Phys. Chem. B

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“…To quantitatively describe the morphologies of GO sheets, the radius of gyration tensor S , the relative shape anisotropy, and the solvent accessible surface area (SASA) are calculated (Supporting Information). The hydrodynamic radius, R h , is computed via Stokes–Einstein relations, with the translational and rotational diffusion coefficients, D t and D r , which are calculated by the mean-square displacement (MSD) and angular mean-square displacement (AMSD), respectively. , …”

Section: Simulation Methodsmentioning

confidence: 99%

Conformational Scaling Relations of Two-Dimensional Macromolecular Graphene Oxide in Solution

et al. 2020

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One of the most celebrated achievements in polymer physics is the finding of simple scaling laws that correlate molecular behaviors with molecular size. Scaling relations of 2D macromolecules between the conformation and size have been extensively investigated in theory. However, in contrast to their 1D counterparts, the fundamental correlation of conformation with the size, bending rigidity, and surface interaction still remains unsolved in both experiments and theory. Here we report the scaling relations of 2D macromolecules by using single-layer graphene oxide as the model, underpinning a general framework to understand and measure their thermodynamic and rheological behaviors. Using Ubbelohde capillary rheology, we experimentally determined the Flory-type and Mark–Houwink–Sakurada scaling rules in the self-avoiding, good-solvent regime through the critical overlapping concentration (C * ∼ L –0.87, L is the lateral size) and intrinsic viscosity ([η] ∼ M α, α = 0.33, M is the molecular weight). The measured exponent γ = 0.87 is well located between self-avoiding (4/5) and rigid (1) limit, indicating a nearly flat conformation and semiflexible nature, and α = 0.33 differs from the value of polymers (0.5–0.8), signaling the dimensional constraint. The discussion of conformational size-scaling relations is complemented by dissipative particle dynamics simulations, which clarify the effects of size and bending resistance of 2D macromolecules as well as the solvent that tunes their surface interaction, resulting in conformation transitions among nearly flat, folded, and crumpled phases.

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“…In previous publications, we have discussed automated coarse-graining protocols to calculate partition coefficients 1 and diffusion coefficients. 2 In this work, we focus on providing a fast and reliable method for calculating the alkane/water partition coefficient of lead-like molecules with a molecular weight of up to 800. As far as modeling is concerned, predicting large-molecule partitioning in a practical industrial setting is extraordinarily difficult.…”

Section: Introductionmentioning

confidence: 99%

Alkane/Water Partition Coefficient Calculation Based on the Modified AM1 Method and Internal Hydrogen Bonding Sampling Using COSMO-RS

Petris

Becherer

Fraaije

2021

J. Chem. Inf. Model.

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We introduce a physics-based model for calculating partition coefficients of solutes between water and alkanes, using a combination of a semi-empirical method for COSMO charge density calculation and statistical sampling of internal hydrogen bonds (IHBs). We validate the model on the experimental partition data (∼3500 molecules) of small organics, drug-like molecules, and statistical assessment of modeling of proteins and ligand drugs. The model combines two novel algorithms: a bond-correction method for improving the calculation of COSMO charge density from AM1 calculations and a sampling method to deal with IHBs. From a comparison of simulated and experimental partition coefficients, we find a root-mean-square deviation of roughly one log 10 unit. From IHB analysis, we know that IHBs can be present in two states: open (in water) and closed (in apolar solvent). The difference can lead to a shift of as much as two log 10 units per IHB; not taking this effect into account can lead to substantial errors. The method takes a few minutes of calculation time on a single core, per molecule. Although this is still much slower than quantitative structure–activity relationship, it is much faster than molecular simulations and can be readily incorporated into any screening method.

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

Cited by 19 publications

References 27 publications

Micellization of Rhamnolipid Biosurfactants and Their Applications in Oil Recovery: Insights from Mesoscale Simulations

Micellization of Rhamnolipid Biosurfactants and Their Applications in Oil Recovery: Insights from Mesoscale Simulations

Conformational Scaling Relations of Two-Dimensional Macromolecular Graphene Oxide in Solution

Alkane/Water Partition Coefficient Calculation Based on the Modified AM1 Method and Internal Hydrogen Bonding Sampling Using COSMO-RS

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