Automated Topology Builder Version 3.0: Prediction of Solvation Free Enthalpies in Water and Hexane

Stroet, Martin; Caron, Bertrand; Visscher, Koen; Geerke, Daan P.; Malde, Alpeshkumar K.; Mark, Alan E.

doi:10.1021/acs.jctc.8b00768

Cited by 346 publications

(232 citation statements)

References 75 publications

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“…No more than 24 molecules were removed during any of the simulations. Charges, van der Waals interactions, and bonded interactions for TCTA were assigned using the Automated Topology Builder (ATB) version 3.0 . The charges and interactions for Ir(ppy) 3 were identical to those used by Tonnelé et al The topology and optimized coordinate files are provided in the Supporting Information.…”

Section: Methodsmentioning

confidence: 99%

“…Charges, van der Waals interactions, and bonded interactions for TCTA were assigned using the Automated Topology Builder (ATB) version 3.0. [25] The charges and interactions for Ir(ppy) 3 were identical to those used by Tonnelé et al [10] The topology and optimized coordinate files are provided in the Supporting Information. Bonds involving hydrogen atoms were constrained using the LINCS algorithm.…”

Section: Methodsmentioning

confidence: 99%

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Revealing the Interplay between Charge Transport, Luminescence Efficiency, and Morphology in Organic Light‐Emitting Diode Blends

Gao

Lee

Burn

et al. 2019

Adv Funct Materials

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Phosphorescent emissive materials in organic light‐emitting diodes (OLEDs) manufactured using evaporation are usually blended with host materials at a concentration of 3–15 wt% to avoid concentration quenching of the luminescence. Here, experimental measurements of hole mobility and photoluminescence are related to the atomic level morphology of films created using atomistic nonequilibrium molecular dynamics simulations mimicking the evaporation process with similar guest concentrations as those used in operational test devices. For blends of fac‐tris[2‐phenylpyridinato‐C2,N]iridium(III) [Ir(ppy)3] in tris(4‐carbazoyl‐9‐ylphenyl)amine (TCTA), it is found that clustering of the Ir(ppy)3 (surface of the molecules within ≈0.4 nm) in the simulated films is directly relatable to the experimentally‐measured hole mobility. Films containing 1–10 wt% of Ir(ppy)3 in TCTA have a mobility of up to two orders of magnitude lower (≈10−6 cm2 V−1 s−1) than the neat TCTA film, which is consistent with the Ir(ppy)3 molecules acting as hole traps due to their smaller ionization potential. Comparison of the simulated film morphologies with the measured photoluminescence properties shows that for luminescence quenching to occur, the Ir(ppy)3 molecules have to have their ligands partially overlapping. Thus, the results show that the effect of guest interactions on charge transport and luminescence are markedly different for OLED light‐emitting layers.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Revealing the Interplay between Charge Transport, Luminescence Efficiency, and Morphology in Organic Light‐Emitting Diode Blends

Gao

Lee

Burn

et al. 2019

Adv Funct Materials

Self Cite

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“…For example, the proprietary OPLS3 force eld denes 124 atom types and 48 142 torsional parameters. 6 Other methods provide options to reparameterize force elds automatically using ab initio calculations, [7][8][9][10][11] although this complicates the simulation workow and can be computationally expensive.…”

Section: Introductionmentioning

confidence: 99%

Simulating protein–ligand binding with neural network potentials

2020

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“…These thermodynamic data are arguably one of the most important properties for ensuring the proper distribution of functional groups between hydrophilic and hydrophobic phases, which is expected to be crucial for accessing sorption properties of small molecules in soil organic matter. Note that very recently an updated version of the automated topology builder became available, leading to excellent reproduction of hydration free energies for hundreds of compounds (Stroet et al, 2018), potentially making manual reparameterization as described here obsolete.…”

Section: Discussionmentioning

confidence: 99%

Molecular modelling of sorption processes of a range of diverse small organic molecules in Leonardite humic acid

Petrov

Tunega

Gerzabek

et al. 2019

European J Soil Science

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Soil organic matter (SOM) is abundant in the environment and plays an important role in several biogeochemical processes, including microbial activity, soil aggregation, plant growth and carbon storage. One of its key functions is the retention and release of various chemical compounds, primarily governed by the sorption process, which strongly affects the environmental fate of nutrients and pollutants. Sorption largely depends on the composition of SOM, as well as its structure, dynamics and the thermodynamic conditions. Although several approaches are available, experimental characterization of sorption mechanisms is not easy. Computational models for predicting sorption coefficients often require a wealth of experimental data for training and are only applicable to compounds and conditions related to the training dataset. Here, we use molecular dynamics (MD) simulations to study the sorption of a range of small organic compounds. As a model SOM system we use the standard Leonardite humic acid (LHA) sample, which physicochemical properties have recently been characterized computationally in detail. This model allowed us to estimate sorption propensities of the systems at two different hydration levels (water activities close to 0 and 1), showing a remarkable correlation with experimental data. Importantly, this molecular modelling approach based on perturbation free‐energy calculations is rigorously derived from statistical thermodynamics and requires no experimental sorption data for training. It is therefore in principle applicable to any SOM model or thermodynamic condition. Moreover, the power of MD simulations to provide high‐resolution insight into atomistic and molecular interactions was employed to explore how sorbate molecules associate with the LHA matrix and which contacts they form. The heteroatoms of both sorbate and sorbent play an important role and water molecules are identified as further key players in facilitating the sorption process. Highlights Modelling of the sorption processes in soil organic matter at atomistic level. Rigorous, physics‐based approach applicable to a range of SOM systems and conditions. Remarkable level of matching with experimental data with additional insight into the molecular mechanism. Interactions between the sorbate and local environment strongly affects the sorption process.

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Automated Topology Builder Version 3.0: Prediction of Solvation Free Enthalpies in Water and Hexane

Cited by 346 publications

References 75 publications

Revealing the Interplay between Charge Transport, Luminescence Efficiency, and Morphology in Organic Light‐Emitting Diode Blends

Revealing the Interplay between Charge Transport, Luminescence Efficiency, and Morphology in Organic Light‐Emitting Diode Blends

Simulating protein–ligand binding with neural network potentials

Molecular modelling of sorption processes of a range of diverse small organic molecules in Leonardite humic acid

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