Molecular fragment dynamics study on the water–air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants

Truszkowski, Andreas; Epple, Matthias; Fiethen, Annamaria; Zielesny, Achim; Kühn, Hubert

doi:10.1016/j.jcis.2013.07.069

Cited by 24 publications

(18 citation statements)

References 29 publications

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“…This is an important topic in making coarse-grained modeling applicable to a wide range of chemistries. For recent case studies in molecular fragment dynamics (MFD), a variation of DPD, along these same lines, the reader is referred to refs − . We consider many thousands of molecules and an arbitrary number of fragments.…”

Section: Introductionmentioning

confidence: 99%

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

Fraaije

Male

Becherer

et al. 2016

J. Chem. Inf. Model.

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We calibrate coarse-grained interaction potentials suitable for screening large data sets in top-down fashion. Three new algorithms are introduced: (i) automated decomposition of molecules into coarse-grained units (fragmentation); (ii) Coarse-Grained Reference Interaction Site Model-Hypernetted Chain (CG RISM-HNC) as an intermediate proxy for dissipative particle dynamics (DPD); and (iii) a simple top-down coarse-grained interaction potential/model based on activity coefficient theories from engineering (using COSMO-RS). We find that the fragment distribution follows Zipf and Heaps scaling laws. The accuracy in Gibbs energy of mixing calculations is a few tenths of a kilocalorie per mole. As a final proof of principle, we use full coarse-grained sampling through DPD thermodynamics integration to calculate log P for 4627 compounds with an average error of 0.84 log unit. The computational speeds per calculation are a few seconds for CG RISM-HNC and a few minutes for DPD thermodynamic integration.

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Section: Introductionmentioning

confidence: 99%

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

Fraaije

Male

Becherer

et al. 2016

J. Chem. Inf. Model.

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“…MFD simulations of the nonionic polyoxyethylene alkyl ether surfactants C 6 E 6 , C 10 E 6 , C 12 E 6 and C 16 E 6 at the water-air interface are performed to study their nanoscale structures and surface properties. The simulations of the self-aggregation of the polyoxyethylene alkyl ether surfactants lead to equilibrium nanoscale structures and computationally determined surface tensions which are in agreement with experimental data for different surfactant concentrations [ 1 ].…”

mentioning

confidence: 52%

Molecular fragment dynamics study on the water-air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants

Truszkowski

Fiethen²,

Kühn³

et al. 2014

J Cheminform

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“…The fragmentation of a distinct chemical compound is not a unique and objective procedure but only an adequate approximation driven by experience and chemical intuition. As an example, non-ionic polyoxyethylene alkyl ether surfactants with the general formula C x H 2 x +1 (OCH 2 CH 2 ) y OH, abbreviated as C x E y , may be approximated by x linearly connected methane fragments followed by y connected dimethyl ether fragments and a terminal methanol fragment [ 20 ]. Alternatively, the initial carbon chain could be represented by larger fragments like ethane, propane or butane, e.g.…”

Section: Resultsmentioning

confidence: 99%

“…The DPD technique is designed to obey the Navier-Stokes equations of hydrodynamics and to rigorously sample the canonical ensemble [ 16 ]. Molecular fragment dynamics (MFD) is a particular chemical intuitive DPD variant: Its beads are chosen to be specific molecules or molecular fragments where each distinct chemical compound is represented by a specific set of fragments which are connected by harmonic springs in an appropriate manner to describe the intra-compound covalent bonding [ 17 ]-[ 20 ].…”

Section: Introductionmentioning

confidence: 99%

A molecular fragment cheminformatics roadmap for mesoscopic simulation

Truszkowski

Daniel²,

Kühn³

et al. 2014

J Cheminform

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BackgroundMesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application.ResultsThe molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted fSMILES) with connected molecular fragments to represent a molecular structure. The fSMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software.ConclusionsMesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and conceptual usage hurdles. Molecular Fragment Cheminformatics may be regarded as a crucial accelerator to propagate MFD and similar mesoscopic simulation techniques in the molecular sciences.Graphical abstractA molecular fragment cheminformatics roadmap for mesoscopic simulation.

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Molecular fragment dynamics study on the water–air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants

Cited by 24 publications

References 29 publications

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

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

Molecular fragment dynamics study on the water-air interface behavior of non-ionic polyoxyethylene alkyl ether surfactants

A molecular fragment cheminformatics roadmap for mesoscopic simulation

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