Accuracy Test of the OPLS-AA Force Field for Calculating Free Energies of Mixing and Comparison with PAC-MAC

Sweere, Augustinus J. M.; Fraaije, J. G. E. M.

doi:10.1021/acs.jctc.6b01106

Cited by 26 publications

(28 citation statements)

References 52 publications

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“…The OPLS-AA force field has previously been used to model mixture of alkane-alcohol, alkane-amine and alcohol-amine with satisfactory results for various thermodynamic properties. 47 Bulk liquid simulations have also been performed in this work to ensure that the OPLS-AA force field represents well the miscibility of ethanol and iso-octane at various temperatures in the range of 270-390 K. We observed that the OPLS-AA force field parameterization used in this work reproduces the bulk experimental density of an equimolar mixture of iso-octane and ethanol (less than 2% deviation), 48 as well as the full miscibility of both components. All LJ interactions have a cutoff of 10Å and electrostatic interactions are handled using the PPPM method.…”

Section: Simulation Methodsmentioning

confidence: 86%

Competitive Adsorption of a Multifunctional Amine and Phenol Surfactant with Ethanol on Hematite from Nonaqueous Solution

et al. 2019

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Surfactants, which contain phenol and amine groups, are commonly used in industry to protect metallic surfaces and their efficiency depends strongly on factors such as pressure and temperature, solvent properties, and the presence of other surfactants in the system. In this work, we present a molecular simulation study of the competitive adsorption between a multi-functional phenol and amine surfactant model and ethanol at the oil/solid interface formed between iso-octane and a model hematite (α -Fe 2 O 3 ) slab. We show that the surfactant strongly adsorbs at the iso-octane/hematite interface in the absence of ethanol at moderate temperatures. As the concentration of ethanol is increased, the ethanol molecules compete effectively for the adsorption sites on the iron oxide surface. This competition drives the surfactant molecules to remain in the bulk-solution while ethanol forms an ordered and strongly coordinated layers at the oil/solid interface, despite the well-known complete miscibility of ethanol in iso-octane in bulk at standard conditions. Potential of mean force calculations show that the free energy of adsorption of the surfactant is approximately two times larger than for a single ethanol molecule, but the simulations also reveal that a single surfactant chain needs to displace up to five ethanol molecules to adsorb onto the surface. The end result is a more favorable ethanol adsorption which agrees with the experimental analysis of similar oil/iron oxide systems also reported in this work.

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Section: Simulation Methodsmentioning

confidence: 86%

Competitive Adsorption of a Multifunctional Amine and Phenol Surfactant with Ethanol on Hematite from Nonaqueous Solution

et al. 2019

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“…Some force fields have been parametrized based on experimental data on binary mixtures, such as vapor-liquid equilibria (e.g., TraPPE), 65 while established force fields have been tested for their performance in reproducing such equilibria 66 or other related thermodynamic properties of mixtures (e.g., the free energy of mixing). 67 We performed mixing assays to estimate whether two Martini solvent models mixed or not, and compared the observed behavior to reference experimental data. Data regarding the most common solvents are commonly available as solvent miscibility tables.…”

Section: Solvent Mixtures: Martini Miscibility Tablementioning

confidence: 99%

Martini 3 Coarse-Grained Force Field: Small Molecules

Alessandri

Barnoud

Gertsen

et al. 2021

Preprint

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The recent re-parametrization of the Martini coarse-grained force field, Martini 3, improved the accuracy of the model in predicting molecular packing and interactions in molecular dynamics simulations. Here, we describe how small molecules can be accurately parametrized within the Martini 3 framework and present a database of validated small molecule models (available at https://github.com/ricalessandri/ Martini3-small-molecules and http://cgmartini.nl). We pay particular attention to the description of aliphatic and aromatic ring-like structures, which are ubiquitous in small molecules such as solvents and drugs or in building blocks constituting macromolecules such as proteins and synthetic polymers. In Martini 3, ring-like structures are described by models that use higher resolution coarse-grained particles (small and tiny particles). As such, the present database constitutes one of the cornerstones of the calibration of the new Martini 3 small and tiny particle sizes. The models show excellent partitioning behavior and solvent properties. Miscibility trends between different bulk phases are also captured, completing the set of thermodynamic properties considered during the parametrization. We also show how the new bead sizes allow for a good representation of molecular volume, which translates into better structural properties such as stacking distances. We further present design strategies to build Martini 3 models for small molecules of increased complexity. The present database, along with the outlined design strategies and the modularity of the Martini force field, constitute a resource of models that 1) can be used "as is" in (bio)molecular simulations; 2) gives reference points for the construction of other small molecule models; 3) provides guidelines and reference data for automated topology builders; and 4) can be used as building blocks for the construction of more complex (macro)molecules, hence enabling investigations of complex biomolecular and soft material systems.

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“…Every structure was neutralized at the physiological pH and a library of 36,229 potential ligands was created including the stereoisomers and tautomers (Srivastava, Pal & Misra, 2018). Target protein structures files were prepared using Schrödinger Protein Preparation Wizard by removing excess waters and were minimized using OPLS 2005 force field (Clark et al, 2019;Sweere & Fraaije, 2017).…”

Section: Virtual Screening Against Npassmentioning

confidence: 99%

VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo

Srivastava

Choudhury

Talwar

et al. 2020

PeerJ

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Vitiligo is a chronic asymptomatic disorder affecting melanocytes from the basal layer of the epidermis which leads to a patchy loss of skin color. Even though it is one of the neglected disease conditions, people suffering from vitiligo are more prone to psychological disorders. As of now, various studies have been done in order to project auto-immune implications as the root cause. To understand the complexity of vitiligo, we propose the Vitiligo Information Resource (VIRdb) that integrates both the drug-target and systems approach to produce a comprehensive repository entirely devoted to vitiligo, along with curated information at both protein level and gene level along with potential therapeutics leads. These 25,041 natural compounds are curated from Natural Product Activity and Species Source Database. VIRdb is an attempt to accelerate the drug discovery process and laboratory trials for vitiligo through the computationally derived potential drugs. It is an exhaustive resource consisting of 129 differentially expressed genes, which are validated through gene ontology and pathway enrichment analysis. We also report 22 genes through enrichment analysis which are involved in the regulation of epithelial cell differentiation. At the protein level, 40 curated protein target molecules along with their natural hits that are derived through virtual screening. We also demonstrate the utility of the VIRdb by exploring the Protein–Protein Interaction Network and Gene–Gene Interaction Network of the target proteins and differentially expressed genes. For maintaining the quality and standard of the data in the VIRdb, the gold standard in bioinformatics toolkits like Cytoscape, Schrödinger’s GLIDE, along with the server installation of MATLAB, are used for generating results. VIRdb can be accessed through “http://www.vitiligoinfores.com/”.

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Accuracy Test of the OPLS-AA Force Field for Calculating Free Energies of Mixing and Comparison with PAC-MAC

Cited by 26 publications

References 52 publications

Competitive Adsorption of a Multifunctional Amine and Phenol Surfactant with Ethanol on Hematite from Nonaqueous Solution

Competitive Adsorption of a Multifunctional Amine and Phenol Surfactant with Ethanol on Hematite from Nonaqueous Solution

Martini 3 Coarse-Grained Force Field: Small Molecules

VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo

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