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Comparison and Validation of Force Fields for Deep Eutectic Solvents in Combination with Water and Alcohol Dehydrogenase

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Comparison and Validation of Force Fields for Deep Eutectic Solvents in Combination with Water and Alcohol Dehydrogenase. / Bittner, Jan Philipp; Huang, Lei; Zhang, Ningning; Kara, Selin; Jakobtorweihen, Sven.

I: Journal of Chemical Theory and Computation, Bind 17, Nr. 8, 08.2021, s. 5322-5341.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

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Bittner, JP, Huang, L, Zhang, N, Kara, S & Jakobtorweihen, S 2021, 'Comparison and Validation of Force Fields for Deep Eutectic Solvents in Combination with Water and Alcohol Dehydrogenase', Journal of Chemical Theory and Computation, bind 17, nr. 8, s. 5322-5341. https://doi.org/10.1021/acs.jctc.1c00274

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Author

Bittner, Jan Philipp ; Huang, Lei ; Zhang, Ningning ; Kara, Selin ; Jakobtorweihen, Sven. / Comparison and Validation of Force Fields for Deep Eutectic Solvents in Combination with Water and Alcohol Dehydrogenase. I: Journal of Chemical Theory and Computation. 2021 ; Bind 17, Nr. 8. s. 5322-5341.

Bibtex

@article{14b308b2ba5b43228a62baa79472ae57,
title = "Comparison and Validation of Force Fields for Deep Eutectic Solvents in Combination with Water and Alcohol Dehydrogenase",
abstract = "Deep eutectic solvents (DESs) have become popular as environmental-friendly solvents for biocatalysis. Molecular dynamics (MD) simulations offer an in-depth analysis of enzymes in DESs, but their performance depends on the force field chosen. Here, we present a comprehensive validation of three biomolecular force fields (CHARMM, Amber, and OPLS) for simulations of alcohol dehydrogenase (ADH) in DESs composed of choline chloride and glycerol/ethylene glycol with varying water contents. Different properties (e.g., protein structure and flexibility, solvation layer, and H-bonds) were used for validation. For two properties (viscosity and water activity) also experiments were performed. The viscosity was calculated with the periodic perturbation method, whereby its parameter dependency is disclosed. A modification of Amber was identified as the best-performing model for low water contents, whereas CHARMM outperforms the other models at larger water concentrations. An analysis of ADH's structure and interactions with the DESs revealed similar predictions for Amber and CHARMM.",
keywords = "Alcohol Dehydrogenase/chemistry, Choline/chemistry, Ethylene Glycol/chemistry, Glycerol/chemistry, Hydrogen Bonding, Molecular Dynamics Simulation, Solvents/chemistry, Thermodynamics, Viscosity, Water/chemistry",
author = "Bittner, {Jan Philipp} and Lei Huang and Ningning Zhang and Selin Kara and Sven Jakobtorweihen",
year = "2021",
month = aug,
doi = "10.1021/acs.jctc.1c00274",
language = "English",
volume = "17",
pages = "5322--5341",
journal = "Journal of Chemical Theory and Computation",
issn = "1549-9618",
publisher = "AMER CHEMICAL SOC",
number = "8",

}

RIS

TY - JOUR

T1 - Comparison and Validation of Force Fields for Deep Eutectic Solvents in Combination with Water and Alcohol Dehydrogenase

AU - Bittner, Jan Philipp

AU - Huang, Lei

AU - Zhang, Ningning

AU - Kara, Selin

AU - Jakobtorweihen, Sven

PY - 2021/8

Y1 - 2021/8

N2 - Deep eutectic solvents (DESs) have become popular as environmental-friendly solvents for biocatalysis. Molecular dynamics (MD) simulations offer an in-depth analysis of enzymes in DESs, but their performance depends on the force field chosen. Here, we present a comprehensive validation of three biomolecular force fields (CHARMM, Amber, and OPLS) for simulations of alcohol dehydrogenase (ADH) in DESs composed of choline chloride and glycerol/ethylene glycol with varying water contents. Different properties (e.g., protein structure and flexibility, solvation layer, and H-bonds) were used for validation. For two properties (viscosity and water activity) also experiments were performed. The viscosity was calculated with the periodic perturbation method, whereby its parameter dependency is disclosed. A modification of Amber was identified as the best-performing model for low water contents, whereas CHARMM outperforms the other models at larger water concentrations. An analysis of ADH's structure and interactions with the DESs revealed similar predictions for Amber and CHARMM.

AB - Deep eutectic solvents (DESs) have become popular as environmental-friendly solvents for biocatalysis. Molecular dynamics (MD) simulations offer an in-depth analysis of enzymes in DESs, but their performance depends on the force field chosen. Here, we present a comprehensive validation of three biomolecular force fields (CHARMM, Amber, and OPLS) for simulations of alcohol dehydrogenase (ADH) in DESs composed of choline chloride and glycerol/ethylene glycol with varying water contents. Different properties (e.g., protein structure and flexibility, solvation layer, and H-bonds) were used for validation. For two properties (viscosity and water activity) also experiments were performed. The viscosity was calculated with the periodic perturbation method, whereby its parameter dependency is disclosed. A modification of Amber was identified as the best-performing model for low water contents, whereas CHARMM outperforms the other models at larger water concentrations. An analysis of ADH's structure and interactions with the DESs revealed similar predictions for Amber and CHARMM.

KW - Alcohol Dehydrogenase/chemistry

KW - Choline/chemistry

KW - Ethylene Glycol/chemistry

KW - Glycerol/chemistry

KW - Hydrogen Bonding

KW - Molecular Dynamics Simulation

KW - Solvents/chemistry

KW - Thermodynamics

KW - Viscosity

KW - Water/chemistry

U2 - 10.1021/acs.jctc.1c00274

DO - 10.1021/acs.jctc.1c00274

M3 - Journal article

C2 - 34232662

VL - 17

SP - 5322

EP - 5341

JO - Journal of Chemical Theory and Computation

JF - Journal of Chemical Theory and Computation

SN - 1549-9618

IS - 8

ER -