Calculation of binding affinities for linear alcohols to α -cyclodextrin by twin-system enveloping distribution sampling simulations

Gebhardt, Julia; Hansen, Niels

doi:10.1016/j.fluid.2016.02.001

Cited by 18 publications

(33 citation statements)

References 114 publications

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“…are based on our compilation reported earlier [56] supplemented by additional data [99]. Simulation results are reported for the GROMOS force field 53A6 GLYC [78] calculated either by alchemical double decoupling (DD) [56] or via the potential or mean force (PMF) and for the force field CHARMM36 [79] calculated via the potential of mean force. Dashed lines are used as guide to the eye.…”

Section: Discussionmentioning

confidence: 99%

“…If the two routes provide the same results within the statistical errors, the calculated binding free enthalpy is most likely the one prescribed by the underlying molecular force field. In a previous work the standard binding free enthalpy of primary alcohols from 1-butanol to 1-dodecanol to a-cyclodextrin for different GROMOS force fields using the alchemical route was calculated [56]. In the present work these simulations were extended for alcohols up to 1-eicosanol (C20) using the GROMOS 53A6 GLYC [78] force field, applying the same methodology as in the previous work [56].…”

Section: Standard Binding Free Enthalpy Of Primary Alcohols To A-cyclmentioning

confidence: 94%

“…The hydration free enthalpies were obtained from molecular dynamics simulations with the GROMOS 53A6 force field. For 1-butanol to 1-octanol the values reported in [55] were used while the increments in hydration free enthalpy with carbon number relative to 1-octanol calculated in a recent work [56] were used to obtain values for 1-decanol and 1-dodecanol. Finally it is noted that if the assumption that all activity coefficients are unity proves to be unrealistic, finite concentration activity coefficients may also be obtained from molecular dynamics free-energy calculations [57].…”

Section: Aqueous Solubility Of N-alkanes and Primary Alcoholsmentioning

confidence: 99%

“…In a previous work the standard binding free enthalpy of primary alcohols from 1-butanol to 1-dodecanol to a-cyclodextrin for different GROMOS force fields using the alchemical route was calculated [56]. In the present work these simulations were extended for alcohols up to 1-eicosanol (C20) using the GROMOS 53A6 GLYC [78] force field, applying the same methodology as in the previous work [56]. Additionally the PMF route was examined for 1-butanol to 1-dodecanol using the GROMOS 53A6 GLYC and CHARMM36 [79] force fields.…”

Section: Standard Binding Free Enthalpy Of Primary Alcohols To A-cyclmentioning

confidence: 99%

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Molecular Simulations of Thermodynamic Properties for the Systemα‐Cyclodextrin/Alcohol in Aqueous Solution

Markthaler

Gebhardt

Jakobtorweihen

et al. 2017

Chemie Ingenieur Technik

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Free-energy calculations based on molecular simulations provide access to a wide range of thermodynamic properties such as the solubility and partitioning of a molecule in and between various phases. It is demonstrated how molecular dynamics free-energy simulations may be used to obtain the solubilities of primary alcohols and n-alkanes in water and binding affinities of primary alcohols to a-cyclodextrin. The equivalence of two distinct routes to calculate binding free energies is shown leading to the conclusion that host-guest binding affinities may be used to probe the underlying molecular force field.

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Section: Discussionmentioning

confidence: 99%

Section: Standard Binding Free Enthalpy Of Primary Alcohols To A-cyclmentioning

confidence: 94%

Section: Aqueous Solubility Of N-alkanes and Primary Alcoholsmentioning

confidence: 99%

Section: Standard Binding Free Enthalpy Of Primary Alcohols To A-cyclmentioning

confidence: 99%

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Molecular Simulations of Thermodynamic Properties for the Systemα‐Cyclodextrin/Alcohol in Aqueous Solution

Markthaler

Gebhardt

Jakobtorweihen

et al. 2017

Chemie Ingenieur Technik

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“…Mat. A, Table A.10), alkali and halide ions 90 , and 2016H66-compatible biomolecular building blocks for peptides, nucleic acids, carbohydrates (including cyclodextrins 124 ), lipids (including mono-and diglycerides 97,101,[107][108][109][110]125 ) and cofactors (see details in the Appendix of Suppl. Mat.…”

Section: Introductionmentioning

confidence: 99%

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Horta

Merz

Fuchs

et al. 2016

J. Chem. Theory Comput.

144

287

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This article reports on the calibration and validation of a new GROMOS-compatible parameter set 2016H66 for small organic molecules in the condensed phase. The calibration is based on 62 organic molecules spanning the chemical functions alcohol, ether, aldehyde, ketone, carboxylic acid, ester, amine, amide, thiol, sulfide, and disulfide, as well as aromatic compounds and nucleic-acid bases. For 57 organic compounds, the calibration targets are the experimental pure-liquid density ρliq and the vaporization enthalpy ΔHvap, as well as the hydration free energy ΔGwat and the solvation free energy ΔGche in cyclohexane, at atmospheric pressure and at (or close to) room temperature. The final root-mean-square deviations (RMSD) for these four quantities over the set of compounds are 32.4 kg m(-3), 3.5 kJ mol(-1), 4.1 kJ mol(-1), and 2.1 kJ mol(-1), respectively, and the corresponding average deviations (AVED) are 1.0 kg m(-3), 0.2 kJ mol(-1), 2.6 kJ mol(-1), and 1.0 kJ mol(-1), respectively. For the five nucleic-acid bases, the parametrization is performed by transferring the final 2016H66 parameters from analogous organic compounds followed by a slight readjustment of the charges to reproduce the experimental water-to-chloroform transfer free energies ΔGtrn. The final RMSD for this quantity over the five bases is 1.7 kJ mol(-1), and the corresponding AVED is 0.8 kJ mol(-1). As an initial validation of the 2016H66 set, seven additional thermodynamic, transport, and dielectric properties are calculated for the 57 organic compounds in the liquid phase. The agreement with experiment in terms of these additional properties is found to be reasonable, with significant deviations typically affecting either a specific chemical function or a specific molecule. This suggests that in most cases, a classical force-field description along with a careful parametrization against ρliq, ΔHvap, ΔGwat, and ΔGche results in a model that appropriately describes the liquid in terms of a wide spectrum of its physical properties.

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Predicting Critical Micelle Concentrations with Molecular Dynamics Simulations and COSMOmic

Jakobtorweihen

Yordanova

Смирнова

2017

Chemie Ingenieur Technik

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Surfactants are amphiphilic molecules which are capable of forming micelles. Therefore, they are used in many applications. The critical micelle concentration (CMC), the surfactant concentration at which micelles start to form, is an important property of these systems. Here, the applicability of COSMOmic (an extension of COSMO‐RS) to predict CMCs is reported for the first time. Molecular dynamics simulations were used as second method to calculate transfer free energies needed for the calculation of CMCs. In particular, CMCs for poly(oxyethylene) monoalkyl ether surfactants are determined.

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Calculation of binding affinities for linear alcohols to α -cyclodextrin by twin-system enveloping distribution sampling simulations

Cited by 18 publications

References 114 publications

Molecular Simulations of Thermodynamic Properties for the Systemα‐Cyclodextrin/Alcohol in Aqueous Solution

Molecular Simulations of Thermodynamic Properties for the Systemα‐Cyclodextrin/Alcohol in Aqueous Solution

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Predicting Critical Micelle Concentrations with Molecular Dynamics Simulations and COSMOmic

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