6533b7d5fe1ef96bd1265253
RESEARCH PRODUCT
Comparison of some dispersion-corrected and traditional functionals as applied to peptides and conformations of cyclohexane derivatives.
Amparo AsensioJ. J. DannenbergMateusz Marianskisubject
CyclohexaneChemistryHydrogen bondMolecular biophysicsMolecular ConformationGeneral Physics and AstronomyThermodynamicsAntiparallel (biochemistry)chemistry.chemical_compoundMolecular geometryCyclohexanesComputational chemistryTheoretical Methods and AlgorithmsQuantum TheoryThermodynamicsPhysical and Theoretical ChemistryPeptidesProtein secondary structureBasis setRamachandran plotdescription
We compare the energetic and structural properties of fully optimized α-helical and antiparallel β-sheet polyalanines and the energetic differences between axial and equatorial conformations of three cyclohexane derivatives (methyl, fluoro, and chloro) as calculated using several functionals designed to treat dispersion (B97-D, ωB97x-D, M06, M06L, and M06-2X) with other traditional functionals not specifically parametrized to treat dispersion (B3LYP, X3LYP, and PBE1PBE) and with experimental results. Those functionals developed to treat dispersion significantly overestimate interaction enthalpies of folding for the α-helix and predict unreasonable structures that contain Ramachandran φ and ψ and C = O...N H-bonding angles that are out of the bounds of databases compiled the β-sheets. These structures are consistent with overestimation of the interaction energies. For the cyclohexanes, these functionals overestimate the stabilities of the axial conformation, especially when used with smaller basis sets. Their performance improves when the basis set is improved from D95∗∗ to aug-cc-pVTZ (which would not be possible with systems as large as the peptides).
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2012-07-28 |