2016
DOI: 10.1021/acs.jctc.6b01045
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Method Dependence of Proline Ring Flexibility in the Poly-l-Proline Type II Polymer

Abstract: We studied the sensitivity of the energetic and geometrical features of the proline ring (pyrrolidine) to the quantum mechanical computational approach by adopting the proline monomer, trimer, and polymer, as simplified collagen protein models. Within the Density Functional Theory (DFT) approach, we tested the ability of different functionals (GGA PBE and the hybrid B3LYP), added with a posteriori empirical dispersion corrections (D), to predict the conformational potential energy surface of the five-membered … Show more

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Cited by 17 publications
(44 citation statements)
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“…This approach was proven to be cost-effective for computing energies and geometries of molecular crystals 5 and protein conformations. 28…”
Section: Introductionmentioning
confidence: 99%
“…This approach was proven to be cost-effective for computing energies and geometries of molecular crystals 5 and protein conformations. 28…”
Section: Introductionmentioning
confidence: 99%
“…In all molecules, the carboxyl group is in the trans conformation, the OH group of the carboxyl group makes an intramolecular H-bond with the nitrogen lone pair. This conformation has been demonstrated to be the most stable one in the case of Pro in gas phase, 12 and it was extensively studied by us in Ref 32 .…”
Section: Molecular Models (Mol)mentioning
confidence: 91%
“…These have been extensively studied with NMR spectroscopy [35][36][37][38][39] and, theoretically, in an all-Pro PPII polymer within our group. 32 Those conformations are called U/D, in association with positive/negative value of the χ 2 dihedral angle (see Figure 4B). The U/D conformer has the C γ on the opposite/same side of the carbonyl group with respect to the pseudo-plane defined by the other ring atoms (N, C α , C β and C δ ), see Figure 4B and 4C.…”
Section: Conformational Analysismentioning
confidence: 99%
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“…HF-3c: The empirically modified minimal basis set Hartree-Fock method accounts for London dispersion and basis set errors in a consistent and cost-effective way (only nine global empirical parameters) [21]. While it has been introduced for molecular complexes, its extension and accuracy for various organic crystals has been demonstrated recently [31,32]. PBE-D3/def2-SVP: As cross check we apply the dispersion corrected GGA PBE functional [22] in a common split-valence orbital set without further corrections [23].…”
Section: Computational Detailsmentioning
confidence: 99%