Method Dependence of Proline Ring Flexibility in the Poly-<scp>l</scp>-Proline Type II Polymer

Several computational techniques for solid-state applications have recently been proposed to enlarge the scope of computer simulations of large molecular systems. In this contribution, we focused on two of these, namely, HF-3c and PBEh-3c. They were recently proposed by the Grimme’s group, as “low-cost” ab initio-based techniques for electronic structure calculation of large systems and were proved to be effective essentially for organic molecules. HF-3c is based on a Hartree–Fock Hamiltonian with a minimal Gaussian quality basis set, whereas PBEh-3c is a density functional theory (DFT) based method with a hybrid functional and a medium-quality basis set. Both HF-3c and PBEh-3c account for dispersion (London) interactions and are free from the basis set superposition error due to limited basis set size, through several pairwise semiempirical corrections. To the best of our knowledge, despite the promising results on the cost-accuracy side of molecular simulations of organic molecules, these methods have been used only in few cases for solid-state applications. In this contribution, we studied the performance of HF-3c and PBEh-3c for predicting the properties of inorganic crystals to enlarge the applicability of these cheap and fast methodologies. As a testing ground, we have chosen a well-known class of material, e.g., microporous all-silica zeolites. We benchmarked geometries, formation energies, vibrational features, and mechanical properties by comparing the results with literature data from both experiment and computer simulation. For structures, HF-3c is extremely accurate in predicting the zeolites cell volume, albeit we do not include any vibrational contribution, neither zero point nor thermal, on the computed volumes, which may introduce small variations in the predicted values. For the energetic, the relative stability of the zeolites using the DFT//HF-3c approach allows predictions within the experimental error for most of the cases taken into consideration when the experimental enthalpies were corrected back to electronic energies by using the HF-3c thermodynamic contributions computed in the harmonic approximation. This strategy is particularly convenient, as the slow step (geometry optimization) is carried out with the cheapest HF-3c method, whereas the fast step (single point energy evaluation) is carried out with costly DFT methods. In this sense, the use of the DFT//HF-3c approach results to be a promising one to predict the stability and structure of microporous materials. Finally, the HF-3c method predicts the mechanical properties of the zeolite set in reasonable agreement with respect to those computed with the state-of-the-art DFT simulations, indicating the HF-3c method as a possible technique for the mechanical stability screenings of microporous materials.

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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%

Cost-Effective Quantum Mechanical Approach for Predicting Thermodynamic and Mechanical Stability of Pure-Silica Zeolites

2019

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“…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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Decoding Collagen Triple Helix Stability by Means of Hybrid DFT Simulations

2019

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Collagen is a protein family defined by a triple helix motif, which comprises roughly one-third of the total human protein content. Decoding the reasons underlying the stability of the collagen triple helix is of both fundamental and applicative relevance, for instance, to guide collagen protein engineering. In principle, full quantum mechanical approaches based on density functional theory (DFT) are ideal to study the subtle physico-chemical features of collagen. Unfortunately, the huge size of the protein prevents the straightforward application of DFT to realistic collagen protein models. In this paper, we propose a new realistic model of the collagen protein based on a periodic approach. The protein model exploits the intrinsic symmetry of the collagen triple helix, dramatically lowering the cost of the simulations. This allows using accurate hybrid DFT simulations (B3LYP-D/TZP) for systematic studies of the collagen protein features. We have tested the proposed model/level-of-theory combination to analyze the well-known proline-conformation/collagen-stability relationship. For this purpose, we have performed an extensive conformational analysis of proline ring within the protein, clarifying some of the reasons linking specific ring conformations to helix positions. Throughout our data analysis, we have also obtained "for free" the collagen inter-strand binding energy. Simulation results demonstrate that London dispersion interactions play the dominant role in the whole helix stability. The good agreement with the experimental data validates the use of the proposed model/level-of-theory to assist the active field of collagen-like peptide synthesis.

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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%

On the hydrogen activation by frustrated Lewis pairs in the solid state: benchmark studies and theoretical insights

Liu

Brandenburg

Grimme

2017

Phil. Trans. R. Soc. A.

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Recently, the concept of small molecule activation by frustrated Lewis pairs (FLPs) has been expanded to the solid state showing a variety of interesting reactivities. Therefore, there is a need to establish a computational protocol to investigate such systems theoretically. In the present study, we selected several FLPs and applied multiple levels of theory, ranging from a semi-empirical tight-binding Hamiltonian to dispersion corrected hybrid density functionals. Their performance is benchmarked for the computation of crystal geometries, thermostatistical contributions, and reaction energies. We show that the computationally efficient HF-3c method gives accurate crystal structures and is numerically stable and sufficiently fast for routine applications. This method also gives reliable values for the thermostatistical contributions to Gibbs free energies. The meta-generalized gradient approximated TPSS-D3 evaluated in a projector augmented plane wave basis set is able to produce sufficiently accurate reaction electronic energies. The established protocol is intended to support experimental studies and to predict new reactions in the emerging field of solid-state FLPs.This article is part of the themed issue 'Frustrated Lewis pair chemistry'.

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Method Dependence of Proline Ring Flexibility in the Poly-l-Proline Type II Polymer

Cited by 17 publications

References 50 publications

Cost-Effective Quantum Mechanical Approach for Predicting Thermodynamic and Mechanical Stability of Pure-Silica Zeolites

Cost-Effective Quantum Mechanical Approach for Predicting Thermodynamic and Mechanical Stability of Pure-Silica Zeolites

Decoding Collagen Triple Helix Stability by Means of Hybrid DFT Simulations

On the hydrogen activation by frustrated Lewis pairs in the solid state: benchmark studies and theoretical insights

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