A Statistically Supported Antioxidant Activity DFT Benchmark—The Effects of Hartree–Fock Exchange and Basis Set Selection on Accuracy and Resources Uptake
Abstract
:1. Introduction
BDE | |
IP | |
EA | |
PA |
2. Results
3. Discussion
3.1. Bond Dissociation Enthalpy
3.2. Adiabatic Ionization Potential
3.3. Adiabatic Electron Affinity
3.4. Proton Affinity
3.5. Section Conclusions
3.6. Performance Evaluation
3.7. Janak’s Theorem Applicability
4. Materials and Methods
4.1. Caffeic Acid as a Reference Structure
4.2. On Functionals and Basis Set Choice
4.3. DFT Calculations
4.4. Linear Regression Models
- %HF at short range (SR, [0, 100]);
- %HF at middle range (MR, [0, 100]);
- %HF at long range (LR, [0, 100]);
- Number of basis functions (NBF, N > 0);
- Presence of valence double basis set (ζ, 0 ∨ 1);
- presence of diffuse function (D, 0 ∨ 1).
4.5. Computational Performance
4.6. Janak’s Theorem Revisited
4.7. Scoring Function
- Hydroxyl bond length at C3;
- Hydroxyl bond length at C4;
- Hydrogen bond length;
- Bond dissociation enthalpy at C3;
- Bond dissociation enthalpy at C4;
- Adiabatic electron affinity;
- Adiabatic ionization potential;
- Proton affinity at C3;
- Proton affinity at C4.
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Sample Availability
References
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BLYP | TPSSh | B3LYP | PW6B95 | MPWB1K | M06-2X | wB97 | wB97X | CAM–B3LYP | M11 | HISSbPBE | |
---|---|---|---|---|---|---|---|---|---|---|---|
6–31G(d,p) | 41% | 41% | 46% | 46% | 41% | 54% | 53% | 51% | 55% | 51% | 46% |
6–31+G(d,p) | 32% | 56% | 51% | 61% | 57% | 66% | 61% | 61% | 65% | 70% | 60% |
6–31++G(d,p) | 32% | 56% | 51% | 61% | 57% | 66% | 61% | 61% | 63% | 70% | 60% |
6–311G(d,p) | 56% | 61% | 60% | 56% | 37% | 78% | 51% | 51% | 61% | 65% | 39% |
6–311+G(d,p) | 46% | 53% | 51% | 63% | 52% | 65% | 58% | 58% | 63% | 65% | 58% |
6–311++G(d,p) | 46% | 53% | 48% | 63% | 52% | 70% | 63% | 58% | 63% | 65% | 58% |
cc–pVDZ | 39% | 46% | 51% | 46% | 44% | 53% | 46% | 46% | 47% | 46% | 44% |
aug–cc–pVDZ | 29% | 51% | 48% | 56% | 42% | 71% | 53% | 56% | 61% | 63% | 51% |
cc–pVTZ | 44% | 48% | 46% | 48% | 32% | 66% | 53% | 48% | 49% | 63% | 48% |
aug–cc–pVTZ | 34% | 48% | 48% | 53% | 40% | 63% | 53% | 53% | 58% | 58% | 48% |
def2–SVP | 41% | 46% | 56% | 46% | 47% | 61% | 46% | 53% | 47% | 56% | 51% |
def2–SVPD | 39% | 53% | 48% | 63% | 52% | 69% | 58% | 53% | 63% | 68% | 68% |
def2–TZVP | 32% | 56% | 51% | 56% | 47% | 65% | 51% | 51% | 56% | 63% | 48% |
def2–TZVPD | 29% | 48% | 44% | 53% | 40% | 64% | 53% | 53% | 58% | 63% | 58% |
Substance | BDEcalc | BDEexp [22] | Δ(BDEcalc − BDEexp) |
---|---|---|---|
Catechin | 76.9 | 83.2 (C4′) | −6.3 |
Chrysin | 92.6 | 85.4 (C7) | 7.2 |
(–)-Epicatechin | 82.4 | 82.0 (C4′) | 0.4 |
(–)-Epigallocatechin | 79.4 | 82.4 (C4′) | −3.0 |
Fisetin | 86.5 | 83.2 (C4′) | 3.3 |
Galangin | 92.5 | 86.8 (C7) | 5.7 |
Gallic acid | 81.0 | 83.0 (C4) | −2.0 |
Luteolin | 78.1 | 81.9 (C4′) | −3.8 |
Myricetin | 79.6 | 81.5 (C4′) | −1.9 |
Quercetin | 78.6 | 82.0 (C4′) | −3.4 |
Taxifolin | 86.6 | 82.1 (C4′) | 4.5 |
MAE: 3.8 kcal/mol | RMSE: 4.2 kcal/mol |
Method | Type | %HF (SR/MR/LR) |
---|---|---|
BLYP [30,31] | GGA | (0%)/0%/(0%) |
TPSSh [32,33] | GH meta–GGA | (10%)/10%/(10%) |
B3LYP [31,34] | GH GGA | (20%)/20%/(20%) |
PW6B95 [35] | GH meta–GGA | (28%)/28%/(28%) |
MPWB1K [36] | GH meta–GGA | (44%)/44%/(44%) |
M06–2X [21] | GH meta–GGA | (54%)/54%/(54%) |
WB97 [37] | RSH GGA | 0%/0%/100% |
WB97X [37] | RSH GGA | 15.77%/0%/100% |
CAM–B3LYP [38] | RSH GGA | 19%/0%/65% |
M11 [39] | RSH meta–GGA | 42.8%/0%/100% |
HISSbPBE [40] | RSH GGA | 0%/60%/0% |
Family | Basis Set | Number of Basis Functions |
---|---|---|
Pople’s [42,43] | 6–31G(d,p) | 235 |
6–31+G(d,p) [41,44,45,46] | 287 | |
6–31++G(d,p) | 295 | |
6–311G(d,p) | 282 | |
6–311+G(d,p) [47,48] | 334 | |
6–311++G(d,p) | 342 | |
Dunning’s [49,50] | cc–pVDZ | 222 |
aug–cc–pVDZ | 371 | |
cc–pVTZ | 502 | |
aug–cc–pVTZ | 782 | |
Ahlrich’s [51,52] | def2–SVP | 222 |
def2–SVPD | 336 | |
def2–TZVP | 451 | |
def2–TZVPD | 565 |
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Spiegel, M.; Gamian, A.; Sroka, Z. A Statistically Supported Antioxidant Activity DFT Benchmark—The Effects of Hartree–Fock Exchange and Basis Set Selection on Accuracy and Resources Uptake. Molecules 2021, 26, 5058. https://doi.org/10.3390/molecules26165058
Spiegel M, Gamian A, Sroka Z. A Statistically Supported Antioxidant Activity DFT Benchmark—The Effects of Hartree–Fock Exchange and Basis Set Selection on Accuracy and Resources Uptake. Molecules. 2021; 26(16):5058. https://doi.org/10.3390/molecules26165058
Chicago/Turabian StyleSpiegel, Maciej, Andrzej Gamian, and Zbigniew Sroka. 2021. "A Statistically Supported Antioxidant Activity DFT Benchmark—The Effects of Hartree–Fock Exchange and Basis Set Selection on Accuracy and Resources Uptake" Molecules 26, no. 16: 5058. https://doi.org/10.3390/molecules26165058