Case Study: S22 Dataset

Case Study: S22 Dataset

We compare interaction energies calculated for the S22 dataset compiled by Jurecka et al. using the Abinit, Qbox, Quantum Espresso, and Siesta codes. In addition, we compare to published results by Zhao & Truhlar using Gaussian 03. Our study focuses on DFT codes using the Perdew-Burke-Ernzerhof (PBE) GGA exchange-correlation functional.

Introduction

The S22 dataset consist of twenty-two biological complexes represent a balanced mixture of noncovalent interactions to evaluate the quality of theoretical methods implemented in these codes. Specifically, the S22 dataset consists of 7 hydrogen-bonded complexes, 8 dispersion-dominated complexes, and 7 mixed complexes. The dispersion-dominated complexes contain systems 8-15, the mixed-complexes consist of 16-22, and the hydrogen-bonded ones are 1-7.

Hydrogen-bonded complexes Dispersion-dominated complexes Mixed complexes
1. (NH3)2 (C2h)
2. (H2O)2 (Cs)
3. Formic acid dimer (C2h)
4. Formic acid dimer (C2h)
5. Uracil dimer (C2h)
6. 2-pyridoxine--2-aminopyridine (C1)
7. Adenine--thymine WC (C1)
8. (CH4)2 (D3d)
9. (C2H4)2 (D2d)
10. Benzene--CH4 (C3)
11. Benzene dimer (C2h)
12. Pyrazine dimer (Cs)
13. Uracil dimer (C2)
14. Indole benzene (C1)
15. Adenine--thymine stack (C1)
16. Ethene--Ethyne (C2v)
17. Benzene H2O (Cs)
18. Benzene NH3 (Cs)
19. Benzene HCN (Cs)
20. Benzene dimer (C2v)
21. Indole benzene T-shaped (C1)
22. Phenol dimer (C1)

Results

The table below gives interaction energies in units of kcal/mol.
System Qbox QE Abinit Siesta Gaussian CP/noCP
1. (NH3)2 (C2h) -2.888 -2.889 -2.861 -3.442 -3.54/-3.8
2. (H2O)2 (Cs) -5.09 -5.09 -5.046 -6.528 -5.59/-6.45
3. Formic acid dimer (C2h) -18.653 -18.656 -18.529 -21.155 -17.47/-18.34
4. Formamide dimer (C2h) -15.017 -15.018 -14.918 -17.489 -14.48/-15.07
5. Uracil dimer (C2h) -18.887 -18.872 -18.676 -21.451 -18.41/-19.21
6. 2-pyridoxine-2-aminopyridine (C1) -15.726 -15.705 -15.573 -18.571 -15.37/-16.07
7. Adenine-thymine WC -14.737 -14.711 -14.543 -17.823 -14.33/-15.1
8. (CH4)2 (D3d) -0.118 -0.119 -0.096 -0.475 -0.05/-0.06
9. (C2H4)2 (D2d) -0.387 -0.387 -0.341 -0.775 -0.29/-0.45
10. Benzene-CH4 (C3) -0.125 -0.126 -0.056 -0.578 -0.02/-0.19
11. Benzene dimer (C2h) 1.597 1.604 1.849 0.02 2.01/1.41
12. Pyrazine dimer (Cs) 0.359 0.361 0.654 -1.409 0.75/0.07
13. Uracil dimer (C2) -3.385 -3.378 -2.768 -5.697 -2.7/-3.88
14. Indole benzene (C1) 1.788 1.799 2.178 -0.44 2.33/1.38
15. Adenine-thymine stack (C1) -2.194 -2.182 -1.445 -5.769 -1.43/-2.93
16. Ethene-Ethyne (C2v) -1.229 -1.228 -1.2 -1.642 -1.26/-1.43
17. Benzene H2O (Cs) -2.159 -2.16 -2.065 -3.46 -2.25/-2.79
18. Benzene NH3 (Cs) -1.036 -1.037 -0.961 -1.793 -1.05/-1.43
19. Benzene HCN (Cs) -2.96 -2.96 -2.893 -3.545 -2.85/-3.21
20. Benzene dimer (C2v) -0.289 -0.269 -0.142 -1.197 -0.18/-0.62
21. Indole benzene T-shaped (C1) -2.314 -2.285 -2.112 -3.621 -2.03/-2.66
22. Phenol dimer (C1) -4.248 -4.219 -4.023 -6.022 -4.14/-5.19
We can also plot these interaction energies

References

  1. Petr Jurecka, Jiri Sponer, Jiri Cerny, and Pavel Hobza. Benchmark database of accurate (mp2 and ccsd(t) complete basis set limit) interaction energies of small model complexes, dna base pairs, and amino acid pairs. Phys. Chem. Chem. Phys., 8:–, 2006. http://dx.doi.org/10.1039/B600027D
  2. John P. Perdew, Kieron Burke, and Matthias Ernzerhof. Generalized gradient approximation made simple. Phys. Rev. Lett., 77:3865–3868, Oct 1996. http://link.aps.org/doi/10.1103/PhysRevLett.77.3865
  3. Yan Zhao and Donald G. Truhlar. Density functionals for noncovalent interaction energies of biological importance. Journal of Chemical Theory and Computation, 3(1):289–300, 2007. http://pubs.acs.org/doi/abs/10.1021/ct6002719

Data Links

DatasetShort URL
S22 Abinithttp://goo.gl/eUSsT
S22 Qboxhttp://goo.gl/pW6c6
S22 Quantum Espressohttp://goo.gl/hpyhG
S22 Siestahttp://goo.gl/ZazUW