Sent to CCL by: Ambrish K Srivastava [ambrishphysics]![gmail.com]
Dear Prof. Zhurko,
I am NOT sure about the effect of dispersion on hydrogen bond.
However, dispersion corrections are indeed required in case of
hydrogen adsorption on some metallic clusters. Recently, we have
studied the same on small MgO clusters (see, A.K. Srivastava & N.
Misra (2015): Molecular Simulation, DOI:
10.1080/08927022.2015.1032278).
The best choice in this case is PBE-D3 rather than B3LYP-D3 as
described by Gebhardt et al. (see, Gebhardt J, Vin˜es F, Bleiziffer P,
Hieringer W, Go¨rling A. Phys Chem Chem Phys. 2014;16:5382 –5392)
Thanks and regards,
AKS
On 6/20/15, Grigoriy Zhurko reg_zhurko#%#chemcraftprog.com
<owner-chemistry : ccl.net> wrote:
Sent to CCL by: Grigoriy Zhurko [reg_zhurko]|[chemcraftprog.com]
Dear All,
My first question is, whether the hydrogen bond is a kind of dispersion
interaction (which can be taken into account by methods like DFT-D)?
I try to compute a molecule of bilirubin (see the structure below), and I
found that different DFT functionals give quite different H..O bond lengths
(from 1.52 to 1.64 A). Which DFT should be chosen? If there is dispersion
interaction in H-bonds, maybe the best choice will be e.g. B3LYP-D3
implemented in the latest Gaussian?
The molecule:
6 0.000000000 5.561929000 -2.050909000
6 0.920495000 4.961635000 -1.068567000
7 0.205382000 4.046911000 -0.365731000
6 -1.111043000 3.976317000 -0.824087000
6 -1.211095000 4.958500000 -1.900895000
6 -2.063857000 3.119331000 -0.399976000
1 0.611747000 3.634373000 0.469199000
6 -3.025202000 1.279200000 1.055237000
6 -1.984634000 2.062973000 0.564997000
7 -0.833436000 1.623524000 1.181168000
6 -1.109020000 0.600704000 2.028487000
6 -2.470241000 0.349674000 1.975049000
1 0.113160000 1.946575000 1.042427000
6 2.470241000 -0.349674000 1.975049000
6 1.109020000 -0.600704000 2.028487000
7 0.833436000 -1.623524000 1.181168000
6 1.984634000 -2.062973000 0.564997000
6 3.025202000 -1.279200000 1.055237000
6 0.000000000 0.000000000 2.844663000
6 1.211095000 -4.958500000 -1.900895000
6 1.111043000 -3.976317000 -0.824087000
7 -0.205382000 -4.046911000 -0.365731000
6 -0.920495000 -4.961635000 -1.068567000
6 0.000000000 -5.561929000 -2.050909000
6 2.063857000 -3.119331000 -0.399976000
1 -0.611747000 -3.634373000 0.469199000
8 2.117092000 5.204802000 -0.891075000
8 -2.117092000 -5.204802000 -0.891075000
6 3.238959000 0.663634000 2.774482000
1 2.575531000 1.148113000 3.492029000
1 4.004810000 0.151009000 3.365790000
6 4.473436000 -1.409878000 0.698541000
1 5.109313000 -1.201973000 1.562048000
1 4.717415000 -2.417234000 0.359059000
1 4.768044000 -0.716453000 -0.095375000
6 3.940086000 1.747526000 1.952147000
1 4.603166000 2.340051000 2.590822000
1 4.580472000 1.324217000 1.177015000
6 3.009070000 2.725417000 1.285739000
8 1.813868000 2.776190000 1.541402000
8 3.613329000 3.515250000 0.438808000
1 2.997128000 4.180234000 -0.008699000
6 -4.473436000 1.409878000 0.698541000
1 -4.717415000 2.417234000 0.359059000
1 -4.768044000 0.716453000 -0.095375000
1 -5.109313000 1.201973000 1.562048000
6 -3.238959000 -0.663634000 2.774482000
1 -2.575531000 -1.148113000 3.492029000
1 -4.004810000 -0.151009000 3.365790000
6 -3.940086000 -1.747526000 1.952147000
1 -4.603166000 -2.340051000 2.590822000
1 -4.580472000 -1.324217000 1.177015000
6 -3.009070000 -2.725417000 1.285739000
8 -3.613329000 -3.515250000 0.438808000
8 -1.813868000 -2.776190000 1.541402000
1 -2.997128000 -4.180234000 -0.008699000
1 -3.036498000 3.230979000 -0.860156000
1 3.036498000 -3.230979000 -0.860156000
1 -0.421543000 -0.769314000 3.495015000
1 1.318885000 -7.468669000 -3.653386000
1 0.421543000 0.769314000 3.495015000
1 -0.113160000 -1.946575000 1.042427000
6 2.442661000 -5.190242000 -2.707594000
1 3.120597000 -4.338263000 -2.667624000
1 2.987984000 -6.067896000 -2.348654000
1 2.185360000 -5.370287000 -3.752753000
6 -0.483709000 -6.574054000 -2.973701000
1 -1.567240000 -6.625471000 -3.030271000
6 0.238784000 -7.426089000 -3.698510000
1 -0.247403000 -8.137346000 -4.354264000
6 -2.442661000 5.190242000 -2.707594000
1 -2.987984000 6.067896000 -2.348654000
1 -2.185360000 5.370287000 -3.752753000
1 -3.120597000 4.338263000 -2.667624000
6 0.483709000 6.574054000 -2.973701000
1 1.567240000 6.625471000 -3.030271000
6 -0.238784000 7.426089000 -3.698510000
1 -1.318885000 7.468669000 -3.653386000
1 0.247403000 8.137346000 -4.354264000
Grigoriy Zhurko>