From owner-chemistry@ccl.net Sat Jun 20 09:03:01 2015 From: "Grigoriy Zhurko reg_zhurko#%#chemcraftprog.com" To: CCL Subject: CCL:G: H-bond and dispersion energy Message-Id: <-51456-150620090043-31712-jzH79cVQA0NPlqKILvnLjA[a]server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Sat, 20 Jun 2015 17:01:02 +0400 MIME-Version: 1.0 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 From owner-chemistry@ccl.net Sat Jun 20 10:58:00 2015 From: "Ambrish K Srivastava ambrishphysics[a]gmail.com" To: CCL Subject: CCL:G: H-bond and dispersion energy Message-Id: <-51457-150620105619-1443-4PzlZAuaHsQwQECSAKDaxA__server.ccl.net> X-Original-From: Ambrish K Srivastava Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Sat, 20 Jun 2015 20:26:13 +0530 MIME-Version: 1.0 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 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> > > -- *Ambrish K. Srivastava CSIR Senior Research Fellow Department of Physics University of Lucknow Lucknow, India-226007* Google Scholar: http://scholar.google.co.in/citations?user=XTcgp1EAAAAJ Research Gate: https://www.researchgate.net/profile/Ambrish_K_Srivastava From owner-chemistry@ccl.net Sat Jun 20 12:24:00 2015 From: "Stefan Grimme grimme]*[thch.uni-bonn.de" To: CCL Subject: CCL:G: H-bond and dispersion energy Message-Id: <-51458-150620115510-24274-nANl1vHuUK5L3Wevg0uu4Q#server.ccl.net> X-Original-From: "Stefan Grimme" Date: Sat, 20 Jun 2015 11:55:08 -0400 Sent to CCL by: "Stefan Grimme" [grimme:-:thch.uni-bonn.de] >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? Dear Grigoriy, here are my answers: 1. any two atoms with at least two electrons in total have dispersion interactions. 2. for O...H at a typical HB-distance this contribution is small on a RELATIVE basis because the HB energy can be relatively large. 3. dispersion effects on HB-bonded systems can NOT be neglected in general in particular for larger complexes. For example DNA base WC complexes are much better with DFT-D than with standard DFT. 4. the range of distances you find is typical for various density functionals. 5. B3LYP-D3/"triple-zeta AO basis" is a reasonable level of theory. Hope this helps Stefan From owner-chemistry@ccl.net Sat Jun 20 13:00:01 2015 From: "Jean-Pierre Djukic_HP djukic[a]unistra.fr" To: CCL Subject: CCL:G: H-bond and dispersion energy Message-Id: <-51459-150620123150-3653-yOKo9hHDmiGySfoE5RpwRQ#,#server.ccl.net> X-Original-From: Jean-Pierre Djukic_HP Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Sat, 20 Jun 2015 18:28:15 +0200 MIME-Version: 1.0 Sent to CCL by: Jean-Pierre Djukic_HP [djukic#unistra.fr] Dear all, Dispersion correction will surely improve the overall geometry of your structure and make the H bonding in question, I assume, "tighter" because of the impact of the correction on the molecule overall. It could be interesting to do calculations with and without any -D correction to figure out the consequence of the correction. There are a host of functionals that can do the job; functionals with suffix D3 , D3(BJ) and dDsC are doing very well in general to produce realistic geometries. if not implemented in Gaussian try to use ORCA. Regards, JP Le 20/06/2015 16:56, Ambrish K Srivastava ambrishphysics[a]gmail.com a écrit : > 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 > 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> >> >> > From owner-chemistry@ccl.net Sat Jun 20 13:34:01 2015 From: "Sebastian Kozuch seb.kozuch]|[gmail.com" To: CCL Subject: CCL:G: H-bond and dispersion energy Message-Id: <-51460-150620105930-2709-9pM+WR8BOeLJOLKh6eneBw,server.ccl.net> X-Original-From: Sebastian Kozuch Content-Transfer-Encoding: 8bit Content-Type: text/html; charset=windows-1252 Date: Sat, 20 Jun 2015 17:59:02 +0300 MIME-Version: 1.0 Sent to CCL by: Sebastian Kozuch [seb.kozuch+/-gmail.com]
Dear Grigoriy,
That is a question that does not have a definitive answer. H Bonds have a dispersion component, but some other factors influence the bond (charge transfer, electrostatic, polarization, it depends on who you ask). Because of that, the use of a dispersion correction is not always adequate, and sometimes overshoots. In the case of B3LYP the dispersion is so badly described that it is hard to have worse results with D3 (actually B3LYP-D3 is quite good, but you can do better). For other functionals it may not be the case, especially with small basis sets (this does not mean that small basis sets can be good, just that adding a dispersion correction may be even worse).
I am sorry for the auto-publicity, but this paper may help you: 
"Conformational Equilibria in Butane-1,4-Diol: A Benchmark of a Prototypical System With Strong Intramolecular H-Bonds."
http://dx.doi.org/10.1021/jp410723v

Best,
Sebastian

On 20/6/2015 4:01 PM, Grigoriy Zhurko reg_zhurko#%#chemcraftprog.com 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


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-- 
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch...........
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
.Ben Gurion University of the Negev .
..........Beer Sheva, Israel.........
.......... kozuch|a|bgu.ac.il .........
....http://www.bgu.ac.il/~kozuch/....
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From owner-chemistry@ccl.net Sat Jun 20 14:09:00 2015 From: "Abrash, Samuel sabrash|,|richmond.edu" To: CCL Subject: CCL:G: H-bond and dispersion energy Message-Id: <-51461-150620132600-27494-rJnw5xQZ62aCGTzZRo5Q4g]_[server.ccl.net> X-Original-From: "Abrash, Samuel" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 20 Jun 2015 17:25:53 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash++richmond.edu] Stefan, What are your thoughts on D3 vs D3BJ? Sam Abrash Sent from my iPhone > On Jun 20, 2015, at 12:49 PM, Stefan Grimme grimme]*[thch.uni-bonn.de wrote: > > > Sent to CCL by: "Stefan Grimme" [grimme:-:thch.uni-bonn.de] >> 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? > > Dear Grigoriy, > here are my answers: > 1. any two atoms with at least two electrons in total have > dispersion interactions. > 2. for O...H at a typical HB-distance this contribution is small > on a RELATIVE basis because the HB energy can be relatively large. > 3. dispersion effects on HB-bonded systems can NOT be neglected > in general in particular for larger complexes. For example DNA > base WC complexes are much better with DFT-D than with standard > DFT. > 4. the range of distances you find is typical for various density > functionals. > 5. B3LYP-D3/"triple-zeta AO basis" is a reasonable level of theory. > > Hope this helps > Stefan> > From owner-chemistry@ccl.net Sat Jun 20 14:44:01 2015 From: "Jim Kress jimkress35^^gmail.com" To: CCL Subject: CCL:G: H-bond and dispersion energy Message-Id: <-51462-150620143102-22018-2Fsauh+3JhF8rsUR7G7rPA+*+server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 20 Jun 2015 14:31:02 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35*o*gmail.com] Grigoriy, What you see is a fundamental flaw in DFT approaches. In the absence of an exact functional representation we have a plethora of approximate functionals, all of which are tuned to "accurately" reproduce differing types of physical phenomena while representation of other physical phenomena is less well represented. DFT has turned into a more rigorous form of semi-empirical methodology. When using DFT, I always use a variety of functionals that are chosen to encompass a variety of physical phenomena to ensure the results I get are reproducible. I believe any DFT calculation that is published should be required to do this. In addition, I always include Stefan Grimme's dispersion and use methods/ functionals that eliminate the double counting that can occur with DFT application. Use of DFT is not a black box method and must be approached with care. Jim -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com**ccl.net [mailto:owner-chemistry+jimkress35==gmail.com**ccl.net] On Behalf Of Grigoriy Zhurko reg_zhurko#%#chemcraftprog.com Sent: Saturday, June 20, 2015 9:01 AM To: Kress, Jim Subject: CCL:G: H-bond and dispersion energy 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 Zhurkohttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sat Jun 20 23:38:00 2015 From: "Jean-Pierre Djukic_HP djukic**unistra.fr" To: CCL Subject: CCL:G: H-bond and dispersion energy Message-Id: <-51463-150620233527-23687-yRqAEb8cATYI5YmnFdSa7w!^!server.ccl.net> X-Original-From: Jean-Pierre Djukic_HP Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Sun, 21 Jun 2015 05:31:52 +0200 MIME-Version: 1.0 Sent to CCL by: Jean-Pierre Djukic_HP [djukic-.-unistra.fr] There is another way of putting the issue. DFT-D is the combination of a native DFT treatment, which treats local interactions (and correlation), with a treatment of long-range acting dispersion. Combining the two requires damping the double counting of the effect of correlation and dispersion in the critical distance range of 2.6-3.8 angstroms where correlation treated by the native functional remains active and starts to deplete and where the dispersion correction takes over. This damping is operated by a "function", all the difference between D3 and D3(BJ) is in the nature of this function, the one used in the latter formulation is to my experience much better especially if a preliminary analysis of such localized interaction is targeted (Stefan Grimme will certainly explain and document this much better than me). Now if one is interested in analysing an interaction between two centers within this range of distances, using DFT-D will not allow a very precise dichotomy of the forces that make the interaction up, however, it is possible but not ideal; knowing that long range dispersion also plays a role in defining the extent of such interaction DFT-D will provide the role of such long range interactions on the specific conformation or geometry. Perhaps a WFT analysis of this DFT-D optimized structure can produce a clean dichotomy of the forces operating within the local H-bond of interest if this is the goal of the study. I personnally use NCI analysis to materialize such local interaction, even though this materialization does not say much on the role of long range dispersion in the establishment of local NCI nor on the intimate nature and energy extent of the localized, intimate NCI; I assume that NCI analysis only makes sense if the geometry analysed has been properly optimized with a DFT-D functional, particularly if the molecule is very large and asymmetric. all the best. Le 20/06/2015 20:31, Jim Kress jimkress35^^gmail.com a écrit : > Sent to CCL by: "Jim Kress" [jimkress35*o*gmail.com] > Grigoriy, > > What you see is a fundamental flaw in DFT approaches. In the absence of an > exact functional representation we have a plethora of approximate > functionals, all of which are tuned to "accurately" reproduce differing > types of physical phenomena while representation of other physical phenomena > is less well represented. > > DFT has turned into a more rigorous form of semi-empirical methodology. > > When using DFT, I always use a variety of functionals that are chosen to > encompass a variety of physical phenomena to ensure the results I get are > reproducible. I believe any DFT calculation that is published should be > required to do this. In addition, I always include Stefan Grimme's > dispersion and use methods/ functionals that eliminate the double counting > that can occur with DFT application. > > Use of DFT is not a black box method and must be approached with care. > > Jim > > -----Original Message----- >> From: owner-chemistry+jimkress35==gmail.com~!~ccl.net > [mailto:owner-chemistry+jimkress35==gmail.com~!~ccl.net] On Behalf Of Grigoriy > Zhurko reg_zhurko#%#chemcraftprog.com > Sent: Saturday, June 20, 2015 9:01 AM > To: Kress, Jim > Subject: CCL:G: H-bond and dispersion energy > > > 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 Zhurkohttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt