From owner-chemistry@ccl.net Sat Jun 20 09:03:01 2015
From: "Grigoriy Zhurko reg_zhurko#%#chemcraftprog.com" <owner-chemistry[a]server.ccl.net>
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 <reg_zhurko/a\chemcraftprog.com>
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Date: Sat, 20 Jun 2015 17:01:02 +0400
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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" <owner-chemistry__server.ccl.net>
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 <ambrishphysics=-=gmail.com>
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
<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>
>
>
--
*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" <owner-chemistry#server.ccl.net>
To: CCL
Subject: CCL:G: H-bond and dispersion energy
Message-Id: <-51458-150620115510-24274-nANl1vHuUK5L3Wevg0uu4Q#server.ccl.net>
X-Original-From: "Stefan Grimme" <grimme~~thch.uni-bonn.de>
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" <owner-chemistry#,#server.ccl.net>
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 <djukic%unistra.fr>
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
> <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>
>>
>>
>
From owner-chemistry@ccl.net Sat Jun 20 13:34:01 2015
From: "Sebastian Kozuch seb.kozuch]|[gmail.com" <owner-chemistry,server.ccl.net>
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 <seb.kozuch%a%gmail.com>
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]
<html style="direction: ltr;">
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
<style type="text/css">body p { margin-bottom: 0cm; margin-top: 0pt; } </style>
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text="#000000">
<div class="moz-cite-prefix">Dear Grigoriy,<br>
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). <br>
I am sorry for the auto-publicity, but this paper may help you:� <br>
"Conformational Equilibria in Butane-1,4-Diol: A Benchmark of a
Prototypical System With Strong Intramolecular H-Bonds."<br>
<a class="moz-txt-link-freetext" href="http://dx.doi.org/10.1021/jp410723v">http://dx.doi.org/10.1021/jp410723v</a><br>
<br>
Best,<br>
Sebastian<br>
<br>
On 20/6/2015 4:01 PM, Grigoriy Zhurko
reg_zhurko#%#chemcraftprog.com wrote:<br>
</div>
<blockquote
cite="mid:-id%233xm-51456-150620090043-31712-EHx8c9ZAyfg25MWMbwzFkg|a|server.ccl.net"
type="cite">
<pre wrap="">
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 ZhurkoE-mail to subscribers: <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY|a|ccl.net">CHEMISTRY|a|ccl.net</a> or use:
<a class="moz-txt-link-freetext" href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a>
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</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
..........Sebastian Kozuch...........
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
.Ben Gurion University of the Negev .
..........Beer Sheva, Israel.........
.......... <a class="moz-txt-link-abbreviated" href="mailto:kozuch|a|bgu.ac.il">kozuch|a|bgu.ac.il</a> .........
....http://www.bgu.ac.il/~kozuch/....
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx</pre>
</body>
</html>
From owner-chemistry@ccl.net Sat Jun 20 14:09:00 2015
From: "Abrash, Samuel sabrash|,|richmond.edu" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL:G: H-bond and dispersion energy
Message-Id: <-51461-150620132600-27494-rJnw5xQZ62aCGTzZRo5Q4g]_[server.ccl.net>
X-Original-From: "Abrash, Samuel" <sabrash(0)richmond.edu>
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 <owner-chemistry#,#ccl.net> 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" <owner-chemistry+*+server.ccl.net>
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" <jimkress35_-_gmail.com>
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" <owner-chemistry!^!server.ccl.net>
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 <djukic,+,unistra.fr>
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 �crit :
> 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