From owner-chemistry@ccl.net Mon Oct 17 08:09:00 2016 From: "Marcel Swart marcel.swart|,|icrea.cat" To: CCL Subject: CCL: CCL #DFT16poll results are out Message-Id: <-52396-161017080840-4097-OlYKeam/l9fGKBJeRV53Gw-*-server.ccl.net> X-Original-From: "Marcel Swart" Date: Mon, 17 Oct 2016 08:08:38 -0400 Sent to CCL by: "Marcel Swart" [marcel.swart . icrea.cat] Dear all, the results for the 2016 edition of the #DFTpoll have been published: http://www.marcelswart.eu/dft-poll/index.html Marcel Swart Matthias Bickelhaupt Miquel Duran _____________________________________ Prof Dr Marcel Swart, FRSC ICREA Research Professor at Institut de Qumica Computacional i Catlisi (IQCC) Univ. Girona (Spain) COST Action CM1305 (ECOSTBio) chair Girona Seminar 2016 organizer IQCC director RSC Advances associate editor Young Academy of Europe member Web http://www.marcelswart.eu vCard addressbook://www.marcelswart.eu/MSwart.vcf From owner-chemistry@ccl.net Mon Oct 17 10:42:00 2016 From: "Jim Kress jimkress35+/-gmail.com" To: CCL Subject: CCL: CCL #DFT16poll results are out Message-Id: <-52397-161017103421-4548-Rvk/GIof0+lKu4W83LdwyA%x%server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 17 Oct 2016 10:34:12 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35%x%gmail.com] Marcel, Matthias, and Miquel; Great work as usual. Thanks for doing this. It is immensely helpful. Jim -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com ~ ccl.net [mailto:owner-chemistry+jimkress35==gmail.com ~ ccl.net] On Behalf Of Marcel Swart marcel.swart|,|icrea.cat Sent: Monday, October 17, 2016 8:09 AM To: Kress, Jim Subject: CCL: CCL #DFT16poll results are out Sent to CCL by: "Marcel Swart" [marcel.swart . icrea.cat] Dear all, the results for the 2016 edition of the #DFTpoll have been published: http://www.marcelswart.eu/dft-poll/index.html Marcel Swart Matthias Bickelhaupt Miquel Duran _____________________________________ Prof Dr Marcel Swart, FRSC ICREA Research Professor at Institut de Qumica Computacional i Catlisi (IQCC) Univ. Girona (Spain) COST Action CM1305 (ECOSTBio) chair Girona Seminar 2016 organizer IQCC director RSC Advances associate editor Young Academy of Europe member Web http://www.marcelswart.eu vCard addressbook://www.marcelswart.eu/MSwart.vcfhttp://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 Mon Oct 17 11:22:00 2016 From: "Jens Spanget-Larsen spanget(0)ruc.dk" To: CCL Subject: CCL: Hydrogen bond order? Message-Id: <-52398-161017103307-4451-/rJwuiT2qHQsfhrt6tZFCQ[a]server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Language: da-DK Content-Type: multipart/alternative; boundary="_000_A94E15A372E6194CA8719D62642F67448BA82E04MBX2adrucdk_" Date: Mon, 17 Oct 2016 14:32:58 +0000 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget^^^ruc.dk] --_000_A94E15A372E6194CA8719D62642F67448BA82E04MBX2adrucdk_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCl: Do you know of any systematic studies of the application of Wiberg Bond Ord= ers in the description of intramolecular hydrogen bonds? Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget,+,ruc.dk DK-4000 Roskilde, Denmark Web: thiele.ruc.dk/~spanget ------------------------------------------------------ --_000_A94E15A372E6194CA8719D62642F67448BA82E04MBX2adrucdk_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCl:

Do you know of any systematic studies of the application of Wiberg Bond Ord= ers in the description of intramolecular hydrogen bonds?

Yours, Jens >--<

  ------------------------------------------------------
  JENS SPANGET-LARSEN        Office= :       +45 4674 2710
  Dept. of Science        &nbs= p;  Fax:          +45= 4674 3011
  Roskilde University        Mobile= :       +45 2320 6246
  P.O.Box 260         &nb= sp;      E-Mail:      spanget,+,ruc.dk
  DK-4000 Roskilde, Denmark  Web: thiele.ruc.dk/~spanget
  ------------------------------------------------------


--_000_A94E15A372E6194CA8719D62642F67448BA82E04MBX2adrucdk_-- From owner-chemistry@ccl.net Mon Oct 17 13:46:00 2016 From: "Safiya Ess Amer amersaf85%%yahoo.com" To: CCL Subject: CCL:G: HOMO-LUMO molecular orbitals Message-Id: <-52399-161016150124-25442-o5moCMx3dJUWM+94kI7o/g|-|server.ccl.net> X-Original-From: "Safiya Ess Amer" Date: Sun, 16 Oct 2016 15:01:23 -0400 Sent to CCL by: "Safiya Ess Amer" [amersaf85 ~ yahoo.com] Hello for all CCL subscribers I'm studying a system of hydrogen molecule adsorbed on an ionic surface. I used Gaussian 03W programme with two methods HF and DFT-b3lyp to obtain molecular orbitals by using GaussView programme. this rout section is used for that: %Chk=Th90 b3lyp #T b3lyp nosymm gen pseudo=read pop=full Now I'm looking forward to explain the difference between what I got by using HF and DFT. in other words, I got a certain shape of molecular orbitals using HF and other different shape using DFT, how can I explain this difference! Thanks in advance Safiya Amer Graduate student Misrata University amersaf85 .. yahoo.com From owner-chemistry@ccl.net Mon Oct 17 15:55:00 2016 From: "Susi Lehtola susi.lehtola ~ alumni.helsinki.fi" To: CCL Subject: CCL: CCL #DFT16poll results are out Message-Id: <-52400-161017142838-9330-ukTunfjnm+qrDsvLwUZNXA:server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 17 Oct 2016 11:28:14 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola~!~alumni.helsinki.fi] On 10/17/2016 07:34 AM, Jim Kress jimkress35+/-gmail.com wrote: > > Sent to CCL by: "Jim Kress" [jimkress35%x%gmail.com] > Marcel, Matthias, and Miquel; > > Great work as usual. Thanks for doing this. It is immensely helpful. I would tend to disagree. What the poll tells you is a very limited picture. Democracy has no say on what is the truth... Especially when you can't vote for what you'd like to, but are presented with a choice between what are essentially bad and worse functionals. The poll is on the popularity - *not* the accuracy - of OLD functionals, which is furthermore limited in its participants. For instance, the first division participants were LDA 1965 BP86 1988 PW91 1991 B3PW91 1993 B3LYP 1994 PBE 1996 (PBE0 1999) B97-D 1997 revPBE 1999 RPBE 1999 HSE 2003 CAM-B3LYP 2004 B2PLYP 2006 LC-wPBE 2006 B3LYP-D 2007? optB88-vdW 2007 wB97X-D 2008 M06-2X 2008 M06 2008 PWPB95-D3 2010 which I would say is really old. 13 out of 19 functionals are over 10 years old. What represents the state of the art, for instance, the wB97X-V, B97M-V and wB97M-V functionals, have not been included in the poll, even though they beat the crap out of basically anything on the list. The poll seems to be centered on getting a picture of the functionals that people use. You could get a much better picture just by tabulating the number of citations to the articles describing these functionals. -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola.:.alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA ----------------------------------------------------------------------- From owner-chemistry@ccl.net Mon Oct 17 16:42:00 2016 From: "Tymofii Nikolaienko tim_mail-$-ukr.net" To: CCL Subject: CCL: Hydrogen bond order? Message-Id: <-52401-161017160010-32651-92p2KUohbYKguRzDNhKzYw\a/server.ccl.net> X-Original-From: Tymofii Nikolaienko Content-Type: multipart/alternative; boundary="------------05D31BD1C89FBC3457E8032E" Date: Mon, 17 Oct 2016 22:59:55 +0300 MIME-Version: 1.0 Sent to CCL by: Tymofii Nikolaienko [tim_mail~~ukr.net] This is a multi-part message in MIME format. --------------05D31BD1C89FBC3457E8032E Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 7bit Dear Jen, as far as I know, this bond index can hardly give any useful results for the hydrogen bond. And not because it is 'bad' -- it is by no way bad, but it was designed to measure to what extent two atoms are _covalently_ bonded, i.e., bonded in a way that their 'valence' electrons are _shared_ between the two atoms [ For more details the papers by I.Mayer can be useful ( Int.J.Quant.Chem.(1986), 29, p. 477 etc. ) ] But the hydrogen bond 'work' in a different manner. Sure, it also has _some_ degree of covalency, but a rather small degree and I don't think that the contribution to its energy from covalency should/can correlate with the 'whole' energy of the hydrogen bond. To summarize, I would not expect that Wiberg bond index can work well to identify / characterize the hydrogen bond. For hydrogen bond, an alternative (although not quite ideal as well) can be found in QTAIM-based criteria, in spectroscopic criteria or in both - see e.g. Phys. Chem. Chem. Phys. - 2012. - Vol. 14. - P. 7441-7447, DOI: 10.1039/C2CP40176B Hope this helps! Regards, Tymofii P.S. Even if I'm wrong - how would you get the value of the Wiberg index provided that it is defined in the basis of _orthogonal_ atomic orbitals only ? (unless a special software like Janpa, http://janpa.sf.net (see Comput.Theor.Chem. (2014), 1050, p. 15 DOI: 10.1016/j.comptc.2014.10.002 ) is used). On 17.10.2016 17:32, Jens Spanget-Larsen spanget(0)ruc.dk wrote: > Dear CCl: > > Do you know of any systematic studies of the application of Wiberg > Bond Orders in the description of intramolecular hydrogen bonds? > > Yours, Jens >--< > > ------------------------------------------------------ > JENS SPANGET-LARSEN Office: +45 4674 2710 > Dept. of Science Fax: +45 4674 3011 > Roskilde University Mobile: +45 2320 6246 > P.O.Box 260 E-Mail: spanget ~ ruc.dk > > DK-4000 Roskilde, Denmark Web: thiele.ruc.dk/~spanget > ------------------------------------------------------ > > --------------05D31BD1C89FBC3457E8032E Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: 8bit

Dear Jen,


as far as I know, this bond index can hardly give any useful results for the hydrogen bond.
And not because it is 'bad' -- it is by no way bad, but it was designed to measure
to what extent two atoms
are _covalently_ bonded, i.e., bonded in a way that their 'valence'
electrons are _shared_ between the two atoms [ For more details the papers by I.Mayer can be useful ( Int.J.Quant.Chem.(1986), 29, p. 477 etc. ) ]
But the hydrogen bond 'work' in a different manner.
Sure, it also has _some_ degree of covalency, but a rather small degree and I don't think
that the contribution to its energy from covalency should/can correlate with the 'whole'
energy of the hydrogen bond.
To summarize, I would not expect that Wiberg bond index can work well to identify / characterize
the hydrogen bond.
For hydrogen bond, an alternative (although not quite ideal as well) can be found in QTAIM-based
criteria, in spectroscopic criteria or in both - see e.g.
Phys. Chem. Chem. Phys. - 2012. - Vol. 14. - P. 7441-7447, DOI: 10.1039/C2CP40176B



Hope this helps!

Regards,
Tymofii



P.S. Even if I'm wrong - how would you get the value of the Wiberg index provided that it is defined in the basis of _orthogonal_ atomic
orbitals  only ? (unless a special software like Janpa, http://janpa.sf.net (see Comput.Theor.Chem. (2014), 1050, p. 15 DOI: 10.1016/j.comptc.2014.10.002 )  is used).






On 17.10.2016 17:32, Jens Spanget-Larsen spanget(0)ruc.dk wrote:
Dear CCl:

Do you know of any systematic studies of the application of Wiberg Bond Orders in the description of intramolecular hydrogen bonds?

Yours, Jens >--<

  ------------------------------------------------------
  JENS SPANGET-LARSEN        Office:       +45 4674 2710
  Dept. of Science           Fax:          +45 4674 3011
  Roskilde University        Mobile:       +45 2320 6246
  P.O.Box 260                E-Mail:      spanget ~ ruc.dk
  DK-4000 Roskilde, Denmark  Web: thiele.ruc.dk/~spanget
  ------------------------------------------------------



--------------05D31BD1C89FBC3457E8032E-- From owner-chemistry@ccl.net Mon Oct 17 17:22:00 2016 From: "Tymofii Nikolaienko tim_mail-,-ukr.net" To: CCL Subject: CCL:G: HOMO-LUMO molecular orbitals Message-Id: <-52402-161017171239-28108-usxS4qVCIS3f7UlSwkzbZQ^-^server.ccl.net> X-Original-From: Tymofii Nikolaienko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 18 Oct 2016 00:12:33 +0300 MIME-Version: 1.0 Sent to CCL by: Tymofii Nikolaienko [tim_mail##ukr.net] Dear Safiya Amer, sorry for saying such not-popular thing, but it is a big question whether any orbitals obtained from DFT do have any physical or chemical sense. Just recall that most of the widely DFT functionals are based on Kohn-Sham formalist - that is, the orbitals you get are the orbitals for 'auxiliary' system of non-interacting electrons and, strictly speaking, the only linkage between this system and your real system is that they have the same electron density. However, having the same density does not imply having the set of the same orbitals. Thus, it you might want to consider an alternative of just ignoring the shapes of DFT orbitals. Best regards, Tymofii On 16.10.2016 22:01, Safiya Ess Amer amersaf85%%yahoo.com wrote: > Sent to CCL by: "Safiya Ess Amer" [amersaf85 ~ yahoo.com] > Hello for all CCL subscribers > I'm studying a system of hydrogen molecule adsorbed on an ionic surface. I > used Gaussian 03W programme with two methods HF and DFT-b3lyp to obtain > molecular orbitals by using GaussView programme. this rout section is used for > that: > > %Chk=Th90 b3lyp > #T b3lyp nosymm gen pseudo=read pop=full > > Now I'm looking forward to explain the difference between what I got by using > HF and DFT. in other words, I got a certain shape of molecular orbitals using > HF and other different shape using DFT, how can I explain this difference! > > Thanks in advance > > > Safiya Amer > Graduate student > Misrata University > amersaf85^yahoo.com> > > From owner-chemistry@ccl.net Mon Oct 17 18:44:00 2016 From: "William F. Polik polik^hope.edu" To: CCL Subject: CCL: CCL #DFT16poll results are out Message-Id: <-52403-161017184037-11836-odpdaMwdZ+BJMNS9pflKNA,server.ccl.net> X-Original-From: "William F. Polik" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 17 Oct 2016 18:40:20 -0400 MIME-Version: 1.0 Sent to CCL by: "William F. Polik" [polik]![hope.edu] Hey, please watch it there.... This is a list about computational chemistry, not about the upcoming United States election! On 10/17/16 2:28 PM, Susi Lehtola susi.lehtola ~ alumni.helsinki.fi wrote: > Democracy has no say on what is the truth... Especially when you can't > vote for what you'd like to, but are presented with a choice between > what are essentially bad and worse From owner-chemistry@ccl.net Mon Oct 17 23:32:00 2016 From: "Dr. Robert Molt Jr. r.molt.chemical.physics(!)gmail.com" To: CCL Subject: CCL: CCL #DFT16poll results are out Message-Id: <-52404-161017185503-19357-id/b+IpiyAG83YmFaZ91/A()server.ccl.net> X-Original-From: "Dr. Robert Molt Jr." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 17 Oct 2016 18:54:45 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Robert Molt Jr." [r.molt.chemical.physics!A!gmail.com] I 100% agree with with Dr. Lehtola; no useful information can be extracted from this poll. Science has nothing to do with democracy. I am interested in reading review papers from experts, like Grimme, Truhlar, Head-Gordon, Gordon, Perdew, Burke, Yang, etc. The evidence in such review papers should guide action. We have reviewers for journal articles because popularity is not a substitute for evidence. I don't revere Maxwell, Boltzmann, Einstein, etc. because they won high school popularity contests. On 10/17/16 2:28 PM, Susi Lehtola susi.lehtola ~ alumni.helsinki.fi wrote: > > Sent to CCL by: Susi Lehtola [susi.lehtola~!~alumni.helsinki.fi] > On 10/17/2016 07:34 AM, Jim Kress jimkress35+/-gmail.com wrote: >> >> Sent to CCL by: "Jim Kress" [jimkress35%x%gmail.com] >> Marcel, Matthias, and Miquel; >> >> Great work as usual. Thanks for doing this. It is immensely helpful. > > I would tend to disagree. What the poll tells you is a very limited > picture. Democracy has no say on what is the truth... Especially when > you can't vote for what you'd like to, but are presented with a choice > between what are essentially bad and worse functionals. > > The poll is on the popularity - *not* the accuracy - of OLD > functionals, which is furthermore limited in its participants. For > instance, the first division participants were > > LDA 1965 > BP86 1988 > PW91 1991 > B3PW91 1993 > B3LYP 1994 > PBE 1996 (PBE0 1999) > B97-D 1997 > revPBE 1999 > RPBE 1999 > HSE 2003 > CAM-B3LYP 2004 > B2PLYP 2006 > LC-wPBE 2006 > B3LYP-D 2007? > optB88-vdW 2007 > wB97X-D 2008 > M06-2X 2008 > M06 2008 > PWPB95-D3 2010 > > which I would say is really old. 13 out of 19 functionals are over 10 > years old. What represents the state of the art, for instance, the > wB97X-V, B97M-V and wB97M-V functionals, have not been included in the > poll, even though they beat the crap out of basically anything on the > list. > > The poll seems to be centered on getting a picture of the functionals > that people use. You could get a much better picture just by > tabulating the number of citations to the articles describing these > functionals.