From owner-chemistry@ccl.net Tue Sep 22 02:15:01 2015 From: "Frank Jensen frj{:}chem.au.dk" To: CCL Subject: CCL: The use of NMR spectra computations for verification of computational method Message-Id: <-51762-150922021324-32506-G2a39anfKjDUeqjnOtizCQ|server.ccl.net> X-Original-From: Frank Jensen Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 22 Sep 2015 06:13:15 +0000 MIME-Version: 1.0 Sent to CCL by: Frank Jensen [frj * chem.au.dk] One cannot help wondering why people still are using B3LYP/6-31G* as the answer to any question. For NMR shielding, there are better functionals and basis sets optimized specifically for NMR. Using such a combination will have essentially the same computational cost, and who knows, may even solve problems like the one posed. Frank Frank Jensen Assoc. Prof., Vice-Chair Dept. of Chemistry Aarhus University http://old.chem.au.dk/~frj -----Original Message----- > From: owner-chemistry+frj==chem.au.dk a ccl.net [mailto:owner-chemistry+frj==chem.au.dk a ccl.net] On Behalf Of Grigoriy Zhurko reg_zhurko^chemcraftprog.com Sent: 21. september 2015 19:20 To: Frank Jensen Subject: CCL: The use of NMR spectra computations for verification of computational method Sent to CCL by: Grigoriy Zhurko [reg_zhurko^chemcraftprog.com] I have been computing NMR spectra of several organic compounds, comparing them with the experiment. Usually these computations show big systematic errors, but correlate well with the experiment (for C13 spectra of organic molecules, I got the correlation coefficient R about 0.9995 with B3LYP/6-311G(D,P) method). Now I have computed some NMR spectra of bilirubin molecule with different DFT functionals, and I found that the correlation coefficient is not a good criteria of computation accuracy in my case. This molecule has internal hydrogen bonds, and different functionals (in particular, B3LYP and PBE) give quite different O..H distance (the difference is about 0.1 A), while other bond lengths in this molecule do not differ significantly (the difference is 0.012 A or less). The PMR spectrum with B3LYP correlates with the experimental one with R=0.997, and with PBE ? R=0.995. These values do not differ very much. But the coefficient B in the equation Y=A+B*X (for the linear approximation of experiment vs theory graph) is 1.02 for B3LYP, and 1.14 for PBE. So, with PBE it is far less from 1. Does that mean that PBE is much less appropriate method for this task? I suppose, that the systematic error of absolute values of the NMR chemical shifts is caused by unclear physical meaning of these chemical shifts and shieldings (maybe the solvent gives some additional shielding in experiment). So, my question is, whether the B coefficient in correlation must be always equal 1. If yes, then instead of correlation coefficients R I should use another criteria of computation accuracy ? the RMS of MAE difference between the computed and experimental chemical shifts, if the shielding of the standard (TMS) simply fitted for best agreement (not computed quantum-chemically). Is that correct? In my case, these MAE difference must be much bigger for PBE functional, than for the B3LYP functional. Grigoriy Zhurko.http://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 Tue Sep 22 04:14:01 2015 From: "Peter Jarowski peterjarowski[-]gmail.com" To: CCL Subject: CCL:G: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51763-150922032909-28207-9v+5YtMolmYuGpjNeV044w]|[server.ccl.net> X-Original-From: Peter Jarowski Content-Type: multipart/alternative; boundary=047d7b6048d8d6ff82052050f32c Date: Tue, 22 Sep 2015 09:29:03 +0200 MIME-Version: 1.0 Sent to CCL by: Peter Jarowski [peterjarowski+*+gmail.com] --047d7b6048d8d6ff82052050f32c Content-Type: text/plain; charset=UTF-8 Dear All: The results of last week's survey can be found following the link below: https://www.surveymonkey.com/results/SM-ZZHHTKW2/ Some preliminary comments: (1) 95% of respondents are computational chemists. So a clear community is being surveyed. (2) ca. 60% are Gaussian users. I note that I didn't include Turbomole in the list, but that this was often filled in in the other category. (3) We have a mixed community in Industry and Academia. (4) There are many resonances to the last question, you can scroll the last section to see all of them, its not obvious. I will leave it all of you to interpret the results without much priming > from me. Best Regards and thanks for participating. Peter On Sun, Sep 13, 2015 at 2:21 AM, Jim Kress jimkress35 * gmail.com < owner-chemistry+/-ccl.net> wrote: > > Sent to CCL by: "Jim Kress" [jimkress35!A!gmail.com] > Bill Goddard and his group at Caltech have a vast body of work that deals > with the successful use of Quantum Chemistry in solving real problems. > Adri > van Duin also is doing the same at Penn State. > > You should investigate their work. > > Jim Kress> > > --047d7b6048d8d6ff82052050f32c Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear All:

<= /div>The results of last week's survey can be found following the link = below:

https://www.surveymonkey.com/results/SM-ZZHHTKW2/

Some pr= eliminary comments:

(1) 95% of respondents are computational c= hemists. So a clear community is being surveyed.
(2) ca. 60% are G= aussian users. I note that I didn't include Turbomole in the list, but = that this was often filled in in the other category.
(3) We have = a mixed community in Industry and Academia.
(4) There are man= y resonances to the last question, you can scroll the last section to see a= ll of them, its not obvious.

I will leave it all of= you to interpret the results without much priming from me.

Be= st Regards and thanks for participating.

Peter

On Sun, Sep 13, 2015 at= 2:21 AM, Jim Kress jimkress35 * gmail.com= <owner-chemistry+/-ccl.net> wrote:

Sent to CCL by: "Jim Kress" [jimkress35!A!gmail.com]
Bill Goddard and his group at Caltech have a vast body of work that deals with the successful use of Quantum Chemistry in solving real problems.=C2= =A0 Adri
van Duin also is doing the same at Penn State.

You should investigate their work.

Jim Kress



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY+/-ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST+/-ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/



--047d7b6048d8d6ff82052050f32c-- From owner-chemistry@ccl.net Tue Sep 22 07:01:00 2015 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor.||.fluor.quimica.uniovi.es" To: CCL Subject: CCL:G: Case Studies of QM Computational Chemistry in Reactivity Message-Id: <-51764-150922065827-18560-CJriOI/0y9H1Or7KgpcW1g||server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-type: text/plain; charset=us-ascii Date: Tue, 22 Sep 2015 12:40:40 +0200 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor[-]fluor.quimica.uniovi.es] On Tue, Sep 22, 2015 at 09:29:03AM +0200, Peter Jarowski peterjarowski[-]gmail.com wrote: > Dear All: > > The results of last week's survey can be found following the link below: > > https://www.surveymonkey.com/results/SM-ZZHHTKW2/ > > Some preliminary comments: > > (1) 95% of respondents are computational chemists. So a clear community is > being surveyed. > (2) ca. 60% are Gaussian users. I note that I didn't include Turbomole in > the list, but that this was often filled in in the other category. > (3) We have a mixed community in Industry and Academia. > (4) There are many resonances to the last question, you can scroll the last > section to see all of them, its not obvious. Pter, I answered your survey and it was not clear for me if the system was accepting more than one answer to the questions. This is relevant because I'm sure most people in this field have used gaussian ... and many other electronic codes too. So a 60% gaussian users may not be 60% users prefering gaussian over other alternatives. Regards, Victor Lua~na From owner-chemistry@ccl.net Tue Sep 22 11:31:01 2015 From: "Grigoriy Zhurko reg_zhurko : chemcraftprog.com" To: CCL Subject: CCL: The use of NMR spectra computations for verification of computational method Message-Id: <-51765-150922111143-17822-vTcxVJlN6W//A84TbFkzeA*_*server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 22 Sep 2015 18:11:54 +0400 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko||chemcraftprog.com] > Sent to CCL by: Frank Jensen [frj * chem.au.dk] > One cannot help wondering why people still are using B3LYP/6-31G* as the answer to any question. > For NMR shielding, there are better functionals and basis sets optimized specifically for NMR. > Using such a combination will have essentially the same > computational cost, and who knows, may even solve problems like the one posed. 1) So, what are these functionals and basis sets? 2) I still need to know, whether the B coefficient in Y=A+B*X equation of the correlation must be equal 1. > Frank > Frank Jensen > Assoc. Prof., Vice-Chair > Dept. of Chemistry > Aarhus University > http://old.chem.au.dk/~frj > -----Original Message----- >> From: owner-chemistry+frj==chem.au.dk::ccl.net [mailto:owner-chemistry+frj==chem.au.dk::ccl.net] On Behalf Of Grigoriy Zhurko reg_zhurko^chemcraftprog.com > Sent: 21. september 2015 19:20 > To: Frank Jensen > Subject: CCL: The use of NMR spectra computations for verification of computational method > Sent to CCL by: Grigoriy Zhurko [reg_zhurko^chemcraftprog.com] I > have been computing NMR spectra of several organic compounds, > comparing them with the experiment. Usually these computations show > big systematic errors, but correlate well with the experiment (for > C13 spectra of organic molecules, I got the correlation coefficient > R about 0.9995 with B3LYP/6-311G(D,P) method). > Now I have computed some NMR spectra of bilirubin molecule with > different DFT functionals, and I found that the correlation > coefficient is not a good criteria of computation accuracy in my > case. This molecule has internal hydrogen bonds, and different > functionals (in particular, B3LYP and PBE) give quite different O..H > distance (the difference is about 0.1 A), while other bond lengths > in this molecule do not differ significantly (the difference is > 0.012 A or less). The PMR spectrum with B3LYP correlates with the > experimental one with R=0.997, and with PBE ? R=0.995. These values > do not differ very much. But the coefficient B in the equation > Y=A+B*X (for the linear approximation of experiment vs theory graph) > is 1.02 for B3LYP, and 1.14 for PBE. So, with PBE it is far less > from 1. Does that mean that PBE is much less appropriate method for this task? > I suppose, that the systematic error of absolute values of the NMR > chemical shifts is caused by unclear physical meaning of these > chemical shifts and shieldings (maybe the solvent gives some > additional shielding in experiment). So, my question is, whether the > B coefficient in correlation must be always equal 1. If yes, then > instead of correlation coefficients R I should use another criteria > of computation accuracy ? the RMS of MAE difference between the > computed and experimental chemical shifts, if the shielding of the > standard (TMS) simply fitted for best agreement (not computed > quantum-chemically). Is that correct? In my case, these MAE > difference must be much bigger for PBE functional, than for the B3LYP functional. From owner-chemistry@ccl.net Tue Sep 22 13:23:01 2015 From: "Frank Jensen frj++chem.au.dk" To: CCL Subject: CCL: The use of NMR spectra computations for verification of computational method Message-Id: <-51766-150922132155-27478-ozbKPj+hPPU8JvLVWHrDrQ%x%server.ccl.net> X-Original-From: Frank Jensen Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 22 Sep 2015 17:21:46 +0000 MIME-Version: 1.0 Sent to CCL by: Frank Jensen [frj++chem.au.dk] A few selected references for a start: > From CCSD(T)/aug-cc-pVTZ-J to CCSD(T) complete basis set limit isotropic nuclear magnetic shieldings via affordable DFT/CBS calculations By: Kupka, Teobald; Stachow, Michal; Nieradka, Marzena; et al. MAGNETIC RESONANCE IN CHEMISTRY Volume: 49 Issue: 5 Pages: 231-236 Published: MAY 2011 Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels By: Flaig, Denis; Maurer, Marina; Hanni, Matti; et al. JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 10 Issue: 2 Pages: 572-578 Published: FEB 2014 Benchmarking density-functional theory calculations of NMR shielding constants and spin-rotation constants using accurate coupled-cluster calculations By: Teale, Andrew M.; Lutnaes, Ola B.; Helgaker, Trygve; et al. JOURNAL OF CHEMICAL PHYSICS Volume: 138 Issue: 2 Article Number: 024111 Published: JAN 14 2013 Segmented Contracted Basis Sets Optimized for Nuclear Magnetic Shielding By: Jensen, Frank JOURNAL OF CHEMICAL THEORY AND COMPUTATION Volume: 11 Issue: 1 Pages: 132-138 Published: JAN 2015 Frank Frank Jensen Assoc. Prof., Vice-Chair Dept. of Chemistry Aarhus University http://old.chem.au.dk/~frj -----Original Message----- > From: owner-chemistry+frj==chem.au.dk^-^ccl.net [mailto:owner-chemistry+frj==chem.au.dk^-^ccl.net] On Behalf Of Grigoriy Zhurko reg_zhurko : chemcraftprog.com Sent: 22. september 2015 16:12 To: Frank Jensen Subject: CCL: The use of NMR spectra computations for verification of computational method Sent to CCL by: Grigoriy Zhurko [reg_zhurko||chemcraftprog.com] > Sent to CCL by: Frank Jensen [frj * chem.au.dk] One cannot help > wondering why people still are using B3LYP/6-31G* as the answer to any question. > For NMR shielding, there are better functionals and basis sets optimized specifically for NMR. > Using such a combination will have essentially the same computational > cost, and who knows, may even solve problems like the one posed. 1) So, what are these functionals and basis sets? 2) I still need to know, whether the B coefficient in Y=A+B*X equation of the correlation must be equal 1. > Frank > Frank Jensen > Assoc. Prof., Vice-Chair > Dept. of Chemistry > Aarhus University > http://old.chem.au.dk/~frj > -----Original Message----- >> From: owner-chemistry+frj==chem.au.dk::ccl.net >> [mailto:owner-chemistry+frj==chem.au.dk::ccl.net] On Behalf Of >> Grigoriy Zhurko reg_zhurko^chemcraftprog.com > Sent: 21. september 2015 19:20 > To: Frank Jensen > Subject: CCL: The use of NMR spectra computations for verification of > computational method > Sent to CCL by: Grigoriy Zhurko [reg_zhurko^chemcraftprog.com] I have > been computing NMR spectra of several organic compounds, comparing > them with the experiment. Usually these computations show big > systematic errors, but correlate well with the experiment (for > C13 spectra of organic molecules, I got the correlation coefficient R > about 0.9995 with B3LYP/6-311G(D,P) method). > Now I have computed some NMR spectra of bilirubin molecule with > different DFT functionals, and I found that the correlation > coefficient is not a good criteria of computation accuracy in my case. > This molecule has internal hydrogen bonds, and different functionals > (in particular, B3LYP and PBE) give quite different O..H distance (the > difference is about 0.1 A), while other bond lengths in this molecule > do not differ significantly (the difference is > 0.012 A or less). The PMR spectrum with B3LYP correlates with the > experimental one with R=0.997, and with PBE ? R=0.995. These values do > not differ very much. But the coefficient B in the equation Y=A+B*X > (for the linear approximation of experiment vs theory graph) is 1.02 > for B3LYP, and 1.14 for PBE. So, with PBE it is far less from 1. Does > that mean that PBE is much less appropriate method for this task? > I suppose, that the systematic error of absolute values of the NMR > chemical shifts is caused by unclear physical meaning of these > chemical shifts and shieldings (maybe the solvent gives some > additional shielding in experiment). So, my question is, whether the B > coefficient in correlation must be always equal 1. If yes, then > instead of correlation coefficients R I should use another criteria of > computation accuracy ? the RMS of MAE difference between the computed > and experimental chemical shifts, if the shielding of the standard > (TMS) simply fitted for best agreement (not computed > quantum-chemically). Is that correct? In my case, these MAE difference > must be much bigger for PBE functional, than for the B3LYP functional.http://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 Tue Sep 22 17:56:01 2015 From: "Alan Shusterman alan=-=reed.edu" To: CCL Subject: CCL: Constructive DFT suggestions appreciated Message-Id: <-51767-150922173829-15939-Go942pWPEeM5HAoEDcCZIA^_^server.ccl.net> X-Original-From: Alan Shusterman Content-Type: multipart/alternative; boundary=089e013cc168599b1405205cbaf3 Date: Tue, 22 Sep 2015 14:31:59 -0700 MIME-Version: 1.0 Sent to CCL by: Alan Shusterman [alan(_)reed.edu] --089e013cc168599b1405205cbaf3 Content-Type: text/plain; charset=UTF-8 I have read several CCL messages over the past few weeks disparaging a correspondent's choice of DFT functional (usually B3LYP, but not always) as being obsolete, useless, or both. These are perfectly fair opinions to share, but they are not constructive. If you want to disparage a computational approach, fine with me, but please recommend at least *one* better alternative. I would like to learn what you think I should use, not just what I should not use. You don't need to cite publications or explain why you prefer a particular functional. I can look that up once you tell me which functional(s) you think are worthy. Alan -- Alan Shusterman Chemistry Department Reed College 3203 SE Woodstock Blvd Portland, OR 97202-8199 503-517-7699 http://blogs.reed.edu/alan/ "Nature doesn't make long speeches." Lao Tzu 23 --089e013cc168599b1405205cbaf3 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
I have read several CCL messages over the past few weeks d= isparaging a correspondent's choice of DFT functional (usually B3LYP, b= ut not always) as being obsolete, useless, or both.

Thes= e are perfectly fair opinions to share, but they are not constructive. If y= ou want to disparage a computational approach, fine with me, but please rec= ommend at least=C2=A0one better alternative. I would like to learn w= hat you think I should use, not just what I should not use.

<= /div>
You don't need to cite publications or explain why you prefer= a particular functional. I can look that up once you tell me which functio= nal(s) you think are worthy.

Alan

<= /div>--
Alan Shusterman=
Chemistry Department
Reed College
3203 SE Woodstock Blvd
Portl= and, OR 97202-8199
503-517-7699
http://blogs.reed.edu/alan/
"Nature doesn&= #39;t make long speeches." Lao Tzu 23
--089e013cc168599b1405205cbaf3-- From owner-chemistry@ccl.net Tue Sep 22 18:32:01 2015 From: "Susi Lehtola susi.lehtola]^[alumni.helsinki.fi" To: CCL Subject: CCL: The use of NMR spectra computations for verification of computational method Message-Id: <-51768-150922182549-27960-s3MoBx0mLW1/twk2BhE5XQ|,|server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Tue, 22 Sep 2015 15:25:36 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola()alumni.helsinki.fi] Dear Grigoriy, if you are asking something, please formulate your message using paragraphs. A wall of text is hard to read, and most people will just skip over it. On 09/21/2015 10:19 AM, Grigoriy Zhurko reg_zhurko^chemcraftprog.com wrote: > The PMR spectrum with B3LYP correlates with the experimental one with > R=0.997, and with PBE ? R=0.995. These values do not differ very > much. But the coefficient B in the equation Y=A+B*X (for the linear > approximation of experiment vs theory graph) is 1.02 for B3LYP, and > 1.14 for PBE. So, with PBE it is far less from 1. So here you are talking about how well the values reproduced by theory agree with experiment, allowing for systematic error in the theory that follows a linear model. Indeed, the R values are close to one, which indicates the linear model is good. The different B (and A?) values just indicate that the functionals produce different values for the shielding constants, but as both R values are good, you should be able to easily convert a PBE value to B3LYP or vice versa. > Does that mean that PBE is much less appropriate method for this > task? I'm not an expert on NMR. However, judging from your data, I would say that the answer is no. Naturally if your theory reproduced experiment exactly you'd have A=0 and B=1. Here, both functionals give somewhat incorrect values, since A!=0 and B!=1. However, the error in the values seems to be systematical, which you can correct for by solving x from y. > I suppose, that the systematic error of absolute values of the NMR > chemical shifts is caused by unclear physical meaning of these > chemical shifts and shieldings (maybe the solvent gives some > additional shielding in experiment). Naturally, effects that aren't included in your modeling will affect the goodness of your model. In general, you might see this as unexpected values of A and B, or by a breakdown of your model (small R). > So, my question is, whether the B coefficient in correlation must be > always equal 1. No. > If yes, then instead of correlation coefficients R I should use > another criteria of computation accuracy? If B were always equal to 1 you wouldn't really need R at all. R is a measure of how well y = a + bx fits your data. > the RMS of MAE difference between the computed and experimental > chemical shifts, if the shielding of the standard (TMS) simply > fitted for best agreement (not computed quantum-chemically). Is that > correct? What? > In my case, these MAE difference must be much bigger for PBE > functional, than for the B3LYP functional. If you took the uncorrected values, sure. But if you applied the correction for the systematical error, both should give similarly accurate results. -- ----------------------------------------------------------------------- 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 Tue Sep 22 19:07:01 2015 From: "Susi Lehtola susi.lehtola!^!alumni.helsinki.fi" To: CCL Subject: CCL: Constructive DFT suggestions appreciated Message-Id: <-51769-150922184927-11247-sbJJxPxZM4NL584iqnWrsw(a)server.ccl.net> X-Original-From: Susi Lehtola Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Tue, 22 Sep 2015 15:49:12 -0700 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola###alumni.helsinki.fi] On 09/22/2015 02:31 PM, Alan Shusterman alan=-=reed.edu wrote: > I have read several CCL messages over the past few weeks disparaging a > correspondent's choice of DFT functional (usually B3LYP, but not always) as > being obsolete, useless, or both. > > These are perfectly fair opinions to share, but they are not constructive. > If you want to disparage a computational approach, fine with me, but please > recommend at least *one* better alternative. I would like to learn what you > think I should use, not just what I should not use. > > You don't need to cite publications or explain why you prefer a particular > functional. I can look that up once you tell me which functional(s) you > think are worthy. This is certainly true. However, this *is* the computational chemistry list, and most of the people here are scientists. The main duty of a scientist is keep up to date with current methodology. Or, at least do a literature search when someone tells you your method is outdated and that you can get much better results with the same resources by using more modern techniques, as has been pointed out (even with some suggestions for alternatives) by many people on the forum. Unlike in the B3LYP/6-31G* days, where all you had was a hammer so every problem started to look like nails, today there are specialized methodologies for each field so general advice is harder to give, and so the responsibility really rests on the researcher. [We wouldn't even be in the current jam if article reviewers were more strict about the use of obsolete methodologies, but at that stage it is somewhat too late. The reviewers might also not be computational chemists.] -- ----------------------------------------------------------------------- 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 Tue Sep 22 20:10:01 2015 From: "Robert Molt r.molt.chemical.physics++gmail.com" To: CCL Subject: CCL: Constructive DFT suggestions appreciated Message-Id: <-51770-150922195848-29215-VuxkDEQQpfR/RU88oDVRWQ!=!server.ccl.net> X-Original-From: Robert Molt Content-Type: multipart/alternative; boundary="------------070906040508040904000701" Date: Tue, 22 Sep 2015 19:58:41 -0400 MIME-Version: 1.0 Sent to CCL by: Robert Molt [r.molt.chemical.physics||gmail.com] This is a multi-part message in MIME format. --------------070906040508040904000701 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Understand, at least for me, part of the reason to not offer a specific functional is to avoid politics/debate about whose functional is the best (there are many smart men working on this). I can offer, unequivocally, B3LYP is not a good choice. I recommend looking at Stefan Grimme's work on functionals, Don Truhlar's, or Martin Head-Gordon's. They do a lot of work dealing with accounting for dispersion through various means. They are always developing new things, so there is a balance between the newest vs. the most tested. Things like B3LYP-D3, M11, M06, wB97X. If you want DFT functionals for the sake of /ab initio /work, John Perdew's work as well as Samuel Trickey's work is nice. On 9/22/15 5:31 PM, Alan Shusterman alan=-=reed.edu wrote: > I have read several CCL messages over the past few weeks disparaging a > correspondent's choice of DFT functional (usually B3LYP, but not > always) as being obsolete, useless, or both. > > These are perfectly fair opinions to share, but they are not > constructive. If you want to disparage a computational approach, fine > with me, but please recommend at least _one_ better alternative. I > would like to learn what you think I should use, not just what I > should not use. > > You don't need to cite publications or explain why you prefer a > particular functional. I can look that up once you tell me which > functional(s) you think are worthy. > > Alan > > -- > Alan Shusterman > Chemistry Department > Reed College > 3203 SE Woodstock Blvd > Portland, OR 97202-8199 > 503-517-7699 > http://blogs.reed.edu/alan/ > "Nature doesn't make long speeches." Lao Tzu 23 -- Dr. Robert Molt Jr. Visiting Associate Professor of Chemistry Department of Chemistry & Chemical Biology Indiana University-Purdue University Indianapolis LD 326 402 N. Blackford St. Indianapolis, IN 46202 --------------070906040508040904000701 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Understand, at least for me, part of the reason to not offer a specific functional is to avoid politics/debate about whose functional is the best (there are many smart men working on this). I can offer, unequivocally, B3LYP is not a good choice.

I recommend looking at Stefan Grimme's work on functionals, Don Truhlar's, or Martin Head-Gordon's. They do a lot of work dealing with accounting for dispersion through various means. They are always developing new things, so there is a balance between the newest vs. the most tested. Things like B3LYP-D3, M11, M06, wB97X.

If you want DFT functionals for the sake of ab initio work, John Perdew's work as well as Samuel Trickey's work is nice.

On 9/22/15 5:31 PM, Alan Shusterman alan=-=reed.edu wrote:
I have read several CCL messages over the past few weeks disparaging a correspondent's choice of DFT functional (usually B3LYP, but not always) as being obsolete, useless, or both.

These are perfectly fair opinions to share, but they are not constructive. If you want to disparage a computational approach, fine with me, but please recommend at least one better alternative. I would like to learn what you think I should use, not just what I should not use.

You don't need to cite publications or explain why you prefer a particular functional. I can look that up once you tell me which functional(s) you think are worthy.

Alan

--
Alan Shusterman
Chemistry Department
Reed College
3203 SE Woodstock Blvd
Portland, OR 97202-8199
503-517-7699
http://blogs.reed.edu/alan/
"Nature doesn't make long speeches." Lao Tzu 23

-- 
Dr. Robert Molt Jr.
Visiting Associate Professor of Chemistry
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
--------------070906040508040904000701-- From owner-chemistry@ccl.net Tue Sep 22 20:59:01 2015 From: "Nico Green nicogreen6!^!gmail.com" To: CCL Subject: CCL: The use of NMR spectra computations for verification of computational method Message-Id: <-51771-150922204516-25994-pRTZMq1A7JzSbNsBeTwp0A!^!server.ccl.net> X-Original-From: Nico Green Content-Type: multipart/alternative; boundary=001a113a723244598505205f6dd9 Date: Wed, 23 Sep 2015 00:45:01 +0000 MIME-Version: 1.0 Sent to CCL by: Nico Green [nicogreen6~!~gmail.com] --001a113a723244598505205f6dd9 Content-Type: text/plain; charset=UTF-8 Dear Grigoriy The values you obtain seems to reproduce correctly the experimental chemical shifts. However, may I suggest you try using the MSTD? Here are the references: for 13C: The Journal of Organic Chemistry 2009; 74(19):7254-60. for 1H: The Journal of Organic Chemistry 2012; 77(14):6059-65. On the other hand, in my humble experience mPW1PW91 is the best cost/accuracy basis set, depending on your structure the functional you'll need to use, but as a start a 6-31G(d) or 6-31G(d,p) should work fine. In GIAO NMR is very common to use one level for the optimization step and another for the NMR calculation. So you may use your geometries and just perform a single point NMR calculation with mPW1PW91/6-31G(d) and check. Hope this helps On Mon, Sep 21, 2015 at 6:28 PM Grigoriy Zhurko reg_zhurko^chemcraftprog.com wrote: > > Sent to CCL by: Grigoriy Zhurko [reg_zhurko^chemcraftprog.com] > I have been computing NMR spectra of several organic compounds, comparing > them with the experiment. Usually these computations show big systematic > errors, but correlate well with the experiment (for C13 spectra of organic > molecules, I got the correlation coefficient R about 0.9995 with > B3LYP/6-311G(D,P) method). > Now I have computed some NMR spectra of bilirubin molecule with different > DFT functionals, and I found that the correlation coefficient is not a good > criteria of computation accuracy in my case. This molecule has internal > hydrogen bonds, and different functionals (in particular, B3LYP and PBE) > give quite different O..H distance (the difference is about 0.1 A), while > other bond lengths in this molecule do not differ significantly (the > difference is 0.012 A or less). The PMR spectrum with B3LYP correlates with > the experimental one with R=0.997, and with PBE ? R=0.995. These values do > not differ very much. But the coefficient B in the equation Y=A+B*X (for > the linear approximation of experiment vs theory graph) is 1.02 for B3LYP, > and 1.14 for PBE. So, with PBE it is far less from 1. Does that mean that > PBE is much less appropriate method for this task? > I suppose, that the systematic error of absolute values of the NMR > chemical shifts is caused by unclear physical meaning of these chemical > shifts and shieldings (maybe the solvent gives some additional shielding in > experiment). So, my question is, whether the B coefficient in correlation > must be always equal 1. If yes, then instead of correlation coefficients R > I should use another criteria of computation accuracy ? the RMS of MAE > difference between the computed and experimental chemical shifts, if the > shielding of the standard (TMS) simply fitted for best agreement (not > computed quantum-chemically). Is that correct? In my case, these MAE > difference must be much bigger for PBE functional, than for the B3LYP > functional. > > Grigoriy Zhurko.> > > --001a113a723244598505205f6dd9 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Grigoriy
=
The values you obtain seems to reproduce correctly the exper= imental chemical shifts.
However,= may I suggest you try using the MSTD?
Here are the re= ferences:
for 13C: The Journal of Organic Chemistry 2009; 74(19):7254-= 60.
for 1H:=C2=A0The Journal of= Organic Chemistry 2012; 77(14):6059-65.=C2=A0<= /span>

On the other hand, in my humble = experience=C2=A0mPW1PW91 is the best cost/accuracy basi= s set, depending on your structure the functional you'll need to use, b= ut as a start a 6-31G(d) or 6-31G(d,p) should work fine.
<= span style=3D"line-height:17px;font-family:arial,helvetica,clean,sans-serif= ;color:rgb(0,0,0)">
In GIAO NMR is= very common to use one level for the optimization step and another for the= NMR calculation. So you may use your geometries and just perform a single = point NMR calculation with=C2=A0mPW1PW91/6-31G(d) and c= heck.

<= /span>
Hope this h= elps

=C2=A0


<= /span>

=

On Mon, Sep 21, 2015 = at 6:28 PM Grigoriy Zhurko reg_zhurko^chemcraftprog.com <owner-chemistry() ccl.net> wrote:

Sent to CCL by: Grigoriy Zhurko [reg_zhurko^chemcraftprog.com]
I have been computing NMR spectra of several organic compounds, comparing t= hem with the experiment. Usually these computations show big systematic err= ors, but correlate well with the experiment (for=C2=A0 C13 spectra of organ= ic molecules, I got the correlation coefficient R about 0.9995 with B3LYP/6= -311G(D,P) method).
Now I have computed some NMR spectra of bilirubin molecule with different D= FT functionals, and I found that the correlation coefficient is not a good = criteria of computation accuracy in my case. This molecule has internal hyd= rogen bonds, and different functionals (in particular, B3LYP and PBE) give = quite different O..H distance (the difference is about 0.1 A), while other = bond lengths in this molecule do not differ significantly (the difference i= s 0.012 A or less). The PMR spectrum with B3LYP correlates with the experim= ental one with R=3D0.997, and with PBE ? R=3D0.995. These values do not dif= fer very much. But the coefficient B in the equation Y=3DA+B*X (for the lin= ear approximation of experiment vs theory graph) is 1.02 for B3LYP, and 1.1= 4 for PBE. So, with PBE it is far less from 1. Does that mean that PBE is m= uch less appropriate method for this task?
I suppose, that the systematic error of absolute values of the NMR chemical= shifts is caused by unclear physical meaning of these chemical shifts and = shieldings (maybe the solvent gives some additional shielding in experiment= ). So, my question is, whether the B coefficient in correlation must be alw= ays equal 1. If yes, then instead of correlation coefficients R I should us= e another criteria of computation accuracy ? the RMS of MAE difference betw= een the computed and experimental chemical shifts, if the shielding of the = standard (TMS) simply fitted for best agreement (not computed quantum-chemi= cally). Is that correct? In my case, these MAE difference must be much bigg= er for PBE functional, than for the B3LYP functional.

Grigoriy Zhurko.



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY() ccl.net or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST() ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/s= end_ccl_message

Subscribe/Unsubscribe:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/chemistry/sub_un= sub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/sear= chccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/


--001a113a723244598505205f6dd9-- From owner-chemistry@ccl.net Tue Sep 22 21:34:01 2015 From: "Ray Merewether Ray.Merewether-#-seescan.com" To: CCL Subject: CCL: Constructive DFT suggestions appreciated Message-Id: <-51772-150922194650-20017-DOdPtMNg4UTE9qECz8C22w-x-server.ccl.net> X-Original-From: Ray Merewether Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Tue, 22 Sep 2015 23:46:42 +0000 MIME-Version: 1.0 Sent to CCL by: Ray Merewether [Ray.Merewether|*|seescan.com] Alan, Here is a paper from 2012: Why the Standard B3LYP/6-31G* Model Chemistry Should Not Be Used in DFT Calculations of Molecular Thermochemistry: Understanding and Correcting the Problem Holger Kruse†, Lars Goerigk‡, and Stefan Grimme*§ J. Org. Chem., 2012, 77 (23), pp 10824–10834 DOI: 10.1021/jo302156p Hope it helps. At the very least it is a place to start. -----Original Message----- > From: owner-chemistry+ray_merewether==deepsea.com#,#ccl.net [mailto:owner-chemistry+ray_merewether==deepsea.com#,#ccl.net] On Behalf Of Susi Lehtola susi.lehtola!^!alumni.helsinki.fi Sent: Tuesday, September 22, 2015 3:49 PM To: Ray Merewether Subject: CCL: Constructive DFT suggestions appreciated Sent to CCL by: Susi Lehtola [susi.lehtola###alumni.helsinki.fi] On 09/22/2015 02:31 PM, Alan Shusterman alan=-=reed.edu wrote: > I have read several CCL messages over the past few weeks disparaging a > correspondent's choice of DFT functional (usually B3LYP, but not > always) as being obsolete, useless, or both. > > These are perfectly fair opinions to share, but they are not constructive. > If you want to disparage a computational approach, fine with me, but > please recommend at least *one* better alternative. I would like to > learn what you think I should use, not just what I should not use. > > You don't need to cite publications or explain why you prefer a > particular functional. I can look that up once you tell me which > functional(s) you think are worthy. This is certainly true. However, this *is* the computational chemistry list, and most of the people here are scientists. The main duty of a scientist is keep up to date with current methodology. Or, at least do a literature search when someone tells you your method is outdated and that you can get much better results with the same resources by using more modern techniques, as has been pointed out (even with some suggestions for alternatives) by many people on the forum. Unlike in the B3LYP/6-31G* days, where all you had was a hammer so every problem started to look like nails, today there are specialized methodologies for each field so general advice is harder to give, and so the responsibility really rests on the researcher. [We wouldn't even be in the current jam if article reviewers were more strict about the use of obsolete methodologies, but at that stage it is somewhat too late. The reviewers might also not be computational chemists.] -- ----------------------------------------------------------------------- Mr. Susi Lehtola, PhD Chemist Postdoctoral Fellow susi.lehtola=alumni.helsinki.fi Lawrence Berkeley National Laboratory http://www.helsinki.fi/~jzlehtol USA -----------------------------------------------------------------------http://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 Tue Sep 22 22:09:01 2015 From: "Lars Goerigk lars.goerigk^unimelb.edu.au" To: CCL Subject: CCL: Constructive DFT suggestions appreciated Message-Id: <-51773-150922201733-8240-uQQQypgINDId3jiHpJLVUw-x-server.ccl.net> X-Original-From: "Lars Goerigk" Date: Tue, 22 Sep 2015 20:17:32 -0400 Sent to CCL by: "Lars Goerigk" [lars.goerigk*|*unimelb.edu.au] Dear Alan, I recommend you read this paper in which Stefan Grimme and I benchmarked nearly 50 methods on a large set of chemically relevant problems. This paper did not only have a look at the overall accuracy of a method but also on its robustness, that means how reliable the method is when you change from one chemical problem to another: PCCP 2011, 13, 6670. The general recommendations are: - The higher you climb on Jacobs Ladder, the more reliable your result is. - Recommended GGA methods: revPBE-D3, B97-D3 - Recommended meta-GGA methods: oTPSS-D3, TPSS-D3 - Hybrid functionals: PW6B95-D3, M062X-D3 Comment: Yes, also Minnesota functionals need dispersion corrections! a) This was shown for the M05 and M06 suites of functionals in ChemPhysChem 2011, 12, 3421. b) For the latest Minnestoa-type methods (the M11, MN12, N12, and SOGGA11 suites of functionals), unusual problems around van-der-Waals minima were reported in J. Phys. Chem. Lett. 2015, 6, 3891. c) Note that B3LYP-D3 is worse than the average of more than 20 tested hybrids! - Double-hybrids are the most accurate DFT methods on the market: DSD-BLYP-D3, DSD-PBEP86-D3, PWPB95-D3 Comment: They may need an additional MP2-type term, however, efficient programs, such as ORCA or Turbomole, make use of the RI approximation to speed up this step. So overall, double-hybrids are not too costly nowadays. However, you need at least a good triple-zeta basis set, do not use double-zeta basis sets for double-hybrids. - Always use a dispersion correction! - As for the famous B3LYP/6-31G* model chemistry, its flaws are discussed herein: JOC 2012, 77, 10824 I hope that helped. Cheers, Lars --- Dr. Lars Goerigk ARC DECRA Fellow School of Chemistry The University of Melbourne VIC 3010 Australia Research profile: http://www.chemistry.unimelb.edu.au/dr-lars-goerigk List of my publications: http://www.researcherid.com/rid/D-3717-2009 Follow me on Twitter: https://twitter.com/lgoer_compchem ----- On 23 Sep 2015, at 7:31 am, Alan Shusterman alan=-=reed.edu wrote: I have read several CCL messages over the past few weeks disparaging a correspondent's choice of DFT functional (usually B3LYP, but not always) as being obsolete, useless, or both. These are perfectly fair opinions to share, but they are not constructive. If you want to disparage a computational approach, fine with me, but please recommend at least one better alternative. I would like to learn what you think I should use, not just what I should not use. You don't need to cite publications or explain why you prefer a particular functional. I can look that up once you tell me which functional(s) you think are worthy. Alan -- Alan Shusterman Chemistry Department Reed College 3203 SE Woodstock Blvd Portland, OR 97202-8199 503-517-7699 http://blogs.reed.edu/alan/ "Nature doesn't make long speeches." Lao Tzu 23