From owner-chemistry@ccl.net Wed Apr 24 09:30:01 2024 From: "Marcos Verissimo Alves marcos_verissimo ~~ id.uff.br" To: CCL Subject: CCL: Strange geometry optimization with breaking of H-bonds Message-Id: <-55128-240424092843-28309-3N61aSd+7+Ww/iz+iH+U8A^-^server.ccl.net> X-Original-From: Marcos Verissimo Alves Content-Type: multipart/alternative; boundary="0000000000007e893a0616d7a53e" Date: Wed, 24 Apr 2024 15:27:54 +0200 MIME-Version: 1.0 Sent to CCL by: Marcos Verissimo Alves [marcos_verissimo|*|id.uff.br] --0000000000007e893a0616d7a53e Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Grigoriy, I have a couple of questions: 1) Why didn't you include D3 or D4 corrections in your first calculation? I might be wrong, but dispersion corrections will improve geometries in most cases, if not all. 2) Why use ORCA 5.0.3 when version 5.0.4 has been out for quite some time now, and many bugs were corrected or detected? Looking at the release notes for version 5.0.3: Regarding the use of D4 in ORCA, in the release notes for version 5.0.3, the first post in the ORCA forum says: "Unfortunately, the C++ implementation of the DFT-D4 code was affected by a bug in the gradient and some further minor bugs. This affects all DFT gradient (and thus also hessian) calculations using D4 in ORCA mainly manifesting in sometimes erroneous geometry optimizations. In most cases this breakdown is indicated by geometry optimizations running up in energy/gradient. The magnitude of the error is not generally assessable and should be checked for each individual case (it can be negligibly small for many systems). In any case, it is recommended to check the convergence behavior/final geometry in comparison to a D3 calculation. Further, some elements (Li, Be, Na, Mg, K, Ca, Sc, Ti, V, Rb, Sr, Y, Zr, Nb, Cs, Ba, Hf, Ta) did not make use of the revised reference polarizabilities given in DOI: 10.1039/D0CP00502A resulting in minor energy differences compared to the current DFT-D4 standalone code provided by Grimme and co-workers. These bugs also affect the r2SCAN-3c composite method. D3, GFN-xTB and GFN-FF methods are NOT affected! In any case, all energies computed with the ORCA implementation of D4 should be checked with the stand alone code (current stable release version 3.5.0, https://github.com/dftd4/dftd4). The bug will be fixed in the upcoming ORCA 5.0.4 release. The Grimme Group DevTeam & ORCA Team" It may be advisable to re-run these calculations with version 5.0.4 using D3 or D4 corrections, checking if you get the same problems. Best regards, Marcos --- Prof. Dr. Marcos Verissimo Alves Prof. Adjunto II, Curso de F=C3=ADsica Computacional Instituto de Ci=C3=AAncias Exatas Universidade Federal Fluminense Volta Redonda - RJ, Brasil Em ter., 23 de abr. de 2024 =C3=A0s 19:47, Grigoriy Zhurko reg_zhurko% chemcraftprog.com escreveu: > I have an Orca 5.0.3 job: > > !B3LYP 6-31++G(D,P) Opt PAL3 CPCM(Water) ANFREQ > > * xyz 0 1 > ... > > The geometry optimization produced a structure at attach 1, with O16-H23 > distance 2.63944, but with negative frequencies. To get rid of them, I > repeated the job with these keywords: > > !B3LYP 6-31++G(D,P) Opt PAL3 CPCM(Water) AnFreq > !TightOpt DefGrid3 VeryTightSCF > > * xyz 0 1 > ... > > Finally I got an optimized geometry without negative frequencies, but the > structure is different - see attach 2. The distance O16-H23 is now 3.8971= 2. > Isn't that strange that the optimized structure does not have this O:H > hydrogen bond? > At attach 3 you can see one more optimized (at the same level ) structure= , > which seems to be ok - the O15..H21 distance is 2.27375. My intuition tel= ls > me that this is a correct calculation. > The structure from attach 1 was also computed at B3LYP-D4 level and > everything seems ok - see attach 4 (O16..H23 distance is 2.21156): > > !B3LYP D4 6-31++G(D,P) Opt PAL3 CPCM(Water) ANFREQ > > * xyz 0 1 > ... > > Maybe this is a bug in Orca? > Grigoriy Zhurko --0000000000007e893a0616d7a53e Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Grigoriy,

I have a couple=C2=A0of = questions:

1) Why didn't you include D3 or D4= =C2=A0corrections=C2=A0in your first calculation? I might be wrong, but dis= persion corrections will improve geometries in most cases, if not all.
2) Why use ORCA 5.0.3 when version 5.0.4 has been out for quite some = time now,=C2=A0and many bugs were corrected or detected?

Looking at the release notes for version 5.0.3:

=
Regarding the use of D4 in ORCA, in the release notes for version 5.0.= 3, the first post in the ORCA forum says:

"Un= fortunately, the C++ implementation of the DFT-D4 code was affected by a bu= g in the gradient and some further minor bugs.

This affects all DFT = gradient (and thus also hessian) calculations using D4 in ORCA mainly manif= esting in sometimes erroneous geometry optimizations.

In most cases = this breakdown is indicated by geometry optimizations running up in energy/= gradient. The magnitude of the error is not generally assessable and should= be checked for each individual case (it can be negligibly small for many s= ystems). In any case, it is recommended to check the convergence behavior/f= inal geometry in comparison to a D3 calculation.

Further, some eleme= nts (Li, Be, Na, Mg, K, Ca, Sc, Ti, V, Rb, Sr, Y, Zr, Nb, Cs, Ba, Hf, Ta) d= id not make use of the revised reference polarizabilities given in DOI: 10.= 1039/D0CP00502A resulting in minor energy differences compared to the curre= nt DFT-D4 standalone code provided by Grimme and co-workers.

These b= ugs also affect the r2SCAN-3c composite method. D3, GFN-xTB and GFN-FF meth= ods are NOT affected!

In any case, all energies computed with the OR= CA implementation of D4 should be checked with the stand alone code (curren= t stable release version 3.5.0, = https://github.com/dftd4/dftd4).

The bug will be fixed in the up= coming ORCA 5.0.4 release.

The Grimme Group DevTeam & ORCA Team&= quot;

It may be advisable to re-run these calculat= ions with version 5.0.4 using D3 or D4 corrections, checking if you get the= same problems.

Best regards,

=
Marcos
---

=
Prof. Dr. Marcos Verissimo Alves
Prof. Adjunto II, Curso de F=C3= =ADsica Computacional
Instituto = de Ci=C3=AAncias Exatas
Universidade Federal Fluminens= e
Volta Redonda - RJ, Brasil


Em ter., 23 de abr. de 2024 =C3=A0s 19:47, G= rigoriy Zhurko reg_zhurko%chemcraftpro= g.com <owner-chemistry.^-^.cc= l.net> escreveu:
I have an Orca 5.0.3 job:

!B3LYP 6-31++G(D,P) Opt PAL3 CPCM(Water) ANFREQ

* xyz 0 1
...

The geometry optimization produced a structure at attach 1, with O16-H23 di= stance 2.63944, but with negative frequencies. To get rid of them, I repeat= ed the job with these keywords:

!B3LYP 6-31++G(D,P) Opt PAL3 CPCM(Water) AnFreq
!TightOpt DefGrid3 VeryTightSCF

* xyz 0 1
...

Finally I got an optimized geometry without negative frequencies, but the s= tructure is different - see attach 2. The distance O16-H23 is now 3.89712.<= br> Isn't that strange that the optimized structure does not have this O:H = hydrogen bond?
At attach 3 you can see one more optimized (at the same level ) structure, = which seems to be ok - the O15..H21 distance is 2.27375. My intuition tells= me that this is a correct calculation.
The structure from attach 1 was also computed at B3LYP-D4 level and everyth= ing seems ok - see attach 4 (O16..H23 distance is 2.21156):

!B3LYP D4 6-31++G(D,P) Opt PAL3 CPCM(Water) ANFREQ

* xyz 0 1
...

Maybe this is a bug in Orca?
Grigoriy Zhurko
--0000000000007e893a0616d7a53e-- From owner-chemistry@ccl.net Wed Apr 24 11:52:01 2024 From: "Grigoriy Zhurko reg_zhurko^chemcraftprog.com" To: CCL Subject: CCL: Strange geometry optimization with breaking of H-bonds Message-Id: <-55129-240424114930-30326-Yjxfoes5uBH5mbqp05xMxg!=!server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 24 Apr 2024 18:48:32 +0300 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko,chemcraftprog.com] > I have a couple of questions: > 1) Why didn't you include D3 or D4 corrections in your first calculation? I > might be wrong, but dispersion corrections will improve geometries in most > cases, if not all. I performed the computations with three methods - B3LYP, B3LYP-D4 and wB97X-D4, and compared the results. As far as I know, it is not 100% proven that D4 correction is always good. > 2) Why use ORCA 5.0.3 when version 5.0.4 has been out for quite some time > now, and many bugs were corrected or detected? Unfortunately, I can't run 5.0.4 version on my Windows PC with PAL3 option, while the 5.0.3 version allows that. For the B3LYP-D4 method, I have checked many times whether the results for my compounds are the same with the 5.0.3 and 5.0.4 versions. I performed the first geometry optimization via 5.0.3 version and then completed it with 5.0.4 version. My molecules contain only C, N, O, H, Cl, F atoms. Grigoriy Zhurko. From owner-chemistry@ccl.net Wed Apr 24 12:27:00 2024 From: "Felipe S. S. Schneider schneider.felipe.5(_)gmail.com" To: CCL Subject: CCL: Strange geometry optimization with breaking of H-bonds Message-Id: <-55130-240423161630-21206-2aeQb10ZPiTJxXKXmUXz1g]~[server.ccl.net> X-Original-From: "Felipe S. S. Schneider" Content-Type: multipart/alternative; boundary="0000000000001a7c7c0616c93afb" Date: Tue, 23 Apr 2024 17:15:43 -0300 MIME-Version: 1.0 Sent to CCL by: "Felipe S. S. Schneider" [schneider.felipe.5*_*gmail.com] --0000000000001a7c7c0616c93afb Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable I think that's fairly common. P.S.: Those yellow carbons... Maybe you should consider using that CPK colour scheme for white backgrounds I've sent to support|,|chemcraftprog.com back in 2017. On Tue, 23 Apr 2024 at 14:51, Grigoriy Zhurko reg_zhurko%chemcraftprog.com = < owner-chemistry|,|ccl.net> wrote: > I have an Orca 5.0.3 job: > > !B3LYP 6-31++G(D,P) Opt PAL3 CPCM(Water) ANFREQ > > * xyz 0 1 > ... > > The geometry optimization produced a structure at attach 1, with O16-H23 > distance 2.63944, but with negative frequencies. To get rid of them, I > repeated the job with these keywords: > > !B3LYP 6-31++G(D,P) Opt PAL3 CPCM(Water) AnFreq > !TightOpt DefGrid3 VeryTightSCF > > * xyz 0 1 > ... > > Finally I got an optimized geometry without negative frequencies, but the > structure is different - see attach 2. The distance O16-H23 is now 3.8971= 2. > Isn't that strange that the optimized structure does not have this O:H > hydrogen bond? > At attach 3 you can see one more optimized (at the same level ) structure= , > which seems to be ok - the O15..H21 distance is 2.27375. My intuition tel= ls > me that this is a correct calculation. > The structure from attach 1 was also computed at B3LYP-D4 level and > everything seems ok - see attach 4 (O16..H23 distance is 2.21156): > > !B3LYP D4 6-31++G(D,P) Opt PAL3 CPCM(Water) ANFREQ > > * xyz 0 1 > ... > > Maybe this is a bug in Orca? > Grigoriy Zhurko --=20 *ORCID | GitHub * Campus Universit=C3=A1rio Trindade, Caixa Postal 476 88040-900, Florian=C3=B3polis/SC, Brazil +55-48-3721-6839 schneider.felipe|,|posgrad.ufsc.br --0000000000001a7c7c0616c93afb Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
I thi= nk that's fairly common.

= P.S.: Those yellow carbons... Maybe you should consider using that CPK colo= ur scheme for white backgrounds I've sent to=C2=A0support|,|chemcraftpro= g.com back in 2017.

On Tue, 23 Apr 2024 at 14:51= , Grigoriy Zhurko reg_zhurko%chemcraft= prog.com <owner-chemistry= |,|ccl.net> wrote:
I have an Orca 5.0.3 job:

!B3LYP 6-31++G(D,P) Opt PAL3 CPCM(Water) ANFREQ

* xyz 0 1
...

The geometry optimization produced a structure at attach 1, with O16-H23 di= stance 2.63944, but with negative frequencies. To get rid of them, I repeat= ed the job with these keywords:

!B3LYP 6-31++G(D,P) Opt PAL3 CPCM(Water) AnFreq
!TightOpt DefGrid3 VeryTightSCF

* xyz 0 1
...

Finally I got an optimized geometry without negative frequencies, but the s= tructure is different - see attach 2. The distance O16-H23 is now 3.89712.<= br> Isn't that strange that the optimized structure does not have this O:H = hydrogen bond?
At attach 3 you can see one more optimized (at the same level ) structure, = which seems to be ok - the O15..H21 distance is 2.27375. My intuition tells= me that this is a correct calculation.
The structure from attach 1 was also computed at B3LYP-D4 level and everyth= ing seems ok - see attach 4 (O16..H23 distance is 2.21156):

!B3LYP D4 6-31++G(D,P) Opt PAL3 CPCM(Water) ANFREQ

* xyz 0 1
...

Maybe this is a bug in Orca?
Grigoriy Zhurko


--
ORCID | GitHub
Campus Universit=C3=A1rio T= rindade, Caixa Postal 476
88040-900, Florian=C3=B3polis/SC, Brazil
+5= 5-48-3721-6839
schneider.felipe|,|posgrad.ufsc.br
--0000000000001a7c7c0616c93afb--