From owner-chemistry@ccl.net Thu Feb 20 08:59:01 2020 From: "Norrby, Per-Ola Per-Ola.Norrby~!~astrazeneca.com" To: CCL Subject: CCL: Radical optimisation Message-Id: <-53986-200220032816-494-w+dTjz201F7JN2S6XgtaRw||server.ccl.net> X-Original-From: "Norrby, Per-Ola" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 20 Feb 2020 08:28:06 +0000 MIME-Version: 1.0 Sent to CCL by: "Norrby, Per-Ola" [Per-Ola.Norrby]![astrazeneca.com] Dear Bonoit, A couple of things. When doing G3, I'd first do the much less expensive geometry optimization at the level of theory specified by the G3 variant you're using (MP2/6-31G* ? ), and check that before starting the full calculation. The structure you are looking at is set up to generate a fairly unstable primary radical. The barrier for rearrangement is pretty low, the optimization could accidentally jump over the barrier. One way to avoid this is to ensure you geometry optimize a symmetric system. You can draw CH2=CH-CH2-CH2. in Cs symmetry, then it will not be able to migrate the single H if you optimize in symmetry. Alternatively, you can specify the geometry as a Z-matrix where you use a single variable for the two C-H bond lengths on carbon 2, that has the same effect. Be very careful when doing this to verify both that the final structure is a real minimum by frequency analysis, and that there are no other lower conformations. You could also try first to optimize at a cheaper level of theory where your structure is a deeper minimum. You may then be able to bring that structure on to the higher level even without symmetry constraints; the closer you are to your desired structure when you start the calculation, the less likely it is that the optimization will skip over low barriers. And if it didn't work, you only wasted a few seconds... Best regards, Per-Ola Norrby -----Original Message----- > From: owner-chemistry+per-ola.norrby==astrazeneca.com|ccl.net On Behalf Of Benoit Gearald ablux13 .. gmail.com Sent: den 19 februari 2020 22:00 To: Norrby, Per-Ola Subject: CCL: Radical optimisation Sent to CCL by: "Benoit Gearald" [ablux13:-:gmail.com] Dear CCLers, I lauched a radical optimisation at G3 level. The radical corresponds to butadiene without a hydrogen atom at carbone 2. but in the output file I don't get this structure. I get two succesive double bond and the alternance is lost. I don't know whether there is a keyword to restrict the strucure or something in this way. Any help is appreciated Bonoithttps://clicktime.symantec.com/3E7BXmZApmZ9Etj1qRVeGgq6H2?u=http%3A%2F%2Fwww.ccl.net%2Fcgi-bin%2Fccl%2Fsend_ccl_messagehttps://clicktime.symantec.com/3E7BXmZApmZ9Etj1qRVeGgq6H2?u=http%3A%2F%2Fwww.ccl.net%2Fcgi-bin%2Fccl%2Fsend_ccl_messagehttps://clicktime.symantec.com/37S9C3FSyqGVspp2sXEGjS36H2?u=http%3A%2F%2Fwww.ccl.net%2Fchemistry%2Fsub_unsub.shtml Before posting, check wait time at: https://clicktime.symantec.com/3Q5gboQnHggvP9a3fJojzGn6H2?u=http%3A%2F%2Fwww.ccl.net Job: https://clicktime.symantec.com/3ThoL7VRvxMews7cSgYY57s6H2?u=http%3A%2F%2Fwww.ccl.net%2Fjobs Conferences: https://clicktime.symantec.com/38qc4GH5yMhdcbWxULovbhg6H2?u=http%3A%2F%2Fserver.ccl.net%2Fchemistry%2Fannouncements%2Fconferences%2F Search Messages: https://clicktime.symantec.com/3ADMNuFDC2uAhGdN1ToQGZo6H2?u=http%3A%2F%2Fwww.ccl.net%2Fchemistry%2Fsearchccl%2Findex.shtmlhttps://clicktime.symantec.com/3NBXvjaxLgF6Ekrx5XPfNWi6H2?u=http%3A%2F%2Fwww.ccl.net%2Fspammers.txt RTFI: https://clicktime.symantec.com/3JvvYcGmj8bwPtF31Hch81m6H2?u=http%3A%2F%2Fwww.ccl.net%2Fchemistry%2Faboutccl%2Finstructions%2F ________________________________ Confidentiality Notice: This message is private and may contain confidential and proprietary information. 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From owner-chemistry@ccl.net Thu Feb 20 09:34:01 2020 From: "Breton, Gary gbreton ~ berry.edu" To: CCL Subject: CCL: Radical optimisation Message-Id: <-53987-200220080817-10338-isKrx7fh1VmCsSOlFYwKpA()server.ccl.net> X-Original-From: "Breton, Gary" Content-Language: en-US Content-Type: multipart/related; boundary="_004_31037CC5F4BB492A90595446A7193C2Aberryedu_"; type="multipart/alternative" Date: Thu, 20 Feb 2020 13:08:06 +0000 MIME-Version: 1.0 Sent to CCL by: "Breton, Gary" [gbreton * berry.edu] --_004_31037CC5F4BB492A90595446A7193C2Aberryedu_ Content-Type: multipart/alternative; boundary="_000_31037CC5F4BB492A90595446A7193C2Aberryedu_" --_000_31037CC5F4BB492A90595446A7193C2Aberryedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 QXNzdW1pbmcgdGhlIGluaXRpYWwgZ2VvbWV0cnkgaXMgcGxhbmFyIGZvciBhbGwgZm91ciBjYXJi b25zLCBteSBndWVzcyB3b3VsZCBiZSB0aGF0IG9wdGltaXphdGlvbiBpcyByZXN1bHRpbmcgaW4g 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X-Original-From: "Welch, Bradley" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_3b252f15474941febcebab2a72c1524fCH2PR12MB41835BEDD7E119_" Date: Thu, 20 Feb 2020 16:38:41 +0000 MIME-Version: 1.0 Sent to CCL by: "Welch, Bradley" [welchbr2=-=msu.edu] --_000_3b252f15474941febcebab2a72c1524fCH2PR12MB41835BEDD7E119_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I have a feeling part of the problem might be relying too heavily on what a= visualization program shows. Gaussview, chemcraft, molden, etc. all use cu= t offs for what is a single, double, triple, etc. bond. Take a look at this paper (Phys.Chem.Chem.Phys.,2017,19, 14543--14554) by R= iberio and Mebel. This molecule is in the SI. I would see how my structure = compares to that. This molecule isn't some multireference monster either. Bradley Welch ________________________________ > From: owner-chemistry+welchbr2=3D=3Dmsu.edu{:}ccl.net on behalf of Norrby, Per-Ola Per-Ola.Norrby~!~astr= azeneca.com Sent: Thursday, February 20, 2020 3:28 AM To: Welch, Bradley Subject: CCL: Radical optimisation Sent to CCL by: "Norrby, Per-Ola" [Per-Ola.Norrby]![astrazeneca.com] Dear Bonoit, A couple of things. When doing G3, I'd first do the much less expensive geo= metry optimization at the level of theory specified by the G3 variant you'r= e using (MP2/6-31G* ? ), and check that before starting the full calculatio= n. The structure you are looking at is set up to generate a fairly unstable pr= imary radical. The barrier for rearrangement is pretty low, the optimizatio= n could accidentally jump over the barrier. One way to avoid this is to ens= ure you geometry optimize a symmetric system. You can draw CH2=3DCH-CH2-CH2= . in Cs symmetry, then it will not be able to migrate the single H if you o= ptimize in symmetry. Alternatively, you can specify the geometry as a Z-mat= rix where you use a single variable for the two C-H bond lengths on carbon = 2, that has the same effect. Be very careful when doing this to verify both= that the final structure is a real minimum by frequency analysis, and that= there are no other lower conformations. You could also try first to optimize at a cheaper level of theory where you= r structure is a deeper minimum. You may then be able to bring that structu= re on to the higher level even without symmetry constraints; the closer you= are to your desired structure when you start the calculation, the less lik= ely it is that the optimization will skip over low barriers. And if it didn= 't work, you only wasted a few seconds... Best regards, Per-Ola Norrby -----Original Message----- > From: owner-chemistry+per-ola.norrby=3D=3Dastrazeneca.com/./ccl.net On Behalf Of Ben= oit Gearald ablux13 .. gmail.com Sent: den 19 februari 2020 22:00 To: Norrby, Per-Ola Subject: CCL: Radical optimisation Sent to CCL by: "Benoit Gearald" [ablux13:-:gmail.com] Dear CCLers, I lauched a radical optimisation at G3 level. The radical corresponds to bu= tadiene without a hydrogen atom at carbone 2. but in the output file I don'= t get this structure. I get two succesive double bond and the alternance is= lost. I don't know whether there is a keyword to restrict the strucure or = something in this way. Any help is appreciated Bonoithttps://clicktime.symantec.com/3E7BXmZApmZ9Etj1qRVeGgq6H2?u=3Dhttp%3A= %2F%2Fwww.ccl.net%2Fcgi-bin%2Fccl%2Fsend_ccl_messagehttps://clicktime.syman= tec.com/3E7BXmZApmZ9Etj1qRVeGgq6H2?u=3Dhttp%3A%2F%2Fwww.ccl.net%2Fcgi-bin%2= Fccl%2Fsend_ccl_messagehttps://clicktime.symantec.com/37S9C3FSyqGVspp2sXEGj= S36H2?u=3Dhttp%3A%2F%2Fwww.ccl.net%2Fchemistry%2Fsub_unsub.shtml Before posting, check wait time at: https://urldefense.com/v3/__https://cli= cktime.symantec.com/3Q5gboQnHggvP9a3fJojzGn6H2?u=3Dhttp*3A*2F*2Fwww.ccl.net= __;JSUl!!HXCxUKc!kD6FjuwHePAf51WV6Z0gR9c76QHUdv0zHn24m7URQSM7Q3r60mDG56_P2E= x77rwP$ Job: https://urldefense.com/v3/__https://clicktime.symantec.com/3ThoL7VRvxM= ews7cSgYY57s6H2?u=3Dhttp*3A*2F*2Fwww.ccl.net*2Fjobs__;JSUlJQ!!HXCxUKc!kD6Fj= uwHePAf51WV6Z0gR9c76QHUdv0zHn24m7URQSM7Q3r60mDG56_P2D3xWjyd$ Conferences: https://urldefense.com/v3/__https://clicktime.symantec.com/38q= c4GH5yMhdcbWxULovbhg6H2?u=3Dhttp*3A*2F*2Fserver.ccl.net*2Fchemistry*2Fannou= ncements*2Fconferences*2F__;JSUlJSUlJQ!!HXCxUKc!kD6FjuwHePAf51WV6Z0gR9c76QH= Udv0zHn24m7URQSM7Q3r60mDG56_P2KVwrRYD$ Search Messages: https://urldefense.com/v3/__https://clicktime.symantec.com= /3ADMNuFDC2uAhGdN1ToQGZo6H2?u=3Dhttp*3A*2F*2Fwww.ccl.net*2Fchemistry*2Fsear= chccl*2Findex.shtmlhttps:**Aclicktime.symantec.com*3NBXvjaxLgF6Ekrx5XPfNWi6= H2*u=3Dhttp*3A*2F*2Fwww.ccl.net*2Fspammers.txt__;JSUlJSUlLy8vPyUlJSU!!HXCxU= Kc!kD6FjuwHePAf51WV6Z0gR9c76QHUdv0zHn24m7URQSM7Q3r60mDG56_P2FFAYJp0$ RTFI: https://urldefense.com/v3/__https://clicktime.symantec.com/3JvvYcGmj8= bwPtF31Hch81m6H2?u=3Dhttp*3A*2F*2Fwww.ccl.net*2Fchemistry*2Faboutccl*2Finst= ructions*2F__;JSUlJSUlJQ!!HXCxUKc!kD6FjuwHePAf51WV6Z0gR9c76QHUdv0zHn24m7URQ= SM7Q3r60mDG56_P2JcwUDTj$ ________________________________ Confidentiality Notice: This message is private and may contain confidentia= l and proprietary information. 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I have a feeling part of the problem might be relying too heavily on what a= visualization program shows. Gaussview, chemcraft, molden, etc. all use cu= t offs for what is a single, double, triple, etc. bond. 

Take a look at this paper (Phys.Chem.Chem.Phys.,2017,19, 14543--14554) by R= iberio and Mebel. This molecule is in the SI. I would see how my structure = compares to that. This molecule isn't some multireference monster either.&n= bsp;


Bradley Welch

From: owner-chemistry+w= elchbr2=3D=3Dmsu.edu{:}ccl.net <owner-chemistry+welchbr2=3D=3Dmsu.edu{:}= ccl.net> on behalf of Norrby, Per-Ola Per-Ola.Norrby~!~astrazeneca.com <owner-chemistry{:}ccl.net>
Sent: Thursday, February 20, 2020 3:28 AM
To: Welch, Bradley <welchbr2{:}msu.edu>
Subject: CCL: Radical optimisation
 

Sent to CCL by: "Norrby, Per-Ola" [Per-Ola.Norrby]![astrazeneca.c= om]
Dear Bonoit,

A couple of things. When doing G3, I'd first do the much less expensive geo= metry optimization at the level of theory specified by the G3 variant you'r= e using (MP2/6-31G* ? ), and check that before starting the full calculatio= n.

The structure you are looking at is set up to generate a fairly unstable pr= imary radical. The barrier for rearrangement is pretty low, the optimizatio= n could accidentally jump over the barrier. One way to avoid this is to ens= ure you geometry optimize a symmetric system. You can draw CH2=3DCH-CH2-CH2. in Cs symmetry, then it will not be= able to migrate the single H if you optimize in symmetry. Alternatively, y= ou can specify the geometry as a Z-matrix where you use a single variable f= or the two C-H bond lengths on carbon 2, that has the same effect. Be very careful when doing this to verify bot= h that the final structure is a real minimum by frequency analysis, and tha= t there are no other lower conformations.

You could also try first to optimize at a cheaper level of theory where you= r structure is a deeper minimum. You may then be able to bring that structu= re on to the higher level even without symmetry constraints; the closer you= are to your desired structure when you start the calculation, the less likely it is that the optimization wil= l skip over low barriers. And if it didn't work, you only wasted a few seco= nds...

Best regards,

Per-Ola Norrby

-----Original Message-----
> From: owner-chemistry+per-ola.norrby=3D=3Dastrazeneca.com/./ccl.ne= t <owner-chemistry+per-ola.norrby=3D=3Dastrazeneca.com/./ccl.net>= On Behalf Of Benoit Gearald ablux13 .. gmail.com
Sent: den 19 februari 2020 22:00
To: Norrby, Per-Ola <Per-Ola.Norrby/./astrazeneca.com>
Subject: CCL: Radical optimisation


Sent to CCL by: "Benoit  Gearald" [ablux13:-:gmail.com] Dear= CCLers,

I lauched a radical optimisation at G3 level. The radical corresponds to bu= tadiene without a hydrogen atom at carbone 2. but in the output file I don'= t get this structure. I get two succesive double bond and the alternance is= lost. I don't know whether there is a keyword to restrict the strucure or something in this way.

Any help is appreciated

Bonoithttps://clicktime.symantec.com/3E7BXmZApmZ9Etj1qRVeGgq6H2?u=3Dhttp%3A= %2F%2Fwww.ccl.net%2Fcgi-bin%2Fccl%2Fsend_ccl_messagehttps://clicktime.syman= tec.com/3E7BXmZApmZ9Etj1qRVeGgq6H2?u=3Dhttp%3A%2F%2Fwww.ccl.net%2Fcgi-bin%2= Fccl%2Fsend_ccl_messagehttps://clicktime.symantec.com/37S9C3FSyqGVspp2sXEGj= S36H2?u=3Dhttp%3A%2F%2Fwww.ccl.net%2Fchemistry%2Fsub_unsub.shtml

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