CCL:G: Not able to optimize structure - bisphosphole



Also, you should consider eliminating the diffuse functions from your basis set and make sure you are using the pure 5D and 7F basis specifications.  With all the diffuse functions in your current calculation, you most certainly have significant linear dependence of your atomic basis functions which will result in no or poor SCF convergence.

 

Jim

 

From: owner-chemistry+jimkress35==gmail.com/a\ccl.net [mailto:owner-chemistry+jimkress35==gmail.com/a\ccl.net] On Behalf Of Daniel Morales Salazar danielmoralessalazar91- -gmail.com
Sent: Monday, May 16, 2016 4:37 PM
To: Kress, Jim <jimkress35/a\gmail.com>
Subject: CCL:G: Not able to optimize structure - bisphosphole

 

I am sorry, I sent the -email while editing.
Hello everybody,

Thanks a lot for the replies.

Dear Dr. Layec, I just realized that the only try that passed had the following input:

# opt=(calcfc, loose, cartesian) pm6 nosymm scf=qc


Dear Dr. Molt, I am not sure if I understood your question correctly, but I believe tungsten is a singlet in these cases, the spin question, I am not sure but, should it be zero? I am not sure how to answer this question right about now (need to read my organometallics textbook! :))
By the way I forgot to mention on the original post that I am trying DFT methods as well but since they are taking so long to finish I started the semi-empirical calculations thinking they would be straight forward (oh was I wrong). For the DFT I am using a combination of basis sets combined with pseudo-core potentials for the tungsten

C H O P S 0

6-311G**

****

W 0

MWB

****

 

W 0

ECP60MWB 5 60

Ultimately, it did not pass on time so I will restart from the last geometry soon.

There were a couple of PM6 that did not finish on time on the interactive session so I do not know if I should restart them now that you said it was ambitious.

I also thought about making the calculation with smaller atoms such as chromium and maybe changing the phenyl ligands for methyl groups, but being a "dimeric" structure, I do not want to obtain something completely different using smaller ligands.

Dear Dr. Shobe,
With the Amber it crashed immediately, but with the UFF it did go through some steps. When I search for Energy in the output I find:

" Convergence criteria             0.00011250 0.00007500 0.00045000 0.00030000

  Step  NS  ND Rises OKQ   Scale  Max. Force  RMS Force Max. Disp.  RMS Disp.     Energy   Flag

.....bunch of steps

 2093   0   0   F    T  1.61D+00 0.00009841 0.00001833 0.00009354 0.00002815    0.3068418 ====

 Energy=    0.306841771"
Then,
" Item               Value     Threshold  Converged?

 Maximum Force            0.000097     0.000450     YES

 RMS     Force            0.000018     0.000300     YES

 Maximum Displacement     0.110212     0.001800     NO

 RMS     Displacement     0.014639     0.001200     NO

 Predicted change in Energy=-1.662896D-05"
Then,
 "Convergence limit is  0.750E-04 MaxStp= 10000 StMxLn= 3.00D-04 StpMin= 1.00D-06.

 Convergence criteria             0.00011250 0.00007500 0.00045000 0.00030000

  Step  NS  ND Rises OKQ   Scale  Max. Force  RMS Force Max. Disp.  RMS Disp.     Energy   Flag

     1   0   0   F    T  1.00D+00 0.00017298 0.00001595 0.00017298 0.00001595    0.3068252 -+++

     2   0   0   F    T  1.47D+00 0.00007243 0.00000955 0.00013885 0.00001595    0.3068252 ====

 Energy=    0.306825172  "

Finally,

 " Item               Value     Threshold  Converged?

 Maximum Force            0.000070     0.000450     YES

 RMS     Force            0.000010     0.000300     YES

 Maximum Displacement          NaN     0.001800     YES

 RMS     Displacement          NaN     0.001200     YES

 Predicted change in Energy=          NaN"

For the other UFF trial, there were more results for the Energy word, so I guess it went slightly better, I will just paste shorter versions starting > from the top of the output:

"Step  NS  ND Rises OKQ   Scale  Max. Force  RMS Force Max. Disp.  RMS Disp.     Energy   Flag

     1   0   0   F    T  1.00D+00 0.00000000 0.00000000 0.00000000 0.00000000    0.8772618 ====

 Energy=    0.877261757     NIter=   0."
" Energy=    0.849329056"
" Energy=    0.813651610"
" Energy=    0.771900194"

"Energy=    0.724817194 "
.....
" Energy=    0.623211212"
" Energy=    0.612600532"

 Item               Value     Threshold  Converged?

 Maximum Force            0.037731     0.000450     NO

 RMS     Force            0.005556     0.000300     NO

 Maximum Displacement     0.051140     0.001800     NO

 RMS     Displacement     0.007356     0.001200     NO

 Predicted change in Energy=-1.136353D-02

 Optimization stopped.

    -- Number of steps exceeded,  NStep=  10

 

 

I do not have an atom type or anything for tungsten, the input of the UFF looks like:

# opt=calcfc uff geom=connectivity

 

I used the ones available in Gaussian 09 , UFF, as I said before.

It has 60 atoms, I realized the typo, and I was waiting for someone to notice thanks.

Yes, for the later jobs I am, but those did not finish on time during the interactive session.

Unfortunately I am way past my allocated hours per month so I get very low priorities in my jobs now.
 
Guess=Read does seem to be working with the later jobs, and I do believe the tungsten is in the correct electronic state. 

Just a friendly reminder that before Gaussian, I preoptimized the structures first in chem3d using MM2 then in Avogadro using UFF. So I was pretty surprised to see that Gaussian failed.

Thank you everybody for the replies. I hope my DFT on queue will pass this time.

Sincerely,

Daniel Morales Salazar

Bachelor of Science in Chemistry, Georgia Institute of Technology

PhD student, Department of Chemistry - Ångström Laboratory

Uppsala University

Box 523

SE-751 20 Uppsala

Sweden

 

On Mon, May 16, 2016 at 10:15 PM, Daniel Morales Salazar <danielmoralessalazar91%gmail.com> wrote:

Hello everybody,

Thanks a lot for the replies.

Dear Dr. Layec, I just realized that the only try that passed had the following input:

# opt=(calcfc, loose, cartesian) pm6 nosymm scf=qc


Dear Dr. Molt, I am not sure if I understood your question correctly, but I believe tungsten is a singlet in these cases, the spin question, I am not sure but, should it be zero? I am not sure how to answer this question right about now (need to read my organometallics textbook! :))
By the way I forgot to mention on the original post that I am trying DFT methods as well but since they are taking so long to finish I started the semi-empirical calculations thinking they would be straight forward (oh was I wrong). For the DFT I am using a combination of basis sets combined with pseudo-core potentials for the tungsten

C H O P S 0

6-311G**

****

W 0

MWB

****

 

W 0

ECP60MWB 5 60

Ultimately, it did not pass on time so I will restart from the last geometry soon.

There were a couple of PM6

I also thought about making the calculation with smaller atoms such as chromium and maybe changing the phenyl ligands for methyl groups, but being a "dimeric" structure, I do not want to obtain something completely different using smaller ligands.

Dear Dr. Shobe,
With the Amber it crashed immediately, I am assuming tungsten was not parametr


Daniel--

A few questions, that may be useful to others even if not to me :-)

First regarding the MM methods.  The error message given is pretty generic.  Does the calculation produce any intermediate geometries, or does it crash on the first geometric-optimization step?  If there are intermediate geometries,does the energy decrease from step to step, or is there a sudden increase in energy?  Do you even have an atom type and parameters for tungsten?  Which MM force field are you using?

[I would have advised opt=calcall as a last resort, but given the size of your molecule (which is surely even bigger than the formula you actually wrote implies: how many carbon atoms again? :-) I might have second thoughts on that.  Hopefully someone has a better idea.]

About the semiemprical method (PM6).  It appears from the error message that you are not getting a decent wavefunction.  Are you using guess=read to get the wavefunction from the checkpoint file in which you were able to optimize with opt=loose?  (Or does guess=read even work with semiempirical methods?)  Are you sure everything (especially the tungsten moieties) are in the correct electronic state? 

Hope this helps,--David Shobe

 

SCF Energy                                 R     -1.229246327147848E+00

Total Energy                               R     -1.229246327147848E+00

RMS Force                                  R      2.869324126432187E-04

 



 

On Sat, May 14, 2016 at 10:42 PM, David Shobe avidshobe-$-yahoo.com <owner-chemistry%ccl.net> wrote:

Daniel--
A few questions, that may be useful to others even if not to me :-)
First regarding the MM methods.  The error message given is pretty generic.  Does the calculation produce any intermediate geometries, or does it crash on the first geometric-optimization step?  If there are intermediate geometries,does the energy decrease from step to step, or is there a sudden increase in energy?  Do you even have an atom type and parameters for tungsten?  Which MM force field are you using?
[I would have advised opt=calcall as a last resort, but given the size of your molecule (which is surely even bigger than the formula you actually wrote implies: how many carbon atoms again? :-) I might have second thoughts on that.  Hopefully someone has a better idea.]
About the semiemprical method (PM6).  It appears from the error message that you are not getting a decent wavefunction.  Are you using guess=read to get the wavefunction from the checkpoint file in which you were able to optimize with opt=loose?  (Or does guess=read even work with semiempirical methods?)  Are you sure everything (especially the tungsten moieties) are in the correct electronic state? 
Hope this helps,--David Shobe







 On Saturday, May 14, 2016 9:10 AM, Daniel Morales Salazar danielmoralessalazar91]_[gmail.com <owner-chemistry++ccl.net> wrote:



Sent to CCL by: "Daniel  Morales Salazar" [danielmoralessalazar91*|*gmail.com]
Hello,

I am trying to optimize a molecule with the chemical formula CH52O18P4S4W2, which contains thiophenes-phospholes, phenyl groups, and
tungsten pentacarbonyl substituents.

It is a large and especially bulky molecule. I have tried using MM and
Semi-empirical methods (PM6) unsuccessfully. The only converged trial so
far was one with the "loose" keyword using PM6, which crashed in the
following calculation with stricter parameters when I did not use the
keyword. I have tried the keywords calcfc, qc, cartesian, etc.

Any advice for these types of cases?

Semi-empirical jobs crash with the message:

"Symmetry turned off by external request.
 DSYEV returned Info=          2 IAlg= 2 N=    3 NDim=    3 NE2=         
2.
 Diagonalization in DiagDN failed."

MM methods crash with the message:

" Error termination request processed by link 9999."

I have the feeling that the initial geometries are not so bad even! Thank
you very much for your help.

Sincerely,

Daniel Morales Salazar



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<html><head></head><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:13px"><div id="yiv3733130765"><div id="yui_3_16_0_ym19_1_1463251158989_27956"><div style="color:#000;background-color:#fff;font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:13px;" id="yui_3_16_0_ym19_1_1463251158989_27955"><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609">Daniel--</div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609"><br></div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609">A few questions, that may be useful to others even if not to me :-)</div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609"><br></div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609">First regarding the MM methods. &nbsp;The error message given is pretty generic. &nbsp;Does the calculation produce any intermediate geometries, or does it crash on the first geometric-optimization step? &nbsp;If there are intermediate geometries,does the energy decrease > from step to step, or is there a sudden increase in energy? &nbsp;Do you even have an atom type and parameters for tungsten? &nbsp;Which MM force field are you using?</div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609"><br></div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609" dir="ltr">[I would have advised opt=calcall as a last resort, but given the size of your molecule (which is surely even bigger than the formula you actually wrote implies: how many carbon atoms again? :-) I might have second thoughts on that. &nbsp;Hopefully someone has a better idea.]</div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609"><br clear="none"></div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609" dir="ltr">About the semiemprical method (PM6). &nbsp;It appears from the error message that you are not getting a decent wavefunction. &nbsp;Are you using guess=read to get the wavefunction from the checkpoint file in which you were able to optimize with opt=loose? &nbsp;(Or does guess=read even work with semiempirical methods?) &nbsp;Are you sure everything (especially the tungsten moieties) are in the correct electronic state?&nbsp;</div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609" dir="ltr"><br></div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609" dir="ltr">Hope this helps,</div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609" dir="ltr">--David Shobe</div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609"><br clear="none"></div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22609"><br clear="none"></div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_22613"><br clear="none"></div><div id="yiv3733130765yui_3_16_0_ym19_1_1463251158989_23060"><br clear="none"></div><div class="yiv3733130765qtdSeparateBR" id="yui_3_16_0_ym19_1_1463251158989_27957"><br clear="none"><br clear="none"></div></div></div></div><div class=".yiv3733130765yahoo_quoted"> <div style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:13px;"> <div style="font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px;"> <div class="qtdSeparateBR"><br><br></div><div class="yiv3733130765yqt3542491216" id="yiv3733130765yqtfd16282"><div dir="ltr"><font size="2" face="Arial"> On Saturday, May 14, 2016 9:10 AM, Daniel Morales Salazar danielmoralessalazar91]_[gmail.com &lt;owner-chemistry++ccl.net&gt; wrote:<br clear="none"></font></div>  <br clear="none"><br clear="none"> <div class="yiv3733130765y_msg_container"><br clear="none">Sent to CCL by: "Daniel&nbsp; Morales Salazar" [danielmoralessalazar91*|*gmail.com]<br clear="none">Hello, <br clear="none"><br clear="none">I am trying to optimize a molecule with the chemical formula CH52O18P4S4W2, which contains thiophenes-phospholes, phenyl groups, and <br clear="none">tungsten pentacarbonyl substituents.<br clear="none"><br clear="none">It is a large and especially bulky molecule. I have tried using MM and <br clear="none">Semi-empirical methods (PM6) unsuccessfully. The only converged trial so <br clear="none">far was one with the "loose" keyword using PM6, which crashed in the <br clear="none">following calculation with stricter parameters when I did not use the <br clear="none">keyword. I have tried the keywords calcfc, qc, cartesian, etc. <br clear="none"><br clear="none">Any advice for these types of cases?<br clear="none"><br clear="none">Semi-empirical jobs crash with the message:<br clear="none"><br clear="none">"Symmetry turned off by external request.<br clear="none"> DSYEV returned Info=&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;  2 IAlg= 2 N=&nbsp; &nbsp;  3 NDim=&nbsp; &nbsp;  3 NE2=&nbsp; &nbsp; &nbsp; &nbsp; &nbsp;  <br clear="none">2.<br clear="none"> Diagonalization in DiagDN failed."<br clear="none"><br clear="none">MM methods crash with the message:<br clear="none"><br clear="none">" Error termination request processed by link 9999."<br clear="none"><br clear="none">I have the feeling that the initial geometries are not so bad even! Thank <br clear="none">you very much for your help.<br clear="none"><br clear="none">Sincerely,<br clear="none"><br clear="none">Daniel Morales Salazar<br clear="none"><br clear="none"><br clear="none"><br clear="none">-= This is automatically added to each message by the mailing script =-<br clear="none">To recover the email address of the author of the message, please change<br clear="none">the strange characters on the top line to the ++ sign. 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--

Daniel Morales Salazar

Bachelor of Science in Chemistry, Georgia Institute of Technology

PhD student, Department of Chemistry - Ångström Laboratory 

Uppsala University 

Box 523

SE-751 20 Uppsala

Sweden

 

 



 

--

Daniel Morales Salazar

Bachelor of Science in Chemistry, Georgia Institute of Technology

PhD student, Department of Chemistry - Ångström Laboratory 

Uppsala University 

Box 523

SE-751 20 Uppsala

Sweden