Subject: Re: CCL:W:problem with solvent effect calculations (fwd)

From: Andreas Klamt <klamt <> cosmologic.de>
Date: Tue, 05 Apr 2005 12:48:12 +0200

Dear Jelena,

as agreed on we did the TURBOMOLE/COSMO optimization of the geometry 
optimization of your large bioorganic
molecule supramolecular structure, which you had problems with using PCM 
and Gaussian. As expected, the geometry optimization was no technical 
problem. It converged from your start structure without any problem. The 
complex had
 NUMBER OF ATOMS:          112
 DEGREES OF FREEDOM:          330
 INTERNAL COORDINATES:          379
We performed a BP DFTcalculation with TZVP basis set resulting in 1413 
atom orbitals.

The calculation took about 9 days on a single 3MHz CPU. It took 145 
geometry optimization steps.

As a result we may conclude, that optimization of such complexes with 
the dielectric continuum solvation model COSMO is technically doable 
with no problems using TURBOMOLE. Obviously, such calculations are for 
such floppy supramolecular complexes are time consuming.

Best regards

Andreas

Jelena Tamuliene wrote:

>
> Dear Professor Klamt,
>
> Thank you for your letter.
> Of course we agree.
>
> Thank you again.
>
> With respect,
>
> Jelena
>
> On Tue, 22 Mar 2005, Andreas Klamt wrote:
>
>> Dear Jelena,
>>
>> we will be happy to do it, but with our default level BP91 and TZVP 
>> basis set. The geometries typically depend very little on the DFT 
>> method. So a well optimized BP91/TZVP optimization should be o.k. for 
>> your applications. And TURBOMOLE is so much faster for non-hybride 
>> functionals due to the RI approximation.
>>
>> If you agree please let me know.
>>
>> Andreas
>>
>> Jelena Tamuliene wrote:
>>
>>>
>>> Dear Professor Klamt,
>>>
>>> Thank you for your help.
>>> Please find attached the coordinates of the derivatives that we 
>>> would like to optimize in water solvent. It will be very kind of you 
>>> to perform the optimization by DFT method PBEPBE or B3PW91 approch 
>>> with 6-31+G** basis set.
>>> Thank you in advance.
>>> With respect,
>>>
>>> J. Tamuliene
>>> ************************************************************************** 
>>> Research Fellow
>>> Vilnius University Institute of Theoretical Physics and Astronomy
>>> A. Gostauto 12, LT-01108 Vilnius
>>> Lithuania
>>>
>>> Phone: 370-5-2620861
>>> Fax: 370-5-2125361
>>> E-mail: gicevic <> itpa.lt
>>>
>>> *************************************************************************** 
>>>
>>>
>>>>
>>>> Dear Arvydas Tamulis, Noel O'Boyle and other CCL Colleagues,
>>>>
>>>> while I do not have much experience with PCM optimization in 
>>>> Gaussian, I can definitely say, that my COSMO in TURBOMOLE is very 
>>>> robust and efficien even for geometry optimization of large 
>>>> molecules. I suggest that you let us have a typical start structure 
>>>> and we try an optimization here. We will communicate the results 
>>>> via CCL.
>>>>
>>>> Andreas
>>>>
>>>> -- 
>>>>
>>>> ----------------------------------------------------------------------------- 
>>>> Dr. habil. Andreas Klamt
>>>> COSMOlogic GmbH&CoKG
>>>> Burscheider Str. 515
>>>> 51381 Leverkusen, Germany
>>>>
>>>> Tel.: +49-2171-73168-1  Fax:  +49-2171-73168-9
>>>> e-mail: klamt <> cosmologic.de
>>>> web:    www.cosmologic.de
>>>>
>>>> ----------------------------------------------------------------------------- 
>>>> COSMOlogic
>>>>       Your Competent Partner for
>>>>       Computational Chemistry and Fluid Thermodynamics
>>>>
>>>> ----------------------------------------------------------------------------- 
>>>>
>>>>
>>>>
>>>> Arvydas Tamulis wrote:
>>>>
>>>>> Dear Noel O'Boyle and other CCL Colleagues,
>>>>>
>>>>> I have never succeeded to get G03 optimization using PCM or iefpcm 
>>>>> of large
>>>>> bioorganic molecule, supermolecular or supramolecular structures 
>>>>> indeed.
>>>>> In the case if somebody else know how to to do this you are 
>>>>> welcome to teach me.
>>>>>
>>>>> Let me correct Noel O'Boyle's sheme of calculations with PCM or 
>>>>> iefpcm.
>>>>>
>>>>> In the case if you will optimize geometry of large bioorganic 
>>>>> molecule, supermolecular or supramolecular structure in the vaacum 
>>>>> you will
>>>>> get not correct mutual displacement. That will not allow later to 
>>>>> get good
>>>>> single point calculations with PCM or iefpcm.
>>>>>
>>>>> We are doing geometry optimization of large bioorganic
>>>>> molecule, supermolecular or supramolecular structures together 
>>>>> with surrounding H2O molecules shell. We remove H2O molecules and 
>>>>> only then doing calculations with PCM or iefpcm of large bioorganic
>>>>> molecule, supermolecular or supramolecular structures.
>>>>>
>>>>> Best regards,
>>>>> Arvydas Tamulis
>>>>> www.itpa.lt/~tamulis/ ******************************************
>>>>>
>>>>> On Wed, 16 Mar 2005, Girish Ssr Suravajhula wrote:
>>>>>
>>>>>>
>>>>>> ----- Forwarded message from noel.oboyle2 <> mail.dcu.ie -----
>>>>>> Date: Tue, 15 Mar 2005 08:56:10 +0000
>>>>>> From: Noel O'Boyle <noel.oboyle2 <> mail.dcu.ie>
>>>>>> Reply-To: noel.oboyle <> ucd.ie
>>>>>> Subject: Re: CCL:W:problem with solvent effect calculations
>>>>>> To: "girish, s, suravajhula" <gss006 <> latech.edu>
>>>>>>
>>>>>> You need to geometry optimise the structure first, starting with a
>>>>>> structure that Gaussian does correctly understand. You don't need 
>>>>>> to use
>>>>>> PCM for this step. After this, geometry with PCM (if possible) or 
>>>>>> just
>>>>>> do a single-point calculation with PCM.
>>>>>>
>>>>>> Regards,
>>>>>> Noel
>>>>>>
>>>>>> On Mon, 2005-03-14 at 17:57, girish, s, suravajhula wrote:
>>>>>>
>>>>>>> Dear all,
>>>>>>>
>>>>>>> I was trying to perform solvent effect calculations on 
>>>>>>> calix[4]arene crown-6
>>>>>>
>>>>>>
>>>>>>
>>>>>> interaction with cesium in chcl3 as solvent.
>>>>>>
>>>>>>>
>>>>>>> For that I placed cesium inside the crown structure did the PCM 
>>>>>>> calculations
>>>>>>>
>>>>>>> But guassian gave me an error. What its actually doing is 
>>>>>>> counting the number
>>>>>>
>>>>>>
>>>>>>
>>>>>> if bonds cesium is formin with all the surrounding atoms. And 
>>>>>> since cesium is
>>>>>> very close to many atoms its showing errors like Hydrogen has two 
>>>>>> bonds.
>>>>>>
>>>>>>>
>>>>>>> could any one suggenst me how to correct this error.
>>>>>>>
>>>>>>> I would be glad if any one can suggest me any other method how I 
>>>>>>> should
>>>>>>
>>>>>>
>>>>>>
>>>>>> perform a solvent effect on calix[4]arene crown-6 and cesium with 
>>>>>> chcl3 as the
>>>>>> solvent.
>>>>>>
>>>>>>>
>>>>>>> Regards.
>>>>>>>
>>>>>>> Girish Suravajhula.
>>>>>>>
>>>>>>>
>>>>>>> To send e-mail to subscribers of CCL put the string CCL: on your 
>>>>>>> Subject: line
>>>>>>>
>>>>>>> Send your subscription/unsubscription requests to: 
>>>>>>> CHEMISTRY-REQUEST <> ccl.net
>>>>>>> HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ----- End forwarded message -----
>>>>>>
>>>>>>
>>>>>> ----------------------------------------------------------------
>>>>>> This message was sent using IMP, the Internet Messaging Program.
>>>>>>
>>>>>
>>>>>
>>>>> To send e-mail to subscribers of CCL put the string CCL: on your 
>>>>> Subject: line
>>>>> and send your message to: CHEMISTRY <> ccl.net
>>>>>
>>>>> Send your subscription/unsubscription requests to: 
>>>>> CHEMISTRY-REQUEST <> ccl.net HOME Page: http://www.ccl.net | Jobs 
>>>>> Page: http://www.ccl.net/jobs
>>>>> Jan Labanowski, jlabanow <> nd.edu (read about it on CCL Home Page)
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -= This is automatically added to each message by the mailing 
>>>> script =-
>>>> To send e-mail to subscribers of CCL put the string CCL: on your 
>>>> Subject: line
>>>> and send your message to:  CHEMISTRY <> ccl.net
>>>>
>>>> Send your subscription/unsubscription requests to: 
>>>> CHEMISTRY-REQUEST <> ccl.net HOME Page: http://www.ccl.net   | Jobs 
>>>> Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET 
>>>> domain send it to the maintainer:
>>>> Jan Labanowski,  jlabanow <> nd.edu (read about it on CCL Home Page)
>>>> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ 
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>> ------------------------------------------------------------------------ 
>>>
>>>
>>> C    -5.785353    -2.228004    -1.689626
>>> N    -5.010075    -1.150248    -2.224425
>>> C    -3.699579    -1.320343    -2.563354
>>> C    -3.109345    -2.544660    -2.479830
>>> C    -3.926052    -3.621260    -2.009317
>>> N    -5.200146    -3.459244    -1.650000
>>> C    -5.630462     0.172775    -2.295998
>>> C    -4.978835     1.207667    -1.380149
>>> O    -3.993791     1.852499    -1.820088
>>> N    -3.422058    -4.878440    -1.914356
>>> O    -6.954957    -1.987828    -1.299134
>>> N    -5.523126     1.487035    -0.150971
>>> C    -4.902880     2.601484     0.596306
>>> C    -5.275090     3.989602     0.051441
>>> N    -4.509067     5.006982     0.754937
>>> C    -6.437089     0.572903     0.559628
>>> C    -7.812709     1.201325     0.825784
>>> O    -8.507819     0.844136     1.803468
>>> C    -5.871084     0.023616     1.875350
>>> C    -4.589688    -0.763961     1.705569
>>> O    -4.166982    -1.146647     0.594791
>>> N    -3.934230    -1.059018     2.873892
>>> C    -2.698590    -1.846054     2.905204
>>> N    -1.469327    -1.070377     3.061173
>>> C    -1.353567    -0.358296     4.331506
>>> C    -0.972661    -0.415722     1.891753
>>> C    -0.310708    -1.198250     0.888144
>>> C     0.104555    -0.575658    -0.335848
>>> C    -0.049582     0.844257    -0.498865
>>> C    -0.644429     1.570007     0.520529
>>> C    -1.117913     0.944449     1.692900
>>> C     0.635396    -1.394868    -1.368213
>>> C     0.835830    -2.748454    -1.176598
>>> C     0.519130    -3.342650     0.068246
>>> C    -0.051784    -2.583730     1.070198
>>> N     0.386162     1.457980    -1.701776
>>> C    -0.359642     2.623812    -2.169598
>>> C     1.834318     1.571963    -1.912350
>>> N    -8.236656     2.106904    -0.096561
>>> C    -9.580931     2.678668    -0.073841
>>> C   -10.496440     2.072639    -1.139266
>>> C     4.857283    -0.674649     2.164412
>>> C     6.226208    -0.494894     1.961274
>>> C     6.830129    -0.939728     0.772399
>>> C     6.039423    -1.566447    -0.206455
>>> C     4.674422    -1.747697     0.000182
>>> C     4.078888    -1.301892     1.186558
>>> C     8.278581    -0.774380     0.500894
>>> C     9.143920    -0.139064     1.581032
>>> O    10.539962    -0.190744     1.209174
>>> C    10.978527     0.786537     0.331415
>>> C    12.369199     0.488174    -0.144061
>>> C    13.028109     1.665639    -0.863589
>>> C    14.417368     1.314552    -1.411403
>>> C    15.087102     2.493117    -2.124473
>>> O     8.789546    -1.134064    -0.573024
>>> O    10.282427     1.754420     0.023021
>>> H    -7.605582     2.350561    -0.845732
>>> H    -6.621488    -0.299412    -0.087346
>>> H    -3.562903     5.150930     0.433265
>>> H    -4.990272     5.861682     0.986686
>>> H    -5.116739     3.999505    -1.037819
>>> H    -6.339906     4.169688     0.235254
>>> H    -3.815271     2.481734     0.556181
>>> H    -5.216818     2.548935     1.639461
>>> H    -6.691924     0.016552    -2.099045
>>> H    -5.505164     0.567408    -3.308759
>>> H    -4.030223    -5.602226    -1.568123
>>> H    -2.463563    -5.087422    -2.128250
>>> H    -2.064537    -2.676571    -2.724488
>>> H    -3.169957    -0.429102    -2.877331
>>> H    -9.505997     3.765681    -0.201915
>>> H   -10.102505     2.240263    -2.148697
>>> H   -10.598727     0.993782    -0.986864
>>> H    -4.334736    -0.747009     3.745982
>>> H    -5.731101     0.821953     2.613966
>>> H    -6.649775    -0.626243     2.294503
>>> H    -2.657189    -2.392382     1.961765
>>> H    -2.765800    -2.554938     3.737531
>>> H    -1.612578     1.550053     2.445575
>>> H    -0.762381     2.643093     0.416265
>>> H     0.857071    -0.930947    -2.322957
>>> H     1.240517    -3.357599    -1.980198
>>> H     0.720982    -4.397063     0.232403
>>> H    -0.299227    -3.024582     2.029783
>>> H    -0.347711     0.058842     4.422839
>>> H    -2.076869     0.466291     4.455311
>>> H    -1.507203    -1.067777     5.153295
>>> H     2.258515     2.447353    -1.388827
>>> H     2.344671     0.680226    -1.544173
>>> H     2.045611     1.679129    -2.982068
>>> H    -0.146849     2.773100    -3.234261
>>> H    -1.432126     2.451424    -2.050119
>>> H    -0.084716     3.557866    -1.644394
>>> H    -9.977932     2.483277     0.926239
>>> H   -11.493638     2.524383    -1.087686
>>> H     6.522791    -1.900091    -1.118551
>>> H     4.067456    -2.232991    -0.756544
>>> H     3.014289    -1.442854     1.343186
>>> H     4.397069    -0.324920     3.082887
>>> H     6.813141    -0.001432     2.729575
>>> H    14.479515     2.837866    -2.969991
>>> H    15.219897     3.342330    -1.442975
>>> H    15.059941     0.970121    -0.587417
>>> H    14.329777     0.466241    -2.106307
>>> H    12.376348     1.998331    -1.681474
>>> H    13.106701     2.517637    -0.174266
>>> H     8.838059     0.902230     1.737313
>>> H     9.073450    -0.692084     2.520197
>>> H    12.965661     0.154540     0.714376
>>> H    12.294316    -0.382749    -0.812011
>>> H    16.074352     2.217054    -2.511644
>>>
>>>
>>
>>
>> -- 
>> ----------------------------------------------------------------------------- 
>>
>> Dr. habil. Andreas Klamt
>> COSMOlogic GmbH&CoKG
>> Burscheider Str. 515
>> 51381 Leverkusen, Germany
>>
>> Tel.: +49-2171-73168-1  Fax:  +49-2171-73168-9
>> e-mail: klamt <> cosmologic.de
>> web:    www.cosmologic.de
>> ----------------------------------------------------------------------------- 
>>
>> COSMOlogic
>>       Your Competent Partner for
>>       Computational Chemistry and Fluid Thermodynamics
>> ----------------------------------------------------------------------------- 
>>
>>
>>
>>
>
>

-- 
-----------------------------------------------------------------------------
Dr. habil. Andreas Klamt
COSMOlogic GmbH&CoKG
Burscheider Str. 515
51381 Leverkusen, Germany

Tel.: +49-2171-73168-1  
Fax:  +49-2171-73168-9
e-mail: klamt <> cosmologic.de
web:    www.cosmologic.de
-----------------------------------------------------------------------------
COSMOlogic
        Your Competent Partner for
        Computational Chemistry and Fluid Thermodynamics
-----------------------------------------------------------------------------