From owner-chemistry@ccl.net Fri Feb 25 01:09:00 2011 From: "asp asp99++yandex.ru" To: CCL Subject: CCL: UV-VIS spectra values obtained computationally are different (TDDFT & CIS) for different concentrations Message-Id: <-44016-110225010631-17466-WS5oSwDEm5oVnQ30WBzhUw(0)server.ccl.net> X-Original-From: asp Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=koi8-r Date: Fri, 25 Feb 2011 09:06:23 +0300 MIME-Version: 1.0 Sent to CCL by: asp [asp99*|*yandex.ru] Hi, Ashu, it looks like that some king of interaction is taking place in your system. It could be assosiation of compound molecules or formation of complexes with the solvent leading to concentartion-dependent absorption band position. If there is an equlibrium in the solution, then it is likely that at lower concentation you will have more unreacted (isolated) molecules of the compound. The results of calculation also give you values for an isolated molecule, so it is more reasonable to compare values obtatined at lower concentrations. However, there is a possibility that you are regestering to completly separete bands corresponding to different electron transitions in the molecule. What are the extinction coefficients for your experimental bands? It is likely that the band at 400 nm has low intensity and you simply could not detect it at low concentration. How this helps to figure things out, Andrei 25.02.2011, 05:05, "ashutosh gupta ashu1809 : gmail.com" : > Hi,Greetings. > > I have a UV-Vis spectra of a compound at different concentrations. (10-2M to 10-5M) > > At higher concentration( ~10-2 M), the experimental peaks match well with TDDFT/6-31+G* values (400nm), whereas at lower concentration (~10-5M), the experimental peaks match with CIS/6-31+G*švalues (280 nm). > > The IR values obtained experimentally and computationally matches well (for DFT values). > > I would be thankful if someone could help me in knowing as to which value (TDDFT or CIS) to consider for assigning UV-VIS spectra computationally. > > thanking you. > ashu From owner-chemistry@ccl.net Fri Feb 25 03:08:00 2011 From: "Marcel Swart marcel.swart]=[icrea.cat" To: CCL Subject: CCL:G: HF or B3LYP for a transition state of an SN2 Rx Message-Id: <-44017-110225030413-29050-9286R8MfinECTAe7UrbDWQ() server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-2-338807651 Date: Fri, 25 Feb 2011 09:04:31 +0100 Mime-Version: 1.0 (Apple Message framework v1082) Sent to CCL by: Marcel Swart [marcel.swart ~~ icrea.cat] --Apple-Mail-2-338807651 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Have a look at M. Swart, M. Sol=E0 and F.M. Bickelhaupt "Energy landscapes of nucleophilic substitution reactions: A comparison = of density functional theory and coupled cluster methods" J. Comput. Chem. 2007, 28, 1551-1560 where you can find all the information you need. Marcel On 24 Feb 2011, at 22:29, Raphael Martinez = raphaelmartinez1983++gmail.com wrote: > Hello everyone,=20 > I am new in the computational chemistry field, and I need to calculate = the transition state of an SN2 reaction. I have access top Gaussian 03. = I was wondering which method is better in order to identify the = Delta-Enthalpy of the transition state, HF or B3LYP /(with 6-31g*). Also = why? > Thanks for the help =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional Universitat de Girona Facultat de Ci=E8ncies Campus Montilivi 17071 Girona Catalunya (Spain) tel +34-972-418861 fax +34-972-418356 e-mail marcel.swart*icrea.cat marcel.swart*udg.edu web http://www.marcelswart.eu =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --Apple-Mail-2-338807651 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 Have = a look at

M. Swart, M. Sol=E0 and F.M. Bickelhaupt
"Energy landscapes of = nucleophilic substitution reactions: A comparison of density functional = theory and coupled cluster methods"
J. Comput. = Chem. 2007, 28, = 1551-1560

where you can find all the = information you = need.

Marcel

On 24 Feb = 2011, at 22:29, Raphael Martinez raphaelmartinez1983++gmail.com = wrote:

Hello = everyone, 
I am new = in the computational chemistry field, and I need to calculate the = transition state of an SN2 reaction. I have access top Gaussian 03. I = was wondering which method is better in order to identify the = Delta-Enthalpy of the transition state, HF or B3LYP /(with 6-31g*). Also = why?
Thanks for the help


=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

Institut de Qu=EDmica = Computacional
Universitat de Girona

Facultat de Ci=E8ncies
Campus = Montilivi
17071 Girona
Catalunya = (Spain)

tel
+34-972-418861
fax
+34-972-418356
e-mailmarcel.swart*udg.edu




= --Apple-Mail-2-338807651-- From owner-chemistry@ccl.net Fri Feb 25 03:54:01 2011 From: "Eli Lam elizabeth.shlam_._gmail.com" To: CCL Subject: CCL:G: Gaussian03 optimisation problems Message-Id: <-44018-110225032651-7292-c4QkJcc6cBvL6QEQ0sYkBA=server.ccl.net> X-Original-From: "Eli Lam" Date: Fri, 25 Feb 2011 03:26:48 -0500 Sent to CCL by: "Eli Lam" [elizabeth.shlam^_^gmail.com] Dear Dave, I've tried to modify as advised and it works! And I have also tried to use the keyword opt(readfc) and opt(calcfc) and for some cases it works for the re-optimisation too. Thank you so much! Best regards, Eli > "Close, David M. CLOSED*o*mail.etsu.edu" wrote: > > Sent to CCL by: "Close, David M." [CLOSED+*+mail.etsu.edu] > Eli: > If you have a viewer you should animate the frequency that has the imaginary eigenvector. This represents a vibration in the direction that will lead to the true minimum. The trick is to > make a few changes in the X Y Z coordinates listed under the frequency and redo the calculation. Some trial and error may be needed, but it is not too difficult to displace the vibration off of the local minima and get it to move towards the true minima. Try this. If you don't succeed, send me the X Y Z coordinates and I will give it a try. > Regards, Dave Close. > > > -----Original Message----- > > From: owner-chemistry+closed==etsu.edu * ccl.net [mailto:owner-chemistry+closed==etsu.edu * ccl.net] On Behalf Of Eli Lam elizabeth.shlam!A!gmail.com > Sent: Saturday, February 19, 2011 8:27 PM > To: Close, David M. > Subject: CCL: Gaussian03 optimisation problems > > > Sent to CCL by: "Eli Lam" [elizabeth.shlam() gmail.com] > Hi, > > Recently when I do optimisation of a organometallic molecules, I've found an imaginary frequency in > the optimized structure, I know it would mean that the structure is not a minima in the PES. But how > should I optimise again to find the true minimum? Thanks! > > Elihttp://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 Fri Feb 25 08:18:00 2011 From: "ashutosh gupta ashu1809() gmail.com" To: CCL Subject: CCL: UV-VIS spectra values obtained computationally are different (TDDFT & CIS) for different concentrations Message-Id: <-44019-110225081720-3525-ed08AOL+UMvUd2a7tvtIdQ * server.ccl.net> X-Original-From: ashutosh gupta Content-Type: multipart/alternative; boundary=20cf3054a2e9a69a93049d1b2589 Date: Fri, 25 Feb 2011 18:47:08 +0530 MIME-Version: 1.0 Sent to CCL by: ashutosh gupta [ashu1809]-[gmail.com] --20cf3054a2e9a69a93049d1b2589 Content-Type: text/plain; charset=ISO-8859-1 Hi Andrei, Thank you very much for such a nice and lucid explanation. indeed the extinction coefficients of bands at 400 nm has low intensity (100 units) whereas at 280nm, it has value of some 30,000 units. What i am worried about is that TDDFT is considered to better than CIS. my TDDFT results are showing values around 400 nm but not at 280 nm, whereas CIS is giving the same as 280 nm. could it be that i am missing out higher level of excitation in case of TDDFT (however S1,S2,S3 values are 399,394,356 nm(s)). why CIS & TDDFT results are varying so much. Is it something to do with theory part? thanks again for your kind reply and your help. thanks indeed. best wishes& kind regards. ashu. 2011/2/25 asp asp99++yandex.ru > > Sent to CCL by: asp [asp99*|*yandex.ru] > Hi, Ashu, > it looks like that some king of interaction is taking place in your system. > It could be assosiation of compound molecules or formation of complexes with > the solvent leading to concentartion-dependent absorption band position. If > there is an equlibrium in the solution, then it is likely that at lower > concentation you will have more unreacted (isolated) molecules of the > compound. The results of calculation also give you values for an isolated > molecule, so it is more reasonable to compare values obtatined at lower > concentrations. > > However, there is a possibility that you are regestering to completly > separete bands corresponding to different electron transitions in the > molecule. What are the extinction coefficients for your experimental bands? > It is likely that the band at 400 nm has low intensity and you simply could > not detect it at low concentration. > How this helps to figure things out, > Andrei > > 25.02.2011, 05:05, "ashutosh gupta ashu1809 : gmail.com" ccl.net>: > > Hi,Greetings. > > > > I have a UV-Vis spectra of a compound at different concentrations. (10-2M > to 10-5M) > > > > At higher concentration( ~10-2 M), the experimental peaks match well with > TDDFT/6-31+G* values (400nm), whereas at lower concentration (~10-5M), the > experimental peaks match with CIS/6-31+G* values (280 nm). > > > > The IR values obtained experimentally and computationally matches well > (for DFT values). > > > > I would be thankful if someone could help me in knowing as to which value > (TDDFT or CIS) to consider for assigning UV-VIS spectra computationally. > > > > thanking you. > > ashu> > > --20cf3054a2e9a69a93049d1b2589 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Andrei,
Thank you very much for such a nice and lucid explanation.

indeed the=A0extinction coefficients of bands at 40= 0 nm has low intensity (100 units) =A0whereas at 280nm, it has value of som= e 30,000 units.

What i am worried about is that TDDFT is considered to = better than CIS.
my TDDFT results are showing values around 400 n= m but not at 280 nm, whereas CIS is giving the same as 280 nm.

could it be that i am missing out higher level of excitation= in case of TDDFT (however S1,S2,S3 values are 399,394,356 nm(s)).

why CIS & TDDFT results are varying so much. Is it som= ething to do with theory part?

thanks again for your kind reply and your help.

thanks indeed.
best wishes& kind regards.
ashu.

2011/2/25 asp asp99+= +yandex.ru <owner-chemistry|ccl.net><= br>

Sent to CCL by: asp [asp99*|*yandex.ru]
Hi, Ashu,
it looks like that some king of interaction is taking place in your system.= It could be assosiation of compound molecules or formation of complexes wi= th the solvent leading to concentartion-dependent absorption band position.= If there is an equlibrium in the solution, then it is likely that at lower= concentation you will have more unreacted (isolated) molecules of the comp= ound. The results of calculation also give you values for an isolated molec= ule, so it is more reasonable to compare values obtatined at lower concentr= ations.

However, there is a possibility that you are regestering to completly separ= ete bands corresponding to different electron transitions in the molecule. = What are the extinction coefficients for your experimental bands? It is lik= ely that the band at 400 nm has low intensity and you simply could not dete= ct it at low concentration.
How this helps to figure things out,
Andrei

25.02.2011, 05:05, "ashutosh gupta ashu1809 : gmail.com" <owner-chemistry^ccl.net>:
> Hi,Greetings.
>
> I have a UV-Vis spectra of a compound at different concentrations. (10= -2M to 10-5M)
>
> At higher concentration( ~10-2 M), the experimental peaks match well w= ith TDDFT/6-31+G* values (400nm), whereas at lower concentration (~10-5M), = the experimental peaks match with CIS/6-31+G*=A0values (280 nm).
>
> The IR values obtained experimentally and computationally matches well= (for DFT values).
>
> I would be thankful if someone could help me in knowing as to which va= lue (TDDFT or CIS) to consider for assigning UV-VIS spectra computationally= .
>
> thanking you.
> ashu



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--20cf3054a2e9a69a93049d1b2589-- From owner-chemistry@ccl.net Fri Feb 25 09:28:00 2011 From: "Patricia Richardson patricia.richardson(~)ed.ac.uk" To: CCL Subject: CCL: UV-VIS spectra values obtained computationally are different Message-Id: <-44020-110225092507-4504-wXyCtGP3xji3lkSM5J/xXA,,server.ccl.net> X-Original-From: "Patricia Richardson" Date: Fri, 25 Feb 2011 09:24:57 -0500 Sent to CCL by: "Patricia Richardson" [patricia.richardson-.-ed.ac.uk] Hi Ashu, CIS tends to systematically overestimate excitation energies, and so people often scale them by a factor of 0.72. See Broo and Holmen for more details. A. Broo and A. Holmen, Calculations and characterization of the electronic spectra of DNA bases based on ab initio MP2 geometries of different tautomeric forms, J. Phys. Chem. 101 (1997), pp. 3589?3600 Scaling your CIS calculated transition energy (280 nm) gives 389 nm, much closer to the TDDFT value. Of course, you should always check that the CIS and TDDFT transitions are giving the same electronic transitions - same orbitals, similar oscillator strengths etc. Certainly high concentrations can lead to the formation of aggregates in solution, which may have a markedly different absorption spectrum than the monomer species. However, could it be that the band at 400 nm simply has a low extinction coefficient, and so you don't see it at lower concentrations? You should be able to measure the extinction coefficients of each band from from your UV-VIS spectra, and use the Beer-Lambert law to get an idea of the concentration/path-length range at which they will be observable. The calculations will also give you the oscillator strength, which is proportional to the extinction coefficient (see Hollas - Modern Spectroscopy). So if there is a big differential between the oscillator strength of your UV peaks and that at 400 nm, that may explain it. I'm assuming you still see the UV peaks in your high concentration spectrum, though they may be completely saturated? In the experimental UV-VIS spectra you'll see transitions to other higher energy electronic states, and you can usually set the number of states you'd like to calculate in your input file, so you can span the full experimental range, which you might need to do if you aren't seeing the UV bands in your TDDFT calculation. Hope this is helpful. Best wishes, Tricia From owner-chemistry@ccl.net Fri Feb 25 11:37:00 2011 From: "Serge Gorelsky gorelsky++gmail.com" To: CCL Subject: CCL:G: help with guassian Message-Id: <-44021-110225113521-25640-lBhT2yEEg1DIZLWeRlgp1g[A]server.ccl.net> X-Original-From: Serge Gorelsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 25 Feb 2011 11:34:57 -0500 MIME-Version: 1.0 Sent to CCL by: Serge Gorelsky [gorelsky]_[gmail.com] Hi Ricardo, the way to do this is by using the fragment orbital approach where you can get p_sigma and p_pi overlap integrals for the interacting donor-acceptor orbital pairs. Gaussian and other QM programs typically give you only overlap integrals between BASIS FUNCTIONS. However, for your applications, one has to get overlap integrals between FRAGMENT ORBITALS. AOMix (see www.sg-chem.net) will process Gaussian output files to give you the overlap integrals between FRAGMENT ORBITALS. Best, S.G. On Thu, Feb 24, 2011 at 9:02 PM, Ricardo Lewis Lambo luiz_iniciante-#-hotmail.com wrote: > > Sent to CCL by: "Ricardo Lewis Lambo" [luiz_iniciante_-_hotmail.com] > Hello CCL Net, >              Gaussian novice here. I need to calculate the p_sigma and p_pi overlap integrals for various alkali metal/rare gas combinations and would like to use the (n+1)p rare gas orbitals and the wave functions for the ground state unoccupied metal valence np orbitals. > > Is it possible to do such a calculation with Gaussian, i.e. calculate the p_sigma and p_pi overlap integrals? If so, does anyone have an example of such code or at least the key command lines. We do not have Young or Foresman and Frisch at our university library, and of all the pages I have seen online about Gaussian none of them deal specifically with the question of overlap integrals. Would it be better then for me to use a different quantum chemistry package? > > Regards, >        Ricardo>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > -- Best regards,   Serge Gorelsky From owner-chemistry@ccl.net Fri Feb 25 12:15:01 2011 From: "James McDonagh jm222||st-andrews.ac.uk" To: CCL Subject: CCL:G: Specifying a new solvent in G03 Message-Id: <-44022-110225102342-20257-EmlQljclorNDOsyaeQrt3A+*+server.ccl.net> X-Original-From: "James McDonagh" Date: Fri, 25 Feb 2011 10:23:39 -0500 Sent to CCL by: "James McDonagh" [jm222+*+st-andrews.ac.uk] Hi all, I am trying carry out solvation free energy calculations in Gaussian 03 (G03). I wish to use n-Octanol as one of the solvents, I am aware that G09 has parameters for this, however G03 does not according to it's manual. I have read conflicting reports about been able to specify enough parameters to define a new solvent in G03, can anyone clarify for me whether this is possible? If it is possible could you recommend a reliable source of information on how to do this? Many thanks in advance, James