From owner-chemistry@ccl.net Tue Jul 12 01:47:01 2016 From: "Visvaldas K. coyote_v2002+*+yahoo.com" To: CCL Subject: CCL: cyclooctane Cartesians Message-Id: <-52292-160712013639-27222-uOko+x2B0wxBIJep1HWuVw#server.ccl.net> X-Original-From: "Visvaldas K." Content-Type: multipart/alternative; boundary="----=_Part_1509019_1288040971.1468301496011" Date: Tue, 12 Jul 2016 05:31:35 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: "Visvaldas K." [coyote_v2002{}yahoo.com] ------=_Part_1509019_1288040971.1468301496011 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Check out the "computed 3D structure" on NIST page http://webbook.nist.gov/cgi/cbook.cgi?ID=3DC292648 Vis =20 =20 Dear CCL-ers, Does anyone have (or know where I can get) the optimized geometry for cyclo= octane in its lowest-energy conformation? =C2=A0Preferably in Cartesian coo= rdinates. =C2=A0(I'm not having good luck in getting the correct geometry f= rom input files that I make). =C2=A0I need the hydrogen atoms' coordinates = as well as the carbon atoms' coordinates. [I did find the following paper online, but it's $40.00 and I don't know wh= ether it has what I'm looking for or not.]Olga V. Dorofeeva, Vladimir S. Ma= stryukov, Norman L. Allinger, Arne AlmenningenJ. Phys. Chem., 1985, 89 (2),= pp 252=E2=80=93257 Regards,--David Shobe ------=_Part_1509019_1288040971.1468301496011 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Check out the "computed 3D structure" on NIST page


Vis



<= div style=3D"display: block;" id=3D"yui_3_16_0_ym19_1_1468301406032_3271" c= lass=3D"yahoo_quoted">


Dear CCL-ers,

Does anyone have (or know where I can get) the optimized geometry for cyc= looctane in its lowest-energy conformation?  Preferably in Cartesian c= oordinates.  (I'm not having good luck in getting the correct geometry= from input files that I make).  I need the hydrogen atoms' coordinate= s as well as the carbon atoms' coordinates.

[I did find the following paper online= , but it's $40.00 and I don't know whether it has what I'm looking for or n= ot.]
Olga V.= Dorofeeva, Vladimir S. Mastryukov, Norman L. Allinger, Arne Almenningen
J.= Phys. Chem., 1985, 89 (2), pp 252=E2=80=93257

Regards,
--David Shobe



------=_Part_1509019_1288040971.1468301496011-- From owner-chemistry@ccl.net Tue Jul 12 02:21:00 2016 From: "Cristian Bologa CBologa!^!salud.unm.edu" To: CCL Subject: CCL: cyclooctane Cartesians Message-Id: <-52293-160712020243-6017-ABF2GAhZuZHbPu87plEQGA#,#server.ccl.net> X-Original-From: Cristian Bologa Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_83afdbb6e34b497ba6b76127fd6c61a5UHXCHMBX10hscadunmedu_" Date: Tue, 12 Jul 2016 06:02:35 +0000 MIME-Version: 1.0 Sent to CCL by: Cristian Bologa [CBologa#%#salud.unm.edu] --_000_83afdbb6e34b497ba6b76127fd6c61a5UHXCHMBX10hscadunmedu_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 RGF2aWQsDQoNCllvdSBzaG91bGQgYmUgYWJsZSB0byBnZXQgb3B0aW1pemVkIENhcnRlc2lhbiBj b29yZGluYXRlcyBmb3IgY3ljbG9vY3RhbmUgYXQgZGlmZmVyZW50IGxldmVscyBvZiB0aGVvcnkg YW5kIHdpdGggZGlmZmVyZW50IGJhc2lzIHNldHMgZnJvbSBoZXJlOg0KDQpodHRwOi8vY2NjYmRi Lm5pc3QuZ292L2dlb20xeC5hc3ANCg0KSnVzdCB0eXBlIEM4SDE2IGluIHRoZSBjaGVtaWNhbCBm 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<-52294-160711230217-24958-YAdytCI983/r/Rr7y42Rzw _ server.ccl.net> X-Original-From: "Chunlin WANG" <623698744|,|qq.com> Date: Mon, 11 Jul 2016 23:02:15 -0400 Sent to CCL by: "Chunlin WANG" [623698744 .. qq.com] Dear CCL-ers, I want to get the potential energy curve between 2 excited atoms, for example, two H both at the first excited state, H(1)-H(1)(what's more H(n)-H(m) is also wanted, n,m<=3). I have tried to treat such systerm as a double excited dimer, with GAUSSIAN (eomccsd). But from the result, I find the double excited conditions but I can not know the excited states of the dimer corresponding to which states of the atom H. I don't know this method is suitable or not. Maybe there should be beter model or software for such problems. I appreciate your help.Thanks. Regards WANG Chunlin From owner-chemistry@ccl.net Tue Jul 12 08:33:00 2016 From: "Colin Lam lam=-=chem.ucla.edu" To: CCL Subject: CCL: cyclooctane Cartesians Message-Id: <-52295-160712025832-17458-5dsmcS9Ycgl/xCm0IsNF1w**server.ccl.net> X-Original-From: Colin Lam Content-Type: multipart/alternative; boundary="Apple-Mail=_267ED866-FCEB-4390-96A3-D1970CA194CD" Date: Mon, 11 Jul 2016 23:58:28 -0700 Mime-Version: 1.0 (Mac OS X Mail 9.3 \(3124\)) Sent to CCL by: Colin Lam [lam{=}chem.ucla.edu] --Apple-Mail=_267ED866-FCEB-4390-96A3-D1970CA194CD Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi David, The lowest-energy conformer of cyclooctane is the boat-chair. K. B. = Wiberg has a paper on a QM computational study of cycloalkane conformers = > from C7 to C10: J. Org. Chem. 2003, 68, 9322. The SI contains the XYZ = coordinates of the different conformers and transition structures for = interconversion between conformers. Regards, Colin > On 11 Jul 2016, at 11:02 PM, Cristian Bologa CBologa!^!salud.unm.edu = wrote: >=20 > David, > =20 > You should be able to get optimized Cartesian coordinates for = cyclooctane at different levels of theory and with different basis sets = > from here: > =20 > http://cccbdb.nist.gov/geom1x.asp > =20 > Just type C8H16 in the chemical formula input box and click the Submit = button. > =20 > Regards, > Cristian > =20 > Cristian Bologa, Ph.D. > Research Professor, > Div. of Translational Informatics,=20 > Dept. of Internal Medicine, > Univ. of New Mexico, School of Medicine, > Innovation Discovery&Training Center, MSC09 5025,=20 > 700 Camino de Salud NE, Albuquerque, NM 87131 > tel: +1 (505) 925-7534 > fax:+1 (505) 925-7625 > =20 > =C2=A0 <> > From: owner-chemistry+cbologa=3D=3Dsalud.unm.edu(0)ccl.net = = [mailto:owner-chemistry+cbologa=3D=3Dsalud.unm.edu(0)ccl.net = ] On Behalf = Of David Shobe avidshobe=3D=3D=3Dyahoo.com > Sent: Monday, July 11, 2016 6:54 PM > To: Cristian Bologa > > Subject: CCL: cyclooctane Cartesians > =20 > Dear CCL-ers, > =20 > Does anyone have (or know where I can get) the optimized geometry for = cyclooctane in its lowest-energy conformation? Preferably in Cartesian = coordinates. (I'm not having good luck in getting the correct geometry = > from input files that I make). I need the hydrogen atoms' coordinates = as well as the carbon atoms' coordinates. > =20 > [I did find the following paper online, but it's $40.00 and I don't = know whether it has what I'm looking for or not.] > Olga V. Dorofeeva, Vladimir S. Mastryukov, Norman L. Allinger, Arne = Almenningen > J. Phys. Chem., 1985, 89 (2), pp 252=E2=80=93257 > =20 > Regards, > --David Shobe --Apple-Mail=_267ED866-FCEB-4390-96A3-D1970CA194CD Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Hi David,

The lowest-energy conformer of cyclooctane is the boat-chair. = K. B. Wiberg has a paper on a QM computational study of cycloalkane = conformers from C7 to C10: J. Org. Chem. 2003, 68, 9322. The SI contains = the XYZ coordinates of the different conformers and transition = structures for interconversion between conformers.

Regards,
Colin

On = 11 Jul 2016, at 11:02 PM, Cristian Bologa CBologa!^!salud.unm.edu <owner-chemistry(0)ccl.net> wrote:

David,
 
You should be able to = get optimized Cartesian coordinates for cyclooctane at different levels = of theory and with different basis sets from here:
 
 
Just type C8H16 in the = chemical formula input box and click the Submit button.
 
Regards,
Cristian
 
Cristian Bologa, = Ph.D.
Research Professor,
Div. of = Translational Informatics, 
Dept. of = Internal Medicine,
Univ. of New Mexico, School of = Medicine,
Innovation Discovery&Training Center, MSC09 = 5025, 
700= Camino de Salud NE, Albuquerque, NM 87131
tel: +1 (505) = 925-7534
fax:+1 (505) 925-7625
 
From: owner-chemistry+cbologa=3D=3Dsalud.unm.edu(0)ccl.net [mailto:owner-chemistry+cbologa=3D=3Dsalud.unm.edu(0)ccl.net]<= span class=3D"Apple-converted-space"> On = Behalf Of David = Shobe avidshobe=3D=3D=3Dyahoo.com
Sent: Monday, July 11, 2016 6:54 = PM
To: Cristian Bologa <CBologa(0)salud.unm.edu>
Subject: CCL: cyclooctane = Cartesians
 
Dear CCL-ers,
 
Does anyone have = (or know where I can get) the optimized geometry for cyclooctane in its = lowest-energy conformation?  Preferably in Cartesian coordinates. =  (I'm not having good luck in getting the correct geometry from = input files that I make).  I need the hydrogen atoms' coordinates = as well as the carbon atoms' coordinates.
 
[I did find the = following paper online, but it's $40.00 and I don't know whether it has = what I'm looking for or not.]
Olga V. Dorofeeva, = Vladimir S. Mastryukov, Norman L. Allinger, Arne Almenningen
J. Phys. Chem., = 1985, 89 (2), pp 252=E2=80=93257
 
Regards,
--David = Shobe

= --Apple-Mail=_267ED866-FCEB-4390-96A3-D1970CA194CD-- From owner-chemistry@ccl.net Tue Jul 12 12:02:01 2016 From: "Javier Cerezo jcb1 _ um.es" To: CCL Subject: CCL:G: GAUSSIAN: Displacement of normal modes in the electronic excited state Message-Id: <-52296-160712113017-12813-qcQqvXOXLkucMGqhMnWLkw**server.ccl.net> X-Original-From: Javier Cerezo Content-Type: multipart/alternative; boundary="------------050405070101080503080300" Date: Tue, 12 Jul 2016 17:30:07 +0200 MIME-Version: 1.0 Sent to CCL by: Javier Cerezo [jcb1=-=um.es] This is a multi-part message in MIME format. --------------050405070101080503080300 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: quoted-printable Dear Shahnawaz, Indeed, the displacement vector (along with the Duschinsky matrix) are=20 used to evaluate the FC integrals, so the right way to proceed is to=20 compute such parameters directly from their definition in terms of the=20 normal mode matrices and structural displacements (see, e.g,=20 http://link.aip.org/link/?JCP/41/3453/1 -Eq. 11). Such analysis can be done with a variety of programs, as, for instance,=20 FCclasses (http://www.pi.iccom.cnr.it/fcclasses), which can interface to = a variaty of QM codes (see https://github.com/jcerezochem/fcc_tools). In = Gaussian09, you can also get the shift vector as explained in the manual = (http://www.gaussian.com/g_tech/g_ur/k_freq.htm). Take a look to the=20 option PrtMat=3D/N/ from Freq=3DReadFC (it seems that PrtMat=3D2 is what = you=20 want). Javier El 11/07/16 a las 17:48, Shahnawaz Rather shahcmt2009()gmail.com escribi=F3= : > Sent to CCL by: "Shahnawaz Rather" [shahcmt2009(-)gmail.com] > Hi Everyone, > I am interested in finding the displacement of all the IR active mode= s in the excited state. For that I started with ground state optimization= and frequency calculations followed by excited state optimization of the= desired electronic state and the frequency calculation of the excited st= ate. I am not sure how to proceed ahead in order to find the displacement= of the IR modes in the excited state? I can probably perform a Franck-Co= ndon analysis and read information from check point files to calculate th= e absorption spectrum and the corresponding Franck-Condon factors for the= 1-0 and 0-0 transition of a particular normal mode, whose ratio will giv= e me the displacement through Huang-Rhys factor and then repeat this for = every other mode. But at the same time, I believe that the Franck-Condon = analysis calculates Franck-Condon factors from the displacement of the no= rmal modes in the excited state itself, so why not to locate those displa= cement values directly. My question is, if ! > whatever I wrote above is true, where can I exactly find these displa= cement values for the normal modes in the excited state??? > =20 > Your immediate response will be highly appreciated. > > Thanks > Shahnawaz Rather > shahcmt2009**gmail.com > Princeton University, USA > > > > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please chang= e=> > --=20 Javier CEREZO BASTIDA PostDoc Researcher ICCOM-CNR, UOS di Pisa 56124 PISA (ITALY) --------------050405070101080503080300 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: 8bit Dear Shahnawaz,

Indeed, the displacement vector (along with the Duschinsky matrix) are used to evaluate the FC integrals, so the right way to proceed is to compute such parameters directly from their definition in terms of the normal mode matrices and structural displacements (see, e.g, http://link.aip.org/link/?JCP/41/3453/1  -Eq. 11).

Such analysis can be done with a variety of programs, as, for instance, FCclasses (http://www.pi.iccom.cnr.it/fcclasses), which can interface to a variaty of QM codes (see https://github.com/jcerezochem/fcc_tools). In Gaussian09, you can also get the shift vector as explained in the manual (http://www.gaussian.com/g_tech/g_ur/k_freq.htm). Take a look to the option PrtMat=N from Freq=ReadFC (it seems that PrtMat=2 is what you want).

Javier

El 11/07/16 a las 17:48, Shahnawaz Rather shahcmt2009()gmail.com escribió:
Sent to CCL by: "Shahnawaz  Rather" [shahcmt2009(-)gmail.com]
Hi Everyone,
 I am interested in finding the displacement of all the IR active modes in the excited state. For that I started with ground state optimization and frequency calculations followed by excited state optimization of the desired electronic state and the frequency calculation of the excited state. I am not sure how to proceed ahead in order to find the displacement of the IR modes in the excited state? I can probably perform a Franck-Condon analysis and read information from check point files to calculate the absorption spectrum and the corresponding Franck-Condon factors for the 1-0 and 0-0 transition of a particular normal mode, whose ratio will give me the displacement through Huang-Rhys factor and then repeat this for every other mode. But at the same time, I believe that the Franck-Condon analysis calculates Franck-Condon factors from the displacement of the normal modes in the excited state itself, so why not to locate those displacement values directly. My question is, if !
 whatever I wrote above is true, where can I exactly find these displacement values for the normal modes in the excited state???
 
Your immediate response will be highly appreciated.

Thanks
Shahnawaz Rather
shahcmt2009**gmail.com
Princeton University, USAE-mail to subscribers: CHEMISTRY . ccl.net or use:
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--
Javier CEREZO BASTIDA
PostDoc Researcher
ICCOM-CNR, UOS di Pisa
56124 PISA (ITALY)
--------------050405070101080503080300-- From owner-chemistry@ccl.net Tue Jul 12 22:23:01 2016 From: "Raphael Martinez raphaelmartinez1983[*]gmail.com" To: CCL Subject: CCL: Radical-to-cation calculation Gaussian Message-Id: <-52297-160712222017-22172-k1JAt8hBLIC38TY5397JSw]~[server.ccl.net> X-Original-From: "Raphael Martinez" Date: Tue, 12 Jul 2016 22:20:16 -0400 Sent to CCL by: "Raphael Martinez" [raphaelmartinez1983^gmail.com] Dear all, Please forgive me in advance if my question is too simple. I have an organic molecule, it is a hydrocarbon which contains a radical. I have optimized the geometry of the structure and calculated its energy using DFT. Now, I am planning to calculate the exact same molecule, but in its cationic form, so minus 1 electron. I need to place this to molecules relative to each other in a reaction path. In order for me to be able to compared the energies between the two structures, do I have to add the energy of an electron to the cationic form?, or do I have to do something else is order to be able to compared them? Or I do not need to do anything at all? Thanks for the help.