From owner-chemistry@ccl.net Tue Jun 12 03:32:00 2012 From: "Jean Jules FIFEN julesfifen#gmail.com" To: CCL Subject: CCL: Contribution from vibrational motion Message-Id: <-47069-120612032914-3009-1mOhaR9xRJlXPGuIauOYwQ(a)server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=20cf300fb21d03f68904c2416c70 Date: Tue, 12 Jun 2012 08:29:07 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen-x-gmail.com] --20cf300fb21d03f68904c2416c70 Content-Type: text/plain; charset=ISO-8859-1 Taking the zero of the energy at the bottom of the well does not take into account the zero-point energy correction (ZPE), which arises rigorously > from the Heisenberg indetermination principle (the Irreducibility of the quantum fluctuations). Obviously, such a correction is sometimes negligible, but it is more reliable from the principle. Thus, reliable computations may take the zero of the energy at the first vibrational level. However, when doing otherwise, there is no difference when the suitable translation is respected. On 10 June 2012 08:14, bonoit bonoit bonoit_10/ayahoo.fr < owner-chemistry*|*ccl.net> wrote: > > Sent to CCL by: "bonoit bonoit" [bonoit_10-*-yahoo.fr] > Dear CClers, > For calculating the Contribution from vibrational motion, we have two ways > to choose the zero of energy: either the bottom of the internuclear > potential energy well, or the first vibrational level. > What is the difference between them? > When can we use one and the other? and why? > Regards > Bonoit> > > -- Jules. --20cf300fb21d03f68904c2416c70 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Taking the zero of the energy at the bottom of the w= ell does not take into account the zero-point energy correction (ZPE), whic= h arises rigorously from the Heisenberg indetermination principle (the Irre= ducibility of the quantum fluctuations). Obviously, such a correction is so= metimes negligible, but it is more reliable from the principle. Thus, relia= ble computations may take the zero of the energy at the first vibrational l= evel. However, when doing otherwise, there is no difference when the suitab= le translation is respected.

On 10 June 2012 08:14, bonoit bonoit = bonoit_10/ayahoo.fr <owner-chemistry*|*ccl.net> wrote:

Sent to CCL by: "bonoit =A0bonoit" [bonoit_10-*-yahoo.fr]
Dear CClers,
For calculating the Contribution from vibrational motion, we have two ways = to choose the zero of energy: either the bottom of the internuclear potenti= al energy well, or the first vibrational level.
What is the difference between them?
When can we use one and the other? and why?
Regards
Bonoit



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Jules.=

--20cf300fb21d03f68904c2416c70-- From owner-chemistry@ccl.net Tue Jun 12 07:29:00 2012 From: "Cory Pye cpye]|[ap.smu.ca" To: CCL Subject: CCL: Contribution from vibrational motion Message-Id: <-47070-120612072536-5653-z8IrXOTAUBlwVEMiamJnNQ .. server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 12 Jun 2012 08:35:51 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye#,#ap.smu.ca] Bonoit, Normally, the vibrational partition function is taken relative to the lowest vibrational energy state. However, the "zero" of the electronic energy is taken at the bottom of the well. There is a small exponential term which takes care of the difference in choice of zero energy. -Cory On Tue, 12 Jun 2012, Jean Jules FIFEN julesfifen#gmail.com wrote: > Taking the zero of the energy at the bottom of the well does not take into > account the zero-point energy correction (ZPE), which arises rigorously > > from the Heisenberg indetermination principle (the Irreducibility of the > quantum fluctuations). Obviously, such a correction is sometimes > negligible, but it is more reliable from the principle. Thus, reliable > computations may take the zero of the energy at the first vibrational > level. However, when doing otherwise, there is no difference when the > suitable translation is respected. > > On 10 June 2012 08:14, bonoit bonoit bonoit_10/ayahoo.fr < > owner-chemistry]~[ccl.net> wrote: > > > > > Sent to CCL by: "bonoit bonoit" [bonoit_10-*-yahoo.fr] > > Dear CClers, > > For calculating the Contribution from vibrational motion, we have two ways > > to choose the zero of energy: either the bottom of the internuclear > > potential energy well, or the first vibrational level. > > What is the difference between them? > > When can we use one and the other? and why? > > Regards > > Bonoit> > > > > > > > -- > Jules. > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye{:}crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Tue Jun 12 09:36:00 2012 From: "John McKelvey jmmckel~!~gmail.com" To: CCL Subject: CCL: "Quasi free rotors" Message-Id: <-47071-120612093018-31373-oL06UMTwNkbLmtknmmkdIA- -server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 12 Jun 2012 09:30:06 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel-,-gmail.com] Folks, Hypothetical: Suppose that one has methyl-benzene (toluene) and one can not get the maximum displacement in a geometry optimization to converge due to the "spinning methyl group", but the energy, MAX & RMS gradients and RMS displacement have converged. Now the target is then to do the IR frequencies. I might suppose or hope that in an ideal case that the lowest frequency above the usual first 6, though probably negative, would be this CH3 rotation, and the remainder of the freqs would be real and close to these when the compete optimization might be achieved, would be useful. Too much wishful thinking? The real application is a metal complex with a loosely bound solvent molecule, and the experimental IR spectrum is known, and is otherwise analogous to the above with respect to max displacement. Reasonable to depend upon the computed IR freqs other than the suspect low energy mode? Many thanks! John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel(!)gmail.com From owner-chemistry@ccl.net Tue Jun 12 11:14:00 2012 From: "Kaliappan Muthukumar muthukumar2k3[]gmail.com" To: CCL Subject: CCL: Call for papers : Doped Nano-structures For Energy and Electronic Applications Message-Id: <-47072-120612051333-9661-ETc9kVj+VqHwexQEb/3djg##server.ccl.net> X-Original-From: Kaliappan Muthukumar Content-Type: multipart/alternative; boundary=047d7b10d1f100e30f04c242e122 Date: Tue, 12 Jun 2012 11:13:25 +0200 MIME-Version: 1.0 Sent to CCL by: Kaliappan Muthukumar [muthukumar2k3 ~ gmail.com] --047d7b10d1f100e30f04c242e122 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL ers, We have the pleasure to inform you that we are organizing a (peer-reviewed) themed issue entitled 'Doped Nano-Materials for Energy and Electronic Applications' to be published in 'Advanced Chemistry Letters'. A journal published by the American Scientific Publishers, this December. If your research field (both experimental and theoretical) matches any of the following themes 1) Doped Nanomaterials for Energy (Photovoltaic and Electrochemical Applications) and Electronic Devices, 2) Synthesis, Growth, Fabrication and Processing of Functional Materials, 3) Characterization of Doped Nanomaterials and Molecules on Surfaces, 4) Dopants, Vacancies and Defects in Surfaces and Interfaces, 5) Further Studies Advancing and Understanding the Function of Doped Materials. we welcome your submission (Article /communication /Review) to this issue. The last date for the submission of manuscript is 15th September 2012, and i suggest you the following webpage http://www.aspbs.com/acl.htm for further information and instructions for the preparation of manuscripts. According to the journal policy, all research papers will be peer-reviewed by experts in the field and we would be grateful if you would inform us about your intention to submit well in advance. Further, If you need more information please do not hesitate to contact me (kaliappan.muthukumar(~)gmail.com) and we look forward to hearing from you. Best regards, Dr. Muthukumar and Dr. Larsson -- -- Dr. Muthukumar Kaliappan, Goethe University, Frankfurt Am Main Germany Email : Kaliappan.Muthukumar(~)gmail.com "To get Profit without risk, Experience without danger & Reward without Hard work is as impossible as it is to live without being born" -'Anonymous' --047d7b10d1f100e30f04c242e122 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCL ers,

We have the p= leasure to inform you that we are organizing
a (peer-review= ed) themed issue entitled 'Doped Nano-Materials for Energy and Electron= ic
Applications' to be published in 'Advanced Chemistry Letters'.<= br>A journal published by the American Scientific Publishers, this December= .

If your research field (both experim= ental and theoretical)
matches any of the following themes=A0

=
1) Doped Nanomaterials for Energy (Photovoltaic and Electrochemi= cal
Applications) and Electronic Devices,

2) Synthesis, Growth,= Fabrication and Processing of Functional Materials,

3) Cha= racterization of Doped Nanomaterials and Molecules on Surfaces,

<= div> 4) Dopants, Vacancies an= d Defects in Surfaces and Interfaces,

5) Further Studies Advancing and Understanding= the Function of Doped
Materials.

we welcome your submission=A0(Article /communication /Review)=A0to thi= s issue.=A0

The last date for the submission of ma= nuscript=A0
is 15th September 2012, and=A0i suggest=A0you the fol= lowing webpage
for fu= rther information and instructions for the preparation of manuscripts.=A0

According to the journal policy, a= ll research papers will be=A0
peer-reviewed by experts=A0in the f= ield and we would be grateful=A0
if you=A0would inform us about your intention to submit well in advanc= e.

Further,=A0If you need more information please do no= t hesitate=A0
and we look forward to hearing from you.

Best= regards,
Dr. Muthukumar and Dr. Larsson


--
--
Dr. Muthukumar Kaliappan,
Goethe University,
Frankfurt Am Main
Germany

Email=A0 : Kaliappan.Muthukumar(~)gmail.com

"To = get Profit without risk, Experience without danger & Reward without Har= d work is as impossible as it is to live without being born"
-'Anonymous'

--047d7b10d1f100e30f04c242e122-- From owner-chemistry@ccl.net Tue Jun 12 12:19:01 2012 From: "John Keller jwkeller__alaska.edu" To: CCL Subject: CCL: "Quasi free rotors" Message-Id: <-47073-120612121751-8970-7/2Bp5XoFy4in1SXN2ckIg:+:server.ccl.net> X-Original-From: John Keller Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 12 Jun 2012 08:17:44 -0800 Mime-Version: 1.0 (1.0) Sent to CCL by: John Keller [jwkeller---alaska.edu] If the methyl group is not directly involved in complex formation, just fix a torsion angle using mod redundant. Or, do Opt=tight and integral=grid=ultraviolet (if you are using a DFT method). John Keller Sent from my iPad On Jun 12, 2012, at 6:40 AM, "John McKelvey jmmckel~!~gmail.com" wrote: > > Sent to CCL by: John McKelvey [jmmckel-,-gmail.com] > Folks, > > Hypothetical: Suppose that one has methyl-benzene (toluene) and one > can not get the maximum displacement in a geometry optimization to > converge due to the "spinning methyl group", but the energy, MAX & RMS > gradients and RMS displacement have converged. > > Now the target is then to do the IR frequencies. I might suppose or > hope that in an ideal case that the lowest frequency above the usual > first 6, though probably negative, would be this CH3 rotation, and the > remainder of the freqs would be real and close to these when the > compete optimization might be achieved, would be useful. Too much > wishful thinking? > > The real application is a metal complex with a loosely bound solvent > molecule, and the experimental IR spectrum is known, and is otherwise > analogous to the above with respect to max displacement. Reasonable > to depend upon the computed IR freqs other than the suspect low energy > mode? > > Many thanks! > > John > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel : gmail.com> > From owner-chemistry@ccl.net Tue Jun 12 13:30:00 2012 From: "John Keller jwkeller%x%alaska.edu" To: CCL Subject: CCL: "Quasi free rotors" Message-Id: <-47074-120612125719-25717-fMM5ZM31vH7bY/eL2tW0qA|*|server.ccl.net> X-Original-From: John Keller Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 12 Jun 2012 08:57:12 -0800 MIME-Version: 1.0 Sent to CCL by: John Keller [jwkeller^alaska.edu] Sorry, use "integral=grid=ultrafine" in your route section, not "...ultraviolet". John Keller On Tue, Jun 12, 2012 at 8:17 AM, John Keller jwkeller__alaska.edu wrote: > > Sent to CCL by: John Keller [jwkeller---alaska.edu] > If the methyl group is not directly involved in complex formation, > just fix a torsion angle using mod redundant. Or, do Opt=tight and > integral=grid=ultraviolet (if you are using a DFT method). > John Keller > > > Sent from my iPad > > On Jun 12, 2012, at 6:40 AM, "John McKelvey jmmckel~!~gmail.com" > wrote: > >> >> Sent to CCL by: John McKelvey [jmmckel-,-gmail.com] >> Folks, >> >> Hypothetical:  Suppose that one has methyl-benzene (toluene) and one >> can not get the maximum displacement in a geometry optimization to >> converge due to the "spinning methyl group", but the energy, MAX & RMS >> gradients and RMS displacement have converged. >> >> Now the target is then to do the IR frequencies.  I might suppose or >> hope that in an ideal case that the lowest frequency above the usual >> first 6, though probably negative, would be this CH3 rotation, and the >> remainder of the freqs would be real and close to these when the >> compete optimization might be achieved, would be useful.  Too much >> wishful thinking? >> >> The real application is a metal complex with a loosely bound solvent >> molecule, and the experimental IR spectrum is known, and is otherwise >> analogous to the above with respect to max displacement.  Reasonable >> to depend upon the computed IR freqs other than the suspect low energy >> mode? >> >> Many thanks! >> >> John >> >> -- >> John McKelvey >> 10819 Middleford Pl >> Ft Wayne, IN 46818 >> 260-489-2160 >> jmmckel : gmail.com>      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> > From owner-chemistry@ccl.net Tue Jun 12 21:28:00 2012 From: "Theodore S. Dibble tsdibble::esf.edu" To: CCL Subject: CCL: "Quasi free rotors" Message-Id: <-47075-120612212652-7119-H8zwSEHiorl8bVIFdA2/7Q(-)server.ccl.net> X-Original-From: "Theodore S. Dibble" Date: Tue, 12 Jun 2012 21:26:50 -0400 Sent to CCL by: "Theodore S. Dibble" [tsdibble-.-esf.edu] John, A comment and a suggestion 1) I do a lot geometry optimizations on radicals with some floppy modes. Sometimes, when I do the frequency calculation, the maximum displacement is reported as exceeding the convergence criterion. If I reoptimize with opt=tight and then repeat the frequency calculation to obtain full convergence, some of the lower frequencies are different by 1-2 wavenumbers. 2) Do you have an example of a solvent-bound metal complex that did optimize fully? If so, you could test the extent of the problem in by running the frequency calculation at one of not-quite-optimized geometries. Then compare these results to those calculated with the fully optimized geometry and see if any frequencies are significantly affected. Best wishes Ted Dibble Theodore S. Dibble Chemistry Department SUNY-Environmental Science and Forestry 1 Forestry Drive Syracuse, NY 13210 (315) 470-6596 (315) 470-6856 (fax) http://www.esf.edu/chemistry/faculty/dibble.htm > "John McKelvey jmmckel~!~gmail.com" wrote: > > Sent to CCL by: John McKelvey [jmmckel-,-gmail.com] > Folks, > > Hypothetical: Suppose that one has methyl-benzene (toluene) and one > can not get the maximum displacement in a geometry optimization to > converge due to the "spinning methyl group", but the energy, MAX & RMS > gradients and RMS displacement have converged. > > Now the target is then to do the IR frequencies. I might suppose or > hope that in an ideal case that the lowest frequency above the usual > first 6, though probably negative, would be this CH3 rotation, and the > remainder of the freqs would be real and close to these when the > compete optimization might be achieved, would be useful. Too much > wishful thinking? > > The real application is a metal complex with a loosely bound solvent > molecule, and the experimental IR spectrum is known, and is otherwise > analogous to the above with respect to max displacement. Reasonable > to depend upon the computed IR freqs other than the suspect low energy > mode? > > Many thanks! > > John > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel(!)gmail.com > >