From owner-chemistry@ccl.net Tue Apr 5 03:22:00 2011 From: "Bonoit Bonoit bonoit_10,+,yahoo.fr" To: CCL Subject: CCL: Transition state Message-Id: <-44284-110405031356-5923-NNcuKTMm5Hn6Q/U/s6rWsg::server.ccl.net> X-Original-From: "Bonoit Bonoit" Date: Tue, 5 Apr 2011 03:13:54 -0400 Sent to CCL by: "Bonoit Bonoit" [bonoit_10|yahoo.fr] Dear CCLers, I'm writing to enquire about if there is a method to localize the transition state of the passage from the singlet to the triplet state. Sincerely, Bonoirt From owner-chemistry@ccl.net Tue Apr 5 03:56:00 2011 From: "Bonoit Bonoit bonoit_10{:}yahoo.fr" To: CCL Subject: CCL: Spin density Message-Id: <-44285-110405031759-10969-CFYjEL0H+ZSG561nOz3BRg:-:server.ccl.net> X-Original-From: "Bonoit Bonoit" Date: Tue, 5 Apr 2011 03:17:57 -0400 Sent to CCL by: "Bonoit Bonoit" [bonoit_10(!)yahoo.fr] Dear CClers, I'm writing to enquire about the spin density, we need the MPA (Mulliken population analysis) to calculate it. My question is, c'd we use another population analysis to calculate it as NPA forexample? Sincerely, Bonoit From owner-chemistry@ccl.net Tue Apr 5 05:38:00 2011 From: "Ajitha. John aji.john07]^[gmail.com" To: CCL Subject: CCL: Relative energy Vs activation barrier Message-Id: <-44286-110405053554-29575-G9De3jDuegmxgWKl6f1fqQ###server.ccl.net> X-Original-From: "Ajitha. John" Content-Type: multipart/alternative; boundary=0016e659f756e35aa904a0289987 Date: Tue, 5 Apr 2011 15:05:47 +0530 MIME-Version: 1.0 Sent to CCL by: "Ajitha. John" [aji.john07:-:gmail.com] --0016e659f756e35aa904a0289987 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL users, There is a bit confusion regarding the selection of best possible pathway in a reaction mechanism. There are two possible pathways with different transition states with equal energy barrier (energy difference between the transition state and its pre-reactant complex) out of which one transition state is having low relative energy compared to the other (relative energy is with respect to the infinitely separated initial reactants). How can we select the most favorable pathway?? Whether it is the one which is having the transition state that passes through low relative energy or the one with low energy barrier?? If the second one is correct, then whether these two pathways mentioned above are equally possible? sincerely, Ajitha --0016e659f756e35aa904a0289987 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL users,

There is a bit confusion regarding the selection of = best possible pathway in a reaction mechanism.

There are two possib= le pathways with different transition states with equal energy barrier (ene= rgy difference between the transition state and its pre-reactant complex) o= ut of which one transition state is having=A0 low relative energy compared = to the other (relative energy is with respect to the infinitely separated i= nitial reactants).

How can we select the most favorable pathway?? Whether it is the one wh= ich is having the transition state that passes through low relative energy = or the one with low energy barrier?? If the second one is correct, then whe= ther these two pathways mentioned above are equally possible?

sincerely,
Ajitha

--0016e659f756e35aa904a0289987-- From owner-chemistry@ccl.net Tue Apr 5 06:13:00 2011 From: "Andras Borosy andras.borosy_+_givaudan.com" To: CCL Subject: CCL: About optical rotation calculation Message-Id: <-44287-110405060021-5559-qqHXYKBQ6c4gMdSaXqlvww^server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 0036EFE5C1257869_=" Date: Tue, 5 Apr 2011 12:00:10 +0200 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy/./givaudan.com] This is a multipart message in MIME format. --=_alternative 0036EFE5C1257869_= Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: base64 RGVhciBFZHVhcmRvLA0KDQpNeSBleHBlcmllbmNlIGlzIHRoYXQgR2F1c3NpYW4gaXMgbm90IGEg dmVyeSByZWxpYWJsZSBhcHBsaWNhdGlvbiBpbiANCmdlbmVyYWwuIEkgZG8gbm90IGtub3cgd2hh dCBpdHMgT1IgbW9kdWxlIGlzIGxpa2UgaW4gcGFydGljdWxhciBidXQgSSANCndvdWxkIHRyeSB0 aGUgc2FtZSBjb21wdXRhdGlvbiBieSB1c2luZyBUdXJib21vbGUuIEl0IGhhcyBhIGRlY2VudCBP 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czogaHR0cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9zZWFyY2hjY2wvaW5kZXguc2h0bWw8YnI+ DQo8YnI+DQpJZiB5b3VyIG1haWwgYm91bmNlcyBmcm9tIENDTCB3aXRoIDUuNy4xIGVycm9yLCBj aGVjazo8YnI+DQogJm5ic3A7ICZuYnNwOyAmbmJzcDtodHRwOi8vd3d3LmNjbC5uZXQvc3BhbW1l cnMudHh0PGJyPg0KPGJyPg0KUlRGSTogaHR0cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9hYm91 dGNjbC9pbnN0cnVjdGlvbnMvPGJyPg0KPGJyPg0KPGJyPg0KPC9mb250PjwvdHQ+DQo8YnI+DQo= --=_alternative 0036EFE5C1257869_=-- From owner-chemistry@ccl.net Tue Apr 5 06:47:00 2011 From: "Sergio Emanuel Galembeck segalemb!^!usp.br" To: CCL Subject: CCL: Spin density Message-Id: <-44288-110405061257-12959-/ZbNOpqCyYI5P2UCF4uNiA . server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Tue, 05 Apr 2011 07:12:47 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb[]usp.br] Dear Bonoit, Yes, you can use NPA analysis to calculate spin densities. For open shell systems NBO program lists the spin densities. At my experience, Mulliken or NPA produces very similar results for spin densites. Best regards, Sergio Citando "Bonoit Bonoit bonoit_10{:}yahoo.fr" : > > Sent to CCL by: "Bonoit Bonoit" [bonoit_10(!)yahoo.fr] > Dear CClers, > I'm writing to enquire about the spin density, we need the MPA > (Mulliken population analysis) to calculate it. My question is, c'd > we use another population analysis to calculate it as NPA forexample? > Sincerely, > Bonoit> > > From owner-chemistry@ccl.net Tue Apr 5 07:25:00 2011 From: "Andreas Uhe Uhe%a%itmc.rwth-aachen.de" To: CCL Subject: CCL: Relative energy Vs activation barrier Message-Id: <-44289-110405071653-25144-VN9RSzBLhaKS6hQf0yRYbA++server.ccl.net> X-Original-From: Andreas Uhe Content-type: multipart/alternative; boundary="Boundary_(ID_Nmzag+tqBlh/3Yx1xqoF6Q)" Date: Tue, 05 Apr 2011 13:16:42 +0200 MIME-version: 1.0 Sent to CCL by: Andreas Uhe [Uhe||itmc.rwth-aachen.de] This is a multi-part message in MIME format. --Boundary_(ID_Nmzag+tqBlh/3Yx1xqoF6Q) Content-type: text/plain; charset=ISO-8859-1; format=flowed Content-transfer-encoding: 8BIT Dear Ajitha, in multistep reactions the single activation barriers are unimportant and the relative energies decide which pathway is favored. If you are interested in catalysis, I recommend that you have a look at the energetic span model: A) Kozuch, S.; Shaik, S. /J. Am. Chem. Soc. /*2006*, /128/, 3355-3365. B) Kozuch, S.; Shaik, S. /J. Phys. Chem. A/ *2008*, /112/, 6032-6041. C) Uhe, A.; Kozuch, S.; Shaik, S. /J. Comp. Chem. /*2011*, /32/, 978-985. D) Kozuch, S.; Shaik, S. /Acc. //Chem. Res. /*2011*, /44/, 101-110. The model shows that the concept of a rate determining reaction step (corresponding to a single activation barrier of a multistep reaction) is misleading. It also allows to calculate the turnover frequency of a catalytic system from relative energies e.g. obtained with DFT. Paper A introduces the model, paper B extends its application to the reactant concentrations, paper C further extends the model and introduces a small computer program helping to apply the model and paper D reviews the model. There are also some papers with further applications. To be fair I have to mention that a similar concept has later been developed also by Campbell: C. Stegelmann, A. Andreasen, C. T. Campbell, J. Am. Chem. Soc. 2009, 131, 8077 --8082. C. Stegelmann, A. Andreasen, C. T. Campbell, J. Am. Chem. Soc. 2009, 131, 13563. Cheers, Andi Am 05.04.2011 11:35, schrieb Ajitha. John aji.john07]^[gmail.com: > Dear CCL users, > > There is a bit confusion regarding the selection of best possible pathway in a reaction mechanism. > > There are two possible pathways with different transition states with equal energy barrier (energy difference between the transition state and its pre-reactant complex) out of which one transition state is having low relative energy compared to the other (relative energy is with respect to the infinitely separated initial reactants). > > How can we select the most favorable pathway?? Whether it is the one which is having the transition state that passes through low relative energy or the one with low energy barrier?? If the second one is correct, then whether these two pathways mentioned above are equally possible? > > sincerely, > Ajitha > -- Dipl. Chem. Andreas Uhe Rheinisch-Westfälische Technische Hochschule Aachen (RWTH) Institut für Technische und Makromolekulare Chemie (ITMC) Lehrstuhl für Technische Chemie und Petrolchemie Worringer Weg 1 52074 Aachen Tel.: 0049 - 241 - 80-26453 E-mail: Uhe|*|itmc.rwth-aachen.de --Boundary_(ID_Nmzag+tqBlh/3Yx1xqoF6Q) Content-type: text/html; charset=ISO-8859-1 Content-transfer-encoding: 7BIT Dear Ajitha,

in multistep reactions the single activation barriers are unimportant and the relative energies decide which pathway is favored. If you are interested in catalysis, I recommend that you have a look at the energetic span model:

A) Kozuch, S.; Shaik, S. J. Am. Chem. Soc. 2006, 128, 3355-3365.
B) Kozuch, S.; Shaik, S. J. Phys. Chem. A 2008, 112, 6032-6041.
C) Uhe, A.; Kozuch, S.; Shaik, S. J. Comp. Chem. 2011, 32, 978-985.
D) Kozuch, S.; Shaik, S. Acc. Chem. Res. 2011, 44, 101-110.

The model shows that the concept of a rate determining reaction step (corresponding to a single activation barrier of a multistep reaction) is misleading. It also allows to calculate the turnover frequency of a catalytic system from relative energies e.g. obtained with DFT. Paper A introduces the model, paper B extends its application to the reactant concentrations, paper C further extends the model and introduces a small computer program helping to apply the model and paper D reviews the model. There are also some papers with further applications.

To be fair I have to mention that a similar concept has later been developed also by Campbell:
C. Stegelmann, A. Andreasen, C. T. Campbell, J. Am. Chem. Soc. 2009, 131, 8077 –8082.
C. Stegelmann, A. Andreasen, C. T. Campbell, J. Am. Chem. Soc. 2009, 131, 13563.

Cheers,
Andi



Am 05.04.2011 11:35, schrieb Ajitha. John aji.john07]^[gmail.com:
Dear CCL users,

There is a bit confusion regarding the selection of best possible pathway in a reaction mechanism.

There are two possible pathways with different transition states with equal energy barrier (energy difference between the transition state and its pre-reactant complex) out of which one transition state is having  low relative energy compared to the other (relative energy is with respect to the infinitely separated initial reactants).

How can we select the most favorable pathway?? Whether it is the one which is having the transition state that passes through low relative energy or the one with low energy barrier?? If the second one is correct, then whether these two pathways mentioned above are equally possible?

sincerely,
Ajitha


-- 
Dipl. Chem. Andreas Uhe

Rheinisch-Westfälische Technische Hochschule Aachen (RWTH)
Institut für Technische und Makromolekulare Chemie (ITMC)
Lehrstuhl für Technische Chemie und Petrolchemie
Worringer Weg 1
52074 Aachen
Tel.: 0049 - 241 - 80-26453
E-mail: Uhe|*|itmc.rwth-aachen.de
--Boundary_(ID_Nmzag+tqBlh/3Yx1xqoF6Q)-- From owner-chemistry@ccl.net Tue Apr 5 08:00:01 2011 From: "Mikael Johansson mikael.johansson . iki.fi" To: CCL Subject: CCL: Spin density Message-Id: <-44290-110405074009-16801-TgxvOZtq55jQeyuUnv6xjA{}server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 5 Apr 2011 14:39:57 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson(~)iki.fi] Hello Bonoit and All! On Tue, 5 Apr 2011, Bonoit Bonoit bonoit_10{:}yahoo.fr wrote: > I'm writing to enquire about the spin density, we need the MPA (Mulliken > population analysis) to calculate it. My question is, c'd we use another > population analysis to calculate it as NPA forexample? It depends on what you mean by spin density. In short, you can get the spin population with practically any method that can provide a total density population. Note, however, that the "charge" of an atom obtained by any of the population analyses is an attempt at emulating the difference of the negative charge of the electrons surrounding a specific atom and the positive charge of the nucleus in question. Thus the "spin density" that you get will simply be one number, the difference of the number of alpha and beta electrons that your partitioning scheme of choice assigns to a specific atom. This is not really the spin density, if you think of it as regions in space dominated by alpha/beta electrons, but rather an average of the differences over a "volume" defined by the population/partitioning scheme. That said, the values of Mulliken "spin densitites" do correspond quite well to what you would expect, giving, for example, roughly the number of unpaired d-electrons for tranition metals. And the sum of the individual "spin densities" will (should) of course add up to the total number of unpaired electrons in your molecule, just like the sum of the atomic charges add up to the charge of the molecule. As a side note, Mulliken spin densities are also much less sensitive towards basis set choice, in contrast to the Mulliken atomic charges, which can turn out quite droll with, for example, diffuse functions. Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/ From owner-chemistry@ccl.net Tue Apr 5 08:35:00 2011 From: "Andrew Voronkov drugdesign**yandex.ru" To: CCL Subject: CCL: question on Phase II metabolism rpedictions Message-Id: <-44291-110405081124-17357-2t+iDqin8OgH0ZX0HMBKAQ^^server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 05 Apr 2011 16:11:12 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign+*+yandex.ru] Dear CCL users, I am interested in Phase II metabolism prediction tools along with different non-CYP hepatic metabolism prediction software packages. Can you please recommend me links to some reviews in this field or to some software packages which you personally like. Until now I was working only with MetaDrug from GeneGo for phase II prediction, but I am interested in additional tools for cross validation. Best regards, Andrew From owner-chemistry@ccl.net Tue Apr 5 09:26:00 2011 From: "Eduardo edulsa- -ufpr.br" To: CCL Subject: CCL:G: About optical rotation calculation Message-Id: <-44292-110405072400-32307-sKFt/Hgs6iQYNm6ZnvScbw,+,server.ccl.net> X-Original-From: Eduardo Content-Type: multipart/alternative; boundary="------------080206040006060909040809" Date: Tue, 05 Apr 2011 08:23:39 -0300 MIME-Version: 1.0 Sent to CCL by: Eduardo [edulsa[A]ufpr.br] This is a multi-part message in MIME format. --------------080206040006060909040809 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 8bit Dear CCLers First it all, thanks to Dr. Borsosy and to Richard J. Wood for their replies. Unfortunately, I do not have access to Turbomole suite. In my case, the molecule that I am interested carries 4 optical active centres (2 of them are fixed), so Dr. Borosy confirmed what I suspected: algoritms were implemented aiming simple enantiomeric molecules (only one optical active center). Please, I would like to know if is there some program, free to academics, which should be able to calculate optical rotation for not too small (40 heavy atoms) molecules. Thank you in advance Yours Eduardo 07:00, Andras Borosy andras.borosy_+_givaudan.com wrote: > > Dear Eduardo, > > My experience is that Gaussian is not a very reliable application in > general. I do not know what its OR module is like in particular but I > would try the same computation by using Turbomole. It has a decent OR > calculation algorithm: Chemical Physics Letters 361 (2002) 321–328. > > If the molecule has too many rotatable bonds, these OR calculation > algorithms do not work: Current Organic Chemistry, 2010, 14, 1612-1628. > > Best wishes, > > > Dr. András Péter Borosy > Scientific Modelling Expert > > Fragrance Research > Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - Dübendorf > - Switzerland > T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com > > > > > > *"Eduardo edulsa^_^ufpr.br" * > Sent by: owner-chemistry+andras.borosy==givaudan.com[a]ccl.net > > 28.03.2011 20:18 > Please respond to > "CCL Subscribers" > > > > To > "Borosy, Andras " > cc > > Subject > CCL:G: About optical rotation calculation > > > > > > > > > > > Sent to CCL by: Eduardo [edulsa|a|ufpr.br] > Dear CCLers > > I am performing some calculations (g03) aiming the optical rotation > properties. My first test was a s-valinol molecule (CAS 2026-48-4). > After a geometry optimization step (opt=tight), I got a value for > Alpha-D equals to -158.98 deg. The experimental value is + 16.9 deg. I > am get confuse because, unless I was strongly wrong, they are not the > same despite -160 and +20 be complementary angles. So please, could > anyone help me to explain and understand what is happening? > > My best wishes > > Eduardo > > -- > Eduardo Lemos de Sa > Associated Professor at Chemistry Department > Universidade Federal do Parana > Dep. Quimica, P. Box 19081, 81531-990 Curitiba PR / Brazil > phone: +55(41)33613300 > fax : +55(41)33613186> > > -- Eduardo Lemos de Sa Associated Professor at Chemistry Department Universidade Federal do Parana Dep. Quimica, P. Box 19081, 81531-990 Curitiba PR / Brazil phone: +55(41)33613300 fax : +55(41)33613186 --------------080206040006060909040809 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit Dear CCLers

First it all, thanks to Dr. Borsosy and to Richard J. Wood for their replies.

Unfortunately, I do not have access to Turbomole suite.  In my case, the molecule that I am interested carries 4 optical active centres (2 of them are fixed), so Dr. Borosy confirmed what I suspected: algoritms were implemented aiming simple enantiomeric molecules (only one optical active center).

Please, I would like to know if is there some program, free to academics, which should be able to calculate optical rotation for not too small (40 heavy atoms) molecules.

Thank you in advance

Yours

Eduardo



07:00, Andras Borosy andras.borosy_+_givaudan.com wrote:

Dear Eduardo,

My experience is that Gaussian is not a very reliable application in general. I do not know what its OR module is like in particular but I would try the same computation by using Turbomole. It has a decent OR calculation algorithm: Chemical Physics Letters 361 (2002) 321–328.

If the molecule has too many rotatable bonds, these OR calculation algorithms do not work: Current Organic Chemistry, 2010, 14, 1612-1628.

Best wishes,


Dr. András Péter Borosy
Scientific Modelling Expert

Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  Dübendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http://www.givaudan.com





"Eduardo edulsa^_^ufpr.br" <owner-chemistry[a]ccl.net>
Sent by: owner-chemistry+andras.borosy==givaudan.com[a]ccl.net

28.03.2011 20:18
Please respond to
"CCL Subscribers" <chemistry[a]ccl.net>

To
 "Borosy, Andras " <andras.borosy[a]givaudan.com>
cc
Subject
 CCL:G: About optical rotation calculation








Sent to CCL by: Eduardo [edulsa|a|ufpr.br]
Dear CCLers

I am performing some calculations (g03) aiming the optical rotation
properties. My first test was a s-valinol molecule (CAS 2026-48-4).
After a geometry optimization step (opt=tight), I got a value for
Alpha-D equals to -158.98 deg. The experimental value is + 16.9 deg. I
am get confuse because, unless I was strongly wrong, they are not the
same despite -160 and +20 be complementary angles. So please, could
anyone help me to explain and understand what is happening?

My best wishes

Eduardo

--
Eduardo Lemos de Sa
Associated Professor at Chemistry Department
Universidade Federal do Parana
Dep. Quimica, P. Box 19081, 81531-990 Curitiba PR / Brazil
phone: +55(41)33613300
fax  : +55(41)33613186



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-- 
Eduardo Lemos de Sa
Associated Professor at Chemistry Department
Universidade Federal do Parana
Dep. Quimica, P. Box 19081, 81531-990 Curitiba PR / Brazil
phone: +55(41)33613300
fax  : +55(41)33613186
--------------080206040006060909040809-- From owner-chemistry@ccl.net Tue Apr 5 10:01:00 2011 From: "Eugene V Horbatenko yevhen.horbatenko#,#udg.edu" To: CCL Subject: CCL:G: IRC for flat PES Message-Id: <-44293-110405085334-26482-JjU6Jq1y6KP6D0u2BCVKlg__server.ccl.net> X-Original-From: "Eugene V Horbatenko" Date: Tue, 5 Apr 2011 08:53:32 -0400 Sent to CCL by: "Eugene V Horbatenko" [yevhen.horbatenko(-)udg.edu] Dear colleagues, I have a problem with IRC (I use Gaussian09). I have 3 TS, two of them have Cs symmetry (TS1 and TS2), the last is asymmetric (TSasy), and I have a minimum as well. These TSs are caracterized by low values of imaginary frequencies of 66i cm-1, 49i cm-1 and 54i cm-1. To check whether they are true TSs or not I reoptimized them with option Integral=(UltraFineGrid). The results are almost the same, with similar corresponding imaginary frequensies. Then I performed IRC on these TSs. To do this I used the command #p tpssh/Gen pseudo=read gfinput IRC=(CalcFC,Forward,MaxPoints=60,StepSize=10) NoSym The problem is that IRC "fails". For TSasy the output is as follows: IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC Error in corrector energy = -0.0000004499 Magnitude of corrector gradient = 0.0005687690 Magnitude of analytic gradient = 0.0006577701 Magnitude of difference = 0.0003392476 Angle between gradients (degrees)= 31.0438 Pt 37 Step number 3 out of a maximum of 20 CORRECTOR INTEGRATION CONVERGENCE: Recorrection delta-x convergence threshold: 0.010000 Delta-x Convergence Met Point Number: 37 Path Number: 1 CHANGE IN THE REACTION COORDINATE = 0.17497 NET REACTION COORDINATE UP TO THIS POINT = 6.34057 # OF POINTS ALONG THE PATH = 37 # OF STEPS = 3 Calculating another point on the path. Point Number 38 in FORWARD path direction. Using LQA Reaction Path Following. LQA: T_Est iteration completed in 2 iterations. PES minimum detected within a second-order step. Calculation of FORWARD path complete. Reaction path calculation complete. Energies reported relative to the TS energy of -1532.778448 -------------------------------------------------------------------------- Summary of reaction path following -------------------------------------------------------------------------- Energy Rx Coord 1 0.00000 0.00000 2 0.00000 0.03446 3 -0.00002 0.20571 4 -0.00003 0.38133 5 -0.00005 0.55710 6 -0.00007 0.73281 7 -0.00008 0.90852 8 -0.00010 1.08423 9 -0.00011 1.25992 10 -0.00013 1.43534 11 -0.00015 1.60923 12 -0.00016 1.78411 13 -0.00018 1.95941 14 -0.00020 2.13383 15 -0.00022 2.30856 16 -0.00023 2.48337 17 -0.00025 2.65833 18 -0.00027 2.83303 19 -0.00030 3.00825 20 -0.00032 3.18283 21 -0.00034 3.35812 22 -0.00037 3.53343 23 -0.00040 3.70864 24 -0.00042 3.88373 25 -0.00045 4.05891 26 -0.00048 4.23433 27 -0.00051 4.40993 28 -0.00054 4.58537 29 -0.00057 4.76150 30 -0.00060 4.93735 31 -0.00063 5.11313 32 -0.00066 5.28897 33 -0.00069 5.46469 34 -0.00073 5.64059 35 -0.00076 5.81574 36 -0.00079 5.99054 37 -0.00082 6.16560 38 -0.00085 6.34057 -------------------------------------------------------------------------- Total number of points: 37 Total number of gradient calculations: 81 Total number of Hessian calculations: 1 IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC But the final geometry is not a minimum, the difference between transition state and this final geometry is only 0.5 kcal/mol, at the same time, the true barrier should be 1.2 kcal/mol. If one performs a geometry optimization using this geometry as a starting point one can reach true minimum. I tried to use the various values for StepSize as 15 and 20, tried to use additional options as Integral=(UltraFineGrid) and Iop(1/7=30) but the results were even worther. (IRC performed less than 38 steps and finished with its usual "PES minimum detected within a second-order step.") For symmtreic TS1 the situation is far worther than for the previous TSasy. For TS1 I used #p tpssh/Gen pseudo=read gfinput IRC=(CalcFC,Forward,MaxPoints=60,StepSize=20) NoSym Integral(UltraFineGrid) and the output is as follows: IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC Error in corrector energy = -0.0000000095 Magnitude of corrector gradient = 0.0000442551 Magnitude of analytic gradient = 0.0000533873 Magnitude of difference = 0.0000353012 Angle between gradients (degrees)= 41.0683 Pt 1 Step number 7 out of a maximum of 20 CORRECTOR INTEGRATION CONVERGENCE: Recorrection delta-x convergence threshold: 0.010000 Delta-x Convergence Met Point Number: 1 Path Number: 1 CHANGE IN THE REACTION COORDINATE = 0.20701 NET REACTION COORDINATE UP TO THIS POINT = 0.20701 # OF POINTS ALONG THE PATH = 1 # OF STEPS = 7 PES minimum detected on this side of the pathway. Magnitude of the gradient = 0.0000401 Calculation of FORWARD path complete. Reaction path calculation complete. Energies reported relative to the TS energy of -1532.775738 -------------------------------------------------------------------------- Summary of reaction path following -------------------------------------------------------------------------- Energy Rx Coord 1 0.00000 0.00000 2 0.00000 0.20701 -------------------------------------------------------------------------- Total number of points: 1 Total number of gradient calculations: 8 Total number of Hessian calculations: 1 IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC If I modify the command line the result is not better. #p tpssh/Gen pseudo=read gfinput IRC=(CalcFC,Forward,MaxPoints=60,StepSize=15) NoSym Integral=(UltraFineGrid) Iop(1/7=30) IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC Error in corrector energy = 0.0000000152 Magnitude of corrector gradient = 0.0000110028 Magnitude of analytic gradient = 0.0001169156 Magnitude of difference = 0.0001150405 Angle between gradients (degrees)= 77.5196 Pt 1 Step number 14 out of a maximum of 20 CORRECTOR INTEGRATION CONVERGENCE: Recorrection delta-x convergence threshold: 0.003162 Delta-x Convergence Met Point Number: 1 Path Number: 1 CHANGE IN THE REACTION COORDINATE = 0.00315 NET REACTION COORDINATE UP TO THIS POINT = 0.00315 # OF POINTS ALONG THE PATH = 1 # OF STEPS = 14 PES minimum detected on this side of the pathway. Magnitude of the gradient = 0.0000348 Calculation of FORWARD path complete. Reaction path calculation complete. Energies reported relative to the TS energy of -1532.775738 -------------------------------------------------------------------------- Summary of reaction path following -------------------------------------------------------------------------- Energy Rx Coord 1 0.00000 0.00000 2 0.00000 0.00315 -------------------------------------------------------------------------- Total number of points: 1 Total number of gradient calculations: 15 Total number of Hessian calculations: 1 IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC-IRC I understand that, in general, all this happened because of a flat potential energy surface. Anyway, I would be grateful for some help and advices. Sincerely, Eugene From owner-chemistry@ccl.net Tue Apr 5 10:35:00 2011 From: "Ralf Tonner tonner++chemie.uni-marburg.de" To: CCL Subject: CCL:G: [Summary] IR intensities from VASP Message-Id: <-44294-110405101015-27964-KrzdJU3GReRwxBsr9crwGw]|[server.ccl.net> X-Original-From: Ralf Tonner Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Tue, 05 Apr 2011 16:09:50 +0200 MIME-Version: 1.0 Sent to CCL by: Ralf Tonner [tonner ~~ chemie.uni-marburg.de] Dear CClers, after several very helpful answers to my above-mentioned post and initial investigations, I want to summarize the results. In VASP, the intensities of IR-active vibrational frequencies are not calculated directly. CASTEP can do this - Raman activities can be calculated as well (thanks to Phil Hasnip). If calculations with VASP are undertaken, two approaches can be followed to obtain the respective IR-intensitites: a) change of dipole moment w.r.t. normal modes ("old" approach, also used in most molecular QC programs, e.g. Gaussian. See e.g. Preuss, Bechstedt Phys. Rev. B 73 2006, 155413 for an application to VASP) b) density functional pertubation theory (a.k.a. linear response theory). For a), a finite difference calculation has to be carried out with displacement of all atoms in all directions (might be reduced by symmetry considerations). The dipole moment has to be calculated for all displacements. Afterwards, the dipole moment change w.r.t the normal modes has to be calculated which is proportional to the IR intensity of the respective mode. Several programs are available for this task (thanks to Alfred Gil Arranz and Kacper Druzbicki). This method is restricted to isolated molecules and slabs in VASP. For b), a linear response calculation has to be carried out and the born effective charges have to be determined for all atoms. Afterwards, the method published by Gianozzi&Baroni (see JCP, 100, 1994, 8537 and Rev. Mod. Phys. 73, 2001, 515) can be applied to derive IR intensities. Many thanks to David Karhanek (ICIQ, Spain) for introducing me to this method and providing a script implementing this scheme. This latter approach is also followed e.g. by CASTEP and seems to be more reliable and more general. Kind regards, Ralf. -- Dr. Ralf Tonner Philipps-Universität Marburg GERMANY Ph +49-(0)6421-28-25418 Fax +49-(0)6421-28-25566 http://www.uni-marburg.de/fb15/ag-tonner ---- From owner-chemistry@ccl.net Tue Apr 5 11:24:01 2011 From: "Andras Borosy andras.borosy ~ givaudan.com" To: CCL Subject: CCL: About optical rotation calculation Message-Id: <-44295-110405110904-18554-ZDrWjlNuGbnrwDgijc0iSQ]-[server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 0053322DC1257869_=" Date: Tue, 5 Apr 2011 17:08:49 +0200 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy::givaudan.com] This is a multipart message in MIME format. --=_alternative 0053322DC1257869_= Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: base64 RGVhciBFZHVhcmRvLA0KDQpJZiBDaGVtc3BpZGVyIHdvcmtzIHdlbGwgdG9kYXksIFMtdmFsaW5v bCANCigyKFMpLTItQW1pbm8tMy1tZXRoeWwtMS1idXRhbm9sKSBoYXMgb25seSBvbmUgY2hpcmFs 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John aji.john07-$-gmail.com" To: CCL Subject: CCL: Relative energy Vs activation barrier Message-Id: <-44296-110405114121-15855-hnR6G9kgjLoPyytDwVW8Og:+:server.ccl.net> X-Original-From: "Ajitha. John" Content-Type: multipart/alternative; boundary=000e0cd5be2ca49b5104a02db4ac Date: Tue, 5 Apr 2011 21:11:11 +0530 MIME-Version: 1.0 Sent to CCL by: "Ajitha. John" [aji.john07(0)gmail.com] --000e0cd5be2ca49b5104a02db4ac Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear Andreas, I had gone through the papers you cited here.. Those papers are really useful in understanding the concept of rate determining states (TDI and TDTS) instead of rate determining step. Thank you so much, Ajitha On Tue, Apr 5, 2011 at 4:46 PM, Andreas Uhe Uhe%a%itmc.rwth-aachen.de < owner-chemistry]![ccl.net> wrote: > Dear Ajitha, > > in multistep reactions the single activation barriers are unimportant and > the relative energies decide which pathway is favored. If you are interes= ted > in catalysis, I recommend that you have a look at the energetic span mode= l: > > A) Kozuch, S.; Shaik, S. *J. Am. Chem. Soc. **2006*, *128*, 3355-3365. > B) Kozuch, S.; Shaik, S. *J. Phys. Chem. A* *2008*, *112*, 6032-6041. > C) Uhe, A.; Kozuch, S.; Shaik, S. *J. Comp. Chem. **2011*, *32*, 978-985. > D) Kozuch, S.; Shaik, S. *Acc. **Chem. Res. **2011*, *44*, 101-110. > The model shows that the concept of a rate determining reaction step > (corresponding to a single activation barrier of a multistep reaction) is > misleading. It also allows to calculate the turnover frequency of a > catalytic system from relative energies e.g. obtained with DFT. Paper A > introduces the model, paper B extends its application to the reactant > concentrations, paper C further extends the model and introduces a small > computer program helping to apply the model and paper D reviews the model= . > There are also some papers with further applications. > > To be fair I have to mention that a similar concept has later been > developed also by Campbell: > C. Stegelmann, A. Andreasen, C. T. Campbell, J. Am. Chem. Soc. 2009, 131, > 8077 =968082. > C. Stegelmann, A. Andreasen, C. T. Campbell, J. Am. Chem. Soc. 2009, 131, > 13563. > > Cheers, > Andi > > > > Am 05.04.2011 11:35, schrieb Ajitha. John aji.john07]^[gmail.com: > > Dear CCL users, > > There is a bit confusion regarding the selection of best possible pathway > in a reaction mechanism. > > There are two possible pathways with different transition states with equ= al > energy barrier (energy difference between the transition state and its > pre-reactant complex) out of which one transition state is having low > relative energy compared to the other (relative energy is with respect to > the infinitely separated initial reactants). > > How can we select the most favorable pathway?? Whether it is the one whic= h > is having the transition state that passes through low relative energy or > the one with low energy barrier?? If the second one is correct, then whet= her > these two pathways mentioned above are equally possible? > > sincerely, > Ajitha > > > -- > Dipl. Chem. Andreas Uhe > > Rheinisch-Westf=E4lische Technische Hochschule Aachen (RWTH) > Institut f=FCr Technische und Makromolekulare Chemie (ITMC) > Lehrstuhl f=FCr Technische Chemie und Petrolchemie > Worringer Weg 1 > 52074 Aachen > Tel.: 0049 - 241 - 80-26453 > E-mail: Uhe:-:itmc.rwth-aachen.de > > --=20 With Regards, Ajitha --000e0cd5be2ca49b5104a02db4ac Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear Andreas,

I had gone through the papers you cited here..
Tho= se papers are really useful in understanding the concept of rate determinin= g states (TDI and TDTS) instead of rate determining step.

Thank you = so much,
Ajitha


On Tue, Apr 5, 2011 at 4:46 PM= , Andreas Uhe Uhe%a%itmc.rwth-aachen= .de <ow= ner-chemistry]![ccl.net> wrote:
=20 =20 =20
Dear Ajitha,

in multistep reactions the single activation barriers are unimportant and the relative energies decide which pathway is favored. If you are interested in catalysis, I recommend that you have a look at the energetic span model:

A) Kozuch, S.; Shaik, S. J. Am. Chem. Soc. 2006, 128, 3355-3365.
B) Kozuch, S.; Shaik, S. J. Phys. Chem. A 2008, 112, 6032-6041.
C) Uhe, A.; Kozuch, S.; Shaik, S. J. Comp. Chem. 2011= , 32, 978-985.
D) Kozuch, S.; Shaik, S. Acc. Chem. Res. 2011, 44, 101-110.

The model shows that the concept of a rate determining reaction step (corresponding to a single activation barrier of a multistep reaction) is misleading. It also allows to calculate the turnover frequency of a catalytic system from relative energies e.g. obtained with DFT. Paper A introduces the model, paper B extends its application to the reactant concentrations, paper C further extends the model and introduces a small computer program helping to apply the model and paper D reviews the model. There are also some papers with further applications.

To be fair I have to mention that a similar concept has later been developed also by Campbell:
C. Stegelmann, A. Andreasen, C. T. Campbell, J. Am. Chem. Soc. 2009, 131, 8077 =968082.
C. Stegelmann, A. Andreasen, C. T. Campbell, J. Am. Chem. Soc. 2009, 131, 13563.

Cheers,
Andi



Am 05.04.2011 11:35, schrieb Ajitha. John aji.john07]^[gmail.com:
Dear CCL us= ers,

There is a bit confusion regarding the selection of best possible pathway in a reaction mechanism.

There are two possible pathways with different transition states with equal energy barrier (energy difference between the transition state and its pre-reactant complex) out of which one transition state is having=A0 low relative energy compared to the other (relative energy is with respect to the infinitely separated initial reactants).

How can we select the most favorable pathway?? Whether it is the one which is having the transition state that passes through low relative energy or the one with low energy barrier?? If the second one is correct, then whether these two pathways mentioned above are equally possible?

sincerely,
Ajitha


--=20
Dipl. Chem. Andreas Uhe

Rheinisch-Westf=E4lische Technische Hochschule Aachen (RWTH)
Institut f=FCr Technische und Makromolekulare Chemie (ITMC)
Lehrstuhl f=FCr Technische Chemie und Petrolchemie
Worringer Weg 1
52074 Aachen
Tel.: 0049 - 241 - 80-26453
E-mail: Uhe:=
-:itmc.rwth-aachen.de



--
With Regards,
Ajitha=
--000e0cd5be2ca49b5104a02db4ac-- From owner-chemistry@ccl.net Tue Apr 5 12:33:00 2011 From: "Pierre Archirel pierre.archirel---u-psud.fr" To: CCL Subject: CCL: IRC for flat PES Message-Id: <-44297-110405122021-17714-wRVe8VpVubvLUsgdRUDTVw%%server.ccl.net> X-Original-From: "Pierre Archirel" Date: Tue, 5 Apr 2011 12:20:18 -0400 Sent to CCL by: "Pierre Archirel" [pierre.archirel..u-psud.fr] This is an answer to E. V. Horbatenko If the PES is very flat there is a difficult issue in the separation of the center of mass of the molecule. It is very useful to compare the "negative" frequency characterising the TS with the six "zero" frequencies coming from the global translation and rotation. I have two examples of this, for the same molecule, with B3LYP and int=ultrafine: Example 1: Low frequencies --- -36.0058 -2.8583 -0.0001 0.0005 0.0009 5.9011 Low frequencies --- 10.3067 18.8761 33.4494 it can be seen that the "TS" frequency (-36.0058) is much larger (by a factor 10) than the first "zero" frequency (-2.8583). Actually the IRC calculation worked nicely. Example 2: Low frequencies --- -13.7156 -6.3252 -3.9374 -0.0003 0.0003 0.0005 Low frequencies --- 5.4561 16.2158 28.6961 In this case the "TS" frequency (-13.7156) is only two times larger than the first "zero" frequency (-6.3252). I could not make the IRC calculation even start. Obviously in this case the "TS" direction is polluted by global rotation. Have you compared these values? Pierre Archirel LCP, Universite Paris-Sud, France pierre.archirel.u-psud.fr From owner-chemistry@ccl.net Tue Apr 5 18:25:00 2011 From: "Olexandr Isayev olexandr.isayev-*-case.edu" To: CCL Subject: CCL: 20th Anniversary Conference on Current Trends in Computational Chemistry (October 27-29, 2011) Message-Id: <-44298-110405154200-21147-jmU2uTHbEYl/1R4AvI7X+w!A!server.ccl.net> X-Original-From: Olexandr Isayev Content-Type: multipart/alternative; boundary=000e0cd2bfec42ff9c04a0311114 Date: Tue, 5 Apr 2011 14:41:30 -0500 MIME-Version: 1.0 Sent to CCL by: Olexandr Isayev [olexandr.isayev]=[case.edu] --000e0cd2bfec42ff9c04a0311114 Content-Type: text/plain; charset=ISO-8859-1 http://cctcc.icnanotox.org *20th Conference on Current Trends in Computational Chemistry (October 27-29, 2011)* We would like to invite you and encourage your students, postdoctoral fellows and colleagues to participate in the 20th anniversary Conference on Current Trends in Computational Chemistry (20th CCTCC) to be held in Jackson, Miss (USA), on October 27-29, 2011. To celebrate two decades of success this CCTCC meeting will gather lectures by two Nobel laureates and twenty five invited speakers who have made prominent contributions to the broad field of computational and quantum chemistry. It will also provide the opportunity to all members of our community, researchers and students, to present and discuss their work through several poster sessions and social events. Contributions in all areas of methods development and applications in theoretical chemistry are welcome. *Important Date:* Early (discounted) registration and abstract submission is open until *September 1, 2011*. *Venue:* As usual the conference will be held at the Hilton Jackson Hotel, Jackson, Miss. (USA). *Confirmed list of invited speakers:* Misako Aida, *Hiroshima University, Japan* Axel D. Becke, *Dalhousie University, Canada* Roberto Cammi, *Universita' di Parma, Italy* Jiali Gao, *University of Minnesota, USA* Sharon Hammes-Schiffer, *Pennsylvania State University, USA* Istvan Hargittai, *Hungarian Academy of Sciences, Hungary* Trygve Helgaker, *University of Oslo, Norway* Yasuyuki Ishikawa, *University of Puerto Rico, USA* William Jorgensen, *Yale University, USA* Miklos Kertesz, *Georgetown University, USA* Kwang S. Kim, *Pohang University of Science and Technology, Korea* Walter Kohn, *University of California, Santa Barbara, USA* Harold W. Kroto, *Florida State University, USA* William Lester, Jr., *University of California, Berkeley, USA* Hans Lischka, *University of Vienna, Austria* William H. Miller, *University of California, Berkeley, USA* Keiji Morokuma, *Emory University, USA* Hiroshi Nakatsuji, *Quantum Chemistry Research Institute, Japan* Vincent Ortiz, *Auburn University, USA* Manthos Papadopoulos, *National Hellenic Research Foundation, Greece* Peter Politzer, *University of New Orleans, USA* Peter Pulay, *University of Arkansas, USA* Henry F. Schaefer III, *University of Georgia, USA* George C. Schatz, *Northwestern University, USA* Harold A. Scheraga, *Cornell University, USA* H. Bernhard Schlegel, *Wayne State University, USA* Bobby G. Sumpter, *Oak Ridge National Laboratory, USA* All details about registration, abstracts and housing may be found at http://cctcc.icnanotox.org Questions? Email us at cctcc:icnanotox.org Please also feel free to forward this invitation to any potentially interested colleagues. We look forward to seeing you in Jackson this Fall! On behalf of the Organizing Committee, Olexandr Isayev ________________________________ Olexandr Isayev, Ph.D. Department of Chemistry Case Western Reserve University 10900 Euclid Avenue Cleveland, OH 44106-7078 USA Phone: 769 218-9812 Fax: 216 368-3006 http://olexandrisayev.com --000e0cd2bfec42ff9c04a0311114 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
http://cctcc.icnanotox.org<= /div>
=A0
20th Conference on Current Trends in Computational Chemistry (= October 27-29, 2011)
=A0
We would like to invite you and encourage your students, postdoctoral = fellows and colleagues to participate in the 20th anniversary Conference on= Current Trends in Computational Chemistry (20th CCTCC) to be held in Jacks= on, Miss (USA), on October 27-29, 2011.
=A0
To celebrate two decades of success this CCTCC meeting will gather lec= tures by two Nobel laureates and twenty five invited speakers who have made= prominent contributions to the broad field of computational and quantum ch= emistry. It will also provide the opportunity to all members of our communi= ty, researchers and students, to present and discuss their work through sev= eral poster sessions and social events. Contributions in all areas of metho= ds development and applications in theoretical chemistry are welcome.
=A0
Important Date:
Early (discounted) registration and abstract submission is open until = September 1, 2011.
=A0
Venue:
As usual the conference will be held at the Hilton Jackson Hotel, Jack= son, Miss. (USA).
=A0
Confirmed list of invited speakers:
Misako Aida, Hiroshima University, Japan
Axel D. Becke, Dalhousie University, Canada
Roberto Cammi, Universita' di Parma, Italy
Jiali Gao, University of Minnesota, USA
Sharon Hammes-Schiffer, Pennsylvania State University, USA
Istvan Hargittai, Hungarian Academy of Sciences, Hungary
Trygve Helgaker, University of Oslo, Norway
Yasuyuki Ishikawa, University of Puerto Rico, USA
William Jorgensen, Yale University, USA
Miklos Kertesz, Georgetown University, USA
Kwang S. Kim, Pohang University of Science and Technology, Korea
Walter Kohn, University of California, Santa Barbara, USA
Harold W. Kroto, Florida State University, USA
William Lester, Jr., University of California, Berkeley, USA<= /div>
Hans Lischka, University of Vienna, Austria
William H. Miller, University of California, Berkeley, USA
Keiji Morokuma, Emory University, USA
Hiroshi Nakatsuji, Quantum Chemistry Research Institute, Japan
Vincent Ortiz, Auburn University, USA
Manthos Papadopoulos, National Hellenic Research Foundation, Greec= e
Peter Politzer, University of New Orleans, USA
Peter Pulay, University of Arkansas, USA
Henry F. Schaefer III, University of Georgia, USA
George C. Schatz, Northwestern University, USA
Harold A. Scheraga, Cornell University, USA
H. Bernhard Schlegel, Wayne State University, USA
Bobby G. Sumpter, Oak Ridge National Laboratory, USA
=A0
All details about registration, abstracts and housing may be found at = http://cctcc.icnanotox.org
=A0
Questions? Email us at cctcc:ic= nanotox.org
=A0
Please also feel free to forward this invitation to any potentially in= terested colleagues.
=A0
We look forward to seeing you in Jackson this Fall!
=A0
On behalf of the Organizing Committee,
Olexandr Isayev
=A0

________________________________
Olexandr Isayev,= Ph.D.
=A0
Department of Chemistry
Case Western Reserve University=
10900 Euclid Avenue
Cleveland, OH 44106-7078 USA

Phone:=A0=A0= 769 218-9812
Fax:=A0 =A0 =A0=A0 216 368-3006

http://olexandrisayev.com

=A0
=A0
=A0
--000e0cd2bfec42ff9c04a0311114-- From owner-chemistry@ccl.net Tue Apr 5 21:13:01 2011 From: "Peng Yun ericyunp~~gmail.com" To: CCL Subject: CCL: Help in Gaussian Message-Id: <-44299-110405211209-29539-xpAcpMC5XycubwQc4AChTg^server.ccl.net> X-Original-From: "Peng Yun" Date: Tue, 5 Apr 2011 21:12:07 -0400 Sent to CCL by: "Peng Yun" [ericyunp#%#gmail.com] Dear CCLers: I'm trying to calculate the open-shell singlet state of a molecule.I run it from open-shell triplet . After affirming its function's stability , I have to reordering its orbitals , but I have no idea which orbital should be reordered , according to its d-orbital(a transition-metal system) or something else?Is there any references? Any suggestions will be appreciated! Best regards! Peng Yun ericyunp ~~ gmail.com