From owner-chemistry@ccl.net Wed Sep 15 00:41:01 2010 From: "Sayed Mesa elsayed.elmes]![yahoo.com" To: CCL Subject: CCL:G: Energy partitioning analysis + Gaussian 09 Message-Id: <-42765-100914234605-28386-0JmAIz969NwWaNOyo3GRzw=server.ccl.net> X-Original-From: "Sayed Mesa" Date: Tue, 14 Sep 2010 23:46:05 -0400 Sent to CCL by: "Sayed Mesa" [elsayed.elmes#,#yahoo.com] Dear CCL Community, It is known that ADF programis able to do "Energy partitioning analysis". My question: is Gaussian program able to do such partitioning? Thanks in advance, Sayed From owner-chemistry@ccl.net Wed Sep 15 05:28:00 2010 From: "Dipl.-Ing. Thomas Mitterfellner thomas.mitterfellner!^!tugraz.at" To: CCL Subject: CCL: How to make an enantiomer? Message-Id: <-42766-100915051810-8193-81+17j4dScK9Hg7UX0c+Ew_._server.ccl.net> X-Original-From: "Dipl.-Ing. Thomas Mitterfellner" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Wed, 15 Sep 2010 11:17:57 +0200 MIME-Version: 1.0 Sent to CCL by: "Dipl.-Ing. Thomas Mitterfellner" [thomas.mitterfellner a tugraz.at] You can also use a shell script (requires an xyz file and awk): #!/bin/bash # 2009 # Requires awk if [ $# -lt 2 ] then echo echo 'Script for generating an enantiomers from an xyz file' echo echo 'Syntax: enant ' echo exit fi awk '{ if (NF == 4) {printf("%2s %12.6f %12.6f %12.6f\n", $1, -$2, -$3, -$4)} else {print} }' $1 > $2 As a sidenote: the command line tool babel comes in very handy when you want to convert from some coordinate file to another (eg. mol2 to xyz). I hope this helps! Thomas From owner-chemistry@ccl.net Wed Sep 15 07:52:00 2010 From: "Marcel Swart marcel.swart^icrea.es" To: CCL Subject: CCL: Density Functionals 2010 (15 days left) Message-Id: <-42767-100915031613-18458-QUMMMr75MM7wzm02Pim1ig . server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-5--862399811 Date: Wed, 15 Sep 2010 09:16:01 +0200 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Marcel Swart [marcel.swart]|[icrea.es] --Apple-Mail-5--862399811 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 There are only 15 days left before the Oct. 1 deadline, so please add your preferences for density functionals: We have recently hosted the IXth Girona Seminar = (http://iqc.udg.edu/gs2010/), which had Density Functional Theory as one of the topics. One of the = things that came up was the popularity of current density functionals, and how = these could be used to generate a "consensus" DFT method by taking a linear combination of a number of popular DFT methods. This "consensus" method will probably be more accurate than the GFSRPM method that was also revealed during the conference, and therefore we have setup a popularity poll for density functional methods for the year 2010. The number of density functionals is limited by choice to 20, with 5-10 = places reserved for additional suggestions; in future editions this may be = extended. Please add your choice for the best (and worst) density functional at: http://bit.ly/cQPX2w The poll is open until Oct. 1 after which a ranking will be made. =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 Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart||icrea.es 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 =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 Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart||icrea.es 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-5--862399811 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 http://iqc.udg.edu/gs2010/),=
which had Density Functional Theory as one of the topics. One of = the things
that came up was the popularity of current density = functionals, and how these
could be used to generate a = "consensus" DFT method by taking a linear
combination of a = number of popular DFT methods.

This = "consensus" method will probably be more accurate = than
the GFSRPM method that was also revealed during the = conference,
and therefore we have setup a popularity poll for = density functional
methods for the year = 2010.

The number of density functionals is = limited by choice to 20, with 5-10 places
reserved for = additional suggestions; in future editions this may be = extended.
Please add your choice for the best (and worst) = density functional at:

http://bit.ly/cQPX2w

The poll is open until = Oct. 1 after which a ranking will be made.

=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

Parc Cient=EDfic i = Tecnol=F2gic
Edifici Jaume Casademont (despatx = A-27)
Pic de Peguera 15
17003 Girona

+34-972-183240
fax
e-mail





=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

Parc Cient=EDfic i = Tecnol=F2gic
Edifici Jaume Casademont (despatx = A-27)
Pic de Peguera 15
17003 Girona

+34-972-183240
fax
e-mail


= --Apple-Mail-5--862399811-- From owner-chemistry@ccl.net Wed Sep 15 10:55:00 2010 From: "Serge Gorelsky gorelsky]=[gmail.com" To: CCL Subject: CCL:G: Energy partitioning analysis + Gaussian 09 Message-Id: <-42768-100915105328-8820-T4PNQ33v7E0zUNtoWYA9Tw(~)server.ccl.net> X-Original-From: Serge Gorelsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 15 Sep 2010 10:52:22 -0400 MIME-Version: 1.0 Sent to CCL by: Serge Gorelsky [gorelsky!=!gmail.com] Gaussian with AOMix-prepared input files (http://www.sg-chem.net) can be used to do parts of the EDA (energy decomposition analysis). Please refer to pages 34-35 in the AOMix manual (http://www.sg-chem.net/aomix/AOMix-manual.pdf) about the details. S.G. On Tue, Sep 14, 2010 at 11:46 PM, Sayed Mesa elsayed.elmes]![yahoo.com wrote: > > Sent to CCL by: "Sayed  Mesa" [elsayed.elmes#,#yahoo.com] > Dear CCL Community, > It is known that ADF programis able to do "Energy partitioning analysis". My question: is Gaussian program able to do such partitioning? > > Thanks in advance, > Sayed>      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 Wed Sep 15 11:29:01 2010 From: "Serge Gorelsky gorelsky###gmail.com" To: CCL Subject: CCL:G: Energy partitioning analysis + Gaussian 09 Message-Id: <-42769-100915105825-10460-nQ4x/dPAAMz9i77JT9yEYw-,-server.ccl.net> X-Original-From: Serge Gorelsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 15 Sep 2010 10:52:22 -0400 MIME-Version: 1.0 Sent to CCL by: Serge Gorelsky [gorelsky%a%gmail.com] Gaussian with AOMix-prepared input files (http://www.sg-chem.net) can be used to do parts of the EDA (energy decomposition analysis). Please refer to pages 34-35 in the AOMix manual (http://www.sg-chem.net/aomix/AOMix-manual.pdf) about the details. S.G. On Tue, Sep 14, 2010 at 11:46 PM, Sayed Mesa elsayed.elmes]![yahoo.com wrote: > > Sent to CCL by: "Sayed  Mesa" [elsayed.elmes#,#yahoo.com] > Dear CCL Community, > It is known that ADF programis able to do "Energy partitioning analysis". My question: is Gaussian program able to do such partitioning? > > Thanks in advance, > Sayed>      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 Wed Sep 15 12:51:00 2010 From: "Justin Finnerty justin.finnerty:+:uni-oldenburg.de" To: CCL Subject: CCL:G: Which is the best way to work with N-OXIDES? Message-Id: <-42770-100915103458-28832-d5/6i4Hijc1UnMcm/dezAw^-^server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 15 Sep 2010 08:28:29 +0200 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty:uni-oldenburg.de] On Tue, 2010-09-14 at 20:37 -0400, Miguel A. Quiliano rifaximina^gmail.com wrote: > Sent to CCL by: "Miguel A. Quiliano" [rifaximina a gmail.com] > Hello CCL users. > > I am a new user of this forum so please be patient jeje. > > Recently, I have a problem, but basically it`s a doubt. I have performed geometrical optimization of one compound (by the way I`m not an expert using QM). It`s a derivate N-oxide. > > In the paper is: after Gaussian, using Gaussview I see this: > > o o > / - \ // ---\ // > I C-C / C- C > I Ar I \ I I \ > I I C- R I Ar I C - R > I I // I I // > \ C- N(+) \ C - N > \ - / / ---- / // > O(-) O The lack of charge is due to the calculation being implicitly calculated in a "gas phase", which will favour a neutral molecule. To obtain the charge species you will need to calculate the molecule in a simulated solvent (probably methanol or water). Note that the QM solvent phase are a continuum model so do not add actual solvent molecules to the calculation so no H-bonding is possible. If you are modelling REDOX in a solvent with H-bonds then you will need to add solvent molecules as well as using the solvent phase model. The PM3 theory is considered very low-level, and will require verification by comparison to experiment or a higher level QM method. If you are going to do a series of these molecules I would suggest doing at least one structure using DFT to compare with the (very) low level PM3 calculations. For example molecules this size using B3LYP/6-31G* takes less than an hour to optimise on my 5yr old desktop. However B3LYP/6-31G* level of theory is considered small these days, so something like B3LYP/6-311+G* would be considered a minimum for your molecule. (As you will need a PM3 frequency calculation to verify that the molecule is a stationary point, optimising from the PM3 geometry using B3LYP/6-311+G* with reading in the PM3 force constants should help reduce the calculation time.) Cheers Justin Finnerty From owner-chemistry@ccl.net Wed Sep 15 14:15:00 2010 From: "Jamin Krinsky jamink^berkeley.edu" To: CCL Subject: CCL:G: Which is the best way to work with N-OXIDES? Message-Id: <-42771-100915140616-766-AOEdAq6Wr8go0ziSJzvvsA(-)server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 15 Sep 2010 11:06:04 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink+/-berkeley.edu] Miguel, With any QM calculation, you only supply the coordinates (and elements) of atoms and overall charge and multiplicity of the system. Bond orders are not used in the calculation, so draw it however you want and it will come out the same (this is NOT true for molecular mechanics calculations). Note that there is no QM expectation value for bond order, so it's meaning in QM theory is not very well defined anyway. Regards, Jamin On Tue, Sep 14, 2010 at 5:43 PM, Miguel Quiliano Meza rifaximina/./gmail.com wrote: > Hello CCL users. > > I am a new user of this forum so please be patient jeje. > > Recently, I have a problem, but basically it`s a doubt. I have performed > geometrical optimization of one compound (by the way I`m not an expert using > QM). It`s a derivate N-oxide. > > > In the paper is: after Gaussian, using Gaussview I see this: > > o o > / - \ // ---\ // > I C-C / C- C > > I Ar I \ I I \ > I I C- R I Ar I C - R > I I // I I // > \ C- N(+) \ C - N > > \ - / / ---- / // > O(-) O > > > I set a simple "# opt pm3 geom=connectivity". I want to study REDOX > properties, but N(+)-O(-) seems totally different to N=O, Although you can > see that nitrogen continuous with 5 bonds, I missed the N-O > > > What do you think about this?? is correct the set of bonds between N=O? I > know that partial double bond is present but is it acceptable for my > objetive? If you were me, what should I do to prevent a posible mistake? > What would you have done, if you have wanted a good conformation to work?? > > Sorry for the long message, perhaps this problem is very easy for you. > > I would be grateful if someone can help me or give me advices > Thanks in advance. > > M.Q > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink++berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Wed Sep 15 18:16:00 2010 From: "Michael Dimitrov mich.dimitrov-,-gmail.com" To: CCL Subject: CCL: ONIOM literature Message-Id: <-42772-100915154209-10413-45xLHN6UZ23bRGEx6JQIgg*server.ccl.net> X-Original-From: Michael Dimitrov Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 15 Sep 2010 23:41:59 +0400 MIME-Version: 1.0 Sent to CCL by: Michael Dimitrov [mich.dimitrov##gmail.com] Hi, In the review J. Mol. Cat. A: Chem. 2010, 324, 104 (http://dx.doi.org/10.1016/j.molcata.2010.03.015 ) Morokuma has compiled recent ONIOM calculations and especially Table 1 in the article is of interest. Looks like DFT:MM or DFT:HF levels were mostly used for transition metal systems. I am wondering, if DFT:Semiempirical can replace DFT:HF with similar accuracy? (in my system DFT:MM gives unreliable geometry, probably due to incorrect treatment of electronic effects). Best regards, Michael Dimitrov. From owner-chemistry@ccl.net Wed Sep 15 22:17:01 2010 From: "zouzou adnani zinebeladnani-*-hotmail.com" To: CCL Subject: CCL: sulfur with 6-31G** and lanl2dz Message-Id: <-42773-100915221511-30350-FTXi51Bp2IOE0vnDhT/gXA|*|server.ccl.net> X-Original-From: "zouzou adnani" Date: Wed, 15 Sep 2010 22:15:10 -0400 Sent to CCL by: "zouzou adnani" [zinebeladnani#,#hotmail.com] hi I'm working on the geometry optimisation of the some quinoxaline derivatives using different basis set , in most of my systems I have almost the same energies with both 6-31G(d,p) and lanl2dz basis sets, except in those containing sulfur atoms, can anyone tell me why? Thanks for taking the time to read this! Regards, Zineb el adnani