From owner-chemistry@ccl.net Sat Sep 4 05:29:01 2010 From: "Shirin Seifert shirin.seifert**gmail.com" To: CCL Subject: CCL:G: Tunneling Barrier Message-Id: <-42689-100904052430-26192-swQmpcoCH44LJO6MEE4Amw#server.ccl.net> X-Original-From: Shirin Seifert Content-Type: multipart/alternative; boundary=000e0cd6a9f0fe2aae048f6b9ce3 Date: Sat, 4 Sep 2010 13:54:24 +0430 MIME-Version: 1.0 Sent to CCL by: Shirin Seifert [shirin.seifert-,-gmail.com] --000e0cd6a9f0fe2aae048f6b9ce3 Content-Type: text/plain; charset=ISO-8859-1 Dear All, How to compute the tunneling barrier in an undriven molecule which has been relaxed into one dipole state. Or in other words I would like to draw the double-well diagram for a specific undriven molecule, familiar in the literature of mixed-valance compounds. The computations are to be done using Gaussian 09W. Thanks for your suggestions in advance. Best regards, SS --000e0cd6a9f0fe2aae048f6b9ce3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,

How to compute the tunneling barrier in an undriven molecu= le which has been relaxed into one dipole state. Or in other words I would = like to draw the double-well diagram for a specific undriven=A0 molecule, f= amiliar in the literature of mixed-valance compounds. The computations are = to be done using Gaussian 09W.

Thanks for your suggestions in advance.

Best regards,
SS
<= br>
--000e0cd6a9f0fe2aae048f6b9ce3-- From owner-chemistry@ccl.net Sat Sep 4 06:04:00 2010 From: "ABHISHEK SHAHI shahi.abhishek1984!A!gmail.com" To: CCL Subject: CCL: 6 degree of freedom for linear molecule ?????? Message-Id: <-42690-100904055721-18977-GGoKle6ScL/KW7ArZtvDRA~~server.ccl.net> X-Original-From: ABHISHEK SHAHI Content-Type: multipart/alternative; boundary=0016367b668a6d9cd4048f6c12ac Date: Sat, 4 Sep 2010 15:27:15 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984(0)gmail.com] --0016367b668a6d9cd4048f6c12ac Content-Type: text/plain; charset=ISO-8859-1 Dear All Here optimization give a linear geometry but on frequency calculation, Job gives 6(translational+rotational) frequencies and they are negative enough to make any sense.My route section is "# MP2=full/aug-cc-PVTZ opt=(verytight,maxcycle=100) nosymm freq=noraman scf=(xqc,vshift=150,tight)".And same problem is faced by me several other complexes.Please help me in this problem.your suggestions are valuable for me. Errors ::::: Full mass-weighted force constant matrix: Low frequencies --- -378.7133 -378.7122 -215.1945 -215.1944 0.0043 0.0046 Low frequencies --- 0.0060 714.7626 2094.2659 Molecule is linear but NTrRo=6. Error termination via Lnk1e in /home/pkg/lic/g09/em64t/g09/l716.exe at Fri Sep 3 19:32:28 2010. Job cpu time: 0 days 3 hours 7 minutes 24.7 seconds. With regards; *ABHISHEK SHAHI* IISc bangalore-12 Official E-mail: shahi/a\ipc.iisc.ernet.in CC: shahi.abhishek1984/a\gmail.com --0016367b668a6d9cd4048f6c12ac Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All

=A0=A0=A0 Here optimization give a linear geometry but on f= requency calculation, Job gives 6(translational+rotational) frequencies and= they are negative enough to make any sense.My route section is "# MP2= =3Dfull/aug-cc-PVTZ opt=3D(verytight,maxcycle=3D100) nosymm freq=3Dnoraman = scf=3D(xqc,vshift=3D150,tight)".And same problem is faced by me severa= l other complexes.Please help me in this problem.your suggestions are valua= ble for me.

Errors :::::





Full mass-weighted force constant m= atrix:
=A0Low frequencies --- -378.7133 -378.7122 -215.1945 -215.1944=A0= =A0=A0 0.0043=A0=A0=A0 0.0046
=A0Low frequencies ---=A0=A0=A0 0.0060=A0 = 714.7626 2094.2659
=A0Molecule is linear but NTrRo=3D6.
=A0Error termination via Lnk1e in /= home/pkg/lic/g09/em64t/g09/l716.exe at Fri Sep=A0 3 19:32:28 2010.
=A0Jo= b cpu time:=A0 0 days=A0 3 hours=A0 7 minutes 24.7 seconds.



=

With regards;
=A0<= font size=3D"4">ABHISHEK SHAHI
=A0 IISc bangalore-12
=A0 Official E-mail: shahi/a\ipc.iisc.ernet.in
=A0 CC:=A0 <= a href=3D"mailto:shahi.abhishek1984/a\gmail.com" target=3D"_blank">shahi.abhi= shek1984/a\gmail.com
--0016367b668a6d9cd4048f6c12ac-- From owner-chemistry@ccl.net Sat Sep 4 06:38:00 2010 From: "Tristan Youngs t.youngs[-]qub.ac.uk" To: CCL Subject: CCL: soft for molecular construction Message-Id: <-42691-100904063306-8976-1mQ8f5oIc1MwnUwh+a3Igg++server.ccl.net> X-Original-From: "Tristan Youngs" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 4 Sep 2010 11:32:59 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: "Tristan Youngs" [t.youngs*_*qub.ac.uk] At the risk of shamelessly self-promoting, you could try out Aten (http://www.projectaten.net). It will certainly do what you want (I have used it with 100,000 atoms in the past). Cheers, Tris. > > Sent to CCL by: Eduard Matito [ematito-#-gmail.com] > Hi, > > Can anyone recommend me a good *free* software to build up molecules? > I would need it to run under Mac > and deal with large molecules (say hundreds of atoms). So far I was > using molden, but now capabilities such > as copy-paste, rotation of translation of small fragments in the > molecule would be highly desirable. > > Thanks in advance, > > Eduard > From owner-chemistry@ccl.net Sat Sep 4 10:28:00 2010 From: "Jeffrey Mo jdmo . mit.edu" To: CCL Subject: CCL:G: Potential energy scans on Gaussian - Possible From Initial Geometry? Message-Id: <-42692-100903222903-25316-TgiT94VD3CdeBrarOhPGYw]_[server.ccl.net> X-Original-From: "Jeffrey Mo" Date: Fri, 3 Sep 2010 22:29:00 -0400 Sent to CCL by: "Jeffrey Mo" [jdmo]=[mit.edu] Hi everyone, My first post! Hopefully I'll get some help from you guys and be able to give some help in the future too. I'm trying to perform a potential energy scan (PES) on short-chain alkyl/alkenyl radical transition states right now, and am running into a problem. Gaussian starts each new optimization in the scan from the previous geometry; therefore, when I get all the way around (360 degrees) a dihedral, for instance, I often don't end up at the same geometry. Is there a way that I can ask Gaussian to perform each new optimization from the initial geometry? That is, let's say we're on scan job #19 of a 36-point dihedral scan (where each scan increments by 10 degrees) -- then, I just want to change the relevant dihedral by 180 degrees from the initial geometry, not by 10 degrees from the geometry of scan job #18. Thanks in advance! Jeffrey Mo MIT Chemical Engineering Doctoral Candidate jdmo(a)mit.edu From owner-chemistry@ccl.net Sat Sep 4 12:23:00 2010 From: "Geoffrey Hutchison geoffh,+,pitt.edu" To: CCL Subject: CCL: soft for molecular construction Message-Id: <-42693-100904122046-6948-4GyjGPRYmQSs2J3RR2gdPQ-*-server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Sat, 04 Sep 2010 12:20:36 -0400 MIME-version: 1.0 (Apple Message framework v1081) Sent to CCL by: Geoffrey Hutchison [geoffh[*]pitt.edu] > Can anyone recommend me a good *free* software to build up molecules? I would need it to run under Mac > and deal with large molecules (say hundreds of atoms). I'm biased, but I think Avogadro http://avogadro.openmolecules.net/ is the best molecule builder and certainly can deal with biomolecules. I develop Avogadro on the Mac, and there are nightly builds of both "stable" and "development" versions: http://avogadro.openmolecules.net/nightly/mac/ Avogadro for Mac includes support for drag-and-drop of files, double-click in the Finder... all the usual goodies. Best regards, -Geoff P.S. I do like Aten -- I think it's very good for building repeating systems like crystals, nanotubes, solvent for MD, etc. --- Prof. Geoffrey Hutchison Assistant Professor, Department of Chemistry University of Pittsburgh http://hutchison.chem.pitt.edu/ Office: (412) 648-0492 From owner-chemistry@ccl.net Sat Sep 4 13:29:00 2010 From: "Arvydas.Tamulis]|[tfai.vu.lt" To: CCL Subject: CCL: Two Variable Quantum Entangled OR Logic Gates Message-Id: <-42694-100904120839-21232-biu6mXxyruqyiyLnuwqQDw~!~server.ccl.net> X-Original-From: Arvydas.Tamulis()tfai.vu.lt Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Sat, 04 Sep 2010 19:08:25 +0300 MIME-Version: 1.0 Sent to CCL by: Arvydas.Tamulis- -tfai.vu.lt Dear Colegues, Who can provide me literature or Truth Tables concerning Two Variable Quantum Entangled OR Logic Gates ? Thanking your in advance. With best regards, Arvydas Tamulis http://www.itpa.lt/~tamulis/