From owner-chemistry@ccl.net Mon Jun 9 04:17:00 2014 From: "Andras Borosy andras.borosy*givaudan.com" To: CCL Subject: CCL: Movie Recommendation Message-Id: <-50186-140609041239-343-U+SVJjY7jCqa4B1UKx5tBw:_:server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 002D0787C1257CF2_=" Date: Mon, 9 Jun 2014 10:12:31 +0200 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy-$-givaudan.com] This is a multipart message in MIME format. --=_alternative 002D0787C1257CF2_= Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: base64 RGVhciBGcmFuaywNCg0KVGhhbmsgeW91IGZvciB0aGUgcmVjb21tZW5kYXRpb24uIFdoZXJlIGNh biBvbmUgYnV5IGl0Pw0KDQpSZWdhcmRzLA0KDQpBbmRyYXMNCg0KDQoNCkZyb206ICAgIk1hcmNo ZXNlLCBQcm9mLiBGcmFuY2lzIFQuIGZtYXJjaGVzZS8uL3BhY2UuZWR1IiANCjxvd25lci1jaGVt aXN0cnlAY2NsLm5ldD4NClRvOiAgICAgIkJvcm9zeSwgQW5kcmFzIC1pZCM0azMtIiA8YW5kcmFz LmJvcm9zeUBnaXZhdWRhbi5jb20+LCANCkRhdGU6ICAgMDYvMDcvMjAxNCAwNTo0OSBQTQ0KU3Vi 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--=_alternative 002D0787C1257CF2_=-- From owner-chemistry@ccl.net Mon Jun 9 08:10:00 2014 From: "Mark Mackey mark(_)cresset-group.com" To: CCL Subject: CCL: Looking for a conformer generator program Message-Id: <-50187-140609065237-17450-Pe1f1CwbacbqxiJyirWugg!=!server.ccl.net> X-Original-From: Mark Mackey Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 9 Jun 2014 10:52:26 +0000 MIME-Version: 1.0 Sent to CCL by: Mark Mackey [mark ~~ cresset-group.com] Hi Gustavo, Xedex from Cresset meets all your criteria apart from the selenium bit, so I can't recommend it directly. However, I did have a comment to make about your "equivalent conformer" criteria. In most conf gen programs, the RMSD criteria for whether conformers are the same calculate the RMSD only over heavy atoms. Conformers which differ only in OH and NH2 rotamers will thus be filtered out - that may have caused the problem you saw with OpenBabel if your compounds have no other rotatable bonds. To fix this, the conf gen program you use either needs to consider hydrogens (or hydrogens on heteroatoms) when doing the RMSD calculations, or it needs to apply additional filters on torsional angles such that OH rotamers are treated as separate even though the RMSD difference is negligible. We've had to do both of these for xedex as our emphasis on molecular electrostatics means that we have to treat OH and NH2 rotamers quite carefully (the electrostatic potentials can obviously change significantly on hydroxyl rotation!). Most conf gen programs out there do neither of these, so you might find your criteria difficult to meet. Regards, Mark -- Dr Mark Mackey CSO, Cresset -----Original Message----- > From: owner-chemistry+mark==cresset-bmd.com:-:ccl.net [mailto:owner-chemistry+mark==cresset-bmd.com:-:ccl.net] On Behalf Of Gustavo L.C. Moura gustavo.moura*_*ufpe.br Sent: 05 June 2014 23:31 To: Mark Mackey Subject: CCL: Looking for a conformer generator program Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura=ufpe.br] Dear CCL community, I have been searching for a conformer generator program that can handle acyclic compounds (none of my molecules have flexible rings, yet). I have already tested a few programs, and so far, none has worked to my satisfaction. The program I am looking for should obey some requirements. The requirements are: 1) The program should use the RMSD of the coordinates to check for equivalent conformers. The first program that I tested employed only the energy to differentiate conformers and was unable to differentiate non-superimposable conformers that happen to have the same energy. 2) I am not overly concerned with the quality of the molecular mechanics forcefield that will be employed by the program to optimize the geometries of the conformers because I will reoptimize them with quantum chemical methods. However, I need to have a forcefield that is able to handle selenium atoms. 3) The program should be capable of generating conformers resulting from the rotation around C-OH and C-NH2 bonds. My interest is in the spectroscopic properties (UV-VIS and NMR) of my molecules and rotations around such bonds are very important to me. So, does anyone on the list know of a conformer generator program that has the characteristics above? Thank you very much in advance. Sincerely yours, Gustavo L.C. Mourahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Jun 9 09:27:00 2014 From: "Ramy EHab Farag romio.1001(~)yahoo.com" To: CCL Subject: CCL: Attachment of dyes on Titanium oxide Message-Id: <-50188-140609092506-24194-nJwagJB1cFSjtRF49FTlVA{}server.ccl.net> X-Original-From: "Ramy EHab Farag" Date: Mon, 9 Jun 2014 09:25:05 -0400 Sent to CCL by: "Ramy EHab Farag" [romio.1001 ~~ yahoo.com] - How to draw Titanium oxide (TiO2)38 and attaching it with an organic dye using Gaussview 05 ? - The dye has cyanoacrylic acid , will the attachment be with one oxygen or two oxygens ? , and what kind of bond & length ? From owner-chemistry@ccl.net Mon Jun 9 12:19:00 2014 From: "Ramesh Kumar rameshchitumalla:gmail.com" To: CCL Subject: CCL: Attachment of dyes on Titanium oxide Message-Id: <-50189-140609121819-3113-9HCU1e1MCR8M9R9kX4ZUTQ ~ server.ccl.net> X-Original-From: Ramesh Kumar Content-Type: multipart/alternative; boundary=047d7bd6ba707c14ec04fb698ece Date: Mon, 9 Jun 2014 21:48:07 +0530 MIME-Version: 1.0 Sent to CCL by: Ramesh Kumar [rameshchitumalla---gmail.com] --047d7bd6ba707c14ec04fb698ece Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Ramy EHab Farag, It is difficult to build the (TiO2)38 cluster using Gaussview 05. It is possible to attache your dye (If I am correct, your dye may be organic D-Pi-A dye with Cyanoacrylic acid as anchoring group) to the (TiO2)38 using Gaussview. For the information regarding how to attach and approximate bond distances from dye to TiO2 you can refer recent PCCP article, ( http://pubs.rsc.org/EN/content/articlelanding/2014/cp/c3cp53613k#!divAbstra= ct). *DOI: * 10.1039/C3CP53613K =E2=80=8BHope it helps you. Regards Dr. Ramesh Kumar Chitumalla.=E2=80=8B On Mon, Jun 9, 2014 at 6:55 PM, Ramy EHab Farag romio.1001(~)yahoo.com < owner-chemistry . ccl.net> wrote: > > Sent to CCL by: "Ramy EHab Farag" [romio.1001 ~~ yahoo.com] > - How to draw Titanium oxide (TiO2)38 and attaching it with an organic dy= e > using Gaussview 05 ? > > - The dye has cyanoacrylic acid , will the attachment be with one oxygen > or two oxygens ? , and what kind of bond & length ? > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 *Best Regards* *CH. Ramesh Kumar* Senior Research fellow Computational Chemistry Lab-II, Indian Institute of Chemical technology, Tarnaka, Hyderabad- 500007 --047d7bd6ba707c14ec04fb698ece Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear Ramy EHab Farag,
It is difficult to build the (TiO2)38 cluster using Gaussview 05.

It is possible to attache your dye (I= f I am correct, your dye may be organic D-Pi-A dye with Cyanoacrylic acid a= s anchoring group) to the (TiO2)38 using Gaussview. For the information reg= arding how to attach and approximate bond distances from dye to TiO2 you ca= n refer recent PCCP article, (http://pubs.rsc.org/EN/content= /articlelanding/2014/cp/c3cp53613k#!divAbstract). DOI: 10.1039/C3CP53613K =C2=A0 =C2= =A0


=E2=80=8BHope it helps you.=

Regards

Dr. Ramesh Kumar Chitumalla.=E2=80=8B




On Mon, Jun 9, 2014 at 6:55 PM, Ramy EHab Farag romio.1001(~)yahoo.com <owner-chemistry . ccl.net= > wrote:

Sent to CCL by: "Ramy EHab Farag" [romio.1001 ~~ yahoo.com]
- How to draw Titanium oxide (TiO2)38 and attaching it with an organic dye = using Gaussview 05 ?

- The dye has cyanoacrylic acid , will the attachment be with one oxygen or= two oxygens ? , and what kind of bond & length ?



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--
<= p>Best Regards=

CH.= Ramesh Kumar
Senior Research fellow
Computational Chemistry Lab-II,
Indian Institute = of Chemical technology,
Tarnaka,
Hyderabad- 500007


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