From owner-chemistry@ccl.net Wed Jan 13 01:36:01 2010 From: "Daniil Bratashov dn2010-*-gmail.com" To: CCL Subject: CCL: freq computation Message-Id: <-41037-100112164947-10992-72VrLE5++047W8ajpucSqA-.-server.ccl.net> X-Original-From: Daniil Bratashov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Tue, 12 Jan 2010 23:46:38 +0300 Mime-Version: 1.0 Sent to CCL by: Daniil Bratashov [dn2010::gmail.com] On Tue, 12 Jan 2010 14:50:09 -0500 "Close, David M. CLOSED]-[mail.etsu.edu" wrote: > There used to be a free program available to perform this > distortion. macmolplt (http://www.scl.ameslab.gov/MacMolPlt/) can do such thing with View->Offset along mode. WBR, Daniil Bratashov. From owner-chemistry@ccl.net Wed Jan 13 03:57:01 2010 From: "Pau Farras pfarras[-]icmab.es" To: CCL Subject: CCL: Radical Vs Anionic Message-Id: <-41038-100113035415-14994-yj41I0he3mUeXjdJN4yGkQ++server.ccl.net> X-Original-From: "Pau Farras" Date: Wed, 13 Jan 2010 03:54:11 -0500 Sent to CCL by: "Pau Farras" [pfarras^_^icmab.es] Good morning! I've got a problem with a reaction mechanism were a compound is broken in an anionic molecule and an iodine. The issue is that this iodine can leave as a radical or an anion. From experimental evidence it seems that the radical pathway is favoured although my calculations indicate that the formation of the I(-1) is energetically less demanding. I was wondering how to calculate a possible transition state for this reaction but I cannot imagine a why about how to distinguish between the I(0) and I(-1). What I've tried is to separate the iodine from the compound and calculate a TS, but in this case I cannot specify the charge of this leaving iodine. Has anybody any idea about how to do that? Thank you! From owner-chemistry@ccl.net Wed Jan 13 05:40:01 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= uekstrom+*+gmail.com" To: CCL Subject: CCL: Radical Vs Anionic Message-Id: <-41039-100113052540-16704-uUisTt9BVjBRr6nQmwBD1g.:.server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 13 Jan 2010 11:25:28 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [uekstrom|*|gmail.com] > I've got a problem with a reaction mechanism were a compound is broken in= an anionic molecule and an iodine. The issue is that this iodine can leave= as a radical or an anion. From experimental evidence it seems that the rad= ical pathway is favoured although my calculations indicate that the formati= on of the I(-1) is energetically less demanding. > I was wondering how to calculate a possible transition state for this rea= ction but I cannot imagine a why about how to distinguish between the I(0) = and I(-1). What I've tried is to separate the iodine from the compound and = calculate a TS, but in this case I cannot specify the charge of this leavin= g iodine. > Has anybody any idea about how to do that? If anion+I(-1) is the lower energy configuration, then molecule+I(0) will be an electronically excited state. If your molecule has high symmetry it may be possible to classify the symmetry of this excited state and directly optimize its wavefunction (using i.e. MCSCF). Otherwise you can calculate the excitation energies of the ground state and try to identi= fy the charge transfer states which would leave the iodine atom neutral. Note that because this will be a charge transfer state you cannot use "normal" time dependent density functional theory to get the excitation energies. There might be other tricks to directly computing the excited state with some sort of constrained optimization, even if your system has no symmetry, perhaps some other person has some idea? Sincerely, Ulf Ekstr=F6m From owner-chemistry@ccl.net Wed Jan 13 08:44:01 2010 From: "John McKelvey jmmckel^-^gmail.com" To: CCL Subject: CCL: Radical Vs Anionic Message-Id: <-41040-100113083538-6570-E0q8qCdrFQFobsmUgWleHQ]=[server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 13 Jan 2010 08:28:07 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel*gmail.com] Since anions don't like "vacuum" very much, if at all, is the calculation disturbed by not including some sort of solvation? John McKelvey 2010/1/13 Ulf Ekstr=F6m uekstrom+*+gmail.com : > > Sent to CCL by: ?ISO-8859-1?Q?Ulf_Ekstr=F6m? [uekstrom|*|gmail.com] >> I've got a problem with a reaction mechanism were a compound is broken i= n an anionic molecule and an iodine. The issue is that this iodine can leav= e as a radical or an anion. From experimental evidence it seems that the ra= dical pathway is favoured although my calculations indicate that the format= ion of the I(-1) is energetically less demanding. >> I was wondering how to calculate a possible transition state for this re= action but I cannot imagine a why about how to distinguish between the I(0)= and I(-1). What I've tried is to separate the iodine from the compound and= calculate a TS, but in this case I cannot specify the charge of this leavi= ng iodine. >> Has anybody any idea about how to do that? > > If anion+I(-1) is the lower energy configuration, then molecule+I(0) > will be an electronically excited state. If your molecule has high symmet= ry > it may be possible to classify the symmetry of this excited state and > directly optimize its wavefunction (using i.e. MCSCF). Otherwise you > can calculate the excitation energies of the ground state and try to iden= tify > the charge transfer states which would leave the iodine atom neutral. > Note that because this will be a charge transfer state you cannot use > "normal" time dependent density functional theory to get the excitation > energies. There might be other tricks to directly computing the excited > state with some sort of constrained optimization, even if your system has > no symmetry, perhaps some other person has some idea? > > Sincerely, > Ulf Ekstr=F6m > > > > - This is automatically added to each message by the mailing script -> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > --=20 John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel~~gmail.com From owner-chemistry@ccl.net Wed Jan 13 11:45:01 2010 From: "Serge Gorelsky sgorelsk**uottawa.ca" To: CCL Subject: CCL: freq computation Message-Id: <-41041-100113083703-6738-fXiAtCTXmcEsuf3eAk9hyw(_)server.ccl.net> X-Original-From: Serge Gorelsky Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8 Date: Wed, 13 Jan 2010 08:06:20 -0500 MIME-Version: 1.0 Sent to CCL by: Serge Gorelsky [sgorelsk,uottawa.ca] http://www.sg-chem.net/alp-vibro/ can do this > On Tue, 12 Jan 2010 14:50:09 -0500 > "Close, David M. CLOSED]-[mail.etsu.edu" > wrote: > >> =C2=A0 There used to be a free program available to perform this >> distortion. > --=20 Best regards, Serge Gorelsky From owner-chemistry@ccl.net Wed Jan 13 13:00:01 2010 From: "Andrew Voronkov drugdesign!^!yandex.ru" To: CCL Subject: CCL: OpenEye software users Message-Id: <-41042-100113125823-3246-5QGIKkhQf/0u6MisCydo7g%a%server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 13 Jan 2010 20:58:09 +0300 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign!=!yandex.ru] Dear CCL users, are there any OpenEye software users? I have a series of questions to them. It would be also nice to make a mailing list for it probably. Best regards, Andrew From owner-chemistry@ccl.net Wed Jan 13 15:50:00 2010 From: "Andrew Dalke dalke,+,dalkescientific.com" To: CCL Subject: CCL: OpenEye software users Message-Id: <-41043-100113153928-13731-XnHnDmaKnB/kXR+85E3e3w~!~server.ccl.net> X-Original-From: Andrew Dalke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Wed, 13 Jan 2010 20:39:17 +0100 Mime-Version: 1.0 (Apple Message framework v1077) Sent to CCL by: Andrew Dalke [dalke#dalkescientific.com] On Jan 13, 2010, at 6:58 PM, Andrew Voronkov drugdesign!^!yandex.ru wrote: > are there any OpenEye software users? I am one, and quite happy with the parts I use. > I have a series of questions to them. Sure. I mostly work with the toolkits, and not Vida, Rocs, or other application level components, which makes me a distinct minority. > It would be also nice to make a mailing list for it probably. Lists are easy to start. You just have to figure out the purpose and get people interested enough to join up. Andrew dalke{}dalkescientific.com