From owner-chemistry@ccl.net Tue Jul 29 08:50:00 2008 From: "Yangsoo Kim vsmember===gmail.com" To: CCL Subject: CCL: Family/Functional Group Identification From 2D/3D mol file Message-Id: <-37434-080729084009-27350-1o9enmOXiGEeBxE4sfyklw:server.ccl.net> X-Original-From: "Yangsoo Kim" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 29 Jul 2008 21:10:41 +0900 MIME-Version: 1.0 Sent to CCL by: "Yangsoo Kim" [vsmember[#]gmail.com] Dear All, I'm looking for a program that can automatically determine the family and/or functional group of molecule from a kind of a 2D or 3D molfile. The groups I want to identify are the followings (total of 31 groups): (1)n-alkane, (2)iso-alkne, (3)cyclo-alkane, (4)n-alkene, (5)iso-alkene, (6)aromatics, (7)alcohol, (8)ketone, (9)aldehyde, (10)acetic acid, (11) ether, (12)ester, (13)hydroperoxide, (14)peroxide, (15)formic acid, (16) amide, (17)amine, (18)imines, (19)azo, (20)cyanate, (21)isocynate, (22) nitrate, (23)nitrile, (24)nitrite, (25)nitro, (26)pyridine, (27)pyrrole, (28)sulfide, (29)sulfoxide, (30)thiol, (31)thiophene I found checkmol (http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html) so far, but some groups are missing in this software. Any information related to this matter will greatly be appreciated. Many thanks in advance, YangSoo Kim. From owner-chemistry@ccl.net Tue Jul 29 09:24:00 2008 From: "Raj S r.subramanian(~)ipc.uni-stuttgart.de" To: CCL Subject: CCL:G: vibration visualization Message-Id: <-37435-080729085305-29574-FA0b0RqRbeMADKOVT1Kp7w{=}server.ccl.net> X-Original-From: "Raj S" Date: Tue, 29 Jul 2008 08:53:01 -0400 Sent to CCL by: "Raj S" [r.subramanian(_)ipc.uni-stuttgart.de] Dear CCL members, Is there a way to hide hydrogen atoms in Molekel 5.3 ???...and view the rest of the atoms vibrating....I could only make .ps files of all atoms vibrating with arrows... or if there is some other (free) software to view the molecular vibration (normal modes) from G03 freq output kindly inform me. thanks for your help regards, raj From owner-chemistry@ccl.net Tue Jul 29 10:08:01 2008 From: "Norma L Rangel Norma.Rangel%%chemail.tamu.edu" To: CCL Subject: CCL: n=4 electron basis set for Au Message-Id: <-37436-080729093624-24554-adt7VlczUyYyJAHbkK4vKw * server.ccl.net> X-Original-From: "Norma L Rangel" Date: Tue, 29 Jul 2008 09:36:20 -0400 Sent to CCL by: "Norma L Rangel" [Norma.Rangel_._chemail.tamu.edu] Dear CCLers, The Gold atom in the LANL2DZ uses only 19 ("valence") electrons thus the Au has the following term 5s2 5p6 5d10 6s1 the other electrons 1s2 2s2 2p6 .... 4s2 3d10 4p6 4d10 4f14 are represented by the ECP, is there a systematic and/or practical way to extend the valence electrons with the n=4 shell? or something that includes the 4f14 electrons too. or even better is there already a basis and ECP that already includes the n=4 in the valence? I searched for this extensively, but not luck so far. your help is strongly appreciated Norma L. Rangel From owner-chemistry@ccl.net Tue Jul 29 10:43:00 2008 From: "Luca bellucci14!^!unisi.it" To: CCL Subject: CCL:G: TD-DFT Message-Id: <-37437-080728133421-17104-oGuO15V1E9bplrR8YGqk2Q(~)server.ccl.net> X-Original-From: Luca Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Mon, 28 Jul 2008 18:59:59 +0200 MIME-Version: 1.0 Sent to CCL by: Luca [bellucci14]^[unisi.it] Dear Mahmoud when you use diffuseve functions, SCF oscillate at the end and do not converge. You can tray to set FDIFF =.FALSE. in $SCF section. (see manual for details) Luca > > Sent to CCL by: "Mahmoud Korani Abdel-Latif" [mkkhedr[#]hotmail.com] > Dear All, > > I am calculating TD-DFT using Gamess package But unfortunately There is Abnormal termination. Although the input I used is Gaussian output. > > I am using the following basis set with B3LYP thepry. > $basis gbasis=N31 ngauss=6 diffsp=.T. ndfunc=1 npfunc=1 $end. > > > I got smething like in the output file: > > THE INPUT BASIS SET CONTAINS APPROXIMATE LINEAR DEPENDENCE. > THE SMALLEST EIGENVALUE OF THE OVERLAP MATRIX IS 2.211503E-09 > THERE ARE 19 EIGENVALUES LESS THAN QMTTOL= 1.00E-06 > EIGENVECTORS BELOW -QMTTOL- ARE DROPPED FROM THE MO SPACE, > IN ORDER TO ELIMINATE THE APPROXIMATE LINEAR DEPENDENCE. > ...... END OF TWO-ELECTRON INTEGRALS > > > > SCF IS UNCONVERGED, TOO MANY ITERATIONS > TIME TO FORM FOCK OPERATORS= 187018.4 SECONDS ( 935.1 SEC/ITER) > FOCK TIME ON FIRST ITERATION= 1764.2, LAST ITERATION= 709.7 > TIME TO SOLVE SCF EQUATIONS= 6727.9 SECONDS ( 33.6 SEC/ITER) > > FINAL R-B3LYP ENERGY IS 0.0000000000 AFTER 200 ITERATIONS > DFT EXCHANGE + CORRELATION ENERGY = -196.7509056337 > TOTAL ELECTRON NUMBER = 287.9994180225 > ...... END OF RHF CALCULATION ...... > STEP CPU TIME =193774.12 TOTAL CPU TIME = 891689.4 (14861.5 MIN) > TOTAL WALL CLOCK TIME= 907324.0 SECONDS, CPU UTILIZATION IS 98.28% > > SCF DID NOT CONVERGE...NO TDDFT=EXCITE CALCULATION > EXECUTION OF GAMESS TERMINATED -ABNORMALLY- AT Mon Jul 28 05:32:46 2008 > 76515198 WORDS OF DYNAMIC MEMORY USED > > > Could you please tell me what should I do to overcome this problem. > > Best regards, > Mahmoud Abdel-Latif, > mkkhedr^-^hotmail.com> > > From owner-chemistry@ccl.net Tue Jul 29 11:18:01 2008 From: "Paul Wilhelm Elsinghorst paul/a\uni-bonn.de" To: CCL Subject: CCL:G: Search for a transition state provides minimum Message-Id: <-37438-080729085803-31694-SD6n+YI/WZ0C5ccRzXd83A!A!server.ccl.net> X-Original-From: Paul Wilhelm Elsinghorst Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 29 Jul 2008 13:57:46 +0200 Mime-Version: 1.0 Sent to CCL by: Paul Wilhelm Elsinghorst [paul++uni-bonn.de] Dear CCLers, using Gaussian03 I'm trying to locate two transition states resulting > from two rotational barriers inside a molecule. I performed a relaxed PES scan at BP86/LANL2DZ to identify suitable input geometries approximately 5° before the rotational barriers. I took those geometries and tried to optimize the TS using #P B3LYP/6-311G** OPT=(TS,NoEigenTest,CalcFC,MaxCycles=1000). Unfortunately the optimization does not provide the TS, let's say doing 5° more, but goes for a local minimum, so to say rewinding the rotation by 80°. What should I do to obtain the TS? Paul From owner-chemistry@ccl.net Tue Jul 29 11:53:00 2008 From: "Forlani Roberto roberto.forlani/./nikemresearch.com" To: CCL Subject: CCL: Family/Functional Group Identification From 2D/3D mol file Message-Id: <-37439-080729100550-12939-cGGj1xLM/NMeE68txuzLNg++server.ccl.net> X-Original-From: "Forlani Roberto" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Tue, 29 Jul 2008 15:33:15 +0200 MIME-Version: 1.0 Sent to CCL by: "Forlani Roberto" [roberto.forlani]-[nikemresearch.com] =20 > -----Original Message----- > From: owner-chemistry^-^ccl.net [mailto:owner-chemistry^-^ccl.net]=20 > Sent: Tuesday, July 29, 2008 2:11 PM > To: Forlani Roberto > Subject: CCL: Family/Functional Group Identification From=20 > 2D/3D mol file >=20 >=20 > Sent to CCL by: "Yangsoo Kim" [vsmember[#]gmail.com] Dear All, >=20 > I'm looking for a program that can automatically determine=20 > the family and/or functional group of molecule from a kind of=20 > a 2D or 3D molfile. The groups I want to identify are the=20 > followings (total of 31 groups): > (1)n-alkane, (2)iso-alkne, (3)cyclo-alkane, (4)n-alkene,=20 > (5)iso-alkene, (6)aromatics, (7)alcohol, (8)ketone,=20 > (9)aldehyde, (10)acetic acid, (11) ether, (12)ester,=20 > (13)hydroperoxide, (14)peroxide, (15)formic acid, (16) amide,=20 > (17)amine, (18)imines, (19)azo, (20)cyanate, (21)isocynate,=20 > (22) nitrate, (23)nitrile, (24)nitrite, (25)nitro,=20 > (26)pyridine, (27)pyrrole, (28)sulfide, (29)sulfoxide,=20 > (30)thiol, (31)thiophene >=20 > I found checkmol=20 > (http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html) > so far, but some groups are missing in this software. >=20 > Any information related to this matter will greatly be appreciated. >=20 > Many thanks in advance, >=20 > YangSoo Kim. Dear YangSoo, I think you can search and/or filter your molecular files by corresponding functional groups SMARTS. For your information Open Babel offers this functionality http://openbabel.org/wiki/SMARTS Hope this helps. Regards, Roberto From owner-chemistry@ccl.net Tue Jul 29 12:27:00 2008 From: "Wolf-D. Ihlenfeldt wdi%%xemistry.com" To: CCL Subject: CCL: Family/Functional Group Identification From 2D/3D mol file Message-Id: <-37440-080729111550-11457-D100UJstY9LGziXnscK5lQ]-[server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: en-us Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 29 Jul 2008 16:14:53 +0200 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi%a%xemistry.com] If you can write your own substructure patterns (for examples as SMARTS strings, or as imported query Molfiles or ChemDraw files, created by the respective standard structure editors), this is something which can = easily be scripted as a small Cactvs toolkit script (www.xemistry.com, free for academic use). Please let me know in case you need more information. W. D. Ihlenfeldt Xemistry GmbH wdi,+,xemistry.com --- xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. = Ihlenfeldt Address: Auf den Stieden 8, D-35094 Lahntal, Germany HR Marburg B4713 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 > -----Original Message----- > From: owner-chemistry,+,ccl.net [mailto:owner-chemistry,+,ccl.net] > Sent: Tuesday, July 29, 2008 2:11 PM > To: Ihlenfeldt, Wolf D > Subject: CCL: Family/Functional Group Identification From 2D/3D mol > file >=20 >=20 > Sent to CCL by: "Yangsoo Kim" [vsmember[#]gmail.com] > Dear All, >=20 > I'm looking for a program that can automatically determine the family > and/or > functional group of molecule from a kind of a 2D or 3D molfile. The > groups I > want to identify are the followings (total of 31 groups): > (1)n-alkane, (2)iso-alkne, (3)cyclo-alkane, (4)n-alkene, = (5)iso-alkene, > (6)aromatics, (7)alcohol, (8)ketone, (9)aldehyde, (10)acetic acid, = (11) > ether, (12)ester, (13)hydroperoxide, (14)peroxide, (15)formic acid, > (16) > amide, (17)amine, (18)imines, (19)azo, (20)cyanate, (21)isocynate, = (22) > nitrate, (23)nitrile, (24)nitrite, (25)nitro, (26)pyridine, > (27)pyrrole, > (28)sulfide, (29)sulfoxide, (30)thiol, (31)thiophene >=20 > I found checkmol > (http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html) > so far, but some groups are missing in this software. >=20 > Any information related to this matter will greatly be appreciated. >=20 > Many thanks in advance, >=20 > YangSoo Kim. >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please > change>=20>=20>=20>=20>=20> Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20 > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search) >=20>=20 From owner-chemistry@ccl.net Tue Jul 29 13:16:00 2008 From: "Mikael Johansson mpjohans]|[chem.au.dk" To: CCL Subject: CCL:G: n=4 electron basis set for Au Message-Id: <-37441-080729131156-4310-HdX8MIWNneCoXK+O0thGxA===server.ccl.net> X-Original-From: Mikael Johansson Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Tue, 29 Jul 2008 18:10:29 +0200 MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mpjohans-#-chem.au.dk] Hello Norma and All! On Tue, 29 Jul 2008 "Norma L Rangel Norma.Rangel%Tue 29 Jul 2008 =20 15:36:20 CESThemail.tamu.edu" wrote: > The Gold atom in the LANL2DZ uses only 19 ("valence") electrons > is there a systematic and/or practical way to extend the valence =20 > electrons with the n=3D4 shell? or something that includes the 4f14 =20 > electrons too. > or even better is there already a basis and ECP that already =20 > includes the n=3D4 in the valence? I'm not aware of a standard 46 electron ECP for gold in connection =20 with Gaussian basis sets either, but assuming you are doing DFT, ADF =20 could be an option. With ADF, you can do ZORA calculations either =20 fully all-electron, as well as with frozen cores of 46 (4d frozen) or =20 60 (4f frozen) electrons. At least it should give some indication on =20 the importance of unfreezing 4f. I suspect that trying to represent scalar relativistic effects with a =20 very small core ECP on gold, without additional measures to account =20 for relativity, could be problematic. I'm no expert on ECP's, so =20 someone correct me if I'm wrong here. Have a nice day, Mikael J. http://www.iki.fi/~mpjohans ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From owner-chemistry@ccl.net Tue Jul 29 14:02:00 2008 From: "Mohamed Naseer Ali MOHAMED mmdnaseer[]gmail.com" To: CCL Subject: CCL:G: vibration visualization Message-Id: <-37442-080729123546-10215-Jz8tNgdJdn/jEYXBKSzjhQ/a\server.ccl.net> X-Original-From: "Mohamed Naseer Ali MOHAMED" Content-Type: multipart/alternative; boundary="----=_Part_48226_22314241.1217342404618" Date: Tue, 29 Jul 2008 10:40:04 -0400 MIME-Version: 1.0 Sent to CCL by: "Mohamed Naseer Ali MOHAMED" [mmdnaseer(0)gmail.com] ------=_Part_48226_22314241.1217342404618 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hey raj, Did you tried with FACIO ? On Tue, Jul 29, 2008 at 8:53 AM, Raj S r.subramanian(~)ipc.uni-stuttgart.de wrote: > > Sent to CCL by: "Raj S" [r.subramanian(_)ipc.uni-stuttgart.de] > Dear CCL members, > Is there a way to hide hydrogen atoms in Molekel 5.3 ???...and view the > rest of the atoms vibrating....I could only make .ps files of all atoms > vibrating with arrows... > or if there is some other (free) software to view the molecular vibration > (normal modes) from G03 freq output kindly inform me. > > thanks for your help > regards, > raj> > > ------=_Part_48226_22314241.1217342404618 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hey raj,

  Did you tried with FACIO ?

On Tue, Jul 29, 2008 at 8:53 AM, Raj S r.subramanian(~)ipc.uni-stuttgart.de <owner-chemistry|*|ccl.net> wrote:

Sent to CCL by: "Raj  S" [r.subramanian(_)ipc.uni-stuttgart.de]
Dear CCL members,
Is there a way to hide hydrogen atoms in Molekel 5.3 ???...and view the rest of the atoms vibrating....I could only make .ps files of all atoms vibrating with arrows...
or if there is some other (free) software to view the molecular vibration (normal modes) from G03 freq output kindly inform me.

thanks for your help
regards,
raj



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------=_Part_48226_22314241.1217342404618-- From owner-chemistry@ccl.net Tue Jul 29 16:03:00 2008 From: "=?ISO-8859-1?Q?Ren=E9_Kanters?= rkanters__richmond.edu" To: CCL Subject: CCL:G: vibration visualization Message-Id: <-37443-080729152130-5685-20ZFsZ8JWxBspU+TVmxpGA|*|server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ren=E9_Kanters?= Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Tue, 29 Jul 2008 15:21:15 -0400 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: =?ISO-8859-1?Q?Ren=E9_Kanters?= [rkanters]*[richmond.edu] Hi Raj, Jmol (http://jmol.sourceforge.net/) is able to show the vibrations =20 > from a G03 frequency analysis. You can turn off/on the hydrogens by =20 right-clicking and select in the popup menu Style:Atoms:Show Hydrogens. Cheers, Ren=E9 On Jul 29, 2008, at 8:53 AM, Raj S r.subramanian(~)ipc.uni-=20 stuttgart.de wrote: > > Sent to CCL by: "Raj S" [r.subramanian(_)ipc.uni-stuttgart.de] > Dear CCL members, > Is there a way to hide hydrogen atoms in Molekel 5.3 ???...and view =20= > the rest of the atoms vibrating....I could only make .ps files of =20 > all atoms vibrating with arrows... > or if there is some other (free) software to view the molecular =20 > vibration (normal modes) from G03 freq output kindly inform me. > > thanks for your help > regards, > raj > > > > -=3D This is automatically added to each message by the mailing =20 > script =3D- > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: =20 > search)> >