From owner-chemistry@ccl.net Tue May 26 00:39:00 2009 From: "Giju Thomas Kalathingal gijukt~!~rediffmail.com" To: CCL Subject: CCL: Carbon footprint Message-Id: <-39375-090525232708-21768-pt7kvjzBHPM8Vocc6i1qPw-.-server.ccl.net> X-Original-From: "Giju Thomas Kalathingal" Date: Mon, 25 May 2009 23:27:04 -0400 Sent to CCL by: "Giju Thomas Kalathingal" [gijukt]![rediffmail.com] Could you please help me with the following question? Which energy source has lowest Carbon footprint? (a) Biodiesel (b) Bioethanol (c) Hydrogen (d) Hydroelectric power Any computational/ experimental data? From owner-chemistry@ccl.net Tue May 26 01:14:00 2009 From: "Giju Thomas Kalathingal gijukt++rediffmail.com" To: CCL Subject: CCL: Carbon footprint Message-Id: <-39376-090525071830-10082-8P6nObCXv/bTxqoOoS+H7g{=}server.ccl.net> X-Original-From: "Giju Thomas Kalathingal" Content-Type: multipart/alternative; boundary="=_b47887d071c05748451b7a31be8f2da2" Date: 25 May 2009 10:16:46 -0000 MIME-Version: 1.0 Sent to CCL by: "Giju Thomas Kalathingal" [gijukt*_*rediffmail.com] --=_b47887d071c05748451b7a31be8f2da2 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="ISO-8859-1" Hi every one, Could you please help me with the following question? Which energy source has lowest Carbon footprint? (a) Biodiesel (b) Bioethanol (c) Hydrogen (d) Hydroelectric power Any computational/ experimental data? Dr. Kalathingal Thomas Giju Kalathingal (house) Kodakara Road, Kallettumkara via Aloor P.O., Thrissur - 680683 Kerala, India. E-mail: gijukt**rediffmail.com --=_b47887d071c05748451b7a31be8f2da2 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="ISO-8859-1" Hi every one,

Could you please help me with the following question?

Which energy source has lowest Carbon footprint?
(a) Biodiesel
(b) Bioethanol
(c) Hydrogen
(d) Hydroelectric power

Any computational/ experimental data?

Dr. Kalathingal Thomas Giju
Kalathingal (house)

Kodakara Road, Kallettumkara via

Aloor P.O., Thrissur - 680683

Kerala, India.

E-mail: gijukt**rediffmail.com
--=_b47887d071c05748451b7a31be8f2da2-- From owner-chemistry@ccl.net Tue May 26 02:53:01 2009 From: "Jan Labanowski janl__speakeasy.net" To: CCL Subject: CCL: Carbon footprint Message-Id: <-39377-090526024954-7576-TgxvOZtq55jQeyuUnv6xjA|server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 26 May 2009 02:49:42 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl-x-speakeasy.net] I wish I was censoring CCL, but I cannot do it for legal reasons. It is pro= bably an "activist" question or, maybe even worse, an attempt to collect readers = IP addresses via an embedded external gif at the end of the message.=20 But obviously hydroelectric power cannot have carbon footprint unless you consider amount of diesel that was needed to build the power plant. Hydrogen does not have carbon so it has no carbon footprint unless it was m= ade > from the electricity produced by fossil fuels burning power plant. I wonder= if omission of nuclear energy is intentional. This one does not have a carbon footprint and it is the only rational option for the future, once we agree = how to dispose radioactive waste rationally (rather than building mountains out of= it). Please respond to me directly. This is not a computational chemistry topic. Jan Labanowski jkl:-:ccl.net > Hi every one, >=20 > Could you please help me with the following question? >=20 > Which energy source has lowest Carbon footprint? > (a) Biodiesel > (b) Bioethanol > (c) Hydrogen > (d) Hydroelectric power >=20 > Any computational/ experimental data? >=20 > Dr. Kalathingal Thomas Giju From owner-chemistry@ccl.net Tue May 26 11:15:01 2009 From: "Barbara Jagoda-Cwiklik barbara[a]fh.huji.ac.il" To: CCL Subject: CCL:G: NON-equilibrium PCM calculation in Gaussian Message-Id: <-39378-090526104306-18788-r0BS1TowSSMtKhSvt0EEhA]~[server.ccl.net> X-Original-From: Barbara Jagoda-Cwiklik Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 26 May 2009 17:17:35 +0300 MIME-Version: 1.0 Sent to CCL by: Barbara Jagoda-Cwiklik [barbara]*[fh.huji.ac.il] Dear Jan, NonEq can take two arguments: NonEq=3Dwrite and NonEq=3Dread. In the first case PCM parameters are written to the checkpoint file, in the second - they are read from the checkpoint (simply speaking, the cavity read > from the disk is used). Take a look at a test job: http://g03.sownar.com/test614.gjf We employed a similar scheme in: J. Phys. Chem. A, Vol. 112 (2008) 3499 Best, Basia On Mon, May 25, 2009 at 4:42 PM, Jan Moens molukken*_*hotmail.com wrote: > > Sent to CCL by: "Jan =A0Moens" [molukken^hotmail.com] > Dear all, > > I am interested in nonequilibrium PCM calculations for vertical ionizatio= n potentials. In the g03 manual, it is indicated that non equilibrium solva= tion can be performed using the NonEq=3Dtype PCM keyword. But this keyword = is not described elsewhere in the manual. Does anyone know how to use this = keyword in a correct way? > > Thanks in advance > > Jan Moens > PhD student > Vrije Universiteit Brussel > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =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 Barbara Jagoda-Cwiklik, Ph.D The Fritz Haber Research Center for Molecular Dynamics Institute of Chemistry The Hebrew University of Jerusalem Jerusalem, ISRAEL e-mail: barbara#,#fh.huji.ac.il From owner-chemistry@ccl.net Tue May 26 12:04:00 2009 From: "Ashwini Bundhun ashwinibilly!=!hotmail.com" To: CCL Subject: CCL: need help in gaussian ts search Message-Id: <-39379-090526120217-12060-RyhGKDb5O7QGC/0mkpNvdw*_*server.ccl.net> X-Original-From: "Ashwini Bundhun" Date: Tue, 26 May 2009 12:02:13 -0400 Sent to CCL by: "Ashwini Bundhun" [ashwinibilly---hotmail.com] Dear tran van tan tvtan The input file should include both the starting reactant and the products structures. This would be a better way to find the TS structure: %chk=TS.chk #p opt=qst2 freq b3lyp/6-311+g(d,p) geom=connectivity Reactants 0 2 C C 1 B1 H 2 B2 1 A1 C 1 B3 2 A2 3 D1 N 4 B4 1 A3 2 D2 H 4 B5 1 A4 2 D3 B1 1.19117810 B2 1.05686011 B3 1.42940095 B4 1.24698289 B5 1.08948293 A1 179.42682237 A2 178.40506719 A3 123.91641107 A4 49.00000000 D1 180.00000000 D2 180.00000000 D3 0.00000000 1 2 3.0 4 1.5 6 1.0 2 3 1.0 3 4 5 2.0 6 1.0 5 6 Products 0 2 C C 1 B1 H 2 B2 1 A1 C 1 B3 2 A2 3 D1 N 4 B4 1 A3 2 D2 H 4 B5 1 A4 2 D3 B1 1.19117810 B2 1.05686011 B3 1.42940095 B4 1.24698289 B5 1.08948293 A1 179.42682237 A2 178.40506719 A3 123.91641107 A4 49.00000000 D1 180.00000000 D2 180.00000000 D3 0.00000000 1 2 3.0 4 1.5 6 1.0 2 3 1.0 3 4 5 2.0 6 1.0 5 6 I hope this helps. Regards Ashwini Bundhun ashwinibilly|gmail.com From owner-chemistry@ccl.net Tue May 26 14:35:01 2009 From: "Ashwini Bundhun ashwinibilly : gmail.com" To: CCL Subject: CCL: need help in gaussian ts search Message-Id: <-39380-090526115311-9044-Gi3azJQW7OgxmNjVxt1d9Q##server.ccl.net> X-Original-From: "Ashwini Bundhun" Date: Tue, 26 May 2009 11:53:08 -0400 Sent to CCL by: "Ashwini Bundhun" [ashwinibilly!A!gmail.com] Dear tran van tan tvtan The input file should include both the starting reactant and the products structures. This would be a better way to find the TS structure: %chk=TS.chk #p opt=qst2 freq b3lyp/6-311+g(d,p) geom=connectivity Reactants 0 2 C C 1 B1 H 2 B2 1 A1 C 1 B3 2 A2 3 D1 N 4 B4 1 A3 2 D2 H 4 B5 1 A4 2 D3 B1 1.19117810 B2 1.05686011 B3 1.42940095 B4 1.24698289 B5 1.08948293 A1 179.42682237 A2 178.40506719 A3 123.91641107 A4 49.00000000 D1 180.00000000 D2 180.00000000 D3 0.00000000 1 2 3.0 4 1.5 6 1.0 2 3 1.0 3 4 5 2.0 6 1.0 5 6 Products 0 2 C C 1 B1 H 2 B2 1 A1 C 1 B3 2 A2 3 D1 N 4 B4 1 A3 2 D2 H 4 B5 1 A4 2 D3 B1 1.19117810 B2 1.05686011 B3 1.42940095 B4 1.24698289 B5 1.08948293 A1 179.42682237 A2 178.40506719 A3 123.91641107 A4 49.00000000 D1 180.00000000 D2 180.00000000 D3 0.00000000 1 2 3.0 4 1.5 6 1.0 2 3 1.0 3 4 5 2.0 6 1.0 5 6 I hope this helps. Regards Ashwini Bundhun ashwinibilly++gmail.com From owner-chemistry@ccl.net Tue May 26 16:54:00 2009 From: "Jan Moens molukken#hotmail.com" To: CCL Subject: CCL:G: NON-equilibrium PCM calculation in Gaussian Message-Id: <-39381-090526165301-4657-ys2nXOuwy+by4qkC4hjeiQ-x-server.ccl.net> X-Original-From: "Jan Moens" Date: Tue, 26 May 2009 16:52:57 -0400 Sent to CCL by: "Jan Moens" [molukken{:}hotmail.com] Thank you Basia for your response! I previously saw your interesting paper and I was wondering if these type of calculations are also possible with DFT (no TD-DFT) instead of the MP or derivative methods , within the G03 version? In particular, I am interested in differences between vertical and adiabatic ionization potentials of metal complexes, where solvent is modelled by pcm. best regards Jan Moens > "Barbara Jagoda-Cwiklik barbara[a]fh.huji.ac.il" wrote: > > Sent to CCL by: Barbara Jagoda-Cwiklik [barbara]*[fh.huji.ac.il] > Dear Jan, > > NonEq can take two arguments: NonEq=3Dwrite and NonEq=3Dread. In the first > case PCM parameters are written to the checkpoint file, in the second > - they are read from the checkpoint (simply speaking, the cavity read > > from the disk is used). > Take a look at a test job: http://g03.sownar.com/test614.gjf > We employed a similar scheme in: J. Phys. Chem. A, Vol. 112 (2008) 3499 > > Best, > Basia > > On Mon, May 25, 2009 at 4:42 PM, Jan Moens molukken*_*hotmail.com > wrote: > > > > Sent to CCL by: "Jan =A0Moens" [molukken^hotmail.com] > > Dear all, > > > > I am interested in nonequilibrium PCM calculations for vertical ionizatio= > n potentials. In the g03 manual, it is indicated that non equilibrium solva= > tion can be performed using the NonEq=3Dtype PCM keyword. But this keyword = > is not described elsewhere in the manual. Does anyone know how to use this = > keyword in a correct way? > > > > Thanks in advance > > > > Jan Moens > > PhD student > > Vrije Universiteit Brussel > > > > > > > > -=3D This is automatically added to each message by the mailing script = > =3D-> =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 > Barbara Jagoda-Cwiklik, Ph.D > The Fritz Haber Research Center for Molecular Dynamics > Institute of Chemistry > The Hebrew University of Jerusalem > Jerusalem, ISRAEL > e-mail: barbara#,#fh.huji.ac.il > > From owner-chemistry@ccl.net Tue May 26 19:14:00 2009 From: "Joe Leonard jleonard42__gmail.com" To: CCL Subject: CCL: Mol2 file example? Message-Id: <-39382-090526190756-22150-DyARyF9wu2A/rYqfyJCU/A]=[server.ccl.net> X-Original-From: Joe Leonard Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Tue, 26 May 2009 19:07:35 -0400 Mime-Version: 1.0 (Apple Message framework v935.3) Sent to CCL by: Joe Leonard [jleonard42*|*gmail.com] Folks, does anybody have (or can they easily generate) a Sybyl mol2 file containing a protein/ligand and waters? Any old PDB file would do, as long as it's a cocrystal with waters. While the mol2 file format is documented on their support website, there's no example file. There's a fair number of entries that would profit from a more- complete example such as the one I'm looking for... Thanks in advance! I've tried googling for such an example and I'm getting papers talking about files rather than the files themselves... Joe Leonard jleonard42+*+gmail.com -- The only solution I see for developers to not have to be diplomatic to get cooperation from other departments is to arm the developers. From owner-chemistry@ccl.net Tue May 26 22:11:00 2009 From: "Benjamin Roberts benjamincharlesroberts,gmail.com" To: CCL Subject: CCL: Mol2 file example? Message-Id: <-39383-090526220344-31043-VuxkDEQQpfR/RU88oDVRWQ#,#server.ccl.net> X-Original-From: Benjamin Roberts Content-Type: multipart/alternative; boundary=000e0cd32982870b9e046ada62aa Date: Wed, 27 May 2009 09:01:35 +0800 MIME-Version: 1.0 Sent to CCL by: Benjamin Roberts [benjamincharlesroberts%x%gmail.com] --000e0cd32982870b9e046ada62aa Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Joe, Open Babel can convert pdb files to mol2 easily enough, http://openbabel.org/wiki/Main_Page. Ben. On Wed, May 27, 2009 at 7:07 AM, Joe Leonard jleonard42__gmail.com < owner-chemistry++ccl.net> wrote: > > Sent to CCL by: Joe Leonard [jleonard42*|*gmail.com] > Folks, does anybody have (or can they easily generate) a Sybyl mol2 file > containing a protein/ligand and waters? Any old PDB file would do, as long > as it's a cocrystal with waters. While the mol2 file format is documented > on their support website, there's no example file. There's a fair number of > entries that would profit from a more-complete example such as the one I'm > looking for... > > Thanks in advance! I've tried googling for such an example and I'm getting > papers talking about files rather than the files themselves... > > Joe Leonard > jleonard42],[gmail.com > -- > The only solution I see for developers to not have to be diplomatic to get > cooperation from other departments is to arm the developers.http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --000e0cd32982870b9e046ada62aa Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Joe, Open Babel can convert pdb files to mol2 easily enough, http://openbabel.org/wiki/Main_Page.
Ben.

On Wed, May 27, 2009 at 7:07 A= M, Joe Leonard jleonard42__gmail.c= om <own= er-chemistry++ccl.net> wrote:

Sent to CCL by: Joe Leonard [jleonard42*|*gmail.com]
Folks, does anybody have (or can they easily generate) a Sybyl mol2 file co= ntaining a protein/ligand and waters? =A0Any old PDB file would do, as long= as it's a cocrystal with waters. =A0While the mol2 file format is docu= mented on their support website, there's no example file. =A0There'= s a fair number of entries that would profit from a more-complete example s= uch as the one I'm looking for...

Thanks in advance! =A0I've tried googling for such an example and I'= ;m getting papers talking about files rather than the files themselves...
Joe Leonard
jleonard42],[gmail.com --
The only solution I see for developers to not have to be diplomatic to get = cooperation from other departments is to arm the developers.



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