From owner-chemistry@ccl.net Wed May 9 01:21:00 2007 From: "Seth Olsen s.olsen1^^^uq.edu.au" To: CCL Subject: CCL: Good Source for History of Oxidation Numbers? Message-Id: <-34216-070508223411-18176-Yg9fpY1MJl5eta30SqNE9g]~[server.ccl.net> X-Original-From: Seth Olsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 09 May 2007 12:03:24 +1000 MIME-Version: 1.0 Sent to CCL by: Seth Olsen [s.olsen1-x-uq.edu.au] Hi CCLers, Can anyone direct me to a good source containing a short review of the history of oxidation-reduction concepts, particularly the history of Oxidation Number notation as a way to balance reactions? I am teaching my first ~400 student Gen. Chem. class this monday, and I think that adding a historical note or two to the powerpoint slides provided to me is a good idea. I remember thinking once that (as a physics student in a chemistry class) some of the rules for Ox. numbers seemed quite arbitrary, which I now appreciate to mean that history must be the cause. I generally do not support the teaching of scientific knowledge as 'I bring this to you from the top of Mt. Zion. Learn it so that ye may be enlightened and pass the exam.', and a good way to get around this problem is to highlight the human (fallible) egos which built any given field. Can someone direct me to a good source to bring this home? Cheers, Seth From owner-chemistry@ccl.net Wed May 9 02:29:01 2007 From: "Chimica Teorica teorica.ch . unito.it" To: CCL Subject: CCL: [SPAM] CCL: Nano Clusters Message-Id: <-34217-070508072406-23643-handEbru20eWbBioXyhJEw[]server.ccl.net> X-Original-From: Chimica Teorica Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Tue, 08 May 2007 12:35:54 +0200 MIME-Version: 1.0 Sent to CCL by: Chimica Teorica [teorica.ch],[unito.it] "Yousef Sharifi ysharifi _ gmail.com" wrote: > > Sent to CCL by: "Yousef Sharifi" [ysharifi|a|gmail.com] > I need a program to create spherical clusters, is there any program to create clusters? > See MOLDRAW : http://www.moldraw.unito.it Bartolomeo Civalleri Theoretical Chemistry Group - Torino http://www.crystal.unito.it From owner-chemistry@ccl.net Wed May 9 04:01:00 2007 From: "Luciano Marchi marchio-$-unipr.it" To: CCL Subject: CCL: Good Source for History of Oxidation Numbers? Message-Id: <-34218-070509033649-29588-zgh25tqwrZSEExbjTO2RLw.:.server.ccl.net> X-Original-From: "Luciano Marchi " Date: Wed, 9 May 2007 03:36:45 -0400 Sent to CCL by: "Luciano Marchi " [marchio,,unipr.it] Hello Seth, This paper points out the differences between oxidation numbers, formal charge and valence. G. Parkin, J. Chem. Educ. 2006, 83, 791 cheers, luciano Sent to CCL by: Seth Olsen [s.olsen1-x-uq.edu.au] Hi CCLers, Can anyone direct me to a good source containing a short review of the history of oxidation-reduction concepts, particularly the history of Oxidation Number notation as a way to balance reactions? I am teaching my first ~400 student Gen. Chem. class this monday, and I think that adding a historical note or two to the powerpoint slides provided to me is a good idea. I remember thinking once that (as a physics student in a chemistry class) some of the rules for Ox. numbers seemed quite arbitrary, which I now appreciate to mean that history must be the cause. I generally do not support the teaching of scientific knowledge as 'I bring this to you from the top of Mt. Zion. Learn it so that ye may be enlightened and pass the exam.', and a good way to get around this problem is to highlight the human (fallible) egos which built any given field. Can someone direct me to a good source to bring this home? Cheers, Seth From owner-chemistry@ccl.net Wed May 9 07:23:00 2007 From: "Sebastian Schwieger sebastian.schwieger-x-chemie.uni-halle.de" To: CCL Subject: CCL: Good Source for History of Oxidation Numbers? Message-Id: <-34219-070509061325-6694-jT+zEsHP98YYYvZUGGhmRw,+,server.ccl.net> X-Original-From: Sebastian Schwieger Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-1 Date: Wed, 09 May 2007 12:11:43 +0200 MIME-version: 1.0 Sent to CCL by: Sebastian Schwieger [sebastian.schwieger_+_chemie.uni-halle.de] Hi Seth, Seth Olsen s.olsen1^^^uq.edu.au wrote: > > Sent to CCL by: Seth Olsen [s.olsen1-x-uq.edu.au] > > Hi CCLers, > > Can anyone direct me to a good source containing a short review of the > history of oxidation-reduction concepts, particularly the history of > Oxidation Number notation as a way to balance reactions? I am teaching > my first ~400 student Gen. Chem. class this monday, and I think that > adding a historical note or two to the powerpoint slides provided to me > is a good idea. I remember thinking once that (as a physics student in > a chemistry class) some of the rules for Ox. numbers seemed quite > arbitrary, which I now appreciate to mean that history must be the > cause. I generally do not support the teaching of scientific knowledge > as 'I bring this to you from the top of Mt. Zion. Learn it so that ye > may be enlightened and pass the exam.', and a good way to get around > this problem is to highlight the human (fallible) egos which built any > given field. Can someone direct me to a good source to bring this home? > > Cheers, > > Seth > my tutor wrote about the concept of oxidation states in metal complexes (2004). I don't have it at hand at the moment, so I am not sure if the paper talks much about history, it does talk about the arbitrariness of oxidation numbers: D. Steinborn, Journal of Chemical Education 81 (8), 2004, 1148-54. I hope this helps, Cheers, Sebastian From owner-chemistry@ccl.net Wed May 9 07:58:00 2007 From: "genevieve miquel genevievelaure:yahoo.fr" To: CCL Subject: CCL: chem3D et ammonium Message-Id: <-34220-070507071309-11241-sE6WzyCvqjwHI3qz0yvukw---server.ccl.net> X-Original-From: genevieve miquel Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-723802570-1178532759=:70266" Date: Mon, 7 May 2007 12:12:39 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: genevieve miquel [genevievelaure!A!yahoo.fr] --0-723802570-1178532759=:70266 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Bonjour J'utilise Chem3D pour modéliser un complexe comportant un atome d'azote secondaire ou tertiaire chélaté à un métal, donc ayant un azote de type amonium. Le programme Chem 3D refuse de prendre en compte cet azote faute de définition. Le programme répond :there are no atom types defined for this nitrogen. Avez vous une solution à ce problème ? merci cordialement G. Miquel --------------------------------- Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international.Téléchargez la version beta. --0-723802570-1178532759=:70266 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Bonjour
J'utilise Chem3D pour modéliser un complexe comportant un atome d'azote secondaire ou tertiaire chélaté à un métal, donc ayant un azote de type amonium.
Le programme Chem 3D refuse de prendre en compte cet azote faute de définition.
Le programme répond :there are no atom types defined for this nitrogen.
 
Avez vous une solution à ce problème ?
merci
cordialement
G. Miquel

Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international. Téléchargez la version beta. --0-723802570-1178532759=:70266-- From owner-chemistry@ccl.net Wed May 9 08:33:01 2007 From: "Sibel Tokdemir sozturk##gyte.edu.tr" To: CCL Subject: CCL:G: hyperfine coupling constans fo transition metals Message-Id: <-34221-070509045911-27118-gHGqa4PijV0577EZP92P/A(a)server.ccl.net> X-Original-From: "Sibel Tokdemir" Date: Wed, 9 May 2007 04:59:08 -0400 Sent to CCL by: "Sibel Tokdemir" [sozturk!A!gyte.edu.tr] Hello, I have experience on calculating hyperfine coupling constant for organic molecules using Gaussian program. I want to do same thing for first raw transition metals. As far as I read I saw that people used ADF program for transition metals.I wonder if anyone used Gaussian98(or 03) for this purpose. Which basis set will be appropriate for DFT method for Sc-Zn? thanks Sibel Tokdemir/ sozturk::gyte.edu.tr From owner-chemistry@ccl.net Wed May 9 09:19:00 2007 From: "Sue Lam chsue2004*o*yahoo.com" To: CCL Subject: CCL: Interplane Angle Message-Id: <-34222-070509073459-21349-pwHVnsQ1wdUfLvs+wm89Fg(!)server.ccl.net> X-Original-From: Sue Lam Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1054255339-1178706843=:31049" Date: Wed, 9 May 2007 03:34:03 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sue Lam [chsue2004]~[yahoo.com] --0-1054255339-1178706843=:31049 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi all, Thank you very much for your information "Phil Hultin hultin%a%cc.umanitoba.ca" wrote: Sent to CCL by: "Phil Hultin" [hultin(~)cc.umanitoba.ca] Basic geometry is one of the things many of us have forgotten (I include myself in this) but whenever I need such things I just google. It's humbling to be reminded that back in freshman year we all knew how to find things like the angle between two planes! If you google the phrase "angle between two planes" you will find thousands of web pages that give you the math - and then a few minutes work with your spreadsheet and you have your answer. Dr. Philip G. Hultin Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin|cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin -----Original Message----- > From: owner-chemistry|ccl.net [mailto:owner-chemistry|ccl.net] Sent: May 6, 2007 11:07 PM To: Hultin, Philip G. Subject: CCL: Interplane Angle Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com] Hi, Does anyone know a program that can measure an interplane angle from calculated structures? Many thanks Suehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar. --0-1054255339-1178706843=:31049 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi all,
 
Thank you very much for your information

"Phil Hultin hultin%a%cc.umanitoba.ca" <owner-chemistry ~~ ccl.net> wrote:

Sent to CCL by: "Phil Hultin" [hultin(~)cc.umanitoba.ca]
Basic geometry is one of the things many of us have forgotten (I include
myself in this) but whenever I need such things I just google. It's
humbling to be reminded that back in freshman year we all knew how to find
things like the angle between two planes!

If you google the phrase "angle between two planes" you will find thousands
of web pages that give you the math - and then a few minutes work with your
spreadsheet and you have your answer.

Dr. Philip G. Hultin

Professor of Chemistry,

University of Manitoba

Winnipeg, MB

R3T 2N2

hultin|cc.umanitoba.ca

http://umanitoba.ca/chemistry/people/hultin

-----Original Message-----
> From: owner-chemistry|ccl.net [mailto:owner-chemistry|ccl.net]
Sent: May 6, 2007 11:07 PM
To: Hultin, Philip G.
Subject: CCL: Interplane Angle


Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com]
Hi,

Does anyone know a program that can measure an interplane angle from
calculated structures?

Many thanks

Suehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtml
http://www.ccl.net/spammers.txt




It's here! Your new message!
Get new email alerts with the free Yahoo! Toolbar. --0-1054255339-1178706843=:31049-- From owner-chemistry@ccl.net Wed May 9 09:43:00 2007 From: "Jeff Hammond jeff.science~!~gmail.com" To: CCL Subject: CCL: chem3D et ammonium Message-Id: <-34223-070509091602-30570-+kLRHPYrfJDI8PzOibj/hg:server.ccl.net> X-Original-From: Jeff Hammond Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 09 May 2007 08:15:45 -0500 MIME-Version: 1.0 Sent to CCL by: Jeff Hammond [jeff.science|a|gmail.com] ENGLISH Miquel, I don't know that the problem is Chem3D, but rather MM2 and MOPAC. Those two theories appear not to contain parameters for 4-coordinated nitrogen. I was able to build a molecule in ChemDraw and input it to Chem3D just fine. The subsequent MM2 minimization failed. MOPAC ran but noted that it didn't have all the necessary parameters. You might try to run it in another program with an ab initio theory. You could do HF/STO-3G if you want complete garbage. B3LYP/6-31G* is a standard low-level theory to optimize at. Best, Jeff PS I don't speak French. Any poor translation is due to Altavista Babelfish (http://babelfish.altavista.com). FRENCH Miquel, Je ne sais pas que le problème est Chem3D, mais plutôt MM2 et MOPAC. Ces deux théories semblent ne pas contenir des paramètres pour l'azote 4-coordinated. Je pouvais construire une molécule dans ChemDraw et l'entrer dans Chem3D juste fin. La minimisation MM2 suivante a échoué. MOPAC a couru mais a noté qu'il n'a pas eu tous les paramètres nécessaires. Vous pourriez essayer de le courir dans un autre programme avec ab initio une théorie. Vous pourriez faire HF/STO-3G si vous voulez les ordures complètes. B3LYP/6-31G* est une théorie de bas niveau standard à optimiser à. Mieux, Jeff La picoseconde I ne parlent pas français. N'importe quelle traduction faible est due à Altavista Babelfish (http://babelfish.altavista.com). ========================================================================== genevieve miquel genevievelaure:yahoo.fr wrote: ENGLISH TRANSLATION Hello I use Chem3D to model a complex comprising an atom of secondary or tertiary nitrogen chelated to a metal, therefore having a nitrogen of the amonium type. The program Chem 3d refuses to take into account this nitrogen for lack of definition. The program answers:there are standard No atom defined for this nitrogen. Have a solution with this problem? thank you cordially G Miquel FRENCH ORIGINAL Bonjour J'utilise Chem3D pour modéliser un complexe comportant un atome d'azote secondaire ou tertiaire chélaté à un métal, donc ayant un azote de type amonium. Le programme Chem 3D refuse de prendre en compte cet azote faute de définition. Le programme répond :there are no atom types defined for this nitrogen. Avez vous une solution à ce problème ? merci cordialement G. Miquel From owner-chemistry@ccl.net Wed May 9 10:37:01 2007 From: "rafi A rafi4dd]|[gmail.com" To: CCL Subject: CCL: Volume of active site in protein Message-Id: <-34224-070509103520-24582-Y2rcXl1SFYz+0EnSu9e9jw|a|server.ccl.net> X-Original-From: "rafi A" Date: Wed, 9 May 2007 10:35:17 -0400 Sent to CCL by: "rafi A" [rafi4dd(a)gmail.com] Hello everyone, Is there any method or software to know the volume of the protein active site or the volume of a particular cavity in protein. Thank you Rafi From owner-chemistry@ccl.net Wed May 9 11:11:00 2007 From: "Phil Hultin hultin]-[cc.umanitoba.ca" To: CCL Subject: CCL: Good Source for History of Oxidation Numbers? Message-Id: <-34225-070509110132-6312-3yl3wM0rVlDXmgb6pSbn+w!^!server.ccl.net> X-Original-From: "Phil Hultin" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 9 May 2007 10:01:13 -0500 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin+*+cc.umanitoba.ca] I like including the history of science into science teaching myself, but I have to note that a large percentage of my class doesn't appreciate the significance of this. Especially when you are teaching large classes containing mostly students who "have to take chemistry" rather than students who want to take chemistry, you can see them wondering "is this going to be on the exam?" You can lead the horse to water, but... Dr. Philip G. Hultin Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin]~[cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin -----Original Message----- > From: owner-chemistry]~[ccl.net [mailto:owner-chemistry]~[ccl.net] Sent: May 8, 2007 9:03 PM To: Hultin, Philip G. Subject: CCL: Good Source for History of Oxidation Numbers? Sent to CCL by: Seth Olsen [s.olsen1-x-uq.edu.au] Hi CCLers, Can anyone direct me to a good source containing a short review of the history of oxidation-reduction concepts, particularly the history of Oxidation Number notation as a way to balance reactions? I am teaching my first ~400 student Gen. Chem. class this monday, and I think that adding a historical note or two to the powerpoint slides provided to me is a good idea. I remember thinking once that (as a physics student in a chemistry class) some of the rules for Ox. numbers seemed quite arbitrary, which I now appreciate to mean that history must be the cause. I generally do not support the teaching of scientific knowledge as 'I bring this to you from the top of Mt. Zion. Learn it so that ye may be enlightened and pass the exam.', and a good way to get around this problem is to highlight the human (fallible) egos which built any given field. Can someone direct me to a good source to bring this home? Cheers, Sethhttp://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 Wed May 9 12:46:00 2007 From: "Elaine Meng meng===cgl.ucsf.edu" To: CCL Subject: CCL: Volume of active site in protein Message-Id: <-34226-070509123945-20600-5DtVt5UGAVOLf8tI3VDqFA,+,server.ccl.net> X-Original-From: "Elaine Meng" Date: Wed, 9 May 2007 12:39:40 -0400 Sent to CCL by: "Elaine Meng" [meng]*[cgl.ucsf.edu] Hi Rafi, Take a look at CASTp - this page links to a server and a publications list. http://sts.bioengr.uic.edu/castp/ I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Wed May 9 13:20:00 2007 From: "Jeff Nauss jnauss-$-accelrys.com" To: CCL Subject: CCL: Volume of active site in protein Message-Id: <-34227-070509123203-19667-SPeJcJZXvF/1F90YGWEP3Q _ server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Wed, 9 May 2007 08:49:51 -0700 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss#%#accelrys.com] owner-chemistry]^[ccl.net wrote on 05/09/2007 07:35:17 AM: > Sent to CCL by: "rafi A" [rafi4dd(a)gmail.com] > > Is there any method or software to know the volume of the protein > active site or the volume of a particular cavity in protein. The binding site analysis functionality in Discovery Studio and InsightII will report a volume for a cavity. The same algorithm is available in Cerius2 but does not report the cavity volume for some reason. Be aware that a fundamental issue in measuring cavity volume is where do you put the top? Where is the boundary between the cavity and the bulk solvent? Different methods will have different definitions. Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/services/training/ From owner-chemistry@ccl.net Wed May 9 14:44:00 2007 From: "Victor Manuel Rosas-Garcia quimico69]*[yahoo.com" To: CCL Subject: CCL: Volume of active site in protein Message-Id: <-34228-070509142955-12160-J+nfq/vOWC9qpbSXXB8DZA,,server.ccl.net> X-Original-From: Victor Manuel Rosas-Garcia Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 9 May 2007 10:29:49 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Victor Manuel Rosas-Garcia [quimico69*|*yahoo.com] You can try alpha shapes see: http://biogeometry.duke.edu/software/alphashapes/ Victor M. Rosas García, PhD Coordinador del Posgrado en Ciencias Facultad de Ciencias Quimicas, UANL e-mail: quimico69[#]yahoo.com Tel: (81) 8329-4010 ext. 6253 Fax: (81) 8376-5375 ----- Original Message ---- > From: rafi A rafi4dd]|[gmail.com To: "Garcis, Rosas " Sent: Wednesday, May 9, 2007 9:35:17 AM Subject: CCL: Volume of active site in protein Sent to CCL by: "rafi A" [rafi4dd(a)gmail.com] Hello everyone, Is there any method or software to know the volume of the protein active site or the volume of a particular cavity in protein. Thank you Rafi ____________________________________________________________________________________ Don't pick lemons. See all the new 2007 cars at Yahoo! Autos. http://autos.yahoo.com/new_cars.html From owner-chemistry@ccl.net Wed May 9 19:21:00 2007 From: "Christa Maria Van Klei Christa.VanKlei__ucfv.ca" To: CCL Subject: CCL: OPLS parameters for Epoxide Message-Id: <-34229-070509172104-20090-Lh9yi+piO4Sj3vi0u1VM3w-,-server.ccl.net> X-Original-From: "Christa Maria Van Klei" Date: Wed, 9 May 2007 17:21:01 -0400 Sent to CCL by: "Christa Maria Van Klei" [Christa.VanKlei|*|ucfv.ca] I am working on MD simulations of an epoxide system and wanted to use OPLS parameters, but was unable to find anything in the literature. If anyone could suggest a reference that contains OPLS parameters for epoxides, it would be very helpful. Thanks, Christa Van Klei From owner-chemistry@ccl.net Wed May 9 19:56:00 2007 From: "Gennady L. Gutsev gennady.gutsev-#-famu.edu" To: CCL Subject: CCL:G: hyperfine coupling constans fo transition metals Message-Id: <-34230-070509165319-123456-P0GL1OO8xxROfCAbCpILZA###server.ccl.net> X-Original-From: "Gennady L. Gutsev" Date: Wed, 9 May 2007 14:39:39 -0400 Sent to CCL by: "Gennady L. Gutsev" [gennady.gutsev .. famu.edu] The basis is 6-311+G* whose content has nothing to do with the basis title. The latter is just traditional. GG -----Original Message----- From: Sibel Tokdemir sozturk##gyte.edu.tr Sent: Wed 5/9/2007 4:59 AM Sent to CCL by: "Sibel Tokdemir" [sozturk!A!gyte.edu.tr] Hello, I have experience on calculating hyperfine coupling constant for organic molecules using Gaussian program. I want to do same thing for first raw transition metals. As far as I read I saw that people used ADF program for transition metals.I wonder if anyone used Gaussian98(or 03) for this purpose. Which basis set will be appropriate for DFT method for Sc-Zn? thanks Sibel Tokdemir/ sozturk(!)gyte.edu.tr