From owner-chemistry@ccl.net Tue Jan 12 06:42:01 2010 From: "Kunal Roy kroy!A!pharma.jdvu.ac.in" To: CCL Subject: CCL: New Article on Validation of QSAR Models Message-Id: <-41027-100112064009-8235-IvAJbr+Q0jbpCp5LDjYSvA%a%server.ccl.net> X-Original-From: "Kunal Roy" Date: Tue, 12 Jan 2010 06:40:03 -0500 Sent to CCL by: "Kunal Roy" [kroy*pharma.jdvu.ac.in] *****************Apology for multiple posting***************** New paper on validation of QSAR models (downloadable free of charge from the publisher site): On further application of rm2 as a metric for validation of QSAR models Mitra I, Roy PP, Kar S, Ojha P, Roy K J Chemometrics, 24, 2010, 22-33, http://dx.doi.org/10.1002/cem.1268 . ========================= Kunal Roy, Ph.D. Reader, Drug Theoretics and Cheminformatics Lab, Department of Pharmaceutical Technology, JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA) Email : kroy[#]pharma.jdvu.ac.in , kunalroy_in[#]yahoo.com URL : http://sites.google.com/site/kunalroyindia/ From owner-chemistry@ccl.net Tue Jan 12 10:45:01 2010 From: "Zong-Jun Li lzjciac=126.com" To: CCL Subject: CCL: The symmetries of neutral C60 molecule and C60 anions Message-Id: <-41028-100112100509-4843-vDRx32rTofxfz+xZIS8+lQ\a/server.ccl.net> X-Original-From: "Zong-Jun Li" Date: Tue, 12 Jan 2010 10:05:05 -0500 Sent to CCL by: "Zong-Jun Li" [lzjciac-*-126.com] Dear, CCl users, I have a question. It is calculated that fullerence C60 has high Ih symmetry, while C60 anions, such as C602- and C603- have lower D2h and Ci symmetry, respectively. (Green, W. H. et al. J. Phys. Chem. 1996, 100, 14892-14898.) Why is it found that the neutral C60 molecule, C602- and C603- anions have only one peak by NMR spectrometer? (Reed, C. A.; Bolskar, R. D. Chem. Rev. 2000, 100, 1075-1120.) Thanks you for your consideration! Zong-Jun LiState Key Laboratory of Electroanaytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of Sciences(CIAC.CAS)Address: 5625 Renmin Street, Changchun 130022 From owner-chemistry@ccl.net Tue Jan 12 11:20:01 2010 From: "Kunal Roy kunalroy_in^_^yahoo.com" To: CCL Subject: CCL: New Article on Validation of QSAR Models Message-Id: <-41029-100112081421-7697-tiJLCfr+E2y1+MHWHWRn4A|-|server.ccl.net> X-Original-From: Kunal Roy Content-Type: multipart/alternative; boundary="0-276616160-1263298446=:69009" Date: Tue, 12 Jan 2010 17:44:06 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Kunal Roy [kunalroy_in[-]yahoo.com] --0-276616160-1263298446=:69009 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable *****************Apology for multiple posting***************** New paper on validation of QSAR models (downloadable free of charge from th= e publisher site): On further application of rm2 as a metric for validation of QSAR models=20 Mitra I, Roy PP, Kar S, Ojha P, Roy K=20 J Chemometrics, 24, 2010, 22-33, http://dx.doi.org/10.1002/cem.1268 . =A0 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D Kunal Roy, Ph.D.=20 Reader, Drug Theoretics and Cheminformatics Lab, Department of Pharmaceutic= al Technology,=20 JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA)=20 Email : kroy\a/pharma.jdvu.ac.in , kunalroy_in\a/yahoo.com=A0=A0 URL :=A0=A0 http://sites.google.com/site/kunalroyindia/=A0=20 =A0 =A0=0A=0A=0A The INTERNET now has a personality. YOURS! See your Yahoo= ! Homepage. http://in.yahoo.com/ --0-276616160-1263298446=:69009 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable

*****************Apology for multiple posting= *****************

<= SPAN style=3D"mso-bidi-font-size: 12.0pt">New paper on validation of QSAR m= odels (downloadable free of charge from the publisher site):

On further applicati= on of rm2 as a metric for validation of= QSAR models

Mitra I, Roy PP, Kar= S, Ojha P, Roy K

J Ch= emometrics, 24= , 2010, 22-33, http://dx.doi.org/10.1002/cem= .1268 .= =

 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D

Kunal Roy, <= FONT size=3D2>Ph.D.
Reader, Drug T= heoretics and Cheminformatics Lab, Department of Pharmaceutical Technology,=
JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA)=
Email : kroy\a/pharma.jdvu.ac.in= , = kunalroy_in\a/yahoo.com  
 


 
=

=0A=0A=0A=0A
=0AThe INTERNET now has a personality. YOURS! See = your Yahoo! Homepage. --0-276616160-1263298446=:69009-- From owner-chemistry@ccl.net Tue Jan 12 13:32:01 2010 From: "sina rastegar sina_rastegar1979:-:yahoo.com" To: CCL Subject: CCL: freq computation Message-Id: <-41030-100112055647-1824-SseN4GkQA55D6nP67Fc5nw^server.ccl.net> X-Original-From: "sina rastegar" Date: Tue, 12 Jan 2010 05:56:43 -0500 Sent to CCL by: "sina rastegar" [sina_rastegar1979,+,yahoo.com] I have uploaded a file which is about freq computation. I have a serious problem which is the negative frequency after optimization and frequency computaion. I want to know what should I do to solve this problem that how to solve the negative frequency after optimization of the compound. with my best regards From owner-chemistry@ccl.net Tue Jan 12 14:15:00 2010 From: "Henry Martinez hmartine:+:gmail.com" To: CCL Subject: CCL: Activation energy Message-Id: <-41031-100112141348-9986-RtUHdgPHJRAIkBfWgbV7TA++server.ccl.net> X-Original-From: "Henry Martinez" Date: Tue, 12 Jan 2010 14:13:44 -0500 Sent to CCL by: "Henry Martinez" [hmartine:gmail.com] What could be consider the maximun activation energy in Kcal/mol that could be consider for a reaction to be possible in the real world. I have calculate this energy for a particular system, but I want to know if it is too high for being done in a real reaction. Thanks From owner-chemistry@ccl.net Tue Jan 12 14:52:00 2010 From: "Close, David M. CLOSED]-[mail.etsu.edu" To: CCL Subject: CCL: freq computation Message-Id: <-41032-100112145054-21272-NxE9/1CiiHfAmF1QnVwwhA-x-server.ccl.net> X-Original-From: "Close, David M." Content-Class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Tue, 12 Jan 2010 14:50:09 -0500 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED|-|mail.etsu.edu] Sina: If you have just one negative eigenvalue, you have converged to a transition structure. The true minimum lies below this structure. You have to distort the molecule in the direction of this eigenvector and do a re-optimization. The first thing to do is animate the frequency with a graphic program to get a feel for the nature of the vibration. =20 There used to be a free program available to perform this distortion. I have not seen mention of this program for a number of years. The problem being that people who know the trick don't need any help. If this is the first time you have encountered this problem, then you may need some help. =20 Regards, Dave Close -----Original Message----- > From: owner-chemistry+closed=3D=3Detsu.edu*ccl.net [mailto:owner-chemistry+closed=3D=3Detsu.edu*ccl.net] On Behalf Of sina rastegar sina_rastegar1979:-:yahoo.com Sent: Tuesday, January 12, 2010 5:57 AM To: Close, David M. Subject: CCL: freq computation Sent to CCL by: "sina rastegar" [sina_rastegar1979,+,yahoo.com] I have uploaded a file which is about freq computation. I have a serious problem which is the negative frequency after optimization and frequency computaion. I want to know what should I do to solve this problem that how to solve the negative frequency after optimization of the compound. with my best regards -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Jan 12 15:30:01 2010 From: "Serdar Bado?lu sbadoglu++gazi.edu.tr" To: CCL Subject: CCL: freq computation Message-Id: <-41033-100112150907-4620-yjm4+2c6+3xhJ5z1fRW/Hg,server.ccl.net> X-Original-From: "Serdar Bado?lu" Date: Tue, 12 Jan 2010 20:08:52 -0000 Sent to CCL by: "Serdar Bado?lu" [sbadoglu^^^gazi.edu.tr] Have you tried to shift the geometry by hand, then re-run the optimization? Generally this works. Regards -- Serdar BADOGLU From owner-chemistry@ccl.net Tue Jan 12 18:01:01 2010 From: "Kaliappan Muthukumar muthukumar2k3-x-gmail.com" To: CCL Subject: CCL: The symmetries of neutral C60 molecule and C60 anions Message-Id: <-41034-100112175205-19935-SJ35gl5Imeg2A5y1+np5eA]=[server.ccl.net> X-Original-From: Kaliappan Muthukumar Content-Type: multipart/alternative; boundary=00032555ac0a9e7da6047cff7edf Date: Tue, 12 Jan 2010 17:51:29 -0500 MIME-Version: 1.0 Sent to CCL by: Kaliappan Muthukumar [muthukumar2k3{}gmail.com] --00032555ac0a9e7da6047cff7edf Content-Type: text/plain; charset=ISO-8859-1 Two things you should consider 1) NMR time scale is very slow. 2) The charge distribution over the fullerene cage (anions) should be uniform. (Although, i didnt calculated it for C60, i observed this on C82-C2v). Best regards, Muthu On Tue, Jan 12, 2010 at 10:05 AM, Zong-Jun Li lzjciac=126.com < owner-chemistry###ccl.net> wrote: > > Sent to CCL by: "Zong-Jun Li" [lzjciac-*-126.com] > Dear, CCl users, I have a question. It is calculated that fullerence C60 > has high Ih symmetry, while C60 anions, such as C602- and C603- have lower > D2h and Ci symmetry, respectively. (Green, W. H. et al. J. Phys. Chem. 1996, > 100, 14892-14898.) Why is it found that the neutral C60 molecule, C602- and > C603- anions have only one peak by NMR spectrometer? (Reed, C. A.; Bolskar, > R. D. Chem. Rev. 2000, 100, 1075-1120.) Thanks you for your consideration! > Zong-Jun LiState Key Laboratory of Electroanaytical ChemistryChangchun > Institute of Applied ChemistryChinese Academy of Sciences(CIAC.CAS)Address: > 5625 Renmin Street, Changchun 130022> > > -- Dr. Muthukumar Kaliappan, University of Cincinnati, Cincinnati, Ohio, USA --00032555ac0a9e7da6047cff7edf Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Two things you should consider
=A0
1) NMR time scale is very slow.
=A0
2) The charge distribution over the fullerene cage (anions)=A0should b= e=A0uniform.
(Although, i didnt calculated it for C60, i observed this on C82-C2v).=
=A0
Best regards,
Muthu
=A0
=A0
=A0
=A0


=A0
On Tue, Jan 12, 2010 at 10:05 AM, Zong-Jun Li lz= jciac=3D126.com <owner-chemistry###ccl.net>= wrote:

Sent to CCL by: "Zong-J= un =A0Li" [lzjciac-*-126= .com]
Dear, CCl users, I have a question. =A0It is calculated that fullerence C60= has high Ih symmetry, while C60 anions, such as C602- and C603- have lower= D2h and Ci symmetry, respectively. (Green, W. H. et al. J. Phys. Chem. 199= 6, 100, 14892-14898.) Why is it found that the neutral C60 molecule, C602- = and C603- anions have only one peak by NMR spectrometer? (Reed, C. A.; Bols= kar, R. D. Chem. Rev. 2000, 100, 1075-1120.) =A0 Thanks you for your consid= eration! Zong-Jun LiState Key Laboratory of Electroanaytical ChemistryChang= chun Institute of Applied ChemistryChinese Academy of Sciences(CIAC.CAS)Add= ress: 5625 Renmin Street, Changchun 130022



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--
=A0 Dr. Muthukumar Kaliappan,
=A0 = University of Cincinnati,
Cincinnati,
Ohio, USA

--00032555ac0a9e7da6047cff7edf-- From owner-chemistry@ccl.net Tue Jan 12 21:28:00 2010 From: "John McKelvey jmmckel(~)gmail.com" To: CCL Subject: CCL: freq computation Message-Id: <-41035-100112165300-11337-oZK/3J9WR4n2ph98FALhQQ-$-server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 12 Jan 2010 16:52:49 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel- -gmail.com] David Giesen offered a free PYMOL based code for visualization recently on = CCL. John McKelvey On Tue, Jan 12, 2010 at 2:50 PM, Close, David M. CLOSED]-[mail.etsu.edu wrote: > > Sent to CCL by: "Close, David M." [CLOSED|-|mail.etsu.edu] > Sina: > > =A0If you have just one negative eigenvalue, you have converged to a > transition structure. =A0The true minimum lies below this structure. =A0Y= ou > have to distort the molecule in the direction of this eigenvector and do > a re-optimization. =A0The first thing to do is animate the frequency with > a graphic program to get a feel for the nature of the vibration. > =A0There used to be a free program available to perform this distortion. > I have not seen mention of this program for a number of years. =A0The > problem being that people who know the trick don't need any help. =A0If > this is the first time you have encountered this problem, then you may > need some help. > =A0Regards, Dave Close > > -----Original Message----- >> From: owner-chemistry+closed=3D=3Detsu.edu:-:ccl.net > [mailto:owner-chemistry+closed=3D=3Detsu.edu:-:ccl.net] On Behalf Of sina > rastegar sina_rastegar1979:-:yahoo.com > Sent: Tuesday, January 12, 2010 5:57 AM > To: Close, David M. > Subject: CCL: freq computation > > > Sent to CCL by: "sina =A0rastegar" [sina_rastegar1979,+,yahoo.com] > > I have uploaded a file which is about freq computation. > I have a serious problem which is the negative frequency after > optimization and frequency computaion. > I want to know what should I do to solve this problem that how to solve > the negative frequency after optimization of the compound. > with my best regards > > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageJ= ob: http://www.ccl.net/jobs> > > - 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 Tue Jan 12 22:03:00 2010 From: "John McKelvey jmmckel#%#gmail.com" To: CCL Subject: CCL: Visualization Message-Id: <-41036-100112214314-24305-eu1NsLLR5OVtozQ9HU8dmg*|*server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 12 Jan 2010 21:43:03 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel _ gmail.com] Correction... David Giesens program was written in PYTHON, not PYMOL. John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel!=!gmail.com