From owner-chemistry@ccl.net Tue Nov 6 00:33:01 2007 From: "Antony Williams tony{:}chemspider.com" To: CCL Subject: CCL: FW: CCL: Looking for strucrue viewer program which can show the charges Message-Id: <-35559-071106002849-15259-SFGwdMI/3am5VS2bc26h0w^_^server.ccl.net> X-Original-From: "Antony Williams" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 5 Nov 2007 23:38:35 -0500 MIME-Version: 1.0 Sent to CCL by: "Antony Williams" [tony[-]chemspider.com] JunJun, I've spent sometime of late looking at the SimBioSys product line and one of their products might be of value to you. Take a look at the CheVi product (http://www.simbiosys.ca/chevi/) If you go under the Molecule -> Label -> Charges then it can show the partial charges coming from the mol2 format. An example is shown here: http://www.simbiosys.ca/chevi/index.html SimBioSys give the CheVi 3D visualization tool free to everyone. It was developed on Linux so is ideal for your needs I think. There's a demo request form online at their website: http://www.simbiosys.ca/products/demo_request.html Antony Williams, Host of ChemSpider (www.chemspider.com) Phone: (919) 341-8375 Mobile: (919) 201-1516 Fax: (919) 300 5321 Email: antony.williams=chemspider.com CONFIDENTIALITY NOTICE Unless expressly stated otherwise, this message is confidential and is intended for the addressee(s) only. If you are not an addressee, please inform the sender immediately or contact feedback=chemspider.com. ---------- Forwarded Message ---------- Subject: CCL: Looking for strucrue viewer program which can show the charges Date: Thursday 01 November 2007 14:10 > From: "JunJun Liu ljjlp03 _ gmail.com" To: "Simon, Aniko " Sent to CCL by: "JunJun Liu" [ljjlp03 * gmail.com] Hello everyone, I'm looking for a free graphical 3D structure viewer program that can easily display atomic partial charges as the label on each atom. Can someone give me a suggestion? My OS is linux, so I'd like the program can be run under Linux. Thanks a lot! -- JunJun Liuhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------- -- Aniko Simon, Ph.D. SimBioSys Inc. http://www.simbiosys.ca/ Tel: 1-416-741-4263 From owner-chemistry@ccl.net Tue Nov 6 04:25:00 2007 From: "Yangsoo Kim vsmember,gmail.com" To: CCL Subject: CCL:G: Hinderedrotor Problem in Gaussian03 Message-Id: <-35560-071106035138-17834-ApsVT/Yx4yRHvzxDW26gpQ[-]server.ccl.net> X-Original-From: "Yangsoo Kim" Content-Type: multipart/alternative; boundary="----=_Part_136_28401318.1194339085312" Date: Tue, 6 Nov 2007 17:51:25 +0900 MIME-Version: 1.0 Sent to CCL by: "Yangsoo Kim" [vsmember * gmail.com] ------=_Part_136_28401318.1194339085312 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCL members, I am trying to use the "HF/6-31G* opt freq=hinderedrotor" keyword in Gaussian03 to correct the themochemical data for contributions of internal rotation. It is normally terminated to calculate the hindered rotor analysis for the normal alkyl-chained systems. But I met the following error messages for various alkyl-substitutied benzene ring systems. (e.q. toluene, ethylbenzene or propylbenzene) === Error Message (propylbenzene) === Hindered Internal Rotation Analysis Internal coordinate list checked Check for planar centers 1 2 3 10 360.000 2 1 6 7 359.984 3 1 4 11 360.000 4 3 5 12 360.000 5 4 6 13 360.000 6 2 5 14 360.000 Check reduced barrier height. Cut-off : V/RT = 33.7561 Check for ring deformation Number of internal rotation degrees of freedom = 3 NNew= 48 NTest= 3 NB= 9 IFrz= 0 IBar= 0 ICyc= 0 Problem with the number of degrees of freedom Error termination... ====================== Does anyone have any suggestions to solve these problems? And please tell me another softwares to calculate the hindered rotor. Thanks in advance. Yangsoo Kim ------=_Part_136_28401318.1194339085312 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

Dear CCL members,

I am trying to use the "HF/6-31G* opt freq=hinderedrotor" keyword in Gaussian03 to correct the themochemical data for contributions of internal rotation.
It is normally terminated to calculate the hindered rotor analysis for the normal alkyl-chained systems.
But I met the following error messages for various alkyl-substitutied benzene ring systems. (e.q. toluene, ethylbenzene or propylbenzene)

=== Error Message (propylbenzene) ===
           Hindered Internal Rotation Analysis
 Internal coordinate list checked
 Check for planar centers
    1         2         3        10      360.000
    2         1         6         7      359.984
    3         1         4        11      360.000
    4         3         5        12      360.000
    5         4         6        13      360.000
    6         2         5        14      360.000
 Check reduced barrier height. Cut-off : V/RT =    33.7561
 Check for ring deformation
 Number of internal rotation degrees of freedom =   3
 NNew=   48 NTest=    3 NB=    9 IFrz=    0 IBar=    0 ICyc=    0
  Problem with the number of degrees of freedom
 Error termination...
======================

Does anyone have any suggestions to solve these problems?
And please tell me another softwares to calculate the hindered rotor.

Thanks in advance.

Yangsoo Kim

------=_Part_136_28401318.1194339085312-- From owner-chemistry@ccl.net Tue Nov 6 09:10:01 2007 From: "Chunsen Li chunsen_li],[yahoo.com.cn" To: CCL Subject: CCL: looking for a software for displaying the molecular structures Message-Id: <-35561-071106023427-12959-WJyp07eESrReU0/9qS5pmg#,#server.ccl.net> X-Original-From: "Chunsen Li" Date: Tue, 6 Nov 2007 02:34:23 -0500 Sent to CCL by: "Chunsen Li" [chunsen_li!A!yahoo.com.cn] Hi , I want know which software can display the molecular structures as shown in Figure 1 of Angew. Chem. Int. Ed. 2005, 44, 2939. The bond in the structure is shown as single line and the labels can be add in the center of the atoms freely. In addition, the atoms can be in different patterns and colors. The similar picture and be found from http://qc.physto.se/home.htm. Which software can do this? Is it free of charge? Thank you. Chunsen Li Center for Theoretical Chemistry, Department of Chemistry, Xiamen University, Xiamen, 361005, China. Tel.: 86-592-2180418 Fax: 86-592-2184708 email: lics01|*|xmu.edu.cn chunsen_li|*|yahoo.com.cn 2007-10-30 From owner-chemistry@ccl.net Tue Nov 6 09:45:01 2007 From: "Ulrich Scharfenort scharfenort{=}ltt.rwth-aachen.de" To: CCL Subject: CCL:G: Hinderedrotor Problem in Gaussian03 Message-Id: <-35562-071106065703-12520-kg1PvDSUUrdzhjNMN8/9uw[a]server.ccl.net> X-Original-From: Ulrich Scharfenort Content-disposition: inline Content-transfer-encoding: 7BIT Content-type: text/plain; charset=iso-8859-1 Date: Tue, 06 Nov 2007 12:25:19 +0100 MIME-version: 1.0 Sent to CCL by: Ulrich Scharfenort [scharfenort .. ltt.rwth-aachen.de] Hello, you may have to use Geom=Modify to get the right set of coordinates for your calculation. Freq=HinderedRotor doesn't work with all. best wishes Ulrich Scharfenort Am Dienstag, 6. November 2007 09:51:25 schrieb Yangsoo Kim vsmember,gmail.com: > am trying to use the "HF/6-31G* opt freq=hinderedrotor" keyword in > Gaussian03 to correct the themochemical data for contributions of internal > rotation. From owner-chemistry@ccl.net Tue Nov 6 10:20:01 2007 From: "Greef, T.F.A. de t.f.a.d.greef(a)tue.nl" To: CCL Subject: CCL:G: Hinderedrotor Problem in Gaussian03 Message-Id: <-35563-071106054838-7906-zAtfsLsAXu3fKNehdoFjMw,,server.ccl.net> X-Original-From: "Greef, T.F.A. de" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C8205D.4EC9811F" Date: Tue, 6 Nov 2007 11:10:50 +0100 MIME-Version: 1.0 Sent to CCL by: "Greef, T.F.A. de" [t.f.a.d.greef.:.tue.nl] This is a multi-part message in MIME format. ------_=_NextPart_001_01C8205D.4EC9811F Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear Yangsoo, I had the same problem a while ago. Dr. Douglas Fox from Gaussian told me that the error here is related to the attempt to classify the internal coordinates and unfortunately it is not uncommon that it fails. I am not aware of any program that can do the trick. =20 Best regards, =20 Tom =20 =20 ________________________________ > From: owner-chemistry(!)ccl.net [mailto:owner-chemistry(!)ccl.net]=20 Sent: Tuesday, November 06, 2007 9:51 AM To: Greef, T.F.A. de Subject: CCL:G: Hinderedrotor Problem in Gaussian03 =20 Dear CCL members, I am trying to use the "HF/6-31G* opt freq=3Dhinderedrotor" keyword in Gaussian03 to correct the themochemical data for contributions of internal rotation. It is normally terminated to calculate the hindered rotor analysis for the normal alkyl-chained systems.=20 But I met the following error messages for various alkyl-substitutied benzene ring systems. (e.q. toluene, ethylbenzene or propylbenzene) =3D=3D=3D Error Message (propylbenzene) =3D=3D=3D Hindered Internal Rotation Analysis Internal coordinate list checked Check for planar centers 1 2 3 10 360.000 2 1 6 7 359.984 3 1 4 11 360.000 4 3 5 12 360.000 5 4 6 13 360.000 6 2 5 14 360.000 Check reduced barrier height. Cut-off : V/RT =3D 33.7561 Check for ring deformation Number of internal rotation degrees of freedom =3D 3 NNew=3D 48 NTest=3D 3 NB=3D 9 IFrz=3D 0 IBar=3D 0 ICyc=3D = 0 Problem with the number of degrees of freedom Error termination...=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Does anyone have any suggestions to solve these problems? And please tell me another softwares to calculate the hindered rotor. Thanks in advance. Yangsoo Kim ------_=_NextPart_001_01C8205D.4EC9811F Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear Yangsoo,

I had the same problem a while ago. Dr. Douglas Fox from = Gaussian told me that the error here is related to the attempt to classify the = internal coordinates and unfortunately it is not uncommon that it fails. I am not = aware of any program that can do the trick.

 

Best regards,

 

Tom

 

 

From: owner-chemistry(!)ccl.net [mailto:owner-chemistry(!)ccl.net]
Sent: Tuesday, November = 06, 2007 9:51 AM
To: Greef, T.F.A. de
Subject: CCL:G: = Hinderedrotor Problem in Gaussian03

 

Dear CCL members,

I am trying to use the "HF/6-31G* opt freq=3Dhinderedrotor" keyword = in Gaussian03 to correct the themochemical data for contributions of = internal rotation.
It is normally terminated to calculate the hindered rotor analysis = for the normal alkyl-chained systems.
But I met the following error messages for various alkyl-substitutied = benzene ring systems. (e.q. toluene, ethylbenzene or = propylbenzene)

=3D=3D=3D Error Message (propylbenzene) =3D=3D=3D
           Hindered = Internal Rotation Analysis
 Internal coordinate list checked
 Check for planar centers
    1         2         3        = 10      360.000
    2         1         6         7      359.984
    3         1         4        = 11      360.000
    4         3         5        = 12      360.000
    5         4         6        = 13      360.000
    6         2         5        = 14      360.000
 Check reduced barrier height. Cut-off : V/RT =3D    = 33.7561
 Check for ring deformation
 Number of internal rotation degrees of freedom =3D   = 3
 NNew=3D   48 NTest=3D    3 = NB=3D    9 IFrz=3D    0 IBar=3D    0 = ICyc=3D    0
  Problem with the number of degrees of freedom
 Error termination...
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

Does anyone have any suggestions to solve these problems?
And please tell me another softwares to calculate the hindered = rotor.

Thanks in advance.

Yangsoo Kim

------_=_NextPart_001_01C8205D.4EC9811F-- From owner-chemistry@ccl.net Tue Nov 6 11:47:00 2007 From: "Deepangi Pandit dnp5 * njit.edu" To: CCL Subject: CCL: looking for a software for displaying the molecular structures Message-Id: <-35564-071106113058-30545-Vj2MaYDSxCq7XZsOMHmBxg=-=server.ccl.net> X-Original-From: "Deepangi Pandit" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 6 Nov 2007 10:32:01 -0500 MIME-Version: 1.0 Sent to CCL by: "Deepangi Pandit" [dnp5+/-njit.edu] Hi Chunsen: You could try ISIS/Draw, Arguslab or ACD Chemsketch. http://www.mdli.com/downloads/downloadable/index.jsp http://www.acdlabs.com/download/chemsk.html http://www.planaria-software.com/ DP On 11/6/07, Chunsen Li chunsen_li],[yahoo.com.cn wrote: > > Sent to CCL by: "Chunsen Li" [chunsen_li!A!yahoo.com.cn] > Hi , > > I want know which software can display the molecular structures as shown in Figure 1 of Angew. Chem. Int. Ed. 2005, 44, 2939. > The bond in the structure is shown as single line and the labels can be add in the center of the atoms freely. In addition, the atoms can be in different patterns and colors. The similar picture and be found from http://qc.physto.se/home.htm. > > Which software can do this? Is it free of charge? > > Thank you. > > > Chunsen Li > Center for Theoretical Chemistry, Department of Chemistry, > Xiamen University, Xiamen, 361005, China. > Tel.: 86-592-2180418 Fax: 86-592-2184708 > email: lics01]-[xmu.edu.cn chunsen_li]-[yahoo.com.cn > 2007-10-30> > > > -- - Deepangi