From chemistry-request@ccl.net Tue Sep 7 02:45:25 2004 Received: from xsmtp.ethz.ch (xsmtp.ethz.ch [129.132.97.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i877jOPS009880 for ; Tue, 7 Sep 2004 02:45:24 -0500 Received: from xfe1.d.ethz.ch ([192.168.36.10]) by xsmtp.ethz.ch with Microsoft SMTPSVC(6.0.3790.0); Tue, 7 Sep 2004 09:54:55 +0200 Received: from [129.132.224.211] ([129.132.224.211]) by xfe1.d.ethz.ch with Microsoft SMTPSVC(6.0.3790.0); Tue, 7 Sep 2004 09:54:54 +0200 Date: Tue, 07 Sep 2004 09:54:54 +0200 From: Urakawa To: chemistry^at^ccl.net Subject: G03 - semiempirical ADMP Message-Id: <20040907094009.5F27.URAKAWA^at^bluewin.ch> MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: Becky! ver. 2.05.06 X-OriginalArrivalTime: 07 Sep 2004 07:54:54.0869 (UTC) FILETIME=[F67B7450:01C494AF] X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCL scientists, I have now a problem with running ADMP in Gaussian 03. When I run ADMP with HF or DFT, there is no problem. However, when I run ADMP with semiempirical methods (AM1, PM3, MNDO), I receive the following error (I have tested on linux and HP-UX). Error termination in NtrErr: NtrErr Called from FileIO As the manual says, I also included the 'Int' keyword (e.g. Int=AM1, Int=MNDO or Int=PM3) in the route section, but doesn't solve the problem. Does anyone know how to solve it? Which keywords I need to specify? I think it should be possible since it is written in the manual... Thank you very much in advance. Atsushi From chemistry-request@ccl.net Tue Sep 7 04:32:08 2004 Received: from web15608.mail.cnb.yahoo.com (web15608.mail.cnb.yahoo.com [202.165.102.62]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i879VsPS018564 for ; Tue, 7 Sep 2004 04:31:55 -0500 Message-ID: <20040907094126.40342.qmail(at)web15608.mail.cnb.yahoo.com> Received: from [202.201.245.195] by web15608.mail.cnb.yahoo.com via HTTP; Tue, 07 Sep 2004 17:41:26 CST Date: Tue, 7 Sep 2004 17:41:26 +0800 (CST) From: =?gb2312?q?yong=20guo?= Subject: ccl:consultation! To: chemistry(at)ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1795882028-1094550086=:24168" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=5.3 required=7.5 tests=DATE_IN_PAST_12_24, DEAR_SOMETHING,FCS_URI_NODOTS,HTML_MESSAGE,J_BACKHAIR_11, MK_BAD_HTML_04,MK_YAHOO_REDIR_01,WLS_URI_OPT_150 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-1795882028-1094550086=:24168 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear Sir: I wanted to calculate the bond energy of H-bond between chloroform and water on the basis of MP2/6-31++G(d,P) level,and compare the calculation result based on the MP2/6-31++G(d,P) level with the result of Second Order Perturbation Theory Analysis of Fock Matrix in NBO Basis of NBO program in Gauss03W program. The reason that I do so is that I think the stable effect of H-bond mainly derive from the orbital interaction between lone pair orbital of O atom and anti-bond ortital of C-H. NBO program can calculate the interaction between orbital. Therefore,I want to make a comparison between the NBO calculation result and the bond energy of H-bond calculated on the basis of MP2/6-31++G(d,P) level. But the comparison result is hard to understand: the energy of orbital interaction calculated with NBO program is larger than the bond energy of H-bond calculated on the MP2/6-31++G(d,P) level. This is abnormal:the energy value calculated with NBO program should less than the bond energy value calculated on the MP2/6-31++G(d,P) level because Hydrogen bond is a combination of static interaction and partial covalent bond between hydrogen (bonded to atoms with high negativity, such as O atom, F atom and N atom) and high negative atom (e.g. O atom, F atom, N atom etc).I do not know why has the queer result? I am eager to wait your reply. Thank you advance! The bond energy calculation of H-bond : E(bond energy of H-bond)= E[dimer energy of chloroform and water , including BBSE] -E[energy of chloroform]-E[energy of water]=#(-1493.649971475258#)-#(-1417.4107645178#)-#(-76.233375740578#)=-0.00583121688 1Hartree=627.5095Kcl/mol, So, E=-0.00583121688 * 627.5095Kcl/mol= -3.65914Kcl/mol The orbital interaction woth NBO program Kcl/mol 34. LP(2) O 7 / 49. RY*( 1) H 2 0.56 1.86 0.029 34. LP(2) O 7 /120. BD*( 1) C 1 - H 2 9.17 1.61 0.109 34. LP (2) O 7 /121. BD*( 1) C 1 -Cl 3 0.09 1.18 0.00 Input file # rmp2/6-31++g(d,p) opt=(calcfc,tight) freq scf=tight 0 1 C H 1 B1 Cl 1 B2 2 A1 Cl 1 B3 2 A2 3 D1 Cl 1 B4 2 A3 4 D2 H 1 B5 2 A4 4 D3 O 1 B6 2 A5 4 D4 H 7 B7 1 A6 2 D5 B1 1.08291447 B2 1.76767156 B3 1.76849461 B4 1.76849461 B5 3.78448696 B6 3.14922668 B7 0.96449625 A1 108.42214171 A2 107.56663818 A3 107.56663818 A4 15.82916059 A5 7.81276324 A6 124.88583699 D1 -120.18166943 D2 -119.63666114 D3 -107.93491134 D4 -59.81833057 D5 103.73430139 Regard! Your sincere:yong guo 2004-9-7 --------------------------------- Do You Yahoo!? 150MrGzMP37h?qKQ#,4xDz43HkRt@V5nLC C(at)E.CwPGS&SP>!SP#,KQ1iC@MMJG1000UW#,QE;"5gSJWTVz@)H]#! --0-1795882028-1094550086=:24168 Content-Type: text/html; charset=gb2312 Content-Transfer-Encoding: 8bit

Dear Sir:

         I wanted to calculate the bond energy of H-bond between chloroform and water on the basis of MP2/6-31++G(d,P) level,and compare the calculation result based on the MP2/6-31++G(d,P) level with the result of Second Order Perturbation Theory Analysis of Fock Matrix in NBO Basis of NBO program in Gauss03W program. The reason that I do so is that I think the stable effect of H-bond mainly derive from the orbital interaction between lone pair orbital of O atom and anti-bond ortital of C-H. NBO program can calculate the interaction between orbital. Therefore,I want to make a comparison between the NBO calculation result and the bond energy of H-bond calculated on the basis of MP2/6-31++G(d,P) level. But the comparison result is hard to understand: the energy of orbital interaction calculated with NBO program is larger than the bond energy of H-bond calculated on the MP2/6-31++G(d,P) level. This is abnormal:the energy value calculated with NBO program should less than the bond energy value calculated on the MP2/6-31++G(d,P) level because Hydrogen bond is a combination of static interaction and partial covalent bond between hydrogen (bonded to atoms with high negativity, such as O atom, F atom and N atom) and high negative atom (e.g. O atom, F atom, N atom etc).I do not know why has the queer result? I am eager to wait your reply. Thank you advance!

 

The bond energy calculation of H-bond :

E(bond energy of H-bond)= E[dimer energy of chloroform  and water , including  BBSE] -E[energy of chloroform]-E[energy of water]=#(-1493.649971475258#)-#(-1417.4107645178#)-#(-76.233375740578#)=-0.00583121688

1Hartree=627.5095Kcl/mol, So,        

E=-0.00583121688 * 627.5095Kcl/mol=

   -3.65914Kcl/mol

 

The orbital interaction woth NBO program

                                                     Kcl/mol

34. LP(2) O   7             / 49. RY*( 1) H   2           0.56    1.86    0.029

34. LP(2) O   7            /120. BD*( 1) C   1 - H   2     9.17    1.61    0.109

34. LP (2) O 7               /121. BD*( 1) C   1 -Cl   3    0.09    1.18    0.00

 

Input file

# rmp2/6-31++g(d,p) opt=(calcfc,tight) freq scf=tight

0 1

 C

 H                  1              B1

 Cl                 1              B2    2              A1

 Cl                 1              B3    2              A2    3              D1

 Cl                 1              B4    2              A3    4              D2

 H                  1              B5    2              A4    4              D3

 O                  1              B6    2              A5    4              D4

 H                  7              B7    1              A6    2              D5

 

   B1             1.08291447

   B2             1.76767156

   B3             1.76849461

   B4             1.76849461

   B5             3.78448696

   B6             3.14922668

   B7             0.96449625

   A1           108.42214171

   A2           107.56663818

   A3           107.56663818

   A4            15.82916059

   A5             7.81276324

   A6           124.88583699

   D1          -120.18166943

   D2          -119.63666114

   D3          -107.93491134

   D4           -59.81833057

   D5           103.73430139

Regard!

                                                        Your sincere:yong guo

                                                          2004-9-7


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C(at)E.CwPGS&SP>!SP#,KQ1iC@M
1G>MJG1000UW#,QE;"5gSJWTVz@)H]#! --0-1795882028-1094550086=:24168-- From chemistry-request@ccl.net Tue Sep 7 01:13:36 2004 Received: from mail.sysarris.soft.net (mail.sysarris.soft.net [164.164.144.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i876DXPS004554 for ; Tue, 7 Sep 2004 01:13:35 -0500 Received: from RAJUV (mobyz.setech.soft.net [164.164.144.12]) (authenticated) by mail.sysarris.soft.net (8.11.2/8.11.2) with ESMTP id i876DrC09321 for ; Tue, 7 Sep 2004 11:43:54 +0530 From: "Raju Vishwanathan" To: Subject: Reg Molecular descriptor calculator for Chemical structures Date: Tue, 7 Sep 2004 11:53:06 +0530 Message-ID: <002901c494a3$23c88360$6666a8c0*at*agi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.2 required=7.5 tests=EXCUSE_16 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello CCL members, I would like to know a list of freely available or commercially available Molecular Descriptor calculator for Chemical structures. Thanking you, Warm Regards, Raju Vishwanathan Sr. Consultant SysArris Software # 120 A, Elephant Rock Road, III Block, Jayanagar,( Opp to HSBC ATM ). Bangalore-560011 India. Tel. No. 91-80-26654965,26655052,26642690, Fax No. 91-80-26650374 <> The information in this message is conf dential and may be legally privileged. It is intended solely for the addressee. Access to this message by anyone else is unauthorised. If you are not the intended recipient, any disclosure, copying, or distribution of the message, or any action or omission taken by you in reliance on it, is prohibited and may be unlawful. Please immediately contact the sender if you have received this message in error.Thank you. From chemistry-request@ccl.net Tue Sep 7 04:15:04 2004 Received: from mailer.gwdg.de (mailer.gwdg.de [134.76.10.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i879F3PS017465 for ; Tue, 7 Sep 2004 04:15:03 -0500 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 4.42) id 1C4cDM-0007gt-OW for chemistry-.at.-ccl.net; Tue, 07 Sep 2004 11:24:37 +0200 Message-ID: <413D7E51.2040307-.at.-mpi-bpc.mpg.de> Date: Tue, 07 Sep 2004 11:24:33 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL List Subject: no. of steps exceeded Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: (clean) by exiscan+sophie X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear CCLers, I appreciate a lot your promt replies to my email that I sent yesterday. The problem is indeed that the no. of steps was exceeded. Now I want to ask you how is the best to get around this: to restart the opt > from where it stopped (using geom=allcheck and guess=read) or to rerun the whole opt using maxcycle=N? And second, gaussian gives me the following: "Number of steps in this run= 102 maximum allowed number of steps= 114". Does this mean that my maxcycle cannot be more than 114?? Could somebody help me on this? Te error: "Optimization stopped. -- Number of steps exceeded, NStep= 102 -- Flag reset to prevent archiving." Thank you in advance vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru-.at.-mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@ccl.net Tue Sep 7 11:55:43 2004 Received: from mb2i1.ns.pitt.edu (mb2i1.ns.pitt.edu [136.142.11.140]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i87GtgPS009994 for ; Tue, 7 Sep 2004 11:55:43 -0500 Received: from CONVERSION-DAEMON by pitt.edu (PMDF V5.2-32 #41462) id <01LEL4X2XI5S002Q3K{at}mb2i1.ns.pitt.edu> for chemistry{at}ccl.net; Tue, 7 Sep 2004 13:04:53 EDT Received: from [127.0.0.1] ([136.142.109.16]) by pitt.edu (PMDF V5.2-32 #41462) with ESMTP id <01LEL4X09JFK002G0H{at}mb2i1.ns.pitt.edu>; Tue, 07 Sep 2004 13:04:49 -0400 (EDT) Date: Tue, 07 Sep 2004 13:04:46 -0400 From: Kadir Diri Subject: Re: CCL:no. of steps exceeded In-reply-to: <413D7E51.2040307{at}mpi-bpc.mpg.de> To: Vlad Cojocaru Cc: CCL List Message-id: <413DEA2E.2020000{at}visual1.chem.pitt.edu> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1; format=flowed Content-transfer-encoding: 7bit User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040803 X-Accept-Language: en-us, en, tr References: <413D7E51.2040307{at}mpi-bpc.mpg.de> X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net You can also just take your last geometry from your output and start a new optimization with that geometry. kadir Vlad Cojocaru wrote: > Dear CCLers, > I appreciate a lot your promt replies to my email that I sent > yesterday. The problem is indeed that the no. of steps was exceeded. > Now I want to ask you how is the best to get around this: to restart > the opt > >> from where it stopped (using geom=allcheck and guess=read) or to rerun > > the whole opt using maxcycle=N? And second, gaussian gives me the > following: "Number of steps in this run= 102 maximum allowed number of > steps= 114". Does this mean that my maxcycle cannot be more than 114?? > Could somebody help me on this? > > Te error: > "Optimization stopped. > -- Number of steps exceeded, NStep= 102 > -- Flag reset to prevent archiving." > > Thank you in advance > vlad > From chemistry-request@ccl.net Tue Sep 7 14:29:35 2004 Received: from smtp1.nodak.edu (smtp1.NoDak.edu [134.129.111.50]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i87JTYPS015562 for ; Tue, 7 Sep 2004 14:29:35 -0500 Received: from ndsu.nodak.edu (dyn216.cie-122.ndsu.NoDak.edu [134.129.122.216]) (authenticated) by smtp1.nodak.edu (8.11.6/8.11.6) with ESMTP id i87Jd5G24074 for ; Tue, 7 Sep 2004 14:39:10 -0500 Message-ID: <413E0EBE.2050207~at~ndsu.nodak.edu> Date: Tue, 07 Sep 2004 14:40:46 -0500 From: Pijush Ghosh User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY~at~ccl.net Subject: CCL: Unit cell coordinates for Aragonite. Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net CCL-friends, I have all the information for the unit cell of Aragonite ( space group, cell dimension, general position etc), but finding some problem to build a model of the same in Cerius2 or in Sybyl6.91. Could anyone help me with the coordinates of unit cell of aragonite. If anyone has tool which is efficient in building unit cell atomic model, please let me know, I can pass on the details needed for building. Thank you. Pijush Ghosh PhD Student Dept. of Civil Engineering. North Dakota State University Fargo. ND-58105. Phone: 701-231-6491(Lab) 701-231-4096(Res) From chemistry-request@ccl.net Tue Sep 7 14:07:30 2004 Received: from hotmail.com (bay10-f36.bay10.hotmail.com [64.4.37.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i87J7TPS014595 for ; Tue, 7 Sep 2004 14:07:29 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 7 Sep 2004 12:17:04 -0700 Received: from 80.108.25.179 by by10fd.bay10.hotmail.msn.com with HTTP; Tue, 07 Sep 2004 19:17:04 GMT X-Originating-IP: [80.108.25.179] X-Originating-Email: [joachimpaier$at$hotmail.com] X-Sender: joachimpaier$at$hotmail.com From: "Joachim Paier" To: chemistry$at$ccl.net Subject: Re: CCL:vibrational spectra of first exc. state w. G03 Date: Tue, 07 Sep 2004 21:17:04 +0200 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1; format=flowed Message-ID: X-OriginalArrivalTime: 07 Sep 2004 19:17:04.0123 (UTC) FILETIME=[4237FCB0:01C4950F] X-Spam-Status: No, hits=3.0 required=7.5 tests=FCS_URI_NODOTS, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net >From: help$at$gaussian.com >To: Joachim Paier >Subject: Re: CCL:vibrational spectra of first exc. state w. G03 >Date: Tue, 7 Sep 2004 10:06:02 -0400 > > > > Dr. Paier, > > The only viable approach for this is CI singles. You would use > ># CIS=(Direct,Root=2) Opt Freq > >to get the second excited state optimized geometry and frequencies. >Check under CIS in the User's Reference for other possible options. > >On Sun, Sep 05, 2004 at 04:08:32PM +0200, Joachim Paier wrote: > > Hi @ all, > > > > I'm interested in calculating the vibrational spectra of > > the first excited state of an > > organic compound (C23H23N2O2+) ... > > > > 1) is it principally possible to 'tackle' this problem with G03 (system > > size!!) > > 2) if yes - which method could I apply? > > > > I would be really grateful for a detailed description of > > the method (keywords etc ...) > > > > regards, > > Joachim > > > > ----------------------------------------------------------------- > > Joachim Paier > > Institut f|r Materialphysik, Univ. Wien > > Sensengasse 8/12, A-1090 Wien, Austria > > mail: joachimpaier$at$hotmail.com > > ----------------------------------------------------------------- > > > > _________________________________________________________________ > > So wird man Teil einer riesigen Chatgemeinde, die ihrer Zeit voraus ist. > > http://messenger.msn.at?DI=1031&XAPID=2532 > > > > > > > > -= This is automatically added to each message by the mailing script =- > > To send e-mail to subscribers of CCL put the string CCL: on your >Subject: > > line > > and send your message to: CHEMISTRY$at$ccl.net > > > > Send your subscription/unsubscription requests to: > > CHEMISTRY-REQUEST$at$ccl.net HOME Page: http://www.ccl.net | Jobs Page: > > http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > > Jan Labanowski, jlabanow$at$nd.edu (read about it on CCL Home Page) > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > >-- >Douglas J. Fox >Technical Support >Gaussian, Inc. >help$at$gaussian.com _________________________________________________________________ Treffen Sie Gleichgesinnte und plaudern Sie |ber gemeinsame Interessen in Foren! http://groups.msn.com/people?pgmarket=de-at From chemistry-request@ccl.net Tue Sep 7 17:30:03 2004 Received: from smtp1.nodak.edu (smtp1.NoDak.edu [134.129.111.50]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i87MU1PS025591 for ; Tue, 7 Sep 2004 17:30:01 -0500 Received: from ndsu.nodak.edu (dyn216.cie-122.ndsu.NoDak.edu [134.129.122.216]) (authenticated) by smtp1.nodak.edu (8.11.6/8.11.6) with ESMTP id i87MdWG13262 for ; Tue, 7 Sep 2004 17:39:36 -0500 Message-ID: <413E3909.2030708-.at.-ndsu.nodak.edu> Date: Tue, 07 Sep 2004 17:41:13 -0500 From: Pijush Ghosh User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY-.at.-ccl.net Subject: CCL:Unit cell coordinates for Aragonite. References: <413E0EBE.2050207-.at.-ndsu.nodak.edu> <1123.152.74.10.94.1094594090.squirrel-.at.-webmail.udec.cl> Content-Type: multipart/alternative; boundary="------------060104000000020208040806" X-Spam-Status: No, hits=0.5 required=7.5 tests=HTML_MESSAGE,HTML_TITLE_EMPTY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --------------060104000000020208040806 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Thanks a lot for this information. But actually what i am looking for is to check if anyone worked with atomic model of aragonite, in that case i can get the coordinate(pdb) of unit cell from them. Because my main difficulty is in developing coordinates of unit cell using the known information. In a more explanatory form, i need coordinates of 20 (8+4+4+4) atoms involved in a unit cell, so that I can use those and extend to form lattice structure. I am new to this field, so i am sorry in case my sentences are unclear.. Antonio Guillermo Buljan Hernandez wrote: >Dear Pijush: > >The Inorganic Crystal Structure Database has 4 entries for >Aragonite Structure. >Here come the structural parameters for these 4 entries. > >Cheers... > > Antonio > > > >>CCL-friends, >> >> I have all the information for the unit cell of Aragonite ( space >>group, cell dimension, general position etc), but finding some problem >>to build a model of the same in Cerius2 or in Sybyl6.91. Could anyone >>help me with the coordinates of unit cell of aragonite. If anyone has >>tool which is efficient in building unit cell atomic model, please let >>me know, I can pass on the details needed for building. >> Thank you. >> >> >>Pijush Ghosh >>PhD Student >>Dept. of Civil Engineering. >>North Dakota State University >>Fargo. ND-58105. >>Phone: 701-231-6491(Lab) >> 701-231-4096(Res) >> >> >>-= This is automatically added to each message by the mailing script =- >>To send e-mail to subscribers of CCL put the string CCL: on your Subject: >>line >>and send your message to: CHEMISTRY-.at.-ccl.net >> >>Send your subscription/unsubscription requests to: >>CHEMISTRY-REQUEST-.at.-ccl.net >>HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs >> >>If your mail is bouncing from CCL.NET domain send it to the maintainer: >>Jan Labanowski, jlabanow-.at.-nd.edu (read about it on CCL Home Page) >>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >> >> >> >> >> >> >> >> >>------------------------------------------------------------------------ >> >> COL ICSD Collection Code 15194 >> DATE Recorded Jan 1, 1980; updated Nov 10, 1997 >> NAME Calcium carbonate >> MINR Aragonite - from Grapevine Mountains, Beatty, Nevada >> FORM Ca C O3 >> = C Ca O3 >> TITL Crystal structures of aragonite, strontianite, and witherite >> REF American Mineralogist >> AMMIA 56 (1971) 758-766 >> AUT de Villiers J P R >> CELL a=4.961(0) b=7.967(0) c=5.740(0) `=90.0 a=90.0 g=90.0 >> V=226.9 Z=4 >> SGR P m c n (62) - orthorhombic >> CLAS mmm (Hermann-Mauguin) - D2h (Schoenflies) >> PRS oP20 >> ANX ABX3 >> PARM Atom__No OxStat Wyck -----X----- -----Y----- -----Z----- -SOF- >> Ca 1 2.000 4c 1/4 0.4150(1) 0.7597(3) >> C 1 4.000 4c 1/4 0.7622(4) -0.0862(10) >> O 1 -2.000 4c 1/4 0.9225(4) -0.0962(9) >> O 2 -2.000 8d 0.4736(4) 0.6810(3) -0.0862(5) >> WYCK d c3 >> >> TF Atom a(1,1) a(2,2) a(3,3) a(1,2) a(1,3) a(2,3) >> Ca 1 0.0062 0.0021 0.0063 0.0000 0.0000 0.0001 >> (1) (1) (4) (2) >> C 1 0.0065 0.0027 0.0025 0.0000 0.0000 -0.0006 >> (9) (3) (25) (3) >> O 1 0.0122 0.0028 0.0086 0.0000 0.0000 -0.0011 >> (9) (3) (18) (5) >> O 2 0.0053 0.0042 0.0069 0.0008 -0.0001 -0.0030 >> (5) (2) (12) (3) (5) (40) >> REM M PDF 41-1475 >> RVAL 0.031 >> >> COL ICSD Collection Code 15198 >> DATE Recorded Jan 1, 1980; updated Nov 10, 1997 >> NAME Calcium carbonate >> MINR Aragonite >> FORM Ca C O3 >> = C Ca O3 >> TITL Refinement of the crystal structure of aragonite >> REF American Mineralogist >> AMMIA 56 (1971) 768-772 >> AUT dal Negro A, Ungaretti L >> CELL a=4.962(0) b=7.970(1) c=5.739(0) `=90.0 a=90.0 g=90.0 >> V=227.0 Z=4 >> SGR P m c n (62) - orthorhombic >> CLAS mmm (Hermann-Mauguin) - D2h (Schoenflies) >> PRS oP20 >> ANX ABX3 >> PARM Atom__No OxStat Wyck -----X----- -----Y----- -----Z----- -SOF- >> Ca 1 2.000 4c 1/4 0.41501(1) 0.2403(1) >> C 1 4.000 4c 1/4 0.7622(45) 0.0862(10) >> O 1 -2.000 4c 1/4 0.9225(4) 0.0962(9) >> O 2 -2.000 8d 0.4736(4) 0.6810(3) 0.0862(5) >> WYCK d c3 >> >> TF Atom a(1,1) a(2,2) a(3,3) a(1,2) a(1,3) a(2,3) >> Ca 1 0.0062 0.0021 0.0063 0.0000 0.0000 0.0001 >> (1) (1) (4) (2) >> C 1 0.0065 0.0027 0.0025 0.0000 0.0000 -0.0006 >> (9) (3) (25) (5) >> O 1 0.0122 0.0028 0.0086 0.0000 0.0000 -0.0011 >> (9) (3) (18) (5) >> O 2 0.0053 0.0042 0.0069 0.0008 -0.0001 -0.0003 >> (5) (2) (12) (3) (5) (4) >> REM M PFD 42-1475 >> RVAL 0.022 >> >> COL ICSD Collection Code 34308 >> DATE Recorded Jan 1, 1980; updated Nov 10, 1997 >> NAME Calcium carbonate >> MINR Aragonite >> FORM Ca C O3 >> = C Ca O3 >> TITL Refinement of the crystal structure of the aragonite phase of Ca C >> O3 >> REF Journal of Research of the National Bureau of Standards, Section >> A. Physics and Chemistry >> JNBAA 75 (1971) 27-32 >> AUT Dickens B, Bowen J S >> CELL a=4.960(1) b=7.964(1) c=5.738(1) `=90.0 a=90.0 g=90.0 >> V=226.6 D=2.95(0) Z=4 >> SGR P m c n (62) - orthorhombic >> CLAS mmm (Hermann-Mauguin) - D2h (Schoenflies) >> PRS oP20 >> ANX ABX3 >> PARM Atom__No OxStat Wyck -----X----- -----Y----- -----Z----- -SOF- >> Ca 1 2.000 4c 1/4 0.58507(5) 0.25974(6) >> C 1 4.000 4c 1/4 0.2386(2) 0.4148(3) >> O 1 -2.000 4c 1/4 0.0770(2) 0.4043(2) >> O 2 -2.000 8d 0.4737(2) 0.3196(1) 0.4131(2) >> WYCK d c3 >> >> TF Atom B(1,1) B(2,2) B(3,3) B(1,2) B(1,3) B(2,3) >> Ca 1 0.6640 0.5990 0.6010 0.0000 0.0000 -0.0100 >> (90) (90) (90) (100) >> C 1 0.7500 0.8500 0.4600 0.0000 0.0000 0.0700 >> (500) (500) (500) (500) >> O 1 1.5000 0.5400 1.0400 0.0000 0.0000 0.0300 >> (500) (400) (400) (400) >> O 2 0.7100 1.0300 1.0200 -0.3200 -0.0200 -0.0900 >> (300) (300) (300) (300) (300) (300) >> REM TEM 298 >> REM M PDF 41-1475 >> RVAL 0.030 >> TEST At least one temperature factor is implausible or meaningless but >> agrees with the value given in the paper. (Code 52) >> >> COL ICSD Collection Code 32100 >> DATE Recorded Mar 16, 1987; updated Nov 10, 1997 >> NAME Calcium carbonate >> MINR Aragonite - from Horenz, Czechoslovakia >> FORM Ca (C O3) >> = C Ca O3 >> TITL Neutron diffraction refinement of the crystal structure of >> Aragonite >> REF TMPM. Tschermaks Mineralogische und Petrographische Mitteilungen >> (1979-) >> TTMMD 35 (1986) 127-131 >> AUT Jarosch D, Heger G >> CELL a=4.961(0) b=7.967(1) c=5.741(0) `=90.0 a=90.0 g=90.0 >> V=226.9 Z=4 >> SGR P m c n (62) - orthorhombic >> CLAS mmm (Hermann-Mauguin) - D2h (Schoenflies) >> PRS oP20 >> ANX ABX3 >> PARM Atom__No OxStat Wyck -----X----- -----Y----- -----Z----- -SOF- >> Ca 1 2.000 4c 1/4 0.41508(5) 0.24046(8) >> C 1 4.000 4c 1/4 0.76211(4) 0.08518(6) >> O 1 -2.000 4c 1/4 0.92224(4) 0.09557(8) >> O 2 -2.000 8d 0.47347(5) 0.68065(3) 0.08726(5) >> WYCK d c3 >> >> TF Atom a(1,1) a(2,2) a(3,3) a(1,2) a(1,3) a(2,3) >> Ca 1 0.0068 0.0026 0.0050 0.0000 0.0000 0.0001 >> (1) (0) (1) (1) >> C 1 0.0045 0.0023 0.0030 0.0000 0.0000 0.0000 >> (1) (0) (1) (0) >> O 1 0.0115 0.0021 0.0066 0.0000 0.0000 -0.0003 >> (1) (0) (1) (0) >> O 2 0.0052 0.0037 0.0070 0.0011 -0.0001 0.0005 >> (7) (0) (1) (0) (1) (0) >> REM NDS (neutron diffraction from a single crystal) >> REM M PDF 41-1475 >> RVAL 0.014 >> >> --------------060104000000020208040806 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Thanks a lot for this information. But actually what i am looking for is to check if anyone worked with atomic model of aragonite, in that case i can get the coordinate(pdb) of unit cell from them. Because my main difficulty is in developing coordinates of unit cell using the known information. In a more explanatory form, i need coordinates of 20 (8+4+4+4) atoms involved in a unit cell, so that I can use those and extend to form lattice structure. I am new to this field, so i am sorry in case my sentences are unclear..

Antonio Guillermo Buljan Hernandez wrote:
Dear Pijush:

The Inorganic Crystal Structure Database has 4 entries for
Aragonite Structure.
Here come the structural parameters for these 4 entries.

Cheers...

          Antonio

  
CCL-friends,

       I have all the information for the unit cell of Aragonite ( space
group, cell dimension, general position etc), but  finding  some problem
to build a model of the same in Cerius2 or in Sybyl6.91. Could anyone
help me with the coordinates of unit cell of aragonite. If anyone has
tool which  is efficient in building unit cell atomic model, please let
me know, I can pass on the details needed for building.
       Thank you.


Pijush Ghosh
PhD Student
Dept. of Civil Engineering.
North Dakota State University
Fargo. ND-58105.
Phone: 701-231-6491(Lab)
           701-231-4096(Res)


-= This is automatically added to each message by the mailing script =-
To send e-mail to subscribers of CCL put the string CCL: on your Subject:
line
and send your message to:  CHEMISTRY-.at.-ccl.net

Send your subscription/unsubscription requests to:
CHEMISTRY-REQUEST-.at.-ccl.net
HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs

If your mail is bouncing from CCL.NET domain send it to the maintainer:
Jan Labanowski,  jlabanow-.at.-nd.edu (read about it on CCL Home Page)
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+






    

 COL  ICSD Collection Code 15194
 DATE Recorded Jan 1, 1980; updated Nov 10, 1997
 NAME Calcium carbonate
 MINR Aragonite - from Grapevine Mountains, Beatty, Nevada
 FORM Ca C O3
      = C Ca O3
 TITL Crystal structures of aragonite, strontianite, and witherite
 REF  American Mineralogist
      AMMIA 56 (1971) 758-766
 AUT  de Villiers J P R
 CELL a=4.961(0) b=7.967(0) c=5.740(0) à=90.0 á=90.0 ç=90.0
      V=226.9 Z=4
 SGR  P m c n       (62) - orthorhombic
 CLAS mmm   (Hermann-Mauguin) - D2h (Schoenflies)
 PRS  oP20
 ANX  ABX3
 PARM Atom__No OxStat  Wyck -----X----- -----Y----- -----Z-----  -SOF-
      Ca     1  2.000    4c  1/4         0.4150(1)   0.7597(3)
      C      1  4.000    4c  1/4         0.7622(4)  -0.0862(10)
      O      1 -2.000    4c  1/4         0.9225(4)  -0.0962(9)
      O      2 -2.000    8d  0.4736(4)   0.6810(3)  -0.0862(5)
 WYCK d c3
ÿ
 TF   Atom   á(1,1)  á(2,2)  á(3,3)  á(1,2)  á(1,3)  á(2,3)
      Ca 1    0.0062  0.0021  0.0063  0.0000  0.0000  0.0001
                 (1)     (1)     (4)                     (2)
      C  1    0.0065  0.0027  0.0025  0.0000  0.0000 -0.0006
                 (9)     (3)    (25)                     (3)
      O  1    0.0122  0.0028  0.0086  0.0000  0.0000 -0.0011
                 (9)     (3)    (18)                     (5)
      O  2    0.0053  0.0042  0.0069  0.0008 -0.0001 -0.0030
                 (5)     (2)    (12)     (3)     (5)    (40)
 REM  M PDF 41-1475
 RVAL 0.031

 COL  ICSD Collection Code 15198
 DATE Recorded Jan 1, 1980; updated Nov 10, 1997
 NAME Calcium carbonate
 MINR Aragonite
 FORM Ca C O3
      = C Ca O3
 TITL Refinement of the crystal structure of aragonite
 REF  American Mineralogist
      AMMIA 56 (1971) 768-772
 AUT  dal Negro A, UngarettiÿL
 CELL a=4.962(0) b=7.970(1) c=5.739(0) à=90.0 á=90.0 ç=90.0
      V=227.0 Z=4
 SGR  P m c n       (62) - orthorhombic
 CLAS mmm   (Hermann-Mauguin) - D2h (Schoenflies)
 PRS  oP20
 ANX  ABX3
 PARM Atom__No OxStat  Wyck -----X----- -----Y----- -----Z-----  -SOF-
      Ca     1  2.000    4c  1/4         0.41501(1)  0.2403(1)
      C      1  4.000    4c  1/4         0.7622(45)  0.0862(10)
      O      1 -2.000    4c  1/4         0.9225(4)   0.0962(9)
      O      2 -2.000    8d  0.4736(4)   0.6810(3)   0.0862(5)
 WYCK d c3
ÿ
 TF   Atom   á(1,1)  á(2,2)  á(3,3)  á(1,2)  á(1,3)  á(2,3)
      Ca 1    0.0062  0.0021  0.0063  0.0000  0.0000  0.0001
                 (1)     (1)     (4)                     (2)
      C  1    0.0065  0.0027  0.0025  0.0000  0.0000 -0.0006
                 (9)     (3)    (25)                     (5)
      O  1    0.0122  0.0028  0.0086  0.0000  0.0000 -0.0011
                 (9)     (3)    (18)                     (5)
      O  2    0.0053  0.0042  0.0069  0.0008 -0.0001 -0.0003
                 (5)     (2)    (12)     (3)     (5)     (4)
 REM  M PFD 42-1475
 RVAL 0.022

 COL  ICSD Collection Code 34308
 DATE Recorded Jan 1, 1980; updated Nov 10, 1997
 NAME Calcium carbonate
 MINR Aragonite
 FORM Ca C O3
      = C Ca O3
 TITL Refinement of the crystal structure of the aragonite phase of Ca C 
      O3
 REF  Journal of Research of the National Bureau of Standards, Section 
      A. Physics and Chemistry
      JNBAA 75 (1971) 27-32
 AUT  Dickens B, BowenÿJÿS
 CELL a=4.960(1) b=7.964(1) c=5.738(1) à=90.0 á=90.0 ç=90.0
      V=226.6 D=2.95(0) Z=4
 SGR  P m c n       (62) - orthorhombic
 CLAS mmm   (Hermann-Mauguin) - D2h (Schoenflies)
 PRS  oP20
 ANX  ABX3
 PARM Atom__No OxStat  Wyck -----X----- -----Y----- -----Z-----  -SOF-
      Ca     1  2.000    4c  1/4         0.58507(5)  0.25974(6)
      C      1  4.000    4c  1/4         0.2386(2)   0.4148(3)
      O      1 -2.000    4c  1/4         0.0770(2)   0.4043(2)
      O      2 -2.000    8d  0.4737(2)   0.3196(1)   0.4131(2)
 WYCK d c3
ÿ
 TF   Atom   B(1,1)  B(2,2)  B(3,3)  B(1,2)  B(1,3)  B(2,3)
      Ca 1    0.6640  0.5990  0.6010  0.0000  0.0000 -0.0100
                (90)    (90)    (90)                   (100)
      C  1    0.7500  0.8500  0.4600  0.0000  0.0000  0.0700
               (500)   (500)   (500)                   (500)
      O  1    1.5000  0.5400  1.0400  0.0000  0.0000  0.0300
               (500)   (400)   (400)                   (400)
      O  2    0.7100  1.0300  1.0200 -0.3200 -0.0200 -0.0900
               (300)   (300)   (300)   (300)   (300)   (300)
 REM  TEM 298
 REM  M PDF 41-1475
 RVAL 0.030
 TEST At least one temperature factor is implausible or meaningless but 
      agrees with the value given in the paper. (Code 52)

 COL  ICSD Collection Code 32100
 DATE Recorded Mar 16, 1987; updated Nov 10, 1997
 NAME Calcium carbonate
 MINR Aragonite - from Horenz, Czechoslovakia
 FORM Ca (C O3)
      = C Ca O3
 TITL Neutron diffraction refinement of the crystal structure of 
      Aragonite
 REF  TMPM. Tschermaks Mineralogische und Petrographische Mitteilungen 
      (1979-)
      TTMMD 35 (1986) 127-131
 AUT  Jarosch D, HegerÿG
 CELL a=4.961(0) b=7.967(1) c=5.741(0) à=90.0 á=90.0 ç=90.0
      V=226.9 Z=4
 SGR  P m c n       (62) - orthorhombic
 CLAS mmm   (Hermann-Mauguin) - D2h (Schoenflies)
 PRS  oP20
 ANX  ABX3
 PARM Atom__No OxStat  Wyck -----X----- -----Y----- -----Z-----  -SOF-
      Ca     1  2.000    4c  1/4         0.41508(5)  0.24046(8)
      C      1  4.000    4c  1/4         0.76211(4)  0.08518(6)
      O      1 -2.000    4c  1/4         0.92224(4)  0.09557(8)
      O      2 -2.000    8d  0.47347(5)  0.68065(3)  0.08726(5)
 WYCK d c3
ÿ
 TF   Atom   á(1,1)  á(2,2)  á(3,3)  á(1,2)  á(1,3)  á(2,3)
      Ca 1    0.0068  0.0026  0.0050  0.0000  0.0000  0.0001
                 (1)     (0)     (1)                     (1)
      C  1    0.0045  0.0023  0.0030  0.0000  0.0000  0.0000
                 (1)     (0)     (1)                     (0)
      O  1    0.0115  0.0021  0.0066  0.0000  0.0000 -0.0003
                 (1)     (0)     (1)                     (0)
      O  2    0.0052  0.0037  0.0070  0.0011 -0.0001  0.0005
                 (7)     (0)     (1)     (0)     (1)     (0)
 REM  NDS (neutron diffraction from a single crystal)
 REM  M PDF 41-1475
 RVAL 0.014

--------------060104000000020208040806--