From chemistry-request ( ( at ) ) 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--