|
|
| From: |
Pijush Ghosh <pijush.ghosh-.at.-ndsu.nodak.edu> |
| Date: |
Tue, 07 Sep 2004 17:41:13 -0500 |
| Subject: |
CCL:Unit cell coordinates for Aragonite. |
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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)
>>
>>
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>>-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
>>
>>
>>
>>
>>
>>
>>
>>
>>------------------------------------------------------------------------
>>
>> 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
>>
>>
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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">http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs">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
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