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Newsgroups: sci.techniques.xtallography From: mbruck@azstarnet.com (Mike Bruck) Subject: help prevent ORTEP of the year Date: Thu, 14 Mar 1996 03:10:26 GMT Organization: Arizona Daily Star - AZSTARNET
I have a structure which is not behaving well and I would like some advice or assistance. The molecule is the meso form of Dimethoxy Dibromo Diketopiperazine
OMe Br
| O |
C " C
/ \ N-C / \
C C-C / \ C-C C
| | >C C< | |
C C-C \ / C-C C
\ / C-N \ /
C " C
| O |
Br OMe
The unit cell is 8.2817 6.1031 21.7360
90.0000 97.2519 90.0000
There is an 0k0 k=2n+1 absence condition There are many exceptions to an h0l h+l=2n+1 condition so I have concluded that it is either P21 (#4) or P21/m (#11)
Surprizingly the Patterson shows a series of weak, monotonically decreasing peaks. There are no distinct Br vectors!
Direct Methods (Shelxs-93) gives a solution in P21, but not in P21/m.
The solution in P21 has TOTALLY disordered Br and OMe groups so that it is not possible to distinquish whether this is meso or a racemic d-l compound. The coordinates are appended to the bottom of this message for those who are interested.
Unfortunately it only refines to an R of 6% and what is worse(!) the ORTEP shows all the characteristics of an improperly solved structure.
Any suggestions or advice will be appreciated.
Mike Bruck
University of Arizona
Department of Chemistry
Tucson AZ 85721
mbruck@xray0.chem.arizona.edu
atoms.dat from Molen, (VAX/VMS version)
Br5 0.128469 -0.471507 0.008544 0.027163 0.045821 0.003037 -0.008107 -0.000228 -0.006707 Br8 0.851728 -0.402233 0.178531 0.017018 0.060790 0.005143 0.006661 0.003677 -0.007259 Br15 0.365973 0.398590 0.492627 0.022662 0.049764 0.003308 -0.008550 0.002012 -0.000845 Br18 -0.349850 0.329514 0.317910 0.022662 0.034667 0.007132 0.008754 0.006707 -0.006838 O5 0.216013 -0.399334 0.024075 5.291246 0.000000 0.000000 0.000000 0.000000 0.000000 O8 0.756489 -0.376800 0.158928 6.280622 0.000000 0.000000 0.000000 0.000000 0.000000 O15 0.315678 0.301081 0.475958 6.890503 0.000000 0.000000 0.000000 0.000000 0.000000 O18 -0.314081 0.272711 0.337257 4.934363 0.000000 0.000000 0.000000 0.000000 0.000000 C5A 0.160286 -0.554202 -0.017289 13.890241 0.000000 0.000000 0.000000 0.000000 0.000000 C8A 0.932448 -0.522617 0.152742 12.050902 0.000000 0.000000 0.000000 0.000000 0.000000 C15A 0.327256 0.468537 0.534906 7.281434 0.000000 0.000000 0.000000 0.000000 0.000000 C18A -0.396610 0.469593 0.339509 5.042902 0.000000 0.000000 0.000000 0.000000 0.000000 O1 0.330063 0.330823 0.190052 0.042674 0.010281 0.004969 0.005982 0.018490 0.003096 O11 0.166999 -0.388135 0.308109 0.026009 0.014399 0.001743 -0.000858 0.006590 0.001528 N1 0.288575 -0.241561 0.232677 0.028239 0.009377 0.001721 0.007421 0.007517 0.000096 N11 0.218433 0.169748 0.268218 0.012730 0.013262 0.003025 -0.000046 0.006008 -0.000155 C1 0.286521 0.160457 0.220380 0.022497 0.006690 0.004030 -0.005519 0.011693 -0.003584 C2 0.339585 -0.067213 0.192207 0.027726 0.004049 0.002326 -0.000149 0.012429 -0.001685 C3 0.257598 -0.093858 0.126123 0.022852 0.029176 0.002291 0.017629 -0.000693 0.003769 C4 0.362455 -0.246014 0.101100 0.019074 0.013992 0.003251 -0.004032 -0.000107 0.001632 C5 0.328710 -0.412091 0.053676 0.013434 0.037925 0.002619 -0.001449 0.001165 -0.002472 C6 0.455876 -0.570064 0.042223 0.021542 0.015390 0.002074 -0.003415 0.003334 -0.004612 C7 0.596182 -0.545046 0.076015 0.038062 0.021064 0.003091 -0.006228 0.015521 -0.003311 C8 0.636387 -0.390151 0.124722 0.011330 0.041116 0.002367 -0.010377 -0.001363 0.004964 C9 0.519831 -0.256081 0.140341 0.009134 0.019729 0.003156 -0.008755 0.006535 0.002467 C10 0.511464 -0.077406 0.190748 0.017107 0.013267 0.002865 -0.003406 0.008159 -0.007461 C11 0.201666 -0.228944 0.282632 0.015021 0.020114 0.001250 0.012704 0.000677 0.004773 C12 0.169209 -0.011933 0.303618 0.009868 0.023692 0.002059 0.004163 -0.000636 0.001387 C13 0.242529 0.035043 0.373245 0.015767 0.010086 0.002570 -0.002117 0.008438 0.000072 C14 0.122526 0.204556 0.395170 0.016170 0.020013 0.000775 0.008643 0.006939 0.002802 C15 0.142918 0.344224 0.442194 0.021988 0.025402 0.001291 -0.004737 0.006385 0.001928 C16 0.027875 0.462322 0.455081 0.037018 0.032486 0.002710 -0.030589 0.011089 -0.008939 C17 -0.126261 0.468957 0.421037 0.011450 0.031638 0.003526 0.014387 0.004207 -0.003196 C18 -0.153165 0.325269 0.370122 0.022234 0.014197 0.003709 0.013014 0.010684 -0.003662 C19 -0.023043 0.180242 0.362781 0.027486 0.012583 0.001793 0.005638 0.005599 -0.001633 C20 -0.026055 0.025355 0.311515 0.013538 0.020609 0.002921 -0.001255 0.002358 0.002786 H6 0.439777 -0.678942 0.010812 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 H7 0.682121 -0.639956 0.068108 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 H3A 0.243344 0.039122 0.103367 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 H3B 0.154789 -0.161718 0.127279 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 H10A 0.566168 -0.130925 0.228832 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 H10B 0.559924 0.056482 0.180371 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 H1 0.314219 -0.385776 0.220621 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 H11 0.192953 0.312672 0.281382 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 H13A 0.350329 0.090622 0.375872 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 H13B 0.242121 -0.094759 0.397348 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 H17 -0.210580 0.564684 0.430100 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 H16 0.052721 0.558181 0.489407 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 H20A -0.068262 -0.109608 0.324308 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000 H20B -0.086663 0.070837 0.273638 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
Newsgroups: sci.techniques.xtallography From: fronz@chxray.dnet.lsu.edu (Frank Fronczek) Subject: Re: help prevent ORTEP of the year Date: Thu, 14 Mar 1996 04:17:07 -0600 Organization: Louisiana State University InterNetNews Site
Mike,
Translation of your coordinates by something like -0.249, 0.029,
-0.249 places the molecule on a center in P2(1)/n with deviations on
the order of a few tenths on an Angstrom across the center. You might
want to try refinement of this centrosymmetric model on the hypothesis
that the n-glide violations are spurious. The Br and OMe groups would
still be disordered, of course.
Good luck!
Newsgroups: sci.techniques.xtallography From: GREGOR@unisi.it (Miguel Gregorkiewitz) Subject: RE: stx2485 help prevent ORTEP of the year Date: Thu, 14 Mar 1996 20:33:32 +0100 (WET) Organization: Dip Scienze della Terra, Universita, SIENA, Europe
Date: Thu, 14 Mar 1996 03:54:42 CST
mbruck@azstarnet.com (Michael Bruck) wrote about an organic crystal stru (dipiperazine....) to behave crazy withpseudo-extinctions and the like.
We had similar problems with a metall-organic structure and zeolites, and found some help thru intensity statistics. There is even a program which does the job - oh, only half of the job, because I never had time to include the less original steps like space group selection. You may have a look at some aspect in Gregorkiewitz & Tudela, Acta Cryst (1990) C46: 210-213, if you think it is of interest for your case, I can send you an abstract with more exhaustive explanations presented at ECM-16 or so some year ago.
Best regards
Prof. Miguel Gregorkiewitz
Dip Scienze della Terra, Universita
Via delle Cerchia 3, I-53100 SIENA, Europe
fon +39'577'298823 fax 298815
Newsgroups: sci.techniques.xtallography From: mbruck@azstarnet.com (Mike Bruck) Subject: Re: help prevent ORTEP of the year Date: Sat, 16 Mar 1996 13:19:12 GMT Organization: Arizona Daily Star - AZSTARNET
Frank Fronczek <fronz@chxray.dnet.lsu.edu> wrote: >Mike, >Translation of your coordinates by something like -0.249, 0.029, >-0.249 places the molecule on a center in P2(1)/n with deviations on >the order of a few tenths on an Angstrom across the center. You might >want to try refinement of this centrosymmetric model on the hypothesis >that the n-glide violations are spurious. The Br and OMe groups would >still be disordered, of course. >Good luck! >Frank Fronczek
THANKS to Frank, Fred Hollander, Larry Henling, Kris Tesh and A. Chandrasekaran!! The advice to ignore the h+l=2n+1 violations seems to be the answer. The structure solves quite nicely in P21/n. The final R-value is slightly lower than in P21, but the data:parameter ratio is much better! since the molecule now sits on an inversion center. The ORTEP no longer gives me nightmares!
Anyone have a good explanation for the h+l=2n+1 exceptions? Maybe the disorder of the Br isn't perfectly distributed? Might this be the source of anomolous reflection intensity? If I have the time and the crystal is stll mounted I'll try some psi-scans when the diffractometer is free.....
Thanks again
Mike
Newsgroups: sci.techniques.xtallography From: boyle@laue.chem.ncsu.edu (Paul D. Boyle) Subject: Re: help prevent ORTEP of the year Date: 19 Mar 1996 14:04:39 GMT Organization: North Carolina State UniversityMichael Bruck (mbruck@azstarnet.com) wrote:
: Anyone have a good explanation for the h+l=2n+1 exceptions? : Maybe the disorder of the Br isn't perfectly distributed? Might this : be the source of anomolous reflection intensity? If I have the time : and the crystal is stll mounted I'll try some psi-scans when the : diffractometer is free.....These could be Renniger reflections. If your crystal is still on the difractometer, go to one of the "violations" and offset psi by couple of degrees and scan through the peak. If it's a Renniger affected reflection, the anomalous intensity should drop off.
You may also find it constructive to read Marsh's recent paper, "Some Thoughts on Choosing the Correct Space Group" in Acta. Cryst. (1995) B51, 897-907. It is a very worthwhile read.
later,
Paul
__ Paul D. Boyle | boyle@laue.chem.ncsu.edu Director, X-ray Structural Facility | phone: (919) 515-7362 Department of Chemistry - Box 8204 | FAX: (919) 515-5079 North Carolina State University | Raleigh, NC, 27695-8204 http://laue.chem.ncsu.edu/web/xray.welcome.html
Newsgroups: sci.techniques.xtallography From: "Graheme J.B. Williams" <GRAHEME@enraf.delftny.com> Subject: (Fwd) Spurious reflections Date: Tue, 19 Mar 1996 15:56:38 EST Organization: Enraf-Nonius, Kipp & ZonenMike,
Pleased to note that you will not be cited in The R Harlow Hall of Shame - this year or any other I am sure.
Obviously your respondents were right in suggesting that the
violations of the h+l=2n rule were spurious. There are two main
reasons for this.
1) Renninger reflections. These are "reflections which use a strong
reflected beam as the x-ray source" They are common when the
crystal is of high quality and good reflection power. Perhaps they
are the cause for you but I do not expect so since the sample is
disordered.
2) Lambda/2 effects. In both a crystal-monochromated beam and in a
filtered beam there exists significant contamination by the "half
wavelength" component of the spectrum. This can give rise to
spurious reflections and, of course, contamination of all
reflections. If the doubled indices of the spurious reflections
correspond to strong reflections then I think that this is a most
likely cause. For example if your reflection 2.0.1 is present but
should not be then look at 4.0.2 Is it strong?
The diagnostic test for this phenomena is to look at a position in
space where ONLY the lambda/2 reflection will occur. For example if
your 1.1.1 is strong look for the reflection 1/2.1/2.1/2 If it's
there then you have contamination. Of course in order to look for a
reflection with fractional indices you need to have a CAD4 or some
other diffractometer which has some sophistocated tools built in!
If this contamination exists then there are two "cures".
1) Don't worry about it.
2) Adjust the window of your Pulse Height Discriminator to reduce
the observability of the double-energy peaks. Of course when you do
this you also will reduce the observabilityof peaks which have double
energy because of two normal pulses arriving at the same time. This
should be too much of a problem however since at high count rates
your diffractometer looks after you!
Cheers. =Graheme=
EEEE N N Graheme J. B. Williams: || // cc cc ddd \\
E NN N 390 Central Ave, : ||// c c d d \\
EEE N N N Bohemia,NY 11716-3147 : ||\\ c c d d //
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Williams@DelftNY.com : HTTP://WWW.Enraf-Nonius.DelftNY.com
Comments on our WWW site are solicited
Newsgroups: sci.techniques.xtallography From: swinnea@weiss.che.utexas.edu (J. Steven Swinnea) Subject: Re: (Fwd) Spurious reflections Date: 20 Mar 1996 16:31:48 GMT Organization: Dept. Chem. Engr., Univ. of Texas at Austin
In article <7F29017BD0@enraf.delftny.com>, Graheme J.B. Williams <williams@delftny.com> wrote: >there then you have contamination. Of course in order to look for a >reflection with fractional indices you need to have a CAD4 or some >other diffractometer which has some sophistocated tools built in!Gee... I didn't know that doubling the unit-cell edges to make the 1/2.1/2.1/2 a 1.1.1 was all that sophisticated. :-)
Steve Swinnea swinnea@che.utexas.edu Department of Chemical Engineering
Newsgroups: sci.techniques.xtallography From: Hakon Hope <hhope@ucdavis.edu> Subject: Re: (Fwd) Spurious reflections Date: Wed, 20 Mar 1996 17:05:18 -0800 Organization: University of California, Davis
:Steve Swinnea says: Gee... I didn't know that doubling the :unit-cell edges to make the :1/2.1/2.1/2 a 1.1.1 was all that sophisticated. :-)The sophistication lies in *not* having to double the cell edges, but to go to fractional indices without further ado. Graheme Williams is quite justified in making fun of some well-known diffractometer software where you have to double, or triple, or quadruple or whatever, just to check some region with non-integer indices.
Hakon Hope