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How to draw ferrocene?
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Reply to topic    Home -> Forums -> Support -> Drawing & visualization: Marvin/Sketch /View /Space -> How to draw ferrocene?

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aruga
Joined: 09 Apr 2005
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Post subject: How to draw ferrocene?
Link to postPosted: Thu Feb 08, 2007 11:12 am  Reply with quote
Could you tell me how to draw ferrocene molecule by Marvin Sketch?
Szilva
Joined: 10 Jul 2004
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Link to postPosted: Thu Feb 08, 2007 12:35 pm  Reply with quote
Hello, unfortunatelly in the current version there are no coordinated bonds and you can not really draw a ferrocene/metallocene. We are working hard on coordinated bonds and multicenter Sgroups - they will be included in the next major release.
aruga
Joined: 09 Apr 2005
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Post subject:
Link to postPosted: Thu Feb 08, 2007 3:25 pm  Reply with quote
Thank you very much.
Szilva
Joined: 10 Jul 2004
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Post subject:
Link to postPosted: Thu Feb 08, 2007 3:53 pm  Reply with quote
This topic is realted to dative/multicenter bonds, maybe useful for you:

http://www.chemaxon.com/forum/ftopic1412.html

cheers
Eric Hart
Joined: 20 Dec 2006
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Post subject: Re: How to draw ferrocene?
Link to postPosted: Sat Feb 10, 2007 1:19 am  Reply with quote
aruga wrote:
Could you tell me how to draw ferrocene molecule by Marvin Sketch?
Szilva
Joined: 10 Jul 2004
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Link to postPosted: Mon Feb 12, 2007 7:06 pm  Reply with quote
Hello, was something missed here? Seems the quiestion did not come through.
bobgr
Joined: 15 Jun 2004
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Link to postPosted: Fri Jan 11, 2008 9:00 pm  Reply with quote
In Marvin 5.0, it's possible to draw ferrocene. You will need to look at these instructions to learn how to do it.

It is also possible to draw a pi-allyl complex. (See Cp2Ti(allyl) below.) I used aromatic bonds to represent the C-C bonds in the allyl group. However, I would like to see a curved line represent the electrons in the allyl group in the picture, rather than the solid-dashed lines that show currently. Is it possible to add that feature to multicenter S groups?

Code:
<?xml version="1.0" ?>
<cml>
<MDocument>
  <MChemicalStruct>
    <molecule molID="m1">
      <atomArray
          atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17"
          elementType="Ti C C C C C X C C C C C X C C C X"
          sgroupRef="0 sg1 sg1 sg1 sg1 sg1 0 sg2 sg2 sg2 sg2 sg2 0 sg3 sg3 sg3 0"
          x2="-3.5199999809265137 -6.215000152587891 -7.460866481604919 -6.985004064217696 -5.444996240958083 -4.969133823570862 -6.215000152587891 -3.7950000762939453 -5.0408664053109735 -4.565003987923751 -3.024996164664138 -2.549133747276917 -3.7950000762939453 -1.9800000190734863 -0.6463208972454506 -0.6463208972454505 -1.0908806045214625"
          y2="1.8700000047683716 4.609992207093841 3.7047756085818406 2.2402281686619485 2.2402281686619485 3.7047756085818406 3.299999952316284 0.3199922452408135 -0.5852243532711867 -2.049771793191079 -2.049771793191079 -0.5852243532711867 -0.9900000095367432 3.4649999141693115 2.6949999141693115 1.1549999141693115 2.4383332475026447"
          />
      <bondArray>
        <bond atomRefs2="a2 a3" order="A" />
        <bond atomRefs2="a2 a6" order="A" />
        <bond atomRefs2="a3 a4" order="A" />
        <bond atomRefs2="a4 a5" order="A" />
        <bond atomRefs2="a5 a6" order="A" />
        <bond atomRefs2="a7 a1" convention="cxn:coord" />
        <bond atomRefs2="a8 a9" order="A" />
        <bond atomRefs2="a8 a12" order="A" />
        <bond atomRefs2="a9 a10" order="A" />
        <bond atomRefs2="a10 a11" order="A" />
        <bond atomRefs2="a11 a12" order="A" />
        <bond atomRefs2="a13 a1" convention="cxn:coord" />
        <bond atomRefs2="a14 a15" order="A" />
        <bond atomRefs2="a15 a16" order="A" />
        <bond atomRefs2="a17 a1" convention="cxn:coord" />
      </bondArray>
      <molecule id="sg1" role="MulticenterSgroup" molID="m2"
         atomRefs="a2 a3 a4 a5 a6"  center="a7"
        />
      <molecule id="sg2" role="MulticenterSgroup" molID="m3"
         atomRefs="a8 a9 a10 a11 a12"  center="a13"
        />
      <molecule id="sg3" role="MulticenterSgroup" molID="m4"
         atomRefs="a14 a15 a16"  center="a17"
        />
    </molecule>
  </MChemicalStruct>
</MDocument>
</cml>
Erika
Joined: 12 Oct 2005
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Post subject:
Link to postPosted: Mon Jan 14, 2008 10:16 pm  Reply with quote
We have considered your request. The representation and visualization of the electrons in the allyl group will be different. We plan to solve this problem in Marvin 5.1 or 5.2.

Best regards,
Erika.
bobgr
Joined: 15 Jun 2004
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Link to postPosted: Mon Jan 14, 2008 10:47 pm  Reply with quote
Pentadienyl groups (not cyclopentadienyl -- they already work fine) too, please.
Erika
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Post subject:
Link to postPosted: Wed Jan 16, 2008 10:45 pm  Reply with quote
Yes, Pentadienyl groups will be represented and visualized similarly.
bobgr
Joined: 15 Jun 2004
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Post subject:
Link to postPosted: Fri Jun 12, 2009 3:05 am  Reply with quote

I want to compliment you on the ease of drawing cyclopentadienyl compounds such as Cp2Fe and Cp2TiCl2 in Marvin 5.2.  I also want to compliment you on the fact that Clean-3D converts both these compounds to their correct 3D structures (linear and tetrahedral, respectively).  One very minor complaint: When the Cp ring is converted to 3D, the circle inside the Cp that represents aromaticity is replaced with five individual aromatic bonds, which are represented by parallel solid and dashed lines.  I would like to see the circle preserved in 3D (though of course it would have to be an oval, depending on the user's perspective).  
akospapp
Joined: 09 Mar 2007
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Post subject: Projected view of aromatic rings
Link to postPosted: Mon Jun 15, 2009 7:32 am  Reply with quote

Hi Bob,

The perspective drawing of aromatic rings (using ellipses for the display of aromaticity) is among our plans, and will hopefully be released in 5.3 coming this autumn.

Best regards,

Akos
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