Hi Henry,
Thanks for your kind comments. I see what you mean about the
"antarafacial" nature of the ozonolysis. I had not intended to imply
any antara/suprafacial aspect to the 3D arrows but like you I think
this could be used specifically to stress this important aspect
perhaps by using a different colour or weight to the arrow (both can
be controlled). [and then another colored arrow for conrotatory and
disrotatory!]
I've done some more pericyclic reactions but have more to do before
they are ready.
I was aiming for an "atom-speciļ¬c" curly arrow passing through the
atom that reacts - Organic Chemistry Clayden et al p 124
As with so much in Jmol, creating the 3D curly arrows is
straightforward.
http://chemapps.stolaf.edu/jmol/docs/examples-11/draw.htm
curves, arrows, OFFSET, set picking DRAW, and show DRAW - you can
experiment here
The process involves drawing any arrow, set picking DRAW, dragging
the three points of the 3D curve to the desired positions (alt or
shift) and then issuing show DRAW - the relevant command can then be
copied into the load command from Console
e.g.
draw arrow1 ARROW {-2.5876317 -0.14727443 -0.49999237} {-0.9625803
2.3060563 -0.9999962} {0.59135246 -0.35723114 2.9140291};
draw arrow1 fill noMesh noDots notFrontOnly fullylit;
color draw opaque [xffa500];
All the best
Nick
--
WWW Pages: http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html
Tel: +44 (0)151-794-3506 (3500 secretary)
On 4 Jan 2008, at 19:57, [EMAIL PROTECTED] wrote:
Message: 6
Date: Fri, 4 Jan 2008 19:56:12 +0000
From: "Rzepa, Henry" <[EMAIL PROTECTED]>
Subject: Re: [Jmol-users] Interactive 3D Organic Reaction Mechanisms
To: [email protected]
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="us-ascii"
Dear Jmol users,
I would like to draw to your attention a new site I have developed
using Jmol (with much help from many of you, especially Bob) to
depict
interactive 3D animations for some of the most important organic
reactions covered during an undergraduate degree with supporting
information on reactivity.
<http://osxs.ch.liv.ac.uk/~ng/external/>http://osxs.ch.liv.ac.uk/~ng/external/
If you are a student or teacher of Organic chemistry, I hope you
will find it interesting and useful. It is intended to supplement
existing textbooks and lectures and I use it regularly projected -
Jmol makes it look great!
What a splendid site Nick.
I have one question. I have for years taught eg pericyclic
mechanisms, where
I drum home to the students that pushed arrows have three
dimensions. Thus suprafacial,
antarafacial, etc etc. Its a specific case of the more general
stereoelectronic theory
of chemistry.
This 3D nature is a little tricky to display. for example, I am
looking at
the 1,3 dipolar cycloaddtion for ozonolysis, where unless I am
mistaken, the arrows could
be taken to indicate antarafacial on the carbonyl and antarafacial
on the 1,3 dipole.
Whilst this is actually "allowed", no 4a + 2a cycloaddition is
actually known.
I must confess to being both impressed and baffled as to how the
arrows
were generated, but is it possible to show the suprafacial/
antarafaciality with
greater precision, ie true 3D arrows (after all, Jmol is the only
tool for arrow
pushing I have ever seen which is capable of doing this!)
Generally, how does one go about authoring this? How long would it
take to eg
position one arrow in a starting set of 3D coordinates?
--
Henry Rzepa.
+44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); [EMAIL PROTECTED]
(iChat)
http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College
London, SW7 2AZ, UK.
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