#pb
8 messages in this thread
hyperchem! I want to:
1) compare the structure I have modeled with the crystallographic data from the
literature…..how can I load the crystallographic coordinates and do an
overlay?
2) pi bond an olefin to a titanocene metal center that has a growing polymer
chain on it….(for rotational studies using the dihedral excel macro)
more later!
..and more replies..
To load the crystallographics coordinates, you would need to format them
according to HIN or some other format. Although the HIN file format can look
pretty intimidating, you can get by with very little. Here is an example of a
minimal HIN file for ethylene:
mol 1 atom 1 – C ** – 0.0 -0.67 0.0 0.0 0 atom 2 – C ** – 0.0 0.67 0.0 0.0 0
endmol
You need the – and **'s, but the column numbers donb't matter. The numbers are
charges (the first 0.0), coordinates (next three numbers) and a 0 for the
number of neighbours.
This doesn't connect them, of course. The trick then is to save the structure
as a Z-matrix, and read it in again. Coupled with the z-matrix reader is a
component that takes a guess at bonding and bond orders. Then do an "Add
hydrogens" to add on the hydrogen atoms.
Hope this helps.
Tom
but once you "add hydrogens" does'nt the structure change to some other optima?
and I don't want a central "dummy" atom, I need a pi bonded olefin….next
release?
R
/
Cp =
\ /
M P
/ \/\/\/\/\/
Cp
\
R'
where = is a substituted olefin, and is pi bonded to the metal center, and
spins around so that the effects of R (or R') on the energy of the system, (and
the optimum orientation) can be mapped….will a dummy atom or disconnected Cp
system work? How do I measure the distance between the Cp centroid and the
metal center? how do I measure the olefin metal center bond distance, and look
at the effect of the R (or R') group?
more later,
ps, thanks!
Larry,
The structure changes after you "Add Hydrogens and Model Build", but there is
also an option to simply add hydrogens, which leaves all other atoms in
unchanged positions.
As for your pi-bonded olefin: hmmm… let me think till tomorrow on that one..
Tom
also, lets put these crystallographic coordinates into an excel file (with the
unit cell parameters, or cartesian coordinates or whatever…..even maybe have
one of those nice little windows like the periodic table window for the
elements you made in the latest release….) and then have that go into the
readable Hyperchem modeling formatted whatever…..
more later….
I'm not sure if I know what you mean here: but given a spreadsheet with
something like
C 1.1 1.2 3.2
O 2.1 1.2 3.0 etc., an Excel macro could be written that
would send those coordinates into HyperChem, using the script commands. At
least, as long as the coordinates are cartesian… Is this the kind of thing
you had in mind?
Tom
yes, that's exactly what I had in mind, and I hope this kind of thing can be
included in a future release…(or even better, written by an interested party
and uploaded to the Hyperchem library forum) I don't know how to write those
macros……I do think that the utility of hyperchem is greatly increased by
having this type of feature avaliable (just like the dihedral macro did)….it
is a formula to convert from crystallographic to cartesian coordinates….this
type of calculation could be included with the macro? ie "will you enter
crystallographic or cartesian coordinates? a: crystallographic, Q: please enter
the angular components of the unit cell: a____,b_____,c_____ etc…)…..
Yes!
To load in a structure from crystallographic data, you need to get it into a
format that HyperChem can read. I would recomend a HIN file format. ALthough
the HIN file can get pretty complicated, it ca also be pretty simple . Here is
an example.
mol 1 atom 1 – C ** – 0.0 -0.67 0.0 0.0 0 atom 2 – C ** – 0.0 0.67 0.0 0.0 0
endmol
This gives you two carbon atoms. You need the -'s and **'s, but can ignore
column numbers: it is just white-space separation that matters. The first 0.0
in each line is the charge. The next three numbers are coordinates, and the
final 0 is the number of neighbours.
To add the bonding information to this, there is a trick. Save the file as a
z-matrix and read it in again. The z-matrix reader has a bond-inferring
component: not completely reliable, but it makes a good first guess. Then
choose "Add hydrogens" under Build to add the hydrogens and you have ethylene.
Hope this helps,
TOm