[BlueObelisk-discuss] OK, I'm catching on, but...

[Robert Hanson]

Can someone shed some light on how this brilliant statement:

Rule 3. When two ligands differ


*only in that one has an atomor atom-group of higher rank in a cis-position
and theother in a trans-position to the core of the stereogenicunit, *then
preference is given to the former.

[Mata, Lobo, et al., J. Chem. Inf. Comput. Sci. 1994, 34, 491-504]

Got turned into this monster?

Rule 3: ... seqcis = 'Z' precedes seqtrans = 'E'.

In other words, rather than being able to assign priority by the very
clever method of just following the path, one has to actually assign all
the priorities of the double bonds first (from scratch, presumably, not the
currently working process) *then *continue.

Or, maybe what I am saying is, they were so close and yet didn't see that
it could have been so so simple. But no....

[I suppose the writer of this rule is on this list, right?....]


Bob
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

[Wolf Ihlenfeldt]

Rule 3. When two ligands differ only in that one has an atom
or atom-group of higher rank in a cis-position and the
other in a trans-position to the core of the stereogenic
unit, then preference is given to the former.
[Mata, Lobo, et al., J. Chem. Inf. Comput. Sci. 1994, 34, 491-504]
Got turned into this monster?
Rule 3: ... seqcis = 'Z' precedes seqtrans = 'E'.
In other words, rather than being able to assign priority by the very clever
method of just following the path, one has to actually assign all the
priorities of the double bonds first (from scratch, presumably, not the
currently working process) then continue.

No, not even that is sufficient. You can have of course stereo double
bonds determining the fate of an atom stereo center which are
themselves E/Z only by virtue of having substituents which differ only
in R and S - which then need to be determined first to get the double
bond descriptor. You cannot determine atom and bond stereochemistry
independently in the CIP system. This must be a single, repetitive,
interwoven process.

Please keep us posted on your implementation line count ;-)

Or, maybe what I am saying is, they were so close and yet didn't see that it
could have been so so simple. But no....
[I suppose the writer of this rule is on this list, right?....]
Bob
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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[Robert Hanson]

Post by Wolf Ihlenfeldt

Rule 3. When two ligands differ only in that one has an atom
or atom-group of higher rank in a cis-position and the
other in a trans-position to the core of the stereogenic
unit, then preference is given to the former.

OK -- I see that the 2013 final version is much simpler than I thought, in
that one can simply take care of most of the E/Z business by itself in Rule
3. (I hear you, Wolf. Not pretending I have this totally worked out for
more complex cases. I consider that the realm of Rule 4.)

Q: Aren't there cases where you have to know the R/S to get E/Z, but you
also have to know E/Z to get the R/S? How is that trap evaded?

No, not even that is sufficient. You can have of course stereo double

Post by Wolf Ihlenfeldt
bonds determining the fate of an atom stereo center which are
themselves E/Z only by virtue of having substituents which differ only
in R and S - which then need to be determined first to get the double
bond descriptor. You cannot determine atom and bond stereochemistry
independently in the CIP system. This must be a single, repetitive,
interwoven process.
Please keep us posted on your implementation line count ;-)

Rules 1-3 implemented. Tracking multiple stereocenters, but not carrying
out much in the way of Rule 4. All cases that I have that do not involve
auxiliary R/S determination (such as inositol) appear to be working ---
basically anything but Rule 4. No pseudochirality; no axial or other more
sophisticated forms of stereochemistry. At this point I can say, though,
that the algorithm is certainly suitable for most typical cases and holds
up pretty well with the sorts of cases illustrated in Chapter 9. All
methods are relatively simple, with efficient recursion and structural
analysis only on a "need-to-know" basis.

412 lines

Bob