Subject: experimental geometry

From: [email-masked] (Brad Thompson)
Date: Tue, 23 Aug 94 09:54:37 CDT

Adel El-Azhary  writes:

> Can someone elaborate on the difference of the geometry by microwave,
> electron diffraction and X-Ray. Can you give references. My ynderstanding 
> is that the microwave geometry is better than the others but I do not know
> exactly why. 

What's "better" depends on the molecule and what information you want.
First off, ED and XRay give you gas-phase, i.e. isolated molecule, info,
which may or may not be what you want.  Also, neither can handle large
species.

When both ED and MW can give you a structure, bond distance differences
are likely to be at the .00x Angstrom level.  It's important to remember
vibrational amplitudes are .0x Angstroms!  Both ED and MW measure some
sort of average distance, and just what average that is depends both on
the experimental method and on the way the distances were deduced from the
data.  And common methods of data treatment, for both ED and MW, can go
pathological in the hands of the naive or careless user.  [But of course,
that sort of thing never happens to theorists. :) ]

So in terms of the real world and the measurements we can make on it,
all those digits (past, say, .01 Angstrom and 1 degree) in geometries
we get from Gaussian 92 don't have a lot of significance.

There's an extensive literature on just what ED and MW distances "mean."
I really don't recommend it to those outside the fields unless you badly
need to know!

                    | H. Bradford Thompson   [Brad]
[email-masked]       | Scholar in Residence, Chemistry & Physics
                    | Gustavus Adolphus College, St. Peter MN 56082-1498

---

From: "William T. Winter" <[email-masked]>
Date: Tue, 23 Aug 1994 22:57:01 -0400 (EDT)

On Tue, 23 Aug 1994, Brad Thompson wrote:

,> What's "better" depends on the molecule and what information you want.
> which may or may not be what you want.  Also, neither can handle large
Not so! electron diffraction, historically, was a gas phase technique but 
there is an expanding literature of crystal structures determined by 
electron diffraction.  X-ray diffraction is the classical approach for 
studying molecular structure in a macroscopic crystal and has been widely 
applied to proteins, nucleic acids, other natural and synthetic polymers  
and a huge range of other crystalline materials.
> data.  

Don't all experimental methods average over the sample in some manner?

A more important point is that the time and sample averaged structure 
in a crystal lattice (XRD and ED) need not be identical to the time and 
space averaged structure in any other phase or even in a different 
crystalline polymorph.

One further key difference is that the atomic form factors used to 
describe scattering of x-rays by atoms increase with increasing atomic 
number.  Thus positions of hydrogen atoms in hydroxyl groups are often 
impossible to define due to a combination of weak scattering power and 
mobility of the atom within the structure.
As in any experimental method the uncertainties in derived results depend 
upon the number and quality of the data.  In well-determined crystal 
structures the esd s in bond lengths is often less than 0.001 Angstrom 
while that in bond angles is in the 0.x degree region.  If one attempts 
to average geometries over a family of related compounds the esds 
increase to 0.001-3 angstrom and the esd in bond angles is 0.5 - 1.5 degrees.

A number of such studies on various structure families were done in the 
1970's and 80's.

For better crystal data on distances involving hydrogen atoms one should 
look at the neutron diffraction literature, since neutron diffraction 
intensities are quite sensitive to hydrogen atom coordinates. 
...
> I really don't recommend it to those outside the fields unless you badly

I do not want to get into a flame war here and will not participate in 
one, but the preceding comment is indicative of the reasons whey 
experimental structural chemists are often less than enthusiastic about 
the proliferation of modeling packages and the embarrassing ease with 
which they can be employed.

It is fortunate that the late Linus Pauling didn't have such tools  or he 
might have tried to invoke cis peptide linkages instead of trans and 
hence would have not found his alpha helix and beta sheet structures. 
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Dr. William T. Winter                  Phone: (315)470-6876
315 Baker Lab                          FAX:   (315)470-6856
SUNY-ESF                               Internet: [email-masked]
Syracuse, NY 13210-2786