Applications of scattering techniques to chemical structure

1
Applications of scattering techniques to chemical
structure
John F. C. Turner
2
Acknowledgements
Collaborators Chris J. Benmore (IPNS) Joan E.
Siewenie (IPNS) Chick C. Wilson (ISIS) Jennifer
C. Green (University of Oxford) Funding Neu
trons CAREER award, NSF IPNS, Argonne
National Lab ACS-PRF ISIS, Rutherford Appleton
Lab University of Tennessee Neutron Sciences
Consortium
3
Group Members
Structure Synthesis Cara Nygren Andrew
Colvin Megan Bragg Michael
Blanchard Jamie Molaison Brian
Harrison Michelle Dolgos (IPNS Laboratory
Graduate) Dr. Sylvia McLain Ryan Quarberg (M.Sc
2003) (NSF post-doctoral fellow, ISIS)
4
Research Themes
Structural chemistry of the proton or hydrogen
atom Superacids Hydrogen bonded
systems Superacid solutions Pure
fluids Fluorine-fluoride chemistry Fluoride-oxide
analogy 214 high Tc analogs Fluoride glasses,
micropores and mesopores Reactive matrix
chemistry Inorganic-neutronic chemistry Solute
structures in solution Inorganic structural
problems Biomimetic catalysis Fundamental
structure and bonding Neutron scattering and
charge density studies
Structural chemistry of the proton or hydrogen
atom Superacids Hydrogen bonded
systems Superacid solutions Pure
fluids Fluorine-fluoride chemistry Fluoride-oxide
analogy 214 high Tc analogs Fluoride glasses,
micropores and mesopores Reactive matrix
chemistry Inorganic-neutronic chemistry Solute
structures in solution Inorganic structural
problems Biomimetic catalysis Fundamental
structure and bonding Neutron scattering and
charge density studies
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Talk structure

• Definition and outline of the structural
  question
• Examples
• Aluminium Trimethyl
• Urotropine-N-oxide formic acid
• 1,2,3,4,5,6,7,8 Octahydro-2a,4a,6a,8a-tetraazacyc
  lopentaf,gacenaphthylene
• Summary

6
The Chemical Structural Question I
The atom is formally and empirically bipartile,
containing Electron density Nuclear
density Simplest description of a molecule
invokes the presence of atoms another
hierarchical level beyond the structure of the
atom Empirical evidence, based on reactivity
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The Chemical Structural Question II
Structure definition requires only a knowledge of
connectivity and identity in general However, the
level of description of the problem is important
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The Chemical Structural Question III
Although structure definition requires only a
knowledge of connectivity and identity the
method by which we investigate the structure is
important, due to the dual nature of the
atom. The standard method is through diffraction
of some description, which gives information
about the distribution of scattering density in
the sample
Length scale Scattering density Distribution
Short Electrons Periodic
Long Nuclear Aperiodic Very long
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Radiation Sources
X-rays vs Neutrons Electron
distribution Nuclear distribution Strong
angular dependence No angular dependence of the
form factor to scattering intensity Scattering
intensity scatters No 'chemical size' with Z2
- the chemical size dependency of the atom
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Neutrons and chemistry
Neutrons and X-rays Scattering power is
decoupled from the chemical nature of the
atom Neutron scattering cross-sections X-ray
intensity scale with Z2 are independent of Z
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Inorganic structures
The majority of structure determinations are
undertaken in the solid state X-ray structures
predominate Inorganic Structures have their own
peculiarities Light vs. heavy atoms
Dissociation Stereochemical lability or
fluxionality
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Inorganic structures
Cp2Zr(Me)MeB(C6F5)3 crucial intermediate in
single site homogenous Ziegler- Natta
catalysis Close ion pair in the solid state
including a CN 5 C atom
Guzei, I. A. Stockland, Jr., R. A. Jordan, R.
F. Acta Cryst. 2000 C56, 635-636
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Inorganic structures
X-ray ZZr 40 ZC 6 ZB 5 ZZr2
1600 ZC2 36 ZB2 25 ZF 9 ZH 1 ZF2
81 ZD2 1
Neutron bCoh, Zr 7.16 fm sCoh, Zr 6.44
barns bCoh,C 6.646 fm sCoh,C 5.551
barns bCoh,B 6.65 fm sCoh,B 5.56
barns bCoh,F 5.654 fm sCoh,F 4.017
barns bCoh,H -3.739 fm sCoh,H 1.76 barns
The radiation source used in a diffraction
experiment alters the distribution of
information in the data
Guzei, I. A. Stockland, Jr., R. A. Jordan, R.
F. Acta Cryst. 2000 C56, 635-636
14
Light atom sensitivity
Consider a material composed of Fe, C, O and H
X-ray scattering Dominated by Fe (Z2262)
Neutron scattering Dominated by H
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The solid state aluminum trimethyl

• Industrially very important
• Co-catalyst for Ziegler-Natta olefin
  polymerization
• Dimer in condensed phases
• Fluxional by NMR in solution
• Dimer-monomer in gas phase

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Intrinsic scattering power in AlMe3
X-ray ZAl 13 ZC 6 ZAl2 169
ZC2 36 ZD 1 ZD2 1
Neutron bCoh,Al 3.449 fm bCoh,C 6.646
fm bCoh,D 6.671 fm
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Synthesis of d9- AlMe3
Neutronically friendly synthesis

• d9-AlMe3 very air sensitive
• Volatile liquid

18
Diffraction data for d9- AlMe3

• Powder formed in situ by condensation
• Preferred orientation on freezing the liquid
• Data from HRPD (ISIS) at 4.5 K (?d/d 5 x 10-4
  back scattering)
• Refined using Rietveld method

a / Å 12.0243(10) b / Å 6.9631(1) c / Å
14.0180(1)
r(Al-Cb) 2.145(7)/2.146(8) Å, r(Al-Ct)
1.945(6)/1.926(5) Å, r(Al...Al) 2.700(10) Å,
r(C-D) 1.061(4)-1.118(5) Å ?Cb-Al-Cb
102.0(3) ?Ct-Al-Ct 125.8(3), ?Cb-Al-Ct
108.8(4), ?D-C-D 99.0(4)-111.6(5)
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Dimer structure of d9- AlMe3
Staggered conformation in the solid state Only
one conformer present in the structure at any
temperature of measurement (4.5 K 180 K)
McGrady, G. S. Turner, J. F. C. Ibberson, R.
M. Prager, M. Organometallics 2000, 19,
4398-4401.
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Urotropine-N-oxide formic acid
Urotropine-N-oxide
Urotropine-N-oxide . formic acid
Proton transfer across the OO bond should allow
two structural extrema in prinicple
Trialkyhydroxyammonium cation
Trialkyl-N-oxide adduct
Lam, Y.-S. Mak, T. C. W. Acta Cryst. B, 1978
B34, 1915-1918
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Urotropine-N-oxide formic acid

• To investigate the structural problem
• Use X-ray and neutron diffraction to determine
• The distribution of electron density
• The distribution of nuclear density
• not only in order to determine the structure but
  also to investigate the correlation between the
  nuclear and electron density distributions

In the urotropine frame work, the nuclear and
electron densities are expected to coincide well
the electron density should be well defined In
the hydrogen bond, this is less certain
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Urotropine-N-oxide formic acid
The electron density Variable temperature X-ray
diffraction at 123, 148, 173, 198, 223, 248 and
298 K Collection strategy -9 h, k 9, -25
l 25 8,500 9,500 independent
reflections Refinement strategy Spherical atom
for all atoms except the H atom involved in
the hydrogen bond Examine and integrate the
Fourier map in order to image the electron
density associated with the hydrogen atom
position Data collected on the departmental
Bruker AXS instrument
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Urotropine-N-oxide formic acid
The experimental electron density
P21/n a 6.774(2) Å ß 95.159(6) º b
6.790(2) Å c 19.472(7) Å at 123 K
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Urotropine-N-oxide formic acid
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Urotropine-N-oxide formic acid
The electron density associated with the hydrogen
atom Isotropic vs. anisotropic refinements
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Urotropine-N-oxide formic acid
Experimental densities from F0bs-FCalc
123 K
223 K
173 K
248 K
148 K
198 K
298 K
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Urotropine-N-oxide formic acid
The nuclear density associated with the hydrogen
atom
Data collected at IPNS using SCD from a 2 mm3
single crystal
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Urotropine-N-oxide formic acid
We have three descriptions of the hydrogen bond
in this system
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Urotropine-N-oxide formic acid
The nuclear density gives the effective nuclear
potential in the Bragg average in which the
electrons move The unrefined electron density
from the Fourier map gives the experimental
electron density, again in the Bragg average The
refinement of the electron density, in this case,
is probably a poor measure of the actual
distribution of electron density associated with
the hydrogen bond
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Urotropine-N-oxide formic acid
The variation of the bond lengths in the formate
residue do not correlate with the position of the
maximum of the electron density associated with
the hydrogen bond Neither of the initial
postulated extrema are applicable Bond
length trends, in general, are not automatically
useful, especially when the assumed correlation
between electron density and atomic position
breaks down.
Trialkyhydroxyammonium cation
Trialkyl-N-oxide adduct
Nygren, C. L. Wilson, C. C. Turner, J. F. C.
J. Phys. Chem. A submitted 2004
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1,2,3,4,5,6,7,8 Octahydro-2a,4a,6a,8a-tetraazacyc
lopentaf,gacenaphthylene
The Alkene
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1,2,3,4,5,6,7,8 Octahydro-2a,4a,6a,8a-tetraazacyc
lopentaf,gacenaphthylene

• Chemical rationale for
• Chelating diamide
• Potential range of ligand behaviors
• L2X2, L3X2 or L4X2
• Potentially interesting small molecule
  activation
• Gibson-Brookhart catalysis
• Biomimetic catalysis

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1,2,3,4,5,6,7,8 Octahydro-2a,4a,6a,8a-tetraazacyc
lopentaf,gacenaphthylene
NMR spectra of many of the intermediates in this
scheme are obscure in the literature. With care
and under strictly anhydrous conditions, the
spectra are tractable, rich and beautiful
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1,2,3,4,5,6,7,8 Octahydro-2a,4a,6a,8a-tetraazacyc
lopentaf,gacenaphthylene

• The side bar formation of the Alkene
• Highly electron rich
• Interesting electronic structure
• Analog of tetrakis(dimethylamino)ethene (TDAE)
• TDAE forms a reductive intercalate with C60
  that proves to be a weak ferromagnet at 16 K

Allemand, P. M. et al. Science 1991 Stephens, P.
W. et al. Nature 1992
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1,2,3,4,5,6,7,8 Octahydro-2a,4a,6a,8a-tetraazacyc
lopentaf,gacenaphthylene
Tetrakis(dimethylamino)ethene (TDAE) has been
termed organic zinc due to the reductive power
and the Alkene is indeed very air sensitive and
highly reducing.
Burkholder, C. et al. Tet. Letts. 1997 38,
821-824
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1,2,3,4,5,6,7,8 Octahydro-2a,4a,6a,8a-tetraazacyc
lopentaf,gacenaphthylene
anti-diurea is known, but not the syn
Surprisingly resistant to reduction Very slow
reaction with liquid Na in toluene
Colvin, A. J. Nygren, C. L. Harrison, B. C.
Schell, F. M. Turner, J. F. C. In preparation
37
1,2,3,4,5,6,7,8 Octahydro-2a,4a,6a,8a-tetraazacyc
lopentaf,gacenaphthylene
The reactivity of the Alkene is peculiar and the
electronic structure is interesting. From X-ray
diffraction, we can extract the spherical atom
structure of the material
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1,2,3,4,5,6,7,8 Octahydro-2a,4a,6a,8a-tetraazacyc
lopentaf,gacenaphthylene
By performing high quality X-ray diffraction
experiments, we can visualize the scattering
density present in the molecule, in the Bragg
average.
Calculated
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1,2,3,4,5,6,7,8 Octahydro-2a,4a,6a,8a-tetraazacyc
lopentaf,gacenaphthylene

• We know that atoms in molecules cannot be
  spherical
• Covalent bonding implies delocalization of
  electron density over several nuclear cores,
  taking the nuclear positions as defining the
  center of the atom.
• This sharing must extend beyond the measure of
  the atomic radius
• In a molecular system, bonding is in general
  directional

These plots are already familiar as the Q
peaks in a standard SHELX i.e. spherical atom,
refinement.
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1,2,3,4,5,6,7,8 Octahydro-2a,4a,6a,8a-tetraazacyc
lopentaf,gacenaphthylene
We can account for the aspherical nature of atoms
revealed in X-ray diffraction experiments by
using the method of Coppens by modeling the
data using a combination of spherical harmonic
functions and radial functions which are then
fitted to the data.
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1,2,3,4,5,6,7,8 Octahydro-2a,4a,6a,8a-tetraazacyc
lopentaf,gacenaphthylene
Analysis of the refined model allows the
extraction of bond properties The central CC
linkage is a double bond There is significant
double bond character in the C-N bonds
Preliminary DFT calculations also reproduce the
structure well
X-ray
Highest Occupied Molecular Orbital
DFT (ADF)
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1,2,3,4,5,6,7,8 Octahydro-2a,4a,6a,8a-tetraazacyc
lopentaf,gacenaphthylene

• Future Alkene and tetramine studies
• Photoelectron spectrum to define the energies
  of the system (in association with Prof. J. C.
  Green (University of Oxford)
• Protonation dynamics of concave tetramines,
  including superacidic solutions
• Electron and hydrogen atom transfer to define
  fundamental redox properties
• Redox chemistry with C60

Nygren, C. L. Colvin, A. J. Green, J. C.,
Schell, F. M. Turner, J. F. C. In preparation
43
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