CHEMISTRY 69600 APPLIED CRYSTALLOGRAPHY SPRING 2011

The Chemistry 69600 Special Topics Course in Applied Crystallography is designed to introduce chemists to the technique of x-ray structure analysis. Most topics are covered in only enough depth so that the experiment can be understood. The course is taught in a computer lab so students can have hands on experience using software.

Instructor: Phillip Fanwick 234 WTHR 44572 pfanwick@purdue.edu

Text: NONE

Website: http://xraylab.chem.purdue.edu/chm696.htm

Course Prerequisites: 1. A basic knowledge of point group symmetry. 2. Minimal knowledge in matrix mathematics

Course Requirements: 1. Attend Lectures 2. Complete all homework sets 3. Collect data and solve a crystal structure in the laboratory

Topics to be Covered:

1. A brief overview of crystallography and its relationship to other analytical methods.2. Crystals, lattices; non-orthogonal coordinate systems: 3. From point groups to space groups, Hermann-Mauguin Notation 4. Symmetry, centering; unit cell selection, space group determination, and more Hermann-Mauguin Notation.5. The nature of x-rays; X-ray generation.6. Scattering and diffraction.7. Fourier synthesis and non-linear least squares refinement.8. Data collection and reduction; cameras, diffractometers; growing,selecting and mounting crystals.9. Solving the structure--Patterson and Direct Methods.10. Refinement in practice--SHELX.11. Out of the Norm--absolute configuration and disorder12. Molecular Graphics.13. Finishing the Structure; crystallographic statistics.14. Crystallographic databases.

Some other comments

The basic idea of the course is to provide an introduction to crystallography

Give some insight into what goes on in the crystallography lob

Build physical not mathematical models wherever possible

Do not derive information that can readily be looked up. However, it is important to know where to find it.

I am not training crystallographers but chemists who can use and understand crystallography

Important Analytical Techniques

It can be argued that since 1950 the two principal analytical techniques that have advanced chemistry are:

1. NMR 2. X-ray Crystallography

Yet while NMR has become central to chemical education, crystallography remains almost unknown.

Cambridge Structural Database

This is a database of all crystallographic structures that contain at least one organic carbon atom.

In general there is one entry per compound per publication.

Date Number of Entries1983 52,3631990 104,3802001 251,515Present 591,860 (544,565 compounds)

Why crystallography is not taught.

The theory is too difficult. The instrumentation is too expensive. Lack of instructors. No course to place it in.

Objectives

A major problem in crystallographic education is the failure to decide what we want students to be able to do with crystallography.

There are a whole spectrum of possible objectives but very few are applicable to the typical chemist.

Objectives

A major problem in crystallographic education is the failure to decide what we want students to be able to do with crystallography.

There are a whole spectrum of possible objectives but very few are applicable to the typical chemist.

Objective 1

Know the Input and Output for the Crystallographic Experiment

What are the sample requirements and needed initial information to conduct the experiment?

What information is the product of the experiment?

Objective 2

Analyze and Work with Crystallographic Data.Understand bond distances and angles, their statistics and their

relation to bonding

Work with simple molecular graphics

Read Crystallographic Information Files (CIF)

Critically analyze crystallographic results.

Graphical Output

Derived Output

Bond Distances and their s.u.'s Bond Angles and their s.u.'s Torsional Angles and s.u.'s Least Square Planes, angles between planes,

and their s.u.'s From these can infer bond orders, types of

bonding etc.

Input A crystal—good faces, transparent The crystal should be single—only one crystal. Size—appropriate to x-ray beam size. Typically

0.3mm on an edge. Since the x-ray beam has a definite size using crystals larger than the beam does not produce more intensity

Shape is important as very thin plates or long needles do not put much crystal in the beam.

Need to have an idea of what elements are present.

Some Comments on Crystals

It would appear easy to get crystals for crystallography but it can be quite difficult.

Some crystals do not grow to give suitable shape or produce layered or multiple crystals.

Some compounds will never give crystals. Remember--

The quality of a structure can never be better than the quality of the crystals!!

Good Crystals

Workable Crystals

Good Crystal

Marginal Crystal

Unusable Crystals

The “spots” are actually the Fourier transformof the electron density!

Working with Crystallographic Data

Like any other data, crystallographic results must be analyzed critically.

Most chemists have no idea how to do this. This has lead to the idea that crystallographic

results are always correct. It is also important that chemists determine

what in the result is significant or interesting.

A Comment

Any crystallographic result must agree with known chemistry.

Generally when a structure produces an unbelievable result it is the structure that is incorrect

“Extraordinary claims require extraordinary evidence”--Carl Sagan

There are levels of quality in structures and marginal structures produce the most extraordinary claims

Crystallographic Information File

All information from a structure is contained in the crystallographic information file (cif)

The cif is formatted such that each datum has a definition (header) and then the entry.

The headers are defined by the International Union of Crystallography (IUCr) committee called COMCIFS.

Each definition is spelled out in a cif dictionary. This can be found at

http://www.iucr.org/resources/cif/dictionaries/cif_core

Part of a CIF

_refine_ls_structure_factor_coef Fsqd _refine_ls_matrix_type full _refine_ls_R_factor_all 0.053 _refine_ls_R_factor_gt 0.044 _refine_ls_wR_factor_ref 0.128 _refine_ls_wR_factor_gt 0.122 _refine_ls_hydrogen_treatment constr _refine_ls_number_reflns 2565 _refine_ls_number_parameters 193 _refine_ls_number_restraints 0 _refine_ls_goodness_of_fit_ref 1.177 _refine_ls_weighting_scheme 'calc ' _refine_ls_weighting_details '1/[\s^2^(Fo^2^)+(0.0639P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3 '

_refine_ls_shift/su_max 0.000 _refine_diff_density_max 0.49 _refine_diff_density_min -0.33 _refine_ls_extinction_method none

CIF Dictionary

S.U.'s and comparisons

Since there is an error in the measured data there are errors in the derived parameters

These errors are expressed as standard uncertainties (s.u.'s)

Two parameters are the same if they differ by less than 3 s.u.'s

Two parameters are different if they differ by more than 3 s.u.'s

Other Cif Ideasloop__geom_bond_atom_site_label_1_geom_bond_atom_site_label_2_geom_bond_distance_geom_bond_site_symmetry_1_geom_bond_site_symmetry_2_geom_bond_publ_flagCl3 C3 1.739(3) . . ?Cl1 C1 1.739(2) . . ?O23 C24 1.364(3) . . ?O23 N22 1.407(3) . . ?N22 C21 1.309(3) . . ?F1 C7 1.321(3) . . ?C1 C6 1.373(3) . . ?C1 C2 1.398(3) . . ?F3 C7 1.313(3) . . ?F2 C7 1.317(3) . . ?C6 C5 1.398(3) . . ?C6 H6 0.9500 . . ?C4 C5 1.376(4) . . ?C4 C3 1.382(3) . . ?C4 H4 0.9500 . . ?C2 C3 1.399(3) . . ?

ORTEP Drawings

ORTEP stands for Oak Ridge Thermal Ellipse Plotting program

The original was written in 1956 by Carol Johnson at Oak Ridge

Thermal Ellipse is an old term for atomic displacement parameter (adp)

The adp's are very important in analyzing a structure.

ADP's and Motion

ADP's and Temperature

ADP's and Element Assignment The crystal structure is refined by calculating

the data from a structural model and adjusting it to the observed data.

The data intensity is related to the electron density.

An assumption is that the atoms are located where the density is.

The element type is assigned. If the number of electrons is mis-assigned then

the atomic volume will be adjusted to get a better fit to the density

Agnew. Chem. Intl. Ed. Engl., 27, 436 (1998)Note heavier atoms should vibrate less thanlight atoms!

Chem. Commun., 1733 (1990)

Disorder

Not all crystals are perfectly ordered Crystal structure sees the average occupancy

Recent Result

(H30)AlF

4 reported

Nothing obviously wrong Crystals grown from solution with pH 8.5 Actually (NH

4)AlF

4

Homework

Read JACS December 1920 2419-2434—The Chemistry and Crystallography...

• Pay attention to what measurements were made.

• What instruments were used?

• How could this information be used?

Make notes but nothing to hand in!!

December 1920 Volume 42, Issue