CHEMISTRY 69600 APPLIED CRYSTALLOGRAPHY

SPRING 2015

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: Dr. Phillip Fanwick 101b 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 of matrix mathematics

Course Requirements: 1. Attend and Participate at Lectures 2. Complete all homework sets 3. Collect data and solve a crystal structure in the laboratory 4. Write up a manuscript for Acta Cryst. E on the structure collected

Topics to be Covered:

1. A brief overview of crystallography and its relationship to other analytical methods 2. An overview of the crystallographic method 3. Unit Cells 4. Crystallographic databases--CSD and Inorganic 5. Linux, X-windows, Connecting to the X-ray Lab Computer 6. The nature of x-rays; X-ray generation, safety. 7. Data collection and reduction; cameras, diffractometers; growing,selecting and mounting crystals. 8. Solving and refining a basic structure 9. Molecular Graphics.10. Finishing the Structure; crystallographic statistics.11. Working with cif and publcif.12. Crystals, lattices; non-orthogonal coordinate systems: 13. From point groups to space groups, Hermann-Mauguin Notation 14. Symmetry, centering; unit cell selection, space group determination, and more Hermann-Mauguin Notation.15. Scattering and diffraction.16. Fourier synthesis and non-linear least squares refinement.17. Solving the structure--Patterson and Direct Methods.18. Refinement in practice--SHELX.19. Out of the Norm--absolute configuration and disorder

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 lab

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

A minimal of theory will be taught and then each member of the class will work on the same basic structure

After this we will return to a more in depth look at what and why procedures were carried out. This means that some topics will be covered twice.

The course will be taught using the Purdue program package which includes many locally written programs

Instruction on operation of diffractometers will be minimized

Now on to the course!

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 frequently untaught and misunderstood .

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 except when the structure is redetermined.

Date Number of Entries1983 52,3631990 104,3802001 251,515Present 744,127

Why crystallography is not taught.

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

Teaching Objectives

A major problem in crystallographic education is the failure to decide what students need 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 obtained from 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

Understand Crystallographic Information Files (CIF)

Critically analyze crystallographic results.

Crystallographic Output The dimensions of the unit cell and its orientation to

the crystal.● The coordinates of all the atoms in the unit cell and

their standard uncertainties (s.u.'s). The motion of the atoms in the crystal—atomic

displacement parameters (adp's) For optically active crystals the absolute configuration

—if the experiment was done correctly.

Graphical Output

Derived Output

Bond Distances and their s.u.'s (standard uncertainty)

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 data bond orders, types of bonding

etc. can be inferred.

Input A crystal—good faces, transparent if not dark The crystal must 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 and may cause problems

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 a 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

Crystallographic Data

The crystallographic data consists of three components for a diffraction spot.

1. The h,k,l values which are the coordinates in reciprocal space which is related to the unit cell space.

2. The intensity of the reflection found by summing over all the pixels (called integration)

3. The standard uncertainty in the intensity.

Since data is collect graphically the data must be integrated to obtain numerical data.

Workable Crystals

Good Crystal

Marginal Crystal

Unusable Crystals

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

Working with Crystallographic Results

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

Most chemists and journal editors have no idea how to do this.

This has lead to the idea that crystallographic results are always correct or unquestionable.

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 frequently 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 data name and then the data entry.

The names have a definition created by an International Union of Crystallography (IUCr) committee called COMCIFS.

Each definition is spelled out in a cif dictionary. The dictionaries 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 '

CIF Dictionary

S.U.'s and comparisons

Since there is an uncertainty in the measured data there are uncertainties in the derived parameters

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

Two parameters are considered to be 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 National Laboratory

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

The adp's are very important in analyzing the quality of 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 the model to obtain agreement with 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 not directly observed and is assigned by the crystallographer.

If the number of electrons add is incorrect then the atomic volume will be adjusted to get a better fit to the density

Incorrect Structures

If the crystallographer mis-assigns the atom type then new and novel compounds can be created

Also certain problems can produce novel but incorrect structues.

Chemists doing their own structures frequently will bias the experiment to obtain a result more in keeping with their conceptions.

Chem. Commun., 1733 (1990)

Disorder

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

The Mysterious Rhodium Compound

The elongated Cl atoms are actually a disorder of a Cl atom and a CO ligand.

The molecule has a crystallographically imposed inversion center requiring the trans ligands to be the same.

Cl and CO are about the same size.The actual compound is RhCl(CO)(PPh

3)

2

This is a Rh(I) compound and should be square planar.

A Sumbitted Result

(H30)AlF

4 reported

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

4)AlF

4 a well known compound

Since H atoms only contain 1 electron they can be difficult to locate using crystallography

Homework 1

Watch the videos http://richannel.org/collections/2013/crystallography#/understanding-crystallography-part-one

http://richannel.org/collections/2013/crystallography#/understanding-crystallography-part-two