Crystallography

SELF PACED COMPUTER EXERCISE

WINGX software version

Introduction
Single Crystal X-ray diffraction is the ultimate tool for the determination of molecular structure. Our goal here
is to introduce you to the basics of structural determination and modern computer software. All chemists make
use of structural data from X-ray crystallography. You will make use of the widely used SHELX software4.
This will give you some insight into the nature of the problem of structural determination and a better
understanding of molecular structure in the solid state. A 4000-level half course is offered for those seeking a
more extensive treatment of X-ray crystallography.
WINGX is a licensed package from Glasgow free to academics which incorporates the SHELX programs for
solving X-ray crystal structures into a user-friendly windows environment The wingx software will guide you
through the steps required to solve the structure starting only from what appears to be a meaningless set of
reflection intensities. YLID will be demonstrated in lecture and the hkl file is available on the website. You
will solve the structure of an iron dimethylglyoxime carbonyl complex which serves as a simple model for the
heme group.
The following steps are part of typical structure determination. They have already been completed for you.
PRELIMINARIES
1. A high quality single crystal is required. Powders, snowflakes, or multiple crystallites stuck together are
unsuitable. Diffraction quality single crystals do not normally just fall out during the standard recrystallization,
they must be grown very slowly. A suitable crystal will have well defined faces 0.1 to 0.5 mm on a side.
Larger crystals are not suitable but sometimes a smaller specimen can be cut from them.
2. The crystal is glued to the end of a glass fibre which is attached to the goniometer head.
3. The head attaches to the goniometer which allows it to be precisely positioned in the X-ray beam. A four
circle diffractometer such as the one in 015 Petrie allows the crystal to be rotated in all directions in order to
bring all lattice planes in position to diffract according to Braggs law.
GEOMETRIC DATA COLLECTION
X-rays are diffracted only at selected angles as given by Braggs law and each reflection is defined in terms of
three integers (h,k,l) called indices. The number of allowed reflections depends on the size of the unit cell (not
the size of the crystal and not on whats in the unit cell) and wavelength of the X-rays. Some 25 to 50 intense
reflections are found and automatically indexed on modern equipment giving the unit cell dimensions. The unit
cell may be cubic, orthorhombic, monoclinic, triclinic, etc. and it may be primitive, face or body centered.
There are 14 Bravais lattices on the basis of these considerations. The geometric data collection establishes the
unit cell dimensions. The centering is established on the basis of systematically absent reflections.
INTENSITY DATA COLLECTION
Once the unit cell is known, the computer calculates the location of all reflections and the automatic
diffractometer rotates the crystal and detector in order to measure the relative intensity of each reflection. In
olden days photographs were taken and eyeball estimates of the intensity of each spot were made. The result of
a several day automatic operation, after a bit of computer massaging, is a set of several thousand indexed
reflections (h,k,l) with their intensity and standard deviation. Area detectors on the latest equipment (CCD) can
collect 40,000 intensities in 6 hours, something that would take a month on our equipment. The YLID data you
will use was collected overnight using Molybdenum radiation on the Siemens diffractometer formerly in 015
Petrie.
The intensities of the reflections are only half of the information needed to deduce the arrangement of the atoms
in the cell. The phases, which are not experimentally measurable, are the other half. Every atom contributes to
every reflection producing a net scattered wave at each Bragg angle. Thus several thousand data points

(intensities) are related to hundreds of atom locations (depending on the size of the molecule) in a complex way.
The strategy used to solve this problem is unlike any you have likely encountered. Do not let the computer
spoil your appreciation of the creativity and intelligence which underlies the software. All of this can be done
by hand - it just takes a lot longer.
STRUCTURE SOLUTION.
To solve the structure you must first determine which one of the 230 space groups correctly describes the
symmetry in the crystal, then crack the phase problem, and finally perform a nonlinear least squares refinement
to minimize the differences, Fobs-Fcalc. The variables in this refinement are the atom locations, expressed as
coordinates, which are fractions of the unit cell dimensions. You will use the wingx program to assist you. This
software is used by practicing crystallographers all over the world.
SPACE GROUP DETERMINATION
There are exactly 230 ways of packing molecules in 3 dimensions. These are called space groups and the
symmetry characteristics of each are tabulated in the International Tables of Crystallography6. Examples are
attached.
Symmetry is of paramount importance in crystallography and space group information provides exactly what
we need. The space group is determined experimentally on the basis of systematic absences - certain reflections
which must have zero intensity because of the presence of glide planes or screw axes in the cell. These arise
because of symmetry elements (screw axes and glide planes) or centering. In special cases, for every atom in
the cell there is another of the same type exactly out of phase with it. These systematic absences are given in
the Int Tables for each space group.
PATTERSON AND DIRECT METHODS
Structure factors have both magnitude and phase, and the X-ray experiment only gives us the magnitude. To
appreciate the dilemma, consider a centrosymmetric space group where Fhkl is real and the phase is simply plus
or minus. (For noncentrosymmetric cases Fhkl is a complex number of the form A + iB but we wont get into
that here). Now imagine a 2000 term series where you know all 2000 coefficients but you dont know which
are + and which are -. Clearly without the signs, it is impossible to know what the function looks like. Thats
the phase problem. A full explanation of the phase problem is presented in an advanced course. Simply stated,
it can be shown that the intensities, Ihkl are proportional to the square of the structure factors Fhkl. The
structure factors Fhkl are in fact coefficients in a Fourier series which defines the electron density in the unit
cell. Further, if the atom locations are known, the structure factors (including their phases) can be calculated
from them. X-ray diffraction doesnt actually find atoms, it finds regions of electron density. It is the electrons,
not the nuclei, which diffract X-rays. No bonds are observed. The graphic software will draw lines between
atoms within bonding distances. The SXGRAPH software translates the electron density map into something
resembling chemical structure to make your task easier. .
Cracking the phase problem SHELXS-97
If one atom is very heavy (a metal) something called a Patterson approach can be used to obtain the phases
based on the tendency for the heavy atom to dominate the X-ray scattering. The Patterson method is used to
locate the heavy atom positions and then phases are calculated using those positions. Hauptmann and Karle
received the Nobel Prize for developing direct methods. This is really complicated and only 0.1% of chemists
using direct methods actually understand it - this doesnt inhibit them from using it. It turns out that once you
assign or guess phases for a few reflections, there is a high probability that selected other reflections have
phases related to these. Nothing is for sure! This form of educated guessing often leads to a solution of the
phase problem. You provide the reflection intensities and the software gives you some good guesses for phases,
then computes the electron density map and tells you where it seems atoms are located. You look at it and
provide chemical intuition/sense. For example, there ought to be 6 carbons in benzene not 5 and there certainly
isnt an atom in the middle of the ring. Trial structures derived from partially correct phasing may often include

artifacts. The key to structure solution is determining what is real and what is an artifact. You will use
SXGRAPH to revise the atom location list and then run the SHELXL-97. The more atom locations you
establish, the more correct phases are obtained and the better the electron density map will look. One basically
works the problem from both ends. The problem cannot be solved otherwise.
LEAST SQUARES REFINEMENT
Once all non-H atoms are located, it remains to find the precise locations of each which minimize the difference
between Fobs (based on the measured intensities) and Fcalc (based on the atom locations). The R factor is a
measure of how good the agreement is. Publishable crystal structures should have R factors below 10%
normally. The accuracy of bond lengths and angles improve as the R factor is lowered.
A full refinement also takes into account the vibration of atoms in the structure (Uiso = thermal parameter).
Highly accurate data includes 6 anisotropic thermal parameters (U11, U12, U13, U13 U23 U33) which define
an ellipsoid. Texts and journal articles routinely display such structural data as ORTEPs. (An acronym for Oak
Ridge Thermal Ellipsoid Program where the program for drawing these was first developed by Johnson.)
References
1. Stout and Jensen, X-ray Structure Determination
2. Drago, Physical Methods in Inorganic Chemistry, Chapter 22.
3. P. W. Atkins, Physical Chemistry. Chapters 16 on symmetry and 21 on diffraction.
4. Louis J. Farrugia , J. Appl. Cryst. (1999). 32, 837 WinGX suite for small molecule single-crystal
crystallography
5. SHELX Sheldrick, G. M. (1997). SHELX97. Programs for Crystal Structure Analysis. Release 97. Institute
fur
Anorganische Chemie der Universitate, Tammanstrasse 4, D-3400 Goettingen, Germany.
6. International Tables for X-ray Crystallography
.
The structure solution boils down to two fundamental equations.
The electron density in the unit cell at a point (x,y,z ) is given by EQ 1 (electrons/cubic Angstrom)
EQ 1
factors.

rho (x,y,z) = 1/V Fhkl {cos (2(hx + ky + lz)} sum over all hkl

Fhkl are the structure

The structure factors are given by EQ 2. For Centrosymmetric structures the sin terms vanish.
EQ 2
atoms, i.

Fhkl = fi (i, hkl ) {cos (2(hxi + kyi + lzi ) + i sin (2 (hxi + kyi + lzi ))} summed over all

SHELX reduces the hundreds of thousands of computations required to a surprisingly small number of
instructions which are contained in the INS (instruction) file. The results are output to the RES file. These and
other files retain the same name (PYCO in this case) with different extensions HKL, INS , RES.LST, etc. You
can examine or edit these files from the pulldown menu under REFINE in wingx and save them to disc for
home use. In addition to the SHELX programs, wingx includes a convenient graphical editor (SXGRAPH) and
the ORTEP program for drawing structures for publication. These and many other options are found in the
toolbar menus.
In the first step under PRELIM you examine the HKL file to obtain the space group, enter the unit cell
dimensions and set up the first instruction file.

SHELXS (S as in solve) reads your first INS file and the HKL file and uses Direct (TREF) or Patterson (PATT)
methods to obtain phases. It then examines the E-map and picks out possible atom locations. It writes these to
the RES file as Qs. You will edit this with SXGRAPH to select only those locations which you believe are real
atoms and you identify which are C O N etc. You then write a new INS file with instructions for SHELXL.
SHELXL (L as in least squares) reads the INS file containing atom locations and computes Fcalc including the
phases from EQ 2. It finally examines the difference e-density map (one using Fobs and the other Fcalc (EQ 1 )
for unaccounted e-density or errors in the atom locations. If all is well the R factor drops below 10% and you
have solved the structure. If not you pick out new atoms or eliminate wrong ones and repeat SHELXL until the
R factor drops to an acceptable level. There are simple tools within wingx to add hydrogens and use anisotropic
thermal factors and to create e-density or difference maps.

Structure of Fe(DMGBF2)2(PY)(CO)-CH2Cl2

SELF DIRECTED Computer EXERCISE

Updated for wingx 1.80.03

SOME CAVEATS ABOUT WINGX

WINGX is professional software used by crystallographers around the world incorporting the SHELX
programmes into a windows environment. It is not an instructional program. There are features of direct
methods etc which you will not comprehend. However nothing else is beyond your ken if you have read the
Intro to crystallography, think about what you are doing in each step, and examine some of the screen output.
There is much to be learned by doing. Like any software, minor errors by the user can be fatal. Watch out for
using zero instead of O. 1 instead of lowercase L, etc
The SHELX programs read the INS file and then output the results to a RES file.ALL files will be named
PYCO with various extensions. The SXGRAPH edit of the RES file overwrites the INS file. Neither
SXGRAPH nor Hg will read a file with an INS extension. If you have errors in your INS file and run SHELXL97, it will abort leaving a useless RES file. To recover you need to manually edit the INS file which has not
changed and correct the errors before re-running SHELXL-97. When in doubt -throw it out is a good policy.
NOTE : You should close the interior windows- not wingx- after each step or things can get confused with
multiple windows open.
DESCRIPTION OF STRUCTURE: The complex contains a bis dimethylglyoximate chelate with BF2 groups
replacing the bridging H. Trans axial sites are occupied by CO and pyridine ligands. The crystal is a
dichloromethane solvate. <solvent is discovered during refinement but we will give you that info > This
structure is somewhat more challenging than YLID demonstrated in lecture .DMG = dimethylglyoxime (A Ni
glyoxime complex is shown on page 633 of Housecroft 3rd or 763 4th.) I INSIST that you draw out the
structure with the labelling as suggested below BEFORE coming to the lab.
You also need to download the PYCO.hkl file from the course website and bring it on a usb drive. (Make sure
the file name is as shown with the hkl extension. (not txt!) You may examine it in notepad. )
http://www.yorku.ca/stynes/PYCO.hkl
LOGIN with your acadlabs login , insert your USB drive with the PYCO.hkl file in it.
into a temp directory you create on the desktop>.

< or download the file

< If you work from your usb all output files will be written to it. Some USB drives seem to crash or run too
slow. In that case copy your hkl file to a temp directory on the desktop and work from there.>
1. Click on the WINGX icon and the wingx toolbar will appear.

INS file not found messages appears- you will create this in the next steps - click OK and continue.
2. FILE select new project.
Browse to your e:drive and select the PYCO.hkl file , it will do the rest including . JOB NAME PYCO
<If you don't have the working directory with the hkl file in it - you won't get started.- file not found error>
3. MODEL PRELIM - ASSIGN SPACE GROUP < prelims set up the first INS file with cell contents and
unit cell dimensions>
Enter the required unit cell data. Tick that the cell is orthorhombic : 12.436 13.246 14.158 90.00 90.00
90.00
.
The hkl file is examined for ALL potential absences and the space group most consistent with the reflection
data is identified.
TICK the box to update the INS file
4. MODEL PRELIM - INITIALIZE FILES - check info and then tick the crystal data tab. You may have to
reenter the unit cell.
the molecular formula is C15 H19 N5 B2 F4 O5 FE CL2. <note spacing, O5 not 05
!!!>
Colour is red and crystal size is 0.1 0.1 0.1. When checking Z (Tick ESTIMATE Z box) it should be 4. If not
look for errors in your formula and correct them.
(The colour and size are not relevant but wingx won't proceed without this info)
The PYCO.INS file ( INS as in instructions) is created.
Under REFINE -OPEN INS file - Look at it, spot any typos. Note the unit cell data in the CELL line , Z, symm
codes for the space group, SFAC lists atoms and defines atom codes. C =1 etc. UNIT line lists number of each
atom in unit cell for SFAC line above (formula times Z). < If no problems proceed to "solve"
5. SOLVE - SHELXS-97
Tick the direct methods tab and then OK < a Patterson method doesn't do well in this case- if you used the
default PATT you won't crack this>
Direct Methods selects certain reflections from the hkl file with high E values. (An E value is a special kind of
structure factor) then tries to obtain their phases. Using about 1000 of the 4000 reflections in the file it
computes an E map, a Fourier series for the electrron density RHO using E's instead of F's, and then examines
that function and picks out some 35 peaks which may correspond to real atom locations. Output this to the
graphic editor SXGRAPH where you will use your knowledge to identify which atoms are which and which are
artifacts due to incorrect phasing , data error, or round off error ( Only an infinite series with exact intensities
can exactly describe the structure.).
6. SXGRAPH is the graphic editor you will use to examine the RES output. If the sxgraph screen does not
appear click the caliper ( compass) icon on the tool bar
Tick label atoms, label Q peaks and show Q bonds if not already ticked at the right so you can see what you are
doing. Using SXGRAPH your task is to identify which atoms are Carbons, nitrogens etc and which are real
atoms and which spurious artifacts. Do not consider H-atoms at this point. On the screen menu : Tick Zoom and
mouse in or out to a reasonable size and then tick XY rotate to examine.
The possible atom locations are Q's. numbered in order of e-density from big to small Q1 is already
identified as Fe since it is easily distinguished from a C N or O. Q2 is a big atom, Q35 a lesser atom or maybe
just junk. Until you identify them, Q's are treated like Carbon and connected to other atoms if they are within
0.5 A of the sum of covalent radii. Hopefully you can see something resembling the proposed structure for
Fe(DMGBF2)2PYCO. Some atoms could be missing and some non-atoms with high Q# may confuse you.
Your task is to identify the atoms and delete the junk to come up with a reasonable looking tentative structure.
1.80 update : You can now automatically select how many Qs to show using the PERCENTAGE Q peaks
scroll bar. You can reduce the clutter, label obvious atoms and then expand the number of Qs using the scroll
bar labelling and deleting as below.

LABEL ATOMS in SXGRAPH To label real atoms I recommend the method below. Bring a page with the
expected structure which YOU generate before coming to the lab labelled as below to avoid confusion.
Recommended Labelling Method - systematic labels make it easy to remember who is who. The scattering
factors will be correctly identified if you proceed as below. However if you decide to change an atom from N1
to O1 you will need to also change the scattering factor. Note that the atom type is determined from the code not
the label.
Left Click the four nitrogen atoms bound to Fe in the planar macrocycle, right mouse click and : label N1 N2
N3 N4. Click OK. Click the four oxime oxygen atoms bound to these Nitrogens and label O1 O2 O3 O4. label
the two borons B1 and B2 and the four fluorines attached to boron as F1 F2 F3 F4. There are 8 carbons in the
planar macrocylic ligand Label those bound to nitrogen C1 thru C4. C1 bound to N1, etc. Then the methyl
carbons C5 thru C8. Label the py nitrogen N5 and the carbonyl carbon and oxygen C99 and O99. Label the
pyridine ring carbons C51 thru C55 - you may not find them all on the first refinement but label those you
recognize. You may not be able to locate the dichloromethane solvate and maybe a few of the pyridine carbons
but you can pick these up later. You should only include atoms which you are certain are correct in your atom
list.
In general deleting and labelling atoms will follow the strategies below. (SEE percentage Q info above.)
Option A . If you can't see something resembling the structure you can get rid of most of the spurious Q's by
selecting only the top Q's but this may also delete a few real atoms. Select only the first 32 or so Q's under
MODEL LIST Q's , click on the first 32 or whereever you want to cut off .You can always find deleted atoms in
round 2 as every atom located improves the Fcalc's. Proceed as in option B to to complete your edit.
Option B. Delete obvious junk one or more at a time and label others. (You will want to rotate the structure
often to get a good look at what you are deleting/labelling.) For deletion start with high Q#'s as these are likely
junk. For labelling start with low Q#'s as these are most likely real atoms. To delete an atom hi-lite it or
several by clicking on them <they turn yellow>. Then hit DELETE selected atoms on SXGRAPH toolbar.
.
The molecule crystallizes with a molecule of CH2Cl2 solvent. Q2 might be a chlorine but you may wish to
delete it and deal with the solvent in round 2. You'll find the rest on the second refinement. Delete any
remaining Q's which don't look like real atoms.
7. WHEN YOU have a reasonable structure ( even if some atoms are missing) Tick the save as INS bar in
SXGRAPH. DO NOT save a structure with extra atoms or Q's as this will only muddy the waters in round 2.
CLOSE SXGRAPH
8. REFINE - OPEN INS FILE -(just looking) note that the Q's are now labelled and have correct sfac codes.
The new INS file has instructions for least squares refinement added. CLOSE
9. REFINE - SHELXL-97 - run the least squares refinement programme. This will read the atom list from the
INS file and compute two e-density maps.
RHO(1) uses the intensity data from HKL file ( /Fobs/) and phases computed from the atom list for the
F(HKL)'s. = Fobs
RHO(2) uses the structure factors calculated from the atom LIST only = Fcalc
RHO(1) has info from all atoms including those yet to be found. RHO(2) only has info from atoms located so
far. The difference MAP then will show missing atoms. Once all atoms are found the difference map will be
relatively flat and the R1 factor less than 0.10.
The R factor is a measure of the agreement between Fobs and F calc. Follow only the R1 based on reflections >
4sigma.
CLICK SXGRAPH ICON to examine the results and edit. After each SHELXL-97, additional Q's are output
for your evaluation. In subsequent refinements the missing atoms should appear among Q1 to Q5 in
SXGRAPH. Label any atoms and delete the rest (or untick the show Q's box),save the ins file and refine again.

< If you don't want to output 20 difference peaks after each refinement you can change the PLAN 20 in the INS
file to PLAN 5. >
The SOLVENT : You are looking for a dichloromethane without its hydrogens. It will have a V shape with CCl bonds in the 1.5 to 1.8 range. Label the chlorines CL1 and CL2 and the carbon C1S.
ABSOLUTE STRUCTURE : If you have been getting a "wrong absolute structure" message under MODEL invert structure.
10. HYDROGENS RIDE -When all heavies are located and R1 around 10%, you can add hydrogens within the
SXGRAPH editor. Delete any Q's or untick the show Q's box.
Select all 4 methyl carbons. MODEL add Hydrogens - methyl
Select all 5 pyridine carbons MODEL add Hydrogen - aromatic
Select the C1S atom
MODEL add Hydrogens- methylene.
This doesn't add the hydrogens but it turns them green and writes the instructions for SHELXL-97 to do it in the
next refinement. Tick the SAVE INS FILE bar in SXGRAPH. to save and close..
11. REFINE - OPEN INS FILE
Before continuing check that you have all your atoms correctly labelled in the atom list , there should be 3 and
ONLY 3 HFIX lines, one for the methyls, one for the aromatics and one for the solvent carbons.
Add the following lines just above the FVAR line.
<All SHELX commands are 4 letter words>
ANIS -99 This will make the next 99 non-hydrogen atoms anisotropic <space between ANIS and -99>
LIST 3
This will output structure factors to an fcf file for use in generating an e-density map later with
MAPS. <space between LIST and 3>
ACTA This will allow you to collect data for your report easily using PUBLISH.
delete any lines that begin with OMIT as ACTA is not compatible with OMIT.
CLOSE and save the edited INS file.
12. REFINE AGAIN- SHELXL-97
Once all atoms are located you can untick the show Q box and they will be ignored. Otherwise if you save
them and run SHELXL-97 , it will crash if there is a Q in the atom list. - unrecognized atom type.
<NOTE: SXGRAPH does not do anything other than write an instruction file. You have to run SHELXL-97
each time to execute those instructions.>
REFINE AGAIN. SHELX will execute the HFIX instruction, save the structure factors in an .fcf file and
refiine 6 thermal parameters for each non-hydrogen atom. The R factor should drop to about 6% and you are
done.
If you get a message suggesting you have the wrong chirality invert the structure ( in SXGRAPH MODEL
invert) FILE and REFINE again. )
13.ORTEP FIGURE. * You may skip this and complete at home using the latest Hg ORTEP drawing option.
OR using wingx : Click on the ORTEP ellipsoid. Labeling is best done by mouse as auto label puts the label on
top of the atom where it cant be read. Select LABELS/set mouse labels. For each atom, click on it to select- a
blue dot appears, them move mouse cursor to where you want the label and click. The label appears in blue.
Then click OK in the bottom left box.. The label turns to white. Select the next atom etc. Then click OK to go to
the next one.
When finished hit ESC and under FILE writes postscript EPS file for your report and close ORTEP window.
14. RECORDS FOR PUBLICATION. To generate a TXT file which includes tables of crystallographic info
including all bond lengths and angles Select publish in the wingx toolbar and CIF TOOLS CIFTAB. The tables
too include are in the Tables section on the right. The defaults are OK. Click OK. Then quit. Be sure that your
TABLES.TXT file is copied to a floppy and paste this text into your final word report or print it out at home.
You may need to fill in a few blanks in the TXT file by hand and clean up any font problems. ( Older wingx
versions name this pyco.tex).

15. MAPS. The MAP tab provides for computation of electron density or difference maps. Before you can do
this you must have run SHEXL-97 with a LIST 3 instruction in the INS file. This will have output structure
factors Fobs and Fcalc into an FCF file which is needed to obtain the e-density maps.
From MAPS select the slant Fourier and then pick out three atoms which will define the plane of interest and
enter them in the space provided (N1 N2 N3 for instance). Tick Fobs for the e-density map. You can expand
the values of x,y, and z from the default options later if your map isnt big enough but for now leave these
defaults alone. If you choose the default option of a difference map (Fo-Fc) by mistake you will see only
random error in the map as all the atoms are accounted for. Under style/options tick show bonds, label atoms.
For hardcopy for your report file/save as bmp .
.
All files should be on your USB stick. Otherwise transfer or e-mail them to yourself.
The PYCO.res file can be read with Hg.
The tables.txt file from PUBLISH has your tables.
The LST files contain output from SHELXS and SHELXL jobs.
Note that the ortep.eps file can be pasted into word
Only the BMP file is useful for the maps figure
In Hg you can select jpegs. You should change the background colour to white and labels to black for best
print results. {This is done for you using the manage style toolbar in latest Hg version 2.3.
These can then be pasted into a word doc for your report. Be sure to provide a label !! Dumping output
without captions or comment is not acceptable.
IMPORTANT. Save the wingx.log file and e-mail it to me
DISCUSSION : USING HG with your PYCO.res file note the conformation of the N4 ligand and the
orientation of the pyridine ligand. Examine any close non bonded contacts between py and the N4 ligand. Note
any distortions in the N4 ligand which may reflect repulsive contacts.
USING HG at home you can easily do the following ( Only requires your PYCO.res file) . You can save all
screens including powder pattern as jpegs and paste these into your report.
1. Determine the displacement of the Fe and two borons from a plane defined by the four oxime nitrogens.
(Calculate/ planes)
2. How many solvent molecules are there in one unit cell?
3. Which regions of the N4 ligand are planar and which not. What is the hybridization of the imine carbons, the
borons, the oximate oxygens?
4. The PY ligand is free to rotate about the Fe-N axis. What determines the orientation in this case?
5. Compute by hand the Fe-NPy and Fe-CO bond lengths and show how you obtained them.
6. Why do you suppose the solvent is located where it is. Provide the closest nonbonded contact between the
solvent and the metal complex.
7. What other techniques would reveal the presence of dichloromethane in the crystals?
8. Compute the density with and without the solvent. Does it make a significant difference?
9. Report the axial and equatorial fluorine bond lengths.
10. What makes this molecule chiral?

WORKSHEET PYCO

Please fill in answers to the following. See EQ1 and Eq2..

Step 1. Record the intensity and standard deviation for a few strong reflections, data given in the hkl file OR.
Using Hg, identify the two strongest reflections and there relative intensity and Bragg angle from the powder
pattern (Mo radiation).

Recall Braggs Law : = 2d sin() AND = 0.71073 for Mo

The unit cell dimensions for an orthorhombic PYCO crystal are 12.436 13.246 14.158
What is the d spacing for the 100 planes and the Bragg angle using Mo radiation. ____________ ___________
What is the d spacing for the 800 planes and the Bragg angle using Mo radiation? ___________ ___________
Ditto for the 001 and 0,0, 23 reflections? ______________ _____________.
Step 2. From the unit cell parameters, 12.436 13.246 14.158 90 90 90 which crystal system does PYCO belong
to? _____________________
On what basis does the software decide the lattice type is P and space group P212121 ?
____________________
Give one reflection which is absent as a result of the 21 parallel to a _____ b ______ and c_____ .
If the computer recommended a value of Z = 5 why would you change it to 4 ?
SHELX INS FILE:
Do the SYMM lines generate the other three general positions? _________
How does the software come up with the number of each type of atom in the UNIT LINE?
_____________________________________________________________
Step 3. While you will not understand much of the direct methods information shown on the screen, what
exactly does direct methods seek to obtain? ________________ Where subsequently is it
used?____________________
Once tentative locations of most of the atoms are obtained from the E-map, the phases are tossed out and new
ones computed using EQ2 in what is called a Fourier synthesis. What information is used to do this?
Which structure factor would be used to obtain the coefficient of a term cos(4z), one of some 2000 terms in
the expression for the electron density RHO = 1/V Fhkl cos(2(hx + ky +lz hkl ) sum over h, k
and l where
hkl is a phase angle between 0 and 2. __________ Assume is zero here.
For F(000) (the zero angle reflection) all atoms scatter in phase and the value = total number of electrons in the
cell. What is F(000) in this case? _________________________
If F001 = 0 and F 002 = 28 what fraction of the electrons are scattering in phase at the angles corresponding to
these reflections? _______________ ____________________

Step 4. Graphical editor SXGRAPH How does the computer determine which atoms are connected to each
other?
What are the Qs displayed on the screen and where did they come from ?
_______________________________
In your own words what happens in a least squares refinement?
Step 5 Least Squares Refinement.
.
Record and explain the entries for the Iron in the atom list in the RES file.
The number of parameters (np) are used for the isotropic least squares refinement is 4N + 1 where N is the
number of non-hydrogen atoms? What exactly are these parameters?
Which most accurately describes what the R factor measures?
a)Agreement between bond lengths and correct values
b) Agreement between magnitudes of Fobs and F calc
c) How good the structure is.
Step 6. What is a difference electron density map? Explain how the coefficients for the 2000 cosine terms in
the Fourier series are obtained. Explain.
Explain how missing atoms in the structure appear in the difference map?
Step 7.
Why do the number of parameters increase to 9N + 1 for an anisotropic refinement?
Step 8. Comment on the Flack parameter and whether you have the correct absolute structure. (see
SHELXL.LST)
SUMMARY : The software contains quite a bit of data which otherwise you could look up.
List below what was needed :
a) in order obtain the space group
b) to compute Fc (see eq 2 of handouts)
c) to connect atoms for graphic displays of the structure.