Study Guide
Bruker Quest Diffractometer
-
University:
Purdue University -
Course:
CHM 62000 | Spectrochemical Instrumentation Academic year:
2022
-
Views:
221
Pages:
43
Author:
Kylan Cox
Standard Operating Procedure – Bruker Quest
Diffractometer with sealed tube molybdenum source
X-ray Crystallography Laboratory
The following is a guide for collecting data and solving structures using the Purdue Bruker
Quest single crystal diffractometer with a sealed tube molybdenum source. It is intended as a
“walk-through” user guide geared especially towards novice users, but also tries to cover more
advanced features of the software where they are important for the collection of normal “simple”
small molecule structural data. A basic knowledge of the fundamentals of diffraction and
crystallography is expected.
This manual is based on an instrument and software produced around the year 2017. Most of
the manual’s content also applies to newer as well as older instrument makes. For the novice user,
changes between different generation instruments are mostly limited to slightly different program
layouts and color schemes. The general procedures described in this manual still apply.
For a more in-depth description of the features of a CCD or CMOS diffractometer, the reader
should refer to the manuals and technique guides on specific topics by the manufacturer of the type
of instrumentation they are using. The gold standard for a more in depth guide towards the use of
Shelxtl for the refinement of single crystal structures is Peter Müller’s book ”Crystal Structure
Refinement”. Every crystallography lab should have at least one copy.
Among the many programs commonly used for crystal structure solution and refinement we
recommend the Bruker Shelxtl package (including XPREP, XS, XM and XT), George Sheldrick’s
refinement program Shelxl2018, the graphical interface Shelxle by Hübschle, Dittrich and
Sheldrick, and Platon by Anthony Spek.
1 Table of Contents
Instrument Overview...............................................................................................3
Checking the Status and Thermostat .......................................................................5
Starting the System .................................................................................................7
Unloading the Previous Sample ..............................................................................8
Selecting and Mounting of Sample .........................................................................9
Crystal Mounting and Centering ...........................................................................11
Crystal and Compound Description ......................................................................13
Unit Cell Determination ........................................................................................14
Data Collection......................................................................................................20
Data Integration .....................................................................................................26
Scaling and Absorption Correction .......................................................................27
Transferring the Data ............................................................................................31
Setting up Data for XPREP ...................................................................................32
XPREP ..................................................................................................................33
The Initial INS File ...............................................................................................40
Solving Structures using XS and XM ...................................................................41
Solving Structures using ShelXT ..........................................................................43
Structure Refinement ............................................................................................43
2 Instrument Overview
The Bruker Quest instrument with sealed tube molybdenum source consists of:
The diffractometer including the X-ray enclosure, PhotonII detector, X-ray tube,
monochromator and optics, video microscope, fixed Chi goniometer, electronic controls,
power supply and other miscellaneous pieces of equipment essential for the operation of the
instrument.
An Oxford Cryosystems 800 plus variable temperature unit (pump, controllers and liquid
nitrogen tanks located outside the enclosure) and an Oxford Cryosystems AD51 dry air unit.
Haskris chillers that cool and circulate cooling water for the power supply and the X-ray
tube.
The instrument computer: This computer runs the Measurement Server, the Bruker
Instrument Service (BIS), Diffrac.Maintenance and Apex3.
3 Figure 1, Inside of the Quest X-ray enclosure with X-ray tube, PhotonII Detector, Variable Temp Unit and
Goniometer. Between X-ray tube and detector are the Optics (Monochromator, Collimator), the Video
Microscope (in back, partially hidden), and the Beam Stop. On the Goniometer is mounted the Goniometer
Head that holds the crystal specimen.
4 Having a promising sample of crystals, it is best to start in the following order:
Checking the Status and Thermostat
All but very high melting samples (inorganics, ceramics, etc) should be measured at lower
temperature to avoid extensive thermal motion of the atom cores, to obtain higher angle diffraction
data and to minimize radiation damage to the sample.
The Oxford Cryosystems variable temperature unit can be operated as a stand-alone unit through
its own controllers. More often, it is controlled via Apex3 or BIS. The sample is embedded in a
stream of cold nitrogen gas supplied by a low pressure liquid nitrogen dewar. To avoid buildup of
ice, the sample is insulated from ambient humidity by an outer layer of warm dry air supplied by
an Oxford Cryosystems AD51 dry air unit (located outside the lab in a facilities closet).
The Oxford Cryosystems variable temperature unit is able to achieve temperatures between 475 K
(+202.5°C) down to ca. 85 K (-188.5°C). The recommended temperature for “low temperature”
data collections is 100 K in winter, and 150 K in summer (due to higher humidity levels that can
cause icing around the sample mount).
• Make sure, the tank is properly connected and full enough for the planned experiment.
• The Oxford Cryostream N2 tank (silver dewar behind the diffractometer) is automatically refilled
from the larger low pressure liquid nitrogen tank (to the left of the dewar). Check that the Liquid
Level Controller (the smaller of the two controllers, Fig. 2) is set to . The fill level
displayed on the controller should be between 20 and 80%. When it is below 20% (despite the
controller set to AUTOFILL) the low pressure N2 tank is empty and needs to be refilled.
5 Figure 2, The external controller (bottom), the
circulation pump (center), and the liquid level
controller (top) of the Oxford Cryosystems
variable temperature unit.
• Check that no data collection is running (e.g., look at the BIS interface, check for “Frames
left” or “Time left”). If a running data collection can be stopped, abort the running data collection
(see below), then make changes to the VT unit.
• Check that the dry air unit providing the shield gas flow is switched on.
• Tap the touchscreen of the Cryostream Controller (larger of the two controllers) to check the
status of the VT unit. If it is running (“Cryostream running” beside the
symbol on the screen),
check if the temperature is appropriate for your experiment. If you need a different temperature,
or if the system is on standby (“Cryostream ready” beside the
symbol on the screen), use the
interface of Apex3 to set the desired temperature (see below, Starting the
System).
• If the unit is completely switched off it needs to be started. Press the main single button on the
front of the controller. Follow the on screen prompts to switch on the unit. Use the interface of Apex3 to set the desired temperature (see below, Starting the System).
6 Starting the System
• Start BIS (Bruker Instrumentation System) if it is not already running. This will also start the
measurement server if it is not active already.
Figure 3, The BIS window
• Check if a data collection is still running (e.g., look at the BIS interface, check for “Frames
left” or “Time left”). If a data collection is active but can be aborted, then stop this data
collection first. Navigate to the active copy of Apex3 and click the STOP symbol in the Apex3
interface.
• Minimize any sessions of Apex3 that might be open.
▪
Start a new session of Apex3. No login is required.
▪
Connect to BIS (, then ).
• Via the dropdown menu, either an existing sample (continuation of old data
collection) or
• Start a
▪
Fill in the project name. Avoid using special characters (including dashes and periods) or
overly long project names.
7 ▪
Leave the Group as “Users” and accept the automatically created project path
(D:\frames\guest\ProjectName)
Figure 4, New Sample pop-up window
• If necessary, ramp the temperature:
▪
Under click on
▪
In the column of the table, click on the top row and select
Enter the target temperature (in K). Set the rate to 360 (K/hr). Click the
button. You can mount and center a crystal while the temperature is ramping. For unit
cell measurements and data collections, wait for the temperature to have settled at the
target value.
Unloading the Previous Sample
• Before using the video for crystal centering, make sure only one copy of Apex3 is open
(trying to open the crystal centering tab from a second copy of Apex3 can crash the video
feed).
• Under , go to
▪
The video feed will automatically open showing you a life picture of the mounted crystal.
Troubleshooting: If the connection to the video feed fails, do the following: Close all
other open copies of Apex3. Then close the “Center Crystal” subwindow. Disconnect
from the Server (Click the dropdown menue, click ). Click
8 under again. If this also fails, close Apex3 entirely. Open
the Task Manager. Find and close “FrameGrabber.exe” (under “Details”, “End Task”).
Restart Apex3 and try again. Repeat if necessary.
▪
Once the live video feed is running, click on in the lower right of the interface.
The angles will drive to a position convenient for mounting a magnetic snap-on mount.
▪
Press the button on the front face of the diffractometer enclosure (to the
right of the front door, below the light button). Doors need to be closed to drive any
mechanical parts other than the phi (spindle) axis of the goniometer.
▪
Carefully dismount the magnetic snap-on mount from the previous experiment. Tilt it
backwards until the magnet comes loose, then take it off.
Figure 4, Goniometer head with magnetic snap on mount and adjustment screw
Selecting and Mounting of Sample
• Crystals can be mounted on glass rods, inside glass capillaries, on Nylon loops, or using mesh
mounts. The Purdue X-ray lab uses Mitegen micromesh mounts for most samples and data
collections.
9 ▪
Two types of micromesh mounts for small (<0.1 mm) and medium and large (0.1 – 0.5 mm)
crystals are stocked in the lab (Fig 5). Crystals collected at low temperature are mounted on
the micromesh with the help of a trace of mineral oil, Fomblin (fluorinated mineral oil) or
polybutene oil (very viscous oil to protect extremely oxygen sensitive samples) and flash
frozen in the cold stream. Crystals collected at room or elevated temperature might need to
be fixed to the mesh with a trace of glue to avoid crystal movement during measurement.
Figure 5, Mitegen Micromesh mounts (Left:
small tipped mount with 15 µm openings for
crystals 0.1 mm and smaller. Right: large
mesh mount with 25 µm openings. Mesh is 0.4
mm across).
▪
For typical crystal selection and mounting, place a drop of oil on a glass slide under a
microscope. Place several representative crystals in the oil. Inspect the crystals and select a
suitable candidate. Crystals on the Quest instrument with sealed tube molybdenum source
should ideally be between 0.2 and 0.55 mm in any direction (size of the X-ray beam is 0.6
mm). The minimum size depends on the diffraction intensity of the crystal. For highly
absorbing samples limit the size of the crystal (make sure the minimum transmission will be
above 10-20%). If no single specimen with suitable dimensions can be found, use a sharp
razor blade to cut off a single piece from a larger crystal or cluster. Remove all smaller pieces
and dirt from the crystal (the micromesh mount can be used to brush off loose pieces from
the crystal).
10 Figure 6, Crystals with well-developed faces on a
microscope slide
▪
Scoop up a crystal with the micromesh mount and place it on the inside of the concave face
of the mount in the center of the mesh. Remove as much excess oil as possible by tipping the
back (convex) side of the mount onto a dry section of the microscope slide until only a
minimum amount of oil remains on the mount and crystal. (If a crystal needs to be glued to
the mount make sure that both crystal and mount are dry without any traces of oil. Dip the
mesh carefully in a small amount of glue and pick up the crystal without touching the glass
slide).
Crystal Mounting and Centering
▪
Make sure exactly one copy of Apex3 is running (trying to open the crystal centering tab
from a second copy of Apex3 will crash the video feed).
▪
Carefully mount the magnetic snap on mount onto the goniometer.
▪
Check the position of the mount by eye (is it aligned with the collimator and the beam stop?)
▪
In Apex3, click in the submenue. The crystal centering live video
feed will automatically open (If the live video feed does not start, see “Unloading of Previous
Sample” for troubleshooting). Is the crystal visible on the video screen? If you cannot see the
crystal, its position is further off than usual and needs to be adjusted by eye on the
goniometer head before the live video feed can be used.
11 Figure 7, Crystal Centering Window and live video feed with mounted sample, cross hair and green measuring line.
▪
If the image is too dark to see the crystal well, you can place a piece of paper between the
goniometer head and the detector.
▪
There are three adjustment screws (metal pins) on the goniometer head: for up-down, rightleft, and forward-backward. Use the bold end of the adjustment screw driver to turn the pins
to position the crystal in the center of the cross hair of the video feed.
▪
When the crystal is centered in the cross hair, click the large button (in the
window of Apex3) to spin the crystal around the phi axis by 90°. Repeat
the centering procedure using the adjustment screws as before. Repeat the process ( followed by centering of the crystal in the cross hair of the video feed) until the crystal
stays positioned in the center of the cross hair in all positions. If the cross hair seems to be
slightly off try to center the crystal so that it “rotates in place”.
For oddly shaped crystals, try to center the mass center of the crystal. For long needles, try to
align them along the axis of the mounting pin.
▪
Measure the dimensions of the crystal: Switch on the measuring tool (double sided arrow
icon on top of window, Fig. 7). Click on one side of the crystal, hold the
left mouse key and drag to the other side. The length of the green line dragged is given in the
12 bar below the video screen (“vector length”, value in µm). Write down the value and repeat
for the other two directions using .
Crystal and Compound Description
• Under , go to
▪
Fill in all values that apply. In the “compound” line, it is best to give the full name of the
person that provided the sample. Crystal dimensions need to be entered in mm (video
screen values are in µm!).
Figure 8, Crystal and compound description
13 Unit Cell Determination
• Under , click on .
▪
Two procedures are available, or .
Figure 9, Starting Window of the Unit Cell determination
We encourage to use the manual procedure. To do so click , this will open
the Unit Cell Data Collection Window.
14 Figure 10, Unit Cell window with active data collection running
▪
Choose an exposure time (default is 10 seconds) and click .
▪
2 × 12 frames will be collected which will be displayed in the frame window.
▪
Make sure that your specimen diffracts to sufficiently high angle. Use the resolution arc
tool to check the resolution limit. Only samples that show at least some diffraction above
ca. 0.9 Å (with ten second exposures) are likely to meet the IUCr requirements for
publication. For crystals diffracting too weakly, consider using the copper microsource
instrument.
▪
When all 24 images are collected, the program will automatically proceed to . Select an I/sigma cutoff value for the diffraction spots to be used (circled in green
in the diffraction image). To obtain a reasonable suggestion for the exposure time use the
default value of 10.0. Click on .
15 Figure 11, Unit Cell Harvesting Window
▪
Proceed to , use all default values and click on at the bottom of the
window.
16 Figure 12, Unit Cell Indexing Result Window
▪
Check the unit cells obtained. The positions of the diffraction spots (ignoring natural
decay events) should agree with the predicted positions (circled in diffraction images). If
there are excess spots not assigned to the cell a non-merohedral twin might be present, or
the crystal is not single. Try to find a better, more obviously single crystal. If this is
the best crystal that can be found, investigate if it can be processed as a twin. Export the
data as a p4p file using , then and use the program Cell Now to
determine the unit cell and relationships between domains (see the Purdue Twinning
Manual for details).
▪
If one of the two unit cells looks reasonable, select it and click . This will open
the Refine Window. Use all defaults and click on to run a least squares
optimization of the unit cell against the diffraction spot position. Select more or less
reflections using the sliding bar and repeat, then click .
17 Figure 13, Unit Cell Refinement Window
▪
Proceed to . A list of possible Bravais lattices will be displayed with the
software's choice highlighted in green.
18 Figure 14, Bravais Result Window
The correct choice should have a Figure of Merit (FOM) value significantly higher than
the others. If several solutions have similarly high FOM values, the one with the highest
symmetry is likely to be correct. If you are not sure (e.g. when a high symmetry solution
has a high FOM value, but significantly lower than a lower symmetry solution) select the
lower symmetry solution to avoid collecting incomplete data.
▪
Make your choice of Bravais lattice, then click . This will open the second
Refine Window.
▪
Use all defaults and click on to run a least squares optimization of the unit cell
against the diffraction spot positions (constrained to the chosen Bravais lattice). Select
more or less reflections as desired and repeat, then click .
▪
▪
Please note the resolution prediction at the bottom of the window
This finishes the Unit Cell Determination.
19 Data Collection
• Click < Calculate Strategy> under .
▪
Under Step 1., change the resolution to d = 0.75 or lower, as required. The worst
acceptable value, by IUCr standard, is 0.83 Å. A resolution better than 0.65 Å will rarely
be required (and will substantially increase data collection time). Click if you
made any changes.
Figure 15, Strategy Starting Window
▪
Under Step 2., click . In the pop-up window, it is usually safe to
use the default values. Click ,
20 Figure 16, Determine Strategy popup window
▪
Under Step 3., click
Related Documents
- Friedel - Craft Alkylation Reaction
- Non-Polar Amino Acid Group Contains S Group
- Phase Transfer Catalyst & Ultrasound Technique
- Carbohydrates Chemistry Lecture
- Reaction for Exo & Endothermic
- Solubility And Precipitation Reactions
- Reactions Stoichiometry
- Fundamental (principles) of Chemistry
- Cyclic Non-Polar Amino Acid Group (Proline)
- Properties of Amino Acid Base
- Aromatic Non-Polar Amino Acid
- Carbohydrate and Monosaccharides
- Electrophilic Aromatic Substition
- Phenyl Ring Effect
- Hammond Postulate & Reaction Profile
- Friedel - Craft Acetylation Reaction
- Delocalised Covalent Bonding
- Elimination Addition Process
- Sulphonation and Its Mechanism
- Factors Affecting SN Reaction
Bruker Quest Diffractometer
of 43
Recommended Documents
⏰ Deadline pressure?
Get your assignment done in just 3 hours. Quick, easy, and available 24/7.
Report
Tell us what’s wrong with it:
Thanks, got it!
We will moderate it soon!
Free up your schedule!
Our EduBirdie Experts Are Here for You 24/7! Just fill out a form and let us know how we can assist you.
Take 5 seconds to unlock
Enter your email below and get instant access to your document