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Molecular Structure Laboratory

Facility


Molecular Structure Laboratory / Facility Updated: February 11, 2015

  • Laboratory
  • Bruker Quazar IµS
  • Bruker SMART APEX2
  • Bruker D8 Advance
  • Microscope
  • Supper Drill
  • Innovations
  • Low Temp Basin
  • Grant info

The Molecular Structure Laboratory occupies room 2121 and 2143 on the second floor of the Shain Tower - the newest addition to the Chemistry Department.

The Laboratory is equipped with two state-of-the-art single-crystal X-ray diffractometers: Bruker Quazar APEX2 with a Mo Kα IµS radiation source (aka Gromit) and Bruker SMART APEX2 with a Cu Kα conventional sealed X-ray tube (aka Bucky). Both instruments are outfitted with Oxford Cryosystems low temperature devices allowing data acquisition in the 90-293 K range on Gromit and 90-400 K range on Bucky.

There is a Nikon SMZ-10A (49x) microscope with a polarizer for crystal selection. The microscope is connected to a high-resolution digital camera and computer for photographing crystals and recording videos of small-scale chemical reactions.

There is also a computer lab (room 2122, below) available to students for data processing.

 

Bruker Quazar SMART APEXII (aka Gromit)

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

This diffractometer equipped with a Mo Kα IµS radiation source is located in room 2121 of the Shain tower.

This instrument is ideally suited for structural characterization of organometallic crystals and crystals of small size.

Most data aquisitions are conducted with an Oxford Cryosystems low temperature device model 700 in the 90-400 K range.

The size of the X-ray beam measures 160 microns in diameter and requires precise crystal alignment.

This instrument was commissioned in November 2009.

 

 

 

 

 

 

 

 

 

 

 

A close-up of the instrument.

 

 

Bruker SMART APEXII (aka Bucky)

This instrument (room 2121) equipped with a Cu Kα conventional sealed X-ray tube is best suited for organic crystals because Cu Kα radiation allows determination of the absolute configuration in the absence of heavy elements (Z < 16).

Bucky is equipped with an Oxford Cryosystems low temperature device model 700 allowing data acquisition in the 90-400 K range. The capability of the low temperature device to maintain temperature in a 310 degree range enables the researchers to study solid state phase transitions in a broad range of temperatures.

The size of the X-ray beam measures 500 microns in diameter and requires precise crystal alignment.

The instrument was commissioned in November 2007.

 

 

 

 

 

 

A close-up of the instrument

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Bruker D8 Advance (aka Sid)

Bruker D8 Advance is a powder diffractometer equipped with a Cu Kα conventional sealed X-ray tube and a Lynxeye detector (room 2143).

The instrument enclosure reads "D8 Discover" because the enclosure of our D8 Advance diffractometer can accommodate a large D8 Discover instrument - ideal for a future instrument upgrade.

The instrument is equipped with an XYZ sample stage.

Several front-loading and back-loading sample holders as well as zero background plates are available to the users.

The Department has nine simultaneous licenses for the Bruker software used in the powder diffraction laboratory and all users are welcome to install it on their lab comuters. However, the software runs only on the computers plugged in directly into an internet port inside the Chemistry department.

The instrument was commissioned in August 2012.

Instrument operation notes are available to trained users.

 

 

 

 

Nikon SMZ-10A

 

This microscope is capable of 49x magnification. The microscope is equipped with a polarizer for crystal selection. A high-resolution digital camera is attached to the microscope (shown in the photo) and a computer for photographing crystals and recording videos of small-scale chemical reactions. There is a source of transient light in the microscope base and an additional source of incident illumination (not shown). The microscope user instructions are posted next to the scope in room 2121.

Supper Drill

The Supper drill is used to build custom molecular models that reflect experimentally observed molecular geometries. For example, a molecule of Vitamin C is accurately represented by a model on the photograph on the right. Additional models can be seen hanging from the ceiling in the laboratory panorama.

This is a Si diod that we use for calibrating our low temperature devices. The diod is a flat disk measuring about 1 mm in diameter and 0.1 mm in thickness. It is mounted on a goniometer head for ease of use. For measuring the temperature at the crystal position it is NOT mounted on the goniometer stage of our three-circle diffractometers because it would not be coaxial with with stream of cold nitrogen. Instead it is raised vertically on a lab jack stand until the diod occupies the position of a centered crystal in the cold nitrogen stream.

Details: Sold by Lakeshore; model DT-421, calibrated between 1.4-325 K.

 

 

 

 

 

On both of our instruments the metal beam supporting the low temp device is attached to the roof of the enclosure. This makes the right-hand side of the instrument substantially less crowded. This is especially handy for instruments with a Cu tube - the roof mount facilitates access to the tube when it is replaced.

The vertical mount was first observed in the lab of Prof. Len Barbour, Stellenbosch, South Africa in 2008.

 

 

 

 

 

 

This is how the mount looks from above - no need for any additional metal plates - the enclosure sheet metal is strong enough.

 

 

 

 

The video camera mount is modified - a horisontal translation stage is inserted between the steel post and the black L-bracket in order to move the camera to and from the crystal for easy focusing. This is seldom needed but it is very handy. Using an X/Y stage for translating the video camera in two directions was considered but such a stage was too bulky for the available space.

 

 

 

Top - our modified mount. Bottom - original mount.

 

 

 

 

 

 

In order to avoid corrosion of the shutter it is constantly purged with a low flow of house nitrogen gas (Joe Reibenspies' (Texas A&M) idea). Chunhua "Tony" Hu has a similar set up at NYU.

 

 

 

 

Nikolay Gerasimchuk (Missouri State) has the nitrogen feed at the bottom. "We do not have a house N2 high pressure line, so we use an N2 gas cylinder, and we also found that the flow rate ~0.4 L/min is sufficient for effective purging."

 

 

 

 

This is the barb needed for the setup. Peter Janutolo, Bruker AXS: "Most tube housings newer than 2008 will have the new coated plate over the S1 and S2 switches that will have a thread hole that you can attach a hose barb to. Then you can use a small pump or a low flow nitrogen line to help the main shutter stay free of debris."

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Low Temperature Basin

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

This is a pretty nifty device for handling air- and moisture-sensitive samples without a glove box. The basin consists of Styrofoam frame, with a piece of glass at the bottom. The glass is attached to the frame with duct tape. The front wall of the basin is lower than the back to allow easy access to the bottom of the basin with scalpels and goniometer heads. Argon gas from an argon tank fills the basin through the Tygon tubings inserted in the holes at the four corners. The Tygon tubing is held in place by friction. The beauty of the device is that you can also cool your crystals in the basin with dry ice because no moisture condensation will occur under argon.

The X-ray Laboratory is equipped with two state-of-the-art single-crystal X-ray diffractometers.

Bruker Quazar APEX2 with a Mo Kα IµS radiation source. The instrument is equipped with an Oxford Cryosystems low temperature device model 700 allowing data acquisition in the 90-400 K range. This instrument is ideally suited for structural characterization of organometallic crystals and crystals of small size. This instrument was purchased by the department with the Bender fund money in November 2009.

Bruker SMART APEX2 with a Cu Kα conventional sealed X-ray tube. The instrument is equipped with an Oxford Cryosystems low temperature device model 700 allowing data acquisition in the 90-400 K range. This instrument is best suited for organic crystals because Cu Kα radiation allows determination of the absolute configuration in the absence of heavy elements (Z < 16). The capability of the low temperature device to maintain temperature in a 310 degree range enables the researchers to study solid state phase transitions in a broad range of temperatures. This diffractometer can also be used for recording powder diffraction patterns. The instrument was purchased with departmental and graduate school funds in November 2007.

Bruker D8 Advance powder diffractometer with a Lynxeye detector and Cu Kα conventional sealed X-ray tube. This instrument was purchased by the department with the Bender fund money in August 2012.



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