Perspective On: An Academic Research Lab

Instrumentation laboratories in the University of Rochester (UR) Department of Chemistry play a key role in both academic research and education.


Instrumentation Lab Plays Key Role in the University of Rochester's Mission

Instrumentation laboratories in the University of Rochester (UR) Department of Chemistry play a key role in both academic research and education. Besides instruments belonging to each professor’s research group, the department also maintains a large group of instruments devoted to the research needs of faculty members and researchers as well as for educating students taking various chemistry department courses.

The Instrumentation Laboratory is housed in the University’s massive Hutchison Hall, home to the Department of Biology and the Department of Earth and Environmental Sciences as well as the Department of Chemistry. The instrumentation specialists in charge of the individual laboratories schedule usage time on the instruments and train students and postdoctoral researchers in their operation. They also maintain the instruments in top operating condition. All are longtime university employees.

Terry O’Connell is the Director of Chemical Operations. With 29 years of experience with the Chemistry Department, O’Connell is responsible for new instrument installation and building renovations to accommodate new instruments. During the 2009-2010 academic year, the Department of Chemistry acquired and installed over $2 million worth of research instrumentation. This includes a Bruker EMS-Plus electron paramagnetic resonance (EPR) spectrometer, a Thermo Scientific LTQ Velos ion trap liquid chromatograph/mass spectrometer, a Bruker Fourier transform mass spectrometer (FTMS), a PerkinElmer 2400 Series II HNS/O elemental analyzer and a Bruker Autoflex III MALDI-TOF mass spectrometer. O’Connell works closely with Senior Lab Engineer Pete Serrino and Research Scientist Ray Teng. Teng has worked at UR since 1987 in the Department of Physics and Astronomy, the Nuclear Structure Research Laboratory, and the Department of Earth Science and Environmental Sciences. In 1987 he joined the Department of Chemistry as Research/Facility Coordinator.

X-ray crystallography and elemental analysis

Bill Brennessel is in charge of the management and operations of the X-ray crystallography and combustion elemental analysis facilities. These instruments are used in the determination of the chemical structure of solid samples. X-ray crystallography enables researchers to determine the structure of a single crystal of a sample, delineating the identity and spatial arrangement of the atoms in a crystal.

Typically only a few crystals are required to find an acceptable crystal specimen. More crystals are better and larger crystals are preferred. Brennessel accepts crystals either dry or still wet in the mother liquor used to perform the sample crystallization.

Absolute stereochemical configuration can be determined for compounds containing at least one heavy atom (silicon or heavier). Relative stereochemistry can be determined for light atom structures. Absolute stereochemical configuration can then be assigned from a known stereochemical center.

Air-sensitive samples are prepared under a nitrogen atmosphere. Experiments are run on a Bruker- AXS SMART Platform diffractometer equipped with an APEX II CCD detector. An X-ray tube (50 kilovolts and 30 milliamperes) delivers molybdenum radiation to the crystal sample. The standard test temperature of 100° K is maintained using a Kryoflex low-temperature device. Operating temperature range is 90°K to 300°K. Samples are examined using a polarizing microscope.

Data manipulation and structural solution and refinement are performed with the SHELXTL package from Bruker-AXS.

Typically, data collection requires 8 to 24 hours and is controlled by Bruker-AXS’s APEX2 software package. The X-ray crystallography laboratory analyzes an average of one new research sample daily.

The submitter receives a full report in PDF format by e-mail plus a crystallographic information file (CIF). The CIF is suitable for journal submission while the PDF file contains experimental data, ORTEP diagrams, bond lengths and angles.

UR research groups pay a fee of $200 per sample. Researchers from other universities pay $250 per sample. The industrial researchers’ fee is $500.

Graduate students learn the theory and operation of the X-ray crystallography instrument as part of a graduate-level chemistry course, Chemistry 416. Students who take this course are considered officially trained users of the instrument and can study their own research samples.

In addition, as part of the undergraduate Chemistry 234 Advanced Laboratory Techniques course, Brennessel provides students with hands-on training on the instrument. This laboratory course provides experience with analytical methods including infrared and ultraviolet-visible spectroscopy, nuclear magnetic resonance spectroscopy, magnetic susceptibility, X-ray crystallography, differential scanning calorimetry, and methods of handling air-sensitive compounds under inert atmospheres. Combustion elemental analysis involves burning a solid sample to produce carbon dioxide, hydrogen and nitrogen. Measuring the amounts of these gases produced enables researchers to determine the absolute percentages of carbon, hydrogen and nitrogen in the sample.

Inorganic chemistry graduate student Thomas Dugan preparing a sample for EPR spectrometer.

Center for Enabling New Technologies Through Catalysis

The Center for Enabling New Technologies Through Catalysis (CENTC) is a National Science Foundation Phase II Center for Chemical Innovation. CENTC brings together researchers from 12 universities across North America and a U.S. national laboratory with the primary purpose of assisting research on development of more cost-effective and environmentally friendly methods to manufacture chemicals and fuels from a variety of feedstocks. The major focus is on catalysis. Effective catalysts can reduce the amount of energy needed to perform chemical conversions. Catalysts can also enable the use of less-expensive and nontoxic starting materials while generating less waste per pound of product formed.

CENTC has established an elemental analysis facility at UR. The facility consists of three main units, a PerkinElmer 2400 Series II analyzer for micro-scale elemental analyses and a PerkinElmer Model AD-6 Autobalance. Air-sensitive materials are prepared in a dedicated VAC Atmosphere glovebox loaded with Ar (argon) gas. Solid and liquid samples are crimp-sealed in special tin capsules and aluminum capsules, respectively.

To improve accuracy, precision and consistency of the analyses, Brennessel is the only person authorized to operate the UR equipment. Helium (99.998%) is used as the carrier gas for the analyses. Accuracy is 0.3% and precision is 0.2% per element.

A calibration standard of known composition is used to determine the correct signal:microgram ratio for each element. It is run as an actual sample before and after all other sample runs. To maintain the calibration, the calibration standard is also run at regular intervals during a long series of samples.

Industrial laboratories can become affiliates of the CENTC program. This provides them with early access to CENTC research results. Possibilities include sponsored research by the industrial affiliates or technology licensing. Among the 14 industrial affiliates nationwide are three oil companies, ExxonMobil, Chevron and BP; chemical firms Dow, BASF, Eastman and Strem Chemicals; Procter & Gamble; and Pfizer.

UR’s CENTC facility will also perform analyses for research groups from other universities and from companies. These organizations must apply and be accepted to have their analyses performed. While the fee for UR research groups and research groups from other CENTC facilities is $25 per sample, it is $30 for external academic researchers. Industrial research groups must pay a $50 fee.

Other instrumentation

Other Department of Chemistry instrumentation includes five nuclear magnetic resonance (NMR) spectrometers: a Varian 500 megahertz (MHZ) spectrometer, a Bruker 500 MHZ spectrometer, two Bruker 400 MHZ spectrometers and a Bruker 300 MHZ spectrometer.

The department’s mass spectrometers include the Bruker FTMS, Bruker MALDI-TOF and Thermo LTQ Velos ion trap LC-MS mentioned above, plus three Shimadzu instruments: an LC-MS 2010 with APCI and electrospray ionization, a GC-MS with dual columns, and a GC-MS with direct injection probe.

Inorganic chemistry graduate student Meghan Rodriguez operating a liquid chromatograph/ mass spectrometer (LC-MS).

The department also has laser systems for absorption, fluorescence, and Raman spectroscopic analysis; nonlinear four-wave mixing; electrooptic sampling; time-resolved electron diffraction; photoelectron spectroscopy; temperature-jump studies; and photoacoustic calorimetry. To initiate photochemical reactions, the department has two kHz regeneratively amplified femtosecond titanium:sapphire lasers. One is equipped with an optical parametric amplifier for generation of continuously tunable UV, visible and infrared femtosecond pulses. The department also has transient absorption systems based on a picosecond Nd:YAG laser and a nanosecond excimerpumped dye laser. There is also a picosecond time-correlated single photon counting fluorescence system based on an Nd:YLF-pumped cavitydumped dye laser. Besides a laser Raman facility, there is also an Nd:YAG/dye laser system. There are also associated optical instruments: monochromators and spectrographs; fast multichannel plate photodetectors; and state-of-theart, highly-sensitive array detectors (CCDs and photodiode arrays).

Organic chemistry graduate student Ria Swanekamp preparing to operate a Bruker Autoflex III MALDI-TOF mass spectrometer.

Other instruments include an infrared spectrometer with probes for remote monitoring and recording of spectra over time. This last probe is useful for monitoring changes in the composition of reaction mixtures over time. To aid in polymer characterization, the department also has thermogravimetric analysis and differential scanning calorimetry instruments.

There is a Digital Instruments Nanoscope IIa atomic force microscope, an ellipsometer, a single molecule time-resolved fluorescence confocal microscope and a Roper Scientific spectrofluorometer with infrared and visible light capabilities. There are also four Shimadzu FT-IR spectrometers and many UV-Vis spectrometers. Finally, the department has an H-cube hydrogenator and a phosphorimager.

In addition to all the instruments mentioned in this article, many of the department’s research groups possess their own instruments dedicated to their own research needs.

The instrument capabilities of the UR Department of Chemistry are essential in performing the research of its members and achieving its educational mission. These capabilities are responsible in no small part for the department being ranked in the Top 50 U.S. chemistry departments in the U.S. News & World Report Annual Survey of Graduate Schools.

All photographs are courtesy of the University of Rochester and were taken by Karen Chiang, a graduate student and aspiring professional photographer.

Published In

Communicating Science Magazine Issue Cover
Communicating Science

Published: November 1, 2011

Cover Story

Communicating Science

The scientific community has historically taken a dim view of communications with nonscientific publics. No thanks, said scientists. What an imposition! Why bother? What good could possibly come from interrupting research, sticking our necks out and dumbing it down for non-scientific dunderheads, only to see them mismanage our findings?