Featured Core Facility: Small Molecule X-ray Diffraction Core (SMXDC)

Asia Marie Riel with her molecule

Under the leadership of Dr. Orion Berryman, CBSD’s Small Molecule X-ray Diffraction Core (SMXDC) has become a competitive, regional facility serving Principal Investigators (PIs) from Montana, Washington, Idaho, Utah, and Wisconsin. In the past year, the facility has evaluated over 500 samples with over 175 data sets collected on the Bruker D8 Venture Duo. The instrument sports two X-ray sources (copper and molybdenum) enabling the facility to select appropriate data collection strategies for diverse compounds such as natural products, transition metal enzyme mimics, uranium clusters, organocatalysts, and metal-organic frameworks. The core provides support, expertise, and infrastructure to researchers who use X-ray crystallography as a tool to determine the three-dimensional atomic structures of organic and inorganic molecules.

The SMXDC provides a resource for training, education, and consultation in X-ray crystallography techniques to assist individuals of any experience level to initiate and complete an X-ray diffraction experiment. Inherently, this ties to the University of Montana’s mission:

The University of Montana transforms lives by providing a high-quality and accessible education and by generating world-class research and creative scholarship in an exceptional place.

On a more granular level, the SMXDC is instrumental in meeting Priority #2 - Drive Excellence and Innovation in Teaching, Learning, and Research of the University of Montana’s Priorities for Action. The Core places emphasis on outreach and teaching by hosting multiple camps in collaboration with UM’s SpectrUM and We Are Montana in the Classroom. Outreach activities so far have brought microscopes and crystals on the road, included 3D printing, and been integrated into Chemistry 122 – Introduction to General Chemistry Lab and Chemistry 222 – Organic Chemistry laboratory.

Small molecule X-ray diffraction is one of the most powerful methods to characterize the atomic structure of molecules. With a structural resolution frequently less than 0.8 angstrom, the researcher receives a 3D molecular picture of their compound including atomic identity and connectivity. Beyond the structure of the molecule, the researcher can learn about how the molecule packs together and interacts in the crystalline state. The primary charge of the SMXDC facility is to generate data for publication and grant applications. The SMXDC offers many valuable services to accomplish this commitment including:

  • Crystallization consultations. Quality crystals are essential for structure determination and growing them can be difficult. The SMXDC is happy to help and work with individual researchers to grow X-ray diffraction quality crystals.
  • Data collection, processing, and analysis. At the facility we harvest, and mount air-, water-, temperature-, light-sensitive, or solvent-containing crystals and collect data from 80 K - 400 K.
  • Structure determination and display. The SMXDC will solve your raw data and determine molecular structure, including absolute configuration of light-atom structures (we recommend at least one oxygen for every ten carbon atoms). Furthermore, we will work with you to generate images that highlight the significance of your work.
  • Manuscript and grant preparation. Not that familiar with X-ray diffraction? At the SMXDC we are happy to discuss how our services can augment your current research efforts. Consider us a collaborator. If the structure is significant to your manuscript or grant, we are here to help write and communicate this clearly and efficiently to other scientists.
  • Training. Want to learn how to run and operate a single crystal X-ray diffractometer? We provide training for excited and dedicated individuals.
  • Data archival. At your request, we will deposit the final data to the Cambridge Crystallographic Data Center (CCDC) to obtain CCDC numbers (a requirement for most journals). Furthermore, we back up your precious data to a cloud service for those rare unfortunate circumstances.

We are here to collaborate and help augment your research efforts. Communication is critical in science, so please don’t hesitate to contact us; we are here to help! To demonstrate this the following are two examples that highlight the utility of the SMXDC.

The Berryman lab was synthesizing long oligomeric molecules designed to fold into discrete structures (akin to how biopolymers fold into proteins). However, when the group started studying the molecules with conventional techniques (NMR spectroscopy, mass spectrometry, etc.) it was clear something more complicated than folding transpired, leaving them with an enigmatic structure persistent in solution. While contemplating complex NMR experiments to help elucidate the structure, single crystals of the compound were isolated. The SMXDC was able to collect data on these challenging crystals, and to the surprise of everyone, the data revealed that the molecule self-assembles into a rare anion assisted triple helix. This one piece of data has enabled an entirely new research project in the lab and has provided a remarkable example of an anion triple helix for the chemistry community at large.

Another example highlights the utility X-ray diffraction experiments at the SMXDC to determine the absolute configuration of a molecule. The importance of the "handedness" of a molecule is often taught in sophomore organic chemistry and biochemistry. Indeed, the biological function of many molecules is determined by this handedness, and X-ray diffraction provides the unambiguous determination of stereochemistry. The Stierle lab isolates complex organic molecules that are grown by fungi and bacteria that thrive in extreme environments like the Berkeley Pit. One of these compounds preaustinoid A1 and a closely related molecule preaustinoid A, both isolated from the Penicillium fungi, underscore the importance and power of small molecule X-ray diffraction. The structure of Preaustinoid A was reported by another group using molybdenum radiation, inhibiting the ability to determine the absolute configuration of the molecule, however using circular dichroism they claimed a particular atomic configuration. Crystals of the closely related preaustinoid A1 were submitted to the SMXDC and data were collected using copper radiation enabling the absolute structure to be determined. What the SMXDC discovered was that this closely related compound contains the opposite configuration than preaustinoid A, shedding some uncertainty on the reported preaustinoid A structure. This anecdote highlights the power of small molecule X-ray diffraction to determine the absolute stereochemistry of molecules unambiguously.

Looking to the future

The SMXDC plans to continue to grow outreach, teaching, and service in the coming year through new equipment and professional development. The atomic 3D information obtained through the diffraction experiments is widely adaptable to all levels of science. Our outreach efforts will be further enhanced by 3D printing. Through the support of the National Science Foundation (NSF MRI CAREER grant, P.I. Berryman), the Vice President of Research and Creative Scholarship (VPRCS), and Student Instructional Equipment Funds, the SMXDC has brought the first color 3D printer to the University of Montana. This unique and versatile equipment will enhance outreach, teaching, and service at the University of Montana.

As such, we enhanced teaching and integrated crystallography and 3D printed models into the teaching curriculum for the Fall 2019 semester. Organic Chemistry Laboratory classes were augmented with tactile color 3D models printed from the facility. These models were used to teach concepts in chemistry like chirality, symmetry and NMR spectroscopy. Expect to see more color 3D models in a classroom near you!

Professional Development

Graduate student Daniel Decato has already benefited from the unique presence of the X-ray diffractometer at the University of Montana. Having spent countless hours on the instrument, he is the department crystallographer and has proven himself a Guru of X-ray diffraction—a skill he likely wouldn’t have cultivated if he had attended many other institutions. To further enhance his professional development Dan will be attending 2019 American Crystallographic Association annual meeting in Covington, Kentucky, where he will continue to network with leaders in the field of crystallography, participate in software workshops and attend sessions on sustaining crystallography education and training which will augment the SMXDC capabilities at the University of Montana. Dan will also be attending an advanced structure refinement workshop at Clarkson University this summer to advance his skills for handling particularly tricky data sets.

The NIH-CoBRE primarily supports CBSD's SMXDC with additional funding provided by UM’s VPRCS. To enhance the sustainability of the Core, it has operated as a recharge facility with an established fee structure. A fee table for SMXDC service is available at hs.umt.edu/cbsd/facilities/small-molecule/fee-structure.php. As a reminder from our January issue, vouchers (hs.umt.edu/cbsd/facilities/voucher-policy.php) are provided by the VPRCS and CBSD to support users who are unable to provide funding for their use of core facilities to acquire preliminary data that leads to a future publication or grant application. Staff and students from individual research laboratories are encouraged to consult with Dr. Orion Berryman (orion.berryman@umontana.edu) about how core resources can advance their research programs.