Identifying the structure of molecules remains a key challenge within modern chemistry. In many cases, a molecule’s structure has a huge influence on both its chemical and biological activities. For example, carvone, a molecule found in many essential oils and fragrances, can either smell like caraway seeds or spearmint, depending on the orientation of one of the chemical substituents in the molecule. While the two forms of carvone are identical in their atomic composition, it is the physical orientation of one of the groups in the molecule that determines which receptors interact within the human nose and ultimately, how we perceive the smell.
There are still very few experimental techniques capable of identifying molecular structures, particularly in the solution phase. X-ray crystallography is probably the most famous structural identification technique, with the 1964 and 1962 Nobel Prizes in Chemistry both being awarded to work determining the structure of biochemical substances including vitamin B12 and globular proteins, respectively. However, X-ray crystallography relies on forming a solid, crystalline sample, often technically challenging and not always representative of the environment in which a compound exists in vivo. It was not until advancements in nuclear magnetic resonance (NMR) in the 1970s that it was possible to capture information on the structure of molecules in solution.
The underlying physics of nuclear magnetic resonance (NMR) spectroscopy is more widely appreciated in the form of magnetic resonance imaging (MRI), a technique used in hospitals to image organs and diagnose diseases. In chemistry, rather than identifying the type of tissue, NMR can be used to identify the chemical groups found in a molecule and their relative connectivities. NMR signals can be translated into chemical structures for a wide variety of molecules, from small molecules to large proteins, either as solids or liquids.
Professor Anthony Serianni at the University of Notre Dame is an expert in utilising modern NMR techniques and computational approaches to identify the structures and reactivities of carbohydrates and nucleic acids. One of his approaches is to use ‘isotopic labelling’ to make it easier to differentiate between different regions of these large complex biomolecules. This technique has been so successful that it has been commercialised by his company, Omicron Biochemicals Inc., which provides services to researchers around the world.
Professor Anthony Serianni at the University of Notre Dame is an expert in utilising modern isotope-based NMR techniques and computational approaches
Saccharides are a large family of molecules, including sugars, starch and cellulose, made mostly from carbon, oxygen and hydrogen. Saccharides are also known as carbohydrates and are ubiquitous in the biological world. Understanding their chemical structures is often key to understanding how they will bind and interact with the receptors in the human body, shaped in such a way that only molecules with complementary structures are able to fit.
The highly complex structures of many saccharides make standard NMR techniques very challenging to use. Professor Serianni’s group has found a way to overcome this limitation by developing a range of new methods capable of introducing isotopic labels into specific sites in the compounds. An isotope is a version of a chemical element that has a different number of neutrons that, in an NMR experiment, acts as a unique flag for the labelled element in the compound. This is very powerful when looking at chemical reactions, as it is possible to follow the position of the label during the reaction to identify the structures of intermediates and end-products.
While introducing isotopic labels is a powerful tool to gain more structural information on molecules by NMR, introducing isotopes is a challenging problem, spanning both synthetic and biological chemistry. Fortunately, Professor Serianni and his team have developed a suite of methods that have transformed the possibilities for the types of compounds that can be precisely isotopically labelled at single sites, multiple sites, or uniformly labelled.
These approaches are currently being used to tackle fundamental chemical problems in the Notre Dame laboratory – the same research location that led to the development and expansion of Omicron Biochemicals, Inc. The work done in the Omicron research facility is somewhat different though, instead focusing exclusively on saccharide isotopic synthesis using chemical, biochemical and biological methods. This work has had an enormous impact worldwide, enabling other researchers to purchase isotopically-labelled compounds for use in their own work.
The University of Notre Dame and Omicron Inc. work in parallel, utilising complementary approaches to push the limits of isotopic labelling and the applications of labelling to solving important problems in chemistry and biochemistry
The labs at both Notre Dame and Omicron now work in parallel, utilising different approaches to push the limits of isotopic labelling and the applications of labelled saccharides to address chemical, biochemical and biomedical problems. Without this synergistic effort, tackling fundamental problems encountered in saccharide isotope labelling would have been difficult, and the core technologies underpinning Omicron would never have been developed or would have been developed more slowly.
In the future, Professor Serianni is optimistic that the innovative approaches pioneered in the Notre Dame Lab will lead to new spin-out companies able to exploit these findings and apply them to solve specific problems that impact human health and well-being.
What are the most important molecular structures you have been able to elucidate using your techniques?
- O-glycosidic linkages in oligosaccharides;
- exocyclic hydroxymethyl group conformation;
- N-acetyl side-chain conformation;
- O-acetyl side-chain conformation;
- hydroxyl group conformation; and
- furanose and pyranose ring conformation.
We have been frustrated with conventional NOE-based and simple J-based methods to characterise these behaviours because they often lead to generally unsatisfying solutions. This situation has led to an over-reliance on MD simulation and related methods to assess these behaviours, yet experimental validation of MD is weak. We contend that a more holistic treatment of NMR J-couplings, which are highly abundant in saccharides, is a potential solution to this problem, and recent studies using circular statistics in conjunction with DFT appear to provide conformational models that can be compared directly to those derived from MD. One of our core research goals is to parameterise all biologically relevant O-glycosidic linkages to enable studies of their conformational behaviours in simple and complex structures. This work hinges on the ability to label target molecules with 13C at one or more sites to allow measurements of JCC values. Recent expansions of this approach to studies of furanosyl rings, such as those found in DNA and RNA, appear promising; this work transcends typical HH analyses, as first applied by Altona, Sundaralingam and others, and offers the potential to characterise their conformational equilibria in greater detail and with greater reliability than has been possible for the past 40 years.
What are the big challenges ahead in 3D structural determination?
What are some of the advantages of using NMR for structural determination?
Did you face any difficulties creating this spin-out company from your fundamental university-based research?
- There was a void in the scientific community that the company filled by widening the range of compounds that could be labelled in an affordable manner and on scales that enabled diverse applications;
- the company serves as a key research resource for academic studies at Notre Dame that require access to labelled compounds, without which the projects would be difficult if not impossible to undertake in a timely manner.
Any success I may have achieved in academic research I attribute in significant measure to the unique opportunities offered by Omicron as a partner in the work.
Do you think it will become more common in the future to see spin-out companies developing from university research groups?