Chemistry and Biochemistry


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            General Background.  In research funded by the National Science Foundation’s Division of Chemistry, our group uses one of the most powerful types of mass spectrometry (Fourier transform ion cyclotron resonance mass spectrometry, FTICR/MS, Figure 1), combined with molecular modeling using high-end supercomputers, to develop methods for characterizing molecule-sized devices (the field for which the 2016 Nobel Prize in Chemistry was awarded).  One technique we have recently developed provides a new way for determining the conformations of molecules in the gas phase using very tiny samples.

Figure 1.  2006 Ph.D. graduate Haizhen Zhang stands in front of the 4.7 Tesla FTICR in the Dearden laboratory.


Molecular nanotechnology,1 the development and application of devices of nanometer size built from single molecules or supramolecular assemblies of a few molecules, is one of the most promising new areas of 21st century research. Most researchers in the nanotechnology area have taken the approach of making existing devices smaller (for example, decreasing the size of transistors used in microchips) or of carrying out existing processes on a smaller scale (for instance, using shorter wavelength radiation to scale down photolithography).  Another approach, one favored by nature, is to redesign the devices using the smallest possible components, atoms and molecules.  The feasibility of this approach is demonstrated in biology; biological systems use extensive molecule-based “nanotechnology,” with DNA acting as a molecular information storage device and various proteins serving as molecular machines.  Many labs around the world are now working to improve on nature by designing new molecular machines that usually consist of a number of smaller molecules held together by weak, non-covalent interactions to form a nanodevice that is a supramolecular complex.

With the push to design and synthesize artificial nanodevices comes an urgent need to develop techniques for characterizing them.  The general goal of our group is to develop new mass spectrometric tools for the sensitive, accurate characterization of fragile supramolecules.  These same tools are also useful for characterizing nature’s supramolecular machines, biomolecular systems.  Along the way, we take advantage of the isolated molecule conditions available inside a mass spectrometer to gain information that would be difficult or impossible to obtain in condensed media.

Much of our recent work has focused on pumpkin-shaped molecules, called cucurbiturils,2 that have hollow cavities inside which other molecules can be trapped (Figure 2).  We have learned to assemble and disassemble these molecular containers, and have found that the rates of these processes are influenced by the not-so-inert contents of the container.3  We have also developed mass spectrometric tests to distinguish between complexes that have one molecule threaded through another, like a string through a bead, and isobaric isomers that are not threaded.4-5 Some of these supramolecular self-assembling molecular complexes might someday become important parts of nanoscale computers or assemblers (Figure 2). 

Figure 2. 1,4-Phenylenediammonium (space filling) bound inside cucurbit[6]uril (tubes). High level ab initio theory is in agreement with experimental results suggesting the other phenylenediamine isomers do not fit inside this ligand.  Structures like these, called “rotaxanes,” are proposed as key components of nano-scale computers and assemblers. machines.

Although mass spectrometry works superbly for measuring molecular weights, specialized methods are required for measuring molecular shapes. The premier technique for doing this is drift ion mobility spectrometry, which measures molecular collision cross sections that can be used to distinguish between different possible shapes. We have used this technique to characterize several cucurbituril-based prototypical molecular machines.6-7  However, drift ion mobility experiments require a specialized instrument. Hence, we have developed a new technique that measures molecular collision cross sections by analyzing the pressure-limited decay of FTICR signal (Figure 3). Originally, we showed our new method, which we call CRAFTI (an acronym for cross sectional areas by Fourier transform ion cyclotron resonance), correlates well with drift ion mobility results.8  We also realized that our method could be run “backward” as a new way to measure neutral gas pressures under high vacuum conditions.9  More recently we analyzed all 20 of the biogenic amino acids (the pieces from which proteins are built) to show that CRAFTI gives useful structural insights.10 Because CRAFTI experiments can be performed over a range of collision energies,11 we are optimistic that we can gain new insights that are not possible with methods that are limited to low collision energies.

Figure 3. CRAFTI measures collision cross sections by examining FTICR signal decay.


1.         Newton, D. E., Recent Advances and Issues in Molecular Nanotechnology. Greenwood Press: Westport, CT, 2002; p 306.

2.         Mock, W. L., Cucurbituril. In Comprehensive Supramolecular Chemistry, Vögtle, F., Ed. Elsevier: New York, 1996; Vol. 2, pp 477-493.

3.         Kellersberger, K. A.; Anderson, J. D.; Ward, S. M.; Krakowiak, K. E.; Dearden, D. V., Encapsulation of N2, O2, Methanol, or Acetonitrile by Decamethylcucurbit[5]uril(NH4+)2 Complexes in the Gas Phase: Influence of the Guest on 'Lid' Tightness. J. Am. Chem. Soc. 2001, 123 (45), 11316-11317.

4.         Zhang, H.; Paulsen, E. S.; Walker, K. A.; Krakowiak, K. E.; Dearden, D. V., Cucurbit[6]uril Pseudorotaxanes:  Distinctive Gas Phase Dissociation and Reactivity. J. Am. Chem. Soc. 2003, 125 (31), 9284-9285.

5.         Zhang, H.; Ferrell, T. A.; Asplund, M. C.; Dearden, D. V., Molecular Beads on a Charged Molecular String: α,ω-Alkyldiammonium Complexes of Cucurbit[6]uril in the Gas Phase. Int. J. Mass Spectrom. 2007, 265 (1-3), 187-196.

6.         Zhang, H.; Grabenauer, M.; Bowers, M. T.; Dearden, D. V., Supramolecular Modification of Ion Chemistry:  Modulation of Peptide Charge State and Dissociation Behavior through Complexation with Cucurbit[n]uril (n = 5, 6) or α-Cyclodextrin. J. Phys. Chem. A 2009, 113, 1508-1517.

7.         Dearden, D. V.; Ferrell, T. A.; Asplund, M. C.; Zilch, L. W.; Julian, R. R.; Jarrold, M. F., One Ring to Bind Them All:  Shape-Selective Complexation of Phenylenediamine Isomers with Cucurbit[6]uril in the Gas Phase. J. Phys. Chem. A 2009, 113, 989-997.

8.         Yang, F.; Voelkel, J.; Dearden, D. V., Collision Cross Sectional Areas from Analysis of Fourier Transform Ion Cyclotron Resonance Line Width: A New Method for Characterizing Molecular Structure. Anal. Chem. 2012, 84 (11), 4851-4857.

9.         Jones, C. A.; Dearden, D. V., Linewidth Pressure Measurement: a New Technique for High Vacuum Characterization. J. Am. Soc. Mass Spectrom. 2015, 26 (2), 323-329.

10.       Anupriya; Jones, C. A.; Dearden, D. V., Collision Cross Sections for 20 Protonated Amino Acids: Fourier Transform Ion Cyclotron Resonance and Ion Mobility Results. J. Am. Soc. Mass Spectrom. 2016, 27 (8), 1366-1375.

11.       Yang, F.; Jones, C. A.; Dearden, D. V., Effects of Kinetic Energy and Collision Gas on Measurement of Cross Sections by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Int. J. Mass Spectrom. 2015, 378, 143-150.