Joel Parks

Trapped Ion Dynamics Group


Rowland Senior Fellow
Rowland Institute at Harvard
Harvard University
100 Edwin H. Land Blvd.
Cambridge, MA 02142
Tel: 617-497-4653
Fax: 617-497-4627
Email: parks@rowland.harvard.edu
Website: Trapped Ion Dynamics Group 

Current research projects in the Trapped Ion Dynamics Group are designed to study the structural dynamics of nanoscale gas-phase species including small metal clusters and biomolecules, by making diffraction measurements of metal cluster symmetry and probing using fluorescence the dynamics and interactions of biomolecules.

Selected Publications

  • "Fluorescence probe of polypeptide conformational dynamics in gas phase and in solution", A. T. Iavarone, J. Meinen, S. Schulze, J. H. Parks, Int. J. Mass Spectrom. (2006) in press.
  • "The Structures of Ag55+ and Ag55- Trapped Ion Electron Diffraction and Density Functional Theory", D. Schooss, M. N. Blom, J. H. Parks, B. von Issendorff, H. Haberland, M. M. Kappes, Nano Letters, 5, 1972-1977 (2005).
  • "Size dependent fivefold and icosahedral symmetry in silver clusters", X. Xing, R. M. Danell, I. L. Garzon, K. Michaelian, M. N. Blom, M. M. Burns, and J. H. Parks, Phys. Rev. B, 72, 081405(R) (2005).

For a complete list of publications.

Metal Clusters

Diffraction Measurements of Metal Cluster Symmetry

The study of small metal clusters has made extensive contributions to understanding the size-dependent, many-body character of nanoscale physics and chemistry. Important examples which have increased our appreciation of the different forms in which size dependence is manifest include measurements and calculations of metal cluster melting, the transition of planar to three-dimensional structures and the reactivity of gold cluster nanocatalysts. Measurements conducted in our laboratory investigate the development of cluster structures with size range to develop an understanding of how these structures evolve through intermediate sizes to achieve “magic number” structures composed of closed electronic or atomic shells. The structural symmetries of cluster ions stored within a quadrupole ion trap are probed by electron diffraction as a function of cluster size and temperature [1]. The experimental configuration enables the accumulation of size selected clusters, collisional relaxation of the vibrational energy and adequate exposure time to collect electron diffraction data from ~104 clusters. It is precisely the ability to isolate a single cluster size having a well defined temperature which provides for a controlled investigation of quantum size effects.

Figure 1


Figure 2

The diffraction instrument design shown in Fig. 1 incorporates a rail structure which allows the entire beamline to be extracted from the UHV chamber. The diffraction beamline shown in Fig. 2 is mounted within the UHV chamber and includes an rf trap, Faraday cup and microchannel plate detector configured to maintain a cylindrical symmetry around the electron beam axis. A CCD camera at the UHV window records the detector phosphor screen image of the electron diffraction pattern.


Figure 2

The sputter ion aggregation source shown in Fig. 3 produces metal cluster in the size range 10<n<100, of interest for current experiments. A quadrupole bender directs the cluster beam to a time of flight mass spectrometer to optimize cluster production in a particular size range after which the bender voltages are changed to direct the ion beam to the trap endcap electrode for ion loading.

(CsI)nCs+ Diffraction

Diffraction experiments [2] on (CsI)nCs+ clusters over the size range n=30-39 revealed that all cluster sizes except n=32 display patterns described by the NaCl rock salt structure of simple cubic symmetry. Data for n=32 indicate that contributions to diffraction are dominated by the CsCl structural isomer having bcc symmetry. This cluster size is unique in that it can form a closed shell rhombic dodecahedron corresponding to the CsI bulk bcc structure. The structural transition observed in these experiments was induced by the change of a single molecule, demonstrating both the enhanced stability of closed shell structures and the importance of measurements on a single cluster size. It will be important to push this technique to a level to enable diffraction measurements on small cluster sizes of 10-30 atoms.


Figure 4

Measurements on (CsI)13 Cs+ clusters shown in Fig. 4 indicate the feasibility of extending diffraction to smaller cluster sizes. This figure shows a CCD image of the electron diffraction ring pattern. (a) A plot of the integrated ring intensity as a function of momentum transfer (s) proportional to scattering angle. (b) The molecular diffraction intensity sM(s) extracted from the ring pattern is compared with a calculated intensity assuming a simple cubic (3x3x3) structure.

Metal Cluster Diffraction: Agn+ n=36-55

The study of small metal clusters has made extensive contributions to understanding the size dependent, many-body character of nanoscale physics and chemistry. Important examples which have increased our appreciation of the different forms in which size dependence is manifest include measurements and calculations of metal cluster melting, the transition of planar to three dimensional structures, and the reactivity of gold cluster nanocatalysts. Trapped ion electron diffraction measurements on silver cluster cations present the first measurements of the structure of mass selected metal clusters by trapped ion electron diffraction. Diffraction techniques have been shown to be particularly sensitive to the measurement of size dependent changes in structural symmetry for small clusters. Measurements recently completed investigate the development of silver cluster structures over the size range 36 to 55 atoms to develop an understanding of how cluster structures evolve through intermediate sizes to achieve “magic number” structures composed of closed electronic or atomic shells. These measurements [3] have discovered an evolution from short range order among nearest neighbors having fivefold symmetry to a global order having icosahedral symmetry at n=55. The local fivefold symmetry does not result from the decoration of an inner icosahedral core of 13 atoms having Ih symmetry. Not a single isomer calculated for cluster sizes below n=55, comprising a total of ~40 DFT optimized cluster structures, contains an icosahedral core. The local order in these calculated structures becomes apparent only after symmetry analysis of the cluster structure.

Current Diffraction Measurements

Diffraction measurements of gold cluster anions were performed throughout the cluster size range 11<n<23. This series of anion cluster sizes has been very actively studied, both theoretically and experimentally. Theory predicts a 2D to 3D transition for surprisingly large size (n=13). Gas phase mobility measurements observed a change in cross section which correlated with a calculated structural change from 2D to 3D at n=12-13. Catalytic reactions of adsorbed O2 and CO also has been identified to take place on gold clusters residing on MgO surfaces. CO2 formation at low temperatures (140 K) was found to require the back donation of negative charge. Experiments underway and those planned will investigate the structures, symmetry and catalytic processes on gold anions Aun- in this size range.

Trapped Ion Dynamics Group

Current research projects in the Trapped Ion Dynamics Group are designed to study the structural dynamics of nanoscale gas-phase species including small metal clusters and biomolecules. Please see our Group Page for a list of past and present researchers who have contributed to these projects.



Diffraction Measurements of Metal Cluster Symmetry

The study of small metal clusters has made extensive contributions to understanding the size-dependent, many-body character of nanoscale physics and chemistry. Important examples which have increased our appreciation of the different forms in which size dependence is manifest include measurements and calculations of metal cluster melting, the transition of planar to three-dimensional structures and the reactivity of gold cluster nanocatalysts. Measurements conducted in our laboratory investigate the development of cluster structures with size range to develop an understanding of how these structures evolve through intermediate sizes to achieve “magic number” structures composed of closed electronic or atomic shells. The structural symmetries of cluster ions stored within a quadrupole ion trap are probed by electron diffraction as a function of cluster size and temperature. The experimental configuration enables the accumulation of size selected clusters, collisional relaxation of the vibrational energy and adequate exposure time to collect electron diffraction data from ~104 clusters. It is precisely the ability to isolate a single cluster size having a well defined temperature which provides for a controlled investigation of quantum size effects.

Biomolecule Dynamics and Interactions Probed by Fluorescence

The three-dimensional structures and dynamics of proteins and other biomolecules play a central role in determining their unique functions in living organisms and their specific interactions with other molecules. One major challenge of life science is to grasp how a given sequence of amino acid residues gives rise to the native structure and function. We have developed a probe of the conformational dynamics of unsolvated proteins and peptides that is based on modulation of the fluorescence of a covalently attached dye through intramolecular quenching by tryptophan (Trp) or other residues. These gas-phase measurements are used in combination with solution measurements and theoretical calculations to advance our understanding of how the solvent environment affects the behavior of biomolecules and non-covalent complexes.

Biomolecule Dynamics

Biomolecule Dynamics and Interactions Probed by Fluorescence

The three-dimensional structures and dynamics of proteins and other biomolecules play a central role in determining their unique functions in living organisms and their specific interactions with other molecules. One major challenge of life science is to grasp how a given sequence of amino acid residues gives rise to the native structure and function. We have developed a probe of the conformational dynamics of unsolvated proteins and peptides that is based on modulation of the fluorescence of a covalently attached dye through intramolecular quenching by tryptophan (Trp) or other residues. These gas-phase measurements are used in combination with solution measurements and theoretical calculations to advance our understanding of how the solvent environment affects the behavior of biomolecules and non-covalent complexes.

For the gas-phase experiments, intact, unsolvated biomolecule ions are formed by electrospray ionization (ESI) and transferred into a radio-frequency Paul trap. A particular ion of interest is isolated by ejecting the unwanted ions which occur at lower or higher mass-to-charge ratios from the trap.



The ions under study are then thermalized by collisions with a helium buffer gas. Laser-induced fluorescence is excited by 532 nm light from a frequency-doubled Nd:YAG laser, isolated by bandpass filters, and detected by gallium arsenide photomultipliers.


The excitation and detection optics have been configured to reduce background noise from scattering to nearly zero. Fluorescence with a signal-to-noise ratio of ~ 400 is routinely measured from ~200 ions in a small volume of the trapped ion cloud (~2x10-5 cm3).



This methodology has been applied to Trp-cage, a miniprotein which is fully structured in aqueous solution at low temperatures.1 The fluorescence of Trp-cage 3+ ions is constant between 303 and 363 K and decreases by ~75% between 363 and 438 K.2 The decrease in fluorescence with increasing temperature is consistent with a conformational change which results in more quenching interactions between the Trp side chain and the fluorescent dye.


The associated enthalpy change for this ion is 51% higher than that in solution,3 most likely a consequence of increased intramolecular hydrogen bonding in the absence of solvent. Hydrogen bond donors and acceptors which are solvated by water molecules in solution can form new intramolecular hydrogen bonds upon desolvation.

Molecular dynamics (MD) simulations indicate a decrease in the number of hydrogen bonds with increasing temperature which agrees well with the experimentally derived change in enthalpy.

A salt bridge between lysine, aspartic acid, and arginine (+ - +) is important for Trp-cage stability in solution, however, replacing negatively charged aspartic acid with uncharged asparagine (D9N mutation) does not significantly change the unfolding enthalpy in gas phase. This indicates that the salt bridge is not a major contributor to the conformational stability of these unsolvated ions.4

Measurements5 have also been made of small (≤12 residues) poly(Pro) and poly(Gly-Ser) peptides to isolate the effects of chain length, amino acid composition, and charge on the measured fluorescence. For the 2+ ions, the longer peptides, Pro10 and (GlySer)5, emit higher intensity fluorescence than the corresponding shorter peptides, Pro4 and (GlySer)2, at all temperatures studied. This suggests dynamics which are dominated by Coulomb repulsion between the two positive charges. For singly charged ions, in which Coulomb repulsion is absent, the dynamics appear to be characterized by the backbone flexibility, i.e., poly(Pro) is less flexible than poly(Gly-Ser). MD simulations in progress will provide more detailed information on the polypeptide dynamics which lead to the differences in measured fluorescence.

Ongoing projects aim to use these methods to investigate secondary structure formation and the dynamic interactions between the components of non-covalent complexes formed between peptides and other molecules of biological and/or therapeutic importance.

References cited

  1. Neidigh, J. W.; Fesinmeyer, R. M.; Andersen, N. H. Nat. Struct. Biol. 2002,9, 425.
  2. Iavarone, A. T.; Parks, J. H. J. Am. Chem. Soc. 2005127, 8606.
  3. Qiu, L.; Pabit, S. A.; Roitberg, A. E.; Hagen, S. J. J. Am. Chem. Soc. 2002,124, 12952.
  4. Iavarone, A. T.; Patriksson, A.; Van der Spoel, D.; Parks, J. H. J. Am. Chem. Soc., submitted.
  5. Iavarone, A. T.; Meinen, J.; Schulze, S.; Parks, J. H. Int. J. Mass Spectrom., in press.