3-mer Dynamics

    The temperature dependent ATDs for the M+PET3 oligomers indicate that the folding dynamics involved with the 3-mers are strongly dependent on the metal cation. "Closed" and "open" conformers are theoretically predicted for all M+PET3 but whether each conformer is experimentally observed depends on the metal cation. For Li+PET3, both conformers are experimentally observed from 80 to 550 K. For Na+PET3, the "closed" and "open" conformers are separated at 80 K but rapidly interconvert at 300 K. For K+PET3, the "closed" and "open" conformers could not be separated at 80 K.
    Click on the links below to get more detailed information concerning each metal cation.
    To better understand how the isomerization process between the "closed" and "open" forms depends on the metal cation, molecular dynamics simulations were run for Li+PET3, Na+PET3, and K+PET3. In each case, the simulations were started with the more stable "closed" form at a temperature of 200 K. The dynamics were run for 1000 ps with structures saved every 1 ps. At the end of the dynamics run, the temperature was increased 100 K and the process repeated. The calculations were stopped at 900 K for Li+PET3 and 800 K for Na+PET3 and K+PET3. For each saved structure, the distance between the metal cation and the carbonyl oxygen nearest the end of the oligomer was measured. M+-O distances of <3 Å indicate that the structure is in a "closed" conformation while M+-O distances of >7 Å indicate the structure is in an "open" conformation. Shown below are the resulting plots of M+-O distance vs. time and temperature for Li+PET3, Na+PET3, and K+PET3.

     Theory predicts that isomerization between the "closed" and "open" forms does not occur for any of the M+PET3 oligomers until 500 K. However, the ion mobility experiments indicate that the Na+PET3 and K+PET3 oligomers are isomerizing between 80 and 300 K. The reason for the difference is most likely due to the time scale. The experimental ATDs are measured over hundreds of microseconds while the dynamics calculations are only run for several nanoseconds.
     Li+PET3 is the last to isomerize and "opens up" about 600 ps into the 600 K run. The structure remains "open" throughout the rest of the dynamics run with a few brief exceptions. Na+PET3 begins to isomerize about 900 ps into the 500 K run. Once the isomerization occurs, the structure remains in an "open" or "closed" conformation for about 1000 ps. K+PET3 isomerizes the earliest, about 400 ps into the 500 K run, and converts much more frequently between "open" and "closed" forms than Na+PET3 or Li+PET3.
     The general trend observed in the dynamics simulations tracks nicely with the trend observed in the experimental data: the rate of isomerization increases in the order Li < Na < K. The "closed" and "open" forms of Li+PET3 are separated in the drift cell under all temperatures, indicating the isomerization barrier between the two conformers must be relatively high. Na+PET3 has a small but noticeable isomerization barrier as the "closed" and "open" forms rapidly interconvert at 300 K but are separated in the 80 K ATDs. K+PET3 has the lowest barrier, as the "closed" and "open" forms cannot be separated, even at 80 K.