Mark Ingratta

Effect of Side-chain Length on the Side-chain Dynamics of α-Helical Poly(l-glutamic acid) as Probed by a Fluorescence Blob Model

Two series of pyrene-labeled poly(glutamic acid) (Py-PGA) were synthesized utilizing two different linkers for pyrene attachment, namely 1-pyrenemethylamine (PMA) and 1-pyrenebutylamine (PBA). Several Py-PGAs were synthesized for each series with pyrene contents ranging from 4 to 15 mol %. Py-PGA forms a rigid alpha-helix in DMF that effectively locks the backbone in place, thus enabling only side-chain or linker motions to be monitored by time-resolved fluorescence. Time-resolved fluorescence decays were acquired for the pyrene monomer of the Py-PGA constructs and the fluorescence blob model (FBM) was used to quantify the dynamics of the different linkers connecting pyrene to the backbone. Nitromethane was used to shorten the lifetime of the pyrene monomer, in effect controlling the probing time of the pyrene group, from 50 to 155 ns for PGA-PBA and from 50 to 215 ns for PGA-PMA. The FBM analysis of the fluorescence decays led to the conclusion that excimer formation around the rigid alpha-helix backbone takes place in a compact environment. The number of glutamic acid units within a blob, N blob, decreased only slightly with decreasing probing time for both Py-PGA constructs as a result of the compact distribution of the chromophores around the alpha-helix. The PGA alpha-helix was modeled using Hyperchem software and the ability of two pyrene groups to encounter was evaluated as they were separated by increasing numbers of amino acids along the alpha-helix. The number of amino acids required for two pyrenes to lose their ability to overlap and form excimer matched closely the N blob values retrieved using the FBM.

Effect of time on the rate of long range polymer segmental intramolecular encounters.

The kinetics of encounters between the pyrene pendants randomly attached along a polystyrene chain (Py-PS) were monitored with a fluorescence blob model (FBM) as an external quencher was added to the solution to decrease the lifetime of the excited pyrene. The fluorescence decays acquired with the Py-PS samples yielded a measure of the volume Vblob probed by an excited pyrene during its lifetime in the form of N0blob, the number of monomers found within Vblob, and K0blob, which is inversely proportional to Vblob. Both N0blob and K0blob(-1) were found to increase with increasing probing time as the excited pyrene was allowed to probe a larger Vblob volume. The rate constant for pyrene-pyrene encounters was obtained from the product (KblobNblob). (KblobNblob) was found to decrease with increasing probing time, in agreement with scaling arguments suggesting that, as the probing time increases, the exited pyrene probes a larger Vblob where the local concentration of ground-state pyrenes in the polymer coil, [Py]loc, is smaller. K0blob, which is inversely proportional to Vblob, was found to scale as N0blob(alpha), where alpha equaled -1.5 and -1.2 in DMF and THF, respectively. The alpha exponents found for the Py-PS samples are in the same range as those found for other polymers exhibiting a random polymer coil conformation in solution and where much smaller than those obtained with more compact structured alpha-helical polypeptides randomly labeled with pyrene. Master curves were also constructed that describe how K0blob and the product (KblobNblob) scale as a function of solvent viscosity, probing time, and N0blob. These scaling laws illustrate the opposite effects that probing time and viscosity have on N0blob, V0blob, and the product (KblobNblob).