Poly (N-isopropylacrylamide) (PNIPAM) is the premier example of a macromolecule that undergoes a hydrophobic collapse when heated above its lower critical solution temperature (LCST). Here we utilize, dynamic light scattering, H-NMR, steady-state and time-resolved UVRR measurements to determine the molecular mechanism of PNIPAM's hydrophobic collapse. Our steady-state results indicate that in the collapsed state the amide bonds of PNIPAM do not engage in inter-amide hydrogen bonding, but are hydrogen bonded to water molecules. At low temperatures, the amide bonds of PNIPAM are predominantly fully water hydrogen bonded, whereas, in the collapsed state one of the two normal C=O hydrogen bonds is lost. The NH-water hydrogen bonding, however, remains unperturbed by the PNIPAM collapse. Our kinetic results indicate a mono-exponential collapse with τ~360 (±85) ns. The collapse rate indicates a persistence length of n~10. At lengths shorter than the persistence length the polymer acts as an elastic rod, whereas, at lengths longer than the persistence length the polymer backbone conformation forms a random coil. Based on these results we propose that at low temperatures PNIPAM adopts an extended, water-exposed conformation that is stabilized by favorable NIPAM-water solvation shell interactions which stabilize large clusters of water molecules. At elevated temperatures, thermal agitation disrupts these interactions. The PNIPAM+water polymer undergoes a volume phase transition, expels water and shrinks to a compact conformation that reduces its hydrophobic solvent accessible surface area. In this compact state, PNIPAM forms small hydrophobic nano-pockets where the (i, i +3) isopropyl groups make hydrophobic contacts. A persistent length of n~10 suggests a cooperative collapse where hydrophobic interactions between adjacent hydrophobic pockets stabilize the collapsed PNIPAM.

Photoinitiation of relaxation of two peptides (labeled 1 and 2) and spectroscopic studies of the ensuing dynamics have led to new information about peptide conformational dynamics. Following photolysis of the aryl disulfide chromophore that constrains a peptide to be distorted from its equilibrium form, the S−S bond is broken in <200 fs, and the liberated thiyl radicals either undergo geminate recombination or diffuse apart to allow the peptides to change conformation. From anisotropy measurements, overall peptide rotation is on the time scale of 600 ps. At an even earlier time (ca. 100 ps), transient IR measurements show a bleaching of the amide I‘ region, arising from a vibrational Stark effect produced upon ring opening of peptide 2. We did not detect any significant shift in the amide I‘ region up to 2 ns, suggesting no significant helix formation in this time domain. Thiyl radicals arising from peptide 2 recombine with a power law rate over the time range from picoseconds to microseconds signaling an unusual type of scaled kinetics.

Nitric oxide myoglobin (MbNO) at 300 K was photodissociated with 405 nm pulses. The NO recombination in several mutants of iron and cobalt myoglobins was investigated at a time resolution of ca. 70 fs. The geminate recombination of NO was nonexponential on sub-nanosecond time scales. For both metals, the change of the detailed structure of the heme pocket (position 68 mutations) caused significant changes in the rates of recombination; however, the metal substitution influenced the recombination much less than did amino acid substitution. The results indicate a primary role of the heme pocket structure in the dynamics, and they suggest that proximal protein relaxation is not the limiting factor in the geminate recombination process. Recombination in cobalt derivatives is somewhat more efficient on the sub-nanosecond time scales than in corresponding iron myoglobins, consistent with other results that show a greater intrinsic reactivity toward the NO of cobalt compared with the iron heme. A comparison of results using Soret band excitation with previous Q-state excitation studies demonstrates that the ligand dissociates with a similar kinetic energy in both cases, suggesting fast intramolecular energy redistribution before dissociation.