Matthijs R. Panman

Operation mechanism of a molecular machine revealed using time-resolved vibrational spectroscopy

Not So Random Walk In rotaxanes, a molecular ring can shuttle back and forth between docking sites along an axle. Panman et al. (p. 1255) traced the intricacies of this shuttling motion using vibrational spectroscopy. The kinetics were dominated by the slow scission of hydrogen bonds tying the ring to its starting site. Varying the length of the axle allowed the extraction of relative rates for forward and backward motion once the ring was free: Somewhat surprisingly, forward motion toward the destination site was slightly hindered relative to regression toward the starting place. Measuring the travel of a molecular ring along an axle explains its shuttling motion. Rotaxanes comprise macrocycles that can shuttle between docking stations along an axle. We explored the nanosecond shuttling mechanism by reversing the relative binding affinities of two stations through ultraviolet-induced transient reduction. We monitored the ensuing changes in the CO-stretching bands of the two stations and the shuttling macrocycle by means of an infrared probing pulse. Because hydrogen-bond scission and formation at the initial and final stations led to well-resolved changes in the respective CO-stretch frequencies, the departure and arrival of the macrocycle could be observed separately. We found that the shuttling involves two steps: thermally driven escape from the initial station, followed by rapid motion along the track ending either at the initial or final station. By varying the track’s length, we found that the rapid motion approximates a biased one-dimensional random walk. However, surprisingly, the direction of the overall motion is opposite that of the bias.

Two-dimensional vibrational spectroscopy of rotaxane-based molecular machines

It has recently become possible to synthesize mechanical devices the size of a single molecule. Although it is tempting to regard such molecular machines as nanoscale versions of their macroscopic analogs, many notions from macroscopic mechanics no longer apply at a molecular level. For instance, the concept of viscous friction is meaningless for a molecular machine because the size of the solvent molecules that cause the friction is comparable to that of the machine itself. Furthermore, in many cases, the interactions between a molecular machine and its surroundings are comparable to the force driving the machine. As a result, a certain amount of intrinsic randomness exists in the motion of molecular machines, and the details of their mechanics are largely unknown. For a detailed understanding of the mechanical behavior of molecular machines, experiments that probe their motion on an ultrafast time scale, such as two-dimensional (2D) vibrational spectroscopy, are essential. This method uses coupling between vibrational modes in a molecule to investigate the molecular conformation. The coupling shows up as off-diagonal peaks in a 2D graph of the vibrational response of the molecule, analogous to the spin coupling observed in multidimensional NMR spectroscopy. Both spin coupling and vibrational coupling are sensitive probes of the molecular conformation, but 2D vibrational spectroscopy shows orders of magnitude better time resolution than NMR. In this Account, we use 2D vibrational spectroscopy to study molecular machines based on rotaxanes. These devices consist of a linear thread and a macrocycle that is noncovalently locked onto the thread. In the rotaxanes we study, the macrocycle and the thread both contain CO and NH groups. By determining the coupling between the stretching modes of these goups from the cross peaks in the 2D spectrum, we directly and quantitatively probe the relative position and orientation of the macrocycle and the thread for both a small model rotaxane and a rotaxane-based molecular shuttle. Our results demonstrate the feasibility of using time-resolved 2D-IR experiments to measure externally triggered structural changes of molecular devices with subpicosecond time resolution. We can observe each of the elementary events that underlie the mechanical motion separately. With this ability to investigate the nature of the mechanical motions at the molecular level and with unprecedented time resolution, we expect that 2D-IR spectroscopy on molecular machines will lead to new insights into their function.

Structure and dynamics of water in nonionic reverse micelles: A combined time-resolved infrared and small angle x-ray scattering study

We study the structure and reorientation dynamics of nanometer-sized water droplets inside nonionic reverse micelles (water/Igepal-CO-520/cyclohexane) with time-resolved mid-infrared pump-probe spectroscopy and small angle x-ray scattering. In the time-resolved experiments, we probe the vibrational and orientational dynamics of the O-D bonds of dilute HDO:H(2)O mixtures in Igepal reverse micelles as a function of temperature and micelle size. We find that even small micelles contain a large fraction of water that reorients at the same rate as water in the bulk, which indicates that the polyethylene oxide chains of the surfactant do not penetrate into the water volume. We also observe that the confinement affects the reorientation dynamics of only the first hydration layer. From the temperature dependent surface-water dynamics, we estimate an activation enthalpy for reorientation of 45 ± 9 kJ mol(-1) (11 ± 2 kcal mol(-1)), which is close to the activation energy of the reorientation of water molecules in ice.

Guanidinium‐Induced Denaturation by Breaking of Salt Bridges

Despite its wide use as a denaturant, the mechanism by which guanidinium (Gdm(+) ) induces protein unfolding remains largely unclear. Herein, we show evidence that Gdm(+) can induce denaturation by disrupting salt bridges that stabilize the folded conformation. We study the Gdm(+) -induced denaturation of a series of peptides containing Arg/Glu and Lys/Glu salt bridges that either stabilize or destabilize the folded conformation. The peptides containing stabilizing salt bridges are found to be denatured much more efficiently by Gdm(+) than the peptides containing destabilizing salt bridges. Complementary 2D-infrared measurements suggest a denaturation mechanism in which Gdm(+) binds to side-chain carboxylate groups involved in salt bridges.

Communication: Nanosecond folding dynamics of an alpha helix: Time-dependent 2D-IR cross peaks observed using polarization-sensitive dispersed pump-probe spectroscopy

We present a simple method to measure the dynamics of cross peaks in time-resolved two-dimensional vibrational spectroscopy. By combining suitably weighted dispersed pump-probe spectra, we eliminate the diagonal contribution to the 2D-IR response, so that the dispersed pump-probe signal contains the projection of only the cross peaks onto one of the axes of the 2D-IR spectrum. We apply the method to investigate the folding dynamics of an alpha-helical peptide in a temperature-jump experiment and find characteristic folding and unfolding time constants of 260 ± 30 and 580 ± 70 ns at 298 K.

Exchanging conformations of a hydroformylation catalyst structurally characterized using two-dimensional vibrational spectroscopy.

Catalytic transition-metal complexes often occur in several conformations that exchange rapidly (<ms) in solution so that their spatial structures are difficult to characterize with conventional methods. Here, we determine specific bond angles in the two rapidly exchanging solution conformations of the hydroformylation catalyst (xantphos)Rh(CO)2H using two-dimensional vibrational spectroscopy, a method that can be applied to any catalyst provided that the exchange between its conformers occurs on a time scale of a few picoseconds or slower. We find that, in one of the conformations, the OC-Rh-CO angle deviates significantly from the canonical value in a trigonal-bipyramidal structure. On the basis of complementary density functional calculations, we ascribe this effect to attractive van der Waals interaction between the CO and the xantphos ligand.