Pavol Bodis

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.

Beta Sheets with a Twist: The Conformation of Helical Polyisocyanopeptides Determined by Using Vibrational Circular Dichroism

Detailed information on the architecture of polyisocyanopeptides based on vibrational circular dichroism (VCD) spectroscopy in combination with DFT calculations is presented. It is demonstrated that the screw sense of the helical polyisocyanides can be determined directly from the C=N-stretch vibrational region of the VCD spectrum. Analysis of the VCD signals associated with the amide I and amide II modes provides detailed information on the peptide side-chain arrangement in the polymer and indicates the presence of a helical β-sheet architecture, in which the dihedral angles are slightly different to those of natural β-sheet helices.

Vibrational self-trapping in beta-sheet structures observed with femtosecond nonlinear infrared spectroscopy

Self-trapping of NH-stretch vibrational excitations in synthetic beta-sheet helices is observed using femtosecond infrared pump-probe spectroscopy. In a dialanine-based beta-sheet helix, the transient-absorption change upon exciting the NH-stretch mode exhibits a negative absorption change at the fundamental frequency and two positive peaks at lower frequencies. These two induced-absorption peaks are characteristic for a state in which the vibrational excitation is self-trapped on essentially a single NH-group in the hydrogen-bonded NH...OC chain, forming a small (Holstein) vibrational polaron. By engineering the structure of the polymer we can disrupt the hydrogen-bonded NH...OC chain, allowing us to eliminate the self-trapping, as is confirmed from the NH-stretch pump-probe response. We also investigate a trialanine-based beta-sheet helix, where each side chain participates in two NH...OC chains with different hydrogen-bond lengths. The chain with short hydrogen bonds shows the same self-trapping behavior as the dialanine-based beta-sheet helix, whereas in the chain with long hydrogen bonds the self-trapping is too weak to be observable.

Bimodal dynamics of mechanically constrained hydrogen bonds revealed by vibrational photon echoes

We have investigated the dynamics of the hydrogen bonds that connect the components of a [2]rotaxane in solution. In this rotaxane, the amide groups in the benzylic-amide macrocycle and the succinamide thread are connected by four equivalent N-H⋅⋅⋅O=C hydrogen bonds. The fluctuations of these hydrogen bonds are mirrored by the frequency fluctuations of the NH-stretch modes, which are probed by means of three-pulse photon-echo peak shift spectroscopy. The hydrogen-bond fluctuations occur on three different time scales, with time constants of 0.1, 0.6, and ≥200 ps. Comparing these three time scales to the ones found in liquid formamide, which contains the same hydrogen-bonded amide motif but without mechanical constraints, we find that the faster two components, which are associated with small-amplitude fluctuations in the strength of the N-H⋅⋅⋅O=C hydrogen bonds, are very similar in the liquid and the rotaxane. However, the third component, which is associated with the breaking and subsequent reformation of hydrogen bonds, is found to be much slower in the rotaxane than in the liquid. It can be concluded that the mechanical bonding in a rotaxane does not influence the amplitude and time scale of the small-amplitude fluctuations of the hydrogen bonds, but strongly slows down the complete dissociation of these hydrogen bonds. This is probably because in a rotaxane breaking of the macrocycle-axle contacts is severely hindered by the mechanical constraints. The hydrogen-bond dynamics in rotaxane-based molecular machines can therefore be regarded as liquidlike on a time scale 1 ps and less, but structurally frozen on longer (up to at least 200 ps) time scales.

Self-trapped vibrational states in synthetic β-sheet helices

Femtosecond vibrational pump-probe spectroscopy on beta-helical polyisocyanopeptides reveals vibrational self-trapping in the well-defined hydrogen-bonded side groups that is absent when non-hydrogen bonded monomers are mixed in.

Structural dynamics of rotaxanes studied by infrared photon echo spectroscopy

The structural dynamics of a rotaxane is investigated using infrared photon echo peak shift spectroscopy on the N-H stretch vibrational mode. The results demonstrate non-Markovian character of the dynamics of this vibrational mode and an oscillatory component related to the presence of low-frequency modes that are anharmonically coupled to the N-H stretch mode.