Jan Helbing

Watching hydrogen-bond dynamics in a β-turn by transient two-dimensional infrared spectroscopy

X-ray crystallography and nuclear magnetic resonance measurements provide us with atomically resolved structures of an ever-growing number of biomolecules. These static structural snapshots are important to our understanding of biomolecular function, but real biomolecules are dynamic entities that often exploit conformational changes and transient molecular interactions to perform their tasks. Nuclear magnetic resonance methods can follow such structural changes, but only on millisecond timescales under non-equilibrium conditions. Time-resolved X-ray crystallography has recently been used to monitor the photodissociation of CO from myoglobin on a subnanosecond timescale, yet remains challenging to apply more widely. In contrast, two-dimensional infrared spectroscopy, which maps vibrational coupling between molecular groups and hence their relative positions and orientations, is now routinely used to study equilibrium processes on picosecond timescales. Here we show that the extension of this method into the non-equilibrium regime allows us to observe in real time in a short peptide the weakening of an intramolecular hydrogen bond and concomitant opening of a β-turn. We find that the rate of this process is two orders of magnitude faster than the ‘folding speed limit’ established for contact formation between protein side chains.

Picosecond conformational transition and equilibration of a cyclic peptide

Ultrafast IR spectroscopy is used to monitor the nonequilibrium backbone dynamics of a cyclic peptide in the amide I vibrational range with picosecond time resolution. A conformational change is induced by means of a photoswitch integrated into the peptide backbone. Although the main conformational change of the backbone is completed after only 20 ps, the subsequent equilibration in the new region of conformational space continues for times >16 ns. Relaxation and equilibration processes of the peptide backbone occur on a discrete hierarchy of time scales. Albeit possessing only a few conformational degrees of freedom compared with a protein, the peptide behaves highly nontrivially and provides insights into the complexity of fast protein folding.

Double-resonance versus pulsed Fourier transform two-dimensional infrared spectroscopy: An experimental and theoretical comparison

In this study we focus on the differences and analogies of two experimental implementations of two-dimensional infrared (2D-IR) spectroscopy: double-resonance or dynamic hole burning 2D-IR spectroscopy and pulsed Fourier transform or heterodyne detected photon echo spectroscopy. A comparison is done theoretically as well as experimentally by contrasting data obtained from both methods. As an example we have studied the strongly coupled asymmetric and symmetric carbonyl stretching vibrations of dicarbonylacetylacetonato rhodium dissolved in hexane. Both methods yield the same peaks in a 2D-IR spectrum. Within certain approximations we derive an analytic expression which shows that the 2D-IR spectra are broadened in one frequency dimension in the double-resonance experiment by convolution with the pump pulse spectral width, while the spectral resolution in the other frequency direction is the same in both cases.

Compact implementation of Fourier transform two-dimensional IR spectroscopy without phase ambiguity

We describe an optimized setup for two-dimensional (2D) IR spectroscopy, which can be implemented at low additional cost and with standard optics in any laboratory equipped for femtosecond mid-IR spectroscopy. An interferometer produces a pair of intense pump pulses, whose interferogram is simultaneously recorded and directly yields the relative phase needed for the calculation of absorptive 2D spectra. We analyze different sampling methods based on a realistic noise model and introduce fast population time modulation as an alternative to the use of choppers in the suppression of scatter. Signal levels are compared to those of a photon-echo setup.

Coherent control by a single phase shaped femtosecond laser pulse

Abstract Coherent control of molecular multiphoton ionization by a single phase shaped femtosecond laser pulse is reported. Electron and ion spectra of the sodium dimer are recorded in a molecular beam experiment and both show a strongly chirp- and pulse-length-dependent behavior. The measured spectra reveal that although for one chirp direction the population in all intermediate molecular states may be higher, the opposite chirp leads to a higher ionization yield. In addition, a strongly chirp-dependent photoionization of atomic sodium is observed.

An artificial molecular switch that mimics the visual pigment and completes its photocycle in picoseconds

Single molecules that act as light-energy transducers (e.g., converting the energy of a photon into atomic-level mechanical motion) are examples of minimal molecular devices. Here, we focus on a molecular switch designed by merging a conformationally locked diarylidene skeleton with a retinal-like Schiff base and capable of mimicking, in solution, different aspects of the transduction of the visual pigment Rhodopsin. Complementary ab initio multiconfigurational quantum chemistry-based computations and time-resolved spectroscopy are used to follow the light-induced isomerization of the switch in methanol. The results show that, similar to rhodopsin, the isomerization occurs on a 0.3-ps time scale and is followed by <10-ps cooling and solvation. The entire (2-photon-powered) switch cycle was traced by following the evolution of its infrared spectrum. These measurements indicate that a full cycle can be completed within 20 ps.

Protein ligand migration mapped by nonequilibrium 2D-IR exchange spectroscopy

2D-IR exchange spectroscopy has been introduced recently to map chemical exchange networks in equilibrium with subpicosecond time resolution. Here, we demonstrate the generalization of 2D-IR exchange spectroscopy to nonequilibrium systems and its application to map light-triggered migration of ligands between different sites in a protein. Within picoseconds after a photodissociating laser pulse, carbon monoxide ligands relocate from their binding site A at the heme prosthetic group of myoglobin to a primary docking site B in the distal heme pocket. Multiple CO stretching bands are observed for the CO ligand in sites A and B, indicating that several distinct conformational substates of the myoglobin:ligand complex coexist in solution. Exchange cross-peaks between the bands associated with substates of heme-bound CO and photodissociated CO in the primary docking site reveal the substate connectivity at physiological temperature.

Folding and unfolding of a photoswitchable peptide from picoseconds to microseconds

Using time-resolved IR spectroscopy, we monitored the kinetics of folding and unfolding processes of a photoswitchable 16-residue alanine-based α-helical peptide on a timescale from few picoseconds to almost 40 μs and over a large temperature range (279–318 K). The folding and unfolding processes were triggered by an ultrafast laser pulse that isomerized the cross linker within a few picoseconds. The main folding and unfolding times (700 ns and 150 ns, respectively, at room temperature) are in line with previous T-jump experiments obtained from similar peptides. However, both processes show complex, strongly temperature-dependent spectral kinetics that deviate clearly from a single-exponential behavior. Whereas in the unfolding experiment the ensemble starts from a well defined folded state, the starting ensemble in the folding experiment is more heterogeneous, which leads to distinctly different kinetics of the experiments, because they are sensitive to different regions of the energy surface. A qualitative agreement with the experimental data-set can be obtained by a model where the unfolded states act as a hub connected to several separated “misfolded” states with a distribution of rates. We conclude that a rather large spread of rates (k1 : kn ≈ 9) is needed to explain the experimentally observed stretched exponential response with stretching factor β = 0.8 at 279 K.

Transient two-dimensional infrared spectroscopy: Exploring the polarization dependence

We present a general expression for the polarization dependence of transient two-dimensional IR spectroscopy (T2D-IR), a technique designed to measure 2D-IR spectra of transient species. T2D-IR is a UV pump narrowband-IR-pump broadband-IR-probe experiment of fifth order in the laser field which involves up to three different transition dipole moments. The UV pulse adds an additional degree of freedom in polarization as compared to 2D-IR spectroscopy and increases the versatility of signal manipulation and the potential structural information content of the signals. The polarization conditions leading to a maximum of structural information are discussed. Important special cases of polarization conditions are formulated. The application of polarization selectivity is demonstrated for different types of T2D-IR experiments on photo triggered metal-to-ligand charge transfer in the model system [Re(CO)(3)(dmbpy)Cl].

Hydration Dynamics of Aqueous Nitrate

Aqueous nitrate, NO3(-)(aq), was studied by 2D-IR, UV-IR, and UV-UV time-resolved spectroscopies in combination with molecular dynamics (MD) simulations with the purpose of determining the hydration dynamics around the anion. In water, the D3h symmetry of NO3(-) is broken, and the degeneracy of the asymmetric-stretch modes is lifted. This provides a very sensitive probe of the ion-water interactions. The 2D-IR measurements reveal excitation exchange between the two nondegenerate asymmetric-stretch vibrations on a 300-fs time scale concomitant with fast anisotropy decay of the diagonal-peak signals. The MD simulations show that this is caused by jumps of the transition dipole orientations related to fluctuations of the hydrogen bonds connecting the nitrate ion to the nearest water molecules. Reorientation of the ion, which is associated with the hydrogen-bond breaking, was monitored by time-resolved UV-IR and UV-UV spectroscopy, revealing a 2-ps time constant. These time scales are very similar to those reported for isotope-labeled water, suggesting that NO3(-)(aq) has a labile hydration shell.