Everything that living things do can be understood in terms of the jigglings and wigglings of atoms (R.P. Feynman)
Part of the Molecular Photonics group investigates the structure and dynamics ("jigglings and wigglings") of complex molecular systems by means of vibrational spectroscopy, in particular time-resolved and two-dimensional infrared (2D-IR) spectroscopy. The investigated molecular systems include
In all of these systems, the molecular motions take place on many time scales, ranging from less than a picosecond to microseconds and longer. Structural dynamics taking place on such vastly different time scales are difficult to investigate with conventional structure-resolving methods, but can be probed directly using time-resolved vibrational spectroscopy.
Active matter (ensembles of particles that consume energy in order to move or exert force) often behaves very differently from normal matter. Using a sample that we bought in the pet shop on a Friday afternoon, we found that active "polymers" show unique phase-separation and shear-thinning behaviour.
Many proteins are located at interfaces for their biofunctionality, which makes them problematic to study with conventional methods. Infrared sum-frequency generation provides the solution.
A shuttling rotaxane synthesized by the group of Fred Brouwer uses a clever harpooning mechanism to speed up the translational motion. Matthijs Panman measured the speed using time-resolved vibrational spectroscopy.
Why are some polyethers (such as POM, used to make Keck clips) completely insoluble in water, whereas others are perfectly miscible? A combination of spectroscopy experiments and computer simulations reveals the answer.
Using two-dimensional infrared spectroscopy, Joen Hermans has unravelled the structures of the zinc complexes involved in the degradation of zinc-white oil paint (used by Vincent van Gogh and other painters of his day). Joen's results shed new light on the humidity sensitivity of oil-paint ageing.
The isotope-dependent response of salt solutions to oscillating electrical fields shows that water molecules surrounding ions behave in a less cooperative way than they do in bulk water. These findings lead to an update of the theory for the dielectric response of salt solutions developed by Nobel Laureate Onsager and his co-worker Hubbard, and enable a reliable determination of hydration numbers, which play a key role in chemistry and biophysics.
Using a combination of calorimetry, molecular dynamics simulations and infrared spectroscopy, we investigated a liquid-liquid transition in supercooled aqueous solution.
Science 359, 1127 (2018) (freely accessible PDF)
The Making Of. The story of how this cooperation started, why supercooled water does not freeze, and what happened during the experiments is told in Sander Woutersen’s inaugural lecture:
Highlights about this article:
A molecular machine fueled by light and operating like the crankshaft and pedals of a bicycle. With infrared pulses you can see it working in real time.
Transient two-dimensional infrared spectroscopy makes it possible to observe the structural changes of a translational molecular machine during its operation.
The pathogenesis of Parkinson's disease is believed to involve the self-assembly of alpha-synuclein into amyloid fibrils. Surprisingly, when its last 32 amino acid are truncated alpha-synuclein forms much more strongly twisted fibrils.
Everyone knows that plants and animals consist mostly of water. Does this water behave the same as normal tap water? To find out, we used time-resolved vibrational spectroscopy and dielectric-relaxation spectroscopy.
The absolute orientation of interfacial proteins can be determined using phase-resolved sum frequency generation spectroscopy in combination with molecular dynamics simulations and spectral calculations.
A combination of interfacial spectroscopy with spectral calculations reveals the molecular properties of extremely water-repelling hydrophobin films.
The protein alpha-synuclein forms fibrillar aggregates that play a key role in the pathogenesis of Parkinson's disease. The morphology of the fibrils changes dramatically depending on the amount of salt in the surrounding buffer. 2D-IR spectroscopy reveals the underlying molecular mechanism.
Time-resolved experiments on the molecular motor of Nobel laureate Ben Feringa show that its operation cycle involves an electronic 'dark state' that results in a small but important stutter in the rotational motion.
Water containing antifreeze (glycerol) can be cooled down all the way to -100°C without freezing. At that temperature, the liquid undergoes a phase transition and changes into… another liquid?! 2DIR Spectroscopy reveals what is going on at the molecular level.
The Homogeneous Catalysis group of HIMS has achieved highly efficient hydrogen production using a synthetic catalyst that mimics the design of the iron-iron hydrogenase enzyme. The unique redox behavior of the catalyst was unraveled using time-resolved IR spectroscopy.
Review article by Sergio Domingos highlighted on the cover:
Guanidinium is a commonly used denaturant, but the mechanism by which it unfolds proteins is still largely unknown. We find that guanidinium disrupts the folded conformation by breaking salt bridges. 2D-IR spectroscopy shows that guanidinium binds to the carboxylate side groups involved in these salt bridges.
Adding a ferrocene-based electrochemically switchable amplifier to a biomolecular system enables localized amplification of vibrational circular dichroism, making it possible to probe chirality in a site-specific manner.
Ultrafast IR spectroscopy combined with molecular dynamics simulations shows that hydrogen-bonded liquids such as ethanol and N-methylacetamide are less 'random' that you might think.
The vibrational circular dichroism of amino acids and oligopeptides can be enhanced by up to 2 orders of magnitude by coupling them to a paramagnetic metal ion.
Salt-bridge geometries can be determined by measuring the couplings between vibrations of the salt-bridged moieties using 2D-IR spectroscopy.
Salt bridges speed up or slow down folding, depending on the distance and orientation of the salt-bridge-forming residues. This suggest an explanation for the surprising fact that many biologically active proteins contain salt bridges that do not stabilize the native conformation: these salt bridges might have a kinetic rather than a thermodynamic function.