Time-Resolved Vibrational Spectroscopy

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 time-resolved vibrational spectroscopy, in particular by means of two-dimensional infrared (2D-IR) spectroscopy. The investigated molecular systems include

  • catalytic transition-metal complexes
  • peptides and proteins
  • molecular machines
  • liquid water and aqueous solutions

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.



Two kinds of deeply supercooled water

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) (PDF, freely accessible)

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:

Online video of the lecture (in Dutch)

Highlights about this article:

"Scientists Watch Water Change Phase From a Liquid... to a Liquid" (Gizmodo)

Highlight on the UvA website

Article in Folia (in Dutch)

Article in Chemistry World

Highlight on the ASU website

Molecular bicycle pedals

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.

Angew. Chem. Int. Ed.  57, 1792 (2018)

Highlight on the UvA website

A new twist to amyloid fibrils

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.

J. Am. Chem. Soc. DOI: 10.1021/jacs.7b07403

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Is "biological water" the same as tap water?

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.

Nature Communications 8, 904 (2017)

Highlight in the Volkskrant (in Dutch)

Highlight on the C2W website (in Dutch)

Highlight in Analytik News (in German)


Measuring the tilt angle of a protein

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.

J. Phys. Chem. Lett. 8, 3101 (2017)

The secrets of a fungal 'raincoat'

A combination of interfacial spectroscopy with spectral calculations reveals the molecular properties of extremely water-repelling hydrophobin films.

J. Phys. Chem. Lett. 8, 1772 (2017)

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New light on Parkinson's

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.

Sci. Rep. 7, 41051 (2017)

Under the hood of molecular motors

Surprising finding under the hood of molecular motors

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.

J. Phys. Chem. A 120, 8606 (2016)

Highlight on the UvA website

Short presentation about molecular motors

Solving water mysteries

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.

J. Phys. Chem. Lett. 7, 795 (2016) 

Hydrogen cell HomKat

The redox behavior of a bio-inspired hydrogen-production catalyst

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.

Sci. Adv. 2, e1501014 (2016)

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Cover story on amplified vibrational circular dichroism

Review article by Sergio Domingos highlighted on the cover:

ChemPhysChem 16, 3363 (2015)

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How guanidinium unfolds proteins

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.

Angewandte Chemie 54, 15255 (2015)

Highlight on the FOM website

Cover Angewandte Chemie 2014 53/51

Switchable Amplification of Vibrational Circular Dichroism

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.

Angewandte Chemie 53, 13943 (2014)

Ethanol chain

Local orientational order in liquids

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.

Phys. Rev. Lett. 113, 207801 (2014)

Highlight on the FOM website

Complex of chiral molecule with cobalt

Amplifying the optical effects of chirality

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.

JACS 136, 3530 (2014) 

Salt bridge

Unraveling the structure of salt bridges in solution

Salt-bridge geometries can be determined by measuring the couplings between vibrations of the salt-bridged moieties using 2D-IR spectroscopy.

PCCP (communication) 16, 15784 (2014)

How salt bridges influence the speed of protein folding

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.

J. Phys. Chem. Lett. 5, 900 (2014)

Published by  HIMS

19 March 2018