RESEARCH

Oxazolidinone
Rapidly interconverting intermediates.
Molecular motions and interactions give rise to exciting phenomena at the intersection of chemistry, physics and biology. They dictate, for example, chemical reactions, folding and function of biomolecules and structure formation in condensed matter. Motions on the molecular scale occur on an incredible range of timescales from femtoseconds (1 fs = 10-15 s) to milliseconds and longer. How do processes on different timescales and length scales couple and give rise to complex molecular behaviour, for instance in the function of biomolecules? How can molecular devices that mimic such function be constructed? How can we resolve shortlived intermediates in chemical reactions and which role do they play in reaction mechanisms? How can a catalyst be optimized for a certain type of reaction? Our research aims at answering such questions by following molecular dynamics over many orders of magnitude in time.

This experimental challenge is met by the development of nonlinear spectroscopic techniques that combine structure resolution, high time resolution and high sensitivity. These fascinating techniques are based on transient and multidimensional infrared spectroscopy. They employ sequences of femtosecond infrared and visible laser pulses to measure couplings and correlations between vibrations in different parts of a molecule or even between different molecules. In this way information on structural changes on the molecular scale can be obtained over a very wide time range down to the femtosecond regime. We are thus approaching the ultimate goal for investigating the relationship of structure, dynamics and function of molecular systems: the development of a method with sufficient time and structure resolution to capture every relevant motion of molecules.

Oxazolidinone
Protein labeled with an artificial amino acid.
Our efforts in spectroscopy are supported by techniques from molecular biology, biochemistry and theoretical chemistry, which we also established in our group. In addition to the ultrafast optics and spectroscopy labs, we therefore run a biochemistry and molecular biology lab.  For more background information, or if you are interested in some current projects, please have a look at the links below.

If you are interested in available research projects please contact us and read the information for prospective students.
2D-IR spectroscopy

To come... For the moment please refer to these overview articles:

[1] J. Bredenbeck, Nachr. Chem. 54, 104-108 (2006) (in German)
[2] J. Bredenbeck, J. Helbing, C. Kolano and P. Hamm, ChemPhysChem 8, 1747-1756 (2007)

[3] J. Bredenbeck, A. Ghosh, H.-K. Nienhuys and M. Bonn, Acc. Chem. Res. 42, 1332-1342 (2009)
[4] L. J. G. W. van Wilderen and J. Bredenbeck, Angew. Chem. Int Ed.
, published online (2015)
[5] L. J. G. W. van Wilderen and J. Bredenbeck, Angew. Chem., published online (2015) (in German)

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Artificial amino acids: Infrared labels provide new observables for protein structure and dynamcis

Time-resolved 1D and 2D-IR spectroscopy are powerful tools to study structure and dynamics of small to medium size molecules. When applied to proteins, these techniques face similar difficulties as known from classical FTIR spectroscopy: The protein spectrum contains many overlapping absorptions of the protein backbone (amide I and amide II modes) and the side chains. IR spectroscopy of proteins therefore frequently suffers from a lack of structural resolution.

In our group we combine time-resolved IR-spectroscopy with the aplication of artificial amino acids featuring functional groups that are not commonly present in proteins. Their infrared absorptions appear in a spectral window (ca. 1800 cm-1 to 3000 cm-1) that is free of native protein absorptions. These infrared labels therefore can provide site-selective information on the single amino acid level. Of special interest are nitriles and azides that can be incorporated cotranslationally by genetic code expansion or as a surrogate of a natural amino acid. 

proteins and labels
Schematic IR spectrum of a protein (blue) and infrared labels (red).

Solid lines are measured spectra of H2O (brown) abd D2O (blue).

Methods, Keywords: biochemistry, molecular biology, artificial amino acid, non-canonical amino acids, artificial genetic code expansion, codon reassignment, FTIR spectroscopy, time-resolved (2D-)IR spectroscopy, CD spectroscopy, ITC (isothermal titration calorimetry), DFT computations, molecular docking, protein structure visualization

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Development of novel pulse sequences

To come...

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Laser syncronization: Molecular dynamics from femtoseconds to milliseconds

The dynamics of proteins is characterized by a continuum of time scales extending from the femtosecond regime of local dynamics involving just a few chemical bonds to the millisecond and longer time scale of correlated global structural changes. How do processes on such different time and length scales couple to each other, e. g. how is an ultrafast local change at the active site or binding site of a protein amplified into a mesoscopic change of structure that executes a biological function? 

To gain access to such a wide range of time scales, we rely on electronically synchronized femtosecond lasers. Traditional femtosecond spectroscopy uses a trigger pulse and a detection pulse that are derived from the same parent pulse of the laser system, simply using partially reflective mirrors. Trigger pulse and measurement pulse are delayed with respect to each other using a delay line with motorized mirrors. Delays that can be achieved with an optical delay line typically are in the range of femtoseconds to 1 ns. 

synchro box
Fig.: Home built femtosecond laser synchronization.

Each of the two synchronized laser systems consists of an oscillator and an amplifier. One system serves as the master and the other as slave. One system provides the trigger pulse and the other the detection pulse. In this way arbitrary delays can be generated. To achieve synchronisation, the cavity length of the slave oscillator is continuously adjusted to match the master oscillator cavity. A phase-looked loop is used to force the difference frequency of both lasersystems to zero. The jitter can be as low as a few 100 fs. An electronic phase shifter generates delay between the oscillator pulses. Longer delays are created by picking different oscillator pulses for amplification in each of the amplifiers. This allows for pump-probe delays up to the repetition time of the laser systems of 1 ms.

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Vibrational energy transfer

To come...

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Catalysis and reaction mechanisms

Determining the structure of reactive intermediates is the key for understanding chemical reaction mechanisms and for developing and optimizing reactions. To resolve intermediate structures, a method combining structure sensitivity and high time resolution is required. Ultrafast polarization-dependent 2D-IR (P2D-IR) spectroscopy is an excellent complement to commonly used methods such as one-dimensional IR and multidimensional NMR spectroscopy for investigating reaction intermediates [1]. P2D-IR allows structure determination by measuring the angles between vibrational transition dipole moments and by determining anharmonic couplings. Its high time resolution makes P2D-IR spectroscopy an attractive method for structure determination in the presence of fast exchange and for short-lived intermediates. The ubiquity of vibrations in molecules ensures broad applicability of the method, particularly in cases in which NMR spectroscopy is challenging due to a low density of active nuclei [1-3]. 

oxazolidinone
P2D-IR spectroscopy resolves reactive intermediates of Lewis acid catalyzed Diels-Alder reactions.
A minor conformer, source of unwanted side reactions, is revealed [3].

[1] A. T. Messmer, K. M. Lippert, S. Steinwand, E.-B. W. Lerch, K. Hof, D. Ley, D. Gerbig, H. Hausmann, P. R. Schreiner, J. Bredenbeck, Chem. Eur. J. 18, 14989-14995 (2012)
[2] A. T. Messmer, S. Steinwand, K. M. Lippert, P. R. Schreiner, J. Bredenbeck, J. Org. Chem. 77, 11091-11095 (2012)
 

[3] A. T. Messmer, K. M. Lippert, P. R. Schreiner, J. Bredenbeck, Phys. Chem. Chem. Phys. 15, 1509-1517 (2013) 

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Photocontrolled catalysts

Starting and stopping chemical reactions by light offers ultimate spatiotemporal control. Photocontrolled catalysts allow to initiate chemical reactions, which are no photochemical reactions themselves, by light. The figure shows the prototype of a reversibly switchable azobenzene-based catalyst. Isomerization of the azobenzene moiety activates the catalyst by exposing the catalytically active site. We study the dynamics of this and related catalysts as well as their interaction with the surrounding solvent and substrate molecules.

azokat
Reversibly photoswitchable catalyst [1].
In the inactive form, the active site is shielded by bulky rests R' on the azobenzene.

[1] M. V. Peters, R. S. Stoll, A. Kühn, S. Hecht, Angew. Chem. Int. Ed. 47, 5968-5972 (2008).

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Ultrafast 2D-IR spectroelectrochemistry

Electron transfer reactions are fundamental processes in chemistry and biology. They are key events in cellular respiration, photosynthesis and catalysis. We introduced the technique of 2D-IR spectroelectrochemistry to be able to carry out 2D-IR experiments under in situ redox control [1]. The cell design allows for rapid redox cycling which is of particular importance for collecting redox induced 2D-IR difference spectra to measure subtle changes in structure and dynamics.

2D-IR spectroelectrochemistry
2D-IR spectroelectrochemistry is carried out in reflection mode
on a gold mirror which is used at the same time as an electrode.[1,2]

[1] Y. El Khoury, L. J. G. W. van Wilderen, J. Bredenbeck, Ultrafast 2D-IR spectroelectrochemistry of flavin mononucleotide, J. Chem. Phys. 142, 212416 (2015).
[2] Y. El Khoury, L. J. G. W. van Wilderen, T. Vogt, E. Winter, J. Bredenbeck
Rev. Sci. Instrum. 86, 083102 (2015).
 

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Dynamics of natural and designed proteins

The dynamics of proteins is characterized by a continuum of time scales extending from the femtosecond regime of local dynamics involving just a few chemical bonds to the microsecond and longer time scale of correlated global structural changes. How do processes on such different time and length scales couple to each other? How is an ultrafast local change at the active site or binding site of a protein amplified into a mesoscopic change of structure that executes a biological function? Related phenomena play a role in light sensitive proteins, where local ultrafast conformational changes of a chromophor drive processes on much larger time and length scales. Understanding the interaction of various degrees of freedom is of particular importance when it comes to the design of proteins. To study these macromolecular machines at work over many orders of magnitude in time with high structure resolution, we apply our tools of laser synchronization, multidimensional spectroscopy and incorporation of infrared labels by artificial amino acids.

gfp
Green fluorescent protein optimized for charge separation using
a genetically encoded metal-chelating amino acid to create an artificial copper redox center [1].

[1] X. Liu, J. Li, J. Dong, C. Hu, W. Gong, J. Wang, Angew. Chem. Int. Ed. 51, 1-6 (2012).

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2D-IR spectroscopy of interfaces

SFG 2D-IR
Fig.: Surface specific 2D-IR spectroscopy by sum frequency generation [1].

To come... For the moment please refer to this article [1].

[1] J. Bredenbeck, A. Ghosh, H.-K. Nienhuys and M. Bonn, Acc. Chem. Res. 42, 1332-1342 (2009)

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Labs and equipment

We are currently running two femtosecond laser labs. Each lab features two oscillator/amplifier systems, that can be synchronized.

Lab 1

  • Spitfire Pro XP (3 mJ, 1 kHz, 100 fs), seeded by a Tsunami oscillator (Spectra Physics)
  • Legend Elite (4 mJ, 1 kHz, 100 fs), seeded by a Mira oscillator modified for laser syncronization (Coherent)

Lab 2

  • Spitfire Ace (5 mJ, 1 kHz, 100 fs), seeded by a Tsunami oscillator, modified for laser synchronization (Spectra Physics)
  • Spitfire Ace (5 mJ, 1-10 kHz, 35-100 fs), seeded by a MaiTai SP oscillator (Spectra Physics)

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