New dynamic probes for ions interacting with biomolecules


Figure 1. DNA double helix embedded in water (angled small molecules, not to scale). The dark red spheres on the helix surface represent oxygen atoms of the negatively charged PO2- units, the blue spheres positively charged ions in the environment.

Pairs of negatively charged phosphate groups and positive magnesium ions represent a key structural feature of DNA and RNA embedded in water. Vibrations of phosphate groups have now been established as selective probes of such contact pairs and allow for a mapping of interactions and structure on the ultrafast time scales of molecular dynamics.

DNA and RNA are charged polymers that encode genetic information in a double helix structure and act as key player in the biosynthesis of proteins. Their negative charges are located in the molecular backbone, which consists of ionic phosphate (PO2) and of sugar groups (Figure 1). Stabilization of the macromolecular structures of DNA and RNA requires a compensation of strong repulsive electric forces between the equally charged phosphate groups by ions of opposite, i.e., positive charge. In this context, magnesium (Mg2+) ions Mg2+ are particularly relevant as Mg2+ ions not only stabilize the structure but also mediate the recognition of binding partners and act as catalytic centers. Moreover, changes of macromolecular structure via dynamic folding processes are connected with a rearrangement of positive ions embedded in the surrounding water shell.


Figure 2. Top: Molecular structure of a contact ion pair consisting of dimethylphosphate (DMP) and a magnesium ion Mg2+ embedded in water, arrows mark elongations of the asymmetric PO2- stretching vibration. Bottom: Two-dimensional infrared (2D-IR) spectra of the asymmetric PO2- stretching vibration showing a component P1 from DMP molecules without a magnesium ion and the contribution P2 from contact ion pairs.

Positive ions are arranged in different geometries around DNA and RNA: in so-called site-bound or contact-pair geometries, a positive ion is located in direct contact with an oxygen atom of a phosphate group. In contrast, the so-called outer ion atmosphere consists of positive ions separated by at least one layer of water molecules from the phosphate groups. The functional role of the different geometries and the underlying interactions are far from being understood. A deeper insight at the molecular level requires highly sensitive probes which allow for discerning the different ion geometries without disturbing them, and for mapping their dynamics on the ultrafast time scale of molecular motions.

In a recent publication, we demonstrate that vibrations of phosphate groups represent sensitive and noninvasive probes of ion geometries in a water environment. Dimethylphosphate (DMP, (CH3O)2PO2), an established model system for the DNA and RNA backbone, was prepared in liquid water with an excess of Mg2+ ions (Figure 2, top) and studied by nonlinear vibrational spectroscopy in the femtosecond time domain (1 fs = 10-15 s). The experiments make use of two-dimensional infrared (2D-IR) spectroscopy, a most sophisticated method for analyzing the ionic interactions and structures on the intrinsic time scale of fluctuating molecular motions.

The experiments map Mg2+ ions in direct contact with a PO2 group via a distinct feature in the 2D-IR spectrum (Figure 2, bottom). The interaction with the Mg2+ ion shifts the asymmetric PO2 stretching vibration to a frequency which is higher than in absence of Mg2+ ions. The lineshape and the time evolution of this new feature reveal fluctuations of the contact ion pair geometry and the embedding water shell on a time scale of hundreds of femtoseconds while the contact pair itself exists for much longer times (~10-6 s). An in-depth theoretical analysis shows that the subtle balance of attractive electrostatic (Coulomb) forces and repulsive forces due to the quantum-mechanical exchange interaction govern the frequency position of the phosphate vibration.

The ability of 2D-IR spectroscopy to characterize the short-ranged phosphate-ion interaction in solution provides a novel analytical tool that complements currently available structural techniques. An extension of this new approach to DNA and RNA and their ionic environment is most promising and expected to provide new insight in the forces stabilizing equilibrium structures and driving folding processes.

Jakob Schauss, Fabian Dahms, Benjamin P. Fingerhut, Thomas Elsaesser: Phosphate-magnesium ion interactions in water probed by ultrafast two-dimensional infrared spectroscopy. Phys. Chem. Lett. 10, 238-243 (2019).


Dr. Benjamin Fingerhut, Phone +49 30 63921404
Prof. Thomas Elsaesser, Phone +49 30 63921400


ERC Starting Grant 2018

LOGO_ERC-FLAG_EU_ 2Dr. Benjamin Fingerhut, junior group leader at the Max Born Institute (MBI), is recipient of the prestigious ERC Starting Grant 2018. The project addresses ultrafast biomolecular dynamics via a non-adiabatic theoretical approach. The award is granted by the European Research Council (ERC) to support excellent researchers at the beginning of their independent research careers.

The European Research Council (ERC) has announced the awardees of its Starting Grants. In the highly competitive selection procedure, the research proposal of Benjamin Fingerhut has been selected for funding. ERC Starting Grants are designed to support excellent early career researchers in establishing their own independent research programme. ERC Starting Grants are awarded to researchers up to 7 years after their PhD to conduct a research programme at a European university or research institute. The grants are awarded under the “excellent science” pillar of Horizon 2020, the EU’s research and innovation programme with a funding of up to Euro 1.5 million for a maximum of 5 years.

The successful project is devoted to the fundamental understanding of ultrafast biomolecular vibrational dynamics in the mid-IR/THz spectral region where biologically highly relevant dynamics occur. The innovative non-adiabatic approach addresses fundamental problems, such as proton transfer, vibrational lifetimes and the dissipation of excess energy. The project aims to elucidate ultrafast biomolecular vibrational dynamics in dipolar liquids, within nanoconfined environments and in the vicinity of biological interfaces. As such the non-adiabatic approach to biomolecular vibrational dynamics facilitates insight into transmembrane proton translocation mechanisms which is highly relevant as microscopic foundation of cell respiration.

Further information on ERC Starting Grants 2018:

Large-amplitude transfer motion of hydrated excess protons mapped by ultrafast 2D IR spectroscopy

our latest work on the solvated excess proton got published as Science First Release paper:

Large-amplitude transfer motion of hydrated excess protons mapped by ultrafast 2D IR spectroscopy

by Fabian Dahms, Benjamin P. Fingerhut, Erik T. J. Nibbering, Ehud Pines, Thomas Elsaesser,

Science DOI: 10.1126/science.aan5144.


Publisher link:

MACGIC-QUAPI method for the treatment of non-Markovian long-time bath memory

our new method got published in J. Chem. Phys.:

Coarse-grained representation of the quasi adiabatic propagator path integral for the treatment of non-Markovian long-time bath memory

by Martin Richter and Benjamin P. Fingerhut

The Journal of Chemical Physics 146, 214101 (2017); doi: 10.1063/1.4984075


Publisher link:

May 2017 Featured Article in Structural Dynamics

Our recent acticle
Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations

by Yingliang Liu, Biswajit Guchhait, Torsten Siebert, Benjamin P. Fingerhut, and Thomas Elsaesser

was selected as May Featured Article in Structural Dynamics.



Robin Hochstrasser Young Investigator Award

Dr. Benjamin Fingerhut, junior group leader at the Max-Born-Institute (MBI) receives the 2016 Robin Hochstrasser Young Investigator Award. The award is granted by an international scientific committee, consisting of members of the editorial board of the journal Chemical Physics, in order to support excellent early career researchers.

To honor Robin Hochstrasser and support young scientists Elsevier has initiated for Chemical Physics the Robin Hochstrasser Young Investigator Award. Professor Hochstrasser was one of the pioneers in ultrafast spectroscopy of molecular systems and has made seminal contributions to our understanding of condensed phase structure and dynamics. His group was the first to introduce 2D IR spectroscopy in 1998 as optical analogue of nuclear magnetic resonance (NMR) spectroscopy. Today, this technique is among the most important in ultrafast science. At MBI, it has been extended into the terahertz range and is being applied to biophysical problems.

The Robin Hochstrasser Young Investigator Award of Chemical Physics is granted to excellent scientists younger than 40 years of age on the basis of their scientific contributions. An international committee of scientists, consisting of five members of the editorial board of Chemical Physics, selects the winner from the nominations.

Benjamin Fingerhut joined the MBI in 2014 and is currently supported by an Emmy Noether Early Career Grant of the German Research Foundation (DFG) which allowed him to establish the new Junior Research Group: Biomolecular Dynamics at the MBI. His research involves the development of state of the art spectroscopic simulation techniques and their application to the real-time determination of ultrafast structural dynamics of molecular and biomolecular systems. The group combines analytical and computational approaches for novel simulation protocols suited to investigate excited-state non-adiabatic dynamics as well as vibrational dynamics of spacio-selective probes like phosphate groups to explore fluctuation induced decoherence dynamics in aqueous and biological environments.


for further information:

Accepted talk at the STC2016

Martin’s contribution entitled “Nonlinear Signals From Nonadiabatic ab-initio Molecular Dynamics Simulations”

was accepted as talk at the Symposium on Theoretical Chemistry 2016.



for more information see:

Symposium on Theoretical Chemistry 2016

Range, Magnitude, and Ultrafast Dynamics of Electric Fields at the Hydrated DNA Surface

our recent work got published in J. Phys. Chem. Lett.:
Range, Magnitude, and Ultrafast Dynamics of Electric Fields at the Hydrated DNA Surface

by Torsten Siebert, Biswajit Guchhait, Yingliang Liu, Benjamin P. Fingerhut, and Thomas Elsaesser


Publisher link:

Anharmonicities and coherent vibrational dynamics of phosphate ions in bulk H2O

our recent work got published in PCCP:
Anharmonicities and coherent vibrational dynamics of phosphate ions in bulk H2O

by Rene Costard, Tobias Tyborski and Benjamin P. Fingerhut


Publisher link:!divAbstract

The new Intel Xeon E5-2650 v2 based 2U Twin2 Nodes arrived at MBI.










Two nodes will be equipped with MIC Xeon Phi support.