DTU Chemistry - Cosine

Shaping the Digital Chemist of Tomorrow

Thursday 18 Jan 18
by Morten Andersen


Sonia Coriani
DTU Chemistry
+45 45 25 23 35


Klaus Braagaard Møller
DTU Chemistry
+45 45 25 24 61

Beneficiary partners in the COSINE – ETN

UHEI - Ruprecht Karls University Heidelberg, Germany (coordinator);
Kungliga Tekniska Högskolan, Stockholm, Sweden;
LMU - Ludwig Maximilians University Munich, Germany;
SNS - Scuola Normale Superiore, Pisa, Italy;
SDU -  
Syddansk Universitet, Odense, Denmark;
ENSCP - Ecole Nationale Superieure de Chimie de Paris, France;
NTNU - Norges Teknisk-Naturvitenskapelige Universitet, Trondheim, Norway.
DTU Chemistry, Kgs. Lyngby, Denmark.

Further, a number of private companies and organizations participate: Elettra Sincrotrone Trieste; Electromagnetic Geoservices ASA; EXACT Lab SRL; NVIDIA GmbH; DELL S.P.A. Bio Tools Inc; PDC Center for High Performance Computing KTH; Dipartimento di Scienze Chimiche e Farmaceutiche,  Trieste.

Total budget is 3.75 million EUR, hereof 580,000 EUR are allocated to DTU Chemistry.

itncosine website

No less than 14 new PhD’s will be recruited and trained in a European network on computational spectroscopy with strong DTU Chemistry participation.

No flasks or test tubes are found in the office of Professor Sonia Coriani. She heads a key work package in a new European training network (ETN) for computational spectroscopy. Seeking 14 new PhD students, the network will shape the digital chemists of tomorrow.

“As facilities such as powerful synchrotron radiation sources and free-electron lasers become available, there is a huge need for computational chemistry. It is simply not possible to interpret results from advanced spectroscopy intuitively. You will need corresponding models and software tools,” explains Sonia Coriani, adding that experts in computational spectroscopy are scarce.

“Education and training of students or early-stage researchers in this field is not part of any standard curriculum, neither in chemistry nor physics. This is in clear contrast to the increasing importance of computational spectroscopy.”

Of the 14 young researchers to be recruited, two will be employed at DTU Chemistry with Sonia Coriani as their supervisor.

“If you a long-term resident in Denmark, actually the other 12 positions are more relevant. As mobility is an embedded ETN requirement, we need to hire our two candidates internationally. However, if candidates already living in Denmark are interested – and willing to accept a stay abroad – we will try to help them get in touch with the relevant academic partner.”

Know which fingerprint to expect
The initiative is named COSINE (COmputational Spectroscopy In Natural science and Engineering). Sonia Coriani heads the work package on modeling of advanced spectroscopies. Besides herself, Klaus B. Møller, Professor in Physical Chemistry at the department, will contribute with his experience from computer simulation of chemical dynamics and interpretation of ultrafast X-ray scattering experiments.

“Scattering and spectroscopy are very different techniques, but they are alike in the sense that they both yield indirect information about the probed molecules. This implies that before you do your experiment you need to have a model,” says Klaus B. Møller. “You need to know which fingerprint you should expect from the experiment. There is just no way of working your way backwards from an experimental result.”

Both professors have extensive experience from large-scale facilities abroad. And with the experience of the seven European academic partners and associated industrial partners included, the network covers a wide range of techniques. Examples are Near-Edge X-ray Absorption Fine Structure for ground and excited states, Resonance Raman Optical Activity, Resonance Inelastic X-ray Scattering, and photo-electron spectroscopy. Importantly, the network also offers specific training on programming and use of High-Performance Scientific Computing resources, both locally and through the PDC Center for High Performance Computing of Kungliga Tekniska Högskolan (KTH) in Stockholm, a partner.

Screen before synthesis

Both in her own research and in the COSINE project, Sonia Coriani focuses on excited electronic states.

“User-friendly software packages for ground-state chemistry already exists, but similar solutions for excited states are lagging behind,” she points out.

Over the last two decades it has become possible to model molecular ground-state properties on the computer with high accuracy. This enables chemists to predict the properties of new molecules virtually. Thereby a huge number of molecules can be pre-screened on computers prior to synthesis, avoiding costs. It is also easily tested whether a proposed change in the structure of a molecule, a particular substitution for example, can be expected to give the desired effect. This approach to design of molecules with specific properties – like molecules with low optical band gaps, high or low electron affinities or ionization potentials – is gaining momentum in both academia and industry.

“The ultimate goal of computational spectroscopy is, similarly, to be able to predict excited-state properties and spectra of real-life molecular species in gas and condensed phases, and to be able to study light-triggered reactions on the computer,” says Sonia Coriani.

How we adjust to sunlight
A recent joint project with experiments executed at the XFEL facility in California illustrates the scope of computational spectroscopy. The subject was thymine which is a key DNA component. The thymine molecules were first excited by an UV laser pulse and then probed with a time-delayed X-ray pulse. This is an example of what is known as pump/probe spectroscopy. The article is published in the high-profile journal Nature Communications.

“Based on computational spectroscopy tools we were able to explain the experimental results found by our American partners and identify the population of the electronic excited states involved in the de-excitation process,” says Sonia Coriani.

The experiment shows how the excited electrons in thymine release a major part of their newly acquired energy in just a few pico-seconds (10-12 second).

“This ultrafast internal conversion is actually a vital mechanism, which contributes to explain why our DNA is surprisingly resistant to the destructive potential of UV radiation from the Sun,” comments Klaus B. Møller.

This example shows how computational spectroscopy can increase fundamental understanding in the field of photo-biology. 

Ultrafast X-ray scattering
One example of the ultrafast X-ray scattering experiments, that Professor Klaus B. Møller has worked with, is described in the scientific article “Atomistic characterization of the active-site solvation dynamics of a model photocatalyst”.

The article was also published in the high-profile journal Nature Communications, and here DTU researchers shows that it is possible experimentally to record ‘molecular movies’ of the interactions between light-activated molecules and their surroundings.

Klaus Møller headed the computational studies that proved invaluable in interpreting and modelling the experimental data. 

High employability ahead
Other applications where light-triggered reactions are important can be found in emerging scientific and technological fields dealing with optically active materials, organic opto-electronics, photo-medicine, and photo-catalysis.

As these fields evolve, the demand for new computational spectroscopic tools will continue to grow.

“The most accurate predictive methods can presently only be applied to relatively simple molecules. It is a natural ambition in computational spectroscopy to extend the most accurate methods to more complex molecules. Also, we constantly strive for simplifications that make our tools cheaper without compromising accuracy,” Sonia Coriani notes, giving an example:

“Sometimes it may be possible to apply the most accurate method to a part of the molecule only, typically the active site, while modelling the rest of the molecule more crudely. This can save extensive computer time and thereby also keep costs down.”

The future digital chemists are to be hired by May 2018, and will start as PhD students by September 1. Besides the opportunity to engage in fascinating science, they can expect to generally boost their careers, promises Sonia Coriani:

“In the spirit of Marie Sklodowska-Curie ETN framework and the European Charter for Researchers, the early-stage researchers trained in COSINE will achieve not only a unique research profile but also management and communication skills. They will become fully qualified for careers in either academia or industry, and the mobility component will contribute further to their employability.”

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