Coherences and organic chromophores
Rhodamine heterodimer tethered on DNA scaffold
This direction of our research is largely inspired by the advances in the 2D-photon-echo spectroscopy of the organic chromophores. The ability to measure both the population and the coherences between the excited electronic states, even for a very short times, like 100-200fs, is very impressing. During my PostDoc research at the University of Liege in collaboration with experimental groups of University of Padova (2D-spectroscopy, E. Collini) and Hebrew University of Jerusalem (synthesis of the dimer, I. Willner) we examined theoretically and experimentally the time-evolution of the vibronic coherences in the rhodamine heterodimer tethered on DNA scaffold [1].
The two rhodamines are tethered on the 3’ and 5’ ends of the suitably designed DNA strands by aliphatic linkers. When the formation of the double helix is promoted, these linkers ensure formation of the heterodimer. Our team at the University of Liege provided MD simulations and analysis of the electronic structure and normal modes in the heterodimer to get better a link between the coherences observed in the 2D-Photon-Echo (2D-PE) experiment and the vibronic structure of the dimer. Indeed MD simulations confirmed the rather short distances in a range 3-6Å (FWHM) between the two dye moieties along 4ns trajectories. We characterized the electronic structure and optically active vibrational modes of the heterodimer based on the simulation and analysis of the absorption lineshape. We computed QM-MM equilibrium geometry of the dimer tethered on DNA and got the normal mode representation. This enabled us to construct the absorption lineshape for different conformations [1]. There were two major findings along this project:
(i) Due to weakly bound nature of the dimer the relative orientation of the two monomers can hardly be described by one or two equilibrium geometries. The intermolecular motion of the two monomers is far from being harmonic, it is more likely to be a shallow bottom of the sea with a lot of local minima present. Such a change in orientation of the monomers affects the electronic structure and consequently absorption spectrum of the dimer in a large extent.
(ii) Having identified the optically active modes for the different types of conformations of the dimer we found that the coherences measured in the experiment can be attributed only to few of them. Namely, the effective Hamiltonian which was able to describe the observed evolution of the coherences had only 4 excited vibronic states in the basis.
In response to (i) in our recent paper [2] on the analysis of the chirality of the heterodimer we used more realistic MD sampling of the dimer conformations. This enabled us to better describe the lineshape and to follow the changes in the electronic structure along the trajectory. However, this was not enough to tackle the issue (ii) – namely, to address the question: why do we observe only some specific set of coherences in the 2D-PE spectrum.
See also the lecture: Chirality of the Rhodamine Heterodimer Linked to DNA Scaffold
Algebraic Mapping of electronic observables onto vibrational Hilbert space
In our current project we examine the use of such artificially designed materials in the field of Quantum Information Processing. The promise is a quantum computer operating at room temperature.
Addressing the chromophores during the 2D-PE experiment gives an output on the population and coherence between N vibronic states at the specific delay time t. This allows having N(N-1) coherence variables and N populations for one specific orientation of the 3 laser pulses. Such a construction enables a basis for the non-binary coherence based logic of the Quantum Computer [3-5].
[1] Coherent electronic and nuclear dynamics in a rhodamine heterodimer-DNA supramolecular complex. Phys. Chem. Chem. Phys., 19, 23043-23051 (2017)
[2] Chirality of the Rhodamine Heterodimer Linked to DNA Scaffold: An Experimental and Computational Study. Phys. Chem. Chem. Phys., 22, 7516-7523 (2020)
[3] Parallel and Multivalued Logic by the Two-Dimensional Photon-Echo Response of a Rhodamine-DNA Complex. J. Phys. Chem. Lett., 6, 1714 (2015)
[4] Quantum Device Emulates Dynamics of Two Coupled Oscillators J.Phys.Chem.Lett. 11, 17, 6990–6995 (2020)
[5] Parallel Quantum Computation of Vibrational Dynamics. K. Komarova, H. Gattuso, R.D. Levine, and F. Remacle. Front. Phys. 8, 590699.