Research
I. On-the-fly hybrid quantum/classical dynamics in a complex environment
II. PySurf: A framework for database accelerated direct dynamics
III. Photo-switchable DNA G-quadruplex; using hybrid quantum mechanics/molecular mechanics approach
IV. Photo-switchable dual-functional molecular motors
V. Singlet fission in molecular solids; using non-orthogonal configuration interaction approach
I. On-the-fly hybrid quantum/classical dynamics in a complex environment
Hybrid and hierarchical approach to study molecular systems in complex environments. We combine three different approaches and tools in computational chemistry: quantum dynamics, quantum mechanics, and molecular mechanics. To ensure a seamless interaction between software packages, we previously developed PySurf (framework for database accelerated direct dynamics, hosting a surface point provider as its core that communicates with a neural network plugin), INAQS (generic QM/MM interface for non-adiabatic dynamics) and Q-Force (automated tool to generate quantum mechanically derived force fields).
PySurf: M. F. S. J. Menger, J. Ehrmaier, S. Faraji* (2020), PySurf: Databased Accelerated Surface Hopping", J. Chem. Theory Comput., 16(12), 7681. https://doi.org/10.1021/acs.jctc.0c00825
INAQS: V. Cofer-Shabica*, M. F. S. J. Menger, Q. Oui, Y. Shao, J. E. Subotnik, S. Faraji* (2022), "INAQS: a generic interface for non-adiabatic QM/MM dynamics: Design, implementation, and validation for GROMACS/Q-CHEM simulations", J. Chem. Theory Comput., 18, 8, 4601. https://doi.org/10.1021/acs.jctc.2c00204
Q-Force: S. Sami*, M. F. S. J. Menger, S. Faraji, R. Broer, R. Havenith, (2021), "Q-Force: Quantum Mechanically Augmented Molecular Force Fields", J. Chem. Theory Comput., 17(8), 4946. https://doi.org/10.1021/acs.jctc.1c00195
II. PySurf: A framework for database accelerated direct dynamics
The greatest bottleneck to study photo-induced processes is computationally expensive electronic structure calculations. With PySurf, we present a novel innovative code framework to tackle the latter. It is especifically designed for rapid prototyping and development in computational chemistry. Results from ab-initio calculations are automatically preserved through a database framework and can be used e.g. for the training of machine learning models. This enables the study of (non-adiabatic) dynamics and potential energy exploration in small to medium sized systems.
III. Photo-switchable DNA G-quadruplex; using hybrid quantum mechanics/molecular mechanics approach
Introducing photoswitches into the DNA G-quadruplex provides excellent opportunities to control folding and unfolding of these assemblies, demonstrating their potential in the development of novel nanodevices with medical and nanotechnology applications. Using molecular dynamics in combination with hybrid quantum mechanics and molecular mechanics, we provide atomistic insights into the photoresponsive formation of photoswitchable G-quadruplex motifs, thus providing design principles for developing azobenzene-based photocontrollable DNA G-quarduplexes.
IV. Photo-switchable dual-functional molecular motors
Light-driven molecular- motors and switches that can exist in two or more distinct (meta)stable states, are excellent candidates for developing modern technologies utilizing light, such as nanomachines or molecular electronic devices. Using advanced electronic structure methods, we explore the excited-state dynamics and model relevant spectra to translate experimental observation into an atomic-level mechanism picture providing detailed insight into the primary photo-chemical reactions.
V. Singlet fission in molecular solids; using non-orthogonal configuration interaction approach
Singlet fission (SF) has been proposed as an alternative to boost solar cells’ efficiency since, in principle, two pairs of charge carries can be generated per single absorbed photon. In this process, two singlet-coupled triplets (1TT) are formed from a photo excited chromophore combined with a neighbor in the ground state (S1S0). The theoretical modelling of SF is often done by employing a gas-phase dimer model which has shown its utility as a first approximation to explain the process. However, it does not always cover all the physics and the effect of surrounding molecules has to be included in such cases. In this project, we explore how the crystal packing (environment) influences the SF process by means of analyzing the electronic couplings and the excited character of the molecules inside the crystal structure.