scholarly journals Using quantum dynamics simulations to follow the competition between charge migration and charge transfer in polyatomic molecules

2017 ◽  
Vol 482 ◽  
pp. 52-63 ◽  
Author(s):  
K.E. Spinlove ◽  
M. Vacher ◽  
M. Bearpark ◽  
M.A. Robb ◽  
G.A. Worth
2019 ◽  
Vol 205 ◽  
pp. 10009 ◽  
Author(s):  
Martin Richter ◽  
Benjamin P. Fingerhut

Dissipative quantum dynamics simulations reveal a branching of charge separation dynamics in Drosophila Cryptochrome due to subtle balanced energetics within the enzyme. In silico mutations of charged amino acids provide control over charge transfer directionality.


Molecules ◽  
2020 ◽  
Vol 25 (20) ◽  
pp. 4810
Author(s):  
Martin Richter ◽  
Benjamin P. Fingerhut

Interconnected transcriptional and translational feedback loops are at the core of the molecular mechanism of the circadian clock. Such feedback loops are synchronized to external light entrainment by the blue light photoreceptor cryptochrome (CRY) that undergoes conformational changes upon light absorption by an unknown photoexcitation mechanism. Light-induced charge transfer (CT) reactions in Drosophila CRY (dCRY) are investigated by state-of-the-art simulations that reveal a complex, multi-redox site nature of CT dynamics on the microscopic level. The simulations consider redox-active chromophores of the tryptophan triad (Trp triad) and further account for pathways mediated by W314 and W422 residues proximate to the C-terminal tail (CTT), thus avoiding a pre-bias to specific W-mediated CT pathways. The conducted dissipative quantum dynamics simulations employ microscopically derived model Hamiltonians and display complex and ultrafast CT dynamics on the picosecond timescale, subtly balanced by the electrostatic environment of dCRY. In silicio point mutations provide a microscopic basis for rationalizing particular CT directionality and demonstrate the degree of electrostatic control realized by a discrete set of charged amino acid residues. The predicted participation of CT states in proximity to the CTT relates the directionality of CT reactions to the spatial vicinity of a linear interaction motif. The results stress the importance of CTT directional charge transfer in addition to charge transfer via the Trp triad and call for the use of full-length CRY models including the interactions of photolyase homology region (PHR) and CTT domains.


Symmetry ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 205
Author(s):  
Dietrich Haase ◽  
Gunter Hermann ◽  
Jörn Manz ◽  
Vincent Pohl ◽  
Jean Christophe Tremblay

Quantum simulations of the electron dynamics of oriented benzene and Mg-porphyrin driven by short (<10 fs) laser pulses yield electron symmetry breaking during attosecond charge migration. Nuclear motions are negligible on this time domain, i.e., the point group symmetries G = D6h and D4h of the nuclear scaffolds are conserved. At the same time, the symmetries of the one-electron densities are broken, however, to specific subgroups of G for the excited superposition states. These subgroups depend on the polarization and on the electric fields of the laser pulses. They can be determined either by inspection of the symmetry elements of the one-electron density which represents charge migration after the laser pulse, or by a new and more efficient group-theoretical approach. The results agree perfectly with each other. They suggest laser control of symmetry breaking. The choice of the target subgroup is restricted, however, by a new theorem, i.e., it must contain the symmetry group of the time-dependent electronic Hamiltonian of the oriented molecule interacting with the laser pulse(s). This theorem can also be applied to confirm or to falsify complementary suggestions of electron symmetry breaking by laser pulses.


Author(s):  
Adrian Dominguez-Castro ◽  
Thomas Frauenheim

Theoretical calculations are an effective strategy to comple- ment and understand experimental results in atomistic detail. Ehrenfest molecular dynamics simulations based on the real-time time-dependent density functional tight-binding (RT-TDDFTB) approach...


2021 ◽  
Author(s):  
Xinyang Li ◽  
Pengfei Huo

<div>We use the ab-initio ring polymer molecular dynamics (RPMD) approach to investigate tunneling controlled reactions in methylhydroxycarbene. Nuclear tunneling effects enable molecules to overcome the barriers which can not be overcome classically. Under low-temperature conditions, intrinsic quantum tunneling effects canfacilitate the chemical reaction in a pathway that is neither favored thermodynamically nor kinetically. This</div><div>behavior is referred to as the tunneling controlled chemical reaction and regarded as the third paradigm of chemical</div><div>reaction controls. In this work, we use the ab-initio RPMD approach to incorporate the tunneling effects in our quantum dynamics simulations. The reaction kinetics of two competitive reaction pathways at various temperatures are investigated with the Kohn-Sham density functional theory (KS-DFT) on-the-fly molecular dynamics simulations and the ring polymer quantization of the nuclei. The reaction rate constants obtained here agree extremely well with the experimentally measured rates. We demonstrate the feasibility of using ab-initio RPMD rate calculations in a realistic molecular system, and provide an interesting and important example for future investigations on reaction mechanisms dominated by quantum tunneling effects.</div>


PRX Quantum ◽  
2021 ◽  
Vol 2 (3) ◽  
Author(s):  
Yong-Xin Yao ◽  
Niladri Gomes ◽  
Feng Zhang ◽  
Cai-Zhuang Wang ◽  
Kai-Ming Ho ◽  
...  

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