Electron transfer within a reaction path model calibrated by constrained DFT calculations: application to mixed-valence organic compounds

Mangaud, Etienne; Lande, Aurélien de la; Meier, Christoph; Desouter-Lecomte, Michèle

doi:10.1039/c5cp01194a

Cited by 20 publications

(27 citation statements)

References 104 publications

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“…The black, red and blue curves correspond to the first, second and third diabatic state respectively. Bottom eqn (33) has been used. Bottom eqn (33) has been used.…”

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confidence: 99%

“…Equations-of-Motion (HEOM) algorithm, simulating as the whole the charge transfer process within the tryptophan triad. In a previous work we used cDFT to build a reaction path model derived from a spin-boson vibronic Hamiltonian 33. This data provide basic material for direct QDD26,27 or Multi-Layers Multi Configuration Time Dependent Hartree (ML-MCTDH) simulations [28][29][30][31][32].…”

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confidence: 99%

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Quantum effects in ultrafast electron transfers within cryptochromes

Firmino

Mangaud

Cailliez

et al. 2016

Phys. Chem. Chem. Phys.

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Cryptochromes and photolyases are flavoproteins that may undergo ultrafast charge separation upon electronic excitation of their flavin cofactors. Charge separation involves chains of three or four tryptophan residues depending on the protein of interest. The molecular mechanisms of these processes are not completely clear. In the present work we investigate the relevance of quantum effects like the occurrence of nuclear tunneling and of coherences upon charge transfer in Arabidopsis thaliana cryptochromes. The possible breakdown of the Condon approximation is also investigated. We have devised a simulation protocol based on the realization of molecular dynamics simulations on diabatic potential energy surfaces defined at the hybrid constrained density functional theory/molecular mechanics level. The outcomes of the simulations are analyzed through various dedicated kinetics schemes related to the Marcus theory that account for the aforementioned quantum effects. MD simulations also provide a basic material to define realistic model Hamiltonians for subsequent quantum dissipative dynamics. To carry out quantum simulations, we have implemented an algorithm based on the Hierarchical Equations of Motion. With this new tool in hand we have been able to model the electron transfer chain considering either two- or three-state models. Kinetic models and quantum simulations converge to the conclusion that quantum effects have a significant impact on the rate of charge separation. Nuclear tunneling involving atoms of the tryptophan redox cofactors as well as of the environment (protein atoms and water molecules) is significant. On the other hand non-Condon effects are negligible in most simulations. Taken together, the results of the present work provide new insights into the molecular mechanisms controlling charge separation in this family of flavoproteins.

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“…The black, red and blue curves correspond to the first, second and third diabatic state respectively. Bottom eqn (33) has been used. Bottom eqn (33) has been used.…”

mentioning

confidence: 99%

mentioning

confidence: 99%

Quantum effects in ultrafast electron transfers within cryptochromes

Firmino

Mangaud

Cailliez

et al. 2016

Phys. Chem. Chem. Phys.

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“…The strategy could be less adequate in other situations with unstructured spectral densities or with many thin peaks of similar intensity. Another definition of a collective coordinate can also be examined [71]. The other necessary conditions are a Markovian secondary bath and a weak residual coupling.…”

Section: Results Of the Vibronic Modelmentioning

confidence: 99%

“…This mapping towards a vibronic or reaction path model has been frequently used in the literature [1,17,70,71]. The collective mode, often called 'effective mode' can still be coupled to a secondary bath.…”

Section: Effective Modementioning

confidence: 99%

Analysis of the non-Markovianity for electron transfer reactions in an oligothiophene-fullerene heterojunction

2017

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a b s t r a c tThe non-Markovianity of the electron transfer in an oligothiophene-fullerene heterojunction described by a spin-boson model is analyzed using the time dependent decoherence canonical rates and the volume of accessible states in the Bloch sphere. The dynamical map of the reduced electronic system is computed by the hierarchical equations of motion methodology (HEOM) providing an exact dynamics. Transitory witness of non-Markovianity is linked to the bath dynamics analyzed from the HEOM auxiliary matrices. The signature of the collective bath mode detected from HEOM in each electronic state is compared with predictions of the effective mode extracted from the spectral density. We show that including this main reaction coordinate in a one-dimensional vibronic system coupled to a residual bath satisfactorily describes the electron transfer by a simple Markovian Redfield equation. Non-Markovianity is computed for three inter fragment distances and compared with a priori criterion based on the system and bath characteristic timescales.

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“…The so-called coherence parameter [110] defined as Ccoh=false〈HDAfalse〉2/false〈HDA2false〉 takes values of 0.006 and 0.003, very close to zero, which indicates that the peptide conformational dynamics strongly affects ET. Other applications of cDFT to model ET processes with deMon2k can be found in References [111,112,113].…”

Section: Applicationsmentioning

confidence: 99%

Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review

et al. 2019

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deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born–Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.

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Electron transfer within a reaction path model calibrated by constrained DFT calculations: application to mixed-valence organic compounds

Cited by 20 publications

References 104 publications

Quantum effects in ultrafast electron transfers within cryptochromes

Quantum effects in ultrafast electron transfers within cryptochromes

Analysis of the non-Markovianity for electron transfer reactions in an oligothiophene-fullerene heterojunction

Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review

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