Non-Markov dissipative dynamics of electron transfer in a photosynthetic reaction center

Poddubnyy, Vladimir V.; Glebov, I. O.; Еремин, В. В.

doi:10.1007/s11232-014-0141-6

Cited by 5 publications

(5 citation statements)

References 14 publications

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“…This spectral function has a peak near 700 cm –1 , which indicates that there is a strong interaction between chromophores and vibrational modes with frequencies close to this value. Such a strong interaction can cause oscillations of population of the charge-transfer state with frequency of ∼700–550 = 150 cm –1 . It should be mentioned, that the shape of this spectral function is very similar to the shape of the spectral function that was determined on the basis of molecular dynamics calculation …”

Section: Resultsmentioning

confidence: 99%

“…This transition is dissipative and occurs only due to interaction of chromophores with vibrations of its protein environment. We showed 10 that oscillations in the time-dependencies of spectral properties might be caused by nonmarkovian effects.…”

Section: ■ Introductionmentioning

confidence: 89%

“…The second group includes protein vibrational frequencies that can be calculated quite accurately using the molecular mechanics method. The last one is a set of interaction parameters that can be calculated on the basis of the wave functions of the chromophore subsystem and forms of the protein normal modes …”

Section: Theoretical Methodsmentioning

confidence: 99%

“…Interaction parameters – ĝ α matrix elements were calculated using the formula where m α is the reduced mass of the αth mode, A α, q b are elements of the transformation matrix from the Cartesian coordinates of protein atoms q b to the normal modes coordinates, and operators F̂ b determine forces that act on the b th protein atom from the chromophore system side. Calculation of F̂ b matrix elements was performed using the one-electron density matrices ⟨ t ( r⃗ ) | P̂ K , L | u ( r⃗ )⟩ in the basis of atomic orbitals | t ( r⃗ )⟩ and | u ( r⃗ )⟩.…”

Section: Theoretical Methodsmentioning

confidence: 99%

“…The last one is a set of interaction parameters that can be calculated on the basis of the wave functions of the chromophore subsystem and forms of the protein normal modes. 10 The first step of the calculation was determination of the RC structure and normal modes of its part, which does not include chromophores, participating in primary ET. These calculations were performed by means of molecular mechanics using GROMACS software.…”

Section: Modelmentioning

confidence: 99%

See 4 more Smart Citations

Protein Vibration Effects on Primary Electron Transfer Dynamics in Rhodobacter sphaeroides Photosynthetic Reaction Center

2017

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Primary electron transfer (ET) in the chromophore subsystem in a bacterial reaction center (RC) is a unique process, and is coupled with the protein motion, which, like the ET, is caused by photoexcitation of these chromophores. ET is also coupled with dissipative processes, which are caused by interaction between chromophores and vibrations of its surrounding protein. We propose a new dynamics calculation method that accounts for both these effects of protein vibrations. Within this method, the photoinduced protein motion causes an addition of coherent component to the ET rate. We performed dynamics calculation using this method and parameters, which were determined from the ab initio wave functions of the chromophore subsystem and protein normal vibrational modes. We showed that it is this protein motion that causes oscillations in the time-dependencies of stimulated emission intensities and of absorption at 1020 nm. Moreover, the latter oscillations are related to the coherent component of the ET rate.

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Section: Resultsmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 89%

Section: Theoretical Methodsmentioning

confidence: 99%

Section: Theoretical Methodsmentioning

confidence: 99%

Section: Modelmentioning

confidence: 99%

See 3 more Smart Citations

Protein Vibration Effects on Primary Electron Transfer Dynamics in Rhodobacter sphaeroides Photosynthetic Reaction Center

2017

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Applicability of the protein environment equilibrium approximation for describing ultrafast biophysical processes

2015

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Transient structures and chemical reaction dynamics

Ischenko¹,

Weber²,

Miller³

2017

Russ. Chem. Rev.

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To study transition structures that are formed in real time during a chemical reaction process, it is necessary to use ultrafast methods to follow the structural dynamics of molecular systems. For many decades, optical methods have been used to study the electronic states and time course giving rise to structural intermediates of chemical reactions with an ever higher time resolution. Although in some cases optical methods show many details, ultimately the results of these observations give only indirect information about the structure of the chemical reaction intermediates. Experimental observation of the behaviour of matter in the space-time continuum on ultrashort time scale is the necessary first step to explain and, subsequently, to control the nonequilibrium processes and functionality of the systems under study, to trace the relationship between the elements of the triad 'Structure–Dynamics–Function' to fully understand material properties. The results of these studies provide the necessary new information for testing theoretical approaches to the description of nonequilibrium chemical dynamics of molecular systems. The study of the time sequence of ultrafast processes occurring during the evolution of intermediate structures in the course of chemical reactions requires the integration of information that can be obtained by using complementary diffraction and spectroscopic methods based on various physical phenomena. Integration of data from ultrafast diffraction and spectroscopy makes it possible to investigate timescales prior to the onset of dissipation in which the coherent dynamics of matter can be observed. The use of quantum chemical calculations has reached a level of sophistication that makes it possible to explain the results of these experimental studies, the features of nonadiabatic behaviour of intermediate structures, and transition states of chemical reactions of molecular systems. This review analyzes the achievements of this rapidly developing field of modern chemistry, femtochemistry, to observe the primary events directing chemistry. The bibliography includes 580 references

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Non-Markov dissipative dynamics of electron transfer in a photosynthetic reaction center

Cited by 5 publications

References 14 publications

Protein Vibration Effects on Primary Electron Transfer Dynamics in Rhodobacter sphaeroides Photosynthetic Reaction Center

Protein Vibration Effects on Primary Electron Transfer Dynamics in Rhodobacter sphaeroides Photosynthetic Reaction Center

Applicability of the protein environment equilibrium approximation for describing ultrafast biophysical processes

Transient structures and chemical reaction dynamics

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