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Dmitry V Matyushov - One of the best experts on this subject based on the ideXlab platform.
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nanosecond stokes shift dynamics dynamical transition and gigantic Reorganization Energy of hydrated heme proteins
Journal of Physical Chemistry B, 2011Co-Authors: Dmitry V MatyushovAbstract:We report numerical simulations of three hydrated heme proteins, myoglobin, cytochrome c, and cytochrome B562. The properties of interest are the dynamics and statistics of the electric field and electrostatic potential at heme's iron, as well as their separation into the protein and water components. We find that the electric field produced by both the protein and the hydration water relaxes on the time scale of 3-6 ns, and the relaxation time of the electrostatic potential is close to 1 ns. The slow dynamics of the electrostatic observables is accompanied by their large variances. For the electrostatic potential, a large amplitude of its fluctuations leads to a gigantic Reorganization Energy of a half redox reaction changing the redox state of the protein. Both a large magnitude and a slow relaxation time of the electric field fluctuations are required to explain the onset of large mean-square displacements of iron at the point of protein's dynamical transition. These requirements are met by the simulations which are used to explain the temperature dependence of heme iron displacements measured by Mossbauer spectroscopy. All three phenomena, (i) nanosecond dynamics, (ii) protein dynamical transition and a large high-temperature excess of atomic mean-square displacements, and (iii) the gigantic Reorganization Energy, are explained here by one physical mechanism. This mechanism involves two components: nanosecond motions of the protein surface residues and polarization of the interfacial water by the protein charges. Global nanosecond conformations of the protein move the surface water. Since water is polarized, these movements create large-amplitude electrostatic fluctuations, sufficient to modify displacements of groups inside the protein and yield Reorganization energies of protein electron transfer far exceeding those found for small molecules. Water follows adiabatically the protein motions. Therefore, the relaxation times of the protein and its hydration layer are close, leading to matching temperatures of the dynamical transition for the two components.
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glassy protein dynamics and gigantic solvent Reorganization Energy of plastocyanin
Journal of Physical Chemistry B, 2008Co-Authors: David N Lebard, Dmitry V MatyushovAbstract:We report the results of molecular dynamics simulations of electron-transfer activation parameters of plastocyanin metalloprotein involved as an electron carrier in natural photosynthesis. We have discovered that slow, non-ergodic conformational fluctuations of the protein, coupled to hydrating water, result in a very broad distribution of donor-acceptor Energy gaps far exceeding those observed for commonly studied inorganic and organic donor-acceptor complexes. The Stokes shift is not affected by these fluctuations and can be calculated from solvation models in terms of the linear response of the solvent dipolar polarization. The non-ergodic character of large-amplitude protein/water mobility breaks the strong link between the Stokes shift and the Reorganization Energy characteristic of equilibrium (ergodic) theories of electron transfer. This mechanism might be responsible for fast electronic transitions in natural electron-transfer proteins characterized by low reaction free Energy.
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glassy protein dynamics and gigantic solvent Reorganization Energy of plastocyanin
arXiv: Biological Physics, 2007Co-Authors: David N Lebard, Dmitry V MatyushovAbstract:We report the results of Molecular Dynamics simulations of electron transfer activation parameters of plastocyanin metalloprotein involved as electron carrier in natural photosynthesis. We have discovered that slow, non-ergodic conformational fluctuations of the protein, coupled to hydrating water, result in a very broad distribution of donor-acceptor Energy gaps far exceeding that observed for commonly studied inorganic and organic donor-acceptor complexes. The Stokes shift is not affected by these fluctuations and can be calculated from solvation models in terms of the response of the solvent dipolar polarization. The non-ergodic character of large-amplitude protein/water mobility breaks the strong link between the Stokes shift and Reorganization Energy characteristic of equilibrium (ergodic) theories of electron transfer. This mechanism might be responsible for low activation barriers in natural electron transfer proteins characterized by low reaction free Energy.
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solvent Reorganization Energy of electron transfer reactions in polar solvents
Journal of Chemical Physics, 2004Co-Authors: Dmitry V MatyushovAbstract:A microscopic theory of solvent Reorganization Energy in polar molecular solvents is developed. The theory represents the solvent response as a combination of the density and polarization fluctuations of the solvent given in terms of the density and polarization structure factors. A fully analytical formulation of the theory is provided for a solute of arbitrary shape with an arbitrary distribution of charge. A good agreement between the analytical procedure and the results of Monte Carlo simulations of model systems is achieved. The Reorganization Energy splits into the contributions from density fluctuations and polarization fluctuations. The polarization part is dominated by longitudinal polarization response. The density part is inversely proportional to temperature. The dependence of the solvent Reorganization Energy on the solvent dipole moment and refractive index is discussed.
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effects of solvent and solute polarizability on the Reorganization Energy of electron transfer
Journal of Physical Chemistry A, 2004Co-Authors: Shikha Gupta, Dmitry V MatyushovAbstract:We report Monte Carlo simulations of the effect of solute and solvent polarizability on the solvent Reorganization Energy of intramolecular electron transfer. In the first set of simulations, the polarizability of the solvent is varied at constant permanent dipole of the solvent molecules (high-frequency dielectric constants is in the range 1−2.5). The Reorganization Energy is calculated on the solvent configurations around a nonpolar solute (charge separation transition) and around a dipolar solute (charge recombination transition). In both cases, the variation of the solvent Reorganization Energy does not exceed 30%, a change much smaller than predicted by dielectric continuum models. In the second set of simulations, the solute polarizability in the charge-separated state was varied while keeping the initial state for charge separation at zero dipole moment and polarizability. The gap between the charge-separation and charge recombination Reorganization energies widens substantially with increasing dif...
Ulf Ryde - One of the best experts on this subject based on the ideXlab platform.
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Reorganization Energy for Internal Electron Transfer in Multicopper Oxidases.
The journal of physical chemistry. B, 2011Co-Authors: Maryam Farrokhnia, Jimmy Heimdal, Sergey Shleev, Lubomír Rulíšek, Ulf RydeAbstract:We have calculated the Reorganization Energy for the intramolecular electron transfer between the reduced type 1 copper site and the peroxy intermediate of the trinuclear cluster in the multicopper oxidase CueO. The calculations are performed at the combined quantum mechanics and molecular mechanics (QM/MM) level, based on molecular dynamics simulations with tailored potentials for the two copper sites. We obtain a Reorganization Energy of 91-133 kJ/mol, depending on the theoretical treatment. The two Cu sites contribute by 12 and 22 kJ/mol to this Energy, whereas the solvent contribution is 34 kJ/mol. The rest comes from the protein, involving small contributions from many residues. We have also estimated the Energy difference between the two electron-transfer states and show that the reduction of the peroxy intermediate is exergonic by 43-87 kJ/mol, depending on the theoretical method. Both the solvent and the protein contribute to this Energy difference, especially charged residues close to the two Cu sites. We compare these estimates with energies obtained from QM/MM optimizations and QM calculations in a vacuum and discuss differences between the results obtained at various levels of theory.
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geometry reduction potential and Reorganization Energy of the binuclear cua site studied by density functional theory
Journal of the American Chemical Society, 2001Co-Authors: Mats Olsson, Ulf RydeAbstract:Abstract in Undetermined The dimeric CuA site found in cytochrome c oxidase and nitrous oxide reductase has been studied with the density functional B3LYP method. We have optimized the structure of the realistic (Im)(S(CH3)2)- Cu(SCH3)2Cu(Im)(CH3CONHCH3) model in the fully reduced, mixed-valence, and fully oxidized states. The optimized structures are very similar to crystal structures of the protein, which shows that the protein does not strain the site significantly. Instead, inorganic model complexes of the protein site are strained by the macrocyclic connections between the ligand models. For the mixed-valence (CuI+CuII) state, two distinct equilibrium structures were found, one with a short Cu-Cu distance, 248 pm, similar to the protein structure, and one with a longer distance, 310 pm, similar to what is found in inorganic models. In the first state, the unpaired electron is delocalized over both copper ions, whereas in the latter, it is more localized to one of the ions. The two states are nearly degenerate. The potential Energy surfaces for the Cu-Cu, Cu-SMet, and Cu-O interactions are extremely flat. In fact, all three distances can be varied between 230 and 310 pm at an expense in Energy of less than 8 kJ/mol, which explains the large variation observed in crystal structures for these interactions. Inclusion of solvation effects does not change this significantly. Therefore, we can conclude that a variation in these distances can change the reduction potential of the CuA site by at most 100 mV. The model complex has a Reorganization Energy of 43 kJ/mol, 20 kJ/mol lower than for a monomeric blue-copper site. This lowering is caused by the delocalization of the unpaired electron in the mixed-valence state. (Less)
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inner sphere Reorganization Energy of iron sulfur clusters studied with theoretical methods
Inorganic Chemistry, 2001Co-Authors: Emma Sigfridsson, Mats Olsson, Ulf RydeAbstract:Models of several types of iron-sulfur clusters (e.g., Fe4S4(SCH3)42-/3-/4-) have been studied with the density functional B3LYP method and medium-sized basis sets. In a vacuum, the inner-sphere Reorganization energies are 40, 76, 40, 62, 43, and 42 kJ/mol for the rubredoxin, [2Fe-2S] ferredoxin, Rieske, [4Fe-4S] ferredoxin, high-potential iron protein, and desulfoferrodoxin models, respectively. The first two types of clusters were also studied in the protein, where the Reorganization Energy was approximately halved. This change is caused by the numerous NH‚‚‚SCys hydrogen bonds to the negatively charged iron-sulfur cluster, giving rise to a polar local environment. The Reorganization Energy of the iron-sulfur clusters is low because the iron ions retain the same geometry and coordination number in both oxidation states. Cysteine ligands give approximately the same Reorganization Energy as imidazole, but they have the advantage of stabilizing a lower coordination number and giving more covalent bonds and therefore more effective electron-transfer paths. (Less)
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structure strain and Reorganization Energy of blue copper models in the protein
International Journal of Quantum Chemistry, 2001Co-Authors: Ulf Ryde, Mats OlssonAbstract:The copper coordination geometry in the blue copper proteins plastocyanin, nitrite reductase, cucumber basic protein, and azurin has been studied by combined density functional (B3LYP) and molecular mechanical methods. Compared to quantum chemical vacuum calculations, a significant improvement of the geometry is seen (toward the experimental structures) not only for the dihedral angles of the ligands but also for the bond lengths and angles around the copper ion. The flexible Cu–SMet bond is well reproduced in the oxidized structures, whereas it is too long in some of the reduced complexes (too short in vacuum). The change in the geometry compared to the vacuum state costs 33–66 kJ/mol. If the covalent bonds between the ligands and the protein are broken, this Energy decreases by ∼25 kJ/mol, which is an estimate of the covalent strain. This is similar to what is found for other proteins, so the blue copper proteins are not more strained than other metalloproteins. The inner-sphere self-exchange Reorganization Energy of all four proteins are ∼30 kJ/mol. This is 30–50 kJ/mol lower than in vacuum. The decrease is caused by dielectric and electrostatic effects in the protein, especially the hydrogen bond(s) to the cysteine copper ligands and not by covalent strain. (Less)
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Quantum chemical calculations of the Reorganization Energy of blue- copper proteins
Protein Science, 1998Co-Authors: Mats H M Olsson, Ulf Ryde, Björn O. RoosAbstract:The inner-sphere Reorganization Energy for several copper complexes related to the active site in blue-copper protein has been calculated with the density functional B3LYP method. The best model of the blue-copper proteins, Cu(Im)2(SCH3)(S(CH3)2)(0/+), has a self-exchange inner-sphere Reorganization Energy of 62 kJ/mol, which is at least 120 kJ/mol lower than for Cu(H2O)4(+/2+). This lowering of the Reorganization Energy is caused by the soft ligands in the blue-copper site, especially the cysteine thiolate and the methionine thioether groups. Soft ligands both make the potential surfaces of the complexes flatter and give rise to oxidized structures that are quite close to a tetrahedron (rather than tetragonal). Approximately half of the Reorganization Energy originates from changes in the copper-ligand bond lengths and half of this contribution comes from the Cu-S(Cys) bond. A tetragonal site, which is present in the rhombic type 1 blue-copper proteins, has a slightly higher (16 kJ/mol) inner-sphere Reorganization Energy than a trigonal site, present in the axial type 1 copper proteins. A site with the methionine ligand replaced by an amide group, as in stellacyanin, has an even higher Reorganization Energy, about 90 kJ/mol.
Xueyu Song - One of the best experts on this subject based on the ideXlab platform.
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a molecular debye huckel approach to the Reorganization Energy of electron transfer reactions in an electric cell
Journal of Chemical Physics, 2014Co-Authors: Tiejun Xiao, Xueyu SongAbstract:Electron transfer near an electrode immersed in ionic fluids is studied using the linear response approximation, namely, mean value of the vertical Energy gap can be used to evaluate the Reorganization Energy, and hence any linear response model that can treat Coulomb interactions successfully can be used for the Reorganization Energy calculation. Specifically, a molecular Debye-Huckel theory is used to calculate the Reorganization Energy of electron transfer reactions in an electric cell. Applications to electron transfer near an electrode in molten salts show that the Reorganization energies from our molecular Debye-Huckel theory agree well with the results from MD simulations.
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Reorganization Energy of electron transfer processes in ionic fluids a molecular debye huckel approach
Journal of Chemical Physics, 2013Co-Authors: Tiejun Xiao, Xueyu SongAbstract:The Reorganization Energy of electron transfer processes in ionic fluids is studied under the linear response approximation using a molecule Debye-Huckel theory. Reorganization energies of some model reactants of electron transfer reactions in molten salts are obtained from molecular simulations and a molecule Debye-Huckel approach. Good agreements between simulation results and the results from our theoretical calculations using the same model Hamiltonian are found. Applications of our theory to electron transfer reactions in room temperature ionic liquids further demonstrate that our theoretical approach presents a reliable and accurate methodology for the estimation of Reorganization energies of electron transfer reactions in ionic fluids.
Robert J. Silbey - One of the best experts on this subject based on the ideXlab platform.
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Efficient Energy transfer in light-harvesting systems, I: optimal temperature, Reorganization Energy, and spatial-temporal correlations
New Journal of Physics, 2010Co-Authors: Fan Liu, Young Shen, Jianshu Cao, Robert J. SilbeyAbstract:Understanding the mechanisms of efficient and robust Energy transfer in light-harvesting systems provides new insights for the optimal design of artificial systems. In this paper, we use the Fenna-Matthews-Olson (FMO) protein complex and phycocyanin 645 (PC 645) to explore the general dependence on physical parameters that help maximize the efficiency and maintain its stability. With the Haken-Strobl model, the maximal Energy transfer efficiency (ETE) is achieved under an intermediate optimal value of dephasing rate. To avoid the infinite temperature assumption in the Haken-Strobl model and the failure of the Redfield equation in predicting the Forster rate behavior, we use the generalized Bloch-Redfield (GBR) equation approach to correctly describe dissipative exciton dynamics and find that maximal ETE can be achieved under various physical conditions, including temperature, Reorganization Energy, and spatial-temporal correlations in noise. We also identify regimes of Reorganization Energy where the ETE changes monotonically with temperature or spatial correlation and therefore cannot be optimized with respect to these two variables.
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efficient Energy transfer in light harvesting systems i optimal temperature Reorganization Energy and spatial temporal correlations
New Journal of Physics, 2010Co-Authors: Fan Liu, Young Shen, Jianshu Cao, Robert J. SilbeyAbstract:Understanding the mechanisms of efficient and robust Energy transfer in light-harvesting systems provides new insights for the optimal design of artificial systems. In this paper, we use the Fenna-Matthews-Olson (FMO) protein complex and phycocyanin 645 (PC 645) to explore the general dependence on physical parameters that help maximize the efficiency and maintain its stability. With the Haken-Strobl model, the maximal Energy transfer efficiency (ETE) is achieved under an intermediate optimal value of dephasing rate. To avoid the infinite temperature assumption in the Haken-Strobl model and the failure of the Redfield equation in predicting the Forster rate behavior, we use the generalized Bloch-Redfield (GBR) equation approach to correctly describe dissipative exciton dynamics, and we find that maximal ETE can be achieved under various physical conditions, including temperature, Reorganization Energy and spatial-temporal correlations in noise. We also identify regimes of Reorganization Energy where the ETE changes monotonically with temperature or spatial correlation and therefore cannot be optimized with respect to these two variables.
Tiejun Xiao - One of the best experts on this subject based on the ideXlab platform.
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a molecular debye huckel approach to the Reorganization Energy of electron transfer reactions in an electric cell
Journal of Chemical Physics, 2014Co-Authors: Tiejun Xiao, Xueyu SongAbstract:Electron transfer near an electrode immersed in ionic fluids is studied using the linear response approximation, namely, mean value of the vertical Energy gap can be used to evaluate the Reorganization Energy, and hence any linear response model that can treat Coulomb interactions successfully can be used for the Reorganization Energy calculation. Specifically, a molecular Debye-Huckel theory is used to calculate the Reorganization Energy of electron transfer reactions in an electric cell. Applications to electron transfer near an electrode in molten salts show that the Reorganization energies from our molecular Debye-Huckel theory agree well with the results from MD simulations.
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Reorganization Energy of electron transfer processes in ionic fluids a molecular debye huckel approach
Journal of Chemical Physics, 2013Co-Authors: Tiejun Xiao, Xueyu SongAbstract:The Reorganization Energy of electron transfer processes in ionic fluids is studied under the linear response approximation using a molecule Debye-Huckel theory. Reorganization energies of some model reactants of electron transfer reactions in molten salts are obtained from molecular simulations and a molecule Debye-Huckel approach. Good agreements between simulation results and the results from our theoretical calculations using the same model Hamiltonian are found. Applications of our theory to electron transfer reactions in room temperature ionic liquids further demonstrate that our theoretical approach presents a reliable and accurate methodology for the estimation of Reorganization energies of electron transfer reactions in ionic fluids.