A QM/MM study on the spinach plastocyanin: Redox properties and absorption spectra

Monari, Antonio; Véry, Thibaut; Rivail, Jean‐Louis; Assfeld, Xavier

doi:10.1016/j.comptc.2011.11.026

Cited by 60 publications

(45 citation statements)

References 44 publications

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“…Finally, note that in order to match experimental results, vertical transitions have been convoluted with Gaussian functions of fixed half-length width of 0.2 eV. As previously reported [26] we underline that, although dealing with charge transfer transitions, in isolated model systems similar to our active site, the use of long range corrected functional gives practically indistinguishable spectra. To be assured of such an occurrence, we also performed more tests computing the absorption spectrum of the isolated plastocyanin active site (at the QM/MM B3LYP optimized geometry) using three more functionals: CAM-B3LYP [55], wB97XD [56], PBE0 [57].…”

Section: Computational Strategymentioning

confidence: 91%

“…Conversely, the influence of the fixed charges on classical atoms can be easily evidenced by setting them to zero and performing another QM computation on the previously optimized fixed geometry. The electronic response of the surroundings (ERS) [26,[31][32][33][34] technique allows us to simulate the role of electronic polarization, that is, the modifications of the electronic distribution of the classical subsystem treated at MM level under the influence of the density modification in the QM part. Indeed, if within the framework of the Franck-Condon principle, the electronic transitions are vertical and do not involve any nuclear position rearrangement, the electronic cloud of the environment can, however, instantaneously adapt itself to the new electronic distribution of the chromophore.…”

Section: Electrostatic Polarization Of the MM Partmentioning

confidence: 99%

“…In a previous paper [26], we have shown that a mixed quantum mechanics/molecular mechanics (QM/MM) approach of the spinach plastocyanin is quite appropriate to address the spectroscopic as well as the redox properties of this molecule and to analyze the influence of the various characteristics of the macromolecular surroundings on these properties. In the present paper, we focus our attention on the influence of the changes of the copper II fourfold coordination on the spectroscopic properties by considering the mutations of the methionine residue by the cysteine anion, cysteine, glutamate and homocysteine anion.…”

Section: Introductionmentioning

confidence: 99%

“…The evolution of the spectroscopic parameters with mutations will be also considered. The use of natural transition orbitals (NTOs) [26,38] techniques will allow us to perform a systematic analysis of the nature and electronic properties of the excited states, Fig. 2 The structure of nitrosocyanin, active site in ball and stick representation.…”

Section: Introductionmentioning

confidence: 99%

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Effects of mutations on the absorption spectra of copper proteins: a QM/MM study

et al. 2012

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The ground and excited state properties of copper proteins are studied and analyzed using hybrid quantum mechanics/molecular mechanics technique. Wildtype plastocyanin, characterized by an intense blue color, and wild-type nitrosocyanin, a red protein, are considered. These proteins differ from some ligands of the copper containing chromophore; we also studied the effects of selective mutations of one of the active site residue in plastocyanin. It is shown that this mutation is able to strongly modify the UV/VIS spectrum continuously modifying the absorption spectrum of the protein that from blue becomes red. Electrostatic and polarization effects of the macromolecular environment on the chromophore are taken into account using original techniques. Principal transitions are analyzed by mean of natural transition orbitals.

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Section: Computational Strategymentioning

confidence: 91%

Section: Electrostatic Polarization Of the MM Partmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Effects of mutations on the absorption spectra of copper proteins: a QM/MM study

et al. 2012

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“…Overall, good agreement with the experiment was obtained, with the excitation energies of the six lowest excitations predicted within 0.25 eV of their experimental values. Time dependent density functional theory (TDDFT) has also been applied to compute the absorption, 20,27 electronic circular dichroism (CD) 27,28 and magnetic circular dichroism (MCD) 27 of blue copper proteins. While the qualitative shape of the absorption spectra was reproduced, the excitation energies were found to be too high and the computed CD spectra show a relatively poor agreement with experiment.…”

Section: Introductionmentioning

confidence: 99%

Computational Study of the Structure and Electronic Circular Dichroism Spectroscopy of Blue Copper Proteins

Deeth

Besley

2013

J. Phys. Chem. B

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The calculation of the electronic circular dichroism (CD) spectra of the oxidised form of the blue copper proteins plastocyanin and cucumber basic protein and the relationship between the observed spectral features and the structure of the active site of the protein is investigated.Excitation energies and transition strengths are computed using multi reference configuration interaction, and it is shown that computed spectra based on coordinates from the crystal structure or a single structure optimised in quantum mechanics/molecular mechanics (QM/MM) or ligand field molecular mechanics (LFMM) are qualitatively incorrect. In particular, the rotational strength of the ligand to metal charge transfer band is predicted to be too small or have the incorrect sign. By considering calculations on active site models with modified structures it is shown that the intensity of this band is sensitive to the non-planarity of the histidine and cysteine ligands coordinated to copper. Calculation of the ultraviolet absorption and CD spectra based upon averaging over many structures drawn from a LFMM molecular dynamics simulation are in good agreement with experiment, and superior to analogous calculations based upon structures from a classical molecular dynamics simulation. This provides evidence that the LFMM force field provides an accurate description of the molecular dynamics of these proteins.

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Charge‐Transfer versus Charge‐Separated Triplet Excited States of [Re^I(dmp)(CO)₃(His124)(Trp122)]⁺ in Water and in Modified Pseudomonas aeruginosa Azurin Protein

Marazzi

Gattuso

Fumanal

et al. 2019

Chemistry A European J

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A computational investigation of the triplet excited states of a rhenium complex electronically coupled with a tryptophan side chain and bound to an azurin protein is presented. In particular, by using high‐level molecular modeling, evidence is provided for how the electronic properties of the excited‐state manifolds strongly depend on coupling with the environment. Indeed, only upon explicitly taking into account the protein environment can two stable triplet states of metal‐to‐ligand charge transfer or charge‐separated nature be recovered. In addition, it is also demonstrated how the rhenium complex plus tryptophan system in an aqueous environment experiences too much flexibility, which prevents the two chromophores from being electronically coupled. This occurrence disables the formation of a charge‐separated state. The successful strategy requires a multiscale approach of combining molecular dynamics and quantum chemistry. In this context, the strategy used to parameterize the force fields for the electronic triplet states of the metal complex is also presented.

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A QM/MM study on the spinach plastocyanin: Redox properties and absorption spectra

Cited by 60 publications

References 44 publications

Effects of mutations on the absorption spectra of copper proteins: a QM/MM study

Effects of mutations on the absorption spectra of copper proteins: a QM/MM study

Computational Study of the Structure and Electronic Circular Dichroism Spectroscopy of Blue Copper Proteins

Charge‐Transfer versus Charge‐Separated Triplet Excited States of [Re^I(dmp)(CO)₃(His124)(Trp122)]⁺ in Water and in Modified Pseudomonas aeruginosa Azurin Protein

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A QM/MM study on the spinach plastocyanin: Redox properties and absorption spectra

Cited by 60 publications

References 44 publications

Effects of mutations on the absorption spectra of copper proteins: a QM/MM study

Effects of mutations on the absorption spectra of copper proteins: a QM/MM study

Computational Study of the Structure and Electronic Circular Dichroism Spectroscopy of Blue Copper Proteins

Charge‐Transfer versus Charge‐Separated Triplet Excited States of [ReI(dmp)(CO)3(His124)(Trp122)]+ in Water and in Modified Pseudomonas aeruginosa Azurin Protein

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Charge‐Transfer versus Charge‐Separated Triplet Excited States of [Re^I(dmp)(CO)₃(His124)(Trp122)]⁺ in Water and in Modified Pseudomonas aeruginosa Azurin Protein