Modelling the spectroscopy and dynamics of plastocyanin

2015

J. Phys. Chem. A

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A note on versions:The version presented here may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher's version. Please see the repository url above for details on accessing the published version and note that access may require a subscription. The electronic structure and photoinduced electron transfer processes in a K + fluorescent sensor that comprises a 4-amino-naphthalimide derived fluorophore with a triazacryptand ligand is investigated using density functional theory (DFT) and time-dependent density functional theory (TDDFT) in order to rationalise the function of the sensor. The absorption and emission energies of the intense electronic excitation localised on the fluorophore are accurately described using a ∆SCF Kohn-Sham DFT approach, which gives excitation energies closer to experiment than TDDFT. Analysis of the molecular orbital diagram arising from DFT calculations for the isolated molecule or with implicit solvent cannot account for the function of the sensor and it is necessary to consider the relative energies of the electronic states formed from the local excitation on the fluorophore and the lowest fluorophore→chelator charge transfer state. The inclusion of solvent in these calculations is critical since the strong interaction of the charge transfer state with the solvent lowers it energy below the local fluorophore excited state making a reductive photoinduced electron transfer possible in the absence of K + , while no such process is possible when the sensor is bound to K + . The rate of electron transfer is quantified using Marcus theory, which gives a rate of electron transfer of k ET =5.98 x 10 6 s −1 .

Section: Methodsmentioning

confidence: 99%

Density Functional Theory Based Analysis of Photoinduced Electron Transfer in a Triazacryptand Based K⁺ Sensor

Briggs

2015

J. Phys. Chem. A

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“…18,19 These functionals work by correcting the core orbital energies while not significantly affecting the valence and virtual orbital energies, and have been shown to give accurate core excitation energies and NEXAFS spectra in a range of applications. 5, [20][21][22][23] In comparison to calculations of NEXAFS spectra, there have been far fewer studies of XES.…”

Section: Introductionmentioning

confidence: 99%

Quantum Chemical Calculations of X-ray Emission Spectroscopy

Wadey

J. Chem. Theory Comput.

2014

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110

The calculation of X-ray emission spectroscopy with equation of motion coupled cluster theory (EOM-CCSD), time dependent density functional theory (TDDFT) and resolution of the identity single excitation configuration interaction with second order perturbation theory (RI-CIS(D)) is studied. These methods can be applied to calculate X-ray emission transitions by using a reference determinant with a core-hole, and they provide a convenient approach to compute the X-ray emission spectroscopy of large systems since all of the required states can be obtained within a single calculation removing the need to perform a separate calculation for each state. For all of the methods, basis sets with the inclusion of additional basis functions to describe core orbitals are necessary, particularly when studying transitions involving the 1s orbitals of heavier nuclei. EOM-CCSD predicts accurate transition energies when compared with experiment, however, its application to larger systems is restricted by its computational cost and difficulty in converging the CCSD equations for a core-hole reference determinant, which become increasing problematic as the size of the system studied increases. While RI-CIS(D)gives accurate transition energies for small molecules containing first row nuclei, its application to larger systems is limited by the CIS states providing a poor zeroth order reference for perturbation theory which leads to very large errors in the computed transition energies for some states. TDDFT with standard exchange-correlation functionals predicts transition energies that are much larger than experiment. Optimization of a hybrid and short-range corrected functional to predict the X-ray emission transitions results in much closer agreement with EOM-CCSD. The most accurate exchange-correlation functional identified is a modified B3LYP hybrid functional with 66% Hartree-Fock exchange, denoted B 66 LYP, which predicts X-ray emission spectra for a range of molecules including fluorobenzene, nitrobenzene, acetone, dimethyl sulfoxide and CF 3 Cl in good agreement with experiment.

“…7,[14][15][16][17][18][19][20] However, there has been less attention on small molecules that incorporate the copper-cysteine bond. Ryde et al have studied the structure and reorganization energy of small models of the copper cysteine bond, including CuSH 0/+ and [Cu(imidazole-CH 3 ) 2 (SC 2 H 5 (CH 3 SC 2 H 5 )] 0/+ , using a number of theoretical methods including density functional theory (DFT) with the B3LYP exchange-correlation functional, perturbation theory and coupled cluster theory.…”

Section: Introductionmentioning

confidence: 99%

Theoretical Study of the Electronic Spectra of Small Molecules That Incorporate Analogues of the Copper–Cysteine Bond

2012

J. Phys. Chem. A

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The copper-sulphur bond which binds cysteinate to the metal centre is a key factor in the spectroscopy of blue copper proteins. We present theoretical calculations describing the electronically excited states of small molecules, including CuSH, CuSCH 3 , (CH 3 ) 2 SCuSH, (imidazole)-CuSH and (imidazole) 2 -CuSH, derived from the active site of blue copper proteins that contain the copper-sulphur bond in order to identify small molecular systems that have electronic structure that is analogous to the active site of the proteins. Both neutral and cationic forms are studied, since these represent the reduced and oxidised forms of the protein, respectively. For CuSH and CuSH + , excitation energies from time-dependent density functional theory with the B97-1 exchange-correlation functional agree well with the available experimental data and multireference configuration interaction calculations. For the positive ions, the singly occupied molecular orbital is formed from an antibonding combination of a 3d orbital on copper and a 3p p orbital on sulphur, which is analogous to the protein. This leads several of the molecules to have qualitatively similar electronic spectra to the proteins. For the neutral molecules, changes in the nature of the low lying virtual orbitals leads the predicted electronic spectra to vary substantially between the different molecules. In particular, addition of a ligand bonded directly to copper results in the low-lying excited states observed in CuSH and CuSCH 3 to be absent or shifted to higher energies.