Electronic Structure of the Perturbed Blue Copper Site in Nitrite Reductase:  Spectroscopic Properties, Bonding, and Implications for the Entatic/Rack State

2012

J. Phys. Chem. A

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.

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

“…17,18 More bands are evident in the CD spectra compared to the optical absorption spectra. For plastocyanin, a small positive band at 10 800 cm À1 and larger negative band at about 13 000 cm À1 are observed.…”

Section: Introductionmentioning

confidence: 99%

Modelling the spectroscopy and dynamics of plastocyanin

Robinson

Phys. Chem. Chem. Phys.

2010

The electronic absorption, electronic circular dichroism and X-ray absorption spectroscopy of the blue copper protein plastocyanin is studied with density functional theory, time-dependent density functional theory and multireference configuration interaction in conjunction with classical molecular dynamics simulations. A strong correlation is observed between the excitation energy of the intense ligand to metal charge transfer band and the copper-cysteine sulfur bond length. The results suggest that the copper-cysteine sulfur bond length in the crystal structure of plastocyanin is too short and should be closer to the corresponding bond lengths in related blue copper proteins. Averaging over many structural conformations is required to reproduce the major features of the experimental circular dichroism spectra. A correlation between the rotational strength of the ligand to metal charge transfer band and the distortion of the copper atom from the plane of the cysteine sulfur and histidine nitrogen atoms is found. X-ray absorption calculations show a smaller sulfur p orbital character in the singly occupied molecular orbital of cucumber basic protein compared to plastocyanin.

“…This leads to a small geometry change on reduction from Cu(II) to Cu(I), 3,4 resulting in a small reorganization energy and high rate of electron transfer. 5 The oxidised forms of blue copper proteins have a d 9 electronic configuration that results in distinctive absorption spectra, [6][7][8][9] with an intense band at about 2.1 eV (16 700 cm 1 ). This band is often referred to as arising from a ligand to metal charge transfer (LMCT) transition, which corresponds to an excitation from the Cys p orbital to the singly occupied orbital (SOMO).…”

Section: Introductionmentioning

confidence: 99%

“…10 Blue copper proteins have also been studied with electronic circular dichroism (CD) spec-troscopy. 6,7 There are more distinct bands in the CD spectra compared to the absorption spectra.…”

Section: Introductionmentioning

confidence: 99%

“…In particular, the intensity of the band arising from the LMCT excitation is reduced relative to the ligand field bands. 6,7 In addition to experimental work, a number of theoretical studies have investigated the structure or spectroscopy of the oxidised form of blue copper proteins. [11][12][13][14][15][16][17][18][19][20]22,[24][25][26] Calculations confirm that the intense band observed in the absorption spectrum arises from an excitation from the orbital comprising a bonding mixture of the Cu 3d x 2 y 2 and S cys 3p p orbitals to the SOMO.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

Deeth

2013

J. Phys. Chem. B

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.