| 1. |
- De Kerpel, Jan O A, et al.
(författare)
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Geometric and Electronic Structure of Co(II)-Substituted Azurin
- 1999
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 103:39, s. 8375-8382
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Tidskriftsartikel (refereegranskat)abstract
- The molecular and electronic structures of Co(II)-substituted azurin have been investigated using several realistic models of the metal coordination sphere. The geometry of the models was optimized using the hybrid density functional B3LYP method and compared to the structures obtained for similar Cu(II) models. It is found that Co(II) prefers a distorted tetrahedral structure with four strong bonds to two histidine nitrogens, the cysteine sulphur, and the backbone carbonyl group. This is in contrast to Cu(II), where two weak axial bonds to methionine and the backbone oxygen are found, combined with three strong bonds to the histidines and cysteine in the equatorial plane of a trigonal bipyramidal structure. The optimal structure of the models conforms with experimental crystal data, indicating that the active-site structure in these proteins is determined by the preferences of the metal ion and its ligand and not by protein strain. The electronic structure and spectrum of the Co(imidazole) 2(SH)(SH) 2(HCONH 2) + model have been investigated in detail using multiconfigurational second-order perturbation theory based on a complete active-space wavefunction (CASPT2). Nine ligand-field transitions and six S cys → Co charge-transfer transitions have been calculated, and all experimentally observed absorption bands in the absorption spectrum of Co(II) azurin have been assigned. It is shown that the Co-S cys bond is more ionic than the Cu-S cys bond and that this causes the blue shift and weakening of the charge-transfer states in the spectrum of Co(II)-substituted azurin compared to native copper protein.
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| 2. |
- De Kerpel, Jan O A, et al.
(författare)
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Theoretical study of the structural and spectroscopic properties of stellacyanin
- 1998
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 102:23, s. 4638-4647
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Tidskriftsartikel (refereegranskat)abstract
- The electronic spectrum of the azurin Met121Gln mutant, a model of the blue copper protein stellacyanin, has been studied by ab initio multiconfigurational second-order perturbation theory (the CASPT2 method), including the effect of the protein and solvent by point charges. The six lowest electronic transitions have been calculated and assigned with an error of less than 2400 cm-1. The ground-state singly occupied orbital is found to be a predominantly π antibonding orbital involving Cu3d and Scys3pπ. However, it also contains a significant amount (18%) of Cu-Scys σ antibonding character. This σ interaction is responsible for the appearance in the absorption spectrum of a band at 460 nm, with a significantly higher intensity than observed for other, axial, type 1 copper proteins (i.e., plastocyanin or azurin). The π-σ mixing is caused by the axial glutamine ligand binding at a much shorter distance to copper than the corresponding methionine ligand in the normal blue copper proteins. This explains why, based on its spectral properties, stellacyanin is classified among the rhombic type 1 copper proteins, although its structure is clearly trigonal, as it is for the axial proteins. Calculations have also been performed on structures where the glutamine model coordinates to the copper ion via the deprotonated N∈ atom instead of the O∈ atom. However, the resulting transition energies do not resemble the experimental spectrum obtained at normal or elevated pH. Thus, the results do not confirm the suggestion that the coordinating atom of glutamine changes at high pH.
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| 3. |
- Delcey, Mickaël G., 1988-, et al.
(författare)
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Accurate calculations of geometries and singlet-triplet energy differences for active-site models of [NiFe] hydrogenase
- 2014
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 16:17, s. 7927-7938
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the geometry and singlet-triplet energy difference of two mono-nuclear Ni2+ models related to the active site in [NiFe] hydrogenase. Multiconfigurational second-order perturbation theory based on a complete active-space wavefunction with an active space of 12 electrons in 12 orbitals, CASPT2(12,12), reproduces experimental bond lengths to within 1 pm. Calculated singlet-triplet energy differences agree with those obtained from coupled-cluster calculations with single, double and (perturbatively treated) triple excitations (CCSD(T)) to within 12 kJ mol(-1). For a bimetallic model of the active site of [NiFe] hydrogenase, the CASPT2(12,12) results were compared with the results obtained with an extended active space of 22 electrons in 22 orbitals. This is so large that we need to use restricted active-space theory (RASPT2). The calculations predict that the singlet state is 48-57 kJ mol(-1) more stable than the triplet state for this model of the Ni-Sl(a) state. However, in the [NiFe] hydrogenase protein, the structure around the Ni ion is far from the square-planar structure preferred by the singlet state. This destabilises the singlet state so that it is only similar to 24 kJ mol(-1) more stable than the triplet state. Finally, we have studied how various density functional theory methods compare to the experimental, CCSD(T), CASPT2, and RASPT2 results. Semi-local functionals predict the best singlet-triplet energy differences, with BP86, TPSS, and PBE giving mean unsigned errors of 12-13 kJ mol(-1) (maximum errors of 25-31 kJ mol(-1)) compared to CCSD(T). For bond lengths, several methods give good results, e. g. TPSS, BP86, and M06, with mean unsigned errors of 2 pm for the bond lengths if relativistic effects are considered.
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| 4. |
- Dong, Geng, et al.
(författare)
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H2 binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods
- 2017
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Ingår i: Physical Chemistry Chemical Physics. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 19:16, s. 10590-10601
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Tidskriftsartikel (refereegranskat)abstract
- [NiFe] hydrogenases catalyse the reversible conversion of molecular hydrogen to protons and electrons. This seemingly simple reaction has attracted much attention because of the prospective use of H2 as a clean fuel. In this paper, we have studied how H2 binds to the active site of this enzyme. Combined quantum mechanical and molecular mechanics (QM/MM) optimisation was performed to obtain the geometries, using both the TPSS and B3LYP density-functional theory (DFT) methods and considering both the singlet and triplet states of the Ni(ii) ion. To get more accurate energies and obtain a detailed account of the surroundings, we performed calculations with 819 atoms in the QM region. Moreover, coupled-cluster calculations with singles, doubles, and perturbatively treated triples (CCSD(T)) and cumulant-approximated second-order perturbation theory based on the density-matrix renormalisation group (DMRG-CASPT2) were carried out using three models to decide which DFT methods give the most accurate structures and energies. Our calculations show that H2 binding to Ni in the singlet state is the most favourable by at least 47 kJ mol-1. In addition, the TPSS functional gives more accurate energies than B3LYP for this system.
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| 5. |
- Dong, Geng, et al.
(författare)
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Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods
- 2018
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Ingår i: Inorganic Chemistry. - : American Chemical Society (ACS). - 0020-1669 .- 1520-510X. ; 57:24, s. 15289-15298
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Tidskriftsartikel (refereegranskat)abstract
- [NiFe] hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons. This seemingly simple reaction has attracted much attention because of the prospective use of H2 as a clean fuel. In this paper, we have studied the full reaction mechanism of this enzyme with various computational methods. Geometries were obtained with combined quantum mechanical and molecular mechanics (QM/MM) calculations. To get more accurate energies and obtain a detailed account of the surroundings, we performed big-QM calculations with 819 atoms in the QM region. Moreover, QM/MM thermodynamic cycle perturbation calculations were performed to obtain free energies. Finally, density matrix renormalisation group complete active space self-consistent field calculations were carried out to study the electronic structures of the various states in the reaction mechanism. Our calculations indicate that the Ni-L state is not involved in the reaction mechanism. Instead, the Ni-C state is reduced by one electron and then the bridging hydride ion is transferred to the sulfur atom of Cys546 as a proton and the two electrons transfer to the Ni ion. This step turned out to be rate-determining with an energy barrier of 58 kJ/mol, which is consistent with the experimental rate of 750 ± 90 s-1 (corresponding to ∼52 kJ/mol). The cleavage of the H-H bond is facile with an energy barrier of 33 kJ/mol, according to our calculations. We also find that the reaction energies are sensitive to the size of the QM system, the basis set, and the density functional theory method, in agreement with previous studies.
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| 6. |
- Olsson, Mats H M, et al.
(författare)
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On the relative stability of tetragonal and trigonal Cu(II) complexes with relevance to the blue copper proteins
- 1998
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Ingår i: Journal of Biological Inorganic Chemistry. - : Springer Science and Business Media LLC. - 0949-8257 .- 1432-1327. ; 3:2, s. 109-125
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Tidskriftsartikel (refereegranskat)abstract
- The role of the cysteine thiolate ligand for the unusual copper coordination geometry in the blue copper proteins has been studied by comparing the electronic structure, geometry, and energetics of a number of small Cu(II) complexes. The geometries have been optimised with the density functional B3LYP method, and energies have been calculated by multi- configurational second-order perturbation theory (the CASPT2 method). Most small inorganic Cu(II) complexes assume a tetragonal geometry, where four ligands make σ bonds to a Cu 3d orbital. If a ligand lone-pair orbital instead forms a π bond to the copper ion, it formally occupies two ligand positions in a square coordination, and the structure becomes trigonal. Large, soft, and polarisable ligands, such as SH- and SeH-, give rise to covalent copper-ligand bonds and structures close to a tetrahedron, which might be trigonal or tetragonal with approximately the same stability. On the other hand, small and hard ligands, such as NH3, OH2, and OH-, give ionic bonds and flattened tetragonal structures. It is shown that axial type 1 (blue) copper proteins have a trigonal structure with a π bond to the cysteine sulphur atom, whereas rhombic type 1 and type 2 proteins have a tetragonal structure with σ bonds to all strong ligands. The soft cysteine ligand is essential for the stabilisation of a structure that is close to a tetrahedron (either trigonal or tetragonal), which ensures a low reorganisation energy during electron transfer.
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| 7. |
- Pierloot, Kristine, et al.
(författare)
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Relation between the structure and spectroscopic properties of blue copper proteins
- 1998
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 120:50, s. 13156-13166
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Tidskriftsartikel (refereegranskat)abstract
- The electronic spectra of three rhombic type 1 blue copper proteins, nitrite reductase, pseudoazurin, and cucumber basic protein, have been studied by ab initio multiconfigurational second-order perturbation theory (the CASPT2 method). The six lowest excitations have been calculated and assigned with an error of less than 1800 cm-1. The singly occupied orbital in the ground-state forms a strongly covalent antibond between the copper ion and the thiolate group of the cysteine ligand with a mixture of σ and π character. This is in contrast to the axial type 1 copper protein plastocyanin which has an almost pure Cu-S(Cys) π interaction. The two brightest lines in the absorption spectrum originate from transitions to the corresponding σ (~460 nm) and π (~600 mm) bonding orbitals. The relative intensity of these two lines is determined by the character of the ground- state orbital. It is possible to obtain a structure closely similar to the one found in nitrite reductase by geometry optimizations with the hybrid density functional B3LYP method in vacuum. It is a tetragonal structure with bonds of mainly σ character to the four ligands like normal square-planar Cu(II) complexes, but the cysteine thiolate group donates much charge to the copper ion and thereby makes the structure strongly distorted toward a tetrahedron. Both this structure and a trigonal π-bonded structure, which also can be obtained for all complexes and is an excellent model of plastocyanin, are equilibrium structures (although usually not with the same ligand models). They have virtually the same energy (within ~7 kJ/mol), and the barrier between them is low. Therefore, small differences in the structure and electrostatics of different proteins may lead to stabilization of one or the other of the structures. The results indicate that axial type 1 proteins have a trigonal structure with an almost pure Cu-S(Cys) π bond, whereas rhombic type 1 proteins have tetragonal structures with a significant σ character in this bond. Type 1.5 and 2 copper-cysteinate proteins arise when the tetragonal structure becomes more flattened than in nitrite reductase, probably by the inclusion of stronger (type 1.5) and more (type 2) ligands.
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| 8. |
- Pierloot, Kristine, et al.
(författare)
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Theoretical study of the electronic spectrum of plastocyanin
- 1997
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Ingår i: Journal of the American Chemical Society. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 119:1, s. 218-226
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Tidskriftsartikel (refereegranskat)abstract
- The electronic spectrum of the blue copper protein plastocyanin has been studied by ab initio multiconfigurational second-order perturbation theory (the CASPT2 method). The six lowest electronic transitions have been calculated and assigned with an error of less than 2000 cm-1. The singly occupied orbital in the ground state is Cu 3d-S(Cys) 3pπ antibonding with some N(His) 2pσ character. The bright blue color originates from an electron transfer to this orbital from the corresponding Cu 3d-S(Cys)3pπ bonding orbital. The influence of different ligand models on the spectrum has been thoroughly studied; Cu(imidazole)2(SCH3)(S(CH3)2)+ as a model of CuHis2CysMet is the smallest system that gives converged results.The spectrum is surprisingly sensitive to changes in the geometry, especially in the Cu-S bond distances; a 5 pm change in the Cu-S(Cys) bond length may change the excitation energies by as much as 2000 cm-1. The effect of the surrounding protein and solvent on the transition energies has been modeled by point charges and is found to be significant for some of the transitions (up to 2000 cm-1).
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| 9. |
- Ryde, Ulf, et al.
(författare)
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On the role of strain in blue copper proteins
- 2000
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Ingår i: Journal of Biological Inorganic Chemistry. - : Springer Science and Business Media LLC. - 0949-8257 .- 1432-1327. ; 5:5, s. 565-574
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Tidskriftsartikel (refereegranskat)abstract
- Theoretical investigations of the structure and function of the blue copper proteins are described. We have studied the optimum vacuum geometry of oxidised and reduced copper sites, the relative stability of trigonal and tetragonal Cu(II) structures, the relation between the structure and electronic spectra, the reorganisation energy, and reduction potentials. Our calculations give no support to the suggestion that strain plays a significant role in the function of these proteins; on the contrary, our results show that the structures encountered in the proteins are close to their optimal vacuum geometries (within 7 kJ/mol). We stress the importance of defining what is meant by strain and of quantifying strain energies or forces in order to make strain hypotheses testable.
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| 10. |
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