1
Ground state and electronic spectrum of Cu(ii) and Cu(iii) complexes of N,N′-1,2-phenylenebis-2-mercaptoacetamide

Type: Object | Advantage: None | Novelty: New | ConceptID: Obj1

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The electronic structure and the UV-vis spectrum of reduced and oxidized model systems of the N,N′-1,2-phenylenebis(2-mercapto-2-methylpropionamide) copper complex have been studied using a multiconfigurational quantum chemical method (CASSCF/CASPT2).

Type: Object | Advantage: None | Novelty: New | ConceptID: Obj2

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The bonds between Cu and the two sulfur ligand atoms have a large covalent character in the oxidized Cu(iii) form.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res1

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As a result of the increased covalency, the effective charge on the Cu atom is actually smaller in the oxidized form.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res2

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The electronic spectrum for both oxidation states of the complex is in agreement with the experiment for excitation energies and intensities showing that the theoretical description of the electronic structure is essentially correct.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con1

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All bands that involve excitations from either Cu or S localized orbitals to the empty or half empty CuS antibonding orbital have been characterized.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res3

Introduction

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The N,N′-1,2-phenylenebis(2-mercapto-2-methylpropionamide) complexes of Cu(ii) and Cu(iii) (Cuphmi), containing the N2S2 chelating group in a square-planar coordination environment, are interesting models of copper proteins.1,2

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac1

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For example, the high affinity for copper and the N2S2 coordination environment are peculiar properties of the active site of methanobactin,3 a copper acquisition protein.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac1

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Hanss and Krüger obtained the X-ray crystal structure of both the oxidized and reduced forms of Cuphmi and also measured the electronic spectrum in acetonitrile solution.2

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The X-ray absorption (XAS) spectra of Cu(iii)phmi and Cu(ii)phmi in solid phase have recently been recorded and analyzed.4

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac1

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The structures of the Cu(ii) and Cu(iii) ionic complexes were obtained using the B3LYP density functional method, with a 6-31G(d,p) basis set, considering different possible spin multiplicities.4

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac1

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The shape of the experimental XAS K-edge region was rationalized in the frame of an orbital approximation, employing HF molecular orbital eigenvalues and eigenvectors of the optimized DFT structures.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac1

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The singlet state of the Cu(iii) complex was shown to be more stable than the triplet state in agreement with the absence of an experimental ESR signal for the oxidized complex.2

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac1

14
A XAS study on similar Cu(ii) and Cu(iii) complexes5 showed that the shape of the corresponding K-edge region depends on the electronic properties and the coordination geometry of the chelating ligand.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac1

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Moreover, a shift of about 2 eV was observed in the assigned resonances when going from Cu(ii) to Cu(iii) ions.

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A Cu(iii) complex with six coordinated sulfur atoms in an octahedral geometry has been characterized, confirming a d8 electron configuration of Cu(iii) with a triplet spin state,6 in contrast to the situation in Cu(iii)phmi.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac1

17
In order to gain a better understanding of the electronic properties of these interesting molecules, we present here results from a theoretical study of the electronic structure of Cu(iii)phmi and Cu(ii)phmi models in the ground and lower excited states originating from excitations within the 3d shell or from the sulfur lone pair orbitals to the empty (or half empty) 3d orbital.

Type: Goal | Advantage: None | Novelty: None | ConceptID: Goa1

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The information obtained can be used to obtain a better understanding of the nature of the XAS K-edge resonances and the present study will be extended to an explicit calculation of the XAS resonances in a forthcoming publication.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac2

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Wave functions and energies have been generated using the complete active space (CAS) SCF method7 with dynamic correlation added using second order perturbation theory (CASPT2).8,9

Type: Method | Advantage: None | Novelty: Old | ConceptID: Met1

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It has been shown recently in a series of papers that this approach, which includes scalar relativistic effects, is to date among the most accurate methodologies that can be used to obtain detailed information on the electronic structure of the ground and low-lying excited states of transition metal complexes.

Type: Method | Advantage: Yes | Novelty: Old | ConceptID: Met1

21
The same approach has been used previously to study the electronic spectrum of a number of blue copper proteins where one of the ligands is cysteine.10–13

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That comprehensive investigation resulted in a paradigm shift for the explanation of the origin of the specific structural characteristics of the blue copper proteins.

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The earlier ideas were based on the assumption of a strained protein structure that forced the specific (tetrahedral) structure of the active Cu(ii) site.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac3

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It was shown in the theoretical work that it is the special nature of the copper sulfur bond that favors a tetrahedral structure instead of the normal tetragonal arrangement of the ligand.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac3

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It is known that the copper sulfur bond is strong and has a dominating covalent character with the bonding and antibonding orbitals delocalized over both centers.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac4

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As a result, the metal–ligand bonding in blue copper proteins can occur either through the sulphur σ lone pair orbital, yielding a tetragonal coordination site, or through the sulphur π lone pair orbital, in this case stabilizing a tetrahedral active center.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac4

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The most prominent spectral features arise from excitations to the half-filled (Cu(ii)) or empty (Cu(iii)) antibonding Cu–S orbital from either the 3d-orbitals, from the sulfur lone pair orbitals, or from the bonding Cu–S orbital.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac4

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The latter transition is supposed to give rise to the strongest band in the low energy part of the electronic spectrum.

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It is traditional to classify these transitions as either d–d or ligand to metal charge transfer (LMCT).

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac4

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However, considering the delocalized nature of the antibonding Cu–S orbital, this picture is not accurate.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac4

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All these transitions contain some charge transfer character, which is special for the thiolate ligand.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac4

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We shall return to this point in the analysis of the excited states.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac4

Computational details

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Two sets of calculations were performed at CASPT2 level8,9 on the structure of the copper model complexes with the ligand N,N′-1,2-phenylenebis-2-mercaptoacetamide, which we call Cuphma: one using the averaged C2v geometry obtained from the X-ray structure of the Cuphmi complexes2 and one using the fully optimized geometry of Cuphmi calculated at unrestricted B3LYP/6-31G(d,p) DFT level.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod1

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The singlet and the triplet states of Cu(iii)phmi and the doublet state of Cu(ii)phmi were considered, by imposing the C2v symmetry (see Table 1).

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod1

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The reason of this choice is that the important Cu–S bond distance is quite different in the two cases, as can be seen in Table 1, while the transition energies strongly depend on this distance, because the energy separation between the bonding and antibonding Cu–S orbitals is strongly linked to it.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod1

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We have shown10 that DFT gives a Cu–S bond which is too long by about 0.08 Å in the active site of plastocyanin.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac5

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In the present case, it becomes more difficult to optimize this bond distance using the CASPT2 method,10 due to the strong coupling to other bonds in the chelating ligand system.

Type: Method | Advantage: None | Novelty: New | ConceptID: Met2

38
On the other hand, the experimental geometry of the small title complexes can be expected to be accurate in contrast to the case of a protein.

Type: Hypothesis | Advantage: None | Novelty: None | ConceptID: Hyp1

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For the same reason, the DFT optimized geometry of Cuphma (see Table 1) was not used in the CASPT2 calculations.

Type: Method | Advantage: None | Novelty: New | ConceptID: Met3

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In Cuphma the methyl groups on the atom C1 are replaced by hydrogen atoms (cf. Fig. 1).

Type: Method | Advantage: None | Novelty: New | ConceptID: Met3

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Such a simplification only influences excited states to a small extent originating from excitations in the active site region.

Type: Method | Advantage: None | Novelty: New | ConceptID: Met3

42
While the calculations have been performed on the isolated Cu(iii)phma1− and Cu(ii)phma2− ions, the experimental spectrum of Cuphmi was measured in acetonitrile solution.2

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac6

43
Clearly, the transition energies are shifted by the solvent.

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac6

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A rough estimate could be obtained from the relative dipole moments in the ground and excited states, but it is also known that acetonitrile molecules are very weakly coordinated to the axial sites of the square planar copper environment.1

Type: Background | Advantage: None | Novelty: None | ConceptID: Bac6

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One of the crucial steps in the calculation is the choice of the active orbitals.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod2

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We are interested in transitions occurring in the active site, that is, within the metal 3d-orbitals and from the sulfur 3p-orbitals to the metal.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod3

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So we need to consider the five 3d- and four S3p-orbitals with 17 (16 for Cu(iii)) active electrons.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod2

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We also need to account for the strong radial correlation effects in the localized 3d-orbitals by adding a second set of orbitals, 3d′ (the so called double shell effect.14)

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod2

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These extra active orbitals are particularly important for excitations where the number of d electrons change.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod2

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Here we need four such orbitals, which yields a total active space of 13 orbitals divided in 5, 2, 3, 3, respectively in the four representations of the C2v point group, a1, b2, b1, a2.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod2

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Basis sets of the Atomic Natural Orbital (ANO) type were used for all atoms.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod3

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Such basis sets have newly been developed that include scalar relativistic effects and correlation of the semi-core electrons,15 for example the 3p electrons on the Cu atom.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod3

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The size of the basis sets were: Cu: 6s5p3d2f, S: 5s4p2d, C,N,O: 4s3p1d, and H: 2s1p.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod3

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The selected basis sets contain enough diffuse functions to ensure a good quality in the calculation of the oscillator strengths.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod3

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These have been computed at CASSCF level of theory.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod3

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All calculations have been performed with the MOLCAS-6.0 quantum chemistry software16.

Type: Experiment | Advantage: None | Novelty: None | ConceptID: Exp1

Results and discussion

The ground states of Cu(iii)phmi1− and Cu(ii)phmi2−

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We first give an overall description of the electronic structure of the region around the metal atom.

Type: Object | Advantage: None | Novelty: New | ConceptID: Obj3

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In Table 1 it is seen that the Cu–S distance in the optimized geometry of Cuphmi is larger than the one observed experimentally, of about 0.03 and 0.05 Å for oxidized and reduced forms, respectively.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs1

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This distance further increases by 0.04 and 0.08 Å in the optimized geometry of Cuphma.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs2

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While the first structural distortion could be associated both to solid state packing effects and to the tendency of DFT methods in predicting larger bond lengths,10 the one observed in Cuphma is to be attributable also to the simplification of the ligand model.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con2

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For this reason we have performed our calculations using the coordinates of Cuphmi.

Type: Experiment | Advantage: None | Novelty: None | ConceptID: Exp2

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The characteristic features of the Cu–S bonding and antibonding (CuS*) orbitals are presented in Fig. 2.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs3

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This figure shows the orbital pair for both Cu(ii)phma and Cu(iii)phma.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs3

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In the oxidized form we would expect to find a stronger covalent character of the bond and this is also what the figure illustrates.

Type: Hypothesis | Advantage: None | Novelty: None | ConceptID: Hyp2

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Actually, we have an almost equal distribution of the electron pair over all three centers in the bonding orbital.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs4

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The orbital has b2 symmetry and thus combines the antisymmetric in plane sulfur lone-pair orbital with the metal 3dxy orbital to form the three center bond.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res4

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The symmetric lone-pair combination (of a1 symmetry) does not interact strongly with the metal center and remains localized on the sulfur atoms.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res5

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The b2 orbital is doubly occupied in both complex ions.

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The antibonding orbital is singly occupied in the reduced form.

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In the oxidized form we find 0.14 electrons in this orbital, showing that there is a strong static correlation effect in the Cu–S bond, which is typical for weak covalent bonds.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con3

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It is obvious from the electronic structure that the ground state of the oxidized form of the complex should be a singlet state.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res6

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In fact, the reduced form has the odd electron in the CuS* orbital and can be easily removed.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res6

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The presence of an electron in an antibonding orbital explains the longer CuS bond distance in Cu(ii)phmi compared to that observed in Cu(iii)phmi (see Table 1).

Type: Result | Advantage: None | Novelty: None | ConceptID: Res6

74
We have computed the energy difference between the lowest singlet, 1A1, and triplet, 3A2, states of Cu(iii)phma and found it to be close to 25 000 cm−1 (3.09 eV), thus showing that the ground state is a singlet.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res7

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The spin–density in Cu(ii)phma is almost entirely localized on the copper ion (92%) with most of the remaining density actually located on the nitrogen atoms of the ligand.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs7

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The localization of the spin is achieved by mixing two configurations, one dominating (weight 83%) with the spin in the antibonding orbital and one (weight 13%) with the spin in the bonding orbital.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res8

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The wave function in the ground state of Cu(iii)phma is dominated by two single closed shell configurations, one with the bonding Cu–S orbital occupied (weight 91%) and one doubly excited configuration where the corresponding antibonding orbital is doubly occupied (weight 6%).

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs8

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This is typical for the formation of a comparably weak covalent bond, in this case between the 3dxy Cu orbital and the antisymmetric combination of the in-plane sulfur lone pair orbitals (see Fig. 2).

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con4

The excited states of Cu(ii)phma2−

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The electronic spectrum of Cu(ii)phma is characterized in the low energy region by excitations into the half empty CuS* orbital (lower right orbital in Fig. 2) from the filled 3d shells and from the sulfur 3p lone pair orbitals.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs9

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Computed energies are shown in Table 2.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs10

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The four first excited states correspond to the ligand field transitions resulting in a hole in one of the four localized 3d orbitals.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res9

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The two transitions with the largest oscillator strengths can be assigned to the first two bands found in the experimental spectrum.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res10

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Then three transitions follow that are characterized as LMCT from the sulfur lone pair orbitals to the CuS* orbital.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res11

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Two of them have appreciable intensity.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res11

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The most intense band (with a peak at 32 258 cm−1) corresponds to excitation from the symmetric in-plane sulfur 3p orbital.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res12

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As expected, we find this transition at a lower energy than the one coming from the antisymmetric 3p combination, which is stabilized by the interaction with the Cu 3dxy orbital.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res13

87
The agreement with the four bands found in the experimental spectrum is satisfactory, but we would like to point out that the transition energies depend strongly on the geometry used.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con5

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The total energy for the ground state (CASSCF and CASPT2) is 1.4 eV lower for the DFT optimized structure than for the structure obtained from the X-ray measurements.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res14

89
This might indicate that the crystal structure is perturbed by the packing in the crystal.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con6

90
The experimental spectrum was measured in acetonitrile, so one can also expect some solvent shifts, in particular for charge transfer excitations.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con6

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The changes in dipole moments are small for the ligand field excitations.The ground state dipole moment is −7.41 D, the four first excited states have dipole moments between −6.52 and −7.41 D, and the following three (LMCT) states have dipole moments in the range −11.93 to −12.13 D. Thus, we can see a clear difference between the ligand field states and the charge transfer states and we can expect a bathochromic shift of the transition energies for the latter transition energies.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con7

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The clear distinction between ligand field and LMCT states is also illustrated by the Mulliken charges on the copper ion (cf. Table 2), which is around 0.8 for the ligand field states and close to zero for the LMCT states, while the ground state charge is +0.7.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res15

The excited states of Cu(iii)phma1−

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The odd electron is removed from the CuS* orbital in the oxidized form.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod4

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Thus, this orbital is now empty.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod4

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All low lying excited states correspond to transitions of an electron into this orbital.

Type: Model | Advantage: None | Novelty: None | ConceptID: Mod4

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The computed excitation energies and oscillator strengths are presented in Table 3.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs11

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The agreement with the three experimental bands in the low energy region is fair.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs12

98
Again we see that computed excitation energies depend on the geometry used, but, analogously to the reduced complex, it is not possible to draw any definitive conclusion about the preferred geometry.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs13

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In fact, the total energy of the DFT optimized geometry is 1.1 eV lower than the one calculated for the experimental structure.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs13

100
The transition at 24 000 cm−1 is intense with an oscillator strength of 0.28.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs14

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Although it is a transition from a 3d orbital to CuS*, there is a reorganization effect in the excited state that diminishes the amount of charge transfer.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res16

102
The created open shell interacts with the sulfur lone pair orbitals such that the orbital is delocalized.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res16

103
Thus charge is back donated into the 3d shell from the sulfur orbitals.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res16

104
Such interaction was not present in the reduced complex.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res17

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It can occur easier here because of the shorter Cu–S bond distance, that decreases up to 0.13 Å for the optimized geometry of the oxidized form of Cuphma.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con8

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The stronger back donation effect also results in larger and more irregular variations of the dipole moments for the different states.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con9

107
The ground state moment is −2.28 D, while the moments for the excited states vary between −5.21 and +9.30 D. The back donation effect is nicely illustrated by the Mulliken charges on copper, as shown in Table 3.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res18

108
The ground state charge is +0.39, which is smaller than the copper charge observed in the reduced form!

Type: Result | Advantage: None | Novelty: None | ConceptID: Res19

109
Moreover, it does not deviate much from this value in the excited states.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs15

110
The charge neutralization effect is a result of the strong covalency in the Cu–S bond and it is much more effective here than it is in Cu(ii)phma, where the interaction of copper with the sulfur atoms is weaker.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con10

Conclusions

111
We have in this report described the electronic structure and spectrum of the reduced and oxidized forms of a copper model complex of N,N′-1,2-phenylenebis(2-mercapto-2-methylpropionamide), with the four methyl groups on the atom C1 replaced by hydrogens.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con11

112
The system is interesting because of the two Cu–S bonds, which do not behave as normal dative bonds, but more like covalent bonds.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res20

113
This is most pronounced in the oxidized form.

Type: Observation | Advantage: None | Novelty: None | ConceptID: Obs16

114
As a result of the increased covalency, the effective charge on the Cu atom is actually smaller in the oxidized form.

Type: Result | Advantage: None | Novelty: None | ConceptID: Res21

115
The correctness of the calculated electronic structure is validated through the calculation of the electronic spectrum for both oxidation states of the complex.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con12

116
All bands that involve excitations from either Cu or S localized orbitals to the empty or half empty Cu–S* orbital have been characterized in terms of ligand field transitions and LMCT states involving sulfur orbitals.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con13

117
These results provide support for the Cu–S* orbital also being involved in the core excitations observed by XAS.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con14

118
The agreement with the experimental excitation energies and intensities shows that the theoretical description of the electronic structure is essentially correct.

Type: Conclusion | Advantage: None | Novelty: None | ConceptID: Con15