Geometry and Electronic Structure of the P-Cluster in Nitrogenase Studied by Combined Quantum Mechanical and Molecular Mechanical Calculations and Quantum Refinement.

We have studied the geometry and electronic structure of the P-cluster in nitrogenase in four oxidation states: PN, P1+, P2+, and P3+. We have employed combined quantum mechanical and molecular mechanical (QM/MM) calculations, using two different density-functional theory methods, TPSS and B3LYP. The calculations confirm that the side chain of Ser-188 is most likely deprotonated in the partly oxidized P1+ state, thereby forming a bond to Fe6. Likewise, the backbone amide group of Cys-88 is deprotonated in the doubly oxidized P2+ state, forming a bond to Fe5. The calculations also confirm the two conformations of the P-cluster in the atomic-resolution crystal structure of the enzyme, representing the PN and P2+ states, but show that the finer differences between the two structures are not fully reflected in the crystal structure, because the coordinates of only two atoms differ between the two conformations. However, the recent crystal structure of the P1+ state seems to be of lower quality with many dubious Fe-Fe and Fe-S distances. Quantum refinement of this structure indicates that it is a mixture of the P1+ and P2+ states but confirms that the side chain of Ser-188 is most likely deprotonated in both states. TPSS gives structures that are appreciably closer to the crystal structures than does B3LYP. In addition, we have studied all 16-48 possible broken-symmetry states of the four oxidation states of the P-cluster with DFT in the one or two observed spin states. For the reduced PN state, we can settle the most likely state from the calculated energies and geometries. However, for the more oxidized states there are large differences in the predictions obtained with the two DFT methods.

Optimizing bidentate N-heterocyclic carbene ligands for the modification of late transition metal surfaces - new insights through theory.

The functionalization of metal surfaces with N-heterocyclic carbenes (NHCs) has gained much interest in the past decade, since the modified materials are highly suitable for the development of specialized applications, for example in heterogeneous catalysis. More recently, multidentate NHC-ligands have been utilized to further improve the properties of the modified materials. However, the influence of the linker, which connects the NHC units, on the adsorption behavior of multidentate NHC-ligands has not been investigated so far. This knowledge is essential in order to access the full potential of applications. Here, we provide a thorough computational study, which compares the performance of bidentate NHC-ligands with twelve different linkers on the Cu(111), Pd(111) and Au(111) surfaces. It is shown that, on the Cu(111) and Au(111) surfaces, linkers should most importantly allow for a favorable arrangement of all NHC units, while aromatic linkers lead to stronger adsorption than aliphatic ones on Pd(111) surfaces. As a consequence, bidentate NHCs with aromatic linkers on Pd(111) surfaces tolerate larger deviations from the optimum single-NHC adsorption mode.

Intermolecular coupling and intramolecular cyclization of aryl nitriles on Au(111).

The on-surface dimerization reaction of an organic nitrile on Au(111) is reported. The formation of the product, which contains five newly formed σ-bonds and a diazapyrene core structure, was investigated and characterized by scanning tunneling microscopy. Experimental and computational studies of reference compounds support our findings.