Experimental Determination of the Electron Density Topology in a Non-centrosymmetric Transition Metal Complex: [Ni(H3L)][NO3][PF6] [H3L = N,N‘,N‘‘-Tris(2-hydroxy-3-methylbutyl)-1,4,7-triazacyclononane]

Probing the Isolobal Relation between Cp'''NiP3 and White Phosphorus by Experimental Charge Density Analysis

An in-depth analysis of the description of bonding within Cp'''Ni-cyclo-P3 (Cp'''=1,2,4-tri-tert-butylcyclopentadienyl, [Ni]P3) employing X-ray diffraction based multipolar modeling, density functional theory (DFT) as well as an "experimental wavefunction" obtained from X-ray restrained wavefunction (XRW) fitting is presented. The results are compared to DFT calculations on white phosphorus - an isolobal analogue to [Ni]P3. A complementary bonding analysis shows insights into the reactivity of [Ni]P3. The isolobal principle is reflected in every aspect of our analysis and the employed methods seamlessly predict the differences in reactivity of [Ni]P3 and P4. Crystallographic modeling, solid-state NMR, and DFT calculations describe the dynamic behavior of the cyclo-P3 unit in the title molecule.

Crystal structure resolution of an insulator due to the cooperative Jahn-Teller effect through Bader's theory: the challenging case of cobaltite oxide Y114

Cobaltite YBaCo4O7, abbreviated as Y114, is one of the most thoroughly investigated perovskites, owing largely to its interesting magnetic properties. Y114 is an insulator as a result of the cooperative Jahn-Teller effect, where one electron jumps quickly from one cobalt site to another, making it impossible to experimentally assign the correct oxidation state for each of the two cobalt sites. The present study solved the ambiguity by means of state-of-the-art DFT calculations. The two cobalt sites were differentiated through an analysis of charge density within the framework of the quantum theory of atoms in molecules.

Charge-density analysis of an iron-sulfur protein at an ultra-high resolution of 0.48 Å

The fine structures of proteins, such as the positions of hydrogen atoms, distributions of valence electrons and orientations of bound waters, are critical factors for determining the dynamic and chemical properties of proteins. Such information cannot be obtained by conventional protein X-ray analyses at 3.0-1.5 Å resolution, in which amino acids are fitted into atomically unresolved electron-density maps and refinement calculations are performed under strong restraints. Therefore, we usually supplement the information on hydrogen atoms and valence electrons in proteins with pre-existing common knowledge obtained by chemistry in small molecules. However, even now, computational calculation of such information with quantum chemistry also tends to be difficult, especially for polynuclear metalloproteins. Here we report a charge-density analysis of the high-potential iron-sulfur protein from the thermophilic purple bacterium Thermochromatium tepidum using X-ray data at an ultra-high resolution of 0.48 Å. Residual electron densities in the conventional refinement are assigned as valence electrons in the multipolar refinement. Iron 3d and sulfur 3p electron densities of the Fe4S4 cluster are visualized around the atoms. Such information provides the most detailed view of the valence electrons of the metal complex in the protein. The asymmetry of the iron-sulfur cluster and the protein environment suggests the structural basis of charge storing on electron transfer. Our charge-density analysis reveals many fine features around the metal complex for the first time, and will enable further theoretical and experimental studies of metalloproteins.

Cryo-crystallography: diffraction at low temperature and more

This chapter comments on the motivations and the methods of crystallographic studies at low temperature. Cry-crystallography is a brunch of Crystallography, a science that is too often confused with a technique. On the other hand, the scientific background to study crystal phases at low temperature is here provided, together with a survey of many possible techniques that provide complementary or supplementary information. Several applications are discussed, in particular in relation with highly accurate studies like electron density determination or phase transition mechanisms.

High- and low-spin Fe(III) complexes of various AGE inhibitors

Density functional theory calculations [CPCM/UM06/6-31+G(d,p)] were used to elucidate the structures and relative stability of Fe(III) complexes with various ligands that inhibit the formation of advanced glycation end products (AGEs) or iron overloaded disease (viz. aminoguanidine, pyridoxamine, LR-74, Amadori compounds, and ascorbic acid). EDTA was used as the free energy reference ligand. The distorted neutral octahedral complex containing one iron atom and three molecules of pyridoxamine [Fe(PM)(3)] was found to be the most stable. The stability of the complexes decreases in the following chelate sequence: pyridoxamine, Amadori complex, aminoguanidine, LR inhibitor, and ascorbic acid.

Metal-metal and metal-ligand bonding at a QTAIM catastrophe: a combined experimental and theoretical charge density study on the alkylidyne cluster Fe3(μ-H)(μ-COMe)(CO)10

The charge density in the tri-iron methoxymethylidyne cluster Fe(3)(μ-H)(μ-COMe)(CO)(10) (1) has been studied experimentally at 100 K and by DFT calculations on the isolated molecule using the Quantum Theory of Atoms in Molecules (QTAIM). The COMe ligand acts as a nearly symmetric bridge toward two of the Fe atoms (Fe-C = 1.8554(4), 1.8608(4) Å) but with a much longer interaction to the third Fe atom, Fe-C = 2.6762(4) Å. Complex 1 provides a classic example where topological QTAIM catastrophes render an exact structure description ambiguous. While all experimental and theoretical studies agree in finding no direct metal-metal interaction for the doubly bridged Fe-Fe vector, the chemical bonding between the Fe(CO)(4) unit and the Fe(2)(μ-H)(μ-COMe)(CO)(6) moiety in terms of conventional QTAIM descriptors is much less clear. Bond paths implying direct Fe-Fe interactions and a weak interaction between the COMe ligand and the Fe(CO)(4) center are observed, depending on the experimental or theoretical density model examined. Theoretical studies using the Electron Localizability Indicator (ELI-D) suggest the metal-metal bonding is more significant, while the delocalization indices imply that both Fe-Fe bonding and Fe···C(alkylidyne) bonding are equally important. The source functions at various interfragment reference points are similar and highly delocalized. The potential-energy surface (PES) for the migration of the alkylidyne group from a μ(2) to a semi-μ(3) coordination mode has been explored by DFT calculations on 1 and the model complexes M(3)(μ-H)(μ-CH)(CO)(10) (M = Fe, 2; Ru, 3; and Os, 4). These calculations confirm a semi-μ(3) bridging mode for the alkylidyne ligand as the minimum-energy geometry for compounds 2-4 and demonstrate that, for 1, both Fe-Fe and Fe···C(alkylidyne) interactions are important in the cluster bonding. The PES between μ(2) and semi-μ(3) alkylidyne coordination for 1 is extremely soft, and the interconversion between several topological isomers is predicted to occur with almost no energy cost. Analysis of the density ρ(r) and the Laplacian of the density ▽(2)ρ(r(b)) in the methoxymethylidyne ligand is consistent with a partial π-bond character of the C-O bond, associated with an sp(2) hybridization for these atoms.

Experimental X-ray Charge Density Studies on the Binary Carbonyls Cr(CO)6, Fe(CO)5, and Ni(CO)4

The experimental charge densities in the binary carbonyls Cr(CO)(6) (1), Fe(CO)(5) (2), and Ni(CO)(4) (3) have been investigated on the basis of high-resolution X-ray diffraction data collected at 100 K. The nature of the metal-ligand interactions has been studied by means of deformation densities and by topological analyses using the Atoms in Molecules (AIM) approach of Bader. A detailed comparison between the experimental results and theoretical results from previous work and from gas-phase and periodic DFT/B3LYP calculations shows excellent agreement, both on a qualitative and quantitative level. An examination of the kappa-restricted multipole model (KRMM) for Cr(CO)(6), using theoretically derived structure factors, showed it to provide a somewhat worse fit than a model with freely refined kappa' values. The experimental atomic graphs for the metal atoms in 2 and 3 were found to be dependent on the multipole model used for that atom. In the case of compound 2, restriction of the multipole populations according to idealized site symmetry of D(3h) gave an atomic graph in essential agreement with the theoretical gas-phase study. For compound 3, all multipole models fail to reproduce the atomic graph obtained from the theoretical gas-phase study. The atomic quadrupole moments for the C atoms in all compounds were consistent with significant pi back-donation from the metal atoms.

Bonding to titanium

The recent synthesis of a crystalline compound containing Ti bonded to cyclopentadienyl and a substituted dienyl fragment prompted the question of whether Ti-C contacts that were found to be shorter than other such bonded contacts in the same molecule should be considered as short nonbonded contacts or "nonclassical metal-to-saturated-carbon atom interactions", fitting the description of agostic interactions. This question has a unique answer within the framework of the quantum theory of atoms in molecules (QTAIM). QTAIM uses the measurable electron density to assign a molecular structure and the physics of an open system to determine the nature of the bonded interactions. All of the classical bonding descriptors, when recast in terms of the topologies of the electron density and the pair density, are faithfully recovered when QTAIM is applied to the hydrocarbon framework of the Ti complex, thereby justifying its application to the analysis of the Ti-C interactions. No bond paths are found to link the Ti to the carbons exhibiting the "short contacts", and the topology of the density gives no indication of an incipient change in structure that would result in their formation.