Ligand Distances Research Articles

Coordination Mode of Nitrate in Uranyl(VI) Complexes: A First-Principles Molecular Dynamics Study

According to Car-Parrinello molecular dynamics simulations for [UO(2)(NO(3))(3)](-), [UO(2)(NO(3))(4)](2-), and [UO(2)(OH(2))(4-)(NO(3))](+) complexes in the gas phase and in aqueous solution, the nitrate coordination mode to uranyl depends on the interplay between ligand-metal attractions, interligand repulsions, and solvation. In the trinitrate, the eta(2)-coordination is clearly favored in water and in the gas phase, leading to a coordination number (CN) of 6. According to pointwise thermodynamic integration involving constrained molecular dynamics simulations, a change in free energy of +6 kcal/mol is predicted for eta(2)- to eta(1)-transition of one of the three nitrate ligands in the gas phase. In the gas phase, the mononitrate-hydrate complex also prefers a eta(2)-binding mode but with a CN of 5, one H(2)O molecule being in the second shell. This contrasts with the aqueous solution where the nitrate binds in a eta(1)-fashion and uranyl coordinates to four H2O ligands. A driving force of ca. -3 kcal/mol is predicted for the eta(2)- to eta(1)- transition in water. This structural preference is interpreted in terms of steric arguments and differential solvation of terminal vs uranyl-coordinated O atoms of the nitrate ligands. The [UO(2)(NO(3))(4)](2-) complex with two eta(2)- and two eta(1)- coordinated nitrates, observed in the solid state, is stable for 1-2 ps in the gas phase and in solution. In the studied series, the modulation of uranyl-ligand distances upon immersion of the complex in water is found to depend on the nature of the ligand and the composition of the complex.

Theoretical study on local lattice structure distortion for octahedral Fe 3+ center in several germanate garnets

Local lattice structure distortion study of octahedral Fe 3+ center in garnets Ca 3M 2Ge 3O 12 (M = Al, Ga, Sc, In, Lu) has been performed systematically based on the diagonalization of the complete energy matrices of the electron–electron repulsion, the spin–orbit coupling and the trigonal ligand–field interaction for a d 5 configuration ion in a trigonal ligand field. From the EPR calculation, the local structure distortion parameters Δ R and Δ θ are determined, respectively. These results illuminate a microscopic origin of various ligand field parameters used empirically for the interpretation of electron paramagnetic resonance experiments. It is found that the theoretical results of the electron paramagnetic resonance spectra for Fe 3+ center in garnets Ca 3M 2Ge 3O 12 (M = Al, Ga, Sc, In, Lu) are in good agreement with the experimental findings. Although the local lattice structures around the M 3+ (M = Al, Ga, Sc, In, Lu) ions are obviously different, the local lattice structures around the dopants are rather similar. Moreover, it is noted that the empirical impurity–ligand distance R ≈ R H + 1 2 ( r i - r h ) is not suitable for Fe 3+ in garnets Ca 3M 2Ge 3O 12 (M = Al, Ga, Sc, In, Lu).

Influence of chemical bond length changes on the crystal field strength and “ligand–metal” charge transfer transitions in Cs 2GeF 6 doped with Mn 4+ and Os 4+ ions

Detailed study of dependence of the crystal field strength 10 Dq and lowest charge transfer (CT) energies for different interionic distances in Cs 2GeF 6:Mn 4+ and Cs 2GeF 6:Os 4+crystals is presented. The calculations were performed using the first-principles discrete-variational Dirac–Slater (DV-DS) method. As a result, the functional dependencies of 10 Dq and lowest CT energy on the metal–ligand distance R were obtained without any fitting or semiempirical parameters. It was shown that 10 Dq depends on R as 1/ R n , with n=4.0612 and 4.3874 for Cs 2GeF 6:Mn 4+ and Cs 2GeF 6:Os 4+, respectively. Two approximations (linear and quadratic) are obtained for the dependence of the lowest CT energy on R; CT energy decreases when R increases with d E( CT)/d R=−638 and −1080 cm −1/pm for Cs 2GeF 6:Mn 4+ and Cs 2GeF 6:Os 4+, respectively, if the linear approximation is used. These values can be used for estimations of the lowest CT energies for Mn 4+ and Os 4+ ions in other hosts with fluorine ligands. Estimations of the electron-vibrational interaction (EVI) constants, Huang–Rhys parameters, and Stokes shifts for all the above-mentioned crystals were performed using the obtained 10 Dq and E( CT) functions.

Identification of the Peroxy Adduct in Multicopper Oxidases by a Combination of Computational Chemistry and Extended X-ray Absorption Fine-Structure Measurements

We have developed a computational method that combines extended X-ray absorption fine structure (EXAFS) refinements with the integrated quantum mechanical and molecular mechanics (QM/MM) method. This method allows us to obtain a structure of a metal site inside a protein that is compatible with both EXAFS data and QM calculations (i.e., that is chemically reasonable). Thereby, the QM/MM calculations play the same role as MM in nearly all NMR and crystallographic refinementsEXAFS ensures that the metal−ligand distances are accurate and QM/MM fills in all the other structural data. We have used this method to show that a structure with a peroxide ion in the center of the trinuclear cluster fits experimental EXAFS data better than a structure with the peroxide ion on the side of the cluster for the peroxide adduct of multicopper oxidases.

Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry

The use of molecular mechanics calculations to supplement experimental data in standard X-ray crystallography and NMR refinements is discussed and it is shown that structures can be locally improved by the use of quantum chemical calculations. Such calculations can also be used to interpret the structures, e.g. to decide the protonation state of metal-bound ligands. They have shown that metal sites in crystal structures are frequently photoreduced or disordered, which makes the interpretation of the structures hard. Similar methods can be used for EXAFS refinements to obtain a full atomic structure, rather than a set of metal-ligand distances.

The effect of halogen atom on the molecular quadratic nonlinearity of half sandwich complexes in the presence of an acceptor

Half sandwich complexes of the type [CpM(CO) n X] {X = Cl, Br, I; If, M = Fe, Ru; n = 2 and if M = Mo; n = 3} and [CpNiPPh 3X] {X = Cl, Br, I} have been synthesized and their second order molecular nonlinearity ( β) measured at 1064 nm in CHCl 3 by the hyper-Rayleigh scattering technique. Iron complexes consistently display larger β values than ruthenium complexes while nickel complexes have marginally larger β values than iron complexes. In the presence of an acceptor ligand such as CO or PPh 3, the role of the halogen atom is that of a π donor. The better overlap of Cl orbitals with Fe and Ni metal centres make Cl a better π donor than Br or I in the respective complexes. Consequently, M–π interaction is stronger in Fe/Ni–Cl complexes. The value of β decreases as one goes down the halogen group. For the complexes of 4d metal ions where the metal–ligand distance is larger, the influence of π orbital overlap appears to be less important, resulting in moderate changes in β as a function of halogen substitution.

Structure of the Oxidized Active Site of Galactose Oxidase from Realistic In Silico Models

A systematic in silico approach is employed to generate an accurate model for the catalytically important oxidized state of galactose oxidase (GO) using spectroscopically calibrated hybrid density-functional theory. GO displays three distinct oxidation states: oxidized [Cu(II)-Y*], semireduced [Cu(II)-Y], and fully reduced [Cu(I)-Y], but only the [Cu(II)-Y*] and the [Cu(I)-Y] states are assumed to be involved in catalysis. We have developed multiple models for the oxidized [Cu(II)-Y*] state, whose structure has not yet been fully characterized. These models were evaluated by comparison of calculated and experimental structural data, singlet-triplet energy gaps, and electronic transitions for the antiferromagnetically coupled oxidized [Cu(II)-Y*] state. An extended model system that includes explicit solvent molecules and second coordination sphere residues (R330, Y405, and W290) is essential to obtain the correct electronic structure of the active site. The model with all the residues that have been shown to affect the radical stability and catalysis resulted in a singlet ground state with the radical centered on the Y272-C228 cofactor. The optimized structure of the oxidized GO [Cu(II)-Y*] reveals a five-coordinated square pyramidal coordination geometry very similar to [Cu(II)-Y] with considerably different Cu-ligand distances. The hydrogen-bonding interactions involving Y495 modulates the spin density distribution and the singlet-triplet energy gaps. The final model as the most reasonable structure of the oxidized [Cu(II)-Y*] state in GO reproduces the spectroscopic signature of oxidized GO.

The Iron-Sulfur Cluster-free Hydrogenase (Hmd) Is a Metalloenzyme with a Novel Iron Binding Motif

The iron-sulfur cluster-free hydrogenase (Hmd) from methanogenic archaea harbors an iron-containing cofactor of yet unknown structure. X-ray absorption spectroscopy of the active, as isolated enzyme from Methanothermobacter marburgensis (mHmd) and of the active, reconstituted enzyme from Methanocaldococcus jannaschii (jHmd) revealed the presence of mononuclear iron with two CO, one sulfur and one or two N/O in coordination distance. In jHmd, the single sulfur ligand is most probably provided by Cys176, as deduced from a comparison of the activity and of the x-ray absorption and Mössbauer spectra of the enzyme mutated in any of the three conserved cysteines. In the isolated Hmd cofactor, two CO, one sulfur, and two nitrogen/oxygen atoms coordinate the iron, the sulfur ligand being most probably provided by mercaptoethanol, which is absolutely required for the extraction of the iron-containing cofactor from the holoenzyme and for the stabilization of the extracted cofactor. In active mHmd holoenzyme, the number of iron ligands increased by one when one of the Hmd inhibitors (CO or KCN) were present, indicating that in active Hmd, the iron contains an open coordination site, which is proposed to be the site of H2 interaction.

Mid-IR transitions of trivalent neodymium in low phonon laser crystals

Mid-IR Nd 3+ transitions perspective for laser oscillation were analyzed in the CaGa 2S 4, PbGa 2S 4, and PbCl 2 crystals and compared with low phonon fluoride crystals. Fluorescence kinetics decay of the high-lying 4G 7/2 and 4G 5/2; 2G 7/2 and low-lying 4I J levels and its temperature dependence in the range of 13–295 K were measured. For 5 μm mid-IR transitions of Nd 3+ the radiative relaxation rates are found to be several times higher and multiphonon relaxation (MR) rates are several times lower in lead and calcium thiogallate crystals compared to low phonon fluoride crystals. MR rate dependence on the Nd 3+ to the nearest ligand distance R 0 is established experimentally and analyzed in the frame of point-charge model of nonlinear theory of multiphonon relaxation. Mid-IR Nd 3+ 4–5.5 μm fluorescence spectra of 4I i – 4I j transitions perspective for laser oscillation were measured for the first time in the studied crystals.

Strong dependence of 10Dq on the metal–ligand distance: Key role played by the s–p hybridization on ligands

The microscopic origin of the strong dependence of the crystal field splitting parameter, 10Dq, upon the metal–ligand distance, R, has been explored using vibronic theory as well as analysing the forces on ligands due to electronic density changes. Both different but complementary methods support that for an octahedral transition metal complex the R dependence of 10Dq mainly comes from a fine detail in the e g (∼ x 2 − y 2, 3 z 2 − r 2) wavefunction: the small admixture of s valence ligand orbitals with the corresponding p orbitals. The implication of this result as regards the Stokes shift involved in the luminescent emission is also underlined.

Delineating the principles controlling polymer formation and topology in zinc(II)- and cadmium(II)-dithiophosphate adducts of diimine-type ligands

The crystal structure determination of polymeric [Cd(S 2P(OCy) 2) 2(3-NC 5H 4C(H) NN C(H)C 5H 4N-3)·(CHCl 3) 2] ∞, where Cy is cyclohexyl and the bridging ligand is 3-pyridinealdazine, shows that the cadmium atom exists within a trans-N 2S 4 donor set and that the resultant polymer topology is of a step-ladder. It is argued that this is the expected structure for the compound as it concurs with the structure of the related iso-propyl derivative. Indeed, in most cases polymer topology in related cadmium dithiophosphate systems is controlled by the nature of the bridging diimine-type ligand. By contrast, in the analogous zinc dithiophosphate adducts, controlling polymer topology is possible by systematically varying the steric profile of the dithiophosphate-bound R groups, a phenomenon ascribed to the fact that in the zinc system, the zinc–ligand distances being shorter, bring all the components of the structure in close proximity and thereby exacerbates steric effects. An overview of our accomplishments in this area ‘crystal engineering of coordination polymers’ is presented herein.

Fac-Tris(tert-butyl isocyanide)tricarbonylmolybdenum(0)

The title compound, [Mo(C5H9N)3(CO)3], was produced from Mo(CO)6 and tert-butyl isocyanide in the presence of 10 atm of carbon monoxide (1 atm = 101325 Pa). The octa­hedral complex shows a facial arrangement of the ligands, the Mo—C distances of the isocyanide ligands being about 0.15 A longer than the corresponding bond lengths of the carbonyl ligands. The crystal structure is influenced by one short C—H⋯·O contact, resulting in infinite chains which are inter­connected by additional weak C—H⋯·O inter­actions.

Cellular Unbinding Forces of Initial Adhesion Processes on Nanopatterned Surfaces Probed with Magnetic Tweezers

To study the dependence of unbinding forces on the distance of molecularly defined and integrin specific c(-RGDfK-) ligand patches in initial cellular adhesion processes, we developed a magnetic tweezers setup for applying vertical forces of up to 200 pN to rat embryonic fibroblasts. The ligand patch distance is controlled with a hexagonally close packed pattern of biofunctionalized gold nanoparticles prepared by block-copolymer micelle nanolithography. Each gold nanoparticle potentially activates up to one alpha(v)beta(3)-integrin. The distances between the gold nanoparticles determine the separation of individual integrins and thus the assembly of integrin clusters. The results show an increase in cellular unbinding forces from approximately 6 to more than 200 pN for a decreasing ligand distance of 145 to 58 nm after 5 min of cell adhesion. Furthermore, we observe a strong dependence on adhesion time during the first 10 min of cell surface contact suggesting an active, cooperative cell response that is controlled by the spacing between individually activated integrins.

New lipophilic 3-hydroxy-4-pyridinonate iron(iii) complexes: synthesis and EXAFS structural characterisation

New tris-iron(III) chelates of 3-hydroxy-4-pyridinone ligands derived from maltol (3-hydroxy-2-methyl-4-pyrone) or ethylmaltol (2-ethyl-3-hydroxy-4-pyrone), including a variety of N-aryl (phenyl, 4'-tolyl, 4'-(n-butyl)phenyl, 4'-(n-hexyl)phenyl) and N-benzyl (4'-methylbenzyl, 4'-fluorobenzyl and 4'-(trifluoromethyl)benzylamine) substituents on the nitrogen atom of the pyridinone ring, have been prepared. Characterization by C,H,N elemental analysis and thermogravimetric measurements indicates that most of the complexes are obtained as hydrates of general formula ML3.xH2O. Structural characterization of these difficult to crystallize lipophilic complexes has been achieved by EXAFS spectroscopy. Solutions of iron(III) complexes of maltol, ethylmaltol, 1,2-dimethyl-3-hydroxy-4-pyridinone and 1-phenyl-2-methyl-3-hydroxy-4-pyridinone in methanol-water mixtures were also examined by EXAFS. Distances from the central atom to ligand atoms, within 6 A of the metal, have been determined in the solid and solution samples and the results show that the structure observed in the powder is maintained in solution. The local structure around the metal centre, bond distances and bond angles, does not change significantly with variable lipophilicity, thus indicating that ligands may be tailored according to specific needs without altering their chelation properties. EXAFS data analysis for this set of tris-iron(III) compounds illustrates the important contribution of both intra-ligand and inter-ligand multiple scattering pathways through the metal centre to a peak observed in the FT spectrum at twice the metal ligand distance (approximately 4 A). The present results demonstrate that EXAFS features at twice the metal-ligand distance are valuable in the assignment of molecular geometry and that location of hydration water molecules, by EXAFS analysis, is limited by the geometry of the complexes, in particular for those in which ligands containing phenyl rings are present.

A Flexible and Versatile Strategy for the Covalent Immobilization of Chiral Catalysts Based on Pyridinebis(oxazoline) Ligands.

AbstractFor Abstract see ChemInform Abstract in Full Text.

The importance of ligand–ligand interactions for molecular geometry and the ligand close-packing model

Abstract It is shown that repulsions between vicinal ligands and groups can be of considerable importance in determining molecular geometry, particularly for small central atoms. The importance of such repulsions was first proposed in the 1960s for molecules with a central carbon atom but has much more recently also been shown to be the case for molecules with other small central atoms. Indeed for such molecules the ligands may be considered to be close-packed around the central atom and from the constant ligand–ligand distances in these molecules a ligand radius for the atom bonded to the central atom may be deduced. These radii decrease across the periodic table as the charge on the ligand decreases with increasing electronegativity of the central atom. It is shown that most of the exceptions to the VSEPR model for molecules with non-metal central atoms can be explained if ligand–ligand repulsions, which are not explicitly considered in the VSEPR model, are taken into account. For example, the VSEPR model predicts that the bond angle in PH 3 would be larger than in NH 3 , whereas it is in fact considerably smaller, which is entirely consistent with ligand close packing (LCP) and the small size of the hydrogen ligand. Indeed, the ligand radius enables bond angles to be predicted quantitatively if the bond length is known, whereas the VSEPR model can only make qualitative predictions. It has long been recognized that steric effects between large nearby groups, in particular geminal groups, can be of importance in determining molecular geometry and reaction rates and mechanisms. However, the effect of steric interactions between vicinal atoms or groups has not been so widely recognized. Several authors have maintained that such interactions may be of considerable importance in determining molecular geometry, although this topic has generally only been discussed in terms of the valence bond theory or the VSEPR model. The purpose of this paper is to review previous relevant work and to review and extend our recent work, which provides strong evidence for the importance of the interaction between vicinal ligands (ligand–ligand repulsion) in determining molecular geometry. This evidence led to the development of the LCP model. To cite this article: R.J. Gillespie C. R. Chimie 08 (2005) .

Structural investigation of lithium iodide in liquid dimethyl sulfoxide: Comparison between experiment and computation

We report a combined experimental (X-ray and neutron diffraction) and theoretical (ab initio calculations and molecular dynamics simulation) study of LiI in dimethyl sulfoxide (DMSO) solution. The total structure function computed from MD agrees well with those obtained from both X-ray and neutron diffraction experiments. Evidence was found for Li–I contact ion pair formation in solution. The overall coordination number of Li + was found to be four, while the Li–DMSO coordination number is below four; the coordination sphere of the I − ion contains eight species (DMSO and lithium) in average and does not show any special geometrical arrangement. Ab initio calculations for clusters containing Li + and up to six DMSO molecules have been performed with the B3LYP density functional and various basis sets. The calculations show an increase of the average ion–ligand distance from about 1.71–1.96 Å when the number of DMSO molecules in the cluster increases from 1 to 4. The corresponding Li–DMSO interaction energy decreases accordingly; additional DMSO molecules are accommodated in the second shell, in agreement with the results from diffraction experiments and the simulation.

Oxidative Addition von N‐Chlortriphenylphosphanimin an Phosphortrichlorid und Antimontrichlorid. Kristallstrukturen von (Cl3PNPPh3)2[PCl6][ClHCl],[SbCl4(HNPPh3)2][SbCl6] und [Sb(NPPh3)4][SbCl6

AbstractOxidative Addition of N‐chlorotriphenylphosphoraneimine onto Phosphorus(III) Chloride and Antimony(III) Chloride. Crystal Structures of (Cl3PNPPh3)2[PCl6][ClHCl], [SbCl4(HNPPh3)2][SbCl6], and [Sb(NPPh3)4][SbCl6]Phosphorus(III) chloride reacts with N‐chlorotriphenylphosphoraneimine, ClNPPh3, in CH2Cl2 solution strongly exothermically via oxidative addition to give (Cl3PNPPh3)2[PCl6][ClHCl] (1). As a by‐product, Ph3PNP(O)Cl2 can be obtained, which is formed from PCl3 and ClNPPh3 in the presence of POCl3. In contrast to these results, antimony(III) chloride reacts with ClNPPh3 in CH2Cl2 solution to give a mixture of the phosphoraneimine complex [SbCl4(HNPPh3)2][SbCl6] (2) and the phosphoraneiminato complex [Sb(NPPh3)4][SbCl6] (3). The complexes 1‐3 were characterized by IR spectroscopy and by single crystal X‐ray determinations.1: Space group C2/c, Z = 4, lattice dimensions at 193 K: a = 3282.0(2), b = 798.7(1), c = 1926.1(2) pm, β = 107.96(1)°, R1 = 0.0302. 1 contains [Cl3PNPPh3]+ cations with PN bond lengths of 152.5(2) and 160.9(2) pm, and a PNP bond angle of 140.5(1)°.2·CH2Cl2: Space group ${\rm P}{\bar 1}$, Z = 2, lattice dimensions at 193 K: a = 1031.2(1), b = 1448.3(2), c = 1811,4(2) pm, α = 70.96(1)°, β = 87.67(1)°, γ = 75.37(1)°, R1 = 0.0713. 2·CH2Cl2 contains cations [SbCl4(HNPPh3)2]+ with octahedrally coordinated Sb atom and the HNPPh3 ligand molecules being in trans‐position. Sb–N bond lengths are 207.6(6) and 209.3(6) pm, PN bond lengths 162.3(7) and 160.8(7), which approximately corresponds with double bonds.3·0.5CH2Cl2: Space group P4/n, Z = 2, lattice dimensions at 193 K: a = b = 1678.8(1), c = 1244.3(1) pm, R1 = 0.0618. 3·0.5CH2Cl2 contains [Sb(NPPh3)4]+ cations with tetrahedrally coordinated Sb atom and short Sb–N bond lengths of 193.7(6) pm. The PN distances of the phosphoraneiminato ligands, (NPPh3)− with 156.5(6) pm, correspond with double bonds, the SbNP bond angles are 130.6(3)°.

Emission and excitation characteristics and internal quantum efficiencies of vacuum-ultraviolet excitedPr3+-doped fluoride compounds

We report on the spectroscopic investigation of ${\mathrm{Pr}}^{3+}$-doped binary, ternary, and quaternary fluoride compounds exhibiting photon cascade emission. Under vacuum-ultraviolet synchrotron excitation at wavelengths below 200 nm in the $4f5d$ bands of the ${\mathrm{Pr}}^{3+}$ ion the emission spectra show intraconfigurational $4f\text{\ensuremath{-}}4f$ transitions originating from the $^{1}S_{0}$ and $^{3}P_{0}$ multiplets. In the ternary and quaternary compounds investigated, i.e., Ca-, Sr-, Ba-, and Rb-fluorides, broadband emission due to transitions from the $4f5d$ level of ${\mathrm{Pr}}^{3+}$ are also observed. The different types of emission transitions observed in the compounds investigated were analyzed in detail. The internal quantum efficiency for the visible spectral range (390 nm--750 nm), ${\ensuremath{\eta}}_{\mathrm{vis}}$, is determined with the help of the Judd-Ofelt theory and the branching ratios of the $^{1}S_{0}$ emission transitions. The dependence of this quantum efficiency ${\ensuremath{\eta}}_{\mathrm{vis}}$ from the ionic radius of the second cation $({R}_{2\mathrm{nd}})$, the effective ligand distance, and the coordination number is investigated.

Synthesis and characterization of scandium complexes with reduced ligands: Crystal structures of Cp∗ScI 2, [Cp∗ScI(bpy)] 2, and [Cp∗ScCl(bpy)] 2

The synthesis and characterization of complexes containing a Cp∗Sc(R 2bpy) (Cp∗ = pentamethylcyclopentadienyl, bpy = 4,4′-R,R-2,2′-bipyridine, R = H, Me) motif are described. Cp∗ScI 2 ( 1) was prepared from Cp∗Sc(acac) 2 (acac = acetylacetonate) and AlI 3 (2 equiv) in pentane. Compound 1 reacted with bipyridine and 4,4′-dimethyl-2,2′-bipyridine (dmb) in benzene to yield Cp∗ScI 2(bpy) ( 3) and Cp∗ScI 2(dmb) ( 4), respectively. Compound 3 was reduced by alkali metal reductants such as Na/Hg, NaK 2, and K in aromatic solvents to yield [Cp∗ScI(bpy)] 2 ( 5). The chloride analog of 5, [Cp∗ScCl(bpy)] 2 ( 7), was prepared from Cp∗ScCl 2 by salt metathesis with Li 2(dme) 2bpy (6) (dme = dimethoxyethane) in toluene. Compounds 1, 5, and 7 have been structurally characterized. Analysis of the bond distances of the bipyridine ligands in 5 and 7, together with infrared and UV/vis spectroscopic data, suggest that the bipyridine ligands in these molecules exist as radical anions. The bipyridine ligands in 5 and 7 are arranged co-facially and are in close proximity (⩽3.30 Å), suggesting the presence of a π–π interaction.