Changes In Bond Distances Research Articles

Dehydrogenation and Transfer Hydrogenation of Alkenones to Phenols and Ketones on Carbon-Supported Noble Metals.

The catalytic dehydrogenation of substituted alkenones on noble metal catalysts supported on carbon (Pt/C, Pd/C, Rh/C, and Ru/C) was investigated in an organic phase under inert conditions. The dehydrogenation and semihydrogenation of the enone starting materials resulted in aromatic compounds (primary products), saturated cyclic ketones (secondary products), and cyclic alcohols (minor products). Pd/C exhibits the highest catalytic activity, followed by Pt/C and Rh/C. Aromatic compounds remain the primary products, even in the presence of hydrogen donors. Joint experimental and theoretical analyses showed that the four catalytic materials stabilize a common dienol intermediate on the metal surfaces, formed by keto-enol tautomerization. This intermediate subsequently forms aromatic products upon dehydrogenation. The binding orientation of the enone reactants on the catalytic surface is strongly metal-dependent, as the M-O bond distance changes substantially according to the metal. The longer M-O bonds (Pt: 2.84 Å > Pd: 2.23 Å > Rh: 2.17 Å > Ru: 2.07 Å) correlate with faster reaction rates and more favorable keto-enol tautomerization, as shorter distances correspond to a more stabilized starting material. Tautomerization is shown to occur via a stepwise surface-assisted pathway. Overall, each of the studied metals exhibits a distinct balance of enthalpy and entropy of activation (ΔH°‡, ΔS°‡), offering unique possibilities in the realm of enone dehydrogenation reactions that can be achieved by suitable selection of catalytic materials.

Effect of oxygen partial pressure on phase, local structure and photoluminescence properties of Hf(1-x)YxO2 thin films prepared by pulsed laser deposition

Hf(1-x)YxO2 (x = 0, 0.10, 0.15, 0.20) epitaxial thin films on YSZ(100) substrate were prepared at different oxygen (O2) partial pressures (100, 70, 30, and 10 sccm) by pulsed laser deposition. The effect of oxygen partial pressure on crystalline and local structure was investigated using X-ray diffraction (XRD), Fourier Transform Infrared (FTIR) and X-ray absorption spectroscopy (XAS). The surface composition was determined by X-ray photoelectron spectroscopy. The XRD and FTIR studies reveal that undoped HfO2 thin films remain in monoclinic phase, and the Hf0.85Y0.15O2 & Hf0.80Y0.20O2 films stabilize in cubic phase at all oxygen pressures, whereas the structure of Hf0.90Y0.10O2 films changes from orthorhombic to cubic as oxygen pressure reduces from 100 sccm. The XAS at Hf-L3 edge and O K-edge shows the changes in bond distances, disorder and hybridization. In monoclinic HfO2 films the Hf–O bond distance and disorder increases and Hf–Hf bond decreases as the O2 partial pressure decreases, whereas disorder in doped films shows anomalous behaviour. The oxygen vacancies are evident from both XAS and photoluminescence studies. The results enlighten a deeper understanding of phase change, local structure, optical properties and pave a way to stabilize and identify different technologically important HfO2 phases for dielectric and ferroelectric applications.

Single-crystal analysis of La-doped pyromorphite [Pb5(PO4)3Cl

Abstract Rare earth elements (REE) in calcium apatite have been widely described in the literature. Based on the investigations of minerals and their synthetic analogs, the mechanism of substitution of REE3+ for Ca2+ and their structural positions are well established. Although the presence of REE in natural pyromorphite has been reported, the structural response of substitution of REE3+ for Pb2+ is not established. A better understanding of REE-rich Pb-apatite may facilitate the potential use of this mineral in industrial processes. Two La-doped pyromorphite analogs [Pb5(PO4)3Cl] and two control pyromorphite analogs (with the absence of La) were synthesized from aqueous solutions at 25 °C. Na+ and K+ were used as charge-compensating ions to facilitate the incorporation of trivalent REE cations (La3+ + Na+ ↔ 2Pb2+ and La3+ + K+ ↔ 2Pb2+). Microprobe analysis, scanning electron microscopy, and Raman spectroscopy were used to confirm the purity of obtained phases. High-precision crystal structure refinements (R1 = 0.0140–0.0225) of all four compounds were performed from single-crystal X-ray diffraction data. The La content varied from 0.12(1) to 0.19(1) atoms per formula unit with the counter ions of K+ and Na+, respectively. Both substituting ions were accommodated at the Pb1 site only. By comparing the La-doped pyromorphite analogs with their control samples, it was possible to detect small changes in bond distances and polyhedral volumes caused by the La substitution. Variations in individual and mean interatomic distances reflected the cumulative effect of both the amount of substitution and ionic radii of substituting ions (La3+, Na+, and K+).

The thermal decomposition of studtite: analysis of the amorphous phase

Studtite is known to exist at the back-end of the nuclear fuel cycle as an intermediate phase formed in the reprocessing of spent nuclear fuel. In the thermal decomposition of studtite, an amorphous phase is obtained at calcination temperatures between 200 and 500 °C. This amorphous compound, referred to elsewhere in the literature as U2O7, has been characterised by analytical spectroscopic methods. The local structure of the amorphous compound has been found to contain uranyl bonding by X-ray absorption near edge (XANES), Fourier transform infrared and Raman spectroscopy. Changes in bond distances in the uranyl group are discussed with respect to studtite calcination temperature. The reaction of the amorphous compound with water to form metaschoepite is also discussed and compared with the structure of schoepite and metaschoepite by X-ray diffraction. A novel schematic reaction mechanism for the thermal decomposition of studtite is proposed.

London Dispersion Corrections to Density Functional Theory for Transition Metals Based on Fitting to Experimental Temperature-Programmed Desorption of Benzene Monolayers.

Standard implementations of generalized gradient approximation (GGA)-based density functional theory (DFT) describe well strongly bound molecules and solids but fail to describe long-range London dispersion or van der Waals (vdW) attraction interactions that are important in molecular crystals and two-dimensional solids. To provide accurate values for the vdW distance and energies for the metals Cu, Ag, Au, Ni, Pd, and Pt, we determined empirical vdW corrections to Perdew, Burke, and Ernzerhof (PBE) DFT by fitting the experimental adsorption enthalpies measured by temperature-programmed desorption (TPD) from benzene monolayers by Campbell and co-workers ( J. Phys. Chem. C 2016, 120, 25161-25172). Benzene physisorbed to these metals without chemical reaction; therefore, we consider the bonding to be vdW. We use the low gradient form for the vdW corrections, EvdW-LG = -C6LG/[R6 + RvdwLG6] with just two parameters per atom (C6LG and RvdwLG). This LG form leads to negligible changes in bond distances and angles, so adjusting the parameters should not sacrifice accuracy for the bonding interactions. We demonstrate that the parameters fitted to benzene also describe well the physisorption enthalpies for other hydrocarbons (naphthalene, cyclohexane, methane, ethane, and propane) on Pt. We also report low gradient vdW correction parameters for the noble gases that fit the equilibrium lattice parameter and heat of vaporization of the crystals.

Stabilization of Plutonium(V) Within a Crown Ether Inclusion Complex

Crystalline coordination complexes of actinides, especially in atypical oxidation states, are not only fundamentally important for expanding the notably limited knowledge on the bonding nature of a...

Crystal Chemistry of an Erythrite-Köttigite Solid Solution (Co3–xZnx) (AsO4)2·8H2O

A wide compositional range, covering about 90% of an expected erythrite-köttigite substitutional solid solution with extreme compositions of (Co2.84Mg0.14Zn0.02) (AsO4)2·8H2O and (Zn2.74Co0.27) (AsO4)2·8H2O, was revealed in a suite of samples from a polymetallic ore deposit in Miedzianka, SW Poland. Members of the solid solution series were examined by means of Electron Probe Microanalysis (EPMA), Scanning Electron Microscopy (SEM)/Energy-Dispersive Spectrometer (EDS), X-ray single-crystal and powder diffraction, and Raman spectroscopy. Metal cations were randomly distributed between two special octahedral sites in the erythrite–köttigite structure. In response to Co ↔ Zn substitutions, small but significant changes in bond distances (particularly in [AsO4] tetrahedra), rotation, and distortion of co-ordination polyhedra were observed. Two sub-series of dominant cationic substitutions (Co-Mg-Ni and Co-Fe-Zn) were noted within the arsenate series of vivianite-group minerals linked by erythrite. The paragenetic sequence erythrite → Zn-rich erythrite → Co-rich köttigite → köttigite reflects the evolution of the solution’s pH towards increased acidity and a relative increase in the concentration of Zn ions following precipitation of erythrite.

Quantifying the Interdependence of Metal–Ligand Covalency and Bond Distance Using Ligand K‐edge XAS

AbstractBond distance is a common structural metric used to assess changes in metal–ligand bonds, but it is not clear how sensitive changes in bond distances are with respect to changes in metal–ligand covalency. Here we report ligand K‐edge XAS studies on Ni and Pd complexes containing different phosphorus(III) ligands. Despite the large number of electronic and structural permutations, P K‐edge pre‐edge peak intensities reveal a remarkable correlation that spectroscopically quantifies the linear interdependence of covalent M−P σ bonding and bond distance. Cl K‐edge studies conducted on many of the same Ni and Pd compounds revealed a poor correlation between M−Cl bond distance and covalency, but a strong correlation was established by analyzing Cl K‐edge data for Ti complexes with a wider range of Ti−Cl bond distances. Together these results establish a quantitative framework to begin making more accurate assessments of metal–ligand covalency using bond distances from readily‐available crystallographic data.

Quantifying the Interdependence of Metal-Ligand Covalency and Bond Distance Using Ligand K-edge XAS.

Bond distance is a common structural metric used to assess changes in metal-ligand bonds, but it is not clear how sensitive changes in bond distances are with respect to changes in metal-ligand covalency. Here we report ligand K-edge XAS studies on Ni and Pd complexes containing different phosphorus(III) ligands. Despite the large number of electronic and structural permutations, P K-edge pre-edge peak intensities reveal a remarkable correlation that spectroscopically quantifies the linear interdependence of covalent M-P σ bonding and bond distance. Cl K-edge studies conducted on many of the same Ni and Pd compounds revealed a poor correlation between M-Cl bond distance and covalency, but a strong correlation was established by analyzing Cl K-edge data for Ti complexes with a wider range of Ti-Cl bond distances. Together these results establish a quantitative framework to begin making more accurate assessments of metal-ligand covalency using bond distances from readily-available crystallographic data.

Photochemical pathways in nucleobases measured with an X-ray FEL.

The conversion of light energy into other molecular energetic degrees of freedom is often dominated by ultrafast, non-adiabatic processes. Femtosecond spectroscopy with optical pulses has helped in shaping our understanding of crucial processes in molecular energy-conversion. The advent of new, ultrashort and bright X-ray free electron laser sources opens the possibility to use X-ray-typical element and site sensitivity for ultrafast molecular research. We present two types of spectroscopy, ultrafast Auger and ultrafast X-ray absorption spectroscopy, and discuss their sensitivity to molecular processes. While Auger spectroscopy is able to monitor bond distance changes in the vicinity of an X-ray created core hole, near-edge absorption spectroscopy can deliver high-fidelity information on non-adiabatic transitions involving lone-pair orbitals. We demonstrate these features on the example of the UV-excited nucleobase thymine, investigated at the oxygen K-edge. We find a C-O bond elongation in the Auger data in addition to ππ*/ nπ* non-adiabatic transition in X-ray near-edge absorption. We compare the results from both methods and draw a conclusive scenario of non-adiabatic molecular relaxation after UV excitation. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.

Evaluating the Effects of Geometry and Charge Flux in Force Field Modeling

We apply a model for analyzing the importance of conformational charge flux to 11 molecules with the R-(CH2) n-R structure (R = Cl, F, OH, SH, COOH, CONH2, and NH2 and n = 4-6). Atomic charges were obtained by fitting to results from density functional theory calculations using the HLY procedure, and their geometry dependence is decomposed into contributions from changes in bond lengths, bond angles, and torsional angles. The torsional degrees of freedom are the main contribution to the conformational dependence of atomic charges and molecular dipole moments, but indirect effects due to changes in bond distances and angles account for ∼15% of the variations. While the magnitude of charge flux and geometry effects have been found to be independent of the number of internal degrees of freedom, the nature of the R- group has a moderate influence. The indirect effects are comparable for all of the R-groups and are approximately one-half the magnitude of the corresponding effects in peptide models. However, the magnitudes are different, yet the relative importance of geometry and charge flux effects are completely similar to those of the peptide models, which suggests that modeling the charge flux effects for changes in bond lengths, bond angles, and torsional angles should be considered for developing improved force fields.

Probing the Importance of Charge Flux in Force Field Modeling.

We analyze the conformational dependence of atomic charges and molecular dipole moments for a selection of ∼900 conformations of peptide models of the 20 neutral amino acids. Based on a set of reference density functional theory calculations, we partition the changes into effects due to changes in bond distances, bond angles, and torsional angles and into geometry and charge flux contributions. This allows an assessment of the limitations of fixed charge force fields and indications for how to design improved force fields. The torsional degrees of freedom are the main contribution to conformational changes of atomic charges and molecular dipole moments, but indirect effects due to change in bond distances and angles account for ∼25% of the variation. Charge flux effects dominate for changes in bond distances and are also the main component of the variation in bond angles, while they are ∼25% compared to the geometry variations for torsional degrees of freedom. The geometry and charge flux contributions to some extent produce compensating effects.

Ultrafast Photoinduced Electron Transfer from Peroxide Dianion.

The encapsulation of peroxide dianion by hexacarboxamide cryptand provides a platform for the study of electron transfer of isolated peroxide anion. Photoinitiated electron transfer (ET) between freely diffusing Ru(bpy)3(2+) and the peroxide dianion occurs with a rate constant of 2.0 × 10(10) M(-1) s(-1). A competing electron transfer quenching pathway is observed within an ion pair. Picosecond transient spectroscopy furnishes a rate constant of 1.1 × 10(10) s(-1) for this first-order process. A driving force dependence for the ET rate within the ion pair using a series of Ru(bpy)3(2+) derivatives allows for the electronic coupling and reorganization energies to be assessed. The ET reaction is nonadiabatic and dominated by a large inner-sphere reorganization energy, in accordance with that expected for the change in bond distance accompanying the conversion of peroxide dianion to superoxide anion.

Supramolecular architectures for controlling slow magnetic relaxation in field-induced single-molecule magnets

In order for molecular magnetic materials to become functional, they must retain their magnetization at reasonable temperatures implying high energy barriers for spin reversal. The field of single-molecule magnets (SMMs) has recently experienced an explosion of research targeting these high anisotropic barriers. Achieving such feats has involved increasing the spin of a complex and/or increasing the inherent magnetic anisotropy. Exerting control over the total spin of a complex has been possible contrary to controlling the global anisotropy. Herein, we report the experimental and theoretical study of local anisotropy alignment on DyIII metal centers and their orientation relative to other centers in rare, dinuclear quadruply-stranded helicate/mesocate complexes. A detailed study of these supramolecular architectures has advanced our knowledge of the origins of magnetic relaxation in SMMs which was shown to arise from minute changes in bond distances around the metal centers leading to changes in the local anisotropy and, in turn, the effective energy barriers.

Computational Studies of Lewis Acidities of Tris(fluorophenyl)-Substituted Boranes: An Additive Relationship between Lewis Acidity and Fluorine Position

Computational studies of the binding energies of all possible tris(fluoroaryl)boranes B(C(6)H(x)F(5-x))(3) to NMe(3) and PMe(3) show that they (and by extension, the Lewis acidities of the boranes) can be tuned to a sizable range of values through judicious placement of fluorines. This holds despite the fact that the B-X bond distance changes little regardless of substitution, save when the aryl ring is 2,6-disubstituted. Fluorine substitution appears to affect the binding energies additively. Least-squares regression finds substitution at the 2-position to increase the binding energy by ca. 13 kcal·mol(-1), while substitution at the 3- and 5-positions increases it by ca. 3 kcal·mol(-1). Substitution at the 4-position has little to no impact, while substitution at the 6-position decreases the binding energy by ca. 3-6 kcal·mol(-1). The last observation arises from steric congestion because the 6-position can only be substituted in tandem with substitution at the 2-position. Models suggest that the pattern arises from polarization effects that decrease exponentially as the distance between boron and fluorine increases.

Local spin-coupled distortions in multiferroic hexagonalHoMnO3

Local structural measurements have been performed on hexagonal HoMnO3 in order to ascertain the specific changes in bond distances which accompany magnetic ordering transitions. The transition from paramagnetic to the antiferromagetic (noncollinear) phase near ~70 K is dominated by changes in the a-b plane Mn-Mn bond distances. The spin rotation transition near ~40 K involves both Mn-Mn and nearest neighbor Ho-Mn interactions while the low temperature transition below 10 K involves all interactions, Mn-Mn, Ho-Mn (nearest and next nearest) and Ho-Ho correlations. These changes in bond distances reveal strong spin-lattice coupling. The similarity in magnitude of the change in J(Mn-Mn) and J(Ho-Mn) enhances the system frustration. The structural changes are interpreted in terms of a model of competing spin order and local structural distortions. Density functional calculations are used to estimate the energies associated with ionic displacements. The calculations also reveal asymmetric polarization of the charge density of Ho, O3 and O4 sites along the z-axis in the ferroelectric phase. This polarization facilitates coupling between Ho atoms on neighboring planes normal to the z-axis.

Interaction of Mg 2+, Ca 2+, Zn 2+ and Cu + with cytosine nucleosides: Influence of metal on sugar puckering and stability of N-Glycosidic bond, a DFT study

The coordination geometries, electronic features, absolute metal ion affinities, geometrical multiplicity and binding strength for the complexes formed by Mg 2+, Ca 2+, Zn 2+ and Cu + with cytidine and deoxycytidine have been determined theoretically employing the hybrid B3LYP exchange-correlation functional and using 6-311++G(d,p) orbital basis sets. Our study shows that the most stable coordination modes of cytosine nucleosides with these cations are rather similar. In the isolated state, the most stable form corresponds to a tridentate complex in which the cation interacts with three oxygen atoms: one from the carbonyl oxygen of cytosine moiety and two from the sugar unit (i.e., O5′ and O4′). The influences of metal cationization on the strength of the N-glycosidic bond, the values of the phase angle of pseudorotation P in the sugar unit and sugar ring conformation have been studied. In all cases, the N1 C1′ bond distance changes upon introducing positive charge in the nucleosides.

Structure, Heat Capacity, and High-Temperature Thermal Properties of Yb14Mn1−xAlxSb11

A series of compounds, Yb_(14)Mn_(1−x)Al_xSb_11 with (0 < x < 1), was prepared via Sn flux and the structures investigated. Single-crystal X-ray diffraction reveals that the volume of the unit cell increases with increasing Al content. Bond-distance changes are less than 2% and the increase in volume of the unit cell is associated with the decreasing distortion of the tetrahedron with increasing Al content. The specific heat, C_p, was measured from 300 to 1100 K. The measured C_p for these compounds is 19% higher than the Dulong-Petit value at the peak zT temperature (1223 K). These measured values permit a recalculation of thermal conductivity, revealing an extremely low lattice thermal conductivity of approximately 0.3−0.4 W/(m K) at 1223 K. The maximum zT of Yb_(14)Mn(1−x)Al_xSb_11 is approximately 0.8 and 1.1 for the x = 0 and x = 0.6 compositions, respectively.

DFT study of the interaction of cytidine and 2′-deoxycytidine with Li +, Na +, and K +: effects of metal cationization on sugar puckering and stability of the N-glycosidic bond

Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li +, Na +, and K + with cytidine and 2′-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li + to Na + and K + for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.5, 55.2, and 41.8 and for 2′-deoxycytidine, 82.8, 57.4, and 42.2 kcal/mol, respectively. It is also interesting to mention that linear correlations between calculated MIA values and the atomic numbers ( Z) of the above metal ions were found. The influence of metal cationization on the coordination modes and the strength of the N-glycosidic bond in cytosine nucleosides have been studied. In all cases, the N1–C1′ bond distance changes upon introducing a positive charge in the nucleosides. It has been found that metal binding significantly changes the values of the phase angle of pseudorotation P in the sugar unit of these nucleosides. With respect to the sugar ring, metal binding changes the values of the glycosyl torsion angle and sugar ring conformation. The present calculations in the gas phase provide the first clues on the intrinsic chemistry of these systems and may be of value for studies of the influence of metal cations on the conformational behavior and function of nucleic acids.

Quenching Mechanism of Zn(Salicylaldimine) by Nitroaromatics

Nitroaromatics and nitroalkanes quench the fluorescence of Zn(Salophen) (H2Salophen = N,N'-phenylene-bis-(3,5-di- tert-butylsalicylideneimine); ZnL(R)) complexes. A structurally related family of ZnL(R) complexes (R = OMe, di-tBu, tBu, Cl, NO2) were prepared, and the mechanisms of fluorescence quenching by nitroaromatics were studied by a combined kinetics and spectroscopic approach. The fluorescent quantum yields for ZnL(R) were generally high (Phi approximately 0.3) with sub-nanosecond fluorescence lifetimes. The fluorescence of ZnL(R) was quenched by nitroaromatic compounds by a mixture of static and dynamic pathways, reflecting the ZnL(R) ligand bulk and reduction potential. Steady-state Stern-Volmer plots were curved for ZnL(R) with less-bulky substituents (R = OMe, NO2), suggesting that both static and dynamic pathways were important for quenching. Transient Stern-Volmer data indicated that the dynamic pathway dominated quenching for ZnL(R) with bulky substituents (R = tBu, DtBu). The quenching rate constants with varied nitroaromatics (ArNO2) followed the driving force dependence predicted for bimolecular electron transfer: ZnL* + ArNO2 --> ZnL(+) + ArNO2(-). A treatment of the diffusion-corrected quenching rates with Marcus theory yielded a modest reorganization energy (lambda = 25 kcal/mol), and a small self-exchange reorganization energy for ZnL*/ZnL(+) (ca. 20 kcal/mol) was estimated from the Marcus cross-relation, suggesting that metal phenoxyls may be robust biological redox cofactors. Electronic structure calculations indicated very small changes in bond distances for the ZnL --> ZnL(+) oxidation, suggesting that solvation was the dominant contributor to the observed reorganization energy. These mechanistic insights provide information that will be helpful to further develop ZnL(R) as sensors, as well as for potential photoinduced charge transfer chemistry.