Differences In Bond Lengths Research Articles

Lattice relaxation and ferromagnetic character of (LaVO3)m/SrVO3superlattices

The experimental observation that vanadate superlattices (LaVO3)m/SrVO3 show ferromagnetism up to room temperature (Lüders U. et al., Phys. Rev. B, 80 (2009) 241102(R)) is investigated by means of density functional theory, and the band structure for m = 5 and 6 is calculated. A buckling of the interface VO2 layers is found in both cases, but subtle differences in bond length lead to very different properties for even and odd values of m: in the even case, the two interface VO2 layers effectively decouple from the adjacent LaO layers due to a strong bond length enhancement. This results into a local inversion of the orbital occupancy and to the confinement of the charge carriers. In the odd case, the amplitude of the bond length variation is smaller, so that the charge carriers spill into the deeper-lying VO2 layers, and spin-polarised interfaces are obtained.

Determination of the molecular structure of the short-lived light-induced high-spin state in the spin-crossover compound [Fe(6-mepy)3tren](PF6)2

In the spin-crossover compound [Fe(6-mepy)(3)tren](PF6)(2), (6-mepy)(3)tren=tris{4-[(6-methyl)-2-pyridyl]-3-aza-butenyl}amine, the high-spin state can be populated as a metastable state below the thermal transition temperature via irradiation into the metal to the ligand charge-transfer absorption band of the low-spin species. At 10 K, the lifetime of thismetastable state is only 1 s. Despite this, it is possible to determine an accurate excited state structure by following the evolution of relevant structural parameters by synchrotron x-ray diffraction under continuous irradiation with increasing intensity. The difference in metal-ligand bond length between the high-spin and the low-spin states is found to be 0.192 angstrom, obtained from an analysis of the experimental data using the mean-field approximation to model cooperative effects.

The influence of (5′R) and (5′S)-5′,8-cyclo-2′-deoxyadenosine for the electronic properties of nucleosides pairs. The theoretical quantum mechanics studies

Abstract Oxidatively generated damage to DNA frequently appears in the human genome as the effect of aerobic metabolism or as the result of exposure to exogenous oxidizing agents such as ionization radiation. In this paper, for the first time, the electronic properties of nucleoside pairs containing 5′,8-cyclo-2′-deoxyadenosine (cdA) in their 5′R and 5′S diastereomeric forms (cdA(R)::T and cdA(S)::T) as the simplest model of ds-DNA have been discussed. The following values of the selected electronic parameters, measured in eV, were found for cdA(R)::T, cdA(S)::T, and dA::T, respectively, adiabatic/vertical electron affinity: 0.39/0.24, 0.35/0.18, 0.33/0.21; and adiabatic/vertical ionization potential: 7.27/7.50, 7.7.25/7.49, 7.03/7.27. Moreover, based on the results of the relaxation energy, the presence of cdA(S)::T should provide the highest barrier for electron transfer in ds-DNA. Analyses of hydrogen bond length deviations reveal that the formation of cationic forms results in higher elongation than that of anionic forms. Moreover, during the electron attachment or detachment for the investigated cdA(R)::T, cdA(S)::T, and dA::T nucleoside pairs, the same scheme of changes in hydrogen bond length was noted.

DFT Studies of Trans and Cis Influences in the Homolysis of the Co–C Bond in Models of the Alkylcobalamins

Density functional theory (DFT) calculations (BP86/6-31+G(d,p)) and an analysis of the electron density using Bader's quantum theory of atoms in molecules (QTAIM) are used to explore factors that influence the bond dissociation energy (BDE) of the Co-C bond in models for the cofactor in the coenzyme B12-dependent enzymes. An increase in the basicity of L in [L-Co(III)(corrin)-CH3](n+), L = NH3, NH2(-), and NH(2-), causes an elongation of the trans Co-C bond, but this does not necessarily cause the BDE to decrease. The bond between the metal and the N-donor of L, Co-Nα, usually becomes shorter after Co-C homolysis as the resulting five-coordinate product permits the metal ion to move toward L. This contraction increases with the basicity of L and stabilizes the five-coordinate product. The BDE is found to correlate well with two variables, the basicity of L and the difference in the Co-Nα bond length between the five-coordinate product and the six-coordinate ground state. When L is a naturally occurring amino acid or a model for its metal-coordinating side chain, the BDE is found to be moderately dependent on L and decrease with an increase in the softness of the donor atom of L. Sulfides produce a BDE < 30 kcal mol(-1), whereas neutral alcohol donors produce a stronger Co-C bond with a BDE of 34-35 kcal mol(-1). All other ligands are associated with a trans Co-C bond that is almost invariant in strength and with a BDE of 31-33 kcal mol(-1). Models of the type [H3N-Co(III)(N4)-CH3](n+), where N4 = bis(dimethylglyoxime), porphyrin, corrin, and corrole, show that the nature of the tetraaza equatorial ligand can change BDE values by over 8 kcal mol(-1); the BDE when N4 = bis(dimethylglyoxime) is significantly larger than for the other three systems, among which differences in BDE are quite small (2.4 kcal mol(-1)). The differential stabilization of the five-coordinate product by the shrinking of the Co-Nα bond (in corrin and in corrole) or its elongation (in porphyrin and in bis(dimethylglyoxime)) is an important factor in determining the BDE of these systems. Corrin has the longest and weakest Co-C bond; this, together with a significant contraction of the Co-Nα after homolysis, is likely to be the origin of its relatively low BDE.

Structural properties and growth evolution of diamond-like carbon films with different incident energies: A molecular dynamics study

Structural properties and growth evolution of diamond-like carbon (DLC) films with different incident energies were investigated systematically by the molecular dynamics simulation using a Tersoff interatomic potential for carbon-carbon interaction. The results revealed that the density, sp3 fraction and residual compressive stress as a function of incident energy increased firstly and then decreased; when the incident energy was 70eV/atom, the density could reach to 3.0g/cm3 with the maximal compressive stress of 15.5GPa. Structure analysis indicated that the deviation of both bond angles and lengths from the equilibrium position led to the generation of a large residual stress, while the high compressive stress mainly attributed to the decrease of both bond angles and lengths among carbon atoms. The growth of DLC films underwent a formation process of “Line-Net” structure accompanied with the interaction of many atomic motion mechanisms, and the “Point” stage was only found for DLC films with low incident energy.

Size‐Selective Encapsulation of Hydrophobic Guests by Self‐Assembled M4L6 Cobalt and Nickel Cages

Subtle differences in metal-ligand bond lengths between a series of [M(4)L(6)](4-) tetrahedral cages, where M = Fe(II), Co(II), or Ni(II), were observed to result in substantial differences in affinity for hydrophobic guests in water. Changing the metal ion from iron(II) to cobalt(II) or nickel(II) increases the size of the interior cavity of the cage and allows encapsulation of larger guest molecules. NMR spectroscopy was used to study the recognition properties of the iron(II) and cobalt(II) cages towards small hydrophobic guests in water, and single-crystal X-ray diffraction was used to study the solid-state complexes of the iron(II) and nickel(II) cages.

Crystallization of salts M3[NpO4(OH)2]·nH2O (M = Na, K, Rb, Cs) from concentrated alkali solutions at low temperatures. Synthesis and structure of a new Np(VII) compound, Na3[NpO4(OH)2]·6H2O

Precipitation of salts M3[NpO4(OH)2]·nH2O (M = Na, K, Rb, Cs) from concentrated alkali solutions at low temperatures (about −10°C) was studied. From solutions with [OH−] > 9.5 M, these compounds are isolated as coarse black crystals in high yield without impurity of other phases. The K, Rb, and Cs salts crystallize in the form of the previously studied compounds K3[NpO4(OH)2]·2H2O and M3[NpO4(OH)2]·3H2O (M = Rb, Cs). In the case of Na, a new hydrate Na3[NpO4(OH)2]·6H2O was obtained, and its crystal structure was determined. Crystals of the hexahydrate consist of centrosymmetrical tetragonal-bipyramidal anions [NpO4(OH)2]3−, crystallographically independent Na(1) and Na(2) cations, and water molecules. The coordination surrounding of the Np atom is characterized by noticeable difference (Δ = 0.0203 A) in the Np-O bond lengths in the equatorial plane of the bipyramid. The [NpO4(OH)2]3− anions are combined with the Na(2) cations to form infinite chains [Na(2)NpO4(OH)2(H2O)2]2− in such a manner that the lateral edges of the anion are simultaneously the lateral edges of the Na(2) coordination polyhedron. Incorporation of one of the two crystallographically independent O atoms of the NpO4 group into the Na(2) coordination surrounding is responsible for a noticeable difference in the Np-O bond lengths in the equator of the [NpO4(OH)2]3− anion. The types of hydrogen bonding in the structures of Na3[NpO4(OH)2]·nH2O (n = 0, 2, 4, 6) are compared.

Investigations on the g factors for the Cu2+ sites in YBa1.9Na0.1Cu3O7−δ and YBa2Cu3O7−δ

The anisotropic g factors gi (i=x, y, z ) for the six-fold coordinated orthorhombic Cu2+(1) site in YBa1.9Na0.1Cu3O7−δ and the five-fold coordinated tetragonal Cu2+(2) site in YBa2Cu3O7−δ are theoretically studied from the perturbation formulas of the g factors for a 3d9 ion in orthorhombically and tetragonally elongated octahedra, respectively. The orthorhombic (or tetragonal) field parameters are obtained using the superposition model and the local structures of the Cu2+ sites. In view of covalency, the contributions from the ligand orbital and spin-orbit coupling interactions are taken into account. For the Cu2+(1) site in YBa1.9Na0.1Cu3O7−δ, the axial anisotropy Δg[=gz−(gx−gy)/2] may be ascribed to the moderate (about 3%) elongation of the Cu–O distance along c axis, while the perpendicular anisotropy δg(=gx−gy) can be characterized by the planar bond length deviation difference δR(≈0.083Å) in the perpendicular (ab) plane. However, for the Cu2+(2) site in YBa2Cu3O7−δ, the anisotropy Δg(=g||−g⊥) is illustrated by the significant elongation of the [CuO5]8− cluster along c axis with about 25% longer axial Cu–O distance than the four planar ones. The theoretical g factors are in good agreement with the experimental data.

Nuclear resonance vibrational spectroscopy (NRVS) of rubredoxin and MoFe protein crystals.

We have applied 57Fe nuclear resonance vibrational spectroscopy (NRVS) for the first time to study the dynamics of Fe centers in Fe-S protein crystals, including oxidized wild type rubredoxin crystals from Pyrococcus furiosus, and the MoFe protein of nitrogenase from Azotobacter vinelandii. Thanks to the NRVS selection rule, selectively probed vibrational modes have been observed in both oriented rubredoxin and MoFe protein crystals. The NRVS work was complemented by extended X-ray absorption fine structure spectroscopy (EXAFS) measurements on oxidized wild type rubredoxin crystals from Pyrococcus furiosus. The EXAFS spectra revealed the Fe-S bond length difference in oxidized Pf Rd protein, which is qualitatively consistent with the X-ray crystal structure.

Redetermination of Ba2CdTe3from single-crystal X-ray data

The previous structure determination of the title compound, dibarium tritelluridocadmate, was based on powder X-ray diffraction data [Wang & DiSalvo (1999 ▶). J. Solid State Chem. 148, 464–467]. In the current redetermination from single-crystal X-ray data, all atoms were refined with anisotropic displacement parameters. The previous structure report is generally confirmed, but with some differences in bond lengths. Ba2CdTe3 is isotypic with Ba2 MX 3 (M = Mn, Cd; X = S, Se) and features 1 ∞[CdTe2/2Te2/1]4− chains of corner-sharing CdTe4 tetra­hedra running parallel [010]. The two Ba2+ cations are located between the chains, both within distorted monocapped trigonal–prismatic coordination polyhedra. All atoms in the structure are located on a mirror plane.

Deciphering the atomic structure of a complex Sr/Ge (100) phase via scanning tunneling microscopy and first-principles calculations

The details of a Sr-induced ($3\ifmmode\times\else\texttimes\fi{}4$) reconstruction on Ge(100) were examined using scanning tunneling microscopy (STM) and density functional theory. At 1/6 ML of Sr, this reconstruction is similar to the 1/6 ML ($3\ifmmode\times\else\texttimes\fi{}2$) Sr phase previously observed on Si. In contrast to Si, however, atomic-resolution images of the Sr-Ge phase exhibit more dramatic and unusual bias dependence in STM that could be explained with the help of first-principles calculations of minimum energy structures. Simulated STM images are in excellent agreement with the experimental data and allow the ($3\ifmmode\times\else\texttimes\fi{}2$) Sr-Si double dimer vacancy alloy model to be extended to the Ge surface through a more complex ($3\ifmmode\times\else\texttimes\fi{}4$) arrangement of its building blocks. The difference between Si and Ge is interpreted in terms of the lower Ge-Ge binding energy and differences in the interatomic bond lengths.

The role of the Auger parameter in XPS studies of nickel metal, halides and oxides

The critical role of the Auger parameter in providing insight into both initial state and final state factors affecting measured XPS binding energies is illustrated by analysis of Ni 2p(3/2) and L(3)M(45)M(45) peaks as well as the Auger parameters of nickel alloys, halides, oxide, hydroxide and oxy-hydroxide. Analyses of the metal and alloys are consistent with other works, showing that final state relaxation shifts, ΔR, are determined predominantly by changes in the d electron population and are insensitive to inter-atomic charge transfer. The nickel halide Auger parameters are dominated by initial state effects, Δε, with increasing positive charge on the core nickel ion induced by increasing electronegativity of the ligands. This effect is much greater than the final state shifts; however, the degree of covalency is reflected in the Wagner plot where the more polarizable iodide and bromide have greater ΔR. The initial state shift for NiO is much smaller than those of Ni(OH)(2) or NiOOH and the effective oxidation state is much less than that inferred from the average electronegativity of the ligand(s). Auger parameter analysis indicates that the bonding in NiO appears to have stronger contributions from initial state charge transfer from the oxygen ligands than that in the hydroxide and oxyhydroxide consistent with the considerable differences in the Ni-O bond lengths in these compounds with some relaxation of this state occurring during final state phenomena. The Auger parameter of NiOOH is, however, shifted positively, like the iodide, indicating greater polarizability of the ligands and covalency in this bonding. There is support for more direct use of relative bond lengths in interpreting differences between related compounds rather than more general electronegativity or similar parameters.

Calculation and analysis of the valence electron structure of MoSi2 and (Mo0.95, Nb0.05)Si2

Based on the empirical electron theory (EET) of solids and molecules, the valence electron structure (VES) and theoretical bond energy of MoSi2 was calculated by the bond length difference method (BLD). According to the average atomic model in substitutional solid solution of EET, the VES and theoretical bond energy of (Mo0.95, Nb0.05)Si2 were analyzed. The results indicated that the Nb alloying into MoSi2 changed the hybridization state of Mo and Si atom, which correspondingly changed the parameters of VES. The ratio of covalent valence electron number to total number of valence electron in MoSi2 is 65.87%, compared with that of MoSi2, the ratio increase to 80.61% in (Mo0.95, Nb0.05)Si2, thus the addition of niobium can improve the strength of MoSi2. The lattice electron decrease from 4.7141 to 2.5526, which reduced the plasticity of MoSi2 by niobium microalloying.

Stone–Wales defects can cause a metal–semiconductor transition in carbon nanotubes depending on their orientation

It has been shown that the two different orientations of Stone–Wales (SW) defects, i.e. longitudinal and circumferential SW defects, on carbon nanotubes (CNTs) result in two different electronic structures. Based on density functional theory we have shown that the longitudinal SW defects do not open a bandgap near the Fermi energy, while a relatively small bandgap emerges in tubes with circumferential defects. We argue that the bandgap opening in the presence of circumferential SW defects is a consequence of long-range symmetry breaking which can spread all the way along the tube. Specifically, the distribution of contracted and stretched bond lengths due to the presence of defects, and hopping energies for low-energy electrons, i.e. the 2pz electrons, show two different patterns for the two types of defects. Interplay between the geometric features and the electronic properties of the tubes have also been studied for different defect concentrations. Considering π-orbital charge density, it has also been shown that the deviations of bond lengths from their relaxed length result in different doping for two defect orientations around the defects—electron-rich for a circumferential defect and hole-rich for a longitudinal one. We have also shown that, in the tubes having both types of defects, circumferential defects would dominate and impose their electronic properties.

Redetermination of (E)-3-(anthracen-9-yl)-1-(2-hydroxyphenyl)prop-2-en-1-one

The redetermined structure of title chalcone derivative, C23H16O2, corrects errors in the title, scheme and synthesis in the previous report of the same structure [Jasinski et al. (2011 ▶). Acta Cryst. E67, o795]. There are two independent mol­ecules in the asymmetric unit with slight differences in bond lengths and angles. The dihedral angle between the benzene ring and the anthracene ring system is 73.30 (4)° in one mol­ecule and 73.18 (4)° in the other. Both mol­ecules feature an intra­molecular O—H⋯O hydrogen bond, which generates an S(6) ring. In the crystal, mol­ecules are arranged into sheets lying parallel to the ac plane and further stacked along the b axis by π–π inter­actions with centroid–centroid distances in the range 3.6421 (6)–3.7607 (6) Å. The crystal structure is further stabilized by C—H⋯π inter­actions. There are also C⋯O [3.2159 (15) Å] short contacts.

Calculation of Valence Electron Structure of Precipitate Phases in Al-Cu Cast Alloy

Based on Empirical Electron Theory in solid (EET) and Bond Length Difference (BLD) the valence electron structures of precipitates in AlCu alloy during aging process were calculated. The results show that the different phase structure factors explain the thermal stability of phases in θ sequence, and the tendency of atoms solution is corresponding with the phase transition during aging from valence electron structure levels, which reveals the inside causes of ageing hardening is closely related to the covalent electron pairs in some bond of the precipitations and matrix.

Face-Dependent Bond Lengths in Molecular Chemisorption: The Formate Species on Cu(111) and Cu(110)

Many previous structural studies of molecular adsorbates on metal surfaces indicate that the local coordination and bonding is closely similar to that in organometallic compounds, implying that the metallic substrate has no significant influence. Here we show that such an influence is detectable for one model system, namely, the formate species, HCOO, adsorbed on the atomically rough and smooth (110) and (111) surfaces of Cu, leading to a statistically significant difference (0.09±0.05 Å) in the Cu-O chemisorption bond length. The effect is reproduced in density functional theory calculations.

Atomic Simulation for Lattice Structure of La/SrMnO&lt;sub&gt;3&lt;/sub&gt; Superlattice

We studied in detail the lattice transition and local lattice structure (including Jahn-Teller distortion) in LaMnO3/SrMnO3surperlattices by classical atomistic simulation. For a certain doping density, it is found that the superlattices with short modulation period have small lattice energies and larger differences among lattice parametersa,b/√2 andc. The average La-Mn (Mn3+-O) distance is larger than the average Sr-Mn (Mn4+-O) distance for all doping densities and superlattice configurations at certain doping density. The standard deviation of Mn-O bond lengths and Jahn-Teller distortion of MnO6octahedra have been calculated. Both the standard deviation and Jahn-Teller distortion of Mn3+O6octahedra in the superlattices are much smaller than those of Mn3+O6octahedra in LaMnO3, while Mn4+O6octahedra in the superlattices have the smallest lattice distortion, but larger than those in SrMnO3.

Photo-switchable spin-crossover iron(III) compound based on intermolecular interactions

Iron(III) spin-crossover compounds, [Fe(qnal)2]CF3SO3·MeOH (1·MeOH) and [Fe(qnal)2]CF3SO3·acetone (1·acetone) were prepared and their spin transition properties were characterized by magnetic susceptibility measurement, Mossbauer spectroscopy and single crystal analysis. Two iron(III) compounds exhibited abrupt spin transition with thermal hysteresis loop (T 1/2↑ = 115 K and T 1/2↓ = 104 K for 1·MeOH, and T 1/2↑ = 133 K and T 1/2↓ = 130 K for 1·acetone). Single crystal analysis revealed both of the structures in high-spin (HS) and low-spin (LS) states for 1·acetone. The difference of bond length between the HS and LS states for 1·acetone was ~0.10 A, which was corresponding to that of typical iron(III) SCO compounds. Specially, it showed strong intermolecular interactions by π–π stacking formed between the neighbor complexes leading to 2-D sheet. Both 1·MeOH and 1·acetone exhibited LIESST effect when it was illuminated at 1000 nm. We also confirmed that the introduction of strong intermolecular interactions, such as π–π stacking, can play an important role in LIESST effect.

Anisotropic ideal strengths of superhard monoclinic and tetragonal carbon and their electronic origin

The mechanical and electronic properties, and the atomic deformation mechanism of recently reported monoclinic ($C$2/$m$) and body-centered-tetragonal ($I$4/mmm) carbon polymorphs are studied by first-principles methods. The calculated elastic moduli and ideal strengths suggest that both polymorphs have low compressibility and are superhard, but their relatively lower ideal strength as compared with diamond indicates that they are intrinsically weaker because of differences in bond lengths and concomitant fluctuation of valence charge density. Analyses of electronic structure and atomic deformation mechanism demonstrate that the polarity of the bonds, which results from the fluctuations, is responsible for the lower strength.