Bond Length Variations Research Articles

Interaction Behavior between Active Hydrogen Bond Donor‐Acceptors as a Binding Decoration for Anion Recognition: Experimental Observation and Theoretical Validation

AbstractInteractions of Harmine (HM), as hydrogen bond donor with different anions as hydrogen bond acceptors were studied using spectroscopic and computational techniques. Significant gradual changes in absorption and emission spectra were observed upon addition of fluoride anions with selectivity. Wide‐ranging theoretical calculations in association with the 1H NMR titration in CDCl3 medium were performed to establish the binding decoration of HM with fluoride ion. Interaction energies, bond length variation, NBO charge transfer, NMR response, MEP 3D surface & 2D contour plot, UV‐Vis spectral simulation, HOMO‐LUMO energy gaps and potential energy curves (PECs) were calculated theoretically employing DFT method for ground state (S0) and TD‐DFT method for first singlet excited electronic state (S1) in ACN. Calculations revealed the proton transfer as ESPT mechanism [extent of proton transfer in S0 (58 %) and S1 (87 %)] behind the molecular interaction and spectral responses. We believe such a fluoride selective sensor like HM may find application to detect and control fluoride content in different commodity products.

The interaction strengths and spectroscopy parameters of the C2H2∙∙∙HX and HCN∙∙∙HX complexes (X = F, Cl, CN, and CCH) and related ternary systems valued by fluxes of charge densities: QTAIM, CCFO, and NBO calculations.

This theoretical work exhibits a new systematic study of structural parameters, electronic properties, infrared vibration modes, and molecular topography of hydrogen complexes, namely linear-type HCN⋯HX and T-type C2H2⋯HX (X = F, Cl, CN, and CCH). Ideally, the knowledge of the ternary systems of C2H2⋯HCN⋯HF and HCN⋯HCN⋯HF whose subparts integrate the linear and T-shaped complexes were used to give support in this current research. By means of computational calculations carried out in both levels B3LYP and MP2, the variations of the HX bond lengths are clearly overestimated in the HCN⋯HX linear complexes. In agreement with the analyses of the electrostatic potentials, the higher intermolecular energies of these complexes agree with the larger red-shifts in the stretch frequencies in HX. Also, the QTAIM descriptors and NBO calculations were used to inspect the interaction strength as well as to confirm the π cloud as a proton accepting center. By taking into account the absorption intensity ratio as a standard parameter to predict the interaction strength and intermolecular characterization, the formalism of the charge-charge flux-overlap modified (CCFO) was applied.

Effect of trivalent transition metal ion substitution in multifunctional properties of Dy2O3 system

The present work describes the systematic study on inducing multiferroic properties in non-magnetic Dy2O3 system. The ceramic compounds of Dy2−xFexO3 (where x = 0.1–1.5) have been prepared by solid state reaction method. The powder X-ray diffraction patterns of all the prepared compounds reveal the strong influence of transition metal ion (Fe) in the Dy2O3 crystal structure. By Rietveld analysis, it is determined that with respect to increasing concentration of Fe3+ ion at Dy3+ site leads to transformation of crystal structure from Cubic to Orthorhombic with varying concentration of DyFeO3 phase and further increase in Fe3+ concentration leads to the formation of Garnet phase in Dy2−xFexO3 compounds. The scanning electron microscopic images of the samples confirm the change in surface morphology with increasing grain boundaries and porosity due to the substitution of Fe in Dy2O3 system which may effects on the electrical transport properties of the materials and increasing concentration of Fe in Dy2O3 system is also analyzed by energy dispersive analysis spectra. By Raman spectral analysis, it is identified that the strong absorption band of Cubic Dy2O3 compound at 373 cm−1 is gradually shifted to 257 cm−1 which indicates the molecular stretching motion of RE–O bond in REO6 octahedra and the large deviation in position of intense Raman bands below 300 cm−1 confirms the incorporation of Fe3+ ion in the host Dy2O3 lattice and imparting large polarizability in the prepared compounds due to translational motions of ReO6 octahedrons by variation in bond length and reduced mass of the bonding atoms. Diffused reflectance spectroscopy analysis implies the semiconducting nature of all the prepared compounds. It is also identified that the energy gap values goes on decreasing till DyFeO3 and then starts increasing due to change in crystal structure by cubic to orthorhombic and then orthorhombic to garnet phase. From the magnetization studies, it is found that till even substitution of Fe (i.e. x = 0.1–0.9) in Dy2−xFexO3 system, the compounds exhibits paramagnetic nature whereas from x = 1.0 i.e. DyFeO3, the samples exhibits ferromagnetic nature. The variation of magnetization behaviour from paramagnetic to ferromagnetic in higher concentration of Fe explicit the feasibility of attaining ferroic behaviour in Garnet mixed phase ceramic compounds. The electric polarization analysis reveal that while substituting Fe3+ ion in Dy3+ site by more than 50% of molecular ratio, the compounds exhibits non-zero remanance and coercivity values with respect to applied d.c. electric field and evident peculiar ferroelectric characteristic of those compounds. The maximum saturation polarization achieved in Dy0.6Fe1.4O3 compound is 0.2 µC/cm2 and found comparable with the results observed from Bismuth Ferrite related compounds.

Investigations on the spin Hamiltonian parameters and the local structures for the irradiation induced Rh2+ and Rh0 centres in NH4Cl

The spin Hamiltonian parameters (SHPs) (i.e., g factors, hyperfine structure constants and superhyperfine parameters) are theoretically investigated for the irradiation induced Rh2+ and Rh0 centres in NH4Cl by use of the perturbation calculations. The tetragonally compressed Rh2+ centre in the form of [RhCl4(H2O)2]2‾ group originates from interstitial Rh2+ (reduced from original Rh3+ of doped RhCl3 by capturing one electron during gamma irradiation) associated with two adjacent axial NH4+ cations substituted by two H2O molecules due to charge compensation. The orthorhombically compressed Rh0 centre in the form of [RhCl4(H2O)2]4‾ group arises from interstitial Rh0 (reduced from Rh3+ by capturing three electrons during gamma irradiation) with two adjacent axial NH4+ replaced by two H2O molecules as charge compensators and the planar Rh0-Cl‾ bond length variation of about 0.042 Ǻ along [011] and [01¯1] axes due to the Jahn-Teller effect. The calculated SHPs are in good agreement with the observed values. The EPR spectra and local structures are discussed for both centres.

Safe-by-Design CuO Nanoparticles via Fe-Doping, Cu-O Bond Length Variation, and Biological Assessment in Cells and Zebrafish Embryos.

The safe implementation of nanotechnology requires nanomaterial hazard assessment in accordance with the material physicochemical properties that trigger the injury response at the nano/bio interface. Since CuO nanoparticles (NPs) are widely used industrially and their dissolution properties play a major role in hazard potential, we hypothesized that tighter bonding of Cu to Fe by particle doping could constitute a safer-by-design approach through decreased dissolution. Accordingly, we designed a combinatorial library in which CuO was doped with 1-10% Fe in a flame spray pyrolysis reactor. The morphology and structural properties were determined by XRD, BET, Raman spectroscopy, HRTEM, EFTEM, and EELS, which demonstrated a significant reduction in the apical Cu-O bond length while simultaneously increasing the planar bond length (Jahn-Teller distortion). Hazard screening was performed in tissue culture cell lines and zebrafish embryos to discern the change in the hazardous effects of doped vs nondoped particles. This demonstrated that with increased levels of doping there was a progressive decrease in cytotoxicity in BEAS-2B and THP-1 cells, as well as an incremental decrease in the rate of hatching interference in zebrafish embryos. The dissolution profiles were determined and the surface reactions taking place in Holtfreter's solution were validated using cyclic voltammetry measurements to demonstrate that the Cu+/Cu2+ and Fe2+/Fe3+ redox species play a major role in the dissolution process of pure and Fe-doped CuO. Altogether, a safe-by-design strategy was implemented for the toxic CuO particles via Fe doping and has been demonstrated for their safe use in the environment.

Spherical aromaticity in C-, Si-, and Ge-containing compounds

Various dismutative structures of the form [E(EX)(EX2)]2 with E being C, Si, and/or Ge and X being some side group (H, CH3, F, or Cl) were studied with the special purpose of identifying signals for aromaticity in those compounds. Also a dismutative analogue of pyridine was studied. In order to identify signals of aromaticity we focused on the total energy, the HOMO–LUMO energy gap, the variation of the nearest-neighbour bond lengths along the backbone, and NICS and NICSzz as functions of the distance along a normal to a plane of the molecule. In many cases, strong distortions from a nearly-planar structure were observed. Only in few cases, the bond lengths could suggest the existence of aromaticity or anti-aromaticity. On the other hand, in many cases NICS and NICSzz give signals that suggest the existence of aromaticity similar to that of spherical cluster compounds.

Cationic Two-Coordinate Complexes of Pd(I) and Pt(I) Have Longer Metal-Ligand Bonds Than Their Neutral Counterparts

Summary One-electron oxidation of known ( t Bu 3 P) 2 M (1, M = Pd; 2, M = Pt) with [Ph 3 C][HCB 11 Cl 11 ] leads to two-coordinate, monovalent cations of the formula [( t Bu 3 P) 2 M][HCB 11 Cl 11 ] (3, M = Pd; 4, M = Pt), which also possess linear geometry but with elongated M–P bonds. Spectroscopic and computational studies consistently show that the unpaired electron of the d 9 configuration of 3 and 4 belongs to largely non-bonding orbitals: the s/d z2 hybrid for Pd and the degenerate d x2-y2 /d xy pair for Pt. We show that molecular-orbital-based arguments alone are incapable of predicting or rationalizing the observed M–P bond lengthening on oxidation; correct prediction and rationalization are achieved only by inclusion of electrostatic and Pauli effects. This emphasizes the dangers of interpreting any perturbative changes in bond metrics solely on the basis of energies and occupancies of molecular orbitals; the inclusion of electrostatic and Pauli components is essential to providing a more complete picture.

Perovskite-spinel composite approach to modify room temperature structural, magnetic and dielectric behavior of BiFeO3

In the present attempt, we report modified features of structural, dielectric, magnetic and ferroelectric behaviour of BiFeO3 (BFO) by perovskite-spinel composite approach. ZnFe2O4 (ZFO) is used as spinel phase. The structural measurement of composite show anisotropically compression in the BiFeO3 lattice with ZFO compositions and stimulates the variation in bond length, bond angle, tilting angle, electron density and resultant polarization. This affects on magnetic and dielectric behaviour of BFO. Room temperature magnetic measurement revealed enhancement of magnetization of BFO in composite, attributed to spin restructuring due to change in magnetic anisotropy, exchange energy and stress energy at interface with ZFO composition. There is around 7 times enhancement in magnetization as compared to pure BFO phase. Dielectric profile of composites shows decrease in dielectric constant as well as dielectric loss as compared to single phase BFO. P-E loop exhibits leaky ferroelectric behaviour of composite system with drop down in leakage current by 2 order of magnitude than pure BFO phase. Magnetic contributions of individual phases in composite are determined by Vegard Law while dielectric contributions are modelled by Maxwell-Garnett (MG) equation. The present work demonstrates that BFO-ZFO: perovskite-spinel composite approach to modify magnetic, dielectric and ferroelectric behaviour and to facilitate BFO as room temperature multiferroic system.

Role of Defects on Regioselectivity of Nano Pristine Graphene.

Here analytical Fukui functions based on density functional theory are applied to investigate the redox reactivity of pristine and defected graphene lattices. A carbon H-terminated graphene structure (with 96 carbon atoms) and a graphene defected surface with Stone-Wales rearrangement and double vacancy defects are used as models. Pristine sp2-hybridized, hexagonal arranged carbon atoms exhibit a symmetric reactivity. In contrast, common carbon atoms at reconstructed polygons in Stone-Wales and double vacancy graphene display large reactivity variations. The improved reactivity and the regioselectivity at defected graphene is correlated to structural changes that caused carbon-carbon bond length variations at defected zones.

Deformation forces in promolecules revisited: Binding of homonuclear diatomic molecules and calculation of stretching vibrational frequencies in diatomic and larger systems

Internuclear forces in a molecule, as an integral over a geometrical factor and the electron density, can be decomposed into a part having as origin promolecular densities of the participating atoms, and a contribution from the deformation density. At the hand of homo-nuclear diatomic molecules we show that the binding energy is linked to the deformation force except for transition metal dimers. However, vibrational frequencies involving pure bond-length variations are rather well reproduced, even for heteroatomic diatomics. For larger assemblies, frequencies for bending modes are underestimated, but the model may serve for a rough analysis of a vibrational spectrum.

A robust molecular probe for Ångstrom-scale analytics in liquids.

Traditionally, nanomaterial profiling using a single-molecule-terminated scanning probe is performed at the vacuum–solid interface often at a few Kelvin, but is not a notion immediately associated with liquid–solid interface at room temperature. Here, using a scanning tunnelling probe functionalized with a single C60 molecule stabilized in a high-density liquid, we resolve low-dimensional surface defects, atomic interfaces and capture Ångstrom-level bond-length variations in single-layer graphene and MoS2. Atom-by-atom controllable imaging contrast is demonstrated at room temperature and the electronic structure of the C60–metal probe complex within the encompassing liquid molecules is clarified using density functional theory. Our findings demonstrates that operating a robust single-molecular probe is not restricted to ultra-high vacuum and cryogenic settings. Hence the scope of high-precision analytics can be extended towards resolving sub-molecular features of organic elements and gauging ambient compatibility of emerging layered materials with atomic-scale sensitivity under experimentally less stringent conditions.

Bond-length distributions for ions bonded to oxygen: alkali and alkaline-earth metals.

Bond-length distributions have been examined for 55 configurations of alkali-metal ions and 29 configurations of alkaline-earth-metal ions bonded to oxygen, for 4859 coordination polyhedra and 38 594 bond distances (alkali metals), and for 3038 coordination polyhedra and 24 487 bond distances (alkaline-earth metals). Bond lengths generally show a positively skewed Gaussian distribution that originates from the variation in Born repulsion and Coulomb attraction as a function of interatomic distance. The skewness and kurtosis of these distributions generally decrease with increasing coordination number of the central cation, a result of decreasing Born repulsion with increasing coordination number. We confirm the following minimum coordination numbers: ([3])Li(+), ([3])Na(+), ([4])K(+), ([4])Rb(+), ([6])Cs(+), ([3])Be(2+), ([4])Mg(2+), ([6])Ca(2+), ([6])Sr(2+) and ([6])Ba(2+), but note that some reported examples are the result of extensive dynamic and/or positional short-range disorder and are not ordered arrangements. Some distributions of bond lengths are distinctly multi-modal. This is commonly due to the occurrence of large numbers of structure refinements of a particular structure type in which a particular cation is always present, leading to an over-representation of a specific range of bond lengths. Outliers in the distributions of mean bond lengths are often associated with anomalous values of atomic displacement of the constituent cations and/or anions. For a sample of ([6])Na(+), the ratio Ueq(Na)/Ueq(bonded anions) is partially correlated with 〈([6])Na(+)-O(2-)〉 (R(2) = 0.57), suggesting that the mean bond length is correlated with vibrational/displacement characteristics of the constituent ions for a fixed coordination number. Mean bond lengths also show a weak correlation with bond-length distortion from the mean value in general, although some coordination numbers show the widest variation in mean bond length for zero distortion, e.g. Li(+) in [4]- and [6]-coordination, Na(+) in [4]- and [6]-coordination. For alkali-metal and alkaline-earth-metal ions, there is a positive correlation between cation coordination number and the grand mean incident bond-valence sum at the central cation, the values varying from 0.84 v.u. for ([5])K(+) to 1.06 v.u. for ([8])Li(+), and from 1.76 v.u. for ([7])Ba(2+) to 2.10 v.u. for ([12])Sr(2+). Bond-valence arguments suggest coordination numbers higher than [12] for K(+), Rb(+), Cs(+) and Ba(2+).

Dipole and quadrupole polarizabilities of the water molecule as a function of geometry.

Dipolar, dipole-quadrupole and quadrupole-quadrupole static polarizabilities of the water molecule have been determined by ab initio calculations at coupled cluster level of theory with single, double and perturbative triple excitations CCSD(T) with an aug-cc-pVTZ basis set using a finite field and field-gradient method. The geometry dependence of polarizability tensor components has been explored and modeled by power series expansion in bond length and angle variations up to sum of powers equal to 4. The results provide a very detailed description of the static polarizability of water up to quadrupolar rank which can be used for the test and development of novel accurate polarizable interaction potentials for modeling aqueous solutions. © 2016 Wiley Periodicals, Inc.

Estimating local bonding/antibonding character of canonical molecular orbitals from their energy derivatives. The case of coordinating lone pair orbitals

According to Koopmans theorem, the derivative of the energy of a canonical molecular orbital (MO) with respect to nuclear coordinates quantifies its bonding/antibonding character. This quantity allows predictions of bond length variation on ionisation in a panel of 19 diatomic species. In polyatomic molecules, the derivative of a MO energy with respect to a given bond length reveals the nature and the degree of the bonding/antibonding contribution of this MO with respect to this bond. Accordingly, the HOMO “lone pairs” of CO and CN− and the HOMO-2 of CH3CN are found to be antibonding with respect to the CX bond (X = N, O), whereas the HOMO of N2 is found to be bonding. With the same approach, the variation of the bonding character in the MOs of CO and CH3CN on interaction with an electron acceptor (modeled through the approach of a proton) or by applying an electric field was studied. © 2016 Wiley Periodicals, Inc.

SU‐C‐204‐03: DFT Calculations of the Stability of DOTA‐Based‐Radiopharmaceuticals

Purpose:Application of the density function theory (DFT) to investigate the structural stability of complexes applied in cancer therapy consisting of the 1,4,7,10‐tetraazacyclododecane‐1,4,7,10‐tetraacetic acid (DOTA) chelated to Ac225, Fr221, At217, Bi213, and Gd68 radio‐nuclei.Methods:The possibility to deliver a toxic payload directly to tumor cells is a highly desirable aim in targeted alpha particle therapy. The estimation of bond stability between radioactive atoms and the DOTA chelating agent is the key element in understanding the foundations of this delivery process. Thus, we adapted the Vienna Ab‐initio Simulation Package (VASP) with the projector‐augmented wave method and a plane‐wave basis set in order to study the stability and electronic properties of DOTA ligand chelated to radioactive isotopes. In order to count for the relativistic effect of radioactive isotopes we included Spin‐Orbit Coupling (SOC) in the DFT calculations. Five DOTA complex structures were represented as unit cells, each containing 58 atoms. The energy optimization was performed for all structures prior to calculations of electronic properties. Binding energies, electron localization functions as well as bond lengths between atoms were estimated.Results:Calculated binding energies for DOTA‐radioactive atom systems were −17.792, −5.784, −8.872, −13.305, −18.467 eV for Ac, Fr, At, Bi and Gd complexes respectively. The displacements of isotopes in DOTA cages were estimated from the variations in bond lengths, which were within 2.32–3.75 angstroms. The detailed representation of chemical bonding in all complexes was obtained with the Electron Localization Function (ELF).Conclusion:DOTA‐Gd, DOTA‐Ac and DOTA‐Bi were the most stable structures in the group. Inclusion of SOC had a significant role in the improvement of DFT calculation accuracy for heavy radioactive atoms. Our approach is found to be proper for the investigation of structures with DOTA‐based‐radiopharmaceuticals and will enhance our understanding of processes occurring at subatomic levels.

Highly strained AlAs-type interfaces in InAs/AlSb heterostructures

Spontaneously formed Al-As type interfaces of the InAs/AlSb system grown by molecular beam epitaxy for quantum cascade lasers were investigated by atomic resolution scanning transmission electron microscopy. Experimental strain profiles were compared to those coming from a model structure. High negative out-of-plane strains with the same order of magnitude as perfect Al-As interfaces were observed. The effects of the geometrical phase analysis used for strain determination were evidenced and discussed in the case of abrupt and huge variations of both atomic composition and bond length as observed in these interfaces. Intensity profiles performed on the same images confirmed that changes of chemical composition are the source of high strain fields at interfaces. The results show that spontaneously assembled interfaces are not perfect but extend over 2 or 3 monolayers.

Influence of nickel doping on oxygen-ionic conductivity of the n = 1 Ruddlesden-Popper Phases La1.85Ca0.15(Cu1−xNix)O4−δ (δ = 0.0905)

The results of the synthesis and characterization of the optimally doped La1.85Ca0.15(Cu1−xNix)O4-δ solid solution with x = 0, 0.1, 0.2 and 0.3 are reported. The versatility of these La1.85Ca0.15(Cu1−xNix)O4−δ materials is explained on the basis of structural features and the ability to accommodate oxygen nonstoichiometry. According to powder X-ray and neutron diffraction data, La1.85Ca0.15(Cu1−xNix)O4−δ adopts the tetragonal structure with oxygen vacancies occurring preferentially at the Oap sites within the {(La/Ca)O} layers of the perovskite blocks and the oxygen deviation from stoichiometry δ was found to be δ=0.0905(6). The bulk conductivity indicated an Arrhenius-type thermally activated process and oxygen vacancies are the possible ionic charge carriers at T=270°C. An increase of the conductivity was detected when Ni was introduced. With nickel ratio variation, a strong correlation was observed between the Cu(Ni)-Oap apical bond length variation and the conductivity variation through controlling the O2− ion migration.

Diaqua(nitrato-κ2O,O′)bis(L-valine-κO)lead(II) nitrate at 296 K

The structure of the title complex, [Pb(NO3)(C5H11NO2)2(H2O)2]NO3, had been determined previously at 173 and 193 K, and is now reported at 296 K, in the same space group. The main difference with the low-temperature structures is that a methyl group of one valine ligand is clearly disordered over two positions, for which the occupancies converged to 0.56 (3) and 0.44 (3). Bond-length variations within the coordination sphere of PbIIas a function ofTare difficult to assess because uncertainties on these parameters are high. On the other hand, Pb...O distances above 2.9 Å cannot be assigned unambiguously to formal Pb—O bonds. As a consequence, the polymeric nature of the complex previously described at 173 K is uncertain, as well as the actual coordination number of PbII, and it is thus not possible to determine if the metal environment is holo- or hemidirected.

Studies of the local distortions for nd1 (Mo5+ and W5+) impurities in KTP crystals

4d1 (Mo5+) and 5d1 (W5+) impurities doped into nonlinear optical crystals KTiOPO4 (KTP) can occupy the inequivalent Ti1 and Ti2 sites and exhibit orthorhombically compressed octahedral nd1 (n=4, 5) centres arising from the Jahn–Teller effect. Closely relevant to the electronic levels as well as optical and magnetic properties of these materials, the above local distortions can be suitably reflected by the anisotropic electron paramagnetic resonance (EPR) signals with the paramagnetic nd1 probes. This work stresses on the theoretical studies of the EPR parameters (g factors gx, gy, gz and hyperfine structure constants Ax, Ay, Az) and local distortions for the above nd1 impurity centres in a consistent way. The local distortions are characterised by the relative axial compression ratios ρ (≈0.040, 0.032 and 0.031) and the relative planar bond length variation ratios τ (≈0.030, 0.015 and 0.012) for Mo5+ centre I and W5+ centres II and III, respectively, which are larger than those of host Ti1 and Ti2 sites.

NEXAFS Sensitivity to Bond Lengths in Complex Molecular Materials: A Study of Crystalline Saccharides.

Detailed analysis of the C K near-edge X-ray absorption fine structure (NEXAFS) spectra of a series of saccharides (fructose, xylose, glucose, galactose, maltose monohydrate, α-lactose monohydrate, anhydrous β-lactose, cellulose) indicates that the precise determination of IPs and σ* shape resonance energies is sensitive enough to distinguish different crystalline saccharides through the variations in their average C-OH bond lengths. Experimental data as well as FEFF8 calculations confirm that bond length variations in the organic solid state of 10(-2) Å can be experimentally detected, opening up the possibility to use NEXAFS for obtaining incisive structural information for molecular materials, including noncrystalline systems without long-range order such as dissolved species in solutions, colloids, melts, and similar amorphous phases. The observed bond length sensitivity is as good as that originally reported for gas-phase and adsorbed molecular species. NEXAFS-derived molecular structure data for the condensed phase may therefore be used to guide molecular modeling as well as to validate computationally derived structure models for such systems. Some results indicate further analytical value in that the σ* shape resonance analysis may distinguish hemiketals from hemiacetals (i.e., derived from ketoses and aldoses) as well as α from β forms of otherwise identical saccharides.