Determination Of Bond Lengths Research Articles

Automated site-directed drug design: searches of the Cambridge Structural Database for bond lengths in molecular fragments to be used for automated structure assembly.

In this paper a database of small frequently occurring molecular fragments is used for the determination of fragment bond lengths from the Cambridge Structural Database. A large number of bond types are described that have not been reported previously.

Structural and spectroscopic studies of rhodium-(I) and -(III) nitrato complexes

Refluxing Rh(NO3)3·2H2O with an excess of PPh3 in MeOH or EtOH for over 48 h gives trans-[Rh(CO)(ONO2)(PPh3)2]1 whereas the same reaction at room temperature gives predominantly [Rh(ONO2)(PPh3)3]2. X-Ray structure determinations of 1 and 2 show the nitrate groups to be monodentate in each case although disorder of the CO and NO3 groups in 1 precludes accurate determination of bond lengths and angles. There is no reaction of trans-[Rh(CO)X(PPh3)2](X = Cl, F or ONO2) with H2 at room temperature and 1 atm pressure, whereas there is an immediate reaction of [Rh(ONO2)(PPh3)3] under the same conditions to give [RhH2(ONO2)(PPh3)3]3, which has been characterised by multinuclear NMR spectroscopy. Compound 3 loses PPh3 to give [RhH2(O2NO)(PPh3)2]6a which has been characterised similarly and by X-ray crystallography; although the metal-bound hydrogens were not located the structure is clearly based on an octahedral geometry with trans phosphines and a bidentate nitrate.

Structural effects in single-crystal photoelectron, Auger-electron, and Kikuchi-electron angular diffraction patterns

The full-hemisphere diffraction patterns of primary photoelectrons, photoemission Auger electrons, and Kikuchi electrons are reported for single-crystal surfaces of Cu(100), Cu(111), Cu(110), Ir(111), and Ag(100), to test models for direct structure determinations from angle-dependent final-state diffraction patterns. Our measurements show a simple correlation between the low-index crystallographic directions of the substrate and local intensity maxima in the electron angular distributions. We find that the angular anisotropy can be qualitatively explained in all cases studied by final-state elastic forward scattering. The strong forward scattering features in photoemission diffraction patterns are used to measure bond angles and determine the structure of Cu ultrathin films on Ir(111). In addition, a radial image function based on a holographic Fourier-transform algorithm is evaluated for the determination of bond lengths from three-dimensional images reconstructed from the two-dimensional diffraction pattern.

A XANES study of the K-absorption edge of copper in some of its compounds and use of the same in the determination of bond length

XANES in the K-edge of copper in the systems CuO, Cu(OH) 2, La 2CuO 4, Cu 3AsO 4 and CuOHF have been investigated and transitions have been assigned to the observed structures. The measurements have been used for calculating the first coordination bond distance in the above systems. It is observed that the values so determined agree fairly well with crystallographic values.

Ethylene monolayer and multilayer on Pt(111) below 52 K: determination of bond lengths by near-edge X-ray fine structure

Ethylene monolayer and multilayer on Pt(111) below 52 K: determination of bond lengths by near-edge X-ray fine structure

Ethylene monolayer and multilayer on Pt(111) below 52 K: determination of bond lengths by near-edge X-ray fine structure

At temperatures lower than 52 K, ethylene condenses on Pt(111). Valence-band analysis shows that the first layer and the condensed phase exhibit almost the same positions of the molecular orbitals. Carbon K-shell excitation leads to the appearance of π∗ and σ∗ resonances from which it is deduced that the low temperature ethylene monolayer is π-bonded to the substrate with minor C-C elongation, namely about 0.004 nm. A comparison is made with C-C bond lengths of ethylene monolayers and multilayers measured using NEXAFS on various substrates and given in the literature. It shows that they correlate nicely with the values of the πσ parameter deduced from HREELS results for the same monolayers.

Determination of carbon-carbon bond length from the absorption spectra of cyanine dyes

A new method of analyzing the traditional conjugated dyes absorption experiment provides a method for calculating the average bond length along a polymethine chain.

X-ray photoelectron holography of ultrathin film and single crystal Cu(111): improving the accuracy of bond-length determination

Forward-scattering diffraction patterns from single-crystal Cu(111) substrates and an epitaxial film of FCC Cu/Ir(111) have been analyzed to produce real-space images of the atomic lattice by Fourier-transform holography. The accuracy of atomic positions is found to be better in the single-crystal holograms than in the ultrathin film of copper. The angular dependence of the atomicscattering factor produces a shift in the position of atoms in the holographic image, and causes the atom image to be asymmetric. Model calculations reproduce the atom shift and asymmetry. A modified Fourier-transform algorithm is shown to correct for both the atom-shift and the image asymmetry.

The determination of bond lengths in solids using the Carr-Purcell sequence

Nutation NMR spectroscopy has been used to measure bond lengths in orientationally disordered solids by suppression of the chemical-shift anisotropy broadening (I ). In this technique, removal of this unwanted broadening is accompanied by a reduction of the splitting in the Pake doublet (2) by a factor of two. In many cases of special interest, however, the isolated pairs of spins involved in the Pake doublet may belong to more than one class. For example, two different bond lengths (3) may be present leading to a superposition of two Pake doublet patterns. A similar situation may occur even if all pairs are characterized by a single bond length but are associated, for example, with two classes of molecules in quite different motional states. If one of these situations prevails, it is highly desirable to take advantage of the best possible resolution to permit correct assignments in increasingly complex spectra. The Carr-Purcell sequence (4) is another method for suppressing the chemical-shift anisotropy broadening; in principle, it should not scale down the dipolar interaction. Although a reduction of the homonuclear dipolar splitting does take place in practice, as shown below, it is not as severe as in the nutation experiment. For the determination of internuclear distances using the Carr-Purcell sequence it is essential to know the scaling behavior of the Pake doublet splitting as the pulse separation and pulse width are varied. We show that under ideal conditions this scaling should be a linear function of the duty factor. Our measurements in two different systems employing a modified Carr-Purcell sequence confirm this prediction over a wide range of duty factors. 13C pulsed NMR experiments were performed at a magnetic field strength of 1.4 1 T ( 15 MHz). Although the suppression of dipolar broadening by protons is partly

Quantitative analysis of ligand effects (QALE). Systematic study of iron-phosphorus bond lengths and their relationship to steric thresholds

Systematic determination of Fe-P bond lengths for the set of complexes (η-Cp)(CO)(L)FeCOMe containing «sterically unencumbered» σ-donor phosphorus(III) ligands shows that the Fe-P bond lengths vary over a narrow range (2.195±0.0015 A) and are only slightly dependent on the σ-donicity and size of the ligand. π-Acid ligands (i.e. P(OR) 3 ) exhibit significantly shorter Fe-P bond lengths around 2.10 A. In light of this virtual constancy of σ bond length for a family of complexes, it is reasonable to expect steric thresholds to be manifest

Electron-energy-loss-based spectroscopies: A molecular viewpoint

A review is given of electron-energy-loss molecular spectroscopies with emphasis on recent studies of core excitation of free molecules by inner-shell electron-energy-loss spectroscopy (ISEELS). Issues discussed include: resolution capabilities, momentum transfer dependence, dipole oscillator strength determination, extended fine structure and bond length determination. Coincidence techniques between inelastically scattered electrons and electrons or ions produced in the decay of electronic excited states are also reviewed.

Nitrogen-hydrogen bond length determinations and implications for the gramicidin channel conformation and dynamics from nitrogen-15-proton dipolar interactions

Nitrogen-hydrogen bond length determinations and implications for the gramicidin channel conformation and dynamics from nitrogen-15-proton dipolar interactions

On the determination of uraniumoxygen bond lengths in dioxouranium(VI) compounds by Raman spectroscopy

On the determination of uraniumoxygen bond lengths in dioxouranium(VI) compounds by Raman spectroscopy

Accurate Bond Length Determination by EXAFS Method

The Extended X-ray Absorption Fine Structure (EXAFS) spectra of pure iron, pure platinum and intermetallic compound Fe 2 Zr, whose strtuctures were well krown, have been measured at lower temperatures (20 K–300 K), and the accuracy of the interatomic-distance determination has been estimated. In order to increase the accuracy in determining the values of the structural parameters, the FABM technique proposed by Teo et al. has been applied. In our results, however the accuracy of the interatomic distance under various temperature could be improved almost an order of magnitude by assuming that the inflection point on the absorption edge represents the edge position.

Study of the structure of azatetrahedranes by quantum-chemical methods

In the present work we studied the geometric structure of tetrahedrane (I), azatetrahedrane (II), diazatetrahedrane (III), triazatetrahedrane (IV), and tetraazatetrahedrane (V) (see Fig. i). The data available from the literature on the structure of these compounds, with the exception of the parental hydrocarbon [5], are basically results obtained by the MINDO/3 method and a nonempirical method in a minimal basis. However, the MINDO/3 method is known to be unsuitable for calculations of compounds with NN bonds, and the latter method is known to be unsuitable for the determination of the structure of stressed compounds. We carried out the optimization of the geometry of molecules I-V by a nonempirical method in the 3-21G basis [6], whose accuracy in the determination of bond lengths in organic molecules is comparable to experimental accuracy. The GAUSSIAN-80 system of programsadapted for the ES1052 computer was used. In addition, semiempirical calculations were performed by the MNDO method, as well as with the use of a variant of the MINDO/3 method with corrected values for the two-center parameters aNN and BNN, which has demonstrated its superiority over the ordinary versionof the method on an extensive group of nitrogen-containing compounds (MINDO/3M [7]). The data from the calculations of the bond lengths in the molecules studied are presented in Table I~ The data from [i, 2] (MINDO/3), [4, 8, 9] (MNDO), and [2] (STO-3G) were used in part in compiling this table. In the literature there are data from the calculation of bond lengths in double-zeta basis: The results for I in [5] differ only slightly from the values which we obtained, but the data for V in [3], which were obtained with the use of a pseudopotential, deviate significantly from the results presented. A possible reason for this disparity is the greater structural lability of the molecules of the tetrahedrane series, as well as the necessity of using gradient methods of optimization in carrying OUt nonempiri -~ cal structural calculations (see, for example, [i0]).

Applications of XANES to surface science.

In this review, the current theoretical methods for the interpretation of XANES are discussed, and some applications of XANES to surface science are illustrated. For theoretical problems, we discuss the cluster size to be included in the calculations, polarization dependence, multiple scatterings and many-body effects. For the applications to surface science, two examples are given. One is the measurement of the surface XANES under nonvacuum conditions, the other is the bond-length determination from intramolecular multiple scattering.

Local structure of silicon films and silicon carbide by surface extended energy loss fine structure

Surface extended energy loss fine structure (SEELFS) has been shown to yield nearest neighbor coordination and bond length for carbon in different structural forms. A standard Auger electron spectrometer(double pass cylindrical mirror analyzer) is used to obtain energy loss spectra in the laboratory. Preliminary work on diamond, graphite and ‘‘Aquadag’’ using spectra in the second derivative mode is now extended to silicon and α- and β-silicon carbide. Silicon has been used as reference for phase and amplitude in the bond length and coordination determination of β-silicon carbide. β-SiC has been used as a standard for α-SiC. The coordination and radius determined agree with known values to within uncertainties estimated. The uncertainties in the determination of bond length and coordination due to the choice of reference phase and amplitude are discussed.

Local structure investigations of carbon by surface extended energy loss fine structure

Surface extended energy loss fine structure (SEELFS) spectroscopy has been used to determine structural parameters for several different forms of carbon. A standard Auger electron spectrometer (double pass cylindrical mirror analyser) was used to obtain energy loss spectra. First shell coordination numbers and bond lengths were obtained for single crystal diamond, pyrolytic graphite, and “Aquadag” (graphite particle suspension) samples. The study of pure carbon surfaces allowed us to probe the limitations on the determination of bond lengths and coordination. The validity of some of the theoretical assumptions is also discussed.

Local structure investigations of carbon by surface extended energy loss fine structure

Surface extended energy loss fine structure (SEELFS) spectroscopy has been used to determine structural parameters for several different forms of carbon. A standard Auger electron spectrometer (double pass cylindrical mirror analyser) was used to obtain energy loss spectra. First shell coordination numbers and bond lengths were obtained for single crystal diamond, pyrolytic graphite, and “Aquadag” (graphite particle suspension) samples. The study of pure carbon surfaces allowed us to probe the limitations on the determination of bond lengths and coordination. The validity of some of the theoretical assumptions is also discussed.

Determination of intramolecular bond lengths in gas phase molecules from K shell shape resonances

A systematic analysis of K shell excitation spectra of gas phase molecules containing B, C, N, O, and F reveals a correlation between the position of a characteristic K shell excitation feature, the σ shape resonance, and the intramolecular bond length. When referenced to the 1s ionization threshold the position of the σ shape resonance is found to vary linearly with the internuclear distance between the pair of atoms which gives rise to the scattering resonance. This linear relationship holds remarkably well within different classes of molecules characterized by the total number of electrons (sum of atomic numbers) for a given pair of atoms. The empirically derived rules are compared with the predictions of a full multiple scattering theory treatment. Comparison of empirical experimental and first-principle theoretical results allows the prediction of the average intramolecular muffin tin potential in the presence of the core hole.