Intramolecular Bond Lengths Research Articles

Resonance electron scattering by adsorbed molecules: [formula omitted] resonance energy versus bond length

This paper explores the relationship between the energy of the σ ∗ negative ion resonance, observed in the cross-section for vibrational excitation of small molecules in electron energy-loss spectroscopy (EELS), and the intramolecular bond length. On the basis of experimental results assembled from studies of electron scattering by both free and adsorbed molecules containing the CO group, we find an approximately linear empirical correlation between the resonance energy and the CO bond length. This correlation is accurately reproduced by multiple-scattering X α calculations for the free CO molecule as a function of bond length, suggesting the possible determination of molecular bond lengths from the σ ∗ resonance energies obtained in EELS. Similar calculations are reported for N 2 and O 2 in addition to CO.

Intramolecular bond length dependence of the anisotropic dispersion coefficients for H2–rare gas interactions

Effective states arising from variational perturbation calculations in a full configuration interaction basis are used to calculate dynamic multipole polarizabilities for H2 at seven different bond lengths. These are combined with previously calculated dynamic polarizabilities for rare gas atoms to obtain the intramolecular bond length dependence of the anisotropic C6, C8, and C10 dispersion coefficients for H2–X (X=He, Ne, Ar, Kr, Xe) interactions. The results are generally in good agreement with previous semiempirical estimates where available.

Structure of Selenium under High Pressure

The high-pressure X-ray structural analysis of rhombohedral selenium has revealed that with increasing pressure, an intermolecular distance decreases rapidly, while an intramolecular covalent bond length increases gradually. On the other hand, the pressure-induced softening of the bond stretching mode, especially A1 mode, has been observed in the Raman spectra of both rhombohedral and α-monoclinic selenium. These findings suggest that the intramolecular covalent bonding in selenium crystal decreases with pressure.

X-ray, Fourier-transform infrared,1H and13C nuclear magnetic resonance, and PM3 studies of (N—H⋯N)+and (O—H⋯O)–intramolecular hydrogen bonds in a complex of 1,8-bis(dimethylamino)naphthalene with maleic acid

The crystal structure of the title compound has been determined by X-ray analysis. The intramolecular hydrogen bond lengths are 2.606(3)A for the (NHN)+ bridge in protonated 1,8-bis(dimethylamino)naphthalene cation (DMAN+H) and 2.401(4)A for the (OHO)– bridge in the hydrogen maleate anion (HM–). The H-bonds are asymmetrical and not strictly linear: NHN, 157(3)° and OHO, 170(5)°. The geometries of the N—H⋯N and O—H⋯C bridges of the investigated cation and anion are dominated by the spherical repulsions of their constituent atoms.The overlapping bands in the absorbance IR spectra of potassium hydrogen (deuteron) maleate are separated in the second-derivative spectra. The strong mixing of the in-plane modes with skeletal modes in the hydrogen maleate ion causes a larger separation (Δν≈ 115 cm–1) of the ν(CO) bands in comparison with those in other type A acid salts containing intermolecular hydrogen bonds (Δν≈ 20–35 cm–1). The observed lack of solvent effect on the IR absorption suggests that the hydrogen bonds in tetrabutylammonium hydrogen maleate and 1,8-bis(dimethylamino)naphthalene hydrogen maleate are not extremely polarizable. 1H and 13C NMR chemical shifts of the investigated compound were measured and identified in two-dimensional (2D) experiments. The 1H NMR spectra show two narrow signals at ca. 19.5 and 18.7 ppm due to the OHO and NHN protons, respectively. The structural parameters of the cation and anion were also determined by quantum-mechanical calculations with the semiempirical MNDO-PM3 method.

High resolution x-ray absorption spectroscopy of linear hydrocarbons adsorbed on noble metal surfaces

Recent progress in the performance of soft x-ray monochromators has revealed new features in soft x-ray molecular photoabsorption spectra. We present here a comprehensive high resolution x-ray absorption study on the linear hydrocarbons C2H2n and C2D2n, adsorbed on Ag(100) and Cu(100) at 50 K and in the solid and the gas phase. A line shape analysis is given, for the bound as well as for the continuum resonances and the absorption thresholds, by means of models easily accessible to the experimentalist, leading to a quantitative understanding of the observed spectra, including the vibrational envelopes. Changes in intramolecular bond lengths upon core-hole excitation can be determined and tracked as a function of deuteration and chemisorption. The effects of the substrate bonding on the vibrational envelopes are analyzed.

Ferroelectric phase transition and crystal structure of the mixed crystals (NH4)2SO4-(NH4)2SeO4

Solid solutions of general formula (NH4)2(SeO4)x(SO4)1-x (0.14 ≥ × ≥ 0) have been prepared. The orthorhombic symmetry of the crystals at room temperature was confirmed. The substitution of sulfate by selenate causes an increase in the Curie temperature for the paraelectric-ferroelectric, Pnam (D162h) to Pna21 (C92v), phase transition. The crystal structure of (NH4)2(SeO4)0.10(SO4)0.90 has been resolved: Fw = 143.86, orthorhombic, Pnam, a = 7.797(1) A, b = 10.664(2) A, c = 5.995(1) A, V = 49889.5(2) A3, Dx = 1.916 g cm-3, Z = 4, F(000) = 298.0, μ(Mo Kα) = 0.71069 A, μ(Mo Kα) = 24.20 cm-1 at 20°C, and Pna21, a = 7.890(2) A, b = 10.589(3) A, c = 5.957(2) A, V = 491.7(4) A3, Dx = 1.919 g cm-3, Z = 4, F(000) = 298.0, μ(Mo Kα) = 24.24 cm-1 at -50°C. The final R factor was 0.041 (wR = 0.045) for 20°C and 0.062 (wR = 0.070) for -50°C with all observed reflections. The mechanism that better justifies the phase transition is a strengthening of hydrogen bond which produces a rotation in sulfate or selenate ions, together with a modification in the intramolecular bond lengths and angles in these anions. In view of this we propose a displacive mechanism for the phase transition.

Studies of σ shape resonance and intramolecular bond length by the multiple-scattering cluster method

The NEXAFS spectra of O 2, CO, and formate molecules have been calculated for the first time in terms of the multiple-scattering cluster method of NEXAFS. Our calculations identify the empirical correlation between σ shape resonance position and intramolecular bond length. By a comparison between the results of theoretical calculation and the experimental NEXAFS spectrum of the formate-Cu system, we have found that the intramolecular bond length L CO in formate is 1.26±0.01 A ̊ , and the OCO bond angle is equal to 134±4°.

A critical interpretation of the near-edge X-ray absorption fine structure of chemisorbed benzene

Near-edge X-ray absorption fine structure (NEXAFS) measurements for submonolayer benzene coverages on Ag(110) are reported and interpreted in light of recent electronic structure calculations for free benzene. Quantitative analysis of the continuum resonances indicates that benzene is bound parallel to Ag(110) while analysis of the C(1s) → π ∗ (e 2u) transition intensities yields a maximum tilt of ~ 10–15°. The apparent tilting suggested by the π ∗ resonances is most likely not a real and global tilt, but probably arises from the presence of tilted minority species. A comparison of the NEXAFS spectra for benzene on Ag(110) with those previously reported for benzene on Pt(111) and Mo(110) and phenyl thiolate on Mo(110) indicates that strong adsorbate-substrate interactions may result in significant perturbations in the bound-state region of the near-edge structure, as well as shifting of the continuum resonances due to changes in intramolecular bond lengths.

Synthesis and structure of cytosine dichloride cuprate: direct bonding of copper to cytosine

Dichlorobis(cytosine)copper(II), [CuCl2-(C4H5N3O)2], Mr = 356.65, monoclinic, P2(1)/n, a = 8.399 (2), b = 13.773 (2), c = 10.775 (2) A, beta = 90.8 (2) degrees, V = 1246.3 (9) A3, Z = 4, Dx = 1.901 Mg m-3, lambda (Mo K alpha) = 0.7107 A, mu = 2.195 mm-1, F(000) = 716, T = 298 K, R = 0.032, wR = 0.037 for 2313 reflections greater than 2 sigma(F). The crystal structure of the title compound consists of two crystallographically independent cytosine molecules attached together through the direct bonding of a Cu2+ ion with two N atoms of the pyrimidine rings. In addition to the N atoms, the Cu ions are coordinated to two Cl atoms forming approximately a square-planar environment. The bond distances of Cu to Cl(1), Cl(2), N(3) and N(3') atoms are 2.299 (1), 2.267 (1), 1.985 (4) and 1.996 (3) A, respectively. Packing of the Cyt(I)-CuCl2-Cyt(II) complex in the crystal is ensured by an extensive extramolecular N--H...Cl and N--H...O network. Hydrogen bonds involving Cl, O and H atoms of the neighboring Cyt(I) and Cyt(II) induce a slight distortion in Cu--Cl, C = O distances but do not significantly affect intramolecular bond lengths and angles in the cytosine rings and their flatness.

Molecular orientational correlation in liquid halogens

The characteristic features of structure factor Sm(Q) of liquid halogens F2, Cl2, Br2, and I2 have been discussed in terms of preferred orientational correlations introduced between the nearest neighbors. The orientational correlations estimated directly from the experimental Sm(Q)’s of these liquids are rather similar to each other and are related to a ‘‘staggered parallel’’ orientation proposed previously for liquid Br2. The characteristic features of these Sm(Q)’s are interpreted quite well by two structurally simple quantities, i.e., the ratio of intramolecular bond length to intermolecular center–center separation of correlated molecules l/Rc and that of intramolecular bond length to effective diameter of uncorrelated molecule l/σ. The characteristic features of the experimental radial distribution functions are also reproduced quite well.

Evidence for molecular dissociation in bromine near 80 GPa.

Synchrotron x-ray diffraction studies using a diamond-anvil cell and an imaging plate reveal that solid bromine begins to undergo a molecular-to-monatomic phase transition near 80 GPa. The structure of the high-pressure phase is found to be body-centered orthorhombic (${D}_{2h}^{25}$-Immm), as previously observed in iodine above 21 GPa. These results on bromine plus the previous data on iodine and iodine monobromide show that the molecular dissociation takes place when the scaled unit-cell volume as v\ifmmode \tilde{}\else \~{}\fi{}=v/8${r}_{s}^{3}$ in the molecular phase (${r}_{s}$ is the intramolecular bond length in the solid) reaches v${\ifmmode \tilde{}\else \~{}\fi{}}_{c}$=1.29. We also observe universal behavior of the scaled lattice constants versus v\ifmmode \tilde{}\else \~{}\fi{} in all solid halogens.

Structure determination in intercalated graphite by polarized XAFS analysis

Highly oriented pyrolytic graphite (HOPG), intercalated with the halogen molecules ICl and IBr, was investigated by x-ray absorption spectroscopy. Information on the structural arrangement of the intercalated halogen molecules was derived from the polarization and temperature dependent near-edge (NEXAFS) and extended (EXAFS) x-ray absorption fine structure of the respective Cl-K, I-LI, III′ and Br-K thresholds. The observed change in the intramolecular bondlength of the halogen molecules in different surroundings is correlated with the energy separation of the σ∗- and π-resonances observed in the NEXAFS spectra.

X-ray diffraction measurements on liquid iodine and some dilute mixtures of KI in I2

Using X-ray diffraction we have determined the structure factor of pure iodine and of a number of dilute mixtures of KI in I2. We show that these liquids exhibit short-range orientational order, adjacent molecules being orient- ed more or less parallel. The intramolecular bond length in pure liquid iodine is 2·70±0·01 A, intermediate between the bond lengths of gaseous and solid iodine. Upon addition of KI the bond length increases, while the distances to atoms in the second and third shell decrease. These effects are related to recent high-pressure diffraction measurements on solid iodine.

K-shell shape resonances and intramolecular bond lengths. Comments on ‘‘The relationship between shape resonances and bond lengths’’

A rebuttal is given to the critique by Piancastelli et al. [J. Chem. Phys. 86, 2765 (1987)] of the relationship between 1s→σ* excitation energies and bond lengths proposed by Sette et al. [J. Chem. Phys. 81, 4906 (1984)]. The anomalous character of σ* resonances in the C1s and O1s spectra of CO2 is explained in terms of dipole selection rules and a large energy splitting between the σ*g and σ*u orbitals.

Röntgenstrukturuntersuchung des flüssigen Silicium‐, Germanium‐ und Zinntetrachlorids. Ein Beitrag zur Frage einer gemeinsamen Flüssigkeitsstruktur I. Streuexperimente an den reinen Komponenten und ihren binären Mischungen

AbstractX‐ray diffraction experiments have been performed for liquid tetrachlorides SiCl4, GeCl4, SnCl4 and special binary mixtures including isoelectronic species. They were analysed to yield experimental evidence regarding the question of a common liquid structure that is essential for separating partial structure factors by isomorphic substitution.—The scattering intensity obtained at 20°C using CuKα and AgKα radiation was corrected for background, absorption, polarisation, multiple scattering, Compton scattering, and for the wavelength distribution of the incident beam. The intramolecular contribution calculated from best fit molecular parameters was separated from the coherent differential cross section. The molecular model parameters compare excellently with those of the literature.—Based on the comparison of the properties of the intermolecular scattering functions, the experimental results point to a common type of short range order but establish that the structure factors are affected by the different intramolecular bond lengths.

Thermodynamic character of the vibron frequencies and equation of state in dense, high-temperature, fluid N2.

The pressure-temperature dependence of the vibron stretching mode frequency, the intramolecular bond lengths, and the pressure-volume curves along various isotherms are calculated for fluid ${\mathrm{N}}_{2}$ in the ranges 2\ensuremath{\le}P\ensuremath{\le}150 kbar and 300\ensuremath{\le}T\ensuremath{\le}1500 K. A constant-pressure Monte Carlo procedure with continuously deformable, periodic boundary conditions is used. The results are in good agreement with recent high-temperature diamond cell, dynamic shock, and earlier P-V data.

NEXAFS and SEXAFS studies of chemisorbed molecules

Near-edge x-ray absorption fine structure (NEXAFS) and surface extended x-ray absorption fine structure (SEXAFS) spectroscopies and their application to the determination of the adsorption geometry and bonding of low-Z molecules on surfaces are discussed. NEXAFS is characterized by intramolecular resonances and probes the internal structure of the molecule (intramolecular bond lengths and possibly bond angles) as well as its orientation relative to the surface. SEXAFS provides information about the adsorption site and the molecule-substrate distances. After demonstrating the full power of SEXAFS in the analysis of oxygen adsorption on Cu(110) and on Ag(110) an example is given of a complete structure determination for the formate species (HCO2) on Cu(110) using NEXAFS and SEXAFS.

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.

The temperature dependence of the crystal structures of the solid halogens, bromine and chlorine

The neutron powder profile refinement technique has been used to determine the crystal structure of solid Br2 at 5, 80, 170 and 250 K and that of solid Cl2 at 22, 55, 100 and 160 K. The results confirm that the structures of the two halogens are isomorphous, with space group Cmca at all temperatures. For both halogens the lattice parameters a and b increase monotonically with temperature, but the lattice parameter c decreases at the highest temperatures. The data were analysed assuming both isotropic and anisotropic thermal parameters. The intramolecular bond length and its orientation relative to the b-axis show little change with temperature. For Br2 at 5 K the bond length is 2·301(2) A while a = 6·5672(3), b = 4·4678(2), c = 8·6938(4) A. For Cl2 at 22 K the bond length is 1·994(2) A while a = 6·1453(2), b = 4·3954(1), c = 8·1537(2) A, where the errors quoted are those produced by the profile fitting program.

Correlation between intramolecular bond lengths and K-shell σ-shape resonances in gas-phase molecules

Analysis of K-shell excitation spectra of gas-phase molecules containing at least two atoms of either B, C. N. O or F reveals the existence of a striking correlation between the bond length of the atomic pair. the sum of their atomic numbers and the associated α-shape resonance energy. Empirical rules are established which allow the derivation of intramolecular distances with accuracies reliably better than ± 0.05 A from the K-.shell absorption spectrum of one of the atoms in the Molecule.