Hydrogen bonding in selected vanadates: a Raman and infrared spectroscopy study

Water plays an important role in the stability of minerals containing the deca and hexavanadates ions. A selection of minerals including pascoite, huemulite, barnesite, hewettite, metahewettite, hummerite has been analysed. Infrared spectroscopy combined with Raman spectroscopy has enabled the spectra of the water HOH stretching bands to be determined. The use of the Libowitsky type function allows for the estimation of hydrogen bond distances to be determined. The strength of the hydrogen bonds can be assessed by these hydrogen bond distances. An arbitrary value of 2.74A was used to separate the hydrogen bonds into two categories such that bond distances less than this value are considered as strong hydrogen bonds whereas hydrogen bond distances greater than this value are considered relatively weaker. Importantly infrared spectroscopy enables the estimation of hydrogen bond distances using an empirical function.     

Theoretical study of structure, bonding, and aromaticity of borazyne and B-substituted borazynes

The density functional theory (DFT) is used to study the geometries, and electronic structures of triplet and singlet of borazyne and B-substituted of borazyne. The aromaticity of these systems is analyzed in the light of nucleus-independent chemical shift (NICS), average of two-center indices (ATI). These methods show increasing of aromaticity in deactivating groups. The relation between electron density in ring critical point (RCP) and NICS(1.0) is observed. The most important interaction in these molecules has been investigated by natural bonding orbital method (NBO).     

Hydrogen bonding in dimers of tritolyl and tritosylurea derivatives of triphenylmethanes

The crystal structure of the homodimer formed by the tritolylurea 3a proves the existence of a belt of six bifurcated hydrogen bonds between both NH and the O=C groups of the adjacent urea residues. For the tritosylurea 3b, four additional three-center hydrogen bonds, also involving the SO2 oxygen, are found in the crystalline state. Molecular dynamics simulations in a chloroform box confirm these patterns of the hydrogen bonds and the resulting elongation of the dimer 3b. 3b in comparison to 3a x 3a. The calculated complexation energies for the three dimeric combinations are nearly identical in agreement with the simultaneous formation of heterodimer 3a x 3b in a mixture of 3a and 3b.     

Photoelectron spectra and electronic structure of aza-boron-dipyridomethene derivatives

The electronic structure of three aza-boron-dipyridomethene derivatives containing different hydrocarbon groups at the boron atom is studied by ultraviolet photoelectron spectroscopy and calculations at the density functional theory level. According to the experimental and theoretical data, the higher occupied molecular orbitals of anthracene, acridine, and the studied complexes are of the same character. For the three studied compounds, the effect of alkyl and phenyl substituents on the electronic structure is determined. The parameters of the electronic structure of aza-boron-dipyridomethene (phenyl groups at the boron atom) and its β-diketonate analogue are compared. It is shown that in an energy range up to 11 eV the calculated results correlate with the ultraviolet photoelectron spectra.     

Hydrogen bonding and multiphonon structure in copper pyrazine coordination polymers

We report a systematic investigation of the temperature-dependent infrared vibrational spectra of a family of chemically related coordination polymer magnets based upon bridging bifluoride (HF(2)-) and terminal fluoride (F-) ligands in copper pyrazine complexes including Cu(HF(2))(pyz)(2)BF(4), Cu(HF(2))(pyz)(2)ClO(4), and CuF(2)(H(2)O)(2)(pyz). We compare our results with several one- and two-dimensional prototype materials including Cu(pyz)(NO(3))(2) and Cu(pyz)(2)(ClO(4))(2). Unusual low-temperature hydrogen bonding, local structural transitions associated with stronger low-temperature hydrogen bonding, and striking multiphonon effects that derive from coupling of an infrared-active fundamental with strong Raman-active modes of the pyrazine building-block molecule are observed. On the basis of the spectroscopic evidence, these interactions are ubiquitous to this family of coordination polymers and may work to stabilize long-range magnetic ordering at low temperature. Similar interactions are likely to be present in other molecule-based magnets.     

Hydrogen bonding NH/pi interactions between betacarboline and methyl benzene derivatives

In the presence of benzene, toluene, m-xylene, mesitylene and durene, the pyrrolic NH stretching band of betacarboline, 9H-pyrido[3,4-b]indole, and its 1-methyl derivative, harmane, in tetrachloroethane diminishes in intensity while a new red-shifted band grows up. The shifts of the associated bands increase linearly with the pi-electron density of the substrates. These spectral changes are attributed to the formation of 1:1 molecular association complexes between the betacarbolines and the benzenoid substrates. The complexes are stabilized by the hydrogen-bonding interaction between the pyrrolic NH group of betacarboline and the pi-delocalized electrons of the benzene derivatives. The influence of these NH/pi hydrogen-bonding interactions in the fluorescence spectra of betacarboline is discussed.     

Crystal structure, electronic structure, and bonding properties of anhydrous nickel oxalate

The results of crystal structure determination and theoretical analysis of electronic structure and bonding properties in relation to thermal decomposition process in anhydrous nickel oxalate are presented. The details of the methods used in this analysis i.e., the Bader’s quantum theory of atoms in molecules and bond order models (as defined by Pauling, Bader, Cioslowski and Mixon—modified by Howard and Lamarche), applied to topological properties of the electron density, obtained from ab initio calculations carried out by Wien2k FP-LAPW package (full potential linearized augmented plane wave method), as well as Brown’s bond valence model (bond valences and strengths, and bond and crystal strains, calculated from experimental crystal structure data) are described. Nickel oxalate dihydrate was prepared by precipitation from water solutions of nickel nitrate (V) with oxalic acid at about 60 °C. The crystalline powder was filtered, washed, and dried at 80 °C on air. Anhydrous nickel oxalate sample was measured by XRD method applying Philips X’Pert Pro MD diffractometer equipped with MRI high temperature cell. Structural as well as qualitative and quantitative phase analyses were made by Phillips X’Pert HighScore Plus version 2.1 software with implemented full-pattern fit by means of Rietveld method. The detailed analysis of the obtained results shows that anhydrous nickel oxalate has monoclinic crystal structure (P2₁/c, sg 14), the carbon–carbon bond is the weakest one, and the process of thermal decomposition of this structure should begin with the breaking of this particular bond followed by nickel-oxygen bonds, which will lead to metallic nickel and carbon dioxide as final products, in agreement with the experiment. These results, supported by our earlier ones show clearly that such methods (topological and structural), when used simultaneously in analysis of the crystal structure and bonding properties, provide us with the additional insight into the behavior of given compound during thermal decomposition process and thus allow predicting and explaining of its most probable pathway.     

Chemical bonding and aromaticity in trinuclear transition-metal halide clusters

Trinuclear transition-metal complexes such as Re(3)X(9) (X = Cl, Br, I), with their uniquely featured structure among metal halides, have posed intriguing questions related to multicenter electron delocalization for several decades. Here we report a comprehensive study of the technetium halide clusters [Tc(3)(μ-X)(3)X(6)](0/1-/2-) (X = F, Cl, Br, I), isomorphous with their rhenium congeners, predicted from density functional theory calculations. The chemical bonding and aromaticity in these clusters are analyzed using the recently developed adaptive natural density partitioning method, which indicates that only [Tc(3)X(9)](2-) clusters exhibit aromatic character, stemming from a d-orbital-based π bond delocalized over the three metal centers. We also show that standard methods founded on the nucleus-independent chemical shift concept incorrectly predict the neutral Tc(3)X(9) clusters to be aromatic.     

Hydrogen bonding and the structure of the HFHCN dimer

The structure and energy of formation of the hydrogen bonded complex HFHCN are predicted by ab initio molecular orbital methods. The charge redistribution upon dimer formation is examined in this complex and related to those charge distributions found in other H-bonded complexes. The total hydrogen bond energy is broken down into components as well as related to experimental work on similar compounds.     

纳米碳管电子结构和键合特性的第一原理研究

利用第一原理方法对一系列尺寸变化的单层纳米碳管电子结构进行了研究,得到了总态密度和态密度随碳管半径R的变化情况与实验结果完全一致,Fermi能级处态密度值随着管径R的增大而减小,说明纳米管的化学活性随着管径的增大而增强。碳管中C-C之间的键合为2s和2p价电子混合而成的弯曲的σ,π键,随着管径R的增大,化学键的弯曲度逐渐减小,C-C之间的键合作用和结合能逐渐增强,电荷密度和对应的势场也逐渐减弱。这些结果表明管径较小的纳米碳管在复合材料的合成中具有一定的优势。     

Accurate redetermination of the X-ray structure and electronic bonding in adenosylcobalamin

The electronic structure of adenosylcobalamin (B12 coenzyme, AdoCbl) has been calculated by a density functional method, using the orthogonalized linear combination of the atomic orbital method (OLCAO). Since a fixed accurately determined geometry was needed in such calculations, the crystal structure of adenosylcobalamin has been redone and refined to R = 0.065, using synchrotron diffraction data. Comparison with the recently reported electronic structures of cyano- (CNCbl) and methylcobalamin (MeCbl) shows that the net charges and bond orders vary only on the axial donors. The values in the three cobalamins suggest that the Co-C bond in MeCbl has a strength similar to that in AdoCbl, but it is significantly weaker that that in CNCbl. Present results are compared with those previously reported for the analogous corrin derivatives; i.e., simplified cobalamins with the side chains a-f replaced by H atoms. Despite a qualitative agreement, a discrepancy in the calculated HOMO-LUMO gap is found.     

Diamagnetism as a structure and bonding related property in semiconductors

The reformulation of the quantum mechanical expression of the diamagnetic susceptibility, in terms of bond and band related parameters, leads us to evaluate separately the Langevin and the Van Vleck components of the lattice magnetic susceptibility of semiconductors. Its validity, checked for a number of semiconductors covering seven different structures and almost the entire range of variability of Suchet's ionicity parameter, confirms that a definite link exists between the diamagnetism of semiconductors and dielectrics and the nature of their interatomic bonds.     

Photoelectron spectra and electronic structure of derivatives of imidazoline

We have obtained for the first time the photoelectron spectra (PES) of 20 diamagnetic and paramagnetic derivatives of imidazole. On the basis of calculations in the MNDO approximation, analysis of the vibrational structure, and comparisons in a series we have interpreted the bands in the range 7–11 eV. In the nitroxyl radicals of 3-imidazoline the highest occupied molecular orbital is the _NO ^* orbital, having also a contribution on the C⁴ atom. On introducing N-oxide groups there is a considerable rearrangement of the electronic structure of the radicals. In the PES of the nitroxyl radicals of 3-imidazoline-3-oxide there is multiplet splitting of the ionization band of the n_o·MO, amounting to 0.3–0.4 eV. Replacement of the methyl groups on the C² atom by methoxyl groups leads to an increase in the interactions of the unshared pairs of the O atoms of the nitronium and nitroxyl groups, while the same replacement on the C⁵ atoms leads to a considerable decrease in this interaction. When the substituent on the N¹ atom in derivatives of 3-imidazoline-3-oxide is varied the energy of ionization of the _C-NO MO decreases in the series: CH₃ < H OH < O < NO.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1769–1777, August, 1990.     

Hydrogen bonding and anaesthesia

General anaesthetics act by perturbing intermolecular associations without breaking or forming covalent bonds. These associations might be due to a variety of van der Waals interactions or hydrogen bonding. Neurotransmitters all contain OH or NH groups, which are prone to form hydrogen bonds with those of the neurotransmitter receptors. These could be perturbed by anaesthetics.

Aromatic rings in amino acids can act as weak hydrogen bond acceptors. On the other hand the acidic hydrogen in halothane type anaesthetics are weak proton donors. These two facts together lead to a probable mechanism of action for all general anaesthetics.