Intramolecular N−H...O hydrogen bonding,quinoid effect,and partial π-electron delocalization in N-aryl Schiff bases of 2-hydroxy-1-naphthaldehyde: the crystal structures of planar N-(α-naphthyl)- and N-(β-naphthyl)-2-oxy-1-naphthaldimine

The structures of N-(-naphthyl)-2-oxy-1-naphthaldimine1 and N-(-naphthyl)-2-oxy-1-naphthaldimine2 have been investigated by X-ray analysis and by spectroscopic methods. Crystals of1 are monoclinic, space groupPn, with cell dimensionsa=10.823(3),b=5.826(2),c=11.899 (3) Å, and =99.66(3)°. Compound2 crystallizes in the orthorhombic space groupPca2₁ witha=17.564(3),b=6.314(2), andc=13.663(4) Å. The IR spectra exhibited neither N–H nor O–H stretching frequencies. The existence of theintramolecular hydrogen bonding of N–H...O type was predicted by spectroscopic experiment but unequivocally established by diffraction experiment in both cases1 and2. The molecules1 and2 are significantly planar with considerable quinoid effect at the 2-oxy-naphthaldimine moiety. Although essentially planar, both molecules1 and2 show the delocalization of -electrons only in the central part of the molecules including C=N imino group with pendent ring carbon atoms.Intermolecular attractions in the crystals belong to weak van der Waals interactions-between discrete planar molecules spatially arranged into the expectedherringbone motif in the solid state.     

Crystal and molecular structure of 2,6-dihydroxybenzoic acid

The crystal and molecular structure of 2,6-dihydroxybenzoic acid has been determined by single crystal X-ray diffraction. The crystals are monoclinic witha=5.4084(5),b=5.2240(7),c=22.986(4) Å, =94.69(3)°, space group P2₁/c,Z=4,V=647.27(16) ų,d _c =1.58Mg m^–3, The acid crystallizes as hydrogen bonded carboxylic dimers which pack to generate a herringbone motif of the type typically encountered in polycyclic aromatic compounds.     

Intramolecular hydrogen bonding and tautomerism in N-(3-pyridil)-2-oxo-1-naphthylidenemethylamine

N-(3-pyridil)-2-oxo-1-naphthylidenemethylamine (C₁₆H₁₂N₂O) was studied by elemental analysis, IR, ¹H NMR, and UV–visible techniques and X-ray diffraction methods. The UV–visible spectrum of the compound was investigated in solutions effect polarity. The polarity of the some solvents was modifierly the additional (CF₃COOH) and [(C₂H₅)₃N]. The compound is in tautomeric equilibrium (phenol-imine O–H···N and keto-amine O···H–N forms) in polar and nonpolar solvents. The keto-amine form is observed in basic solutions of DMSO, ethanol, chloroform, benzene, cyclohexane, and in acidic solutions of chloroform and benzene, but not in acidic solutions of DMSO and ethanol. The compound crystallizes in the monoclinic, space group P2₁/a with a = 7.010(5) Å, b = 13.669(4) Å, c = 12.764(4) Å, = 101.23(4)°, V = 1199.6(10) ų, Z = 4, D _c = 1.375 g/cm³, (Mo K) = 0.088 mm^–1, R = 0.045 for 1658 reflections [I > 2(I)]. The title compound is not planar two Schiff base moieties A [C1–C11, O1] and B [N1, C12, C13, N2, C14, C15, C16] are inclined at an angle of 27.4(1)° reflecting mainly the twist about C12–N1 [C11–C12–N1–C13, 29.7(2)°]. There is a strong intramolecular hydrogen bond (O–H···N) of 2.529(2) Å.     

Molecular interactions between pyrazine and n-propanol, chloroform, or tetrahydrofuran

The molecular interactions of pyrazine (PZ) with n-propanol, chloroform, and tetrahydrofuran (THF) have been investigated by employing ultraviolet spectroscopy and quantum chemical calculation methods. A new quantity, excess absorption coefficient, was introduced to represent the strength of the interaction. It was found that the interaction decreased in the order: PZ-propanol>PZ-chloroform>PZ-THF. The Benesi-Hildebrand method indicated that the interaction stoichiometries of the PZ-chloroform and PZ-THF systems were both 1:1 and the equilibrium constants were determined to be 2.07 and 0.64M(-1), respectively. Using a nonlinear fitting method, we demonstrated that the PZ-propanol was a two-step 1:2 interaction pair and the equilibrium constants were determined to be 8.8 and 0.19M(-1). Quantum chemical calculations showed the existence of hydrogen-bonding interactions in all the three system: normal Ncdots, three dots, centeredH-O hydrogen bond in the PZ-propanol system, unconventional Ncdots, three dots, centeredH-C hydrogen bond in the PZ-chloroform, and weak N-C-Hcdots, three dots, centeredO hydrogen bond in the PZ-THF system. Methodologically, we pointed out that special care must be taken when the Benesi-Hildebrand method is used to evaluate 1:2 interactions.     

A note on Michael Weisberg’s: challenges to the structural conception of chemical bonding

Michael Weisberg’s recent 2007 paper on the chemical bond makes the claim that the chemical notion of the covalent bond is in trouble. This note casts doubts on that claim.

Wavelength dependence of matrix-assisted laser desorption and ionization using a tunable mid-infrared laser

Matrix-assisted laser desorption and ionization by infrared laser (IR-MALDI) is expected to be an effective methods for soft-ionization of high-molecular weight proteins and intracellular proteins. IR-MALDI is not widely used because its low sensitivity, complexity, high cost, and as it does not work well on commercial MALDI time-of-flight mass spectrometers (TOFMSs). We employed a tunable mid-infrared (MIR) laser as a light source for MALDI to investigate the IR-MALDI. The laser wavelength can be tuned within a range from 5.5 to 10.0 μm, and included several biomaterial group vibration modes. We evaluated the wavelength dependence of ionization in IR-MALDI for four matrices: succinic acid, urea, 3,5-dimethoxy-4-hydroxycinnamic acid (sinapic acid) and 2,5-dihydroxybenzoic acid (DHB). These matrices contained various groups of vibration modes, and absorbed an infrared (IR) energy at a specific wavelength. The mass spectra of angiotensin II was obtained at a specific wavelength corresponding to the CO stretching and benzene ring vibration mode. In IR-MALDI, we considered the strong molecular bond attracting an electron from a neighboring hydrogen atom, possibly protonating the hydrogen atom.     

A definition for the covalent and ionic bond index in a molecule

Formulae for hermitian operators representing covalent, ionic, and total bond indices are derived. The eigenstates of these operators come in pairs, and can be considered as bonding, anti-bonding and lone-pair orbitals. The form of these operators is derived by generalising the rule that the bond order be defined as the net number of bonding electron pairs. The percentage of covalency and ionicity of a chemical bond may be obtained, and bond indices can also be defined between groups of atoms. The calculation of the bond indices depends only on the electron density operator, and certain projection operators used to represent each atom in the molecule. Bond indices are presented for a series of first and second row hydrides and fluorides, hydrocarbons, a metal complex, a Diels–Alder reaction and a dissociative reaction. In general the agreement between the bond indices is in accord with chemical intuition. The bond indices are shown to be stable to basis set expansion.     

The strength of the σ-, π- and δ-bonds in Re2Cl 8 2−

The geometry of Re₂Cl₈²⁻ has been optimized for the eclipsed (D _4h ) equilibrium conformation and for the staggered (D _4d ) conformation at BP86/TZ2P. The nature of the Re–Re bond which has a formal bond order four has been studied with an energy decomposition analysis (EDA). The EDA investigation indicates that the contribution of the b ₂ (δ _xy ) orbitals to the Re–Re bond in the ground state is negligibly small. The vertical excitation of one and two electrons from the bonding δ orbital into the antibonding δ* orbitals yielding the singly and doubly excited states and gives a destabilization of 17.5 and 36.1 kcal/mol, respectively, which is nearly the same as the total excitation energies. The preference for the D _4h geometry with eclipsing Re–Cl bonds is explained in terms of hyperconjugation rather than δ bonding. This is supported by the calculation of the triply bonded Re₂Cl₈ which also has an eclipsed energy minimum structure. The calculations also suggest that the Re–Re triple bond in Re₂Cl₈ is stronger than the Re–Re quadruple bond in Re₂Cl₈²⁻. A negligible contribution of the δ orbital to the metal–metal bond strength is also calculated for Os₂Cl₈ which is isoelectronic with Re₂Cl₈²⁻. Contribution of the Mark S. Gordon 65th Birthday Festschrift Issue. Theoretical Studies of Inorganic Compounds. 38. Part 37 (2006) Bessac F, Frenking G, Inorg Chem 45:6956.