Rationalizing the effect of halogenation on the molecular structure of simple cyclobutene derivatives by topological real-space analysis of their electron density.

The accurate gas-phase equilibrium structures on the ground-state potential energy surface of the complete series of fluorinated and chlorinated cyclobutene derivatives with C(2v) symmetry have been evaluated at DFT PBE0/6-311++G(d,p) theory level. The optimized geometries have been compared with all the available experimental data reported in the literature, as obtained by microwave spectroscopy (MW) and gas-phase electron diffraction (GED) techniques. For hexafluorocyclobutene and 1,2-dichloro-3,3',4,4'-tetrafluorocyclobut-1-ene, the results of accurate low-temperature single-crystal X-ray diffraction experiments have also been considered. Structural changes within the cyclobutene ring, as induced by fluorination and chlorination at allylic and vinylic positions, have been correlated with changes in the corresponding theoretical charge densities. To this aim, several local and nonlocal topological descriptors provided by the quantum theory of atoms in molecules, QTAIM, have been employed, with particular emphasis on the delocalization indices and integrated source function decomposition schemes. Key factors for the resulting molecular structures are the chemical nature and the steric hindrance of the substituents, as well as quantum-mechanical effects, such as delocalization and partial conjugation. When fluorine atoms replace hydrogens at allylic or vinylic positions, the corresponding Csp(3)-Csp(3) or Csp(2)═Csp(2) bonds between the substituted carbons undergo a significant strengthening, while chlorination has just the opposite effect. In the latter case the steric hindrance between bulky chlorine atoms occupying vicinal positions is crucial in determining the single Csp(3)-Csp(3) bond length. These findings are discussed in the context of the reactivity of chemically related chlorofluorocarbon compounds.

The puzzle of bond length variation in substituted cyclobutenes. A new example: molecular structure and conformations of 1,2-dimethoxy-3,3,4,4-tetrafluorocyclobut-1-ene.

The structure and composition of 1,2-dimethoxy-3,3,4,4-tetrafluorocyclobut-1-ene (DMCB) have been measured by electron diffraction from the gas at a temperature of 370 K with the help of auxiliary data from molecular orbital and normal coordinate calculations, the former at several levels of theory and basis-set size, most importantly B3LYP/cc-pVTZ. The compound was found to exist primarily as a rotamer of C(s) symmetry (ca. 98%; 2sigma = 11%) with the remainder one of C(2v) symmetry; theory predicts about 88% C(s). Values for some of the more important parameters (r(g)/A; angle(alpha)/deg) of the C(s) form are r(C=C) = 1.337(21), r(C1-C4) = 1.496(8), r(C2-C3) = 1.501(8), r(C3-C4) = 1.567(12), r(C1-O) = 1.318(12), r(C2-O) = 1.340(12), r(C3-F) = 1.375(4), r(C4-F) = 1.368(4), angle(ave)(C=C-C) = 94.4(4), angle(ave)(C=C-O) = 133.5(12), angle(ave)(C-O-C) = 119.6(13), and angle(ave)(F-C-F) = 104.4(7). Surprisingly, although electron-diffraction values for the fluorinated C3-C4 bond in other cyclobutenes are greater than that for cyclobutene itself, that is not the case for DMCB where it is found to be about the same. Details of the DMCB structure, together with possible reasons for the observed variations in the length of the C3-C4 bond in fluorinated cyclobutene-like molecules, are discussed.

Effect of methoxy substituents on the structural and electronic properties of fluorinated cyclobutenes: a study of hexafluorocyclobutene and its vinyl methoxy derivatives by XRD and periodic DFT calculations.

The effect of the methoxy substituent on the structure, crystal packing, and electrostatic properties of hexafluorocyclobutene (C(4)F(6)) was investigated in the solid-state with DFT-B3LYP calculations. Full geometry optimizations were done for the parent compound and its two vinyl methoxy derivatives C(4)F(5)OCH(3) and C(4)F(4)(OCH(3))(2), starting from the structures obtained by single-crystal X-ray diffraction at low temperature. A full topological analysis, followed by the calculation of several electrostatic properties, was performed on the periodic electron density using the quantum theory of atoms in molecules. Eventually, the cohesive energies of the three crystals were estimated. In the cyclobutene plane, the methoxy substitution yields a significant electronic rearrangement involving the pi-electrons. The solid-state (periodic) results agree with those obtained by gas-phase calculations on C(4)F(6) and its derivatives at a comparable level of theory. It was found that the substitution of one or two vinylic fluorine atoms with the OCH(3) group considerably influences the molecular dipole moment, which undergoes an enhancement in both the solid and the gas phase as large as 200% and 235% for C(4)F(5)OCH(3) and C(4)F(4)(OCH(3))(2), respectively, with respect to that calculated for C(4)F(6). The charge rearrangement due to the substituents provides a significant electrostatic contribution to the lattice energy, and in turn it can be related to the change in the observed crystal packing on going from C(4)F(6) (space group P2(1)/c) to both of its derivatives (space group P1). It is also shown that the dispersion energy significantly contributes to the lattice stability in all three compounds. Since the DFT calculations, in the limit of large separations, entirely miss the dispersion term, this was estimated by applying a recently proposed dampening function to the semiempirical atom-atom C(6) R(-6) potentials in the mainframe of Spackman's energy decomposition scheme for Mulliken multipoles.

Accessory allowing an optical cell of 6-10,000 microm path for liquids and gases to be filled in vacuum and used under pressure.

An accessory for introducing liquid or gaseous samples without any contamination into an evacuated cell for optical spectrometry is described. The procedure for its use is similar to that of sample injection into a gas-liquid chromatograph, no glove box or glove bag being needed. Main benefits are the wide choice of size of the samples, their recoverability, safety, and a range of optical paths allowing to measure the absorbance of strongly absorbing liquids and gases, very dilute liquid solutions, and liquefied gases under moderate pressure. Short path spectra of gaseous water pressure standards consent quantification of water partial pressure measured in common gas cells.

Interaction of bovine serum albumin with chrysotile: spectroscopic and morphological studies.

The biodurability of chrysotile fibers, which is related to their cytotoxicity and mutagenic responses, is strongly affected by the surface chemical adsorption of biological molecules. Natural chrysotile is a heterogeneous material in both structure and composition. The availability of synthetic stoichiometric chrysotile of constant structure and uniform morphology has allowed us to investigate its interaction with bovine serum albumin (BSA). By using transmission electron microscopy (TEM) and atomic force microscopy (AFM), we have obtained the first morphological evidence of albumin adsorption onto chrysotile nanocrystals. FTIR spectroscopy was used to quantify modifications of BSA secondary structure that were induced by the surface interaction. The protein transition to beta-turns allows a stronger interaction between the protein hydrophilic side-chains and the charged asbestos surface, which is consistent with hydrogen bonds involving the superficial OH groups. Synthetic stoichiometric chrysotile nanocrystals were shown to be an ideal reference standard with which to study the interaction of asbestos fibers with biological systems, in order to elucidate the chemical mechanisms of asbestos toxicity.