Towards an unified chemical model of secondary bonding.

The concept of secondary bond covers a wide range of non-covalent interactions involving an acceptor (or electrophilic) molecule and an electron donor (or nucleophilic) one. It involves triel, tetrel, pnictogen, chalcogen, halogen, and aerogen bonds as well as hydrogen bonds. Such interactions yield complexes in which the internuclear distance of the electrophilic and nucleophilic centers is intermediate between the sums of the covalent and van der Waals radii of these atoms. These complexes can be considered as precursors of hypothetical nucleophilic substitution or addition reactions. As a consequence of the least motion principle, in the complex, the arrangement of the ligands around the electrophilic center should look like that of the hypothetical transition state or addition product. In a same fashion, the geometry around the nucleophilic center is determined by the location of the lone pair or of the bond involved in the interaction. In this picture of secondary bonding, the structure of the valence shell of the electrophilic atoms determines the geometry of the complex rather than the group to which belongs the elemental atom. The reorganization of the complexes in terms of the arrangement of the bonding and non-bonding electronic domains around the electrophilic center enables to rationalize the geometries in a systematic fashion. A set of VSEPR inspired rules enabling the building up of secondary bonded isomers are proposed and checked by quantum chemical calculations performed on representative test systems of the AX4-nEn type. Graphical Abstract An example of secondary interaction: FClO[Formula: see text].

Hydrogen bonding and delocalization in the ELF analysis approach.

Delocalization of the electron density in the proton donor fragment has been studied for 21 complexes, A-HB (A = F, Cl; B = Ne, Ar, CO2, N2, FH, ClH, H2O, PH3, NH3, Cl-, F-, covering the whole range of hydrogen bond strength. The proton donor and proton acceptor fragments are defined by a minimum variance principle achieved by the ELF partition. It is shown that the variance of the proton donor population as well as the charge transfer between the fragments calculated from the ELF partition is always smaller than that evaluated within the QTAIM framework. For both partition schemes, the variance and the charge transfer are correlated with the hydrogen bond strength. It is shown that the variance varies as the square root of the value of the ELF at the hydrogen bond interaction point (i.e. the saddle point at the boundary of the proton donor and proton acceptor moieties)ηvv' providing a numerical proof of the conjecture that the ELF partition satisfies a minimum variance condition and an explanation of the success of the core valence bifurcation index as an indicator of the hydrogen bond strength. The ELF technique has been then applied to the study of hydrogen bonded crystals for which the variance of the fragment population has been estimated from ηvv'. The systems investigated are KHF2, KDP and ice VIII. The results are consistent with very strong hydrogen bonds in the two former crystals and medium-weak bonding in ice. In ice VIII the variance, and therefore the hydrogen bond strength, increases with pressure yielding a phase transition toward ice X in which the hydrogen bond is characterized as very strong. Our study emphasizes the importance of the partition scheme which defines the proton donor fragment and the role of electron density delocalization between the fragments which is, according to us, often improperly termed as covalence.

Polarised IR and Raman spectra of the gamma-glycine single crystal.

Complete (full) set of the polarised IR and Raman spectra for the gamma-glycine single crystal at room temperature are presented. The polarised IR spectra were measured by the specular reflection method and the spectra of the imaginary parts of the refractive indices were computed by Kramers-Kronig transformation. The polarised properties of the bands are discussed with respect to the normal coordinate analysis (literature data) and diffraction crystal data (oriented gas model approximation). A very good agreement between the polarised properties of the bands and simple models of vibrations are observed for the stretching vibrations of the CH2 and COO- group. It is not the case for most of the deformation vibrations of the carboxylic group and of the skeleton. The polarization properties of the stretching vibrations of the NH3+ group are determined by their hydrogen bondings.

Chronic liver and renal diseases differently affect structure of human serum albumin.

Human serum albumin (HSA) binding with endogenous metabolites and drugs is substantially decreased in chronic renal and liver diseases. To test the hypothesis that the decreased binding ability is caused by conformational changes of the protein, we analyzed infrared and Raman spectra of HSA isolated from healthy donors and patients with chronic uremia and liver cirrhosis. Uremia did not affect the secondary structure of HSA but modified the environment of its Asp/Glu residues. Liver cirrhosis increased the amount of extended and beta-structures, modified the environment of Asp/Glu and Tyr side chains, and changed the configuration of disulfide bridges in albumin molecules. The conformational changes of "cirrhotic" albumin were not caused by reversibly bound ligands and resembled a partial unfolding of the protein induced by adsorption on the charcoal surface. The dramatic structural alterations of HSA in liver cirrhosis may be caused by its oxidative modification and might underlie the decreased binding ability and changed body distribution of albumin.