|
| ||
|
|
||
Bonding Effects (bonding + effects)
Selected AbstractsAnisotropic and hydrogen bonding effects in phenylglyoxamides and mandelamides: theoretical and NMR conformational evaluationMAGNETIC RESONANCE IN CHEMISTRY, Issue 5 2008Biank T. Gonçalves Abstract Interesting anisotropic effects were observed for phenylglyoxamides and their respective mandelamides. Such effects were observed in experimental 1H and 13C NMR (in CDCl3, CD3OD, and DMSO- d6 solvents) and in some cases with good correlation to theoretical 1H and 13C NMR DFT,GIAO (B3LYP/6-311 + + G**//B3LYP/6-31G*) calculations. A systematic conformational analysis of these compounds was performed in a two-step methodology, using PM3 and DFT (B3LYP/6-31G*) calculations; with good accomplishment and computational time economy. It was observed that intramolecular hydrogen bonding plays a significant role in the conformation of such compounds. Finally, a geminal nonequivalence of an NCH2 moiety, in one of the alkyl side chain (R1 = R2), was found for the tertiary mandelamides studied. Copyright © 2008 John Wiley & Sons, Ltd. [source] Correlation between the reactivity and spectroscopic properties of N -substituted secondary thioamides.MAGNETIC RESONANCE IN CHEMISTRY, Issue 3 2003New intramolecular N···H+···N binding approach, proton complexes based on thioamide ligation Abstract On the basis of a comparison of chemical shifts and wavenumbers of several secondary thioamides and amides having monocationic substituents attached to thiocarbamoyl or carbamoyl groups by a polymethylene chain, new intramolecular unconventional N···H+···N hydrogen bonding effects were discovered. It is argued that the CH2,N rotation is hindered and two +H···NHCH3 non-equivalent protons occur in a proton spectrum of hydrochloride 1a (at 10.68 and 2.77 ppm, respectively) instead of two +NH2CH3 protons. Presumably, the above steric factors inhibit the acidic hydrolysis of 1a (stabilized by strong intramolecular N···H+···N hydrogen bonds) to an amide and prevent intramolecular cyclization of 2a (stabilized by strong intramolecular neutral,neutral N···HN hydrogen bonds) to a cyclic amidine. Postulation of additional dihydrogen bond formation is helpful in understanding the spectroscopic differences of 4 and 5. The above new bonding is also compared with intramolecular N···H,N+ hydrogen bonds in primary amine salts 7 and 8. In contrast to 3, a cooperative hydrogen bonded system is observed in 9 and 10. The weak hydrogen bonds in 7,10 facilitate the hydrolysis and cyclization reactions of secondary thioamides. The spectroscopic data for secondary (thio)amides are especially useful for characterizing the electronic situation at the (thio)carbamoyl nitrogen atoms and they are perfectly correlated with the reactivity. Examples of chelation of protons by thioamides (11 and 12), which contain strongly electron-donating pyrimidine groups, are presented to show the contribution of dihydrogen bonding in the protonation reaction similar to 1 and 4. Copyright © 2003 John Wiley & Sons, Ltd. [source] Structure correlation study of four-coordinate copper(I) and (II) complexesACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2000Paul R. Raithby The geometries of four-coordinate CuI and CuII complexes in the Cambridge Structural Database (CSD) have been analysed systematically and compared using symmetry-deformation coordinates and principal component analysis. The observed stereochemistries have been rationalized in terms of the d -electron configurations, interligand repulsion and ,-bonding effects. The results confirm that the majority of four-coordinate copper(I) complexes in the CSD adopt tetrahedral geometries and deviations from tetrahedral symmetry are caused by the presence of chelating ligands or by the incorporation of copper centres into dimeric or polymeric structures. Four-coordinate copper(II) complexes generally adopt geometries close to square planar; this is particularly evident for bis(chelate) complexes where ,-bonding is important. Distortions towards tetrahedral geometries are attributable to steric interactions of bulky substituents in the bidentate ligands. [source] Polarizable atomic multipole X-ray refinement: application to peptide crystalsACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2009Michael J. Schnieders Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussian multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA,IAS model lowered Rfree by 20,40% relative to the original spherically symmetric scattering model. [source] | ||||||||||