Conformational isomerism

About: Conformational isomerism is a research topic. Over the lifetime, 11563 publications have been published within this topic receiving 199312 citations.

Combined FTIR Matrix Isolation and Ab Initio Studies of Pyruvic Acid: Proof for Existence of the Second Conformer

Abstract: The molecular structure of pyruvic acid was investigated by matrix isolation FTIR spectroscopy, density functional theory (DFT), and ab initio calculations performed at the RHF, MP2, MP4(SDQ), and CCSD(T) levels of theory with the aug-cc-pVDZ basis set. In these calculations, the geometries of the three lowest energy conformers of pyruvic acid were fully optimized at the DFT/B3LYP/aug-cc-pVDZ and MP2/aug-cc-pVDZ levels. Additionally, the relative energies of the conformers were calculated at the MP4, CCSD, and CCSD(T) levels. Harmonic frequencies and IR intensities were then calculated for these three conformers and were used to account for the zero point vibrational energy corrections and to assist the assignment of the observed bands to the different forms. We found that two conformers are present in the Ar matrix, and both forms exhibit a planar framework with the carbonyl bonds in a trans arrangement but differ in the orientation of the hydroxyl hydrogen. By varying the temperature of the pyruvic acid...

Spectra and structure of silicon‐containing compounds. XXXVI—Raman and infrared spectra, conformational stability, ab initio calculations and vibrational assignment of ethyldibromosilane

Abstract: The Raman spectrum of liquid ethyldibromosilane, CH3CH2SiHBr2, was recorded at various temperatures between 298 and 218 K, and the spectrum of the crystal was obtained at 210 K from a sample sealed in a capillary. Additional spectra of the amorphous and annealed crystals, which were deposited on a copper finger cooled with boiling liquid nitrogen, were recorded. The infrared spectra were recorded of the vapor and amorphous and crystalline solid in the range 4000–50 cm−1 and mid-infrared spectra isolated at 4.8 K in argon and nitrogen matrices were also observed. These vibrational spectra show that two conformers, anti and gauche, are present in the vapor and in the liquid, but only the anti conformer remains in the crystalline solid. Three conformer pairs in the Raman spectrum of the liquid phase were used to obtain the enthalpy difference, which gave an average value of 128 ± 17 cm−1 (1.53 ± 0.2 kJ mol−1) with the anti form lower in energy. At ambient temperature it is estimated that there is 52 ± 2% of the gauche conformer present in the liquid. The optimized geometries, infrared and Raman intensities, and scaled vibrational wavenumbers for the anti and gauche conformers were obtained from ab initio MP2/6–31G(d) calculations with full electron correlation. The conformational energy difference was also obtained from ab initio MP2/6–311 + G(d,p) calculations which gave a predicted energy difference of 97 cm−1 with the anti form the conformer of lower energy. These spectroscopic and theoretical results are discussed and compared with the corresponding quantities for some similar molecules. Copyright © 2003 John Wiley & Sons, Ltd.

Intramolecular photochemical electron transfer. 2. Fluorescence studies of linked porphyrin-quinone compounds

Abstract: Systematic studies of absorption spectra and fluorescence spectra and lifetimes have been carried out on a series of meso-tetratolylporphyrins to which various molecular entities have been covalently attached via diamide linkages with the two amides being separated by n methylene groups (n=2, 3, or 4). The attached end groups include p-benzoquinone, hydroquinone, and dimethoxybenzene. These studies reveal the existence of at least two more or less distinct forms: a family of ''complexed'' conformers in which the end group is likely folded so as to interact with the porphyrin, and one or more ''extended'' conformers in which the porphyrin moiety is relatively unperturbed by the end group. The complexed conformers exhibit perturbations of spectra and diminished fluorescence lifetimes and quantum yields as compared with the extended conformer(s). Oxidation of the porphyrin-linked hydroquinone form to the quinone form does not significantly affect the absorption or fluorescence spectra but causes strong quenching of fluorescence and diminution of the fluorescence lifetimes. This quenching is interpreted primarily in terms of electron transfer from the lowest excited singlet state of the porphyrin to the quinone moiety. On the basis of the assumption that these shorter fluorescence lifetimes of the quinone relative to the hydroquinone are duemore » entirely to electron transfer, apparent electron-transfer rate constants k/sup et/ at room temperature range from <1 x 10/sup 8/ to <7 x 10/sup 9/ s-/sup 1/, depending on solvent and probably the specific geometry of the conformers. Quenching in both sets of conformers appears to be thermally activated and is strongly inhibited in frozen matrices. Parallel studies of porphyrin-quinone molecules with various methylene chains (n=2, 3, and 4) indicate that the geometry of the linkage is critical to the rate of electron transfer. A methylene chain with n = 3 appears to be optimum. 4 figures, 6 tables.« less

Computational study of bond dissociation enthalpies for substituted β-O-4 lignin model compounds.

Abstract: The biopolymer lignin is a potential source of valuable chemicals. Phenethyl phenyl ether (PPE) is representative of the dominant β-O-4 ether linkage. DFT is used to calculate the Boltzmann-weighted carbon-oxygen and carbon-carbon bond dissociation enthalpies (BDEs) of substituted PPE. These values are important for understanding lignin decomposition. Exclusion of all conformers that have distributions of less than 5% at 298 K impacts the BDE by less than 1 kcal mol(-1). We find that aliphatic hydroxyl/methylhydroxyl substituents introduce only small changes to the BDEs (0-3 kcal mol(-1)). Substitution on the phenyl ring at the ortho position substantially lowers the C-O BDE, except in combination with the hydroxyl/methylhydroxyl substituents, for which the effect of methoxy substitution is reduced by hydrogen bonding. Hydrogen bonding between the aliphatic substituents and the ether oxygen in the PPE derivatives has a significant influence on the BDE. CCSD(T)-calculated BDEs and hydrogen-bond strengths of ortho-substituted anisoles, when compared with M06-2X values, confirm that the latter method is sufficient to describe the molecules studied and provide an important benchmark for lignin model compounds.

The evaluation of type I and type II β-turn mixtures: Circular dichroism, NMR and molecular dynamics studies*

Abstract: Circular dichroism (CD) and 1H-(1H)NOE spectra were obtained for Piv-Pro-Ser-NHCH3 (1), [Piv-(CH3)3-C-CO], Boc-Pro-Ser-NHCH3 (2) and Boc-Val-Ser-NHCH3 (3), to determine the solution conformation of these beta-turn models. In the crystal, 1 and 3 adopt an ideal type I beta-turn, while 2 is characterized by a semifolded backbone geometry incorporating a cis Boc-Pro tert-amide bond. The predominance of a beta-turn conformation in solution was suggested for models 1-3 on the basis of 1H-(1H)NOE data. In a nonpolar solvent the prevailing trans rotamer form (> 80%) of 2 has a beta-turn conformation according to heteronuclear NOE measurement. Positive 1H-(1H)NOEs were detected between the H alpha(Pro)/NH(Ser), H alpha(Ser)/NH(Ser) and NH(NHCH3)/HN(Ser) protons in the trans Boc-Pro rotamer form of 2 at -20 degrees in CDCl3. Similar positive homonuclear NOE enhancements were also observed on the appropriate proton signals in other models, such as Boc-Val-Ser-NHCH3 (3), Boc-Val-D-Ser-NHCH3 (4) and Boc-Pro-D-Ser-NHCH3 (5), in various solvents. The 1H-(1H)NOE experiments carried out in CD3CN clearly showed that besides the type I (or III) beta-turn structure, one of the main conformations of models 1-5 is close to the type II beta-turn backbone geometry in a nonpolar solvent. Unexpectedly, the conformational mixture of models 1-3 were characterized by class C (helix-like) CD spectra, although class C spectra are generally only correlated with the type I beta-turn conformation. These acyclic models are the first carefully investigated examples of -L-L- triamide systems, containing a significant amount of a type II beta-turn, as well as the type I beta-turn and, however, yielding a class C circular dichroism spectra. The CD spectra recorded for 3 and 4 in acetonitrile were 'calibrated' using the 1H-(1H)NOE data. Such a "calibration", as well as the semi-quantitative CD and NMR comprehensive analyses, demonstrated that class C, class B, as well as class C' CD spectra may be obtained from the linear combination of the same two-component spectra, with different conformational weights. Therefore, it is suggested that the extraction of the conformational components of such models, simply on the basis of their CD spectra, must be made with caution.