Completely geometrically optimized DFT/ONIOM triple-helical collagen-like structures containing the ProProGly, ProProAla, ProProDAla, and ProProDSer triads

We report completely optimized ONIOM DFT/AM1 molecular orbital calculations on several collagen-like triple helices based upon the repeating triad, ProProGly. The requirement of Gly as every third amino acid in collagen can be attributed to its enantiomorphic nature, as it behaves as a Damino acid in collagen. We, therefore, explored related collagen-like triple helices with one of the central Gly's mutated to either L or DAla; l-Ala appreciably destabilizes, while d-Ala slightly stabilizes the triple helical structure. Mutation of the same Gly to DSer, which is simply DAla with an OH in place of one of the methyl H's, induces a much greater stabilization due to an additional H-bond formed between this OH and a C=O on an adjacent peptide strand. Energies are presented for the triple helices and their component strands (both optimized and distorted to their triple helical geometries) relative to the component amino acids. The variation of relative energies with the chosen reference is delineated.     

γ-Keto Esters and γ-Butyrolactones From the Reaction of Dialkoxydihydrofurans With Trimethylsilyl Iodide

Dimethoxydihydrofurans are converted into γ-keto esters and γ-butyrolactones by a new procedure using an equimolar quantity and an excess of trimethylsilyl iodide, respectively.     

Strukturaufkl?rung organischer Verbindungen nach chemischen und physikalischen Methoden

Ohne Zusammenfassung     

Comparison of fully optimized alpha- and 3(10)-helices with extended beta-strands. An ONIOM density functional theory study

We compare the structures and energies of beta-strands, alpha-helices, and 3(10)-helices for capped polyalanines, acetyl(ala)(N)()NH(2), for values of N from 2 to 18, using completely optimized mixed DFT/AM1 calculations. Non-pairwise additive cooperativity is manifest from the variation of the relative energies, helical strain, dipole moments, and H-bond lengths of both types of helices, but especially for the alpha-helices. While the gas-phase 3(10)-helices are more stable for small polyalanines, largely due to the additional H-bond, the alpha-helices become relatively more stable as the polyalanines increase in size.     

Shortcut to a Fermi-degenerate gas of molecules via cooperative association

We theoretically examine the creation of a Fermi-degenerate gas of molecules by considering a photoassociation or Feshbach resonance applied to a degenerate Bose-Fermi mixture of atoms. This problem raises interest because, unlike bosons, fermions in general do not behave cooperatively, so that the collective conversion of a degenerate gas atoms into a macroscopic number of diatomic molecules is not to be expected. Nevertheless, we find that the coupled Fermi system displays collective Rabi-like oscillations and a rapid adiabatic passage between atoms and molecules, thereby mimicking Bose-Einstein statistics. Cooperative association of a degenerate mixture of Bose and Fermi gases could therefore serve as a shortcut to a degenerate gas of Fermi molecules.     

An o-iminothioquinone: its cycloaddition to produce an indologlycoside and its self-dimerization to form a dithio-diazocycloctane, the structure assignment of which is based on the DFT prediction of its IR spectrum

An unusual heterodiene, an indolothiono quinone, undergoes cycloaddition with a glycal to form an indole-N-glycoside. A novel dimer of the indolothionoquinone is assigned its structure on the basis of a match between its predicted and observed IR spectrum.     

Attempts to prepare aromatic O-acyl-hydroxylamines—I : Dehydrohalogenation of 1-bromo-4-acetoxyimino-1,2,3,4-tetrahydrophenanthrene by tetramethylammonium dimethylphosphate

The dehydrohalogenation of 1-bromo-4-acetoxyimino-1,2,3,4-tetrahydrophenanthrene by tetramethylammonium dimethylphosphate gave a mixture of products. Ten of these were identified and together account for 70% of the total yield. The proposed reaction mechanism implicates the corresponding O-acetyl-hydroxylamine 15 as an intermediate. Attempts to prepare O-esters or O-ethers of aromatic hydroxylamines by dehydrogenation, with quinones, of the corresponding oximino-derivatives of oxo-1,2,3,4-tetrahydro-naphthalene and oxo-1,2,3,4-tetrahydro-phenanthrene were without success.     

Amide I vibrational frequencies of alpha-helical peptides based upon ONIOM and density functional theory (DFT) studies

We present ONIOM and pure DFT calculations on infrared spectra of alpha-helical-capped polyalanines. The calculations used two-layer ONIOM (B3LYP/D95**:AM1) calculations of the amide I vibrational frequencies for acetyl(ala)NNH2 (N=8, 10, 12-18) whose structures have been previously completely optimized by the same method. These are the first such calculations based upon structures of alpha-helical peptides that are completely optimized using DFT or molecular orbital methods. As the peptide becomes longer, the amide I band becomes both more intense and more red shifted. However, the individual absorptions that contribute most to the band vary between three patterns: one very intense absorption, two absorptions of similar intensity, and two strong absorptions where one is roughly twice as intense as the other. This pattern appears to be related to the relative number of H bonds in the individual H-bonding chains; however, there is one exception. Using 14C=O's to selectively decouple specific C=O's, we found that the couplings between the C=O's within each of the three individual H-bonding chains within the helices follow the same pattern previously reported for planar H-bonding chains of formamides. The coupling between the H-bonding chains appears to involve through-space coupling between the H-bonding chains. While decoupling individual C=O's always decreases the intensity of the amide I band, it leads to complex changes in the individual amide I absorptions that contribute to the band. Depending upon the position of the 14C=O, the amide I band can either red or blue shift. Moreover, the individual absorptions that contribute to the band can increase or decrease in intensity as well as shift. The patterns of the individual absorptions (mentioned above) also change. Using the C=O stretch of acetamide as a reference, we calculate the red shifts for the most intense absorptions to be much greater than predicted by the transition dipole method.     

Direct calculation of trans-hydrogen-bond 13C-15N 3-bond J-couplings in entire polyalanine alpha-helices. A density functional theory study

We present the first trans-H-bond 13C-15N 3-bond J couplings calculated from entire neutral and protonated alpha-helical polyalanines. The neutral helices considered are those of the capped peptides, acetyl(Ala)NNH2, where N = 8, 16, 17, and 18, while the protonated peptides are the uncapped (Ala)17 protonated at three different positions. The calculated J values correlate well with O...H distances and somewhat less well with N...O distances, particularly if the terminal H-bonds are eliminated from the correlation. The J values calculated using the entire helix are about 6% lower in magnitude than those recently reported for H-bonding chains whose geometries were extracted from the same helices. Aqueous solvation favors protonation of the alpha-helix on the terminal COOH. Experimental measurements of the trans-H-bond 13C-15N 3-bond J couplings in acidic solution should be interpreted with this context.