Ring Torsion Angles Research Articles

Conformational differences and steric energies for compounds containing α- d-glucopyranose chairs having a range of 0–4-0–1 distances

Conformations corresponding to minimal energies are predicted with molecular mechanics for a series of compounds containing α- d-glucopyranose rings. These model rings, in the 4 C 1 conformation, were constrained to have O-4-O-1 distances ranging from 360 to 500 pm. The predicted conformation of lowest energy has an O-4-O-1 distance of 426 pm, close to the midpoint of the observed 400–460-pm range. The predicted monomers with O-4-O-1 distances of 400 and 460 pm have energies ∼2.51 kJ.mol −1 (∼0.6 kcal.mol −1) above the minimum. Systematic relationships of valence and torsion angles to the O-4-O-1 distance were examined with these molecular models, and the predicted relationships were compared to changes observed by single-crystal diffraction-studies. All of the ring torsion-angles, except C-1-C-2-C-3-C-4, several ring-valence angles, and the virtual angles involving O-1, C-1, C-4, and O-4, showed systematic changes with change in O-4-O-1 distance. Discrepancies between the observed and predicted rings include the values for the virtual angle C-1-C-4-O-4, values for the C-1-C-4 distance (10 pm) and its rate of change, and values for CO bond-lengths.

Description of ring puckering of furanose: An analytical approach

An analytical approach for the description of the ring puckerings from the endocyclic ring torsion angles of a five-membered saturated ring is given. This description is independent of any reference conformation. For the description, a revised notation for the endocyclic ring torsion angles has been suggested. The application of this method to the furanose ring is described in detail.

The application of molecular mechanics to the structures of carbohydrates

AbstractA study is reported of the accuracy with which the geometries of pyranose and methyl pyranoside molecules are predicted by molecular mechanics. Calculations of the conformational energies of the model compounds dihydroxymethane, methoxymethanol, and dimethoxymethane, made with the program MMI, produced results that compare well with previous ab initio molecular orbital calculations. This indicates that MMI gives a satisfactory account of the energetic and conformational aspects of the anomeric effect, a conclusion further supported by calculations on 2‐methoxytetrahydropyran. The prediction of the observed preferred conformations of the primary alcohol group in aldohexopyranoses appears to be less satisfactory. MMI‐CARB, a version of MMI with changes in some of the equilibrium CO bond lengths of the program, has been used to calculate the geometries of 13 pyranose and methyl pyranoside molecules, the crystal structures of which have been studied by neutron diffraction. When the CCOH torsion angles are constrained to approximately the values observed in the crystal structures, good agreement is obtained between the theoretical and experimental molecular geometries. The rms deviation for CC and CO bonds, excluding those significantly affected by thermal motion in the crystal structure determinations, is 0.005 Å. Corresponding figures for the valence angles that do not involve hydrogen atoms and for the ring torsion angles are 1.2° and 2.0°, respectively. The Cremer and Pople puckering parameters for the pyranose rings are reproduced within 0.026 Å in Q and 5.4° in θ.

Conformational studies. Part 13.1H N.m.r. and X-ray analyses of 2β-bromo-3α-hydroxy-5α-pregnane-11,20-dione, 3α-hydroxy-2β-methoxy-5α-pregnane-11,20-dione, and 3α-hydroxy-2α-methyl-5α-pregnane-11,20-dione

To investigate the potential relationship between structure and anaesthetic activity, the title steroids have been analysed by 1H n.m.r. spectroscopy, and by X-ray crystallography. The three compounds crystallise in the monoclinic space group P21 with two molecules per unit cell. Crystals of the 2β-bromo-derivative (2) have a= 10.288(4), b= 7.480(5), c= 13.646(4)A, β= 107.78(2)°. The structure was solved by the heavy-atom method and refined by full-matrix least-squares calculations: R= 0.083 for 1 428 reflections. The 2β-methoxy-derivative (3) has a= 10.814(3), b= 7.207(2), c= 13.963(3)A, β= 106.73(1)°. Structure solution was by direct methods and refinement as for (2) lowered R= 0.052 for 1 505 reflections. Crystals of the 2α-methyl derivative (4) are isomorphous with those of (2) with a= 10.183(8), b= 7.552(7), c= 13.772(9)A, β= 106.73(4)°; refinement by full-matrix least-squares calculations lowered R to 0.072 for 698 reflections.The torsion angles in ring A of (2) involving atom C(2) are smaller than standard values because of a slight flattening of the ring. In (3) this flattening is marginally less marked whereas in (4) the ring A conformation is close to a ‘normal’ chair. The 1H n.m.r. (solution) data are compatible with these observations.

Flexibility of the pyranose ring in α‐ and β‐D‐glucoses

AbstractConformational energies of α‐ and β‐D‐glucopyranoses were computed by varying all the ring bond angles and torsional angles using semiempirical potential functions. Solvent accessibility calculations were also performed to obtain a measure of solvent interaction.The results indicate that the 4C1 (D) chair is the most favored conformation, both by potential energy and solvent accessibility criteria. The 4C1 (D) chair conformation is also found to be somewhat flexible, being able to accommodate variations up to 10° in the ring torsional angles without appreciable change in energy. Observed solid‐state conformations of these sugars and their derivatives lie in the minimum‐energy region, suggesting that the substituents and crystal field forces play a minor role in influencing the pyranose ring conformation. Theory also predicts the variations in the ring torsional angles, i.e., CCCC < CCCO < CCOC, in agreement with the experimental results. The boat and twist‐boat conformations are found to be at least 5 kcal mol−1 higher in energy compared to the 4C1 (D) chair, suggesting that these forms are unlikely to be present in a polysaccharide chain. The 1C4 (D) chair has energy intermediate between that of the 4C1 (D) chair and that of the twist‐boat conformation. The calculated energy barrier between 4C1 (D) and 1C4 (D) conformations is high—about 11 kcal mol−1.

Studies on the reactions of (η 5cyclopentadienyl)dicarbonylcobalt with phenyl-1-naphthylacetylene and with phenyl-2-naphthylacetylene, and an X-ray crystallographic determination of one of the products: (η 5cyclopentadienyl)-[η 4-3,3-di-(1-naphthyl)-2,4diphenylcyclobutadiene]cobalt

The reactions of (η 5-C 5H 5)Co(CO) 2 with both phenyl-1-naphthylacetylene and phenyl-2-naphthylacetylene have been shown to produce all four possible η 5-cyclobutadiene-cobalt complexes and all six possible η 4-cyclopentadienone-cobalt derivatives. The structures of the η 4-cyclobutadiene-cobalt complexes have been assigned on the basis of proton NMR and mass spectral studies, and unequivocally established by means of an X-ray diffraction investigation for one of the isomers as (η 5-cyclopentadienyl)[η 4-1,3-di(1-naphthyl)-2,4-diphenylcyclobutadiene]cobalt. This compound is triclinic, a = 10.88(2), b = 15.710(6), c = 8.728(4) Å, α = 95.09(4)°, β = 101.94(2)°, γ = 86.93(3)°. The space group is P 1 with Z = 2. The structure was solved by Patterson and Fourier methods and refined by full-matrix least squares methods (4128 reflections above 3σ) to a final R = 0.036. Bond distances and angles are normal but the cyclobutadiene ring is not quite planar. One of the atoms is 0.047 Å out of the plane of the other three apparently to relieve steric stress. The two phenyl rings are almost coplanar with the cyclobutadiene ring (torsion angles 3.9 and 20.4°) while the naphthyl rings are almost perpendicular to it (torsion angles 63.8, 64°).

Conformational analysis of tertiobutyl-4, d-4, thiacyclohexane:by proton nmr spectroscopy

Abstract Proton NMR studies of tertiobutyl-4, D-4, thiacyclohexane, which has a fixed chair conformation, have allowed a direct determination of the various coupling constants. A discussion of the values of the ring torsion angles calculated from the different gauche constants 3 J shows that the most probable value is given by J Hαe ,H βa for which there is no hydrogen atom antiperiplanar to the S atom.

The Crystal and Molecular Structure of Daphnetin 8-β-d-Glucopyranoside Dihydrate Isolated from Daphne odora

Abstract The crystal structure of daphnetin 8-β-d-glucopyranoside dihydrate has been determined by the X-ray method. The crystal is monoclinic, space group P21, with the lattice parameters a=7.773(1), b=22.478(5), c=4.715(1) Å, β=99.77(2)°, and Z=2. The structure was determined by the direct method and refined by least-squares to a final R of 0.041 for 2690 observed reflexions. The daphnetin moiety is approximately planar, and little effect from glucosylation is observed in the bond lengths and angles, compared with daphnetin itself. The glucopyranoside is in C1 chair conformation, with the ring torsion angles ranging from 48 to 66°. The anomeric C–O bond is twisted by 78.2° against the coumarin plane, which is the largest value in aromatic glycopyranosides so far reported and which is concomitant with a small valence angle, 114.4°, at the oxygen atom linking the coumarin and the glucose group.

1H n.m.r. study and conformation of 3,3‐dimethyl‐3‐sila‐1‐heterocyclohexanes and derivatives (heteroatom SiCl2, SiMe2, O, NMe, S, Se, Te)

AbstractIt is found that the basic form of the 3,3‐dimethyl‐3‐sila‐1‐heterocyclohexane family (heteroatom X = O, NMe, S, Se, Te, SiMe2, SiCl2) is the chair, having ring torsion angles in the aliphatic region tending to be somewhat more puckered (up to 7°) than in cyclohexane, except next to Si when the other heteroatom is relatively small. The 5‐tertiarybutyl‐, 6‐methyl‐ and 2‐phenyl derivatives are all anancomeric, except for the latter two derivatives when X = NMe. A 5‐tertiarybutyl group causes an additional deformation, e.g. an increased puckering of the aliphatic C‐4C‐5C‐6 region (buttressing effect). Other 1H n.m.r. features are discussed in detail, and the behaviour of the 3‐sila‐1‐heterocyclohexanes is compared with other 1,3‐diheterocyclohexanes.

Model compounds for simple saturated 7–9 membered rings: the X-ray crystal structure of hexa-, hepta-, and octa-methyleneammonium salts

The structures of the title compounds have been determined by X-ray crystallography, and ring torsional angles are given for all three compounds; the conformation of the seven-membered ring is a slightly ‘twisted chair’ and that of the eight-membered ring a ‘boat chair,’ while the nine-membered ring does not possess any obvious symmetry.

The effects of changes in ring geometry on computer models of amylose

A review of single-crystal studies shows that α- D-glucopyranose, residues of which constitute the monomeric units of amylose, is flexible within the constraints of the Cl conformation, and that the internal differences among the rings are most clearly indicated by the variety in ring-torsion angles (or conformation angles). An index of the cumulative effect of changes in these angles is provided by the length of the virtual bond, O-1—O-4, and classification of residue geometries by virtual bond-length permits a systematic selection of suitable residues for the construction of models of amylose. By the use of D-glucopyranose residues having different geometries, it is possible to build models of ( a) V-amylose helices having 6, 7, and 8 residues per turn, ( b) single and double helical B-amyloses, and ( c) KBr-amylose, all of which satisfy reasonable stereochemical criteria. Because no single residue can satisfactorily model all of the well known polymorphs of amylose, it is suggested that structural determinations that utilize a rigid residue approximation should make use of the full range of known, residue geometries.

Intramolecular energy functions for conformation and vibrational analysis

Calculations of helical conformations of macromolecules depend on the intramolecular energy functions used. The reliability of such energy functions can be checked by applying them to medium size molecules for the calculation of the stable conformations and their energies, as well as of the vibrations around these conformations. In this way a comparison of theoretical prediction with a wealth of experimental data derived from X-ray and electron diffraction, thermodynamic measurements and vibrational spectra is made possible. Conversely, such comparison may be used as a powerful tool to check and improve upon the energy functions and the numerical values of their parameters. The homologous series of ring molecules like cycloalkanes have been shown to be of particular interest since the condition of ring closure forces bond angles and torsional angles out of their equilibrium values. This helps in checking the dependence of the energy functions on these variables. Some of the results of these calculations are discussed.