Showing papers on "Dihedral angle published in 1973"

Disulfide bond dihedral angles from Raman spectroscopy.

Abstract: Raman spectra of several compounds containing the CS-SC moiety were obtained (in the solid phase) from 450-800 cm(-1) to investigate the S-S and C-S stretching behavior. The S-S stretching frequency varied linearly with the CS-SC dihedral angle (obtained from either x-ray or neutron diffraction or ultraviolet absorption) for compounds whose CC-SS dihedral angles were not very different. The ratio of the intensities of the S-S and C-S stretching bands exhibited no recognizable correlation with either the CS-SC dihedral angle or the CSS bond angle, probably because this ratio is sensitive to the crystalline environment. The linear dependence of the S-S stretching frequency on dihedral angle leads to a dihedral angle for the plant hormone, malformin A, that is in excellent agreement with that estimated from the longest wavelength CS-SC ultraviolet absorption band.

A dihedral angle-vicinal proton coupling constant correlation for the α–β bond of amino acid residues

Abstract: A coupling constant-dihedral angle correlation for the HCαCβH system of amino acid residues in peptides has been derived from a set of model compounds covering the full range of dihedral angles. The expression obtained, J = 11.0 cos2 θ −1.4 cos θ + 1.6 sin2θ, is close to those already used in pmr studies of peptide conformation, and provides a firmer foundation for them. A factor limiting the precision of this and other “Karplus relations” is illustrated.

Dihedral angle of biphenyl in solution and the molecular force field

Abstract: The dihedral angle between the rings of biphenyl is determined to be 32 ± 2° in the molten and solution states. Observed vibrational frequency shifts on going from the planar configuration held in the crystal to the non-planar solution state are compared with computed frequency shifts. To improve the accuracy in the computed frequencies the force constants were refined. The values of the force constants associated with the inter-ring bond are discussed.

Molecular orbital calculations on the conformation of nucleic acids and their constituents

Abstract: The conformational properties of the furanose ring of purine- and pyrimidine-β-nucleosides and-nucleotides are studied quantum-mechanically with the help of the PCILO method, using the pseudorotational concept. The computations point to the existence of two stable conformational zones centered around the C(3′)-endo and C(2′)-endo conformations which in the isolated furanose ring are separated by barriers of the order of 4 kcal/mole. In nucleosides one of the barriers (the one running through the O(1′)-exo-C(2′)-exo path) becomes very high. A detailed study is made of the relation between the phase angle of pseudorotation, P, and the torsion angle about the glycosyl bond, χ CN. A very satisfactory agreement with the available experimental data is observed.

Investigations of Substituent Effects by Nuclear Magnetic Resonance Spectroscopy and All-valence Electron Molecular Orbital Calculations. II. 4-Substituted α-Methylstyrenes and α-t-Butylstyrenes

Abstract: Substituent-induced 1H chemical shifts (S.C.S.) for 19 4-substituted α-methyl- and α-t-butylstyrenes have been determined at infinite dilution in C6H12 and 13C S.C.S. have been determined for 0.4 M solutions in CCl4. S.C.S. are correlated with field and resonance substituent parameters and compared with charge densities determined by CNDO/2 MO calculations. The variation of S.C.S. with the dihedral angle, ρ, between phenyl and vinyl groups and the overall pattern of S.C.S. can be largely accounted for by a model of substituent effects based on field, resonance, and π polarization effects, with conjugative interactions varying as cos2ρ. Both 13C chemical shifts and charge densities indicate that the π polarization effect consists of two components: (1) a through-space polarization of the vinyl system by the polar C—X bond and (2) polarization of the entire conjugated styrene π electron system. However, significant deviations are noted for some of the 1H S.C.S. correlations. The CNDO/2 calculations indicate...

Some aspects of NMR techniques for the conformational analysis of peptides

Abstract: An outline is given of some new NMR spectroscopic approaches to the spatial structure of peptides in solution which have been recently suggested and tested in the Shemyakin Institute for Chemistry of Natural Products. The previously derived angular dependence of the peptide vicinal 3'NHCH coupling constant has been refined on the basis of the latest experimental data. It has been found that ion—dipole interaction of the type C==-O M +(where M is an alkali metal ion) leads to a low field shift of the '3C signal of the carbonyl group. This effect permits determination of the number and location of the ligand groups which form the internal cavity of peptide and depsipeptide complexones. The effect of 'shift reagents' on the NMR spectra sheds certain light on the spatial structure of peptides in solution, and, in particular, gives considerable information on the configuration of the amide bond and on the rotational states of the C—-C" bond. The INDOR and signals on combination frequency have been used for detection of 'hidden' signals (their multiplicity, chemical shift and splitting) and on the assignment of the NH signals in the proton NMR spectra of peptides. High resolution NMR spectroscopy is becoming the most powerful means for the study of the spatial structure of peptides in solution. The progress in this field has required the development of new spectroscopic approaches. The subject matter of this paper is to outline some of those which have been suggested and tested recently in the Shemyakin Institute for Chemistry of Natural Products. I. THE ANGULAR DEPENDENCE OF THE PEPTIDE VICINAL NH-C8H COUPLING CONSTANT With the accumulation of more experimental data it has now become possible to refine the earlier proposed"2 dependence of the 3NflCH constant on the dihedral angle U between the H—N---C' and N—C-----H planes.

Crystal and molecular structure of [NN′-ethylenebis(salicylideneiminato)](methanol)dioxouranium

Abstract: The crystal and molecular structure of the title compound has been determined by three-dimensional X-ray methods. Crystals are monoclinic, space group P21/n with cell dimensions: a= 18·695(15), b= 9·012(9), c= 10·652(10)A, γ= 97·52°(5), and Z= 4. The structure was solved by the heavy-atom method from 2239 reflections collected by counter, and refined by least-squares methods to R 0·055.Four atoms of the Schiff base and the oxygen of the methanol are co-ordinated in a plane, forming a slightly irregular pentagon, with the uranyl group perpendicular to this plane. Equatorial U–O(3) and U–O(4) distances are 2·25(2) and 2·33(3)A, while U–O(MeOH) is 2·45(3)A U–N(1) and U–N(2) are 2·57(2) and 2·54(5)A. The only short intermolecular distance, O(4)⋯ O(5) of two neighbouring molecules 2·58A, suggests the presence of a hydrogen bond. The N(1)–CH2–CH2–N(2) group is in a near-gauche conformation (torsion angle 51·8°) and the complex exhibits an overall ‘stepped’ geometry. The stereochemistry and chemical properties of 3dtransition-metal compounds of such ligands are compared.

Retrodirective reflector visible over wide range of observation angles

Abstract: The reflector is constructed of transparent material and has a plurality of reflector elements at the rear and a light-receiving face at the front. Each reflector element has three faces intersecting at three edges, three dihedral angles being respectively defined by the intersection of adjacent faces. Two of the dihedral angles of all of the reflector elements are substantially 90*. The third dihedral angle of at least some of the reflector elements is substantially greater than the angle of the other two dihedral angles, so that light reflected by the reflector is diverged into an elongated pattern.

Structure of guanosine‐3′,5′‐cytidine monophosphate. I. Semi‐empirical potential energy calculations and model‐building

Abstract: synopsis The conformation and packing scheme for guanosine-3’,5’-cytidine monophosphate, GpC, were computed by minimizing the classical potential energy. The lowest energy conformation of the isolated molecule had dihedral angles in the range of helical RNA’s, and the sugar pucker was C3‘ endo. This was used as the starting conformation in a packing search over orientation space, the dihedral angles being flexible in this step also. The packing search was restricted by constraints from our x-ray data, namely, (1) the dimensions of the monoclinic unit cell and its pseudo-C2 symmetry (the real space group is P21), (2) t,he location of the phosphorous atom, and (3) the orientation of the bases. In addition, a geometric function was devised to impose Watson-Crick base pairing. Thus, a trial structure could be sought without explicit inclusion of intermolecular potentials. An interactive computer graphics system was used for visualizing the calculated structures. The packing searches yielded two lowest energy schemes in which the molecules had the same conformation (similar to double-helical RNA) but different orientations within the unit cell. One of these was refined by standard x-ray methods to a discrepancy index of 14.4% in the C2 pseudocell. This served as the starting structure for the subsequent refinement in the real P21 cell.5

Conformational studies on alamethicin.

Abstract: A conformational analysis has been carried out for the cyclic peptide antibiotic alamethicin. Unlikely structures were first eliminated by constructing van der Waals' energy maps for near-neighbor contacts and using these maps to generate forty complete alamethicin structures free of steric overlaps. The energies of the forty conformations were minimized; optimizing all dihedral angles first in sets and then simultaneously, to give a family of five low-energy structures. In the conformation of lowest energy three of the seven α-amino isobutyric acid residues occur in a six-residue α-helix and three at the two chain reversals. Judged by the change in conformational energy as a function of the change in dihedral angle, the flexibility of the chain is determined by both the type of peptide unit and its position in the molecule. The model has features consistent with reported circular dichorism and surface balance measurements and has two polar centers separated by a lipophilic region. It does not contain the large central pore required by some theories for the action of alamethicin on cell membrances. It therefore probably acts by altering membrance structres rather than by shuttling ions through a pore in the membrance.

The conformational problem of biphenyl in solution as investigated by the liquid crystal nuclear magnetic resonance spectrum of 3,3′,5,5′-tetrachlorobiphenyl

Abstract: The interpretation of the 1H n.m.r. spectrum of a meta-substituted biphenyl (3,3′,5,5′-tetrachlorobiphenyl) dissolved in the nematic phase of a liquid crystalline solvent showed unambiguously that in solution it has neither a planar structure nor free rotation but exists in a twisted conformation. A fairly accurate measurement of the twisting angle could also be obtained (34° 20′), the experimental error being similar to that reported in the electron diffraction studies of the vapour phase. The effects of the substituents and of the nematic solvent upon the conformation are discussed and the conclusion is reached that they are rather small and acting in opposite directions. Biphenyl is thus expected to have a similar dihedral angle in solution.

The surface energy anisotropy of 3% silicon iron

Abstract: The surface energy anisotropy of a high-purity 3% silicon iron alloy has been determined at various temperatures between 1000° and 1400°C by measuring the variation in grain boundary dihedral angle in those wires exhibiting a bamboo texture The μ-plots have been obtained by numerical analysis of these data and have been normalized to the absolute values of the (110) surface energy obtained under identical experimental conditions using a zero creep technique The present results are explained in terms of a silicon/oxygen complex adsorbate on the (111) and (100) planes at the lower temperatures which dissociates between 1300° and 1400°C, giving rise to a decrease in the surface energies of the (111) and (100) planes at 1400°C

Conformational energy and circular dichroism computed for cyclo-(pro-gly)3.

Abstract: An analytic cyclization procedure has allowed the complete specification of c-(Pro-Gly)3 conformation by three dihedral angles. Utilizing this simplification, the intramolecular potential energy of c-(Pro-Gly)3 has been computed over all of conformational space. Conformers with all peptide bonds trans have the lowest total potential energy. Circular dichroism spectra calculated for the low-energy regions provide the basis for the interpretation of experimental CD spectra.

Proposed Tertiary Structure for the Hypothalamic Thyrotropin-Releasing Factor

Abstract: Semiempirical energy calculations were performed to determine the conformation of the thyrotropin-releasing factor, L-pyroglutamyl-L-histidyl-L-prolineamide. Our results strongly suggest a “hairpin turn” conformation stabilized by two specific hydrogen bonds. Experimental support for this structure was obtained from proton magnetic resonance by use of chemical shifts and coupling constants with the implied dihedral angles.

Electron redistribution in disulfide bonds under torsion

Abstract: The origin of the conformational preference of acyclic disulfides is elucidated with population analyses and electron density maps of extended Huckel wave functions for HSSH and H3CSSCH3. Overlap population between the sulfurs is greatest when the dihedral angle about the S-S bond is near 90° because the negative contributions from the repulsive interactions of the lone-pair electrons are minimized in this conformation. Electron density maps are introduced to illustrate the rearrangement of the valence electrons in HSSH when the molecule is formed from the isolated atoms and the redistribution which occurs when the molecule is twisted about the S-S bond. A “C”-shaped distribution is found for the lone-pair clouds around each sulfur. The spacing between these clouds and the transfer of density away from the sulfurs toward the hydrogens are enhanced when the dihedral angle is near 90°.

The conformational analysis of saturated heterocycles. Part L. Computer program for strain energy minimisation in six-membered rings and recalculation of conformational equilibria

Abstract: Computer programs are developed which allow (a) the calculation of ring geometry including vector angles for dipole-moment components and (b) the energy minimisation of bond and torsion angle strain.Conformational equilibria are recalculated for 1-alkylpiperidines, 1,3-dialkylhexahydropyrimidines, 3-alkyltetrahydro-1,3-oxazines, 5-alkyldihydro-1,3,5-dithiazines, and 1,3,5-trialkylhexahydro-1,3,5-triazines. The previous conclusions are little, for the most part insignificantly, affected.