Showing papers on "Dihedral angle published in 1980"

Empirical Correlations Between Conformational Parameters in β‐D‐Furanoside Fragments Derived from a Statistical Survey of Crystal Structures of Nucleic Acid Constituents Full Description of Nucleoside Molecular Geometries in Terms of Four Parameters

Abstract: A data file was created containing internal coordinates and derived parameters for 178 β-D-furanoside fragments, occurring in X-ray structures of ribo-, 2′-deoxyribo- and arabinonucleoside derivatives. The variability in bond angles and torsion angles can be described by four conformational parameters; the kind and degree of ring puckering as expressed in phase angle of pseudorotation P and puckering amplitude vm, the conformation of the side-chain δ and the glycosidic torsion angle χ. Comparison between out-of-plane and torsion angle methods for calculation of pseudorotation parameters revealed that the latter method is better suited to describe the internal coordinates of the non-equilateral five-membered ring. Inspection of the distribution of phase angles and puckering amplitudes lends additional support to the hypothesis that conformational interconversion of the familiar N and S type ring conformers is a process of hindered pseudorotation, proceeding through the O4′endo conformation (P = 90°) and maintaining a constant puckering amplitude. Both syn-anti distribution and preferred ranges of χ are correlated with furanose conformation in ribonucleosides; the distribution is also affected by the type of base, purines showing higher syn/anti ratios than pyrimidines. Three modes are observed for the backbone torsion angle δ(C4′–C5′); the most abundant rotamer is δ+, followed by δa. The δ− rotamer has so far been found only in S-type furanosides. Regressions based on existing or modified equations were used to express variations in internal coordinates in terms of the four parameters involved. As a consequence of its anomeric character, the glycosidic bond length can be described by a cyclic function of χ. Endocyclic bond angles' and torsion angles show small but systematic deviations from the pseudorotation equations derived for equilateral rings. Based on observed correlations with the four parameters, reasonably accurate coordinates for exocyclic atoms, including hydrogen atoms, could also be obtained. Coordinates for model β-D-furanoside fragments with preferred χ and δ orientations and variable pseudorotation parameters, covering a part of the N ⇌ S interconversion pathway, are presented. Their usefulness in future theoretical and experimental studies on nucleic acid conformations, both in the solid state and in solution, is discussed.

Vibrational analysis of peptides, polypeptides, and proteins. V. Normal vibrations of β‐turns

Abstract: modes are given for the latter three structures. Calculations have been done for structures with standard dihedral angles, as well as for structures whose dihedral angles differ from these by amounts found in protein structures. The force field was that refined in our previous work on polypeptides. Transition dipole coupling was included, and is crucial to predicting frequency splittings in the amide I and amide I1 modes. The results show that in the amide I region, P-turn frequencies can overlap with those of the cu-helix and @-sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region. The amide I11 modes of 0-turns are predicted at significantly higher frequencies than those of (?-helix and 0-sheet structures, and this region therefore provides the hest possibility of identifying 0-turn structures. Amide V frequencies of fl-turns may also he distinctive for such structures.

Structure and Phase Transformation of Rhombohedral Selenium Composed of Se 6 Molecules

Abstract: A new allotrope of selenium has been found. X-ray analysis has revealed that the new form consists of hexameric molecules, Se6, with symmetry D3d. It has been ascertained by rotational and Weissenberg methods that the crystal has a rhombohedral unit cell with lattice parameters in hexagonal axes, a=11.362±0.001 A, c=4.429±0.008 A, and belongs to space group R. Refinement of atomic parameters using the full matrix least squares method gives the following structural quantities: x=0.16021±0.00048, y=0.20227±0.00047, z=0.12045±0.00120, bond length 2.356±0.009 A, bond angle 101.1±0.3°, and dihedral angle 76.2±0.4°. Studies on the transformation by DSC and X-ray measurements revealed that the rhombohedral phase is irreversibly converted to the polycrystalline trigonal phase at temperatures above 105°C.

Intermediate range order in amorphous solids

Abstract: Information about local atomic arrangements in amorphous solids is derived by a variety of techniques, X-ray RDF's, vibrational spectroscopy, NMR and EXAFS's; however, there is a scarcity of information about intermediate range order, in particular the distribution of dihedral angles. We show that this information can frequently be obtained from an analysis of polarized features in the Raman response.

The Conformations of 2-Phenylpropionaldehyde and Some Aliphatic Ketones. The Possible Importance of the CH/π and CH/n Interactions in Determining the Molecular Geometry of a Mobile System

Abstract: The conformations have been studied by means of NMR spectroscopy, largely by the computer simulation of the lanthanoid-induced shifts, for a series of aliphatic carbonyl compounds with the following structures: CH3CH(C6H5)CO–R; R=H, CH3, C2H5, i-C3H7, and t-C4H9. It has been suggested that two rotamers are important in the conformational equilibria of these ketones, in which the R–C–C–C6H5 dihedral angle is ca. 30° and ca. 90°. The relative stability of the above two rotamers has been found to depend on the nature of the alkyl group, R. The results have been discussed in light of the possible weak attractive forces, the CH/π and CH/n interactions.

Local structure and vibrational spectra of vAs2O3

Abstract: We discuss the atomic displacements of the optically active vibrational modes of vitreous (v-)As2O3 through comparisons of the infrared (ir) and Raman response with the corresponding spectra of the two crystalline polymorphs, claudetite, a layer crystal similar to orpiment, and arsenolite, a molecular crystal based on the As4O6 molecule. We conclude from these comparisons that the structure of the glass is composed of AsO 3 2 pyramidal units that are corner connected to form a continuous random network. The character of the strong ir and polarized Raman modes in the vitreous form, suggests that the interconnection of these pyramidal units cannot be described by a random distribution of dihedral angles, but rather has peaks at angles characteristic of the different ordering in two-dimensional macromolecular layer basis of claudetite, and the As4O6 molecule. The comparisons are extended to v-As2S3 and vAs2Se3 where we conclude the dihedral angle distributions characteristic of an As4O6-like local geometry are less prevalent.

Conformational analysis of sterols: comparison of X-ray crystallographic observations with data from other sources.

Abstract: Cystallographic data on over 400 steroids collected in the Atlas of Steroid Structure provide information concerning preferred conformations, relative stabilities and substituent influence of the interactive potential of steroid hormones. Analysis of these data indicates that observed conformational details are intramolecularly controlled and that the influence of crystal packing forces is negligible. Crystallographic data on the orientation of the progesterone side chain contradict published force-field calculations. In 84 of 88 structures having a 20-one substituent, the C(16)-C(17)-C(20)-O(20) torsion angle is between 0 degrees and -46 degrees. The 4 torsion angles that lie outside this range do so because of a 16 beta-substituent and not because of crystal packing forces. Not one of the 88 structures is found to have a conformation in which the C(16)-C(17)-C(20)-O(20) torsion angle is within +/- 15 degrees of the most commonly calculated minimum energy value. The narrow range of side chain conformations seen in very different crystalline environments in the 88 crystal structure determinations and the predictable substituent influence apparent in the data strongly suggest that crystallographically observed conformers seldom deviate from minimum energy positions, regardless of hypothetical broad energy minima, metastable states and small barriers to rotation. The 96 crystallographically independent determinations of the cholestane 17-side chain show that the chain has 4 principal conformations (A:B:C:D), occurring in the ratio 69:8:8:11. Although the fully extended side chain is clearly the energetically most favored one, in 16 observations of cholesterol itself only 6 are in the extended conformation. Some of the correlated conformational changes in the chains can be rationalized on the basis of model studies, but others apparently result from subtle intramolecular forces. The unsaturated B ring provides another element of flexibility in the structure of cholesterol. The 5-ene B ring is normally observed in an 8 beta, 9 alpha-half-chair conformation. However, in structures containing more than one molecular in the crystallographic asymmetric unit, at least one of the 2 molecules is found to differ significantly from this form. It may be that this inherent flexibility is responsible for the presence of conformationally distnct molecules in the same crystal. The intermolecular interaction observed in the crystal structure of cholesterol and its fatty acid derivatives illustrate the type of interaction between the steroid ring system and hydrocarbon chains that can be expected in membrane bilayers.

A strong asymmetric N–H–N hydrogen bond: Neutron diffraction and IR spectroscopic studies of 4‐aminopyridine hemiperchlorate

Abstract: The structure of 4‐aminopyridine hemiperchlorate, C5H6N2⋅1/2HClO4, has been determined from three‐dimensional neutron diffraction data The crystals are monoclinic, space group P21/n, with cell dimensions a=11224 (7) A, b=9325 (6) A, c=16631 (9) A, β=10272 (3) ° and Z=4 The structure was refined to an R(F02) =0102 for 862 reflections with F02≳σF02 The structure consists of perchlorate anions and asymmetrically H‐bridged (NH2Py⋅H⋅⋅PyNH2)+ cations The cations contain a short, asymmetric, nearly linear (N⋅H⋅⋅⋅N)+ hydrogen bond (N⋅⋅⋅N=2698 (8) A, N–H=117 (2) A) The dihedral angle between the planes of the N–H⋅⋅N bridged pyridine rings is 85° The IR spectra are consistent with those predicted for this type of bridge system Strong temperature effects were found to occur both in the stretching frequency region νNH2 and in the low‐frequency broad absorption band below 800 cm−1 The νNH+band shift towards lower frequencies indicating that the bridge becomes shortened which, in turn, results in an incr

Erratum: Energetics of defect motion which transports polyethylene molecules along their axis

Abstract: Defect energy was calculated as a function of dihedral angles of the bonds in a point dislocation for sequences of conformations that resulted in motion of the dislocation along the polyethylene chain. Paths that presented low barriers to diffusive motion of the defect were found by incrementing, in a particular sequence, selected dihedral angles around two separated bonds near the opposite ends of the defect as the computer searched for the lowest energy conformation of all the other parts of the defect. Thus, the diffusion of a point dislocation provides a plausible mechanism for diffusion of the chain along its axis.

Crystal structure of γ-monoclinic selenium

Abstract: The crystallization of a new allotrope of cyclo-octaselenium, named γ-monoclinic selenium, from a solution of dipiperidinotetraselane in carbon disulphide is described. The allotrope γ-Se8 crystallizes in space group P21/c(no. 14) with a= 15.018(1), b= 14.713(1), c= 8.789(1)A, β= 93.61(1)°, and z= 64 (atoms). The crystal structure has been determined by X-ray diffraction from Mo-Kα diffractometer data and refined to R 0.047 for 2 525 observed reflections. There are two crown-shaped Se8 rings in the asymmetric unit, with bond lengths, bond angles, and dihedral angles in the ranges 2.326(3)–2.344(3)A, 103.3(1)–109.1(1)°, and 96.5–107.2° respectively. The overall averages, 2.334 ± 0.005 A, 105.8 ± 1.4°, and 101.1 ± 2.2°, are the same, within error limits, as in α- and β-monoclinic selenium. There are more short contacts between the rings than in the α and β forms, the shortest ones being 3.346(3) and 3.404(3)A.

N,N′ -dialkylsubstituted Imidazolidine-2-thionecopper(I) complexes. X-ray analysis of chloro-bis( N,N′ -dimethylimidazolidine-2-thione)copper(I)

Abstract: New complexes of copper(I) withN,N′-dialkylsubstituted imidazolidine-2-thione ligands were prepared by reduction of CuX2 (X = Cl or Br). The i.r. spectra show that in all the complexes the ligand coordinates through the sulphur atom. The crystal structure of chloro-bis(N,N′-dimethylimidazolidine-2-thione)copper(I) has been determined from x-ray diffraction data. Crystals are monoclinic. space groupC 2, with unit cell dimensions:a = 16.022(15),b = 9.942(10),c = 15.112(15) A, β = 139.84(10)2, Z = 4. The final R index is 5.2%. The copper coordination is trigonal, involving sulphur atoms of the two ligands and One chlorine atom. The steric effect of the two methyls imposes a rotation of the imidazolidine rings with respect to the coordination plane. The dihedral angle between the mean plane of thiourea moieties. parallel one with the other. and the coordination plane is 119.3°.

The conformational dependence of vicinal 13C13C spin–spin coupling constants in alicyclic compounds

Abstract: A series of alicyclic compounds with dihedral angles of 0°, 60°, 90°, 120° and 180° between a 13C-labelled carbon atom and a carbon atom separated by three bonds from the label has been synthesized. The vicinal 13C13C spin coupling constants were measured, and from the results a Karplus-type relationship between 13C13C spin coupling and dihedral angle is proposed.

The crystal and molecular structure of chlorpropamide

Abstract: Chlorpropamide, C10H13N2O3SCl, forms orthorhombic crystals of space group P212121 with a 9.066±0.004, b=5.218±0.003, c=26. 604±0.008 A, and four molecules per cell. Three dimensional photographic data were collected with Mo-Kα radiation. The structure was determined using Patterson, Fourier and Difference syntheses methods and refined by the block-diagonal least-squares methods with anisotropic thermal parameters for all nonhydrogen atoms and isotropic thermal parameters for all hydrogen atoms. The final R value was 0.10 for the 1823 observed independent reflections. The dihedral angle between the planes through the benzene ring and the urea group is 99° The conformational angle formed by the projection of the S−C(1) with that of N(1)−C(7) when the projection is taken along the S−N(1) bond is 76°. The molecule appears to form with neighbouring molecules two hydrogen bonds, N(1)−H…0(3) and N(2)−H…O(2) of lengths 2.774 and 2.954A respectively related by screw diads parallel to the a axis. Adjacent molecules parallel to b and c axis are bound together by van der Waals forces.

Variable dihedral angle tail unit for supersonic aircraft

Abstract: An aircraft having supersonic and subsonic flight capabilities which utilizes a variable dihedral angle tail unit to vary the aircraft geometry to improve aerodynamic efficiency, especially when changing from subsonic to supersonic speeds and vice versa, which saves propulsion energy and can be used to present minimal radar cross section from a given direction.

Liquid state torsional dynamics of butane: The Kramers rate and the torsion angle correlation times

Abstract: The diffusion equation for hindered internal rotation of a butane molecule in the liquid state is solved for the Kramers‐like rate for trans–gauche isomerization and the torsion angle correlation times. High accuracy solutions obtained by numerical quadrature and approximate asymptotic results are compared with previous molecular dynamics calculations of butane in several thermodynamic states.

Highly disordered amorphous selenium studied by ultraviolet photoemission spectroscopy

Abstract: Highly disordered amorphous (HDA) selenium films were prepared by vapor deposition onto a cold substrate held at 77 K under ultrahigh vacuum. HeI photoemission spectra of these films were found to be considerably different from the previously observed spectrum of the amorphous film prepared at room temperature (RT film). Characteristic features in the spectra of the HDA films compared with those in the spectrum of the RT film are as follows: (1) the width of the $4p$ nonbonding band is remarkably narrower; (2) the intensity of the upper $4p$ bonding band is decreased, and the intensity ratio of the upper and lower $4p$ bonding bands is reversed; (3) the upper $4p$ bonding band is located at higher initial energy; and (4) a part of the $4s$ band is well resolved. The HDA films underwent thermal annealing effects and at room temperature gave a photoemission spectrum similar to that observed in earlier work. In order to interpret the experimental results, CNDO molecular-orbital calculations were made on a newly proposed model for amorphous selenium, in which distorted infinite chains consist of small spiral units including a few selenium atoms. On this model, dependence of the density of states on the following factors was studied: (1) the number of atoms in a unit cluster, (2) the dihedral angle for the bonds on the junction of the units, and (3) the bond angle. The results of the calculations well explained the spectrum of HDA selenium and its thermally induced changes. The importance of the above three factors for the structure of amorphous selenium was stressed.

Purification, growth, structure, optical and electrical properties of single crystals of the π‐molecular complex of phenothiazine with pyromellitic dianhydride

Abstract: Single crystals of the black phenothiazine : pyromellitic dianhydride (PTZ:PMDA) 1:1 donor–acceptor complex, have been grown by sublimation from the zone‐refined components. The PTZ:PMDA complex crystalizes with P1 symmetry (Z=2), a=7.197(1), b=19.072(5), c=6.886(1) A, α=84.79(1) °, β=72.98(1) °, γ=85.72(2) ° at T=23 °C. The crystal structure model was refined with 5214 data { (sin ϑ/λ)max=0.8071 A−1} to give R=0.049 and Rw=0.089. The crystal packing consists of two polar endless ...DADA... stacks related to one another by 1. The packing is compared with that in the analogous anthracene : PMDA complex. The PTZ molecule displays a modest fold about the N...S axis (dihedral angle 176.4°), however, the deviation from planarity is small in comparison with that in PTZ crystals. The stack axis is nearly perpendicular to the molecular planes, consequently the CT‐dichroism lies essentially in the principal axis system of the indicatrix. The absorption edge is not very sharp, even at 4.2 K; it is located at 900±...

An electron spin resonance study of sulphuranyl radicals of the type R2S–SX [X = CF3 or R′C(O)]

Abstract: Photochemically generated trifluoromethyl- or acyl-thiyl radicals add to dialkyl sulphides to form the sulphuranyl radicals R2S1–S2X [X = CF3 or R′C(O)], the e.s.r. spectra of which have been detected. These adducts appear to be non-planar at the three-co-ordinate sulphur and the unpaired electron is thought to occupy an S–S σ* orbital. The β-hydrogen splittings from the S1-alkyl groups probably arise mainly through a hyperconjugative mechanism of spin transmission and appear to depend upon the spin density (ρ) in the S1-3pσ orbital and the dihedral angle (θ) between the S1CHβ and S2S1C planes according to the approximate equation a(Hβ)= 25.2 ρcos2θ G. The g factors of the sulphuranyl radicals are markedly dependent upon temperature and the nature of R. At low temperatures, the adducts generally decay by a second-order process, presumably bimolecular self-reaction. Different behaviour is observed when R2S = [graphic omitted] or (Et2N)2S and rapid ring-opening or S–N cleavage, respectively, occurs even at low temperatures. Temperature-dependent lineshape effects are evident in the spectra of R2S–SX, and several different processes appear to be responsible for these effects, including efficient spin–rotation relaxation, conformational interconversion, and the bimolecular sulphide exchange reaction R2S + R2S–SX ⇌ R2S–SX + R2S.