Showing papers on "Dihedral angle published in 1979"

Mechanical and thermodynamic constraints on fluid distribution in partial melts

Abstract: In this paper we examine the mechanical and thermodynamic criteria which are necessary for equilibrium to exist in partial melts that are subject to hydrostatic stress. Existing theory satisfactorily demonstrates (1) that crystal-liquid interfaces will have no sharp edges and will approach constant curvature and (2) that the liquid will form a continuously interconnected network by distributing itself in channels along intergranular edge intersections provided that the liquid wetting angle is less than 60°. However, the full textural implications of the thermodynamics have apparently not been realized previously. Currently accepted theoretical developments have been extended to show how equilibrium melt distribution varies with wetting angle. We find that contrary to a widely accepted view a homogeneous fluid phase cannot completely wet intergranular faces, regardless of the exact wetting angle. As a result the intercrystalline faces will remain in mechanical contact throughout the assemblage even when it is characterized by a 0° dihedral angle.

A molecular dynamics and Monte Carlo study of solvent effects on the conformational equilibrium of n‐butane in CCl4a),b)

Abstract: We report on a computer simulation study of the gauche–trans conformational equilibrium of n‐butane in liquid carbon tetrachloride solvent. The study is made possible by implementing an exact statistical mechanical theorem which relates the full intramolecular distribution function for a butane molecule to that of a hypothetical species which does not possess a large potential barrier separating the trans and gauche states. In addition to determining the trans–gauche equilibrium constant, the potential of mean torsion, that is, the reversible work required to alter the conformation is determined as a function of the dihedral angle. Recent theoretical work is compared with these computer experiments, and while qualitative agreement is found, the approximate theory overestimates the solvent effect. Finally, the change in solvent structure in response to a conformational change in the solute is determined.

Structural phase transition in polyphenyls. VII. A neutron diffraction study of the structural phase transition in biphenyl-d10

Abstract: Recently a soft mode has been observed in biphenylhl0 (hydrogenated) by Raman spectroscopy below T c = 40 K. The structural phase transition in biphenyld l0 (deuterated) has been investigated by neutron diffraction. Surprisingly, superlattice reflections appeared below 40 K, corresponding to a doubling of the b parameter only, and not to the doubling of a and b, as was found for p-terphenyl and p-quaterphenyl. The torsion angle between the planes of the phenyl groups is about 10 °, and is in opposite directions for two neighbouring molecules along b. The intensity of the superlattice reflections shows a linear behaviour with temperature, in agreement with Landau theory.

Vibrational approach to the dynamics of an α‐helix

Abstract: The dynamics of a finite α-helix have been studied in the harmonic approximation by a vibrational analysis of the atomic motions about their equilibrium positions. The system were represented by an empirical potential energy function, and all degrees of freedom (bond lengths, bond angles, and torsional angles) were allowed to vary. The complete results were compared with a more restrictive model in which the peptide dihedral angle was kept rigid; also, a model potential excluding hydrogen bonds was examined. Thermal fluctuations in the backbone dihedral angles ϕ and ψ are 12° to 15°. The fluctuations of adjacent dihedral angles are highly correlated, and the correlation pattern is affected by the flexibility of the peptide dihedral angle. Time-dependent autocorrelations in the motion of ϕ and ψ appear to decay due to dephasing in less than 1 psec, while the motions of the carbonyl oxygen and amide hydrogens out of the peptide plane are more harmonic. Length fluctuations have been evaluated and exhibit a strong end effect; the calculated elastic modulus is in agreement with other values. Rigid and adiabatic total energy surfaces corresponding to dihedral angle rotations in the middle of the helix have been obtained and compared with the quadratic approximation to those surfaces. The magnitudes and correlations between the fluctuations obtained by averaging over the adiabatic energy surface most closely resemble the vibrational results. Of particular interest is the fact that hydrogen bonds play a relatively small role in the local dihedral angle fluctuations, though the hydrogen bonds are important in the energy of overall length changes.

Solution conformation of enkephalin. A nuclear magnetic resonance study of 13C-enriched carbonyl carbons in [Leu5]-enkephalin

Abstract: By using 13C enrichment in [Leu5]-enkephalin, it has been possible to improve the assignment of carbonyl resonances in the nuclear resonance spectrum and to remove some of the ambiguities in the derived phi and chi dihedral angles, thereby providing information about the conformation of this molecule in solution. The combined use of 13C and 1H nuclear magnetic resonance experiments leads to the conclusion that [Leu5]0enkephalin contains a type I beta bend at residues Gly3-Phe4 in dimethyl-d6 sulfoxide (Me2SO0d6) solution. Furthermore, the side chains of Tyr1, Phe4, and Leu5 exist predominantly in one conformation (tg-) in this solvent. A comparison is made between the conformation found in Me2SO-d6 and those determined by X-ray diffraction and conformational energy calculations.

The Crystal and Molecular Structure of Benzanilide

Abstract: The crystal structure of benzanilide has been determined from Weissenberg photographs using Cu Kα radiations and refined to an R value of 0.075 for 766 independent reflections. The crystals are monoclinic, space group C2/c, Z=4, with a=24.34(4), b=5.325(3), c=8.012(8) A, β=107.2(3)°, Dm=1.32 and Dx=1.321 g cm−3. Dihedral angle between the benzene rings is 62.6°, and each benzene ring makes dihedral angle of 31.3 and 31.6° with the plane of amido group as found in Kevlar and Nomex polymers. The molecules related by a b-translation are linked together by N–H…O hydrogen bond [N…O 3.112(6), H…O 2.03 A, N–H…O 157°] to form a chain along b. The chains are held together primarily by dipole forces of carbonyl groups of the molecules related by inversion centers to form a sheet parallel to the bc plane. The sheets are stacked along a with disorder by van der Waals interactions.

Atomic resolution analysis of a 2:1 complex of CpG and acridine orange

Abstract: Cytidylyl-3', 5'-guanosine and acridine orange crystallize in a highly-ordered triclinic lattice which diffracts X-rays to 0.85 angstrom resolution. The crystal structure has been solved and refined to a residual factor of 9.5%. The two dinucleoside phosphate molecules form an antiparallel double helix with the acridine orange intercalated between them. The two base pairs of the double helical fragment have a twist angle of 10 degrees and it is found to have a C3' endo-(3', 5')-C2' endo mixed sugar puckering along the nucleotide backbone as has been observed for other simple intercalator complexes. Twenty-five water molecules have been located in the lattice together with a sodium ion. The intercalator double helical fragments form sheets which are held together by van der Waals interactions in one direction and hydrogen bonding interactions in the other. The crystal lattice contains aqueous channels in which sixteen water molecules are hydrogen bonded to the nucleotide, none to the intercalator, five water molecules are coordinated about the sodium ion and four water molecules bind solely to other water molecules. The bases in the base pairs have a dihedral angle of 7 to 8 degrees between them.

Conformational analysis by photoelectron spectroscopy

Abstract: The conformation of organic molecules may be determined by means of photoelectron (PE) spectroscopy if there are orbital interactions present which depend on a dihedral angle. Straightforward application of the method requires that all ionization bands of interest can be assigned unambiguously and that inductive effects and secondary orbital interactions do not occur or can be accounted for appropriately. In many cases, this method complements conventional methods of conformational analysis. PE conformational analysis is particularly suited to compounds containing vicinal lone pairs of ..pi.. systems. 105 references, 10 figures, 2 tables.

13C, 13C coupling constants in phenyl substituted ethylene, naphthalene, phenanthrene and cyclopentadienone. Dependence on dihedral angles. Determination of signs by the symmetrical double labelling (SDL) method. IV

Abstract: Carbon-13, carbon-13 coupling constants and carbon-13 chemical shifts have been measured in a series of phenyl substituted ethylenes and aromatics all doubly labelled with 13C at the olefinic positions (α,β-) or at neighbouring aromatic positions, tetraphenylcyclopentadienone labelled at the 3,4-positions, and dichlorodiphenylmethane labelled at the α-carbon. Signs of coupling constants were determined by the symmetrical double labelling (SDL) method. Coupling constants over as many as five bonds are reported. Two-bond couplings between carbons in the aromatic skeleton belong to different classes according to the nature of the coupling path. The magnitudes of three-bond coupling constants between such carbons correlate linearly with π-bond orders and a separation of the δ- and π-contributions is evident. The three-bond couplings between the 2-position in a phenyl substituent and the olefinic β-position or a corresponding aromatic position depend on the out-of-plane twist of the phenyl ring and may lead to information about the twist angle. Contrary to findings with aromatic carbonyl compounds two- and three-bond couplings to the α-carbon in the present compounds are fairly constant. The reported data suggest that the signs of coupling constants over more than two bonds alternate in aromatic systems. Carbon-13, carbon-13 coupling constants in naphthalene have been calculated by the INDO-SOS method.

An ENDOR study of the geometry of the lowest triplet state of benzil

Abstract: We present the results of our optically detected ENDOR investigation of the lowest triplet state of benzil. The interaction between the total electron spin and nuclear spins placed at strategic positions throughout the molecule was used to probe the molecular geometry. 13C substitution at the carbonyl carbons led to the dihedral angle, while proton A tensors were used to deduce the ring twist. The geometric information resulted from a point–dipole calculation which reproduced the 13C and proton A tensors by optimizing geometry and spin density distribution. A dihedral angle of 157° was found, substantially larger than the ground state value of 111°, though significantly different from a trans‐planar configuration. The ring twist angle was found to be 24°.

Molecular structure of bis(dimethylamino)difluorosulfurane. The first x-ray crystal structure of a fluorosulfurane

Abstract: : The molecular structure of (Me2N)2SF2 has been determined by single crystal X-ray diffraction methods. The compound crystallizes in the monoclinic system, space group C2/c, with a = 11.00 (2) A, b = 5.693 (6) A, c = 12.24 (3) A, beta = 92.79 (10) deg., and Z = 4. The symmetry of (Me2N)2SF2 is C2, and the structure is essentially trigonal bipyramidal with the fluorine and Me2N ligands occupying axial and equatorial sites, respectively. The third equatorial site is occupied by the sulfur 'lone pair' which lies along the C2 symmetry axis. Since the dihedral angle between the C-N-C and N-S-N planes is 48.2 deg., the nitrogen lone pairs are disposed approximately midway between the sulfur lone pair and the sulfur-fluorine axial (S-F2) bonds. The sum of the bond angles around the nitrogen atoms is 342.3 deg.; hence the hybridization at these centers is approximately halfway between sp(2) and sp(3). The Fa-S-Fa bonds are bent toward the sulfur lone pair by 5.3 deg., and the equatorial N-S-N bond angle is 102.3(1) deg. The S-F and S-N bond distances are 1.770(2) A and 1.648(2) A, respectively. (Author)

Molecular and crystal structure of bis(.mu.-acetato)-bis(norbornadiene)dirhodium(I): a catalyst for the isomerization of quadricyclane to norbornadiene

Abstract: Bis(..mu..-acetato)-bis(norbornadiene)dirhodium(I) has been structurally characterized. The compound has been shown to be an active catalyst for the isomerization of quadricyclane to norbornadiene. This material crystallizes in the centrosymmetric monoclinic space group P2/sub 1//c with unit cell constants (T = 20/sup 0/C) a = 9.7733 (10) A, b = 15.2859 (15) A, c = 12.1815 (14) A, and ..beta.. = 103.563 (8)/sup 0/. All 3151 unique reflections were used in the x-ray structure analysis which refined to an R/sub F/ of 0.028. The Rh(1)--Rh(2) distance is 3.1050 (7) A. Each Rh atom is bonded to two oletin moieties of a norbornadiene ligand and to two oxygen atoms of the bridging acetate ligands. Each Rh coordination sphere has two approximate square-planar configuration with average Rh--oletin and Rh--O distances of 1.975 (4) and 2.106 (7) A, respectively. The Rh atoms lie 0.098 and 0.157 A out of their respective coordination planes. The dihedral angle formed between these planes is 50.1/sup 0/, while the angle between the planes defined only by the Rh and acetate oxygens is 40.2/sup 0/. Hydrogen atoms on the norbornadiene groups are within van der Waals contact distances, indicative of strong steric interactions between the ligands of the dimer. 4more » figures, 8 tables.« less

The conformation and reorientation of enclathrated 1,2-dichloroethane

Abstract: The rigid-lattice nmr line shape of the four-proton system in 1,2-dihaloethanes has been obtained by spectral simulation as a function of dihedral angle and used to show that 1,2-dichloroethane is encaged in the structure II hydrate in a gauche configuration with Very broad low-temperature dielectric absorption is associated with an average activation energy of 0.87 kcal/mol for guest-molecule reorientation.

Torsion angle dynamics in three bond chainsa)

Abstract: The correlation times for torsion angle fluctuations of three bond molecules in a liquid are investigated as a function of the barrier hindering internal rotation. The algorithm for the correlation time is general and can be applied for any torsional potential and bond angle. Correlation times obtained from this analysis are in basic accord with the Kramers theory.

Crystal and molecular structures of two dithieno[l,4]dithiins, C8H4S4

Abstract: The structures of two isomeric dithieno-[ 1,4]-dithiins, CsH4S 4, dithieno[ 3,4-b; 3 ',4'-el-p-dithiin (I) and dithieno[2,3-b;3',2'-el-p-dithiin (II), have been determined. Both compounds crystallize in space group P21/c with Z = 4; a = 14.093 (2), b = 8.118 (2), c = 8.061 (2)/~, fl = 98.06 (2) ° for (I), a = 11.672 (2), b = 6.152 (2), c = 13.607 (3) A, fl = 110.63 (2) ° for (II). Refinement of (I) and (II) with respectively 2308 and 2532 independent reflections gave Rw(IFi ) = 0.057 and 0.073, R(IFI) = 0.051 and 0.063 respectively. Both molecules are folded along the S-S axis of the [1,4]-dithiin ring. The dihedral angle is 136.2 ° for (I) and 130.3 o for (II). The molecular symmetry is mm for (I) and m for (II).

Psi-angle dependence of geminal proton–carbonyl-13C coupling constants in peptides. A theoretical investigation†

Abstract: Theoretical calculations of the geminal carbonyl-13C- proton coupling constant, 2J(C′H), in α-amino acids have been carried out using Dirac Vector model and Penney-Dirac bond order formulations. The results indicate that the couplings are dependent on the backbone torsion angle psi (ψ) of the amino acid residues in peptides. The meagre available experimental data seem to support the theoretical findings.

Photophysics of aryl substituted 1,3,4-oxadiazoles. I. SCF CI calculations in different molecular configurations and assignment of the T1→Tn spectrum of 2,5-di-(1-naphthyl)-1,3,4-oxadiazole

Abstract: An SCF MO calculation followed by configuration interaction has been performed for 2,5-di-(1-naphthyl)-1,3,4-oxadiazole as a function of the dihedral angles. The use of the configuration analysis method shows an important contribution of a resonance exciton state of the binaphthyl type to the lowest triplet state. As the molecule becomes more nearly planar, there is an increase in the charge-transfer character of the lowest triplet, which is directly responsible for the two absorption bands in the long wavelength part of the T-T spectrum. The supermolecule αNND is well depicted in terms of a binaphthyl fragment interacting with an oxadiazole ring.