Showing papers on "Dihedral angle published in 1974"
TL;DR: An objective assessment of the upper limit of the error in the atomic coordinates of the final model is possible by comparing the inhibitor component in the model of the complex with the refined structure of the free inhibitor (Deisenhofer & Steigemann, 1974).
526 citations
TL;DR: It is suggested that the enhanced stability of thermostable proteins relative to thermolabile ones cannot be attributed to a common determinant such as metal ion or hydrophobic stabilization, but in a given instance may be due to rather subtle differences inhydrophobic character, metal binding, hydrogen bonding, ionic interactions, or a combination of all of these.
306 citations
TL;DR: The relationship between the CD spectra of the chiral biaryls and their stereochemical configuration, as a function of the dihedral angle between the molecular planes of the aromatic moieties, has been investigated in this article.
200 citations
TL;DR: In this paper, a model of grain edge porosity is presented which is equally applicable to liquid precipitates, to fission gas swelling in nuclear fuels and to powder compacts, and the morphology of the pores is shown to depend on the ratio of their surface to grain boundary energies and their volumes.
182 citations
TL;DR: The similarity of the Mössbauer spectrum of the model complex, 1, with oxyhemoglobin indicates that 1 may be a good model for oxygen binding in the oxygen transport hemeproteins.
Abstract: The preliminary structural characterization of a reversible ferrous dioxygen complex is reported. Mono(N-methyl imidazole) (dioxygen) meso-tetra (α,α,α,α-o-pivalamidephenyl) porphinatorino(II), [Fe(O2)-(N-Me imid) (α,α,α,α-TpivPP)], 1, isolated from toluene solution, crystallizes in the monoclinic system with four molecules in a unit cell of dimensions a = 18.690 (3), b = 19.514 (3), c = 18.638 (3) A, and β = 91.00 (1)°. R = 0.15 for 841 reflections having F2 > 3σ (F2).
The complex 1 has four pivalamido groups on one side of the porphyrin forming a hydrophobic pocket of 5.4-A depth which encloses coordinated dioxygen. The dioxygen is coordinated “end-on,” with a bent Fe-O-O bond. The Fe-O-O plane bisects an N-Fe-N right angle of the equatorial iron porphyrin plane and is four way statistically disordered. In addition there is a crystallographic 2-fold axis through iron, coordinated oxygen, and nitrogen of the axially bound N-methyl imidazole. Thus there are two types of coordinated dioxygen with the Fe-O-O plane either parallel or perpendicular to the trans axial imidazole plane. Corresponding values for the Fe-O-O bond angles are 135-(4)° and 137(4)° and for the O-O bond lengths are 1.23 (0.08) and 1.26 (0.08) A, with a dihedral angle of 90° between alternative orientations of the Fe-O-O plane. The Fe-O distance is 1.75 (0.02) A and Fe-N (imidazole) is 2.07 (0.02) A, suggesting multiple bond character in the Fe-O moiety. The similarity of the Mossbauer spectrum of the model complex, 1, with oxyhemoglobin indicates that 1 may be a good model for oxygen binding in the oxygen transport hemeproteins.
174 citations
TL;DR: Two elastic-energy-relaxed continuous random network (CRN) models for tetrahedrally bonded amorphous semiconductors have been obtained: a 201-atom model built entirely at Yale and a 519-atomic model relaxed from a structure built by Polk and Boudreaux.
Abstract: Two elastic-energy-relaxed continuous random network (Polk) models for tetrahedrally bonded amorphous semiconductors have been obtained: a 201-atom model built entirely at Yale and a 519-atom model relaxed from a structure built by Polk and Boudreaux which originated at Harvard. In relaxing the coordinates to minimize the total energy the Keating potential was used for the interatomic interactions. The models are analyzed in terms of density, elastic distortion energy, elastic constants, numbers of five-, six- and seven-fold rings, distribution of dihedral angles, and radial distribution functions. We find that, despite their different origins, the models have essentially identical characteristics. Our principal conclusions are as follows: (a) The density of the CRN model is, to within 1%, that of diamond cubic. (b) The bulk modulus is about 3% lower than that for the diamond cubic structure and the shear modulus lies between the two diamond cubic shear moduli. (c) There are, to within ± 10% (and with corrections for surface effects), 0.38 five-fold, 0.91 six-fold and 1.04 seven-fold rings per atom. (d) For a reasonable value of the bond bending force constant, rms bond length distortions are about 1.0% and bond angle distortions are about 7.0°. (e) The radial distribution function agrees very well with experiment for all four principal peaks.
144 citations
TL;DR: In this paper, a method for manipulating the conformation in which only one atom is moved at a time is described, hence the name, local method, where small displacements are calculated and applied for each atom in turn and this is repeated a number of times for the entire molecule.
Abstract: In computer manipulation of macromolecules bond lengths and bond angles as well as some dihedral angles frequently are held fixed at ideal values observed in small model compounds. Changes of the conformation are then made by internal rotation about chemical bonds. The result of each rotation is the relative motion of large parts of the molecule; this will therefore be referred to as the global method of changing the conformation. The effect of this method is similar to manipulation of a stick model of the molecule. A method is described for manipulating the conformation in which only one atom is moved at a time; hence the name, local method. Each movement is made in order to improve the immediate environment of the atom by decreasing the differences between bond lengths, bond angles and fixed dihedral angles near this atom and their ideal values. Small displacements are calculated and applied for each atom in turn, and this is repeated a number of times for the entire molecule. At the same time, one may require that the position of each atom is not moved too far away from the starting position, so as to give idealization of the starting conformation or model building. Alternatively, inclusion of a term tending to lower the contributions to the intramolecular energy (van der Waals attractive energy, repulsive energy, electrostatic energy) gives energy minimization. A description is given of the progress of the model-building calculation with a fifteen-residue segment of the protein rubredoxin as a test case. The resulting conformation is found to be very close to the best global fit obtainable. This best global fit is obtained by constructing a global fit to the locally fit model and further adjusting this intermediate conformation to improve the agreement with the starting coordinates. A global fit constructed to the original data is found to be inferior. It corresponds to a higher relative minimum of the sum of the squares of the distances between the model coordinates and those to be fitted; the conformation of two side chains is qualitatively different in the two global fits. An example shows how the method is suitable for building trial conformations of chain segments. Finally, advantages of the local method are pointed out which, it is believed, make its use preferable for model building in an interactive computing environment.
102 citations
TL;DR: The literature concerning the structures of compounds containing saturated, 4-carbon rings is reviewed in this article, and the variety of conformations (dihedral angles of 0° to 30° ± 6°) of the cyclobutane ring are tabulated and discussed.
62 citations
TL;DR: In this article, the energy of each stable conformational isomer (rotamer) of these molecules was calculated for various temperatures and solvent dielectric constants, including intrinsic potentials for rotation about single bonds, intramolecular dispersion and repulsive interaction.
Abstract: As a theoretical analysis of the conformational equilibria of ethylene glycol, methoxyethanol and dimethoxyethane, the energy of each stable conformational isomer (rotamer) of these molecules was calculated for various temperatures and solvent dielectric constants. Classical semi-empirical potential functions were used. Besides intrinsic potentials for rotation about single bonds, intramolecular dispersion and repulsive interaction, dipole-dipole interaction and hydrogen bonding energies were included. Interaction with the solvent was considered only in terms of a continuous dielectric medium interacting with the local dipoles and quadrupoles of the molecule. For each rotamer, the dihedral angles giving the lowest energy were determined. From the energies of each rotamer, Boltzmann distributions of populations were obtained, and total concentrations were calculated in various physically distinguishable states, e.g. those with and without internal hydrogen bonds, or those in which the central C-C bond take...
56 citations
TL;DR: The He 1 photoelectron spectrum of hydrogen peroxide is reported in this paper, showing a splitting of 1.0 eV between the first two bands due to the oxygen nonbonding orbitals.
46 citations
TL;DR: In this article, the He I photoelectron spectra of peri-amino and dimethylamino naphthalenes are presented, and the differences in the ionization energies of the π-bands are interpreted by separation of the perturbation of the amino substituent into an inductive destabilization and conjugative stabilization.
Abstract: The He I photoelectron spectra of peri-amino and dimethylamino naphthalenes are presented. The differences in the ionization energies of the π-bands are interpreted by separation of the perturbation of the amino substituent into an inductive destabilization and conjugative stabilization. This affords the assignment of the photoelectron bands of ionization energies below 11 eV and an estimation of the dihedral angle in the peri-dimethylamino derivatives. The data on the peri-amino naphthalenes indicate some angular distortion in contrast to 2-aminonaphthalene.
TL;DR: It is concluded that TRF in DMSO–d6 does not contain intramolecular hydrogen bonds and there is evidence for a tautomeric equilibrium corresponding to an exchange of imidazole proton between the two nitrogen atoms N‐δ and N‐ε.
Abstract: The proton magnetic resonance spectrum of thyrotropin releasing factor (TRF) in solution in deuterium oxide and deuterated dimethylsulfoxide (DMSO–d6) has been analyzed. Two forms differing in cis–trans isomerism about the His-Pro peptide bond are observed. From the temperature dependence of chemical shift of the amide protons, it is concluded that TRF in DMSO–d6 does not contain intramolecular hydrogen bonds. Measurement of NHCαH coupling constant provides an estimate of the histidine dihedral angle ϕ. Structural information about the histidine side-chain is deduced from CαHCβH coupling constants and from the nonequivalence of the two prolyl δ-protons. In DMSO–d6, there is evidence for a tautomeric equilibrium corresponding to an exchange of imidazole proton between the two nitrogen atoms N-δ and N-e. In water, the N-eH tautomer is found to be the predominant tautomeric form of the imidazole ring. These results in combination with energy calculation, vibrational analysis, and carbon nmr studies allow the determination of the conformationof TRF.
TL;DR: The spin-coupling constants of the proton magnetic resonance spectrum of this cyclic nucleoside derivative measured in C2HCl3 solution confirm the conformation found in the solid state by X-ray methods.
Patent•
01 Oct 1974
TL;DR: An electro-mechanical sign which alternatively exhibits two different kinds of information, for example clock or sign display information, on two respective faces of several adjacent dihedral angles as mentioned in this paper.
Abstract: An electro-mechanical sign which alternatively exhibits two different kinds of information, for example clock or sign display information, on two respective faces of several adjacent dihedral angles.
TL;DR: X-ray analyses have shown that the glucopyranose rings of GlcNAc-Asn and Glc- asparagine both have the C-1 chair conformation and also that the glucose-asparagine linkage of each molecule is present in the beta-anomeric configuration.
Abstract: X-ray analyses have shown that the glucopyranose rings of GlcNAc-Asn [4-N-(2-acetamido-2-deoxy-beta-d-glucopyranosyl)-l-asparagine] and Glc-Asn [4-N-(beta-d-glucopyranosyl)-l-asparagine] both have the C-1 chair conformation and also that the glucose-asparagine linkage of each molecule is present in the beta-anomeric configuration. The dimensions (the estimated standard deviations of the last digit are in parentheses) of the glycosidic bond in GlcNAc-Asn and Glc-Asn are, respectively, C((1))-N((1)) 0.1441(6)nm, 0.146(2)nm; angle O((5))-C((1))-N((1)) 106.8(3) degrees , 105.7(8) degrees ; angle C((2))-C((1))-N((1)) 111.1(4) degrees , 110.4(9) degrees ; angle C((1))-N((1))-C((9)) 121.4(4) degrees , 120.5(9) degrees . The glycosidic torsion angle C((9))-N((1))-C((1))-C((2)) is 141.0 degrees and 157.6 degrees in GlcNAc-Asn and Glc-Asn respectively. Hydrogen-bonding is extensive in these two crystal structures and does affect one torsion angle in particular. Two very different values of chi(1)(N-C(alpha)-C(beta)-C(gamma)) occur for the asparagine residue of the two different molecules; the values of chi(1), -69.0 degrees in GlcNAc-Asn and 61.9 degrees in Glc-Asn, correspond to two different staggered conformations about the C(alpha)-C(beta) bond as the NH(3) (+) group is adjusted to different hydrogen-bonding patterns. The two trans-peptide groups in GlcNAc-Asn show small distortions in planarity whereas that in Glc-Asn is more non-planar. The mean plane through the atoms of the amide group at C((2)) in GlcNAc-Asn is approximately perpendicular (69 degrees ) to the mean plane through the C((2)), C((3)), C((5)) and O((5)) atoms of the glucose ring and that at C((1)) is less perpendicular (65 degrees ). The mean plane through the atoms of the amide group in Glc-Asn makes an angle of only 55 degrees with the mean plane through these same four atoms of the glucose ring. The N((1))-H bond of the amide at C((1)) is trans to the C((1))-H bond in these two compounds; the N((2))-H bond of the amide at C((2)) is trans to the C((2))-H bond in GlcNAc-Asn. The values of the observed and final calculated structure amplitudes have been deposited as Supplementary Publication SUP 50035 (26 pages) at the British Library (Lending Division), (formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1973) 131, 5.
TL;DR: In this article, an X-ray structure analysis of tri-O-acetyl-α-D-arabinopyranosyl azide (1a) (space group rhombic P212121; Z = 4, R = 4.4%) shows that the azido group is oriented towards the ring oxygen with a torsion angle O6Cl.
Abstract: Die Rontgenstrukturanalyse von Tri-O-acetyl-α-D-arabinopyranosylazid (1a) (Raumgruppe rhombisch P212121;Z = 4, R = 4.4%) zeigt, das die Azidogruppe mit einem Torsionswinkel O6Cl.…N1N2 von 75.6° erheblich in Richtung zum Ringsauerstoff ausgelenkt ist. Damit besitzt die N3-Gruppe einen exo-anomeren Effekt von gleicher Grosenordnung wie die OCH3-Gruppe in Methyl-β-D -pyranosiden mit einer Auslenkung von 70–76°. Die Acetyl-Methylgruppen weisen im Kristall statistisch verteilt zwei Konformationen (a und b in Abb. 1) im Verhaltnis 1:1 auf. Axiale und aquatoriale Acetoxygruppen sind beide planar und zum Ring so angeordnet, das die CO-Gruppe und die CH-Bindung des Ring-C-Atoms etwa synparallel stehen.
Conformational Analysis, IV. exo-Anomeric Effect of the Azido Group in Crystalline Tri-O-acetyl-α-D-arabinopyranosyl Azide
An X-ray structure analysis of tri-O-acetyl-α-D-arabinopyranosyl azide (1a) (space group rhombic P212121; Z = 4, R = 4.4%) shows that the azido group is oriented towards the ring oxygen with a torsion angle O6Cl…N1N2 of 75.6°. This can be compared with a bending of the OCH3 bond in methyl β-D-pyranosides in the range of 70–76°. Thus the exo-anomeric effect of an azido group is demonstrated to be of the same magnitude as the effect an alkoxy group. In the crystal the acetyl methyl groups occupy two conformations (a and b in fig. 1) in a statistical ratio of 1:1. The planar acetyl groups in both equatorial and axial positions at the ring are arranged in such a way that the carbonyl-bond and the CH bond of the ring atom to which the acetyl groups is attached are nearly synparallel.
TL;DR: In this article, the microwave spectrum of gaseous ethylene glycol was investigated, and a very thorough search was made for low J a-, b-, and c-type transitions in the 8-38 GHz spectral region.
TL;DR: The solution conformation of xanthosine in liquid N2H3 has been determined by nuclear magnetic resonance and it is deduced that the N ribose is correlated with an anti conformed of the base while the S form of the sugar is coupled to a glycosyl torsion angle in the syn range.
Abstract: The solution conformation of xanthosine in liquid N2H3 has been determined by nuclear magnetic resonance. The correlation times for rotational diffusion were derived from 13C relaxation measurements. A Karplus analysis of the high-resolution spectra of the ribose moiety yields the conformation of the sugar from the H–H coupling constants. The mole fraction of the sugar in the N conformation is 0.4 at room temperature and increases slightly as the temperature decreases. From nuclear Overhauser enhancement studies, and T1 measurements of the various protons it is deduced that the N ribose is correlated with an anti conformation of the base (Y∼ 210°) while the S form of the sugar is coupled to a glycosyl torsion angle in the syn range (Y ∼ 50°–90°).
TL;DR: In this paper, the carboxyl radical anion trapped in irradiated single crystals of L•valine hydrochloride monohydrate has been studied by Endor, and the coupling tensors and their orientations clearly indicate that the amino proton in the neighboring NH3 group is transferred to the anion through the intermolecular hydrogen bond.
Abstract: The so‐called carboxyl radical anion trapped in irradiated single crystals of L‐valine hydrochloride monohydrate has been studied by ENDOR. The spectra exhibited two OHβ proton couplings, indicating that the anion is protonated to form a radical of the type R–Ċ(OH)2. The coupling tensors and their orientations clearly indicate that the amino proton in the neighboring NH3 group is transferred to the anion through the intermolecular hydrogen bond. Combining the results with those previously obtained for L‐alanine and succinic acid, the variation of the dipolar tensor elements with the isotropic values has been examined for the OHβ proton couplings in this type of radical. It is then shown that the anisotropic coupling is approximately independent of the dihedral angle of the O–Hβ bond. The dipolar tensors were also calculated as a function of the dihedral angle, and the results are in good agreement with the observations.
TL;DR: In this article, the authors used 1 H NMR spectra of rifamycin S in different solvents and at different temperatures to study the conformation of the ansa chain.
TL;DR: In this article, a dihedral angle criterion is employed to quantitatively assess shape parameters for polyhedra found in coordination compounds and cluster molecules and it is demonstrated through an analysis of structural data for five coordinate complexes that the Berry type of rearrangement is the lowest energy physical pathway for rearrangements in ML5 molecules or ions.
TL;DR: The crystal and molecular structure of a disubstituted acetylene complex of palladium, [Pd{C2(CO2Me)2}(PPh3)2], has been determined from three-dimensional X-ray diffraction data as discussed by the authors.
Abstract: The crystal and molecular structure of a disubstituted acetylene complex of palladium, [Pd{C2(CO2Me)2}(PPh3)2], has been determined from three-dimensional X-ray diffraction data. The complex crystallises in space group P21/c,C2h5, of the monoclinic system, with four molecules in a unit cell of dimensions a= 11·816(3), b= 15·331(4), c= 21·891(6)A, β= 113·22(1)°. No crystallographic symmetry is imposed upon the molecules and there is one molecule in the asymmetric unit. The structural parameters were refined by least squares techniques, the R-factor on F converging to 5·2% for the 3365 reflections, collected using a four-circle diffractometer, for which F > 0. Co-ordination around palladium is approximately planar: the dihedral angle between the plane defined by the palladium and two phosphorus atoms and that defined by the palladium and the two acetylenic carbon atoms is 9·7(4)°. The acetylenic carbon–carbon separation in the complex is 1·28(1)A, longer than expected for the free acetylene. Each substituent upon acetylene is planar to a reasonable approximation and is bent away from the metal by about 35° from the CC bond axis. The acetylenic carbon atoms are separated from the metal by 2·074(6) and 2·051(6)A and the metal–phosphorus bond lengths are 2·321(2) and 2·330(2)A. This slight asymmetry in the bond lengths to palladium is tentatively ascribed to the electronic effects of the differing orientations of the substituents upon acetylene.
Journal Article•
TL;DR: Sulfadiazine was determined using Patterson and Fourier synthesis methods and refined by block diagonal least squares methods with isotropic thermal parameter for all non-hydrogen atoms as mentioned in this paper.
Abstract: Sulfadiazine, , forms monoclinic crystals of space group from a mixture of acetone and ethanol with , and four molecules per cell. Three dimensional photographic data were collected with radiation. The structure was determined using Patterson and Fourier synthesis methods and refined by block diagonal least-squares methods with isotropic thermal parameter for all non-hydrogen atoms. The final R value was 0.15 for the 1517 observed independent reflections. The dihedral angle between the planes through the benzene ring and the pyrimidine ring is . The conformational angle formed by the projection of the S-C(5) bond with that of N(1)-C(1) where the projection is taken along the S-N(1) bond is . The imino nitrogen atom, N(1), and pyrimidine nitrogen atom, N(3), form intermolecular hydrogen bond between the molecules related by center of symmetry. Amino nitrogen atom, N(4), forms two intermolecular hydrogen bonds, with O(1) and O(2) atoms of different molecules separated by b. A two dimensional network of hydrogen bonds form infinite molecular sheets parallel to the (100) plane. Adjacent sheets are bound together by van der Waals forces.
TL;DR: In this article, the crystal and molecular structure of the cobalt and nickel derivatives of dithioacetylacetone (sacsacH) have been determined by X-ray diffraction methods.
Abstract: The crystal and molecular structure of the cobalt(II) and nickel(II) derivatives of dithioacetylacetone (sacsacH) have been determined by X-ray diffraction methods. Both crystals, being isomorphous, are orthorhombic, with space group Cmca and Z= 4. For Co(sacsac)2: a= 15·64(2), b= 14·35(2), and c= 6·05(1)A; for Ni(sacsac)2: a= 15·592(6), b= 14·348(8), and c= 5·950(3)A. The cobalt(II) structure was solved by conventional Patterson and Fourier methods and was refined by a least-squares method to R 0·11 for 437 independent reflections derived by photographic methods. For the nickel structure, 585 independent reflections, collected by counter methods, were used and the structure refined, by least squares, to R 0·044. The crystals are molecular with discrete monomeric molecular units of composition M (sacsac)2. Each metal atom, located a site of symmetry 2/m, is precisely coplanar with the four sulphur atoms bonded to it and, with an S–M–S intraligand bond angle of ca. 97°, the metal environment is conveniently described as square planar. However, the molecule as a whole is not planar being folded so that the dihedral angle between the MS4 and the ligand planes is ca. 6°. The metal–sulphur bond distance is ca. 2·17 A.
TL;DR: It is suggested that a change in the charge density of the amino group perturbs the dihedral angle of the -CH( 2)-S-S-CH(2)- moiety of oxytocin, which in turn significantly affects the overall conformation of the 20-membered ring of the hormone.
Abstract: The effects of hydrogen ion concentrations on the carbon-13 nuclear magnetic resonance spectra of oxytocin were investigated. The starting pD of 3.0 was increased stepwise to 8.4. A change of the state of protonation of the N-terminal amino group of oxytocin is accompanied by changes in chemical shifts of carbon-13 nuclei of amino-acid residues located in the 20-membered ring of the hormone. The resonance positions of the acyclic peptide portion, Pro-Leu-Gly-NH2, remain constant. The pD-induced chemical-shift changes of carbons up to five bonds removed from the site of protonation are interpreted in terms of “through-bond” and “through-space” mechanisms. Chemical-shift changes of carbons more than five bonds removed are proposed to have a conformational origin. It is suggested that a change in the charge density of the amino group perturbs the dihedral angle of the —CH2—S—S—CH2— moiety of oxytocin, which in turn significantly affects the overall conformation of the 20-membered ring of the hormone.