Showing papers on "Dihedral angle published in 1978"
TL;DR: Configurations that are rare for exposed residues are even rarer for buried residues, suggesting that, while the folded structure puts little strain on side-chain conformations, the side- chain positions with the lowest energy in the unfolded structure are chosen preferentially during folding.
759 citations
TL;DR: In this paper, a novel resolution enhancement technique which applies a sinusoidal half-wave window to the free induction decay combined with multiplication by an increasing exponential was used to extract resonances out of crowded spectral regions.
Abstract: The thus far unexplored aliphatic region of the proton magnetic resonance spectra of ferrichrome peptides was investigated at 360 MHz. Six isomorphic diamagnetic analogues of the ferric cyclohexapeptide differing in the coordinated cation (AL3+ or Ga3+) and the amino acid composition were studied in d6-DMSO solution. By use of a novel resolution enhancement technique which applies a sinusoidal half-wave window to the free induction decay combined with multiplication by an increasing exponential, the proton chemical shifts and spin-spin couplings were accurately measured. Homonuclear decoupling combined with Fourier difference spectroscopy was used to selectively extract resonances out of crowded spectral regions. The spectra revealed unique features of fine structure in the proton resonance lines. Thus, the conformation-dependent geminal coupling constants of glycyl α-protons were found to be constant throughout the suite of analogue peptides. A similar invariance was observed for the vicinal coupling constants between α-, β-, γ-, and δ-protons in the ornithyl side chains. Comparison of the proton spin–spin coupling constants with the crstallographic dihedral angles led to a unique stereochemical assignment of the side-chain resonances. The combined data sets of x-ray atomic coordinates and 1H-nmr spin-spin coupling parameters have been used to calibrate the coefficients for a Karplus curve related to the torsional x angles in amino acid side chains:
Structurial information was also obtained for the seryl residues, where the multiplet structures of the OH resonances indicate preferred spatial arrangements of the side chains.
154 citations
TL;DR: Methyl β-cellobioside (2) has been deuterated at positions C-2, -3, - 3′, -4, -6, and -6′ by 1H-2H exchange with deuterium oxide in the presence of Raney nickel catalyst.
Abstract: Methyl β-cellobioside (2) has been deuterated at positions C-2, -3, -3′, -4, -6, and -6′ by 1H–2H exchange with deuterium oxide in the presence of Raney nickel catalyst. The resulting simplificatio...
95 citations
TL;DR: In this paper, the authors reported the determination of two-and three-bond 1H-15N spin-spin couplings in the nmr spectra of a polypeptide.
Abstract: We report the determination of two- and three-bond 1H-15N spin–spin couplings in the nmr spectra of a polypeptide. The 1H- and 15N-nmr spectra of 99.2% 15N-enriched alumichrome have been studied at 360 MHz and 10.1 MHz, repectively. While some 2J and 3J coupling are of the order of 5 Hz, most splitting resulting from the heteronuclear interaction are ≲2 Hz, which introduces strigent requirements of spectral resolution. In the 1H spectra these requirements were met by digital deconvolution with a sine bell routine combined with positive exponential filtering. Although the 15N spectra clearly exhibit features of fine structure, mainly because of the intrinsic higher nmir sensitivity of protons, observation of 1H-15N spin–spin couplings was found to be more practical in the 1H than in the 15N spectra. We find that the alumichrome data do not satisfy a simple cyclic relationship linking the heteronuclear couplings to the crystallographic ψ dihedral angles. It is suggested that a formal treatment of the ψ-related interresidue 1H-15N coupling might have to take into account a more complex dependence of the intervening 3J on the overall local electronic structure, which is dependent on ϕ,ψ, and ω simultaneoulsy. In contrast, our analysis indicates that χ1 can be readily determined from the measurement of the corresponding heteronuclear 3J coupling in the 1Hβ or in the amide 15N resonances. Karplus relationships are proposed that relate this heteronuclear 3J to the corresponding dihedral angle θ and which, on average, yield
62 citations
TL;DR: In this paper, the bond distances (rg) and angles (rα) in ethyl methyl ether have been determined by gas electron diffraction as follows: average of C(methyl)−O and c(methylene)-O=1.418±0.004 A, ∠C−O−C=111.9± 0.5°, √ O−C−C-C=109.4 ± 0.3°,
Abstract: The bond distances (rg) and angles (rα) in ethyl methyl ether have been determined by gas electron diffraction as follows: average of C(methyl)–O and C(methylene)–O=1.418±0.002 A, C–C=1.520±0.004 A, C–H=1.118±0.004 A, ∠C–O–C=111.9±0.5°, ∠O–C–C=109.4±0.3°, ∠H–C–H=109.0±0.4°, where uncertainties represent estimated limits of experimental error. The two rg(C–O) distances have been estimated independently with the aid of the rotational constants for the trans conformer reported by Hayashi et al.: C(methyl)–O=1.413±0.009 A and C(methylene)–O=1.422±0.007 A. The dihedral angle for the gauche conformer, 84±6°, and the relative abundance of the trans and gauche conformers in the gas phase at 20 °C, nt⁄(nt+ng)=0.80±0.08, have also been determined.
57 citations
TL;DR: It is considered that the bulky, tetrahedral, neutral 8-substituent, with an effective van der Waals radius of 3.5--4.0 A, provides an adenosine analogue which should exhibit the syn conformation about the glycosidic bond in solution as well as in solid state, irrespective of the nature of the sugar pucker, suitable for studies of interactions with enzyme systems requiring the anti conformation of the nucleoside or nucleotide.
34 citations
TL;DR: In this paper, the carbon-13 chemical shifts for a number of relatively rigid ketoximes are presented, and it is shown that the chemical shift difference, A6 (sj~rr-onri), for the carbons a to the oxime carbon depends on the dihedral angle between the C=N and C.-H bonds.
Abstract: The carbon-13 chemical shifts for a number of relatively rigid ketoximes are presented. It is shown that the chemical shift difference, A6 (sj~rr-onri), for the carbons a to the oxime carbon depends on the dihedral angle between the C=N and C.-H bonds. This stereochernical dependence is then used to determine the preferred conforn~ation of substituted cyclohexanone oximes.
34 citations
TL;DR: In this paper, the radial distribution function (RDF) of a tetrahedrally bonded solids is taken to be the sum of n-bond neighbor distributions Jn(r), and limits are placed on the dihedral angle distribution, indicating that staggered configurations are more probable than eclipsed configurations.
Abstract: A theory is presented in which the radial distribution function (RDF) of a tetrahedrally bonded solids is taken to be the sum of n-bond neighbor distributions Jn(r). The Jn(r) are calculated, for n = 1–4, using parameters estimated from crystalline studies, and free parameters governing the dihedral angle distribution, ring statistics and bond-angle distortion. The accuracy of the theory is established by comparison with the results of structural models of amorphous Ge. Application of the theory to the structure of amorphous Ge accounts quantitatively for the experimental RDF out to a radius of 6 A. Limits are placed on the dihedral angle distribution, indicating that staggered configurations are more probable than eclipsed configurations. In general, the location of the third peak in the RDF is found to correlate with the fraction of staggered configurations.
32 citations
TL;DR: The hypothesis is formulated that receptor binding involves a specific conformation of the side-chain, different from the lowest energy state, for fifteen steroids studied.
29 citations
TL;DR: Two stable derivatives of 4a,5-dihydroflavin serving as models for enzymic catalytic intermediates have been synthesized and crystallized as mentioned in this paper.
Abstract: Two stable derivatives of'reduced' 4a,5-dihydroflavin serving as models for enzymic catalytic intermediates have been synthesized and crystallized: 4a-isopropyl-3-methyl-4a,5-dihydrolumiflavin (C~7H22N402) (I)and 4a,5-epoxyethano-3-methyl-4a,5-dihydrolumiflavin (C 16 H 18N403) (IV); (I) belongs to space group C2/c, Z = 8, with unit-cell dimensions a = 11.757 (2), b = 14.060 (2), c = 19.785 (2) A, fl = 91.38 (2)°; (IV) is monoclinic, space group P21/n, Z = 4, a = 12.665 (2), b = 15.217 (2), c = 7.804 (2) A, fl = 95.66 (2) °. Both structures have been solved by means of direct methods and refined by full-matrix least squares to final weighted R values of 0.046 for (I) and 0.041 for (IV). In contrast to the non-planar 1,5-dihydroflavins these 4a,5-dihydroflavins are almost planar, the dihedral angle measured along the N(5)-N(10) axis being 3.2 ° in the first case and 4.9 ° in the second. Ordinary van der Waals contacts are found in (IV), while in (I) two hydrogen bonds link two molecules to one another. Data for two further flavin derivatives [compounds (II) and (III)l have been collected. 821
28 citations
TL;DR: The crystal structure of carboxycobaltocenium hexafluorophosphate has been determined by single crystal X-ray diffraction techniques using three-dimensional data gathered at −35°C by counter methods.
TL;DR: In this paper, photoelectron spectra of 1,2-dialkyl-1,2diazetidines were used to study the conformations of tetraalkylhydrazines.
Abstract: Photoelectron spectra of 1,2-dialkyl- 1,2-diazetidines show that the 1,2-dimethyl compound (1) exists overwhelming- ly in the "diequatorial" trans conformation, while a significant amount of the "diaxial" trans conformation is detected for the diisopropyl compound (2), and the tricyclic structure holds the diazetidine ring in nearly eclipsed geometry for 3,4-dimethyl- 3,4-diazatricyclo(4.2.1 .02~5)non-7-ene (4) and its saturated analogue (3). Although N-dimethylaminoazetidine (5), N-dipro- pylaminoazetidine (6), and biazetidine (8) are predominantly in gauche conformations, the anti conformation predominates for N-piperidinylazetidine (7). The rates of double nitrogen inversion for 3 and 4 are nearly identical and increase slightly with increasing solvent polarity, and AG*298 is about 3.8 kcal/mol lower than for 1. The ESR splitting constants for the cations from 1,2, and 8 are reported, and compared to those for other tetraalkylhydrazine radical cations. Although many techniques have been used to study the conformations of tetraalkylhydrazines,2 two of the most useful are NMR and photoelectron (PE) spectroscopy. NMR allows accurate quantitation of the relative amounts of conformations if their interconversion is slow on the NMR time scale, and also determination of the rates for conformational equilibration. NMR does not directly yield information on the dihedral angle between the nitrogen long pairs (e), but the cis or trans dis- position of the N-alkyl groups attached to a ring may be es- tablished. This allows inferring 0 to within several degrees from a knowledge of the CN,NC endocyclic torsional angle allowed by the ring system in bicyclic233 and monocyclic The PE technique measures the vertical ionization potentials for the lone pair combination orbitals. Their separation is rather sensitive to 0, experimentally varying from a maximum of 2.3 eV near 0 = 180 and 0°5,6 to a minimum of about 0.5 eV near 0 = 90O.' The PE time scale is exceedingly short, so even if conformational interconversiuri ;S iuo rapid to be "frozen out" by NMR spectroscopy, the PE spectrum observed is the su- perposition of those for the conformations present. Although the relative amounts of different 0 value conformations thus detected cannot be nearly as accurately quantitated as in NMR experiments, the qualitative predominance of conformations in six-ring hydrazines determined by PE experiments has al- ways agreed with that determined by 13C NMR in solu- tion." Conformational information on tetraalkylhydrazine radical cations has come almost exclusively from ESR studies,* which have established that the barrier for double nitrogen inversion is quite low, and that for some cases in which the planar form is strained, the equilibrium geometry is not planar at nitro- gen.
TL;DR: The crystal and molecular structure of 1,1′,2,2′,4,4′-tris(trimethylene)ferrocene has been determined by X-ray diffraction.
TL;DR: The structure of 1,1′,2,2′,3,4,4′,5′-tetrakis(trimethylene)ferrocene has been determined by X-ray diffraction as discussed by the authors.
TL;DR: In this paper, the spectra of a cyclopropanol rotamer were fitted to a single set of rotational constants common to the 0+ and 0+ states and a 0−â†� 0+ excitation energy of 163.74(1.80) MHz.
Abstract: The Microwave spectra of cyclopropanol and cyclopropan-[2H1]-ol slow the gauche-conformation is the dominant species present in the vapour at 293K. No evidence for the existence of the trans-conformation has been obtained. The spectra of this rotamer show transitions associated with dipole components in all three inertial axes, the b-type transitions, which form an appreciable part of the spectra, being split into doublets separated by ≈ 8200 MHz in the normal form and by ≈ 326 MHz in the [2H1] form an account of contributions of the torisonal frequence 0–â†� 0+ to these absorptions. Many lines of the normal form depart from rigid rotor behaviour. An analysis has been made in terms of nine parameters for this form, and confirmed by numerous double reasonances. The 0–â†� 0+ excitation energy for this species is 4115.25(42) MHz. Spectra of gauche-cyclopropan-[2H1]-ol can be fitted to a single set of rotational constants common to the 0+ and 0– states and a 0–â†� 0+ excitation energy of 163.74(1.80) MHz. The dipole moment components of the [2H12] from are determined from Stark effect measurements as : µa= 1.58(10)× 10–30 C m, [0.48(3)D]′µb= 3.75(50)× 10–30 C m, [1.12(15) D]; µc= 2.70(57)10–30 C m, [0.81(17) D]; and µtotal= 4.88(67)× 10–30 C m, [1.46(20) D];. Substitution coordinates of the hydroxyl hydrogen accord with an equilibrium dihedral angle of internal rotation, α, of 106°± 5° relative to a zero at the trans-conformation. The 0–â†� 0+ energy differences are used in conjunction with this value of α and the assumption that no stable trans-from occurs, to yield an approximate potential function for internal rotation. The cis-barrier separating the gauche-minima is 7.9(1.5)kJ mol–1, while the barrier via the trans-conformation is 17(6) kJ mol–1, while the barrier via the trans-conformation is 17(6) kJ mol–1.
TL;DR: In this paper, electron diffraction and IR spectroscopic studies of furan-2-aldehyde and 2-furanmethanethiol were carried out to obtain information on the conformational properties and geometry of these molecules.
TL;DR: The method to obtain the dihedral angles for a low-energy structure of a protein is applied here to examine the degree of flexibility of bovine pancreatic trypsin inhibitor, indicating that the conformation of low energy is flexible to some extent in a restricted region of phi, psi space.
TL;DR: In this article, the dihedral-angle dependence of the geminal C-1-H-2 coupling is shown to be invariant to the presence of the amino group and appears to be a useful conformational probe.
TL;DR: In this article, it was shown that a significant fraction of the coupled vibrations of dihedral angles in real globular proteins are collective ones, i.e., those involving the whole protein molecules.
Abstract: Based on the assumption that the conformational energy surface of a protein molecule can be approximated near the global minimum point by a multidimensional parabola, conformational fluctuations in the native state are discussed. In this approximation the conformational fluctuations can be viewed as excitations of coupled harmonic oscillations of dihedral angles. For the purpose of estimating the range of frequencies vibrations, globular proteins are assumed to made of homogeneous continuous elastic material. The number of vibrational modes in such an elastic body, with the wavelength no less than the characteristic length of an amino acid residue, are estimated roughly to be three times the number of amino acid residues in a protein, which is slightly less than the number of variable dihedral angles in a protein. Their frequencies, when converted to the wavenumber of corresponding light, are found to range from 1.8 × 10 cm−1 to 2.1 × 102cm−1 for a protein with the diameter d = 40 A, when Young's E = 1011 dyne/cm2 is assumed. A significant fraction of the coupled vibrations of dihedral angles in real globular proteins are collective ones, i.e., those involving the whole protein molecules. Based on these results, it concluded that the depth of the global minimum s at least 150 Kcal/mol.
TL;DR: In this article, the authors analyzed the ring conformation of [S]-Proline (l -thiazolidine-4-carboxylic acid) with its Cδ atom enriched at 90% in 13C. The results suggest that the ring has an average planar conformation only in a narrow range of pH close to the pK of the amine group.
TL;DR: In this article, significant couplings over two, three and four bonds were observed between the hydroxyl proton and aromatic carbons for some acylphloroglucinol derivatives.
Abstract: Proton coupled 13C NMR spectra have been recorded for some acylphloroglucinol derivatives. Significant couplings over two, three and four bonds were observed between the hydroxyl proton and aromatic carbons for those compounds where the hydroxyl group is hydrogen bonded strongly enough to the carbonyl carbon of the acyl side chain. Typical values were 2J = 4.8 Hz, and 3J = 5.6 Hz or 6.7 Hz corresponding to dihedral angles of c. 0° and c. 180°, respectively; the dihedral angle is defined as the angle between the O—H bond and the plane of the aromatic ring. A stereospecific 4J(COH) value of 1.2 Hz for a ‘W’ arrangement of coupled atoms was also found. An interesting example of ‘virtual’ J(CH) coupling was observed in the proton coupled spectrum of 1-butyrylphloroglucinol 2-monomethyl ether in acetone-d6 caused by the accidentally equal chemical shifts of the two ring protons.
TL;DR: In this article, it was shown that the minima of these energies for ψ in acetamide and N-methylacetamide correspond well to 0 °-30 °, and that the total crystallographic conformational energy corresponds also to ψ = 0 ° −30 ° in agreement with the experimental data.
Abstract: SCFab initio and PCILO computations indicate the intrinsic preference of the ψ torsion angle for 60 °. In the crystal structure of simple methylamides and peptides the observed values for this torsion angle lie between 0 °–30 °. Different procedures for computing lattice energies and total crystallographic conformational energies (lattice + torsional) utilized by other authors, failed to account for this situation. We show that the procedure developed recently in our laboratory for computing lattice energies indicates that the minima of these energies for ψ in acetamide and N-methylacetamide correspond well to 0 °–30 °. Because of the low value of the barrier of the torsional potential for this angle, the total crystallographic conformational energy corresponds also to ψ = 0 °–30 ° in agreement with the experimental data.
TL;DR: In this paper, the infrared spectra of hexa-1,2-diene-5-yne (propargylallene, HC�C-CH 2 -CHCCH 2 ) were obtained for the vapour and liquid states and for a solid (−180°C) in the region 4000-200 cm −1.
TL;DR: The coupling constant for the bound saccharides indicates that the dihedral angle between C1 and C2 for the reducing saccharide is not significantly changed upon binding to lysozyme, which is discussed in terms of other evidence for the role of distortion of thesaccharide bound in subsite D in the lyso enzyme-catalyzed hydrolysis of cell wall oligosaccharides.
Abstract: The binding of the trisaccharide (2-acetamido-2-deoxy-D-muramic acid)-β(1→4)-(2-aceta-mido-2-deoxy-D-glucosyl)-β(1→4)-(2-acetamido-2-deoxy-D-muramic acid) to subsites B, C, and D in lysozyme has been studied by 1H nuclear magnetic resonance methods. In particular, the coupling constant between H1 and H2 of the reducing saccharide bound in subsite D has been determined. The coupling constant for the bound saccharide indicates that the dihedral angle between C1 and C2 for the reducing saccharide is not significantly changed upon binding to lysozyme. This result is discussed in terms of other evidence for the role of distortion of the saccharide bound in subsite D in the lysozyme-catalyzed hydrolysis of cell wall oligosaccharides.
TL;DR: In this paper, the 4-31G basis set was used to study the bond length variations as functions of dihedral angels in methanediol and the possible reason for bond length shorteing in the trans trans configuration was analyzed.
TL;DR: The absolute configuration of four isomeric steroidal molecules containing the isoxazolidine-[2,3-d]-oxadiazoline moiety has been determined by circular dichroism and X-ray diffraction methods as mentioned in this paper.
TL;DR: In this paper, a prismatic yellow compound C 13 H 9 FeN 3 O 6, which is a 1,5-cycloaddition of tricarbonylcycloheptatrieneiron and Nethyltriazolinedione was given.
Patent•
03 Jan 1978
TL;DR: In this paper, the authors describe an aerodynamic structure having lift for use on an aerodyne, which comprises first and second essentially identical planar sections hingedly connected at their roots to one another at dihedral angles.
Abstract: The specification describes an aerodynamic structure having lift for use on an aerodyne. The structure comprises first and second essentially identical planar sections hingedly connected at their roots to one another at dihedral angles. The sections are moveable in unison to vary the angle between each section and its transverse axis.
TL;DR: In this article, a Fourier-type expansion of the potential function was applied to the study of internal rotation in hydroxylamine and its fluorinated derivatives, and the computed energies were analyzed in terms of a decomposition of the total potential function into onefold, twofold, threefold and fourfold components.