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Showing papers on "Dihedral angle published in 1986"


Journal ArticleDOI
TL;DR: In this article, the morphological stability criteria of melts in edge and corner regions in a partially molten system containing several solid phases (three) under textural equilibrium are proposed in terms of dihedral angles.
Abstract: The morphological stability criteria of melts in edge and corner regions in a partially molten system containing several solid phases (three) under textural equilibrium are proposed in terms of dihedral angles. Owing to the variety of edge and corner regions due to combination of the crystalline phases in the multi-solid phase system, melts are morphologically stable in some types of edges and corners, and unstable in others. In order to apply the stability criteria to the partially molten regions in the upper mantle we conducted a partial melting experiment with a peridotite mainly composed of olivine (OL), orthopyroxene (OPX), and clinopyroxene (CPX) crystals at 1300°C, 1 GPa and for 300 hours. Various types of dihedral angles were measured on the run product which contained about 7% melt. The melt versus OL/OL dihedral angle was significantly smaller than other types of melt versus solid/solid dihedral angles. Applying the stability criteria to these experimental results, we predict that in the partially molten peridotite the melts are morphologically stable only in OL-OL-OL edge regions and in OL-OL-OL-OL and OL-OL-OL-OPX corner regions. The connectivity of the melt phase is determined by the melt distribution in the stable edge and corner regions at melt fractions less than 29%. The melt distribution can be modeled by the bond distribution in a lattice, that is, bond percolation. The connectivity of the melt phase is estimated as a function of the modal composition and grain size distribution of the matrix and is graphically presented as a connectivity diagram (OL-OPX-CPX modal composition diagram). The trajectory of modal composition of the solid matrix in the connectivity diagram determines the connectivity history of a rock during progressive partial melting in the upper mantle. Three different cases of connectivity history are discerned depending upon the modal composition before melting and are characterized by the critical melt fractions ϕmc, at which the melt phase suddenly becomes connecting, such as ϕmc = 0, 0 < ϕmc < 0.29, and ϕmc ≒ 0.29. In a peridotite the modal portion of olivine but also the relative grain size are the most important determinant of the connectivity behavior in the upper mantle.

248 citations


Journal ArticleDOI
TL;DR: Haddon and Scott as mentioned in this paper showed that the skeletal dihedral angle may be a poor index of ir-orbital alignment, and that rehybridization from sp2 may have a significant effect on ir-orbital alignment.
Abstract: The field of bridged annulene chemistry began twenty years ago with the synthesis of 1,6methano[10]annulene, and since that time a great many variations on this theme have been reported. By their very nature it is usually impossible for these systems to attain complete coplanarity, and irorbital misalignment often occurs in the periphery. In many cases these deformations have been confirmed by structural, spectroscopic and theoretical investigation, and it has often been noted that these compounds tolerate remarkably high ir-orbital misalignment (as measured by the peripheral dihedral (torsional) angles), without quenching of the cyclic delocalization and aromatic character. It is the purpose of this communication to point out that in nonplanar conjugated molecules: (i) the skeletal dihedral angle may be a poor index of ir-orbital alignment; (ii) rehybridization (from sp2) may have a significant effect on ir-orbital alignment; (iii) the ir-orbital alignment obtained in molecules such as the bridged annulenes is far better than hitherto realized. This process is accomplished by development of a general analytical method for the location of the ir-orbital axis vector (POAV) in nonplanar conjugated molecules. The field of bridged annulene chemistry began twenty years ago with the synthesis of 1,6-methanoL 10]annulene,' and since that time a great many variations on this theme have been reported.2 By their very nature it is usually impossible for these systems to attain complete coplanarity, and ir-orbital misalignment often occurs in the periphery. In many cases these deformations have been confirmed by structural, spectroscopic and theoretical investigation,328 and it has often been noted that these compounds tolerate remarkably high ir-orbital misalignment (as measured by the peripheral (skeletal) dihedral angles), without quenching of the cyclic delocalization and aromatic character.29 It is the purpose of this study to point out that in nonplanar conjugated molecules: (i) the skeletal dihedral angle may be a poor index of ir-orbital alignment; (ii) rehybridization (from sp2) may have a significant effect on ir-orbital alignment; (iii) the ir-orbital alignment obtained in molecules such as the bridged annulenes is far better than hitherto realized. This process is accomplished by development of a general analytical method for the location of the ir-orbital axis vector (POAV) in nonplanar conjugated molecules. We begin by noting that in order for the dihedral (torsional) angle to provide a unique and accurate picture of ir-orbital alignment, each of the bonded pair of atoms must (separately) lie in the same plane as its nearest neighbors. Thus Cl, C2, C3 and R2 (Figure 1) are required to be coplanar, as are C2, C3, C4 and R3 if the dihedral angle (usually taken as Cl, C2, C3, C4) is to provide a meaningful index of ir-orbital alignment. Clearly as the restriction on coplanarity is removed, the dihedral angle is no longer unique, and in general there exist four possible choices (Cl, C2, C3, C4; Cl, C2, C3, R3; R2, C2, C3, C4; R2, C2, C3, R3). The point really at issue of course, is the state of hybridization of C2 and C3, and a more fruitful approach is to pursue the ir-orbital axis vector (POAV) directly, which is the real quantity of interest in the present context. 137 138 ft C. HADDON and L. T. SCOTT X2 — + JPx) Figure 2. Hybrid orbitals Xi, • X for hybridization intermediate between sp2 and sp3. Xi is colinear with the ic-orbital axis vector and is constructed so as to make an equal inclination to the edges of the trihedral angle formed by Xi X3 and X4 and is defined to lie along the Z-axis. 0 is the angle of inclination made by X2, X3 and X4 to the X, Y plane. X3 — — jPx — .jPy) X4 = —=(s — + /fpy) and Xi — Fs + /Pz) X2 — }(s — *Pz + jfpx) 1 1 X3 — Pz — .JfPx — JPy) X4 --(s *PzJfPx +py) (pure sp2)

247 citations


Journal ArticleDOI
TL;DR: The determination of the three‐dimensional solution structure of α1‐purothionin is that of the capital letter L, similar to that of crambin, with the longer arm comprising two approximately parallel α‐helices and the shorter arm a strand and a mini anti‐parallel β sheet.
Abstract: The determination of the three-dimensional solution structure of α1-purothionin using a combination of metric matrix distance geometry and restrained molecular dynamics calculations based on n.m.r. data is presented. The experimental data comprise complete sequence-specific proton resonance assignments, a set of 310 approximate interproton distance restraints derived from nuclear Overhauser effects, 27 O backbone torsion angle restraints derived from vicinal coupling constants, 4 distance restraints from hydrogen bonds and 12 distance restraints from disulphide bridges. The average atomic rms difference between the final nine converged structures and the mean structure obtained by averaging their coordinates is 1.5 ± 0.1 a for the backbone atoms and 2.0 ± 0.1 a for all atoms. The overall shape of α1-purothionin is that of the capital letter L, similar to that of crambin, with the longer arm comprising two approximately parallel α-helices and the shorter arm a strand and a mini anti-parallel β sheet.

242 citations


Journal ArticleDOI
TL;DR: In this article, the authors showed that the MII-H and MII−C bond distances are significantly larger (by 4-10 pm) than their MIV−H and mIV−C counterparts, and valence angles at M increase in the series GeH2= SnH2 < GeMe2 = SnMe2= GeR2 > GeMe 2 < GeR 2 < SnR2> < GeH 2> < SnH 2 > SnR 2> > Ge R 2.
Abstract: Bis[bis(trimethylsilyl)methyl]germanium, GeR2[R = CH(SiMe3)2], is conveniently prepared from GeCl2(diox)(diox = 1,4-dioxane)(for which an improved synthesis, from GeCl4 and SnHBun3, is reported) and 2MgCl(R)(OEt2), MgR2(diox)0.5, or MgR2(OEt2) in OEt2. The corresponding tin(II) alkyl is accessible from SnCl4 and successively 2LiR (to yield SnCl2R2) and Li2(cot)(cot = cyclooctatetraene) in OEt2. Gas-phase electron diffraction (g.e.d.) patterns, recorded with nozzle temperatures of 155 °C for GeR2 and 120 °C for SnR2, show that the gas consists of V-shaped monomers. Least-squares refinements of models of C2 symmetry yielded the bond distances Ge–C 203.8(15) and Sn–C 222(2) pm and the angles CGeC 107(2) and CSnC 97(2)°. In GeR2 the –CH(SiMe3)2 ligands are oriented so that the HCiMCiH moiety (Ci= inner, or methine, C) has a nearly planar syn,syn conformation but in SnR2 the dihedral angles CiMCiH are ca. 15°. Ab initio molecular-orbital calculations with a better than DZ (double zeta) basis were carried out on the model compounds MH2 and GeMe2, and yielded the optimal bond distances Ge–H 158, Ge–C 202, and Sn–H 177 pm, and valence angles HGeH 93, CGeC 97, and HSnH 93°. Correlation of experimental and calculated structures shows that MII–H and MII–C bond distances are significantly larger (by 4–10 pm) than their MIV–H and MIV–C counterparts, and valence angles at M increase in the series GeH2= SnH2 < GeMe2= SnMe2 < GeR2 < SnR2. Both the long bond distances and the less-than-tetrahedral valence angles are rationalised by assuming the metal lone pair to occupy atomic orbitals of predominant s character and the M–H and M–C σ-bonding orbitals to be formed from metal atomic orbitals of predominant p character.

121 citations


Journal ArticleDOI
TL;DR: The crystal and molecular structure of quercetin, one of the bioflavonoids found in plants, is described in this article, and the structure is of interest because of the variety of biological systems affected by it.

112 citations


Journal ArticleDOI
TL;DR: In this paper, molecular dynamics simulations of hen egg-white lysozyme in the free and substrate-bound states are reported and the nature of the average structures and atomic fluctuations are analyzed.

102 citations


Journal ArticleDOI
TL;DR: The structure and dynamics of an 8-base-pair DNA fragment in aqueous solution has been simulated by using the molecular-dynamics method and averaged MD structures are compared with ideal A-DNA and B-DNA structures in terms of helix parameters, dihedral angles, and so forth.
Abstract: The structure and dynamics of an 8-base-pair DNA fragment (dCGCAACGC/dGCGTTGCG) in aqueous solution (14 Na+ ions, 1231 water molecules) have been simulated by using the molecular-dynamics method. Interproton distances have been calculated for various structures and are compared with a set of 174 distances which have been derived from 2D NOE experiments. The averaged MD structures are compared with ideal A-DNA and B-DNA structures in terms of helix parameters, dihedral angles, and so forth. The hydration of various atoms of the DNA fragment and of the Na+ ions is analyzed by calculating coordination numbers and first-neighbor shell residence times.

100 citations


Journal ArticleDOI
TL;DR: In this article, a theory for predicting the distribution of apparent angles observed on a random planar section of a three-dimensional aggregate with one true dihedral angle is reviewed and comparisons are made between apparent angle distributions obtained from partial melting experiments and various theoretical distributions.
Abstract: The distribution of apparent solid-liquid dihedral angles, normally observed on planar sections of partial melting experiments, is examined in terms of a normal distribution of “true” dihedral angles present in any sample. A theory for predicting the distribution of apparent angles observed on a random planar section of a three-dimensional aggregate with one true dihedral angle is reviewed and comparisons are made between apparent angle distributions obtained from partial melting experiments and various theoretical distributions. The results of these comparisons suggest that the observed distribution of solid-liquid dihedral angles in partial melting experiments rarely yield a satisfactory match to the theoretical distribution for a single unique dihedral angle. However, good agreement is generally obtained assuming a normal distribution of true dihedral angles about a mean value. The origin of this normal distribution is discussed both in terms of measuring error and crystalline anisotropy with respect to interfacial energies.

100 citations


Journal ArticleDOI
TL;DR: The crystal structure of wheat germ agglutinin isolectin 2 has been refined by the restrained least-squares method of Hendrickson & Konnert (1980) and side-chains involved in hydrogen bonds were found to be relatively flexible and able to adapt their conformation to changes in environment.

94 citations


Journal ArticleDOI
TL;DR: In this paper, the product rotation is generated by an axial torsion about the O-O axis, consistent with a change in dihedral angle in the upper state.

74 citations


Journal ArticleDOI
TL;DR: The crystal and electronic structures of molecular superconductor θ-(BEDT-TTF)2(I3)1−x(AuI2)x (x < 0.02) were examined as discussed by the authors.
Abstract: The crystal and electronic structures of molecular superconductor θ-(BEDT-TTF)2(I3)1−x(AuI2)x (x<0.02) were examined. BEDT-TTF molecules form a two-dimensional network. The dihedral angle between the planes of the neighbouring molecules interrelated by the screw axis is about 80°. Examination of the band structure suggests that this complex is the first example of the molecular conductor with a completely round two-dimensional Fermi surface.

Journal ArticleDOI
TL;DR: In this paper, an improved refinement procedure was proposed for the lac repressor headpiece, which combines model building with restrained energy minimization (EM) and molecular dynamics (MD) techniques.
Abstract: In recent years a procedure has been developed by which the three-dimensional (3D) structure of biomolecules can be derived from 2D NMR data. This procedure combines model building with restrained energy minimization (EM) and molecular dynamics (MD) techniques. Distance information from NOE's is incorporated in the form of an upper limit distance restraining term that is added to the interatomic potential function. Here, two improvements of the refinement procedure are introduced. First, the information that is contained in empty parts of 2D-NOE spectra is transformed into, so-called, non-NOE's which are modelled by adding a lower limit distance restraining term to the potential function for each non-NOE proton pair. Secondly, the information that is contained in the occurrence of large J-coupling constants for specific dihedrals is modelled by adding a sinusoidal dihedral angle restraining term to the potential function for each dihedral angle with a large J-value. The improved refinement procedure is tested by application of the lac repressor headpiece. Both the inclusion of non-NOE data and the inclusion of J-coupling information markedly improve the result of the restrained MD refinement of headpiece. In the refinement procedure MD simulation is used for searching configuration space. Energy barriers which are too high to be crossed by MD are surmounted by manually changing the model structures on a picture system. The resulting close non-bonded contacts are relaxed by EM. The final structure of headpiece satisfies essentially all 169 NOE and 9529 non-NOE distance constraints as well as the 6Cα – Cβ dihedral angle values corresponding to the measured J-coupling values.

Journal ArticleDOI
01 Jun 1986-Polymer
TL;DR: In this paper, the crystal structure of oriented fibres of poly(ether-ether-ketone) (PEEK) has been analyzed by X-ray diffraction and refined by the linked-atom least squares procedure.

Journal ArticleDOI
TL;DR: In this paper, MNDO calculations on polyaniline segments of the polymer were carried out to get a quantitative picture of the geometry, and the results indicated that the structure is unchanged upon protonation and that the injected charge is delocalized.

Journal ArticleDOI
TL;DR: This work has confirmed that dithioglycolic acid can crystallize in two different forms, one with trans and the other with gauche conformations about both C-S bonds, and that these have S-S stretching bands at 536 and 510 cm-1, respectively.
Abstract: Two hypotheses have been advanced to explain the conformational dependence of the disulfide stretching frequency of the CCSSCC moiety in unstrained disulfides. Such compounds can adopt conformations that exhibit disulfide stretching bands near 510, 525, and 540 cm-1. Sugeta et al. [Sugeta, H., Go, A. & Miyazawa, T. (1973) Bull. Chem. Soc. Jpn. 46, 3407-3411] have attributed these three bands to conformations having none, one, and two trans conformations, respectively, about the C-S bonds. In apparent contradiction to this correlation, Van Wart and Scheraga [Van Wart, H. E. & Scheraga, H. A. (1976) J. Phys. Chem. 80, 1812-1823] found that dithioglycolic acid crystals, believed at the time to exist only in the trans conformation about both C-S bonds, exhibited the S-S stretching band near 510 cm-1. On the basis of this observation, it was suggested instead that the 510, 525, and 540 cm-1 bands arose from CCSSCC moieties having none, one, and two A conformations (i.e., those with CC-SS dihedral angles close to 30 degrees), respectively, about the C-S bonds. It has recently been shown by Nash et al. [Nash, C. P., Olmstead, M. M., Weiss-Lopez, B., Musker, W. K., Ramasubbu, M. & Parthasarathy, R. (1985) J. Am. Chem. Soc. 107, 7194-7195] that dithioglycolic acid can crystallize in two different forms, one with trans and the other with gauche conformations about both C-S bonds, and that these have S-S stretching bands at 536 and 510 cm-1, respectively. These results are confirmed here and it is shown that our earlier data were collected on the all-gauche (rather than the all-trans) form. Thus, the correlation proposed by Sugeta et al. is correct.

Journal ArticleDOI
TL;DR: In this paper, a semi-empirical Hartree-Fock and valence effective Hamiltonian (VEH) calculations on polyaniline in its oxidized (so-called 2A) form are presented.

Journal ArticleDOI
TL;DR: A computer program has been developed which allows exhaustive exploration of the conformation of medium sized rings (8 to 22-membered) and provides for inclusion of experimental data from NMR measurements in the form of dihedral angles estimated by the Karplus equation and NOE close contacts.

Journal ArticleDOI
TL;DR: In this paper, the S-S dihedral angle of disulfide groups was analyzed using the split-valence 6-31G(*) basis set, and it was shown that the hyperconjugation between the s-H bond and the electron pair on the other sulfur plays an important role in determining the characteristic s-S dilation angle.
Abstract: The characteristics of disulfide groups concerning the S-S dihedral angle are represented by ab initio SCF calculations using the split-valence 6-31G(*) basis set. It is shown that the hyperconjugation between the S-H bond and the electron pair on the other sulfur plays an important role in determining the characteristic S-S dihedral angle. The S 3d orbitals do not participate in such characteristics. The nature of the S-S bond is compared with that of the O-O bond. The S-S bond length varies largely depending on the S-S dihedral angle. This is related to the frequency-conformation correlation of the disulfide group.

Journal ArticleDOI
TL;DR: In this article, two model liquids each composed of linear chain molecules containing six interaction sites have been investigated using molecular dynamics computer simulation at constant density at temperatures of 300 K and 200 K, the latter being close to the normal freezing temperature of real hexane.
Abstract: Two model liquids each composed of linear chain molecules containing six interaction sites have been investigated using molecular dynamics computer simulation. One of the liquids has features which resemble those of n-hexane. For the other liquid the interaction parameters are identical except that the dihedral angle potential restricting the torsional motions is set to zero. This flexible form of hexane is called flexane. Simulations have been performed at constant density at temperatures of 300 K and 200 K, the latter being close to the normal freezing temperature of real n-hexane. The molecular conformational distributions for the two liquids are quite different although this has little effect on the intermolecular configurational properties; it is shown that the two liquids are in closely corresponding thermodynamic states at both temperatures. The unrestricted torsional motions in flexane result, however, in a 70 per cent enhancement of the self diffusion coefficient at 200 K as compared to the more ...

Journal ArticleDOI
TL;DR: In this paper, the sensitivity of jet-cooled benzophenone to the S/sub 1/(n,..pi../sup */) transition has been measured and it was found that the spectrum consists exclusively of several long progressions of 60 cm/sup -1/ which is the in-phase torsional mode of the phenyl rings.
Abstract: The sensitized phosphorescence excitation spectrum of jet-cooled benzophenone due to the S/sub 1/(n,..pi../sup */) produced from S/sub 0/ transition has been measured. It was found that the spectrum consists exclusively of several long progressions of 60 cm/sup -1/ which is the in-phase torsional mode of the phenyl rings. The vibrational analysis and the potential calculation shows that the in the S/sub 1/(n,..pi../sup */) state great geometry changes occur in the dihedral angle between the phenyl rings, the C=O bond distance, and the C-C bonds adjacent to the C=O bond.

Journal ArticleDOI
TL;DR: In this article, the tin atom was determined by direct methods and refined to a final R value of 0.031 for 3736 observed Mo-Kα reflections, and the structure was shown to have a 9.2,2′-Bipyridyldichlorodi(p-tolyl)tin(IV), C24H22N2Cl2Sn, crystallizes in the monoclinic space group P21/c.

Journal ArticleDOI
TL;DR: In this paper, the authors investigated the coupling of torsion and OH vibration in hydrogen peroxide by high level ab initio calculations within a Born-Oppenheimer framework, and calculated the trans barrier and equilibrium torsional angle as a function of OH stretch and averaged over Morse local-mode wavefunctions for the nine lowest overtone states.
Abstract: The authors investigated the coupling of torsion and OH overtone vibration in hydrogen peroxide by high level ab initio calculations. Within a Born-Oppenheimer framework, the trans barrier and equilibrium torsional angle were calculated as a function of OH stretch and averaged over Morse local-mode wavefunctions for the nine lowest overtone states. Using MP2 and GVB methods at the highly extended 6-311G(3d,2p) basis set level, they obtain near-quantitative agreement with experiment for the dihedral angle and the observed increase of the trans barrier with OH overtone stretching, based purely on potential energy coupling terms of electronic origin.

Journal ArticleDOI
TL;DR: In this article, the three-dimensional structure was determined by x-ray crystallography for d(T[p](CE)T), a uv photoproduct of the cyanoethyl (CE) derivative of d (TpT), having the cis-syn cyclobutane (CB) geometry and the S-configuration at the chiral phosphorus atom.
Abstract: The three-dimensional structure was determined by x-ray crystallography for d(T[p](CE)T), a uv photoproduct of the cyanoethyl (CE) derivative of d(TpT), having the cis-syn cyclobutane (CB) geometry and the S-configuration at the chiral phosphorus atom. The crystals of C23H30N5O12P · 2H2O belong to the orthorhombic space group P212121 (Z = 4), with cell dimensions a = 11.596 A, b = 14.834 A, and c = 15.946 A, containing two water molecules per asymmetric unit. The CB ring is puckered with a dihedral angle of 151°. The two pyrimidine bases are rotated by –29° from the position of direct overlap of their corresponding atoms. This represents a major distortion of DNA, since in DNA adjacent thymines are rotated by +36°. The pyrimidine rings are puckered with Cremer–Pople parameters for T[p] and in parentheses [p]T: Q: 0.24 A (0.31 A); θ: 123° (120°); ϕ: 141° (86°). These represent half-chairs designated as 6H1 (T[p]) and 6H5 ([p]T). The CB and pyrimidine ring conformations are interrelated, and we postulate that they execute a coupled interconversion in solution. The T[p] segment has the syn glycosyl conformation, a 2T3 sugar pucker, and gauche− conformation at C4′-C5′; the [p]T segment is anti, 3T4, trans. The C5′-O5′ torsion of the [p]T unit is –124.5°, and the C3′-O3′ torsion of the T[p] unit is –152.9°. Bond angles and bond lengths involving the phosphorus atom are similar to those of other phosphotriesters. The P-O3′ and P-05′ torsion angles are –138.1° and 58.6°, respectively. Several intermolecular (but no intramolecular) hydrogen bonds are found in the crystal.

Journal ArticleDOI
TL;DR: In this article, the isotopic multiplets observed in the /sup 13/C NMR spectra of amides, carbohydrates, or amines with partially deuterated NH or OH groups can be very helpful in spectral assignments.
Abstract: Recent reports have demonstrated that isotopic multiplets observed in the /sup 13/C NMR spectra of amides, carbohydrates, or amines with partially deuterated NH or OH groups can be very helpful in spectral assignments. These multiplets are due to upfield deuterium isotope effects on the /sup 13/C chemical shifts and can be observed in the slow hydrogen exchange conditions. This paper presents the first application of the isotopic multiplets to the /sup 13/C NMR spectra of the coordination compounds, which can provide interesting examples of dihedral angular dependence of the three-bond isotope effects. 17 references, 2 tables.

Journal ArticleDOI
TL;DR: In this paper, the molecular structure of 1,1,2,2-tetrabromodisilane has been investigated using gas-phase electron diffraction data obtained at 110°C.

Journal ArticleDOI
TL;DR: Comparison of the solid state molecular structures of methoxypromazine and N-monodesmethyl chlorpromazine sulphoxide reveals that these compounds exist in two different conformations, which have the side-chain on opposite sides of the ring system.

Journal ArticleDOI
TL;DR: The structure and internal motions of the protein hen egg white lysozyme are studied by analysis of simulation and experimental data and the regions that have large deviations among the x‐ray crystal structures, which indicates flexibility, are found to have large fluctuations in the simulation.
Abstract: The structure and internal motions of the protein hen egg white lysozyme are studied by analysis of simulation and experimental data. A molecular dynamics simulation and an energy minimization of the protein in vacuum have been made and the results compared with high-resolution structures and temperature factors of hen egg white lysozyme in two different crystal forms and of the homologous protein human lysozyme. The structures obtained from molecular dynamics and energy minimization have root-mean-square deviations for backbone atoms of 2.3 A and 1.1–1.3 A, respectively, relative to the crystal structures; the different crystal structures have root-mean-square deviations of 0.73–0.81 A for the backbone atoms. In comparing the backbone dihedral angles, the difference between the dynamics and the crystal structure on which it is based is the same as that between any two crystal structures. The internal fluctuations of atomic positions calculated from the molecular dynamics trajectory agree well with the temperature factors from the three structures. Simulation and crystal results both show that there are large motions for residues involved in exposed turns of the backbone chain, relatively smaller motions for residues involved in the middle of helices or β-sheet structures, and relatively small motions of residues near disulfide bridges. Also, both the simulation and crystal data show that side-chain atoms have larger fluctuations than main-chain atoms. Moreover, the regions that have large deviations among the x-ray crystal structures, which indicates flexibility, are found to have large fluctuations in the simulation.

Journal ArticleDOI
TL;DR: In this paper, the average value of the dihedral angle at the edge of a microstructural feature was determined by an appropriate combination of two simple stereological counting measurements, and the result also provided a demonstration that the average dihedral angles measured on a section through the edge is equal to average of the true angle measured in three dimensions.

Journal ArticleDOI
TL;DR: In this article, two conformers were identified, a planar isomer with the S atom syn to the 0 atom and a less stable planar (or near planar) anti form.

Journal ArticleDOI
TL;DR: In this article, the natural abundance 17O n.m.r. spectra of thirteen hindered aryl ketones are reported and correlated with the torsion angle, predicted by molecular mechanics calculations, between the carbonyl group and the aromatic ring.
Abstract: The natural abundance 17O n.m.r. spectra of thirteen variously hindered aryl ketones are reported and correlated with the torsion angle, predicted by molecular mechanics calculations, between the carbonyl group and the aromatic ring.