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Dihedral angle

About: Dihedral angle is a research topic. Over the lifetime, 15718 publications have been published within this topic receiving 174904 citations.


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Journal ArticleDOI
TL;DR: A new formulation for a dihedral angle autocorrelation function is introduced and applied to study side-chain dynamics in L-Enk, finding that the side- chain dynamics of the large Tyr and Phe residues cannot be adequately sampled in 2.0-ns simulations, while this does seem to be possible for the smaller Leu side chain.

122 citations

Journal ArticleDOI
Chang Seop Hong1, Ja Eung Koo1, Sang-Kil Son1, Yoon Sup Lee1, Yaung Soo Kim, Youngkyu Do1 
TL;DR: The MO calculations indicate that the quasiorthogonality between the magnetic orbital of metal ions and the p atomic orbitals of the bridging azide is possible in the observed structures and leads to the ferromagnetism.
Abstract: Two new one-dimensional single azide-bridged metal(II) compounds [[M(5-methylpyrazole)4(N3)]n](ClO4)n(H2O)n [M = Co (1a), Ni (2a)] were prepared by treating an M(II) ion with stoichiometric amount of sodium azide in the presence of four equivalents of the 3(5)-methylpyrazole ligand. The isostructural compounds 1a and 2a crystallize in the monoclinic space group P2(1)/n. The azide bridging ligands have a unique end-to-end coordination mode that brings two neighboring metal centers into a cis-position with respect to the azide unit to form single end-to-end azide-bridged cobalt(II) and nickel(II) chains. The two neighboring metal atoms at inversion centers adopt octahedral environments with four equatorial 3(5)-methylpyrazole ligands and two axial azide bridges. Two adjacent equatorial least-squares planes form dihedral angles of 60.5 degrees and 60.6 degrees for Co and Ni, respectively. In addition, the metal-azide-metal units form large M-N3-M torsion angles, which are magnetically important geometrical parameters, of 71.6 degrees for M=Co and 75.7 degrees for M=Ni. It should also be noted that the M-N-N angles associated with end-to-end azide group, another magnetically important structural parameter, fall into the experimentally observed range of 120-140 degrees as 128.3(3) and 147.8(3) degrees for cobalt species and 128.4(2) and 146.1(3) degrees for nickel species; these values deviate from the theoretical value of around 164 degrees at which the incidental orthogonality is achieved under the torsion angle of 0 degrees. The compounds 1a and 2a have unique magnetic properties of ferromagnetism, zero-field splitting, and spin canting. The MO calculations indicate that the quasiorthogonality between the magnetic orbitals of metal ions and the p atomic orbitals of the bridging azide is possible in the observed structures and leads to the ferromagnetism. The spin canting related to the perturbation of ferromagnetism arises from the magnetic anisotropy and antisymmetric interactions judged by the structural parameters of the zero-field splitting and the tilted MN4 planes in a chain. The enhancement of magnetic interactions was accomplished by dehydrating the chain compounds to afford two soft magnets with critical temperature T(C) and coercive field of 2 K and 35 G for 1b and 2.3 K and 20 G for 2b, respectively.

122 citations

Journal ArticleDOI
TL;DR: The dihedral angle between the rings of biphenyl is determined to be 32 ± 2° in the molten and solution states as mentioned in this paper, and the values of the force constants associated with the inter-ring bond are discussed.
Abstract: The dihedral angle between the rings of biphenyl is determined to be 32 ± 2° in the molten and solution states. Observed vibrational frequency shifts on going from the planar configuration held in the crystal to the non-planar solution state are compared with computed frequency shifts. To improve the accuracy in the computed frequencies the force constants were refined. The values of the force constants associated with the inter-ring bond are discussed.

122 citations

Journal ArticleDOI
TL;DR: In this paper, the authors introduced a map, where the mutual distance between C α -atoms of i -th and j -th residue, r i j, is listed against the residue number, in row and column.
Abstract: A protein conformation can be computed by connecting peptide units of usual trans-planar structure successively with a given set of dihedral angles ϕ and ψ. It is, however, not easy to generate the native conformations such as myoglobin and lysozyme by the computation. In order to show the discrepancy between the native conformation and the computed one, we have introduced a map, where the mutual distance between C α -atoms of i -th and j -th residue , r i j , is listed against the residue number, in row and column. This map represents a tertiary structure of the protein (e. g. α-helix, β-structure) as the characteristic patterns. It becomes possible to estimate the difference of the computed conformation from the native one numerically by comparing the corresponding maps. The improvement of the dihedral angles, ϕ and ψ, as made by minimizing the deviation of the computed map from the native one on both myoglobin and lysozyme.

122 citations

Journal ArticleDOI
TL;DR: The crystal structure of [Ni3(bipyam-H)4Cl2] has been determined using X-ray diffractometer data; C415H355Cl2N12Ni3O075, monoclinic, space group C2/c, with a= 37525(7), b= 16237(3), c= 22550(6)A, β= 11012(2), Z= 12; 5778 measured and 5519 unique reflections gave a final R value of 0051.
Abstract: The crystal structure of [Ni3(bipyam–H)4Cl2]·023H2O·05(CH3)2CO 1[bipyam–H = bis(2-pyridyl)-amide] has been determined using X-ray diffractometer data; C415H355Cl2N12Ni3O075, monoclinic, space group C2/c, with a= 37525(7), b= 16237(3), c= 22550(6)A, β= 11012(2), Z= 12; 5778 measured and 5519 unique reflections gave a final R value of 0051 The structure involves two independent Ni3(bipyam–H)4Cl2 units, (1) and (2)[(1) occupies a general position and (2) is on a C2 axis], one non-co-ordinated water molecule [site occupation factor (sof) 023], and one acetone molecule (sof 05) The Ni3N12Cl2 chromophores of (1) and (2) involve a nearly linear Ni3 unit, mean Ni–Ni–Ni angle 1784(1)°, terminated by the two chloride anions The four separate bipyam–H ligands act as tridentate ligands, involving co-ordination to three separate nickel(II) ions with Ni–Ni distances 2443(1)(twice) and 2431(1)A for units (1) and (2), respectively If the Ni–Ni separations are ignored the central Ni atom in both units involves a four-co-ordinate rhombic coplanar NiN4 chromophore, generated by the four central amido nitrogens of the bipyam–H ligands The two terminal Ni atoms involve a square-based pyramidal NiN4Cl chromophore, involving the four pyridine nitrogens of the bipyam–H ligands and an axial Cl atom A dihedral angle of ca 54° is involved between the planes of the individual pyridine rings of each bipyam–H ligand and results in a spiral configuration in the Ni3(bipyam–H)4Cl2 unit The room-temperature magnetic moment µeff of compound 1 is 246, consistent with a diamagnetic central NiN4 chromophore and two paramagnetic terminal NiN4Cl chromophores The electronic spectrum involves a low-energy peak at 6500 cm–1, an intense peak at 17 700 cm–1, and a low-intensity shoulder at 10 800 cm–1, consistent with the two nickel(II) stereochemistries present

121 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
2023203
2022473
2021160
2020195
2019193
2018216