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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: In this paper, the authors applied molecular dynamics method to predict the Tg of isomeric polyimide (PI) which were prepared based on 4,4'-oxydianiline (ODA) and 3,3',4,4-, biphenyltetracar-boxylic dianhydride (3,3,4, 4'-BPDA).
Abstract: It is an abnormal phenomenon that glass transition temperature (Tg) of isomeric polyimide (PI) is higher than its corresponding symmetrical PI. To illustrate this phenomenon at the molecular scale, we applied molecular dynamics method to predict the Tg of PI, which were prepared based on 4,4'-oxydianiline (ODA) and 3,3',4,4'-biphenyltetracar- boxylic dianhydride (3,3',4,4'-BPDA), and its isomeric system (2,2',3,3'-BPDA-ODA). Simulation result is consistent with experimental value. Non-bond energy plays an important role in glass transition process, for it has an abrupt change near Tg. The higher free volume fraction of isomeric PI can provide the polymer with more space to obtain segmental motion. However, from the torsion angle distribution calculations, it is shown that the torsion angle of its biphenyl group is constrained. Furthermore, from mean square displacement and vector autocorrelation functions calculations, this group is observed to rotate against other groups in the glassy state, and increases the chain rigidity to a great extent. So the isomeric PI needs much more relaxation time for the segment motion. Therefore, the higher Tg of isomeric PI is mainly attributed to the chain rigidity for the time scale, not the free volume for the space scale.

51 citations

Journal ArticleDOI
TL;DR: Many of the main chain dihedral angle changes measured in a comparison of the crystallographic structures of "open" and "closed" conformations of cAPK correspond to the highly flexible residues found during dynamics.
Abstract: Molecular dynamics simulations of the catalytic subunit of cAMP dependent protein kinase (cAPK) have been performed in an aqueous environment. The relations among the protein hydrogen-bonding network, secondary structural elements, and the internal motions of rigid domains were examined. The values of fluctuations of protein dihedral angles during dynamics show quite distinct maxima in the regions of loops and minima in the regions of a-helices and b-strands. Analyses of conformation snapshots throughout the run show stable subdomains and indicate that these rigid domains are constrained during the dynamics by a stable network of hydrogen bonds. The most stable subdomain during the dynamics was in the small lobe including part of the carboxy-terminal tail. The most significant flexible region was the highly conserved glycine-rich loop between b strands 1 and 2 in the small lobe. Many of the main chain dihedral angle changes measured in a comparison of the crystallographic structures of "open" and "closed" conformations of cAPK correspond to the highly flexible residues found during dynamics. © 1999 John Wiley & Sons, Inc. Biopoly 50: 513-524, 1999

51 citations

Book ChapterDOI
TL;DR: In this article, the minimum energy path between the reactants and the products may not be represented by a simple reaction coordinate, but may involve a concerted deformation of bonds, bond angles, and dihedral angles.
Abstract: Publisher Summary A chemical reaction can be viewed as occurring via the formation of an excited state that can be any one of the degrees of freedom of the collection of N atoms. That is, translational, rotational, vibrational, and electronic excitation can lead to a chemical reaction. Most elementary chemical reactions can be categorized as unimolecular or bimolecular events. However, further phenomenological classification is useful for the development of detailed chemical kinetic models to estimate rate parameters for new reactions by analogy to similar reactions in the same phenomenological class. The transition state would be stable to all geometric deformations except the reaction coordinate, which may be a bond distance, bond angle, or dihedral angle, depending on the nature of the reaction for simple molecules. However, when large molecules are involved, such as those observed in biochemical reactions, complex reaction coordinates are possible. That is, the minimum energy path between the reactants and the products may not be represented by a simple reaction coordinate, but may involve a concerted deformation of bonds, bond angles, and dihedral angles.

51 citations

Journal ArticleDOI
TL;DR: In this article, the synthesis and properties of a fixed-distance symmetric bis-pyrochlorophyllide-a molecule are described, which consists of two MePChlidea moieties sharing a common vinyl group at the 2-position of each macrocycle.
Abstract: The synthesis and properties of a fixed-distance symmetric bis-pyrochlorophyllide-a molecule are described. The molecule, 1, consists of two methyl pyrochlorophyllide-a (MePChlide-a) moieties which share a common vinyl group at the 2-position of each macrocycle. The two chlorophylls are trans to one another across the vinyl linkage. The dihedral angle between the plane of each macrocycle and the vinyl linkage is about 50°. The Qy absorption band of this dimer occurs at 689 nm and is essentially independent of solvent. The band is red-shifted by about 27 run relative to that of MePChlide-a. The fluorescence maximum of 1 occurs at 722 nm. This is a red-shift of 49 nm relative to methyl MePChlide-a. The circular dichroism spectrum of 1 shows strong, nonconservative bands in the red region. The fluorescence quantum yield, fluorescence lifetimes, and picosecond transient absorbance kinetics all exhibit a very strong dependence on solvent polarity. The fluorescence quantum yields of 1 in toluene, butyronitrile, and N, N-dimethyl formamide (DMF) are 0.18, 0.008, and 0.002, respectively. The bleach of the 689 nm band (following excitation with a 1.5-ps, 610-nm laser pulse) recovers with single exponential time constants of 2.51 ns, 100 ps, and 64 ps in toluene, butyronitrile, and DMF, respectively. Possible mechanisms for the polarity-dependent increase of the nonradiative decay rate of 1 are considered.

51 citations


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