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In chemistry, pyramidal inversion (also umbrella inversion) is a fluxional process in compounds with a pyramidal molecule, such as ammonia (NH 3) "turns inside out". [1] [2] It is a rapid oscillation of the atom and substituents, the molecule or ion passing through a planar transition state. [3]
on this side of) [2] and trans (lat. over, beyond) [3] are used in various contexts for the description of chemical configurations: [4] [5] In organic structural chemistry , the configuration of a double bond can be described with cis and trans , in case it has a simple substitution pattern with only two residues.
According to one definition, a turn is a structural motif where the C α atoms of two residues separated by a few (usually 1 to 5) peptide bonds are close (less than 7 Å [0.70 nm]). [1] The proximity of the terminal C α atoms often correlates with formation of an inter main chain hydrogen bond between the corresponding residues.
The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with single letter codes. The secondary structure is assigned based on hydrogen bonding patterns as those initially proposed by Pauling et al. in 1951 (before any protein structure had ever been experimentally determined).
As stated above, a chair flip is a ring inversion specifically of cyclohexane (and its derivatives) from one chair conformer to another, often to reduce steric strain.The term, "flip" is misleading, because the direction of each carbon remains the same; what changes is the orientation.
A spiro compound, or spirane, from the Latin spīra, meaning a twist or coil, [22] [5]: 1138 [23] is a chemical compound, typically an organic compound, that presents a twisted structure of two or more rings (a ring system), in which 2 or 3 rings are linked together by one common atom, [2]: SP-0
Beta turns are especially common at the loop ends of beta hairpins; they have a different distribution of types from the others; type I' is the most common, followed by types II', I and II. Additional turn types have been defined by clustering turn conformations within very high-resolution protein structures. [11]
In chemistry, a reaction mechanism is the step by step sequence of elementary reactions by which overall chemical reaction occurs. [1] A chemical mechanism is a theoretical conjecture that tries to describe in detail what takes place at each stage of an overall chemical reaction. The detailed steps of a reaction are not observable in most cases.