Ramachandran plotIn biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a [φ,ψ] plot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. The figure on the left illustrates the definition of the φ and ψ backbone dihedral angles (called φ and φ' by Ramachandran).
Newman projectionA Newman projection is a drawing that helps visualize the 3-dimensional structure of a molecule. This projection most commonly sights down a carbon-carbon bond, making it a very useful way to visualize the stereochemistry of alkanes. A Newman projection visualizes the conformation of a chemical bond from front to back, with the front atom represented by the intersection of three lines (a dot) and the back atom as a circle. The front atom is called proximal, while the back atom is called distal.
Eclipsed conformationIn chemistry an eclipsed conformation is a conformation in which two substituents X and Y on adjacent atoms A, B are in closest proximity, implying that the torsion angle X–A–B–Y is 0°. Such a conformation can exist in any open chain, single chemical bond connecting two sp3-hybridised atoms, and it is normally a conformational energy maximum. This maximum is often explained by steric hindrance, but its origins sometimes actually lie in hyperconjugation (as when the eclipsing interaction is of two hydrogen atoms).
Elimination reactionAn elimination reaction is a type of organic reaction in which two substituents are removed from a molecule in either a one- or two-step mechanism. The one-step mechanism is known as the E2 reaction, and the two-step mechanism is known as the E1 reaction. The numbers refer not to the number of steps in the mechanism, but rather to the kinetics of the reaction: E2 is bimolecular (second-order) while E1 is unimolecular (first-order). In cases where the molecule is able to stabilize an anion but possesses a poor leaving group, a third type of reaction, E1CB, exists.
PentanePentane is an organic compound with the formula C5H12—that is, an alkane with five carbon atoms. The term may refer to any of three structural isomers, or to a mixture of them: in the IUPAC nomenclature, however, pentane means exclusively the n-pentane isomer; the other two are called isopentane (methylbutane) and neopentane (dimethylpropane). Cyclopentane is not an isomer of pentane because it has only 10 hydrogen atoms where pentane has 12. Pentanes are components of some fuels and are employed as specialty solvents in the laboratory.
AtropisomerAtropisomers are stereoisomers arising because of hindered rotation about a single bond, where energy differences due to steric strain or other contributors create a barrier to rotation that is high enough to allow for isolation of individual conformers. They occur naturally and are important in pharmaceutical design. When the substituents are achiral, these conformers are enantiomers (atropoenantiomers), showing axial chirality; otherwise they are diastereomers (atropodiastereomers).
HyperconjugationIn organic chemistry, hyperconjugation (σ-conjugation or no-bond resonance) refers to the delocalization of electrons with the participation of bonds of primarily σ-character. Usually, hyperconjugation involves the interaction of the electrons in a sigma (σ) orbital (e.g. C–H or C–C) with an adjacent unpopulated non-bonding p or antibonding σ* or π* orbitals to give a pair of extended molecular orbitals. However, sometimes, low-lying antibonding σ* orbitals may also interact with filled orbitals of lone pair character (n) in what is termed negative hyperconjugation.
Vicinal (chemistry)In chemistry the descriptor vicinal (from Latin vicinus = neighbor), abbreviated vic, describes any two functional groups bonded to two adjacent carbon atoms (i.e., in a 1,2-relationship). For example, the molecule 2,3-dibromobutane carries two vicinal bromine atoms and 1,3-dibromobutane does not. Mostly, the use of the term vicinal is restricted to two identical functional groups. Likewise in a gem-dibromide the prefix gem, an abbreviation of geminal, signals that both bromine atoms are bonded to the same atom (i.
Ring strainIn organic chemistry, ring strain is a type of instability that exists when bonds in a molecule form angles that are abnormal. Strain is most commonly discussed for small rings such as cyclopropanes and cyclobutanes, whose internal angles are substantially smaller than the idealized value of approximately 109°. Because of their high strain, the heat of combustion for these small rings is elevated. Ring strain results from a combination of angle strain, conformational strain or Pitzer strain (torsional eclipsing interactions), and transannular strain, also known as van der Waals strain or Prelog strain.
Staggered conformationIn organic chemistry, a staggered conformation is a chemical conformation of an ethane-like moiety abcX–Ydef in which the substituents a, b, and c are at the maximum distance from d, e, and f; this requires the torsion angles to be 60°. It is the opposite of an eclipsed conformation, in which those substituents are as close to each other as possible. Such a conformation exists in any open chain single chemical bond connecting two sp3-hybridised atoms, and is normally a conformational energy minimum.
