Alpha and beta carbon

The alpha carbon () in organic molecules refers to the first carbon atom that attaches to a functional group, such as a carbonyl. The second carbon atom is called the beta carbon (),[1] and the system continues naming in alphabetical order with Greek letters.

The nomenclature can also be applied to the hydrogen atoms attached to the carbon atoms. A hydrogen atom attached to an alpha carbon atom is called an alpha-hydrogen atom, a hydrogen atom on the beta-carbon atom is a beta hydrogen atom, and so on.

This naming standard may not be in compliance with IUPAC nomenclature, which encourages that carbons be identified by number, not by Greek letter, but it nonetheless remains very popular, in particular because it is useful in identifying the relative location of carbon atoms to other functional groups.

Organic molecules with more than one functional group can be a source of confusion. Generally the functional group responsible for the name or type of the molecule is the 'reference' group for purposes of carbon-atom naming. For example, the molecules nitrostyrene and phenethylamine are very similar; the former can even be reduced into the latter. However, nitrostyrene's α-carbon atom is adjacent to the phenyl group; in phenethylamine this same carbon atom is the β-carbon atom, as phenethylamine (being an amine rather than a styrene) counts its atoms from the opposite "end" of the molecule.[1]

Alpha and beta positions of benzylacetone-structure
Alpha and beta carbons in the skeletal formula of benzylacetone. The carbonyl has two β-hydrogens and five γ-hydrogens

Examples

Butyric acid carbons 2
Skeletal formula of butyric acid with the alpha, beta, and gamma carbons marked

Proteins and amino acids

Alpha-carbon (α-carbon) is also a term that applies to proteins and amino acids. It is the backbone carbon before the carbonyl carbon atom in the molecule. Therefore, reading along the backbone of a typical protein would give a sequence of –[N—Cα—carbonyl C]n– etc. (when reading in the N to C direction). The α-carbon is where the different substituents attach to each different amino acid. That is, the groups hanging off the chain at the α-carbon are what give amino acids their diversity. These groups give the α-carbon its stereogenic properties for every amino acid except for glycine. Therefore, the α-carbon is a stereocenter for every amino acid except glycine. Glycine also does not have a β-carbon, while every other amino acid does.

The α-carbon of an amino acid is significant in protein folding. When describing a protein, which is a chain of amino acids, one often approximates the location of each amino acid as the location of its α-carbon. In general, α-carbons of adjacent amino acids in a protein are about 3.8 ångströms (380 picometers) apart.

Enols and enolates

The α-carbon is important for enol- and enolate-based carbonyl chemistry as well. Chemical transformations affected by the conversion to either an enolate or an enol, in general, lead to the α-carbon acting as a nucleophile, becoming, for example, alkylated in the presence of primary haloalkane. An exception is in reaction with silyl -chlorides, -bromides, and -idides, where the oxygen acts as the nucleophile to produce silyl enol ether.

References

  1. ^ "Nomenclature". Ask Dr. Shulgin Online. Retrieved August 5, 2010.
  1. ^ Hackh's Chemical Dictionary, 1969, page 30.
  2. ^ Hackh's Chemical Dictionary, 1969, page 95.

External links

Gamma

Gamma (uppercase Γ, lowercase γ; Greek: γάμμα gámma) is the third letter of the Greek alphabet. In the system of Greek numerals it has a value of 3. In Ancient Greek, the letter gamma represented a voiced velar stop /ɡ/. In Modern Greek, this letter represents either a voiced velar fricative or a voiced palatal fricative.

In the International Phonetic Alphabet and other modern Latin-alphabet based phonetic notations, it represents the voiced velar fricative.

Isocitrate dehydrogenase

Isocitrate dehydrogenase (IDH) (EC 1.1.1.42) and (EC 1.1.1.41) is an enzyme that catalyzes the oxidative decarboxylation of isocitrate, producing alpha-ketoglutarate (α-ketoglutarate) and CO2. This is a two-step process, which involves oxidation of isocitrate (a secondary alcohol) to oxalosuccinate (a ketone), followed by the decarboxylation of the carboxyl group beta to the ketone, forming alpha-ketoglutarate. In humans, IDH exists in three isoforms: IDH3 catalyzes the third step of the citric acid cycle while converting NAD+ to NADH in the mitochondria. The isoforms IDH1 and IDH2 catalyze the same reaction outside the context of the citric acid cycle and use NADP+ as a cofactor instead of NAD+. They localize to the cytosol as well as the mitochondrion and peroxisome.

Kinetic isotope effect

In physical organic chemistry, a kinetic isotope effect (KIE) is the change in the reaction rate of a chemical reaction when one of the atoms in the reactants is replaced by one of its isotopes. Formally, it is the ratio of rate constants for the reactions involving the light (kL) and the heavy (kH) isotopically substituted reactants (isotopologues):

This change in reaction rate is a quantum mechanical effect that primarily results from heavier isotopologues having lower vibrational frequencies compared to their lighter counterparts. In most cases, this implies a greater energetic input needed for heavier isotopologues to reach the transition state (or, in rare cases, the dissociation limit), and consequently, a slower reaction rate. The study of kinetic isotope effects can help the elucidation of the reaction mechanism of certain chemical reactions and is occasionally exploited in drug development to improve unfavorable pharmacokinetics by protecting metabolically-vulnerable C-H bonds.

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