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Preparation and In Vivo Use of an Activity-based Probe for N-acylethanolamine Acid Amidase
Published on: November 23, 2016
N-(5-Bromo-pyridin-2-yl)acetamide.
Acta Crystallographica. Section E, Structure Reports Online
|November 18, 2011
Summary
This study characterizes the crystal structure of a novel brominated pyridine derivative. Molecular analysis reveals specific dihedral angles and disordered methyl groups, with hydrogen bonding forming extended crystal chains.
Area of Science:
- Crystallography
- Organic Chemistry
- Materials Science
Background:
- Understanding the crystal packing and intermolecular interactions of organic molecules is crucial for predicting material properties.
- Pyridine derivatives are important scaffolds in medicinal chemistry and materials science.
Purpose of the Study:
- To elucidate the crystal structure of the title compound, C(7)H(7)BrN(2)O.
- To investigate the molecular conformation, including dihedral angles and atom disorder.
- To analyze the hydrogen bonding network and resulting supramolecular architecture.
Main Methods:
- Single-crystal X-ray diffraction was employed to determine the crystal structure.
- Analysis of the asymmetric unit, bond lengths, bond angles, and dihedral angles.
- Identification and analysis of intermolecular interactions, specifically hydrogen bonds (N-H⋯O, C-H⋯O).
Main Results:
- The asymmetric unit contains two molecules, with one exhibiting disordered methyl hydrogen atoms (0.57:0.43 ratio).
- Dihedral angles between the pyridine rings and acetamide groups were measured as 7.27(11)° and 8.46(11)°.
- Hydrogen bonds form bifurcated R(2)(1)(5) ring motifs, leading to the formation of [110] chains in the crystal lattice.
Conclusions:
- The crystal structure of C(7)H(7)BrN(2)O has been successfully determined.
- The study highlights the role of hydrogen bonding in directing the self-assembly of these molecules into specific chain structures.
- The observed disorder and specific molecular conformations provide insights into the solid-state behavior of this compound.
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The IUPAC and common names of amides are derived from the parent carboxylic acid, by replacing the suffix “oic acid” and “ic acid,” respectively, with “amide.” In the following example, the IUPAC name ethanamide is derived from ethanoic acid, and the common name, acetamide, is obtained from acetic acid.
The IUPAC and common names of amides are derived from the parent carboxylic acid, by replacing the suffix “oic acid” and “ic acid,” respectively, with “amide.” In the following example, the IUPAC name ethanamide is derived from ethanoic acid, and the common name, acetamide, is obtained from acetic acid.
Amines to Amides: Acylation of Amines
Various carboxylic acid derivatives (such as acid chlorides, esters, and anhydrides) can be used for the acylation of amines to yield amides. The reaction requires two equivalents of amines. The first amine molecule functions as a nucleophile and attacks the carbonyl carbon to produce a tetrahedral intermediate. This is followed by the loss of the leaving group and restoration of the C=O bond.
Next, the second equivalent of amine serves as a Brønsted base and deprotonates the quaternary amide...
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Preparation of 1° Amines: Gabriel Synthesis
Direct alkylation is not a suitable method for synthesizing amines because it produces polyalkylated products. Gabriel synthesis is the most preferred method to exclusively make primary amines. The method uses phthalimide, which contains a protected form of nitrogen that participates in alkylation only once to predominantly give primary amines.
Strong bases like NaOH or KOH deprotonate the phthalimide to form the corresponding anion, which acts as a nucleophile. Further, the anion attacks an...
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The acidic strength of hydrocarbons follows the order: Alkynes > Alkenes > Alkanes. The strength of an acid is commonly expressed in units of pKa — the lower the pKa, the stronger the acid. Among the hydrocarbons, terminal alkynes have lower pKa values and are, therefore, more acidic. For example, the pKa values for ethane, ethene, and acetylene are 51, 44, and 25, respectively, as shown here.
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Alkylation of terminal alkynes with primary alkyl halides in the presence of a strong base like sodium amide is one of the common methods for the synthesis of longer carbon-chain alkynes. For example, treatment of 1-propyne with sodium amide followed by reaction with ethyl bromide yields 2-pentyne.
Alkylation of terminal alkynes with primary alkyl halides in the presence of a strong base like sodium amide is one of the common methods for the synthesis of longer carbon-chain alkynes. For example, treatment of 1-propyne with sodium amide followed by reaction with ethyl bromide yields 2-pentyne.

