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N-(3-Methyl-phen-yl)pyrimidin-2-amine.
Edura Badaruddin1, Zaharah Aiyub, Zanariah Abdullah
1Department of Chemistry, University of Malaya, 50603 Kuala Lumpur, Malaysia.
Summary
Two independent molecules of C(11)H(11)N(3) exhibit distinct aromatic ring orientations and varied hydrogen bonding patterns, leading to unique crystal packing. This study details their structural and intermolecular interactions.
Area of Science:
- Crystallography
- Organic Chemistry
- Molecular Structure
Background:
- The asymmetric unit of crystal structures can contain multiple independent molecules.
- Intermolecular interactions, such as hydrogen bonding and C-H interactions, are crucial for crystal packing.
- The relative orientation of aromatic rings influences molecular conformation and crystal packing.
Purpose of the Study:
- To characterize the crystal structure of the title compound, C(11)H(11)N(3).
- To analyze the differences in molecular conformation between independent molecules.
- To investigate the hydrogen bonding patterns and their role in crystal packing.
Main Methods:
- Single-crystal X-ray diffraction was used to determine the crystal structure.
- Analysis of dihedral angles between aromatic rings quantified their relative orientations.
- Hydrogen bonding networks and other intermolecular interactions were identified and analyzed.
Main Results:
- Two independent molecules of C(11)H(11)N(3) were identified in the asymmetric unit.
- The molecules showed variations in the dihedral angles between the pyrimidine and phenyl rings (39.00(8)° and 4.59(11)°).
- Distinct hydrogen bonding patterns were observed, including centrosymmetric dimers and tetrameric aggregates, stabilized by N-H⋯N, C-H⋯N, and C-H⋯π interactions.
Conclusions:
- The crystal structure of C(11)H(11)N(3) is characterized by two conformationally distinct molecules.
- Specific hydrogen bonding motifs, such as centrosymmetric dimers and tetrameric aggregates, dictate the overall crystal packing.
- Intermolecular interactions play a significant role in stabilizing the observed crystal structure.
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01:10Nomenclature of Aryl and Heterocyclic Amines
The simplest aromatic amine is phenylamine, which contains an –NH2 functionality directly attached to an aromatic ring. The name aniline is designated for this skeleton. As shown in Figure 1, the common names of the functionalized anilines involve prefixes ortho-, meta-, and para- to indicate the substitution position. Different functionalized aniline derivatives also have notable trivial names.
01:17Nomenclature of Primary Amines
Primary, secondary, and tertiary amines are compounds consisting of one, two, and three alkyl groups connected to the amino group (–NH2), respectively. As depicted in Figure 1, the common name of the primary amines is obtained by adding the suffix -amine to the alkyl substituent attached to the amino group as the corresponding alkylamine.
01:26Physical Properties of Amines
Amines with low molecular weight are usually gaseous at room temperature, while those with high molecular weight are liquid or solids in nature. Usually, low molecular weight amines have a rotten fish-like smell. Diamines typically have a pungent smell. For instance, cadaverine and putrescine, depicted in Figure 1, are two molecules responsible for decaying tissue.
01:25Basicity of Heterocyclic Aromatic Amines
Heterocyclic amines, where the N atom is a part of an alicyclic system, are similar in basicity to alkylamines. Interestingly, the heterocyclic amine having a nitrogen atom as part of an aromatic ring has much less basicity than its corresponding alicyclic counterpart. For this reason, as presented in Figure 1, piperidine (pKb = 2.8) is significantly more basic than pyridine (pKb = 8.8).
01:19Structure of Amines
The hybridized nitrogen atom in amines possesses a lone pair of electrons and is bound to three substituents with a bond angle of around 108°, which is less than the tetrahedral angle of 109.5°. However, the C–N–H bond angle is slightly larger at 112°, with a carbon–nitrogen bond length of 147 pm. This carbon–nitrogen bond length of of amines is longer than the carbon–oxygen bond of alcohols (143 pm) but shorter than alkanes’ carbon–carbon bond (154 pm). These aspects are illustrated in Figure...
01:12Nomenclature of Secondary and Tertiary Amines
The secondary and tertiary amines are derivatives of ammonia, where two and three of its hydrogens are replaced by alkyl groups, respectively. Secondary and tertiary amines can be symmetrical with identical alkyl groups attached to the nitrogen atom or unsymmetrical when more than one type of alkyl group is present. The standard nomenclature of secondary and tertiary amines is similar to the names given to the primary amines. They are generally named alkylamines. As depicted in Figure 1, for...