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Updated: Jun 1, 2026

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Synthesis of pH Dependent Pyrazole, Imidazole, and Isoindolone Dipyrrinone Fluorophores using a Claisen-Schmidt Condensation Approach
Published on: June 10, 2021
4,6-Dichloro-5-methoxy-pyrimidine.
Summary
This study details the crystal structure of a novel compound, C(5)H(4)Cl(2)N(2)O. The molecule is nearly planar, with short chlorine-nitrogen contacts forming a 3D framework in the crystal lattice.
Area of Science:
- Crystallography
- Organic Chemistry
- Materials Science
Background:
- Understanding molecular structure and intermolecular interactions is crucial for predicting material properties.
- Crystal engineering relies on identifying specific non-covalent interactions to design functional materials.
Purpose of the Study:
- To elucidate the crystal structure of the title compound, C(5)H(4)Cl(2)N(2)O.
- To analyze the molecular geometry and intermolecular interactions within the crystal.
Main Methods:
- Single-crystal X-ray diffraction was employed to determine the molecular and crystal structure.
- Analysis of atomic coordinates and bond lengths/angles provided geometric insights.
Main Results:
- The molecule C(5)H(4)Cl(2)N(2)O exhibits near-planarity, with a deviation of 0.013 Å (r.m.s.d.).
- The methoxy group's carbon atom deviates significantly (1.082 Å) from the molecular plane.
- Short chlorine-nitrogen (Cl⋯N) contacts (3.0940 Å and 3.1006 Å) were observed.
- These contacts facilitate the formation of a three-dimensional framework in the crystal.
Conclusions:
- The determined crystal structure reveals specific molecular packing driven by Cl⋯N interactions.
- The nearly planar structure with specific intermolecular contacts suggests potential applications in crystal engineering and materials design.
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Five-Membered Heterocyclic Aromatic Compounds: Overview
Heterocyclic aromatic compounds are cyclic compounds that are aromatic and have one or more heteroatoms—atoms other than carbon, in the ring. Depending upon the number of atoms present in the ring, they can be either five or six-membered. Examples of five-membered heterocyclic aromatic compounds include pyrrole, furan, thiophene, and imidazole. Pyrrole consists of one nitrogen atom having one lone pair of electrons. Furan and thiophene have one oxygen and one sulfur heteroatom, respectively.
Basicity 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).
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