A series of novel salts based on aromatic polyamines and 2,3-pyrazinedicarboxylic acid, such as C
10H
12N
6O
5 (
1), C
10H
9ClN
6O
4 (
2), C
11H
10N
8O
4 (
3), and C
14H
17N
16O
5.5 (
4) or 3,4-thiophenedicarboxylic acid, such as C
10H
10N
4O
4S (
5), C
10H
9ClN
4O
4S (
6), and C
10H
10N
4O
4S
2 (
7), were synthesized and characterized by single-crystal X-ray diffraction. All compounds crystallize in a monoclinic space group. The structure was subjected to complex Hirshfeld surface analysis, molecular electrostatic potential, enrichment ratio, and energy framework calculations. The influence of different cations on the packing of 3-carboxypyrazine-2-carboxylate and 4-carboxythiophene-3-carboxylate anions in the crystal lattice was studied. O
…H/H
…O interactions are the main contributor in all crystals. In addition, in a series of pyrazine-containing structures, N(C)
…H/H
…N(C) interactions have relevance, while in a series of thiophene-based compounds, C
…H/H
…C and S
…H(O)/H(O)
…S. In addition, Cl-based interactions are observed in compound
2. According to the enrichment ratio calculations, O
…H/H
…O and C
…C are the most preferable interactions in all structures. The energy frameworks are dominated by the dispersive contribution, only in compound
3 is the electrostatic term dominant. The analyzed structures reveal intra- and intermolecular recurrent supramolecular synthons. In both series of crystals, the robust H-bonded centrosymmetric dimer
R22(8) as homo- or as heterosynthon (in compounds
2,
3,
6, and
7) and the intramolecular synthon
S(7) generated by O-H
…O interactions (in compounds
2,
6, and
7) are present. The supramolecular patterns formed by π
…π (C
…C) and C-O(Cl,S)
…C are also noticeable. Notably, a dual synthon linking the supramolecular chain via π
…π interactions and the homosynthon
R22(8) via N-H
…N interactions is visible in both series of new salts. A library of H-bonding motifs at diverse levels of supramolecular architecture is provided. We extended the analysis of intramolecular H-bonding motifs to similar structures deposited in the Cambridge Structural Database. Another important feature is the existence of an intramolecular O
…H
…O bridge between two neighboring carboxylic groups as substituents in anions in compounds
3 and
5. In this context, we performed quantum theory of atoms-in-molecule calculations to reveal more details.
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