*3.2. Crystal Structure of DPA\_PA Salt*

recently reported in [55].

DPA and PA in the 1: 1 stoichiometric molar ratio were crystallized from acetone at ambient condition to obtain a colorless block shape crystal. The ∆pKa difference between DPA (pka: 8.36) and coformer PA (pKa: 2.94, 5.41) is more than 3 and salt formation was expected based on the basic rule of three [56]. The X-ray single-crystal structure confirmed the formation of DPA\_PA salt with approximately similar C–O bond lengths C28-O2, 1.2438 (18), C28-O3, 1.2676 (19) Å) of the (COO¯) carboxylate group of PA. These approximate

similarities in the bond length of C–O confirmed the transfer of an acidic proton from one of the carboxylic acidic group of PA to the N3-nitrogen atom of the tertiary amino group (chain moiety) of DPA. DPA\_PA salt crystalized in the monoclinic centrosymmetric *P*21/*n* space group comprising one protonated DPA and one PA¯ anion in an asymmetric unit, revealing the molecular salt in the 1:1 molar ratio. In the crystal structure of DPA\_PA salt, protonated DPA molecules displayed positional disorder and ratio fixed 0.5/0.5 for the two disordered components. DPA is a racemic compound consisting of R and S configurations. These two racemic components R and S are found to occupy the same site with 0.5 and 0.5 occupancy in DPA\_PA. In this disorder model, phenyl and pyridine ring were exchanged between R and S, and the other part of DPA molecule was completely overlapped in DPA\_PA salt. (Figure 7a). *Crystals* **2021**, *11*, x FOR PEER REVIEW 10 of 20

**Figure 7.** (**a**) ORTEP diagram of DPA\_PA salt, showing the atom numbering scheme wherein C1, N4A and N1, and C1A share the same position. Thermal ellipsoid drawn at 50% probability level, and H-atoms are shown as small spheres with arbitrary radii. DPA\_PA salts, displaying intramolecular hydrogen bonds O5-H5A∙∙∙O3, C17-H17C∙∙∙O1, C22-H22∙∙∙O2, C25-H25∙∙∙O4 C15-H15B∙∙∙N1 and intermolecular hydrogen bonds N2–H2A∙∙∙O4 and C9–H9∙∙∙O4, C═O4∙∙∙π between the salt pair. (**b**) The disordered DPA molecule in salt crystal. R and S configuration molecules occupied the same site with 0.5 and 0.5 occupancy. **Figure 7.** (**a**) ORTEP diagram of DPA\_PA salt, showing the atom numbering scheme wherein C1, N4A and N1, and C1A share the same position. Thermal ellipsoid drawn at 50% probability level, and H-atoms are shown as small spheres with arbitrary radii. DPA\_PA salts, displaying intramolecular hydrogen bonds O5-H5A···O3, C17-H17C···O1, C22-H22···O2, C25-H25···O4 C15-H15B···N1 and intermolecular hydrogen bonds N2–H2A···O4 and C9–H9···O4, C=O4···π between the salt pair. (**b**) The disordered DPA molecule in salt crystal. R and S configuration molecules occupied the same site with 0.5 and 0.5 occupancy.

Hereafter, one conformer of disordered protonated DPA molecule used for discussion of crystal structure and packing of DPA\_PA salt. Crystal structure of DPA\_PA salt

(Table 2 and Figure 8a). There is no direct association between the PA¯-PA¯ anion observed in DPA\_PA salt. However the protonated DPA molecule linked PA¯ anions alternatively through N–H∙∙∙O, and charge assisted the N+–H∙∙∙O¯ hydrogen bond shown in Figure 8b, in which one PA¯ anion associated with the protonated DPA molecule by forming the N–H∙∙∙O hydrogen bond involving carbonyl C=O4 oxygen of the carboxyl group of PA¯ anion and amide N-H2A hydrogen of protonated DPA. Whereas the other PA¯ anion associated by forming a charge assisted N+–H∙∙∙O¯ hydrogen bond by using carboxylate (COO¯) O2-oxygen of the PA anion and the protonated tertiary amino group N3+-

A similar phenomenon was also observed in the crystal structure of ketoconazole [57]. Interestingly, in the one configuration, the phenyl ring is roughly coplanar with chain moiety (excluding the *iso*-propyl moiety), whereas in other configuration, the 2-pyridine moiety is roughly coplanar with the chain moiety (excluding the *iso*-propyl moiety). (Figure 7b).

Both the component in the asymmetric unit, that is, protonated DPA and PA¯ anion linked by strong N2–H2A···O4 hydrogen bond and C9–H9···O4 hydrogen bonds and such assembly in salt facilitated the formation C=O···π interaction between the carboxyl C=O4 of PA¯ anion and phenyl ring Cg2 in one configuration/2-pyridine ring Cg3- in other configuration. In the crystal structure of salt, PA¯ displaying an intramolecular strong O5-H5A···O3 hydrogen bond in which hydroxyl (O5-H5A) of the carboxyl group of the PA¯ anion donates H5A hydrogen intramolecularly to an O3-oxygen atom of the carboxylate group of the PA¯ anion and other C-H···O intramolecular hydrogen bonds namely, C22-H22···O2, C25-H25···O4 present in PA¯ anion and C17-H17C···O1, C15-H15B···N1 in protonated DPA which stabilize the conformation the salt as shown in Figure 7a. The crystallographic information and geometrical parameters for the hydrogen bonding interaction are summarized in Tables 1 and 2.

Hereafter, one conformer of disordered protonated DPA molecule used for discussion of crystal structure and packing of DPA\_PA salt. Crystal structure of DPA\_PA salt reveals the presence of a dimeric association between the protonated DPA molecule through the N–H···O hydrogen bond like DPA alone with different symmetry operation (Table 2 and Figure 8a). There is no direct association between the PA¯-PA¯ anion observed in DPA\_PA salt. However the protonated DPA molecule linked PA¯ anions alternatively through N–H···O, and charge assisted the N+–H···O¯ hydrogen bond shown in Figure 8b, in which one PA¯ anion associated with the protonated DPA molecule by forming the N–H···O hydrogen bond involving carbonyl C=O4 oxygen of the carboxyl group of PA¯ anion and amide N-H2A hydrogen of protonated DPA. Whereas the other PA¯ anion associated by forming a charge assisted N+–H···O¯ hydrogen bond by using carboxylate (COO¯) O2-oxygen of the PA anion and the protonated tertiary amino group N3<sup>+</sup> -H3A hydrogen of protonated DPA; both associations were supported by C–H···O interaction as shown in Figure 8b.

In the crystal structure of DPA\_PA salt, two inversion-symmetry related protonated DPA molecules form amide homodimer, via a pair of strong N2–H2B···O1 hydrogen bonds in R<sup>2</sup> <sup>2</sup>(8) ring motif that involve two acceptor and two donor atoms. In this association, protonated DPA donates amide hydrogen N2–H2B to amide carbonyl (C=O1) oxygen of inversion-symmetry related protonated DPA molecules in dimeric N2–H2B···O1 hydrogen bonding interaction. Further, this amide homodimer of protonated DPA molecule linked to two PA anions through N2–H2A···O4 hydrogen bonding interaction between the second hydrogen of amide N2–H2A and carbonyl (C=O4) oxygen of the carboxyl group of the PA¯ anion and further supported by C9–H9···O4 interaction, between C9–H9 hydrogen of the phenyl ring of protonated DPA and carbonyl (C=O4) oxygen of the carboxyl group of the PA¯ anion resulting basic dimeric unit shown in Figure 9.

The dimeric unit linked to four *n*-glide related neighboring dimeric units through charge assisted strong and linear N+–H···O¯ hydrogen bonding interaction and supported by two longer and non-linear C–H ···O¯ interactions, namely C17–H17A ···O2¯, C14– H14B ···O2¯ resulting 2-D packing. In this association, the carboxylate (COO¯) O2 oxygen of PA¯ anion is made hydrogen bond with N3+–H3A (protonated tertiary amino nitrogen) hydrogen of protonated DPA via the charge assisted strong N3+–H3A···O2¯ hydrogen bond; such association was further supported by longer and non-linear C– H···O¯ interaction, namely C17–H17A···O2¯, C14–H14B···O2¯ interactions and resulting packing view down the *a*-axis is shown in Figure 10a (above). In this packing, the dimeric unit assembled along the *b*-axis through the short C2–H2···O1 hydrogen bond between amide carbonyl (C=O1) oxygen and C2–H2 hydrogen of 2-pyridine moieties of the next dimeric unit along the *b*-axis and supported by weak C18-H18A···Cg5 interaction between the C18–H18A hydrogen of *iso*-propyl moieties of protonated DPA and the π cloud of the

aromatic ring (C22-C23-C24-C25-C26-C27) of PA¯ anion; the resulting association is shown in Figure 10a (down). Similar packing views in the *ac-*plane, reveal that the neighboring dimeric unit assembled along the *ac-*diagonal through hydrogen bonding, wherein there is an alternate arrangement of protonated DPA amide dimer and PA¯ anion as shown in Figure 10b. *Crystals* **2021**, *11*, x FOR PEER REVIEW 11 of 20 H3A hydrogen of protonated DPA; both associations were supported by C–H∙∙∙O interaction as shown in Figure 8b.

**Figure 8.** (**a**) Association between protonated DPA molecules through a pair of strong N–H∙∙∙O hydrogen bonds in R22(8) ring motif; and(**b**) Association between the protonated DPA and PA¯ anions in DPA\_PA salt, hereby protonated DPA molecules engaging both carboxylate and carboxyl groups of the PA¯ anion alternatively through a strong N–H∙∙∙O and charge assisted N+–H∙∙∙O¯ hydrogen bond and further supported by C–H∙∙∙O interaction. In the crystal structure of DPA\_PA salt, two inversion-symmetry related protonated DPA molecules form amide homodimer, via a pair of strong N2–H2B∙∙∙O1 hydrogen **Figure 8.** (**a**) Association between protonated DPA molecules through a pair of strong N–H···O hydrogen bonds in R<sup>2</sup> 2 (8) ring motif; and(**b**) Association between the protonated DPA and PA¯ anions in DPA\_PA salt, hereby protonated DPA molecules engaging both carboxylate and carboxyl groups of the PA¯ anion alternatively through a strong N–H···O and charge assisted N+–H···O¯ hydrogen bond and further supported by C–H···O interaction. *Crystals* **2021**, *11*, x FOR PEER REVIEW 12 of 20

bonds in R22(8) ring motif that involve two acceptor and two donor atoms. In this associ-

**Figure 9.** Dimeric unit of DPA\_PA salt in crystal. Dotted lines indicate the non-covalent interaction (hydrogen atoms not involved in the hydrogen bonding were removed for clarity). **Figure 9.** Dimeric unit of DPA\_PA salt in crystal. Dotted lines indicate the non-covalent interaction (hydrogen atoms not involved in the hydrogen bonding were removed for clarity).

The dimeric unit linked to four *n*-glide related neighboring dimeric units through charge assisted strong and linear N+–H∙∙∙O¯ hydrogen bonding interaction and supported

∙∙∙O2¯ resulting 2-D packing. In this association, the carboxylate (COO¯) O2-oxygen of PA¯ anion is made hydrogen bond with N3+–H3A (protonated tertiary amino nitrogen) hydrogen of protonated DPA via the charge assisted strong N3+–H3A∙∙∙O2¯ hydrogen bond; such association was further supported by longer and non-linear C–H∙∙∙O¯ interaction, namely C17–H17A∙∙∙O2¯, C14–H14B∙∙∙O2¯ interactions and resulting packing view down the *a*-axis is shown in Figure 10a (above). In this packing, the dimeric unit assembled along the *b*-axis through the short C2–H2∙∙∙O1 hydrogen bond between amide carbonyl (C═O1) oxygen and C2–H2 hydrogen of 2-pyridine moieties of the next dimeric unit along the *b*axis and supported by weak C18-H18A∙∙∙Cg5 interaction between the C18–H18A hydrogen of *iso*-propyl moieties of protonated DPA and the π cloud of the aromatic ring (C22- C23-C24-C25-C26-C27) of PA¯ anion; the resulting association is shown in Figure 10a (down). Similar packing views in the *ac-*plane, reveal that the neighboring dimeric unit assembled along the *ac-*diagonal through hydrogen bonding, wherein there is an alternate arrangement of protonated DPA amide dimer and PA¯ anion as shown in Figure 10b.

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(**a**)

**Figure 10.** *Cont.*

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**Figure 10.** (**a**) Packing view down the *a*-axis, with each dimeric unit linked to four *n*-glide related neighboring dimeric units, resulting in 2-D packing (above). The inset shows the association between the neighboring dimeric unit shown in different colors through C2–H2∙∙∙O1 interaction and supported by C18-H18A∙∙∙Cg5 along the *b*-axis. (down) (**b**) Similar packing view in the *ac-*plane. **Figure 10.** (**a**) Packing view down the *a*-axis, with each dimeric unit linked to four *n*-glide related neighboring dimeric units, resulting in 2-D packing (above). The inset shows the association between the neighboring dimeric unit shown in different colors through C2–H2···O1 interaction and supported by C18-H18A···Cg5 along the *b*-axis. (down) (**b**) Similar packing view in the *ac-*plane.

Further, such a two-dimensional network of dimeric unit assembled centrosymmetrically along the *a*-axis (parallel to the *ac*-diagonal) through longer and weak C11–H11∙∙∙O2¯ interaction between C11-H11 hydrogen of the phenyl ring of protonated DPA and carboxylate (COO¯) O2-oxygen of PA¯ anions resulting in three-dimensional packing of the dimeric unit in the *ac*-plane, as shown in Figure 11. Further, such a two-dimensional network of dimeric unit assembled centrosymmetrically along the *a*-axis (parallel to the *ac*-diagonal) through longer and weak C11–H11···O2¯ interaction between C11-H11 hydrogen of the phenyl ring of protonated DPA and carboxylate (COO¯) O2-oxygen of PA¯ anions resulting in three-dimensional packing of the dimeric unit in the *ac*-plane, as shown in Figure 11.

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**Figure 11.** 2-Dimentonal network of dimeric unit assembled centrosymmetric fashion through weak and longer C11- H11∙∙∙O2¯ interaction resulting in 3-D packing of dimeric unit in the *ac*-plane. **Figure 11.** 2-Dimentonal network of dimeric unit assembled centrosymmetric fashion through weak and longer C11- H11···O2¯ interaction resulting in 3-D packing of dimeric unit in the *ac*-plane.

#### *3.3. Structural Overlay 3.3. Structural Overlay*

DPA (Figure 12a), has freely rotatable groups connected to asymmetric carbon marked by a star and anticipated to display conformational or orientational changes in its solid forms. The structural overlay of the DPA molecule by overlapping the (C-C-C-N) backbone chain, shown in Figure 12b, reveals conformational and orientational differences owing to rotational freedom around the C−C, C-N bonds. Conformational difference in both solid forms could be characterized by torsion angles τ1, τ2, τ3 and τ4 as shown in Figure 12a, and the dihedral angle between the phenyl and 2-pyridine moieties and values listed in Table 3. In pure DPA crystal structure, both conformers in the pure DPA crystal display slight difference in torsion angles τ1 (−179.78, −171.37), while values of τ2 (177.67, 177.17) and τ3 (−1.01, 3.01) are comparable and indicate that the (C-C-C-N) backbone chain moiety connecting to the phenyl ring are nearly coplanar in molecule A, while there is a slight deviation observed in coplanarity in B molecules. On the other hand, the 2-pyridine ring is roughly perpendicular to the planar part of A and B molecules. The dihedral angle DPA (Figure 12a), has freely rotatable groups connected to asymmetric carbon marked by a star and anticipated to display conformational or orientational changes in its solid forms. The structural overlay of the DPA molecule by overlapping the (C-C-C-N) backbone chain, shown in Figure 12b, reveals conformational and orientational differences owing to rotational freedom around the C−C, C-N bonds. Conformational difference in both solid forms could be characterized by torsion angles τ1, τ2, τ<sup>3</sup> and τ<sup>4</sup> as shown in Figure 12a, and the dihedral angle between the phenyl and 2-pyridine moieties and values listed in Table 3. In pure DPA crystal structure, both conformers in the pure DPA crystal display slight difference in torsion angles τ<sup>1</sup> (−179.78, −171.37), while values of τ<sup>2</sup> (177.67, 177.17) and τ<sup>3</sup> (−1.01, 3.01) are comparable and indicate that the (C-C-C-N) backbone chain moiety connecting to the phenyl ring are nearly coplanar in molecule A, while there is a slight deviation observed in coplanarity in B molecules. On the other hand, the 2-pyridine ring is roughly perpendicular to the planar part of A and B molecules. The dihedral

angle between the phenyl and 2-pyridine rings is 87.16◦ and 79.83◦ in molecules A and B, respectively. In DPA\_PA salt crystal structure, the torsion angles τ<sup>1</sup> and τ<sup>2</sup> are −177.58◦ , −175.47◦ suggesting coplanarity in the backbone chain as pure DPA, whereas torsion angles τ<sup>3</sup> −16.81◦ indicate deviation in coplanarity in backbone chain moiety and the phenyl ring. Further, the dihedral angle between the phenyl and 2-pyridine moiety is significantly changed to 59.43◦and such deviation in orientation of 2-pyridine and phenyl moiety could be due to the association of salt former (PA) with drug (DPA) through hydrogen bond in this direction. However, the torsional value τ<sup>4</sup> is for the orientation of the amide group with a planar part; it is nearly similar for both conformers in pure DPA, and such orientation of the amide group brings 2-pyridine moiety close enough to facilitate an intramolecular hydrogen bond between amide N-H hydrogen and N-atom of 2-pyridine moiety. Whereas in the DPA\_PA salt a conformational twist is observed at amide group as shown in Figure 12b to facilitate the intermolecular hydrogen bond between amide N-H hydrogen of protonated DPA and carbonyl oxygen (C=O) of the carboxyl group PA¯ anion. Moreover, *iso*-propyl moiety present on tertiary nitrogen in all molecules shows conformational/orientational difference. changed to 59.43°and such deviation in orientation of 2-pyridine and phenyl moiety could be due to the association of salt former (PA) with drug (DPA) through hydrogen bond in this direction. However, the torsional value τ4 is for the orientation of the amide group with a planar part; it is nearly similar for both conformers in pure DPA, and such orientation of the amide group brings 2-pyridine moiety close enough to facilitate an intramolecular hydrogen bond between amide N-H hydrogen and N-atom of 2-pyridine moiety. Whereas in the DPA\_PA salt a conformational twist is observed at amide group as shown in Figure 12b to facilitate the intermolecular hydrogen bond between amide N-H hydrogen of protonated DPA and carbonyl oxygen (C=O) of the carboxyl group PA¯ anion. Moreover, *iso*-propyl moiety present on tertiary nitrogen in all molecules shows conformational/orientational difference. Crystal structure analysis showed that the drug–drug amide homosynthon retained in salt as in pure DPA (differed in symmetry operation). Further, the density of DPA alone and its salt DPA\_PA calculated from single crystal X-ray diffraction were found to increase from 1.140 g/cm3 in DPA to 1.269 g/cm3 in the salt, indicating denser packing in salt.

between the phenyl and 2-pyridine rings is 87.16° and 79.83° in molecules A and B, respectively. In DPA\_PA salt crystal structure, the torsion angles τ1 and τ2 are −177.58°, −175.47° suggesting coplanarity in the backbone chain as pure DPA, whereas torsion angles τ<sup>3</sup> −16.81° indicate deviation in coplanarity in backbone chain moiety and the phenyl ring. Further, the dihedral angle between the phenyl and 2-pyridine moiety is significantly

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**Figure 12.** (**a**) Chemical structure of DPA, in which the (C-C-C-N) backbone chain is marked by a red color bond and (**b**) Structural overlay of DPA molecules in both solid forms showing significant conformational variation; Green-Molecule A, Red-Molecule B` in DPA, Light green-DPA molecules from DPA\_PA salt. **Figure 12.** (**a**) Chemical structure of DPA, in which the (C-C-C-N) backbone chain is marked by a red color bond and (**b**) Structural overlay of DPA molecules in both solid forms showing significant conformational variation; Green-Molecule A, Red-Molecule B' in DPA, Light green-DPA molecules from DPA\_PA salt.


In DPA Molecule A: τ1—C7-C14-C15-N3, τ2—C6-C7-C14-C15, τ3—C1-C6-C7-C14, τ4—C13-C7-C14- C15; In DPA Molecule B`: τ1—C28-C35-C36-N6, τ2—C27-C28-C35-C36, τ3—C22-C27-C28-C35, τ4— In DPA Molecule A: τ1—C7-C14-C15-N3, τ2—C6-C7-C14-C15, τ3—C1-C6-C7-C14, τ4—C13-C7-C14-C15; In DPA Molecule B': τ1—C28-C35-C36-N6, τ2—C27-C28-C35-C36, τ3—C22-C27-C28-C35, τ4—C34-C28-C35-C36; DPA from Salt: τ1—C7-C14-C15-N3, τ2—C8-C7-C14-C15, τ3—C4-C8-C7-C14, τ4—C13-C7-C14-C15. The dihedral angle is the angle between planes of the phenyl and 2-pyridine ring in DPA.

C34-C28-C35-C36; DPA from Salt: τ1—C7-C14-C15-N3, τ2—C8-C7-C14-C15, τ3—C4-C8-C7-C14, τ4—C13-C7-C14-C15. The dihedral angle is the angle between planes of the phenyl and 2-pyridine ring in DPA. Crystal structure analysis showed that the drug–drug amide homosynthon retained in salt as in pure DPA (differed in symmetry operation). Further, the density of DPA alone and its salt DPA\_PA calculated from single crystal X-ray diffraction were found to increase from 1.140 g/cm<sup>3</sup> in DPA to 1.269 g/cm<sup>3</sup> in the salt, indicating denser packing in salt.
