Chapter 3 Supramolecular Photochemistry of Naphthalene and Quinoline based systems
3.3. Multipoint solvent recognition within Napthyl based thiourea receptor
3.3.1. Synthesis and characterization of different solvated trans-1,2-Bis-3-(naphthalen-1-yl)-thioureido
The compound was dissolved in methanol at 50 °C under agitation to get a saturated solution. Then, the solvent methanol was allowed to evaporate gradually by using a pierced film cover at 20 °C. Anal. Calcd (%) for C29H32N4OS2: C, 67.41; H, 6.24; N, 10.85 Found: C, 67.44; H, 6.22; N, 10.84%. Similarly the compound L4 was dissolved in MeCN at 50 °C under agitation to get a saturated solution. Single-crystals suitable for X-ray diffraction were obtained from slow evaporation after five days. Anal. Calcd (%) for C30H31N5S2: C, 68.54; H, 5.94; N, 13.33 Found: C, 68.56; H, 5.95; N, 13.35%. On the other hand L was dissolved in higher than the boiling point solvent like DMF at 120°C under agitation to get a saturated solution. Single-crystals suitable for X-ray diffraction were obtained from slow evaporation after fifteen days. Anal. Calcd (%) for C31H35N5OS2: C, 66.75; H, 6.33; N, 12.56 Found: C, 66.78; H, 6.34; N, 12.55%.
3.3.2. Crystal structure analysis
Solvent induced polymorph synthesis is facile for a host molecule with more flexibility or less rigidity. Urea/thiourea is well known building block for generating hydrogen bonded network in the solid-state.3.3.2 Approaches involving crystallization of organic solvents with hydrogen bond donor and acceptor groups has been used to the formation of 1-, 2- and 3-D networks stabilized by several non covalent interactions. Since methanol solvent was found to be able to enter the crystal lattice via hydrogen bonding, therefore we have tried to crystallize L4 from MeOH. L4•MeOH also crystallized in triclinic P-1 space group and asymmetric unit contain only one ligand and MeOH molecule (Figure 3.3.2a).
Interestingly, compound L4 reorganizes in the solid-state to form a channel along a axis to accommodate solvent molecule (Figure 3.3.2b). Each of these channels is filled with discrete dimmer of MeOH molecules stacked in opposite orientation via C–H····O
interactions (Figure 3.3.2c). Each dimmer is separated by 7.17 Å along a axis and 10.32 Å along b axis. The cavity dimension is 7.16 Å x 7.71 Å, which almost a square. MeOH molecule acts as a hydrogen bond acceptor as well as donor in the lattice. One of the NH attached to cyclohexyl unit form N-H····O type bonding with solvent. MeOH is also form O-H····S type hydrogen bond with neighboring thiourea unit. Adjacent thiourea unit form complementary N-H····S type hydrogen bond, which resulted in the formation of 1D hydrogen bonded chain along the diagonal of bc plane in the lattice. Two napthyl moieties in the pendant arm are oriented in the opposite direction with respect to the cyclohexyl unit. In crystal lattice neighbouring molecules are linked by thioamide····thioamide
Chapter-3 Supramolecular Photochemistry of Naphthalene and Quinoline based systems
hydrogen bonding forming a 1D chain along c axis (see appendix), which common to thiourea compound and its derivatives.3.3.3, 3.3.4
Figure 3.3.2. (a) Encapsulation of MeOH (b) Packing diagram highlighting the guest dimmer in the channel and (c) MeOH dimmer formation via C-H····O interaction.
Other supramolecular interaction like C-H····π, O-H····S type interactions are also present in the solid-state (see supporting information). Each thiourea unit has common syn and anti geometry. Both the anti conformation is having similar close to 180° dihedral angle.
However, one of the syn N–H has dihedral angle very close to 0°, while other is little larger (6.87°). The dihedral angles of anti conformation are within the range. FT-IR spectrum of the crystal shows a broad band around 3300 cm-1, which can be assigned to the O-H stretching vibrations of MeOH.
Similar observations have been found in acetonitrile solvated system as shown in Figure 3.3.3a. Similar to the MeOH solvate crystal, here also flexible compound L4 reorganizes to accommodate the solvent in the crystal lattice to accommodate the larger, linear MeCN unit in comparison to the previous crystal. 1D channel is running along a axis and each cavity along the channel contain a dimmer of solvent molecules, as observed in the case of
Figure 3.3.3. (a) Encapsulation of MeCN; (b) Perspective view highlighting the solvent dimmer in the cavities and (c) Non-covalent interaction associated with solvent in the lattice.
MeOH solvent (Figure 3.3.3b). It forms a rectangular cavity with dimension of 9.73 Å x 7.83 Å. The cavity size is larger than the MeOH solvate crystal to accommodate larger solvent, MeCN. Each of these solvent dimmer is separated by hydrophobic naphthalene
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Chapter-3 Supramolecular Photochemistry of Naphthalene and Quinoline based systems
ring along c axis with a distance of 9.31 Å and along b axis they are separated by 12.95 Å by cyclohexyl unit. MeCN forms N-H····N, C-H····N and C-H····π type non- covalent interactions with the ligand (Figure 3.3.3c). However, in contrast to the MeOH crystal there is no such non-covalent interactions are observed between the solvent molecules.
Similar to the previous two crystals only nitrogen atoms attached to the aromatic ring are involved in N–H····S hydrogen bonding interactions resulting in the formation of 1D chain.
In the MeOH solvate crystal syn conformations more deviated than un-solvated crystal.
FT-IR spectrum of the crystal shows the bands appearing at 2100 and 2356 cm-1, which can be assigned to the C=N stretching frequencies of CH3CN. In MeCN solvate crystal both the syn and anti N–H groups are within the normal range of dihedral angle (see appendix).
The switch from MeOH or MeCN to amide group containing solvent, DMF had a dramatic effect on the network structure (Figure 3.3.4a). Larger DMF molecule exists as a monomer in the crystal lattice, in contrast to the previous solvated crystal (Figure 3.3.5b). In the lattice it is included in a cylindrical cavity with a dimension of 9.58 Å x 7.96 Å. Along b axis the minimum distance between two DMF molecules is 8.38 Å and along c axis this distance is 8.61 Å. Similar to the previous crystals only nitrogen atoms attached to the aromatic ring (syn to C=S) are involved in N–H····S hydrogen bonding interactions resulting in the formation of 1D chain. In contrast to the previous all crystals, in DMF solvated crystal naphthalene unit forms C-H····S type bond with thiourea unit (see appendix). Each DMF molecule is stacked between two naphthalene rings in the solid- state and C=O group is pointed towards the thiourea unit (see appendix).
Figure 3.3.4. (a) ORTEP view of L4⋅DMF with atom labelling scheme (hydrogen atoms are omitted for clarity); (b) Perspective views of L4⋅DMF highlighting the guest molecules in the cavities and (c) Perspective views of the lone pair ···· π interaction in L4⋅DMF via Olp····π and Nlp····π in DMF molecule.
This particular orientation of the DMF molecules helps in the formation of two rare type of non-covalent interactions viz. C=O····π3.3.5 and lone pair (lp)····π 3.3.5, 3.3.6 (Figure 3.3.4c) interaction with the naphthalene unit in addition to the common N-H····O type hydrogen bonds (see appendix). FT-IR spectrum of crystal shows a lower C=O stretching frequency
Chapter-3 Supramolecular Photochemistry of Naphthalene and Quinoline based systems
at 1680 cm-1 than an unsubstituted C=O bond. Also, peaks at 1500, 1250, 1120 and 860 cm-1 are because of the partial double bond character, the rotation about the C-N bond. In this case, we have seen the more deformation of syn and anti conformation of the dihedral angle of S=C-N-H bonds than the previous systems. Comparisons of all the pseudopolymorph structures are presented in Figure 3.3.5. For easy comparison in the 3D conformation of the flexible ligand, all the solvent molecules are omitted and cyclohexyl unit is shown in the most stable chair conformation. Relative orientation of C=S groups in the pendent arms are largely differ in case of MeOH solvated system. However, relative orientation of the naphthalene units is similar in un-solvated ligand and MeCN solvated crystal. In other two solvated crystals these two aromatic rings are oriented in a different manner and large deviation is observed in DMF solvated crystal.
Figure 3.3.5. Comparison of conformation of ligand in different crystal form (solvent mocules are removed for clarity).