Topology of Ladder Supramolecular Assemblies in Azahetorocyclic

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Topology of ladder supramolecular assemblies in azaheterocyclic phosphonates. A structural and computational approach Anna Pietrzak, Jakub Modranka, Jakub Wojciechowski, Tomasz Janecki, and Wojciech M. Wolf Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.7b01087 • Publication Date (Web): 22 Nov 2017 Downloaded from http://pubs.acs.org on November 23, 2017

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Crystal Growth & Design

Topology of ladder supramolecular assemblies in azahetorocyclic phosphonates. A structural and computational approach Anna

Pietrzaka*,

Jakub

Modrankab,

Jakub

Wojciechowskia*,

Tomasz

Janeckib,

Wojciech M. Wolfa AUTHOR ADDRESS a

Institute of General and Ecological Chemistry, Lodz University of Technology,

Żeromskiego 116, Łódź, Poland b

Institute of Organic Chemistry, Lodz University of Technology, Żeromskiego 116, Łódź,

Poland KEYWORDS crystal packing, single crystal X-ray analysis, azaheterocyclic phosphonates, PIXEL method, self assembly

ABSTRACT

Topologies of ladder packing arrangements in crystal structures of five azaheterocyclic phosphonates were characterized by four geometrical descriptors introduced in the paper.

ACS Paragon Plus Environment

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Crystal Growth & Design 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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The structural analysis was augmented by detailed calculations on interactions stabilizing the

molecular

assemblies.

Intermolecular

energies

were

evaluated

using

PIXEL

and DFT(M062x-GD3) methods. Additionally, fingerprint plots derived from the Hirshfeld surfaces, were generated for each structure to characterize the crystal packing arrangement in detail. All structures are stabilized by the relatively weak hydrogen bonds and nonbonding interactions involving aromatic rings i.e. π...π, C-H...π and (lp)...π effects. Distribution of the molecular electrostatic potential demonstrates that positively charged, endocyclic sulfur atoms are prone to chalcogen-chalcogen (S...O) bonding. Analysis of the supramolecular motifs shows the lack of a common synthon responsible for the ladder packing arrangements. However, the striking geometry similarity of all molecules indicates that ladder packing is based on a shape oriented molecular recognition and mostly driven by the van der Waals forces. The intermolecular electrostatic effects are crucial for stabilizing and fixing geometry of the already formed molecular clusters. INTRODUCTION Phosphonates and their derivatives are important compounds for medicine1–5, chemical industry6–10 and agriculture11–13. On the contrary to phosphates with their highly energetic P-O–C moieties prone to biochemical cleavage, phosphonates with the sturdy P-C bond are chemically and biochemically stable. In particular, they are quite resistant to enzymatic hydrolysis14, thermal decomposition15 and photolysis16. The geometry of phosphorus coordination sphere is similar in both groups of compounds and subsequently they are often recognized by enzyme active sites in a similar fashion. The stronger stability of phosphonates makes them useful inhibitors and antimetabolites of several vital processes in living organisms17. The phosphoryl bond has a strong dipolar character with substantial positive charge located


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on phosphorus atom18. The real structure of this bond was a matter of controversy over last fifty years19. The former view of dπ back-bonding is now being challenged by the negative hyperconjugation formalism20–22. Structurally, phosphoryl group is generally regarded as a longer and more polar equivalent of carbonyl bond. Its oxygen atom is a good acceptor of hydrogen bonds of diversified topology23–25. Therefore, phosphonates are interesting alternative for crystal engineering and important enhancement to carboxylic acids and carboxylates widely used in crystal engineering

strategies26–29 which are based

on principal building blocks, namely synthons and tectons30–33. The former consist of molecular fragments together with the resulting interactions and the similarity of supramolecular assemblies is often characterized by the common synthons34–39. The tecton concept addresses the importance of shape and rigidity of molecular building blocks. This strategy has been introduced by Simard et al., who pointed out that incorporation of multiple sticky sites into a rigid framework may induce the self-assembly of multidimensional molecular networks40,41. The tecton concept is specially dedicated to porous systems42–46. Its application to more densely packed organic crystals is quite limited indeed47. In this paper we describe crystal structures of five azaheterocyclic phosphonates with endocyclic sulfur atoms incorporated into the fluorene fragments (Scheme 1). Despite the lack of common synthons, all structures are stabilized by a number of intermolecular interactions. Their crystal packing is dominated by homogenous ladder molecular assemblies which are characterized in detail by novel geometrical descriptors.


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Scheme 1. Structural schemes of 1 - 5. EXPERIMENTAL SECTION Materials and methods. All solvents and reagents were purchased from commercial vendors and used without further purification. NMR spectra were recorded on a Bruker Avance II instrument at 700 MHz for 1H, 176 MHz for

13

31

C, and 283 MHz for

tetramethylsilane as internal and 85% H3PO4 as external standard.

P NMR using

31

P NMR spectra

were recorded using broadband proton decoupling. HRMS spectra were performed on Waters Acquity UPLC/Q-TOF LC-HRMS apparatus. Column chromatography was performed on Sigma Aldrich silica gel 60 (230-400 mesh). Synthetic procedures. Synthesis and NMR data of Diethyl (4-oxo-4H-benzo[4,5]thiazolo[3,2a]pyrimidin-3-yl)phosphonate 1 were reported previously48. Synthetic procedure of 2 and 3: to a solution of 2-amino-6-methoxybenzothiazole or 2-amino-6-chlorobenzothiazole (10.0 mmol) in


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ethanol (50 mL) 2-diethoxyphosphoryl-3-methoxyacrylate (2.66 g, 10.0 mmol) was added and the mixture was stirred for 24 hours. Next, the methanol was evaporated and Dowtherm A (150 mL) was added. The mixture was heated under reflux for 30 minutes. After cooling, the reaction mixture was applied to a silica gel column. The column was washed in turn with hexane (150 mL), ethyl acetate (150 mL) and ethanol (150 mL). The ethanol fraction was evaporated and the residue purified by column chromatography (eluent: EtOAc–MeOH, 10:1). Diethyl (8-chloro-4-oxo-4H-benzo[4,5]thiazolo[3,2-a]pyrimidin-3-yl)phosphonate

2: (63%);

yellow crystals; mp 145-147 °C, 1H NMR (700 MHz, CDCl3) δ 9.07 (d, J = 9.0 Hz, 1H), 8.56 (d, J = 9.6 Hz, 1H), 7.74 (d, J = 2.1 Hz, 1H), 7.55 (dd, J = 9.0, 2.1 Hz, 1H), 4.34 – 4.22 (m, 4H), 1.39 (t, J = 7.1 Hz, 6H); 13C NMR (176 MHz, CDCl3) δ 165.96, 159.26 (d, J = 11.3 Hz), 158.67 (d, J = 12.7 Hz), 134.18, 133.52, 127.91, 125.69, 121.79, 121.23 (d, J = 3.6 Hz), 109.30 (d, J = 197.3 Hz), 62.89 (d, J = 5.7 Hz), 16.40 (d, J = 6.3 Hz);

31

P NMR (283 MHz, CDCl3) δ 13.37.

HRMS m/z, calcd [M+H]+ 373.01732, observed 373.01749. Diethyl (8-methoxy-4-oxo-4H-benzo[4,5]thiazolo[3,2-a]pyrimidin-3-yl)phosphonate 3: (48%); yellow crystals; mp 116-117 °C, 1H NMR (700 MHz, CDCl3) δ 8.99 (d, J = 9.3 Hz, 1H), 8.50 (d, J = 9.5 Hz, 1H), 7.19 (d, J = 2.6 Hz, 1H), 7.07 (dd, J = 9.3, 2.6 Hz, 1H), 4.37 – 4.14 (m, 4H), 3.88 (s, 3H), 1.37 (t, J = 7.0 Hz, 6H); 13C NMR (176 MHz, CDCl3) δ 166.16, 159.14 (d, J = 2.6 Hz), 159.10, 159.07 (d, J = 2.7 Hz), 158.86 (d, J = 12.7 Hz), 129.67, 125.86, 121.67, 114.67, 108.70 (d, J = 197.4 Hz), 106.14, 62.95 (d, J = 5.5 Hz), 55.99, 16.54 (d, J = 6.3 Hz); 31P NMR (283 MHz, CDCl3) δ 14.26. HRMS m/z, calcd [M+H]+ 353.08970, observed 353.08948. Synthesis of 4: To a solution of phosphonate 1 (5.0 mmol) in toluene (50 mL) PCl5 (1.46 g, 7.0 mmol) was added. The mixture was heated at 100oC for 48 h. The precipitate was filtered.


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Then, the solution was cooled to 0oC and treated with Et3N (3.48 mL, 25 mmol) and (R)- 1-phenylethan-1-amine (1,29 mL, 10 mmol). After 24 h at r.t. the 1M HClaq (50 mL) were added. The organic layer was separated and washed with brine (50 ml), dried over MgSO4, filtered and concentrated. Obtained mixture of diastereoisomers of 4 was purified and separated by column chromatography on silica gel (eluent : Et2O). (R)-P-(4-oxo-4H-benzo[4,5]thiazolo[3,2-a]pyrimidin-3-yl)-N-((R)-1phenylethyl)phosphonamidate 4; (42%), white crystals;

1

H NMR (700 MHz, CDCl3)

δ 9.03 – 9.01 (m, 1H), 8.35 (d, J = 9.1 Hz, 1H), 7.75 – 7.73 (m, 1H), 7.60 – 7.54 (m, 2H), 7.20 – 7.17 (m, 2H), 6.99 – 6.96 (m, 2H), 6.86 – 6.83 (m, 1H), 4.59 – 4.52 (m, 1H), 4.16 – 4.09 (m, 2H), 3.77 – 3.69 (m, 1H), 1.54 (d, J = 6.7 Hz, 3H), 1.33 (t, J = 7.0 Hz, 3H); 13

C NMR (176 MHz, CDCl3) δ 165.27, 159.60 (d, J = 9.0 Hz), 158.01 (d, J = 10.2 Hz),

144.47, 135.63, 127.92, 127.61, 127.31, 126.53, 125.98, 124.09, 121.94, 120.29, 111.33 (d, J = 171.0 Hz), 61.00 (d, J = 4.9 Hz), 51.21, 24.95 (d, J = 8.4 Hz), 16.45 (d, J = 6.6 Hz); 31

P NMR (283 MHz, CDCl3) δ 16.64. HRMS m/z, calcd [M+H]+ 414.10358, observed

414.10349. Synthesis of 5: To the solution of phosphonate 1 (5.0 mmol) in DCM (50 mL) under argon atmosphere, TMSBr (1,98 mL, 15 mmol) was added in one portion. The reaction mixture was stirred at ambient temperature for 24 h. Then EtOH (10 mL) was added. After 15 min. solvents were evaporated. The obtained crude phosphonic acid was treated by (COCl)2 (1,69 mL, 20 mmol) in DCM (50 mL) with catalytic amount of DMF (0.2 mL) and the mixture was refluxed for 3 h. Next, the solvent was evaporated. To the residue DCM (50 mL), Et3N (3.45 mL, 25 mmol) and (S)-1-phenylethanol (1.51 mL, 12.5 mmol). After 24 h at r.t. the 1M HClaq (50 mL) were added. The organic layer was separated and washed with brine (50 ml), dried over


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MgSO4, filtered and concentrated. Obtained crude product was purified by column chromatography on silica gel (eluent : Et2O). Bis((S)-1-phenylethyl)(4-oxo-4H-benzo[4,5]thiazolo[3,2-a]pyrimidin-3-yl)phosphonate 5 (92%), white crystals; 1H NMR (700 MHz, CDCl3) δ 9.10 – 9.07 (m, 1H), 8.29 (d, J = 9.8 Hz, 1H), 7.73 – 7.70 (m, 1H), 7.60 – 7.53 (m, 2H), 7.49 – 7.46 (m, 2H), 7.37 – 7.33 (m, 2H), 7.29 – 7.24 (m, 3H), 7.12 – 7.08 (m, 2H), 7.03 – 7.00 (m, 1H), 5.81 (dq, J = 8.3, 6.6 Hz, 1H), 5.58 (p, J = 6.7 Hz, 1H), 1.68 (d, J = 6.6 Hz, 3H), 1.51 (d, J = 6.5 Hz, 3H);

13

C NMR (176 MHz, CDCl3)

δ 166.12, 158.56 (d, J = 11.4 Hz), 158.46 (d, J = 12.8 Hz), 142.04 (d, J = 4.2 Hz), 141.33 (d, J = 3.9 Hz), 135.63, 128.37, 128.11, 127.91, 127.77, 127.54, 127.33, 126.23, 126.13, 123.96, 121.91, 120.27 (d, J = 4.1 Hz), 109.89 (d, J = 198.8 Hz), 76.26 (d, J = 5.4 Hz), 76.02 (d, J = 6.0 Hz), 24.58 (d, J = 6.9 Hz), 24.18 (d, J = 4.9 Hz);

31

P NMR (283 MHz, CDCl3)

δ 12.22. HRMS m/z, calcd [M+H]+ 491.11889, observed 491.11884. Crystal structure determination. Single crystals suitable for X-ray diffraction studies were recrystallized by slow evaporation from isopropanol at room temperature for 1-4 and from acetonitrile at 2−6 °C for 5. Saturated solutions were prepared with 3-6 mg of particular compound and a solvent added on a drop by drop basis. A magnetic stirrer was applied. All beakers with saturated solutions were subsequently sealed with plastic paraffin film. Compounds 1-4 and 5 crystallized after about four and fourteen days, respectively. The single-crystal X-ray diffraction experiments for 1, 2, 4 and 5 were performed on a Bruker Smart Apex2 diffractometer at 100 K using Incoatec IµS Cu-Kα (λ =1.54178 Å) as a source of radiation. Data integration was done in APEX2 using SAINT49. Intensities for absorption were corrected using SADABS50. X-ray data for 3 were collected on a XtaLAB Synergy, Dualflex, Pilatus 200K diffractometer. The crystal was kept at 100.0(1) K during data collection. All structures were


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solved with the ShelXT51 structure solution program using Intrinsic Phasing and refined in the ShelXle52 by the full-matrix least-squares on F2 with the ShelXL53 refinement package. All nonhydrogen atoms were refined anisotropically, N−H and O−H hydrogens were located from difference electron density maps, and C−H hydrogens were generated geometrically using the HFIX command as in ShelXL. Structure 3 was refined as a two component twin with twin scale factor of 0.179(5). Molecular plots and packing diagrams were drawn using Mercury54 and additional metrical data were calculated using PLATON55 . The crystallographic data are given in Table 1. The CIF files for each refinement are available from the Cambridge Crystallographic Data Centre (CCDC)56 (deposition numbers CCDC: 1478184, 1478182, 1564989, 1491372, 1478183 for 1-5, respectively). Modeling of Disorder. The 1-phenylethylamino group in 4 was observed to be disordered over two orientations, with occupancy ratio 0.783(9):0.217(9). The disorder associated with this molecule was carefully modeled using the PART command. The N-H bond length of amino group was constrained using DFIX command . Thermal parameters were constrained to be equal using SIMU and RIGU instructions.


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Table 1. Selected Structural Data Crystal structure

1

2

3

4

5

Formula

C14H15N2O4PS

C14H14Cl N2O4PS

C15 H17 N2 O5P S

C20H20N3O3PS

C26H23N2O4PS

M, g·mol-1 Crystal system Space group

338.31 triclinic Pī



413.42 monoclinic P 21

490.49 orthorombic P21212

T, K

100.0(2)

100.0(2)

100.0(2)

100.0(2)

100.0(2)

a, Å

8.0173(3)

8.1807(2)

8.2178(2)

7.0770(1)

14.6230(4)

b, Å

8.0856(3)

9.2313(3)

9.1537(2)

12.9400(2)

23.0577(7)

c, Å

13.3095(5)

11.2238(4)

11.1457(4)

11.0190(1)

13.6791(4)

α, degree

84.6420(10)

92.842(2)

96.051(2)

90

90

β, degree

76.5540(10)

91.6010(10)

97.684(2)

103.994(1)

90

γ, degree

60.8780(10)

113.6310(10)

101.113(2)

90

90

Z

2

2

2

2

8

V, Å

732.86(5)

774.51(4)

807.85(4)

979.13(2)

4612.2(2)

R1 [I > 2( I)]

0.0310

0.0267

0.0296

0.0338

0.0260

wR2 (all)

0.0813

0.0757

0.0859

0.0882

0.0713

GOF

1.109

1.033

1.045

1.032

1.020

3

Theoretical calculations. Hirshfeld surface and 2-D Fingerprint Plots. The Hirschfield surfaces (HS) were calculated with the methodology implemented in CrystalExplorer 3.1 program57. Molecular geometries were taken directly from the relevant crystal structure with H atoms at their neutron positions. The distances from the HS to the nearest atom interior and exterior to the surface (di and de respectively) were calculated. The fingerprint plots (FP) were drawn as scattergrams of di and de for each HS point58. A quantitative decomposition analysis of atoms to surface contact was calculated as percentage of points in HS with di or de for specific pair of atoms. The molecular electrostatic potentials (ESP) mapped on HS59 were generated from wave functions calculated for single molecule in Gaussian 09 D.01 program60. The DFT methodology with M062x density functional and 6-31++G(d,p) basis set were used as implemented in Gaussian.


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Energy calculations. The Lattice Energies, crystal intermolecular interaction energies (further abbreviated as Etot) and their Coulumbic (ECoul), polarization (Epol), dispersion (Edisp) and repulsion (Erep) contributions were computed using PIXELC module as in the CLP-PIXEL software package (ver. 3.0)61,62. Geometries of molecules were as determined by the X-ray crystal analysis. Hydrogen atom positions were normalized to be consistent with the respective neutron structural data. The electron density distribution of individual molecules were obtained with the Gaussian 09 D.01 package. MP2 calculations were in the Pople’s basis sets [631++G(d,p)], while DFT computations used the Truhlar’s Minnesota Functional M062x in the same basis sets. The Grimme’s original D3 damping function as an empirical dispersion correction was applied for the latter. Complexation energies for isolated dimers were computed with the DFT method. The basis set superposition error was evaluated using the Gaussian counterpoise correction. RESULTS AND DISCUSSION General Crystal Structure and Conformation Description. Molecular conformations of 1-5 as determined by the X-ray analysis are shown in Figure 1. Compounds 1-3 crystallize in the triclinic system while 4 and 5 are in monoclinic and orthorhombic settings, respectively. In all structures, a rigid planar fused aromatic system is linked to the phosphonic group. In 1-3 this latter fragment is terminated by diethoxyphosphoryl moiety. The C6 atoms at the fluorene skeleton are substituted by H, Cl or OMe as in 1, 2, 3, respectively. In 4 the central phosphorus atom is linked to ethoxy- and 1-phenylethyloamino- groups while in 5 it bears two identical phenylethoxy moieties. All endocyclic nitrogen atoms exist in a planar configuration, their lone pairs are conjugated with the aromatic π electron system.


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Figure 1. ORTEP plots of 1-5 with the atom numbering scheme. Displacement ellipsoids are drawn at the 50% probability level. “Cgn” represents the centroid of the n-th ring as shown by the green spheres. For clarity only one molecule of asymmetric unit in 5 is displayed.


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Molecules 1-3 and 5 adopt T-shaped conformation which minimizes the usual steric interactions, while 4 exists in a folded arrangement additionally stabilized by the intramolecular stacking. The phosphoryl groups in 1, 3, 4 and 5 are almost coplanar with the fluorene skeleton, while in 2 the phosphoryl group is placed out of the benzothiazolopyrimidynone system and the respective torsion angle O4-P1-C1-C10 is -61.33(13)°. Endocyclic S-C bond lengths are quite consistent over all investigated compounds. The average bond [1.741 Å] is shorter than typical S-C (aromatic) bond as reported for the model phenothiazine system 1.764 Å63 and indicates involvement of sulfur π lone pair in the aromatic electron ring system. Molecular geometry details are summarized in Table 1S, Supporting Information. Crystal packing. In all crystals 1 - 5, conjugated aromatic rings create stacks which form ladders, Figure 2. In 1, 2, and 3 supramolecular ladders run along [100], [110] and [010] directions, respectively. Inversion centers located in spaces between rungs, prompt “parallel rung” ladder architecture. All planar benzothiazolopirymidynone moieties are involved in π···π interactions which stabilize centrosymmetric dimers. This “parallel rungs” architecture is distorted in 4 and 5 by a single phenylethyloamino or two phenylethoxy substituents at the phosphorus, respectively. It is also affected by the lacking inversion center between rungs. The resulting ladders run in [010] or [100] directions, accordingly. The ladder geometry parameters, (Figure 3) for 1-5 are summarized in Table 2. The ladder width w is defined as the smallest gap between rails. The ladder propagation distance S is the shortest separation between equivalent phosphorus atoms positioned along the ladder rail. The ladder rung separation r is the distance between least-squares plane defined by the particular rung atoms and the centroid of the next rung.


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Figure 2. Ladder packing motifs in crystals 1-5. Rails are defined as planes spanned over phosphorus atoms. Only single layer of ladders is presented for clarity.

Figure 3. Ladder geometry descriptors: r - inter-rung distance; w - ladder width; E- distance between neighboring ladders, S – propagation distance


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Ladder geometry descriptors clearly show that the widest ladder (w=9.615 Å) exists in 1 while in the similar structures 2 and 3 ladders are significantly slimmer. The respective ladder widths are 4.456 Å and 6.841 Å. In 4, phenylethyloamino group generates additional half-rung and elongates the respective ladder propagation parameter to S=12.657 Å. Asymmetric unit of 5 contains two independent molecules named hereafter A and B. Both adopts similar T-shaped conformation (Figure 1). Molecules related by the 2-fold axis form two types of distinct dimers AA and BB stabilized by stacking interactions between respective benzothiazolopyrimidinone moieties. These structures form ladders with three types of inter-rung interactions, namely A…A, B…B and A…B. The resulting elongation of ladder repetitive unit is reflected by the propagation parameter value S=14.623 Å, higher than those calculated for 1–4. Figures with ladder geometry parameters plotted for 1-5 are presented in Figures 2S-6S, Supporting Information. Table 2. Supramolecular ladder geometry descriptors calculated for 1-5. In 4, parameters were computed for consecutive benzothiazolopirymidynone and phenyl moieties while in 5 symmetry independent molecules (A and B) were taken into the consideration. Descriptor [Å]

1

2

3

4

5

w

9.615

4.456

6.841

7.014

9.308

E

3.327

6.738

1.121

1.199

2.532

3.380

3.407

3.417

3.498

3.396

3.971

3.341

3.649

8.017

9.571

9.154

12.657

r S

3.558 A…A 3.516 A…B 3.583 B…B 14.623


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The Crystal Explorer was used to gain more quantitative insight into the packing arrangement of investigated structures. Fingerprint plots (FPs), derived from the Hirshfeld surfaces, were generated for each crystal structure, Figure 4.

Figure 4. Fingerprint plots generated for asymmetric unit of 1–5. In 5 both symmetry independent molecules ( A and B) were taken into the consideration. Surprisingly, FPs are not highly complementary albeit similarities in the crystal packing. The strongest similarity exists between 1 and 3. It follows the overall intermolecular contacts topology which in 3 is slightly distorted by the terminal methoxy group at the fluorene moiety. FPs of 1,3 and 5 show a single pair of spikes generated by donor-acceptor interactions of the C-H...O type. In 2 the out of plane position of the phosphoryl group combined with the terminal chlorine substituent generates the most distinctive set of intermolecular contacts. They are represented by two pairs of small humps without the clearly defined spikes. Surprisingly, only in 3 a characteristic feature corresponding to aromatic rings stacking interactions is clearly visible. In 4 the three separate pairs of spikes correspond to N-H...N, C-H...O and C-H...S interactions. Percentage contributions to the Hirshfeld surface


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area for the various intermolecular contacts as summarized in Figure 5 indicate lack of the mutual quantitative correlations.

Figure 5. Percentage contributions to the Hirshfeld surface area for various intermolecular contacts as in structures 1-5. Percentages are given for the major contacts only. The H...H contacts dominate on all FPs with their contribution varying from 30.9% to 57.5% for 2 and 4, respectively. The total contribution of N...H, O...H and S...H contacts in 1-3 approaches one third (33.9, 28.9, 32.9% respectively) and is significantly higher than in 4, and 5 ( 23.4 and ~17.0%, respectively). Intermolecular Energy Calculation. The lattice energies and intermolecular interactions were characterized using the Gavezzotti methodology61 as implemented in the PIXELC. This method takes into consideration the periodicity of the crystal and allows partitioning of the particular energy into the contributing Coulombic, polarization, dispersion and repulsion terms, Table 3.


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Table 3. Lattice energy (kcal mol-1) Etot computed by the PIXEL method. Electron density of individual molecules were calculated at the MP2 level of theory. (For comparison, the DFT(M062x-GD3) results are given in the Table 2S Supporting Information). Ecoul

Epol

Edisp

Erep

Etot

1

-28,4

-11,8

-46,6

60,1

-26,7

2

-31,3

-12,5

-50,9

63,1

-31,5

3

-31,8

-10,9

-49,3

62,3

-29,7

4

-32,1

-13,4

-47,1

63,8

-28,9

5

-30,5

-12,8

-59,9

72,0

-31,2

The lattice energies are quite similar over all investigated crystals, the smallest being observed for 1. Dispersion accounts for 51-58% of stabilization components. This value is lower than respective contributions in organic crystals governed by stacking effects64 and indicates that in 1-5 the electrostatics (i.e. ECoul and Epol) should be acknowledged. The latter is of particular importance when N, O or S are involved in a specific interaction or contribution of C-H...π effects increases. The resulting electrostatic complementarities of aromatic moieties explain the relatively low dispersion contribution originated from stacking interactions (Figure 1S Supporting Information). The most relevant interaction energies (Etot), partitioned into Coulombic (Ecoul), polarization (Epol), dispersion (Edisp) and repulsion (Erep) contributions computed for pairs of molecules are summarized in Table 5. They represent intermolecular contacts describing packing arrangement in 1-5. Visualization of intra-ladder and side to side as well as layer to layer inter-ladder molecular clusters stabilized by the lowest interaction energies Etot are shown in Figures 6 – 8, respectively.


17


Page 18 of 35

Table 4. Selected intermolecular energies Etot (kcal mol-1) computed by the PIXEL method and the relevant intermolecular contacts involved. Electron density of individual molecules was determined at the MP2 level of theory (For comparison, the M062x-GD3 results are given in the Table 3S Supporting Information).

Motif

Symmetry operator

Da

ECoul

Epol

Edisp

Erep

Etot

Intermolecular contacts

1 1-a

-x+1, -y+2, -z+1

6.164

-13.5

-4.8

-20.4

31.7

-7.1

Cg1...Cg1, Cg2...Cg3, Cg3...Cg2, O1...Cg3

1-b

x-1, y, z

8.017

-1.6

-0.8

-4.6

5.1

-2.0

C32-H32a…Cg2

1-c

-x+1 -y+1 –z

10.903

-6.7

-2.7

-7.0

9.3

-7.0

C31-H31a...O4

1-d

-x+2, -y+1, -z

8.527

-4.9

-1.9

-7.0

8.3

-5.4

C22-H22c...O4

1-e

x, y-1, z

8.086

-7.0

-2.8

-8.7

13.1

-5.5

C31-H31a…N1, C32-H32c…N1, O1…S1; O3…S1

1-f

-x+2, -y+1, -z+1

8.318

-2.9

-1.7

-6.4

6.5

-4.5

C6-H6...H22b-C22

2 2-a

-x, -y+1,-z+1

5.618

-15.3

-7.0

-14.4

25.3

-11.4

P1-O4…Cg2, C21-H21a ...Cg3

2-b

-x+1 -y+2 -z+1

4.123

-13.8

-6.0

-24.1

33.9

-10.0

S1…O3,S1…Cg2, Cg2...Cg1, Cg1…Cg2

2-c

-x, -y+1, -z+2

12.816

-2.0

-1.2

-5.7

5.8

-3.1

C31-H31b…H31b-C31

2-d

-x, -y+2,-z+1

8.124

-5.7

-2.8

-8.9

11.4

-6.0

C21-H21b…S1

2-e

-x+1, -y+1, -z+1

6.566

-13.0

-4.8

-11.0

15.0

-13.7

C7-H7...O4, C8-H8…O1

3 3-a

-x+1, -y+1, -z+1

4.551

-17.5

-6.1

-22.5

34.5

-11.6

C51-H51A…O4, Cg1…Cg2, S1-O2

3-b

-x+1, -y, -z+1

8.340

-9.8

-3.9

-17.7

25.7

-5.8

C51-H51c…Cg2, Cg3…Cg3

3-c

-x+2, -y+1, -z+1

6.683

-6.3

-3.0

-11.3

15.5

-5.0

C32-H32a…S1

3-d

x+1, y+1, z

11.060

-6.5

-1.8

-4.1

6.2

-6.2

C2-H2…O5, O4…C7-H7

3-e

-x+2,-y+1, -z+2

8.564

-7.9

-2.7

-8.9

11.7

-7.9

C31-H31a…O1, C32-H32b…O3

3-f

-x+2, -y+2, -z+2

11.899

-6.1

-2.4

-6.5

8.4

-6.5

P-O4…C21

4 4-a

-x+2, y-0.5, -z+1

7.141

-6.4

-2.5

-12.4

17.9

-3.4

Cg4...Cg1; Cg4...Cg2

4-b

x-1, y, z

7.077

-10.3

-5.6

-13.0

21.3

-7.6

N3-H3n...N1, C8-H8...S1, O1...S1

4-c

x, y, z+1

11.019

-3.3

-1.2

-2.5

3.0

-3.9

C7-H7...O4


18

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4-d

-x+1, y+0.5, -z

11.083

-3.1

-1.4

-4.8

5.2

-4.2

C22 H22a...O4

4-e

x+1, y, z+1

11.567

-6.9

-2.2

-5.3

8.1

-6.4

C5-H5...O4

5b A…A 5-a

-x+1, -y, z

5-b

x-0.5, -y+0.5, -z+1

6.061 9.841

-16.8 -6.8

-5.8 -3.2

-27.5

34.8

-8.0

-15.3

11.0

-7.0

35.3

-7.8

Cg3…Cg2, C8-H8…Cg5 C37-H37...O4, O4…H24-C24

A…B / B…A S1...Cg5, C21-H21...N1, 5-c

x, y, z

6.527

-14.2

-5.7

-23.2

Cg2...Cg2 5-d

x, y, z+1

9.06

-7.2

-2.9

-14.6

18.6

-6.1

C32-H32B…Cg4 / C32-H32D…Cg4

10.6

-6.1

O4...H35-C35

B …B 5-e

x-0.5, -y+0.5, -z

10.167

-5.3

-3.1

-8.2

C37-H37 ...O1, Cg2...Cg3 5-f

-x+2, -y, z

6.112

-17.7

-6.2

-26.9

35.8

-15.1

C8-H8...Cg5, C8-H8...H38-C38 C8-H8...H37-C37, C37-H37...O1

a

Intermolecular distances D (Å) were calculated between mass centers of relevant molecules

b

Asymmetric unit of 5 contains two independent molecules A and B. A…A, A…B, and B…B indicate interactions between those molecules


19


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Figure 6. Visualization of intra-ladder molecular clusters stabilized by the highest interaction energies. Motifs are as in Table 4. The highest stabilization in 1-3 and 5 follows from the diversified aromatic rings effects (i.e. π-π and CH-π interactions) and extends along the ladder propagation direction. In 1 it mostly arises from the stacking interactions (Etot = -7.1 kcal mol-1) between benzothiazolopyrimidynone moieties as represented by motif 1-a, further augmented by weak (Etot = -2.0 kcal mol-1) C(sp3)-H…π effect (motif 1-b). The electrostatics (ECoul+Epol) is mostly associated with the heteroatom, namely N,O,S participation. Single ladder in 2 is defined by two types of strong stabilizing motifs 2-a and 2-b with interaction energies -13.4 kcal mol-1 and -11.9 kcal mol-1, respectively. Motif 2-a involves axial phosphoryl oxygen interaction with the aromatic pyrimidinone ring system P1-O4...Cg2 supported by the C(sp3)-H…π effect, while motif 2-b includes stacking between aromatic moieties accompanied by chalcogen-


20

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chalcogen interaction, S1…O3. Similarly, molecular ladder in 3 is formed simultaneously by two interaction motifs. The highest stabilization (Etot = -11.6 kcal mol-1) arises from the Cg1…Cg2 stacking augmented by the C51-H51a…O4 interaction. Second motif 3-b (Etot = -5.8 kcal mol-1) is combined with C51-H51c…Cg1 interaction and Cg3…Cg3 π stacking. The latter involves terminal six membered rings of fused aromatic moieties. In 4, a single ladder is stabilized solely by the relatively weak (Etot = -3.4 kcal mol-1) stacking between phenyl ring Cg4 which is positioned approximately under the centre of benzothiazolopyrimidine fragment Cg1. The resulting interaction area is therefore smaller than those in 1-3 and 5. On the contrary, the resulting dispersion contribution in 4 (58%) is the largest of all examined structures. The highest stabilization along the ladder propagation direction is observed in 5. This structure contains two molecules (A and B) in the asymmetric unit. Therefore, three types of stabilizing motifs are recognized 5-a

(AA), 5-c (AB) and 5-f (BB). Analogous motifs 5-a and 5-f

characterized by similar stabilizing energies -15.3 kcal mol-1 and -15.1 kcal mol-1 are formed by symmetry equivalent molecules and are constituted of Cg3…Cg2 stacking combined with the C8-H8…Cg5 interaction. Symmetrically independent molecules A and B are associated by significantly weaker (Etot = -7.8 kcal mol-1) interactions as described by motif 5-c. It is defined by the hydrogen bond C21-H21…N1* and S1…Cg4* contact (asterisk “*” indicates the second molecule in the asymmetric unit of 5). The dispersion component contribution of interactions between the fused aromatic ring systems of molecules A and B (54%) suggests the distinct stacking interaction participation. Side to side inter-ladder contacts in 1,3 and 5 are dominated by C-H…O hydrogen bonds between phosphoryl and ethoxy (motifs 1-c

and 1-d), fluorene (motif 3-d) and phenyl moieties

(motifs 5-b and 5-e), respectively. Regardless diversified nature their stabilizing effects


21


Page 22 of 35

are comparable as indicated by the relevant energies Etot ranging in value from -5.4 to -7.0 kcal mol-1. In 3 additional hydrogen bonds between the single ethoxy group and the endocyclic sulfur atom C32-H32a…S1 (motif 3-c) are involved in the neighboring ladders stabilization (Etot = -5.0 kcal mol-1). Adjacent ladders of 2 are connected by the relatively weak (Etot = -3.1 kcal mol-1) homopolar, symmetrical interactions C31-H31b...H31b-C31 (motif 2-c). In 4, the highest stabilization (Etot = -7.6 kcal mol-1) is observed between neighboring ladders (motif 4-b). It is constituted of the chalcogen-chalcogen contact between endocyclic sulfur atom S1 and carbonyl oxygen atom O1 and further supported by the hydrogen bond N3H3n...N1.

Figure 7. Visualization of side to side inter-ladder molecular clusters stabilized by the highest interaction energies. Motifs are as in Table 4.


22

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In all structures 1-5 molecular ladders are arranged in layers. In 1 and 3-5 they are stabilized by motifs characterized by energies similar to those associated with side to side arrangements, Figure 8. The highest interlayer stabilization is observed in 2. The ladders are linked through two motifs 2-d and 2-e. The former is a single hydrogen bond C21-H21b…S1, while the latter is constructed with two C7-H7...O4 and C8-H8…O1 hydrogen bonds. The respective stabilization energies (Etot) are -6.0 and -13.7 kcal mol-1.

Figure 8. Visualization of layer to layer inter-ladder molecular clusters stabilized by the highest interaction energies. Motifs are as in Table 4. PIXEL interaction energy calculations were determined using electron density distributions calculated by the MP2 and DFT (M062x-GD3) methods. The latter, less computationally demanding procedure was given for comparison (Table 3S, Supporting Information). The cost


23


Page 24 of 35

effective M062x-GD3 approach gave results similar to those calculated with the MP2 methodology. Especially, the best agreement was observed for dispersion contribution values. Moreover, the complexation energies for the isolated molecular pairs were computed with the DFT method as used for electron density calculations (Table 4S, Supporting Information). Interestingly, this approach overestimated interactions involving

aromatic fragments as

determined by PIXEL in the periodic crystal framework, while donor-acceptor interaction energies were similar in both methodologies. Therefore, in systems with high dispersion effects participation, periodicity should always be taken into the consideration. Hirshfeld Surfaces and Molecular Electrostatic Potential. Hirshfeld surface which defines the boundary of electron density related to particular molecule65 were generated for single molecules as in crystals 1-5, Figure 9. All surfaces adopt T-shape and the largest distortion observed in 4 follows the folded 1-phenylethyloamino group. Molecular electrostatic potentials (ESP) mapped over the Hirshfeld surfaces identify parts of molecules prone to electrostatic interactions. In all structures highly negative potential area is placed around the phosphoryl O4 atoms. The latter are involved in either C-H…O hydrogen bonds as in 1 and 3-5 or the lone pair (lp)…π interactions66 with aromatic rings Cg2 and Cg3 observed in 2. Although, the ESP around endocyclic N1 atom is negative, it accepts hydrogen bonds in 1, 4 and 5 only. All endocyclic S1 atoms are positively charged and prone to forming chalcogen-chalcogen contacts67 of diversified length with carbonyl O1 or ethoxy O3 oxygens. Interestingly, sulfur atoms may also act as hydrogen acceptors in C-H…S interactions. This effect is reflected by H…S contacts contribution to the Hirshfeld surface area (7% – 2%) as shown in Figure 5.


24

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Figure 9. Front (left column) and back (right column) views of the molecular electrostatic potential (ESP) mapped over the Hirshfeld surface for 1-5 over -0.06 (red) through 0.0 (white) to 0.06 au (blue).


25


Page 26 of 35

CONCLUSIONS In all structures 1-5, a ladder-like supramolecular arrangements were identified. All ladders were characterized by novel geometrical descriptors. They were introduced for the first time to quantify differences in ladders geometry and may be applied to similar crystal assemblies elsewhere. Detailed examination of stabilizing motifs demonstrated their diversified character over

all

arrangements.

for the formation of

Therefore,

the

common

synthon

responsible

ladders in crystals could not be identified. Intermolecular energies

calculated by PIXEL in the periodic crystal framework showed that in 1-3 and 5 the intra-ladder stabilization plays a vital role while in 4 the highest stabilization is observed for the inter-ladder side to side arrangement. The former is governed by stacking effects accompanied by C-H…π and (lp)…π interactions, while the latter are stabilized by N-H…N hydrogen bonds and S…O interactions. Hirshfeld surfaces (which are derivatives of van der Waals surfaces68) show similar T-shape of molecules in 1-5. We therefore speculate that ladder packing is based on shape oriented molecular recognition and mostly driven by the van der Waals forces. The intermolecular electrostatic effects are crucial for stabilizing and fixing geometry of the already formed molecular clusters. Packing of molecular crystal may be conveniently interpreted by the simplified supramolecular tecton concept in which weak interactions support organization of molecular entities69. This approach may be useful when applied to rigid molecules of the limited conformational freedom (like 1–5), where identification of common synthon is not possible. In the future we would like to extend this approach to similar systems.


26

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ASSOCIATED CONTENT Supporting Information The following files are available free of charge. Selected geometric parameters for the studied azaheterocyclic phosphonates, lattice energies computed by the PIXEL method where electron densities of individual molecules were calculated using MP2 and DFT methods, selected interaction energies computed by the PIXEL method where electron densities of individual molecules were calculated using MP2 and DFT methods, comparison of interaction energies computed by the PIXEL relevant complexation energies for isolated dimers computed by the DFT method, electrostatic complementarities visualized by Hirshfeld surfaces with mapped ESP and relevant fingerprints showing the decomposition for S…O and C…C contacts, ladder geometry descriptors visualized for crystal structures 1 - 5. (PDF) Accession Codes CCDC 1478182-1478184, 1491372, 1564989 contain the supplementary crystallographic data for

this

paper.

These

data

can

be

obtained

free

of

charge

via

www.ccdc.cam.ac.uk./data_request/cif, or by emailing [email protected], or by contacting The Cambridge Crystallographic Data Centre, 12, Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223 336033 AUTHOR INFORMATION Corresponding Author *Anna Pietrzak. E-mail: [email protected]; Tel.:+48 42 6313119


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*Jakub Wojciechowski. E-mail: [email protected]; Tel.:+48 42 6313119 Notes The authors declare no competing financial interest. ACKNOWLEDGMENT The calculations presented in this paper were performed using the PLATON project’s infrastructure at the Lodz University of Technology Computer Center. REFERENCES (1)

Troev, K. D. Chemistry and Application of H-Phosphonates; Elsevier Science, 2006; pp 253-280.

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For Table of Contents Use Only

Topology of ladder supramolecular assemblies in azahetorocyclic phosphonates. A structural and computational approach Anna

Pietrzaka*,

Jakub

Modrankab,

Jakub

Wojciechowskia*,

Tomasz

Janeckib,

Wojciech M. Wolfa

Synopsis Five investigated phosphorylated azaheterocycles adopt ladder packing arrangement. Analysis of the supramolecular motifs using PIXEL and DFT methods shows the lack of a common synthon responsible for the packing similarity. Geometry of all molecules indicates that ladder packing is induced by self-assembly of “T-shaped” units rather than common interaction patterns. The ladder topologies were characterized by four novel geometrical descriptors.


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Topology of Ladder Supramolecular Assemblies in Azahetorocyclic

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