The Supramolecular Assemblies of N-Phthalimide Protected (E)- and

HR-10000 Zagreb, Croatia. ReceiVed January 25, 2008; ReVised Manuscript ReceiVed April 21, 2008. ABSTRACT: The supramolecular structures of three ...
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CRYSTAL GROWTH & DESIGN

The Supramolecular Assemblies of N-Phthalimide Protected (E)and (Z)-4-Amino-2-butenyl 5-Substituted Pyrimidine Derivatives: From Dimers to Two-Dimensional and Three-Dimensional Networks

2008 VOL. 8, NO. 8 2975–2981

Mario Cetina,*,† Ante Nagl,† Vedran Krisˇtafor,‡ Kresˇimir Benci,‡ and Mladen Mintas‡ Department of Applied Chemistry, Faculty of Textile Technology, UniVersity of Zagreb, Prilaz baruna FilipoVic´a 28a, HR-10000 Zagreb, Croatia, and Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, UniVersity of Zagreb, Marulic´eV trg 20, P.O. Box 177, HR-10000 Zagreb, Croatia ReceiVed January 25, 2008; ReVised Manuscript ReceiVed April 21, 2008

ABSTRACT: The supramolecular structures of three (E)-N-phthalimide protected 4-amino-2-butenyl 5-substituted pyrimidine derivatives, uracil derivative (1), 5-fluorouracil derivative (2), and 5-(trifluoromethyl)uracil derivative (3), were analyzed in order to understand how variations in their molecular structure influence their supramolecular aggregation. The structure of 5-fluorouracil derivative (2) is compared also with its (Z)-isomer (4). The molecules of 1-3 are assembled by self-complementary N-H · · · O hydrogen bonds into centrosymmetric dimers. Compound 4 crystallized with two independent molecules in the asymmetric unit that are linked also by two N-H · · · O hydrogen bonds into dimers. In supramolecular assembling of 1-4 C-H · · · O hydrogen bonds participate also, while supramolecular structures of 2, 3, and 4 additionally contain C-H · · · F interactions. The C-H · · · O hydrogen bonds in 1 and C-H · · · O hydrogen bonds and C-H · · · F interactions in 3 and 4 complete a three-dimensional network. The structure of 2 is built of dimers that generate a two-dimensional network. Introduction The rational design and synthesis of novel solid-state architectures are of current interest in the field of supramolecular chemistry and crystal engineering1,2 due to intriguing structural motifs that can be created by various intermolecular interactions. Supramolecular chemistry uses molecular recognition processes that rely heavily on the understanding of the recognition properties of the functional groups involved in these interactions. It is important to understand their nature in order to design new materials with desirable physical and chemical properties. Besides conventional strong hydrogen bonds (O-H · · · O, N-H · · · O, etc.) that play a dominant role in supramolecular assembling, the successful building of supramolecular architectures can be accomplished also by much weaker and more subtle intermolecular interactions, such as C-H · · · O and C-H · · · N hydrogen bonds, C-H · · · π and π · · · π interactions.3,4 Among the weakest types of interactions in molecular selfassembling are C-H· · ·X (X ) F, Cl, Br, I)5 andhalogen · · · halogen6 interactions, and their general application in crystal design is still challenging. Each crystal structure is the result of a delicate balance between a range of intermolecular interactions, and even a small change in the molecular structure may lead to unpredictable changes in supramolecular structure. Understanding the relationship between molecular and crystal structures, which represents the fundamental aspect in crystal engineering, becomes quite complicated if the molecules possess multiple functional groups. Therefore, it is important to study crystal structures of compounds with small differences in molecular structure and almost similar hydrogen-bonding functionalities in order to understand how these small differences can influence supramolecular assembling. It is particularly important to study molecules that * To whom correspondence should be addressed. Tel.: ++385 1 3712 590; fax: ++385 1 3712 599; e-mail: [email protected]. † Department of Applied Chemistry, Faculty of Textile Technology, University of Zagreb. ‡ Faculty of Chemical Engineering and Technology, University of Zagreb.

Chart 1

do not contain flexibility, because flexibility can cause several different molecular conformations. We have recently published syntheses and biological activities of pyrimidine nucleoside analogues containing 4-amino-2butenyl spacer between pyrimidine and phthalamide rings.7 Herein we present supramolecular structures of two (E)-Nphthalimide protected 4-amino-2-butenyl pyrimidine analogues that differ only in the pyrimidine ring C-5 atom substituent (Chart 1), uracil derivative (1) and 5-fluorouracil derivative (2) and compared them with the redetermined structure of 5-(trifluoromethyl)uracil derivative (3) that had been shortly presented in our previous paper.7 We have chosen to study these molecules because of their very small flexibility. Additionally, in order to find out how configurations’ change influences supramolecular assembling we also grew single crystals of (Z)-N-phthalimide protected 4-amino-2-butenyl 5-fluorouracil derivative (4). In this work we particularly pay attention to the role of weak intermolecular interactions, particularly C-H · · · F and F · · · F interactions8 in 2-4, in the formation of higher dimensional supramolecular architectures. A clear understanding of the nature of C-H · · · F and F · · · F interactions has not been reached yet and is still a matter of debate.9 The recent charge density study10 of intermolecular interactions involving organic fluorine has established that C-H · · · F contacts display characteristics of a weak hydrogen bond and has classified F · · · F contacts as a welldefined weak intermolecular interactions. These two weak, but important, interactions can provide stability of the supramo-

10.1021/cg800090n CCC: $40.75  2008 American Chemical Society Published on Web 07/10/2008

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Table 1. X-ray Crystallographic Data for 1-4 1 formula formula weight crystal system space group unit cell dimensions a (Å) b (Å) c (Å) R (°) β (°) γ (°) V (Å3) Z Dcalc. (g cm-3) absorption coefficient µ (mm-1) θ range (°) collected reflections no. independent reflections no./Rint. reflections no. I g 2σ(I) refined parameters no. goodness-of-fit on F2, S R [I g 2σ(I)]/R [all data] wR [I g 2σ(I)]/wR [all data] max/min electron density (e Å-3)

2

3

4

C16H13N3O4 311.29 monoclinic P21/c

C16H12FN3O4 329.29 triclinic P1j

C17H12F3N3O4 379.30 monoclinic C2/c

C16H12FN3O4 329.29 triclinic P1j

10.1870(2) 13.4049(3) 10.6494(2) 90.00 92.792(2) 90.00 1452.51(5) 4 1.424 0.105 3.83-27.00 9066 3114/0.0136 2562 212 0.972 0.0368/0.0461 0.1161/0.1239 0.187/-0.148

9.4250(4) 9.7967(4) 10.3001(3) 63.852(4) 68.655(3) 63.734(4) 748.52(5) 2 1.461 0.115 4.03-26.99 11521 3256/0.0187 2524 221 1.022 0.0416/0.0535 0.1359/0.1479 0.186/-0.198

27.2485(6) 6.8993(2) 18.0188(5) 90.00 96.858(2) 90.00 3363.22(15) 8 1.498 0.130 3.81-27.00 26770 3643/0.0428 2321 248 0.947 0.0382/0.0782 0.0996/0.1199 0.155/-0.196

9.8863(6) 10.3331(6) 16.5554(9) 77.454(5) 83.765(5) 61.683(6) 1453.28(15) 4 1.505 0.119 3.79-27.00 37487 6343/0.0579 3468 441 0.922 0.0420/0.0916 0.1005/0.1252 0.132/-0.180

Table 2. Hydrogen-Bonding and C-H · · · F Interactions Geometry for 1-4

1

2

3

4

D-H · · · A

H · · · A (Å)

D · · · A (Å)

N3-H3 · · · O2 C5-H5 · · · O1′ C8′-H8′ · · · O2′ N3-H3 · · · O1 C6-H6 · · · O1′ C9′-H9′ · · · F C10-H10B · · · O2 C6-H6 · · · F3 N3-H3 · · · O2 C6-H6 · · · O1′ C6′-H6′ · · · O1 C7-H7B · · · O2′ C8-H8 · · · F3 C71-H71A · · · O11 C72-H72B · · · O12 N31-H31 · · · O12 N32-H32 · · · O11 C61-H61 · · · O11′ C62-H62 · · · O12′ C62′-H62′ · · · O21′ C81-H81 · · · F2 C82′-H82′ · · · O22 C91′-H91′ · · · F1 C92-H92 · · · O21

2.06(2) 2.39 2.43 1.96(2) 2.29 2.47 2.58 2.35 1.93(2) 2.59 2.44 2.33 2.49 2.40 2.32 1.86(2) 2.15(2) 2.42 2.39 2.42 2.48 2.47 2.36 2.55

2.947(2) 3.266(2) 3.083(2) 2.805(2) 3.207(2) 3.389(2) 3.410(2) 2.694(2) 2.845(2) 3.224(2) 3.271(2) 3.277(2) 3.341(2) 2.767(3) 2.731(2) 2.745(2) 2.974(2) 3.324(3) 3.291(2) 3.216(3) 3.338(2) 3.338(3) 3.281(3) 3.448(3)

lecular assemblies acting with or without other intermolecular forces.11 For these reasons we aim to study these interactions in structurally related molecules containing fluorine and 4-amino2-butenyl acyclic side chain. Experimental Section Preparation of 1-4. The syntheses of (E)-N-phthalimide protected 4-amino-2-butenyl uracil derivative (1), 5-fluorouracil derivative (2), and 5-(trifluoromethyl)uracil derivative (3), and (Z)-N-phthalimide protected 4-amino-2-butenyl 5-fluorouracil derivative (4) have been described previously.7 Crystal Structure Determination. Colorless single crystals of 1, 2, and 3 suitable for X-ray single crystal analysis were obtained at room temperature by partial evaporation from ethanol solution, while colorless single crystal of 4 was obtained from methanol solution. The intensities for 1-4 were collected at 295 K on a Oxford Diffraction Xcalibur2 diffractometer with a Sapphire 3 CCD detector using graphite monochromated MoKR radiation (λ ) 0.71073 Å). The data collection and reduction were carried out with the CrysAlis programs.12 The structure of 37 was redetermined using the better quality single crystal in order to achieve higher accuracy in molecular and hydrogen-bonding

D-H · · · A (°) 160(2) 157 127 172(2) 170 172 144 102 168(2) 126′ 149 164 153 102 104 173(2) 169(2) 164 162 143 153 156 169 163

symmetry codes -x, -1 - y, 1 - z -x, -1/2 + y, 3/2 - z 1 - x, 1/2 + y, 1/2 - z 1 - x, 1 - y, 1 - z -x, 1 - y, -z -x, 1 - y, -z 1 - x, 1 - y, -z -x, -y, 1 - z 1/2 - x, 1/2 + y, 1/2 - z 1/2 - x, -3/2 - y, 1 - z x, 1 + y, z x, -1 + y, z

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

geometry. Redetermination resulted in much better standard uncertainties and final R-indices compared to those we published previously7 (e.g., R [I g 2σ(I)] ) 3.8 vs 6.9%). Details of crystal data, data collection, and refinement parameters are given in Table 1. The crystal structures were solved by direct methods.13 All non-hydrogen atoms were refined anisotropically by full-matrix least-squares calculations based on F2.14 The hydrogen atoms attached to the N3 atom in 1-3 and the N31 and N32 atoms in 4 were found in a difference Fourier maps and their coordinates and isotropic thermal parameter have been refined freely. All other hydrogen atoms were included in calculated positions as riding atoms, with SHELXL9714 defaults. For structure analysis and molecular and crystal structure drawings preparation were used PLATON15 and MERCURY16 programs.

Results and Discussion The hydrogen-bonding geometries for crystals 1-4 are listed in Table 2 and schematic representations of synthons17 are presented in Scheme 1. As these structures contain a pyrimidine ring, possessing a strong hydrogen-bond donor, N-H group, and strong hydrogen-

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Scheme 1. Schematic Representation of Supramolecular Synthons in 1-4

bond acceptor, CdO group, it can be predicted that the N-H · · · O hydrogen bond in 1-4 forms a characteristic supramolecular synthon, designated as I in Scheme 1. This is in accord with “hydrogen-bonds rules for organic compounds” that the best proton donors and acceptors form intermolecular hydrogen bonds to one another.18 The probability of formation of such N-H · · · O hydrogen bonded ring is 24%.19 Indeed, the molecules of 1-3 are assembled into centrosymmetric dimers via eight-membered rings defined by graph-set notation as R22(8).20 In 1 (Figure 1), the action of N-H · · · O hydrogen bond (Figure 2a) is reinforced by two C-H · · · O hydrogen bonds, as shown in synthons II and III (Scheme 1). The first one, C5 · · · O1′, forms a C(11) chain around the 21 screw axis, while the second hydrogen bond, C8′ · · · O2′, generates a C(7) chain around the 21 screw axis. The combination of these two chain motifs, two C5 · · · O1′ and two C8′ · · · O2′ hydrogen bonds, generates a sheets built of R44(35) rings and leads to a (4,4) net21 (Figure 2b). The crystal packing diagram along the b axis (Figure 2c) reveals that the C-H · · · O hydrogen-bonding sheets are mutually parallel and parallel to (101). The phthalamide and pyrimidine rings of the neighboring sheets’ molecules are not parallel and make an angle of 36° and 55° between neighboring phthalamide

and pyrimidine rings, respectively. The distance between the planes passing through the center of the sheets amounts approximately 3.0 Å. The N-H · · · O hydrogen bond and hydrogen-bonding sheets built of two C-H · · · O hydrogen bonds generate three-dimensional network (Figure 2c). The hydrogen-bonding pattern of 2 (Figure 3) is, unexpectedly, almost completely different than that of 1. The crystal structure of 2 also contains centrosymmetric dimers formed by a symmetry-related N-H · · · O hydrogen bond (Scheme 1, synthon I), but in this structure, the acceptor atom is carbonyl O1 atom of the pyrimidine ring (Table 2).

Figure 1. The molecular structure and labeling of 1. Displacement ellipsoids are drawn at the 30% probability level.

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Figure 2. (a) Centrosymmetric dimer of 1 formed by a pair of self-complementary N-H · · · O hydrogen bond. (b) Part of the crystal structure of 1, showing the C5 · · · O1′ and C8′ · · · O2′ hydrogen bonds that generate (4,4) net. (c) A crystal packing diagram of 1, viewed along the b axis, showing the three-dimensional network formed by N-H · · · O (blue) and C-H · · · O (red) hydrogen bonds.

Figure 3. The molecular structure and labeling of 2. Displacement ellipsoids are drawn at the 30% probability level.

All other intermolecular interactions in this structure also form dimers (Figure 4a). Thus, the C6 · · · O1′ hydrogen bond and C9′ · · · F interactions generate dimers via R22(20) and R22(26) rings, respectively, while the combination of these two interactions forms a new R22(9) ring (synthon IV). Finally, atom C10 acts as a donor to the O2 atom of the neighboring molecule, thus giving rise to a new centrosymmetric ring motif, R22(20) ring (synthon V). These intermolecular interactions link the molecules into a two-dimensional network parallel to the c axis (Figure 4b). The molecules are mutually parallel and form zigzag

channels with the distance of approximately 3.25 Å between the neighboring molecules. This extraordinary supramolecular architecture was obtained only by replacing the hydrogen atom with fluorine atom at 5-position of the pyrimidine ring. Besides, this completely different arrangement was not caused by this replacement because these dimers would be formed anyway by a slightly stronger interaction, C6 · · · O1′ hydrogen bond. In 3 (Figure 5), the hydrogen atom of the pyrimidine ring participates in an intramolecular C-H · · · F interaction (Table 2), so forming an S(5) ring. Besides the R22(8) rings generated by self-complementary intermolecular N-H · · · O hydrogen bond (Scheme 1, synthon I), the C6′ · · · O1 hydrogen bond forms dimers also via R22(24) rings (synthon VI). Two C-H · · · O hydrogen bonds and one C-H · · · F interaction in 3 link the molecules into chains parallel to the b axis (Figure 6a). While the C6 · · · O1′ hydrogen bond generates a C(10) spiral around the 21 screw axis (synthon IV), the C7 · · · O2′ hydrogen bond (synthon VII) and C8 · · · F3 interaction (synthon VIII) form C(8) chains generated by translation. Finally, the combination of the C6 · · · O1′ and C7 · · · O2′ hydrogen bonds form R33(20) rings, while the C7 · · · O2′ hydrogen bond and C8 · · · F3 interaction generate R22(14) chain of rings. The

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Figure 4. (a) Part of the crystal structure of 2, showing the C-H · · · O hydrogen bonds (red) and C-H · · · F interactions (green) that generate dimers. (b) A crystal packing diagram of 2, viewed along the a axis, showing the two-dimensional network formed by N-H · · · O (blue) and C-H · · · O (red) hydrogen bonds and C-H · · · F interactions (green).

One short intermolecular F · · · F contact (Figure 6a,b) is also present in this structure [F1 · · · F1i ) 2.777(2) Å; (i): -x, y, 1/2 - z ]. The F · · · F distance is shorter than the mean value of 2.85 Å for 1536 intermolecular F2C-F · · · F-C contacts in 784 trifluoromethyl derivatives found in Cambridge Structural Database22 (error-free and disorder-free structures of organic compounds with R < 0.075 and with distance shorter than the sum of the van der Waals radii). This F · · · F interaction can be classified as type-I interaction,6a as both, C11-F1 · · · F1i and F1 · · · F1i-C11i angles amount 169.37(12)°. Although in the absence of any other significant intermolecular interactions, F · · · F interaction could provide stability of molecular assembly, it seems that in 3 fluorine atoms closeness is just a consequence of molecular assembling lead by other numerous intermolecular interactions.

Figure 5. The molecular structure and labeling of 3. Displacement ellipsoids are drawn at the 30% probability level.

molecules are assembled in such manner that they are related by a 2-fold axis passing through midway between the neighboring molecules (Figure 6a), and that the supramolecular structure of 3 is a three-dimensional network.

Figure 6. (a) A crystal packing diagram of 3, showing the molecules that are related by a 2-fold axis. (b) A crystal packing diagram of 3, viewed along the c axis, showing the three-dimensional network formed by N-H · · · O (blue) and C-H · · · O (red) hydrogen bonds, C-H · · · F (green) and F · · · F (green) interactions. Table 3. Dihedral Angles between the Mean Planes of Pyrimidine Ring Phthalamide Ring and Butenyl Moiety for 1-4 plane

dihedral angle (A/B) /°

A

B

1

2

3

4

pyrimidine ring (N1/C2/N3/C4-C6) pyrimidine ring (N1/C2/N3/C4-C6) phthalamide ring (N1′/C2′-C9′)

phthalamide ring (N1′/C2′-C9′) butenyl moiety (C7-C10) butenyl moiety (C7-C10)

9.99(5)

3.61(6)

3.60(7)

74.10(13)

72.08(16)

69.09(17)

66.49(13)

68.87(15)

65.51(17)

1.69(8) 7.71(8) 77.43(13) 76.90(12) 78.95(12) 81.03(11)

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Figure 8. The molecular structure and labeling of 4. For clarity, only one of two independent molecules of the asymmetric unit is shown. Displacement ellipsoids are drawn at the 30% probability level.

Figure 7. Overlapping diagrams of: (a) compounds 1 and 2; (b) compounds 1 and 3; (c) compounds 2 and 3.

Thus, these three structures built different supramolecular architectures that can have implications on their physical properties, but, at the molecular level, they do not differ significantly. The bond lengths and angles in 1-3 agree well and present no unexpected features (see Supporting Information). The butenyl moiety adopts E-configuration, as confirmed by the C7-C8-C9-C10 torsion angle of -177.43(11), -179.97(12), and 177.55(14)° in 1, 2, and 3, respectively. The main conformational difference arises from the dihedral angle between the pyrimidine and phthalamide rings (Table 3). The pyrimidine and phthalamide rings in 1-3 are mutually parallel, but the angle for 1 is slightly bigger than that of 2 and 3. Furthermore, the small differences in the dihedral angles between the pyrimidine and the phthalamide rings with respect to the butenyl moiety show that these two rings possess also almost identical orientation toward the butenyl moiety. However, the overlapping diagrams (Figure 7) show that phthalamide and pyrimidine rings are shifted slightly with respect to the other. This shifting is the most pronounced in 3, as structures of 1 and 2 have almost identical conformation (Figure 7a) and could be a result of intermolecular interactions. 5-Fluorouracil derivative (4) (Figure 8), which possesses Z-configuration of the butenyl moiety [C71-C81-C91-C101 ) 2.4(3)°; C72-C82-C92-C102 ) 0.4(3)°], crystallized in the same space group as E-isomer 2, P1j, but with two independent molecules in the asymmetric unit. Bond distances and angles in these two independent molecules agree well with the equivalent ones in (E)-phthalamide protected derivatives. In both independent molecules of 4, the C7 · · · O1 intramolecular hydrogen bond forms S(5) rings (Table 2). There are a lot of similarities in intermolecular interactions of 2 and 4 [N3 · · · O1 and C6 · · · O1′ hydrogen bonds, C9′ · · · F interaction; synthons I and IV]. Only one interaction in 4 does not generate a finite pattern. The C82′ · · · O22 hydrogen bond (synthon IX) joins the molecules into C(15) chains along the

Figure 9. (a) A crystal packing diagram of 4, viewed along the a-axis, showing molecules aligned parallel to the c-axis. (b) A crystal packing diagram of 4, viewed along the c-axis, showing a three-dimensional network formed by N-H · · · O (blue) and C-H · · · O (red) hydrogen bonds and C-H · · · F (green) interactions.

c-axis generated by translation. All other interactions form finite D(2) patterns. The hydrogen-bonded molecules of 4 are aligned parallel to the c axis (Figure 9a) and, in the middle of the unit cell form cavities along the a-axis. The crystal packing diagram along c-axis reveals that the butenyl moiety atoms are disposed

4-Amino-2-butenyl 5-Substituted Pyrimidine Derivatives

almost perpendicularly to the pyrimidine and phthalamide rings (Table 3; Figure 9b), and that the molecules are arranged in interconnected layers. The mutually parallel molecules, linked by nine intermolecular interactions, generate a three-dimensional network.

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Conclusions The intermolecular hydrogen bond dimerization by the N-H · · · O R22(8) rings is the principal and strongest intermolecular association in 1-4. The supramolecular structures of 1-4 also contain C-H · · · O hydrogen bonds, while structures 2-4, additionally, contain C-H · · · F interactions. These weaker intermolecular interactions, the C-H · · · O hydrogen bonds in 1, and C-H · · · O hydrogen bonds and C-H · · · F interactions in 3 and 4, self-assemble the molecules into a three-dimensional network. The structure of 2 is exclusively built of dimers that are interconnected into a two-dimensional network. The C-H · · · F interactions in 2-4 do not play a significant role in higher supramolecular architecture formation since: (a) they form dimers together with the C-H · · · O hydrogen bond (in 2 and 4), (b) link the molecules in the same direction as C-H · · · O hydrogen bonds (in 3), or (c) form finite patterns (in 4). Thus, the similarities in molecular geometries of 1-3 have not resulted in the similarities in their supramolecular architectures. A supramolecular structures of (E)-5-fluorouracil derivative (2) and (Z)-5-fluorouracil derivative (4) differ also in spite of similarities in their intermolecular interactions. Finally, it should be added also that although aromatic rings are present in these structures neither C-H · · · π nor π · · · π interactions participate in supramolecular aggregation.

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Acknowledgment. Support for this study was provided by the Ministry of Science, Education and Sports of the Republic of Croatia (Project Nos. 125-0982464-2922 and 119-11930793069). Supporting Information Available: X-ray crystallographic information file (CIF) for 1-4 (CCDC Nos. 675299-675302). This information is available free of charge via the Internet at http:// pubs.acs.org.

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