Polymorphic and hydrate supramolecular solid state structures of a uracil derived nitronyl nitroxide

Inorganica Chimica Acta 361 (2008) 4094–4099

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Polymorphic and hydrate supramolecular solid state structures of a uracil derived nitronyl nitroxide Robert Feher a, Klaus Wurst b, David B. Amabilino a,*, Jaume Veciana a,* a b

Institut de Ciència de Materials de Barcelona (CSIC), Campus Universitari, 08193 Bellaterra, Spain Institut für Allgemeine Anorganische und Theoretische Chemie, Universität Innsbruck, A-6020, Innrain 52a, Austria

a r t i c l e

i n f o

Article history: Received 16 January 2008 Received in revised form 14 March 2008 Accepted 14 March 2008 Available online 20 March 2008 Dedicated to Dante Gatteschi. Keywords: Polymorph Radical Crystal engineering Hydrogen bonds Supramolecular organizations Nitronyl nitroxides

a b s t r a c t A nitronyl nitroxide bearing a uracil moiety has been shown to exist in at least three different forms in  contains a hydrogen bonded tape with two molecules crystals. The first polymorph (space group P1) stacked in the plane of the tape, while in the second (space group P21/c) unlike the a-phase shows cyclic non-covalent tetramers which come together to form a layer. The hydrate has quite a different structure, in which the amide groups interact with each other and the nitroxide group enters into weaker hydrogen bonds than in the pure material. All the materials are dominated by paramagnetic behaviour, but the structures suggest ways in which hydrogen bonds might be used to influence the packing of this kind of radical in the solid state. Ó 2008 Elsevier B.V. All rights reserved.

1. Introduction The organic radicals of the nitronyl nitroxide family have found widespread use for the preparation of purely organic magnets [1– 4], not to mention their rich coordination chemistry [5–10]. The introduction of groups with a propensity for hydrogen bond formation has provided a valuable way to influence in the packing of the spin-bearing nitroxide moieties [10–15], as well as to promote magnetic exchange interactions [16,17]. An elegant cytosine derived nitronyl nitroxide provides a nice example of the hydrogen bonding networks that can be formed [18]. To this end, we prepared the uracil-substituted nitronyl nitroxide (UrNN) [19]. The uracil group was attractive to us because it is known to generate hydrogen bonded networks of various types [20–28], and it has been used for the preparation of unique molecular materials [29– 33]. Compound UrNN was shown to self-assemble in solution, and a crystal structure of what we shall refer to as the a-phase was isolated (Fig. 1) [19]. The a-phase structure of UrNN is comprised principally of a hydrogen bonded ribbon, in which two uracil NH groups are hydrogen bonded to one of the NO group of the nitronyl nitroxide moiety. The NO group is well documented as being a good acceptor of hydro* Corresponding authors. E-mail addresses: [email protected] (D.B. Amabilino), [email protected] (J. Veciana). 0020-1693/$ - see front matter Ó 2008 Elsevier B.V. All rights reserved. doi:10.1016/j.ica.2008.03.066

gen bonds [34–40], and in this case it proves a better hydrogen bond acceptor than the carbonyl groups of the uracil moiety, which do not form any specific hydrogen bonding interactions but enter into dipole–dipole interactions between the sheets in the crystal. Aware that the uracil moiety can form polymorphic chain structures [27], we explored further the solid state chemistry of this molecule and report here a new polymorph of the compound as well as a hydrate form.

2. Experimental The compound 2-(50 -Uracilyl)-4,4,5,5-tetramethyl-4,5-dihydro1H-imidazolyl-1-oxyl-3-oxide (UrNN) was prepared by condensation of 2,3-bis(hydroxylamino)-2,3-dimethylbutane with 5-formyl uracil (Aldrich) in a methanol–water mixture (2:1) followed by in situ oxidation with sodium periodate using the classic route developed by Ullmann (R.W. Kreilick, J. Becher, E.F. Ullman, J. Am. Chem. Soc. 91 (1969) 5121). The product was isolated by evaporation of the solvent in vacuo and extraction with methanol, followed by crystallisation from acetone–hexane to give a fine microcrystalline powder. Analytical data: Elemental Anal. Calc. for C11H15N4O4: C, 49.43; H, 5.66; N, 20.96. Found: C, 48.99; H, 5.83; N, 20.71%. Laser desorption-ionization mass spectrometry. [M]+ 267.4 Da. IR (KBr disc) 543 (m), 605 (m), 781 (m), 1146 (m, N–O) 1166 (m), 1223 (s), 1331 (m), 1364 (s), 1406 (s), 1497 (m),

R. Feher et al. / Inorganica Chimica Acta 361 (2008) 4094–4099

O N

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N O

O H

N

N

H

O

Fig. 1. Radical UrNN and the crystal packing of the compound in the a-phase.

Table 1 Crystal data and details of the structure refinement

Crystal system Space group Unit cell dimensions a (Å) b (Å) c (Å) a (°) b (°) c (°) Volume (Å3) Temperature (K) Z F(0 0 0) Absorption coefficient (mm1) Crystal size (mm3) Formula weight Density (g/cm3) Independent reflections Reflections [I > 2r(I)] Final R indices [I > 2r(I)] Goodness-of-fit on F2 Data/restraints/ parameters

and refined against F2 SHELX93. All non-hydrogen atoms were refined with anisotropic displacement parameters. Hydrogen atoms attached to carbon and nitrogen atoms were calculated and refined with isotropic displacement parameters 1.2 (or 1.5 for methyl groups) times higher than the value of their carbon or nitrogen atoms with N–H distances of 0.87 Å. Hydrogen atoms of the water molecule of the hydrate were found and refined with isotropic displacement parameters. All crystals had small crystal size, leading to a weak diffraction, and were refined only to a 2H range of around 40°. The crystal of the b-phase shows poor quality by a large crystal mosaicity, maybe the reason for the higher R-value. Further details are listed in Table 1. SHELXS86

a-Phase

b-Phase

Hydrate

triclinic  P1

monoclinic P21/c

monoclinic C2/c

7.090(2) 7.832(1) 11.328(2) 90.85(1) 96.45(2) 96.66(2) 620.6(2) 218 2 282 0.111

13.441(4) 8.001(2) 12.396(3) 90 107.61(2) 90 1270.6(6) 218 4 564 0.108

22.391(1) 6.578(3) 20.952(4) 90 118.10(1) 90 2722.2(14) 218 8 1208 0.111

0.3  0.25  0.2 267.27 1.430 1316 1176 R1 = 0.0344 wR2 = 0.0904 1.074 1271/0/177

0.15  0.1  0.04 267.27 1.397 870 737 R1 = 0.0635 wR2 = 0.1551 1.217 827/0/177

0.1  0.06  0.02 285.29 1.392 944 744 R1 = 0.0347 wR2 = 0.0821 1.087 896/0/194

1533 (w), 1646 (m), 1688 (s), 1725 (s), 1763 (s), 2607 (w), 2900 (m), 2968 (m), 3124 (bm). 2.1. X-ray measurement and structure determination Data collection were performed on a Siemens P4 for the a-phase and on a Nonius Kappa CCD for the b-phase and hydrate, both equipped with graphite-monochromatized Mo Ka-radiation (k = 0.71073 Å). The structures were solved with direct methods

3. Results and discussion The crystallisation of UrNN from acetonitrile–diisopropyl ether by slow evaporation results in crystals of the b-phase which belong to the space group P21/c (unlike the a-phase which crystallises in  The main factor determining the polymorph the space group P 1). seems to be the solvent, the a-phase was grown from a mixture of toluene, water and methanol. The most striking feature of the crystal structure in the b-phase is the formation of a cyclic tetramer in which the hydrogen bonding interactions between the NH groups of the uracil moiety and the oxygen atoms of the nitronyl nitroxide unit again seem to be the driving force for the crystallisation in this form, but importantly there are clear [C–H  O] hydrogen bonds between the C@O groups in the uracil moiety and the methyl groups which stabilise the nitronyl nitroxide as well as the C–H groups in the uracil moiety (see Fig. 2). It is evident that these non-covalent tetramers have ‘‘hanging” hydrogen bond accepting and donating groups, and therefore in turn they join together through [N–H  O] hydrogen bonds to form a sheet-like structure two molecules wide (Fig. 3) in which the methyl groups attached to the five-membered ring are located at the interphases of adjoining sheets. There are also [C–H  O]

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hydrogen bonds between the C@O groups in the uracil moiety and the methyl groups which stabilise the nitronyl nitroxide between the sheets (not shown). The hydrate of the uracil derived radical (UrNN  H2O, referred to as the hydrate from now on), crystallised from wet ethanol, displays a completely different arrangement of the spin-bearing units

and base moieties to the previous structures of this molecule. The structure, which is in the C2/c space group, contains a complex network of hydrogen bonds involving all the hydrogen bond donor and acceptor units of the uracil moiety, and one of the NO groups of the nitronyl nitroxide function is involved in a strong hydrogen bond with the water molecule while the other has a weaker

Fig. 2. View of the cyclic hydrogen-bonded tetramer present in crystals of the b-phase of UrNN.

Fig. 3. Sheets formed by the supramolecular tetramers in the crystals of the b-phase of UrNN.

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Fig. 4. A view of the principle hydrogen bonded chain in crystals of UrNN  H2O.

[N–O  H–C] interaction (Fig. 4). The principle secondary structure is a hydrogen bonded chain in which three hydrogen bonding pathways unite adjacent molecules: firstly there is an [N–H  O@C] bond between the uracil moieties, then a water molecule bridges and the NH group of one uracil to a carbonyl of the neighbour, and finally there is a weak [N–O  H–C] interaction. These hydrogen bonded chains form a dimer row thanks to further hydrogen bonds involving the ‘‘free” hydrogen atom in the principle non-covalent chain in the crystals with an oxygen atom of the nitroxide (Fig. 5). Furthermore, there is a close contact of only 3.304 Å between carbon atoms at the 2-position of the uracil

Fig. 5. The hydrogen bonded dimer rows in UrNN  H2O.

ring with the oxygen atom of the carbonyl group located over the nitrogen atom of the NH group. This stacking interaction is presumably electrostatic in origin, as proposed by Hunter and coworkers in another context [41]. The dimer rows are then packed together such that the methyl groups protecting the radical moiety form a region parallel to the b-axis of the crystal (Fig. 6) and weak hydrogen bonds are also formed between one of the C–H groups of the carbonyl group at the 4-position of the uracil residue. The three structures of UrNN have certain common features: at the molecular level, there is a significant twist angle between the uracil ring and the spin-bearing unit because of the electrostatic repulsion of the carbonyl group in the uracil residue and the spin-bearing oxygen atoms, but the magnitude of the angle is different in all cases (Fig. 7). In the a and b polymorphs, the angle is close to 65°, and the global conformation is pseudo-eclipsed, meaning that the helical sense of the angle between the rings is opposite to that of the angle between the ONCNO group and the C–C bond at the ‘‘back” of the molecule as viewed in Fig. 7 [42]. On the other hand, in the hydrate of UrNN the conformation is pseudo-anti, and while the angle between the uracil and imidazolyl rings is very significantly less the global conformation of the molecule is very similar. That said, the orientation of the hydrogen bond acceptors with respect to the donors is evidently different. The reduction in twist angle in this crystal form is most likely caused by the hydrogen bonding orientation to the water molecule which in the crystal favours this slightly more planar conformation. In terms of the non-covalent interactions, the most conspicuous forces in all the structures are hydrogen bonds, which are detailed in Table 2. In the polymorphs the amide N–H to nitroxide hydrogen bond is determining in the structure, while in the hydrate the more familiar amide N–H to carbonyl bond is present, with the nitroxide hydrogen bonded to water and methylene type groups. The structural richness seen in the solid state for this radical is not matched by its magnetic properties. The magnetic susceptibility behaviour of a ground sample of the significant differences in the magnetic response, the materials have a room temperature value of vmT (about 0.375 emu K mol1) required for the isolated S = 1/2 paramagnetic centres with no magnetic interactions, in agreement with the Curie constant, and are essentially paramagnetic down to 10 K and show slight variations below that, but the radicals are apparently located so far apart (a minimum distance between any part of the O–N–C–N–O fragment of 4.8 Å in

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Fig. 6. Crystal packing of UrNN  H2O viewed along the b-axis.

Fig. 7. The molecules of UrNN in the different crystalline forms, highlighting the angle between the ONCNO unit and the uracil ring.

the a-phase and the hydrate, and 5.5 Å in the case of the b-phase) and in such an orientation – in all the polymorphs – that the exchange interactions are very weak. The estimated J/k values in every case are less than 0.5 K. With such weak interactions, and with no clear exchange pathways in the solids, it is meaningless to propose a dominant magnetic interaction between the spin carriers – either through space or non-covalent bonds. Despite the supramolecular structures of the system, it appears that this neutral uracil-derived nitronyl nitroxide does not favour significant exchange interactions between the spins, possibly because of the conformation of the molecule. 4. Conclusions The uracil-derived nitronyl nitroxide described in this article shows three solid state structures for the moment, which all involve relatively complex hydrogen bonding networks. In all the structures the uracil ring is twisted well away from the plane of the spin-bearing unit because of the proximity of one of the car-

bonyl groups of the uracil moiety. The lack of significant magnetic interactions in these molecular materials may well be because of this same molecular feature which affects the packing of the molecule, such that the areas of significant spin density are held apart, and does not facilitate delocalisation of the spin over the uracil part of the ring. Nonetheless, they stand as elegant solid state structures which suggest strategies towards the crystal engineering of the nitroxide-based molecular magnets. Acknowledgements This work was supported by grants from DGI (Project CTQ200606333/BQU) and from the EU in Marie Curie RTN ‘‘QuEMolNa” (MRTN-CT-2003-504880) and NoE MAGMANet (515767-2). Appendix A. Supplementary material CCDC 680884, 680885 and 680886 contain the supplementary crystallographic data for this paper. These data can be obtained

R. Feher et al. / Inorganica Chimica Acta 361 (2008) 4094–4099 Table 2 Close contacts between hydrogen and oxygen atoms in the different crystal forms of Ur-NN Type of contact

[H  O] (Å)

[X–H  O] (Å)

[X–H–O] angle (°)

a-Phase

N–O  H–N N–O  H–N C–H  O–N C–H  O–N C–H  O–N C–H  O@C

1.939 2.127 2.404 2.638 2.672 2.646

2.773(3) 2.886(3) 3.307(3) 3.581(3) 3.326(3) 3.565(3)

164.7 154.4 154.5 164.0 125.1 158.1

b-Phase

N–O  H–N N–O  H–N Cur–H  O@C C–H  O@C C–H  O@C C–H  O–N C–H  O@C

1.951 1.985 2.371 2.603 2.607 2.657 2.676

2.755(7) 2.821(7) 3.275(9) 3.563(9) 3.554(8) 3.509(8) 3.312(8)

153.0 160.8 161.4 170.6 165.3 146.8 123.6

Hydrate

C@O  H–N H2–O  H–N H–O–H  O–N C@O  H–O–H C–H  O@C C–H  O–N C–H  O–N C–H  O@C C–H  O–N

1.839 1.981 1.997 2.197 2.536 2.546 2.604 2.617 2.665

2.672(5) 2.845(4) 2.863(5) 2.945(6) 3.482(5) 3.442(5) 3.476(5) 3.242(5) 3.421(5)

159.7 171.9 171.1 170.6 165.2 153.5 149.6 122.3 135.1

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