A Case Study of Supramolecular Organization : One Ferrocene Substituted Iminodiacetamide and its Chloroform Solvate

This paper describes the synthesis of an amide based conjugate of ferrocene (Fc), ethylenediamine (eda) and iminodiacetamide (imda), Fc-eda-imda (2). The compound (2) is characterized by various spectroscopic, crystallographic and thermoanalytical techniques in solid state and in solution. By crystallization of the title compound 2 from methanol or chloroform, two different crystalline forms 2a and 2b were obtained, respectively. In their X-ray single crystal structures, 2a and 2b reveal similar 2D hydrogen bonding networks, but differ by supramolecular organization, namely aromatic π – π stacking interactions in the third spatial dimension.


INTRODUCTION
HE field of supramolecular chemistry, defined as "chemistry beyond the molecule", has progressed greatly since Charles Pedersen's discovery of crown ethers that exhibit host-guest interactions. [1]Supramolecular chemistry, based on molecules held together by noncovalent interactions such as hydrogen bonds, electrostatic, van der Waals, π---π stacking or hydrophobic interactions, is a wide field of study, with many applications, [2] such as sensing, [3] molecular machines, [4] drug delivery [5] and catalysis. [6]n supramolecular chemistry, the secondary amide group is an important building block that is a starting point for understanding the formation of secondary and tertiary protein structures.When adopting such structures, proteins rely on noncovalent interactions, such as H-bonds between the amide groups that can act both as H-bond donors (N-H) and H-bond acceptors (C=O). [7]Amide derived iminodiacetamide (imda) derivatives are well known ligands for late transition metals that give access to a great variety of structural motifs. [8,9]In addition, the stability of amide conjugated ferrocenoly group in aerobic media, and aqueous as well as organic solvents, gives access to a large variety of derivatives, and its favorable electrochemical properties have made ferrocene and its derivatives very popular molecules for biological applications and for conjugation with biomolecules. [10]n this work, we present the crystal and molecular structures of two crystalline forms of a ferrocene amide conjugate Fc-eda-imda, 2a, and Fc-eda-imda × CDCl3, 2b.The difference between the bulk solid state structures of 2MeOH and 2CHCl3 is described in detail, using single crystal and powder X-ray diffraction, differential scanning calorimetry and thermogravimetry.Also, the difference between the structure in the solid state and in CHCl3 solution is studied with 1 H NMR and IR spectroscopy.

EXPERIMENTAL
General remarks.Reactions were carried out in ordinary glassware and chemicals were used as purchased from commercial suppliers without further purification.The synthesis of 2 was carried out in a microwave reactor (CEM T Discover).Reactions were monitored by TLC on silica gel 60 F254 plates and detected with a UV lamp (254 nm); crude products were purified using automated flash chromatography (Teledyne Isco CombiFlash Rf) equipped with a UV detector (254 nm) and pre-packed silica columns.
Mass spectra were recorded on a HPLC-MS system (Agilent Technologies 1200) coupled with a 6410 Triple-Quadrupole mass spectrometer, operating in a positive ESI mode.NMR spectra were obtained on a Bruker Avance 300 or 600 spectrometer, operating at 300 or 600 MHz for 1 H and 75 or 150 MHz for 13 C, the spectra were recorded at room temperature.Chemical shifts, δ (ppm), indicate a downfield shift from the internal standard, tetramethylsilane, TMS.Coupling constants, J, are given in Hz.Infrared spectra were recorded using KBr pellets or in chloroform solution (in a KBr solution cell) with a Bruker Alpha FT-IR spectrometer, in the 4000-350 cm −1 region.The UV-Vis spectra were recorded on Varian Cary 50 spectrophotometer using a 1 cm Suprasil quartz cell.
For the DSC measurements approximately 2-5 mg of sample was placed in a standard aluminum crucible (40 μL) and heated at a 10°C/min rate in the temperature range 25-500 °C, under nitrogen flow of 180 mL/min using a Mettler-Toledo DSC 823 e instrument.For the thermogravimetry measurements approximately 5-7 mg of sample was placed in a standard platinum crucible (140 μL), heated at a 10 °C/min rate, under flow of 50 mL/min air, in the temperature range of 25−1000 °C on a Shimadzu DTG-60H instrument.
The powder diffractograms were measured on a PANalytical Aeris instrument; conditions: Bragg-Brentano geometry (ϑ-2ϑ), source Cu-Kα (λ = 1.5418Å), measurement from 5° to 70° (2ϑ), with 5.2°/min (0.0216° step and 0.25 s/step).Consistency of sample 2MeOH with single crystal structure 2a have been checked by LaBail fit of powder data in the 2Θ region of 5 o −32 o , while for sample 2CHCl3 the phase analysis was performed using both structural models from the single crystal data (2a and 2b), in the 2Θ region of 5 o −28 o .The calculations were performed by using GSAS and EXPGUI programs. [11,12]ray single crystal diffraction.The X-ray intensity data were collected on Oxford diffraction Xcalibur CCD diffractometer using monochromatic Cu-Kα (λ = 1.54184Å) radiation at 293 K.The data were processed with CrysalisPro program [13] (unit cell determination and data reduction).Both crystals were of low quality: 2b diffracted poorly at high angles and reflections up to Θmax = 59° were taken into calculations, while for 2a reflections up to Θmax = 76° were used.For 2b, lower number of reflections and lower quality of measured intensities at high angles resulted in a relatively high R value (14.19 %), although procedure of solving the crystal structure by direct methods [14] undoubtedly recognized the correct form of the molecule, plus several peaks in residual density were interpreted as an additional chloroform solvate molecule.During indexation of the measured CCD frames for 2b (which were collected after compound 2a), it was clear that unit cell volume of 2b is slightly larger than one half of the unit cell of 2a, confirming assumption of an additional smaller molecule in the unit cell (chloroform).For 2a the unit cell dimensions were consistent with eight Fc-edaimda molecules.Lower number of reflections for 2b also led to low precision of C−C bonds and large Hirshfeld differences for some atoms in the structure (C28 and C29). [15]During refinement of both structures with SHELXL program, [16] all non-hydrogen atoms were treated anisotropically.For 2b, displacement parameters for carbon atoms in ferrocene unit were restrained to isotropic values (ISOR restrain).Also, the occupancy of chloroform was refined using additional free variable (FVAR).All hydrogen atoms were included in the model at geometrically calculated positions and refined using riding model.As crystals of 2b were grown from deuterated chloroform, deuterium has been explicitly included in UNIT and SFAC instructions, as well as in the atom list.Experimental data for X-ray diffraction studies in this publication are collected in Table 1.The structures are deposited in CCDC database and numbers 1811729 and 1811730 contain the supplementary crystallographic data for this paper.These data can be obtained free of charge from The Cambridge Crystallographic Data Centre via www.ccdc.cam.ac.uk/data_request/cif. [17] A solution of aniline (9.13 mL, 0.10 mol) in acetic acid (conc., 85 mL) was cooled to 10 °C and chloroacetyl chloride (8.75 mL, 0.11 mol) was added at once.With vigorous stirring, a solution of CH3COONa × 3H2O (33 g, 0.24 mol) in 140 mL of water was rapidly added.After 30 minutes, the precipitated product was filtered under vacuum through a Büchner funnel, washed with water and dried.No further purification was required.Yield: 13.9 g (0.08 mol, 82%), white powder, Rf = 0.62, 5% methanol in dichloromethane. 1 H NMR (300 MHz, CD3CN) δ/ppm: 8.57 (s, 1H), 7.61-7.51(m, 2H), 7.41-7.29 (m, 2H), 7.14 (t, J = 7.4 Hz, 1H), 4.15 (s, 2H).
, where n is the number of reflections and p is the total number of parameters refined.
Preparation of crystals suitable for X-ray single crystal analysis.In the first experiment, Fc-eda-imda (25 mg) was dissolved in methanol (5 mL) and left in a partly covered vial at room temperature for slow evaporation.After 5 days, flower-like crystals of 2a were obtained.In a second experiment, Fc-eda-imda (1 mg) was dissolved in CDCl3 (0.5 mL) and left in a NMR tube for slow evaporation.After 3 months, needle-like crystals of 2b were obtained.
Preparation of samples for powder X-ray diffraction, thermal analysis and IR spectrometry.Fc-eda-imda (41.3 mg and 40.9 mg) was dissolved in methanol (7 mL) or chloroform (10 mL) respectively and left in a partly covered vial at room temperature for slow evaporation.After 2 days, the volume of the solutions was reduced to 2 mL by rotary evaporation and after 5 days, orange flower-like crystals (2MeOH) were obtained from the methanol solution and a mixture of orange flower-like and needle-like crystals (2CHCl3) was obtained from the chloroform solution.

Synthesis and Basic Characterization
The title compound Fc-eda-imda (2) was obtained in two synthetic steps in solution, Scheme 1.In the first step, Fceda-boc (1) was synthesized by amide coupling of commercially available precursors, ferrocenecarboxylic acid and N-boc-ethylenediamine.The desired Fc-eda-imda ligand was prepared in a second synthetic step, where the Boc protecting group of Fc-eda-boc was removed in standard conditions (TFA in DCM), and the free primary amine group subsequently reacted in a microwave enhanced nucleophilic substitution reaction with 2-chloro-N-phenylacetamide in DMF with the addition of KI.Crystals suitable for X-ray single crystal analysis were grown from methanol (2a) or chloroform (2b).The corresponding bulk powder samples, 2MeOH (obtained from methanol) and 2CHCl3 (obtained from chloroform) were used for infrared spectroscopy (IR, KBr), thermal analyses (DSC, TG) and for X-ray powder diffraction, see discussion below.
Both products Fc-eda-boc (1) and Fc-eda-imda (2) were characterized by 1 H and 13 C NMR, IR and UV-Vis spectroscopy and ESI mass spectrometry.The ESI MS spectra reveal molecular ions for both compounds, M+Na + and 2M+Na + for 1 and M+H + for 2, at m/z 395.0, 767.1 and 539.1, respectively.In the UV-Vis (CHCl3) spectra the characteristic ferrocene absorption peak is found at 443 nm for both 1 and 2, suggesting that the substitution at the distant amide group moiety has no effect on the ferrocene chromophor. [19,20]Most interesting for the study of supramolecular interactions are the IR and NMR spectra.Secondary amide N-H groups without hydrogen bonding are characterized by stretching bands in the range 3500−3400 cm −1 , while hydrogen bonded secondary amide groups show these bands under 3400 cm −1 . [21]The IR (KBr) spectra are very similar for both samples 2MeOH and 2CHCl3, showing NH stretching at 3276 and 3132 cm −1 , while the IR (CHCl3) spectrum of 2 shows a band at 3284 cm −1 .In the

X-ray Single Crystal Structures
Molecular structures of 2a and 2b, with atomic numbering schemes are given in Figure 1; [22] the structural determination procedures are given in the Experimental part.In the crystal structure of 2a, the asymmetric unit is  2). [21]Angles at imda amine nitrogen atom (N21 and N22 in 2a and N2 in 2b) are typical for sp 3 hybridization.Molecular conformation of the three independent Fc-eda-imda molecules in 2a and 2b is almost identical, Figure 1c. Figure 1 also shows the intramolecular hydrogen bonds listed in Table 3; in both structures 2a and 2b they exist between nitrogen atom N4 (N41 and N42 in 2a) and oxygen atom O2 (O21 and O22 in 2a).As the lone electron pair in the sp 3 hybridized atom N2 (N21 and N22 in 2a) can act as the hydrogen bonding acceptor, intramolecular hydrogen bonds N4−H4A•••N2 (N41−H41A•••N21 and N42−H42•••N22 in 2a) should be considered as additional intramolecular stabilization interaction.In the literature, several examples of similar intramolecular hydrogen bonding in imda derivatives are described. [23,24]n the single crystal structure of 2a, two molecules in the asymmetric unit are connected with two N−H 2a and Table 3), forming a pseudo-centrosymmetric ring pattern with graph-set notation R2 2 (16). [25]The same structural motif exists in the crystal structure of 2b.3), together with its centrosymmetric equivalent, connects two molecules related by center of symmetry into a structural dimer having the same ring R2 2 (16) notation (Figure 2b).
Both crystallographic structures 2a and 2b show completely analogous 2D supramolecular aggregation as a consequence of other intermolecular N−H•••O types of hydrogen bonds.In particular, in the structure of 2a, hydrogen bond N31−H3A1•••O12 i (Table 3) forms a onedimensional chain consistent with a two-fold screw symmetry axis extruding along the crystallographic axis b (Figure 2a).Second hydrogen bond N32−H3A2•••O11 ii Table 2. Characteristic structural parameters for the ferrocene moiety in 2a and 2b. [21]iety (a) ω Table 3. Hydrogen bonding parameters in 2a and 2b (including   (Table 3) also forms a one-dimensional chain extruding in the direction of axis b, but consistent with a two-fold screw axis which is not equivalent to the previous one: the second axis is moved in the direction of axis a by half of the period (Figure 2a).Therefore, a dimer of Fc-eda-imda molecules in the asymmetric unit 2a is surrounded by four nearest neighboring equivalent dimers and 2D supramolecular aggregation in the ab plane of the unit cell is formed.In the structure of 2b, the pseudo-centrosymmetric dimer is replaced by the exact structural dimer formed by the above mentioned hydrogen bond N1−H1A•••O3 v .The role of the intermolecular hydrogen bond N3−H3A•••O1 vi (Table 3) is equivalent to the role of hydrogen bond N31−H3A1•••O11 i in the structure of 2a, i.e. it forms a one-dimensional chain consistent with a two-fold screw axis extruding in the direction of axis b (Figure 2b).By combination of screw axis with the crystallographic center of symmetry existing in the center of the dimer in 2b, a second screw axis is generated.This axis is moved in the direction of axis c by half of the period (Figure 2b).Again, the centrosymmetric dimers in 2b are connected by four nearest neighbors in complete analogy with the structure of 2a.In the case of 2b, the 2D supramolecular aggregation is formed in the bc plane of the unit cell.In 2a, this 2D supramolecular layer is additionally stabilized with two C−H It is interesting that similar, but not equivalent hydrogen bonding motifs are described in the literature for the crystal structure of nitrilotriacetanilide. [24]ntramolecular hydrogen bonds in that compound are completely analogous to those in 2a and 2b, while one type of intermolecular N−H•••O hydrogen bonds form the centrosymmetric dimer that can also be described by the R2 2 (16) graph set notation. [25]However, the ring motif in nitrilotriacetanilide is not completely analogous to the ring motif in 2a and 2b, because it doesn't possess the -CH2−CH2group and one amide group in the ring is reversely oriented compared with the one connected to the ferrocene in 2a and 2b.Finally, the other type of intermolecular N−H•••O hydrogen bonds form additional connections of the centrosymmetric dimers in 1D ladder type of supramolecular aggregation, contrary to 2D layers encountered in 2a and 2b.
In the third spatial dimension, the supramolecular hydrogen bonded 2D layers in 2a and 2b are connected by weak van der Waals interactions or by weak π•••π stacking interactions.Stacking interactions seem to be more important in 2a.Several selected interactions are illustrated in Figure 3 and their geometry parameters are given in Table 4.Although the distances between centers of phenyl rings which are involved are significant (≈5 Å), the perpendicular distances of some ring centroids on the planes of associate rings are less than 3.4 Å, the value that can be used as the contact distance between two carbon atoms. [26]Also, it was recently demonstrated that stacking interactions exist even at larger distances. [27]As evident from Figure 3a, the neighboring 2D layers in the crystal structure of 2a are not just translated in the stacking direction, but they are also shifted in direction of axis b.The stacking of neighboring layers in crystal structure of 2b is different, the supramolecular hydrogen bonding 2D layers are now just translated in the stacking direction one above the other and a thin layer of chloroform molecules divides the layers (Figure 3b).Chloroform solvent molecules interact with the 2D layers only by one C−D•••π interaction (C-D group from chloroform and Ph1 phenyl ring from the Fc-eda-imda molecule (Figure 1b and Table 3) and by weak Van der Waals interactions with surrounding molecules.If we take into account weak long range π•••π interactions, only one interaction could be recognized, Ph2•••Ph2 xi (Table 4).
−30] From presented analysis it is

Figure 1 .
Figure1.ORTEP-3 drawings[22] of molecular structures of compounds 2a (a) and 2b (b), with atomic numbering scheme.Intramolecular hydrogen bonds are shown as black dashed lines.C-H•••π interaction in 2b) is shown as grey dashed line (c) Overlap of three independent molecules of 2a and 2b, showing almost identical molecular conformation.

Figure 2 .
Figure 2. Intermolecular hydrogen bonding aggregation of molecules into 2D layers in 2a (a) and 2b (b).Atoms involved in hydrogen bonds are labelled and represented as small ball, other parts are represented in stick style.The left parts of pictures represent hydrogen bonding skeletons.Dimers formed by hydrogen bonds N11-H1A1•••O32 and N12_H1A2•••O31 in 2a (a) and N1-H1A•••O3 vi in 2b (b) are colored in purple and one-dimensional chains formed by other intermolecular hydrogen bonds (consistent with two-fold screw axes) are given in orange.One hydrogen bonded dimer (purple) is surrounded with four nearest neighbors, and layers formed by whole molecules are given in right part pictures.

( a )Figure 3 .
Figure 3. Representation of stacking of hydrogen bonded layers in third dimension in 2a (a) and 2b (b), where selected π•••π interactions are labelled and colored in red.In case of crystal packing in 2b, layers formed by solvent chloroform molecules are represented in space-filling (CPK) style.

Table 1 .
Crystal data and details of crystal structure refinement for 2a and 2b