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Supramolecular solid-state architectures formed by co-crystallization of melamine and 2-, 3- and 4-chlorophenylacetic acids
Accepted Manuscript Supramolecular solid-state architectures formed by co-crystallization of melamine and 2-, 3- and 4-chlorophenylacetic acids Jan Janczak PII:
S0022-2860(16)30693-7
DOI:
10.1016/j.molstruc.2016.07.022
Reference:
MOLSTR 22725
To appear in:
Journal of Molecular Structure
Received Date: 10 May 2016 Revised Date:
1 July 2016
Accepted Date: 8 July 2016
Please cite this article as: J. Janczak, Supramolecular solid-state architectures formed by cocrystallization of melamine and 2-, 3- and 4-chlorophenylacetic acids, Journal of Molecular Structure (2016), doi: 10.1016/j.molstruc.2016.07.022. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
ACCEPTED MANUSCRIPT Graphical Abstract Supramolecular complexes of melamine with 2-, 3- and 4-chlorophenylacetic acid isomers (1-3) were obtained. The hydrogen-bonded supramolecular complexes were characterized by X-ray single
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(3)
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crystal diffraction, Hirshfeld surface and analysis and vibrational spectroscopy.
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Supramolecular solid-state architectures formed by co-crystallization of melamine and 2-, 3- and 4-chlorophenylacetic acids
Jan Janczak*
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Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okólna 2 str., P.O. Box 1410,
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50-950 Wrocław, Poland
Abstract
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A family of supramolecular complexes of melamine with chlorophenylacetic acid isomers using solvent-assisted and evaporation-based techniques has been prepared. Crystallization of melamine with 2-chlorophenylacetic acid yield hydrated ionic supramolecular complex (1), whereas crystallization of melamine with 3- and 4-chlorophenylacetic acids leads to formation of neutral supramolecular complexes (2, 3), all with base to acid ratio of 1:2.
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Within chlorophenylacetic acid isomers only in 2-chlorophenylacetic acid isomer as the stronger acid the proton transfer to melamine takes place. The crystal structures of supramolecular complexes have been determined. The supramolecular assembly is driven by the noncovalent interactions, most commonly by the hydrogen bonds. The components of
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the crystals interact via NH…O and OH…N with a graph of R22(8) forming respective ionic or neutral supramolecular complexes. All three supramolecular complexes studied interact other via a pair of NH…O hydrogen
bonds forming pseudo one-dimensional
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each
supramolecular chains along [1-10] and [-110] in 1 and along [010] in 2 and 3. Hirshfeld surface and analysis of 2D fingerprint plots have been analysed both quantitatively and qualitatively interactions governing the supramolecular organisation. The IR and Raman vibrational characterization of the supramolecular complexes 1-3 was supported by the spectra of their deuterated analogues.
*E-mail: [email protected]. Tel. +48 71 39 54 145. Fax: +48 71 34 410 29.
1
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1. Introduction The understanding of the interactions between the molecules in the context of design of new solids has considerably expanding the research branch of materials science over past few decades [1]. Despite these advantages, the prediction of the crystalline structure from solely its molecular constituents is still not yet possible. Crystal engineering
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involving a combination of non-covalent synthesis of new solids with designed architecture in solids seems to solve this predicament [2]. A productive strategy in supramolecular synthesis and the crystal engineering is to build supramolecular architectures from molecules containing complementary arrays of the hydrogen-bonding sites [3]. The non-
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covalent interactions such as hydrogen bonding, π-π stacking interactions, and the van der Waals forces have been used in the self-assembly and design a large number of
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supramolecular architectures in solids like as types, rosettes, rods, layers, spheres and sheets [4]. Among the self-assembly organisation forces, the hydrogen bond is the most important interaction and the recognition events for rational design of extending supramolecular architecture in solids, due to its abundance, strength and specific and directional properties [5]. A focal point of the crystal engineering is the concept of supramolecular synthons,
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structural units formed by predictable intermolecular interactions [6]. The supramolecular synthons are powerful tools for predicting not only local intermolecular interactions, but also often provide little insight into a global topology of a crystal structure.
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Melamine is highly symmetric and is trigonal planar (D3h), and is useful in the crystal engineering as a building blocks, since it contains multiple hydrogen-bonding sites, can act
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both as an excellent hydrogen donor and hydrogen acceptor in hydrogen bonding. Furthermore in solids the strong π-π stacking interactions between the aromatic rings of it contribute to their packing arrangement [7]. Melamine is potentially hazardous to health [8], but important in supramolecular non-covalent synthesis of solids [9]. Within the body, melamine is metabolised to cyanuric acid, a process that leads to precipitation of co-crystals of melamine-cyanuric acid within the kidneys, causing renal failure [10]. The complementarity of the melamine and cyanuric acid units has been used to rationalise the stability and relatively poor aqueous solubility of melamine-cyanuric acid co-crystal, as well as a model to realise a wide variety of supramolecular assemblies in solids [11]. Crystallization of melamine and the aromatic carboxylic acids or 1,5-napthtalenedisulfonic 2
ACCEPTED MANUSCRIPT acid leads to the crystals with a characteristic helical water chain assemblies [12]. A porous hydrogen-bonded organic frameworks have been also reported for solvent dependent structures of melamine [13]. Co-crystallization of melamine with inorganic and various organic small carboxylic and sulfonic acids has produced various supramolecular
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architectures [14]. In the present work the supramolecular architecture in solid formed by cocrystallization of melamine with chlorophenylacetic acid isomers has been examined (Scheme 1). In addition, this study is aimed at how the melamine to acid molar ratio used in
architecture of the formed crystals or co-crystals. COOH
COOH
COOH
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NH2
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the crystallization influences the composition and the topology of the supramolecular
Cl N H2N
N N
Cl
NH2
Cl
(a)
(b)
(c)
(d)
isomers (b-d).
2.1.
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2. Experimental
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Scheme 1. Structure of melamine (a) and the 2-, 3- and 4-chlorophenylacetic acid
Materials: The reagents melamine (99%), 2-cholorophenylacetic acid (99%), 3-
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chlorophenylacetic acid (98%) and 4-chlorophenylacetic acid (99%) were purchased from Sigma-Aldrich and were used without further purification. Elemental analysis was carried out with a Perkin Elmer 240 elemental analyser. 2.2.
Synthesis. Melamine and respective isomer of chlorophenylacetic acid isomer were
added to hot water in a molar proportion of 1:1. When the solutions became homogeneous they were cooled slowly and kept at room temperature. After several days, transparent colourless crystals of the respective compounds 1 - 3 suitable for the X-ray single crystal measurements were formed. The crystals have been separated by filtration and dried in air.
3
ACCEPTED MANUSCRIPT Melamin-1-ium 2-chlorophenylacetate – 2-chloropheylacetic acid hemihydrate, (C3H7N6) (C8H6ClO2).(C8H7ClO2). ½(H2O) (1). Analysis: calculated for C38H42Cl4N12O9: C, 47.91; Cl, 14.89; N, 17.64; O, 15.12 and H, 4.44 %. Found: C, 47.80; Cl, 14.81; N, 17.52; O, 15.39 and H, 4.48 %. Melamine – 3-chlorophenyacetic acid co-crystal, (C3H6N6) .2(C8H7ClO2) (2). Analysis:
48.77; Cl, 15.08; N, 17.90; O, 13.90 and H, 4.35 %.
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calculated for C19H20Cl2N6O4: C, 48.84; Cl, 15.17; N, 17.98; O, 13.70 and H, 4.31 %. Found: C,
Melamine – 4-chlorophenylacetic acid co-crystal, (C3H6N6) .2(C8H7ClO2) (3). Analysis:
48.73; Cl, 15.11; N, 17.92; O, 13.88 and H, 4.36 %.
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calculated for C19H20Cl2N6O4: C, 48.84; Cl, 15.17; N, 17.98; O, 13.70 and H, 4.31 %. Found: C,
The deuterated analogues of the respective 1 - 3 co-crystals were prepared by the usual
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reaction with heavy water. The respective protiated samples were dissolved in heavy water, and left in the atmosphere saturated with heavy water for one-two weak, in order to avoid the contamination of the crystals and next this procedure was repeated twice.
2.3. X-ray single crystal data collection. X-ray intensity data for the 1-3 crystals were
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collected using graphite monochromatic MoKα radiation on a four-circle κ geometry KUMA KM-4 diffractometer with a two-dimensional area CCD detector. The ω-scan technique with ∆ω = 1.0o for each image was used for data collection. Data collections were made using the
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CrysAlis CCD program [15]. Integration, scaling of the reflections, correction for Lorenz and polarisation effects and absorption corrections were performed using the CrysAlis Red
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program [15]. The structures were solved by the direct methods using SHELXT [16] and refined using SHELXL-2014/7 program [17]. The positions of hydrogen atoms involving in the hydrogen bonds were located in difference Fourier maps and were refined with Uiso=1.2Ueq of N joined H or Uiso=1.5Ueq of O atom joined H. The hydrogen atoms joined to aromatic carbon atoms were introduced in their geometrical positions and treated as rigid. The final difference Fourier maps showed no peaks of chemical significance. Details of the data collection parameters, crystallographic data and final agreement parameters are collected in Table 1. Visualisations of the structures were made with the Diamond 3.0 program [18]. Selected geometrical parameters are listed in Table S1 (in Supporting Information) and the geometry of hydrogen bonding interactions is collected in Table 2-4. 4
ACCEPTED MANUSCRIPT 2.5. Powder X-ray Diffraction (PXRD). Powder X-ray diffraction patterns of the powdered protiated and deuterated 1-3 compounds were checked on
a PANanalytical X’Pert
diffractometer equipped with a Cu-Kα radiation source (λ=1.54182 Å). The diffraction data were recorded in the range of 5-45o at room temperature. The powder diffraction patterns
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of H- and D-compounds are included in supporting information (Figs. S1–S3). The obtained deuterated analogues crystallise, similar as H-compounds, in the same crystal systems with quite similar lattice parameters.
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2.6. Vibrational Spectra Measurements. The vibrational measurements of H-compound and its deuterated analogues were carried out at room temperature. The Fourier transform
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infrared spectrum was recorded from nujol mulls between 4000 and 400 cm-1 on a Bruker IFS 113 V FTIR spectrometer. Resolution was set up to 2 cm-1. The Fourier Transform Raman spectra for 1-3 were recorded on a FRA-106 attached to the Bruker 113 V FTIR spectrometer equipped with Ge detector cooled to liquid nitrogen temperature. Resolution was set up to 2 cm-1, signal/noise ratio was established by 32 scans. Nd3+ - YAG air-cooled diode pumped laser of power ca. 200 mW was used as an exciting source. The incident laser excitation was
1
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1064 nm. The scattered light was collected at the angle of 180o in the region of 3600÷80 cm, resolution 2 cm-1, 256 scans. Vibrational spectra for all compounds are included in
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supplementary (Figs S5-S7).
3. Results and Discussion
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3.1. Synthesis and preliminary characterization of 1-3. Initially, crystallization of melamine with chlorophenylacetic acid isomers taken in a molar ratio of 1:1 has been performed. Crystallization of melamine with 2-chlorophenylacetic acid yield hydrated ionic supramolecular complex (1), whereas crystallization of melamine with 3- and 4chlorophenylacetic acids lead to formation of neutral supramolecular complexes (2, 3) with the 1:2 composition, since the melamine contains multiple hydrogen-bonding sites. Therefore, the crystallization was repeated starting with the melamine to acid molar ratio of 1:2 and 1:3. Independent of the molar ratio of melamine to acid the formed supramolecular complexes have the same composition of 1:2 and they are most stable in applied conditions of the crystallization. Within the obtained supramolecular complexes only in the case of 5
ACCEPTED MANUSCRIPT melamine with 2- chlorophenylacetic acid isomer gave hydrated crystals (1). Within chlorophenylacetic acid isomers only in 2-chlorophenylacetic acid isomer as the stronger acid the proton transfer to melamine takes place yielding melamin-1-ium cation that interacts with 2-chlorophenylacetate(-) anion and neutral acid molecule forming ionic supramolecular complex, the other two are neutral supramolecular complexes. Melamine is
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a relatively basic compound with pKa of 5.1 in an aqueous solution [19]. Depending on the acidity of the studied acid, salts or co-crystals may form. The pKa of the 2-, 3- and 4chlorophenylacetic acid isomers are 4.07 , 4.14 and 4.19, respectively [20]. A comparison of ΔpKa (ΔpKa = pKa(base) – pKa(acid)) between melamine and 2-, 3-, and 4- acid isomers ( 0.97;
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0.86 and 0.81, respectively) shows that with the values of ΔpKa the formation of the neutral hydrogen bonded supramolecular complex takes place. The formation of melamin-1-ium 2-
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chlorophenylacetate(-) co-crystallizes with 2-chlorophenylacetic acid occurred with the greater value of ΔpKa (~0.97). These observation are in good agreement with Brittain’s method for predicting neutral or ionic formation (salt) supramolecular complexes in aqueous solution by calculating the percentage of salt formation as a function of pKa and pKb [21]. The purity of solid phase of each complex was checked by elemental analysis and by the XRPD.
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Recrystallization of these 1-3 compounds in heavy water yield respective deuterated analogues, which was checked by the XRPD experiment. The XRPD patterns of protiated and deuterated complexes 1-3 together with the calculated ones (Figure S1-S3, in Supporting Information) confirm that the deuterated analogues crystallize, similar as H-compounds, in
Geometry of protonated and neutral melamine and acid units. Within 1-3
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3.2.
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the same space groups with quite similar lattice parameters.
supramolecular complexes only in 1 the melamine is protonated forming melamin-1-ium cation (MH+). The protonation of the perfectly symmetrical melamine results in increasing of the C−N−C bond angle at the protonated ring N atom, which is about four degree larger when comparing with the C−N−C bond angles in neutral melamine ring (Table S1 in supplementary). The differences between the C−N−C bond angles within protonated and non-protonated melamine rings are in agreement with the valence-shell electron-pair repulsion model, VSEPR [22], according to which the lone pair on non-protonated aza nitrogen atoms afford a wider region than the covalent bond N−H causing the internal angle of the last to be greater than on the non-protonated N-ring atoms. As a result of the 6
ACCEPTED MANUSCRIPT protonation of the melamine ring at one of three N-ring atoms, the internal N−C−N angle involving non-protonated N atoms is significantly greater than the remaining two N−C−N angle involving protonated and non-protonated N atoms (Table S1). Ab-initio gas-phase geometry calculated for neutral melamine molecule and its singly protonated cation shows similar correlation between the internal C−N−C and N−C−N angles within the rings as in the
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crystals of 1-3 [23]. Thus the ring distortion of MH+ in comparison to neutral melamine molecule results mainly from protonation, and to a lesser degree, from the hydrogenbonding system. The conformation of the neutral 2- chlorophenylacetic acid or its deprotonated unit in 1 is very similar. The dihedral angle between the plane of aromatic ring
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and the planes of COOH or COO- groups is 100.5(2)o and 96.5(2)o, respectively. The nonplanar conformation of the 2-chlorophenylacetic acid molecule with a dihedral angle of
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74.8(2)o is observed in the crystal of pure acid [24]. The molecule of 3- and 4-chlorophenyl acetic acid isomers in the crystals 2 and 3 is also non-planar, the dihedral angle between the plane of the ring and the plane of COOH group is 77.7(2)o and 74.2(2)o in 3 and 4, respectively. In the crystal of pure 4-chlorophenyl acetic acid the plane of carboxylic group forms an angle of ~85o with the plain of the ring [25]. The crystal structure of the pure 3-
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chlorophenyl acetic acid isomer is till now unknown.
3.3. Analysis of supramolecular structures:
Melamin-1-ium 2-chlorophenylacetate – 2-
chloro-phenylacetic acid hemihydrate co-crystal (1). Compound 1 crystallizes in the
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monoclinic centrosymmetric space group C2/c. Asymmetric unit of 1 consists of protonated melamin-1-ium cation (MH+), 2-chlorophenylacetate anion, neutral molecule of 2-
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chlorophenylacetic acid and half water molecule (Fig. 1a). Besides the ionic interaction, the oppositely charged units additionally interact each other via two N−H…O hydrogen bonds with a graph of R22(8) forming supramolecular {MH…2-chlorophenylacetate} complex that further interacts with neutral acid molecule by a combination of O-H...N and N-H...O hydrogen bonds also with a graph of R22(8) (Table 2). The water molecule acts as a donor and as an acceptor in two hydrogen bonds forming hydrogen bonded ring with a graph of R32(8) (see Fig. 1). The triazine ring of MH+ is almost coplanar with R32(8) and both R22(8) rings formed by hydrogen bonds. The dihedral angles between the plane of triazine ring of MH+ and the planes of R32(8) ring and the R22(8) rings formed by COOH and COO- groups are 23.8(2)o, 11.7(2)o and 17.7(2)o, respectively. Whereas the phenyl rings of deprotonated and 7
ACCEPTED MANUSCRIPT non-deprotonated acid form with the plane of triazine ring of MH+ angles of 97.0(2)o and 61.1(2)o, respectively, and they lie on the same side of the plain of the triazine ring of MH+. The hydrogen bonded supramolecular units of 1 interact each other via two N−H…O hydrogen bonds with a graph of R32(12) formed by donation to O atoms of COOH and COOgroups of one unit from amine groups of the neighbor, extend them into one-dimensional
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ribbons (Fig. 1b). In the ribbons the triazine ring of MH+ units lie on the plane, whereas the phenyl rings of non- and deprotonated of 2-chlorophenylacetic acid units lie on the same side of the plane of the of MH+ units and are inclined to this plane by 61.1(2)o and 97.0(2)o, respectively. The ribbons are further arranged alternatively along the [1-10] and [-110]
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directions (Fig. 1c). The alternatively arranged neighboring ribbons are linked by water molecules that lie on twofold axis via hydrogen bonds, in which they act as acceptors in two
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N-H...O and as donors in two O-H...O hydrogen bonds linking the ribbons aligned along [1-10] with the ribbons aligned along the [-110] into two-dimensional layer parallel to (001) crystallographic plane (Fig. 1c). Weak π…π interactions between the Cg…Cg with a distance of ~3.47 Å (Cg = gravity center of the ring) are established between the triazine ring of MH+ units from the ribbons aligned along [110] and the phenyl ring of 2-chlorophenylacetate anions from another ribbons aligned along [-110] and inversely, which additionally stabilize
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the layer (Fig. 1c). Between the layers the Cg…Cg distances between the phenyl rings of the non-deprotonated 2-chlorophenylacetic acid units are much longer, so the π…π interactions
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between them are relatively very low.
Melamine - 3-chlorophenylacetic acid (1:2) co-crystal (2). Compound 2 crystallizes in the
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centrosymmetric space group Pbcn of the orthorhombic system with Z=4 per unit cell. The asymmetric unit of 2 consists of one 3-chlorophenylacetic acid molecule and half of melamine, which lies on the two-fold symmetry axis (Fig. 2a). The carboxyl group of 3chlorophenylacetic acid molecule interacts with melamine via N-H...O and O-H...N hydrogen bonds with a graph of R22(8). The R22(8) graph is formed by donation to ring N atom of melamine form the OH of COOH group and by donation from amine group to carbonyl O atom of COOH. The first O-H...N hydrogen bond is stronger [D…A = 2.574 (2) Å] than the second N-H...O hydrogen bond [D…A = 2.875 (2) Å]. The R22(8) ring is co-planar with the triazine ring of melamine, whereas the plane of the phenyl ring of 3-chlorophenylacetic acid molecule is inclined to this plane by 75.9(2)o. In the whole supramolecular complex of 8
ACCEPTED MANUSCRIPT melamine - 3-chlorophenylacetic acid of 1:2 due to two-fold symmetry axis the phenyl rings of acid molecules lie on the opposite sides of the plane defined by melamine molecule and both hydrogen-bonded R22(8) rings (Table 3). Translationally related along b-axis hydrogen bonded supramolecular complexes of 2 interact each other via a pair of N-H...O hydrogen bonds (Table 3) with a graphs of R32(12) forming one-dimensional ribbons arranged along
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[010] direction (Fig. 2b). The hydrogen-bonded ribbons related by two-fold axis parallel to [010] are arranged in stacking two-dimensional layer parallel to (100) plane (Fig. 2c). Within the stacks the Cg…Cg distance between the melamine rings is 5.04(2) Å. Since the shifting angle between the melamine ring is 40.9(2)o, the planes of the melamine rings are much
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closer (3.25(2) Å) than the distance of ~3.4 Å pointing on the π-π stacking interactions between the aromatic rings of melamine units. This interactions contribute to their packing
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arrangement. Neighboring stacks related by a plane c perpendicular to the a-axis interact only by the van der Waals forces, which are much weaker than within the stacks and therefore the (100) plane is a cleavage plane of the co-crystal 2.
Melamine - 4-chlorophenylacetic acid (1:2) co-crystal (3). Compound 3 crystallizes in the
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centrosymmetric space group C2/c of the monoclinic system with four molecules per unit cell. Asymmetric unit of 3 consists of one 4-chlorophenylacetic acid molecule and half of melamine, which lies on the two-fold symmetry axis (Fig. 3a). The carboxyl group of 4chlorophenylacetic acid interacts with melamine molecule via N-H...O and O-H...N hydrogen
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bonds with a graph of R22(8). The hydrogen bonded R22(8) ring is formed by donation to the ring N atom of melamine from the non-deprotonated carboxyl group and by donation from
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amine to carbonyl O atom of carboxyl group. In the R22(8) ring the O-H...N hydrogen bond is stronger [O…N = 2.594 (2) Å] than the N-H...O hydrogen bond [D…A = 2.864 (1) Å]. The R22(8) ring is almost co-planar with the triazine ring of melamine, whereas the plane of the phenyl ring of 4-chlorophenylacetic acid molecule is inclined to this plane by 74.1(2)o. In the whole supramolecular complex of melamine - 4-chlorophenylacetic acid of 1:2 due to two-fold symmetry axis the phenyl rings of acid molecules lie on the opposite sides of the plane defined by melamine molecule and both hydrogen-bonded R22(8) rings (Table 4). Translationally related along b-axis hydrogen-bonded supramolecular complexes of melamine - 4-chlorophenylacetic acid
(1:2) interact each other
via a pair of N-H...O
hydrogen bonds with a graph of R32(12) forming ribbons arranged along [010] direction (Fig. 9
ACCEPTED MANUSCRIPT 3b). Within the ribbon the triazine ring of melamine moieties and the hydrogen bonded R22(8) rings are co-planar, while the phenyl rings of 4-chlorophenylacetic acid molecules lie on the opposite sides of this plane. The hydrogen-bonded ribbons related by two-fold axis parallel to [010] and translation along c-axis are arranged in the stacking two-dimensional layer parallel to (100) plane (Fig. 3c). Within the stack the Cg…Cg distance between the
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melamine rings is 5.10(1) Å. However the distance between the planes of melamine rings due to the shifting angle of 40.4(2)o is 3.24(1) Å. So the π-π interactions between the shifted melamine rings within the stack takes place. Inversion related neighboring stacks interact much weaker since the plane of the shifted phenyl rings of 4-chlorophenylacetic acid
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molecules are separated by 3.63(1) Å. Therefore the (100) plane is a cleavage plane of the
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co-crystal 3.
3.4. Hirshfeld surface analysis. Hirshfeld surface is recently developed technique which
allows insight into all interactions constituting crystal structures [26]. This method uses visual recognition of properties of atom contacts through mapping of a range of functions (dnorm, shape index, curvedness, etc.) onto this surface [27]. The increasing popularity of this tool comes from the fact that is allows for recognition not only the hydrogen-bonding
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interactions but also the less directional contacts, for instance C–H…A (A=acceptor) or H…H dispersion forces. Another essential advantage is that all (di, de) contacts created by a molecule of interest can be expressed in the form of a two dimensional plot, known as the
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2D fingerprint plot. The di and de are defined, respectively, as the distance from the Hirshfeld surface to the nearest nucleus outwards from the surface and the distance from
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the surface to the nearest atom in the molecule itself. The shape of this plot, which is unique for each molecule, is determined by dominating intermolecular contacts [28]. The Hirshfeld surface was calculated using the Crystal Explorer v.3.1 program package and the 2D fingerprint was prepared using the same software [29]. The Hirshfeld surface mapped with a dnorm function for the melamin-1-ium cation and for melamine (Fig. 4) and for 2chlorophenylacetic acid and its deprotonated anion as well as for 3- and 4-chloropheylacetic acid molecules (Fig. S4) in the co-crystals 1-3 clearly shows the red spots derived from N-H...O and O-H...N hydrogen bonding interactions. The respective plot of 2D fingerprint for the melamine units (Fig. 4) shows the most significant N-H...O and O-H...N interactions with contribution of 26.5 % and 18.4 % in 1, 17.6 % and 24.1 % in 2 and 18.3 % and 24.4 % in 3, 10
ACCEPTED MANUSCRIPT respectively. The percentage contributions from the major intermolecular interactions to the Hirshfeld surface of melamine units in the 1-3 crystals is shown in Fig 4d. In all supramolecular complexes the types of interactions are similar, but their contributions to the major intermolecular contacts and the structure stabilisation slightly vary. Protonation of melamine as found in 1 is concerned in increasing of contribution of H…O (26.5%) in relation
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to the contributions in supramolecular complexes of neutral melamine as found in 2 and 3, in which the contribution of H…O contacts is very similar (Fig. 4d). However, the opposite relation of the N…H contribution is found in these supramolecular 1-3 complexes. These results confirm the results of crystal structure analysis and reflect the peculiarities of the
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connectivity and the packing patterns.
3.5. Vibrational characterization. In order to gain an insight into the structure and the nature
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of the interaction between the melamine and 2-, 3- and 4-chlorophenylacetic acid isomers in the crystalline form of supramolecular complexes 1-3, the vibrational spectra were measured and discussed with those of melamine [30] and 2-, 3- and 4-chlorophenylacetic acid isomers [31,32]. Assignment of the IR bands was supported by the spectra of their deuterated analogues. The infrared spectra (protiated and deuterated) and Raman spectra
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(protiated) of 1-3 supramolecular complexes are included in the Supporting Information (Figs. S5-S7). Bands corresponding to the vibration of the functional groups were identified with the aid of infrared and Raman correlation charts [33,34]. Within the investigated supramolecular complexes of melamine with chlorophenylacetic acid isomers with a
neutral)
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composition of 1:2, only in 1 both form of 2-chlorophenylacetic acid units (deprotonated and and the protonated melamin-1-ium residue (MH+) exist, but in 2 and 3 the
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supramolecular complexes are formed via N-H...O and O-H...N hydrogen bonds between neutral melamine and 3- or 4-chlorophenylacetic acid molecules. In addition, only 1 is hydrated complex. Therefore in the vibrational spectra the vibrational bands corresponding to these components should be observed and implies the differences in the vibrational spectra (IR and Raman) of these supramolecular complexes (Figs. S5-S7). In the IR spectrum of 1 the band of the hydrated water molecule that acts as a donor in two O-H...O hydrogen bonds with O…O distances of 2.581(2) Å and as an acceptor also two N-H...O hydrogen bonds with distances of 2.797(2) Å is observed at 3575 cm-1. This band, as expected, is shifted to ~2620 cm-1 in the spectrum of its deuterated analogue (Fig. S5a and S5b), and is absent in 11
ACCEPTED MANUSCRIPT the vibrational spectra of 2 and 3, which are anhydrous (Fig. S6 and S7). The isotopic ratio of 1.364 is consistent with the medium and weak hydrogen bonds in which the water molecule is involved. A careful inspection of the IR spectra of the 1-3 compounds the medium-strong intensity bands in the spectral region of 3500-3000 cm-1observed in the spectra of all compounds are attributed to the asymmetric and symmetric stretching of the three NH2
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groups of the melamine units. The bands of asymmetric stretching νa(NH2) vibrations are observed at higher frequency than the symmetric stretching νs(NH2) bands (Fig. S5a, S6a and S7a). These bands, as expected, are shifted in the spectra of deuterated analogues to the spectral region of 2650-2050 cm-1 (Fig. S5b, S6b and S7b). Theoretical calculation23 of the
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IR spectrum of singly protonated melamin-1-ium residue MH+ shows that shows that additional band with frequency between the νa(NH2) and νs(NH2) is assigned to stretching
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vibration of N–H bond with a proton directly bonded to triazine ring nitrogen atom. This band is not observed in 1 as well as in the spectra of other singly protonated melamin-1-ium slats [35]. The melamin-1-ium cation in crystal 1 and neutral melamine molecule in crystals 2 and 3 are involved in N-H...O and O-H...N hydrogen bonds. These interactions result in the IR spectra of these supramolecular complexes as a broad band in the spectral region of 3300-
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250 cm-1, which is shifted to 2500-2000 cm-1 in the spectra of deuterated analogues. In addition, the broad band in the spectral region of 1600 – 1100 cm-1, which is overlapped with several other bands, point on the presence of this types of N-H...O and O-H...N interactions. The spectra of chlorophenylacetic acid isomers, which in solids form dimeric
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structures with O…O distances of 2.64-2.76 Å show similar bands related with the carboxylic group. The vibration bands of the COOH group contain the C=O, C-O and O-H vibration
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modes. The C=O stretching appears a strong intensity band around 1700 cm-1, while for the O-H involved in the dimers is observed in the frequency region ~3000 cm-1 as a broad band. The vibration bands of deprotonated COO- group is observed at ~1630 cm-1 (νasCOOasymmetric stretching) and at ~1440 cm-1 (νsCOO- symmetric stretching). These bands related with the COO- group are observed in the spectrum of 1, whereas in the spectra of 2 and 3 only bands related with the neutral 3- or 4- chlorophenylacetic acid isomers could be found. The C-H stretching modes of the methylene group (CH2) of the chlorophenylacetic acid isomers are at lower frequencies than those of the aromatic C-H ring stretching. The CH2 antisymmetric stretching vibration appear at higher and CH2 symmetric stretching at lower frequency. These bands are clearly evidenced in the Raman spectra of all supramolecular 12
ACCEPTED MANUSCRIPT complexes around 3000 cm-1 (Fig. S5c,d-S7c,d in SI). The vibrations corresponding to bonding between the ring and chloride (C-Cl) are significant due to possibility of mixing of vibrations on lowering of the molecular symmetry and the presence of heavy atom joined to phenyl ring of the acid isomers. The calculated frequencies of C-Cl are 1011 and 666 cm-1, which well correlate with the values of ~1020 and ~687 cm-1 observed for chlorophenylacetic acid
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isomers [31,32]. These bands could be found in the spectra of 1-3 supramolecular complexes. Conclusion
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In the present contribution the structural study of three supramolecular complexes of melamine with 2-, 3- and 4-chlorophenylacetic acid isomers are described. Within these
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supramolecular complexes only one with 2- chlorophenylacetic acid isomers (1) is ionic, in the other two with 3- and 4-chlorophenylacetic acid isomers (2, 3) the supramolecular complexes are formed between neutral melamine and acid units. Independent of the molar ratio of melamine to chlorophenylacetic acid isomers the formed supramolecular complexes have the same composition of 1:2. In solid-state all supramolecular complexes form one dimensional ribbons. Weak π…π interactions between the ribbons stabilize the
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supramolecular assembly of all complexes. Additionally in 1 the ribbons are interconnected via hydrogen bonds with water molecule. The Hirshfeld surface and the 2D fingerprint plots clearly evidenced the differences in the interactions between the building blocks of the
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supramolecular complexes. The medium and weak N-H...O and O-H...N hydrogen-bonding interactions have been confirmed by vibrational spectroscopy. This work confirms the
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usefulness of melamine as a multiple hydrogen-bonding building blocks in the crystal engineering.
Supplementary Materials
Additional material comprising selected geometrical parameters (Å, o) for 1-3, the XRPD diagrams
for protiated and deuterated analogues of 1-3, Hirshfeld surface and 2D
fingerprint for the acid units of 1-3 and the IR and Raman spectra for protiated and deuterated analogues of 1-3. Full details of the X-ray data collection and final refinement
13
ACCEPTED MANUSCRIPT parameters including anisotropic thermal parameters and full list of the bond lengths and angles have been deposited with the Cambridge Crystallographic Data Center in the CIF format as supplementary publications no. CCDC 1474011-1474013 for 1-3, respectively. Copies of the data can be obtained free of charge on the application to CCDC, 12 Union
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Road, Cambridge, CB21EZ, UK, (fax: (+44) 1223-336-033; email: [email protected] ).
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[12] X. Zhang, X. Chen, Cryst. Growth Des., 2005, 5, 617-622; X. Zhang, B. Ye, X. Chen, Cryst. Growth Des., 2005, 5, 1609-1616.
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Des., 2015, 15, 1871-1875.
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Zhu, Acta Crystallogr. Sect. E: Crystallogr. Commun., 2005, 61, o811-o813; J. Janczak, G.J. Perpétuo, Acta Crystallogr. Sect. C: Cryst. Struct. Commun., 2002, 58, o339-o341; J. Janczak, G.J. Perpétuo, Acta Crystallogr. Sect. C: Cryst. Struct. Commun., 2002, 58, o112o114; G.J. Perpétuo, M.A. Ribeiro, J. Janczak, Acta Crystallogr. Sect. E: Crystallogr. Commun., 2005, 61, o1818-o1820; C.S. Choi, R. Venkatraman, E.H. Kim, H.S. Hwang, S.K.
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Kang, Acta Crystallogr. Sect. C: Cryst. Struct. Commun., 2004, 60, o295-o296; J. Janczak, G.J. Perpétuo, Acta Crystallogr. Sect. C: Cryst. Struct. Commun., 2001, 57, 1431-1433; J. Janczak, G.J. Perpétuo, Acta Crystallogr. Sect. C: Cryst. Struct. Commun., 2001, 57, 11201122; I. Karle, R.D. Gilardi, Ch.C. Rao, K.M. Muraleedharan, S. Ranganathan, J. Chem.
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Crystallogr., 2003, 33, 727-749; G.J. Perpétuo, J. Janczak, J. Mol. Struct., 2008, 891, 429436; S. Kohmoto, S. Sekizawa, S. Hisamatsu, H. Masu, M. Takahashi, K. Kishikawa, Cryst.
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Growth Des., 2014, 14, 2209–2217. [15] Oxford Diffraction Poland, CrysAlis CCD and CrysAlis Red, Version 1.171.33.42, 2009. [16] G.M. Sheldrick, Acta Crystallogr. Sect. A: Found. Adv., 2015, 71, 3-8. [17] G.M. Sheldrick, Acta Crystallogr. Sect. C: Cryst. Struct. Commun., 2015, 71, 3-8. [18] K. Brandenburg, H. Putz, DIAMOND Version 3.0, Crystal Impact GbR, Bonn, Germany, 2006. [19] R.C. Hirt, R.G. Schmitt, Spectrochim. Acta, 1958, 12, 127–138. 16
ACCEPTED MANUSCRIPT [20] A. Habibi-Yangjeh, M. Danandeh-Jenagharad, Indian J. Chem., 2007, 46B, 478-487. [21] H.G. Brittain, Am. Pharm. Rev., 2009, 12, 62-65. [22] R.J. Gillespie, Chem. Soc. Rev., 1992, 21, 59-69.
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110, 343–347.
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Crystal Explorer ver. 3.1, University of Western Australia, Perth, Australia, 2013. [30] W.J. Jones, W.J. Orville-Thomas, Trans. Farady Soc., 1959, 55, 203-210; J.R. Schneider, B. Schrader, J. Mol. Struct., 1975, 29, 1-14; R.J. Meier, A. Tiller, S.A.M. Vanhommerig, J. Phys.
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Spectrosc., 2012, 62, 165-171; W.-Ch. Chen, S.-Y. Wu, H.-P. Liu, Ch.-H. Chang, H.-Y. Chen, H.-Y. Chen, Ch.-H. Tsai, Y.-Ch. Chang, F.-J. Tsai, K.-M. Man, P.-L. Liu, F.-Y. Lin, J.-L. Shen, W.Y. Lin, Y.-H. Chen, J. Clin. Lab. Anal., 2010, 24, 92-99.
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ACCEPTED MANUSCRIPT [33] G. Socrates, Infrared Characteristic Group Frequencies; Wiley-Interscience: Chichester, U.K., 1980. [34] G. Socrates, Infrared and Raman Characteristic Group Frequencies Tables and Charts, 3rd ed.; Wiley: Chinchester, West Sussex, England, 2004.
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[35] S. Debrus, M.K. Marchewka, M. Drozd, H. Ratajczak, Opt. Mater., 2007, 29, 1058-1062; M.K. Marchewka, J. Janczak, S. Debrus, J. Baran, H. Ratajczak, Solid State Sci., 2003, 5,
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643-652.
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ACCEPTED MANUSCRIPT 3 C19H20Cl2N6O4 467.31 monoclinic C 2/c 26.6583(15)
b (Å)
10.5687(5)
7.8659(3)
26.6583(15)
c (Å)
34.2869(16)
9.9892(4)
β (o )
90.263(4)
V (Å3)
4321.1(3)
2096.93(14)
Z
8
4
Dcalc/Dobs (g·cm–3)
1.464 / 1.46
1.480 /1.48
μ (mm–1)
0.343
0.350
Crystal size (mm)
0.29 × 0.26 × 0.22
0.31 × 0.27 × 0.23
Radiation, λ (Å)
Mo Kα , 0.71073
Temp. (K)
295(2)
Tmin/Tmax
0.911 / 0.927
θ range, (o)
3.13 ÷ 29.43
Refls collected/
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unique/
5611
observed
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Rint
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Table 1. Crystal Data and Structure Refinement for Compounds 1-3. 1 2 Formula C19H21Cl2N6O4.5 C19H20Cl2N6O4 f.w. (g·mol–1) 476.31 467.31 Crystal system monoclinic orthorhombic space group C 2/c Pbcn a (Å) 11.9247(5) 26.6873(11)
10.1176(6) 97.854(6) 2109.6(2) 4
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1.471 / 1.47 0.348
0.33 × 0.28 × 0.23 Mo Kα , 0.71073
295(2)
295(2)
0.905 / 0.932
0.903 / 0.932
3.05 ÷ 29.42
3.09 ÷ 29.22
27371
14029
2776
2665
1406
1543
0.0345
0.0333
0.0206
R[F2>2σ(F2)]
0.0360
0.0322
0.0311
wR(F2) all refls
0.0889
0.0838
0.0791
1.000
1.002
1.002
+0.277; -0.410
+0.207; -0.254
+0.223; -0.294
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Δρmax; Δρmin (e Å–3)
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Goodness-of-fit, S
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Mo Kα , 0.71073
wR={Σ [w(Fo2–Fc2)2]/ΣwFo4}½; w–1=1/[σ2(Fo2) + (aP)2] where a is 0.0362 for 1, 0.0385 for 2, 0.0405 for 3, and P = (Fo2 + 2Fc2)/3.
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ACCEPTED MANUSCRIPT Table 2. Hydrogen-bond geometry in 1 (Å,o). D—H 0.84 (1) 0.84 (1) 0.85 (1) 0.85 (1) 0.85 (1) 0.87 (1) 0.85 (1) 0.87 (1) 0.87 (1)
H···A 1.75 (1) 2.06 (1) 1.80 (1) 2.11 (1) 2.66 (2) 2.02 (1) 1.91 (1) 1.94 (1) 2.09 (1)
D···A 2.581 (2) 2.797 (2) 2.642 (2) 2.958 (2) 3.295 (2) 2.878 (2) 2.750 (2) 2.796 (2) 2.923 (2)
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Symmetry codes: (i) −x+2, y, −z+1/2; (ii) x+1/2, y−1/2, z.
Table 3. Hydrogen-bond geometry in 2 (Å,o). D—H 0.83 (1) 0.87 (1) 0.86 (1) 0.86 (1)
Symmetry code: (i) x, y+1, z.
H···A 1.75 (1) 2.01 (1) 2.61 (1) 2.04 (1)
D···A 2.574 (2) 2.863 (2) 3.257 (2) 2.875 (2)
D—H···A 171 (2) 169 (1) 133 (1) 165 (2)
D···A 2.594 (2) 2.864 (1) 3.277 (2) 2.872 (2)
D—H···A 167 (2) 177 (1) 138 (1) 171 (1)
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D—H···A O2—H2O···N2 N3—H31···O1i N3—H32···O2 N4—H41···O1
D—H···A 167 (3) 146 (2) 172 (2) 173 (2) 133 (2) 170 (2) 173 (2) 170 (2) 162 (2)
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D—H···A O12—H12···N2 O1—H1···O21ii N3—H3···O21 N4—H4A···O11ii N4—H4B···O12 N5—H5A···O11 N5—H5B···O22 N6—H6A···O22ii N6—H6B···O1
D—H 0.83 (1) 0.87 (1) 0.85 (1) 0.87 (1)
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D—H···A O2—H2O···N2 N3—H31···O1 N4—H41···O2 N4—H42···O1i
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Table 4. Hydrogen-bond geometry in 3 (Å,o).
H···A 1.78 (1) 2.00 (1) 2.60 (1) 2.01 (1)
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Symmetry code: (i) x, y−1, z.
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Figure 1. View of molecular structure of 1 with displacement ellipsoids at the 50% probability level (a), hydrogen-bonded ribbon of 1 (b) and the packing pattern demonstrating the inter-ribbon interactions (c). Dashed lines represent N−H…O, O-H...N and O-H...O hydrogen bonds.
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(b)
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(c) Figure 2. View of molecular structure of 2 with displacement ellipsoids at the 50% probability level (a), hydrogen-bonded ribbon of 1 (b) and the packing pattern demonstrating the inter-ribbon interactions (c). Dashed lines represent N−H…O, O-H...N and O-H...O hydrogen bonds. 22
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(c)
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(c) Figure 3. View of molecular structure of 3 with displacement ellipsoids at the 50% probability level (a), hydrogen-bonded ribbon of 3 (b) and the packing pattern demonstrating the inter-ribbon interactions (c). Dashed lines represent N−H…O, O-H...N and O-H...O hydrogen bonds. 23
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(c)
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(d) Figure 4. The Hirshfeld surface mapped with a dnorm function and the 2D fingerprint for the
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melamin-1-ium cation in 1 (a) and for melamine in 2 (b) and 3 (c), and the percentage contributions from major intermolecular interactions to the Hirshfeld surfaces (d).
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ACCEPTED MANUSCRIPT Highlights
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► Supramolecular complexes of melamine with chlorophenylacetic acid isomers are obtained. ► Hydrogen bonding R22(8) motif forms supramolecular complexes. ► Hirshfeld surface and 2D fingerprint plots have been analysed. ► The characteristic vibrational bands of the H and D analogues are discussed.
S0022-2860(16)30693-7
DOI:
10.1016/j.molstruc.2016.07.022
Reference:
MOLSTR 22725
To appear in:
Journal of Molecular Structure
Received Date: 10 May 2016 Revised Date:
1 July 2016
Accepted Date: 8 July 2016
Please cite this article as: J. Janczak, Supramolecular solid-state architectures formed by cocrystallization of melamine and 2-, 3- and 4-chlorophenylacetic acids, Journal of Molecular Structure (2016), doi: 10.1016/j.molstruc.2016.07.022. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
ACCEPTED MANUSCRIPT Graphical Abstract Supramolecular complexes of melamine with 2-, 3- and 4-chlorophenylacetic acid isomers (1-3) were obtained. The hydrogen-bonded supramolecular complexes were characterized by X-ray single
(2)
(3)
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crystal diffraction, Hirshfeld surface and analysis and vibrational spectroscopy.
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Supramolecular solid-state architectures formed by co-crystallization of melamine and 2-, 3- and 4-chlorophenylacetic acids
Jan Janczak*
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Institute of Low Temperature and Structure Research, Polish Academy of Sciences, Okólna 2 str., P.O. Box 1410,
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50-950 Wrocław, Poland
Abstract
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A family of supramolecular complexes of melamine with chlorophenylacetic acid isomers using solvent-assisted and evaporation-based techniques has been prepared. Crystallization of melamine with 2-chlorophenylacetic acid yield hydrated ionic supramolecular complex (1), whereas crystallization of melamine with 3- and 4-chlorophenylacetic acids leads to formation of neutral supramolecular complexes (2, 3), all with base to acid ratio of 1:2.
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Within chlorophenylacetic acid isomers only in 2-chlorophenylacetic acid isomer as the stronger acid the proton transfer to melamine takes place. The crystal structures of supramolecular complexes have been determined. The supramolecular assembly is driven by the noncovalent interactions, most commonly by the hydrogen bonds. The components of
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the crystals interact via NH…O and OH…N with a graph of R22(8) forming respective ionic or neutral supramolecular complexes. All three supramolecular complexes studied interact other via a pair of NH…O hydrogen
bonds forming pseudo one-dimensional
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supramolecular chains along [1-10] and [-110] in 1 and along [010] in 2 and 3. Hirshfeld surface and analysis of 2D fingerprint plots have been analysed both quantitatively and qualitatively interactions governing the supramolecular organisation. The IR and Raman vibrational characterization of the supramolecular complexes 1-3 was supported by the spectra of their deuterated analogues.
*E-mail: [email protected]. Tel. +48 71 39 54 145. Fax: +48 71 34 410 29.
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1. Introduction The understanding of the interactions between the molecules in the context of design of new solids has considerably expanding the research branch of materials science over past few decades [1]. Despite these advantages, the prediction of the crystalline structure from solely its molecular constituents is still not yet possible. Crystal engineering
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involving a combination of non-covalent synthesis of new solids with designed architecture in solids seems to solve this predicament [2]. A productive strategy in supramolecular synthesis and the crystal engineering is to build supramolecular architectures from molecules containing complementary arrays of the hydrogen-bonding sites [3]. The non-
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covalent interactions such as hydrogen bonding, π-π stacking interactions, and the van der Waals forces have been used in the self-assembly and design a large number of
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supramolecular architectures in solids like as types, rosettes, rods, layers, spheres and sheets [4]. Among the self-assembly organisation forces, the hydrogen bond is the most important interaction and the recognition events for rational design of extending supramolecular architecture in solids, due to its abundance, strength and specific and directional properties [5]. A focal point of the crystal engineering is the concept of supramolecular synthons,
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structural units formed by predictable intermolecular interactions [6]. The supramolecular synthons are powerful tools for predicting not only local intermolecular interactions, but also often provide little insight into a global topology of a crystal structure.
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Melamine is highly symmetric and is trigonal planar (D3h), and is useful in the crystal engineering as a building blocks, since it contains multiple hydrogen-bonding sites, can act
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both as an excellent hydrogen donor and hydrogen acceptor in hydrogen bonding. Furthermore in solids the strong π-π stacking interactions between the aromatic rings of it contribute to their packing arrangement [7]. Melamine is potentially hazardous to health [8], but important in supramolecular non-covalent synthesis of solids [9]. Within the body, melamine is metabolised to cyanuric acid, a process that leads to precipitation of co-crystals of melamine-cyanuric acid within the kidneys, causing renal failure [10]. The complementarity of the melamine and cyanuric acid units has been used to rationalise the stability and relatively poor aqueous solubility of melamine-cyanuric acid co-crystal, as well as a model to realise a wide variety of supramolecular assemblies in solids [11]. Crystallization of melamine and the aromatic carboxylic acids or 1,5-napthtalenedisulfonic 2
ACCEPTED MANUSCRIPT acid leads to the crystals with a characteristic helical water chain assemblies [12]. A porous hydrogen-bonded organic frameworks have been also reported for solvent dependent structures of melamine [13]. Co-crystallization of melamine with inorganic and various organic small carboxylic and sulfonic acids has produced various supramolecular
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architectures [14]. In the present work the supramolecular architecture in solid formed by cocrystallization of melamine with chlorophenylacetic acid isomers has been examined (Scheme 1). In addition, this study is aimed at how the melamine to acid molar ratio used in
architecture of the formed crystals or co-crystals. COOH
COOH
COOH
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NH2
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the crystallization influences the composition and the topology of the supramolecular
Cl N H2N
N N
Cl
NH2
Cl
(a)
(b)
(c)
(d)
isomers (b-d).
2.1.
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2. Experimental
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Scheme 1. Structure of melamine (a) and the 2-, 3- and 4-chlorophenylacetic acid
Materials: The reagents melamine (99%), 2-cholorophenylacetic acid (99%), 3-
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chlorophenylacetic acid (98%) and 4-chlorophenylacetic acid (99%) were purchased from Sigma-Aldrich and were used without further purification. Elemental analysis was carried out with a Perkin Elmer 240 elemental analyser. 2.2.
Synthesis. Melamine and respective isomer of chlorophenylacetic acid isomer were
added to hot water in a molar proportion of 1:1. When the solutions became homogeneous they were cooled slowly and kept at room temperature. After several days, transparent colourless crystals of the respective compounds 1 - 3 suitable for the X-ray single crystal measurements were formed. The crystals have been separated by filtration and dried in air.
3
ACCEPTED MANUSCRIPT Melamin-1-ium 2-chlorophenylacetate – 2-chloropheylacetic acid hemihydrate, (C3H7N6) (C8H6ClO2).(C8H7ClO2). ½(H2O) (1). Analysis: calculated for C38H42Cl4N12O9: C, 47.91; Cl, 14.89; N, 17.64; O, 15.12 and H, 4.44 %. Found: C, 47.80; Cl, 14.81; N, 17.52; O, 15.39 and H, 4.48 %. Melamine – 3-chlorophenyacetic acid co-crystal, (C3H6N6) .2(C8H7ClO2) (2). Analysis:
48.77; Cl, 15.08; N, 17.90; O, 13.90 and H, 4.35 %.
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calculated for C19H20Cl2N6O4: C, 48.84; Cl, 15.17; N, 17.98; O, 13.70 and H, 4.31 %. Found: C,
Melamine – 4-chlorophenylacetic acid co-crystal, (C3H6N6) .2(C8H7ClO2) (3). Analysis:
48.73; Cl, 15.11; N, 17.92; O, 13.88 and H, 4.36 %.
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calculated for C19H20Cl2N6O4: C, 48.84; Cl, 15.17; N, 17.98; O, 13.70 and H, 4.31 %. Found: C,
The deuterated analogues of the respective 1 - 3 co-crystals were prepared by the usual
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reaction with heavy water. The respective protiated samples were dissolved in heavy water, and left in the atmosphere saturated with heavy water for one-two weak, in order to avoid the contamination of the crystals and next this procedure was repeated twice.
2.3. X-ray single crystal data collection. X-ray intensity data for the 1-3 crystals were
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collected using graphite monochromatic MoKα radiation on a four-circle κ geometry KUMA KM-4 diffractometer with a two-dimensional area CCD detector. The ω-scan technique with ∆ω = 1.0o for each image was used for data collection. Data collections were made using the
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CrysAlis CCD program [15]. Integration, scaling of the reflections, correction for Lorenz and polarisation effects and absorption corrections were performed using the CrysAlis Red
AC C
program [15]. The structures were solved by the direct methods using SHELXT [16] and refined using SHELXL-2014/7 program [17]. The positions of hydrogen atoms involving in the hydrogen bonds were located in difference Fourier maps and were refined with Uiso=1.2Ueq of N joined H or Uiso=1.5Ueq of O atom joined H. The hydrogen atoms joined to aromatic carbon atoms were introduced in their geometrical positions and treated as rigid. The final difference Fourier maps showed no peaks of chemical significance. Details of the data collection parameters, crystallographic data and final agreement parameters are collected in Table 1. Visualisations of the structures were made with the Diamond 3.0 program [18]. Selected geometrical parameters are listed in Table S1 (in Supporting Information) and the geometry of hydrogen bonding interactions is collected in Table 2-4. 4
ACCEPTED MANUSCRIPT 2.5. Powder X-ray Diffraction (PXRD). Powder X-ray diffraction patterns of the powdered protiated and deuterated 1-3 compounds were checked on
a PANanalytical X’Pert
diffractometer equipped with a Cu-Kα radiation source (λ=1.54182 Å). The diffraction data were recorded in the range of 5-45o at room temperature. The powder diffraction patterns
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of H- and D-compounds are included in supporting information (Figs. S1–S3). The obtained deuterated analogues crystallise, similar as H-compounds, in the same crystal systems with quite similar lattice parameters.
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2.6. Vibrational Spectra Measurements. The vibrational measurements of H-compound and its deuterated analogues were carried out at room temperature. The Fourier transform
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infrared spectrum was recorded from nujol mulls between 4000 and 400 cm-1 on a Bruker IFS 113 V FTIR spectrometer. Resolution was set up to 2 cm-1. The Fourier Transform Raman spectra for 1-3 were recorded on a FRA-106 attached to the Bruker 113 V FTIR spectrometer equipped with Ge detector cooled to liquid nitrogen temperature. Resolution was set up to 2 cm-1, signal/noise ratio was established by 32 scans. Nd3+ - YAG air-cooled diode pumped laser of power ca. 200 mW was used as an exciting source. The incident laser excitation was
1
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1064 nm. The scattered light was collected at the angle of 180o in the region of 3600÷80 cm, resolution 2 cm-1, 256 scans. Vibrational spectra for all compounds are included in
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supplementary (Figs S5-S7).
3. Results and Discussion
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3.1. Synthesis and preliminary characterization of 1-3. Initially, crystallization of melamine with chlorophenylacetic acid isomers taken in a molar ratio of 1:1 has been performed. Crystallization of melamine with 2-chlorophenylacetic acid yield hydrated ionic supramolecular complex (1), whereas crystallization of melamine with 3- and 4chlorophenylacetic acids lead to formation of neutral supramolecular complexes (2, 3) with the 1:2 composition, since the melamine contains multiple hydrogen-bonding sites. Therefore, the crystallization was repeated starting with the melamine to acid molar ratio of 1:2 and 1:3. Independent of the molar ratio of melamine to acid the formed supramolecular complexes have the same composition of 1:2 and they are most stable in applied conditions of the crystallization. Within the obtained supramolecular complexes only in the case of 5
ACCEPTED MANUSCRIPT melamine with 2- chlorophenylacetic acid isomer gave hydrated crystals (1). Within chlorophenylacetic acid isomers only in 2-chlorophenylacetic acid isomer as the stronger acid the proton transfer to melamine takes place yielding melamin-1-ium cation that interacts with 2-chlorophenylacetate(-) anion and neutral acid molecule forming ionic supramolecular complex, the other two are neutral supramolecular complexes. Melamine is
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a relatively basic compound with pKa of 5.1 in an aqueous solution [19]. Depending on the acidity of the studied acid, salts or co-crystals may form. The pKa of the 2-, 3- and 4chlorophenylacetic acid isomers are 4.07 , 4.14 and 4.19, respectively [20]. A comparison of ΔpKa (ΔpKa = pKa(base) – pKa(acid)) between melamine and 2-, 3-, and 4- acid isomers ( 0.97;
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0.86 and 0.81, respectively) shows that with the values of ΔpKa the formation of the neutral hydrogen bonded supramolecular complex takes place. The formation of melamin-1-ium 2-
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chlorophenylacetate(-) co-crystallizes with 2-chlorophenylacetic acid occurred with the greater value of ΔpKa (~0.97). These observation are in good agreement with Brittain’s method for predicting neutral or ionic formation (salt) supramolecular complexes in aqueous solution by calculating the percentage of salt formation as a function of pKa and pKb [21]. The purity of solid phase of each complex was checked by elemental analysis and by the XRPD.
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Recrystallization of these 1-3 compounds in heavy water yield respective deuterated analogues, which was checked by the XRPD experiment. The XRPD patterns of protiated and deuterated complexes 1-3 together with the calculated ones (Figure S1-S3, in Supporting Information) confirm that the deuterated analogues crystallize, similar as H-compounds, in
Geometry of protonated and neutral melamine and acid units. Within 1-3
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3.2.
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the same space groups with quite similar lattice parameters.
supramolecular complexes only in 1 the melamine is protonated forming melamin-1-ium cation (MH+). The protonation of the perfectly symmetrical melamine results in increasing of the C−N−C bond angle at the protonated ring N atom, which is about four degree larger when comparing with the C−N−C bond angles in neutral melamine ring (Table S1 in supplementary). The differences between the C−N−C bond angles within protonated and non-protonated melamine rings are in agreement with the valence-shell electron-pair repulsion model, VSEPR [22], according to which the lone pair on non-protonated aza nitrogen atoms afford a wider region than the covalent bond N−H causing the internal angle of the last to be greater than on the non-protonated N-ring atoms. As a result of the 6
ACCEPTED MANUSCRIPT protonation of the melamine ring at one of three N-ring atoms, the internal N−C−N angle involving non-protonated N atoms is significantly greater than the remaining two N−C−N angle involving protonated and non-protonated N atoms (Table S1). Ab-initio gas-phase geometry calculated for neutral melamine molecule and its singly protonated cation shows similar correlation between the internal C−N−C and N−C−N angles within the rings as in the
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crystals of 1-3 [23]. Thus the ring distortion of MH+ in comparison to neutral melamine molecule results mainly from protonation, and to a lesser degree, from the hydrogenbonding system. The conformation of the neutral 2- chlorophenylacetic acid or its deprotonated unit in 1 is very similar. The dihedral angle between the plane of aromatic ring
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and the planes of COOH or COO- groups is 100.5(2)o and 96.5(2)o, respectively. The nonplanar conformation of the 2-chlorophenylacetic acid molecule with a dihedral angle of
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74.8(2)o is observed in the crystal of pure acid [24]. The molecule of 3- and 4-chlorophenyl acetic acid isomers in the crystals 2 and 3 is also non-planar, the dihedral angle between the plane of the ring and the plane of COOH group is 77.7(2)o and 74.2(2)o in 3 and 4, respectively. In the crystal of pure 4-chlorophenyl acetic acid the plane of carboxylic group forms an angle of ~85o with the plain of the ring [25]. The crystal structure of the pure 3-
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chlorophenyl acetic acid isomer is till now unknown.
3.3. Analysis of supramolecular structures:
Melamin-1-ium 2-chlorophenylacetate – 2-
chloro-phenylacetic acid hemihydrate co-crystal (1). Compound 1 crystallizes in the
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monoclinic centrosymmetric space group C2/c. Asymmetric unit of 1 consists of protonated melamin-1-ium cation (MH+), 2-chlorophenylacetate anion, neutral molecule of 2-
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chlorophenylacetic acid and half water molecule (Fig. 1a). Besides the ionic interaction, the oppositely charged units additionally interact each other via two N−H…O hydrogen bonds with a graph of R22(8) forming supramolecular {MH…2-chlorophenylacetate} complex that further interacts with neutral acid molecule by a combination of O-H...N and N-H...O hydrogen bonds also with a graph of R22(8) (Table 2). The water molecule acts as a donor and as an acceptor in two hydrogen bonds forming hydrogen bonded ring with a graph of R32(8) (see Fig. 1). The triazine ring of MH+ is almost coplanar with R32(8) and both R22(8) rings formed by hydrogen bonds. The dihedral angles between the plane of triazine ring of MH+ and the planes of R32(8) ring and the R22(8) rings formed by COOH and COO- groups are 23.8(2)o, 11.7(2)o and 17.7(2)o, respectively. Whereas the phenyl rings of deprotonated and 7
ACCEPTED MANUSCRIPT non-deprotonated acid form with the plane of triazine ring of MH+ angles of 97.0(2)o and 61.1(2)o, respectively, and they lie on the same side of the plain of the triazine ring of MH+. The hydrogen bonded supramolecular units of 1 interact each other via two N−H…O hydrogen bonds with a graph of R32(12) formed by donation to O atoms of COOH and COOgroups of one unit from amine groups of the neighbor, extend them into one-dimensional
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ribbons (Fig. 1b). In the ribbons the triazine ring of MH+ units lie on the plane, whereas the phenyl rings of non- and deprotonated of 2-chlorophenylacetic acid units lie on the same side of the plane of the of MH+ units and are inclined to this plane by 61.1(2)o and 97.0(2)o, respectively. The ribbons are further arranged alternatively along the [1-10] and [-110]
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directions (Fig. 1c). The alternatively arranged neighboring ribbons are linked by water molecules that lie on twofold axis via hydrogen bonds, in which they act as acceptors in two
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N-H...O and as donors in two O-H...O hydrogen bonds linking the ribbons aligned along [1-10] with the ribbons aligned along the [-110] into two-dimensional layer parallel to (001) crystallographic plane (Fig. 1c). Weak π…π interactions between the Cg…Cg with a distance of ~3.47 Å (Cg = gravity center of the ring) are established between the triazine ring of MH+ units from the ribbons aligned along [110] and the phenyl ring of 2-chlorophenylacetate anions from another ribbons aligned along [-110] and inversely, which additionally stabilize
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the layer (Fig. 1c). Between the layers the Cg…Cg distances between the phenyl rings of the non-deprotonated 2-chlorophenylacetic acid units are much longer, so the π…π interactions
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between them are relatively very low.
Melamine - 3-chlorophenylacetic acid (1:2) co-crystal (2). Compound 2 crystallizes in the
AC C
centrosymmetric space group Pbcn of the orthorhombic system with Z=4 per unit cell. The asymmetric unit of 2 consists of one 3-chlorophenylacetic acid molecule and half of melamine, which lies on the two-fold symmetry axis (Fig. 2a). The carboxyl group of 3chlorophenylacetic acid molecule interacts with melamine via N-H...O and O-H...N hydrogen bonds with a graph of R22(8). The R22(8) graph is formed by donation to ring N atom of melamine form the OH of COOH group and by donation from amine group to carbonyl O atom of COOH. The first O-H...N hydrogen bond is stronger [D…A = 2.574 (2) Å] than the second N-H...O hydrogen bond [D…A = 2.875 (2) Å]. The R22(8) ring is co-planar with the triazine ring of melamine, whereas the plane of the phenyl ring of 3-chlorophenylacetic acid molecule is inclined to this plane by 75.9(2)o. In the whole supramolecular complex of 8
ACCEPTED MANUSCRIPT melamine - 3-chlorophenylacetic acid of 1:2 due to two-fold symmetry axis the phenyl rings of acid molecules lie on the opposite sides of the plane defined by melamine molecule and both hydrogen-bonded R22(8) rings (Table 3). Translationally related along b-axis hydrogen bonded supramolecular complexes of 2 interact each other via a pair of N-H...O hydrogen bonds (Table 3) with a graphs of R32(12) forming one-dimensional ribbons arranged along
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[010] direction (Fig. 2b). The hydrogen-bonded ribbons related by two-fold axis parallel to [010] are arranged in stacking two-dimensional layer parallel to (100) plane (Fig. 2c). Within the stacks the Cg…Cg distance between the melamine rings is 5.04(2) Å. Since the shifting angle between the melamine ring is 40.9(2)o, the planes of the melamine rings are much
SC
closer (3.25(2) Å) than the distance of ~3.4 Å pointing on the π-π stacking interactions between the aromatic rings of melamine units. This interactions contribute to their packing
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arrangement. Neighboring stacks related by a plane c perpendicular to the a-axis interact only by the van der Waals forces, which are much weaker than within the stacks and therefore the (100) plane is a cleavage plane of the co-crystal 2.
Melamine - 4-chlorophenylacetic acid (1:2) co-crystal (3). Compound 3 crystallizes in the
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centrosymmetric space group C2/c of the monoclinic system with four molecules per unit cell. Asymmetric unit of 3 consists of one 4-chlorophenylacetic acid molecule and half of melamine, which lies on the two-fold symmetry axis (Fig. 3a). The carboxyl group of 4chlorophenylacetic acid interacts with melamine molecule via N-H...O and O-H...N hydrogen
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bonds with a graph of R22(8). The hydrogen bonded R22(8) ring is formed by donation to the ring N atom of melamine from the non-deprotonated carboxyl group and by donation from
AC C
amine to carbonyl O atom of carboxyl group. In the R22(8) ring the O-H...N hydrogen bond is stronger [O…N = 2.594 (2) Å] than the N-H...O hydrogen bond [D…A = 2.864 (1) Å]. The R22(8) ring is almost co-planar with the triazine ring of melamine, whereas the plane of the phenyl ring of 4-chlorophenylacetic acid molecule is inclined to this plane by 74.1(2)o. In the whole supramolecular complex of melamine - 4-chlorophenylacetic acid of 1:2 due to two-fold symmetry axis the phenyl rings of acid molecules lie on the opposite sides of the plane defined by melamine molecule and both hydrogen-bonded R22(8) rings (Table 4). Translationally related along b-axis hydrogen-bonded supramolecular complexes of melamine - 4-chlorophenylacetic acid
(1:2) interact each other
via a pair of N-H...O
hydrogen bonds with a graph of R32(12) forming ribbons arranged along [010] direction (Fig. 9
ACCEPTED MANUSCRIPT 3b). Within the ribbon the triazine ring of melamine moieties and the hydrogen bonded R22(8) rings are co-planar, while the phenyl rings of 4-chlorophenylacetic acid molecules lie on the opposite sides of this plane. The hydrogen-bonded ribbons related by two-fold axis parallel to [010] and translation along c-axis are arranged in the stacking two-dimensional layer parallel to (100) plane (Fig. 3c). Within the stack the Cg…Cg distance between the
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melamine rings is 5.10(1) Å. However the distance between the planes of melamine rings due to the shifting angle of 40.4(2)o is 3.24(1) Å. So the π-π interactions between the shifted melamine rings within the stack takes place. Inversion related neighboring stacks interact much weaker since the plane of the shifted phenyl rings of 4-chlorophenylacetic acid
SC
molecules are separated by 3.63(1) Å. Therefore the (100) plane is a cleavage plane of the
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co-crystal 3.
3.4. Hirshfeld surface analysis. Hirshfeld surface is recently developed technique which
allows insight into all interactions constituting crystal structures [26]. This method uses visual recognition of properties of atom contacts through mapping of a range of functions (dnorm, shape index, curvedness, etc.) onto this surface [27]. The increasing popularity of this tool comes from the fact that is allows for recognition not only the hydrogen-bonding
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interactions but also the less directional contacts, for instance C–H…A (A=acceptor) or H…H dispersion forces. Another essential advantage is that all (di, de) contacts created by a molecule of interest can be expressed in the form of a two dimensional plot, known as the
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2D fingerprint plot. The di and de are defined, respectively, as the distance from the Hirshfeld surface to the nearest nucleus outwards from the surface and the distance from
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the surface to the nearest atom in the molecule itself. The shape of this plot, which is unique for each molecule, is determined by dominating intermolecular contacts [28]. The Hirshfeld surface was calculated using the Crystal Explorer v.3.1 program package and the 2D fingerprint was prepared using the same software [29]. The Hirshfeld surface mapped with a dnorm function for the melamin-1-ium cation and for melamine (Fig. 4) and for 2chlorophenylacetic acid and its deprotonated anion as well as for 3- and 4-chloropheylacetic acid molecules (Fig. S4) in the co-crystals 1-3 clearly shows the red spots derived from N-H...O and O-H...N hydrogen bonding interactions. The respective plot of 2D fingerprint for the melamine units (Fig. 4) shows the most significant N-H...O and O-H...N interactions with contribution of 26.5 % and 18.4 % in 1, 17.6 % and 24.1 % in 2 and 18.3 % and 24.4 % in 3, 10
ACCEPTED MANUSCRIPT respectively. The percentage contributions from the major intermolecular interactions to the Hirshfeld surface of melamine units in the 1-3 crystals is shown in Fig 4d. In all supramolecular complexes the types of interactions are similar, but their contributions to the major intermolecular contacts and the structure stabilisation slightly vary. Protonation of melamine as found in 1 is concerned in increasing of contribution of H…O (26.5%) in relation
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to the contributions in supramolecular complexes of neutral melamine as found in 2 and 3, in which the contribution of H…O contacts is very similar (Fig. 4d). However, the opposite relation of the N…H contribution is found in these supramolecular 1-3 complexes. These results confirm the results of crystal structure analysis and reflect the peculiarities of the
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connectivity and the packing patterns.
3.5. Vibrational characterization. In order to gain an insight into the structure and the nature
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of the interaction between the melamine and 2-, 3- and 4-chlorophenylacetic acid isomers in the crystalline form of supramolecular complexes 1-3, the vibrational spectra were measured and discussed with those of melamine [30] and 2-, 3- and 4-chlorophenylacetic acid isomers [31,32]. Assignment of the IR bands was supported by the spectra of their deuterated analogues. The infrared spectra (protiated and deuterated) and Raman spectra
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(protiated) of 1-3 supramolecular complexes are included in the Supporting Information (Figs. S5-S7). Bands corresponding to the vibration of the functional groups were identified with the aid of infrared and Raman correlation charts [33,34]. Within the investigated supramolecular complexes of melamine with chlorophenylacetic acid isomers with a
neutral)
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composition of 1:2, only in 1 both form of 2-chlorophenylacetic acid units (deprotonated and and the protonated melamin-1-ium residue (MH+) exist, but in 2 and 3 the
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supramolecular complexes are formed via N-H...O and O-H...N hydrogen bonds between neutral melamine and 3- or 4-chlorophenylacetic acid molecules. In addition, only 1 is hydrated complex. Therefore in the vibrational spectra the vibrational bands corresponding to these components should be observed and implies the differences in the vibrational spectra (IR and Raman) of these supramolecular complexes (Figs. S5-S7). In the IR spectrum of 1 the band of the hydrated water molecule that acts as a donor in two O-H...O hydrogen bonds with O…O distances of 2.581(2) Å and as an acceptor also two N-H...O hydrogen bonds with distances of 2.797(2) Å is observed at 3575 cm-1. This band, as expected, is shifted to ~2620 cm-1 in the spectrum of its deuterated analogue (Fig. S5a and S5b), and is absent in 11
ACCEPTED MANUSCRIPT the vibrational spectra of 2 and 3, which are anhydrous (Fig. S6 and S7). The isotopic ratio of 1.364 is consistent with the medium and weak hydrogen bonds in which the water molecule is involved. A careful inspection of the IR spectra of the 1-3 compounds the medium-strong intensity bands in the spectral region of 3500-3000 cm-1observed in the spectra of all compounds are attributed to the asymmetric and symmetric stretching of the three NH2
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groups of the melamine units. The bands of asymmetric stretching νa(NH2) vibrations are observed at higher frequency than the symmetric stretching νs(NH2) bands (Fig. S5a, S6a and S7a). These bands, as expected, are shifted in the spectra of deuterated analogues to the spectral region of 2650-2050 cm-1 (Fig. S5b, S6b and S7b). Theoretical calculation23 of the
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IR spectrum of singly protonated melamin-1-ium residue MH+ shows that shows that additional band with frequency between the νa(NH2) and νs(NH2) is assigned to stretching
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vibration of N–H bond with a proton directly bonded to triazine ring nitrogen atom. This band is not observed in 1 as well as in the spectra of other singly protonated melamin-1-ium slats [35]. The melamin-1-ium cation in crystal 1 and neutral melamine molecule in crystals 2 and 3 are involved in N-H...O and O-H...N hydrogen bonds. These interactions result in the IR spectra of these supramolecular complexes as a broad band in the spectral region of 3300-
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250 cm-1, which is shifted to 2500-2000 cm-1 in the spectra of deuterated analogues. In addition, the broad band in the spectral region of 1600 – 1100 cm-1, which is overlapped with several other bands, point on the presence of this types of N-H...O and O-H...N interactions. The spectra of chlorophenylacetic acid isomers, which in solids form dimeric
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structures with O…O distances of 2.64-2.76 Å show similar bands related with the carboxylic group. The vibration bands of the COOH group contain the C=O, C-O and O-H vibration
AC C
modes. The C=O stretching appears a strong intensity band around 1700 cm-1, while for the O-H involved in the dimers is observed in the frequency region ~3000 cm-1 as a broad band. The vibration bands of deprotonated COO- group is observed at ~1630 cm-1 (νasCOOasymmetric stretching) and at ~1440 cm-1 (νsCOO- symmetric stretching). These bands related with the COO- group are observed in the spectrum of 1, whereas in the spectra of 2 and 3 only bands related with the neutral 3- or 4- chlorophenylacetic acid isomers could be found. The C-H stretching modes of the methylene group (CH2) of the chlorophenylacetic acid isomers are at lower frequencies than those of the aromatic C-H ring stretching. The CH2 antisymmetric stretching vibration appear at higher and CH2 symmetric stretching at lower frequency. These bands are clearly evidenced in the Raman spectra of all supramolecular 12
ACCEPTED MANUSCRIPT complexes around 3000 cm-1 (Fig. S5c,d-S7c,d in SI). The vibrations corresponding to bonding between the ring and chloride (C-Cl) are significant due to possibility of mixing of vibrations on lowering of the molecular symmetry and the presence of heavy atom joined to phenyl ring of the acid isomers. The calculated frequencies of C-Cl are 1011 and 666 cm-1, which well correlate with the values of ~1020 and ~687 cm-1 observed for chlorophenylacetic acid
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isomers [31,32]. These bands could be found in the spectra of 1-3 supramolecular complexes. Conclusion
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In the present contribution the structural study of three supramolecular complexes of melamine with 2-, 3- and 4-chlorophenylacetic acid isomers are described. Within these
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supramolecular complexes only one with 2- chlorophenylacetic acid isomers (1) is ionic, in the other two with 3- and 4-chlorophenylacetic acid isomers (2, 3) the supramolecular complexes are formed between neutral melamine and acid units. Independent of the molar ratio of melamine to chlorophenylacetic acid isomers the formed supramolecular complexes have the same composition of 1:2. In solid-state all supramolecular complexes form one dimensional ribbons. Weak π…π interactions between the ribbons stabilize the
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supramolecular assembly of all complexes. Additionally in 1 the ribbons are interconnected via hydrogen bonds with water molecule. The Hirshfeld surface and the 2D fingerprint plots clearly evidenced the differences in the interactions between the building blocks of the
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supramolecular complexes. The medium and weak N-H...O and O-H...N hydrogen-bonding interactions have been confirmed by vibrational spectroscopy. This work confirms the
AC C
usefulness of melamine as a multiple hydrogen-bonding building blocks in the crystal engineering.
Supplementary Materials
Additional material comprising selected geometrical parameters (Å, o) for 1-3, the XRPD diagrams
for protiated and deuterated analogues of 1-3, Hirshfeld surface and 2D
fingerprint for the acid units of 1-3 and the IR and Raman spectra for protiated and deuterated analogues of 1-3. Full details of the X-ray data collection and final refinement
13
ACCEPTED MANUSCRIPT parameters including anisotropic thermal parameters and full list of the bond lengths and angles have been deposited with the Cambridge Crystallographic Data Center in the CIF format as supplementary publications no. CCDC 1474011-1474013 for 1-3, respectively. Copies of the data can be obtained free of charge on the application to CCDC, 12 Union
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Road, Cambridge, CB21EZ, UK, (fax: (+44) 1223-336-033; email: [email protected] ).
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References
[1] G.R. Desiraju, Chem. Commun., 1997, 1475-1482; G.R. Desiraju, J. Mol. Struct. 2003, 656,
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5-15; L. Brammer, Chem. Soc. Rev. 2004, 33, 476-489; D. Bragga, F. Grepioni, Coord. Chem. Rev., 1999, 183, 19-41; C. Janiak, Dalton Trans. 2003, 2781-2804; N. Shan, M.J. Zaworotko, Drug Discovery Today, 2008, 13, 440-446; A.V. Trask, Mol. Pharma., 2007, 4, 301-309; W. Jones, W.D. Samuel Motherwell, A.V. Trask, MRS Bull., 2006, 31, 875-879. [2] G.R. Desiraju, Crystal Engineering. The Design of Organic Solids; Elsevier, Amsterdam,
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1989; B. Moulton, M.J. Zaworotko, Chem. Rev. 2001, 101, 1629-1658; M.J. Zaworotko, Chem. Commun. 2001, 1-9; G.R. Desiraju, Angew. Chem. Int. Ed., 2007, 46, 8342-8356; S. Varughese, M.S.R.N. Kiran, U. Ramamurty, G.R. Desiraju, Angew. Chem. Int. Ed., 2012, 52,
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667-675; S.L. Price, Acc. Chem. Res., 2009, 42, 117-126. [3] M.J. Krische, J.M. Lehn, Structure Bonding, 2000, 96, 3-29; J.M. Lehn, Angew. Chem. Int. Ed., 1990, 29, 1304–1319; G.R. Desiraju, Acc. Chem. Res., 2002, 35, 565-573; S.C. Zimmerman, P.S. Corbin, Structure Bonding, 2000, 96, 63-94; R.P. Sijbesma, F.H. Beijer, L. Brunsveld, B.J.B. Folmer, J.H.K. Ky Hirschberg, R.F.M. Lange, J.K.L. Lowe, E.W. Meijer, Science, 1997, 278 , 1601-1604; C.-Ch. Cheng, Y.-Ch. Yen, F,-Ch. Chang, RSC Adv., 2011, 1, 1190-1194; M. Ikeda, T. Nobori, M. Schmutz, J.M. Lehn, Chem. Eur. J., 2005, 11, 662668.
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ACCEPTED MANUSCRIPT [4] G.R. Desiraju, Acc. Chem. Res., 1996, 29, 441-449; G.R. Desiraju, T. Steiner, The weak hydrogen bond in structural chemistry and biology; Oxford OUP, 1999; R.E. Melendez, A.J. Carr, B.R. Linton, A.D. Hamilton, Structure Bonding, 2000, 96, 31-61; (d) G.S. Nichol, W. Clegg, Cryst. Growth Des., 2006, 6, 451-460; K. Aoki, M. Nakagawa, T. Seki, K. Ichimura, Bull. Chem. Soc. Jpn., 2002, 75, 2533-2539; M. Ma, D. Bong, Langmuir, 2011, 27, 8841-
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[9] P. Timmerman, L.J. Prins, Eur. J. Org. Chem., 2001, 3191-3205; A. Ranganathan, J. Am. Chem. Soc., 1999, 121, 1752-1753; J.A. Zerkowski, J.C. MacDonald, C.T. Seto, D.A. Wierda, G.M. Whitesides, J. Am. Chem. Soc., 1994, 116, 2382-2391; J.A. Zerkowski, C.T. Seto, G.M.
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Whitesides, J. Am. Chem. Soc., 1992, 114, 5473-5475. [10] T. Kobayashi, A. Okada, Y. Fujii, K. Niimi, S. Hamamoto, T. Yasui, K. Tozawa, K. Kohri,
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Urol. Res., 2010, 38, 117–125; N. Guan, Q. Fan, J. Ding, Y. Zhao, J. Lu, Y. Ai, G. Xu, S. Zhu, Ch. Yao, L. Jiang, J. Miao, H. Zhang, D. Zhao, X. Liu, Y. Yao, New Engl. J. Med., 2009, 360, 1067–1074; R. Reimschuessel, C.M. Gieseker, R.A. Miller, J. Ward, J. Boehmer, N. Rummel, D.N. Heller, C. Nochetto, G.K. Hemakanthi de Alwis, N. Bataller, W.C. Andersen, S.B. Turnipseed, C.M. Karbiwnyk, R.D. Satzger, J.B. Crowe, N.R. Wilber, M.K. Reinhard, J.F. Roberts, M.R. Witkowski, Am. J. Veterinary Res., 2009, 69, 1217-1228; Q. Sun, Y. Shen, N. Sun, G.J Zhang, Z. Chen, J.F. Fan, L.Q. Jia, H.Z. Xiao, X.R. Li, B. Puschner, Eur. J. Pediatr., 2010, 169, 483-489.
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[12] X. Zhang, X. Chen, Cryst. Growth Des., 2005, 5, 617-622; X. Zhang, B. Ye, X. Chen, Cryst. Growth Des., 2005, 5, 1609-1616.
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Des., 2015, 15, 1871-1875.
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Zhu, Acta Crystallogr. Sect. E: Crystallogr. Commun., 2005, 61, o811-o813; J. Janczak, G.J. Perpétuo, Acta Crystallogr. Sect. C: Cryst. Struct. Commun., 2002, 58, o339-o341; J. Janczak, G.J. Perpétuo, Acta Crystallogr. Sect. C: Cryst. Struct. Commun., 2002, 58, o112o114; G.J. Perpétuo, M.A. Ribeiro, J. Janczak, Acta Crystallogr. Sect. E: Crystallogr. Commun., 2005, 61, o1818-o1820; C.S. Choi, R. Venkatraman, E.H. Kim, H.S. Hwang, S.K.
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Kang, Acta Crystallogr. Sect. C: Cryst. Struct. Commun., 2004, 60, o295-o296; J. Janczak, G.J. Perpétuo, Acta Crystallogr. Sect. C: Cryst. Struct. Commun., 2001, 57, 1431-1433; J. Janczak, G.J. Perpétuo, Acta Crystallogr. Sect. C: Cryst. Struct. Commun., 2001, 57, 11201122; I. Karle, R.D. Gilardi, Ch.C. Rao, K.M. Muraleedharan, S. Ranganathan, J. Chem.
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Crystallogr., 2003, 33, 727-749; G.J. Perpétuo, J. Janczak, J. Mol. Struct., 2008, 891, 429436; S. Kohmoto, S. Sekizawa, S. Hisamatsu, H. Masu, M. Takahashi, K. Kishikawa, Cryst.
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Growth Des., 2014, 14, 2209–2217. [15] Oxford Diffraction Poland, CrysAlis CCD and CrysAlis Red, Version 1.171.33.42, 2009. [16] G.M. Sheldrick, Acta Crystallogr. Sect. A: Found. Adv., 2015, 71, 3-8. [17] G.M. Sheldrick, Acta Crystallogr. Sect. C: Cryst. Struct. Commun., 2015, 71, 3-8. [18] K. Brandenburg, H. Putz, DIAMOND Version 3.0, Crystal Impact GbR, Bonn, Germany, 2006. [19] R.C. Hirt, R.G. Schmitt, Spectrochim. Acta, 1958, 12, 127–138. 16
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[23] M. Drozd, M.K. Marchewka, J. Mol. Struct. THEOCHEM, 2005, 716, 175-192. [24] R. Kant, V.K. Gupta, K. Kapoor, B. Narayana, Acta Crystallogr. Sect. E: Crystallogr. Commun., 2012, 68, o1940.
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[27] J.J. MacKimon, M.A. Spackman, A.S. Mitchell, Acta Crystallogr., Sect. B: Struct. Sci., 2004, 60, 627-668.
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Crystal Explorer ver. 3.1, University of Western Australia, Perth, Australia, 2013. [30] W.J. Jones, W.J. Orville-Thomas, Trans. Farady Soc., 1959, 55, 203-210; J.R. Schneider, B. Schrader, J. Mol. Struct., 1975, 29, 1-14; R.J. Meier, A. Tiller, S.A.M. Vanhommerig, J. Phys.
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Chem., 1995, 99, 5457-5464; R.J. Meier, J.R. Maple, M.J. Hwang, A.T. Hagler, J. Phys. Chem., 1995, 99, 5445-5446; N.E. Mircescu, M. Oltean, V. Chiş, N. Leopold, Vib.
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Spectrosc., 2012, 62, 165-171; W.-Ch. Chen, S.-Y. Wu, H.-P. Liu, Ch.-H. Chang, H.-Y. Chen, H.-Y. Chen, Ch.-H. Tsai, Y.-Ch. Chang, F.-J. Tsai, K.-M. Man, P.-L. Liu, F.-Y. Lin, J.-L. Shen, W.Y. Lin, Y.-H. Chen, J. Clin. Lab. Anal., 2010, 24, 92-99.
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ACCEPTED MANUSCRIPT [33] G. Socrates, Infrared Characteristic Group Frequencies; Wiley-Interscience: Chichester, U.K., 1980. [34] G. Socrates, Infrared and Raman Characteristic Group Frequencies Tables and Charts, 3rd ed.; Wiley: Chinchester, West Sussex, England, 2004.
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[35] S. Debrus, M.K. Marchewka, M. Drozd, H. Ratajczak, Opt. Mater., 2007, 29, 1058-1062; M.K. Marchewka, J. Janczak, S. Debrus, J. Baran, H. Ratajczak, Solid State Sci., 2003, 5,
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643-652.
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ACCEPTED MANUSCRIPT 3 C19H20Cl2N6O4 467.31 monoclinic C 2/c 26.6583(15)
b (Å)
10.5687(5)
7.8659(3)
26.6583(15)
c (Å)
34.2869(16)
9.9892(4)
β (o )
90.263(4)
V (Å3)
4321.1(3)
2096.93(14)
Z
8
4
Dcalc/Dobs (g·cm–3)
1.464 / 1.46
1.480 /1.48
μ (mm–1)
0.343
0.350
Crystal size (mm)
0.29 × 0.26 × 0.22
0.31 × 0.27 × 0.23
Radiation, λ (Å)
Mo Kα , 0.71073
Temp. (K)
295(2)
Tmin/Tmax
0.911 / 0.927
θ range, (o)
3.13 ÷ 29.43
Refls collected/
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unique/
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observed
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Table 1. Crystal Data and Structure Refinement for Compounds 1-3. 1 2 Formula C19H21Cl2N6O4.5 C19H20Cl2N6O4 f.w. (g·mol–1) 476.31 467.31 Crystal system monoclinic orthorhombic space group C 2/c Pbcn a (Å) 11.9247(5) 26.6873(11)
10.1176(6) 97.854(6) 2109.6(2) 4
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1.471 / 1.47 0.348
0.33 × 0.28 × 0.23 Mo Kα , 0.71073
295(2)
295(2)
0.905 / 0.932
0.903 / 0.932
3.05 ÷ 29.42
3.09 ÷ 29.22
27371
14029
2776
2665
1406
1543
0.0345
0.0333
0.0206
R[F2>2σ(F2)]
0.0360
0.0322
0.0311
wR(F2) all refls
0.0889
0.0838
0.0791
1.000
1.002
1.002
+0.277; -0.410
+0.207; -0.254
+0.223; -0.294
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Δρmax; Δρmin (e Å–3)
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Mo Kα , 0.71073
wR={Σ [w(Fo2–Fc2)2]/ΣwFo4}½; w–1=1/[σ2(Fo2) + (aP)2] where a is 0.0362 for 1, 0.0385 for 2, 0.0405 for 3, and P = (Fo2 + 2Fc2)/3.
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ACCEPTED MANUSCRIPT Table 2. Hydrogen-bond geometry in 1 (Å,o). D—H 0.84 (1) 0.84 (1) 0.85 (1) 0.85 (1) 0.85 (1) 0.87 (1) 0.85 (1) 0.87 (1) 0.87 (1)
H···A 1.75 (1) 2.06 (1) 1.80 (1) 2.11 (1) 2.66 (2) 2.02 (1) 1.91 (1) 1.94 (1) 2.09 (1)
D···A 2.581 (2) 2.797 (2) 2.642 (2) 2.958 (2) 3.295 (2) 2.878 (2) 2.750 (2) 2.796 (2) 2.923 (2)
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Symmetry codes: (i) −x+2, y, −z+1/2; (ii) x+1/2, y−1/2, z.
Table 3. Hydrogen-bond geometry in 2 (Å,o). D—H 0.83 (1) 0.87 (1) 0.86 (1) 0.86 (1)
Symmetry code: (i) x, y+1, z.
H···A 1.75 (1) 2.01 (1) 2.61 (1) 2.04 (1)
D···A 2.574 (2) 2.863 (2) 3.257 (2) 2.875 (2)
D—H···A 171 (2) 169 (1) 133 (1) 165 (2)
D···A 2.594 (2) 2.864 (1) 3.277 (2) 2.872 (2)
D—H···A 167 (2) 177 (1) 138 (1) 171 (1)
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D—H···A O2—H2O···N2 N3—H31···O1i N3—H32···O2 N4—H41···O1
D—H···A 167 (3) 146 (2) 172 (2) 173 (2) 133 (2) 170 (2) 173 (2) 170 (2) 162 (2)
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D—H···A O12—H12···N2 O1—H1···O21ii N3—H3···O21 N4—H4A···O11ii N4—H4B···O12 N5—H5A···O11 N5—H5B···O22 N6—H6A···O22ii N6—H6B···O1
D—H 0.83 (1) 0.87 (1) 0.85 (1) 0.87 (1)
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D—H···A O2—H2O···N2 N3—H31···O1 N4—H41···O2 N4—H42···O1i
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Table 4. Hydrogen-bond geometry in 3 (Å,o).
H···A 1.78 (1) 2.00 (1) 2.60 (1) 2.01 (1)
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Symmetry code: (i) x, y−1, z.
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Figure 1. View of molecular structure of 1 with displacement ellipsoids at the 50% probability level (a), hydrogen-bonded ribbon of 1 (b) and the packing pattern demonstrating the inter-ribbon interactions (c). Dashed lines represent N−H…O, O-H...N and O-H...O hydrogen bonds.
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(c) Figure 2. View of molecular structure of 2 with displacement ellipsoids at the 50% probability level (a), hydrogen-bonded ribbon of 1 (b) and the packing pattern demonstrating the inter-ribbon interactions (c). Dashed lines represent N−H…O, O-H...N and O-H...O hydrogen bonds. 22
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(a)
(c) Figure 3. View of molecular structure of 3 with displacement ellipsoids at the 50% probability level (a), hydrogen-bonded ribbon of 3 (b) and the packing pattern demonstrating the inter-ribbon interactions (c). Dashed lines represent N−H…O, O-H...N and O-H...O hydrogen bonds. 23
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(d) Figure 4. The Hirshfeld surface mapped with a dnorm function and the 2D fingerprint for the
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melamin-1-ium cation in 1 (a) and for melamine in 2 (b) and 3 (c), and the percentage contributions from major intermolecular interactions to the Hirshfeld surfaces (d).
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ACCEPTED MANUSCRIPT Highlights
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► Supramolecular complexes of melamine with chlorophenylacetic acid isomers are obtained. ► Hydrogen bonding R22(8) motif forms supramolecular complexes. ► Hirshfeld surface and 2D fingerprint plots have been analysed. ► The characteristic vibrational bands of the H and D analogues are discussed.