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The study of crystal structures and vibrational spectra of inorganic salts of 2,4-diaminopyrimidine
Journal of Molecular Structure 1103 (2016) 82e93
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Journal of Molecular Structure journal homepage: http://www.elsevier.com/locate/molstruc
The study of crystal structures and vibrational spectra of inorganic salts of 2,4-diaminopyrimidine a, Jana Mathauserova a, Ivana Císarova a, Ivan Ne mec a, *, Jan Fa bry b Irena Matulkova a b
Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 128 43 Praha 2, Czech Republic Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Praha 8, Czech Republic
a r t i c l e i n f o
a b s t r a c t
Article history: Received 26 June 2015 Received in revised form 12 August 2015 Accepted 2 September 2015 Available online 9 September 2015
Six novel salts of 2,4-diaminopyrimidine were prepared and studied by X-ray single-crystal structure analysis and vibrational spectroscopy. All but one of the title compounds, i.e. (2,4-diaminopyrimidine) 2,4-diaminopyrimidinium perchlorate, 2,4-diaminopyrimidinium nitrate, 2,4-diaminopyrimidinium perchlorate, bis(2,4-diaminopyrimidinium) hydrogen phosphate tetrahydrate and bis(2,4-diamino pyrimidinium) selenate dihydrate, crystallize in the triclinic system with the centrosymmetric space group P1 while the crystals of the remaining compound e 2,4-diaminopyrimidinium chloride hemihydrate e belong to the monoclinic system (space group C2/c). All the crystal structures contain the characteristic graph set motif R22 (8) with NeH… N hydrogen bonds. This graph set motif can be formed by one of three possible arrangements of a pair of 2,4-diaminopyrimidinium cations and all these arrangements have been observed in the title structures. The title salts were also investigated by vibrational spectroscopy (FTIR and FT Raman). The presented interpretation of the vibrational spectra is based on DFT calculations of 2,4-diaminopyrimidine molecule and 2,4-diaminopyrimidinium cation. © 2015 Elsevier B.V. All rights reserved.
Keywords: 2,4-diaminopyrimidine 2,4-diaminopyrimidinium Crystal structure Hydrogen bonds Crystal engineering Vibrational spectroscopy DFT calculations
1. Introduction The crystal engineering is a general branch of supramolecular chemistry, which covers processes of purposeful design of functional three-dimensional crystal structures from molecule-scale components. It actually represents one of the most promising fields of the design of novel materials with desired properties. However, the synthesis of crystals is a much more difficult process to control since it involves manipulation of simultaneous effects of long- and short-range interactions while kinetic effects are difficult to take into account. Hydrogen bonds and dipolar interactions may play most important role in interconnection of synthons. Formation of a crystal from molecules and ions depends not only on symmetry and size of the molecules involved but mainly on intermolecular (supramolecular) interactions, which control mutual assembly of building blocks. From the whole range of these interactions of a different nature (i.e. particularly ioneion interactions, ionedipole interactions, dipoleedipole interactions, cationep interactions, anionep interactions, pep interactions and the van der Waals forces) the hydrogen bonds can be considered as
* Corresponding author. mec). E-mail address: [email protected] (I. Ne http://dx.doi.org/10.1016/j.molstruc.2015.09.002 0022-2860/© 2015 Elsevier B.V. All rights reserved.
the most important and powerful ones, which are sometimes classified as dipoleedipole interactions. Hydrogen bonds can also act as effective means how to override tendency of organic bases with high dipole moments to form centrosymmetric pairs. 2,4-diaminopyrimidine and its derivatives are successfully used in the field of medical research. They can act as antagonists of allergic rhinitis or solid tumours [1,2], inhibitors of cancer cells [3], antifilarial agents [4] and DNA modificators [5e7]. But only one crystal structure containing 2,4-diaminopyrimidinium cation with inorganic acid is present in the Cambridge Structural Database [8]. This is the crystal structure of bis(2,4-diaminopyrimidinium) sulphate monohydrate [9] (REFCODE TEGZIO). This work is a part of our project which is focused on preparation and study of new materials with potential non-linear optical (NLO) properties. We are mainly interested in compounds which are composed of heteroaromatic nitrogen-containing organic bases and inorganic oxyacids and where variety of hydrogen bonds is expected. The formation of crystalline salts with different anionic species (ranging from simple chlorides to planar nitrates or tetrahedral sulfates, selenates, perchlorates or phosphates), which also differ in their role as proton donors/acceptors, can lead to noncentrosymmetric phases which are suitable for nonlinear optics [10e21]. Unfortunately, all the title structures are centrosymmetric
et al. / Journal of Molecular Structure 1103 (2016) 82e93 I. Matulkova
and therefore our attention has been focused mainly on crystallographic and spectroscopic point of aspects. The other motivation for this paper has been the fact that the description of different arrangements of the title cation in the solid state has been neglected. This cation is also interesting for investigation of the configuration of the primary-amine group [22]. The Cambridge Structural Database yielded only five crystal structures containing diaminopyrimidinium cations with the following REFCODES: DICCOJ e 2,3-diaminopyrimidinium 4-nitrophenol 4nitrophenolate [23]; TEGZIO e bis(2,4-diaminopyrimidinium) sulphate monohydrate [9]; TEGZIO01 e hydroxonium bis(2,4diaminopyrimidinium) phosphate [24]; WUJROI e 2,6-diamino pyrimidinium 1,3-cyclopentanedionate monohydrate [25] and WUJRUO e 2,6-diaminopyridinium 1,3-cyclohexanedionate 1,3cyclohexanedione enol monohydrate [25]. Very questionable crystal structure of TEGZIO01 surprisingly exhibits the same lattice parameters and the positional parameters of the non-hydrogen atoms as TEGZIO. Therefore TEGZIO01 has been excluded from other considerations and discussion. The present study is focused on crystal structures and vibrational spectra of six new compounds: 2,4-diaminopyrimidinium chloride hemihydrate (dapClH2O), (2,4-diaminopyrimidine) 2,4diaminopyrimidinium perchlorate (dap2ClO4), 2,4-diamino pyrimidinium perchlorate (dapClO4), 2,4-diaminopyrimidinium nitrate (dapNO3), bis(2,4-diaminopyrimidinium) selenate dihydrate (dap2SeO42H2O) and bis(2,4-diaminopyrimidinium) hydrogen phosphate tetrahydrate (dap2HPO44H2O). 2. Experimental The products derived from 2,4-diaminopyrimidine (dap, Aldrich 98%) were obtained by crystallization of reaction mixtures prepared by dissolving dap in 20e50 mL of distilled water and adding the corresponding amount of 2 mol/L of acid solution (hydrochloric, perchloric, nitric, selenic and phosphoric). The molar ratio (base: acid) was chosen to follow the expected stoichiometry of the potential products. After slow evaporation of water at room temperature, the products were colourless crystals of dapClH2O (starting molar ratio 1: 1), dap2ClO4 (starting molar ratio 1: 1), dapClO4 (starting molar ratio 1: 2), dapNO3 (starting molar ratio 1: 1), dap2SeO42H2O (starting molar ratios 1: 1 and 2: 1), and dap2HPO44H2O (starting molar ratio 2: 1). The obtained crystals were filtered off and dried in air. Single-crystal X-ray diffraction data of dapClH2O, dap2ClO4, dapClO4, dapNO3, dap2SeO42H2O and dap2HPO44H2O were collected on a Nonius Kappa diffractometer (MoKa radiation, graphite monochromator) equipped with Bruker APEX-II CCD array detector (computing programs SAINT [26], Diamond [27], PLATON [28]). The temperature of each sample was controlled by an Oxford Cryosystems liquid nitrogen Cryostream cooler. The phase problem was solved by direct methods (SIR-97 software [29]) and the nonhydrogen atoms were refined anisotropically, using the fullmatrix least-squares procedure (SHELXL-97 [30] and JANA2006 software [31] into which extinction correction by Becker & Coppens [32] is included). For all the title structures, the difference electron density maps revealed all the hydrogens. There have been tested various refinement models with different constraints and restraints regarding the hydrogens' parameters. Therefore, the treatment of the hydrogens can differ in the respective structures, nevertheless, in all the cases the aryl hydrogens were constrained with CaryleH ¼ 0.94 Å and Uiso(H) ¼ 1.2Ueq(Caryl) assuming trigonal configuration of the carrier carbon atom. The detailed refinement of hydrogen atoms in the title crystal structures is included into the Supplementary materials. The basic crystallographic data, measurement and refinement details are summarized in Table 1. The
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selected bond lengths and angles, including those of hydrogen bonds, are presented in Supplementary materials, Tables 1Se6S Crystallographic data for dapClH2O, dap2ClO4, dapClO4, dapNO3, dap2SeO42H2O and dap2HPO44H2O have been deposited with the Cambridge Crystallographic Data Centre as supplementary publications CCDC 1406427, CCDC 1406428, CCDC 1406431, CCDC 1406432, CCDC 1406430 and CCDC 1406429, respectively. Copies of the data can be obtained free of charge on application to CCDC, 12 Union Road, Cambridge CG21, EZ, UK (fax: (44) 1223-336-033; email: [email protected]). The phase purity of the prepared polycrystalline samples was also controlled by powder X-ray diffraction at room temperature using the Bragg-Brentano geometry on a Philips X'pert PRO MPD Xray diffraction system equipped with an ultra fast X'Celerator detection using Cu-anode (Cu-Ka; l ¼ 1.5418 Å). Recorded diffraction patterns (see Tables 7Se13S; Supplementary materials) are consistent with the calculated diffraction maxima (FullProf software [33]). The infrared spectra were recorded using nujol and fluorolube mulls (KBr windows) technique on a Nicolet 6700 FTIR spectrometer with 2 cm1 resolution and Happ-Genzel apodization in the 400e4000 cm1 region. The FAR IR spectra were recorded down to 50 cm1 (4 cm1 resolution, Solid Substrate™ beamsplitter, DTGS detector, Happ-Genzel apodization) in PE pellets. The Raman spectra of the polycrystalline samples were recorded at room temperature on a Nicolet 6700 FTIR spectrometer equipped with the Nicolet Nexus FT Raman module (2 cm1 resolution, Happ-Genzel apodization, 1064 nm Nd:YVO4 laser excitation, 450 mW power at the sample) in the 150e3700 cm1 region. Quantum-chemical calculation (GAUSSIAN09W [34]) of 2,4diaminopyrimidine and 2,4-diaminopyrimidinium (1þ) cation was performed employing the closed-shell restricted density functional method (B3LYP) with the 6-311þG(d, p) basis set. The visualization of the results was carried out with the GaussView [35] program package. The geometry optimizations, also yielding the molecular energies, were followed by frequency calculations together with IR intensities and Raman activities using the same method and the basis set. The optimal scaling scheme for calculated frequencies was inferred from comparison of results, which were obtained by application of WLS (Wavenumber-Linear Scale) procedure [36] and dual scaling [37] procedures with the experimental values recorded for dap base or dapClH2O. The spectra were analysed in terms of the PED (Potential Energy Distribution) contributions by using the VEDA (Vibrational Energy Distribution Analysis) program [38]. The theoretical Raman intensities of the computed normal modes were calculated (RAINT program [39]) for 1064 nm excitation wavelength taking Raman scattering activities from the Gaussian output. 3. Results and discussion 3.1. Crystal structures In the title structures, the most intriguing feature is the hydrogen bond pattern between 2,4-diaminopyrimidine or 2,4diaminopyrimidinium molecules and different anions, which have a varying ability to act as hydrogen-bond acceptors. For example, the excess of the donating hydrogens in 2,4diaminopyrimidinium chloride hemihydrate with respect to the chloride anion can be mitigated by the involvement of the water molecules into this structure. 2,4-diaminopyrimidinium has two primary amine groups involving atoms N3 and N4 as well as N1 or N2 atoms, which are part of the aromatic ring. N1 tends to be hydrogenated in a sufficiently acid environment and N2 can act as a hydrogen bond
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Table 1 Basic crystallographic data and structure refinement details of dapClH2O, dap2ClO4, dapClO4, dapNO3, dap2HPO44H2O and dap2SeO42H2O salts. Chemical formula Mr Crystal system, space group Temperature (K) a, b, c (Å)
a, b, g ( )
C8H13N8$ClO4 320.7 Triclinic, P-1 150 5.8370 (2) 8.2675 (3) 13.8279 (5) 86.715 (2) 86.782 (2) 89.538 (2) 665.14 (14) 2 332 Mo Ka 0.32 1.601 Colourless, needle 0.42 0.38 0.14 5172, 5.895, 55.10
C4H7N4$NO3 173.1 Triclinic, P-1 150 3.5981 (3) 9.7412 (7) 10.5523 (8) 73.658 (4) 87.077 (4) 86.416 (4) 354.00 (5) 2 180
C4H7N4$ClO4 210.6 Triclinic, P-1 150 5.8754 (2) 8.1800 (3) 9.0878 (4) 113.351 (1) 100.109 (1) 92.150 (1) 391.99 (3) 2 216
C8H14N8$PO4H$4H2O 390.3 Triclinic, P-1 150 6.4965 (3) 10.7603 (6) 12.598 (6) 82.956 (2) 88.907 (2) 77.985 (2) 854.84 (7) 2 412
V (Å3) Z F (000) Radiation type 0.14 0.48 0.22 m (mm1) rX-ray (gcm3) 1.624 1.784 1.516 Crystal description Colourless, needle Colourless, prism Colourless, prism Crystal size (mm) 0.41 0.08 0.04 0.62 0.38 0.27 0.42 0.38 0.21 995, 8.054, 51.56 4520, 2.731, 27.65 4600, 2.688, 27.55 Number of diffractions for the cell determination, qmin, qmax Diffractometer Bruker APEX-II CCD diffractometer Monochromator graphite Measurement method 4 and uscans Absorption correction Multi-scan SADABS [26] Tmin, Tmax 0.879, 0.955 0.946, 0.994 0.756, 0.881 0.911, 0.955 No. of measured, independent and observed 8195, 3053, 2644 3848, 1405, 858 5751, 1804, 1675 9121, 3948, 3268 [I > 3s(I)] reflections Rint/Robs 0.026/0.024 0.030/0.046 0.013/0.012 0.018, 0.025 qmin, qmax, completeness 2.47, 27.65, 0.98 2.01, 26.10, 0.99 2.50, 27.57, 0.99 1.63, 27.55, 1.00 1 (sin q/l)max (Å ) 0.653 0.619 0.651 0.651 Weighting scheme 1/(s2(I) þ 0.0004I2) R [F2 > 3s(F2)], 0.0369 0.0413 0.0277 0.0365 wR [F2 > 3s(F2)], 0.1004 0.0812 0.0922 0.0836 R[all] 0.0425 0.8 0.0299 0.0469 wR[all] 0.1024 0.0893 0.093 0.087 S [all] 2.49 1.56 3.2 2.03 2 2 S [F > 3s(F )] 2.64 1.87 3.3 2.17 No. of reflections (all) 3053 1405 1804 3948 No. of parameters 222 124 133 284 No. of constraints 25 13 13 35 No. of restraints 10 5 5 19 H-atom treatment H atoms treated by a mixture of independent and constrained refinement 3 Drmax, Drmin (e Å ) 0.32, 0.45 0.25, 0.26 0.28, 0.41 0.46, 0.48 Extinction method none none none type 1 Lorentzian isotropic [32] Extinction coefficient 1600 (400)
acceptor. Thus 2,4-diaminopyrimidinium has five hydrogens to offer into the hydrogen bond pattern and one ring nitrogen atom to accept the hydrogen bond. Moreover, the primary amines can also be involved into the hydrogen bond pattern as hydrogen bond acceptors. All the crystal structures exhibit a characteristic graph set motif [40,41] R22 (8) with NeH…N hydrogen bonds, which can be formed by three possible arrangements of a pair of the 2,4diaminopyrimidinium cations (Fig. 1), and all these arrangements
C4H7N4$Cl$0.5H2O 155.6 Monoclinic, C2/c 150 20.4070 (9) 5.0299 (2) 16.5030 (6) 90 125.064 (1) 90 1386.52 (10) 8 648
C8H14N8$SeO4$2H2O 401.2 Triclinic, P-1 150 6.8859 (4) 10.5955 (6) 11.5092 (7) 70.058 (3) 77.205 (3) 89.237 (2) 767.98 (8) 2 408
0.48 1.491 Colourless, prism 0.40 0.31 0.29 5294, 3.016, 27.44
2.49 1.735 Colourless, plate 0.20 0.17 0.03 2267, 3.040, 26.64
0.829, 0.871 5306, 1609, 1344
0.637, 0.922 8880, 3539, 2598
0.026/0.023 2.44, 27.63, 0.99 0.653
0.045/0.067 1.93, 27.60, 0.99 0.652
0.0267 0.0684 0.0347 0.0711 1.74 1.84 1609 105 14 1
0.0374 0.0667 0.0595 0.0751 1.16 1.21 3539 254 26 7
0.25, 0.24 none
0.45, 0.37 none
have been observed among the title structures. The forms (I) and (II) are compatible with the centre of symmetry in difference to the form (III), and, indeed, they are truly centrosymmetric in the title structures where they occur. The motif (I) is present in dap2ClO4, dapClO4, and dapClH2O, the motif (II) in dapNO3 while the motif (III) has been found in dap2HPO44H2O as well as in dap2SeO42H2O. In the above mentioned already determined structures there are known forms (I) for WUJROI [25] and (II) for DICCOJ [23] as well as for TEGZIO [9]. WUJRUO [25] seems to be exceptional because there
Fig. 1. Possible schemes of the formation of motifs R22 (8) by a pair of NeH…N hydrogen bonds between two 2,4-diaminopyrimidinium ions.
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Fig. 2. Packing scheme of the dap2ClO4 (view along [100] direction). The dashed lines indicate the hydrogen bonds.
is no motif (I), (II) or (III) present in its structure. Instead of that there are NeH…O hydrogen bonds. In addition to the hydrogen bonds, there are p-electron…pelectron ring interactions in all the structures except for dapClH2O. The crystal structure of dap2ClO4 (Fig. 2 and 2S; Supplementary
materials) is the most interesting structure because the secondary amine hydrogen acts as a bridging hydrogen between 2,4diaminopyrimidine molecule and 2,4-diaminopyrimidinium cation (Table 1S; Supplementary materials). This hydrogen is displaced towards the centre of the connecting line N1…N5 and is
Fig. 3. Packing scheme of the dapNO3 (view along [100] direction). The dashed lines indicate the hydrogen bonds.
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Fig. 4. Packing scheme of the dapClO4 (view along [100] direction). The dashed lines indicate the hydrogen bonds.
disordered between two positions (Figs. 1S and 3S; Supplementary materials) in unequal occupancies. The hydrogen bonds connecting N4…N5 are of moderate strength and are the strongest ones in the title structure. Presence of the centred N…H…N hydrogen bond is relatively rare. The Cambridge Structural Database indicated 22 hits of such structures. Moreover, there have also been indicated some suspicious structures where the pertinent hydrogen was incorrectly attached and constrained to one of the nitrogens involved. Among them was cytosiniumehydrogen maleateecytosine (1/1/1) with
the REFCODE DUJCAN, which corresponds to the publication by Benali-Cherif et al. [42]. The recalculation detected an ill-positioned hydrogen. The recalculation yielded similar splitting of the hydrogen bond as in dap2ClO4 and its improved structure determination is going to be reported elsewhere. The graph-set motif NeH…N is formed by the primary amine hydrogens in dap2ClO4 structure. The hydrogen bonds involved in this graph set motif are of moderate strength. The hydrogen bonds NeH…O are rather weak (Fig. 3S and Table 1S; Supplementary materials). The graph set motifs R22 (8) with NeH…N hydrogen
Fig. 5. Packing scheme of the dap2HPO44H2O (view along [010] direction). The dashed lines indicate the hydrogen bonds.
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Fig. 6. Packing scheme of the dap2Cl2H2O (view along [010] direction). The dashed lines indicate the hydrogen bonds.
bonds of a moderate strength [43] are truly centrosymmetric of the type (I) (Fig. 2). The NeH…O bonds are slightly longer, exceeding a little bit 3.2 Å which is considered to be a limit for distinguishing the hydrogen bonds of the moderate strength from the weak ones [43]. Cf. dapClO4 where the NeH…O bonds are substantially weaker. In dapNO3 (Fig. 3), the motif R22 (8) with the NeH…N is of the type (II) and is truly centrosymmetric (Figs. 4S and 5S, Table 2S; Supplementary materials). The hydrogen bond pattern also contains NeH…O hydrogen bonds of the moderate strength which are involved in the graph set motifs R22 (8), R24 (8) and R33 (10).
In dapClO4 (Fig. 4), there is present a truly centrosymmetric motif R22 (8) of the type (I) with NeH…N hydrogen bonds of the moderate strength (Figs. 6S and 7S; Supplementary materials). The NeH…O hydrogen bonds are weak and bifurcated (Fig. 7S and Table 3S; Supplementary materials). In dap2HPO44H2O (Fig. 5), there are present two motifs R22 (8) of the type (III) between symmetry independent molecules with NeH…N hydrogen bonds of both moderate and weak strength (Figs. 8S and 9S, Table 4S; Supplementary materials). It is of interest that the molecules involved in this interaction are symmetry independent. Concomitantly, these hydrogen bond motifs are not
Fig. 7. Packing scheme of the dap2SeO42H2O (view along [100] direction). The dashed lines indicate the hydrogen bonds.
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centrosymmetric. There are NeH…O and OeH…O hydrogen bonds of moderate strength in the structure. The shortest hydrogen bond in the structure is N1eH1N1…Ow3. In dapClH2O (Fig. 6), there is present a truly centrosymmetric motif R22 (8) of the type (I) with NeH…N hydrogen bonds of a moderate strength (Figs. 10S and 11S; Supplementary materials). There are also present NeH…Cl and OwatereH…Cl hydrogen bonds (Table 5S; Supplementary materials). There is a motif NH2…Cl… HeOwatereH…Cl…H2N in the structure, in which Cl atoms are acceptors of four hydrogen bonds. Water is situated at the special position being on the two-fold axis. Crystal structure of dap2SeO42H2O (Fig. 7) contains a motif R22 (8) of the type (III) with moderate and weak NeH…N hydrogen bonds (Figs. 12S and 13S, Table 6S; Supplementary materials) There are NeH…O and OeH…O moderate and weak hydrogen bonds in the structure. 3.2. Vibrational spectroscopy FTIR and FT Raman spectra of the investigated dap-based compounds have been recorded at room temperature and the results are presented in Figs. 8 and 9 and Tables 2e7. The assignment of the spectra is based on the calculation of the vibrational spectra of an isolated dap molecule and its cation dap(1þ) - see Tables 15Se19S (Supplementary materials). The presented data confirm that WLS procedure [36] is the best approach for the scaling of the calculated frequencies of 2,4-diaminopyrimidine and 2,4-diaminopyrimidinum (1þ) cations. The interpretation of the
Fig. 9. FT Raman spectra of dapClH2O, dap2ClO4, dapClO4, dapNO3, dap2HPO44H2O and dap2SeO42H2O salts.
Fig. 8. FTIR spectra (compiled from nujol and fluorolube mulls) of dapClH2O, dap2ClO4, dapClO4, dapNO3, dap2HPO44H2O and dap2SeO42H2O salts.
bands of stretching and out-of-plane bending vibrations of the NeH and OeH groups involved in the hydrogen bonds arises from the correlation curves [44,45] concerning the appropriate band positions and the hydrogen bond lengths. It is obvious that B3LYP/6-311þG(d,p) calculations provide frequencies which reasonably match the experimental ones. The only discrepancies refer to the NeH stretching modes spectral region (3150e3500 cm1 for dap and 3400e3500 cm1 for dap(1þ)). The reason for these differences follows from the fact that the formation of NeH…X (X ¼ N, O or Cl) hydrogen bonds has not been considered in the calculations for the isolated molecule/cation in vacuum. The overall character of the spectra of dap molecule and dap(1þ) cation is very similar e see Figs. 8 and 9. The main difference can be observed in the 2000e3500 cm1 region in the IR spectra due to the different hydrogen bonding patterns. The other difference can be observed in the position, shape and splitting of the bands of the 2,4-diaminopyrimidine skeleton in the Raman spectra, see Fig. 10. The positions of several characteristic ring vibrations bands of pure dap base and its cation (in dapClH2O) are slightly shifted. The first example is a strong dap band at 791 cm1 (dap(1þ) e 784 cm1) which can be attributed to the ring out-ofplane and out-of-plane CeH vibrations in the Raman spectra. Also, two bands can be observed in the 600e500 cm1 region in the Raman spectra of pure dap in contrast to three bands in the spectra of dapClH2O. The first two bands (601 and 558 cm1 e dap; 589 and 554 cm1 e dapClH2O) can be assigned to the deformation vibration of the pyrimidine ring while the band at 516 cm1
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Table 2 Experimental FTIR and FT Raman wavenumbers (cm1) of dapClH2O and their assignment. FTIR
FT Raman
Assignment
FTIR
FT Raman
Assignment
3323 sb 3150 sb
3304 3162 3082 3066
n NeH n CH n CH, n NeH(…N) n CH n NeH(…O)
1170 m 1121 m 1049 m 987 m 863 mb 826 s 780 s 764 s 722 sh 706 sb 647 sb 598 s 581 sh 546 s 510 sh 436 m 400 m 238 m 220 m 201 m 161 m 151 w 127 m 109 w 71 m
1174 w 1118 m 1043 w 984 s 863 w 828 w 784 vs
r NH2, d CH, d rg d rg, d CH, d NH r NH2 g CH, g rg r NH2, d CH, d rg g CH, g rg g rg, g CH
3066 2954 2907 2846 2646 2512 2444 2379 2192 2153 1966 1764 1683
s s s s m w w w wb wb m w s
1660 1633 1578 1525 1517 1464 1400 1341 1250
s s m sh s m m m m
wb wb m m
Combinational modes
d NH2, n CN, n rg(CN) 1681 1670 1651 1627
m m m m
1526 1508 1466 1397 1341 1249
m w w s s m
d NH2, n CN, n rg(CC) d NH2, n CN, n rg d NH2, d NH d NH2, n CN, d CH, d rg n rg (CC), d CH, r NH2 n rg, d CH, d NH g NH, n rg(CN) d CH, d NH, d rg d CH, d NH, d rg
g NH, t NH2, g rg d rg 589 554 516 436 387 227
s m m w m m
ds rg g NH, t NH2 t NH2, g CH, g rg r NH2 u NH2, gs rg External modes
Note: Abbreviations and symbols: vs, very strong; s, strong; m, medium; w, weak; b, broad; sh, shoulder; n, stretching; d, deformation or in-plane bending; g, out-of-plane bending; r, rocking; u, wagging; t, torsion; s, symmetric; as, antisymmetric.
(dapClH2O) can be assigned to the g NH and t NH2 vibrations. The medium intensity bands recorded at 1397, 1341, 1118 and 984 cm1 in the Raman spectrum of dapClH2O can be assigned to the g NH, n rg(CN); d CH, d NH, d rg; d rg, d CH, d NH and g CH, g rg vibrations, respectively. The medium intensity bands at 1371, 1265, 1115 and 974 cm1 found in the Raman spectrum of dap molecule can be assigned to d NH2, n CN, d rg, d CH; n rg(CN), d CH, u NH2; d CH, n rg(CC) and g rg vibrations, respectively. The detailed assignment of the vibrational spectra of pure dap base and dap(1þ) in dapClH2O are listed in Tables 2 and 19S (Supplementary materials). The comparison of vibrational manifestations of the molecule and its mono-protonated cation can be particularly interesting in the case of dap2ClO4 where both forms should be present e see Fig. 10 and Table 3. Surprisingly dap2ClO4 spectrum (see Fig. 10) manifests in principle presence of just one “intermediate” form of
2,4-diaminopyrimidine skeleton rather than features of both expected forms. However, this feature is fully in accord with the formation of disordered bridging hydrogen bond between 2,4diaminopyrimidine molecule and 2,4-diaminopyrimidinium cation (leading to their considerable structural “similarity”) in the crystal structure of dap2ClO4. Characteristic strong IR bands recorded at 1135, 1108 and 1055 cm1 (Raman 1046, 1122 and 1133 cm1) in the spectrum of dapClO4, and the strong structured band with the maxima at 1096 and 1046 cm1 (Raman 1042, 1090 and 1122 cm1) in dap2ClO4 (partially mixed with vibrational manifestation of dap e i.e. r NH2, d CH, n rg(CC), d NH and d rg vibrations) correspond to the n3 perchlorate vibrations. Dominant, very strong Raman bands at 935 cm1 (dap2ClO4) and 925 cm1 (dapClO4) (very weak in the IR spectra at 934 and 924 cm1) were assigned to the symmetric
Table 3 Experimental FTIR and FT Raman wavenumbers (cm1) of dap2ClO4 and their assignment. FTIR 3434 3360 3338 3166
FT Raman m m m mb
Assignment
FTIR
FT Raman
Assignment
n NeH(…O)
1046 mb 1000 sh
n CH, n NeH(…N)
935 vw
v3 ClO 4 , r NH2 g CH, g rg, r NH2, d rg g rg v1 ClO 4
Combinational modes
815 m 804 m 777 m
1042 w 989 m 978 m 935 vs 909 w 812 w
3382 vw
3092 m 1994 1931 1660 1632 1598 1552 1501 1456 1390
wb w sb sb sh mb m s mb
1256 m 1166 sh 1096 sb
1657 1636 1604 1555 1507 1466 1385 1337 1255 1184 1122 1090
m m m vw m vw s m m w m w
d NH2, n CN, n rg, d rg d NH2, d NH d NH2, d rg d rg, d NH2 n rg(CC), d CH, r NH2 d CH, d NH, d rg d NH2, n CN, d rg, d CH d CH, d NH, d rg n rg(CN), d CH, u NH2 r NH2, d CH v3 ClO 4 , d rg, d NH, d CH v3 ClO 4
689 627 602 573 506 458 436 372 228 207
mb m w w mb w wb m m w
787 vs 714 vw 626 594 573 503 457 437 366 229 218
m s m m m w m vw m
?
d rg g rg, g CH g CH, g rg d rg
v4 ClO 4 t NH2, g CH, g NH, d rg d rg g NH, t NH2 v2 ClO 4 , r NH2 t NH2, g CH, g rg u NH2 u NH2, gs rg u NH2, d rg
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Table 4 Experimental FTIR and FT Raman wavenumbers (cm1) of dapClO4 and their assignment. FTIR 3443 3371 3349 3311 3292 3239 3159 3104 2980 1952 1681 1664
s m m m m m mb m sh vw s s
1625 m 1611 m 1515 m
1378 1341 1311 1236
w w vw m
1136 s 1108 s 1055 s
FT Raman
Assignment
FTIR
3446 w 3375 w
n NH(…O)
987 962 933 925
n CH, n NeH(…N) n CH
3153 wb 3106 m
820 m 780 w 765 m
Combinational modes 1950 1691 1656 1641
vw w m m
1612 1508 1452 1429 1381 1344
m m w w m m
1237 1178 1132 1122
w w sh m
vw w w w
d NH2, n CN, n rg(CC) d NH2, n CN, n rg
669 mb
?
623 s 602 m 591 m 550 m 507 w 478 wb 467 w 454 w 430 m 377 m 225 m 195 w 124 m 115 m 75 m
d NH2, d NH ?
n rg(CC), d CH, r NH2 n rg, d CH, d NH ?
g NH, n rg(CN) d CH, d NH, d rg ?
d CH, d NH, d rg r NH2, d CH, d rg
v3 ClO 4
1046 wb
stretching vibration (n1 ClO 4 ) of the anion. Medium intensity IR bands at 627 cm1 (broad Raman band at 626 cm1) and 623 cm1 (Raman 631 and 621 cm1) in the infrared spectra of dap2ClO4 and dapClO4, respectively, were assigned to the n4 ClO 4 vibration. The n2 ClO 4 vibrations can be attributed to the weak bands at 458 and 466 cm1 in the IR spectra (dap2ClO4 and dapClO4) and one band at 457 cm1 (dap2ClO4) or two bands at 466 and 456 cm1 (dapClO4) in the Raman spectra. In these cases, the observed factor group splitting is quite consistent with the results of the correlation analysis presented in Table 20S (Supplementary materials). Table 4 contains the assignment of the other vibrational bands of dapClO4. Strong bands recorded at 1385 and 1339 cm1 in the IR spectrum of dapNO3 (the medium intensity Raman band at 1404 cm1
FT Raman
Assignment
986 967 933 925 909 858 825 784
m w s vs m w w vs
g CH, g rg ? v1 ClO 4
713 663 631 621
vw vw m m
?
r NH2, d CH, d rg g CH, g rg g rg, g CH ?
586 s 555 s 503 m 466 456 429 370 231 207
m m vw m w w
g rg, g CH g NH, t NH2, g rg v4 ClO 4
t NH2, g CH, g NH d rg ds rg g NH, t NH2 u NH2 v2 ClO 4
t NH2, g CH, g rg r NH2 u NH2 u NH2, gs rg External modes
e mixed with g NH and n rg(CN) vibrations of dap cation) correspond to the n3 nitrate vibrations. A very strong band at 1051 cm1 in the Raman spectrum and the medium intensity band at 1050 cm1 in the IR spectrum correspond to the symmetric stretching vibrations of anion (n1 NO 3 ). The band of the medium intensity at 809 cm1 has been observed in the IR spectrum only and it can be assigned to the n2 NO 3 vibrations. The Raman active band at 725 cm1 was assigned to the n4 NO 3 vibrations. The expected level of the factor group splitting (Table 21S; Supplementary materials) was not observed in the vibrational spectra of dapNO3. Table 5 contains the assignment of other vibrational bands of dapNO3. The assignment of the hydrogen phosphate (HPO-4) vibrations is
Table 5 Experimental FTIR and FT Raman wavenumbers (cm1) of dapNO3 and their assignment. FTIR 3431 3311 3286 3172 3142 3099 2960 2932 2860 2323 1958
s m m sh sb s m m m wb w
1690 s 1649 1525 1456 1385 1339 1238 1187 1122
s m m s s m w m
FT Raman
Assignment
FTIR
3416 vw
n NeH (…O)
1074 m 1050 m 980 m
3293 wb 3196 vw 3105 m
FT Raman
n CH, n NeH(…N), n NeH(…O) n CH, n NeH(…O) n NeH (…O)
819 809 785 759
sh m m m
700 670 591 553 517 482 437 402 237
m m w w w wb w w w
Combinational modes
1704 1679 1657 1539 1517 1452 1405 1344 1244 1197 1116
m m m m m m s s m w m
?
d NH2, n CN, n rg(CC) d NH2, n CN, n rg d NH2, n CN, d CH, d rg n rg, d CH, d NH
v3 NO 3 v3 NO 3 , d CH, d NH, d rg d CH, d NH, d rg r NH2, d CH, d rg d rg, d CH, d NH
173 m 132 mb 94 m
1051 vs 981 m 876 vw
785 757 725 710
vs w m w
594 s 548 m 512 m 439 394 232 193 177
m mb w w w
Assignment ? v1 NO 3 , r NH2 g CH, g rg r NH2, d CH, d rg g CH, g rg v2 NO 3 , d rg g rg, g CH v4 NO 3 , g rg, g CH g rg, g CH g NH, t NH2, g rg t NH2, g CH, g NH ds rg g NH, t NH2 r NH2 t NH2, g CH, g rg r NH2 u NH2, gs rg External modes
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Table 6 Experimental FTIR and FT Raman wavenumbers (cm1) of dap2HPO44H2O and their assignment. FTIR
FT Raman
3451 sh 3278 sb 3111 sb 3096 m 1996 1886 1695 1662
wb wb s s
1518 s 1459 m 1401 m 1334 1259 1241 1195 1168
w m m w w
1094 sh 1070 s 1058 s
Assignment
FTIR
FT Raman
Assignment
n NeH(…O), n NeH(…N), n OeH(…O)
984 s 972 sh
985 s
g CH, g rg, n1 PO4 r NH2, d CH, d rg, n1 PO4
864 809 782 761 656
889 w 864 w
?
n CH Combinational modes
1713 1661 1622 1525 1456 1401 1348 1337 1265 1242 1196
d NH2, n CN, n rg(CC) d NH2, n CN, n rg d NH2, d NH d NH2, n CN, d CH, d rg n rg, d CH, d NH g NH, n rg(CN) d CH, d NH, d rg
w m s m m s m m m m m
528 442 424 400 386
m m m m mb
vs w w m m
r NH2, d CH, d rg
1127 m
n3 PO4
1050 w
r NH2, n3 PO4
based on free phosphate ion (PO3 4 ) vibrational bands labelling (see Table 22S; Supplementary materials). In dap2HPO44H2O, medium to strong IR bands at 1094, 1070 and 1058 cm1 can be assigned to the modes derived from the originally triply degenerate n3 phosphate vibrations. The medium band at 1127 cm1 recorded in the Raman spectrum corresponds to n3 PO4 in IR spectrum of dap2HPO44H2O. The band observed at 970 cm1 as a shoulder overlapped by a medium intensity vibrational manifestation of 2,4diaminopyrimidinium cation (g CH and g rg vibrations) can be assigned to the symmetric stretching mode derived from n1 PO4 in both spectra. The medium intense IR band at 865 cm1 (864 cm1 Raman) can be attributed to the n PeOH vibrations. The assignment of the bands observed at 555 and 521 cm1 in the Raman spectrum (547 and 527 cm1 in the IR spectrum) can be derived from the
187 mb 134 m 102 m 77 w
n PeOH g CH, g rg g rg, g CH
785 vs
592 556 521 444 430 391
s m m w w m
244 231 215 196
w w w m
g NH, t NH2, g rg d rg ds rg, n4 PO4 g NH, t NH2, n4 PO4 u NH2 t NH2, g CH, g rg n2 PO4 u NH2, gs rg
External modes
originally triple degenerate n4 phosphate vibrations. The band recorded at 401 cm1 (partially overlapped by the band at 389 cm1 attributed to the r NH2 vibrations) in the Raman spectrum was assigned to the originally doubly degenerate n2 PO4 vibrations. The observed factor group splitting is consistent with the results of a correlation analysis presented in Table 22S (Supplementary materials). Table 6 contains the assignment of other vibrational bands of dap2HPO44H2O. The manifestations of n3 SeO2 vibrations (originally triple 4 degenerate) were observed as structured medium intensity bands at 865 and 856, 865 and 892 cm1 in the IR spectrum and as a weak band at 871 cm1 in the Raman spectrum of dap2SeO42H2O. A very strong band found at 825 cm1 in the Raman spectrum (832 cm1 IR spectrum) was assigned to the characteristic n1 SeO2 4 vibration.
Table 7 Experimental FTIR and FT Raman wavenumbers (cm1) of dap2SeO42H2O and their assignment. FTIR
FT Raman
Assignment
FTIR
3112 m
n OeH(…O), n NeH(…O) n CH
865 856 832 814 785 760 655 629 597 592 551 524 511 442 433 417 401
3319 mb 3088 2945 2876 2819 2749 2640 1760 1698 1659
1523 1459 1400 1347 1334 1251 1242
mb wb wb wb wb wb wb s s
m m m w w sh m
1129 w 1073 w 1052 w 987 m 979 m 892 sh
n NeH(…O), n NeH(…N) n NeH(…O)
1678 1657 1624 1530 1516 1441 1406
m m sh m m m s
d NH2, n CN, n rg(CN) d NH2, n CN, n rg(CC) d NH2, n CN, n rg d NH2, d NH d NH2, n CN, d CH, d rg n rg(CC), d CH, r NH2 n rg, d CH, d NH g NH, n rg(CN) d CH, d NH, d rg
vs sh s s m m mb mb m sh m m sh sh s s m
1337 s 1241 m 1191 m 1113 m
d rg, d CH, d NH
1064 w 982 m 971 m
r NH2 d rg g CH, g rg v3 SeO2 4
332 w 237 w 226 w 186 sh 170 w 116 w 101 sh 83 w
FT Raman
Assignment
871 m
v3 SeO2 4
825 vs 784 vs
592 s 545 s 515 m
v1 SeO2 4
g CH, g rg d rg g rg, g CH g NH, t NH2, g rg d rg ds rg v4 SeO2 4
430 m
r NH2 409 394 358 331 235
m mb m m vs
v2 SeO2 4 External modes
et al. / Journal of Molecular Structure 1103 (2016) 82e93 I. Matulkova
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Appendix A. Supplementary data Supplementary data related to this article can be found at http:// dx.doi.org/10.1016/j.molstruc.2015.09.002. References
Fig. 10. Comparison on FT Raman spectra of dap, dapClH2O and dap2ClO4.
A medium intensity band at 430 cm1 recorded in the Raman spectrum was assigned to the originally triple degenerate n4 SeO2 4 vibrations (structured band at ca. 430 cm1 in the IR spectrum). The n2 SeO2 4 mode can be observed as a medium intense band at 331 cm1 in the Raman spectrum. The expected level of a factor group splitting (Table 23S; Supplementary materials) is quite consistent with the recorded vibrational spectra. Table 7 contains the assignment of the other vibrational bands of dap2SeO42H2O. 4. Conclusions Six novel inorganic salts of 2,4-diaminopyrimidine have been presented as an example of interesting structural arrangements of the title organic base. All three possible motifs R22 (8) (Fig. 1) are present in the series of the title salts of 2,4-diaminopyrimidine. The first two ones are potentially centrosymmetric and e indeed e these motifs if present in the title structures are truly centrosymmetric. The arrangement (I) is present in 2,4-diaminopyrimidinium perchlorate, 2,4diaminopyrimidinium chloride hemihydrate, while the arrangement (II) has been observed in 2,4-diaminopyrimidinium nitrate. The non-centrosymmetric arrangement (III) has been found to exist in bis(2,4-diaminopyrimidinium) selenate dihydrate. The latter arrangement is characterized by simultaneous presence of relatively short and relatively long NeH…N hydrogen bonds (N3 … N2 and N4 … N). The presence of water molecules is among others affected by the size of the anion, by the number of the potential acceptors (cf. 2,4-diaminopyrimidinium nitrate and bis(2,4diaminopyrimidinium) selenate dihydrate) as well as by the charges of the anions. The recorded vibrational spectra of title inorganic salts and 2,4diaminopyrimidine were assigned according to quantum chemical calculations. The spectra are in agreement with the determined crystal structures. Vibrational manifestations of the inorganic anions are quite consistent with expectations based on the correlation analysis. Acknowledgement This work was supported by the Czech Science Foundation (grant no. 14-05506S).
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The study of crystal structures and vibrational spectra of inorganic salts of 2,4-diaminopyrimidine a, Jana Mathauserova a, Ivana Císarova a, Ivan Ne mec a, *, Jan Fa bry b Irena Matulkova a b
Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 128 43 Praha 2, Czech Republic Institute of Physics, Academy of Sciences of the Czech Republic, Na Slovance 2, 182 21 Praha 8, Czech Republic
a r t i c l e i n f o
a b s t r a c t
Article history: Received 26 June 2015 Received in revised form 12 August 2015 Accepted 2 September 2015 Available online 9 September 2015
Six novel salts of 2,4-diaminopyrimidine were prepared and studied by X-ray single-crystal structure analysis and vibrational spectroscopy. All but one of the title compounds, i.e. (2,4-diaminopyrimidine) 2,4-diaminopyrimidinium perchlorate, 2,4-diaminopyrimidinium nitrate, 2,4-diaminopyrimidinium perchlorate, bis(2,4-diaminopyrimidinium) hydrogen phosphate tetrahydrate and bis(2,4-diamino pyrimidinium) selenate dihydrate, crystallize in the triclinic system with the centrosymmetric space group P1 while the crystals of the remaining compound e 2,4-diaminopyrimidinium chloride hemihydrate e belong to the monoclinic system (space group C2/c). All the crystal structures contain the characteristic graph set motif R22 (8) with NeH… N hydrogen bonds. This graph set motif can be formed by one of three possible arrangements of a pair of 2,4-diaminopyrimidinium cations and all these arrangements have been observed in the title structures. The title salts were also investigated by vibrational spectroscopy (FTIR and FT Raman). The presented interpretation of the vibrational spectra is based on DFT calculations of 2,4-diaminopyrimidine molecule and 2,4-diaminopyrimidinium cation. © 2015 Elsevier B.V. All rights reserved.
Keywords: 2,4-diaminopyrimidine 2,4-diaminopyrimidinium Crystal structure Hydrogen bonds Crystal engineering Vibrational spectroscopy DFT calculations
1. Introduction The crystal engineering is a general branch of supramolecular chemistry, which covers processes of purposeful design of functional three-dimensional crystal structures from molecule-scale components. It actually represents one of the most promising fields of the design of novel materials with desired properties. However, the synthesis of crystals is a much more difficult process to control since it involves manipulation of simultaneous effects of long- and short-range interactions while kinetic effects are difficult to take into account. Hydrogen bonds and dipolar interactions may play most important role in interconnection of synthons. Formation of a crystal from molecules and ions depends not only on symmetry and size of the molecules involved but mainly on intermolecular (supramolecular) interactions, which control mutual assembly of building blocks. From the whole range of these interactions of a different nature (i.e. particularly ioneion interactions, ionedipole interactions, dipoleedipole interactions, cationep interactions, anionep interactions, pep interactions and the van der Waals forces) the hydrogen bonds can be considered as
* Corresponding author. mec). E-mail address: [email protected] (I. Ne http://dx.doi.org/10.1016/j.molstruc.2015.09.002 0022-2860/© 2015 Elsevier B.V. All rights reserved.
the most important and powerful ones, which are sometimes classified as dipoleedipole interactions. Hydrogen bonds can also act as effective means how to override tendency of organic bases with high dipole moments to form centrosymmetric pairs. 2,4-diaminopyrimidine and its derivatives are successfully used in the field of medical research. They can act as antagonists of allergic rhinitis or solid tumours [1,2], inhibitors of cancer cells [3], antifilarial agents [4] and DNA modificators [5e7]. But only one crystal structure containing 2,4-diaminopyrimidinium cation with inorganic acid is present in the Cambridge Structural Database [8]. This is the crystal structure of bis(2,4-diaminopyrimidinium) sulphate monohydrate [9] (REFCODE TEGZIO). This work is a part of our project which is focused on preparation and study of new materials with potential non-linear optical (NLO) properties. We are mainly interested in compounds which are composed of heteroaromatic nitrogen-containing organic bases and inorganic oxyacids and where variety of hydrogen bonds is expected. The formation of crystalline salts with different anionic species (ranging from simple chlorides to planar nitrates or tetrahedral sulfates, selenates, perchlorates or phosphates), which also differ in their role as proton donors/acceptors, can lead to noncentrosymmetric phases which are suitable for nonlinear optics [10e21]. Unfortunately, all the title structures are centrosymmetric
et al. / Journal of Molecular Structure 1103 (2016) 82e93 I. Matulkova
and therefore our attention has been focused mainly on crystallographic and spectroscopic point of aspects. The other motivation for this paper has been the fact that the description of different arrangements of the title cation in the solid state has been neglected. This cation is also interesting for investigation of the configuration of the primary-amine group [22]. The Cambridge Structural Database yielded only five crystal structures containing diaminopyrimidinium cations with the following REFCODES: DICCOJ e 2,3-diaminopyrimidinium 4-nitrophenol 4nitrophenolate [23]; TEGZIO e bis(2,4-diaminopyrimidinium) sulphate monohydrate [9]; TEGZIO01 e hydroxonium bis(2,4diaminopyrimidinium) phosphate [24]; WUJROI e 2,6-diamino pyrimidinium 1,3-cyclopentanedionate monohydrate [25] and WUJRUO e 2,6-diaminopyridinium 1,3-cyclohexanedionate 1,3cyclohexanedione enol monohydrate [25]. Very questionable crystal structure of TEGZIO01 surprisingly exhibits the same lattice parameters and the positional parameters of the non-hydrogen atoms as TEGZIO. Therefore TEGZIO01 has been excluded from other considerations and discussion. The present study is focused on crystal structures and vibrational spectra of six new compounds: 2,4-diaminopyrimidinium chloride hemihydrate (dapClH2O), (2,4-diaminopyrimidine) 2,4diaminopyrimidinium perchlorate (dap2ClO4), 2,4-diamino pyrimidinium perchlorate (dapClO4), 2,4-diaminopyrimidinium nitrate (dapNO3), bis(2,4-diaminopyrimidinium) selenate dihydrate (dap2SeO42H2O) and bis(2,4-diaminopyrimidinium) hydrogen phosphate tetrahydrate (dap2HPO44H2O). 2. Experimental The products derived from 2,4-diaminopyrimidine (dap, Aldrich 98%) were obtained by crystallization of reaction mixtures prepared by dissolving dap in 20e50 mL of distilled water and adding the corresponding amount of 2 mol/L of acid solution (hydrochloric, perchloric, nitric, selenic and phosphoric). The molar ratio (base: acid) was chosen to follow the expected stoichiometry of the potential products. After slow evaporation of water at room temperature, the products were colourless crystals of dapClH2O (starting molar ratio 1: 1), dap2ClO4 (starting molar ratio 1: 1), dapClO4 (starting molar ratio 1: 2), dapNO3 (starting molar ratio 1: 1), dap2SeO42H2O (starting molar ratios 1: 1 and 2: 1), and dap2HPO44H2O (starting molar ratio 2: 1). The obtained crystals were filtered off and dried in air. Single-crystal X-ray diffraction data of dapClH2O, dap2ClO4, dapClO4, dapNO3, dap2SeO42H2O and dap2HPO44H2O were collected on a Nonius Kappa diffractometer (MoKa radiation, graphite monochromator) equipped with Bruker APEX-II CCD array detector (computing programs SAINT [26], Diamond [27], PLATON [28]). The temperature of each sample was controlled by an Oxford Cryosystems liquid nitrogen Cryostream cooler. The phase problem was solved by direct methods (SIR-97 software [29]) and the nonhydrogen atoms were refined anisotropically, using the fullmatrix least-squares procedure (SHELXL-97 [30] and JANA2006 software [31] into which extinction correction by Becker & Coppens [32] is included). For all the title structures, the difference electron density maps revealed all the hydrogens. There have been tested various refinement models with different constraints and restraints regarding the hydrogens' parameters. Therefore, the treatment of the hydrogens can differ in the respective structures, nevertheless, in all the cases the aryl hydrogens were constrained with CaryleH ¼ 0.94 Å and Uiso(H) ¼ 1.2Ueq(Caryl) assuming trigonal configuration of the carrier carbon atom. The detailed refinement of hydrogen atoms in the title crystal structures is included into the Supplementary materials. The basic crystallographic data, measurement and refinement details are summarized in Table 1. The
83
selected bond lengths and angles, including those of hydrogen bonds, are presented in Supplementary materials, Tables 1Se6S Crystallographic data for dapClH2O, dap2ClO4, dapClO4, dapNO3, dap2SeO42H2O and dap2HPO44H2O have been deposited with the Cambridge Crystallographic Data Centre as supplementary publications CCDC 1406427, CCDC 1406428, CCDC 1406431, CCDC 1406432, CCDC 1406430 and CCDC 1406429, respectively. Copies of the data can be obtained free of charge on application to CCDC, 12 Union Road, Cambridge CG21, EZ, UK (fax: (44) 1223-336-033; email: [email protected]). The phase purity of the prepared polycrystalline samples was also controlled by powder X-ray diffraction at room temperature using the Bragg-Brentano geometry on a Philips X'pert PRO MPD Xray diffraction system equipped with an ultra fast X'Celerator detection using Cu-anode (Cu-Ka; l ¼ 1.5418 Å). Recorded diffraction patterns (see Tables 7Se13S; Supplementary materials) are consistent with the calculated diffraction maxima (FullProf software [33]). The infrared spectra were recorded using nujol and fluorolube mulls (KBr windows) technique on a Nicolet 6700 FTIR spectrometer with 2 cm1 resolution and Happ-Genzel apodization in the 400e4000 cm1 region. The FAR IR spectra were recorded down to 50 cm1 (4 cm1 resolution, Solid Substrate™ beamsplitter, DTGS detector, Happ-Genzel apodization) in PE pellets. The Raman spectra of the polycrystalline samples were recorded at room temperature on a Nicolet 6700 FTIR spectrometer equipped with the Nicolet Nexus FT Raman module (2 cm1 resolution, Happ-Genzel apodization, 1064 nm Nd:YVO4 laser excitation, 450 mW power at the sample) in the 150e3700 cm1 region. Quantum-chemical calculation (GAUSSIAN09W [34]) of 2,4diaminopyrimidine and 2,4-diaminopyrimidinium (1þ) cation was performed employing the closed-shell restricted density functional method (B3LYP) with the 6-311þG(d, p) basis set. The visualization of the results was carried out with the GaussView [35] program package. The geometry optimizations, also yielding the molecular energies, were followed by frequency calculations together with IR intensities and Raman activities using the same method and the basis set. The optimal scaling scheme for calculated frequencies was inferred from comparison of results, which were obtained by application of WLS (Wavenumber-Linear Scale) procedure [36] and dual scaling [37] procedures with the experimental values recorded for dap base or dapClH2O. The spectra were analysed in terms of the PED (Potential Energy Distribution) contributions by using the VEDA (Vibrational Energy Distribution Analysis) program [38]. The theoretical Raman intensities of the computed normal modes were calculated (RAINT program [39]) for 1064 nm excitation wavelength taking Raman scattering activities from the Gaussian output. 3. Results and discussion 3.1. Crystal structures In the title structures, the most intriguing feature is the hydrogen bond pattern between 2,4-diaminopyrimidine or 2,4diaminopyrimidinium molecules and different anions, which have a varying ability to act as hydrogen-bond acceptors. For example, the excess of the donating hydrogens in 2,4diaminopyrimidinium chloride hemihydrate with respect to the chloride anion can be mitigated by the involvement of the water molecules into this structure. 2,4-diaminopyrimidinium has two primary amine groups involving atoms N3 and N4 as well as N1 or N2 atoms, which are part of the aromatic ring. N1 tends to be hydrogenated in a sufficiently acid environment and N2 can act as a hydrogen bond
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Table 1 Basic crystallographic data and structure refinement details of dapClH2O, dap2ClO4, dapClO4, dapNO3, dap2HPO44H2O and dap2SeO42H2O salts. Chemical formula Mr Crystal system, space group Temperature (K) a, b, c (Å)
a, b, g ( )
C8H13N8$ClO4 320.7 Triclinic, P-1 150 5.8370 (2) 8.2675 (3) 13.8279 (5) 86.715 (2) 86.782 (2) 89.538 (2) 665.14 (14) 2 332 Mo Ka 0.32 1.601 Colourless, needle 0.42 0.38 0.14 5172, 5.895, 55.10
C4H7N4$NO3 173.1 Triclinic, P-1 150 3.5981 (3) 9.7412 (7) 10.5523 (8) 73.658 (4) 87.077 (4) 86.416 (4) 354.00 (5) 2 180
C4H7N4$ClO4 210.6 Triclinic, P-1 150 5.8754 (2) 8.1800 (3) 9.0878 (4) 113.351 (1) 100.109 (1) 92.150 (1) 391.99 (3) 2 216
C8H14N8$PO4H$4H2O 390.3 Triclinic, P-1 150 6.4965 (3) 10.7603 (6) 12.598 (6) 82.956 (2) 88.907 (2) 77.985 (2) 854.84 (7) 2 412
V (Å3) Z F (000) Radiation type 0.14 0.48 0.22 m (mm1) rX-ray (gcm3) 1.624 1.784 1.516 Crystal description Colourless, needle Colourless, prism Colourless, prism Crystal size (mm) 0.41 0.08 0.04 0.62 0.38 0.27 0.42 0.38 0.21 995, 8.054, 51.56 4520, 2.731, 27.65 4600, 2.688, 27.55 Number of diffractions for the cell determination, qmin, qmax Diffractometer Bruker APEX-II CCD diffractometer Monochromator graphite Measurement method 4 and uscans Absorption correction Multi-scan SADABS [26] Tmin, Tmax 0.879, 0.955 0.946, 0.994 0.756, 0.881 0.911, 0.955 No. of measured, independent and observed 8195, 3053, 2644 3848, 1405, 858 5751, 1804, 1675 9121, 3948, 3268 [I > 3s(I)] reflections Rint/Robs 0.026/0.024 0.030/0.046 0.013/0.012 0.018, 0.025 qmin, qmax, completeness 2.47, 27.65, 0.98 2.01, 26.10, 0.99 2.50, 27.57, 0.99 1.63, 27.55, 1.00 1 (sin q/l)max (Å ) 0.653 0.619 0.651 0.651 Weighting scheme 1/(s2(I) þ 0.0004I2) R [F2 > 3s(F2)], 0.0369 0.0413 0.0277 0.0365 wR [F2 > 3s(F2)], 0.1004 0.0812 0.0922 0.0836 R[all] 0.0425 0.8 0.0299 0.0469 wR[all] 0.1024 0.0893 0.093 0.087 S [all] 2.49 1.56 3.2 2.03 2 2 S [F > 3s(F )] 2.64 1.87 3.3 2.17 No. of reflections (all) 3053 1405 1804 3948 No. of parameters 222 124 133 284 No. of constraints 25 13 13 35 No. of restraints 10 5 5 19 H-atom treatment H atoms treated by a mixture of independent and constrained refinement 3 Drmax, Drmin (e Å ) 0.32, 0.45 0.25, 0.26 0.28, 0.41 0.46, 0.48 Extinction method none none none type 1 Lorentzian isotropic [32] Extinction coefficient 1600 (400)
acceptor. Thus 2,4-diaminopyrimidinium has five hydrogens to offer into the hydrogen bond pattern and one ring nitrogen atom to accept the hydrogen bond. Moreover, the primary amines can also be involved into the hydrogen bond pattern as hydrogen bond acceptors. All the crystal structures exhibit a characteristic graph set motif [40,41] R22 (8) with NeH…N hydrogen bonds, which can be formed by three possible arrangements of a pair of the 2,4diaminopyrimidinium cations (Fig. 1), and all these arrangements
C4H7N4$Cl$0.5H2O 155.6 Monoclinic, C2/c 150 20.4070 (9) 5.0299 (2) 16.5030 (6) 90 125.064 (1) 90 1386.52 (10) 8 648
C8H14N8$SeO4$2H2O 401.2 Triclinic, P-1 150 6.8859 (4) 10.5955 (6) 11.5092 (7) 70.058 (3) 77.205 (3) 89.237 (2) 767.98 (8) 2 408
0.48 1.491 Colourless, prism 0.40 0.31 0.29 5294, 3.016, 27.44
2.49 1.735 Colourless, plate 0.20 0.17 0.03 2267, 3.040, 26.64
0.829, 0.871 5306, 1609, 1344
0.637, 0.922 8880, 3539, 2598
0.026/0.023 2.44, 27.63, 0.99 0.653
0.045/0.067 1.93, 27.60, 0.99 0.652
0.0267 0.0684 0.0347 0.0711 1.74 1.84 1609 105 14 1
0.0374 0.0667 0.0595 0.0751 1.16 1.21 3539 254 26 7
0.25, 0.24 none
0.45, 0.37 none
have been observed among the title structures. The forms (I) and (II) are compatible with the centre of symmetry in difference to the form (III), and, indeed, they are truly centrosymmetric in the title structures where they occur. The motif (I) is present in dap2ClO4, dapClO4, and dapClH2O, the motif (II) in dapNO3 while the motif (III) has been found in dap2HPO44H2O as well as in dap2SeO42H2O. In the above mentioned already determined structures there are known forms (I) for WUJROI [25] and (II) for DICCOJ [23] as well as for TEGZIO [9]. WUJRUO [25] seems to be exceptional because there
Fig. 1. Possible schemes of the formation of motifs R22 (8) by a pair of NeH…N hydrogen bonds between two 2,4-diaminopyrimidinium ions.
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Fig. 2. Packing scheme of the dap2ClO4 (view along [100] direction). The dashed lines indicate the hydrogen bonds.
is no motif (I), (II) or (III) present in its structure. Instead of that there are NeH…O hydrogen bonds. In addition to the hydrogen bonds, there are p-electron…pelectron ring interactions in all the structures except for dapClH2O. The crystal structure of dap2ClO4 (Fig. 2 and 2S; Supplementary
materials) is the most interesting structure because the secondary amine hydrogen acts as a bridging hydrogen between 2,4diaminopyrimidine molecule and 2,4-diaminopyrimidinium cation (Table 1S; Supplementary materials). This hydrogen is displaced towards the centre of the connecting line N1…N5 and is
Fig. 3. Packing scheme of the dapNO3 (view along [100] direction). The dashed lines indicate the hydrogen bonds.
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Fig. 4. Packing scheme of the dapClO4 (view along [100] direction). The dashed lines indicate the hydrogen bonds.
disordered between two positions (Figs. 1S and 3S; Supplementary materials) in unequal occupancies. The hydrogen bonds connecting N4…N5 are of moderate strength and are the strongest ones in the title structure. Presence of the centred N…H…N hydrogen bond is relatively rare. The Cambridge Structural Database indicated 22 hits of such structures. Moreover, there have also been indicated some suspicious structures where the pertinent hydrogen was incorrectly attached and constrained to one of the nitrogens involved. Among them was cytosiniumehydrogen maleateecytosine (1/1/1) with
the REFCODE DUJCAN, which corresponds to the publication by Benali-Cherif et al. [42]. The recalculation detected an ill-positioned hydrogen. The recalculation yielded similar splitting of the hydrogen bond as in dap2ClO4 and its improved structure determination is going to be reported elsewhere. The graph-set motif NeH…N is formed by the primary amine hydrogens in dap2ClO4 structure. The hydrogen bonds involved in this graph set motif are of moderate strength. The hydrogen bonds NeH…O are rather weak (Fig. 3S and Table 1S; Supplementary materials). The graph set motifs R22 (8) with NeH…N hydrogen
Fig. 5. Packing scheme of the dap2HPO44H2O (view along [010] direction). The dashed lines indicate the hydrogen bonds.
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Fig. 6. Packing scheme of the dap2Cl2H2O (view along [010] direction). The dashed lines indicate the hydrogen bonds.
bonds of a moderate strength [43] are truly centrosymmetric of the type (I) (Fig. 2). The NeH…O bonds are slightly longer, exceeding a little bit 3.2 Å which is considered to be a limit for distinguishing the hydrogen bonds of the moderate strength from the weak ones [43]. Cf. dapClO4 where the NeH…O bonds are substantially weaker. In dapNO3 (Fig. 3), the motif R22 (8) with the NeH…N is of the type (II) and is truly centrosymmetric (Figs. 4S and 5S, Table 2S; Supplementary materials). The hydrogen bond pattern also contains NeH…O hydrogen bonds of the moderate strength which are involved in the graph set motifs R22 (8), R24 (8) and R33 (10).
In dapClO4 (Fig. 4), there is present a truly centrosymmetric motif R22 (8) of the type (I) with NeH…N hydrogen bonds of the moderate strength (Figs. 6S and 7S; Supplementary materials). The NeH…O hydrogen bonds are weak and bifurcated (Fig. 7S and Table 3S; Supplementary materials). In dap2HPO44H2O (Fig. 5), there are present two motifs R22 (8) of the type (III) between symmetry independent molecules with NeH…N hydrogen bonds of both moderate and weak strength (Figs. 8S and 9S, Table 4S; Supplementary materials). It is of interest that the molecules involved in this interaction are symmetry independent. Concomitantly, these hydrogen bond motifs are not
Fig. 7. Packing scheme of the dap2SeO42H2O (view along [100] direction). The dashed lines indicate the hydrogen bonds.
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centrosymmetric. There are NeH…O and OeH…O hydrogen bonds of moderate strength in the structure. The shortest hydrogen bond in the structure is N1eH1N1…Ow3. In dapClH2O (Fig. 6), there is present a truly centrosymmetric motif R22 (8) of the type (I) with NeH…N hydrogen bonds of a moderate strength (Figs. 10S and 11S; Supplementary materials). There are also present NeH…Cl and OwatereH…Cl hydrogen bonds (Table 5S; Supplementary materials). There is a motif NH2…Cl… HeOwatereH…Cl…H2N in the structure, in which Cl atoms are acceptors of four hydrogen bonds. Water is situated at the special position being on the two-fold axis. Crystal structure of dap2SeO42H2O (Fig. 7) contains a motif R22 (8) of the type (III) with moderate and weak NeH…N hydrogen bonds (Figs. 12S and 13S, Table 6S; Supplementary materials) There are NeH…O and OeH…O moderate and weak hydrogen bonds in the structure. 3.2. Vibrational spectroscopy FTIR and FT Raman spectra of the investigated dap-based compounds have been recorded at room temperature and the results are presented in Figs. 8 and 9 and Tables 2e7. The assignment of the spectra is based on the calculation of the vibrational spectra of an isolated dap molecule and its cation dap(1þ) - see Tables 15Se19S (Supplementary materials). The presented data confirm that WLS procedure [36] is the best approach for the scaling of the calculated frequencies of 2,4-diaminopyrimidine and 2,4-diaminopyrimidinum (1þ) cations. The interpretation of the
Fig. 9. FT Raman spectra of dapClH2O, dap2ClO4, dapClO4, dapNO3, dap2HPO44H2O and dap2SeO42H2O salts.
Fig. 8. FTIR spectra (compiled from nujol and fluorolube mulls) of dapClH2O, dap2ClO4, dapClO4, dapNO3, dap2HPO44H2O and dap2SeO42H2O salts.
bands of stretching and out-of-plane bending vibrations of the NeH and OeH groups involved in the hydrogen bonds arises from the correlation curves [44,45] concerning the appropriate band positions and the hydrogen bond lengths. It is obvious that B3LYP/6-311þG(d,p) calculations provide frequencies which reasonably match the experimental ones. The only discrepancies refer to the NeH stretching modes spectral region (3150e3500 cm1 for dap and 3400e3500 cm1 for dap(1þ)). The reason for these differences follows from the fact that the formation of NeH…X (X ¼ N, O or Cl) hydrogen bonds has not been considered in the calculations for the isolated molecule/cation in vacuum. The overall character of the spectra of dap molecule and dap(1þ) cation is very similar e see Figs. 8 and 9. The main difference can be observed in the 2000e3500 cm1 region in the IR spectra due to the different hydrogen bonding patterns. The other difference can be observed in the position, shape and splitting of the bands of the 2,4-diaminopyrimidine skeleton in the Raman spectra, see Fig. 10. The positions of several characteristic ring vibrations bands of pure dap base and its cation (in dapClH2O) are slightly shifted. The first example is a strong dap band at 791 cm1 (dap(1þ) e 784 cm1) which can be attributed to the ring out-ofplane and out-of-plane CeH vibrations in the Raman spectra. Also, two bands can be observed in the 600e500 cm1 region in the Raman spectra of pure dap in contrast to three bands in the spectra of dapClH2O. The first two bands (601 and 558 cm1 e dap; 589 and 554 cm1 e dapClH2O) can be assigned to the deformation vibration of the pyrimidine ring while the band at 516 cm1
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Table 2 Experimental FTIR and FT Raman wavenumbers (cm1) of dapClH2O and their assignment. FTIR
FT Raman
Assignment
FTIR
FT Raman
Assignment
3323 sb 3150 sb
3304 3162 3082 3066
n NeH n CH n CH, n NeH(…N) n CH n NeH(…O)
1170 m 1121 m 1049 m 987 m 863 mb 826 s 780 s 764 s 722 sh 706 sb 647 sb 598 s 581 sh 546 s 510 sh 436 m 400 m 238 m 220 m 201 m 161 m 151 w 127 m 109 w 71 m
1174 w 1118 m 1043 w 984 s 863 w 828 w 784 vs
r NH2, d CH, d rg d rg, d CH, d NH r NH2 g CH, g rg r NH2, d CH, d rg g CH, g rg g rg, g CH
3066 2954 2907 2846 2646 2512 2444 2379 2192 2153 1966 1764 1683
s s s s m w w w wb wb m w s
1660 1633 1578 1525 1517 1464 1400 1341 1250
s s m sh s m m m m
wb wb m m
Combinational modes
d NH2, n CN, n rg(CN) 1681 1670 1651 1627
m m m m
1526 1508 1466 1397 1341 1249
m w w s s m
d NH2, n CN, n rg(CC) d NH2, n CN, n rg d NH2, d NH d NH2, n CN, d CH, d rg n rg (CC), d CH, r NH2 n rg, d CH, d NH g NH, n rg(CN) d CH, d NH, d rg d CH, d NH, d rg
g NH, t NH2, g rg d rg 589 554 516 436 387 227
s m m w m m
ds rg g NH, t NH2 t NH2, g CH, g rg r NH2 u NH2, gs rg External modes
Note: Abbreviations and symbols: vs, very strong; s, strong; m, medium; w, weak; b, broad; sh, shoulder; n, stretching; d, deformation or in-plane bending; g, out-of-plane bending; r, rocking; u, wagging; t, torsion; s, symmetric; as, antisymmetric.
(dapClH2O) can be assigned to the g NH and t NH2 vibrations. The medium intensity bands recorded at 1397, 1341, 1118 and 984 cm1 in the Raman spectrum of dapClH2O can be assigned to the g NH, n rg(CN); d CH, d NH, d rg; d rg, d CH, d NH and g CH, g rg vibrations, respectively. The medium intensity bands at 1371, 1265, 1115 and 974 cm1 found in the Raman spectrum of dap molecule can be assigned to d NH2, n CN, d rg, d CH; n rg(CN), d CH, u NH2; d CH, n rg(CC) and g rg vibrations, respectively. The detailed assignment of the vibrational spectra of pure dap base and dap(1þ) in dapClH2O are listed in Tables 2 and 19S (Supplementary materials). The comparison of vibrational manifestations of the molecule and its mono-protonated cation can be particularly interesting in the case of dap2ClO4 where both forms should be present e see Fig. 10 and Table 3. Surprisingly dap2ClO4 spectrum (see Fig. 10) manifests in principle presence of just one “intermediate” form of
2,4-diaminopyrimidine skeleton rather than features of both expected forms. However, this feature is fully in accord with the formation of disordered bridging hydrogen bond between 2,4diaminopyrimidine molecule and 2,4-diaminopyrimidinium cation (leading to their considerable structural “similarity”) in the crystal structure of dap2ClO4. Characteristic strong IR bands recorded at 1135, 1108 and 1055 cm1 (Raman 1046, 1122 and 1133 cm1) in the spectrum of dapClO4, and the strong structured band with the maxima at 1096 and 1046 cm1 (Raman 1042, 1090 and 1122 cm1) in dap2ClO4 (partially mixed with vibrational manifestation of dap e i.e. r NH2, d CH, n rg(CC), d NH and d rg vibrations) correspond to the n3 perchlorate vibrations. Dominant, very strong Raman bands at 935 cm1 (dap2ClO4) and 925 cm1 (dapClO4) (very weak in the IR spectra at 934 and 924 cm1) were assigned to the symmetric
Table 3 Experimental FTIR and FT Raman wavenumbers (cm1) of dap2ClO4 and their assignment. FTIR 3434 3360 3338 3166
FT Raman m m m mb
Assignment
FTIR
FT Raman
Assignment
n NeH(…O)
1046 mb 1000 sh
n CH, n NeH(…N)
935 vw
v3 ClO 4 , r NH2 g CH, g rg, r NH2, d rg g rg v1 ClO 4
Combinational modes
815 m 804 m 777 m
1042 w 989 m 978 m 935 vs 909 w 812 w
3382 vw
3092 m 1994 1931 1660 1632 1598 1552 1501 1456 1390
wb w sb sb sh mb m s mb
1256 m 1166 sh 1096 sb
1657 1636 1604 1555 1507 1466 1385 1337 1255 1184 1122 1090
m m m vw m vw s m m w m w
d NH2, n CN, n rg, d rg d NH2, d NH d NH2, d rg d rg, d NH2 n rg(CC), d CH, r NH2 d CH, d NH, d rg d NH2, n CN, d rg, d CH d CH, d NH, d rg n rg(CN), d CH, u NH2 r NH2, d CH v3 ClO 4 , d rg, d NH, d CH v3 ClO 4
689 627 602 573 506 458 436 372 228 207
mb m w w mb w wb m m w
787 vs 714 vw 626 594 573 503 457 437 366 229 218
m s m m m w m vw m
?
d rg g rg, g CH g CH, g rg d rg
v4 ClO 4 t NH2, g CH, g NH, d rg d rg g NH, t NH2 v2 ClO 4 , r NH2 t NH2, g CH, g rg u NH2 u NH2, gs rg u NH2, d rg
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Table 4 Experimental FTIR and FT Raman wavenumbers (cm1) of dapClO4 and their assignment. FTIR 3443 3371 3349 3311 3292 3239 3159 3104 2980 1952 1681 1664
s m m m m m mb m sh vw s s
1625 m 1611 m 1515 m
1378 1341 1311 1236
w w vw m
1136 s 1108 s 1055 s
FT Raman
Assignment
FTIR
3446 w 3375 w
n NH(…O)
987 962 933 925
n CH, n NeH(…N) n CH
3153 wb 3106 m
820 m 780 w 765 m
Combinational modes 1950 1691 1656 1641
vw w m m
1612 1508 1452 1429 1381 1344
m m w w m m
1237 1178 1132 1122
w w sh m
vw w w w
d NH2, n CN, n rg(CC) d NH2, n CN, n rg
669 mb
?
623 s 602 m 591 m 550 m 507 w 478 wb 467 w 454 w 430 m 377 m 225 m 195 w 124 m 115 m 75 m
d NH2, d NH ?
n rg(CC), d CH, r NH2 n rg, d CH, d NH ?
g NH, n rg(CN) d CH, d NH, d rg ?
d CH, d NH, d rg r NH2, d CH, d rg
v3 ClO 4
1046 wb
stretching vibration (n1 ClO 4 ) of the anion. Medium intensity IR bands at 627 cm1 (broad Raman band at 626 cm1) and 623 cm1 (Raman 631 and 621 cm1) in the infrared spectra of dap2ClO4 and dapClO4, respectively, were assigned to the n4 ClO 4 vibration. The n2 ClO 4 vibrations can be attributed to the weak bands at 458 and 466 cm1 in the IR spectra (dap2ClO4 and dapClO4) and one band at 457 cm1 (dap2ClO4) or two bands at 466 and 456 cm1 (dapClO4) in the Raman spectra. In these cases, the observed factor group splitting is quite consistent with the results of the correlation analysis presented in Table 20S (Supplementary materials). Table 4 contains the assignment of the other vibrational bands of dapClO4. Strong bands recorded at 1385 and 1339 cm1 in the IR spectrum of dapNO3 (the medium intensity Raman band at 1404 cm1
FT Raman
Assignment
986 967 933 925 909 858 825 784
m w s vs m w w vs
g CH, g rg ? v1 ClO 4
713 663 631 621
vw vw m m
?
r NH2, d CH, d rg g CH, g rg g rg, g CH ?
586 s 555 s 503 m 466 456 429 370 231 207
m m vw m w w
g rg, g CH g NH, t NH2, g rg v4 ClO 4
t NH2, g CH, g NH d rg ds rg g NH, t NH2 u NH2 v2 ClO 4
t NH2, g CH, g rg r NH2 u NH2 u NH2, gs rg External modes
e mixed with g NH and n rg(CN) vibrations of dap cation) correspond to the n3 nitrate vibrations. A very strong band at 1051 cm1 in the Raman spectrum and the medium intensity band at 1050 cm1 in the IR spectrum correspond to the symmetric stretching vibrations of anion (n1 NO 3 ). The band of the medium intensity at 809 cm1 has been observed in the IR spectrum only and it can be assigned to the n2 NO 3 vibrations. The Raman active band at 725 cm1 was assigned to the n4 NO 3 vibrations. The expected level of the factor group splitting (Table 21S; Supplementary materials) was not observed in the vibrational spectra of dapNO3. Table 5 contains the assignment of other vibrational bands of dapNO3. The assignment of the hydrogen phosphate (HPO-4) vibrations is
Table 5 Experimental FTIR and FT Raman wavenumbers (cm1) of dapNO3 and their assignment. FTIR 3431 3311 3286 3172 3142 3099 2960 2932 2860 2323 1958
s m m sh sb s m m m wb w
1690 s 1649 1525 1456 1385 1339 1238 1187 1122
s m m s s m w m
FT Raman
Assignment
FTIR
3416 vw
n NeH (…O)
1074 m 1050 m 980 m
3293 wb 3196 vw 3105 m
FT Raman
n CH, n NeH(…N), n NeH(…O) n CH, n NeH(…O) n NeH (…O)
819 809 785 759
sh m m m
700 670 591 553 517 482 437 402 237
m m w w w wb w w w
Combinational modes
1704 1679 1657 1539 1517 1452 1405 1344 1244 1197 1116
m m m m m m s s m w m
?
d NH2, n CN, n rg(CC) d NH2, n CN, n rg d NH2, n CN, d CH, d rg n rg, d CH, d NH
v3 NO 3 v3 NO 3 , d CH, d NH, d rg d CH, d NH, d rg r NH2, d CH, d rg d rg, d CH, d NH
173 m 132 mb 94 m
1051 vs 981 m 876 vw
785 757 725 710
vs w m w
594 s 548 m 512 m 439 394 232 193 177
m mb w w w
Assignment ? v1 NO 3 , r NH2 g CH, g rg r NH2, d CH, d rg g CH, g rg v2 NO 3 , d rg g rg, g CH v4 NO 3 , g rg, g CH g rg, g CH g NH, t NH2, g rg t NH2, g CH, g NH ds rg g NH, t NH2 r NH2 t NH2, g CH, g rg r NH2 u NH2, gs rg External modes
et al. / Journal of Molecular Structure 1103 (2016) 82e93 I. Matulkova
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Table 6 Experimental FTIR and FT Raman wavenumbers (cm1) of dap2HPO44H2O and their assignment. FTIR
FT Raman
3451 sh 3278 sb 3111 sb 3096 m 1996 1886 1695 1662
wb wb s s
1518 s 1459 m 1401 m 1334 1259 1241 1195 1168
w m m w w
1094 sh 1070 s 1058 s
Assignment
FTIR
FT Raman
Assignment
n NeH(…O), n NeH(…N), n OeH(…O)
984 s 972 sh
985 s
g CH, g rg, n1 PO4 r NH2, d CH, d rg, n1 PO4
864 809 782 761 656
889 w 864 w
?
n CH Combinational modes
1713 1661 1622 1525 1456 1401 1348 1337 1265 1242 1196
d NH2, n CN, n rg(CC) d NH2, n CN, n rg d NH2, d NH d NH2, n CN, d CH, d rg n rg, d CH, d NH g NH, n rg(CN) d CH, d NH, d rg
w m s m m s m m m m m
528 442 424 400 386
m m m m mb
vs w w m m
r NH2, d CH, d rg
1127 m
n3 PO4
1050 w
r NH2, n3 PO4
based on free phosphate ion (PO3 4 ) vibrational bands labelling (see Table 22S; Supplementary materials). In dap2HPO44H2O, medium to strong IR bands at 1094, 1070 and 1058 cm1 can be assigned to the modes derived from the originally triply degenerate n3 phosphate vibrations. The medium band at 1127 cm1 recorded in the Raman spectrum corresponds to n3 PO4 in IR spectrum of dap2HPO44H2O. The band observed at 970 cm1 as a shoulder overlapped by a medium intensity vibrational manifestation of 2,4diaminopyrimidinium cation (g CH and g rg vibrations) can be assigned to the symmetric stretching mode derived from n1 PO4 in both spectra. The medium intense IR band at 865 cm1 (864 cm1 Raman) can be attributed to the n PeOH vibrations. The assignment of the bands observed at 555 and 521 cm1 in the Raman spectrum (547 and 527 cm1 in the IR spectrum) can be derived from the
187 mb 134 m 102 m 77 w
n PeOH g CH, g rg g rg, g CH
785 vs
592 556 521 444 430 391
s m m w w m
244 231 215 196
w w w m
g NH, t NH2, g rg d rg ds rg, n4 PO4 g NH, t NH2, n4 PO4 u NH2 t NH2, g CH, g rg n2 PO4 u NH2, gs rg
External modes
originally triple degenerate n4 phosphate vibrations. The band recorded at 401 cm1 (partially overlapped by the band at 389 cm1 attributed to the r NH2 vibrations) in the Raman spectrum was assigned to the originally doubly degenerate n2 PO4 vibrations. The observed factor group splitting is consistent with the results of a correlation analysis presented in Table 22S (Supplementary materials). Table 6 contains the assignment of other vibrational bands of dap2HPO44H2O. The manifestations of n3 SeO2 vibrations (originally triple 4 degenerate) were observed as structured medium intensity bands at 865 and 856, 865 and 892 cm1 in the IR spectrum and as a weak band at 871 cm1 in the Raman spectrum of dap2SeO42H2O. A very strong band found at 825 cm1 in the Raman spectrum (832 cm1 IR spectrum) was assigned to the characteristic n1 SeO2 4 vibration.
Table 7 Experimental FTIR and FT Raman wavenumbers (cm1) of dap2SeO42H2O and their assignment. FTIR
FT Raman
Assignment
FTIR
3112 m
n OeH(…O), n NeH(…O) n CH
865 856 832 814 785 760 655 629 597 592 551 524 511 442 433 417 401
3319 mb 3088 2945 2876 2819 2749 2640 1760 1698 1659
1523 1459 1400 1347 1334 1251 1242
mb wb wb wb wb wb wb s s
m m m w w sh m
1129 w 1073 w 1052 w 987 m 979 m 892 sh
n NeH(…O), n NeH(…N) n NeH(…O)
1678 1657 1624 1530 1516 1441 1406
m m sh m m m s
d NH2, n CN, n rg(CN) d NH2, n CN, n rg(CC) d NH2, n CN, n rg d NH2, d NH d NH2, n CN, d CH, d rg n rg(CC), d CH, r NH2 n rg, d CH, d NH g NH, n rg(CN) d CH, d NH, d rg
vs sh s s m m mb mb m sh m m sh sh s s m
1337 s 1241 m 1191 m 1113 m
d rg, d CH, d NH
1064 w 982 m 971 m
r NH2 d rg g CH, g rg v3 SeO2 4
332 w 237 w 226 w 186 sh 170 w 116 w 101 sh 83 w
FT Raman
Assignment
871 m
v3 SeO2 4
825 vs 784 vs
592 s 545 s 515 m
v1 SeO2 4
g CH, g rg d rg g rg, g CH g NH, t NH2, g rg d rg ds rg v4 SeO2 4
430 m
r NH2 409 394 358 331 235
m mb m m vs
v2 SeO2 4 External modes
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Appendix A. Supplementary data Supplementary data related to this article can be found at http:// dx.doi.org/10.1016/j.molstruc.2015.09.002. References
Fig. 10. Comparison on FT Raman spectra of dap, dapClH2O and dap2ClO4.
A medium intensity band at 430 cm1 recorded in the Raman spectrum was assigned to the originally triple degenerate n4 SeO2 4 vibrations (structured band at ca. 430 cm1 in the IR spectrum). The n2 SeO2 4 mode can be observed as a medium intense band at 331 cm1 in the Raman spectrum. The expected level of a factor group splitting (Table 23S; Supplementary materials) is quite consistent with the recorded vibrational spectra. Table 7 contains the assignment of the other vibrational bands of dap2SeO42H2O. 4. Conclusions Six novel inorganic salts of 2,4-diaminopyrimidine have been presented as an example of interesting structural arrangements of the title organic base. All three possible motifs R22 (8) (Fig. 1) are present in the series of the title salts of 2,4-diaminopyrimidine. The first two ones are potentially centrosymmetric and e indeed e these motifs if present in the title structures are truly centrosymmetric. The arrangement (I) is present in 2,4-diaminopyrimidinium perchlorate, 2,4diaminopyrimidinium chloride hemihydrate, while the arrangement (II) has been observed in 2,4-diaminopyrimidinium nitrate. The non-centrosymmetric arrangement (III) has been found to exist in bis(2,4-diaminopyrimidinium) selenate dihydrate. The latter arrangement is characterized by simultaneous presence of relatively short and relatively long NeH…N hydrogen bonds (N3 … N2 and N4 … N). The presence of water molecules is among others affected by the size of the anion, by the number of the potential acceptors (cf. 2,4-diaminopyrimidinium nitrate and bis(2,4diaminopyrimidinium) selenate dihydrate) as well as by the charges of the anions. The recorded vibrational spectra of title inorganic salts and 2,4diaminopyrimidine were assigned according to quantum chemical calculations. The spectra are in agreement with the determined crystal structures. Vibrational manifestations of the inorganic anions are quite consistent with expectations based on the correlation analysis. Acknowledgement This work was supported by the Czech Science Foundation (grant no. 14-05506S).
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