Crystal structure and vibrational spectra of salts of 1H-pyrazole-1-carboxamidine and its protonation route

Crystal structures of five salts of 1H-pyrazole-1-carboxamidine, PyCA, with various inorganic acids were determined, (HPyCA)Cl, (HPyCA)Cl·H2O, (HPyCA)Br, (HPyCA)2(I)I3, and (HPyCA)HSO4. Theoretical calculations of the protonation route of PyCA showed that the cationic form present in the studied crystals is energetically privileged. Tautomeric equilibrium constants indicated two isomers as the most stable neutral forms. Calculations for two other tautomers failed resulting in pyrazole and carbodiimid tautomer of cyanamide. Such decomposition is important in a view of guanylation reaction. Hydrogen bonding patterns were studied by means of the graph-set approach. Similarities of the patterns in different crystal structures were demonstrated by the algebraic relations between descriptors of the patterns. The strength of hydrogen bonding network in the crystals was assessed analyzing vibrational spectra. The bands were assigned on the basis of theoretical calculations for the complex [(HPyCA)2Cl4]2– ion and potential energy distribution analysis. The strength of hydrogen bonds was set in the following ascending series (HPyCA)2(I)I3 (4) < (HPyCA)Br (3) < (HPyCA)Cl (1) < (HPyCA)Cl·H2O (2) < (HPyCA)HSO4 (5).


Introduction
The 1H-pyrazole-1-carboxamidine, hereafter PyCA, has been a next-generation substrate for guanylation of amines after Smethylisothiouronium sulfate, cyanamide or 3,5-dimethyl-1guanylpyrazole nitrate [1]. For instance, it was successfully used in the introduction of guanidinium group as the last step of synthetic procedure of zanamivir, an influenza A and B drug [2], or Boc protected PyCA was a guanylation agent in synthesis of dengue and West Nile virus protease inhibitors [3].
The 1H-pyrazole-1-carboxamidine is commercially available as a hydrochloride and is widely used in organic synthesis for years. It can be synthesized by mixing equimolar amount of pyrazole and cyanamide, and further crystallization from the reaction mixture [1]. This very simple one-step procedure and very simple isolation method of pure compound make the PyCA a low-cost reagent in organic synthesis. The (HPyCA)Cl has very good solubility in water or DMF and is stable even at basic conditions, i.e., 1 M water solution of 1 M Na 2 CO 3 [1]. So, it was suggested that the guanylation mechanism proceeds with cationic form of 1H-pyrazole-1carboxamidine and deprotonated form of respective amine. However, our preliminary search in Cambridge Structural Database revealed that crystal structure of PyCA or its salts have not been studied so far [4,5].
Apart from pyrazole ring, a molecule of PyCA possesses three hydrogen atoms at the carboxyamidine residue forming NH 2 and NH groups. It is worth noticing that a free nitrogen atom of the pyrazole ring may be theoretically faced to the NH 2 or NH groups. Besides, the hydrogen atom of the NH group can be oriented in syn or anti position. In the first protonation step, the proton can be accepted either to the NH group or to the free nitrogen atom in the pyrazole ring. So, all these facts indicate that a few tautomers of neutral as well as cationic speciation forms of PyCA are expected in the solution. Here, we present theoretical investigation of the route of protonation of PyCA, which has an importance for Supplementary Information The online version contains supplementary material available at https://doi.org/10.1007/s11224-020-01671-0. understanding guanylation reaction. Crystal structures of new PyCA salts with inorganic acids are described. Hydrogen bonding networks are analyzed by topological approach and graph-set descriptors [6,7]. The compounds are also characterized by infra-red and Raman spectra. The bands are assigned with the help of theoretical simulations and potential energy distribution (PED) analysis.  (3) and (HPyCA)HSO 4 (5) were obtained after 1 to 5 days by slow evaporation of the mixture in air at room temperature. The crystals of (HPyCA) 2 (I)I 3 (4) were formed after 2 months, whereas (HPyCA)Cl·H 2 O (2) was obtained instead of fluoride salt.

Synthesis
Single crystal X-ray diffraction studies X-ray diffraction data were collected on an Oxford Diffraction four-circle single crystal diffractometer equipped with a CCD detector using graphite-monochromatized MoK α radiation (λ = 0.71073 Å). The raw data were treated with the CrysAlis Data Reduction Program (version 1.171.38.43). The intensities of the reflection were corrected for Lorentz and polarization effects. The crystal structures were solved by direct methods [8] and refined by full-matrix least-squares method using SHELXL-2017 program [9]. Non-hydrogen atoms were refined using anisotropic displacement parameters. All Hatoms were visible on the Fourier difference maps, but placed by geometry and allowed to refine "riding on" the parent atom (with U iso = 1.2 U eq for sp 2 -carbon atoms, and U iso = 1.5 U eq for other atoms). Visualizations of the structure were made using Diamond 3.2 k [10]. Low temperature X-ray diffraction experiments were carried out using Oxford Cryosystems device in the range of 295-100 K with temperature step ΔT = 10 K, but no phase transition was observed for all the crystals. Crystal data and refinement details are presented in Table 1.

Spectroscopic measurements
Room temperature FT-IR spectra in the 4000-400 cm -1 range were measured on the Bruker IFS-88 spectrometer with 2 cm -1 resolution. Nujol and fluorolube mull techniques have been used in the measurements. Nd:YAG laser (1064 nm) was used to collect room temperature FT-Raman spectra, which were

Computational details
All the computations were performed with the Gaussian 16 program [11]. The calculations were carried out using densityfunctional theory (DFT) and hybrid Becke's three-parameter and the Lee-Yang-Parr correlation functionals (B3LYP) [12][13][14][15] with Grimme's correction for dispersion with Becke-Johnson damping [16]. The 6-311G(d,p) basis set was used, because it gives satisfactory results for vibrational and thermochemical data with respect to the computational costs [17]. For all the neutral and protonated forms of the PyCA, the minima were found for the singlet electronic state. Calculated total energy, zero-point energy (ZPE) plus thermal corrections and entropy are listed in Table 2, whereas Gibbs free energy and tautomer equilibrium constant for tautomeric equilibria of the neutral and protonated forms of 1H-pyrazole-1-carboxamidine are shown in Table 3. Vibrational frequencies were calculated for protonated form of 1H-Pyrazole-1-carboxamidine, i.e., HPyCA + ion. Since the HPyCA + ion is involved in hydrogen bonding network in the studied crystal structures, the calculations were also carried out for the centrosymmetric [(HPyCA) 2 Cl 4 ] 2ionic system present in the crystal structure of (HPyCA)Cl (1). The positions of all the atoms were taken from crystallographic data, and a constrain with C i point group symmetry for geometry parameters was applied. Additionally, positions of four chloride anions were frozen in order to prevent the ions from escaping to infinity. Frequency of normal modes was

Results and discussion
Protonation of 1H-pyrazole-1-carboxamidine Theoretically, the neutral molecule of 1H-pyrazole-1carboxamidine has as many as eight tautomers (Scheme 1). In this work, the tautomers are named after the labels of hydrogen atoms connected to the nitrogen atoms. This labeling scheme is inherited from crystallographic data (Fig. 1). For instance, the 3ab4a abbreviation means that two hydrogen atoms are bound to the N3 atom in a and b positions, one H-atom is connected to the N4 atom in a position, but aromatic N2 atom is free, because its label does not occur in the abbreviation. A protonation route for the PyCA is presented in Scheme 1. Table 2 shows that the most stable geometry is observed for 3ab4a form. However, calculations for the 23b4a, 23b4b, and 23a4b isomers failed revealing their instability. In the case of 23a4b isomer, a hydrogen atom bound to pyrazole N2 atom moved to the 3b position during geometry optimization. As a result, another isomer was formed, 3ab4b, which is the second most stable tautomer of PyCA neutral molecule. Surprisingly, there is one stable tautomer where the hydrogen atom is attached to the N2 atom, 23a4a, although it is featured by the highest energy ( Table 2). The 23a4a form is probably a zwitterion consisting of a positively charged pyrazole and a negatively charged carboxamidine residue. It is worth noting that possible hopping of the hydrogen atom from N2 atom to 3b position in 23a4a results in the most stable 3ab4a form. Such proton transfer proceeds by analogy to the transformation between 23a4b and 3ab4b isomers, and it is very likely due to low ΔG for tautomerization to the energetically privileged 3ab4a form.
The calculations also revealed decomposition of both 23b4a and 23b4b isomers into pyrazole and cyanamide (its carbodiimid tautomer) during optimization of their structure. These results indicate strongly unfavorable binding of two hydrogen atoms to the N2 atom and at 3b site. Therefore, free energy for formation of PyCA from pyrazole and carbodiimid was calculated for five stable species. The only three isomers are featured by negative ΔG and the value for 23a4a relatively highly positive ( Table 3). The tautomeric equilibrium constants clearly reveal that the main neutral form of PyCA is 3ab4a which stays in quite relevant equilibrium with 3ab4b tautomer. The first protonation step theoretically gives five products. All these reactions are featured by large negative free energy. However, they differ from each other as much as one cationic form 3ab4ab + is a dominant product at the first protonation step. The tautomeric equilibrium constants for the cations indicate that approximately only one molecule of the second energetically stable 23a4ab + ion may appear over a billion 3ab4ab + ions. Besides, a molecule of the highest unfavorable 23ab4b + tautomer can be found in the surroundings of 1 mmol of 3ab4ab + ions. So, the latter is reasonably expected in solution as well as in a crystalline product obtained from acidic conditions.
The protonation route of PyCA eventually ends at the second stage leading to the formation of the 23ab4ab 2+ ion. Here, all the proton acceptors are occupied. Since the protonation free energy is negative, formation of the 23ab4ab 2+ ion bearing compound is also probable. However, it is worth noticing that the value of ΔG is twice lower than in the first protonation stage. So, any effort to obtain a crystalline product containing 23ab4ab 2+ cation requires a strongly acidic condition.

Role of pyrazole and carboxamidine residue in formation of hydrogen bonding patterns
All the presented salts of 1H-pyrazole-1-carboxamidine crystallize in centrosymmetric space groups of monoclinic or triclinic symmetry ( Table 1). The common feature of the studied compounds is the presence of the same cationic form of HPyCA + ion, labeled as 3ab4ab + in the former theoretical section, which is the most energetically privileged tautomer among all the HPyCA + cations. Since the N2 atom of pyrazole ring is not protonated, it may play an acceptor role in a hydrogen bonding network. In the crystal structures of (HPyCA)Cl (1), (HPyCA)Cl·H 2 O (2), and (HPyCA)Br (3), two HPyCA + are complementary arranged around the inversion center. The ions are connected to each other by two N3-H3B···N2 hydrogen bonds forming a ring pattern, R 2 2 (10) (Fig. 2a). Interestingly, it is the only characteristic motif created by the N2 atom in the studied crystal structures. Two NH 2 groups of the carboxamidine residue and two anions create another ring pattern R 2 4 (8), which is composed similarly to the R 2 2 (10) ring around the inversion center (Fig. 2b). This pattern occurs in the crystal structure of bisulfate and two chloride salts.
Figure 2c-f shows also small rings arranged in an ascending order R 1 2 (6) < R 2 2 (8) < R 2 3 (8). Formation of these patterns can be expressed by the sum of the elementary graph-set descriptors, E a d (n), which were originally invented for description of atomic pathways in each independent molecule [6,7]. A juxtaposition of the molecules and formation of hydrogen bonding patterns are represented by the algebraic equation of elementary graph-set descriptors. Thus, the aforementioned rings are created as follows: The first one occurs in the chloride salt (1) and bases on the bifurcated hydrogen bonding interaction of one chloride anion. The same two rings are found in (HPyCA) 2 (I)I 3 (4) and they are arranged in the pseudo centrosymmetric binary system. So, one iodide anion takes part in as many as four hydrogen bonds and such surrounding of the anion is not present in the other studied crystal structures. In the bisulfate salt (5), the ring pattern is naturally enlarged due to two oxygen atoms are involved in hydrogen bonding network. Therefore, the simplest ring R 1 2 (6) is expanded by the S-O two-atomic pathway, which can be expressed by the elementary graph-set E 1 0 (2) SO . Using algebraic approach, a relation between two patterns found in chloride and bisulfate is written as R 1 2 (6) + E 1 0 (2) = R 2 2 (8). Similarly, the ring R 2 3 (8) present in (HPyCA)Cl· H 2 O (2) results from expansion of the simplest R 1 2 (6) pattern by the O-H pathway R 1 2 (6) + E 1 1 (2) = R 2 3 (8). Apart from the rings, the chain patterns have got high importance in a view of propagation of the crystal structure and of the crystal growth. In (HPyCA)HSO 4 (5), (HPyCA)Cl·H 2 O (2), and (HPyCA)Cl (1), very short chain patterns containing only four atoms are found, C 1 1 (4) or C 1 2 (4). The former is created by the only one symmetry independent O1-H1O···O4 hydrogen bond and exists in the crystal structure of (HPyCA)HSO 4 (5) (Fig. 3a). The latter C 1 2 (4) chain is observed in (HPyCA)Cl·H 2 O (2) and it runs through the Clanions and water molecules. In the case of (HPyCA)Br (3) and (HPyCA)Cl (1), the C 1 2 (4) chain is constructed by the NH 2 group and anions. So, the organic cations are involved in stabilization of the hydrogen bonding network in the crystal structure of bromide and chloride salts, but interestingly the HPyCA + ions are completely omitted in those short chains in bisulfate and hydrated chloride salts. Such architecture of the network is probably connected to the high tendency of the bisulfate anions to associate with each other, as a data mining of Cambridge Structural Database reveals a lot of crystal structures containing the (HSO 4 -) n chains [4,5]. A branched molecular structure of the HSO 4 ion may also be important in this question. Figure 3 shows that the chain patterns are connected to each other by the HPyCA + associated in dimers forming aforementioned R 2 2 (10) or R 2 4 (8) rings. So, one can infer that the rings play a supporting role in stabilization of the crystal structures. However, their role cannot be regarded as secondary, as creation of the dimers allows crystal growth along orthogonal direction to the chains.

Vibrational characteristics
Geometry data taken from crystal structure analysis show weak nature of N/O-H···donor hydrogen bonds in the studied compounds except one O-H···O interaction. The shortest do-nor···acceptor distance is observed for the O-H···O hydrogen bond, 2.5969(19) Å (Table S1), formed by the adjacent bisulfate anions in (HPyCA)HSO 4 (5). According to earlier Novak's work, the band associated with the stretching vibration of hydroxyl group νOH is seen at 2453 cm -1 [18]. This value correlates very well with a dependence of OH stretching frequency on O···O distance and indicates medium-strong feature of O-H···O hydrogen bond in the (HPyCA)HSO 4 crystal. A medium hydrogen bond of the N-H···O type is created in (HPyCA)Cl·H 2 O (2). Since the N···O distance is 2.800(3) Å, the νNH band is observed in higher frequency region than νOH in the bisulfate salt, 3136 cm -1 (Fig. 4). Geometry data for the other N-H···donor hydrogen bonds indicate their weak nature, and therefore, the respective νNH bands are expected near the νCH ones. So, theoretical calculations have been carried out for the HPyCA + ion and potential energy distribution analysis was performed (Table S2). However, such kind of calculations can provide artificial results; theoretical frequencies of normal modes were also determined for the complex [(HPyCA) 2 Cl 4 ] 2ionic system with C i point group symmetry constrain for geometry parameters. Generally, Table 4 shows good agreement of the theoretical and experimental frequencies and PED analysis reveals a character of each mode.
According to the crystallographic data, the HPyCA + ions are arranged in pairs and connected to each other by two relatively long N3-H3B···N2 hydrogen bonds, 3.028(3) Å. (HPyCA)HSO 4 (5). The fundamental vibration for the I 3 is observed as the most intense band at the low frequency region in the Raman spectrum of 4. The maximum lies at 110 cm -1 and the first and the second overtones are seen at 221 and 334 cm -1 . In the case of the bisulfate anion, its ν 3 stretching vibration of F 2 symmetry in tetrahedral SO 4 2anion splits into two components, 1068 and 1026 cm -1 , due to lowering of symmetry from T d (SO 4 2-) to C 3v (HSO 4 -). Also, the ν 1 mode is associated to the stretching vibration of the S-OH bond. The Raman components for both ν 3 and ν 1 modes are observed at 1023 and 878 cm -1 . Among the bending modes ν 4 and ν 2 , the one maximum at 433 cm -1 in the infra-red spectrum can be tentatively assigned to the ν 4 vibration, whereas the Raman spectrum reveals its two-component feature, 431 and 417 cm -1 .

Conclusions
The (HPyCA)Cl (1) was used to obtain four new salts of 1Hpyrazole-1-carboxamidine with various inorganic acids. The simplicity of synthetic procedure of presented compounds can be optionally used in organic synthesis wherever other salt than commercially available (HPyCA)Cl (1) is required.
Since the literature data as well as Cambridge Structural Database do not contain any structural data about the salts of PyCA, five crystal structures were determined by means of single-crystal X-ray diffraction and presented here. The topological analysis with algebraic approach on the graphset descriptors of hydrogen bonding patterns showed similarities in formation of particular patterns regardless of the counterion present in the structure. This fact was also confirmed by vibrational spectroscopy, where some differences in the infra-red spectra were observed in the high frequency region for νNH modes. In all the studied compounds, the HPyCA + possesses protonated carboxamidine group, whereas the nitrogen atom of pyrazole ring is deprotonated. Theoretical calculations on the protonation route of PyCA revealed that aforementioned speciation cationic form of 1H-pyrazole-1-carboxamidine is the only favored one. Besides, these calculations showed two relatively numerous stable neutral forms and also two other tautomers that are unstable. The molecules decomposed into pyrazole and carbodiimid tautomer of cyanamide. This result seems only seemingly insignificant, but it shows possible mechanism of guanylation by PyCA which is important step in synthesis of some biological active compounds including antiviral drugs.