Insights into the interactions between salt molecules: A combined experimental and computational study

The proton transfer (PT) complex of 2-amino 4-methoxy 6-methyl pyrimidinium (2A4M6MP) 4-aminosalicylate (4AMSA), C 6 H 10 ON 3+ C 7 H 6 NO 3− , (I), and 5-chlorosalicylate (5ClSA), C 6 H 10 ON 3+ C 7 H 4 O 3 Cl − (II) were synthesized and crystallized. The crystal structures of both salt molecules were investigated by SC-XRD. Further, the calculated ∆ pKa values clearly demonstrate that 2A4M6MP is a good salt former when combined with carboxylic acids. Hirshfeld surface analysis provides the quantifying interactions in the solid state and energy framework shows the stability of hydrogen bonding. QTAIM analysis reveals the nature of chemical bonding and electron density distribution of intermolecular interactions of pyrimidine based salt molecules.


Introduction
Co-crystals are the products of crystal engineering, which aims to bring two or more different molecules into one crystal lattice via non-covalent interactions, e.g. hydrogen bonds, without breaking any covalent bond [1]. In designing co-crystals, an important factor for consideration is, which of the two possible intermolecular bonds is favored, i.e. hetromeric (co-crystal) or homomeric (single molecule) [2,3]. Functional groups that show a high tendency of forming a heteromeric interaction include carboxylic acid, pyrimidine and amide [4]. Molecules containing these groups are potentially good supramolecular synthons for co-crystal formation [5]. Proton transfer complexes are gaining considerable interest in the research from the last decade, due to their wide potential applications in the eld of pharmaceutical science [6,7], material science [8,9], bio-electrochemical energy transfer process [10], biological science [11,12], optoelectronic, optical communication, organic semiconductor [13,14] and DNA binding [15], antibacterial and antifungal activity [16].
Pyrimidine and amino pyrimidine derivatives are biologically important compounds and they occur in nature as components of nucleic acids such as cytosine, uracil and thymine [17]. Pyrimidine derivatives also developed as the antiviral agents such as AZT, which is the most widely used anti-HIV drug and in biology it has many applications in the areas of pesticides and pharmaceutical agents [18]. Furthermore, the pyrimidine group offers two protonation sites (the two ring nitrogen) and the site of protonation depends on the nature of the substituent [19,20]. 4-Amino salicylic acid (4AMSA) is a well-known antibiotics for tuberculosis treatment and also encouraging anticancer drug [1,21]. 5-Chlorosalicylic acid (5ClSA) is a potential candidate have found enormous application in medical and pharmaceutical research and industry, particularly in the treatment of acene, psoriasis, calluses, corns, keratosis pilaris and warts [22]. 5-Chlorosalicylic acid is presently nding burgeoning use in cosmetic industry [23]. The title salts, namely, 2-amino 4-methoxy 6-methyl pyrimidinium 4-amino salicylate (2A4M6MP-4AMSA) (I), and 2-amino 4-methoxy 6-methyl pyrimidinium 5-chloro salicylate (2A4M6MP-5ClSA) (II), have been investigated in order to study the hydrogen bonding patterns and supramolecular architectures in the crystalline state. The wide range importance of 2A4M6MP and salicylic acid motivated to synthesize their proton transfer complex [5]. Their single crystal has been grown by slow evaporation technique and it was investigated by crystal and molecular structure analysis. The ngerprint plots associated with the Hirshfeld surface clearly displays each signi cant interaction involved in the structure, by quantifying them in an effective visual manner. The ∆pKa values for both base-acid complexes (I & II) were calculated to con rm the formation of molecular salts.

Synthesis and Crystallization
The title compound was synthesized by the reaction of 1:1 stoichiometric mixture of 2-amino 4-methoxy 6-methyl pyrimidine (34.79 mg, 0.25 mmol) with 4-amino salicylic acid (38.28 mg, 0.25 mmol) or 5chlorosalicylic acid (43.14 mg, 0.25 mmol) in 20ml of hot methanol solution, after warming a few minutes over a water bath for 30 min. The solution was cooled and kept at room temperature. Within few days, block-shaped brown color crystal of salt-I and colorless needle-shaped crystal of salt-II were obtained by slow evaporation at room temperature. Both crystals (I & II) were found suitable for the single crystal X-ray structure analysis.

X-ray Crystallography
Single crystal X-ray diffraction intensity data for the crystals of (I) & (II) were collected on Bruker D8 QUEST ECO diffractometer [24] equipped with APEX III photon detector and Molybdenum monochromator (MoKα radiation, λ = 0.71073 Å). The unit cell re nement and data reduction were carried out using Bruker SAINT [24] and the necessary absorption corrections were performed by multiscan method using SADABS [24]. The structure of both crystals (I & II) were solved by direct methods using SHELXS [25] incorporated to WinGX-2014 [26] program suit and re ned by full-matrix least-squares techniques using SHELXL [25,26]. All non-hydrogen atoms were re ned anisotropically and thereafter, all hydrogen atoms were placed in their geometrically idealized positions and constrained to ride on their parent atoms. The unit cell, X-ray intensity data collection and crystal structure re nement details of salt (I) and (II) are presented in Table 1. All H-atoms except the methyl group H-atoms were located in difference Fourier maps and re ned isotropically. The remaining methyl group H-atom positions were calculated geometrically [C-H = 0.96 Å] and re ned using the riding model with U iso (H) = 1.5U eq (C). Diagrams and publication material were generated using Olex2 [27], PLATON [28] and MERCURY softwares [29].

Hirshfeld Surface Analysis
The Hirshfeld surface of the crystal is being used to analyze the intermolecular interactions of the molecules in the crystal, which is de ned by using the weight function [the division of the sum of the promolecule density (spherical atom electron densities) to the sum of the same procrystal electron density [30,31]. The intermolecular contact information was obtained from the two d i parameters (distance from the surface to the nearest atom interior to the surface) and d e (distance from the surface to the nearest atom exterior to the surface), which is derived from the triangulation of surface points. The Hirshfeld surface and ngerprint plots of the salts (I) & (II) were generated using Crystal Explorer 17.5 [32]. Fingerprint plots are based on Hirshfeld surface, which allows to identify strength of intermolecular interactions and crystal packing modes in molecular crystals to be explored [33]. The sums of four different energy components as electrostatic, polarization, dispersion and repulsion energies were used to calculate the total intermolecular interaction energy (Eq. 1). The graphical representation of energy frameworks of individual energy components was carried out to depict the centroids of interacting molecular pairs as color-coded cylinders. 1

QTAIM Calculation
To view the electronic level information of two different salt molecules, single point energy calculation of DFT (B3LYP) [34][35][36] method with the basis set 6-311G** was performed directly using the crystallographic coordinates GAUSSIAN03 software [37]. Then, topological properties of electron density of both molecules were retrieved from the wave function. The topological properties of electron density at the bond critical point (bcp); [where ] of the molecule were determined from the charge density analysis using Bader's theory of atoms in molecules (AIM) [38]. The bcp for all bonds has been located from the where the rst derivative of electron density is zero, which implies that the electron density is maximum. The second order derivative of electron density is Laplacian of electron density which is formulated in Hessian matrix

Impact of ∆pKa value on the occurrence of acid base dimmers
In a reaction, the acid and base involves, the transfer of proton from acid to base gives rise to a salt, whereas the co-crystal arises, when the proton intact with the acid. For a carboxylic acid pyrimidine reaction [41][42][43], the COO − H···N arom and molecular salts have COO -···H-N + arom heterosynthon. The ∆pKa [pKa(base) -pKa(acid)] rule is an empirical indicator which predicts whether a molecular complex will result as a salt [44][45][46]. The 'rule of three' is commonly employed to predict the outcome of a solid resulting from acid-base molecular reactions [42,43,47]. As a general rule, ∆pKa < 0 yields a co-crystal while ∆pKa > 3.75 leads to a salt. It is generally believed that the co-crystal or salt or both can appear in the domain between 0 and 3.75 [42,48]. Furthermore, a report outline that [49], the ∆pKa region can be classi ed into three zones; in the rst zone, the value of ∆pKa < -1, where one can expect the co-crystal; in the second zone the values range -1 < ∆pKa < 4, this comprises the co-crystal and salt; while in the third zone, the value of ∆pKa > 4 [50,51], which is the molecular salt and this is in good agreement with the molecular complexes salicylic acid and pyrimidine derivative. The pKa value of 2A4M6MP, 4-amino salicylic acid and 5-chlorosalicylic acid are 5.77, 3.68 and 2.59 respectively. In the present study, the calculated values of ∆pKa values of acid-base complexes fall in the range 2.0 to 4.0 (Table S9), this con rms the formation of molecular salts.

Hirshfeld surface analysis
The three-dimensional d norm surface is a useful tool for analyzing and visualizing the intermolecular interactions, as it shows negative or positive values depending on whether an intermolecular contact is shorter or longer, respectively, than the sum of the van der Waals radii [18]. analyses of synthon, the crystal packing of salts were con rmed by light red spots on the d norm surfaces of two salts. Further, inter-contacts are plotted with ngerprint plots (Fig. 5). The Fig. 5(a) shows large surfaces for all inter-contacts, Fig. 5(c) shows large surface for H···H interatomic contacts, the N···H contact plot is shown in Fig. 5(d) and the Fig. 5(e) shows the presence of O···H contact with the two characteristic wings and the "butter ies" are identi ed as a consequence of C-H interactions reveals the information of intermolecular hydrogen bonding. The ngerprint plot studies have been characterized the non-covalent interaction and their reactive proportions to the present organic salt molecules.

Interaction energy calculation
To understand the geometric and electronic relationship between the structure of molecules and to predictive structure-property relationship in crystal engineering, energy frameworks offer a powerful path to visualize the supramolecular architecture of molecular crystal structures. The successful calculation of interaction energies with color-coded molecular crystals was performed for both salts (I&II); the values are tabulated (Table S10 & S11). The total energies of all interacting molecules with respect to corresponding reference molecule along with the different symmetry operation and centroid-centroid distance. In the salt I, the total energy for the hetrosynthon is -52.7 kJ/mol and for the homosynthon, the value is -20.5 kJ/mol. Whereas in the salt II, the total energy is -36.2 kJ/mol and − 68.3 kJ/mol for the hetro and homosynthon respectively. On comparing the salts, the total energy values clearly con rm that, in the crystal phase, the salts are forming strong hydrogen bonding interactions. In the energy framework, the strength of intermolecular interactions is directly correlated to the radii of the color-coded cylinders. Figure 6 shows, the energy frameworks of the salt I and II were generated for a cluster of 3×3×3-unit cells to understand the overall topology of the energy distribution in the solid-state phase. In short, by using NCIPLOT the reduced density gradient is plotted as the function of the density (mapped as isosurfaces) over the molecule of interest. Fig S25 shows the sign of the second Hessian eigen value times the electron density (sign of (λ 2 )ρ in atomic units) enables the identi cation of attractive/stabilizing or repulsive interactions (Salt-I:-105.90; Salt -II:-114.01 kcal/mole). Overall, the interacting energy topologies of the molecules are concluded that these interacting energies are playing crucial role in the assembly of the molecules in the solid state and in the crystal engineering.

Topological properties
The QTAIM (Bader's quantum theory of atoms in molecules) analysis is a powerful tool to understand the nature of chemical bonding, reactive nature and intermolecular interactions of the molecular system at electronic level. The topological parameters such as electron density, Laplacian of electron density of both salts obtained from the wave function have carried out to understand the stability of the molecule when it forms together. To visualize the lone pair position and charge accumulation of the salt molecules, deformation electron density map of both salts were plotted, it displays the lone pair position of O-atom of C = O group (Fig. 7a). Similarly, the Laplacian of electron density (Fig. 7b) −5 ]. The small electron density and positive Laplacian of electron density con rms that the interactions are closed-shell interaction. Furthermore, the kinetic energy, potential energy, total energy and dissociation energy of these interactions were calculated and summarized in the Table 3. Figure 7c shows  Electrostatic potential of both salts (I and II) were calculated to understand the characteristic regions of positive (attracting the nucleophiles) and negative (attracting electrophiles) potentials of the cofomers of salt molecules which were clearly visible and well separated. In which, the vicinity of electronegative potential are shown on the acid group of both salts (Fig. 7d). The obtained energy from the HOMO and LUMO of both salts used to determine the band gap and various reactivity descriptors such as electron a nity (A), ionization potential (I), global hardness ( ), electrophilicity (ω) and electronegativity ( ) shown in Table 4

Conclusions
In both crystal structures of salt molecules, one of the pyrimidine N atoms was protonated which was con rmed from the ∆pKa values, molecular and topological analysis. In general, apart from the hydrogen bonding interactions, it was identi ed that the molecular arrangements of both salts (I) and (II) also