Crystal structure of pentasodium hydrogen dicitrate from synchrotron X-ray powder diffraction data and DFT comparison

The crystal structure of pentasodium hydrogen dicitrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques.

The crystal structure of pentasodium hydrogen dicitrate, Na 5 H(C 6 H 5 O 7 ) 2 , has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Each of the two independent citrate anions is joined into a dimer by very strong centrosymmetric O-HÁ Á ÁO hydrogen bonds, with OÁ Á ÁO distances of 2.419 and 2.409 Å . Four octahedrally coordinated Na + ions share edges to form open layers parallel to the ab plane. A fifth Na + ion in trigonal-bipyramidal coordination shares faces with NaO 6 octahedra on both sides of these layers.

Structural commentary
The compound Na 5 H(C 6 H 5 O 7 ) 2 was unexpectedly synthesized by heating Na 2 HC 6 H 5 O 7 (H 2 O) 1.5 . The asymmetric unit of the title compound is shown in Fig. 1. The root-mean-square deviation of the non-hydrogen atoms in the Rietveld-refined and DFT-optimized structures is 0.216 Å (Fig. 2). The reasonable agreement between the two structures is evidence that the experimental structure is correct (van de Streek & Neumann, 2014). This discussion uses the DFT-optimized structure. Most of the bond lengths, bond angles, and torsion angles fall within the normal ranges indicated by a Mercury Mogul geometry check (Macrae et al., 2008). Both the O28-C10 bond length of 1.249 Å [Z-score = 3.4; average = 1.213 (13) Å ] and the O28-C10-C8 angle of 120.4 [Z-score = 4.0; average = 126.9 (16) ] are flagged as unusual. Since this oxygen atom also coordinates to an Na + cation, it is not unreasonable to encounter some slightly unusual geometry. Each Na + cation is chelated by at least one citrate anion. The chelation modes include hydroxyl/terminal carboxyl, terminal/ central carboxyl, and coordination of both oxygen atoms of a terminal carboxyl group.
The structure contains five independent Na + cations. Na37, Na38, Na39, and Na40 exhibit octahedral coordination spheres, with bond-valence sums of 1.19, 1.24, 1.04, and 1.17 valence units, respectively. Na41 is only five-coordinate with a trigonal-bipyramidal coordination sphere, but its bondvalence sum is 1.26. The only O atom not coordinating to an Na + cation is O26, which participates in very strong centrosymmetric hydrogen bonds. The octahedra involving Na37-Na40 share edges to form open layers parallel to the ab plane. Trigonal-bipyramidal Na41O 5 polyhedra share faces with Na37O 6 and Na39O 6 octahedra on both sides of these layers. The crystal structure is illustrated in Fig. 3.
The Mulliken overlap populations and atomic charges indicate that the metal-oxygen bonding is ionic. Comparison of the structures of the starting material Na 2 HC 6 H 5 O 7 (H 2 O) 1.5 and the title compound does not suggest any plausible mechanism for the conversion.
The Bravais-Friedel-Donnay-Harker (Bravais, 1866;Friedel, 1907;Donnay & Harker, 1937) morphology suggests that we might expect elongated morphology for pentasodium hydrogen dicitrate, with {100} as the principal axis. A 4th-order spherical harmonic texture model was included in the refinement. The texture index was 1.014, indicating that preferred orientation was slight for this rotated capillary specimen.

Supramolecular features
The layers are connected by very strong centrosymmetric O26-H44Á Á ÁO26 and O25-H43Á Á ÁO25 hydrogen bonds ( The asymmetric unit of Na 5 H(C 6 H 5 O 7 ) 2 , with the atom numbering. The atoms are represented by 50% probability spheroids.

Figure 3
Crystal structure of Na 5 H(C 6 H 5 O 7 ) 2 , viewed down the a axis.
O25Á Á ÁO25 distance is 2.409 Å , making these among the shortest hydrogen bonds. The Mulliken overlap populations in the hydrogen bonds are 0.145 and 0.136 e, which correspond to 20.8 and 20.2 kcal mol À1 for each hydrogen bond (Rammohan & Kaduk, 2017a). These hydrogen bonds link two citrates into dimers. The Mulliken overlap populations indicate that the hydroxyl groups O33-H35 and O34-H36 each act as donors in three hydrogen bonds. One [with graph set S(5)] is to the central carboxylate group, and another is intramolecular to a terminal carboxyl group. The third hydrogen bond is intermolecular. These hydrogen bonds are much weaker than the centrosymmetric ones, contributing 5-8 kcal mol À1 to the crystal energy.

Database survey
Details of the comprehensive literature search for citrate structures are presented in Rammohan & Kaduk (2017a). A reduced cell search of the cell of pentasodium hydrogen dicitrate in the Cambridge Structural Database (Groom et al., 2016) (increasing the default tolerance from 1.5 to 2.0%) yielded 98 hits, but combining the cell search with the elements C, H, Na, and O only yielded no hits.

Synthesis and crystallization
The title compound was prepared by heating commercial reagent Na 2 HC 6 H 5 O 7 (H 2 O) 1.5 (Sigma-Aldrich lot BCBC6031V) from 295-453K at 14 K min À1 in air. The crystal structure of this reagent is reported in Rammohan et al. (2016). After holding at 453 K for two minutes, the sample began to discolour (turn yellow), and it was taken from the oven and sealed in a glass jar to cool.

Refinement details
Crystal data, data collection and structure refinement details are summarized in Table 2. The sample was blended with NIST SRM 640b silicon internal standard in a Spex 8000 mixer/mill, and packed into a standard sample holder. It was protected from the atmosphere by a thin Kapton window attached to the cell edges with Vaseline. The pattern was measured on a Bruker D2 Phaser at IIT, and eventually at 11-BM at APS/ANL (Lee et al., 2008;Wang et al., 2008). The structure was solved and refined using the synchrotron data. Diffraction data are displayed in Fig. 4.
The synchrotron pattern was indexed with Jade 9.5 (MDI, 2012) on a primitive triclinic unit cell having a = 6.263, b = 12.029, c = 12.132 Å , = 74.145, = 81.530, = 80.8 6 , and V = 863.06 Å 3 . The volume corresponds to four citrate anions per cell. A Le Bail fit using this cell yielded a reduced 2 = 2.866, but it was not possible to solve the crystal structure using this unit cell.
Removing  The same symmetry and lattice parameters were used for the DFT calculation. Computer programs: DIFFRAC.Measurement (Bruker, 2009)  cell, and space group P1 was assumed. A Le Bail fit yielded a reduced 2 of 2.716. The structure was solved in the sub-cell using DASH 3.3.2 (David et al., 2006), with a citrate anion and two Na + cations as fragments. Two of the 25 simulated annealing runs yielded figures of merit much lower than the rest. Since two O13 atoms were 2.53 Å apart (related by a centre of symmetry), a hydrogen was placed at the centre. Refinement of this model yielded a reduced 2 of 2.6, but the charge did not balance. A difference-Fourier map indicated a peak 2.33 Å from O13; this is too close to be an oxygen atom, but is reasonable for an Na atom. Refinement of this model yielded a reduced 2 of 1.85, and an Na occupancy of 1/2.
The structure was transformed (matrix [010/210/111]) to the original cell using Materials Studio (Dassault Systemes, 2014). The occupancies of the now two half-Na were refined. They refined to 1/0, and the low-occupancy Na moved too close to other atoms. Refinement of the resulting Na 5 H(citrate) 2 model yielded a reduced 2 of 1.829. This larger cell accounts for the 2.510 peak and several other very weak peaks not explained by the sub-cell. A possible C-centering, as suggested by PLATON (Spek, 2009), is not present.
Pseudo-Voigt profile coefficients were as parameterized in Thompson et al. (1987) with profile coefficients for Simpson's rule integration of the pseudo-Voigt function according to Howard (1982). The asymmetry correction of Finger et al. (1994) was applied, and microstrain broadening by Stephens (1999). The structure was refined by the Rietveld method using GSAS/EXPGUI (Larson & Von Dreele, 2004;Toby, 2001). All C-C and C-O bond lengths were restrained, as were all bond angles. The C-C bonds between the terminal carboxyl carbon atoms and the adjacent carbon atoms were restrained at 1.51 (1) Å , the C-C bonds between the central carbon atoms and the adjacent carbon atoms at 1.54 (1) Å , the C-C bond between the central carbon atom and the central carboxyl carbon at 1.55 (1) Å , the C-O bond to the hydroxyl group at 1.42 (3) Å , and the C-O bonds in the carboxylate groups at 1.27 (3) Å . The tetrahedral carbon bond angles were restrained at 109 (3) , and the angles in the planar carboxyl groups at 120 (3) . The hydrogen atoms were included at fixed positions, which were recalculated during the course of the refinement using Materials Studio (Dassault Systemes, 2014). The U iso values of the C and O atoms were constrained to be equal, and the U iso values of the hydrogen atoms were constrained to be 1.3 times those of the atoms to which they are attached. A common U iso value was refined for the Na atoms.

DFT calculations
A density functional geometry optimization (fixed experimental unit cell) was carried out using CRYSTAL09 (Dovesi et al., 2005). The basis sets for the C, H, and O atoms were those of Gatti et al. (1994), and the basis set for Na was that of Dovesi et al. (1991). The calculation used 8 k-points and the B3LYP functional, and took about eight days on a 2.4 GHz PC. U iso values were assigned to the optimized fractional coordinates based on the U eq from the refined structure.