Sodium dirubidium citrate, NaRb2C6H5O7, and sodium dirubidium citrate dihydrate, NaRb2C6H5O7(H2O)2

The crystal structures of sodium dirubidium citrate and sodium dirubidium citrate dihydrate have been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. Both structures contain Na chains and Rb layers, which link to form different three-dimensional frameworks.

The crystal structures of sodium dirubidium citrate {poly[-citrato-dirubidium(I)sodium(I)], [NaRb 2 (C 6 H 5 O 7 )] n } and sodium dirubidium citrate dihydrate {poly[diaqua(-citrato)dirubidium(I)sodium(I)], [NaRb 2 (C 6 H 5 O 7 )-(H 2 O) 2 ] n } have been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. Both structures contain Na chains and Rb layers, which link to form different threedimensional frameworks. In each structure, the citrate triply chelates to the Na + cation. Each citrate also chelates to Rb + cations. In the dihydrate structure, the water molecules are bonded to the Rb + cations; the Na + cation is coordinated only to citrate O atoms. Both structures contain an intramolecular O-HÁ Á ÁO hydrogen bond between the hydroxy group and one of the terminal carboxylate groups. In the structure of the dihydrate, each hydrogen atom of the water molecules participates in a hydrogen bond to an ionized carboxylate group.

Chemical context
A systematic study of the crystal structures of Group 1 (alkali metal) citrate salts has been reported in Rammohan & Kaduk (2018). The study was extended to lithium metal hydrogen citrates in Cigler & Kaduk (2018), and to sodium metal hydrogen citrates in Cigler & Kaduk (2019). These two compounds (Figs. 1 and 2) are a further extension to sodium dirubidium citrates.

Structural commentary
For NaRb 2 C 6 H 5 O 7 , the root-mean-square deviation of the non-hydrogen atoms in the refined and optimized structures is 0.095 Å (Fig. 3). The excellent agreement between the structures is strong evidence that the experimental structure is correct (van de Streek & Neumann, 2014). For NaRb 2-ISSN 2056-9890 C 6 H 5 O 7 (H 2 O) 2 , the agreement of the refined and optimized structures is poorer (Fig. 4); the r.m.s. cartesian displacement is 0.45 Å . The largest differences are in the carboxyl group C5/ O13/O14. Removing O13 and O14 from the displacement calculation yields a value of 0.222 Å , in the upper range of correct structures according to van de Streek & Neumann (2014). Apparently the refined structure is in error, perhaps because it was refined using laboratory X-ray powder data and the structure contains two heavy Rb atoms. This discussion uses the DFT-optimized structures.
In both structures, all of the citrate bond lengths, bond angles, and torsion angles fall within the normal ranges indicated by a Mercury Mogul Geometry Check (Macrae et al., 2008). The citrate anion in both structures occurs in the trans,trans-conformation (about C2-C3 and C3-C4), which is one of the two low-energy conformations of an isolated citrate (Rammohan & Kaduk, 2018). The central carboxylate group and the hydroxy group exhibit small twists (O15-C6-C3-O17 torsion angles of À16.0 and À18.2 ) from the normal planar arrangement.
In NaRb 2 C 6 H 5 O 7 , the citrate anion triply chelates to Na19 through the terminal carboxylate O14, the central carboxylate O15, and the hydroxyl group O17. The citrate also chelates to Rb21 through the terminal carboxylate O11 and the central carboxylate O15. Each citrate oxygen atom bridges multiple metal atoms. The Na + cation is six-coordinate, with a bondvalence sum of 1.12. The two Rb + cations are seven-coordinate, with bond-valence sums of 0.99 and 1.16.
In the dihydrate, the citrate anion similarly triply chelates to Na19 through the terminal carboxylate O12, the central carboxylate O15, and the hydroxy group O17 (the numberings of the oxygen atoms are partially arbitrary). Each terminal carboxylate group chelates to a different Rb21 cation. Most of the oxygen atoms bridge multiple metal atoms, but O13 and Comparison of the refined and optimized structures of sodium dirubidium citrate. The refined structure is in red, and the DFT-optimized structure is in blue.

Figure 4
Comparison of the refined and optimized structures of sodium dirubidium citrate dihydrate. The refined structure is in red, and the DFT-optimized structure is in blue.

Figure 1
The asymmetric unit of NaRb 2 C 6 H 5 O 7 , with the atom numbering and 50% probability spheroids.
O14 bind only to Rb cations, and O17 binds only to the Na + cation. The Na coordination sphere is composed only of citrate oxygen atoms. Rb20 is coordinated by four H 2 O, and Rb21 is bonded to two H 2 O molecules. Each water molecule is coordinated to two Rb20 and and one Rb21 cations. The Na + cation is six-coordinate (distorted octahedral), with a bondvalence sum of 1.19. The Rb20 and Rb21 cations are eight-and nine-coordinate, respectively. The coordination polyhedra are irregular, and the bond-valence sums are 0.94 and 1.03. The Mulliken overlap populations in both structures indicate that the Rb-O bonds are ionic, but that the Na-O bonds have some covalent character.

Supramolecular features
In the crystal structure of NaRb 2 C 6 H 5 O 7 (Fig. 5), the distorted octahedral NaO6 coordination polyhedra share edges to form zigzag double chains along the a-axis direction. The RbO 7 polyhedra share edges to form layers parallel to the ac plane. These layers link the Na chains, forming a three-dimensional framework. The hydrophobic methylene groups of the citrate anions occupy cavities in this framework.
In the crystal structure of NaRb 2 C 6 H 5 O 7 (H 2 O) 2 (Fig. 6), the NaO 6 coordination polyhedra share corners to form double zigzag chains along the c-axis direction. The Rb polyhedra share edges to form layers parallel to the ac plane. These layers share corners with each other and share edges with the Na chains, forming a three-dimensional framework. The hydrophobic methylene groups of the citrate anions also occupy cavities in this framework.

Figure 5
Crystal structure of NaRb 2 C 6 H 5 O 7 , viewed down the a axis.

Figure 6
Crystal structure of NaRb 2 C 6 H 5 O 7 (H 2 O) 2 , viewed down the a axis.
hydrogen bond contributes 14.0 kcal mol À1 to the crystal energy. A weak C-HÁ Á ÁO hydrogen bond also contributes to the crystal energy.
In NaRb 2 C 6 H 5 O 7 (H 2 O) 2 , each water molecule hydrogen atom acts as a donor in an O-HÁ Á ÁO hydrogen bond to a carboxylate oxygen (Table 2). By the correlation of Rammohan & Kaduk (2018), these hydrogen bonds range from 11.0-14.0 kcal mol À1 in energy. There is an intramolecular O17-H18Á Á ÁO13 hydrogen bond between the hydroxyl group and one of the terminal carboxylate groups, as well as a C-HÁ Á ÁO hydrogen bond.
The two structures exhibit some similarities ( Fig. 7), but a mechanism for interconversion of the structures is not obvious by visual inspection.

Database survey
Details of the comprehensive literature search for citrate structures are presented in Rammohan & Kaduk (2018). A reduced cell search for NaRb 2 HC 6 H 5 O 7 in the Cambridge Structural Database (Groom et al., 2016)  Rietveld plot for NaRb 2 C 6 H 5 O 7 . The red crosses represent the observed data points, and the green line is the calculated pattern. The magenta curve is the difference pattern, plotted at the same scale as the other patterns. The vertical scale has been multiplied by a factor of 8 for 2 > 44.0 . The row of black tick marks indicates the reflection positions for this phase.

Figure 9
Rietveld plot for NaRb 2 C 6 H 5 O 7 (H 2 O) 2 . The red crosses represent the observed data points, and the green line is the calculated pattern. The magenta curve is the difference pattern, plotted at the same scale as the other patterns. The vertical scale has been multiplied by a factor of 10 for 2 > 44.0 . The row of black tick marks indicates the reflection positions for this phase.

Figure 7
Comparison of the crystal structures of sodium dirubidium citrate (left) and sodium dirbuidium citrate dihydrate (right).
including the chemistry of C, H, Na, O, and Rb only it yielded no hits.

Synthesis and crystallization
NaRb 2 C 6 H 5 O 7 (H 2 O) 2 was prepared by adding stoichiometric quantities of Na 2 CO 3 and Rb 2 CO 3 to a solution of 10 mmol H 3 C 6 H 5 O 7 in 10 ml of water. After the fizzing subsided, the clear solution was dried overnight at 348 K to yield a glass. This glass was heated at 450 K for 30 min to yield a pale-yellow solid. This solid was equilibrated in air at ambient conditions for 3 h. The anhydrous salt was prepared by heating the dihydrate at 450 K for 30 min.

Refinement
Crystal data, data collection and structure refinement (Fig. 8) details are summarized in Table 3. The diffraction patterns of both compounds were indexed using N-TREOR (Altomare et al., 2013), and the cells were reduced using the tools in the PDF-4+ database (Fawcett et al., 2017). The systematic absences in the the pattern of NaRb 2 C 6 H 5 O 7 (H 2 O) 2 suggested the space groups Pna2 1 and Pnam. The unit-cell volume indicates that Z = 4, so Pna2 1 was chosen, and confirmed by successful solution and refinement of the structure.
The structure of NaRb 2 HC 6 H 5 O 7 was solved using Monte Carlo simulated annealing techniques as implemented in EXPO2014 (Altomare et al., 2013). A citrate anion, a Na cation, and two Rb cations were used as fragments. The position of the active hydrogen atom H18 was deduced from the potential intramolecular hydrogen-bonding pattern.
Pseudovoigt profile coefficients were as parameterized in Thompson et al. (1987) and the asymmetry correction of Finger et al. (1994) was applied and microstrain broadening by Stephens (1999). The hydrogen atoms were included in fixed positions, which were re-calculated during the course of the refinement. The U iso values of C2, C3, and C4 were constrained to be equal, and those of H7, H8, H9, and H10 were constrained to be 1.3 times that of these carbon atoms. The U iso values of C1, C5, C6, and the oxygen atoms were constrained to be equal, and that of H18 was constrained to be 1.3 times this value. The U iso values of Rb20 and Rb21 were constrained to be equal.
The structure of NaRb 2 C 6 H 5 O 7 (H 2 O) 2 was solved using Monte Carlo simulated annealing techniques as implemented in EXPO2014 (Altomare et al., 2013). A citrate anion, a Na cation, two Rb cations, and three O atoms were used as fragments. In the best solution, one of the oxygen atoms was 1.30 Å from one of the Rb atoms, and was removed from the model. The positions of the active hydrogen atoms were deduced from potential hydrogen-bonding patterns. The same refinement strategy was used as for the anhydrous compound, and the U iso values of the two water molecule oxygen atoms were constrained to be equal. Comparison of the initial refined model to that from the DFT calculation revealed that the orientations of the carboxyl group C5/O13/O14 differed, so the Rietveld refinement ( Fig. 9) was re-started from the DFT model.
Density functional geometry optimizations (fixed experimental unit cells) were carried out using CRYSTAL14 . The basis sets for the H, C, and O atoms were those of Gatti et al. (1994), the basis sets for Na was that  Step Step 2 values ( ) 2 min = 5.001 2 max = 100.007 2 step = 0.020 2 min = 5.001 2 max = 100.007 2 step = 0.020 The same symmetry and lattice parameters were used for the DFT calculations as for each powder diffraction study. Computer programs: Diffrac.Measurement (Bruker, 2009) of Dovesi et al. (1991), and the basis set for Rb was that of Sophia et al. (2014). The calculations were run on eight 2.1 GHz Xeon cores (each with 6 GB RAM) of a 304-core Dell Linux cluster at Illinois Institute of Technology, using 8 kpoints and the B3LYP functional, and took approximately 5 and 29 h.