Crystal structure of trirubidium citrate monohydrate from laboratory X-ray powder diffraction data and DFT comparison

The crystal structure of trirubidium citrate monohydrate has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques.


Chemical context
In the course of a systematic study of the crystal structures of Group 1 (alkali metal) citrate salts to understand the anion's conformational flexibility, deprotonation, coordination tendencies, and hydrogen bonding, we have determined several new crystal structures. Most of the new structures were solved using powder diffraction data (laboratory and/or synchrotron), but single crystals were used where available. The general trends and conclusions about the sixteen new compounds and twelve previously characterized structures are being reported separately (Rammohan & Kaduk, 2017a). Seven of the new structures -NaKHC 6 H 5 O 7 , NaK 2 C 6 H 5 O 7 , Na 3 C 6 H 5 O 7 , NaH 2 C 6 H 5 O 7 , Na 2 HC 6 H 5 O 7 , K 3 C 6 H 5 O 7 , and Rb 2 HC 6 H 5 O 7 -have been published recently (Rammohan & Kaduk, 2016a,b,c,d,f, 2017bRammohan et al. (2016)), and two additional structures -KH 2 C 6 H 5 O 7 and KH 2 C 6 H 5 O 7 (H 2 O) 2have been communicated to the CSD (Kaduk & Stern, 2016a,b).

Structural commentary
The asymmetric unit of the title compound is shown in Fig. 1. The root-mean-square deviation of the non-hydrogen atoms in ISSN 2056-9890 the Rietveld-refined and DFT-optimized structures is 0.127 Å (Fig. 2). The good agreement between the two structures is strong evidence that the experimental structure is correct (van de Streek & Neumann, 2014). This discussion uses the DFToptimized 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). Only the O11-C4-C5-C6 torsion angle involving a terminal carboxylate group is flagged as unusual, but as shown in Rammohan & Kaduk (2017a) these torsion angles exhibit no real preference. The citrate anion occurs in the trans,transconformation, which is one of the two low-energy conformations of an isolated citrate trianion. The central carboxylate group and the hydroxyl group occur in the normal planar arrangement. The Bravais-Friedel-Donnay-Harker (Bravais, 1866;Friedel, 1907;Donnay & Harker, 1937) morphology suggests that we might expect platy morphology for the title compound, with {011} as the principal faces. A 4th-order spherical harmonic texture model was included in the refinement. The texture index was 1.014, indicating that preferred orientation was negligible for this rotated flat-plate specimen.

Supramolecular features
The three independent Rb + ions are 7-, 6-and 6-coordinate (upper threshold for Rb-O bond lengths = 3.40 Å ), with bond-valence sums of 0.84, 1.02, and 0.95, respectively. These polyhedra share edges and corners to form a three-dimensional network (Fig. 3). Hydrogen bonds (Table 1)  The asymmetric unit, with the atom numbering. The atoms are represented by 50% probability spheroids.

Figure 2
Comparison of the refined and optimized structures of trirubidium citrate monohydrate. The refined structure is in red, and the DFT-optimized structure is in blue.

Figure 3
Crystal structure of trirubidium citrate monohydrate, viewed down the b axis. outline of the unit cell needs to be added Table 1 Hydrogen-bond geometry (Å , ).

Synthesis and crystallization
H 3 C 6 H 5 O 7 (H 2 O) (10.0 mmol, 2.0972 g) was dissolved in 10 ml deionized water. Rb 2 CO 3 (15.0 mmol, 3.4659 g, Sigma-Aldrich) was added to the citric acid solution slowly with stirring. The resulting clear colourless solution was evaporated to dryness at ambient conditions to yield a white powder.

Refinement
Crystal data, data collection and structure refinement details are summarized in Table 2. The specimen was blended with a NIST SRM 640 Si internal standard (a = 5.43105 Å ). The powder pattern ( Fig. 4) was indexed using Jade 9.4 (MDI, 2012), which yielded a primitive monoclinic cell having a = 7.44769 (10), b = 11.87554 (16), c = 13.41675 (18) Å , = 97.8820 (9) , V = 1175.44 (3) Å 3 , and Z = 4. The suggested space group was P2 1 /n, which was confirmed by successful solution and refinement. Three intense peaks from a structure solution using charge flipping as implemented in Jana2006 (Petříček et al., 2014) were used to carry out a Le Bail fit in GSAS (Larson & Von Dreele, 2004). The resulting peak list was imported into Endeavour 1.7b (Putz et al., 1999), which was used to solve the structure with a citrate anion and 3 Rb atoms as fragments. A significant peak in a difference Fourier map in GSAS corresponded to the oxygen atom of a water molecule, indicating that the compound was a monohydrate. 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 hydrogen atoms were included at fixed positions, which were recalculated during the course of  The same symmetry and lattice parameters were used for the DFT calculation. Computer programs: DIFFRAC.Measurement (Bruker, 2009), (GSAS, Larson & Von Dreele, 2004), DIAMOND (Crystal Impact, 2015) and publCIF (Westrip, 2010).

Figure 4
Rietveld plot for the refinement of trirubidium citrate monohydrate. The vertical scale is not the raw counts but the counts multiplied by the least squares weights. This plot emphasizes the fit of the weaker peaks. 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 row of black tick marks indicates the reflection positions, and the red tick marks indicate the Si internal standard peak positions.
the refinement using Materials Studio (Dassault Systemes, 2014). The U iso values of the C and O atoms in the citrate anion 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.

DFT calculations
After the Rietveld refinement, 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 Rb was that of Schoenes et al. (2008).