research communications Acta Cryst. (2019). E75, 223–227 https://doi.org/10.1107/S205698901900063X 223 Received 23 November 2018 Accepted 12 January 2019 Edited by A. Van der Lee, Universite ´ de Montpellier II, France Keywords: powder diffraction; density func- tional theory; citrate; sodium; rubidium; caesium; crystal structure. CCDC references: 1890745; 1890746; 1890747; 1890748 Supporting information: this article has supporting information at journals.iucr.org/e Sodium rubidium hydrogen citrate, NaRbHC 6 H 5 O 7 , and sodium caesium hydrogen citrate, NaCsHC 6 H 5 O 7 : crystal structures and DFT comparisons Andrew J. Cigler and James A. Kaduk* Department of Chemistry, North Central College, 131 S. Loomis St., Naperville IL 60540, USA. *Correspondence e-mail: [email protected]The crystal structure of sodium rubidium hydrogen citrate, NaRbHC 6 H 5 O 7 or [NaRb(C 6 H 6 O 7 )] n , has been solved and refined using laboratory powder X-ray diffraction data, and optimized using density functional techniques. This compound is isostructural to NaKHC 6 H 5 O 7 . The Na atom is six-coordinate, with a bond-valence sum of 1.16. The Rb atom is eight-coordinate, with a bond- valence sum of 1.17. The distorted [NaO 6 ] octahedra share edges to form chains along the a-axis direction. The irregular [RbO 8 ] coordination polyhedra share edges with the [NaO 6 ] octahedra on either side of the chain, and share corners with other Rb atoms, resulting in triple chains along the a-axis direction. The most prominent feature of the structure is the chain along [111] of very short, very strong hydrogen bonds; the OO distances are 2.426 and 2.398 A ˚ . The Mulliken overlap populations in these hydrogen bonds are 0.140 and 0.143 electrons, which correspond to hydrogen-bond energies of about 20.3 kcal mol 1 . The crystal structure of sodium caesium hydrogen citrate, NaCsHC 6 H 5 O 7 or [NaCs(C 6 H 6 O 7 )] n , has also been solved and refined using laboratory powder X-ray diffraction data, and optimized using density functional techniques. The Na atom is six-coordinate, with a bond-valence sum of 1.15. The Cs atom is eight-coordinate, with a bond-valence sum of 0.97. The distorted trigonal–prismatic [NaO 6 ] coordination polyhedra share edges to form zigzag chains along the b-axis direction. The irregular [CsO 8 ] coordination polyhedra share edges with the [NaO 6 ] polyhedra to form layers parallel to the (101) plane, unlike the isolated chains in NaKHC 6 H 5 O 7 and NaRbHC 6 H 5 O 7 .A prominent feature of the structure is the chain along [100] of very short, very strong O—HO hydrogen bonds; the refined OO distances are 2.398 and 2.159 A ˚ , and the optimized distances are 2.398 and 2.347 A ˚ . The Mulliken overlap populations in these hydrogen bonds are 0.143 and 0.133 electrons, which correspond to hydrogen-bond energies about 20.3 kcal mol 1 . 1. 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). The two title compounds (Figs. 1 and 2) are a further extension to citrates that contain more than one alkali metal cation. ISSN 2056-9890
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research communications Sodium rubidium …...2. Structural commentary Sodium rubidium hydrogen citrate is isostructural to NaKHC 6 H 5 O 7 (Rammohan & Kaduk, 2016). Sodium caesium
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hydrogen citrate has a related but different structure. The
root-mean-square deviations of the non-hydrogen atoms in
the refined and optimized structures are 0.116 and 0.105 A for
NaRbHC6H5O7 and NaCsHC6H5O7, respectively. Compar-
isons of the refined and optimized structures are given in Figs.
3 and 4. The excellent agreement between the structures is
strong evidence that the experimental structures are correct
(van de Streek & Neumann, 2014). This discussion uses the
DFT-optimized structures. All of the citrate bond distances,
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 occur in the normal planar
arrangement.
In the Rb compound, the citrate chelates to Na19 through
the terminal carboxylate oxygen O11 and the central
carboxylate oxygen O16. The Na+ cation is six-coordinate,
with a bond-valence sum of 1.16. The Rb+ cation is eight-
coordinate, with a bond-valence sum of 1.17. Both cations are
thus slightly crowded.
In the Cs compound, the citrate triply chelates to Na20
through the terminal carboxylate oxygen O12, the central
carboxylate oxygen O15, and the hydroxyl oxygen O17. The
Na+ cation is six-coordinate, with a bond-valence sum of 1.15.
The Cs+ cation is eight-coordinate, with a bond-valence sum of
0.97. The Rb—O and Cs—O bonds are ionic, but the Na—O
bonds have slight covalent character, according to the
Mulliken overlap populations.
The Bravais–Friedel–Donnay–Harker (Bravais, 1866;
Friedel, 1907; Donnay & Harker, 1937) method suggests that
we might expect a platy morphology for NaRbHC6H5O7, with
{001} as the principal faces, and an elongated morphology for
NaCsHC6H5O7, with {010} as the long axis. Fourth-order
spherical harmonic preferred orientation models were
included in the refinements; the texture indices were 1.050 and
1.011, indicating that preferred orientation was slight for the
rotated flat-plate specimen of NaRbHC6H5O7, but not
significant in this rotated capillary specimen of
NaCsHC6H5O7. Examination of the products under an optical
microscope indicated that the morphologies were not
especially anisotropic.
3. Supramolecular features
In the crystal structure of NaRbHC6H5O7 (Fig. 5), distorted
[NaO6] octahedra share edges to form chains along the a-axis
direction. The irregular [RbO8] coordination polyhedra share
224 Cigler and Kaduk � [NaRb(C6H6O7)], and [NaCs(C6H6O7)] Acta Cryst. (2019). E75, 223–227
research communications
Figure 2The asymmetric unit of NaCsHC6H5O7, with the atom numbering and50% probability spheroids.
Figure 3Comparison of the refined and optimized structures of sodium rubidiumhydrogen citrate. The refined structure is in red, and the DFT-optimizedstructure is in blue.
Figure 4Comparison of the refined and optimized structures of sodium caesiumhydrogen citrate. The refined structure is in red, and the DFT-optimizedstructure is in blue.
Figure 1The asymmetric unit of NaRbHC6H5O7, with the atom numbering and50% probability spheroids.
edges with the [NaO6] octahedra on either side of the chain,
resulting in triple chains along the a-axis direction. The most
prominent feature of the structure is the chain along [111] of
very short, very strong O—H� � �O hydrogen bonds (Table 1);
the refined O� � �O distances are 2.180 (9) and 2.234 (20) A,
and the optimized distances are 2.426 and 2.398 A. The
Mulliken overlap populations in these hydrogen bonds are
0.140 and 0.143 electrons, which correspond to hydrogen-bond
energies about 20.6 kcal mol�1, according to the correlation in
Rammohan & Kaduk (2018). H18 forms bifurcated hydrogen
bonds: one is intramolecular to O15, and the other is inter-
molecular to O11.
In the crystal structure of NaCsHC6H5O7 (Fig. 6), distorted
trigonal–prismatic [NaO6] share edges to form zigzig chains
along the b-axis direction. The irregular [CsO8] coordination
polyhedra share edges with the [NaO6] polyhedra to form
layers parallel to the (101) plane, unlike the isolated chains in
NaKHC6H5O7 and NaRbHC6H5O7. A prominent feature of
the structure is the chain along [100] of very short, and very
strong O—H� � �O hydrogen bonds (Table 2); the refined
O11� � �O11 and O14� � �O14 distances are 2.398 and 2.159 A,
and the optimized distances are 2.398 and 2.347 A. The
Mulliken overlap populations in these hydrogen bonds are
0.143 and 0.133 electrons, which correspond to hydrogen-bond
energies about 20.3 kcal mol�1. H18 forms an intramolecular
hydrogen bond to O13, one of the terminal carboxylate
oxygen atoms.
4. Database survey
Details of the comprehensive literature search for citrate
structures are presented in Rammohan & Kaduk (2018). After
manually locating the peaks in the pattern of NaRbHC6H5O7,
research communications
Acta Cryst. (2019). E75, 223–227 Cigler and Kaduk � [NaRb(C6H6O7)], and [NaCs(C6H6O7)] 225
Figure 5Crystal structure of NaRbHC6H5O7, viewed down the a axis.
Figure 6Crystal structure of NaCsHC6H5O7, viewed down the b axis.
the pattern was indexed using Jade9.8 (MDI, 2017). A
reduced-cell search in the Cambridge Structural Database
(CSD Version 5.39, update of November 2018; Groom et al.,
2016) yielded 39 hits, among which was NaKHC6H5O7
(Rammohan & Kaduk, 2016).
After manually locating the peaks in the pattern of
NaCsHC6H5O7, the pattern was indexed on a C-centered
monoclinic cell using Jade9.8 (MDI, 2017). A reduced-cell
search in the CSD yielded no hits. The cell was converted to I-
centered, to yield a � angle closer to 90�.
5. Synthesis and crystallization
Stoichiometric quantities of Na2CO3 and Rb2CO3 were added
to a solution of 10.0 mmol citric acid monohydrate in 10 mL
water. After the fizzing subsided, the clear solution was dried
in an oven at 403 K to yield the white solid NaRbHC6H5O7.
2.0236 g (10.0 mmol) of H3C6H5O7(H2O) were dissolved in
10 mL of deionized water. 0.5318 g of Na2CO3 (1.0 mmol Na,
Sigma–Aldrich) and 1.6911 g of Cs2CO3 (10.0 mmol of Ca,
Sigma–Aldrich) were added to the citric acid solution slowly
with stirring. The resulting clear colorless solution was
evaporated to dryness in a 403 K oven to yield NaCsHC6H5O7.
6. Refinement
The initial structural model for NaRbHC6H5O7 was taken
from Rammohan & Kaduk (2016), replacing the K by Rb and
changing the lattice parameters to the observed values.
Pseudovoigt profile coefficients were as parameterized in
Thompson et al. (1987) and the asymmetry correction of
Finger et al. (1994) was applied as well as the microstrain
broadening description by Stephens (1999). The hydrogen
atoms were included in fixed positions, which were re-calcu-
lated during the course of the refinement. Crystal data, data
collection and structure refinement (Fig. 7) details are
summarized in Table 3. The Uiso of C2, C3, and C4 were
constrained to be equal, and those of H7, H8, H9, and H10
were constrained to be 1.3 � that of these carbon atoms. The
Uiso of C1, C5, C6, and the oxygen atoms were constrained to
be equal, and that of H18 was constrained to be 1.3 � this
value. The Uiso of H21 and H22 were fixed.
Analysis of the systematic absences in the pattern of
NaCsHC6H5O7 suggested the space groups I2, Im, or I2/m.
The volume of the unit cell corresponded to Z = 4. Space
group I2 was selected, and confirmed by successful solution
and refinement of the structure. The structure was solved with
FOX (Favre-Nicolin & Cerny, 2002). The maximum sin �/�used for structure solution was 0.55 A, and a citrate, Cs, Na,
and O (water molecule) were used as fragments. The solution
with the lowest cost factor has the Cs, Na, and O on top of each
other, but the Cs was eight-coordinate and all six carboxylate
oxygen atoms were coordinated to the Cs atom. The structure
was examined for voids using Materials Studio (Dassault
Systemes, 2017). One void at approximately 0.375,0.600,0.379
had acceptable coordination to O atoms, and was assigned as
Na20. Another void was assigned as O21, but this moved too
close to the citrate anion on refinement and was discarded.
Active hydrogen atoms were placed by analysis of hydrogen-
bonding interactions. The refinement strategy (Fig. 8) was
similar to that used for the Rb compound. Cs19 was refined
anisotropically.
Density functional geometry optimizations (fixed experi-
mental unit cells) were carried out using CRYSTAL14
(Dovesi et al., 2014). The basis sets for the H, C, and O atoms
226 Cigler and Kaduk � [NaRb(C6H6O7)], and [NaCs(C6H6O7)] Acta Cryst. (2019). E75, 223–227
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Figure 8Rietveld plot for NaCsHC6H5O7. The red crosses represent the observeddata points, and the green line is the calculated pattern. The magentacurve is the difference pattern, plotted at the same scale as the otherpatterns. The vertical scale has been multiplied by a factor of 10 for 2� >28.8�. The row of black tick marks indicates the reflection positions forthis phase.
Figure 7Rietveld plot for NaRbHC6H5O7. The red crosses represent the observeddata points, and the green line is the calculated pattern. The magentacurve is the difference pattern, plotted at the same scale as the otherpatterns. The vertical scale has been multiplied by a factor of 10 for 2� >46.0�. The row of black tick marks indicates the reflection positions forthis phase.
were those of Gatti et al. (1994), the basis sets for Na was that
of Dovesi et al. (1991), and the basis sets for Rb and Cs were
those 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 k-points and the B3LYP functional, and took 10.8 and
7.5 h.
Acknowledgements
We thank Andrey Rogachev for the use of computing
resources at the Illinois Institute of Technology.
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Acta Cryst. (2019). E75, 223–227 Cigler and Kaduk � [NaRb(C6H6O7)], and [NaCs(C6H6O7)] 227
R(F 2) = 0.08622, �2 = 5.570No. of parameters 84 80No. of restraints 29 29H-atom treatment Only H-atom displacement parameters refined Only H-atom displacement parameters refined
The same symmetry and lattice parameters were used for the DFT calculations as for each powder diffraction study. Computer programs: DIFFRAC.Measurement (Bruker, 2009), FOX(Favre-Nicolin & Cerny, 2002), GSAS (Larson & Von Dreele, 2004), Mercury (Macrae et al., 2008), DIAMOND (Crystal Impact, 2015) and publCIF (Westrip, 2010).