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

Rammohan, A.; Kaduk, J.A.

doi:10.1107/S2056989017001256

research communications

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ISSN: 2056-9890

Volume 73| Part 2| February 2017| Pages 286-290

https://doi.org/10.1107/S2056989017001256

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

Alagappa Rammohan ^a and James A. Kaduk ^b ^*

^aAtlantic International University, Honolulu HI, USA, and ^bIllinois Institute of Technology, Chicago IL, USA
^*Correspondence e-mail: kaduk@polycrystallography.com

Edited by A. Van der Lee, Université de Montpellier II, France (Received 4 January 2017; accepted 24 January 2017; online 27 January 2017)

The crystal structure of pentasodium hydrogen dicitrate, Na₅H(C₆H₅O₇)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—H⋯O hydrogen bonds, with O⋯O 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 NaO₆ octahedra on both sides of these layers.

Keywords: powder diffraction; crystal structure; density functional theory; citrate; sodium.

CCDC references: 1529603; 1529604; 1529605

1. 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, ionization, coordination tendencies, and hydrogen bonding, we have determined several new crystal structures. Most of the new structures were solved using X-ray 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 ). Nine of the new structures – NaKHC₆H₅O₇, NaK₂C₆H₅O₇, Na₃C₆H₅O₇, NaH₂C₆H₅O₇, Na₂HC₆H₅O₇, K₃C₆H₅O₇, Rb₂HC₆H₅O₇, Rb₃C₆H₅O₇(H₂O), and Rb₃C₆H₅O₇ – have been published recently (Rammohan & Kaduk, 2016a ,b ,c ,d ,e , 2017b ,c ,d ; Rammohan et al., 2016 ), and two additional structures – KH₂C₆H₅O₇ and KH₂C₆H₅O₇(H₂O)₂ – have been communicated to the CSD (Kaduk & Stern, 2016a ,b ).

2. Structural commentary

The compound Na₅H(C₆H₅O₇)₂ was unexpectedly synthesized by heating Na₂HC₆H₅O₇(H₂O)_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.

Figure 1
The asymmetric unit of Na₅H(C₆H₅O₇)₂, with the atom numbering. The atoms are represented by 50% probability spheroids.

Figure 2
Comparison of the refined and optimized structures of pentasodium hydrogen dicitrate. The refined structure is in red, and the DFT-optimized structure is in blue.

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 bond-valence 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 Na41O₅ polyhedra share faces with Na37O₆ and Na39O₆ octahedra on both sides of these layers. The crystal structure is illustrated in Fig. 3.

Figure 3
Crystal structure of Na₅H(C₆H₅O₇)₂, viewed down the a axis.

The Mulliken overlap populations and atomic charges indicate that the metal–oxygen bonding is ionic. Comparison of the structures of the starting material Na₂HC₆H₅O₇(H₂O)_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.

3. Supramolecular features

The layers are connected by very strong centrosymmetric O26—H44⋯O26 and O25—H43⋯O25 hydrogen bonds (Table 1). The O26⋯O26 distance is 2.419 Å and the O25⋯O25 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⁻¹ for each hydrogen bond (Rammohan & Kaduk, 2017a). These hydrogen bonds link two citrates into dimers.

Table 1
Hydrogen-bond geometry (Å, °) for Na5Hcit2_DFT

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O26—H44⋯O26ⁱ	1.210	1.210	2.419	180.0
O25—H43⋯O25ⁱⁱ	1.205	1.205	2.409	180.0
O33—H35⋯O23ⁱⁱⁱ	0.975	2.045	2.799	132.8
O33—H35⋯O29	0.975	2.450	2.664	91.7
O34—H36⋯O30	0.971	2.212	2.631	104.6
O34—H36⋯O28	0.971	2.302	2.831	113.4
O34—H36⋯O24ⁱⁱⁱ	0.971	2.385	3.223	144.3
Symmetry codes: (i) -x+2, -y+1, -z+1; (ii) -x+1, -y+2, -z+1; (iii) x+1, y, z.

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⁻¹ to the crystal energy.

4. 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.

5. Synthesis and crystallization

The title compound was prepared by heating commercial reagent Na₂HC₆H₅O₇(H₂O)_1.5 (Sigma–Aldrich lot BCBC6031V) from 295–453K at 14 K min⁻¹ 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.

6. 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.

Table 2
Experimental details

Crystal data
Chemical formula	Na₅H(C₆H₅O₇)₂
M_r	494.16
Crystal system, space group	Triclinic, P $[\overline{1}]$
Temperature (K)	295
a, b, c (Å)	6.35262 (9), 11.98628 (18), 12.16544 (16)
α, β, γ (°)	73.8374 (13), 80.8808 (15), 80.7103 (10)
V (Å³)	871.72 (2)
Z	2
Radiation type	Synchrotron, λ = 0.413891 Å
Specimen shape, size (mm)	Cylinder, 1.5 × 1.5

Data collection
Diffractometer	11-BM APS
Specimen mounting	Kapton capillary
Data collection mode	Transmission
Scan method	Step
T_min, T_max	1.000, 1.000
2θ values (°)	2θ_min = 0.5 2θ_max = 50.0 2θ_step = 0.001

Refinement
R factors and goodness of fit	R_p = 0.083, R_wp = 0.097, R_exp = 0.073, R(F²) = 0.085, χ² = 1.823
No. of parameters	145
No. of restraints	58
The same symmetry and lattice parameters were used for the DFT calculation. Computer programs: DIFFRAC.Measurement (Bruker, 2009 ), DASH (David et al., 2006), GSAS (Larson & Von Dreele, 2004), DIAMOND (Crystal Impact, 2015 ) and publCIF (Westrip, 2010 ).

Figure 4
Rietveld plot for the refinement of Na₅H(C₆H₅O₇)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 2.0 at 2.2°, and by 5.0 at 10.8°. The row of black tick marks indicates the reflection positions. The red tick marks indicate the positions of the peaks of the Si internal standard.

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, α = 74.145, β = 81.530, γ = 80.8 6°, and V = 863.06 Å³. The volume corresponds to four citrate anions per cell. A Le Bail fit using this cell yielded a reduced χ² = 2.866, but it was not possible to solve the crystal structure using this unit cell.

Removing the weak peak at 2.510° yielded a new cell, with a = 6.131, b = 6.352, c = 12.142 Å, α = 100.486, β = 98.839, γ = 110.4 0°, and V = 435.852 Å³. This is a sub-cell of the original cell. The volume corresponds to two citrate anions per cell, and space group P $[\overline1]$ was assumed. A Le Bail fit yielded a reduced χ² 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 χ² 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 χ² of 1.85, and an Na occupancy of 1/2.

The structure was transformed (matrix [0 $[\overline{1}]$ 0/ $[\overline{2}]$ $[\overline{1}]$ 0/ $[\overline{1}]$ $[\overline{1}]$ $[\overline{1}]$ ]) 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 Na₅H(citrate)₂ model yielded a reduced χ² 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.

7. 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.

Supporting information

CCDC references: 1529603; 1529604; 1529605

Crystal structure: contains datablocks NA2HCITRATE_2_publ, Na5Hcit2_DFT, NA2HCITRATE_2_overall, NA2HCITRATE_2_phase_1, NA2HCITRATE_2_phase_2, NA2HCITRATE_2_p_01. DOI: https://doi.org/10.1107/S2056989017001256/vn2125sup1.cif

Supporting information file. DOI: https://doi.org/10.1107/S2056989017001256/vn2125NA2HCITRATE_2_phase_2sup2.cml

checkCIF report

Computing details top

Program(s) used to solve structure: DASH (David et al., 2006) for NA2HCITRATE_2_phase_1.

(NA2HCITRATE_2_phase_1) Pentasodium hydrogen dicitrate top

Crystal data top

5Na⁺·H⁺·2C₆H₅O₇³⁻	α = 73.8374 (13)°
M_r = 494.16	β = 80.8808 (15)°
Triclinic, P1	γ = 80.7103 (10)°
Hall symbol: -P 1	V = 871.72 (2) Å³
a = 6.35262 (9) Å	Z = 2
b = 11.98628 (18) Å	D_x = 1.883 Mg m⁻³
c = 12.16544 (16) Å	T = 295 K

Data collection top

11-BM APS
diffractometer

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
C1	−0.2177 (12)	0.5862 (7)	0.8244 (8)	0.0106 (6)*
C2	0.2860 (11)	0.0939 (6)	0.8273 (7)	0.0106 (6)*
C3	−0.1531 (12)	0.6732 (7)	0.7124 (6)	0.0160 (15)*
C4	0.3818 (13)	0.1567 (7)	0.7088 (6)	0.0160 (15)*
C5	0.0541 (9)	0.7213 (5)	0.7189 (4)	0.0160 (15)*
C6	0.5481 (10)	0.2314 (5)	0.7211 (5)	0.0160 (15)*
C7	0.0934 (13)	0.8216 (7)	0.6099 (6)	0.0160 (15)*
C8	0.5470 (10)	0.3460 (6)	0.6243 (8)	0.0160 (15)*
C9	0.2718 (13)	0.8898 (7)	0.6129 (7)	0.0106 (6)*
C10	0.7654 (12)	0.3882 (8)	0.6007 (7)	0.0106 (6)*
C11	0.0204 (12)	0.7688 (6)	0.8273 (5)	0.0106 (6)*
C12	0.4917 (12)	0.2646 (7)	0.8374 (5)	0.0106 (6)*
H13	−0.28788	0.74876	0.69457	0.0209 (19)*
H14	0.24908	0.21558	0.65961	0.0209 (19)*
H15	−0.12367	0.62941	0.63910	0.0209 (19)*
H16	0.46380	0.08980	0.65996	0.0209 (19)*
H17	−0.05905	0.88634	0.59836	0.0209 (19)*
H18	0.42159	0.41571	0.65167	0.0209 (19)*
H19	0.13431	0.78343	0.53201	0.0209 (19)*
H20	0.50574	0.32991	0.54259	0.0209 (19)*
O21	−0.0775 (13)	0.5070 (8)	0.8710 (8)	0.0106 (6)*
O22	0.3882 (14)	0.0013 (7)	0.8837 (7)	0.0106 (6)*
O23	−0.4076 (12)	0.5956 (8)	0.8744 (8)	0.0106 (6)*
O24	0.0872 (12)	0.1157 (7)	0.8570 (8)	0.0106 (6)*
O25	0.3428 (14)	0.9557 (8)	0.5183 (6)	0.0106 (6)*
O26	0.8231 (13)	0.4548 (8)	0.5025 (6)	0.0106 (6)*
O27	0.3893 (13)	0.8613 (8)	0.6940 (7)	0.0106 (6)*
O28	0.8709 (14)	0.3768 (9)	0.6843 (7)	0.0106 (6)*
O29	0.1237 (15)	0.7164 (7)	0.9116 (6)	0.0106 (6)*
O30	0.6331 (15)	0.2353 (8)	0.9069 (7)	0.0106 (6)*
O31	−0.1520 (14)	0.8339 (7)	0.8448 (7)	0.0106 (6)*
O32	0.3407 (14)	0.3458 (8)	0.8468 (7)	0.0106 (6)*
O33	0.2312 (11)	0.6322 (6)	0.7256 (8)	0.0106 (6)*
O34	0.7524 (11)	0.1640 (6)	0.7170 (8)	0.0106 (6)*
H35	0.30788	0.65287	0.77888	0.0138 (8)*
H36	0.80788	0.15287	0.77888	0.0138 (8)*
Na37	0.4491 (12)	0.8035 (6)	0.8933 (6)	0.0127 (6)*
Na38	0.9726 (14)	0.3022 (6)	0.8899 (6)	0.0127 (6)*
Na39	0.2243 (13)	0.9924 (6)	0.0661 (6)	0.0127 (6)*
Na40	0.7348 (11)	0.4891 (6)	0.0844 (6)	0.0127 (6)*
Na41	0.6543 (10)	0.9874 (5)	0.6852 (5)	0.0127 (6)*
H43	0.5	1.0	0.5	0.01472*
H44	1.0	0.5	0.5	0.01472*

Geometric parameters (Å, º) top

C1—C3	1.5099 (13)	O25—Na41^vii	2.375 (10)
C1—O21	1.267 (3)	O25—H43	1.168 (8)
C1—O23	1.265 (3)	O26—C10	1.274 (3)
C2—C4	1.5102 (13)	O26—H44	1.317 (8)
C2—O22	1.268 (3)	O27—C9	1.270 (3)
C2—O24	1.263 (3)	O27—Na37	2.404 (10)
C3—C1	1.5099 (13)	O27—Na41	2.409 (9)
C3—C5	1.5416 (13)	O28—C10	1.269 (3)
C3—H13	0.733 (7)	O28—Na38	2.560 (10)
C3—H15	1.216 (10)	O29—C11	1.265 (3)
C4—C2	1.5102 (13)	O29—Na37	2.416 (12)
C4—C6	1.5397 (13)	O29—Na38^viii	2.352 (10)
C4—H14	0.932 (9)	O29—Na40ⁱⁱⁱ	2.472 (11)
C4—H16	0.966 (10)	O30—C12	1.272 (3)
C5—C3	1.5416 (13)	O30—Na37^viii	2.333 (10)
C5—C7	1.5396 (13)	O30—Na38	2.379 (12)
C5—C11	1.5483 (13)	O30—Na39ⁱⁱⁱ	2.679 (11)
C5—O33	1.416 (3)	O31—C11	1.263 (3)
C6—C4	1.5397 (13)	O31—Na37ⁱ	2.570 (12)
C6—C8	1.5404 (13)	O31—Na39^ix	2.551 (10)
C6—C12	1.5468 (13)	O31—Na41ⁱ	2.590 (10)
C6—O34	1.416 (3)	O32—C12	1.268 (3)
C7—C5	1.5396 (13)	O32—Na38ⁱ	2.422 (12)
C7—C9	1.5103 (13)	O32—Na40ⁱⁱⁱ	2.309 (10)
C7—H17	1.206 (11)	O33—C5	1.416 (3)
C7—H19	0.817 (8)	O33—H35	0.974 (8)
C8—C6	1.5404 (13)	O33—Na40ⁱⁱⁱ	2.386 (10)
C8—C10	1.5103 (13)	O34—C6	1.416 (3)
C8—H18	0.790 (8)	O34—H36	0.850 (9)
C8—H20	1.072 (11)	O34—Na39ⁱⁱⁱ	2.789 (11)
C9—C7	1.5103 (13)	O34—Na41^iv	2.445 (10)
C9—O25	1.263 (3)	H35—O33	0.974 (8)
C9—O27	1.270 (3)	H36—O34	0.850 (9)
C10—C8	1.5103 (13)	Na37—O22^x	2.313 (11)
C10—O26	1.274 (3)	Na37—O23^xi	2.571 (11)
C10—O28	1.269 (3)	Na37—O27	2.404 (10)
C11—C5	1.5483 (13)	Na37—O29	2.416 (12)
C11—O29	1.265 (3)	Na37—O30^viii	2.333 (10)
C11—O31	1.263 (3)	Na37—O31^xi	2.570 (12)
C12—C6	1.5468 (13)	Na38—O21^xi	2.374 (12)
C12—O30	1.272 (3)	Na38—O24^xi	2.359 (11)
C12—O32	1.268 (3)	Na38—O28	2.560 (10)
H13—C3	0.733 (7)	Na38—O29^viii	2.352 (10)
H14—C4	0.932 (9)	Na38—O30	2.379 (12)
H15—C3	1.216 (10)	Na38—O32^xi	2.422 (12)
H16—C4	0.966 (10)	Na39—O22^xii	2.279 (9)
H17—C7	1.206 (11)	Na39—O22ⁱⁱⁱ	2.646 (11)
H18—C8	0.790 (8)	Na39—O24^xii	2.758 (11)
H19—C7	0.817 (8)	Na39—O24^vi	2.457 (10)
H20—C8	1.072 (11)	Na39—O30ⁱⁱⁱ	2.679 (11)
O21—C1	1.267 (3)	Na39—O31^ix	2.551 (10)
O21—Na38ⁱ	2.374 (12)	Na39—O34ⁱⁱⁱ	2.789 (11)
O21—Na40ⁱⁱ	2.645 (10)	Na40—O21^xiii	2.645 (10)
O21—Na40ⁱⁱⁱ	2.336 (11)	Na40—O21ⁱⁱⁱ	2.336 (11)
O22—C2	1.268 (3)	Na40—O23^xiii	2.742 (12)
O22—Na37^iv	2.313 (11)	Na40—O23^vi	2.382 (10)
O22—Na39^v	2.279 (9)	Na40—O29ⁱⁱⁱ	2.472 (11)
O22—Na39ⁱⁱⁱ	2.646 (11)	Na40—O32ⁱⁱⁱ	2.309 (10)
O22—Na41^iv	2.749 (10)	Na40—O33ⁱⁱⁱ	2.386 (10)
O23—C1	1.265 (3)	Na41—O22^x	2.749 (10)
O23—Na37ⁱ	2.571 (11)	Na41—O25	3.183 (11)
O23—Na40ⁱⁱ	2.742 (12)	Na41—O25^vii	2.375 (10)
O23—Na40^vi	2.382 (10)	Na41—O27	2.409 (9)
O24—C2	1.263 (3)	Na41—O31^xi	2.590 (10)
O24—Na38ⁱ	2.359 (11)	Na41—O34^x	2.445 (10)
O24—Na39^v	2.758 (11)	H43—O25	1.168 (8)
O24—Na39^vi	2.457 (10)	H43—O25^vii	1.168 (8)
O25—C9	1.263 (3)	H44—O26	1.317 (8)
O25—Na41	3.183 (11)	H44—O26^xiv	1.317 (8)

C3—C1—O21	119.5 (3)	C6—O34—Na41^iv	100.0 (4)
C3—C1—O23	120.5 (4)	H36—O34—Na39ⁱⁱⁱ	38.5 (4)
O21—C1—O23	120.0 (4)	H36—O34—Na41^iv	114.5 (6)
C4—C2—O22	119.8 (3)	Na39ⁱⁱⁱ—O34—Na41^iv	78.4 (3)
C4—C2—O24	119.1 (4)	O33—H35—Na40ⁱⁱⁱ	98.3 (5)
O22—C2—O24	118.8 (3)	O34—H36—Na39ⁱⁱⁱ	127.5 (5)
C1—C3—C5	110.6 (4)	O22^x—Na37—O23^xi	167.4 (4)
C2—C4—C6	109.1 (4)	O22^x—Na37—O27	85.7 (4)
C3—C5—C7	108.1 (3)	O22^x—Na37—O29	113.4 (4)
C3—C5—C11	108.3 (4)	O22^x—Na37—O30^viii	88.7 (4)
C3—C5—O33	110.6 (3)	O22^x—Na37—O31^xi	85.3 (3)
C7—C5—C11	109.8 (4)	O23^xi—Na37—O27	89.6 (4)
C7—C5—O33	110.0 (3)	O23^xi—Na37—O29	77.3 (4)
C11—C5—O33	110.0 (3)	O23^xi—Na37—O30^viii	99.8 (4)
C4—C6—C8	110.9 (3)	O23^xi—Na37—O31^xi	83.3 (4)
C4—C6—C12	109.7 (3)	O27—Na37—O29	81.3 (3)
C4—C6—O34	107.8 (3)	O27—Na37—O30^viii	158.3 (5)
C8—C6—C12	107.6 (4)	O27—Na37—O31^xi	92.9 (3)
C8—C6—O34	110.6 (3)	O29—Na37—O30^viii	81.8 (4)
C12—C6—O34	110.2 (5)	O29—Na37—O31^xi	159.7 (5)
C5—C7—C9	114.0 (3)	O30^viii—Na37—O31^xi	107.5 (4)
C6—C8—C10	110.0 (3)	O21^xi—Na38—O24^xi	163.1 (4)
C7—C9—O25	116.8 (5)	O21^xi—Na38—O28	80.0 (4)
C7—C9—O27	122.9 (3)	O21^xi—Na38—O29^viii	85.6 (4)
O25—C9—O27	117.4 (3)	O21^xi—Na38—O30	109.5 (5)
C8—C10—O26	119.7 (4)	O21^xi—Na38—O32^xi	78.9 (4)
C8—C10—O28	119.4 (4)	O24^xi—Na38—O28	89.3 (4)
O26—C10—O28	119.5 (4)	O24^xi—Na38—O29^viii	109.8 (4)
C5—C11—O29	119.7 (4)	O24^xi—Na38—O30	80.3 (4)
C5—C11—O31	117.9 (4)	O24^xi—Na38—O32^xi	89.8 (4)
O29—C11—O31	118.7 (4)	O28—Na38—O29^viii	148.9 (5)
C6—C12—O30	117.9 (4)	O28—Na38—O30	77.0 (4)
C6—C12—O32	118.9 (3)	O28—Na38—O32^xi	97.6 (4)
O30—C12—O32	120.0 (4)	O29^viii—Na38—O30	82.2 (4)
C1—O21—Na38ⁱ	130.6 (10)	O29^viii—Na38—O32^xi	106.5 (4)
C1—O21—Na40ⁱⁱ	95.2 (6)	O30—Na38—O32^xi	168.7 (5)
C1—O21—Na40ⁱⁱⁱ	132.9 (10)	O22^xii—Na39—O22ⁱⁱⁱ	85.5 (5)
Na38ⁱ—O21—Na40ⁱⁱ	94.5 (4)	O22^xii—Na39—O24^xii	50.2 (2)
Na38ⁱ—O21—Na40ⁱⁱⁱ	94.3 (4)	O22^xii—Na39—O24^vi	120.6 (5)
Na40ⁱⁱ—O21—Na40ⁱⁱⁱ	94.5 (4)	O22^xii—Na39—O30ⁱⁱⁱ	81.4 (4)
C2—O22—Na37^iv	138.9 (9)	O22^xii—Na39—O31^ix	123.8 (4)
C2—O22—Na39^v	100.9 (5)	O22^xii—Na39—O34ⁱⁱⁱ	136.3 (4)
C2—O22—Na39ⁱⁱⁱ	119.6 (8)	O22ⁱⁱⁱ—Na39—O24^xii	122.2 (4)
C2—O22—Na41^iv	89.3 (4)	O22ⁱⁱⁱ—Na39—O24^vi	139.8 (4)
Na37^iv—O22—Na39^v	99.3 (4)	O22ⁱⁱⁱ—Na39—O30ⁱⁱⁱ	82.6 (4)
Na37^iv—O22—Na39ⁱⁱⁱ	93.8 (4)	O22ⁱⁱⁱ—Na39—O31^ix	79.2 (3)
Na37^iv—O22—Na41^iv	75.6 (3)	O22ⁱⁱⁱ—Na39—O34ⁱⁱⁱ	75.3 (3)
Na39^v—O22—Na39ⁱⁱⁱ	94.5 (5)	O24^xii—Na39—O24^vi	97.5 (4)
Na39^v—O22—Na41^iv	168.6 (5)	O24^xii—Na39—O30ⁱⁱⁱ	117.4 (3)
Na39ⁱⁱⁱ—O22—Na41^iv	75.9 (3)	O24^xii—Na39—O31^ix	95.5 (3)
C1—O23—Na37ⁱ	113.8 (6)	O24^xii—Na39—O34ⁱⁱⁱ	162.2 (4)
C1—O23—Na40ⁱⁱ	90.8 (7)	O24^vi—Na39—O30ⁱⁱⁱ	72.9 (4)
C1—O23—Na40^vi	143.0 (9)	O24^vi—Na39—O31^ix	104.8 (4)
Na37ⁱ—O23—Na40ⁱⁱ	102.4 (4)	O24^vi—Na39—O34ⁱⁱⁱ	64.7 (3)
Na37ⁱ—O23—Na40^vi	100.1 (4)	O30ⁱⁱⁱ—Na39—O31^ix	147.1 (4)
Na40ⁱⁱ—O23—Na40^vi	96.1 (3)	O30ⁱⁱⁱ—Na39—O34ⁱⁱⁱ	57.7 (3)
C2—O24—Na38ⁱ	115.7 (6)	O31^ix—Na39—O34ⁱⁱⁱ	91.0 (3)
C2—O24—Na39^v	79.2 (5)	O21^xiii—Na40—O21ⁱⁱⁱ	85.5 (4)
C2—O24—Na39^vi	138.3 (6)	O21^xiii—Na40—O23^xiii	47.98 (16)
Na38ⁱ—O24—Na39^v	101.1 (4)	O21^xiii—Na40—O23^vi	113.9 (5)
Na38ⁱ—O24—Na39^vi	104.4 (4)	O21^xiii—Na40—O29ⁱⁱⁱ	77.7 (3)
Na39^v—O24—Na39^vi	82.5 (4)	O21^xiii—Na40—O32ⁱⁱⁱ	119.2 (4)
C9—O27—Na37	153.7 (7)	O21^xiii—Na40—O33ⁱⁱⁱ	139.4 (4)
C9—O27—Na41	117.3 (4)	O21ⁱⁱⁱ—Na40—O23^xiii	124.8 (4)
Na37—O27—Na41	80.9 (3)	O21ⁱⁱⁱ—Na40—O23^vi	150.1 (4)
C10—O28—Na38	157.8 (5)	O21ⁱⁱⁱ—Na40—O29ⁱⁱⁱ	82.7 (4)
C11—O29—Na37	109.6 (7)	O21ⁱⁱⁱ—Na40—O32ⁱⁱⁱ	82.0 (4)
C11—O29—Na38^viii	130.2 (6)	O21ⁱⁱⁱ—Na40—O33ⁱⁱⁱ	71.4 (4)
C11—O29—Na40ⁱⁱⁱ	114.1 (5)	O23^xiii—Na40—O23^vi	83.9 (3)
Na37—O29—Na38^viii	96.9 (4)	O23^xiii—Na40—O29ⁱⁱⁱ	108.4 (3)
Na37—O29—Na40ⁱⁱⁱ	102.0 (4)	O23^xiii—Na40—O32ⁱⁱⁱ	95.5 (4)
Na38^viii—O29—Na40ⁱⁱⁱ	99.8 (4)	O23^xiii—Na40—O33ⁱⁱⁱ	163.3 (4)
C12—O30—Na37^viii	123.5 (6)	O23^vi—Na40—O29ⁱⁱⁱ	79.9 (4)
C12—O30—Na38	129.9 (7)	O23^vi—Na40—O32ⁱⁱⁱ	105.3 (5)
C12—O30—Na39ⁱⁱⁱ	108.7 (6)	O23^vi—Na40—O33ⁱⁱⁱ	79.5 (4)
Na37^viii—O30—Na38	98.5 (4)	O29ⁱⁱⁱ—Na40—O32ⁱⁱⁱ	156.1 (4)
Na37^viii—O30—Na39ⁱⁱⁱ	88.3 (4)	O29ⁱⁱⁱ—Na40—O33ⁱⁱⁱ	66.9 (3)
Na38—O30—Na39ⁱⁱⁱ	97.4 (4)	O32ⁱⁱⁱ—Na40—O33ⁱⁱⁱ	90.8 (4)
C11—O31—Na37ⁱ	134.6 (8)	O22^x—Na41—O25^vii	140.9 (4)
C11—O31—Na39^ix	130.3 (7)	O22^x—Na41—O27	76.6 (4)
C11—O31—Na41ⁱ	124.9 (5)	O22^x—Na41—O31^xi	76.7 (3)
Na37ⁱ—O31—Na39^ix	90.2 (3)	O22^x—Na41—O34^x	79.3 (3)
Na37ⁱ—O31—Na41ⁱ	74.5 (3)	O25^vii—Na41—O27	88.0 (4)
Na39^ix—O31—Na41ⁱ	80.4 (3)	O25^vii—Na41—O31^xi	140.6 (4)
C12—O32—Na38ⁱ	119.5 (8)	O25^vii—Na41—O34^x	100.5 (4)
C12—O32—Na40ⁱⁱⁱ	140.3 (7)	O27—Na41—O31^xi	92.3 (4)
Na38ⁱ—O32—Na40ⁱⁱⁱ	93.7 (4)	O27—Na41—O34^x	150.5 (4)
C5—O33—Na40ⁱⁱⁱ	114.0 (4)	O31^xi—Na41—O34^x	98.4 (4)
H35—O33—Na40ⁱⁱⁱ	57.8 (5)	O25—H43—O25^vii	180.0
C6—O34—Na39ⁱⁱⁱ	106.7 (5)	O26—H44—O26^xiv	180.0

Symmetry codes: (i) x−1, y, z; (ii) x−1, y, z+1; (iii) −x+1, −y+1, −z+1; (iv) x, y−1, z; (v) x, y−1, z+1; (vi) −x, −y+1, −z+1; (vii) −x+1, −y+2, −z+1; (viii) −x+1, −y+1, −z+2; (ix) −x, −y+2, −z+1; (x) x, y+1, z; (xi) x+1, y, z; (xii) x, y+1, z−1; (xiii) x+1, y, z−1; (xiv) −x+2, −y+1, −z+1.

(NA2HCITRATE_2_phase_2) Silicon top

Crystal data top

Si	V = 160.20 (1) Å³
M_r = 28.09	Z = 8
Cubic, Fd3m	D_x = 2.329 Mg m⁻³
Hall symbol: -F 4vw 2vw	T = 295 K
a = 5.431046 (9) Å

Data collection top

2θ_min = 0.5°, 2θ_max = 50.0°, 2θ_step = 0.001°

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
Si1	0.125	0.125	0.125	0.0056 (3)*

Geometric parameters (Å, º) top

Si1—Si1ⁱ	2.3517	Si1—Si1ⁱⁱⁱ	2.3517
Si1—Si1ⁱⁱ	2.3517	Si1—Si1^iv	2.3517

Si1ⁱ—Si1—Si1ⁱⁱ	109.4712 (1)	Si1ⁱⁱ—Si1—Si1ⁱⁱⁱ	109.4712 (1)
Si1ⁱ—Si1—Si1ⁱⁱⁱ	109.4712 (1)	Si1ⁱⁱ—Si1—Si1^iv	109.4712 (1)
Si1ⁱ—Si1—Si1^iv	109.4712 (1)	Si1ⁱⁱⁱ—Si1—Si1^iv	109.4712 (1)

Symmetry codes: (i) x+1/4, y+1/4, −z; (ii) −z, x+1/4, y+1/4; (iii) y+1/4, −z, x+1/4; (iv) −x, −y, −z.

(Na5Hcit2_DFT) top

Crystal data top

Na₅H(C₆H₅O₇)₂	α = 73.8374°
M_r = 494.13	β = 80.8808°
Triclinic, P1	γ = 80.7103°
Hall symbol: -P 1	V = 871.72 Å³
a = 6.3526 Å	Z = 2
b = 11.9863 Å	D_x = 1.883 Mg m⁻³
c = 12.1654 Å	T = 295 K

Data collection top

Density functional calculation	k = →
h = →	l = →

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
C1	−0.21093	0.58380	0.83744	0.01060*
C2	0.28547	0.08699	0.82748	0.01060*
C3	−0.11904	0.65713	0.72068	0.01600*
C4	0.34300	0.18316	0.71790	0.01600*
C5	0.06950	0.72103	0.72811	0.01600*
C6	0.53786	0.24180	0.72599	0.01600*
C7	0.11665	0.81156	0.61196	0.01600*
C8	0.55181	0.35732	0.63154	0.01600*
C9	0.29966	0.88149	0.60472	0.01060*
C10	0.77028	0.40070	0.61710	0.01060*
C11	0.00917	0.77940	0.83069	0.01060*
C12	0.50875	0.26301	0.84778	0.01060*
O21	−0.08985	0.50169	0.89446	0.01060*
O22	0.43125	0.00445	0.86367	0.01060*
O23	−0.40674	0.61148	0.87458	0.01060*
O24	0.09817	0.09733	0.88046	0.01060*
O25	0.34064	0.95546	0.50492	0.01060*
O26	0.82824	0.46330	0.51541	0.01060*
O27	0.40445	0.86921	0.68646	0.01060*
O28	0.87727	0.37570	0.70033	0.01060*
O29	0.11832	0.74256	0.91351	0.01060*
O30	0.65064	0.21054	0.91295	0.01060*
O31	−0.15265	0.85830	0.82412	0.01060*
O32	0.34170	0.32615	0.87533	0.01060*
O33	0.25360	0.63635	0.74506	0.01060*
O34	0.72908	0.16202	0.71125	0.01060*
H35	0.36530	0.67271	0.76366	0.01380*
H36	0.83443	0.18009	0.75138	0.01380*
Na37	0.46548	0.79769	0.89886	0.01270*
Na38	0.97393	0.30775	0.88552	0.01270*
Na39	0.22004	0.98848	0.06887	0.01270*
Na40	0.71654	0.49717	0.07535	0.01270*
Na41	0.66889	0.98575	0.69266	0.01270*
H13	−0.24775	0.72123	0.68279	0.02090*
H15	−0.05830	0.59958	0.66395	0.02090*
H14	0.62099	0.85243	0.35789	0.02090*
H16	0.79387	0.74936	0.29832	0.02090*
H18	0.47857	0.65251	0.45109	0.02090*
H20	0.57361	0.57501	0.34726	0.02090*
H17	−0.16193	0.23620	0.45478	0.02090*
H19	0.02421	0.12681	0.41491	0.02090*
H43	0.50000	1.00000	0.50000	0.01470*
H44	1.00000	0.50000	0.50000	0.01470*

Bond lengths (Å) top

C1—C3	1.529	C8—H18ⁱ	1.094
C1—O21	1.259	C8—H20ⁱ	1.096
C1—O23	1.278	C9—O25	1.305
C2—C4	1.538	C9—O27	1.245
C2—O22	1.273	C10—O26	1.287
C2—O24	1.265	C10—O28	1.249
C3—C5	1.549	C11—O29	1.251
C3—H13	1.091	C11—O31	1.276
C3—H15	1.094	C12—O30	1.266
C4—C6	1.547	C12—O32	1.257
C4—H14ⁱ	1.098	O25—H43	1.205
C4—H16ⁱ	1.090	O26—H44	1.210
C5—C7	1.543	O33—H35	0.975
C5—C11	1.563	O34—H36	0.971
C5—O33	1.420	H14—C4ⁱ	1.098
C6—C8	1.539	H16—C4ⁱ	1.090
C6—C12	1.550	H18—C8ⁱ	1.094
C6—O34	1.440	H20—C8ⁱ	1.096
C7—C9	1.518	H17—C7ⁱⁱ	1.096
C7—H17ⁱⁱ	1.096	H19—C7ⁱⁱ	1.095
C7—H19ⁱⁱ	1.095	H43—O25ⁱⁱⁱ	1.205
C8—C10	1.527	H44—O26^iv	1.210

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) −x, −y+1, −z+1; (iii) −x+1, −y+2, −z+1; (iv) −x+2, −y+1, −z+1.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O26—H44···O26^iv	1.210	1.210	2.419	180.0
O25—H43···O25ⁱⁱⁱ	1.205	1.205	2.409	180.0
O33—H35···O23^v	0.975	2.045	2.799	132.8
O33—H35···O29	0.975	2.450	2.664	91.7
O34—H36···O30	0.971	2.212	2.631	104.6
O34—H36···O28	0.971	2.302	2.831	113.4
O34—H36···O24^v	0.971	2.385	3.223	144.3

Symmetry codes: (iii) −x+1, −y+2, −z+1; (iv) −x+2, −y+1, −z+1; (v) x+1, y, z.

Acknowledgements

Use of the Advanced Photon Source at Argonne National Laboratory was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02–06CH11357. This work was partially supported by the International Centre for Diffraction Data. We thank Lynn Ribaud for his assistance in data collection.

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ISSN: 2056-9890

Volume 73| Part 2| February 2017| Pages 286-290

https://doi.org/10.1107/S2056989017001256

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research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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

1. Chemical context

2. Structural commentary

3. Supra­molecular features

4. Database survey

5. Synthesis and crystallization

6. Refinement details

7. DFT calculations

Supporting information

Acknowledgements

References

research communications

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

3. Supramolecular features