Crystal structure of caesium di­hydrogen citrate from laboratory X-ray powder diffraction data and DFT comparison

Rammohan, A.; Kaduk, J.A.

doi:10.1107/S2056989017000135

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ISSN: 2056-9890

Volume 73| Part 2| February 2017| Pages 133-136

https://doi.org/10.1107/S2056989017000135

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Crystal structure of caesium dihydrogen citrate from laboratory 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 2 January 2017; accepted 4 January 2017; online 10 January 2017)

The crystal structure of caesium dihydrogen citrate, Cs⁺·H₂C₆H₅O₇⁻, has been solved and refined using laboratory X-ray powder diffraction data, and optimized using density functional techniques. The coordination polyhedra of the nine-coordinate Cs⁺ cations share edges to form chains along the a-axis. These chains are linked by corners along the c-axis. The un-ionized carboxylic acid groups form two different types of hydrogen bonds; one forms a helical chain along the c-axis, and the other is discrete. The hydroxy group participates in both intra- and intermolecular hydrogen bonds.

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

CCDC references: 1525625; 1525624

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 powder diffraction data (laboratory and/or synchrotron), but single crystals were used where available. The general trends and conclusions about the 16 new compounds and 12 previously characterized structures are being reported separately (Rammohan & Kaduk, 2017a ). Ten of the new structures – NaKHC₆H₅O₇, NaK₂C₆H₅O₇, Na₃C₆H₅O₇, NaH₂C₆H₅O₇, Na₂HC₆H₅O₇, K₃C₆H₅O₇, Rb₂HC₆H₅O₇, Rb₃C₆H₅O₇(H₂O), Rb₃C₆H₅O₇, and Na₅H(C₆H₅O₇)₂ – have been published recently (Rammohan & Kaduk, 2016a ,b ,c ,d ,e , 2017b ,c ,d ,e ; 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 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 0.387 Å (Fig. 2). This agreement is at the upper end of the range of correct structures as discussed by van de Streek & Neumann (2014 ). Re-starting the Rietveld refinement from the DFT-optimized structure led to higher residuals (R_wp = 0.1287 and χ² = 26.43). Accurate determination of the positions of C and O atoms in the presence of the heavy Cs atoms using X-ray powder data might be expected to be difficult. 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 ), but the torsion angles involving the central carboxylate and hydroxyl group are flagged as unusual; the central portion of the molecule is less-planar than usual. In the refined structure, the O8—C1 and O10—C6 bonds, as well as the C3—C2—C1 angle, were flagged as unusual. The citrate anion occurs in the trans,trans conformation, which is one of the two low-energy conformations of an isolated citrate. The central carboxylate O10 and the terminal carboxylate O12 atoms chelate to the Cs⁺cation. The Mulliken overlap populations and atomic charges indicate that the metal-oxygen bonding is ionic.

Figure 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 caesium dihydrogen citrate. The refined structure is in red, and the DFT-optimized structure is in blue.

The Bravais–Friedel–Donnay–Harker (Bravais, 1866 ; Friedel, 1907 ; Donnay & Harker, 1937 ) morphology suggests that we might expect a platy morphology for cesium dihydrogen citrate, with {020} as the principal faces. A 4th-order spherical harmonic texture model was included in the refinement. The texture index was 1.183, indicating that preferred orientation was significant for this rotated flat-plate specimen.

3. Supramolecular features

The nine-coordinate Cs⁺ cation (bond-valence sum 0.96) share edges to form chains along the a axis (Fig. 3). These chains are linked by corners along the c axis. The O7—H20⋯O8 hydrogen bonds (Table 1) form a helical chain along the c axis, and the O11—H21⋯O10 hydrogen bonds are discrete. The Mulliken overlap populations in these hydrogen bonds are 0.064 and 0.095 e, respectively. By the correlation in Rammohan & Kaduk (2017a), these hydrogen bonds contribute 13.8 and 16.8 kcal mol⁻¹ to the crystal energy. The hydroxy group O13—H16 acts as a donor in two hydrogen bonds. The one to O10 is intramolecular, with a graph-set symbol S(5). The one to O9 is intermolecular, with a graph set symbol S(7). These hydrogen bonds are weaker, contributing 11.2 and 9.1 kcal mol⁻¹ to the crystal energy.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O11—H21⋯O10ⁱ	1.028	1.575	2.600	174.4
O7—H20⋯O8ⁱⁱ	0.996	1.674	2.637	161.7
O13—H16⋯O9ⁱⁱⁱ	0.979	1.985	2.865	148.4
O13—H16⋯O10	0.979	2.149	2.691	113.3
Symmetry codes: (i) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, z]$ ; (ii) $[-x, -y, z+{\script{1\over 2}}]$ ; (iii) x, y, z+1.

Figure 3
Crystal structure of CsH₂C₆H₅O₇, viewed down the c-axis.

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 cesium dihydrogen citrate in the Cambridge Structural Database (Groom et al., 2016 ) (increasing the default tolerance from 1.5 to 2.0%) yielded 60 hits, but combining the cell search with the elements C, H, Cs, and O only yielded no hits.

5. Synthesis and crystallization

H₃C₆H₅O₇(H₂O) (2.0766 g, 10.0 mmol) was dissolved in 10 ml deionized water. Cs₂CO₃ (1.6508 g, 5.0 mmol, Sigma–Aldrich) was added to the citric acid solution slowly with stirring. A white precipitate formed in about two minutes, and the colourless solution was evaporated to dryness at ambient conditions.

6. Refinement details

Crystal data, data collection and structure refinement details are summarized in Table 2. The powder pattern (Fig. 4) was indexed using DICVOL06 (Louer & Boultif, 2007 ) [M/F(18) = 64/117] on a primitive orthorhombic unit cell having a = 8.7362 (2), b = 20.5351 (2), c = 5.1682 (5) Å, V = 927.17 (9) Å³, and Z = 4. The peak list from a Le Bail fit in GSAS was imported into Endeavour 1.7b (Putz et al., 1999 ), and used for structure solution. The successful solution used a citrate, a Cs atom, and two oxygen atoms from water molecules. Initial Rietveld refinements moved the oxygens close to the Cs site, so they were deleted from the refinement.

Table 2
Experimental details

	Powder data
Crystal data
Chemical formula	Cs⁺·H₂C₆H₅O₇⁻
M_r	323.97
Crystal system, space group	Orthorhombic, Pna2₁
Temperature (K)	300
a, b, c (Å)	8.7362 (2), 20.53510 (16), 5.1682 (5)
V (Å³)	927.17 (9)
Z	4
Radiation type	Kα₁, Kα₂, λ = 1.540629, 1.544451 Å
Specimen shape, size (mm)	Flat sheet, 24 × 24

Data collection
Diffractometer	Bruker D2 Phaser
Specimen mounting	Standard holder
Data collection mode	Reflection
Scan method	Step
2θ values (°)	2θ_min = 5.042 2θ_max = 70.050 2θ_step = 0.020

Refinement
R factors and goodness of fit	R_p = 0.068, R_wp = 0.089, R_exp = 0.026, R(F²) = 0.171, χ² = 11.765
No. of parameters	57
No. of restraints	29
H-atom treatment	Only H-atom displacement parameters refined
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 CsH₂C₆H₅O₇. 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.

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. The C—C bonds were restrained at 1.54 (1) Å, and the C3—O13 bond at 1.42 (2) Å. The C—O bonds in the carboxylate groups were restrained at 1.26 (2) Å. All angles were also restrained; the restraints were 109 (3)° for the angles around tetrahedral carbon atoms, and 120 (3)° for the angles in the planar carboxylate groups. The restraints contributed 3.0% to the final χ². The hydrogen atoms were included at fixed positions, which were recalculated during the course of the refinement using Materials Studio (Dassault Systèmes, 2014 ).

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 Cs was that of Prencipe (1990 ). The calculation used 8 k-points and the B3LYP functional, and took about 59 h on a 2.4 GHz PC. U_iso were assigned to the optimized fractional coordinates based on the U_iso from the refined structure.

Supporting information

CCDC references: 1525625; 1525624

Crystal structure: contains datablocks RAMM013_publ, ramm013_DFT. DOI: https://doi.org/10.1107/S2056989017000135/vn2124sup1.cif

checkCIF report

Computing details top

Data collection: DIFFRAC.Measurement (Bruker, 2009) for RAMM013_publ. Program(s) used to refine structure: GSAS (Larson & Von Dreele, 2004) for RAMM013_publ. Molecular graphics: DIAMOND (Crystal Impact, 2015) for RAMM013_publ. Software used to prepare material for publication: publCIF (Westrip, 2010) for RAMM013_publ.

(RAMM013_publ) cesium dihydrogen citrate top

Crystal data top

Cs⁺·C₆H₇O₇⁻	Z = 4
M_r = 323.97	D_x = 2.321 Mg m⁻³
Orthorhombic, Pna2₁	Kα₁, Kα₂ radiation, λ = 1.540629, 1.544451 Å
Hall symbol: P 2c -2n	T = 300 K
a = 8.7362 (2) Å	white
b = 20.53510 (16) Å	flat_sheet, 24 × 24 mm
c = 5.1682 (5) Å	Specimen preparation: Prepared at 295 K
V = 927.17 (9) Å³

Data collection top

Bruker D2 Phaser diffractometer	Scan method: step
Specimen mounting: standard holder	2θ_min = 5.042°, 2θ_max = 70.050°, 2θ_step = 0.020°
Data collection mode: reflection

Refinement top

Least-squares matrix: full	57 parameters
R_p = 0.068	29 restraints
R_wp = 0.089	Only H-atom displacement parameters refined
R_exp = 0.026	Weighting scheme based on measured s.u.'s
R(F²) = 0.17055	(Δ/σ)_max = 0.05
3217 data points	Background function: GSAS Background function number 1 with 6 terms. Shifted Chebyshev function of 1st kind 1: 1098.70 2: -707.295 3: 219.700 4: -87.7806 5: 41.2782 6: -44.6612
Profile function: CW Profile function number 4 with 18 terms Pseudovoigt profile coefficients as parameterized in P. Thompson, D.E. Cox & J.B. Hastings (1987). J. Appl. Cryst.,20,79-83. Asymmetry correction of L.W. Finger, D.E. Cox & A. P. Jephcoat (1994). J. Appl. Cryst.,27,892-900. Microstrain broadening by P.W. Stephens, (1999). J. Appl. Cryst.,32,281-289. #1(GU) = 1.718 #2(GV) = 0.000 #3(GW) = 4.751 #4(GP) = 0.000 #5(LX) = 2.847 #6(ptec) = 0.00 #7(trns) = 1.83 #8(shft) = 5.2787 #9(sfec) = 0.00 #10(S/L) = 0.0315 #11(H/L) = 0.0005 #12(eta) = 0.9000 #13(S400) = 1.7E-04 #14(S040) = 5.1E-06 #15(S004) = 1.4E-02 #16(S220) = -4.1E-05 #17(S202) = 5.1E-02 #18(S022) = 4.5E-04 Peak tails are ignored where the intensity is below 0.0100 times the peak Aniso. broadening axis 0.0 0.0 1.0

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

	x	y	z	U_iso*/U_eq
C1	0.1876 (17)	0.0459 (9)	0.281 (8)	0.065 (4)*
C2	0.347 (2)	0.0446 (9)	0.166 (6)	0.009 (9)*
C3	0.4423 (18)	0.0965 (6)	0.304 (5)	0.009 (9)*
C4	0.609 (2)	0.0896 (10)	0.212 (7)	0.009 (9)*
C5	0.706 (2)	0.1464 (9)	0.317 (6)	0.065 (4)*
C6	0.380 (3)	0.1665 (7)	0.241 (6)	0.065 (4)*
O7	0.130 (2)	−0.0065 (11)	0.333 (9)	0.065 (4)*
O8	0.107 (2)	0.0874 (9)	0.223 (13)	0.065 (4)*
O9	0.371 (5)	0.1862 (12)	0.010 (7)	0.065 (4)*
O10	0.351 (4)	0.2037 (12)	0.418 (7)	0.065 (4)*
O11	0.716 (3)	0.1978 (11)	0.185 (7)	0.065 (4)*
O12	0.730 (3)	0.1503 (12)	0.552 (7)	0.065 (4)*
O13	0.436 (3)	0.0847 (9)	0.577 (5)	0.065 (4)*
H14	0.39911	−0.00564	0.19584	0.012 (11)*
H15	0.34027	0.05603	−0.04959	0.012 (11)*
H16	0.31496	0.11870	0.64320	0.085 (6)*
H17	0.65810	0.04163	0.28558	0.012 (11)*
H18	0.61212	0.09008	−0.00850	0.012 (11)*
Cs19	0.0454 (3)	0.20017 (14)	0.7594	0.0505 (15)*
H20	0.06940	−0.05097	0.56860	0.05*
H21	0.67528	0.24300	0.25240	0.05*

Geometric parameters (Å, º) top

C1—C2	1.509 (10)	O9—Cs19ⁱⁱ	3.07 (3)
C1—O7	1.218 (18)	O10—C6	1.217 (19)
C1—O8	1.148 (17)	O10—O9	2.15 (2)
C2—C1	1.509 (10)	O10—Cs19	3.20 (4)
C2—C3	1.532 (10)	O10—Cs19ⁱⁱⁱ	3.14 (4)
C3—C2	1.532 (10)	O11—C5	1.260 (19)
C3—C4	1.537 (10)	O11—O12	2.14 (3)
C3—C6	1.569 (9)	O11—Cs19^iv	3.62 (3)
C3—O13	1.429 (11)	O11—Cs19ⁱⁱ	3.38 (3)
C4—C3	1.537 (10)	O11—Cs19ⁱⁱⁱ	3.93 (3)
C4—C5	1.542 (10)	O12—C5	1.24 (2)
C5—C4	1.542 (10)	O12—O11	2.14 (3)
C5—O11	1.260 (19)	O12—Cs19^v	3.13 (3)
C5—O12	1.24 (2)	O12—Cs19ⁱⁱⁱ	3.63 (3)
C6—C3	1.569 (9)	O13—C3	1.429 (11)
C6—O9	1.267 (19)	Cs19—O8	3.65 (5)
C6—O10	1.217 (19)	Cs19—O8^vi	3.37 (5)
O7—C1	1.218 (18)	Cs19—O9^vi	3.14 (4)
O7—O8	2.02 (2)	Cs19—O9^vii	3.07 (3)
O8—C1	1.148 (17)	Cs19—O10	3.20 (4)
O8—O7	2.02 (2)	Cs19—O10^viii	3.14 (4)
O8—Cs19ⁱ	3.37 (5)	Cs19—O11^ix	3.62 (3)
O8—Cs19	3.65 (5)	Cs19—O11^viii	3.93 (3)
O9—C6	1.267 (19)	Cs19—O11^vii	3.38 (3)
O9—O10	2.15 (2)	Cs19—O12^x	3.13 (3)
O9—Cs19ⁱ	3.14 (4)	Cs19—O12^viii	3.63 (3)

C2—C1—O7	116.8 (10)	C5—O11—Cs19ⁱⁱ	147.2 (15)
C2—C1—O8	118.6 (10)	C5—O12—Cs19^v	120.3 (19)
O7—C1—O8	117.4 (10)	C3—O13—H16	114.5 (15)
C1—C2—C3	107.9 (8)	O8^vi—Cs19—O9^vi	60.0 (7)
C2—C3—C4	108.0 (8)	O8^vi—Cs19—O9^vii	107.5 (11)
C2—C3—C6	110.6 (8)	O8^vi—Cs19—O10	106.0 (7)
C2—C3—O13	108.6 (9)	O8^vi—Cs19—O10^viii	156.2 (7)
C4—C3—C6	110.2 (9)	O8^vi—Cs19—O11^vii	83.9 (9)
C4—C3—O13	109.1 (9)	O8^vi—Cs19—O12^x	99.1 (6)
C6—C3—O13	110.3 (8)	O9^vi—Cs19—O9^vii	110.2 (11)
C3—C4—C5	110.1 (9)	O9^vi—Cs19—O10	58.2 (5)
C4—C5—O11	118.7 (9)	O9^vi—Cs19—O10^viii	141.1 (6)
C4—C5—O12	119.1 (9)	O9^vi—Cs19—O11^vii	52.3 (7)
O11—C5—O12	118.0 (10)	O9^vi—Cs19—O12^x	155.4 (7)
C3—C6—O9	120.8 (8)	O9^vii—Cs19—O10	129.0 (7)
C3—C6—O10	119.5 (8)	O9^vii—Cs19—O10^viii	59.5 (5)
O9—C6—O10	119.5 (8)	O9^vii—Cs19—O11^vii	58.4 (7)
C1—O8—Cs19ⁱ	142 (2)	O9^vii—Cs19—O12^x	87.4 (8)
C6—O9—Cs19ⁱ	119 (3)	O10—Cs19—O10^viii	97.2 (9)
C6—O9—Cs19ⁱⁱ	127 (3)	O10—Cs19—O11^vii	88.6 (7)
Cs19ⁱ—O9—Cs19ⁱⁱ	101.9 (7)	O10—Cs19—O12^x	123.6 (10)
C6—O10—Cs19	125 (3)	O10^viii—Cs19—O11^vii	102.4 (6)
C6—O10—Cs19ⁱⁱⁱ	135 (3)	O10^viii—Cs19—O12^x	62.5 (7)
Cs19—O10—Cs19ⁱⁱⁱ	98.9 (9)	O11^vii—Cs19—O12^x	144.4 (7)

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

(ramm013_DFT) top

Crystal data top

CsH₂C₆H₅O₇	c = 5.1682 Å
M_r = 323.97	V = 927.17 Å³
Orthorhombic, Pna2₁	Z = 4
Hall symbol: P 2c -2n	D_x = 2.321 Mg m⁻³
a = 8.7362 Å	Cu Kα radiation, λ = 1.5418 Å
b = 20.5351 Å	T = 300 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	0.14729	0.01007	0.32268	0.06500*
C2	0.28682	0.02722	0.16639	0.00900*
C3	0.35878	0.08945	0.28492	0.00900*
C4	0.52514	0.09664	0.18015	0.00900*
C5	0.60947	0.15212	0.30828	0.06500*
C6	0.26991	0.15158	0.20135	0.06500*
O7	0.15730	−0.04600	0.44742	0.06500*
O8	0.03401	0.04586	0.34061	0.06500*
O9	0.23818	0.15901	−0.03279	0.06500*
O10	0.24301	0.19347	0.37889	0.06500*
O11	0.62642	0.20442	0.15627	0.06500*
O12	0.65699	0.15090	0.53096	0.06500*
O13	0.36027	0.08089	0.55685	0.06500*
H14	0.36802	−0.01307	0.17323	0.01200*
H15	0.25479	0.03604	−0.03477	0.01200*
H16	0.31496	0.11870	0.64320	0.08500*
H17	0.58685	0.05170	0.22176	0.01200*
H18	0.52243	0.10375	−0.02890	0.01200*
Cs19	−0.05606	0.21080	0.74122	0.05030*
H20	0.06940	−0.05097	0.56860	0.05000*
H21	0.67528	0.24300	0.25240	0.05000*

Bond lengths (Å) top

C1—C2	1.504	C4—H17	1.090
C1—O7	1.322	C4—H18	1.091
C1—O8	1.354	C5—O11	1.339
C2—C3	1.550	C5—O12	1.224
C2—H14	1.090	C6—O9	1.251
C2—H15	1.092	C6—O10	1.279
C3—C4	1.558	O7—H20ⁱ	0.996
C3—C6	1.555	O11—H21	1.028
C3—O13	1.416	O13—H16	0.979
C4—C5	1.510	H20—O7ⁱⁱ	0.996

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

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O11—H21···O10ⁱⁱ	1.028	1.575	2.600	174.4
O7—H20···O8ⁱⁱⁱ	0.996	1.674	2.637	161.7
O13—H16···O9^iv	0.979	1.985	2.865	148.4
O13—H16···O10	0.979	2.149	2.691	113.3

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

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Volume 73| Part 2| February 2017| Pages 133-136

https://doi.org/10.1107/S2056989017000135

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

Crystal structure of caesium di­hydrogen citrate from laboratory 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

References

research communications

Crystal structure of caesium dihydrogen citrate from laboratory X-ray powder diffraction data and DFT comparison

3. Supramolecular features