Possible strong symmetric hydrogen bonding in disodium tri­hydrogen bis(2,2′-oxydi­acetate) nitrate

Price, D.J.; Fritsch, S.; Wood, P.T.; Powell, A.K.

doi:10.1107/S1600536805014819

metal-organic compounds

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ISSN: 2056-9890

Volume 61| Part 6| June 2005| Pages m1174-m1177

https://doi.org/10.1107/S1600536805014819

Possible strong symmetric hydrogen bonding in disodium trihydrogen bis(2,2′-oxydiacetate) nitrate

Daniel J. Price,^a ^*‡ Stefan Fritsch,^a Paul T. Wood ^a § and Annie K. Powell ^a ¶

^aSchool of Chemical Sciences, University of East Anglia, University Plain, Norwich NR4 7TJ, England
^*Correspondence e-mail: d.price@chem.gla.ac.uk

(Received 21 April 2005; accepted 10 May 2005; online 21 May 2005)

In the title compound, 2Na⁺·C₈H₁₁O₁₀⁻·NO₃⁻, the Na^I atom is heptacoordinate with an approximately pentagonal–bipyramidal geometry. A possible strong symmetric hydrogen bond, with the H atom located at an inversion centre and an O⋯O distance of 2.450 (2) Å, is observed in the crystal structure.

Comment

The nature of short hydrogen-bonding interactions is still a subject of much interest and debate (Meot-Ner, 2005 ). It appears that, for O—H—O interactions where O⋯O is less than about 2.50 Å, examples can be found of truly symmetric hydrogen bonds (Catti & Ferraris, 1976 ), most of which have crystallographic equivalence between donor–acceptor atoms. The title sodium compound, (I), displays just such a short and possibly symmetric hydrogen-bonding interaction.

The compound can be viewed as a mixed sodium salt containing two monoanionic components, viz. nitrate and trihydrogen bis(2,2′-oxydiacetate) (a hydrogen-bonded adduct formed by the loss of a single H atom from two of the dicarboxylic acid molecules). These 2,2′-oxydiacetate molecules adopt the fairly common planar all-trans configuration (Albertsson & Grenthe, 1973 ; Albertsson et al., 1973a ,b; Hatfield et al., 1987 ). The Na^I cation in (I) is heptacoordinate with an approximately pentagonal–bipyramidal geometry (Fig. 1); Na—O distances range from 2.4075 (17) to 2.5861 (18) Å. A tridentate chelating 2,2′-oxydiacetate molecule occupies three of the equatorial sites bonding through the two carboxyl and one ether O atoms. Symmetry-equivalent carboxyl atoms O2ⁱⁱⁱ, O5^iv and O1^v [symmetry codes: (iii) 1 − x, 1 − y, 1 − z; (iv) 1 − x, −y, 1 − z; (v) x − ½, y − ½, z] from neighbouring 2,2′-oxydiacetate molecules and atom O6 of a bridging nitrate make up the rest of the coordination sphere.

The nitrate anion lies on the crystallographic twofold axis and links pairs of Na^I ions in an anti–anti-1,3-bridging coordination mode. The carboxyl O atoms act in a bis-μ-bridging capacity between Na^I ions, forming the polymeric structure.

In addition to these ionic interactions, the crystal structure is also held together by a network of two types of hydrogen bonds. The first is formed between the O4-carboxyl group and the nitrate anion (Table 1). This hydrogen bond is asymmetric and non-linear. The nature of the second type of hydrogen bond is ambiguous. Certainly there exists a short hydrogen-bond interaction between the O1-carboxyl group and its crystallographically equivalent group; the O1⋯O1ⁱ distance of 2.450 (2) Å [symmetry code:(i) $[3\over2]$ − x, $[3\over2]$ − y, 1 − z] falls within the normal range for symmetric hydrogen bonds (Catti & Ferraris, 1976). A Fourier map section in the O1/C1/O2 plane (MAPVIEW; Farrugia, 1999 ) clearly indicates a peak of electron density centred on the crystallographic inversion (Fig. 2). Two alternative structural models have been studied. Placing atom H1 on the inversion centre gives a symmetric structure. Full-matrix least-squares refinement converged to a stable solution which is reported here. The residual difference Fourier map has a largest peak and hole of 0.16 and −0.23 e Å⁻³, respectively. The crystallographic symmetry constrains the hydrogen-bond angle to 180° and the O1—H1 distance to 1.23 Å. A second structural model is one with the H1-atom site half occupied and displaced from the inversion centre towards O1. Free refinement of the x, y, z and U_iso parameters for the H1 atom (118 parameters in total) converged to give a sensible asymmetric hydrogen-bonding interaction; the crystallographic residuals are insignificantly different and the difference map shows essentially the same features. The limited data quality and resolution mean that we cannot unambiguously determine the nature of this hydrogen-bonding interaction. The compound clearly merits further study, if only to resolve this issue. Despite this uncertainty in the H-atom position, such a linear hydrogen-bonding interaction linking two 2,2′-oxydiacetate molecules in a trans fashion is not an unusual motif when an H atom is shared between two carboxylic acid groups (Nahringbauer, 1969 ; Longo & Richardson, 1982 ; Misaki et al., 1989 ).

An examination of the Cambridge Structural Database (CSD; Version 5.25; Allen, 2002 ) for short hydrogen bonds between two carboxylate groups reveals three distinct conformational/geometric groups (Fig. 3). Group 1 have a C—O⋯O—C torsion angles of about 0° and have O⋯O separations mostly in the range 2.38–2.43 Å. Group 2 have C—O⋯O—C torsion angles of 180° (invariably fixed by crystallographic symmetry) and O⋯O separations in the range 2.43–2.53 Å. Group 3 have intermediate torsion angles (unrestricted by symmetry) and have O⋯O distances all within the range 2.42–2.47 Å. The possibly symmetric hydrogen bond observed in (I) falls well within the known range for group 2 conformations, and this geometry is seen for many other dicarboxylate compounds (see, for example, Kalsbeek & Larsen, 1991 ; Leban & Rupnik, 1992 ; Flensburg et al., 1995 ) and also in other 2,2′-oxydiacetate salts (Albertsson & Grenthe, 1973; Albertsson et al., 1973a,b ; Herbertsson & Hedman, 1982 ; Urbańczyk-Lipkowska, 2000 ).

We also note that the first hydrogen-bonding pattern (between the carboxylic acid and the nitrate anion), although asymmetric, seems to be a strong and important structural motif. In nine out of 14 reported structures that contain both a carboxylic acid and a nitrate anion, the acid is hydrogen bonded to the nitrate, and none of the structures displays the common R₂²(8) dimeric carboxylic acid motif (see, for example, Sridhar et al., 2002 ).

Together, these two hydrogen-bonded motifs form a network. Using the nomenclature for graph theoretical analysis developed by Etter et al. (1990 ), we can describe this system as N₁ = D₂²(4)D; N₂ = C₃³(20), where the second-order net consists of infinite chains that zigzag through the crystal structure (Fig. 4).

Figure 1
The molecular structure and sodium environment, with 50% probability displacement ellipsoids and the atom-labelling scheme. Dashed lines indicate hydrogen bonds. [Symmetry codes: (i) $[3\over2]$ − x, $[3\over2]$ − y, 1 − z; (ii) x, y − 1, z; (iii) 1 − x, 1 − y, 1 − z; (iv) 1 − x, −y, 1 − z; (v) x − $[1\over2]$ , y − $[1\over2]$ , z; (vi) 1 − x, y, $[3\over2]$ − z].

Figure 2
Difference Fourier map from a refined model where atom H1 is absent. The O1/C1/O2 plane is shown with the crystallographic inversion in the centre of the plot.

Figure 3
Graph showing the distribution of C—O⋯O—C torsion angles as a function of O⋯O interatomic separations for short hydrogen-bonded interactions between two carboxylic acid groups. Data taken from 78 structures in the CSD (Version 5.25; Allen, 2002

Figure 4
The hydrogen-bonded network formed by both types of hydrogen-bonding interaction (dashed lines).

Experimental

Crystals of (I) were grown by slow evaporation from a methanolic solution which contained the bis(2,2′-oxydiacetic acid), sodium hydroxide and aluminium nitrate nonahydrate.

Crystal data

2Na⁺·C₈H₁₁O₁₀⁻·NO₃⁻
M_r = 375.16
Monoclinic, C2/c
a = 12.010 (2) Å
b = 7.0290 (14) Å
c = 16.382 (3) Å
β = 94.84 (3)°
V = 1378.0 (4) Å³
Z = 4
D_x = 1.808 Mg m⁻³
Mo Kα radiation
Cell parameters from 101 reflections
θ = 3.2–24.8°
μ = 0.22 mm⁻¹
T = 293 (2) K
Block, colourless
0.16 × 0.16 × 0.06 mm

Data collection

Rigaku R-AXIS-IIc diffractometer
φ scans
Absorption correction: none
1999 measured reflections
1124 independent reflections
996 reflections with I > 2σ(I)
R_int = 0.016
θ_max = 24.8°
h = 0 → 14
k = −8 → 8
l = −19 → 19

Refinement

Refinement on F²
R[F² > 2σ(F²)] = 0.033
wR(F²) = 0.103
S = 1.17
1124 reflections
115 parameters
H atoms treated by a mixture of independent and constrained refinement
w = 1/[σ²(F_o²) + (0.0446P)² + 1.8079P] where P = (F_o² + 2F_c²)/3
(Δ/σ)_max < 0.001
Δρ_max = 0.16 e Å⁻³
Δρ_min = −0.23 e Å⁻³

Table 1
Hydrogen-bonding geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯O1ⁱ	1.225	1.225	2.450 (2)	180
O4—H4⋯O6ⁱⁱ	0.92 (4)	1.82 (4)	2.703 (3)	160 (3)
Symmetry codes: (i) $[{\script{3\over 2}}-x,{\script{3\over 2}}-y,1-z]$ ; (ii) x,y-1,z.

All methylene H atoms were located in idealized positions and refined in riding mode. C—H distances were set at 0.97Å and U_iso(H) values were constained to be 1.5U_eq of the parent C atom. Both H atoms involved in hydrogen bonding were found in a Fourier difference map and were refined, subject only to the inversion centre constraint.

Data collection: MSC R-AXIS-II Control Software; cell refinement: DENZO (Otwinowski & Minor, 1997 ); data reduction: SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS86 (Robinson & Sheldrick, 1988 ); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997 ) in WinGX (Farrugia, 1999); molecular graphics: DIAMOND (Brandenburg, 1999 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: https://doi.org/10.1107/S1600536805014819/xu6006sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536805014819/xu6006Isup2.hkl

Computing details top

Data collection: MSC R-AXIS-II control Software; cell refinement: DENZO (Otwinowski & Minor, 1997); data reduction: SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SHELXS86 (Robinson & Sheldrick, 1988); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997) in WinGX (Farrugia, 1999); molecular graphics: DIAMOND (Brandenburg, 1999).

disodium trihydrogen bis(2,2'-oxydiacetate) nitrate top

Crystal data top

2Na⁺·C₈H₁₁O₁₀⁻·NO₃⁻	F(000) = 768
M_r = 375.16	D_x = 1.808 Mg m⁻³
Monoclinic, C2/c	Melting point: not measured K
Hall symbol: -C 2yc	Mo Kα radiation, λ = 0.71073 Å
a = 12.010 (2) Å	Cell parameters from 101 reflections
b = 7.0290 (14) Å	θ = 3.2–24.8°
c = 16.382 (3) Å	µ = 0.22 mm⁻¹
β = 94.84 (3)°	T = 293 K
V = 1378.0 (4) Å³	Block, colourless
Z = 4	0.16 × 0.16 × 0.06 mm

Data collection top

Rigaku R-AXIS-IIc diffractometer	996 reflections with I > 2σ(I)
Radiation source: Mo rotating anode	R_int = 0.016
Graphite monochromator	θ_max = 24.8°, θ_min = 3.4°
φ scans	h = 0→14
1999 measured reflections	k = −8→8
1124 independent reflections	l = −19→19

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.033	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.103	H atoms treated by a mixture of independent and constrained refinement
S = 1.17	w = 1/[σ²(F_o²) + (0.0446P)² + 1.8079P] where P = (F_o² + 2F_c²)/3
1124 reflections	(Δ/σ)_max < 0.001
115 parameters	Δρ_max = 0.16 e Å⁻³
0 restraints	Δρ_min = −0.23 e Å⁻³

Special details top

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F² against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F², conventional R-factors R are based on F, with F set to zero for negative F². The threshold expression of F² > σ(F²) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F² are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

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

	x	y	z	U_iso*/U_eq
Na1	0.48509 (7)	0.24986 (12)	0.55036 (5)	0.0308 (3)
O3	0.67561 (12)	0.1858 (2)	0.60051 (9)	0.0301 (4)
O2	0.62402 (12)	0.4925 (2)	0.51549 (9)	0.0296 (4)
O6	0.48709 (15)	0.4402 (3)	0.68343 (9)	0.0407 (5)
N1	0.5000	0.3494 (4)	0.7500	0.0348 (7)
C1	0.71748 (17)	0.4937 (3)	0.55231 (11)	0.0228 (5)
C2	0.75705 (17)	0.3318 (3)	0.60802 (13)	0.0269 (5)
H2A	0.8281	0.2839	0.5926	0.040*
H2B	0.7671	0.3756	0.6643	0.040*
C3	0.70115 (18)	0.0316 (3)	0.65405 (12)	0.0276 (5)
H3A	0.7083	0.0754	0.7104	0.041*
H3B	0.7713	−0.0263	0.6421	0.041*
O7	0.5000	0.1751 (4)	0.7500	0.0792 (11)
O5	0.53165 (13)	−0.0997 (2)	0.58891 (9)	0.0317 (4)
O4	0.62185 (14)	−0.2512 (2)	0.69492 (10)	0.0364 (4)
C4	0.60827 (17)	−0.1102 (3)	0.64181 (12)	0.0241 (5)
O1	0.78860 (12)	0.6300 (2)	0.54870 (9)	0.0310 (4)
H4	0.568 (3)	−0.341 (5)	0.6805 (17)	0.058 (9)*
H1	0.7500	0.7500	0.5000	0.071 (14)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Na1	0.0263 (5)	0.0288 (5)	0.0361 (5)	−0.0002 (4)	−0.0038 (4)	0.0014 (3)
O3	0.0254 (8)	0.0217 (8)	0.0416 (9)	−0.0057 (7)	−0.0069 (6)	0.0124 (7)
O2	0.0235 (8)	0.0269 (8)	0.0374 (8)	−0.0024 (7)	−0.0043 (6)	0.0074 (6)
O6	0.0509 (11)	0.0411 (10)	0.0298 (8)	−0.0082 (9)	0.0018 (7)	−0.0005 (7)
N1	0.0335 (15)	0.0254 (15)	0.0480 (17)	0.000	0.0173 (12)	0.000
C1	0.0228 (10)	0.0199 (11)	0.0260 (10)	−0.0012 (9)	0.0040 (8)	−0.0001 (8)
C2	0.0240 (11)	0.0228 (11)	0.0331 (11)	−0.0050 (9)	−0.0031 (8)	0.0043 (9)
C3	0.0273 (11)	0.0250 (11)	0.0291 (10)	−0.0020 (9)	−0.0051 (8)	0.0084 (9)
O7	0.120 (3)	0.0227 (15)	0.104 (3)	0.000	0.064 (2)	0.000
O5	0.0286 (8)	0.0313 (9)	0.0340 (8)	−0.0041 (7)	−0.0051 (6)	0.0038 (6)
O4	0.0427 (10)	0.0282 (9)	0.0365 (9)	−0.0095 (8)	−0.0073 (7)	0.0121 (7)
C4	0.0270 (11)	0.0217 (11)	0.0237 (10)	0.0004 (9)	0.0032 (8)	0.0019 (8)
O1	0.0258 (8)	0.0243 (8)	0.0420 (9)	−0.0068 (7)	−0.0027 (6)	0.0080 (7)

Geometric parameters (Å, º) top

Na1—O3	2.4075 (17)	N1—O6^iv	1.262 (2)
Na1—O2ⁱ	2.4333 (17)	C1—O1	1.288 (2)
Na1—O2	2.4860 (17)	C1—C2	1.511 (3)
Na1—O1ⁱⁱ	2.5038 (17)	C2—H2A	0.9700
Na1—O5ⁱⁱⁱ	2.5065 (18)	C2—H2B	0.9700
Na1—O6	2.5562 (19)	C3—C4	1.496 (3)
Na1—O5	2.5861 (18)	C3—H3A	0.9700
Na1—Na1ⁱⁱⁱ	3.9100 (18)	C3—H3B	0.9700
Na1—Na1ⁱ	3.9135 (18)	O5—C4	1.212 (2)
O3—C3	1.412 (2)	O5—Na1ⁱⁱⁱ	2.5065 (18)
O3—C2	1.416 (3)	O4—C4	1.320 (3)
O2—C1	1.229 (2)	O4—H4	0.92 (3)
O2—Na1ⁱ	2.4333 (17)	O1—Na1^v	2.5038 (17)
O6—N1	1.262 (2)	O1—H1	1.2250 (14)
N1—O7	1.225 (4)

O3—Na1—O2ⁱ	138.69 (6)	C3—O3—C2	112.97 (15)
O3—Na1—O2	64.51 (5)	C3—O3—Na1	120.39 (12)
O2ⁱ—Na1—O2	74.59 (6)	C2—O3—Na1	121.61 (12)
O3—Na1—O1ⁱⁱ	143.96 (6)	C1—O2—Na1ⁱ	130.39 (14)
O2ⁱ—Na1—O1ⁱⁱ	76.93 (6)	C1—O2—Na1	119.67 (13)
O2—Na1—O1ⁱⁱ	151.48 (6)	Na1ⁱ—O2—Na1	105.41 (6)
O3—Na1—O5ⁱⁱⁱ	103.47 (7)	N1—O6—Na1	117.66 (15)
O2ⁱ—Na1—O5ⁱⁱⁱ	84.90 (6)	O7—N1—O6^iv	120.38 (13)
O2—Na1—O5ⁱⁱⁱ	94.80 (6)	O7—N1—O6	120.38 (13)
O1ⁱⁱ—Na1—O5ⁱⁱⁱ	81.09 (6)	O6^iv—N1—O6	119.2 (3)
O3—Na1—O6	82.33 (7)	O2—C1—O1	124.38 (18)
O2ⁱ—Na1—O6	87.40 (6)	O2—C1—C2	121.28 (18)
O2—Na1—O6	83.03 (6)	O1—C1—C2	114.34 (17)
O1ⁱⁱ—Na1—O6	97.27 (7)	O3—C2—C1	108.29 (16)
O5ⁱⁱⁱ—Na1—O6	172.29 (7)	O3—C2—H2A	110.0
O3—Na1—O5	63.86 (5)	C1—C2—H2A	110.0
O2ⁱ—Na1—O5	155.85 (6)	O3—C2—H2B	110.0
O2—Na1—O5	124.92 (6)	C1—C2—H2B	110.0
O1ⁱⁱ—Na1—O5	82.36 (5)	H2A—C2—H2B	108.4
O5ⁱⁱⁱ—Na1—O5	79.71 (6)	O3—C3—C4	107.92 (16)
O6—Na1—O5	107.62 (6)	O3—C3—H3A	110.1
O3—Na1—Na1ⁱⁱⁱ	81.83 (5)	C4—C3—H3A	110.1
O2ⁱ—Na1—Na1ⁱⁱⁱ	123.13 (5)	O3—C3—H3B	110.1
O2—Na1—Na1ⁱⁱⁱ	115.62 (6)	C4—C3—H3B	110.1
O1ⁱⁱ—Na1—Na1ⁱⁱⁱ	79.21 (5)	H3A—C3—H3B	108.4
O5ⁱⁱⁱ—Na1—Na1ⁱⁱⁱ	40.60 (4)	C4—O5—Na1ⁱⁱⁱ	128.54 (14)
O6—Na1—Na1ⁱⁱⁱ	146.66 (6)	C4—O5—Na1	111.59 (14)
O5—Na1—Na1ⁱⁱⁱ	39.10 (4)	Na1ⁱⁱⁱ—O5—Na1	100.29 (6)
O3—Na1—Na1ⁱ	101.17 (5)	C4—O4—H4	107.3 (18)
O2ⁱ—Na1—Na1ⁱ	37.76 (4)	O5—C4—O4	124.1 (2)
O2—Na1—Na1ⁱ	36.83 (4)	O5—C4—C3	124.60 (18)
O1ⁱⁱ—Na1—Na1ⁱ	114.68 (5)	O4—C4—C3	111.24 (17)
O5ⁱⁱⁱ—Na1—Na1ⁱ	89.88 (5)	C1—O1—Na1^v	151.39 (13)
O6—Na1—Na1ⁱ	83.95 (5)	C1—O1—H1	109.02 (14)
O5—Na1—Na1ⁱ	158.59 (6)	Na1^v—O1—H1	94.58 (8)
Na1ⁱⁱⁱ—Na1—Na1ⁱ	127.91 (5)

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x−1/2, y−1/2, z; (iii) −x+1, −y, −z+1; (iv) −x+1, y, −z+3/2; (v) 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
O1—H1···O1^vi	1.23	1.23	2.450 (2)	180
O4—H4···O6^vii	0.92 (4)	1.82 (4)	2.703 (3)	160 (3)

Symmetry codes: (vi) −x+3/2, −y+3/2, −z+1; (vii) x, y−1, z.

Footnotes

‡Present address: WestCHEM, Department of Chemistry, University of Glasgow, University Avenue, Glasgow G12 8QQ, Scotland

§Present address: University Chemistry Laboratory, Lensfield Road, Cambridge CB2 1EW, England

¶Present address: Institut für Anorganische Chemie der Universität, D-76128 Karlsruhe, Germany

Acknowledgements

The authors are grateful to the EPSRC, UK, for financial support and the Wellcome Trust for the provision of X-ray facilities.

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