A redetermination of the structure of poly[[μ4-(R)-2-ammonio-3-sulfonato­propano­ato]aqua­sodium], originally reported as poly[[μ7-l-cysteato(2−)]disodium]

Brown, I.D.

doi:10.1107/S1600536812009683

metal-organic compounds

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Volume 68| Part 4| April 2012| Page m393

doi:10.1107/S1600536812009683

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A redetermination of the structure of poly[[μ₄-(R)-2-ammonio-3-sulfonatopropanoato]aquasodium], originally reported as poly[[μ₇-L-cysteato(2−)]disodium]

I. David Brown ^a ^*

^aBrockhouse Institute for Materials Research, McMaster University Hamilton, Ontario, Canada L8S 4M1
^*Correspondence e-mail: idbrown@mcmaster.ca

(Received 27 February 2012; accepted 5 March 2012; online 10 March 2012)

The structure originally reported as poly[[μ₇-L-cysteato(2−)]disodium], [Na₂(C₃H₅NO₅S)]_n [Liu (2002). Acta Cryst. E67, m1346–m1347], has been redetermined with one of the sodium atoms replaced with a water molecule and an additional proton attached to the amine group, resulting in the revised formula [Na{CO₂CH(CH₂SO₃)NH₃}(H₂O)]_n. The agreement index, wR, has been reduced from 0.159 to 0.087 and the global instability index from 0.56 vu (valence units) to the acceptable value of 0.11 vu.

Related literature

The original structure determination of this compound was reported by Liu (2011 ). The bond-valence methods are described in Brown (2002 ).

Experimental

Crystal data

[Na(C₃H₆NO₅S)(H₂O)]
M_r = 209.15
Monoclinic, P 2₁ /c
a = 5.7574 (12) Å
b = 11.875 (2) Å
c = 11.691 (3) Å
β = 109.15 (3)°
V = 755.1 (3) Å³
Z = 4
Mo Kα radiation
μ = 0.48 mm⁻¹
T = 298 K
0.24 × 0.22 × 0.20 mm

Data collection

Rigaku SCX-Mini CCD diffractometer
Absorption correction: multi-scan (ABSCOR; Higashi, 1995 ) T_min = 0.894, T_max = 0.911
7845 measured reflections
1740 independent reflections
1463 reflections with I > 2Σ(I)
R_int = 0.044

Refinement

R[F² > 2σ(F²)] = 0.038
wR(F²) = 0.087
S = 1.10
1740 reflections
118 parameters
2 restraints
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.39 e Å⁻³
Δρ_min = −0.35 e Å⁻³

Table 1
Selected bond lengths (Å)

Na1—O4ⁱ	2.3512 (19)
Na1—O5ⁱⁱ	2.3619 (19)
Na1—O3	2.4183 (18)
Na1—O2ⁱⁱⁱ	2.4272 (19)
Na1—O1W	2.450 (2)
Na1—O1	2.4778 (18)
Symmetry codes: (i) x-1, y, z; (ii) $[x, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ ; (iii) $[-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]$ .

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1A⋯O1W^iv	0.89	2.16	2.981 (3)	153
N1—H1B⋯O1^v	0.89	1.97	2.842 (2)	166
N1—H1C⋯O2^iv	0.89	1.88	2.766 (2)	173
O1W—H1WA⋯O3ⁱⁱ	0.85 (1)	2.10 (1)	2.912 (3)	160 (4)
O1W—H1WB⋯O5^vi	0.85 (1)	2.08 (1)	2.930 (2)	178 (3)
Symmetry codes: (ii) $[x, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ ; (iv) x+1, y, z; (v) -x+1, -y+2, -z+1; (vi) $[x-1, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]$ .

Data collection: PROCESS-AUTO (Rigaku, 1998 ); cell refinement: PROCESS-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002 ); method used to solve structure: coordinates taken from the previous refinement (Liu, 2011); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ); molecular graphics: Mercury (Macrae et al., 2006 ); software used to prepare material for publication: publCIF (Westrip, 2010 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536812009683/sj5205sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536812009683/sj5205Isup2.hkl

checkCIF report

Comment top

In a recent issue of this journal, Liu (2011) reported the structure of the title compound, but a close examination of this structure shows a serious problem with the environment of one of the sodium atoms, Na2. In the Comment the author describes this atom as 'tetracoordinated within an NO₃ coordination sphere. The Na⁺ ion binds to the amino N atom, to one of the O atom of the carboxylic residue and to two O atoms of the sulfonate group in a distorted tetrahedral arrangement'. The Comment does not point out that the atomic displacement parameter of Na2 is almost three times larger than the next largest atomic displacement parameter, nor does it point out that the lengths of the four bonds around Na2 all lie in the range 2.90 to 3.03 Å, distances whose bond valence sum of 0.21 vu (valence unit) indicates that they are much longer than would be expected for a four-coordinate sodium cation. The global instability index [root mean square deviation of the bond valence sums of all atoms from their atomic valence, (Brown, 2002)] is 0.56 vu, much higher than the generally accepted limit of 0.20 vu for a stable structure. The environment of Na2 is, however, one that would be expected for a water molecule that forms moderate to weak hydrogen bonds. An additional hydrogen ion is required for charge neutrality, but protonating the water molecule is unlikely as this would require much shorter hydrogen bonds than are observed for this site, but protonating the amine group would not only increase the bond valence sum around the nitrogen from 2.51 vu to a value closer to the expected 3.00 vu, it would also result in an N—H bond positioned to form a hydrogen bond with the water molecule.

This proposed model has been refined and is reported in this paper. The bond valence sum of 0.21 vu around the original Na2 has been replaced by a sum of 1.94 vu around the oxygen of water, and the sum around the N1 atom has been increased to 3.17 vu. Moreover, Na1 now has a meaningful octahedral environment (Fig. 1) with a Na1—O1W contact of 2.450 (2) Å instead of a Na1—Na2 contact as in the original model.

Based on the rerefinement of the structure, this crystal must be reformulated as sodium (R)-2-ammonium-3-sulfopropanoate monohydrate, Na(CO₂CH(CH₂SO₃)NH₃)(H₂O).

Related literature top

The original structure determination of this compound was reported by Liu (2011). The bond-valence methods are described in Brown (2002).

Experimental top

The preparation of the compound is detailed in the original report (Liu, 2011).

Structure description top

Based on the rerefinement of the structure, this crystal must be reformulated as sodium (R)-2-ammonium-3-sulfopropanoate monohydrate, Na(CO₂CH(CH₂SO₃)NH₃)(H₂O).

The original structure determination of this compound was reported by Liu (2011). The bond-valence methods are described in Brown (2002).

Computing details top

Data collection: PROCESS-AUTO (Rigaku, 1998); cell refinement: PROCESS-AUTO (Rigaku, 1998); data reduction: CrystalStructure (Rigaku/MSC, 2002); program(s) used to solve structure: coordinates taken from the previous refinement (Liu, 2011); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2006); software used to prepare material for publication: publCIF (Westrip, 2010).

Figures top

Fig. 1. The environment of the Na⁺ cation with atomic displacement parameters drawn at the 50% probability level. [Symmetry codes: (i) x - 1, y, z; (ii) x, -y + 3/2, z + 1/2; (iii) -x, y - 1/2, -z + 1/2.]

poly[[µ₄-(R)-2-ammonio-3-sulfonatopropanoato]aquasodium] top

Crystal data top

[Na(C₃H₆NO₅S)(H₂O)]	F(000) = 432
M_r = 209.15	D_x = 1.840 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 7309 reflections
a = 5.7574 (12) Å	θ = 3.4–27.5°
b = 11.875 (2) Å	µ = 0.48 mm⁻¹
c = 11.691 (3) Å	T = 298 K
β = 109.15 (3)°	Prism, colourless
V = 755.1 (3) Å³	0.24 × 0.22 × 0.20 mm
Z = 4

Data collection top

Rigaku SCX-Mini CCD diffractometer	1740 independent reflections
Radiation source: fine-focus sealed tube	1463 reflections with I > 2Σ(I)
Graphite monochromator	R_int = 0.044
ω scans	θ_max = 27.5°, θ_min = 3.4°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −7→7
T_min = 0.894, T_max = 0.911	k = −15→15
7845 measured reflections	l = −15→15

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)] = 0.038	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.087	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	w = 1/[σ²(F_o²) + (0.0337P)² + 0.5281P] where P = (F_o² + 2F_c²)/3
1740 reflections	(Δ/σ)_max = 0.001
118 parameters	Δρ_max = 0.39 e Å⁻³
2 restraints	Δρ_min = −0.35 e Å⁻³

Crystal data top

[Na(C₃H₆NO₅S)(H₂O)]	V = 755.1 (3) Å³
M_r = 209.15	Z = 4
Monoclinic, P2₁/c	Mo Kα radiation
a = 5.7574 (12) Å	µ = 0.48 mm⁻¹
b = 11.875 (2) Å	T = 298 K
c = 11.691 (3) Å	0.24 × 0.22 × 0.20 mm
β = 109.15 (3)°

Data collection top

Rigaku SCX-Mini CCD diffractometer	1740 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	1463 reflections with I > 2Σ(I)
T_min = 0.894, T_max = 0.911	R_int = 0.044
7845 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.038	2 restraints
wR(F²) = 0.087	H atoms treated by a mixture of independent and constrained refinement
S = 1.10	Δρ_max = 0.39 e Å⁻³
1740 reflections	Δρ_min = −0.35 e Å⁻³
118 parameters

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	0.04743 (15)	0.74874 (7)	0.32550 (8)	0.0227 (2)
C1	0.2113 (4)	1.00587 (18)	0.31408 (19)	0.0187 (4)
C2	0.4306 (4)	1.03306 (18)	0.27159 (19)	0.0183 (4)
H2	0.4392	1.1153	0.2677	0.022*
C3	0.3962 (4)	0.98919 (18)	0.14342 (19)	0.0202 (5)
H3A	0.5201	1.0241	0.1155	0.024*
H3B	0.2371	1.0146	0.0905	0.024*
N1	0.6664 (3)	0.99540 (16)	0.36077 (16)	0.0229 (4)
H1A	0.6638	0.9210	0.3694	0.034*
H1B	0.6869	1.0284	0.4318	0.034*
H1C	0.7900	1.0143	0.3347	0.034*
O1	0.2380 (3)	0.93424 (13)	0.39576 (13)	0.0244 (4)
O2	0.0199 (3)	1.06104 (14)	0.26136 (16)	0.0294 (4)
O3	0.2321 (3)	0.78831 (14)	0.17151 (15)	0.0310 (4)
O4	0.6636 (3)	0.80928 (14)	0.19436 (15)	0.0300 (4)
O5	0.3578 (3)	0.82358 (14)	−0.00367 (13)	0.0251 (4)
S1	0.41302 (9)	0.84075 (4)	0.12587 (5)	0.01761 (15)
O1W	−0.1946 (4)	0.76543 (17)	0.46236 (17)	0.0356 (4)
H1WA	−0.090 (5)	0.759 (4)	0.5329 (15)	0.090 (15)*
H1WB	−0.326 (3)	0.740 (3)	0.471 (3)	0.058 (10)*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
Na1	0.0214 (5)	0.0242 (5)	0.0216 (5)	0.0005 (4)	0.0058 (4)	0.0015 (4)
C1	0.0195 (11)	0.0171 (10)	0.0209 (11)	−0.0036 (9)	0.0087 (9)	−0.0060 (9)
C2	0.0178 (10)	0.0169 (10)	0.0221 (11)	0.0000 (8)	0.0091 (9)	−0.0003 (8)
C3	0.0228 (11)	0.0187 (11)	0.0209 (11)	0.0011 (9)	0.0094 (9)	0.0013 (9)
N1	0.0174 (9)	0.0297 (10)	0.0223 (10)	−0.0022 (8)	0.0073 (8)	−0.0045 (8)
O1	0.0275 (9)	0.0259 (8)	0.0216 (8)	−0.0031 (7)	0.0105 (7)	0.0012 (7)
O2	0.0195 (8)	0.0306 (9)	0.0411 (10)	0.0060 (7)	0.0139 (7)	0.0091 (8)
O3	0.0366 (10)	0.0311 (9)	0.0319 (9)	−0.0106 (8)	0.0203 (8)	−0.0026 (7)
O4	0.0256 (9)	0.0286 (9)	0.0291 (9)	0.0075 (7)	0.0000 (7)	−0.0007 (7)
O5	0.0264 (8)	0.0309 (9)	0.0184 (8)	−0.0045 (7)	0.0079 (7)	−0.0053 (6)
S1	0.0193 (3)	0.0179 (3)	0.0160 (3)	−0.0013 (2)	0.0063 (2)	−0.0006 (2)
O1W	0.0274 (10)	0.0517 (12)	0.0302 (10)	0.0023 (9)	0.0127 (9)	0.0119 (9)

Geometric parameters (Å, º) top

Na1—O4ⁱ	2.3512 (19)	C3—S1	1.781 (2)
Na1—O5ⁱⁱ	2.3619 (19)	C3—H3A	0.9700
Na1—O3	2.4183 (18)	C3—H3B	0.9700
Na1—O2ⁱⁱⁱ	2.4272 (19)	N1—H1A	0.8900
Na1—O1W	2.450 (2)	N1—H1B	0.8900
Na1—O1	2.4778 (18)	N1—H1C	0.8900
C1—O1	1.250 (3)	O3—S1	1.4567 (16)
C1—O2	1.256 (3)	O4—S1	1.4505 (17)
C1—C2	1.535 (3)	O5—S1	1.4561 (16)
C2—N1	1.484 (3)	O1W—H1WA	0.8499 (11)
C2—C3	1.537 (3)	O1W—H1WB	0.8500 (11)
C2—H2	0.9800

O4ⁱ—Na1—O5ⁱⁱ	162.02 (7)	C2—C3—H3A	108.1
O4ⁱ—Na1—O3	90.22 (7)	S1—C3—H3A	108.1
O5ⁱⁱ—Na1—O3	107.74 (7)	C2—C3—H3B	108.1
O4ⁱ—Na1—O2ⁱⁱⁱ	91.21 (7)	S1—C3—H3B	108.1
O5ⁱⁱ—Na1—O2ⁱⁱⁱ	89.57 (7)	H3A—C3—H3B	107.3
O3—Na1—O2ⁱⁱⁱ	85.17 (6)	C2—N1—H1A	109.5
O4ⁱ—Na1—O1W	77.69 (7)	C2—N1—H1B	109.5
O5ⁱⁱ—Na1—O1W	84.94 (7)	H1A—N1—H1B	109.5
O3—Na1—O1W	162.46 (7)	C2—N1—H1C	109.5
O2ⁱⁱⁱ—Na1—O1W	107.49 (7)	H1A—N1—H1C	109.5
O4ⁱ—Na1—O1	99.41 (7)	H1B—N1—H1C	109.5
O5ⁱⁱ—Na1—O1	85.01 (6)	C1—O1—Na1	114.94 (13)
O3—Na1—O1	79.58 (6)	C1—O2—Na1^iv	132.70 (14)
O2ⁱⁱⁱ—Na1—O1	161.39 (6)	S1—O3—Na1	153.84 (11)
O1W—Na1—O1	89.79 (7)	S1—O4—Na1^v	172.12 (12)
O1—C1—O2	126.7 (2)	S1—O5—Na1^vi	140.97 (10)
O1—C1—C2	118.85 (19)	O4—S1—O5	112.10 (10)
O2—C1—C2	114.45 (18)	O4—S1—O3	112.88 (11)
N1—C2—C1	111.67 (17)	O5—S1—O3	112.51 (10)
N1—C2—C3	112.25 (17)	O4—S1—C3	105.86 (10)
C1—C2—C3	112.80 (17)	O5—S1—C3	104.88 (10)
N1—C2—H2	106.5	O3—S1—C3	107.96 (10)
C1—C2—H2	106.5	Na1—O1W—H1WA	105 (3)
C3—C2—H2	106.5	Na1—O1W—H1WB	140 (2)
C2—C3—S1	116.96 (15)	H1WA—O1W—H1WB	103 (3)

Symmetry codes: (i) x−1, y, z; (ii) x, −y+3/2, z+1/2; (iii) −x, y−1/2, −z+1/2; (iv) −x, y+1/2, −z+1/2; (v) x+1, y, z; (vi) x, −y+3/2, z−1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1W^v	0.89	2.16	2.981 (3)	153
N1—H1B···O1^vii	0.89	1.97	2.842 (2)	166
N1—H1C···O2^v	0.89	1.88	2.766 (2)	173
O1W—H1WA···O3ⁱⁱ	0.85 (1)	2.10 (1)	2.912 (3)	160 (4)
O1W—H1WB···O5^viii	0.85 (1)	2.08 (1)	2.930 (2)	178 (3)

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

Experimental details

Crystal data
Chemical formula	[Na(C₃H₆NO₅S)(H₂O)]
M_r	209.15
Crystal system, space group	Monoclinic, P2₁/c
Temperature (K)	298
a, b, c (Å)	5.7574 (12), 11.875 (2), 11.691 (3)
β (°)	109.15 (3)
V (Å³)	755.1 (3)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.48
Crystal size (mm)	0.24 × 0.22 × 0.20

Data collection
Diffractometer	Rigaku SCX-Mini CCD
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.894, 0.911
No. of measured, independent and observed [I > 2Σ(I)] reflections	7845, 1740, 1463
R_int	0.044
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.038, 0.087, 1.10
No. of reflections	1740
No. of parameters	118
No. of restraints	2
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.39, −0.35

Computer programs: PROCESS-AUTO (Rigaku, 1998), CrystalStructure (Rigaku/MSC, 2002), coordinates taken from the previous refinement (Liu, 2011), SHELXL97 (Sheldrick, 2008), Mercury (Macrae et al., 2006), publCIF (Westrip, 2010).

Selected bond lengths (Å) top

Na1—O4ⁱ	2.3512 (19)	Na1—O2ⁱⁱⁱ	2.4272 (19)
Na1—O5ⁱⁱ	2.3619 (19)	Na1—O1W	2.450 (2)
Na1—O3	2.4183 (18)	Na1—O1	2.4778 (18)

Symmetry codes: (i) x−1, y, z; (ii) x, −y+3/2, z+1/2; (iii) −x, y−1/2, −z+1/2.

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1A···O1W^iv	0.89	2.16	2.981 (3)	152.5
N1—H1B···O1^v	0.89	1.97	2.842 (2)	166.3
N1—H1C···O2^iv	0.89	1.88	2.766 (2)	172.6
O1W—H1WA···O3ⁱⁱ	0.8499 (11)	2.100 (14)	2.912 (3)	160 (4)
O1W—H1WB···O5^vi	0.8500 (11)	2.081 (3)	2.930 (2)	178 (3)

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

Acknowledgements

I wish to thank Dr Liu for supplying the original diffraction measurements through the editorial office of the journal.

References

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