Sodium 2-(N-morpholino)­ethane­sulfonate monohydrate

In this study, we report on the X-ray diffraction analysis of the common buffer salt sodium 2-(N-morpholino)­ethane­sulfonate (NaMES), Na·C₆H₁₂NO₄S·H₂O. MES is one of the `Good' buffers and is frequently used in biological and biochemical research. Following the method employed by Kunkel [(2000); Utilities for estimating the diffusion coefficients of weak electrolytes, URL: http://www.bio.umass.edu/biology/kunkel/probe/buffers/], the Stokes radius for this compound is 4.18 Å. This is significantly different from the value of 3.54 Å previously estimated from a molecular model.

Key indicators

• Single-crystal X-ray study
• T = 93 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.036
• wR factor = 0.089
• Data-to-parameter ratio = 18.6

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry


 Alert Level C:



PLAT_731  Alert C Bond    Calc   3.2150(8), Rep   3.2150(3) ....       2.67 s.u-Ratio
                     NA1  -NA1     1.555   6.656

General Notes



FORMU_01  There is a discrepancy between the atom counts in the
          _chemical_formula_sum and _chemical_formula_moiety. This is
          usually due to the moiety formula being in the wrong format.
          Atom count from _chemical_formula_sum:   C6 H14 N1 Na1 O5 S1
          Atom count from _chemical_formula_moiety:


 0 Alert Level A = Potentially serious problem

 0 Alert Level B = Potential problem

 1 Alert Level C = Please check

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S1. Comment

In this study, we report the results of a structural study on a sodium salt of 2-(N-morpholino)ethanesulfonate (MES), (I). MES crystallized as a monohydrate of the sodium salt in the orthorhombic space group Pbca, with one molecule of MES, one sodium cation and one water molecule in the asymmetric unit. Low-temperature data (93 K) allowed refinement of the position of the solvent H atoms. The water molecule acts as a donor in hydrogen bonds to N1 and a sulfur O atom (O2).

The structure of a monohydrate of 2-(N-morpholino)ethanesulfonic acid was previously reported (Christensen et al., 1993). Comparing the results of the present study with the previously published room-temperature study results in an r.m.s. deviation of 0.098 Å for all atoms (except the sulfur O atoms) in the sulfonic acid.

Good buffers are commonly used in biochemistry and biology based on their relatively inert behavior with regard to affecting cell functions (Good et al., 1966; Good & Izawa, 1972; Ferguson et al., 1980). Some studies require a knowledge of diffusion coefficients in order to properly interpret the results from an experiment. Diffusion coefficients can be estimated from the Stokes radius (Kunkel, 2000). Lacking the results from a three-dimensional structural study, Kunkel (2000) used a molecular model and estimated the Stokes radius to be 3.54 Å. This resulted in an estimated diffusion coefficient of 0.820 (expressed as D × 10⁵/cm² sec^-1). Applying the method of Kunkel to the results from this study yields a Stokes radius of 4.18 Å (using the distance from O1 to H5A) and a corresponding diffusion coefficient of 0.744. This is in good agreement with the results from the previous X-ray study (i.e. Stokes radius of 4.15 Å for O1 to H13 and a diffusion coefficient of 0.744). The large difference in the estimated Stokes radius (3.54 Å) and those derived from X-ray studies (4.18 and 4.15 Å) translates to an error of approximately 10% in the diffusion coefficient.

S2. Experimental

Crystals of (I) were grown by slow evaporation of a solution containing 0.1 M NaMES (pH 6.0) and 40% methyl pentanediol (MPD). The data crystal was cleaved from a larger plate.

S3. Refinement

All H atoms were located in the difference map. Coordinates and isotropic displacement parameters were refined for the H atoms on the solvent (water) molecule. All other H atoms were refined using the riding model.

Computing details

Data collection: SMART (Bruker, 1999); cell refinement: SMART; data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXTL (Sheldrick, 2000); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

Figures

Fig. 1. The structure of (I) showing the water molecule bound to the N atom. Displacement ellipsoids are shown at the 50% probability level.

sodium 2-[N-morpholino]ethanesulfonate hydrate

Crystal data

Na^+·C6H12NO4S^−·H2O	Dx = 1.532 Mg m^−3
Mr = 235.23	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, Pbca	Cell parameters from 5332 reflections
a = 6.3673 (5) Å	θ = 2.9–28.3°
b = 11.3245 (9) Å	µ = 0.36 mm^−1
c = 28.297 (2) Å	T = 93 K
V = 2040.4 (3) Å^3	Prism, colorless
Z = 8	0.40 × 0.40 × 0.20 mm
F(000) = 992

Data collection

Bruker SMART1000 CCD diffractometer	2516 independent reflections
Radiation source: sealed tube	2272 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.027
ϕ and ω scans	θmax = 28.3°, θmin = 2.9°
Absorption correction: multi-scan (SADABS; Bruker, 2001)	h = −8→8
Tmin = 0.833, Tmax = 0.943	k = −15→14
14538 measured reflections	l = −35→37

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.036	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.089	H atoms treated by a mixture of independent and constrained refinement
S = 1.12	w = 1/[σ^2(Fo^2) + (0.0405P)^2 + 1.6377P] where P = (Fo^2 + 2Fc^2)/3
2516 reflections	(Δ/σ)max = 0.001
135 parameters	Δρmax = 0.46 e Å^−3
2 restraints	Δρmin = −0.36 e Å^−3

Special details

Experimental. Final cell refinement and decay correction applied after integration as part of merge process in SAINT v6.02 A.

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 (Ų)

	x	y	z	Uiso*/Ueq
Na1	−0.04058 (9)	0.13677 (5)	0.24209 (2)	0.01324 (15)
N1	0.5411 (2)	0.06214 (11)	0.10008 (4)	0.0126 (3)
C2	0.6779 (2)	−0.02585 (14)	0.07802 (5)	0.0153 (3)
H2A	0.5955	−0.0745	0.0556	0.018*
H2B	0.7365	−0.0787	0.1026	0.018*
C3	0.8546 (3)	0.03474 (16)	0.05200 (6)	0.0213 (3)
H3A	0.9386	0.0818	0.0746	0.026*
H3B	0.9480	−0.0255	0.0378	0.026*
O4	0.77609 (19)	0.11016 (11)	0.01573 (4)	0.0219 (3)
C5	0.6452 (3)	0.19790 (14)	0.03660 (6)	0.0211 (3)
H5A	0.5898	0.2504	0.0116	0.025*
H5B	0.7299	0.2467	0.0585	0.025*
C6	0.4635 (2)	0.14337 (14)	0.06336 (6)	0.0169 (3)
H6A	0.3787	0.2065	0.0782	0.020*
H6B	0.3721	0.0997	0.0411	0.020*
C7	0.3606 (2)	0.00662 (14)	0.12326 (5)	0.0155 (3)
H7A	0.2708	−0.0308	0.0989	0.019*
H7B	0.2764	0.0684	0.1392	0.019*
C8	0.4244 (2)	−0.08635 (13)	0.15948 (5)	0.0136 (3)
H8A	0.5488	−0.0587	0.1773	0.016*
H8B	0.4622	−0.1607	0.1431	0.016*
S1	0.21366 (5)	−0.11227 (3)	0.198900 (13)	0.01066 (11)
O1	0.26616 (17)	−0.22069 (10)	0.22390 (4)	0.0140 (2)
O2	0.02574 (17)	−0.12316 (10)	0.16982 (4)	0.0163 (2)
O3	0.20724 (16)	−0.00894 (9)	0.22975 (4)	0.0145 (2)
O1S	−0.20766 (19)	−0.32879 (11)	0.18371 (4)	0.0186 (3)
H1S	−0.172 (4)	−0.359 (2)	0.1570 (7)	0.039 (7)*
H2S	−0.159 (4)	−0.2619 (16)	0.1813 (8)	0.039 (7)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
Na1	0.0082 (3)	0.0126 (3)	0.0189 (3)	0.0006 (2)	0.0005 (2)	−0.0005 (2)
N1	0.0111 (6)	0.0126 (6)	0.0142 (6)	0.0010 (5)	0.0016 (5)	0.0013 (5)
C2	0.0156 (7)	0.0161 (7)	0.0142 (7)	0.0031 (6)	0.0025 (5)	0.0000 (5)
C3	0.0156 (8)	0.0260 (8)	0.0221 (8)	0.0042 (7)	0.0048 (6)	0.0053 (6)
O4	0.0204 (6)	0.0247 (6)	0.0208 (6)	0.0034 (5)	0.0064 (5)	0.0065 (5)
C5	0.0211 (8)	0.0161 (7)	0.0261 (8)	−0.0009 (6)	0.0041 (7)	0.0047 (6)
C6	0.0146 (8)	0.0172 (7)	0.0190 (7)	0.0030 (6)	0.0023 (6)	0.0046 (6)
C7	0.0101 (7)	0.0201 (7)	0.0164 (7)	0.0014 (6)	0.0015 (5)	0.0048 (6)
C8	0.0106 (7)	0.0145 (7)	0.0156 (7)	0.0011 (5)	0.0023 (5)	0.0023 (5)
S1	0.00779 (18)	0.00962 (17)	0.01455 (18)	−0.00004 (12)	0.00029 (12)	0.00116 (12)
O1	0.0112 (5)	0.0126 (5)	0.0183 (5)	0.0011 (4)	0.0009 (4)	0.0037 (4)
O2	0.0104 (5)	0.0184 (5)	0.0200 (5)	−0.0028 (4)	−0.0038 (4)	0.0031 (4)
O3	0.0116 (5)	0.0124 (5)	0.0196 (5)	0.0006 (4)	0.0013 (4)	−0.0026 (4)
O1S	0.0208 (6)	0.0153 (5)	0.0197 (6)	−0.0040 (5)	0.0060 (5)	−0.0035 (5)

Geometric parameters (Å, º)

Na1—O3	2.3096 (12)	C5—C6	1.515 (2)
Na1—O1S^i	2.3347 (13)	C5—H5A	0.9900
Na1—O1S^ii	2.6569 (14)	C5—H5B	0.9900
Na1—O1^ii	2.3655 (12)	C6—H6A	0.9900
Na1—O1^iii	2.4339 (12)	C6—H6B	0.9900
Na1—O3^iv	2.4364 (12)	C7—C8	1.524 (2)
Na1—Na1^v	3.2150 (3)	C7—H7A	0.9900
N1—C2	1.4635 (19)	C7—H7B	0.9900
N1—C7	1.4648 (19)	C8—S1	1.7695 (15)
N1—C6	1.4732 (19)	C8—H8A	0.9900
C2—C3	1.510 (2)	C8—H8B	0.9900
C2—H2A	0.9900	S1—O1	1.4558 (11)
C2—H2B	0.9900	S1—O2	1.4574 (11)
C3—O4	1.426 (2)	S1—O3	1.4606 (11)
C3—H3A	0.9900	O1S—H1S	0.858 (16)
C3—H3B	0.9900	O1S—H2S	0.822 (16)
O4—C5	1.425 (2)
O3—Na1—O1S^i	118.79 (5)	N1—C2—H2A	109.7
O3—Na1—O1^ii	164.55 (5)	C3—C2—H2A	109.7
O1S^i—Na1—O1^ii	75.94 (4)	N1—C2—H2B	109.7
O3—Na1—O1^iii	87.21 (4)	C3—C2—H2B	109.7
O1S^i—Na1—O1^iii	103.44 (5)	H2A—C2—H2B	108.2
O1^ii—Na1—O1^iii	93.98 (5)	O4—C3—C2	111.21 (14)
O3—Na1—O3^iv	90.91 (4)	O4—C3—H3A	109.4
O1S^i—Na1—O3^iv	83.80 (4)	C2—C3—H3A	109.4
O1^ii—Na1—O3^iv	85.92 (4)	O4—C3—H3B	109.4
O1^iii—Na1—O3^iv	172.52 (5)	C2—C3—H3B	109.4
O3—Na1—O1S^ii	79.51 (4)	H3A—C3—H3B	108.0
O1S^i—Na1—O1S^ii	160.58 (6)	C5—O4—C3	108.95 (13)
O1^ii—Na1—O1S^ii	86.53 (4)	O4—C5—C6	111.69 (13)
O1^iii—Na1—O1S^ii	69.06 (4)	O4—C5—H5A	109.3
O3^iv—Na1—O1S^ii	103.48 (4)	C6—C5—H5A	109.3
O3—Na1—Na1^v	49.04 (3)	O4—C5—H5B	109.3
O1S^i—Na1—Na1^v	141.12 (4)	C6—C5—H5B	109.3
O1^ii—Na1—Na1^v	123.00 (3)	H5A—C5—H5B	107.9
O1^iii—Na1—Na1^v	47.04 (3)	N1—C6—C5	110.54 (13)
O3^iv—Na1—Na1^v	127.38 (3)	N1—C6—H6A	109.5
O1S^ii—Na1—Na1^v	45.64 (3)	C5—C6—H6A	109.5
O3—Na1—Na1^iv	134.23 (3)	N1—C6—H6B	109.5
O1S^i—Na1—Na1^iv	54.45 (3)	C5—C6—H6B	109.5
O1^ii—Na1—Na1^iv	48.85 (3)	H6A—C6—H6B	108.1
O1^iii—Na1—Na1^iv	137.76 (3)	N1—C7—C8	112.87 (12)
O3^iv—Na1—Na1^iv	45.72 (3)	N1—C7—H7A	109.0
O1S^ii—Na1—Na1^iv	118.62 (4)	C8—C7—H7A	109.0
Na1^v—Na1—Na1^iv	163.99 (4)	N1—C7—H7B	109.0
S1—O1—Na1^vi	129.33 (6)	C8—C7—H7B	109.0
S1—O1—Na1^vii	145.78 (7)	H7A—C7—H7B	107.8
Na1^vi—O1—Na1^vii	84.10 (4)	C7—C8—S1	109.66 (10)
S1—O3—Na1	132.99 (7)	C7—C8—H8A	109.7
S1—O3—Na1^v	136.03 (6)	S1—C8—H8A	109.7
Na1—O3—Na1^v	85.24 (4)	C7—C8—H8B	109.7
Na1^viii—O1S—Na1^vi	79.91 (4)	S1—C8—H8B	109.7
Na1^viii—O1S—H1S	137.8 (18)	H8A—C8—H8B	108.2
Na1^vi—O1S—H1S	118.6 (17)	O1—S1—O2	113.05 (6)
Na1^viii—O1S—H2S	118.3 (17)	O1—S1—O3	113.06 (7)
Na1^vi—O1S—H2S	88.6 (17)	O2—S1—O3	112.48 (6)
C2—N1—C7	111.46 (12)	O1—S1—C8	105.79 (7)
C2—N1—C6	108.91 (12)	O2—S1—C8	106.30 (7)
C7—N1—C6	108.70 (12)	O3—S1—C8	105.38 (7)
N1—C2—C3	110.02 (13)	H1S—O1S—H2S	101 (2)

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

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O1S—H1S···N1^vii	0.86 (2)	2.02 (2)	2.8724 (17)	170 (2)
O1S—H2S···O2	0.82 (2)	1.99 (2)	2.7902 (16)	165 (2)

Symmetry code: (vii) −x+1/2, y−1/2, z.