Redetermined structure of β-dl-me-thio-nine at 105 K: an example of the importance of freely refining the positions of the amino-group H atoms.

Diffraction data were taken from the contribution named 'β-dl-Me-thio-nine at 105 K' by Alagar et al. [Acta Cryst. (2005 ▶). E61, o1165-o1167]. Refinement of the coordinates of the three amino H atoms, previously constrained to an idealized geometry, shows that the amino group is in fact rotated 13.5° from the perfectly staggered orientation. This apparently modest change has a profound impact on the calculated hydrogen-bond geometries.

Chemical context

Upon comparing the hydrogen-bond geometries of the high-temperature α-phase of the amino acid racemate dl-me­thio­nine (Görbitz et al., 2014 ▶) with the best published structure of the β-phase [Alagar et al., 2005 ▶; refcode DLMETA05 in the Cambridge Structural Database (CSD), Version 5.35; Allen, 2002 ▶], we noted that H⋯O distances surprisingly appeared to get shorter at 340 K than at 105 K. This was judged to be an artefact resulting from different ways of handling the amino H atoms. Alagar et al. (2005 ▶) used an idealized geometry and a perfectly staggered orientation for this group in their refinement; while we found a 14° counterclockwise rotation (for the l-enanti­omer) that served to give three shorter and more linear inter­actions. The experimental and structural data of Alagar et al. (2005 ▶), with coordinates for the d-enanti­omer as the asymmetric unit, were subsequently downloaded and refined again with free amino H atoms, thus increasing the number of parameters from 82 (nine parameters for nine atoms + scale factor) to 91. In the improved structural model displayed in Fig. 1 ▶ [R(F) = 0.0377 versus 0.411 and wR(F 2) = 0.0918 versus 0.1001], the amino group is shifted slightly away from the staggered orientation through a 13.5° clockwise rotation (for the d-enanti­omer), Table 1 ▶.

Figure 1

(a) The structure of dl-me­thio­nine, (I), viewed approximately along the N1—C2 bond vector, with 50% probability thermal displacement ellipsoids. The racemate contains mol­ecules of both hands; the one depicted here is the d-enanti­omer. Carboxyl­ate groups of three neighboring amino acids accepting hydrogen bonds are shown in a lighter tone. O2i is at (−x, y + , −z + ), O2ii at (x + , −y, z) and Oiii at (x + , −y + 1, z), see Table 2 ▶. Compared to the previously published structure shown in capped sticks representation in (b) (Alagar et al., 2005 ▶), the amino group has been rotated clockwise by about 13.5° to give shorter and more linear hydrogen bonds.

Table 1

Selected torsion angles ()

N1C2C3C4	54.4(2)	C1C2N1H1	46.5(17)
C1C2C3C4	173.53(15)	C1C2N1H2	75.3(15)
C2C3C4S1	179.23(12)	C1C2N1H3	167.4(15)
C3C4S1C5	175.03(14)

Supra­molecular features

The hydrogen-bond geometries listed in Table 2 ▶ show that the free refinement of amino-group H atoms gives close to linear N—H⋯O inter­actions with substanti­ally shorter H⋯O distances. There are no significant changes for geometric parameters involving only C, N and O atoms. This example demonstrates that in order not to unduly bias the statistics of hydrogen-bond geometries in the CSD, it is imperative that H atoms of amino groups and other hydrogen-bond donating functional groups whenever possible are refined in a normal manner and not constrained to theoretical positions. The data set used here (Alagar et al., 2005 ▶) is of good, but not excellent quality. Nevertheless, H atoms can be refined with decent accuracy [standard uncertainties (s.u.’s) = 0.03 Å for N—H distances], allowing experimental determination of hydrogen-bond geometries. In the event that s.u.’s get much higher and/or N—H distances are clearly unreasonably short or long, a rigid rotation refinement of the group (e.g. by an AFIX 37 command in SHELXL; Sheldrick, 2008 ▶) should be performed. The results of such a refinement for (I), which adds just a single refinement parameter compared to DLMETA05, but reaches the same R factor as for (I), are included in Table 2 ▶. The listed values are very close to those of the unconstrained refinement, but are obviously devoid of s.u.’s for geometric parameters involving H atoms.

Table 2

Hydrogen-bond geometry (, )

DHA	Parameter	DLMETA05a	(I)-rigidb	(I)
N1H1O2i	NH	0.89	0.91	0.88(3)
	HO	1.93	1.88	1.91(3)
	NO	2.788(2)	2.787(2)	2.788(2)
	NHO	162	173	174(2)
N1H2O1ii	NH	0.89	0.91	0.94(3)
	HO	2.02	1.92	1.89(3)
	NO	2.814(2)	2.815(2)	2.815(2)
	NHO	148	167	169(2)
N1H3O1iii	NH	0.89	0.91	0.92(3)
	HO	2.02	1.91	1.91(3)
	NO	2.794(2)	2.795(2)	2.795(2)
	NHO	144	163	161(2)

Symmetry codes: (i) x, y+, z+; (ii) x+, y, z; (iii) x+, y+1, z. Notes: (a) Alagar et al. (2005 ▶), 82 parameters; atoms H1, H2 and H3 were called H1A, H1B and H1C, respectively, by the original authors; the labels used in the CSD entry DLMETA05 have been retained here. (b) Rigid rotation refinement of (I), 83 parameters. 0.91 is the standard NH bond length in SHELXL (Sheldrick, 2008 ▶) at 105K.

Under other circumstances restraints on covalent geometry may be employed. Accordingly, we have found that it is often useful to restrain O—H bond distances and H—O—H bond angles (through the 1–3 distances) during refinement of water mol­ecules in crystal hydrates. For a single mol­ecule with atom labels H1W—O1W—H2W, the appropriate SHELXL commands would be DFIX 0.85 0.02 O1W H1W O1W H2W and DFIX 1.35 0.03 H1W H2W (the s.u.’s of 0.02 and 0.03 Å being subject to discussion). Similar approaches may be used for groups like –OH and –NH2 for which AFIX 37 commands (or equivalent) are not applicable.

Experimental

For crystallization details, see Alagar et al. (2005 ▶). Crystal data, data collection and structure refinement details are summarized in Table 3 ▶.

Table 3

Experimental details

Crystal data
Chemical formula	C5H11NO2S
M r	149.21
Crystal system, space group	Monoclinic, I2/a
Temperature (K)	105
a, b, c ()	9.877(2), 4.6915(10), 32.603(6)
()	106.25(1)
V (3)	1450.4(5)
Z	8
Radiation type	Mo K
(mm1)	0.38
Crystal size (mm)	0.32 0.24 0.22
Data collection
Diffractometer	Bruker SMART CCD area detector
Absorption correction	Multi-scan (SADABS; Bruker, 1998 ▶)
T min, T max	0.85, 0.92
No. of measured, independent and observed [I > 2(I)] reflections	6469, 1436, 1373
R int	0.023
(sin /)max (1)	0.623
Refinement
R[F 2 > 2(F 2)], wR(F 2), S	0.038, 0.092, 1.26
No. of reflections	1436
No. of parameters	91
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
max, min (e 3)	0.35, 0.23

Computer programs: SMART-NT and SAINT-NT (Bruker, 1999 ▶), SHELXS97, SHELXL2013 (Sheldrick, 2008 ▶) and SHELXTL (Sheldrick, 2008 ▶).

Coordinates were refined for amino H atoms; other H atoms were positioned with idealized geometry, with fixed C—H = 0.98 (meth­yl), 0.99 (methyl­ene) or 1.00 Å (methine). U iso(H) values were set at 1.2U eq of the carrier atom or at 1.5U eq for methyl and amino groups.

Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536814022223/hb7289sup1.cif

Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536814022223/hb7289Isup2.hkl

Click here for additional data file.

Supporting information file. DOI: 10.1107/S1600536814022223/hb7289Isup3.cml

CCDC reference: 1028065

Additional supporting information: crystallographic information; 3D view; checkCIF report

C5H11NO2S	F(000) = 640
Mr = 149.21	Dx = 1.367 Mg m−3
Monoclinic, I2/a	Mo Kα radiation, λ = 0.71073 Å
a = 9.877 (2) Å	Cell parameters from 1012 reflections
b = 4.6915 (10) Å	θ = 2.6–26.1°
c = 32.603 (6) Å	µ = 0.38 mm−1
β = 106.25 (1)°	T = 105 K
V = 1450.4 (5) Å3	Block, colourless
Z = 8	0.32 × 0.24 × 0.22 mm

Bruker SMART CCD area-detector diffractometer	1436 independent reflections
Radiation source: fine-focus sealed tube	1373 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.023
Detector resolution: 8.3 pixels mm-1	θmax = 26.3°, θmin = 2.6°
Sets of exposures each taken over 0.5° ω rotation scans	h = −12→11
Absorption correction: multi-scan (SADABS; Bruker, 1998)	k = 0→5
Tmin = 0.85, Tmax = 0.92	l = 0→40
6469 measured reflections

Refinement on F2	0 restraints
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.038	H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.092	w = 1/[σ2(Fo2) + (0.0233P)2 + 2.4782P] where P = (Fo2 + 2Fc2)/3
S = 1.26	(Δ/σ)max = 0.001
1436 reflections	Δρmax = 0.35 e Å−3
91 parameters	Δρmin = −0.23 e Å−3

Experimental. Diffraction data and experimental conditions are taken from Alagar et al. (2005), CSD refcode DLMETA05.

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 amino H atom coordinates.

	x	y	z	Uiso*/Ueq
S1	0.39652 (6)	0.15681 (12)	0.44292 (2)	0.03291 (18)
O1	−0.14523 (13)	0.2025 (3)	0.31403 (4)	0.0240 (3)
O2	−0.01841 (13)	−0.0810 (3)	0.28411 (4)	0.0216 (3)
N1	0.19296 (17)	0.3000 (3)	0.29733 (5)	0.0193 (3)
H1	0.142 (3)	0.332 (5)	0.2710 (8)	0.029*
H2	0.238 (2)	0.122 (6)	0.2999 (7)	0.029*
H3	0.263 (2)	0.436 (5)	0.3054 (7)	0.029*
C1	−0.03289 (18)	0.1301 (4)	0.30562 (5)	0.0185 (4)
C2	0.09967 (18)	0.3087 (4)	0.32589 (5)	0.0183 (4)
H4	0.0719	0.5103	0.3294	0.022*
C3	0.17639 (19)	0.1831 (4)	0.36982 (5)	0.0214 (4)
H5	0.1148	0.2038	0.3889	0.026*
H6	0.1911	−0.0232	0.3664	0.026*
C4	0.3196 (2)	0.3214 (4)	0.39143 (6)	0.0246 (4)
H7	0.3068	0.5281	0.3952	0.030*
H8	0.3837	0.2973	0.3731	0.030*
C5	0.5659 (2)	0.3326 (5)	0.45830 (7)	0.0350 (5)
H9	0.6208	0.2627	0.4864	0.053*
H10	0.6169	0.2916	0.4371	0.053*
H11	0.5521	0.5388	0.4597	0.053*

	U11	U22	U33	U12	U13	U23
S1	0.0351 (3)	0.0337 (3)	0.0231 (3)	−0.0067 (2)	−0.0031 (2)	0.0074 (2)
O1	0.0225 (7)	0.0168 (6)	0.0333 (7)	0.0012 (5)	0.0089 (5)	−0.0003 (5)
O2	0.0253 (7)	0.0156 (6)	0.0222 (6)	−0.0010 (5)	0.0037 (5)	−0.0028 (5)
N1	0.0207 (7)	0.0169 (8)	0.0190 (7)	−0.0010 (6)	0.0035 (6)	0.0008 (6)
C1	0.0213 (8)	0.0138 (8)	0.0181 (8)	0.0006 (7)	0.0019 (7)	0.0034 (6)
C2	0.0212 (8)	0.0128 (8)	0.0208 (8)	0.0005 (7)	0.0059 (7)	−0.0008 (7)
C3	0.0248 (9)	0.0186 (9)	0.0197 (8)	−0.0008 (7)	0.0043 (7)	−0.0002 (7)
C4	0.0273 (10)	0.0216 (9)	0.0213 (9)	−0.0016 (8)	0.0007 (7)	0.0017 (7)
C5	0.0309 (11)	0.0416 (13)	0.0272 (10)	−0.0024 (9)	−0.0008 (8)	0.0012 (9)

S1—C5	1.806 (2)	C2—H4	1.0000
S1—C4	1.8104 (19)	C3—C4	1.536 (2)
O1—C1	1.262 (2)	C3—H5	0.9900
O2—C1	1.245 (2)	C3—H6	0.9900
N1—C2	1.483 (2)	C4—H7	0.9900
N1—H1	0.88 (3)	C4—H8	0.9900
N1—H2	0.94 (3)	C5—H9	0.9800
N1—H3	0.92 (3)	C5—H10	0.9800
C1—C2	1.539 (2)	C5—H11	0.9800
C2—C3	1.538 (2)
C5—S1—C4	100.27 (10)	C4—C3—H5	108.6
C2—N1—H1	108.9 (15)	C2—C3—H5	108.6
C2—N1—H2	109.2 (14)	C4—C3—H6	108.6
H1—N1—H2	111 (2)	C2—C3—H6	108.6
C2—N1—H3	110.5 (14)	H5—C3—H6	107.6
H1—N1—H3	110 (2)	C3—C4—S1	109.80 (13)
H2—N1—H3	107 (2)	C3—C4—H7	109.7
O2—C1—O1	125.67 (17)	S1—C4—H7	109.7
O2—C1—C2	117.19 (15)	C3—C4—H8	109.7
O1—C1—C2	117.03 (15)	S1—C4—H8	109.7
N1—C2—C3	110.09 (14)	H7—C4—H8	108.2
N1—C2—C1	108.59 (14)	S1—C5—H9	109.5
C3—C2—C1	109.25 (14)	S1—C5—H10	109.5
N1—C2—H4	109.6	H9—C5—H10	109.5
C3—C2—H4	109.6	S1—C5—H11	109.5
C1—C2—H4	109.6	H9—C5—H11	109.5
C4—C3—C2	114.57 (15)	H10—C5—H11	109.5
N1—C2—C3—C4	54.4 (2)	O2—C1—C2—C3	−87.60 (18)
C1—C2—C3—C4	173.53 (15)	O1—C1—C2—C3	88.98 (18)
C2—C3—C4—S1	179.23 (12)	C1—C2—N1—H1	46.5 (17)
C3—C4—S1—C5	175.03 (14)	C1—C2—N1—H2	−75.3 (15)
O2—C1—C2—N1	32.5 (2)	C1—C2—N1—H3	167.4 (15)
O1—C1—C2—N1	−150.93 (15)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2i	0.88 (3)	1.91 (3)	2.788 (2)	175 (3)
N1—H2···O1ii	0.94 (3)	1.89 (3)	2.815 (2)	169 (2)
N1—H3···O1iii	0.92 (2)	1.91 (2)	2.795 (2)	161 (2)
C2—H4···O2iv	1.00	2.43	3.244 (2)	138