research communications
Redetermined structure of β-DL-methionine at 105 K: an example of the importance of freely refining the positions of the amino-group H atoms
aDepartment of Chemistry, University of Oslo, PO Box 1033 Blindern, N-0315 Oslo, Norway
*Correspondence e-mail: c.h.gorbitz@kjemi.uio.no
Diffraction data were taken from the contribution named `β-DL-Methionine at 105 K′ by Alagar et al. [Acta Cryst. (2005). E61, o1165–o1167]. 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.
Keywords: hydrogen-bond geometry; amino group; refinement model; β-DL-methionine; crystal structure.
CCDC reference: 1028065
1. 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 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 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(F2) = 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.
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2. Supramolecular features
The hydrogen-bond geometries listed in Table 2 show that the free 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 of the group (e.g. by an AFIX 37 command in SHELXL; Sheldrick, 2008) should be performed. The results of such a for (I), which adds just a single 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 but are obviously devoid of s.u.'s for geometric parameters involving H atoms.
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 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.
of water molecules in crystal hydrates. For a single molecule with atom labels H1W—O1W—H2W, the appropriate3. Experimental
For crystallization details, see Alagar et al. (2005). Crystal data, data collection and structure details are summarized in Table 3.
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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). Uiso(H) values were set at 1.2Ueq of the or at 1.5Ueq for methyl and amino groups.
Supporting information
CCDC reference: 1028065
10.1107/S1600536814022223/hb7289sup1.cif
contains datablocks I, global. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536814022223/hb7289Isup2.hkl
Supporting information file. DOI: 10.1107/S1600536814022223/hb7289Isup3.cml
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 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 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(F2) = 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). As seen from Table 1, this change 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. Selected torsion angles are given in Table 2.
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
of the group (e.g. by an AFIX 37 command in SHELXL; Sheldrick, 2008) should be performed. The results of such a for (I), which adds just a single parameter compared to DLMETA05, but reaches the same factor as for (I), are included in Table 3. The listed values are very close to those of the unconstrained but are obviously devoid of s.u.'s for geometric parameters involving H atoms.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
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.Crystal data, data collection and structure
details are summarized in Table 3. 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). Uiso(H) values were set at 1.2Ueq of the or at 1.5Ueq for methyl and amino groups.Data collection: SMART-NT (Bruker, 1999); cell
SAINT-NT (Bruker, 1999); data reduction: SAINT-NT (Bruker, 1999); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXL2013 (Sheldrick, 2008).(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+1/2, -z+1/2, O2ii at (x+1/2, -y, z) and Oiii at (x+1/2, -y+1, z), see Table 1. 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. |
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 |
C5H11NO2S | V = 1450.4 (5) Å3 |
Mr = 149.21 | Z = 8 |
Monoclinic, I2/a | Mo Kα radiation |
a = 9.877 (2) Å | µ = 0.38 mm−1 |
b = 4.6915 (10) Å | T = 105 K |
c = 32.603 (6) Å | 0.32 × 0.24 × 0.22 mm |
β = 106.25 (1)° |
Bruker SMART CCD area-detector diffractometer | 1436 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 1998) | 1373 reflections with I > 2σ(I) |
Tmin = 0.85, Tmax = 0.92 | Rint = 0.023 |
6469 measured reflections |
R[F2 > 2σ(F2)] = 0.038 | 0 restraints |
wR(F2) = 0.092 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.26 | Δρmax = 0.35 e Å−3 |
1436 reflections | Δρmin = −0.23 e Å−3 |
91 parameters |
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 |
Symmetry codes: (i) −x, y+1/2, −z+1/2; (ii) x+1/2, −y, z; (iii) x+1/2, −y+1, z; (iv) x, y+1, z. |
N1—C2—C3—C4 | 54.4 (2) | C1—C2—N1—H1 | 46.5 (17) |
C1—C2—C3—C4 | 173.53 (15) | C1—C2—N1—H2 | −75.3 (15) |
C2—C3—C4—S1 | 179.23 (12) | C1—C2—N1—H3 | 167.4 (15) |
C3—C4—S1—C5 | 175.03 (14) |
D—H···A | Parameter | DLMETA05a | (I)-rigidb | (I) |
N1—H1···O2i | N—H | 0.89 | 0.91 | 0.88 (3) |
H···O | 1.93 | 1.88 | 1.91 (3) | |
N···O | 2.788 (2) | 2.787 (2) | 2.788 (2) | |
N—H···O | 162 | 173 | 174 (2) | |
N1—H2···O1ii | N—H | 0.89 | 0.91 | 0.94 (3) |
H···O | 2.02 | 1.92 | 1.89 (3) | |
N···O | 2.814 (2) | 2.815 (2) | 2.815 (2) | |
N—H···O | 148 | 167 | 169 (2) | |
N1—H3···O1iii | N—H | 0.89 | 0.91 | 0.92 (3) |
H···O | 2.02 | 1.91 | 1.91 (3) | |
N···O | 2.794 (2) | 2.795 (2) | 2.795 (2) | |
N—H···O | 144 | 163 | 161 (2) |
Symmetry codes: (i) -x, y+1/2, -z+1/2; (ii) x+1/2, -y, z; (iii) x+1/2, -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 Å is the standard N—H bond length in SHELXL (Sheldrick, 2008) at 105 K. |
Experimental details
Crystal data | |
Chemical formula | C5H11NO2S |
Mr | 149.21 |
Crystal system, space group | Monoclinic, I2/a |
Temperature (K) | 105 |
a, b, c (Å) | 9.877 (2), 4.6915 (10), 32.603 (6) |
β (°) | 106.25 (1) |
V (Å3) | 1450.4 (5) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.38 |
Crystal size (mm) | 0.32 × 0.24 × 0.22 |
Data collection | |
Diffractometer | Bruker SMART CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 1998) |
Tmin, Tmax | 0.85, 0.92 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 6469, 1436, 1373 |
Rint | 0.023 |
(sin θ/λ)max (Å−1) | 0.623 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), 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 |
Δρmax, Δρmin (e Å−3) | 0.35, −0.23 |
Computer programs: SMART-NT (Bruker, 1999), SAINT-NT (Bruker, 1999), SHELXS97 (Sheldrick, 2008), SHELXL2013 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
References
Alagar, M., Krishnakumar, R. V., Mostad, A. & Natarajan, S. (2005). Acta Cryst. E61, o1165–o1167. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Allen, F. H. (2002). Acta Cryst. B58, 380–388. Web of Science CrossRef CAS IUCr Journals Google Scholar
Bruker (1998). SADABS. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Bruker (1999). SMART-NT and SAINT-NT. Bruker AXS Inc., Madison, Wisconsin, USA. Google Scholar
Görbitz, C. H., Qi, L., Mai, N. T. K. & Kristiansen, H. (2014). Acta Cryst. E70, 337–340. CSD CrossRef IUCr Journals Google Scholar
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122. Web of Science CrossRef CAS IUCr Journals Google Scholar
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