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

By refining positional coordinates for the three amino H atoms of a previously published amino acid structure, an improved structural model with shorter and more linear hydrogen bonds is obtained.


Chemical context
Upon comparing the hydrogen-bond geometries of the hightemperature -phase of the amino acid racemate dl-methionine (Gö rbitz et al., 2014) with the best published structure of the -phase [Alagar et al., 2005; refcode DLMETA05 in the Cambridge Structural Database (CSD), Version 5.35; Allen, 2002], we noted that HÁ Á ÁO 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.

Supramolecular features
The hydrogen-bond geometries listed in Table 2 show that the free refinement of amino-group H atoms gives close to linear ISSN 1600-5368 N-HÁ Á ÁO interactions with substantially shorter HÁ Á ÁO 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 hydrogenbond 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. 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 -NH 2 for which AFIX 37 commands (or equivalent) are not applicable. (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. O2 i is at (Àx, y + 1 2 , Àz + 1 2 ), O2 ii at (x + 1 2 , Ày, z) and O iii at (x + 1 2 , Ày + 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 ( ).

Experimental
For crystallization details, see Alagar et al. (2005). Crystal data, data collection and structure refinement 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). U iso (H) values were set at 1.2U eq of the carrier atom or at 1.5U eq for methyl and amino groups.

Special details
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.