Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807039505/zl2057sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807039505/zl2057Isup2.hkl |
CCDC reference: 660286
The title compound, asparagine oxygen-17 isotope enriched at the carboxyl group, was synthesized with the aim to perform solid-state 17O NMR experiments. L-Asparagine was obtained by deprotection of both the N-terminus and side-chain groups from 17O-enriched N-α-Fmoc-N-β-trityl-L-asparagine. Detailed procedures have been described elsewhere (Yamada et al., 2007).
Colorless crystals of L-asparagine monohydrate can be obtained by slow cooling of an aqueous solution (Verbist et al., 1972; Ramanadham et al., 1972). Colorless platelike crystals of anhydrous L-asparagine used in the present study, on the other hand, were obtained from a saturated aqueous solution after it was left standing at room temperature for a few months.
All H atoms were found in difference density Fourier maps. Their positions and isotropic displacement parameters were freely refined. The refined C—H and N—H bond lengths are in the expected range: 1.00 (3) Å and 107.6 (18)–109.8 (15)° for the methyne C—H distance and the C/N—C—H angle, respectively; 1.01 (3)–1.03 (3) Å, 107.3 (15)–110.9 (18)° and 110 (2)° for the methylene C—H, C—C—H and H—C—H values, respectively; 0.92 (4)–1.01 (3) Å, 109 (2)–114.5 (18)° and 105 (2)–112 (3)° for the ammonium N—H, C—N—H and H—N—H values, respectively; 0.92 (3)–0.94 (3) Å, 118.6 (15)–120.2 (16)° and 121 (2)° for the amide N—H, C—N—H and H—N—H values, respectively. The range of the Uiso values for the H atoms is 0.020 (7)–0.044 (9) Å2.
L-Asparagine is one of the fundamental natural amino acid residues in proteins. It has been believed that it plays an important role in the formation of the secondary structures in proteins due to the fact that the side chain can form efficient hydrogen bonds with the peptide backbone. In general, amino acids very often have polymorphs. The crystal structures of L-asparagine monohydrate (Kartha & de Vries, 1961; Verbist et al., 1972; Ramanadham et al., 1972; Wang et al., 1985; Weisinger-Lewin et al., 1989; Smirnova et al., 1990; Arnold et al., 2000; Flaig et al., 2002; Chandrasekhar et al., 2003) and D-asparagine monohydrate (Chandrasekhar et al., 2003) have been reported so far. A powder X-ray diffraction study (PDF:37–1659) has been also reported for anhydrous L-asparagine. In the present study, a single-crystal structure determination of anhydrous L-asparagine, (I), is reported.
The single-crystal diffraction analysis confirms the space group and the unit-cell dimensions previously proposed by the powder diffraction study, and shows that, as expected, the title molecule exists as a zwitter ion in the crystal (Fig. 1). The distances of the C≐O bonds in the carboxylate group are significantly different although the group is deprotonated. The corresponding distances are 1.2407 (19) and 1.262 (2) Å for C2—O1 and C2—O2, respectively. The discrepancy is attributed to the number and kind of the intermolecular hydrogen bonds each O atom of the carboxylate participates in. The O2 atom forms two strong hydrogen bonds with neighboring cationic ammonium groups. O1, on the other hand, forms only one relatively weak hydrogen bond with the neutral amide group (Table 2 and Fig. 2). Owing to the formation of two strong hydrogen bonds, the C1—O2 bond is strongly polarized, and the distance of the C1—O2 bond is elongated accordingly. The carbonyl oxygen in the side chain, O3, also forms two hydrogen bonds with each one ammonium and amide group of neighboring molecules.
It is of interest to compare the present structure with that of L-asparagine monohydrate (Ramanadham et al., 1972). In the L-asparagine monohydrate crystal, the C≐O bonds in the ionized carboxyl group are 1.243 and 1.257 Å, which is in good agreement with those in (I), but with a slightly less pronounced difference in C—O bond lengths. Both oxygen atoms in the monohydrate exhibit each one relatively weak N—H···O hydrogen bond to an amide group, but the oxygen atom with the longer C—O distance forms two additional strong H bonds with solvate water molecules. The oxygen atom with the shorter C—O bond, on the other hand, forms only one strong hydrogen bond, in this case to the ammonium group. As the difference in the hydrogen bonding environment is thus less pronouced for the monohydrate than in the anhydrous structure this may also explain the more pronounced difference in the C—O distances found in the structure of the title compound.
The conformation of the backbone of (I) is quite different from that of the monohydrate. In (I), the torsion angle of C2—C1—C3—C4 is 170.64 (14)°, while, in the monohydrate, the corresponding angle is -53.08°. As mentioned, there are significant differences between the crystal structures and the side-chain conformations of anhydrous and monohydrate asparagines, which can be attributed most likely to the different hydrogen bonding environment induced by the presence of the water molecules. Similar differences are also found in the crystal structures of L-aspartic acid (Derissen et al., 1968) and L-aspartic acid monohydrate (Umadevi et al., 2003). The corresponding torsion angles of the side-chains, for example, are 178.2° and 52.8°, for L-aspartic acid and its monohydrate, respectively.
For related literature on single-crystal diffraction studies of L-asparagine monohydrate, see: Arnold et al. (2000); Flaig et al. (2002); Kartha & de Vries (1961); Ramanadham et al. (1972); Smirnova et al. (1990); Verbist et al. (1972); Wang et al. (1985); Weisinger-Lewin et al. (1989). The unit cell and space group of the title compound were previously determined by powder X-ray diffraction (PDF: 37–1659). For the sample preparation of the title compound, see Yamada et al. (2007)·For other related literature, see: Chandrasekhar et al. (2003); Derissen et al. (1968); Umadevi et al. (2003).
Data collection: CrystalClear SM (Rigaku/MSC Inc., 2005); cell refinement: CrystalClear SM; data reduction: HKL-2000 (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: SHELXL97.
C4H8N2O3 | F(000) = 140 |
Mr = 132.12 | Dx = 1.607 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 1254 reflections |
a = 5.0622 (4) Å | θ = 2.5–32.2° |
b = 6.7001 (5) Å | µ = 0.14 mm−1 |
c = 8.0543 (5) Å | T = 90 K |
β = 91.706 (5)° | Plate, colourless |
V = 273.06 (3) Å3 | 0.65 × 0.36 × 0.08 mm |
Z = 2 |
AFC-8 with Saturn70 CCD diffractometer | 815 reflections with I > 2σ(I) |
Radiation source: fine-focus rotating anode | Rint = 0.045 |
Confocal monochromator | θmax = 30.1°, θmin = 2.5° |
Detector resolution: 28.5714 pixels mm-1 | h = −7→7 |
ω scans | k = −9→9 |
3379 measured reflections | l = −11→11 |
865 independent reflections |
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)] = 0.032 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.085 | All H-atom parameters refined |
S = 1.08 | w = 1/[σ2(Fo2) + (0.0469P)2 + 0.0383P] where P = (Fo2 + 2Fc2)/3 |
865 reflections | (Δ/σ)max < 0.001 |
114 parameters | Δρmax = 0.22 e Å−3 |
1 restraint | Δρmin = −0.29 e Å−3 |
C4H8N2O3 | V = 273.06 (3) Å3 |
Mr = 132.12 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 5.0622 (4) Å | µ = 0.14 mm−1 |
b = 6.7001 (5) Å | T = 90 K |
c = 8.0543 (5) Å | 0.65 × 0.36 × 0.08 mm |
β = 91.706 (5)° |
AFC-8 with Saturn70 CCD diffractometer | 815 reflections with I > 2σ(I) |
3379 measured reflections | Rint = 0.045 |
865 independent reflections |
R[F2 > 2σ(F2)] = 0.032 | 1 restraint |
wR(F2) = 0.085 | All H-atom parameters refined |
S = 1.08 | Δρmax = 0.22 e Å−3 |
865 reflections | Δρmin = −0.29 e Å−3 |
114 parameters |
Experimental. All Friedel pairs were merged, and all f"s of containing atoms were set to zero. |
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 > 2σ(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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.2240 (2) | 0.1487 (2) | 0.59976 (15) | 0.0152 (3) | |
O2 | −0.1823 (2) | 0.1359 (2) | 0.48234 (15) | 0.0146 (3) | |
O3 | 0.5526 (2) | 0.0384 (3) | −0.00341 (16) | 0.0159 (3) | |
N1 | 0.4009 (3) | 0.3459 (2) | 0.32483 (18) | 0.0113 (3) | |
H1NA | 0.353 (6) | 0.451 (6) | 0.391 (4) | 0.044 (9)* | |
H1NB | 0.458 (5) | 0.393 (5) | 0.212 (4) | 0.031 (8)* | |
H1NC | 0.563 (5) | 0.287 (5) | 0.380 (3) | 0.024 (7)* | |
N2 | 0.1172 (3) | 0.0801 (2) | −0.06008 (19) | 0.0137 (3) | |
H2NA | 0.151 (5) | 0.112 (5) | −0.171 (3) | 0.028 (7)* | |
H2NB | −0.051 (5) | 0.079 (5) | −0.022 (3) | 0.020 (7)* | |
C1 | 0.1734 (3) | 0.2065 (3) | 0.3083 (2) | 0.0097 (3) | |
H1 | 0.034 (5) | 0.273 (5) | 0.237 (3) | 0.019 (6)* | |
C2 | 0.0645 (3) | 0.1617 (3) | 0.48026 (19) | 0.0097 (3) | |
C3 | 0.2553 (4) | 0.0114 (3) | 0.2244 (2) | 0.0126 (3) | |
H3A | 0.420 (6) | −0.049 (5) | 0.283 (3) | 0.025 (7)* | |
H3B | 0.102 (5) | −0.084 (4) | 0.231 (3) | 0.021 (7)* | |
C4 | 0.3218 (3) | 0.0440 (3) | 0.04381 (19) | 0.0108 (3) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0139 (6) | 0.0228 (7) | 0.0088 (5) | 0.0022 (6) | 0.0002 (4) | 0.0018 (5) |
O2 | 0.0096 (6) | 0.0183 (6) | 0.0160 (6) | −0.0017 (6) | 0.0020 (4) | 0.0045 (5) |
O3 | 0.0106 (7) | 0.0229 (7) | 0.0143 (5) | 0.0015 (5) | 0.0016 (4) | −0.0015 (5) |
N1 | 0.0128 (7) | 0.0115 (7) | 0.0097 (6) | −0.0022 (6) | 0.0017 (5) | −0.0008 (5) |
N2 | 0.0127 (7) | 0.0190 (8) | 0.0096 (6) | −0.0011 (6) | 0.0013 (5) | −0.0007 (5) |
C1 | 0.0090 (7) | 0.0120 (7) | 0.0081 (6) | −0.0011 (6) | 0.0013 (5) | 0.0016 (5) |
C2 | 0.0116 (8) | 0.0076 (8) | 0.0099 (7) | 0.0007 (6) | 0.0024 (5) | 0.0007 (5) |
C3 | 0.0166 (8) | 0.0123 (8) | 0.0091 (6) | 0.0016 (7) | 0.0028 (5) | 0.0004 (6) |
C4 | 0.0129 (8) | 0.0094 (8) | 0.0103 (7) | −0.0010 (6) | 0.0018 (5) | −0.0011 (6) |
O1—C2 | 1.2407 (19) | N2—H2NA | 0.94 (3) |
O2—C2 | 1.262 (2) | N2—H2NB | 0.92 (3) |
O3—C4 | 1.240 (2) | C1—C3 | 1.535 (3) |
N1—C1 | 1.485 (2) | C1—C2 | 1.536 (2) |
N1—H1NA | 0.92 (4) | C1—H1 | 1.00 (3) |
N1—H1NB | 1.01 (3) | C3—C4 | 1.518 (2) |
N1—H1NC | 1.00 (3) | C3—H3A | 1.03 (3) |
N2—C4 | 1.334 (2) | C3—H3B | 1.01 (3) |
C1—N1—H1NA | 109 (2) | C2—C1—H1 | 109.8 (15) |
C1—N1—H1NB | 111.0 (18) | O1—C2—O2 | 126.99 (15) |
H1NA—N1—H1NB | 112 (3) | O1—C2—C1 | 118.07 (14) |
C1—N1—H1NC | 114.5 (18) | O2—C2—C1 | 114.90 (13) |
H1NA—N1—H1NC | 106 (3) | C4—C3—C1 | 111.70 (14) |
H1NB—N1—H1NC | 105 (2) | C4—C3—H3A | 107.3 (15) |
C4—N2—H2NA | 118.6 (15) | C1—C3—H3A | 110.9 (18) |
C4—N2—H2NB | 120.2 (16) | C4—C3—H3B | 109.5 (15) |
H2NA—N2—H2NB | 121 (2) | C1—C3—H3B | 107.4 (15) |
N1—C1—C3 | 110.86 (14) | H3A—C3—H3B | 110 (2) |
N1—C1—C2 | 109.90 (14) | O3—C4—N2 | 122.28 (15) |
C3—C1—C2 | 109.84 (14) | O3—C4—C3 | 121.80 (14) |
N1—C1—H1 | 107.6 (18) | N2—C4—C3 | 115.92 (15) |
C3—C1—H1 | 108.8 (17) | ||
N1—C1—C2—O1 | −36.1 (2) | N1—C1—C3—C4 | −67.71 (17) |
C3—C1—C2—O1 | 86.1 (2) | C2—C1—C3—C4 | 170.64 (14) |
N1—C1—C2—O2 | 145.97 (16) | C1—C3—C4—O3 | 107.35 (19) |
C3—C1—C2—O2 | −91.81 (18) | C1—C3—C4—N2 | −72.2 (2) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1NA···O2i | 0.92 (4) | 1.83 (4) | 2.741 (2) | 167 (3) |
N1—H1NB···O3ii | 1.01 (3) | 1.94 (3) | 2.908 (2) | 159 (3) |
N1—H1NC···O2iii | 1.00 (3) | 1.82 (3) | 2.807 (2) | 169 (3) |
N2—H2NA···O1iv | 0.94 (3) | 1.91 (3) | 2.8456 (19) | 174 (3) |
N2—H2NB···O3v | 0.92 (3) | 2.03 (3) | 2.921 (2) | 163 (2) |
Symmetry codes: (i) −x, y+1/2, −z+1; (ii) −x+1, y+1/2, −z; (iii) x+1, y, z; (iv) x, y, z−1; (v) x−1, y, z. |
Experimental details
Crystal data | |
Chemical formula | C4H8N2O3 |
Mr | 132.12 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 90 |
a, b, c (Å) | 5.0622 (4), 6.7001 (5), 8.0543 (5) |
β (°) | 91.706 (5) |
V (Å3) | 273.06 (3) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.14 |
Crystal size (mm) | 0.65 × 0.36 × 0.08 |
Data collection | |
Diffractometer | AFC-8 with Saturn70 CCD |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3379, 865, 815 |
Rint | 0.045 |
(sin θ/λ)max (Å−1) | 0.705 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.032, 0.085, 1.08 |
No. of reflections | 865 |
No. of parameters | 114 |
No. of restraints | 1 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.22, −0.29 |
Computer programs: CrystalClear SM (Rigaku/MSC Inc., 2005), CrystalClear SM, HKL-2000 (Otwinowski & Minor, 1997), SIR2004 (Burla et al., 2005), SHELXL97 (Sheldrick, 1997), ORTEP-3 for Windows (Farrugia, 1997), SHELXL97.
O1—C2 | 1.2407 (19) | O3—C4 | 1.240 (2) |
O2—C2 | 1.262 (2) | ||
C2—C1—C3—C4 | 170.64 (14) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1NA···O2i | 0.92 (4) | 1.83 (4) | 2.741 (2) | 167 (3) |
N1—H1NB···O3ii | 1.01 (3) | 1.94 (3) | 2.908 (2) | 159 (3) |
N1—H1NC···O2iii | 1.00 (3) | 1.82 (3) | 2.807 (2) | 169 (3) |
N2—H2NA···O1iv | 0.94 (3) | 1.91 (3) | 2.8456 (19) | 174 (3) |
N2—H2NB···O3v | 0.92 (3) | 2.03 (3) | 2.921 (2) | 163 (2) |
Symmetry codes: (i) −x, y+1/2, −z+1; (ii) −x+1, y+1/2, −z; (iii) x+1, y, z; (iv) x, y, z−1; (v) x−1, y, z. |
L-Asparagine is one of the fundamental natural amino acid residues in proteins. It has been believed that it plays an important role in the formation of the secondary structures in proteins due to the fact that the side chain can form efficient hydrogen bonds with the peptide backbone. In general, amino acids very often have polymorphs. The crystal structures of L-asparagine monohydrate (Kartha & de Vries, 1961; Verbist et al., 1972; Ramanadham et al., 1972; Wang et al., 1985; Weisinger-Lewin et al., 1989; Smirnova et al., 1990; Arnold et al., 2000; Flaig et al., 2002; Chandrasekhar et al., 2003) and D-asparagine monohydrate (Chandrasekhar et al., 2003) have been reported so far. A powder X-ray diffraction study (PDF:37–1659) has been also reported for anhydrous L-asparagine. In the present study, a single-crystal structure determination of anhydrous L-asparagine, (I), is reported.
The single-crystal diffraction analysis confirms the space group and the unit-cell dimensions previously proposed by the powder diffraction study, and shows that, as expected, the title molecule exists as a zwitter ion in the crystal (Fig. 1). The distances of the C≐O bonds in the carboxylate group are significantly different although the group is deprotonated. The corresponding distances are 1.2407 (19) and 1.262 (2) Å for C2—O1 and C2—O2, respectively. The discrepancy is attributed to the number and kind of the intermolecular hydrogen bonds each O atom of the carboxylate participates in. The O2 atom forms two strong hydrogen bonds with neighboring cationic ammonium groups. O1, on the other hand, forms only one relatively weak hydrogen bond with the neutral amide group (Table 2 and Fig. 2). Owing to the formation of two strong hydrogen bonds, the C1—O2 bond is strongly polarized, and the distance of the C1—O2 bond is elongated accordingly. The carbonyl oxygen in the side chain, O3, also forms two hydrogen bonds with each one ammonium and amide group of neighboring molecules.
It is of interest to compare the present structure with that of L-asparagine monohydrate (Ramanadham et al., 1972). In the L-asparagine monohydrate crystal, the C≐O bonds in the ionized carboxyl group are 1.243 and 1.257 Å, which is in good agreement with those in (I), but with a slightly less pronounced difference in C—O bond lengths. Both oxygen atoms in the monohydrate exhibit each one relatively weak N—H···O hydrogen bond to an amide group, but the oxygen atom with the longer C—O distance forms two additional strong H bonds with solvate water molecules. The oxygen atom with the shorter C—O bond, on the other hand, forms only one strong hydrogen bond, in this case to the ammonium group. As the difference in the hydrogen bonding environment is thus less pronouced for the monohydrate than in the anhydrous structure this may also explain the more pronounced difference in the C—O distances found in the structure of the title compound.
The conformation of the backbone of (I) is quite different from that of the monohydrate. In (I), the torsion angle of C2—C1—C3—C4 is 170.64 (14)°, while, in the monohydrate, the corresponding angle is -53.08°. As mentioned, there are significant differences between the crystal structures and the side-chain conformations of anhydrous and monohydrate asparagines, which can be attributed most likely to the different hydrogen bonding environment induced by the presence of the water molecules. Similar differences are also found in the crystal structures of L-aspartic acid (Derissen et al., 1968) and L-aspartic acid monohydrate (Umadevi et al., 2003). The corresponding torsion angles of the side-chains, for example, are 178.2° and 52.8°, for L-aspartic acid and its monohydrate, respectively.