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The title compound,
rac-(
R,
R)-
N,N'-bis(1-hydroxy-3-methyl-2-butyl)oxalamide, C
12H
24N
2O
4, crystallizes as a non-merohedral twin in the triclinic space group
. The twin is generated by a twofold rotation about
c*. The terminal hydroxy groups of molecules related by an inversion center form hydrogen-bonded dimers. This hydrogen-bonding pattern is further extended into a one-dimensional chain by N-H
O hydrogen bonds.
Supporting information
CCDC reference: 254948
The synthesis of (I) was described by Makarević et al. (2003).
Reflections for indexing were obtained by a locally written peaksearch program on the first 40 frames. These reflections were indexed using DIRAX (Duisenberg, 1992), resulting in two triclinic lattices related by a twofold rotation about hkl (001). Cell parameters and orientation were refined with PEAKREF (Schreurs, 2003). Reflection intensitities for both domains were integrated using the EVALCCD program suite (Duisenberg et al., 2003). Single reflections of the first domain and overlapping reflections of both domains were merged with MERGEHKLF5 (Schreurs, 2003). The twin refinement was performed with SHELXL97 (Sheldrick, 1997) using the data in HKLF5 format and refinement of batch scale factors (Herbst-Irmer & Sheldrick, 1998). The refinement resulted in a ratio of 80.6 (2):19.4 (2) for the two twin domains. H-atom coordinates were calculated geometrically and refined using a riding model. PLATON (Spek, 2003) was used in the preparation of material for publication.
Crystal data top
C12H24N2O4 | Z = 2 |
Mr = 260.33 | F(000) = 284 |
Triclinic, P1 | Dx = 1.247 Mg m−3 |
Hall symbol: -P 1 | Mo Kα radiation, λ = 0.71073 Å |
a = 5.0475 (9) Å | Cell parameters from 212 reflections |
b = 10.0957 (9) Å | θ = 4.1–20.5° |
c = 13.735 (3) Å | µ = 0.09 mm−1 |
α = 88.674 (12)° | T = 150 K |
β = 83.414 (19)° | Prism, colorless |
γ = 85.922 (10)° | 0.1 × 0.05 × 0.01 mm |
V = 693.5 (2) Å3 | |
Data collection top
Nonius KappaCCD diffractometer | Rint = 0.097 |
CCD rotation images, thick slices scans | θmax = 27.5°, θmin = 1.0° |
3065 measured reflections | h = −6→6 |
3065 independent reflections | k = −13→13 |
2017 reflections with I > 2σ(I) | l = −16→17 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | H-atom parameters constrained |
R[F2 > 2σ(F2)] = 0.063 | w = 1/[σ2(Fo2) + (0.0193P)2 + 0.8157P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.126 | (Δ/σ)max < 0.001 |
S = 1.21 | Δρmax = 0.24 e Å−3 |
1690 reflections | Δρmin = −0.23 e Å−3 |
164 parameters | |
Crystal data top
C12H24N2O4 | γ = 85.922 (10)° |
Mr = 260.33 | V = 693.5 (2) Å3 |
Triclinic, P1 | Z = 2 |
a = 5.0475 (9) Å | Mo Kα radiation |
b = 10.0957 (9) Å | µ = 0.09 mm−1 |
c = 13.735 (3) Å | T = 150 K |
α = 88.674 (12)° | 0.1 × 0.05 × 0.01 mm |
β = 83.414 (19)° | |
Data collection top
Nonius KappaCCD diffractometer | 2017 reflections with I > 2σ(I) |
3065 measured reflections | Rint = 0.097 |
3065 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.063 | 0 restraints |
wR(F2) = 0.126 | H-atom parameters constrained |
S = 1.21 | Δρmax = 0.24 e Å−3 |
1690 reflections | Δρmin = −0.23 e Å−3 |
164 parameters | |
Special details top
Experimental. Intensity data were measured on a Nonius KappaCCD with a detector distance of 30.0 mm, a rotation increment of 1.8° per frame and a total integration time of 630.22 s per frame. |
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
C1 | 0.6144 (9) | 0.2053 (4) | 0.0692 (3) | 0.0147 (11) | |
C11 | 0.6506 (8) | 0.2012 (4) | 0.1782 (3) | 0.0138 (11) | |
C2 | 0.8588 (8) | 0.2284 (4) | −0.0968 (3) | 0.0166 (11) | |
C21 | 0.4105 (8) | 0.1679 (4) | 0.3438 (3) | 0.0170 (11) | |
C3 | 0.9904 (8) | 0.0991 (5) | −0.1379 (3) | 0.0205 (12) | |
C31 | 0.2920 (9) | 0.0363 (5) | 0.3703 (4) | 0.0264 (12) | |
C4 | 0.9874 (9) | 0.3544 (4) | −0.1374 (3) | 0.0199 (12) | |
C41 | 0.2546 (9) | 0.2896 (5) | 0.3936 (3) | 0.0238 (12) | |
C5 | 0.8116 (9) | 0.4791 (5) | −0.1059 (4) | 0.0273 (12) | |
C51 | 0.4197 (10) | 0.4096 (5) | 0.3767 (4) | 0.0326 (13) | |
C6 | 1.0449 (9) | 0.3500 (5) | −0.2487 (3) | 0.0283 (13) | |
C61 | 0.1825 (11) | 0.2667 (5) | 0.5043 (4) | 0.0409 (15) | |
N1 | 0.8352 (7) | 0.2262 (4) | 0.0106 (3) | 0.0170 (9) | |
N11 | 0.4278 (7) | 0.1852 (4) | 0.2367 (2) | 0.0160 (9) | |
O1 | 0.3944 (5) | 0.1899 (3) | 0.0409 (2) | 0.0201 (8) | |
O11 | 0.8739 (5) | 0.2114 (3) | 0.2053 (2) | 0.0196 (8) | |
O2 | 1.2716 (5) | 0.0830 (3) | −0.1318 (2) | 0.0210 (8) | |
O21 | 0.4542 (7) | −0.0740 (3) | 0.3275 (2) | 0.0338 (9) | |
H11N | 0.2818 | 0.1848 | 0.21 | 0.019* | |
H1N | 0.9761 | 0.2395 | 0.0377 | 0.02* | |
H2 | 0.676 | 0.2348 | −0.1149 | 0.02* | |
H21 | 0.5924 | 0.163 | 0.3627 | 0.02* | |
H21O | 0.5192 | −0.0594 | 0.2663 | 0.051* | |
H2O | 1.3028 | 0.1052 | −0.0774 | 0.032* | |
H31A | 0.116 | 0.0376 | 0.3482 | 0.032* | |
H31B | 0.2708 | 0.025 | 0.441 | 0.032* | |
H3A | 0.9595 | 0.0939 | −0.206 | 0.025* | |
H3B | 0.9057 | 0.026 | −0.1027 | 0.025* | |
H4 | 1.158 | 0.3584 | −0.1103 | 0.024* | |
H41 | 0.0887 | 0.3077 | 0.3634 | 0.029* | |
H51A | 0.5846 | 0.3927 | 0.4049 | 0.049* | |
H51B | 0.4574 | 0.4262 | 0.3076 | 0.049* | |
H51C | 0.3217 | 0.4857 | 0.407 | 0.049* | |
H5A | 0.8999 | 0.5564 | −0.13 | 0.041* | |
H5B | 0.6438 | 0.4779 | −0.1324 | 0.041* | |
H5C | 0.7806 | 0.4811 | −0.0357 | 0.041* | |
H61A | 0.0826 | 0.344 | 0.532 | 0.061* | |
H61B | 0.3434 | 0.2506 | 0.5351 | 0.061* | |
H61C | 0.0766 | 0.1913 | 0.5148 | 0.061* | |
H6A | 0.8799 | 0.3474 | −0.2769 | 0.042* | |
H6B | 1.1327 | 0.4277 | −0.2723 | 0.042* | |
H6C | 1.1584 | 0.2721 | −0.267 | 0.042* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C1 | 0.015 (3) | 0.008 (3) | 0.020 (3) | 0.006 (2) | −0.002 (2) | 0.001 (2) |
C11 | 0.012 (3) | 0.008 (3) | 0.021 (3) | 0.000 (2) | −0.001 (2) | 0.002 (2) |
C2 | 0.012 (2) | 0.024 (3) | 0.015 (3) | −0.004 (2) | −0.004 (2) | −0.003 (2) |
C21 | 0.016 (2) | 0.023 (3) | 0.011 (3) | 0.005 (2) | −0.002 (2) | −0.002 (2) |
C3 | 0.015 (2) | 0.025 (3) | 0.021 (3) | −0.003 (2) | −0.002 (2) | −0.002 (2) |
C31 | 0.026 (3) | 0.029 (3) | 0.023 (3) | −0.002 (2) | 0.004 (2) | 0.005 (2) |
C4 | 0.022 (3) | 0.016 (3) | 0.021 (3) | −0.001 (2) | 0.001 (2) | −0.003 (2) |
C41 | 0.021 (2) | 0.026 (3) | 0.023 (3) | 0.008 (2) | −0.002 (2) | −0.003 (2) |
C5 | 0.032 (3) | 0.018 (3) | 0.031 (3) | 0.001 (2) | −0.002 (2) | −0.002 (2) |
C51 | 0.041 (3) | 0.026 (3) | 0.030 (3) | 0.006 (3) | −0.007 (2) | −0.007 (3) |
C6 | 0.035 (3) | 0.025 (3) | 0.024 (3) | −0.005 (2) | −0.002 (2) | 0.005 (2) |
C61 | 0.052 (4) | 0.043 (4) | 0.023 (3) | 0.013 (3) | 0.011 (3) | −0.008 (3) |
N1 | 0.012 (2) | 0.022 (2) | 0.017 (2) | −0.0012 (17) | −0.0008 (18) | −0.0028 (18) |
N11 | 0.0086 (19) | 0.025 (2) | 0.014 (2) | 0.0022 (17) | −0.0009 (17) | −0.0008 (18) |
O1 | 0.0116 (17) | 0.031 (2) | 0.0181 (17) | −0.0004 (14) | −0.0007 (14) | −0.0042 (15) |
O11 | 0.0122 (18) | 0.030 (2) | 0.0165 (18) | −0.0006 (15) | −0.0037 (14) | −0.0024 (15) |
O2 | 0.0191 (17) | 0.0239 (19) | 0.0205 (18) | 0.0014 (14) | −0.0046 (14) | −0.0059 (15) |
O21 | 0.047 (2) | 0.023 (2) | 0.028 (2) | 0.0097 (17) | 0.0029 (17) | 0.0040 (16) |
Geometric parameters (Å, º) top
O1—C1 | 1.239 (5) | C4—C6 | 1.524 (6) |
O11—C11 | 1.239 (5) | C4—C5 | 1.528 (6) |
O2—C3 | 1.429 (5) | C4—H4 | 0.98 |
O2—H2O | 0.82 | C31—H31B | 0.97 |
C1—N1 | 1.325 (5) | C31—H31A | 0.97 |
C1—C11 | 1.529 (6) | C41—C51 | 1.517 (7) |
N1—C2 | 1.466 (5) | C41—C61 | 1.538 (6) |
N1—H1N | 0.86 | C41—H41 | 0.98 |
O21—C31 | 1.430 (5) | C5—H5C | 0.96 |
O21—H21O | 0.8804 | C5—H5B | 0.96 |
C2—C3 | 1.513 (6) | C5—H5A | 0.96 |
C2—C4 | 1.533 (6) | C51—H51C | 0.96 |
C2—H2 | 0.98 | C51—H51B | 0.96 |
C3—H3B | 0.97 | C51—H51A | 0.96 |
C3—H3A | 0.97 | C6—H6C | 0.96 |
C11—N11 | 1.322 (5) | C6—H6B | 0.96 |
N11—C21 | 1.472 (5) | C6—H6A | 0.96 |
N11—H11N | 0.86 | C61—H61C | 0.96 |
C21—C31 | 1.515 (6) | C61—H61A | 0.96 |
C21—C41 | 1.540 (6) | C61—H61B | 0.96 |
C21—H21 | 0.98 | | |
| | | |
C3—O2—H2O | 109.5 | C2—C4—H4 | 108 |
O1—C1—N1 | 124.6 (4) | O21—C31—C21 | 112.5 (3) |
O1—C1—C11 | 121.2 (4) | O21—C31—H31B | 109.1 |
N1—C1—C11 | 114.2 (4) | C21—C31—H31B | 109.1 |
C1—N1—C2 | 125.3 (4) | O21—C31—H31A | 109.1 |
C1—N1—H1N | 117.4 | C21—C31—H31A | 109.1 |
C2—N1—H1N | 117.4 | H31B—C31—H31A | 107.8 |
C31—O21—H21O | 113.4 | C51—C41—C61 | 109.6 (4) |
N1—C2—C3 | 111.0 (4) | C51—C41—C21 | 109.4 (4) |
N1—C2—C4 | 110.3 (3) | C61—C41—C21 | 112.2 (4) |
C3—C2—C4 | 115.6 (4) | C51—C41—H41 | 108.5 |
N1—C2—H2 | 106.5 | C61—C41—H41 | 108.5 |
C3—C2—H2 | 106.5 | C21—C41—H41 | 108.5 |
C4—C2—H2 | 106.5 | C4—C5—H5C | 109.5 |
O2—C3—C2 | 114.1 (3) | C4—C5—H5B | 109.5 |
O2—C3—H3B | 108.7 | H5C—C5—H5B | 109.5 |
C2—C3—H3B | 108.7 | C4—C5—H5A | 109.5 |
O2—C3—H3A | 108.7 | H5C—C5—H5A | 109.5 |
C2—C3—H3A | 108.7 | H5B—C5—H5A | 109.5 |
H3B—C3—H3A | 107.6 | C41—C51—H51C | 109.5 |
O11—C11—N11 | 125.5 (4) | C41—C51—H51B | 109.5 |
O11—C11—C1 | 120.5 (4) | H51C—C51—H51B | 109.5 |
N11—C11—C1 | 114.0 (4) | C41—C51—H51A | 109.5 |
C11—N11—C21 | 125.0 (4) | H51C—C51—H51A | 109.5 |
C11—N11—H11N | 117.5 | H51B—C51—H51A | 109.5 |
C21—N11—H11N | 117.5 | C4—C6—H6C | 109.5 |
N11—C21—C31 | 107.8 (4) | C4—C6—H6B | 109.5 |
N11—C21—C41 | 109.6 (3) | H6C—C6—H6B | 109.5 |
C31—C21—C41 | 114.9 (3) | C4—C6—H6A | 109.5 |
N11—C21—H21 | 108.1 | H6C—C6—H6A | 109.5 |
C31—C21—H21 | 108.1 | H6B—C6—H6A | 109.5 |
C41—C21—H21 | 108.1 | C41—C61—H61C | 109.5 |
C6—C4—C5 | 110.6 (4) | C41—C61—H61A | 109.5 |
C6—C4—C2 | 110.8 (4) | H61C—C61—H61A | 109.5 |
C5—C4—C2 | 111.2 (4) | C41—C61—H61B | 109.5 |
C6—C4—H4 | 108 | H61C—C61—H61B | 109.5 |
C5—C4—H4 | 108 | H61A—C61—H61B | 109.5 |
| | | |
O1—C1—N1—C2 | −3.0 (7) | C11—N11—C21—C31 | −121.3 (4) |
C11—C1—N1—C2 | 177.0 (4) | C11—N11—C21—C41 | 112.9 (4) |
C1—N1—C2—C3 | −101.3 (5) | N1—C2—C4—C6 | 172.9 (4) |
C1—N1—C2—C4 | 129.4 (4) | C3—C2—C4—C6 | 46.1 (5) |
N1—C2—C3—O2 | −73.9 (5) | N1—C2—C4—C5 | −63.6 (5) |
C4—C2—C3—O2 | 52.6 (5) | C3—C2—C4—C5 | 169.6 (4) |
O1—C1—C11—O11 | 177.1 (4) | N11—C21—C31—O21 | 61.5 (5) |
N1—C1—C11—O11 | −2.9 (6) | C41—C21—C31—O21 | −175.9 (4) |
O1—C1—C11—N11 | −2.3 (6) | N11—C21—C41—C51 | −69.1 (5) |
N1—C1—C11—N11 | 177.7 (4) | C31—C21—C41—C51 | 169.3 (4) |
O11—C11—N11—C21 | −4.2 (7) | N11—C21—C41—C61 | 169.0 (4) |
C1—C11—N11—C21 | 175.1 (4) | C31—C21—C41—C61 | 47.5 (5) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2O···O1i | 0.82 | 1.97 | 2.780 (4) | 169 |
N1—H1N···O1i | 0.86 | 2.14 | 2.896 (5) | 147 |
O21—H21O···O2ii | 0.88 | 2.03 | 2.880 (4) | 161.9 |
N11—H11N···O11iii | 0.86 | 2.07 | 2.870 (4) | 156 |
N1—H1N···O11 | 0.86 | 2.32 | 2.704 (5) | 108 |
N11—H11N···O1 | 0.86 | 2.33 | 2.713 (5) | 108 |
Symmetry codes: (i) x+1, y, z; (ii) −x+2, −y, −z; (iii) x−1, y, z. |
Experimental details
Crystal data |
Chemical formula | C12H24N2O4 |
Mr | 260.33 |
Crystal system, space group | Triclinic, P1 |
Temperature (K) | 150 |
a, b, c (Å) | 5.0475 (9), 10.0957 (9), 13.735 (3) |
α, β, γ (°) | 88.674 (12), 83.414 (19), 85.922 (10) |
V (Å3) | 693.5 (2) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.09 |
Crystal size (mm) | 0.1 × 0.05 × 0.01 |
|
Data collection |
Diffractometer | Nonius KappaCCD diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 3065, 3065, 2017 |
Rint | 0.097 |
(sin θ/λ)max (Å−1) | 0.650 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.063, 0.126, 1.21 |
No. of reflections | 1690 |
No. of parameters | 164 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.24, −0.23 |
Selected torsion angles (º) topC11—C1—N1—C2 | 177.0 (4) | C1—C11—N11—C21 | 175.1 (4) |
C1—N1—C2—C3 | −101.3 (5) | C11—N11—C21—C31 | −121.3 (4) |
C1—N1—C2—C4 | 129.4 (4) | C11—N11—C21—C41 | 112.9 (4) |
N1—C2—C3—O2 | −73.9 (5) | N11—C21—C31—O21 | 61.5 (5) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O2—H2O···O1i | 0.82 | 1.97 | 2.780 (4) | 169.3 |
N1—H1N···O1i | 0.86 | 2.14 | 2.896 (5) | 146.5 |
O21—H21O···O2ii | 0.88 | 2.03 | 2.880 (4) | 161.9 |
N11—H11N···O11iii | 0.86 | 2.07 | 2.870 (4) | 155.5 |
N1—H1N···O11 | 0.86 | 2.32 | 2.704 (5) | 107.7 |
N11—H11N···O1 | 0.86 | 2.33 | 2.713 (5) | 107.5 |
Symmetry codes: (i) x+1, y, z; (ii) −x+2, −y, −z; (iii) x−1, y, z. |
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The present structure determination forms part of a systematic study related to hydrogen bonding and gelation properties of bis(amino acid) (Makarević et al., 2001; Perić et al., 2001) and bis(amino alcohol) oxalamide derivatives (Makarević et al., 2003). Fig. 1 shows the molecule of (I), with the atom-numbering scheme. The two iso-butyl residues are located on the same side of the oxalamide bridge and have similar geometries (Table 1). Atoms O1 and O11 of the central oxalamide unit are in a trans conformation and are almost coplanar, with an O1—C1—C11—O11 torsion angle of 177.1 (3)°. The terminal hydroxy groups form a hydrogen-bonded dimer (O21—H21O···O2) related by inversion symmetry (Table 2 and Fig. 2). Consequently, the two molecules of the dimer have opposite chirality. These dimers are further interconnected by N1—H1N···O1 and N11—H11N···O11 hydrogen bonds involving the oxalamide units. The molecules linked by the latter motif have the same chirality and form a one-dimensional ladder pattern (Fig. 3) typical of that found in the crystal structures of many retropeptides (Makarević et al., 2001, 2003). This ladder pattern involves intra- and intermolecular interactions, which form bifurcated (three-centred) hydrogen bonds; oxalamide atoms O11 and O1 act as double acceptors, while atoms N11 and N1 are double donors (Fig. 3 and Table 2). In addition to the ladder pattern involving the oxalamide groups there is an intermolecular hydrogen bond between the oxalamide group and the terminal hydroxy O atom (O2—H2O···O1; Table 2 and Fig. 3), and thus oxalamide atom O1 acts as a triple acceptor. The hydrogen-bonding pattern is an one-dimensional or α-network (Coe et al., 1997), composed of tunnels running along the crystallographic a axis. The inside of the tunnel is hydrophilic, featuring hydroxy and amide groups. The outside of the tunnel is dominated by iso-butyl groups and is thus hydrophobic (Fig. 2). The triclinic crystal is non-merohedrally twinned with a twofold rotation about c* (see Experimental). The corresponding twin supercell is approximately monoclinic (a=5.070 Å, b=40.991 Å, c=12.290 Å, α=90.74°, β=93.71° and γ=89.93°), with three times the volume of the triclinic cell. The twofold axis of the pseudo-monoclinic cell is coaxial to the c* axis of the triclinic cell (Fig. 4). A preliminary study with a Nonius CAD-4 point detector found the monoclinic cell. Only reflections with h+k=3n for any l were present, and scan profiles were split, indicating a possible twin supercell (Fig. 4). After transformation to the triclinic subcell, the twin relation was revealed using ROTAX (Cooper et al., 2002). However, since the data processing with EVALCCD (see Experimental) is much more appropriate than the treatment with ROTAX, we have chosen to use the EVALCCD data. EVALCCD uses physically relevant parameters, such as detector setup and crystal dimensions, to predict reflection shapes and consequently treats overlapping reflections correctly. This physical information is not available in the ROTAX approach.