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The title compound [systematic name: (3
S,6S)-3,6-bis(
S-
sec-butyl)-2,5-piperazine-2,5-dione], C
12H
22N
2O
2, was crystallized from a solution of the corresponding linear peptide
L-isoleucyl-
L-isoleucine. In the crystal structure, molecules form traditional N—H
O hydrogen-bonded tapes along the
a axis [
a = 6.242 (9) Å].
Supporting information
CCDC reference: 610843
Key indicators
- Single-crystal X-ray study
- T = 105 K
- Mean (C-C) = 0.004 Å
- R factor = 0.036
- wR factor = 0.106
- Data-to-parameter ratio = 11.1
checkCIF/PLATON results
No syntax errors found
Alert level A
PLAT063_ALERT_3_A Crystal Probably too Large for Beam Size ....... 1.30 mm
| Author Response: This is no problem for a light atom structure, see Gorbitz, Acta
Cryst. B55 (1999) 1090-98.
|
Alert level B
CRYSS02_ALERT_3_B The value of _exptl_crystal_size_max is > 1.0
Maximum crystal size given = 1.300
PLAT220_ALERT_2_B Large Non-Solvent C Ueq(max)/Ueq(min) ... 3.99 Ratio
PLAT222_ALERT_3_B Large Non-Solvent H Ueq(max)/Ueq(min) ... 4.81 Ratio
Alert level C
ABSTM02_ALERT_3_C The ratio of expected to reported Tmax/Tmin(RR') is < 0.90
Tmin and Tmax reported: 0.766 0.994
Tmin(prime) and Tmax expected: 0.905 0.994
RR(prime) = 0.847
Please check that your absorption correction is appropriate.
PLAT029_ALERT_3_C _diffrn_measured_fraction_theta_full Low ....... 0.98
PLAT061_ALERT_3_C Tmax/Tmin Range Test RR' too Large ............. 0.85
PLAT480_ALERT_4_C Long H...A H-Bond Reported H71 .. O1 .. 2.61 Ang.
Alert level G
REFLT03_ALERT_1_G ALERT: Expected hkl max differ from CIF values
From the CIF: _diffrn_reflns_theta_max 28.18
From the CIF: _reflns_number_total 1739
From the CIF: _diffrn_reflns_limit_ max hkl 8. 14. 21.
From the CIF: _diffrn_reflns_limit_ min hkl -7. -9. -24.
TEST1: Expected hkl limits for theta max
Calculated maximum hkl 8. 14. 26.
Calculated minimum hkl -8. -14. -26.
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
correct. If it is not, please give the correct count in the
_publ_section_exptl_refinement section of the submitted CIF.
From the CIF: _diffrn_reflns_theta_max 28.18
From the CIF: _reflns_number_total 1739
Count of symmetry unique reflns 1906
Completeness (_total/calc) 91.24%
TEST3: Check Friedels for noncentro structure
Estimate of Friedel pairs measured 0
Fraction of Friedel pairs measured 0.000
Are heavy atom types Z>Si present no
1 ALERT level A = In general: serious problem
3 ALERT level B = Potentially serious problem
4 ALERT level C = Check and explain
2 ALERT level G = General alerts; check
1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
1 ALERT type 2 Indicator that the structure model may be wrong or deficient
6 ALERT type 3 Indicator that the structure quality may be low
2 ALERT type 4 Improvement, methodology, query or suggestion
Data collection: SMART (Bruker, 1998); cell refinement: SAINT-Plus (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Bruker, 2000); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.
(3
S,6S)-3,6-bis(
S-sec-butyl)-2,5-piperazine-2,5-dione
top
Crystal data top
C12H22N2O2 | F(000) = 496 |
Mr = 226.32 | Dx = 1.125 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 4248 reflections |
a = 6.242 (9) Å | θ = 2.1–28.2° |
b = 10.814 (15) Å | µ = 0.08 mm−1 |
c = 19.79 (3) Å | T = 105 K |
V = 1336 (3) Å3 | Needle, colourless |
Z = 4 | 1.30 × 0.10 × 0.08 mm |
Data collection top
Siemens SMART CCD diffractometer | 1739 independent reflections |
Radiation source: fine-focus sealed tube | 1557 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.040 |
Detector resolution: 8.3 pixels mm-1 | θmax = 28.2°, θmin = 2.1° |
Sets of exposures each taken over 0.3° ω rotation scans | h = −7→8 |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | k = −9→14 |
Tmin = 0.766, Tmax = 0.994 | l = −24→21 |
7470 measured reflections | |
Refinement top
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)] = 0.036 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.106 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.09 | w = 1/[σ2(Fo2) + (0.0514P)2 + 0.2942P] where P = (Fo2 + 2Fc2)/3 |
1739 reflections | (Δ/σ)max = 0.006 |
156 parameters | Δρmax = 0.30 e Å−3 |
0 restraints | Δρmin = −0.19 e Å−3 |
Special details top
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. Data were collected by measuring three sets of exposures with the detector set
at 2θ = 29°, crystal-to-detector distance 5.00 cm. Refinement of F2
against ALL reflections. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O1 | 0.2228 (2) | 0.63275 (14) | 0.38440 (7) | 0.0252 (3) | |
O2 | 0.9431 (2) | 0.59081 (13) | 0.53186 (7) | 0.0242 (3) | |
N1 | 0.7847 (2) | 0.62047 (15) | 0.43045 (8) | 0.0187 (3) | |
H1 | 0.915 (4) | 0.626 (2) | 0.4124 (11) | 0.022* | |
N2 | 0.3810 (2) | 0.59519 (16) | 0.48512 (8) | 0.0193 (3) | |
H2 | 0.245 (4) | 0.590 (2) | 0.5013 (11) | 0.023* | |
C1 | 0.6032 (3) | 0.64716 (16) | 0.38577 (9) | 0.0178 (4) | |
H11 | 0.6096 | 0.7372 | 0.3744 | 0.021* | |
C2 | 0.6208 (3) | 0.57451 (19) | 0.31863 (10) | 0.0232 (4) | |
H21 | 0.4883 | 0.5924 | 0.2920 | 0.028* | |
C3 | 0.6267 (4) | 0.4342 (2) | 0.33129 (12) | 0.0386 (6) | |
H32 | 0.7563 | 0.4143 | 0.3580 | 0.046* | |
H31 | 0.5004 | 0.4110 | 0.3587 | 0.046* | |
C4 | 0.6278 (6) | 0.3557 (3) | 0.26683 (16) | 0.0676 (10) | |
H43 | 0.7643 | 0.3670 | 0.2432 | 0.101* | |
H42 | 0.5099 | 0.3817 | 0.2374 | 0.101* | |
H41 | 0.6100 | 0.2684 | 0.2787 | 0.101* | |
C5 | 0.8121 (3) | 0.6206 (3) | 0.27678 (11) | 0.0401 (6) | |
H53 | 0.9459 | 0.5943 | 0.2983 | 0.060* | |
H52 | 0.8083 | 0.7111 | 0.2742 | 0.060* | |
H51 | 0.8042 | 0.5858 | 0.2311 | 0.060* | |
C6 | 0.3868 (3) | 0.62341 (17) | 0.41899 (9) | 0.0183 (4) | |
C7 | 0.5611 (3) | 0.59603 (16) | 0.53249 (9) | 0.0182 (4) | |
H71 | 0.5470 | 0.6722 | 0.5608 | 0.022* | |
C8 | 0.5530 (3) | 0.48314 (17) | 0.58103 (9) | 0.0209 (4) | |
H81 | 0.6841 | 0.4870 | 0.6100 | 0.025* | |
C9 | 0.5599 (4) | 0.35908 (18) | 0.54281 (11) | 0.0313 (5) | |
H92 | 0.4175 | 0.3433 | 0.5225 | 0.038* | |
H91 | 0.6650 | 0.3654 | 0.5055 | 0.038* | |
C10 | 0.6205 (5) | 0.2492 (2) | 0.58803 (13) | 0.0463 (7) | |
H103 | 0.5267 | 0.2476 | 0.6277 | 0.069* | |
H102 | 0.7698 | 0.2577 | 0.6026 | 0.069* | |
H101 | 0.6038 | 0.1720 | 0.5626 | 0.069* | |
C11 | 0.3586 (3) | 0.4927 (2) | 0.62814 (11) | 0.0313 (5) | |
H113 | 0.2266 | 0.4880 | 0.6014 | 0.047* | |
H112 | 0.3631 | 0.5717 | 0.6524 | 0.047* | |
H111 | 0.3617 | 0.4245 | 0.6607 | 0.047* | |
C12 | 0.7784 (3) | 0.60210 (17) | 0.49755 (9) | 0.0169 (4) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0143 (6) | 0.0410 (8) | 0.0201 (7) | 0.0013 (6) | −0.0015 (5) | 0.0035 (6) |
O2 | 0.0139 (6) | 0.0393 (8) | 0.0195 (7) | 0.0003 (6) | −0.0004 (5) | 0.0022 (6) |
N1 | 0.0123 (7) | 0.0268 (8) | 0.0171 (7) | −0.0011 (6) | 0.0019 (6) | −0.0004 (6) |
N2 | 0.0108 (7) | 0.0291 (8) | 0.0180 (8) | 0.0001 (6) | 0.0018 (6) | 0.0032 (6) |
C1 | 0.0147 (8) | 0.0204 (8) | 0.0182 (8) | −0.0004 (7) | −0.0003 (7) | 0.0017 (7) |
C2 | 0.0171 (9) | 0.0338 (10) | 0.0188 (9) | 0.0018 (8) | −0.0015 (8) | −0.0034 (8) |
C3 | 0.0454 (14) | 0.0306 (11) | 0.0398 (13) | 0.0081 (10) | −0.0105 (12) | −0.0126 (10) |
C4 | 0.082 (2) | 0.0570 (17) | 0.0636 (19) | 0.0110 (17) | −0.0232 (19) | −0.0375 (15) |
C5 | 0.0222 (10) | 0.0745 (18) | 0.0236 (11) | −0.0044 (11) | 0.0042 (9) | −0.0079 (12) |
C6 | 0.0156 (8) | 0.0215 (8) | 0.0179 (8) | 0.0014 (7) | 0.0002 (7) | 0.0010 (7) |
C7 | 0.0130 (8) | 0.0227 (9) | 0.0188 (9) | 0.0001 (7) | 0.0016 (7) | −0.0010 (7) |
C8 | 0.0167 (8) | 0.0271 (9) | 0.0189 (8) | 0.0007 (7) | −0.0006 (7) | 0.0044 (7) |
C9 | 0.0357 (11) | 0.0267 (10) | 0.0314 (11) | −0.0008 (9) | −0.0029 (10) | 0.0023 (8) |
C10 | 0.0582 (16) | 0.0305 (12) | 0.0503 (15) | 0.0069 (11) | 0.0150 (14) | 0.0120 (11) |
C11 | 0.0196 (9) | 0.0468 (13) | 0.0275 (11) | 0.0046 (9) | 0.0049 (8) | 0.0135 (9) |
C12 | 0.0126 (8) | 0.0205 (9) | 0.0177 (9) | −0.0001 (7) | −0.0001 (7) | −0.0015 (7) |
Geometric parameters (Å, º) top
O1—C6 | 1.236 (3) | C4—H41 | 0.9800 |
O2—C12 | 1.238 (3) | C5—H53 | 0.9800 |
N1—C12 | 1.343 (3) | C5—H52 | 0.9800 |
N1—C1 | 1.466 (3) | C5—H51 | 0.9800 |
N1—H1 | 0.89 (2) | C7—C12 | 1.524 (3) |
N2—C6 | 1.345 (3) | C7—C8 | 1.554 (3) |
N2—C7 | 1.464 (3) | C7—H71 | 1.0000 |
N2—H2 | 0.91 (2) | C8—C11 | 1.534 (3) |
C1—C6 | 1.524 (3) | C8—C9 | 1.541 (3) |
C1—C2 | 1.548 (3) | C8—H81 | 1.0000 |
C1—H11 | 1.0000 | C9—C10 | 1.535 (3) |
C2—C5 | 1.536 (3) | C9—H92 | 0.9900 |
C2—C3 | 1.539 (4) | C9—H91 | 0.9900 |
C2—H21 | 1.0000 | C10—H103 | 0.9800 |
C3—C4 | 1.532 (4) | C10—H102 | 0.9800 |
C3—H32 | 0.9900 | C10—H101 | 0.9800 |
C3—H31 | 0.9900 | C11—H113 | 0.9800 |
C4—H43 | 0.9800 | C11—H112 | 0.9800 |
C4—H42 | 0.9800 | C11—H111 | 0.9800 |
| | | |
C12—N1—C1 | 127.06 (16) | O1—C6—N2 | 122.36 (17) |
C12—N1—H1 | 115.7 (14) | O1—C6—C1 | 118.80 (18) |
C1—N1—H1 | 116.8 (14) | N2—C6—C1 | 118.84 (16) |
C6—N2—C7 | 126.96 (16) | N2—C7—C12 | 113.16 (17) |
C6—N2—H2 | 112.5 (14) | N2—C7—C8 | 111.49 (16) |
C7—N2—H2 | 119.4 (14) | C12—C7—C8 | 110.05 (14) |
N1—C1—C6 | 113.06 (17) | N2—C7—H71 | 107.3 |
N1—C1—C2 | 111.30 (16) | C12—C7—H71 | 107.3 |
C6—C1—C2 | 110.35 (15) | C8—C7—H71 | 107.3 |
N1—C1—H11 | 107.3 | C11—C8—C9 | 112.27 (18) |
C6—C1—H11 | 107.3 | C11—C8—C7 | 110.38 (16) |
C2—C1—H11 | 107.3 | C9—C8—C7 | 112.30 (19) |
C5—C2—C3 | 112.9 (2) | C11—C8—H81 | 107.2 |
C5—C2—C1 | 110.70 (18) | C9—C8—H81 | 107.2 |
C3—C2—C1 | 111.25 (18) | C7—C8—H81 | 107.2 |
C5—C2—H21 | 107.2 | C10—C9—C8 | 113.2 (2) |
C3—C2—H21 | 107.2 | C10—C9—H92 | 108.9 |
C1—C2—H21 | 107.2 | C8—C9—H92 | 108.9 |
C4—C3—C2 | 114.2 (2) | C10—C9—H91 | 108.9 |
C4—C3—H32 | 108.7 | C8—C9—H91 | 108.9 |
C2—C3—H32 | 108.7 | H92—C9—H91 | 107.7 |
C4—C3—H31 | 108.7 | C9—C10—H103 | 109.5 |
C2—C3—H31 | 108.7 | C9—C10—H102 | 109.5 |
H32—C3—H31 | 107.6 | H103—C10—H102 | 109.5 |
C3—C4—H43 | 109.5 | C9—C10—H101 | 109.5 |
C3—C4—H42 | 109.5 | H103—C10—H101 | 109.5 |
H43—C4—H42 | 109.5 | H102—C10—H101 | 109.5 |
C3—C4—H41 | 109.5 | C8—C11—H113 | 109.5 |
H43—C4—H41 | 109.5 | C8—C11—H112 | 109.5 |
H42—C4—H41 | 109.5 | H113—C11—H112 | 109.5 |
C2—C5—H53 | 109.5 | C8—C11—H111 | 109.5 |
C2—C5—H52 | 109.5 | H113—C11—H111 | 109.5 |
H53—C5—H52 | 109.5 | H112—C11—H111 | 109.5 |
C2—C5—H51 | 109.5 | O2—C12—N1 | 122.17 (17) |
H53—C5—H51 | 109.5 | O2—C12—C7 | 119.08 (18) |
H52—C5—H51 | 109.5 | N1—C12—C7 | 118.75 (16) |
| | | |
C12—N1—C1—C6 | −13.7 (2) | C6—C1—C2—C3 | −67.0 (2) |
N1—C1—C6—N2 | 7.1 (2) | C5—C2—C3—C4 | −59.0 (3) |
C1—C6—N2—C7 | 6.6 (3) | C7—N2—C6—O1 | −172.20 (17) |
N1—C1—C2—C3 | 59.4 (2) | N1—C1—C6—O1 | −174.02 (17) |
N1—C1—C2—C5 | −67.0 (2) | C2—C1—C6—O1 | −48.7 (2) |
C1—C2—C3—C4 | 175.8 (2) | C2—C1—C6—N2 | 132.51 (19) |
C6—N2—C7—C12 | −14.3 (2) | C6—N2—C7—C8 | −138.94 (19) |
N2—C7—C12—N1 | 7.7 (2) | C12—C7—C8—C11 | 166.93 (15) |
C7—C12—N1—C1 | 6.0 (3) | C12—C7—C8—C9 | −67.0 (2) |
N2—C7—C8—C9 | 59.4 (2) | C11—C8—C9—C10 | −72.4 (3) |
N2—C7—C8—C11 | −66.7 (2) | C1—N1—C12—O2 | −173.51 (17) |
C7—C8—C9—C10 | 162.49 (19) | N2—C7—C12—O2 | −172.80 (18) |
C12—N1—C1—C2 | −138.5 (2) | C8—C7—C12—O2 | −47.3 (2) |
C6—C1—C2—C5 | 166.59 (16) | C8—C7—C12—N1 | 133.14 (18) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O1i | 0.89 (2) | 2.00 (2) | 2.885 (4) | 172 (2) |
N2—H2···O2ii | 0.91 (2) | 1.98 (2) | 2.886 (4) | 175 (2) |
C5—H53···O1i | 0.98 | 2.46 | 3.336 (4) | 148 |
C7—H71···O1iii | 1.00 | 2.61 | 3.511 (4) | 149 |
C11—H113···O2ii | 0.98 | 2.50 | 3.389 (4) | 150 |
Symmetry codes: (i) x+1, y, z; (ii) x−1, y, z; (iii) x+1/2, −y+3/2, −z+1. |
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