The title compound, C
8H
14N
2O
2, exists in the solid state in a zwitterionic form. The imidazolidinium fragment adopts an envelope conformation. The carboxylate group is involved in an intramolecular N
+—H
O
− hydrogen bond.
Supporting information
CCDC reference: 618313
Key indicators
- Single-crystal X-ray study
- T = 150 K
- Mean (C-C) = 0.002 Å
- R factor = 0.029
- wR factor = 0.071
- Data-to-parameter ratio = 9.2
checkCIF/PLATON results
No syntax errors found
Alert level C
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........ 2
Alert level G
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 26.37
From the CIF: _reflns_number_total 1005
Count of symmetry unique reflns 1008
Completeness (_total/calc) 99.70%
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
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2 = . S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4 = . R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C5 = . R
0 ALERT level A = In general: serious problem
0 ALERT level B = Potentially serious problem
1 ALERT level C = Check and explain
4 ALERT level G = General alerts; check
3 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
0 ALERT type 2 Indicator that the structure model may be wrong or deficient
0 ALERT type 3 Indicator that the structure quality may be low
2 ALERT type 4 Improvement, methodology, query or suggestion
0 ALERT type 5 Informative message, check
Data collection: CrysAlis CCD (Oxford Diffraction, 2004; cell refinement: CrysAlis CCD; data reduction: CrysAlis RED (Oxford Diffraction, 2004); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: Stereochemical Workstation (Siemens, 1989) and
Mercury (Macrae et al., 2006); software used to prepare material for publication: SHELXL97.
(
R,
R)-Perhydrobenzimidazolium-2-carboxylate
top
Crystal data top
C8H14N2O2 | Dx = 1.366 Mg m−3 |
Mr = 170.21 | Melting point: 453 K |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 3652 reflections |
a = 5.6176 (4) Å | θ = 4–25° |
b = 9.1414 (5) Å | µ = 0.10 mm−1 |
c = 16.1195 (7) Å | T = 150 K |
V = 827.78 (8) Å3 | Plate, colourless |
Z = 4 | 0.4 × 0.25 × 0.08 mm |
F(000) = 368 | |
Data collection top
Kuma KM4 CCD κ geometry diffractometer | Rint = 0.017 |
ω scans | θmax = 26.4°, θmin = 3.8° |
5897 measured reflections | h = −6→7 |
1005 independent reflections | k = −11→7 |
988 reflections with I > 2σ(I) | l = −19→20 |
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)] = 0.029 | Hydrogen site location: difference Fourier map |
wR(F2) = 0.071 | H-atom parameters constrained |
S = 1.08 | w = 1/[σ2(Fo2) + (0.0379P)2 + 0.2085P] where P = (Fo2 + 2Fc2)/3 |
1005 reflections | (Δ/σ)max < 0.001 |
109 parameters | Δρmax = 0.19 e Å−3 |
0 restraints | Δρmin = −0.17 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. 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 >
σ(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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O1 | 0.6565 (2) | 0.66458 (12) | 0.48708 (9) | 0.0337 (4) | |
O2 | 0.83759 (19) | 0.46996 (13) | 0.42995 (6) | 0.0189 (3) | |
N1 | 0.2438 (2) | 0.53370 (13) | 0.51308 (8) | 0.0152 (3) | |
H1NA | 0.2881 | 0.6283 | 0.5143 | 0.018* | |
H1NB | 0.1166 | 0.5245 | 0.4796 | 0.018* | |
C2 | 0.4488 (3) | 0.43702 (16) | 0.48305 (10) | 0.0158 (3) | |
H2A | 0.4014 | 0.3823 | 0.4334 | 0.019* | |
N3 | 0.5063 (3) | 0.33674 (13) | 0.55064 (8) | 0.0193 (3) | |
H3N | 0.4292 | 0.2511 | 0.5446 | 0.023* | |
C4 | 0.4247 (3) | 0.41455 (17) | 0.62499 (9) | 0.0182 (3) | |
H4A | 0.5357 | 0.4949 | 0.6360 | 0.022* | |
C5 | 0.1873 (3) | 0.48007 (17) | 0.59862 (9) | 0.0164 (3) | |
H5A | 0.0716 | 0.4003 | 0.5937 | 0.020* | |
C6 | 0.0924 (3) | 0.58922 (19) | 0.66091 (10) | 0.0256 (4) | |
H6A | −0.0594 | 0.6282 | 0.6426 | 0.031* | |
H6B | 0.2032 | 0.6697 | 0.6678 | 0.031* | |
C7 | 0.0631 (4) | 0.5051 (2) | 0.74287 (11) | 0.0350 (5) | |
H7A | 0.0130 | 0.5728 | 0.7858 | 0.042* | |
H7B | −0.0618 | 0.4327 | 0.7362 | 0.042* | |
C8 | 0.2913 (4) | 0.4280 (2) | 0.77112 (10) | 0.0305 (4) | |
H8A | 0.2572 | 0.3709 | 0.8204 | 0.037* | |
H8B | 0.4090 | 0.5011 | 0.7858 | 0.037* | |
C9 | 0.3956 (3) | 0.32667 (18) | 0.70422 (10) | 0.0248 (4) | |
H9A | 0.5486 | 0.2890 | 0.7221 | 0.030* | |
H9B | 0.2897 | 0.2446 | 0.6947 | 0.030* | |
C10 | 0.6662 (3) | 0.53467 (17) | 0.46410 (9) | 0.0163 (3) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0232 (7) | 0.0136 (5) | 0.0645 (9) | −0.0037 (5) | 0.0125 (7) | −0.0039 (6) |
O2 | 0.0135 (5) | 0.0208 (5) | 0.0225 (5) | 0.0009 (5) | 0.0020 (4) | −0.0008 (4) |
N1 | 0.0112 (6) | 0.0123 (5) | 0.0222 (6) | 0.0002 (6) | −0.0003 (5) | −0.0003 (5) |
C2 | 0.0122 (7) | 0.0124 (7) | 0.0229 (7) | 0.0009 (6) | 0.0004 (6) | −0.0029 (6) |
N3 | 0.0180 (6) | 0.0108 (6) | 0.0292 (7) | 0.0008 (5) | 0.0027 (6) | 0.0040 (5) |
C4 | 0.0155 (7) | 0.0145 (7) | 0.0248 (8) | −0.0015 (7) | −0.0030 (6) | 0.0016 (6) |
C5 | 0.0145 (7) | 0.0159 (7) | 0.0187 (7) | −0.0017 (6) | −0.0010 (6) | −0.0010 (6) |
C6 | 0.0284 (9) | 0.0258 (8) | 0.0226 (7) | 0.0071 (8) | −0.0005 (7) | −0.0054 (7) |
C7 | 0.0420 (12) | 0.0405 (11) | 0.0225 (8) | 0.0058 (10) | 0.0053 (8) | −0.0056 (8) |
C8 | 0.0419 (11) | 0.0283 (9) | 0.0214 (8) | −0.0053 (9) | −0.0057 (8) | 0.0013 (7) |
C9 | 0.0257 (9) | 0.0212 (8) | 0.0274 (8) | −0.0024 (7) | −0.0046 (8) | 0.0060 (7) |
C10 | 0.0135 (7) | 0.0153 (7) | 0.0202 (7) | −0.0005 (7) | −0.0016 (6) | 0.0025 (6) |
Geometric parameters (Å, º) top
O1—C10 | 1.245 (2) | C5—C6 | 1.512 (2) |
O2—C10 | 1.2572 (18) | C5—H5A | 0.9800 |
N1—C5 | 1.4975 (19) | C6—C7 | 1.538 (2) |
N1—C2 | 1.5301 (19) | C6—H6A | 0.9700 |
N1—H1NA | 0.9000 | C6—H6B | 0.9700 |
N1—H1NB | 0.9000 | C7—C8 | 1.532 (3) |
C2—N3 | 1.4601 (19) | C7—H7A | 0.9700 |
C2—C10 | 1.543 (2) | C7—H7B | 0.9700 |
C2—H2A | 0.9800 | C8—C9 | 1.538 (2) |
N3—C4 | 1.467 (2) | C8—H8A | 0.9700 |
N3—H3N | 0.9000 | C8—H8B | 0.9700 |
C4—C9 | 1.518 (2) | C9—H9A | 0.9700 |
C4—C5 | 1.523 (2) | C9—H9B | 0.9700 |
C4—H4A | 0.9800 | | |
| | | |
C5—N1—C2 | 105.18 (11) | C5—C6—C7 | 106.15 (13) |
C5—N1—H1NA | 110.7 | C5—C6—H6A | 110.5 |
C2—N1—H1NA | 110.7 | C7—C6—H6A | 110.5 |
C5—N1—H1NB | 110.7 | C5—C6—H6B | 110.5 |
C2—N1—H1NB | 110.7 | C7—C6—H6B | 110.5 |
H1NA—N1—H1NB | 108.8 | H6A—C6—H6B | 108.7 |
N3—C2—N1 | 107.04 (12) | C8—C7—C6 | 113.31 (16) |
N3—C2—C10 | 109.62 (12) | C8—C7—H7A | 108.9 |
N1—C2—C10 | 108.91 (11) | C6—C7—H7A | 108.9 |
N3—C2—H2A | 110.4 | C8—C7—H7B | 108.9 |
N1—C2—H2A | 110.4 | C6—C7—H7B | 108.9 |
C10—C2—H2A | 110.4 | H7A—C7—H7B | 107.7 |
C2—N3—C4 | 103.65 (11) | C7—C8—C9 | 112.80 (14) |
C2—N3—H3N | 111.0 | C7—C8—H8A | 109.0 |
C4—N3—H3N | 111.1 | C9—C8—H8A | 109.0 |
N3—C4—C9 | 117.68 (13) | C7—C8—H8B | 109.0 |
N3—C4—C5 | 103.67 (12) | C9—C8—H8B | 109.0 |
C9—C4—C5 | 110.41 (13) | H8A—C8—H8B | 107.8 |
N3—C4—H4A | 108.2 | C4—C9—C8 | 108.21 (13) |
C9—C4—H4A | 108.2 | C4—C9—H9A | 110.1 |
C5—C4—H4A | 108.2 | C8—C9—H9A | 110.1 |
N1—C5—C6 | 118.04 (13) | C4—C9—H9B | 110.1 |
N1—C5—C4 | 101.54 (11) | C8—C9—H9B | 110.1 |
C6—C5—C4 | 112.51 (13) | H9A—C9—H9B | 108.4 |
N1—C5—H5A | 108.1 | O1—C10—O2 | 127.75 (15) |
C6—C5—H5A | 108.1 | O1—C10—C2 | 117.29 (14) |
C4—C5—H5A | 108.1 | O2—C10—C2 | 114.88 (12) |
| | | |
N1—C2—N3—C4 | −24.89 (15) | C7—C8—C9—C4 | 53.2 (2) |
C2—N3—C4—C5 | 41.71 (14) | C8—C9—C4—C5 | −57.06 (18) |
N3—C4—C5—N1 | −42.04 (13) | C9—C4—C5—C6 | 63.90 (17) |
C4—C5—N1—C2 | 25.92 (13) | N1—C2—C10—O2 | −172.28 (11) |
C5—N1—C2—N3 | −1.42 (14) | N1—C2—C10—O1 | 10.69 (19) |
C4—C5—C6—C7 | −59.59 (18) | N3—C2—C10—O1 | −106.12 (16) |
C5—C6—C7—C8 | 54.6 (2) | N3—C2—C10—O2 | 70.91 (16) |
C6—C7—C8—C9 | −54.2 (2) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1NA···O1 | 0.90 | 2.14 | 2.6425 (18) | 114 |
N1—H1NA···O1i | 0.90 | 2.03 | 2.8014 (17) | 143 |
N1—H1NB···O2ii | 0.90 | 1.83 | 2.7098 (17) | 167 |
N3—H3N···O2iii | 0.90 | 2.13 | 2.9760 (17) | 157 |
Symmetry codes: (i) x−1/2, −y+3/2, −z+1; (ii) x−1, y, z; (iii) x−1/2, −y+1/2, −z+1. |