Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807045874/ez2097sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807045874/ez2097Isup2.hkl |
CCDC reference: 663814
To a solution of (4R,5S)-1,3-dibenzyl-5-((R)-2-(hydroxydiphenylmethyl) pyrrolidine-1-carbonyl)-2- oxoimidazolidine-4-carboxylic acid (8 g, 13.68 mmol) in acetone (100 ml) was added NaOH (1.13 g, 27.36 mmol). After stirring at r.t. for 2 h, Me2SO4 (2.57 ml, 27.36 mmol) was added, followed by a catalytic amount of Bu4NI. Then the reaction mixture was heated under reflux for 10 h. The solvent was evaporated in vacuo, 5% aq NH4Cl (50 ml) was added and extracted with CH2Cl2. The combined organic layers were washed with 5% aq NaHCO3 (50 ml), H2O (50 ml) and brine (50 ml), and dried (MgSO4). Evaporation of the solvent under reduced pressure gave the crude product, which was washed with Et2O to afford a white powder (6.4 g, 78%), m.p. 444 K. Recrystallization from 2-propanol yielded colorless crystals of the title compound suitable for X-ray diffraction.
All H atoms were placed in geometrically idealized positions and constrained to ride on their parent atoms, with C—H distances in the range 0.93–0.98 Å, and with Uiso(H) = 1.5Ueq(C) for methyl H atoms and 1.2Ueq(C) for other H atoms. Methyl groups were allowed to rotate freely about the C—C bond.
In our ongoing research on the total synthesis of d-biotin, an efficient and highly diastereoselective approach was developed with (4R,5S)-methyl 1,3-dibenzyl-5- ((R)-2-(hydroxydiphenylmethyl)pyrrolidine-1-carbonyl)-2- oxoimidazolidine-4-carboxylate(I) prepared as a key intermediate. Determination of the three-dimensional structure would help us to investigate the absolute configurations of the three chiral centers. Herein, we report the crystal structure of the title compound (I).
Fig. 1 shows the molecular structure of (I). Due to the certainty of C24 being R-configuration, based on the synthesis, the diffraction analysis indicates that the two other chiral carbon atoms (C4 and C5) have R– and S-configurations respectively. The strong O5—H5X···O4 intramolecular hydrogen bond may enhance the molecular stability of this compound. Intermolecular C—H···O hydrogen bonds lead to a three-dimensional network.
Please provide reference(s) to some related literature.
Data collection: SMART (Bruker, 2000); cell refinement: SAINT (Bruker, 2000); data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2000); software used to prepare material for publication: SHELXTL (Bruker, 2000).
C37H37N3O5 | F(000) = 640 |
Mr = 603.70 | Dx = 1.260 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 793 reflections |
a = 12.075 (4) Å | θ = 2.5–21.2° |
b = 10.907 (4) Å | µ = 0.08 mm−1 |
c = 12.328 (4) Å | T = 293 K |
β = 101.396 (5)° | Prism, colorless |
V = 1591.5 (10) Å3 | 0.20 × 0.12 × 0.10 mm |
Z = 2 |
Bruker SMART APEX CCD area-detector diffractometer | 3679 independent reflections |
Radiation source: fine-focus sealed tube | 2645 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.029 |
φ and ω scans | θmax = 27.2°, θmin = 2.2° |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | h = −7→15 |
Tmin = 0.983, Tmax = 0.992 | k = −13→13 |
8080 measured reflections | l = −15→14 |
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)] = 0.042 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.111 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | w = 1/[σ2(Fo2) + (0.0606P)2] where P = (Fo2 + 2Fc2)/3 |
3679 reflections | (Δ/σ)max < 0.001 |
411 parameters | Δρmax = 0.13 e Å−3 |
2 restraints | Δρmin = −0.13 e Å−3 |
C37H37N3O5 | V = 1591.5 (10) Å3 |
Mr = 603.70 | Z = 2 |
Monoclinic, P21 | Mo Kα radiation |
a = 12.075 (4) Å | µ = 0.08 mm−1 |
b = 10.907 (4) Å | T = 293 K |
c = 12.328 (4) Å | 0.20 × 0.12 × 0.10 mm |
β = 101.396 (5)° |
Bruker SMART APEX CCD area-detector diffractometer | 3679 independent reflections |
Absorption correction: multi-scan (SADABS; Sheldrick, 1996) | 2645 reflections with I > 2σ(I) |
Tmin = 0.983, Tmax = 0.992 | Rint = 0.029 |
8080 measured reflections |
R[F2 > 2σ(F2)] = 0.042 | 2 restraints |
wR(F2) = 0.111 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.02 | Δρmax = 0.13 e Å−3 |
3679 reflections | Δρmin = −0.13 e Å−3 |
411 parameters |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.01834 (19) | 0.4307 (2) | −0.02044 (17) | 0.0663 (6) | |
O2 | −0.23633 (19) | 0.5563 (3) | 0.19449 (19) | 0.0850 (7) | |
O3 | −0.16338 (16) | 0.7314 (2) | 0.27063 (17) | 0.0651 (5) | |
O4 | 0.03920 (15) | 0.54484 (17) | 0.32417 (14) | 0.0531 (4) | |
O5 | 0.24961 (16) | 0.56160 (19) | 0.46064 (15) | 0.0568 (5) | |
H5X | 0.1866 (18) | 0.535 (3) | 0.432 (2) | 0.064 (10)* | |
N1 | 0.07821 (18) | 0.5786 (2) | 0.11061 (18) | 0.0528 (5) | |
C2 | 0.0000 (2) | 0.5168 (3) | 0.0374 (2) | 0.0494 (6) | |
N3 | −0.10202 (19) | 0.5674 (2) | 0.03674 (18) | 0.0563 (6) | |
C4 | −0.0978 (2) | 0.6659 (3) | 0.1152 (2) | 0.0485 (6) | |
H4 | −0.1218 | 0.7420 | 0.0752 | 0.058* | |
C5 | 0.03034 (19) | 0.6750 (2) | 0.16817 (19) | 0.0456 (6) | |
H5 | 0.0605 | 0.7551 | 0.1527 | 0.055* | |
C6 | 0.1946 (2) | 0.5416 (3) | 0.1395 (2) | 0.0644 (8) | |
H6A | 0.2011 | 0.4594 | 0.1113 | 0.077* | |
H6B | 0.2160 | 0.5376 | 0.2195 | 0.077* | |
C7 | 0.2781 (2) | 0.6236 (4) | 0.0971 (2) | 0.0673 (9) | |
C8 | 0.3910 (3) | 0.5966 (7) | 0.1312 (3) | 0.120 (2) | |
H8 | 0.4132 | 0.5337 | 0.1817 | 0.144* | |
C9 | 0.4715 (4) | 0.6629 (10) | 0.0905 (5) | 0.151 (3) | |
H9 | 0.5478 | 0.6470 | 0.1159 | 0.181* | |
C10 | 0.4386 (6) | 0.7515 (7) | 0.0132 (6) | 0.145 (3) | |
H10 | 0.4931 | 0.7932 | −0.0161 | 0.174* | |
C11 | 0.3266 (5) | 0.7808 (4) | −0.0226 (4) | 0.1065 (15) | |
H11 | 0.3046 | 0.8425 | −0.0745 | 0.128* | |
C12 | 0.2469 (3) | 0.7147 (3) | 0.0215 (3) | 0.0752 (9) | |
H12 | 0.1707 | 0.7333 | −0.0012 | 0.090* | |
C13 | −0.1988 (2) | 0.5433 (3) | −0.0507 (2) | 0.0642 (8) | |
H13A | −0.2667 | 0.5504 | −0.0202 | 0.077* | |
H13B | −0.1943 | 0.4593 | −0.0753 | 0.077* | |
C14 | −0.2106 (2) | 0.6261 (3) | −0.1498 (2) | 0.0553 (7) | |
C15 | −0.1246 (3) | 0.6958 (3) | −0.1739 (3) | 0.0680 (8) | |
H15 | −0.0548 | 0.6953 | −0.1259 | 0.082* | |
C16 | −0.1398 (4) | 0.7672 (3) | −0.2687 (3) | 0.0838 (11) | |
H16 | −0.0810 | 0.8153 | −0.2836 | 0.101* | |
C17 | −0.2416 (5) | 0.7661 (4) | −0.3396 (3) | 0.1025 (14) | |
H17 | −0.2527 | 0.8137 | −0.4035 | 0.123* | |
C18 | −0.3259 (5) | 0.6967 (6) | −0.3174 (4) | 0.136 (2) | |
H18 | −0.3951 | 0.6958 | −0.3664 | 0.163* | |
C19 | −0.3110 (4) | 0.6273 (4) | −0.2236 (4) | 0.1092 (16) | |
H19 | −0.3705 | 0.5798 | −0.2097 | 0.131* | |
C20 | −0.1737 (2) | 0.6415 (3) | 0.1980 (2) | 0.0556 (7) | |
C21 | −0.2295 (3) | 0.7239 (5) | 0.3560 (3) | 0.0907 (12) | |
H21A | −0.1970 | 0.6637 | 0.4098 | 0.136* | |
H21B | −0.3055 | 0.7007 | 0.3237 | 0.136* | |
H21C | −0.2298 | 0.8022 | 0.3914 | 0.136* | |
C22 | 0.05575 (19) | 0.6489 (2) | 0.2923 (2) | 0.0435 (6) | |
N23 | 0.09866 (16) | 0.7391 (2) | 0.36102 (17) | 0.0465 (5) | |
C24 | 0.1154 (2) | 0.7207 (3) | 0.4816 (2) | 0.0496 (6) | |
H24 | 0.0571 | 0.6641 | 0.4965 | 0.060* | |
C25 | 0.0911 (3) | 0.8475 (3) | 0.5232 (3) | 0.0693 (9) | |
H25A | 0.1362 | 0.8622 | 0.5964 | 0.083* | |
H25B | 0.0119 | 0.8555 | 0.5266 | 0.083* | |
C26 | 0.1229 (3) | 0.9373 (3) | 0.4395 (3) | 0.0792 (10) | |
H26A | 0.0771 | 1.0108 | 0.4350 | 0.095* | |
H26B | 0.2019 | 0.9602 | 0.4603 | 0.095* | |
C27 | 0.1008 (3) | 0.8700 (3) | 0.3306 (3) | 0.0633 (8) | |
H27A | 0.0291 | 0.8948 | 0.2856 | 0.076* | |
H27B | 0.1603 | 0.8859 | 0.2899 | 0.076* | |
C28 | 0.2328 (2) | 0.6636 (3) | 0.5283 (2) | 0.0471 (6) | |
C29 | 0.3256 (2) | 0.7552 (3) | 0.5229 (2) | 0.0548 (7) | |
C30 | 0.3740 (2) | 0.7603 (4) | 0.4306 (3) | 0.0726 (9) | |
H30 | 0.3523 | 0.7048 | 0.3731 | 0.087* | |
C31 | 0.4557 (3) | 0.8490 (5) | 0.4238 (4) | 0.1074 (15) | |
H31 | 0.4884 | 0.8525 | 0.3616 | 0.129* | |
C32 | 0.4875 (4) | 0.9301 (6) | 0.5076 (6) | 0.130 (2) | |
H32 | 0.5432 | 0.9876 | 0.5031 | 0.156* | |
C33 | 0.4378 (4) | 0.9283 (4) | 0.5999 (4) | 0.1076 (15) | |
H33 | 0.4570 | 0.9867 | 0.6554 | 0.129* | |
C34 | 0.3595 (3) | 0.8387 (3) | 0.6081 (3) | 0.0752 (10) | |
H34 | 0.3289 | 0.8340 | 0.6715 | 0.090* | |
C35 | 0.2425 (2) | 0.6118 (3) | 0.6452 (2) | 0.0516 (7) | |
C36 | 0.1531 (3) | 0.6007 (3) | 0.6997 (2) | 0.0658 (9) | |
H36 | 0.0834 | 0.6351 | 0.6696 | 0.079* | |
C37 | 0.1683 (4) | 0.5377 (4) | 0.8000 (3) | 0.0817 (11) | |
H37 | 0.1077 | 0.5297 | 0.8357 | 0.098* | |
C38 | 0.2689 (4) | 0.4881 (3) | 0.8464 (3) | 0.0838 (11) | |
H38 | 0.2769 | 0.4454 | 0.9128 | 0.101* | |
C39 | 0.3598 (3) | 0.5011 (4) | 0.7949 (3) | 0.0831 (10) | |
H39 | 0.4299 | 0.4685 | 0.8267 | 0.100* | |
C40 | 0.3455 (3) | 0.5627 (3) | 0.6962 (3) | 0.0706 (8) | |
H40 | 0.4072 | 0.5718 | 0.6621 | 0.085* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0971 (15) | 0.0533 (11) | 0.0537 (12) | −0.0013 (11) | 0.0272 (10) | −0.0088 (11) |
O2 | 0.0767 (14) | 0.106 (2) | 0.0775 (15) | −0.0347 (15) | 0.0281 (11) | −0.0103 (14) |
O3 | 0.0695 (12) | 0.0692 (13) | 0.0625 (12) | 0.0099 (11) | 0.0273 (9) | −0.0043 (12) |
O4 | 0.0664 (11) | 0.0444 (11) | 0.0489 (10) | −0.0070 (9) | 0.0123 (8) | 0.0011 (9) |
O5 | 0.0564 (11) | 0.0635 (12) | 0.0511 (10) | 0.0091 (10) | 0.0119 (9) | −0.0118 (10) |
N1 | 0.0516 (11) | 0.0598 (14) | 0.0484 (12) | 0.0059 (10) | 0.0132 (9) | −0.0049 (11) |
C2 | 0.0643 (16) | 0.0521 (16) | 0.0343 (13) | −0.0061 (13) | 0.0157 (12) | 0.0027 (13) |
N3 | 0.0583 (13) | 0.0635 (15) | 0.0456 (12) | −0.0017 (12) | 0.0065 (9) | −0.0038 (11) |
C4 | 0.0532 (14) | 0.0468 (14) | 0.0451 (14) | 0.0035 (12) | 0.0088 (11) | 0.0043 (12) |
C5 | 0.0517 (13) | 0.0424 (14) | 0.0447 (14) | −0.0008 (11) | 0.0145 (11) | 0.0011 (11) |
C6 | 0.0613 (16) | 0.080 (2) | 0.0540 (16) | 0.0163 (16) | 0.0176 (12) | 0.0009 (16) |
C7 | 0.0549 (15) | 0.094 (2) | 0.0537 (17) | −0.0020 (16) | 0.0129 (13) | −0.0258 (18) |
C8 | 0.059 (2) | 0.214 (6) | 0.084 (3) | 0.000 (3) | 0.0053 (18) | −0.009 (3) |
C9 | 0.058 (2) | 0.269 (9) | 0.125 (4) | −0.015 (4) | 0.016 (3) | −0.028 (5) |
C10 | 0.110 (4) | 0.177 (7) | 0.166 (6) | −0.068 (4) | 0.074 (4) | −0.073 (5) |
C11 | 0.134 (4) | 0.076 (3) | 0.131 (4) | −0.022 (3) | 0.078 (3) | −0.026 (3) |
C12 | 0.078 (2) | 0.066 (2) | 0.091 (2) | −0.0051 (17) | 0.0397 (18) | −0.014 (2) |
C13 | 0.0658 (17) | 0.073 (2) | 0.0515 (15) | −0.0191 (16) | 0.0059 (13) | −0.0018 (16) |
C14 | 0.0603 (15) | 0.0552 (17) | 0.0482 (15) | −0.0049 (13) | 0.0051 (12) | −0.0015 (13) |
C15 | 0.0721 (19) | 0.070 (2) | 0.0630 (18) | 0.0012 (15) | 0.0174 (15) | 0.0069 (16) |
C16 | 0.116 (3) | 0.065 (2) | 0.081 (2) | 0.006 (2) | 0.045 (2) | 0.0091 (19) |
C17 | 0.159 (4) | 0.080 (3) | 0.060 (2) | 0.008 (3) | 0.001 (3) | 0.014 (2) |
C18 | 0.125 (4) | 0.142 (5) | 0.113 (4) | −0.033 (4) | −0.044 (3) | 0.052 (4) |
C19 | 0.092 (3) | 0.116 (3) | 0.102 (3) | −0.031 (3) | −0.025 (2) | 0.035 (3) |
C20 | 0.0508 (14) | 0.0655 (19) | 0.0503 (16) | 0.0021 (14) | 0.0093 (11) | 0.0036 (14) |
C21 | 0.090 (2) | 0.118 (3) | 0.075 (2) | 0.020 (2) | 0.0433 (18) | −0.005 (2) |
C22 | 0.0414 (12) | 0.0437 (16) | 0.0470 (14) | −0.0007 (11) | 0.0126 (10) | −0.0006 (12) |
N23 | 0.0476 (11) | 0.0422 (12) | 0.0491 (12) | 0.0006 (9) | 0.0083 (9) | −0.0042 (10) |
C24 | 0.0499 (13) | 0.0555 (16) | 0.0460 (14) | −0.0032 (12) | 0.0155 (11) | −0.0104 (13) |
C25 | 0.0664 (18) | 0.073 (2) | 0.067 (2) | 0.0124 (16) | 0.0112 (15) | −0.0271 (18) |
C26 | 0.092 (2) | 0.0491 (18) | 0.088 (3) | 0.0115 (17) | −0.0027 (19) | −0.0128 (18) |
C27 | 0.0743 (19) | 0.0384 (15) | 0.073 (2) | 0.0020 (13) | 0.0058 (16) | −0.0025 (14) |
C28 | 0.0484 (13) | 0.0523 (15) | 0.0419 (13) | −0.0010 (12) | 0.0122 (10) | −0.0043 (12) |
C29 | 0.0455 (13) | 0.0647 (19) | 0.0527 (15) | −0.0017 (13) | 0.0058 (11) | 0.0128 (14) |
C30 | 0.0514 (15) | 0.096 (3) | 0.0727 (19) | −0.0014 (16) | 0.0182 (13) | 0.0189 (19) |
C31 | 0.073 (2) | 0.140 (4) | 0.112 (3) | −0.023 (3) | 0.026 (2) | 0.042 (3) |
C32 | 0.074 (3) | 0.154 (5) | 0.148 (4) | −0.053 (3) | −0.013 (3) | 0.064 (4) |
C33 | 0.106 (3) | 0.094 (3) | 0.103 (3) | −0.043 (3) | −0.030 (3) | 0.017 (3) |
C34 | 0.072 (2) | 0.077 (2) | 0.068 (2) | −0.0200 (18) | −0.0070 (16) | 0.0021 (18) |
C35 | 0.0585 (16) | 0.0525 (16) | 0.0451 (14) | −0.0079 (12) | 0.0137 (12) | −0.0065 (13) |
C36 | 0.0645 (17) | 0.087 (2) | 0.0488 (16) | −0.0235 (16) | 0.0178 (13) | −0.0123 (16) |
C37 | 0.107 (3) | 0.096 (3) | 0.0486 (17) | −0.044 (2) | 0.0316 (18) | −0.0157 (19) |
C38 | 0.132 (4) | 0.070 (2) | 0.0475 (18) | −0.019 (2) | 0.014 (2) | −0.0023 (17) |
C39 | 0.112 (3) | 0.079 (2) | 0.0565 (19) | 0.020 (2) | 0.0122 (19) | 0.0123 (18) |
C40 | 0.079 (2) | 0.077 (2) | 0.0581 (17) | 0.0140 (17) | 0.0210 (15) | 0.0108 (17) |
O1—C2 | 1.225 (3) | C18—H18 | 0.9300 |
O2—C20 | 1.194 (4) | C19—H19 | 0.9300 |
O3—C20 | 1.317 (4) | C21—H21A | 0.9599 |
O3—C21 | 1.443 (4) | C21—H21B | 0.9599 |
O4—C22 | 1.230 (3) | C21—H21C | 0.9599 |
O5—C28 | 1.429 (3) | C22—N23 | 1.335 (3) |
O5—H5X | 0.825 (18) | N23—C24 | 1.473 (3) |
N1—C2 | 1.350 (3) | N23—C27 | 1.477 (4) |
N1—C6 | 1.438 (4) | C24—C25 | 1.524 (4) |
N1—C5 | 1.451 (3) | C24—C28 | 1.552 (4) |
C2—N3 | 1.348 (4) | C24—H24 | 0.9800 |
N3—C4 | 1.439 (4) | C25—C26 | 1.526 (5) |
N3—C13 | 1.449 (4) | C25—H25A | 0.9700 |
C4—C20 | 1.524 (4) | C25—H25B | 0.9700 |
C4—C5 | 1.559 (3) | C26—C27 | 1.506 (5) |
C4—H4 | 0.9800 | C26—H26A | 0.9700 |
C5—C22 | 1.527 (3) | C26—H26B | 0.9700 |
C5—H5 | 0.9800 | C27—H27A | 0.9700 |
C6—C7 | 1.516 (5) | C27—H27B | 0.9700 |
C6—H6A | 0.9700 | C28—C29 | 1.513 (4) |
C6—H6B | 0.9700 | C28—C35 | 1.531 (4) |
C7—C12 | 1.364 (5) | C29—C30 | 1.379 (4) |
C7—C8 | 1.377 (5) | C29—C34 | 1.389 (4) |
C8—C9 | 1.383 (9) | C30—C31 | 1.396 (6) |
C8—H8 | 0.9300 | C30—H30 | 0.9300 |
C9—C10 | 1.360 (10) | C31—C32 | 1.357 (8) |
C9—H9 | 0.9300 | C31—H31 | 0.9300 |
C10—C11 | 1.375 (9) | C32—C33 | 1.387 (8) |
C10—H10 | 0.9300 | C32—H32 | 0.9300 |
C11—C12 | 1.395 (5) | C33—C34 | 1.377 (5) |
C11—H11 | 0.9300 | C33—H33 | 0.9300 |
C12—H12 | 0.9300 | C34—H34 | 0.9300 |
C13—C14 | 1.503 (4) | C35—C36 | 1.384 (4) |
C13—H13A | 0.9700 | C35—C40 | 1.386 (4) |
C13—H13B | 0.9700 | C36—C37 | 1.395 (5) |
C14—C19 | 1.364 (5) | C36—H36 | 0.9300 |
C14—C15 | 1.365 (4) | C37—C38 | 1.349 (6) |
C15—C16 | 1.386 (5) | C37—H37 | 0.9300 |
C15—H15 | 0.9300 | C38—C39 | 1.380 (6) |
C16—C17 | 1.360 (6) | C38—H38 | 0.9300 |
C16—H16 | 0.9300 | C39—C40 | 1.371 (5) |
C17—C18 | 1.339 (7) | C39—H39 | 0.9300 |
C17—H17 | 0.9300 | C40—H40 | 0.9300 |
C18—C19 | 1.364 (6) | ||
C20—O3—C21 | 117.5 (3) | H21A—C21—H21B | 109.5 |
C28—O5—H5X | 107 (2) | O3—C21—H21C | 109.5 |
C2—N1—C6 | 123.1 (2) | H21A—C21—H21C | 109.5 |
C2—N1—C5 | 113.3 (2) | H21B—C21—H21C | 109.5 |
C6—N1—C5 | 123.2 (2) | O4—C22—N23 | 123.1 (2) |
O1—C2—N3 | 125.4 (2) | O4—C22—C5 | 118.6 (2) |
O1—C2—N1 | 126.0 (2) | N23—C22—C5 | 118.3 (2) |
N3—C2—N1 | 108.5 (2) | C22—N23—C24 | 119.8 (2) |
C2—N3—C4 | 113.0 (2) | C22—N23—C27 | 125.2 (2) |
C2—N3—C13 | 122.2 (2) | C24—N23—C27 | 112.5 (2) |
C4—N3—C13 | 123.4 (2) | N23—C24—C25 | 102.6 (2) |
N3—C4—C20 | 111.9 (2) | N23—C24—C28 | 111.25 (19) |
N3—C4—C5 | 103.27 (19) | C25—C24—C28 | 117.5 (2) |
C20—C4—C5 | 114.1 (2) | N23—C24—H24 | 108.4 |
N3—C4—H4 | 109.1 | C25—C24—H24 | 108.4 |
C20—C4—H4 | 109.1 | C28—C24—H24 | 108.4 |
C5—C4—H4 | 109.1 | C24—C25—C26 | 105.3 (2) |
N1—C5—C22 | 109.6 (2) | C24—C25—H25A | 110.7 |
N1—C5—C4 | 101.96 (19) | C26—C25—H25A | 110.7 |
C22—C5—C4 | 113.22 (18) | C24—C25—H25B | 110.7 |
N1—C5—H5 | 110.6 | C26—C25—H25B | 110.7 |
C22—C5—H5 | 110.6 | H25A—C25—H25B | 108.8 |
C4—C5—H5 | 110.6 | C27—C26—C25 | 105.5 (3) |
N1—C6—C7 | 115.6 (3) | C27—C26—H26A | 110.7 |
N1—C6—H6A | 108.4 | C25—C26—H26A | 110.7 |
C7—C6—H6A | 108.4 | C27—C26—H26B | 110.7 |
N1—C6—H6B | 108.4 | C25—C26—H26B | 110.7 |
C7—C6—H6B | 108.4 | H26A—C26—H26B | 108.8 |
H6A—C6—H6B | 107.4 | N23—C27—C26 | 104.7 (3) |
C12—C7—C8 | 119.1 (4) | N23—C27—H27A | 110.8 |
C12—C7—C6 | 123.6 (3) | C26—C27—H27A | 110.8 |
C8—C7—C6 | 117.0 (4) | N23—C27—H27B | 110.8 |
C7—C8—C9 | 120.1 (6) | C26—C27—H27B | 110.8 |
C7—C8—H8 | 119.9 | H27A—C27—H27B | 108.9 |
C9—C8—H8 | 119.9 | O5—C28—C29 | 107.3 (2) |
C10—C9—C8 | 119.8 (5) | O5—C28—C35 | 105.6 (2) |
C10—C9—H9 | 120.1 | C29—C28—C35 | 111.5 (2) |
C8—C9—H9 | 120.1 | O5—C28—C24 | 108.7 (2) |
C9—C10—C11 | 121.5 (5) | C29—C28—C24 | 110.4 (2) |
C9—C10—H10 | 119.3 | C35—C28—C24 | 113.04 (19) |
C11—C10—H10 | 119.3 | C30—C29—C34 | 119.2 (3) |
C10—C11—C12 | 117.7 (5) | C30—C29—C28 | 120.1 (3) |
C10—C11—H11 | 121.2 | C34—C29—C28 | 120.7 (3) |
C12—C11—H11 | 121.2 | C29—C30—C31 | 119.8 (4) |
C7—C12—C11 | 121.7 (4) | C29—C30—H30 | 120.1 |
C7—C12—H12 | 119.2 | C31—C30—H30 | 120.1 |
C11—C12—H12 | 119.2 | C32—C31—C30 | 120.2 (4) |
N3—C13—C14 | 115.4 (2) | C32—C31—H31 | 119.9 |
N3—C13—H13A | 108.4 | C30—C31—H31 | 119.9 |
C14—C13—H13A | 108.4 | C31—C32—C33 | 120.8 (4) |
N3—C13—H13B | 108.4 | C31—C32—H32 | 119.6 |
C14—C13—H13B | 108.4 | C33—C32—H32 | 119.6 |
H13A—C13—H13B | 107.5 | C34—C33—C32 | 119.0 (5) |
C19—C14—C15 | 117.6 (3) | C34—C33—H33 | 120.5 |
C19—C14—C13 | 118.5 (3) | C32—C33—H33 | 120.5 |
C15—C14—C13 | 123.9 (3) | C33—C34—C29 | 120.9 (4) |
C14—C15—C16 | 121.1 (3) | C33—C34—H34 | 119.5 |
C14—C15—H15 | 119.4 | C29—C34—H34 | 119.5 |
C16—C15—H15 | 119.4 | C36—C35—C40 | 117.5 (3) |
C17—C16—C15 | 119.3 (4) | C36—C35—C28 | 124.6 (2) |
C17—C16—H16 | 120.3 | C40—C35—C28 | 117.6 (2) |
C15—C16—H16 | 120.3 | C35—C36—C37 | 119.7 (3) |
C18—C17—C16 | 120.0 (4) | C35—C36—H36 | 120.2 |
C18—C17—H17 | 120.0 | C37—C36—H36 | 120.2 |
C16—C17—H17 | 120.0 | C38—C37—C36 | 121.6 (3) |
C17—C18—C19 | 120.6 (4) | C38—C37—H37 | 119.2 |
C17—C18—H18 | 119.7 | C36—C37—H37 | 119.2 |
C19—C18—H18 | 119.7 | C37—C38—C39 | 119.6 (3) |
C14—C19—C18 | 121.4 (4) | C37—C38—H38 | 120.2 |
C14—C19—H19 | 119.3 | C39—C38—H38 | 120.2 |
C18—C19—H19 | 119.3 | C40—C39—C38 | 119.1 (4) |
O2—C20—O3 | 125.3 (3) | C40—C39—H39 | 120.4 |
O2—C20—C4 | 124.9 (3) | C38—C39—H39 | 120.4 |
O3—C20—C4 | 109.7 (3) | C39—C40—C35 | 122.5 (3) |
O3—C21—H21A | 109.5 | C39—C40—H40 | 118.8 |
O3—C21—H21B | 109.5 | C35—C40—H40 | 118.8 |
C6—N1—C2—O1 | −7.2 (4) | C4—C5—C22—O4 | 66.3 (3) |
C5—N1—C2—O1 | −179.1 (2) | N1—C5—C22—N23 | 131.0 (2) |
C6—N1—C2—N3 | 174.1 (2) | C4—C5—C22—N23 | −116.0 (2) |
C5—N1—C2—N3 | 2.2 (3) | O4—C22—N23—C24 | −7.5 (3) |
O1—C2—N3—C4 | 178.9 (2) | C5—C22—N23—C24 | 174.9 (2) |
N1—C2—N3—C4 | −2.3 (3) | O4—C22—N23—C27 | −168.1 (3) |
O1—C2—N3—C13 | −14.3 (4) | C5—C22—N23—C27 | 14.4 (3) |
N1—C2—N3—C13 | 164.5 (2) | C22—N23—C24—C25 | −145.6 (2) |
C2—N3—C4—C20 | −121.7 (2) | C27—N23—C24—C25 | 17.3 (3) |
C13—N3—C4—C20 | 71.7 (3) | C22—N23—C24—C28 | 88.0 (3) |
C2—N3—C4—C5 | 1.5 (3) | C27—N23—C24—C28 | −109.2 (3) |
C13—N3—C4—C5 | −165.1 (2) | N23—C24—C25—C26 | −28.8 (3) |
C2—N1—C5—C22 | 119.0 (2) | C28—C24—C25—C26 | 93.6 (3) |
C6—N1—C5—C22 | −52.8 (3) | C24—C25—C26—C27 | 30.6 (3) |
C2—N1—C5—C4 | −1.2 (3) | C22—N23—C27—C26 | 163.1 (2) |
C6—N1—C5—C4 | −173.0 (2) | C24—N23—C27—C26 | 1.3 (3) |
N3—C4—C5—N1 | −0.2 (2) | C25—C26—C27—N23 | −19.6 (3) |
C20—C4—C5—N1 | 121.5 (2) | N23—C24—C28—O5 | −47.9 (3) |
N3—C4—C5—C22 | −117.8 (2) | C25—C24—C28—O5 | −165.8 (2) |
C20—C4—C5—C22 | 3.9 (3) | N23—C24—C28—C29 | 69.5 (3) |
C2—N1—C6—C7 | 109.6 (3) | C25—C24—C28—C29 | −48.4 (3) |
C5—N1—C6—C7 | −79.4 (3) | N23—C24—C28—C35 | −164.9 (2) |
N1—C6—C7—C12 | −10.7 (4) | C25—C24—C28—C35 | 77.3 (3) |
N1—C6—C7—C8 | 174.6 (3) | O5—C28—C29—C30 | 27.7 (3) |
C12—C7—C8—C9 | 1.2 (7) | C35—C28—C29—C30 | 142.9 (3) |
C6—C7—C8—C9 | 176.1 (5) | C24—C28—C29—C30 | −90.5 (3) |
C7—C8—C9—C10 | −2.7 (10) | O5—C28—C29—C34 | −155.2 (2) |
C8—C9—C10—C11 | 2.8 (10) | C35—C28—C29—C34 | −40.0 (3) |
C9—C10—C11—C12 | −1.2 (8) | C24—C28—C29—C34 | 86.5 (3) |
C8—C7—C12—C11 | 0.4 (5) | C34—C29—C30—C31 | −0.2 (5) |
C6—C7—C12—C11 | −174.2 (3) | C28—C29—C30—C31 | 176.9 (3) |
C10—C11—C12—C7 | −0.4 (6) | C29—C30—C31—C32 | 0.0 (6) |
C2—N3—C13—C14 | −87.1 (3) | C30—C31—C32—C33 | −1.5 (7) |
C4—N3—C13—C14 | 78.2 (4) | C31—C32—C33—C34 | 3.3 (7) |
N3—C13—C14—C19 | −165.8 (4) | C32—C33—C34—C29 | −3.6 (6) |
N3—C13—C14—C15 | 17.9 (4) | C30—C29—C34—C33 | 2.0 (5) |
C19—C14—C15—C16 | 1.4 (5) | C28—C29—C34—C33 | −175.0 (3) |
C13—C14—C15—C16 | 177.8 (3) | O5—C28—C35—C36 | −110.4 (3) |
C14—C15—C16—C17 | −1.0 (5) | C29—C28—C35—C36 | 133.4 (3) |
C15—C16—C17—C18 | 0.1 (7) | C24—C28—C35—C36 | 8.3 (4) |
C16—C17—C18—C19 | 0.5 (8) | O5—C28—C35—C40 | 63.6 (3) |
C15—C14—C19—C18 | −0.9 (7) | C29—C28—C35—C40 | −52.6 (4) |
C13—C14—C19—C18 | −177.4 (5) | C24—C28—C35—C40 | −177.7 (3) |
C17—C18—C19—C14 | −0.1 (9) | C40—C35—C36—C37 | −2.4 (4) |
C21—O3—C20—O2 | 2.9 (4) | C28—C35—C36—C37 | 171.6 (3) |
C21—O3—C20—C4 | 180.0 (3) | C35—C36—C37—C38 | 0.8 (5) |
N3—C4—C20—O2 | −5.5 (4) | C36—C37—C38—C39 | 0.9 (6) |
C5—C4—C20—O2 | −122.3 (3) | C37—C38—C39—C40 | −1.1 (6) |
N3—C4—C20—O3 | 177.4 (2) | C38—C39—C40—C35 | −0.5 (6) |
C5—C4—C20—O3 | 60.5 (3) | C36—C35—C40—C39 | 2.3 (5) |
N1—C5—C22—O4 | −46.7 (3) | C28—C35—C40—C39 | −172.1 (3) |
D—H···A | D—H | H···A | D···A | D—H···A |
O5—H5X···O4 | 0.83 (2) | 2.00 (2) | 2.762 (3) | 153 (3) |
C4—H4···O1i | 0.98 | 2.57 | 3.328 (3) | 135 |
C5—H5···O1i | 0.98 | 2.57 | 3.320 (3) | 133 |
C16—H16···O4i | 0.93 | 2.62 | 3.383 (4) | 139 |
C17—H17···O5i | 0.93 | 2.80 | 3.544 (5) | 138 |
C32—H32···O5ii | 0.93 | 2.58 | 3.435 (5) | 153 |
C37—H37···O1iii | 0.93 | 2.50 | 3.336 (4) | 150 |
Symmetry codes: (i) −x, y+1/2, −z; (ii) −x+1, y+1/2, −z+1; (iii) x, y, z+1. |
Experimental details
Crystal data | |
Chemical formula | C37H37N3O5 |
Mr | 603.70 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 293 |
a, b, c (Å) | 12.075 (4), 10.907 (4), 12.328 (4) |
β (°) | 101.396 (5) |
V (Å3) | 1591.5 (10) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.08 |
Crystal size (mm) | 0.20 × 0.12 × 0.10 |
Data collection | |
Diffractometer | Bruker SMART APEX CCD area-detector |
Absorption correction | Multi-scan (SADABS; Sheldrick, 1996) |
Tmin, Tmax | 0.983, 0.992 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8080, 3679, 2645 |
Rint | 0.029 |
(sin θ/λ)max (Å−1) | 0.643 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.042, 0.111, 1.02 |
No. of reflections | 3679 |
No. of parameters | 411 |
No. of restraints | 2 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.13, −0.13 |
Computer programs: SMART (Bruker, 2000), SAINT (Bruker, 2000), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), SHELXTL (Bruker, 2000).
D—H···A | D—H | H···A | D···A | D—H···A |
O5—H5X···O4 | 0.825 (18) | 2.00 (2) | 2.762 (3) | 153 (3) |
C4—H4···O1i | 0.98 | 2.57 | 3.328 (3) | 134.5 |
C5—H5···O1i | 0.98 | 2.57 | 3.320 (3) | 133.0 |
C16—H16···O4i | 0.93 | 2.62 | 3.383 (4) | 139.4 |
C17—H17···O5i | 0.93 | 2.80 | 3.544 (5) | 138.2 |
C32—H32···O5ii | 0.93 | 2.58 | 3.435 (5) | 152.7 |
C37—H37···O1iii | 0.93 | 2.50 | 3.336 (4) | 150.3 |
Symmetry codes: (i) −x, y+1/2, −z; (ii) −x+1, y+1/2, −z+1; (iii) x, y, z+1. |
In our ongoing research on the total synthesis of d-biotin, an efficient and highly diastereoselective approach was developed with (4R,5S)-methyl 1,3-dibenzyl-5- ((R)-2-(hydroxydiphenylmethyl)pyrrolidine-1-carbonyl)-2- oxoimidazolidine-4-carboxylate(I) prepared as a key intermediate. Determination of the three-dimensional structure would help us to investigate the absolute configurations of the three chiral centers. Herein, we report the crystal structure of the title compound (I).
Fig. 1 shows the molecular structure of (I). Due to the certainty of C24 being R-configuration, based on the synthesis, the diffraction analysis indicates that the two other chiral carbon atoms (C4 and C5) have R– and S-configurations respectively. The strong O5—H5X···O4 intramolecular hydrogen bond may enhance the molecular stability of this compound. Intermolecular C—H···O hydrogen bonds lead to a three-dimensional network.