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
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (C-C) = 0.006 Å
- R factor = 0.042
- wR factor = 0.111
- Data-to-parameter ratio = 9.0
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical . ? PLAT152_ALERT_1_C Supplied and Calc Volume s.u. Inconsistent ..... ? PLAT153_ALERT_1_C The su's on the Cell Axes are Equal (x 100000) 400 Ang. PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) ... 3.47 Ratio PLAT222_ALERT_3_C Large Non-Solvent H Ueq(max)/Ueq(min) ... 3.29 Ratio PLAT230_ALERT_2_C Hirshfeld Test Diff for C9 - C10 .. 5.02 su PLAT230_ALERT_2_C Hirshfeld Test Diff for C31 - C32 .. 6.48 su PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C9 PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C10 PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C18 PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C32 PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C7 PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C14 PLAT331_ALERT_2_C Small Average Phenyl C-C Dist. C14 -C19 1.37 Ang. PLAT340_ALERT_3_C Low Bond Precision on C-C Bonds (x 1000) Ang ... 6 PLAT480_ALERT_4_C Long H...A H-Bond Reported H16 .. O4 .. 2.62 Ang. PLAT480_ALERT_4_C Long H...A H-Bond Reported H17 .. O5 .. 2.80 Ang.
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 27.18 From the CIF: _reflns_number_total 3679 Count of symmetry unique reflns 3722 Completeness (_total/calc) 98.84% 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 PLAT199_ALERT_1_G Check the Reported _cell_measurement_temperature 293 K PLAT200_ALERT_1_G Check the Reported _diffrn_ambient_temperature . 293 K PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4 = . R PLAT791_ALERT_1_G Confirm the Absolute Configuration of C5 = . S PLAT791_ALERT_1_G Confirm the Absolute Configuration of C24 = . R PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints ....... 2
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 17 ALERT level C = Check and explain 7 ALERT level G = General alerts; check 8 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 10 ALERT type 2 Indicator that the structure model may be wrong or deficient 3 ALERT type 3 Indicator that the structure quality may be low 3 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
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. |
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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.