Benzhydryl 2-(3-benzyl-7-oxo-4-thia-2,6-diaza­bicyclo­[3.2.0]hept-2-en-6-yl)-3-morpholinobut-2-enoate

The title compound, C₃₂H₃₁N₃O₄S, is an important inter­mediate in the synthesis of cephem compounds, which can be converted into broad-spectrum cephalosporin anti­biotics. Inter­molecular C—H...O and C—H...S contacts are observed in the crystal structure.

Key indicators

• Single-crystal X-ray study
• T = 113 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.040
• wR factor = 0.081
• Data-to-parameter ratio = 18.3

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?

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           27.92
           From the CIF: _reflns_number_total               6676
           Count of symmetry unique reflns         3778
           Completeness (_total/calc)            176.71%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured      2898
           Fraction of Friedel pairs measured     0.767
           Are heavy atom types Z>Si present        yes
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3     = .          R

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   1 ALERT level C = Check and explain
   3 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
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

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Computing details

Data collection: CrystalClear (Rigaku, 2005); cell refinement: CrystalClear; data reduction: CrystalClear; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 1997); software used to prepare material for publication: CrystalStructure (Rigaku/MSC, 2005).

Benzhydryl 2-(3-benzyl-7-oxo-4-thia-2,6-diazabicyclo[3.2.0]hept-2-en-6-yl)- 3-morpholinobut-2-enoate

Crystal data

C32H31N3O4S	Dx = 1.320 Mg m^−3
Mr = 553.66	Melting point: 532 K
Orthorhombic, P212121	Mo Kα radiation, λ = 0.7107 Å
Hall symbol: P 2ac 2ab	Cell parameters from 6900 reflections
a = 8.648 (3) Å	θ = 1.6–27.9°
b = 12.278 (4) Å	µ = 0.16 mm^−1
c = 26.246 (8) Å	T = 113 K
V = 2786.6 (15) Å^3	Block, colourless
Z = 4	0.24 × 0.20 × 0.18 mm
F(000) = 1168

Data collection

Rigaku Saturn CCD diffractometer	6676 independent reflections
Radiation source: rotating anode	6023 reflections with I > 2σ(I)
Confocal monochromator	Rint = 0.051
Detector resolution: 7.31 pixels mm^-1	θmax = 27.9°, θmin = 1.6°
ω scans	h = −10→11
Absorption correction: multi-scan (Jacobson, 1998)	k = −16→16
Tmin = 0.963, Tmax = 0.972	l = −32→34
25624 measured reflections

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.040	w = 1/[σ^2(Fo^2) + (0.0378P)^2] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.081	(Δ/σ)max = 0.001
S = 1.03	Δρmax = 0.24 e Å^−3
6676 reflections	Δρmin = −0.18 e Å^−3
364 parameters	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.0078 (6)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 3304 Friedel pairs
Secondary atom site location: difference Fourier map	Absolute structure parameter: −0.01 (6)

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq
S1	0.23693 (5)	0.31495 (3)	0.379793 (16)	0.02412 (11)
N1	0.04148 (16)	0.14912 (11)	0.34627 (5)	0.0189 (3)
N2	−0.01637 (17)	0.30813 (12)	0.43581 (5)	0.0251 (3)
N3	0.31607 (16)	0.03079 (11)	0.36876 (5)	0.0215 (3)
O1	−0.17125 (14)	0.08171 (10)	0.39244 (5)	0.0294 (3)
O2	0.03623 (15)	−0.02916 (9)	0.23717 (5)	0.0275 (3)
O3	−0.10038 (13)	0.11815 (9)	0.26099 (4)	0.0219 (3)
O4	0.44708 (15)	−0.08033 (10)	0.45332 (5)	0.0296 (3)
C1	−0.08456 (19)	0.15220 (14)	0.37780 (6)	0.0216 (4)
C2	−0.0688 (2)	0.27663 (14)	0.38563 (7)	0.0241 (4)
H2	−0.1592	0.3196	0.3729	0.029*
C3	0.0675 (2)	0.26774 (13)	0.34665 (6)	0.0219 (4)
H3	0.0480	0.3045	0.3133	0.026*
C4	0.1288 (2)	0.32463 (13)	0.43737 (6)	0.0224 (4)
C5	0.2171 (2)	0.35312 (15)	0.48529 (7)	0.0299 (4)
H5A	0.1450	0.3843	0.5107	0.036*
H5B	0.2626	0.2861	0.5000	0.036*
C6	0.3440 (2)	0.43411 (14)	0.47428 (6)	0.0242 (4)
C7	0.3121 (2)	0.54505 (14)	0.47514 (7)	0.0269 (4)
H7	0.2135	0.5699	0.4861	0.032*
C8	0.4234 (2)	0.61949 (16)	0.46009 (7)	0.0324 (4)
H8	0.4008	0.6952	0.4608	0.039*
C9	0.5665 (2)	0.58429 (18)	0.44413 (7)	0.0382 (5)
H9	0.6415	0.6353	0.4327	0.046*
C10	0.6005 (2)	0.47460 (19)	0.44476 (8)	0.0414 (5)
H10	0.7002	0.4501	0.4347	0.050*
C11	0.4899 (2)	0.40030 (16)	0.45996 (8)	0.0340 (5)
H11	0.5146	0.3249	0.4606	0.041*
C12	0.10392 (19)	0.06848 (13)	0.31287 (6)	0.0183 (3)
C13	0.01682 (19)	0.04501 (12)	0.26731 (6)	0.0199 (4)
C14	−0.1857 (2)	0.10910 (14)	0.21382 (6)	0.0211 (4)
H14	−0.1999	0.0303	0.2055	0.025*
C15	−0.0944 (2)	0.16276 (14)	0.17143 (6)	0.0201 (4)
C16	−0.0410 (2)	0.26893 (14)	0.17698 (7)	0.0228 (4)
H16	−0.0627	0.3083	0.2073	0.027*
C17	0.0441 (2)	0.31760 (14)	0.13832 (7)	0.0262 (4)
H17	0.0824	0.3896	0.1426	0.031*
C18	0.0731 (2)	0.26159 (16)	0.09379 (7)	0.0274 (4)
H18	0.1308	0.2952	0.0673	0.033*
C19	0.0186 (2)	0.15745 (16)	0.08766 (7)	0.0290 (4)
H19	0.0373	0.1195	0.0567	0.035*
C20	−0.0637 (2)	0.10733 (14)	0.12660 (6)	0.0253 (4)
H20	−0.0991	0.0346	0.1225	0.030*
C21	−0.3423 (2)	0.16010 (14)	0.22263 (7)	0.0230 (4)
C22	−0.3785 (2)	0.21656 (14)	0.26690 (7)	0.0259 (4)
H22	−0.3037	0.2237	0.2932	0.031*
C23	−0.5246 (2)	0.26273 (16)	0.27278 (8)	0.0332 (4)
H23	−0.5484	0.3016	0.3031	0.040*
C24	−0.6349 (2)	0.25263 (17)	0.23521 (8)	0.0361 (5)
H24	−0.7340	0.2849	0.2394	0.043*
C25	−0.6003 (2)	0.19505 (18)	0.19123 (8)	0.0396 (5)
H25	−0.6762	0.1863	0.1654	0.048*
C26	−0.4546 (2)	0.15037 (17)	0.18516 (7)	0.0320 (4)
H26	−0.4310	0.1122	0.1547	0.038*
C27	0.2510 (2)	0.02702 (12)	0.32211 (6)	0.0202 (4)
C28	0.3476 (2)	−0.02104 (15)	0.28080 (7)	0.0267 (4)
H28A	0.4330	0.0286	0.2727	0.040*
H28B	0.2839	−0.0321	0.2503	0.040*
H28C	0.3895	−0.0911	0.2922	0.040*
C29	0.2296 (2)	0.01985 (14)	0.41620 (6)	0.0240 (4)
H29A	0.1175	0.0145	0.4090	0.029*
H29B	0.2474	0.0841	0.4382	0.029*
C30	0.2859 (2)	−0.08308 (15)	0.44271 (7)	0.0288 (4)
H30A	0.2284	−0.0924	0.4750	0.035*
H30B	0.2632	−0.1468	0.4208	0.035*
C31	0.5305 (2)	−0.07203 (15)	0.40687 (7)	0.0274 (4)
H31A	0.5105	−0.1374	0.3858	0.033*
H31B	0.6427	−0.0692	0.4142	0.033*
C32	0.48351 (19)	0.02895 (14)	0.37760 (7)	0.0252 (4)
H32A	0.5141	0.0946	0.3971	0.030*
H32B	0.5383	0.0305	0.3445	0.030*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0280 (2)	0.0228 (2)	0.0216 (2)	−0.00499 (18)	0.00167 (19)	−0.00164 (17)
N1	0.0196 (7)	0.0185 (7)	0.0185 (7)	−0.0004 (6)	−0.0001 (6)	0.0003 (5)
N2	0.0277 (8)	0.0256 (7)	0.0221 (7)	0.0020 (7)	−0.0001 (6)	−0.0051 (6)
N3	0.0173 (7)	0.0269 (7)	0.0205 (8)	0.0011 (6)	0.0002 (6)	0.0024 (6)
O1	0.0220 (7)	0.0338 (7)	0.0323 (7)	−0.0043 (6)	0.0036 (6)	−0.0028 (6)
O2	0.0357 (7)	0.0218 (6)	0.0248 (7)	0.0050 (6)	−0.0046 (6)	−0.0049 (5)
O3	0.0232 (6)	0.0244 (6)	0.0181 (6)	0.0060 (5)	−0.0052 (5)	−0.0014 (5)
O4	0.0258 (7)	0.0358 (7)	0.0273 (7)	0.0039 (6)	−0.0040 (6)	0.0059 (6)
C1	0.0170 (8)	0.0301 (9)	0.0177 (9)	0.0016 (7)	−0.0042 (7)	−0.0010 (7)
C2	0.0241 (9)	0.0266 (9)	0.0215 (9)	0.0058 (7)	−0.0025 (8)	−0.0038 (7)
C3	0.0271 (10)	0.0201 (8)	0.0186 (9)	0.0018 (7)	−0.0041 (7)	0.0004 (7)
C4	0.0292 (10)	0.0186 (8)	0.0193 (9)	−0.0006 (7)	−0.0008 (7)	−0.0003 (7)
C5	0.0379 (11)	0.0316 (9)	0.0203 (9)	−0.0056 (9)	−0.0019 (8)	−0.0001 (7)
C6	0.0278 (10)	0.0288 (9)	0.0161 (9)	−0.0018 (8)	−0.0055 (8)	−0.0024 (7)
C7	0.0269 (10)	0.0324 (10)	0.0214 (9)	0.0035 (8)	−0.0030 (8)	−0.0022 (7)
C8	0.0436 (12)	0.0269 (9)	0.0268 (10)	−0.0035 (9)	−0.0103 (9)	0.0039 (8)
C9	0.0365 (12)	0.0505 (13)	0.0276 (11)	−0.0161 (10)	−0.0046 (9)	0.0015 (10)
C10	0.0237 (10)	0.0630 (15)	0.0376 (12)	−0.0029 (10)	0.0003 (9)	−0.0167 (11)
C11	0.0314 (11)	0.0332 (10)	0.0375 (11)	0.0055 (9)	−0.0084 (9)	−0.0086 (9)
C12	0.0199 (9)	0.0171 (8)	0.0180 (8)	0.0000 (7)	0.0014 (7)	0.0001 (6)
C13	0.0212 (9)	0.0188 (8)	0.0196 (8)	−0.0002 (7)	0.0028 (7)	0.0038 (7)
C14	0.0259 (9)	0.0224 (8)	0.0150 (8)	−0.0013 (7)	−0.0046 (7)	0.0003 (7)
C15	0.0170 (9)	0.0232 (9)	0.0200 (9)	0.0014 (7)	−0.0031 (7)	0.0009 (7)
C16	0.0226 (9)	0.0227 (8)	0.0231 (9)	0.0039 (7)	−0.0008 (7)	−0.0021 (7)
C17	0.0217 (9)	0.0222 (8)	0.0348 (10)	0.0023 (7)	0.0011 (8)	0.0053 (8)
C18	0.0164 (9)	0.0398 (11)	0.0260 (10)	−0.0010 (8)	0.0008 (7)	0.0087 (8)
C19	0.0255 (10)	0.0435 (11)	0.0181 (9)	−0.0033 (9)	0.0012 (8)	−0.0058 (8)
C20	0.0256 (9)	0.0276 (9)	0.0227 (9)	−0.0039 (7)	−0.0005 (8)	−0.0024 (7)
C21	0.0216 (9)	0.0265 (9)	0.0210 (9)	−0.0014 (7)	0.0017 (7)	0.0076 (7)
C22	0.0238 (9)	0.0317 (10)	0.0221 (9)	−0.0012 (7)	0.0015 (8)	0.0035 (8)
C23	0.0285 (10)	0.0355 (10)	0.0356 (11)	0.0009 (8)	0.0111 (9)	0.0077 (9)
C24	0.0212 (10)	0.0478 (12)	0.0391 (12)	0.0062 (9)	0.0085 (9)	0.0187 (10)
C25	0.0245 (10)	0.0603 (14)	0.0340 (11)	0.0002 (10)	−0.0060 (9)	0.0201 (11)
C26	0.0257 (10)	0.0479 (12)	0.0223 (10)	−0.0006 (9)	−0.0005 (8)	0.0063 (8)
C27	0.0220 (9)	0.0163 (7)	0.0223 (9)	−0.0038 (7)	−0.0011 (8)	0.0017 (6)
C28	0.0222 (10)	0.0294 (9)	0.0284 (10)	0.0025 (8)	0.0029 (8)	−0.0012 (8)
C29	0.0241 (9)	0.0280 (9)	0.0198 (9)	0.0017 (8)	0.0004 (8)	0.0026 (7)
C30	0.0231 (10)	0.0360 (10)	0.0271 (10)	0.0046 (8)	0.0002 (8)	0.0064 (8)
C31	0.0219 (9)	0.0315 (10)	0.0288 (10)	0.0029 (8)	−0.0023 (8)	0.0040 (8)
C32	0.0196 (9)	0.0287 (9)	0.0273 (9)	−0.0008 (7)	−0.0016 (8)	0.0033 (8)

Geometric parameters (Å, º)

S1—C4	1.7809 (18)	C14—C15	1.515 (2)
S1—C3	1.8002 (18)	C14—H14	1.000
N1—C1	1.369 (2)	C15—C20	1.385 (2)
N1—C12	1.428 (2)	C15—C16	1.391 (2)
N1—C3	1.474 (2)	C16—C17	1.389 (2)
N2—C4	1.272 (2)	C16—H16	0.950
N2—C2	1.446 (2)	C17—C18	1.379 (3)
N3—C27	1.348 (2)	C17—H17	0.950
N3—C29	1.459 (2)	C18—C19	1.372 (3)
N3—C32	1.467 (2)	C18—H18	0.950
O1—C1	1.208 (2)	C19—C20	1.389 (2)
O2—C13	1.2179 (19)	C19—H19	0.950
O3—C13	1.3642 (19)	C20—H20	0.950
O3—C14	1.4453 (19)	C21—C26	1.388 (2)
O4—C31	1.420 (2)	C21—C22	1.389 (2)
O4—C30	1.422 (2)	C22—C23	1.393 (3)
C1—C2	1.548 (2)	C22—H22	0.950
C2—C3	1.564 (2)	C23—C24	1.378 (3)
C2—H2	1.000	C23—H23	0.950
C3—H3	1.000	C24—C25	1.386 (3)
C4—C5	1.512 (2)	C24—H24	0.950
C5—C6	1.509 (3)	C25—C26	1.383 (3)
C5—H5A	0.990	C25—H25	0.950
C5—H5B	0.990	C26—H26	0.950
C6—C11	1.381 (3)	C27—C28	1.491 (2)
C6—C7	1.390 (2)	C28—H28A	0.980
C7—C8	1.385 (3)	C28—H28B	0.980
C7—H7	0.950	C28—H28C	0.980
C8—C9	1.376 (3)	C29—C30	1.522 (2)
C8—H8	0.950	C29—H29A	0.990
C9—C10	1.379 (3)	C29—H29B	0.990
C9—H9	0.950	C30—H30A	0.990
C10—C11	1.381 (3)	C30—H30B	0.990
C10—H10	0.950	C31—C32	1.514 (2)
C11—H11	0.950	C31—H31A	0.990
C12—C27	1.391 (2)	C31—H31B	0.990
C12—C13	1.442 (2)	C32—H32A	0.990
C14—C21	1.510 (2)	C32—H32B	0.990
C4—S1—C3	90.23 (8)	C17—C16—C15	120.20 (16)
C1—N1—C12	133.71 (14)	C17—C16—H16	119.9
C1—N1—C3	95.16 (13)	C15—C16—H16	119.9
C12—N1—C3	129.17 (14)	C18—C17—C16	120.06 (17)
C4—N2—C2	112.43 (15)	C18—C17—H17	120.0
C27—N3—C29	123.93 (14)	C16—C17—H17	120.0
C27—N3—C32	123.72 (15)	C19—C18—C17	120.13 (17)
C29—N3—C32	111.69 (14)	C19—C18—H18	119.9
C13—O3—C14	115.64 (12)	C17—C18—H18	119.9
C31—O4—C30	109.36 (14)	C18—C19—C20	120.15 (17)
O1—C1—N1	131.82 (16)	C18—C19—H19	119.9
O1—C1—C2	136.03 (16)	C20—C19—H19	119.9
N1—C1—C2	92.15 (13)	C15—C20—C19	120.38 (17)
N2—C2—C1	114.38 (14)	C15—C20—H20	119.8
N2—C2—C3	112.21 (14)	C19—C20—H20	119.8
C1—C2—C3	84.86 (12)	C26—C21—C22	118.55 (17)
N2—C2—H2	114.1	C26—C21—C14	118.93 (16)
C1—C2—H2	114.1	C22—C21—C14	122.52 (16)
C3—C2—H2	114.1	C21—C22—C23	120.02 (17)
N1—C3—C2	87.63 (13)	C21—C22—H22	120.0
N1—C3—S1	116.46 (12)	C23—C22—H22	120.0
C2—C3—S1	105.95 (11)	C24—C23—C22	120.80 (19)
N1—C3—H3	114.5	C24—C23—H23	119.6
C2—C3—H3	114.5	C22—C23—H23	119.6
S1—C3—H3	114.5	C23—C24—C25	119.49 (18)
N2—C4—C5	124.16 (16)	C23—C24—H24	120.3
N2—C4—S1	118.70 (13)	C25—C24—H24	120.3
C5—C4—S1	117.14 (13)	C26—C25—C24	119.67 (19)
C6—C5—C4	111.12 (14)	C26—C25—H25	120.2
C6—C5—H5A	109.4	C24—C25—H25	120.2
C4—C5—H5A	109.4	C25—C26—C21	121.46 (19)
C6—C5—H5B	109.4	C25—C26—H26	119.3
C4—C5—H5B	109.4	C21—C26—H26	119.3
H5A—C5—H5B	108.0	N3—C27—C12	121.81 (15)
C11—C6—C7	118.71 (18)	N3—C27—C28	116.12 (15)
C11—C6—C5	121.26 (17)	C12—C27—C28	122.04 (15)
C7—C6—C5	119.89 (17)	C27—C28—H28A	109.5
C8—C7—C6	120.29 (18)	C27—C28—H28B	109.5
C8—C7—H7	119.9	H28A—C28—H28B	109.5
C6—C7—H7	119.9	C27—C28—H28C	109.5
C9—C8—C7	120.29 (18)	H28A—C28—H28C	109.5
C9—C8—H8	119.9	H28B—C28—H28C	109.5
C7—C8—H8	119.9	N3—C29—C30	107.61 (14)
C8—C9—C10	119.68 (19)	N3—C29—H29A	110.2
C8—C9—H9	120.2	C30—C29—H29A	110.2
C10—C9—H9	120.2	N3—C29—H29B	110.2
C9—C10—C11	120.1 (2)	C30—C29—H29B	110.2
C9—C10—H10	120.0	H29A—C29—H29B	108.5
C11—C10—H10	120.0	O4—C30—C29	112.54 (15)
C10—C11—C6	120.87 (19)	O4—C30—H30A	109.1
C10—C11—H11	119.6	C29—C30—H30A	109.1
C6—C11—H11	119.6	O4—C30—H30B	109.1
C27—C12—N1	119.49 (15)	C29—C30—H30B	109.1
C27—C12—C13	123.28 (15)	H30A—C30—H30B	107.8
N1—C12—C13	116.74 (14)	O4—C31—C32	110.98 (15)
O2—C13—O3	121.03 (15)	O4—C31—H31A	109.4
O2—C13—C12	128.02 (15)	C32—C31—H31A	109.4
O3—C13—C12	110.94 (13)	O4—C31—H31B	109.4
O3—C14—C21	107.13 (13)	C32—C31—H31B	109.4
O3—C14—C15	109.26 (13)	H31A—C31—H31B	108.0
C21—C14—C15	113.54 (14)	N3—C32—C31	110.97 (14)
O3—C14—H14	108.9	N3—C32—H32A	109.4
C21—C14—H14	108.9	C31—C32—H32A	109.4
C15—C14—H14	108.9	N3—C32—H32B	109.4
C20—C15—C16	119.06 (16)	C31—C32—H32B	109.4
C20—C15—C14	120.68 (15)	H32A—C32—H32B	108.0
C16—C15—C14	120.26 (15)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
C3—H3···O2^i	1.00	2.54	3.444 (2)	150
C16—H16···O2^i	0.95	2.48	3.350 (2)	152
C23—H23···S1^ii	0.95	2.74	3.543 (2)	142

Symmetry codes: (i) −x, y+1/2, −z+1/2; (ii) x−1, y, z.