N^[epsilon]-Benzyl­oxy­carbonyl-N^α-(2-nitro­benzene­sulfonyl)-L-lysine

The title compound, C₂₀H₂₃N₃O₈S, is in an extended conformation. The COOH group does not form hydrogen-bonded carboxyl dimers, but forms an intermolecular hydrogen bond with the NCOO carbonyl O atom [O...O 2.666 (2) Å]. The N atom bonded to S is pyramidal, and forms a bifurcated intramolecular hydrogen bond with carboxy and nitro O atoms.

Key indicators

• Single-crystal X-ray study
• T = 120 K
• Mean [sigma](C-C) = 0.003 Å
• R factor = 0.039
• wR factor = 0.077
• Data-to-parameter ratio = 14.4

checkCIF results

No syntax errors found

ADDSYM reports no extra symmetry

General Notes



REFLT_03
         From the CIF: _diffrn_reflns_theta_max           27.50
         From the CIF: _reflns_number_total               4345
         Count of symmetry unique reflns         2906
         Completeness (_total/calc)            149.52%
         TEST3: Check Friedels for noncentro structure
         Estimate of Friedel pairs measured      1439
         Fraction of Friedel pairs measured     0.495
         Are heavy atom types Z>Si present          yes
          WARNING: Large fraction of Friedel related reflns may
                   be needed to determine absolute structure

---

S1. Comment

The solid-phase peptide synthesis by the use of N^α-protecting groups such as Fmoc (9-fluorenylmethoxycarbonyl) is widely used as described by Wenschuh et al. (1994). In an effort to increase the yield of the amino acid coupling reaction, the title compound, (I), was synthesized. The 2-nitrobenzenesulfonyl protecting group is smaller than the Fmoc group and is expected to increase the amino acid coupling yield due to decreased steric interactions with the nucleophile. The crystal structure determination of the title compound was carried out to confirm its successful synthesis.

The title compound is in an extended conformation. The COOH group does not form hydrogen-bonded carboxy dimers, but forms an intermolecular hydrogen bond with the carbonyl O5 atom. The lysine N1 atom is pyramidal, and forms a bifurcated intramolecular hydrogen bond with the carboxy O3 and nitro O8 atoms.

The cell dimensions of the title compound at 296 K are a = 11.8092 (13), b = 34.832 (4), c = 5.4033 (6) Å and V = 2222.6 (7) ų.

S2. Experimental

The title compound was prepared by reacting N^ε-benzyloxycarbonyl-L-lysine with chlorotrimethylsylane (1.85 equivalents), diisopropylethylamine (2.3 equivalents) and ortho-nitrobenzenesulfonyl chloride (0.9 equivalents) in anhydrous dichloromethane under argon over 12 h (273 K to reflux), followed by aqueous work-up and extraction. The amino acid derivative was recrystalized by dissolving the crude material in a hot ethanol solution, followed by slow cooling to room temperature.

S3. Refinement

H atoms on C atoms were placed in calculated positions with C—H bond distances in the range 0.95–1.00 Å and U_iso = 1.2U_eq of the attached atom, and thereafter treated as riding. H atoms on O and N atoms were placed by difference maps and refined individually. The absolute configuration was determined by refinement of the Flack (1983) parameter, and corresponds with that of L-lysine.

Computing details

Data collection: COLLECT (Nonius 2000); cell refinement: DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: direct methods using SIR (Altomare et al., 1993); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.

Figures

Fig. 1. The atom-numbering scheme for (I) with displacement ellipsoids at the 50% probability level.

N^α(2-nitrobenzenesulfonyl)-N^ε-benzyloxycarbonyl-L-lysine

Crystal data

C20H23N3O8S	Dx = 1.422 Mg m^−3
Mr = 465.47	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P21212	Cell parameters from 13981 reflections
a = 11.7629 (2) Å	θ = 2.5–27.5°
b = 34.5731 (6) Å	µ = 0.20 mm^−1
c = 5.3477 (2) Å	T = 120 K
V = 2174.8 (2) Å^3	Fragment, colorless
Z = 4	0.23 × 0.12 × 0.10 mm
F(000) = 976

Data collection

KappaCCD (with Oxford Cryostream) diffractometer	4345 independent reflections
Radiation source: fine-focus sealed tube	3563 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.050
ω scans with κ offsets	θmax = 27.5°, θmin = 3.4°
Absorption correction: multi-scan (HKL SCALEPACK; Otwinowski & Minor, 1997)	h = −15→15
Tmin = 0.937, Tmax = 0.980	k = −44→44
13981 measured reflections	l = −5→5

Refinement

Refinement on F^2	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F^2 > 2σ(F^2)] = 0.039	w = 1/[σ^2(Fo^2) + (0.0239P)^2 + 0.7661P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.077	(Δ/σ)max = 0.001
S = 1.05	Δρmax = 0.21 e Å^−3
4345 reflections	Δρmin = −0.24 e Å^−3
302 parameters	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.0039 (6)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983); 1439 Friedel pairs
Secondary atom site location: difference Fourier map	Absolute structure parameter: −0.07 (7)

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	0.43876 (4)	0.677475 (15)	0.47852 (10)	0.02199 (14)
O1	0.44420 (14)	0.68264 (4)	0.7440 (3)	0.0298 (4)
O2	0.53146 (12)	0.69058 (4)	0.3276 (3)	0.0273 (4)
O3	0.26251 (14)	0.58376 (5)	0.2702 (3)	0.0360 (4)
O4	0.34781 (14)	0.57133 (5)	−0.0963 (3)	0.0345 (4)
H40	0.290 (2)	0.5532 (9)	−0.110 (6)	0.060 (9)*
O5	0.82527 (14)	0.47725 (4)	0.8337 (3)	0.0304 (4)
O6	0.95282 (12)	0.45492 (4)	0.5520 (3)	0.0294 (4)
O7	0.09305 (15)	0.68765 (6)	0.8123 (4)	0.0580 (6)
O8	0.22750 (15)	0.64804 (5)	0.7149 (3)	0.0424 (5)
N1	0.42408 (17)	0.63207 (5)	0.4233 (3)	0.0230 (4)
H1N	0.371 (2)	0.6243 (7)	0.501 (5)	0.040 (8)*
N2	0.81842 (16)	0.49541 (5)	0.4267 (4)	0.0269 (5)
H2N	0.839 (2)	0.4895 (7)	0.276 (5)	0.032 (7)*
N3	0.17488 (17)	0.67823 (6)	0.6835 (4)	0.0363 (5)
C1	0.43581 (19)	0.61725 (6)	0.1663 (4)	0.0220 (5)
H1	0.4274	0.6394	0.0475	0.026*
C2	0.3387 (2)	0.58930 (6)	0.1230 (5)	0.0261 (5)
C3	0.55223 (18)	0.59877 (6)	0.1248 (4)	0.0241 (5)
H3A	0.5581	0.5902	−0.0514	0.029*
H3B	0.6119	0.6185	0.1538	0.029*
C4	0.57374 (19)	0.56441 (6)	0.2952 (4)	0.0275 (5)
H4A	0.5652	0.5729	0.4710	0.033*
H4B	0.5152	0.5445	0.2623	0.033*
C5	0.69042 (19)	0.54635 (6)	0.2627 (4)	0.0256 (5)
H5A	0.6970	0.5352	0.0927	0.031*
H5B	0.7496	0.5665	0.2815	0.031*
C6	0.70880 (18)	0.51500 (7)	0.4550 (5)	0.0290 (6)
H6A	0.7045	0.5265	0.6242	0.035*
H6B	0.6470	0.4957	0.4404	0.035*
C7	0.86202 (18)	0.47584 (6)	0.6171 (5)	0.0254 (5)
C8	0.31738 (19)	0.70416 (6)	0.3731 (4)	0.0249 (5)
C9	0.20813 (18)	0.70432 (7)	0.4782 (5)	0.0295 (5)
C10	0.1252 (2)	0.72941 (8)	0.3929 (6)	0.0447 (7)
H10	0.0516	0.7291	0.4659	0.054*
C11	0.1496 (3)	0.75489 (8)	0.2017 (6)	0.0537 (8)
H11	0.0929	0.7723	0.1435	0.064*
C12	0.2561 (3)	0.75510 (8)	0.0954 (5)	0.0492 (7)
H12	0.2725	0.7723	−0.0382	0.059*
C13	0.3390 (2)	0.73034 (6)	0.1824 (4)	0.0341 (6)
H13	0.4127	0.7312	0.1100	0.041*
C14	0.9993 (2)	0.43026 (7)	0.7471 (5)	0.0330 (6)
H14A	0.9370	0.4185	0.8453	0.040*
H14B	1.0474	0.4457	0.8618	0.040*
C15	1.06902 (18)	0.39928 (6)	0.6233 (4)	0.0256 (5)
C16	1.17252 (19)	0.38867 (6)	0.7264 (4)	0.0281 (5)
H16	1.2004	0.4021	0.8689	0.034*
C17	1.2359 (2)	0.35880 (7)	0.6246 (5)	0.0317 (6)
H17	1.3061	0.3515	0.6988	0.038*
C18	1.1968 (2)	0.33967 (7)	0.4152 (5)	0.0350 (6)
H18	1.2406	0.3194	0.3435	0.042*
C19	1.0939 (2)	0.34998 (7)	0.3097 (4)	0.0340 (6)
H19	1.0668	0.3366	0.1665	0.041*
C20	1.03010 (18)	0.37977 (7)	0.4121 (4)	0.0293 (6)
H20	0.9597	0.3869	0.3380	0.035*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
S1	0.0248 (3)	0.0211 (3)	0.0201 (3)	0.0001 (2)	−0.0005 (2)	0.0015 (2)
O1	0.0403 (9)	0.0300 (9)	0.0193 (8)	−0.0023 (8)	−0.0030 (8)	−0.0006 (7)
O2	0.0258 (8)	0.0265 (8)	0.0296 (9)	−0.0019 (7)	0.0020 (7)	0.0024 (7)
O3	0.0341 (9)	0.0370 (10)	0.0368 (10)	−0.0086 (8)	0.0043 (9)	−0.0038 (8)
O4	0.0327 (9)	0.0404 (10)	0.0303 (10)	−0.0036 (8)	−0.0036 (8)	−0.0103 (8)
O5	0.0320 (9)	0.0307 (9)	0.0285 (10)	0.0056 (7)	0.0067 (8)	0.0034 (7)
O6	0.0250 (8)	0.0324 (8)	0.0308 (9)	0.0086 (7)	0.0055 (8)	0.0068 (7)
O7	0.0385 (11)	0.0708 (14)	0.0648 (14)	−0.0056 (10)	0.0281 (10)	−0.0226 (11)
O8	0.0453 (11)	0.0405 (11)	0.0414 (11)	−0.0045 (9)	0.0156 (9)	0.0007 (9)
N1	0.0261 (10)	0.0238 (10)	0.0191 (10)	0.0010 (9)	0.0029 (9)	0.0030 (8)
N2	0.0253 (10)	0.0286 (11)	0.0267 (13)	0.0064 (9)	0.0037 (9)	0.0042 (10)
N3	0.0274 (11)	0.0430 (13)	0.0386 (13)	−0.0059 (11)	0.0075 (10)	−0.0188 (11)
C1	0.0287 (12)	0.0202 (11)	0.0171 (12)	0.0034 (10)	−0.0002 (10)	0.0018 (9)
C2	0.0269 (12)	0.0248 (12)	0.0267 (13)	0.0054 (10)	−0.0044 (11)	0.0000 (11)
C3	0.0245 (11)	0.0280 (12)	0.0199 (11)	−0.0005 (10)	0.0031 (11)	−0.0001 (10)
C4	0.0276 (12)	0.0282 (12)	0.0267 (12)	0.0039 (10)	0.0006 (11)	0.0025 (10)
C5	0.0266 (12)	0.0278 (12)	0.0225 (12)	0.0055 (10)	0.0020 (10)	−0.0011 (11)
C6	0.0225 (11)	0.0288 (12)	0.0358 (15)	0.0055 (10)	0.0028 (10)	0.0062 (12)
C7	0.0211 (11)	0.0202 (12)	0.0349 (15)	−0.0030 (9)	0.0048 (11)	0.0008 (11)
C8	0.0319 (13)	0.0226 (11)	0.0204 (12)	0.0041 (10)	−0.0015 (11)	−0.0056 (10)
C9	0.0296 (12)	0.0295 (12)	0.0296 (13)	0.0029 (10)	−0.0013 (11)	−0.0105 (11)
C10	0.0293 (14)	0.0488 (16)	0.0560 (19)	0.0134 (13)	−0.0055 (13)	−0.0257 (16)
C11	0.063 (2)	0.0445 (17)	0.054 (2)	0.0306 (15)	−0.0231 (16)	−0.0134 (15)
C12	0.077 (2)	0.0320 (14)	0.0390 (16)	0.0223 (15)	−0.0072 (15)	0.0022 (12)
C13	0.0493 (16)	0.0245 (12)	0.0285 (14)	0.0098 (12)	−0.0005 (12)	−0.0029 (11)
C14	0.0351 (13)	0.0346 (14)	0.0293 (14)	0.0118 (11)	0.0010 (11)	0.0052 (12)
C15	0.0239 (12)	0.0258 (11)	0.0270 (12)	−0.0011 (10)	0.0039 (11)	0.0055 (10)
C16	0.0278 (13)	0.0291 (12)	0.0274 (13)	0.0016 (11)	−0.0027 (11)	−0.0017 (11)
C17	0.0282 (12)	0.0345 (13)	0.0323 (13)	0.0088 (11)	−0.0032 (11)	−0.0030 (12)
C18	0.0340 (13)	0.0319 (13)	0.0392 (15)	0.0044 (11)	0.0031 (12)	−0.0075 (12)
C19	0.0368 (14)	0.0359 (14)	0.0293 (14)	−0.0055 (11)	−0.0010 (11)	−0.0054 (11)
C20	0.0229 (12)	0.0342 (13)	0.0308 (13)	0.0009 (10)	−0.0022 (11)	0.0060 (11)

Geometric parameters (Å, º)

S1—O2	1.4301 (15)	C5—H5A	0.99
S1—O1	1.4323 (15)	C5—H5B	0.99
S1—N1	1.6065 (18)	C6—H6A	0.99
S1—C8	1.791 (2)	C6—H6B	0.99
O3—C2	1.207 (3)	C8—C13	1.387 (3)
O4—C2	1.331 (3)	C8—C9	1.403 (3)
O4—H40	0.93 (3)	C9—C10	1.383 (3)
O5—C7	1.238 (3)	C10—C11	1.380 (4)
O6—C7	1.336 (3)	C10—H10	0.95
O6—C14	1.454 (3)	C11—C12	1.376 (4)
O7—N3	1.228 (3)	C11—H11	0.95
O8—N3	1.225 (3)	C12—C13	1.379 (4)
N1—C1	1.473 (3)	C12—H12	0.95
N1—H1N	0.80 (3)	C13—H13	0.95
N2—C7	1.326 (3)	C14—C15	1.503 (3)
N2—C6	1.464 (3)	C14—H14A	0.99
N2—H2N	0.87 (2)	C14—H14B	0.99
N3—C9	1.474 (3)	C15—C16	1.386 (3)
C1—C2	1.514 (3)	C15—C20	1.393 (3)
C1—C3	1.527 (3)	C16—C17	1.385 (3)
C1—H1	1.00	C16—H16	0.95
C3—C4	1.519 (3)	C17—C18	1.380 (3)
C3—H3A	0.99	C17—H17	0.95
C3—H3B	0.99	C18—C19	1.382 (3)
C4—C5	1.518 (3)	C18—H18	0.95
C4—H4A	0.99	C19—C20	1.387 (3)
C4—H4B	0.99	C19—H19	0.95
C5—C6	1.509 (3)	C20—H20	0.95
O2—S1—O1	119.06 (10)	C5—C6—H6B	109.0
O2—S1—N1	106.72 (10)	H6A—C6—H6B	107.8
O1—S1—N1	107.98 (9)	O5—C7—N2	124.3 (2)
O2—S1—C8	105.49 (10)	O5—C7—O6	123.0 (2)
O1—S1—C8	106.47 (10)	N2—C7—O6	112.7 (2)
N1—S1—C8	111.09 (10)	C13—C8—C9	117.4 (2)
C2—O4—H40	109.0 (18)	C13—C8—S1	114.92 (18)
C7—O6—C14	115.53 (17)	C9—C8—S1	127.33 (18)
C1—N1—S1	120.09 (15)	C10—C9—C8	121.1 (2)
C1—N1—H1N	116.2 (19)	C10—C9—N3	116.3 (2)
S1—N1—H1N	108.4 (18)	C8—C9—N3	122.6 (2)
C7—N2—C6	119.8 (2)	C11—C10—C9	119.9 (3)
C7—N2—H2N	119.2 (16)	C11—C10—H10	120.1
C6—N2—H2N	116.7 (17)	C9—C10—H10	120.1
O8—N3—O7	123.0 (2)	C12—C11—C10	119.9 (3)
O8—N3—C9	119.32 (19)	C12—C11—H11	120.0
O7—N3—C9	117.6 (2)	C10—C11—H11	120.0
N1—C1—C2	107.09 (18)	C11—C12—C13	120.1 (3)
N1—C1—C3	111.42 (17)	C11—C12—H12	119.9
C2—C1—C3	112.79 (17)	C13—C12—H12	119.9
N1—C1—H1	108.5	C12—C13—C8	121.6 (3)
C2—C1—H1	108.5	C12—C13—H13	119.2
C3—C1—H1	108.5	C8—C13—H13	119.2
O3—C2—O4	124.1 (2)	O6—C14—C15	107.89 (19)
O3—C2—C1	124.1 (2)	O6—C14—H14A	110.1
O4—C2—C1	111.8 (2)	C15—C14—H14A	110.1
C4—C3—C1	112.91 (17)	O6—C14—H14B	110.1
C4—C3—H3A	109.0	C15—C14—H14B	110.1
C1—C3—H3A	109.0	H14A—C14—H14B	108.4
C4—C3—H3B	109.0	C16—C15—C20	118.9 (2)
C1—C3—H3B	109.0	C16—C15—C14	119.5 (2)
H3A—C3—H3B	107.8	C20—C15—C14	121.5 (2)
C5—C4—C3	113.82 (18)	C17—C16—C15	120.9 (2)
C5—C4—H4A	108.8	C17—C16—H16	119.5
C3—C4—H4A	108.8	C15—C16—H16	119.5
C5—C4—H4B	108.8	C18—C17—C16	119.8 (2)
C3—C4—H4B	108.8	C18—C17—H17	120.1
H4A—C4—H4B	107.7	C16—C17—H17	120.1
C6—C5—C4	110.31 (18)	C17—C18—C19	120.0 (2)
C6—C5—H5A	109.6	C17—C18—H18	120.0
C4—C5—H5A	109.6	C19—C18—H18	120.0
C6—C5—H5B	109.6	C18—C19—C20	120.3 (2)
C4—C5—H5B	109.6	C18—C19—H19	119.9
H5A—C5—H5B	108.1	C20—C19—H19	119.9
N2—C6—C5	112.82 (19)	C19—C20—C15	120.1 (2)
N2—C6—H6A	109.0	C19—C20—H20	119.9
C5—C6—H6A	109.0	C15—C20—H20	119.9
N2—C6—H6B	109.0
O2—S1—N1—C1	−40.33 (19)	S1—C8—C9—C10	173.24 (19)
O1—S1—N1—C1	−169.43 (16)	C13—C8—C9—N3	−179.4 (2)
C8—S1—N1—C1	74.18 (19)	S1—C8—C9—N3	−6.7 (3)
S1—N1—C1—C2	−135.06 (16)	O8—N3—C9—C10	157.0 (2)
S1—N1—C1—C3	101.17 (18)	O7—N3—C9—C10	−21.4 (3)
N1—C1—C2—O3	5.7 (3)	O8—N3—C9—C8	−23.1 (3)
C3—C1—C2—O3	128.6 (2)	O7—N3—C9—C8	158.5 (2)
N1—C1—C2—O4	−173.85 (17)	C8—C9—C10—C11	−0.2 (4)
C3—C1—C2—O4	−50.9 (2)	N3—C9—C10—C11	179.8 (2)
N1—C1—C3—C4	61.1 (2)	C9—C10—C11—C12	0.4 (4)
C2—C1—C3—C4	−59.4 (2)	C10—C11—C12—C13	−1.1 (4)
C1—C3—C4—C5	−178.21 (18)	C11—C12—C13—C8	1.5 (4)
C3—C4—C5—C6	174.65 (19)	C9—C8—C13—C12	−1.3 (3)
C7—N2—C6—C5	160.1 (2)	S1—C8—C13—C12	−174.8 (2)
C4—C5—C6—N2	177.72 (19)	C7—O6—C14—C15	159.54 (18)
C6—N2—C7—O5	−11.2 (3)	O6—C14—C15—C16	138.4 (2)
C6—N2—C7—O6	170.50 (18)	O6—C14—C15—C20	−44.1 (3)
C14—O6—C7—O5	6.5 (3)	C20—C15—C16—C17	−1.0 (3)
C14—O6—C7—N2	−175.15 (19)	C14—C15—C16—C17	176.5 (2)
O2—S1—C8—C13	−0.69 (19)	C15—C16—C17—C18	1.1 (4)
O1—S1—C8—C13	126.71 (17)	C16—C17—C18—C19	−0.9 (4)
N1—S1—C8—C13	−115.97 (18)	C17—C18—C19—C20	0.6 (4)
O2—S1—C8—C9	−173.5 (2)	C18—C19—C20—C15	−0.5 (4)
O1—S1—C8—C9	−46.1 (2)	C16—C15—C20—C19	0.7 (3)
N1—S1—C8—C9	71.2 (2)	C14—C15—C20—C19	−176.7 (2)
C13—C8—C9—C10	0.6 (3)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
O4—H40···O5^i	0.93 (3)	1.75 (3)	2.666 (2)	172 (3)
N1—H1N···O3	0.80 (3)	2.26 (3)	2.659 (3)	111 (2)
N1—H1N···O8	0.80 (3)	2.19 (3)	2.843 (3)	138 (2)
N2—H2N···O5^ii	0.87 (2)	2.41 (3)	3.233 (3)	160 (2)
C1—H1···O1^ii	1.00	2.22	3.197 (3)	167
C11—H11···O1^iii	0.95	2.42	3.254 (4)	146

Symmetry codes: (i) −x+1, −y+1, z−1; (ii) x, y, z−1; (iii) x−1/2, −y+3/2, −z+1.