(S)-Benzyl 2-(6-methyl-2-pyridylamino­carbon­yl)pyrrolidine-1-carboxyl­ate

Kang, T.-R.; Ng, S.W.; He, L.

doi:10.1107/S1600536807036689

(S)-Benzyl 2-(6-methyl-2-pyridylaminocarbonyl)pyrrolidine-1-carboxylate

The molecules of the title compound, C₁₉H₂₁N₃O₃, are linked by a hydrogen bond between the amide NH group and the ester substituent in the 1-position of the pyrrolidine ring. This gives rise to a helical chain that propagates along the a axis of the orthorhombic cell by a 2₁ screw translation.

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Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807036689/im2028sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536807036689/im2028Isup2.hkl Contains datablock I

CCDC reference: 660316

checkCIF report

Key indicators

Single-crystal X-ray study
T = 153 K
Mean (C-C) = 0.003 Å
R factor = 0.032
wR factor = 0.092
Data-to-parameter ratio = 9.7

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT036_ALERT_1_A No s.u. Given for Flack Parameter ..............          ?

Author Response: Friedel pairs were merged.


Alert level C
PLAT066_ALERT_1_C Predicted and Reported Transmissions Identical .          ?
PLAT094_ALERT_2_C Ratio of Maximum / Minimum Residual Density ....       2.63
PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 =          3

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           27.48
           From the CIF: _reflns_number_total               2261
           Count of symmetry unique reflns         2266
           Completeness (_total/calc)             99.78%
           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 C8     = .          S
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          8

   1 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   3 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
   1 ALERT type 2 Indicator that the structure model may be wrong or deficient
   2 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

Comment top

A recent study of benzyl (S)-2-(5-methyl-2-pyridylaminocarbonyl)-pyrrolidine-1-carboxylate shows a hydrogen-bonded chain [N···O 2.927 (2) Å] that runs along b-axis [11.4256 (3) Å] of the orthorhombic unit cell. In the isomeric title compound, the molecules are linked by the corresponding amido-carbonyl hydrogen bond [N···O 3.036 (2) Å] into a helical chain that runs along the a-axis of the orthorhombic cell. The mode of propagation differs between the two, as noted from the pitch of the helix.

Related literature top

For benzyl (S)-2-(5-methyl-2-pyridylaminocarbonyl)-pyrrolidine-2-carboxylate, see He (2006).

For related literature, see: Flack (1983).

Experimental top

The procedure for synthesizing benzyl (S)-2-(5-methyl-2-pyridylaminocarbonyl)-pyrrolidine-1-carboxylate (He, 2006) was used, with 6-methylpyridyl-2-amine in place of 5-methylpyridyl-2-amine. Crystals were grown from an ethanolic solution of the compound.

Structure description top

For benzyl (S)-2-(5-methyl-2-pyridylaminocarbonyl)-pyrrolidine-2-carboxylate, see He (2006).

For related literature, see: Flack (1983).

Computing details top

Data collection: RAPID-AUTO (Rigaku, 1998); cell refinement: RAPID-AUTO; data reduction: CrystalStructure (Rigaku/MSC, 2002); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: X-SEED (Barbour, 2001); software used to prepare material for publication: publCIF (Westrip, 2007).

Figures top

Fig. 1. Thermal ellipsoid plot of C₁₉H₂₁N₃O₃. Displacement ellipsoids are drawn at the 70% probability level, H atoms are drawn as spheres of arbitrary radiui.

(S)-Benzyl 2-(6-methyl-2-pyridylaminocarbonyl)pyrrolidine-1-carboxylate top

Crystal data top

C₁₉H₂₁N₃O₃	F(000) = 720
M_r = 339.39	D_x = 1.309 Mg m⁻³
Orthorhombic, P2₁2₁2₁	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 16166 reflections
a = 6.9065 (1) Å	θ = 3.2–27.5°
b = 15.7480 (4) Å	µ = 0.09 mm⁻¹
c = 15.8380 (4) Å	T = 153 K
V = 1722.60 (7) Å³	Block, colorless
Z = 4	0.45 × 0.44 × 0.22 mm

Data collection top

Rigaku R-AXIS RAPID IP diffractometer	2261 independent reflections
Radiation source: rotating anode tube	2207 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.019
ω scans	θ_max = 27.5°, θ_min = 3.2°
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	h = −8→8
T_min = 0.961, T_max = 0.981	k = −20→20
16810 measured reflections	l = −20→20

Refinement top

Refinement on F²	Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: full	H atoms treated by a mixture of independent and constrained refinement
R[F² > 2σ(F²)] = 0.032	w = 1/[σ²(F_o²) + (0.0611P)² + 0.4025P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.092	(Δ/σ)_max = 0.001
S = 1.04	Δρ_max = 0.53 e Å⁻³
2261 reflections	Δρ_min = −0.20 e Å⁻³
232 parameters	Extinction correction: SHELXL97, Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
8 restraints	Extinction coefficient: 0.033 (3)
Primary atom site location: structure-invariant direct methods	Absolute structure: Friedel pairs were merged
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0

Crystal data top

C₁₉H₂₁N₃O₃	V = 1722.60 (7) Å³
M_r = 339.39	Z = 4
Orthorhombic, P2₁2₁2₁	Mo Kα radiation
a = 6.9065 (1) Å	µ = 0.09 mm⁻¹
b = 15.7480 (4) Å	T = 153 K
c = 15.8380 (4) Å	0.45 × 0.44 × 0.22 mm

Data collection top

Rigaku R-AXIS RAPID IP diffractometer	2261 independent reflections
Absorption correction: multi-scan (ABSCOR; Higashi, 1995)	2207 reflections with I > 2σ(I)
T_min = 0.961, T_max = 0.981	R_int = 0.019
16810 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.032	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.092	Δρ_max = 0.53 e Å⁻³
S = 1.04	Δρ_min = −0.20 e Å⁻³
2261 reflections	Absolute structure: Friedel pairs were merged
232 parameters	Absolute structure parameter: 0
8 restraints

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.9391 (2)	0.09533 (8)	0.58395 (7)	0.0265 (3)
O2	0.91177 (19)	0.29212 (8)	0.61477 (7)	0.0234 (3)
O3	1.00096 (19)	0.27940 (8)	0.75267 (7)	0.0226 (3)
N1	0.9295 (2)	0.09490 (8)	0.31762 (8)	0.0196 (3)
N2	1.0429 (2)	0.12574 (9)	0.44994 (8)	0.0198 (3)
H2	1.134 (3)	0.1534 (12)	0.4225 (13)	0.032 (6)*
N3	1.1779 (2)	0.21679 (9)	0.65344 (8)	0.0196 (3)
C1	0.8381 (3)	0.07319 (13)	0.17138 (10)	0.0289 (4)
H1A	0.9745	0.0672	0.1554	0.043*
H1B	0.7958	0.1317	0.1611	0.043*
H1C	0.7592	0.0342	0.1376	0.043*
C2	0.8148 (2)	0.05246 (10)	0.26361 (10)	0.0215 (3)
C3	0.6786 (3)	−0.00678 (11)	0.29092 (11)	0.0254 (4)
H3	0.6003	−0.0365	0.2515	0.030*
C4	0.6600 (3)	−0.02138 (11)	0.37685 (12)	0.0277 (4)
H4	0.5674	−0.0612	0.3969	0.033*
C5	0.7765 (3)	0.02218 (11)	0.43353 (10)	0.0245 (4)
H5	0.7653	0.0134	0.4927	0.029*
C6	0.9107 (2)	0.07922 (9)	0.40043 (10)	0.0188 (3)
C7	1.0491 (2)	0.13158 (9)	0.53608 (9)	0.0183 (3)
C8	1.2178 (2)	0.18583 (10)	0.56818 (9)	0.0183 (3)
H8	1.2434	0.2343	0.5289	0.022*
C9	1.4007 (3)	0.13120 (11)	0.57953 (11)	0.0249 (4)
H9A	1.3667	0.0703	0.5837	0.030*
H9B	1.4907	0.1392	0.5315	0.030*
C10	1.4912 (3)	0.16248 (13)	0.66126 (11)	0.0301 (4)
H10A	1.5743	0.2127	0.6511	0.036*
H10B	1.5698	0.1174	0.6881	0.036*
C11	1.3167 (3)	0.18557 (11)	0.71607 (10)	0.0239 (4)
H11A	1.2658	0.1353	0.7463	0.029*
H11B	1.3499	0.2302	0.7576	0.029*
C12	1.0218 (2)	0.26492 (10)	0.66888 (9)	0.0181 (3)
C13	0.8416 (3)	0.33562 (11)	0.77456 (10)	0.0251 (4)
H13A	0.7232	0.3188	0.7436	0.030*
H13B	0.8739	0.3949	0.7591	0.030*
C14	0.8084 (2)	0.32899 (10)	0.86799 (10)	0.0193 (3)
C15	0.7404 (3)	0.25312 (11)	0.90256 (11)	0.0242 (3)
H15	0.7205	0.2052	0.8671	0.029*
C16	0.7017 (3)	0.24711 (14)	0.98825 (12)	0.0309 (4)
H16	0.6578	0.1950	1.0116	0.037*
C17	0.7273 (3)	0.31743 (15)	1.03973 (11)	0.0344 (5)
H17	0.6986	0.3136	1.0983	0.041*
C18	0.7942 (3)	0.39275 (13)	1.00651 (12)	0.0322 (4)
H18	0.8111	0.4408	1.0420	0.039*
C19	0.8372 (3)	0.39844 (11)	0.92059 (11)	0.0250 (3)
H19	0.8863	0.4500	0.8980	0.030*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0286 (6)	0.0308 (6)	0.0200 (5)	−0.0078 (6)	0.0056 (5)	0.0008 (5)
O2	0.0228 (6)	0.0309 (6)	0.0167 (5)	0.0053 (5)	−0.0015 (5)	0.0009 (4)
O3	0.0220 (5)	0.0312 (6)	0.0145 (5)	0.0091 (5)	−0.0007 (4)	−0.0024 (4)
N1	0.0188 (6)	0.0221 (6)	0.0179 (6)	−0.0021 (6)	−0.0003 (5)	−0.0033 (5)
N2	0.0201 (7)	0.0229 (6)	0.0163 (6)	−0.0061 (5)	0.0015 (5)	0.0002 (5)
N3	0.0199 (7)	0.0260 (6)	0.0129 (5)	0.0038 (6)	−0.0018 (5)	−0.0020 (5)
C1	0.0268 (9)	0.0396 (9)	0.0204 (7)	−0.0062 (8)	−0.0010 (7)	−0.0081 (7)
C2	0.0170 (7)	0.0251 (7)	0.0224 (7)	0.0008 (7)	−0.0003 (6)	−0.0068 (6)
C3	0.0204 (8)	0.0257 (7)	0.0299 (8)	−0.0041 (7)	−0.0022 (7)	−0.0079 (7)
C4	0.0224 (9)	0.0256 (8)	0.0352 (9)	−0.0076 (7)	0.0029 (7)	−0.0013 (7)
C5	0.0246 (8)	0.0258 (8)	0.0230 (7)	−0.0052 (7)	0.0016 (7)	0.0011 (7)
C6	0.0176 (7)	0.0181 (6)	0.0207 (7)	0.0001 (6)	0.0006 (6)	−0.0024 (5)
C7	0.0198 (8)	0.0178 (6)	0.0174 (7)	0.0007 (6)	0.0002 (6)	0.0009 (5)
C8	0.0197 (7)	0.0221 (7)	0.0131 (6)	−0.0003 (6)	0.0007 (6)	−0.0016 (5)
C9	0.0206 (8)	0.0313 (8)	0.0227 (7)	0.0052 (7)	0.0012 (7)	−0.0030 (7)
C10	0.0258 (9)	0.0345 (9)	0.0301 (9)	0.0048 (8)	−0.0021 (8)	−0.0008 (7)
C11	0.0250 (8)	0.0313 (8)	0.0155 (7)	0.0069 (7)	−0.0044 (7)	0.0004 (6)
C12	0.0185 (7)	0.0209 (6)	0.0150 (6)	−0.0008 (6)	−0.0001 (6)	−0.0004 (5)
C13	0.0247 (8)	0.0308 (8)	0.0198 (7)	0.0110 (7)	0.0020 (7)	0.0008 (6)
C14	0.0141 (7)	0.0247 (7)	0.0189 (7)	0.0043 (6)	−0.0004 (6)	−0.0013 (6)
C15	0.0215 (8)	0.0259 (8)	0.0252 (8)	−0.0020 (7)	−0.0026 (7)	−0.0033 (6)
C16	0.0215 (8)	0.0409 (9)	0.0302 (9)	−0.0044 (8)	0.0016 (7)	0.0095 (8)
C17	0.0240 (9)	0.0612 (13)	0.0180 (8)	0.0038 (9)	0.0023 (7)	−0.0025 (8)
C18	0.0266 (9)	0.0422 (10)	0.0277 (8)	0.0050 (8)	−0.0014 (8)	−0.0162 (8)
C19	0.0212 (8)	0.0235 (7)	0.0302 (8)	0.0010 (7)	0.0009 (7)	−0.0044 (7)

Geometric parameters (Å, º) top

O1—C7	1.216 (2)	C8—C9	1.539 (2)
O2—C12	1.223 (2)	C8—H8	1.0000
O3—C12	1.3541 (18)	C9—C10	1.520 (2)
O3—C13	1.455 (2)	C9—H9A	0.9900
N1—C6	1.341 (2)	C9—H9B	0.9900
N1—C2	1.344 (2)	C10—C11	1.530 (2)
N2—C7	1.3682 (19)	C10—H10A	0.9900
N2—C6	1.409 (2)	C10—H10B	0.9900
N2—H2	0.880 (10)	C11—H11A	0.9900
N3—C12	1.341 (2)	C11—H11B	0.9900
N3—C8	1.4618 (18)	C13—C14	1.501 (2)
N3—C11	1.4642 (19)	C13—H13A	0.9900
C1—C2	1.505 (2)	C13—H13B	0.9900
C1—H1A	0.9800	C14—C19	1.389 (2)
C1—H1B	0.9800	C14—C15	1.396 (2)
C1—H1C	0.9800	C15—C16	1.386 (2)
C2—C3	1.393 (2)	C15—H15	0.9500
C3—C4	1.386 (2)	C16—C17	1.387 (3)
C3—H3	0.9500	C16—H16	0.9500
C4—C5	1.387 (2)	C17—C18	1.377 (3)
C4—H4	0.9500	C17—H17	0.9500
C5—C6	1.393 (2)	C18—C19	1.396 (2)
C5—H5	0.9500	C18—H18	0.9500
C7—C8	1.531 (2)	C19—H19	0.9500

C12—O3—C13	114.62 (13)	C8—C9—H9B	110.8
C6—N1—C2	118.28 (14)	H9A—C9—H9B	108.9
C7—N2—C6	127.62 (14)	C9—C10—C11	103.66 (14)
C7—N2—H2	115.9 (15)	C9—C10—H10A	111.0
C6—N2—H2	116.4 (15)	C11—C10—H10A	111.0
C12—N3—C8	120.57 (13)	C9—C10—H10B	111.0
C12—N3—C11	126.34 (13)	C11—C10—H10B	111.0
C8—N3—C11	112.99 (13)	H10A—C10—H10B	109.0
C2—C1—H1A	109.5	N3—C11—C10	102.19 (13)
C2—C1—H1B	109.5	N3—C11—H11A	111.3
H1A—C1—H1B	109.5	C10—C11—H11A	111.3
C2—C1—H1C	109.5	N3—C11—H11B	111.3
H1A—C1—H1C	109.5	C10—C11—H11B	111.3
H1B—C1—H1C	109.5	H11A—C11—H11B	109.2
N1—C2—C3	122.23 (15)	O2—C12—N3	124.75 (14)
N1—C2—C1	116.52 (15)	O2—C12—O3	124.17 (15)
C3—C2—C1	121.24 (15)	N3—C12—O3	111.08 (13)
C4—C3—C2	118.59 (16)	O3—C13—C14	107.95 (13)
C4—C3—H3	120.7	O3—C13—H13A	110.1
C2—C3—H3	120.7	C14—C13—H13A	110.1
C3—C4—C5	119.96 (17)	O3—C13—H13B	110.1
C3—C4—H4	120.0	C14—C13—H13B	110.1
C5—C4—H4	120.0	H13A—C13—H13B	108.4
C4—C5—C6	117.47 (16)	C19—C14—C15	119.13 (15)
C4—C5—H5	121.3	C19—C14—C13	120.97 (16)
C6—C5—H5	121.3	C15—C14—C13	119.85 (15)
N1—C6—C5	123.45 (15)	C16—C15—C14	120.49 (17)
N1—C6—N2	112.70 (14)	C16—C15—H15	119.8
C5—C6—N2	123.84 (14)	C14—C15—H15	119.8
O1—C7—N2	124.79 (15)	C15—C16—C17	119.77 (19)
O1—C7—C8	122.04 (14)	C15—C16—H16	120.1
N2—C7—C8	113.10 (14)	C17—C16—H16	120.1
N3—C8—C7	110.45 (13)	C18—C17—C16	120.39 (16)
N3—C8—C9	103.48 (12)	C18—C17—H17	119.8
C7—C8—C9	110.57 (13)	C16—C17—H17	119.8
N3—C8—H8	110.7	C17—C18—C19	119.94 (17)
C7—C8—H8	110.7	C17—C18—H18	120.0
C9—C8—H8	110.7	C19—C18—H18	120.0
C10—C9—C8	104.84 (13)	C14—C19—C18	120.25 (16)
C10—C9—H9A	110.8	C14—C19—H19	119.9
C8—C9—H9A	110.8	C18—C19—H19	119.9
C10—C9—H9B	110.8

C6—N1—C2—C3	−0.1 (2)	C7—C8—C9—C10	−139.34 (14)
C6—N1—C2—C1	178.90 (15)	C8—C9—C10—C11	34.49 (18)
N1—C2—C3—C4	0.8 (3)	C12—N3—C11—C10	−161.55 (16)
C1—C2—C3—C4	−178.13 (17)	C8—N3—C11—C10	21.96 (18)
C2—C3—C4—C5	−0.5 (3)	C9—C10—C11—N3	−33.99 (18)
C3—C4—C5—C6	−0.5 (3)	C8—N3—C12—O2	−6.1 (2)
C2—N1—C6—C5	−1.0 (2)	C11—N3—C12—O2	177.70 (16)
C2—N1—C6—N2	178.20 (14)	C8—N3—C12—O3	173.69 (14)
C4—C5—C6—N1	1.3 (3)	C11—N3—C12—O3	−2.6 (2)
C4—C5—C6—N2	−177.80 (16)	C13—O3—C12—O2	−3.9 (2)
C7—N2—C6—N1	172.46 (15)	C13—O3—C12—N3	176.36 (14)
C7—N2—C6—C5	−8.4 (3)	C12—O3—C13—C14	166.87 (14)
C6—N2—C7—O1	1.0 (3)	O3—C13—C14—C19	115.82 (17)
C6—N2—C7—C8	178.08 (14)	O3—C13—C14—C15	−66.7 (2)
C12—N3—C8—C7	−59.16 (18)	C19—C14—C15—C16	0.1 (3)
C11—N3—C8—C7	117.55 (15)	C13—C14—C15—C16	−177.40 (17)
C12—N3—C8—C9	−177.53 (14)	C14—C15—C16—C17	1.2 (3)
C11—N3—C8—C9	−0.81 (18)	C15—C16—C17—C18	−1.1 (3)
O1—C7—C8—N3	−24.6 (2)	C16—C17—C18—C19	−0.2 (3)
N2—C7—C8—N3	158.28 (13)	C15—C14—C19—C18	−1.5 (3)
O1—C7—C8—C9	89.38 (19)	C13—C14—C19—C18	176.02 (17)
N2—C7—C8—C9	−87.78 (16)	C17—C18—C19—C14	1.5 (3)
N3—C8—C9—C10	−21.06 (17)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2···O2ⁱ	0.88 (1)	2.18 (1)	3.036 (2)	163 (2)

Symmetry code: (i) x+1/2, −y+1/2, −z+1.

Experimental details

Crystal data
Chemical formula	C₁₉H₂₁N₃O₃
M_r	339.39
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	153
a, b, c (Å)	6.9065 (1), 15.7480 (4), 15.8380 (4)
V (Å³)	1722.60 (7)
Z	4
Radiation type	Mo Kα
µ (mm⁻¹)	0.09
Crystal size (mm)	0.45 × 0.44 × 0.22

Data collection
Diffractometer	Rigaku R-AXIS RAPID IP
Absorption correction	Multi-scan (ABSCOR; Higashi, 1995)
T_min, T_max	0.961, 0.981
No. of measured, independent and observed [I > 2σ(I)] reflections	16810, 2261, 2207
R_int	0.019
(sin θ/λ)_max (Å⁻¹)	0.649

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.032, 0.092, 1.04
No. of reflections	2261
No. of parameters	232
No. of restraints	8
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.53, −0.20
Absolute structure	Friedel pairs were merged
Absolute structure parameter	0

Computer programs: RAPID-AUTO (Rigaku, 1998), RAPID-AUTO, CrystalStructure (Rigaku/MSC, 2002), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), X-SEED (Barbour, 2001), publCIF (Westrip, 2007).