Methyl 2(S)-(N-fluoren-9-yl­methoxy­carbonyl­amino)-3-(2-pyridyl)­propionate

The title compound, C₂₄H₂₂N₂O₄, is a methyl ester of a 2-pyridyl­alanine in which the amine group is protected. The mol­ecule has four essentially planar segments. Apart from a relatively weak N—H...O hydrogen bond, mol­ecules are held together in the solid state only by van der Waals interactions.

Key indicators

• Single-crystal X-ray study
• T = 173 K
• Mean [sigma](C-C) = 0.007 Å
• R factor = 0.052
• wR factor = 0.090
• Data-to-parameter ratio = 6.8

checkCIF/PLATON results

No syntax errors found



Alert level A
PLAT029_ALERT_3_A _diffrn_measured_fraction_theta_full Low .....       0.92

Alert level B
RINTA01_ALERT_3_B  The value of Rint is greater than 0.15
            Rint given   0.158
PLAT020_ALERT_3_B The value of Rint is greater than 0.10 .......       0.16

Alert level C
GOODF01_ALERT_2_C  The least squares goodness of fit parameter lies
            outside the range 0.80 <> 2.00
            Goodness of fit given =      0.797
REFLT03_ALERT_1_C  Reflection count < 95% complete
           From the CIF: _diffrn_reflns_theta_max           25.00
           From the CIF: _diffrn_reflns_theta_full           0.00
           From the CIF: _reflns_number_total               1863
           TEST2: Reflns within _diffrn_reflns_theta_max
           Count of symmetry unique reflns         2023
           Completeness (_total/calc)             92.09%
REFNR01_ALERT_3_C  Ratio of reflections to parameters is < 8 for a
            non-centrosymmetric structure, where ZMAX < 18
            sine(theta)/lambda               -0.1862
            Proportion of unique data used    1.0000
            Ratio reflections to parameters   6.8242
PLAT022_ALERT_3_C Ratio Unique / Expected Reflections too Low ..       0.92
PLAT089_ALERT_3_C Poor Data / Parameter Ratio (Zmax .LT. 18) ...       6.82
PLAT125_ALERT_4_C No _symmetry_space_group_name_Hall Given .....          ?
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang..          7

Alert level G
REFLT03_ALERT_1_G ALERT: Expected hkl max differ from CIF values
           From the CIF: _diffrn_reflns_theta_max           25.00
           From the CIF: _reflns_number_total               1863
           From the CIF: _diffrn_reflns_limit_ max hkl    6.   15.   28.
           From the CIF: _diffrn_reflns_limit_ min hkl   -6.  -11.  -28.
           TEST1: Expected hkl limits for theta max
           Calculated maximum hkl    6.   17.   28.
           Calculated minimum hkl   -6.  -17.  -28.
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           25.00
           From the CIF: _reflns_number_total               1863
           Count of symmetry unique reflns         2023
           Completeness (_total/calc)             92.09%
           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

   1 ALERT level A = In general: serious problem
   2 ALERT level B = Potentially serious problem
   7 ALERT level C = Check and explain
   2 ALERT level G = General alerts; check

   2 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
   7 ALERT type 3 Indicator that the structure quality may be low
   2 ALERT type 4 Improvement, methodology, query or suggestion

---

S1. Comment

The title compound, (I), was prepared in a study of the preparation of enantiomerically pure pyridylamino acids (Tabanella et al., 2003). It was obtained from a palladium-catalysed coupling reaction of 2-bromopyridine with a fluorenylmethyoxycarbonyl-protected (Fmoc-protected) zinc reagent derived from iodoalanine methyl ester. Its structure was determined in order to confirm the identity of the product and to establish the nature of any inter- or intramolecular hydrogen bonding.

The molecule consists of four planar segments (Fig. 1), viz. the fluorene group, the ester and amine linkage from C7 to C11, the methyl ester attached to C7, and the pyridylmethyl group. The main torsion angles defining the conformational arrangement of these segments are given in Table 1. Bond lengths and angles are unexceptional.

Only one, relatively weak, intermolecular hydrogen bond is found, linking the single donor, the N—H group, with atom O2 of an adjacent molecule, with an N···O distance of 3.214 (5) Å and an angle of 142° at the H atom. Neither of the carbonyl O atoms acts as a hydrogen-bond acceptor.

Although complexes with deprotonated β-(2-pyridyl)-α-alanine as a ligand have been crystallographically characterized (Ebner et al., 1979, 1980; Ebner & Angelici, 1981), no crystal structures have been reported for the amino acid itself or for protected derivatives.

S2. Experimental

The synthesis of the title compound is described by Tabanella et al. (2003).

S3. Refinement

H atoms were positioned geometrically and refined with a riding model (including free rotation about C—C bonds), and with U_iso constrained to be 1.2 (1.5 for methyl groups) times U_eq of the carrier atom. In the absence of significant anomalous scattering effects, the absolute configuration could not be confirmed from the diffraction data; it was assumed from the known configuration of the starting material, and Friedel pairs were merged.

Computing details

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXTL (Sheldrick, 2001); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL and local programs.

Figures

Fig. 1. The molecular structure with atom labels and 50% probability ellipsoids for non-H atoms.

Methyl 2(S)-(N-fluoren-9-ylmethoxycarbonylamino)-3-(2-pyridyl)propionate

Crystal data

C24H22N2O4	Dx = 1.371 Mg m^−3
Mr = 402.44	Mo Kα radiation, λ = 0.71073 Å
Orthorhombic, P212121	Cell parameters from 2523 reflections
a = 5.524 (4) Å	θ = 2.2–25.8°
b = 14.988 (11) Å	µ = 0.09 mm^−1
c = 23.557 (18) Å	T = 173 K
V = 1950 (3) Å^3	Needle, colourless
Z = 4	0.48 × 0.09 × 0.06 mm
F(000) = 848

Data collection

Bruker SMART 1K CCD diffractometer	1042 reflections with I > 2σ(I)
Radiation source: sealed tube	Rint = 0.158
Graphite monochromator	θmax = 25.0°, θmin = 1.7°
Detector resolution: 8.192 pixels mm^-1	h = −6→6
narrow–frame ω scans	k = −11→15
6519 measured reflections	l = −28→28
1863 independent reflections

Refinement

Refinement on F^2	Secondary atom site location: difference Fourier map
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F^2 > 2σ(F^2)] = 0.052	H-atom parameters constrained
wR(F^2) = 0.090	w = 1/[σ^2(Fo^2) + (0.0258P)^2] where P = (Fo^2 + 2Fc^2)/3
S = 0.80	(Δ/σ)max < 0.001
1863 reflections	Δρmax = 0.19 e Å^−3
273 parameters	Δρmin = −0.23 e Å^−3
0 restraints	Extinction correction: SHELXTL, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
Primary atom site location: structure-invariant direct methods	Extinction coefficient: 0.0073 (12)

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
C1	0.3623 (8)	0.5721 (4)	0.5524 (2)	0.0315 (14)
N1	0.4492 (8)	0.6179 (3)	0.50819 (16)	0.0370 (12)
C2	0.6059 (10)	0.6832 (4)	0.5197 (2)	0.0479 (16)
H2	0.6654	0.7176	0.4888	0.058*
C3	0.6875 (9)	0.7044 (4)	0.5736 (2)	0.0466 (16)
H3	0.8014	0.7509	0.5797	0.056*
C4	0.5957 (10)	0.6547 (4)	0.6180 (2)	0.0525 (18)
H4	0.6437	0.6671	0.6559	0.063*
C5	0.4364 (9)	0.5880 (4)	0.6069 (2)	0.0435 (16)
H5	0.3761	0.5523	0.6371	0.052*
C6	0.1889 (8)	0.4990 (4)	0.53975 (17)	0.0330 (14)
H6A	0.0228	0.5237	0.5411	0.040*
H6B	0.2016	0.4536	0.5701	0.040*
C7	0.2238 (8)	0.4524 (3)	0.48228 (19)	0.0334 (14)
H7	0.1217	0.3973	0.4837	0.040*
C8	0.1370 (8)	0.5049 (4)	0.4303 (2)	0.0310 (14)
O1	0.2444 (6)	0.5094 (3)	0.38623 (13)	0.0479 (11)
O2	−0.0756 (5)	0.5433 (2)	0.43985 (12)	0.0369 (10)
C9	−0.1820 (8)	0.5855 (4)	0.39104 (19)	0.0436 (15)
H9A	−0.2013	0.5415	0.3606	0.065*
H9B	−0.0766	0.6339	0.3780	0.065*
H9C	−0.3408	0.6099	0.4013	0.065*
N2	0.4662 (6)	0.4224 (3)	0.47369 (14)	0.0295 (11)
H2N	0.5880	0.4576	0.4826	0.035*
C10	0.5101 (9)	0.3413 (4)	0.45225 (18)	0.0274 (14)
O3	0.3698 (6)	0.2803 (3)	0.44961 (13)	0.0363 (10)
O4	0.7398 (5)	0.3359 (2)	0.43328 (12)	0.0320 (9)
C11	0.8216 (8)	0.2504 (3)	0.41180 (18)	0.0325 (15)
H11A	0.6871	0.2068	0.4130	0.039*
H11B	0.9551	0.2275	0.4358	0.039*
C12	0.9088 (8)	0.2619 (3)	0.35102 (17)	0.0274 (14)
H12	1.0297	0.3115	0.3491	0.033*
C13	0.7100 (9)	0.2773 (4)	0.30720 (19)	0.0309 (14)
C14	0.7130 (8)	0.2090 (4)	0.26681 (19)	0.0302 (14)
C15	0.5458 (9)	0.2071 (4)	0.22334 (19)	0.0389 (16)
H15	0.5476	0.1601	0.1963	0.047*
C16	0.3776 (10)	0.2737 (4)	0.2197 (2)	0.0447 (16)
H16	0.2623	0.2732	0.1898	0.054*
C17	0.3740 (9)	0.3424 (4)	0.2596 (2)	0.0419 (16)
H17	0.2562	0.3882	0.2561	0.050*
C18	0.5392 (9)	0.3457 (4)	0.3046 (2)	0.0365 (15)
H18	0.5352	0.3922	0.3320	0.044*
C19	1.0234 (8)	0.1756 (3)	0.32964 (18)	0.0264 (13)
C20	0.9025 (8)	0.1454 (4)	0.2814 (2)	0.0301 (13)
C21	0.9781 (9)	0.0691 (4)	0.25342 (19)	0.0371 (15)
H21	0.8979	0.0494	0.2200	0.045*
C22	1.1738 (9)	0.0221 (4)	0.2752 (2)	0.0459 (16)
H22	1.2251	−0.0317	0.2576	0.055*
C23	1.2932 (9)	0.0534 (4)	0.3225 (2)	0.0436 (16)
H23	1.4323	0.0225	0.3358	0.052*
C24	1.2155 (8)	0.1289 (3)	0.35116 (19)	0.0323 (14)
H24	1.2939	0.1479	0.3850	0.039*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.021 (3)	0.035 (4)	0.039 (3)	0.006 (3)	−0.002 (2)	−0.007 (3)
N1	0.042 (3)	0.028 (4)	0.041 (2)	−0.006 (2)	−0.003 (2)	0.002 (3)
C2	0.043 (3)	0.044 (5)	0.057 (4)	−0.008 (3)	−0.002 (3)	0.004 (4)
C3	0.029 (3)	0.049 (5)	0.062 (4)	−0.005 (3)	−0.007 (3)	−0.020 (4)
C4	0.035 (3)	0.086 (6)	0.036 (3)	−0.011 (4)	0.001 (3)	−0.018 (4)
C5	0.033 (3)	0.061 (5)	0.036 (3)	−0.011 (3)	0.001 (3)	−0.007 (3)
C6	0.029 (3)	0.042 (4)	0.028 (2)	0.004 (3)	0.004 (2)	0.004 (3)
C7	0.024 (3)	0.036 (4)	0.040 (3)	0.006 (3)	0.008 (3)	−0.008 (3)
C8	0.019 (3)	0.037 (4)	0.037 (3)	−0.002 (3)	−0.002 (3)	−0.009 (3)
O1	0.028 (2)	0.085 (3)	0.0312 (18)	−0.001 (2)	0.0046 (19)	−0.001 (2)
O2	0.0220 (19)	0.051 (3)	0.0376 (19)	0.0104 (18)	0.0038 (17)	0.002 (2)
C9	0.025 (3)	0.060 (4)	0.046 (3)	0.007 (3)	−0.011 (3)	0.002 (3)
N2	0.021 (2)	0.026 (3)	0.041 (2)	0.003 (2)	−0.002 (2)	−0.014 (2)
C10	0.024 (3)	0.036 (5)	0.022 (3)	0.000 (3)	0.003 (2)	−0.003 (3)
O3	0.0234 (19)	0.034 (3)	0.051 (2)	−0.0078 (19)	0.0073 (17)	−0.009 (2)
O4	0.0190 (18)	0.039 (3)	0.0381 (17)	0.0017 (19)	0.0068 (16)	−0.0047 (19)
C11	0.022 (3)	0.040 (4)	0.036 (3)	0.004 (3)	0.001 (2)	−0.004 (3)
C12	0.019 (3)	0.028 (4)	0.035 (3)	−0.008 (3)	0.008 (2)	−0.007 (3)
C13	0.025 (3)	0.036 (4)	0.032 (3)	−0.011 (3)	0.009 (2)	−0.001 (3)
C14	0.028 (3)	0.034 (4)	0.028 (3)	−0.011 (3)	0.005 (2)	0.006 (3)
C15	0.035 (3)	0.053 (5)	0.028 (3)	−0.013 (3)	0.000 (3)	0.003 (3)
C16	0.033 (3)	0.055 (5)	0.046 (3)	−0.005 (3)	−0.009 (3)	0.012 (4)
C17	0.024 (3)	0.051 (5)	0.050 (3)	−0.001 (3)	0.001 (3)	0.024 (4)
C18	0.030 (3)	0.039 (4)	0.040 (3)	−0.001 (3)	0.011 (3)	0.006 (3)
C19	0.016 (3)	0.032 (4)	0.031 (3)	−0.005 (3)	0.001 (2)	0.001 (3)
C20	0.024 (3)	0.032 (4)	0.034 (3)	−0.006 (3)	0.001 (2)	−0.003 (3)
C21	0.033 (3)	0.048 (5)	0.030 (3)	−0.007 (3)	0.000 (3)	−0.006 (3)
C22	0.041 (4)	0.057 (5)	0.039 (3)	0.003 (3)	0.007 (3)	−0.008 (3)
C23	0.024 (3)	0.056 (5)	0.050 (3)	0.009 (3)	0.003 (3)	−0.003 (3)
C24	0.023 (3)	0.042 (4)	0.031 (3)	−0.005 (3)	−0.002 (2)	0.004 (3)

Geometric parameters (Å, º)

C1—N1	1.338 (6)	C11—H11A	0.990
C1—C5	1.368 (6)	C11—H11B	0.990
C1—C6	1.485 (7)	C11—C12	1.521 (6)
N1—C2	1.334 (6)	C12—H12	1.000
C2—H2	0.950	C12—C13	1.525 (6)
C2—C3	1.383 (6)	C12—C19	1.525 (6)
C3—H3	0.950	C13—C14	1.398 (6)
C3—C4	1.381 (7)	C13—C18	1.394 (6)
C4—H4	0.950	C14—C15	1.379 (6)
C4—C5	1.357 (7)	C14—C20	1.457 (6)
C5—H5	0.950	C15—H15	0.950
C6—H6A	0.990	C15—C16	1.366 (7)
C6—H6B	0.990	C16—H16	0.950
C6—C7	1.536 (6)	C16—C17	1.394 (7)
C7—H7	1.000	C17—H17	0.950
C7—C8	1.533 (6)	C17—C18	1.400 (6)
C7—N2	1.427 (6)	C18—H18	0.950
C8—O1	1.197 (5)	C19—C20	1.394 (6)
C8—O2	1.327 (5)	C19—C24	1.368 (6)
O2—C9	1.438 (5)	C20—C21	1.384 (6)
C9—H9A	0.980	C21—H21	0.950
C9—H9B	0.980	C21—C22	1.390 (7)
C9—H9C	0.980	C22—H22	0.950
N2—H2N	0.880	C22—C23	1.377 (6)
N2—C10	1.338 (6)	C23—H23	0.950
C10—O3	1.201 (5)	C23—C24	1.386 (6)
C10—O4	1.347 (5)	C24—H24	0.950
O4—C11	1.450 (5)
N1—C1—C5	122.3 (5)	O4—C11—C12	109.1 (4)
N1—C1—C6	117.0 (4)	H11A—C11—H11B	108.3
C5—C1—C6	120.7 (5)	H11A—C11—C12	109.9
C1—N1—C2	116.8 (5)	H11B—C11—C12	109.9
N1—C2—H2	117.7	C11—C12—H12	109.8
N1—C2—C3	124.5 (6)	C11—C12—C13	115.2 (4)
H2—C2—C3	117.7	C11—C12—C19	110.3 (4)
C2—C3—H3	121.6	H12—C12—C13	109.8
C2—C3—C4	116.9 (5)	H12—C12—C19	109.8
H3—C3—C4	121.6	C13—C12—C19	101.8 (4)
C3—C4—H4	120.4	C12—C13—C14	110.0 (4)
C3—C4—C5	119.3 (5)	C12—C13—C18	128.9 (5)
H4—C4—C5	120.4	C14—C13—C18	121.1 (5)
C1—C5—C4	120.2 (5)	C13—C14—C15	120.8 (5)
C1—C5—H5	119.9	C13—C14—C20	109.1 (4)
C4—C5—H5	119.9	C15—C14—C20	130.0 (5)
C1—C6—H6A	108.4	C14—C15—H15	120.4
C1—C6—H6B	108.4	C14—C15—C16	119.1 (5)
C1—C6—C7	115.6 (4)	H15—C15—C16	120.4
H6A—C6—H6B	107.4	C15—C16—H16	119.8
H6A—C6—C7	108.4	C15—C16—C17	120.5 (5)
H6B—C6—C7	108.4	H16—C16—C17	119.8
C6—C7—H7	105.9	C16—C17—H17	119.1
C6—C7—C8	115.5 (4)	C16—C17—C18	121.8 (5)
C6—C7—N2	112.7 (4)	H17—C17—C18	119.1
H7—C7—C8	105.9	C13—C18—C17	116.6 (5)
H7—C7—N2	105.9	C13—C18—H18	121.7
C8—C7—N2	110.0 (4)	C17—C18—H18	121.7
C7—C8—O1	124.5 (4)	C12—C19—C20	110.2 (4)
C7—C8—O2	111.4 (4)	C12—C19—C24	129.3 (4)
O1—C8—O2	124.1 (5)	C20—C19—C24	120.5 (5)
C8—O2—C9	114.7 (4)	C14—C20—C19	108.9 (5)
O2—C9—H9A	109.5	C14—C20—C21	130.2 (5)
O2—C9—H9B	109.5	C19—C20—C21	120.8 (5)
O2—C9—H9C	109.5	C20—C21—H21	120.7
H9A—C9—H9B	109.5	C20—C21—C22	118.6 (5)
H9A—C9—H9C	109.5	H21—C21—C22	120.7
H9B—C9—H9C	109.5	C21—C22—H22	120.1
C7—N2—H2N	119.7	C21—C22—C23	119.9 (5)
C7—N2—C10	120.6 (4)	H22—C22—C23	120.1
H2N—N2—C10	119.7	C22—C23—H23	119.2
N2—C10—O3	126.5 (5)	C22—C23—C24	121.6 (5)
N2—C10—O4	110.5 (5)	H23—C23—C24	119.2
O3—C10—O4	123.0 (5)	C19—C24—C23	118.5 (4)
C10—O4—C11	117.5 (4)	C19—C24—H24	120.7
O4—C11—H11A	109.9	C23—C24—H24	120.7
O4—C11—H11B	109.9
C5—C1—N1—C2	−2.7 (7)	C12—C13—C14—C15	178.5 (4)
C6—C1—N1—C2	−179.7 (4)	C12—C13—C14—C20	1.2 (5)
C1—N1—C2—C3	1.8 (8)	C18—C13—C14—C15	−0.3 (7)
N1—C2—C3—C4	−1.1 (8)	C18—C13—C14—C20	−177.6 (4)
C2—C3—C4—C5	1.0 (8)	C13—C14—C15—C16	0.7 (7)
C3—C4—C5—C1	−1.9 (9)	C20—C14—C15—C16	177.4 (5)
N1—C1—C5—C4	2.8 (8)	C14—C15—C16—C17	−0.3 (8)
C6—C1—C5—C4	179.7 (5)	C15—C16—C17—C18	−0.4 (8)
N1—C1—C6—C7	30.3 (6)	C12—C13—C18—C17	−179.0 (4)
C5—C1—C6—C7	−146.7 (5)	C14—C13—C18—C17	−0.4 (7)
C1—C6—C7—C8	−75.6 (5)	C16—C17—C18—C13	0.8 (7)
C1—C6—C7—N2	52.0 (6)	C11—C12—C19—C20	121.5 (4)
C6—C7—C8—O1	138.5 (5)	C11—C12—C19—C24	−58.4 (6)
C6—C7—C8—O2	−42.9 (6)	C13—C12—C19—C20	−1.3 (5)
N2—C7—C8—O1	9.5 (7)	C13—C12—C19—C24	178.8 (5)
N2—C7—C8—O2	−171.9 (4)	C12—C19—C20—C14	2.1 (5)
C7—C8—O2—C9	−173.3 (4)	C12—C19—C20—C21	178.3 (4)
O1—C8—O2—C9	5.3 (7)	C24—C19—C20—C14	−178.0 (4)
C6—C7—N2—C10	136.1 (4)	C24—C19—C20—C21	−1.8 (7)
C8—C7—N2—C10	−93.4 (5)	C13—C14—C20—C19	−2.1 (5)
C7—N2—C10—O3	−17.0 (7)	C13—C14—C20—C21	−177.8 (5)
C7—N2—C10—O4	163.1 (4)	C15—C14—C20—C19	−179.1 (5)
N2—C10—O4—C11	176.3 (3)	C15—C14—C20—C21	5.2 (9)
O3—C10—O4—C11	−3.6 (6)	C14—C20—C21—C22	176.8 (5)
C10—O4—C11—C12	122.7 (4)	C19—C20—C21—C22	1.5 (7)
O4—C11—C12—C13	−72.2 (5)	C20—C21—C22—C23	−2.3 (7)
O4—C11—C12—C19	173.4 (3)	C21—C22—C23—C24	3.5 (7)
C11—C12—C13—C14	−119.3 (4)	C12—C19—C24—C23	−177.3 (4)
C11—C12—C13—C18	59.4 (7)	C20—C19—C24—C23	2.8 (7)
C19—C12—C13—C14	0.0 (5)	C22—C23—C24—C19	−3.7 (7)
C19—C12—C13—C18	178.7 (5)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N2—H2N···O2^i	0.88	2.47	3.214 (5)	142

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