(2S,4R)-4-Ammonio-5-oxopyrrolidine-2-carboxylate

Kaczmarek, K.; Wojciechowski, J.; Wolf, W.M.

doi:10.1107/S1600536810004277

organic compounds

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ISSN: 2056-9890

Volume 66| Part 4| April 2010| Pages o831-o832

doi:10.1107/S1600536810004277

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(2S,4R)-4-Ammonio-5-oxopyrrolidine-2-carboxylate

Krzysztof Kaczmarek,^a Jakub Wojciechowski ^b and Wojciech M. Wolf ^b ^*

^aInstitute of Organic Chemistry, Technical University of Łódź, ul. Żeromskiego 116, 90-924 Łódź, Poland, and ^bInstitute of General and Ecological Chemistry, Technical University of Łódź, ul. Żeromskiego 116, 90-924 Łódź, Poland
^*Correspondence e-mail: wmwolf@p.lodz.pl

(Received 1 February 2010; accepted 3 February 2010; online 13 March 2010)

In the crystal structure of the title compound, C₅H₈N₂O₃, the molecules exist in the zwitterionic form. The pyrrolidine ring adopts an envelope conformation with the unsubstituted endocyclic C atom situated at the flap. The other four endocyclic atoms are coplanar with the exocyclic carbonyl O atom, with an r.m.s. deviation from the mean plane of 0.06 Å. The carboxylate substituent is located axially, while the ammonium group occupies an equatorial position. In the crystal structure, the molecules are linked through N—H⋯O hydrogen bonds, forming a three-dimensional network.

Related literature

For molecular recognition in N-methyl amino acids and proline residues, see: Dugave & Demange (2003 ). For the construction of modified amino acids, see: Dumy et al. (1997 ); Keller et al. (1998 ); Mutter et al. (1999 ); Tuchscherer & Mutter (2001 ); Paul et al. (1992 ). For pyroglutamic acid derivatives, see: Zabrocki et al. (1988 ); Kaczmarek et al. (2005 ). For the preparation of the title compound, see: Kaczmarek et al. (2001 ); Kaczmarek (2009 ). For asymmetry parameters, see: Griffin et al. (1984 ).

Experimental

Crystal data

C₅H₈N₂O₃
M_r = 144.13
Orthorhombic, P 2₁ 2₁ 2₁
a = 5.9790 (3) Å
b = 9.3665 (4) Å
c = 11.3809 (5) Å
V = 637.36 (5) Å³
Z = 4
Cu Kα radiation
μ = 1.08 mm⁻¹
T = 293 K
0.40 × 0.40 × 0.10 mm

Data collection

Bruker SMART APEX diffractometer
Absorption correction: multi-scan (SADABS; Bruker, 2003 ) T_min = 0.707, T_max = 0.900
7227 measured reflections
1169 independent reflections
1168 reflections with I > 2σ(I)
R_int = 0.030

Refinement

R[F² > 2σ(F²)] = 0.027
wR(F²) = 0.069
S = 1.08
1169 reflections
125 parameters
H atoms treated by a mixture of independent and constrained refinement
Δρ_max = 0.13 e Å⁻³
Δρ_min = −0.17 e Å⁻³
Absolute structure: Flack (1983 ), 461 Friedel pairs
Flack parameter: 0.1 (2)

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1⋯O2ⁱ	0.82 (2)	2.07 (2)	2.8535 (15)	161.2 (18)
N2—H2⋯O1ⁱⁱ	0.88 (2)	1.87 (2)	2.7346 (16)	168.5 (17)
N2—H3⋯O1ⁱⁱⁱ	0.897 (17)	1.886 (17)	2.7788 (14)	173.4 (17)
N2—H4⋯O2^iv	0.868 (17)	1.935 (17)	2.7967 (15)	172.3 (17)
Symmetry codes: (i) $[x+{\script{1\over 2}}, -y+{\script{1\over 2}}, -z+1]$ ; (ii) $[-x+2, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (iii) $[-x+{\script{3\over 2}}, -y, z+{\script{1\over 2}}]$ ; (iv) $[-x+1, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ .

Data collection: SMART (Bruker, 2003); cell refinement: SAINT-Plus (Bruker, 2003); data reduction: SAINT-Plus; program(s) used to solve structure: SHELXTL (Sheldrick, 2008 ); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL and Mercury (Macrae et al., 2008 ); software used to prepare material for publication: SHELXTL and publCIF (Westrip, 2010 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536810004277/bt5187sup1.cif

Structure factors: contains datablock I. DOI: 10.1107/S1600536810004277/bt5187Isup2.hkl

checkCIF report

Comment top

N-methyl amino acids and proline residues in the peptide chain may cause the cis-trans isomerisation of the amide bond and lead to conformational changes, which influence the molecular recognition (Dugave & Demange, 2003). Importance of the cis-amide bonds for the peptide bioactivity led to the construction of modified amino acids, which could lock a peptide bond in the cis-geometry (Dumy et al., 1997; Keller et al., 1998; Mutter et al., 1999; Tuchscherer & Mutter, 2001). In particular, Paul et al. (1992) designed mimetics of the cis-peptide bond based on the substitituted pyroglutamic acid residue. In contrast with a tetrazole replacement for the peptide bond, the pyroglutamic acid derivatives are more rigid (Zabrocki et al., 1988). Their carboxylic group could be either donor or acceptor of hydrogen bond without invloving the polypeptide main chain amide moieties (Kaczmarek et al., 2005).

The 4-aminopyroglutamic acid is a particularly useful residue for building the conformationally restricted peptide chains. Depending on the absolute configuration at both chiral centers it may be applied to construct the VIa or VIb β-turn mimetics.

The title compound may be obtained by two different methods elaborated by us, i.e. by electrophilic amination reaction of N-protected (S)-pyroglutamate ester, which gives separable 9:1 mixture of (2S,4R) and (2S,4S) diastereoisomers (Kaczmarek et al., 2001) or through Michael addition of dehydroalanine derivatives to sodium salt of N-benzyloxycarbonylaminomalonate ester, which gives after hydrolysis and decarboxylation mixture of all four possible stereomers. The details of the last reaction and resolution of stereoisomers will be described elsewhere (Kaczmarek, 2009).

A view of the title compound is given in Fig. 1. The molecule has two chiral centres viz. C3 and C5. Their absolute configurations follow from the synthetic procedure and are R and S, respectively.

The pyrrolidine ring adopts an envelope conformation with N1, C2, C3 and C5 almost coplanar and the C4 situated at the flap.

Additionally, the former four endocyclic atoms are coplanar with the exocyclic carbonyl oxygen, the average r.m.s. deviation from the mean plane is 0.06 Å.

The three lowest ring asymmetry parameters (Griffin et al., 1984) are: C_S(C4) = 1.26 (14), C₂(C2) = 11.92 (14), C₂(N1) = 15.46 (14)°. The carboxylate substituent is located axially in conformation stabilized by the short N1···O2 contact [2.787 (2) Å], while the ammonium group occupies equatorial position.

In the crystal each molecule is linked through N—H ···O hydrogen bonds with eight adjacent molecules, their deatils are shown in Table 2 and Fig. 2.

Related literature top

For molecular recognition in N-methyl amino acids and proline residues, see: Dugave & Demange (2003). For the construction of modified amino acids, see: Dumy et al. (1997); Keller et al. (1998); Mutter et al. (1999); Tuchscherer & Mutter (2001); Paul et al. (1992). For pyroglutamic acid derivatives, see: Zabrocki et al. (1988); Kaczmarek et al. (2005). For the preparation of the title compound, see: Kaczmarek et al. (2001); Kaczmarek (2009). For asymmetry parameters, see: Griffin et al. (1984).

Experimental top

An optically pure (ee>99%) N'-benzyloxycarbonyl protected precursor of the title compound was hydrogenated in methanol solution over 10% palladium on charcoal, which resulted in precipitation of the final product. After filtration of solids final product was washed out of the catalyst with the aim of water. The (2S,4R)-4-aminopyroglutamic acid crystals were grown from this water solution by slow evaporation.

Computing details top

Data collection: SMART (Bruker, 2003); cell refinement: SAINT-Plus (Bruker, 2003); data reduction: SAINT-Plus (Bruker, 2003); program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008) and publCIF (Westrip, 2010).

Figures top

	Fig. 1. Molecule of the title compound. Displacement ellipsoids are drawn at the 50% probability level.
	Fig. 2. View of hydrogen bonding in the crystal of the title compound. Symmetry codes: I (x, y, z); II (x + 1/2,-y+1/2,-z+1); III (-x + 2, y + 1/2,-z+3/2); IV (-x + 1, y + 1/2,-z+3/2); V (-x + 3/2,-y, z + 1/2).

(2S,4R)-4-Ammmonio-5-oxopyrrolidine-2-carboxylate top

Crystal data top

C₅H₈N₂O₃	D_x = 1.502 Mg m⁻³
M_r = 144.13	Melting point: 423(2) K
Orthorhombic, P2₁2₁2₁	Cu Kα radiation, λ = 1.54178 Å
Hall symbol: P 2ac 2ab	Cell parameters from 7056 reflections
a = 5.9790 (3) Å	θ = 6.1–70.8°
b = 9.3665 (4) Å	µ = 1.08 mm⁻¹
c = 11.3809 (5) Å	T = 293 K
V = 637.36 (5) Å³	Prism, colourless
Z = 4	0.40 × 0.40 × 0.10 mm
F(000) = 304

Data collection top

Bruker SMART APEX diffractometer	1169 independent reflections
Radiation source: fine-focus sealed tube	1168 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.030
ω scans	θ_max = 70.8°, θ_min = 6.1°
Absorption correction: multi-scan (SADABS; Bruker, 2003)	h = −6→5
T_min = 0.707, T_max = 0.900	k = −11→11
7227 measured reflections	l = −13→13

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)] = 0.027	w = 1/[σ²(F_o²) + (0.0468P)² + 0.0681P] where P = (F_o² + 2F_c²)/3
wR(F²) = 0.069	(Δ/σ)_max < 0.001
S = 1.08	Δρ_max = 0.13 e Å⁻³
1169 reflections	Δρ_min = −0.17 e Å⁻³
125 parameters	Extinction correction: SHELXL97 (Sheldrick, 2008), Fc^*=kFc[1+0.001xFc²λ³/sin(2θ)]^-1/4
0 restraints	Extinction coefficient: 0.047 (3)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 461 Friedel pairs
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.1 (2)

Crystal data top

C₅H₈N₂O₃	V = 637.36 (5) Å³
M_r = 144.13	Z = 4
Orthorhombic, P2₁2₁2₁	Cu Kα radiation
a = 5.9790 (3) Å	µ = 1.08 mm⁻¹
b = 9.3665 (4) Å	T = 293 K
c = 11.3809 (5) Å	0.40 × 0.40 × 0.10 mm

Data collection top

Bruker SMART APEX diffractometer	1169 independent reflections
Absorption correction: multi-scan (SADABS; Bruker, 2003)	1168 reflections with I > 2σ(I)
T_min = 0.707, T_max = 0.900	R_int = 0.030
7227 measured reflections

Refinement top

R[F² > 2σ(F²)] = 0.027	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.069	Δρ_max = 0.13 e Å⁻³
S = 1.08	Δρ_min = −0.17 e Å⁻³
1169 reflections	Absolute structure: Flack (1983), 461 Friedel pairs
125 parameters	Absolute structure parameter: 0.1 (2)
0 restraints

Special details top

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds 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 (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.85679 (17)	−0.10762 (9)	0.57781 (8)	0.0373 (3)
H2	0.838 (4)	0.3509 (18)	0.9130 (15)	0.042 (4)*
O2	0.57914 (17)	0.04638 (10)	0.55325 (8)	0.0383 (3)
O3	0.6519 (2)	0.46234 (9)	0.68254 (10)	0.0469 (3)
N1	0.8566 (2)	0.27436 (11)	0.61237 (10)	0.0353 (3)
H1	0.917 (4)	0.3094 (19)	0.5549 (17)	0.054 (5)*
C1	0.7725 (2)	0.01571 (13)	0.58351 (10)	0.0283 (3)
C5	0.9163 (2)	0.12935 (13)	0.64357 (11)	0.0304 (3)
H51	1.078 (3)	0.1140 (16)	0.6258 (13)	0.032 (4)*
C4	0.8646 (3)	0.12504 (13)	0.77672 (11)	0.0340 (3)
H41	0.807 (3)	0.0354 (17)	0.8009 (15)	0.045 (5)*
H42	0.995 (4)	0.156 (2)	0.8147 (18)	0.056 (5)*
C3	0.6848 (2)	0.23810 (12)	0.79144 (11)	0.0297 (3)
H31	0.541 (3)	0.1976 (15)	0.7877 (14)	0.030 (4)*
N2	0.7038 (2)	0.31400 (11)	0.90532 (10)	0.0310 (3)
H4	0.607 (3)	0.3822 (18)	0.9140 (14)	0.036 (4)*
H3	0.695 (3)	0.249 (2)	0.9630 (14)	0.042 (4)*
C2	0.7255 (2)	0.34135 (13)	0.68928 (11)	0.0319 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0425 (6)	0.0262 (4)	0.0432 (5)	0.0027 (4)	−0.0079 (4)	−0.0062 (4)
O2	0.0334 (6)	0.0347 (5)	0.0466 (5)	−0.0016 (4)	−0.0093 (4)	0.0089 (4)
O3	0.0561 (7)	0.0309 (5)	0.0536 (6)	0.0133 (5)	0.0046 (5)	0.0104 (4)
N1	0.0451 (7)	0.0234 (5)	0.0374 (6)	−0.0044 (5)	0.0072 (5)	0.0050 (4)
C1	0.0331 (7)	0.0267 (6)	0.0251 (5)	−0.0021 (4)	0.0001 (5)	0.0034 (4)
C5	0.0311 (7)	0.0241 (6)	0.0361 (6)	−0.0008 (5)	0.0004 (5)	0.0004 (5)
C4	0.0435 (8)	0.0250 (6)	0.0335 (6)	0.0040 (5)	−0.0074 (6)	0.0002 (5)
C3	0.0294 (7)	0.0257 (5)	0.0340 (6)	−0.0027 (5)	−0.0020 (4)	0.0037 (5)
N2	0.0327 (7)	0.0257 (5)	0.0345 (5)	0.0022 (5)	0.0027 (4)	0.0029 (4)
C2	0.0321 (7)	0.0270 (6)	0.0367 (6)	−0.0015 (5)	−0.0022 (5)	0.0044 (5)

Geometric parameters (Å, º) top

O1—C1	1.2621 (16)	C4—C3	1.5187 (19)
O2—C1	1.2399 (17)	C4—H41	0.949 (17)
O3—C2	1.2179 (16)	C4—H42	0.94 (2)
N1—C2	1.3321 (17)	C3—N2	1.4826 (16)
N1—C5	1.4485 (15)	C3—C2	1.5318 (16)
N1—H1	0.82 (2)	C3—H31	0.939 (17)
C1—C5	1.5295 (17)	N2—H2	0.88 (2)
C5—C4	1.5470 (17)	N2—H4	0.867 (18)
C5—H51	0.997 (17)	N2—H3	0.898 (18)

C2—N1—C5	115.19 (10)	C3—C4—H41	109.0 (11)
O3—C2—N1	127.55 (12)	C5—C4—H41	112.3 (10)
O3—C2—C3	125.30 (12)	C3—C4—H42	108.7 (13)
N1—C2—C3	107.15 (11)	C5—C4—H42	106.1 (13)
N1—C5—C1	113.86 (10)	H41—C4—H42	116.4 (17)
N1—C5—C4	102.44 (10)	N2—C3—C4	112.11 (10)
C1—C5—C4	107.90 (10)	N2—C3—C2	110.40 (10)
C3—C4—C5	103.37 (10)	N2—C3—H31	107.7 (9)
C4—C3—C2	104.12 (10)	C4—C3—H31	111.1 (9)
C2—N1—H1	126.6 (13)	C2—C3—H31	111.5 (9)
C5—N1—H1	117.8 (13)	C3—N2—H2	110.3 (11)
O2—C1—O1	124.76 (12)	C3—N2—H4	113.6 (11)
O2—C1—C5	119.14 (11)	H2—N2—H4	107.9 (16)
O1—C1—C5	115.82 (11)	C3—N2—H3	108.0 (11)
N1—C5—H51	108.9 (9)	H2—N2—H3	104.4 (16)
C1—C5—H51	110.7 (9)	H4—N2—H3	112.3 (15)
C4—C5—H51	112.9 (8)

N1—C5—C4—C3	26.38 (13)	O2—C1—C5—N1	−26.96 (16)
C5—C4—C3—C2	−25.98 (13)	O1—C1—C5—N1	158.87 (11)
C5—N1—C2—O3	−179.48 (14)	O2—C1—C5—C4	86.02 (13)
C5—N1—C2—C3	1.41 (16)	O1—C1—C5—C4	−88.15 (13)
C4—C3—C2—N1	16.23 (14)	C1—C5—C4—C3	−94.06 (11)
C4—C3—C2—O3	−162.91 (14)	C5—C4—C3—N2	−145.33 (10)
C2—N1—C5—C4	−17.99 (15)	N2—C3—C2—O3	−42.41 (18)
C2—N1—C5—C1	98.23 (14)	N2—C3—C2—N1	136.73 (12)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2ⁱ	0.82 (2)	2.07 (2)	2.8535 (15)	161.2 (18)
N2—H2···O1ⁱⁱ	0.88 (2)	1.87 (2)	2.7346 (16)	168.5 (17)
N2—H3···O1ⁱⁱⁱ	0.897 (17)	1.886 (17)	2.7788 (14)	173.4 (17)
N2—H4···O2^iv	0.868 (17)	1.935 (17)	2.7967 (15)	172.3 (17)

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

Experimental details

Crystal data
Chemical formula	C₅H₈N₂O₃
M_r	144.13
Crystal system, space group	Orthorhombic, P2₁2₁2₁
Temperature (K)	293
a, b, c (Å)	5.9790 (3), 9.3665 (4), 11.3809 (5)
V (Å³)	637.36 (5)
Z	4
Radiation type	Cu Kα
µ (mm⁻¹)	1.08
Crystal size (mm)	0.40 × 0.40 × 0.10

Data collection
Diffractometer	Bruker SMART APEX diffractometer
Absorption correction	Multi-scan (SADABS; Bruker, 2003)
T_min, T_max	0.707, 0.900
No. of measured, independent and observed [I > 2σ(I)] reflections	7227, 1169, 1168
R_int	0.030
(sin θ/λ)_max (Å⁻¹)	0.613

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.027, 0.069, 1.08
No. of reflections	1169
No. of parameters	125
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	0.13, −0.17
Absolute structure	Flack (1983), 461 Friedel pairs
Absolute structure parameter	0.1 (2)

Computer programs: SMART (Bruker, 2003), SAINT-Plus (Bruker, 2003), SHELXTL (Sheldrick, 2008) and Mercury (Macrae et al., 2008), SHELXTL (Sheldrick, 2008) and publCIF (Westrip, 2010).

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1···O2ⁱ	0.82 (2)	2.07 (2)	2.8535 (15)	161.2 (18)
N2—H2···O1ⁱⁱ	0.88 (2)	1.87 (2)	2.7346 (16)	168.5 (17)
N2—H3···O1ⁱⁱⁱ	0.897 (17)	1.886 (17)	2.7788 (14)	173.4 (17)
N2—H4···O2^iv	0.868 (17)	1.935 (17)	2.7967 (15)	172.3 (17)

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

Acknowledgements

Financial support from the Ministry of Science and Higher Education, Poland (project No. 2P05F00129) is gratefully acknowledged.

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