DL-Proline

In the structure of DL-proline, C₅H₉NO₂, the mol­ecules are connected via classical inter­molecular N—H...O hydrogen bonds involving the amine and carbox­yl groups [N...O = 2.7129 (15) and 2.8392 (16) Å], and form chains along the b-axis direction and parallel to (01). The chains are linked into sheets via weak non-classical hydrogen bonds. The conformation of the mol­ecule and its packing are notably different from the monohydrated DL-proline form.

S1. Comment

Structural data of amino acids are fundamentally important. Aside from recent electron density studies (Flaig et al., 2002; Abramov et al., 2000) and quantum chemical investigations (Brauer et al., 2004; Czinki & Császár, 2003; Stepanian et al., 2001; Improta et al., 2001), the study of amino acid clusters in the gas phase has attracted considerable attention (Cooks et al., 2001; Julian et al., 2002; Counterman & Clemmer, 2001; Myung et al., 2004). Although the majority of amino acids have been crystallized as enantiopure L and racemic DL forms and their structures are known, a few remain elusive, notably DL-proline.

Proline is an abundant amino acid in collagen and exceptional among the amino acids; it is the only one in which the amine group is part of a pyrrolidine ring, making it rigid and directional in biological systems despite its conformational flexibility. So far, the crystal structures of L-proline (Kayushina & Vainshtein, 1965), the monohydrates of L– and DL-proline (Janczak & Luger, 1997; Padmanabhan et al., 1995, respectively), and numerous other solvates and salts of proline have been determined. We report here the crystal structure of DL-proline, (I) (Fig, 1).

DL-proline crystallizes in its zwitterionic form with long C—N bond lengths [1.4907 (18) and 1.5104 (19) Å] and a slightly unsymmetrical carboxyl group [C—O =1.2733 (17) and 1.2387 (18) Å]. The pyrrolidine ring adopts a C₂—C^γ-endo conformation (Ashida & Kakudo, 1974) similar to L-proline (Kayushina & Vainshtein, 1965). The C4 atom (or C^γ) is located 0.988 (3) Å above the N1/C2/C3 (or N/C^α/C^β) plane. The angle between atom C1 and the N1/C2/C3 plane is 126.0 (4)°. The ring puckering parameters (Cremer & Pople, 1975) for the pyrrolidine ring are q₂ = 0.4029 (16) Å and ϕ₂ = 57.7 (2)°. For comparison, the puckering parameters of L-proline are q₂ = 0.404 Å and ϕ₂ = 89.1°. In contrast, the puckering parameters for the monohydrates are q₂ = 0.4033 (5) Å and ϕ₂ = 308.63 (7)°, and q₂ = 0.395 (4) Å and ϕ₂ = 309.9 (6)°, for the DL and L forms, respectively.

Classical hydrogen bonds between carboxyl and ammonium ion groups link the molecules into pairs of parallel chains (Table 2 and Fig. 2) parallel to (−101), which can be described by the graph sets R²₂(10) and R²₄(8) (Etter et al., 1990). Interestingly, only one of the carboxyl O atoms (O1), showing a slightly elongated C—O distance, is involved in classical hydrogen bonding. The second O atom (O2) is surrounded by aliphatic H atoms at distances greater than 2.6 Å. Considering the rather long distances, both O atoms form non-classical hydrogen bonds to C atoms that group the hydrogen-bonded chains into slip-stacked layers parallel to (100), with the hydrophobic regions of the layers facing each other (Fig. 3). For comparison, in both L– and DL-proline monohydrate, the molecules are linked into three-dimensional hydrogen-bonded networks that include the water molecules in channels. In L-proline, the molecules form sheets via hydrogen bonding with both carboxyl O atoms participating in the N—H···O interaction.

The study of conformational differences of proline is of interest because of its importance in collagen (DeRider et al., 2002). To achieve a general understanding of proline's conformational flexibility, we carried out DFT-based geometry optimizations. Crystallographic data available for L-proline (Kayushina & Vainshtein, 1965), the monohydrates of L– and DL-proline (Janczak & Luger, 1997; Padmanabhan et al., 1995), and our own results provided initial geometries. Not surprisingly, standard gas phase calculations indicate that in all cases the zwitterionic form of proline is not a well defined minimum on the gas phase molecular potential energy surface. As expected, all geometry optimizations converged to a neutral form. The zwitterionic structures could be optimized successfully, however, by including a continuum field in the computation of the gradient, which, one could argue, mimics the environment in a crystal or protein. The COSMO method was used (Klamt & Schüürmann, 1993), which was originally designed to mimic charge screening due to a solvent. As COSMO, like any other continuum solvation method, simply simulates the response of a dielectric continuum to the charge density of the solute, it is reasonable to make use of this protocol for simulating the effects of the electrostatic response potential present in the proline crystal. Since continuum models use a simple scaling factor to account for different dielectric constants, the potential energy surface does not change its shape as a function of the dielectric constant. Thus, for the purpose of obtaining the geometry of a proline molecule embedded in the continuum potential and evaluating the relative energies of different conformers, the choice of the actual parameter for the dielectric constant is not physically relevant. We used the dielectric constant of water (ε = 78.4) because the continuum models are best calibrated to this dielectric constant.

The geometry optimizations gave rise to only small adjustments of the different X-ray structures. Both endo and exo conformers of the zwitterionic proline are obtained as stable structures, and conformations were maintained for unsolvated and monohydrated prolines, respectively. The energies of the four different structures with and without the COSMO potential [E(COSMO) and E(GP), respectively] are included in the supplementary material. Interestingly, the endo and exo conformers are practically isoenergetic when the continuum potential is included, the computed energy difference being 0.7 kcal mol⁻¹ at best. However, the gas phase energies E(GP) evaluated at the same geometry reveal that there is a slight electronic preference of 2 kcal mol⁻¹ for the endo conformer.

S2. Experimental

The title compound (I) was recrystallized by slow evaporation from a concentrated solution of dry methanol (Aldrich) using commercially available material (Aldrich), m.p. 481 (3) K. All calculations were carried out using density functional theory (Parr & Yang, 1989; Ziegler, 1991) as implemented in the Amsterdam Density Functional 2004.01 package (ADF) (Velde et al., 2001), using a triple-z STO basis set with one set of polarization functions as provided in the ADF package (Basis Set TZP), together with the BLYP functional (Becke, 1988; Lee et al., 1988). The COSMO potential, (Pye & Ziegler, 1999) was included in the SCF procedure and the following radii were used to obtain the solute cavity: C: 1.9 Å; O: 1.6 Å; N 1.6 Å; H: 1.15 Å. The dielectric constant ε was set to 78.4. A l l calculations are carried out using the restricted spin formalism (closed-shell).

S3. Refinement

H atoms participating in classical hydrogen bonding were located in a difference map and refined. All other H atoms were placed in idealized positions, with C—H distances of 0.99 Å for the secondary (CH₂) groups at C3, C4 and C5, and 1.00 Å for the tertiary (CH) group at C2, and treated using a riding model but with individual refined displacement parameters for all H atoms apart from H2, for which the U_iso(H) value was fixed at 1.2U_eq of the parent C2 atom. The residual electron density is small, as expected for an organic system without disorder, and the highest peak is located on the C2–C3 bond. Additional peaks are located in the vicinity of the O atoms and on bonds.

Computing details

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2003); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker, 2003), XTEL (local library) and PLATON (Spek, 2002); software used to prepare material for publication: SHELXTL.

Figures

	Fig. 1. A view of DL-proline with the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level, with H atoms represented by circles of arbitrary size.
	Fig. 2. The hydrogen-bonding pattern along (010), chains parallel to (−101). The secondary CH2 H atoms have been omitted for clarity. Symmetry codes are as in Table 2; atoms marked with an asterisk (*) are at (x, 1 + y, z).
	Fig. 3. The molecular packing of DL-proline viewed along the b axis. Dashed lines show classical and non-classical hydrogen bonding.

DL-proline

Crystal data

C5H9NO2	F(000) = 248
Mr = 115.13	Dx = 1.409 Mg m^−3
Monoclinic, P21/c	Melting point: 481 K
Hall symbol: -P 2ybc	Mo Kα radiation, λ = 0.71073 Å
a = 8.9906 (6) Å	Cell parameters from 1925 reflections
b = 5.2987 (4) Å	θ = 2.3–50.0°
c = 11.4786 (8) Å	µ = 0.11 mm^−1
β = 97.041 (2)°	T = 120 K
V = 542.70 (7) Å^3	Block, colorless
Z = 4	0.24 × 0.11 × 0.10 mm

Data collection

Bruker SMART 6000 diffractometer	963 independent reflections
Radiation source: fine-focus sealed tube	855 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.021
Detector resolution: 44.52 pixels mm^-1	θmax = 25.0°, θmin = 2.3°
ω–scans	h = −10→10
Absorption correction: multi-scan (SADABS; Blessing, 1995)	k = −6→5
Tmin = 0.974, Tmax = 0.990	l = −13→12
3327 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.040	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.114	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ^2(Fo^2) + (0.0745P)^2 + 0.1713P] where P = (Fo^2 + 2Fc^2)/3
963 reflections	(Δ/σ)max < 0.001
87 parameters	Δρmax = 0.37 e Å^−3
0 restraints	Δρmin = −0.19 e Å^−3

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.

Computed electronic energies and energy differences with and without the COSMO potential switched on at the COSMO-optimized geometries.

E(COSMO)/ DE(COSMO)/ E(GP)/ DE(GP)/ eV kcal/mol eV kcal/mol

DL-Proline −103.1375 0 − 101.5864 0 L-Proline −103.1364 0.02 − 101.5846 0.04 DL-Proline Monohydrate −103.1159 0.50 − 101.5123 1.71 L-Proline Monohydrate −103.1081 0.68 − 101.4970 2.06

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
C1	0.14911 (15)	0.6303 (3)	0.20445 (11)	0.0172 (4)
O1	0.08960 (12)	0.72120 (18)	0.10706 (9)	0.0206 (3)
O2	0.18382 (13)	0.74758 (19)	0.29715 (9)	0.0254 (3)
N1	0.13004 (14)	0.2269 (2)	0.09138 (11)	0.0178 (3)
H1N	0.1100 (19)	0.059 (4)	0.1016 (15)	0.025 (4)*
H1M	0.044 (2)	0.295 (4)	0.0555 (16)	0.026 (5)*
C2	0.18069 (15)	0.3453 (3)	0.20726 (11)	0.0164 (4)
H2	0.1307	0.2626	0.2705	0.020*
C3	0.34771 (16)	0.2873 (3)	0.22334 (13)	0.0207 (4)
H3A	0.3669	0.1100	0.2480	0.031 (4)*
H3B	0.4025	0.4008	0.2823	0.031 (5)*
C4	0.39296 (17)	0.3345 (3)	0.10138 (13)	0.0264 (4)
H4A	0.4830	0.2351	0.0893	0.041 (6)*
H4B	0.4141	0.5156	0.0901	0.034 (5)*
C5	0.25664 (19)	0.2483 (3)	0.01675 (13)	0.0243 (4)
H5A	0.2323	0.3736	−0.0467	0.033 (5)*
H5B	0.2764	0.0834	−0.0189	0.041 (5)*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0204 (7)	0.0145 (8)	0.0171 (7)	−0.0007 (5)	0.0041 (5)	−0.0005 (6)
O1	0.0312 (6)	0.0125 (5)	0.0174 (6)	0.0012 (4)	0.0005 (4)	0.0011 (4)
O2	0.0402 (7)	0.0179 (6)	0.0174 (6)	0.0009 (4)	0.0011 (5)	−0.0042 (4)
N1	0.0260 (7)	0.0117 (7)	0.0153 (7)	0.0005 (5)	0.0003 (5)	0.0000 (5)
C2	0.0243 (7)	0.0129 (7)	0.0120 (7)	−0.0012 (5)	0.0015 (5)	−0.0005 (5)
C3	0.0250 (8)	0.0189 (7)	0.0178 (8)	0.0011 (6)	0.0013 (6)	0.0008 (6)
C4	0.0288 (8)	0.0295 (9)	0.0222 (8)	0.0012 (7)	0.0076 (6)	0.0022 (6)
C5	0.0382 (10)	0.0209 (8)	0.0153 (8)	0.0015 (6)	0.0087 (6)	−0.0005 (6)

Geometric parameters (Å, º)

C1—O2	1.2387 (18)	C3—C4	1.526 (2)
C1—O1	1.2733 (17)	C3—H3A	0.9900
C1—C2	1.5361 (19)	C3—H3B	0.9900
N1—C2	1.4907 (18)	C4—C5	1.537 (2)
N1—C5	1.5104 (19)	C4—H4A	0.9900
N1—H1N	0.92 (2)	C4—H4B	0.9900
N1—H1M	0.904 (19)	C5—H5A	0.9900
C2—C3	1.5217 (19)	C5—H5B	0.9900
C2—H2	1.0000
O2—C1—O1	126.79 (13)	C4—C3—H3A	111.2
O2—C1—C2	116.66 (12)	C2—C3—H3B	111.2
O1—C1—C2	116.55 (12)	C4—C3—H3B	111.2
C2—N1—C5	107.78 (11)	H3A—C3—H3B	109.1
C2—N1—H1N	109.7 (11)	C3—C4—C5	104.46 (12)
C5—N1—H1N	108.5 (11)	C3—C4—H4A	110.9
C2—N1—H1M	112.9 (11)	C5—C4—H4A	110.9
C5—N1—H1M	111.8 (12)	C3—C4—H4B	110.9
H1N—N1—H1M	106.0 (15)	C5—C4—H4B	110.9
N1—C2—C3	102.25 (11)	H4A—C4—H4B	108.9
N1—C2—C1	111.08 (11)	N1—C5—C4	105.18 (11)
C1—C2—C3	112.23 (11)	N1—C5—H5A	110.7
N1—C2—H2	110.3	C4—C5—H5A	110.7
C3—C2—H2	110.3	N1—C5—H5B	110.7
C1—C2—H2	110.3	C4—C5—H5B	110.7
C2—C3—C4	103.04 (11)	H5A—C5—H5B	108.8
C2—C3—H3A	111.2
C5—N1—C2—C3	−32.85 (13)	N1—C2—C3—C4	41.68 (13)
C5—N1—C2—C1	87.06 (13)	C1—C2—C3—C4	−77.42 (14)
O2—C1—C2—N1	178.49 (12)	C2—C3—C4—C5	−35.12 (15)
O1—C1—C2—N1	−1.34 (17)	C2—N1—C5—C4	11.14 (14)
O2—C1—C2—C3	−67.73 (16)	C3—C4—C5—N1	15.07 (15)
O1—C1—C2—C3	112.44 (13)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···O1^i	0.92 (2)	1.80 (2)	2.7129 (15)	171.9 (16)
N1—H1M···O1^ii	0.904 (19)	2.094 (19)	2.8392 (16)	139.0 (16)
C2—H2···O1^iii	1.00	2.58	3.4857 (17)	151
C5—H5A···O2^iv	0.99	2.69	3.6759 (18)	173

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