organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

Glycyl-L-proline hemihydrate at 298 K

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aSchool of Chemistry, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JJ, Scotland, and bInstitute for Cell and Molecular Biology, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JR, Scotland
*Correspondence e-mail: s.parsons@ed.ac.uk

(Received 3 February 2006; accepted 9 February 2006; online 15 February 2006)

The crystal structure of glycyl-L-proline (GLY–PRO) hemihydrate, C7H12N2O3·0.5H2O, has two mol­ecules of GLY–PRO in the asymmetric unit; one mol­ecule adopts the cis configuration at the peptide bond and the other adopts the trans configuration.

Comment

The trans form of the peptide bond is generally favoured over the cis form by a ratio of around 1000 to 1 (ca 7.5 kJ mol−1 at 300 K) as the result of more favourable steric inter­actions between side chains (Glusker et al., 1994[Glusker, J. P., Lewis, M. & Rossi, M. (1994). Crystal Structure Analysis for Chemists and Biologists, p. 483. New York: VCH.]). In the case of proline, however, this ratio drops to 4 to 1 (see, for example, Creighton, 1993[Creighton, T. E. (1993). Proteins: Structure and Molecular Properties, 2nd ed., p. 174. New York: W. H. Freeman.]).

[Scheme 1]

Glycyl-L-proline (GLY–PRO), a dipeptide consisting of a glycine (GLY) residue at the N-terminus and a proline (PRO) residue at the carb­oxy terminus, provides an excellent example of a simple structure relevant to protein folding. cistrans Isomerization of the prolyl peptide bond has been implicated in the slow refolding of proteins (e.g. Brandts et al., 1975[Brandts, J. F., Halvorson, H. R. & Brennan, M. (1975). Biochemistry, 14, 4953-4963.]) and nature has overcome this potential restriction by providing a prolyl isomerase.

Recrystallization of GLY–PRO by slow diffusion of ethanol into an aqueous solution yielded crystals of the hemihydrate, (I)[link]. The structure of (I)[link] contains two GLY–PRO mol­ecules in the asymmetric unit, viz. one (based on N11) in the trans form and the other in the cis form (Figs. 1[link] and 2[link], respectively). The relevant ω torsion angles are, in the trans form, τ(C21—C31—N51—C91) = −174.3 (4)° and, in the cis form, τ(C22—C32—N52—C92) = −3.3 (7)°.

The two mol­ecules inter­act with each other via hydrogen bonds between the carboxyl­ate and ammonium groups. The water mol­ecules are double hydrogen-bond donors, linking cis to trans isomers via their carboxyl­ate groups. Overall, the hydrogen bonds form double layers which stack along the a direction (Figs. 3[link] and 4[link]).

[Figure 1]
Figure 1
The structure of GLY–PRO in (I)[link] in its trans configuration. The ellipsoids enclose 30% probability surfaces.
[Figure 2]
Figure 2
Structure of GLY–PRO in (I)[link] in its cis configuration. The ellipsoids enclose 30% probability surfaces.
[Figure 3]
Figure 3
Hydrogen bonding (dashed lines) in layers formed in the structure of (I)[link], viewed along [100].
[Figure 4]
Figure 4
Pairs of layers depicted in Fig. 3[link] are connected though further hydrogen bonds (dashed lines). The double layers so formed stack along the a direction. This view is along [010]; Mol. 1 and Mol. 2 contain atoms N11, C21 etc. and N12, C22 etc., respectively.

Experimental

A sample of glycyl-L-proline was obtained from Sigma–Aldrich. Crystals were grown at room temperature by slow diffusion of ethanol into an aqueous solution over a period of 7 d. Data were collected at room temperature, rather than low temperature, as a preliminary to a high-pressure study, which was also to have been carried out at room temperature. In the event, the crystals proved too weakly diffracting for the high-pressure study.

Crystal data
  • C7H12N2O3·0.5H2O

  • Mr = 181.19

  • Monoclinic, P 21

  • a = 11.171 (4) Å

  • b = 6.619 (3) Å

  • c = 12.371 (5) Å

  • β = 110.818 (7)°

  • V = 855.0 (6) Å3

  • Z = 4

  • Dx = 1.408 Mg m−3

  • Mo Kα radiation

  • Cell parameters from 685 reflections

  • θ = 4–20°

  • μ = 0.11 mm−1

  • T = 293 K

  • Block, colourless

  • 0.12 × 0.11 × 0.09 mm

Data collection
  • Bruker SMART diffractometer

  • ω scans

  • Absorption correction: multi-scan(SADABS; Siemens, 1996[Siemens (1996). SADABS. Siemens Analytical X-ray Instruments Inc., Madison, WIisconsin, USA.])Tmin = 0.73, Tmax = 0.99

  • 5465 measured reflections

  • 1909 independent reflections

  • 1487 reflections with I > 2σ(I)

  • Rint = 0.063

  • θmax = 26.4°

  • h = −13 → 12

  • k = −8 → 8

  • l = −15 → 15

Refinement
  • Refinement on F2

  • R[F2 > 2σ(F2)] = 0.058

  • wR(F2) = 0.143

  • S = 0.98

  • 1908 reflections

  • 233 parameters

  • H atoms treated by a mixture of independent and constrained refinement

  • w = 1/[σ2(F2) + (0.05P)2 + 0.49P] where P = [max(Fo2,0) + 2Fc2]/3

  • (Δ/σ)max < 0.001

  • Δρmax = 0.24 e Å−3

  • Δρmin = −0.24 e Å−3

Table 1
Selected geometric parameters (Å, °)

N11—C21 1.467 (6)
C21—C31 1.526 (6)
C31—O41 1.219 (5)
C31—N51 1.332 (5)
N51—C61 1.474 (5)
N51—C91 1.471 (5)
C61—C71 1.511 (7)
C71—C81 1.515 (7)
C81—C91 1.538 (6)
C91—C101 1.529 (6)
C101—O111 1.253 (6)
C101—O121 1.253 (5)
N12—C22 1.461 (5)
C22—C32 1.515 (6)
C32—O42 1.217 (5)
C32—N52 1.334 (5)
N52—C62 1.470 (6)
N52—C92 1.467 (5)
C62—C72 1.503 (9)
C72—C82 1.521 (7)
C82—C92 1.549 (7)
C92—C102 1.524 (6)
C102—O112 1.231 (6)
C102—O122 1.268 (5)
N11—C21—C31 108.8 (4)
C21—C31—O41 120.8 (4)
C21—C31—N51 115.6 (4)
O41—C31—N51 123.6 (4)
C31—N51—C61 127.3 (3)
C31—N51—C91 119.9 (3)
C61—N51—C91 112.8 (3)
N51—C61—C71 103.3 (3)
C61—C71—C81 104.0 (4)
C71—C81—C91 104.5 (4)
C81—C91—N51 102.1 (3)
C81—C91—C101 112.9 (3)
N51—C91—C101 111.3 (3)
C91—C101—O111 118.3 (4)
C91—C101—O121 117.9 (4)
O111—C101—O121 123.7 (4)
N12—C22—C32 110.3 (3)
C22—C32—O42 119.3 (4)
C22—C32—N52 117.4 (4)
O42—C32—N52 123.3 (4)
C32—N52—C62 120.8 (4)
C32—N52—C92 127.0 (3)
C62—N52—C92 112.1 (4)
N52—C62—C72 102.3 (4)
C62—C72—C82 104.2 (4)
C72—C82—C92 104.3 (4)
C82—C92—N52 103.5 (3)
C82—C92—C102 111.4 (4)
N52—C92—C102 113.9 (4)
C92—C102—O112 120.6 (4)
C92—C102—O122 114.8 (4)
O112—C102—O122 124.6 (4)

Table 2
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N11—H112⋯O122i 0.90 1.95 2.728 (5) 143
N11—H113⋯O13ii 0.90 2.11 2.789 (6) 131
N12—H121⋯O121iii 0.90 2.11 2.876 (5) 142
N12—H122⋯O121iv 0.90 2.15 2.896 (6) 140
N12—H123⋯O111 0.90 1.95 2.839 (5) 168
O13—H131⋯O111 0.85 (1) 1.91 (2) 2.739 (5) 164 (5)
O13—H132⋯O112i 0.85 (1) 2.06 (3) 2.872 (5) 160 (6)
Symmetry codes: (i) [-x+1, y-{\script{1\over 2}}, -z+1]; (ii) x, y-1, z; (iii) [-x+1, y+{\script{1\over 2}}, -z+1]; (iv) x, y+1, z.

H atoms in the GLY–PRO mol­ecules were all placed in calculated positions, with Uiso(H) = 1.2Ueq(C,N), C—H = 0.99 and 1.00 Å, and N—H = 0.90 Å. The H atoms of the water of crystallization (O13) were located in a difference map and refined, subject to the restraints O—H = 0.85 (1) Å and H—O—H = 105 (1)°. A common isotropic displacement parameter was also refined. The 102 reflection was omitted from the refinement since it seemed to suffer from the effects of extinction. In the absence of significant anomalous dispersion effects, Friedel pairs were averaged. The absolute configuration of the model reported here is based on the known configuration of the sample.

Data collection: SMART (Siemens, 1993[Siemens (1993). SMART. Siemens Analytical X-ray Instruments Inc., Madison, WIisconsin, USA.]); cell refinement: SAINT (Siemens, 1995[Siemens (1995). SAINT. Siemens Analytical X-ray Instruments Inc., Madison, WIisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SIR92 (Altomare et al., 1994[Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G. & Camalli, M. (1994). J. Appl. Cryst. 27, 435.]); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003[Betteridge, P. W., Carruthers, J. R., Cooper, R. I., Prout, K. & Watkin, D. J. (2003). J. Appl. Cryst. 36, 1487.]); molecular graphics: XP (Sheldrick, 1997[Sheldrick, G. M. (1997). XP. University of Göttingen, Germany.]) and DIAMOND (Crystal Impact, 2004[Crystal Impact (2004). DIAMOND. Version 3.0. Crystal Impact GbR, Postfach 1251, 53002 Bonn, Germany. (https://www.crystalimpact.com/diamond.)]); software used to prepare material for publication: CRYSTALS.

Supporting information


Computing details top

Data collection: SMART (Siemens, 1993); cell refinement: SAINT (Siemens, 1995); data reduction: SAINT; program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: XP (Sheldrick, 1997) and DIAMOND (Crystal Impact, 2004); software used to prepare material for publication: CRYSTALS.

Glycyl-proline hemihydrate top
Crystal data top
C7H12N2O3·0.5H2OF(000) = 388
Mr = 181.19Dx = 1.408 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ybCell parameters from 685 reflections
a = 11.171 (4) Åθ = 4–20°
b = 6.619 (3) ŵ = 0.11 mm1
c = 12.371 (5) ÅT = 293 K
β = 110.818 (7)°Plate, colourless
V = 855.0 (6) Å30.12 × 0.11 × 0.09 mm
Z = 4
Data collection top
Bruker SMART
diffractometer
1487 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.063
ω scansθmax = 26.4°, θmin = 2.0°
Absorption correction: multi-scan
(SADABS; Siemens, 1996)
h = 1312
Tmin = 0.73, Tmax = 0.99k = 88
5465 measured reflectionsl = 1515
1909 independent reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.058Hydrogen site location: calc + difmap
wR(F2) = 0.143H atoms treated by a mixture of independent and constrained refinement
S = 0.98 w = 1/[σ2(F2) + (0.05P)2 + 0.49P]
where P = [max(Fo2,0) + 2Fc2]/3
1908 reflections(Δ/σ)max = 0.000089
233 parametersΔρmax = 0.24 e Å3
4 restraintsΔρmin = 0.24 e Å3
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
N110.4213 (3)0.0745 (6)0.9062 (3)0.0365
C210.3273 (4)0.0884 (7)0.8627 (4)0.0372
C310.3095 (4)0.1297 (6)0.7365 (4)0.0309
O410.3646 (3)0.0276 (5)0.6866 (3)0.0443
N510.2299 (3)0.2803 (6)0.6865 (3)0.0307
C610.1708 (4)0.4258 (7)0.7427 (4)0.0373
C710.1209 (4)0.5894 (7)0.6527 (4)0.0413
C810.0901 (4)0.4790 (7)0.5387 (4)0.0372
C910.1968 (4)0.3201 (7)0.5622 (3)0.0296
C1010.3126 (4)0.3972 (7)0.5360 (4)0.0305
O1110.3764 (3)0.5397 (5)0.5957 (3)0.0397
O1210.3350 (3)0.3195 (6)0.4528 (3)0.0450
N120.3938 (3)0.8920 (6)0.4713 (3)0.0340
C220.3539 (4)0.8173 (8)0.3525 (4)0.0365
C320.2154 (4)0.7497 (6)0.3115 (4)0.0306
O420.1453 (3)0.8150 (6)0.3594 (3)0.0457
N520.1772 (3)0.6175 (6)0.2245 (3)0.0319
C620.0492 (4)0.5256 (9)0.1888 (4)0.0462
C720.0702 (5)0.3248 (10)0.1418 (5)0.0621
C820.1663 (5)0.3697 (8)0.0833 (5)0.0513
C920.2534 (4)0.5365 (7)0.1593 (4)0.0324
C1020.2890 (4)0.6934 (7)0.0858 (4)0.0342
O1120.2605 (3)0.8723 (5)0.0893 (3)0.0483
O1220.3500 (3)0.6245 (6)0.0247 (3)0.0492
O130.4923 (4)0.5626 (8)0.8312 (3)0.0655
H1110.43250.09990.98060.0574*
H1120.49640.03680.90080.0574*
H1130.39270.18670.86370.0574*
H2110.35860.21210.90910.0458*
H2120.24460.04720.86830.0458*
H6110.23500.48050.81440.0474*
H6120.10010.36220.76100.0474*
H7110.04300.65280.65840.0509*
H7120.18690.69430.66160.0509*
H8110.00510.41330.51600.0446*
H8120.09140.57320.47700.0446*
H910.16230.19470.51670.0359*
H1210.47610.93170.49460.0526*
H1220.34430.99740.47440.0526*
H1230.38550.79280.51790.0526*
H2210.36340.92670.30150.0458*
H2220.40870.70160.34930.0458*
H6210.02080.50850.25540.0570*
H6220.01450.60750.12850.0570*
H7210.10560.22550.20490.0770*
H7220.01080.27240.08510.0770*
H8210.12220.41890.00330.0636*
H8220.21690.24770.08170.0636*
H920.33320.47340.21420.0401*
H1310.468 (4)0.569 (11)0.7577 (10)0.063 (12)*
H1320.5720 (17)0.535 (10)0.854 (3)0.063 (12)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N110.042 (2)0.034 (2)0.039 (2)0.0020 (17)0.0208 (18)0.0087 (17)
C210.037 (2)0.040 (3)0.038 (2)0.008 (2)0.017 (2)0.011 (2)
C310.039 (2)0.024 (2)0.031 (2)0.0047 (19)0.0155 (19)0.0002 (19)
O410.066 (2)0.0355 (18)0.0388 (17)0.0153 (17)0.0277 (17)0.0031 (16)
N510.0358 (18)0.0305 (19)0.0295 (18)0.0023 (16)0.0160 (15)0.0013 (16)
C610.041 (2)0.038 (3)0.039 (2)0.001 (2)0.022 (2)0.006 (2)
C710.041 (2)0.038 (3)0.048 (3)0.006 (2)0.020 (2)0.000 (2)
C810.032 (2)0.040 (3)0.039 (3)0.003 (2)0.013 (2)0.004 (2)
C910.030 (2)0.028 (2)0.031 (2)0.0039 (18)0.0117 (17)0.000 (2)
C1010.031 (2)0.028 (2)0.032 (2)0.0063 (19)0.0102 (18)0.006 (2)
O1110.0356 (16)0.0392 (18)0.0446 (17)0.0080 (15)0.0146 (14)0.0018 (17)
O1210.0510 (19)0.050 (2)0.0417 (17)0.0031 (17)0.0258 (15)0.0027 (18)
N120.0358 (19)0.0326 (19)0.037 (2)0.0046 (17)0.0165 (17)0.0076 (17)
C220.036 (2)0.047 (3)0.031 (2)0.004 (2)0.0179 (18)0.007 (2)
C320.030 (2)0.033 (3)0.032 (2)0.0012 (19)0.0146 (18)0.005 (2)
O420.0383 (17)0.061 (2)0.0488 (18)0.0016 (17)0.0287 (15)0.0135 (19)
N520.0283 (18)0.035 (2)0.0357 (19)0.0008 (16)0.0154 (16)0.0006 (18)
C620.037 (2)0.061 (3)0.045 (3)0.011 (2)0.019 (2)0.010 (3)
C720.064 (3)0.056 (4)0.072 (4)0.024 (3)0.032 (3)0.011 (3)
C820.064 (3)0.036 (3)0.058 (3)0.008 (2)0.028 (3)0.007 (3)
C920.034 (2)0.034 (2)0.032 (2)0.007 (2)0.0154 (18)0.005 (2)
C1020.032 (2)0.040 (3)0.031 (2)0.004 (2)0.0124 (19)0.002 (2)
O1120.063 (2)0.037 (2)0.052 (2)0.0063 (17)0.0292 (18)0.0093 (17)
O1220.055 (2)0.057 (2)0.0492 (19)0.0046 (19)0.0356 (18)0.0030 (19)
O130.069 (3)0.080 (3)0.047 (2)0.023 (3)0.0198 (19)0.016 (2)
Geometric parameters (Å, º) top
N11—C211.467 (6)N12—H1210.900
N11—H1110.900N12—H1220.900
N11—H1120.900N12—H1230.900
N11—H1130.900C22—C321.515 (6)
C21—C311.526 (6)C22—H2210.990
C21—H2110.990C22—H2220.990
C21—H2120.990C32—O421.217 (5)
C31—O411.219 (5)C32—N521.334 (5)
C31—N511.332 (5)N52—C621.470 (6)
N51—C611.474 (5)N52—C921.467 (5)
N51—C911.471 (5)C62—C721.503 (9)
C61—C711.511 (7)C62—H6210.990
C61—H6110.990C62—H6220.990
C61—H6120.990C72—C821.521 (7)
C71—C811.515 (7)C72—H7210.989
C71—H7110.990C72—H7220.990
C71—H7120.990C82—C921.549 (7)
C81—C911.538 (6)C82—H8210.990
C81—H8110.990C82—H8220.990
C81—H8120.990C92—C1021.524 (6)
C91—C1011.529 (6)C92—H921.000
C91—H911.000C102—O1121.231 (6)
C101—O1111.253 (6)C102—O1221.268 (5)
C101—O1211.253 (5)O13—H1310.852 (10)
N12—C221.461 (5)O13—H1320.853 (10)
C21—N11—H111109.5C22—N12—H122109.5
C21—N11—H112109.5H121—N12—H122109.5
H111—N11—H112109.5C22—N12—H123109.5
C21—N11—H113109.5H121—N12—H123109.5
H111—N11—H113109.5H122—N12—H123109.5
H112—N11—H113109.5N12—C22—C32110.3 (3)
N11—C21—C31108.8 (4)N12—C22—H221109.3
N11—C21—H211109.6C32—C22—H221109.3
C31—C21—H211109.6N12—C22—H222109.3
N11—C21—H212109.6C32—C22—H222109.3
C31—C21—H212109.6H221—C22—H222109.5
H211—C21—H212109.5C22—C32—O42119.3 (4)
C21—C31—O41120.8 (4)C22—C32—N52117.4 (4)
C21—C31—N51115.6 (4)O42—C32—N52123.3 (4)
O41—C31—N51123.6 (4)C32—N52—C62120.8 (4)
C31—N51—C61127.3 (3)C32—N52—C92127.0 (3)
C31—N51—C91119.9 (3)C62—N52—C92112.1 (4)
C61—N51—C91112.8 (3)N52—C62—C72102.3 (4)
N51—C61—C71103.3 (3)N52—C62—H621111.2
N51—C61—H611111.0C72—C62—H621111.2
C71—C61—H611111.0N52—C62—H622111.2
N51—C61—H612111.0C72—C62—H622111.2
C71—C61—H612111.0H621—C62—H622109.5
H611—C61—H612109.5C62—C72—C82104.2 (4)
C61—C71—C81104.0 (4)C62—C72—H721110.8
C61—C71—H711110.8C82—C72—H721110.8
C81—C71—H711110.8C62—C72—H722110.8
C61—C71—H712110.8C82—C72—H722110.7
C81—C71—H712110.8H721—C72—H722109.5
H711—C71—H712109.5C72—C82—C92104.3 (4)
C71—C81—C91104.5 (4)C72—C82—H821110.8
C71—C81—H811110.7C92—C82—H821110.7
C91—C81—H811110.7C72—C82—H822110.7
C71—C81—H812110.7C92—C82—H822110.8
C91—C81—H812110.7H821—C82—H822109.4
H811—C81—H812109.5C82—C92—N52103.5 (3)
C81—C91—N51102.1 (3)C82—C92—C102111.4 (4)
C81—C91—C101112.9 (3)N52—C92—C102113.9 (4)
N51—C91—C101111.3 (3)C82—C92—H92109.3
C81—C91—H91110.1N52—C92—H92109.3
N51—C91—H91110.1C102—C92—H92109.3
C101—C91—H91110.1C92—C102—O112120.6 (4)
C91—C101—O111118.3 (4)C92—C102—O122114.8 (4)
C91—C101—O121117.9 (4)O112—C102—O122124.6 (4)
O111—C101—O121123.7 (4)H131—O13—H132105.1 (10)
C22—N12—H121109.5
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N11—H112···O122i0.901.952.728 (5)143
N11—H113···O13ii0.902.112.789 (6)131
N12—H121···O121iii0.902.112.876 (5)142
N12—H122···O121iv0.902.152.896 (6)140
N12—H123···O1110.901.952.839 (5)168
O13—H131···O1110.85 (1)1.91 (2)2.739 (5)164 (5)
O13—H132···O112i0.85 (1)2.06 (3)2.872 (5)160 (6)
Symmetry codes: (i) x+1, y1/2, z+1; (ii) x, y1, z; (iii) x+1, y+1/2, z+1; (iv) x, y+1, z.
 

Acknowledgements

We thank the EPSRC for funding.

References

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