organic compounds
Glycyl-L-proline hemihydrate at 298 K
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
The L-proline (GLY–PRO) hemihydrate, C7H12N2O3·0.5H2O, has two molecules of GLY–PRO in the one molecule adopts the cis configuration at the peptide bond and the other adopts the trans configuration.
of glycyl-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). In the case of proline, however, this ratio drops to 4 to 1 (see, for example, Creighton, 1993).
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. cis–trans Isomerization of the prolyl peptide bond has been implicated in the slow refolding of proteins (e.g. Brandts et al., 1975) 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). The structure of (I) contains two GLY–PRO molecules in the viz. one (based on N11) in the trans form and the other in the cis form (Figs. 1 and 2, 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 and 4).
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
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Refinement
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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 since it seemed to suffer from the effects of extinction. In the absence of significant effects, Friedel pairs were averaged. The of the model reported here is based on the known configuration of the sample.
Data collection: SMART (Siemens, 1993); cell 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.
Supporting information
https://doi.org/10.1107/S1600536806004922/wn2003sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536806004922/wn2003Isup2.hkl
Data collection: SMART (Siemens, 1993); cell
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.C7H12N2O3·0.5H2O | F(000) = 388 |
Mr = 181.19 | Dx = 1.408 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 685 reflections |
a = 11.171 (4) Å | θ = 4–20° |
b = 6.619 (3) Å | µ = 0.11 mm−1 |
c = 12.371 (5) Å | T = 293 K |
β = 110.818 (7)° | Plate, colourless |
V = 855.0 (6) Å3 | 0.12 × 0.11 × 0.09 mm |
Z = 4 |
Bruker SMART diffractometer | 1487 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.063 |
ω scans | θmax = 26.4°, θmin = 2.0° |
Absorption correction: multi-scan (SADABS; Siemens, 1996) | h = −13→12 |
Tmin = 0.73, Tmax = 0.99 | k = −8→8 |
5465 measured reflections | l = −15→15 |
1909 independent reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.058 | Hydrogen site location: calc + difmap |
wR(F2) = 0.143 | H 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 parameters | Δρmax = 0.24 e Å−3 |
4 restraints | Δρmin = −0.24 e Å−3 |
x | y | z | Uiso*/Ueq | ||
N11 | 0.4213 (3) | −0.0745 (6) | 0.9062 (3) | 0.0365 | |
C21 | 0.3273 (4) | 0.0884 (7) | 0.8627 (4) | 0.0372 | |
C31 | 0.3095 (4) | 0.1297 (6) | 0.7365 (4) | 0.0309 | |
O41 | 0.3646 (3) | 0.0276 (5) | 0.6866 (3) | 0.0443 | |
N51 | 0.2299 (3) | 0.2803 (6) | 0.6865 (3) | 0.0307 | |
C61 | 0.1708 (4) | 0.4258 (7) | 0.7427 (4) | 0.0373 | |
C71 | 0.1209 (4) | 0.5894 (7) | 0.6527 (4) | 0.0413 | |
C81 | 0.0901 (4) | 0.4790 (7) | 0.5387 (4) | 0.0372 | |
C91 | 0.1968 (4) | 0.3201 (7) | 0.5622 (3) | 0.0296 | |
C101 | 0.3126 (4) | 0.3972 (7) | 0.5360 (4) | 0.0305 | |
O111 | 0.3764 (3) | 0.5397 (5) | 0.5957 (3) | 0.0397 | |
O121 | 0.3350 (3) | 0.3195 (6) | 0.4528 (3) | 0.0450 | |
N12 | 0.3938 (3) | 0.8920 (6) | 0.4713 (3) | 0.0340 | |
C22 | 0.3539 (4) | 0.8173 (8) | 0.3525 (4) | 0.0365 | |
C32 | 0.2154 (4) | 0.7497 (6) | 0.3115 (4) | 0.0306 | |
O42 | 0.1453 (3) | 0.8150 (6) | 0.3594 (3) | 0.0457 | |
N52 | 0.1772 (3) | 0.6175 (6) | 0.2245 (3) | 0.0319 | |
C62 | 0.0492 (4) | 0.5256 (9) | 0.1888 (4) | 0.0462 | |
C72 | 0.0702 (5) | 0.3248 (10) | 0.1418 (5) | 0.0621 | |
C82 | 0.1663 (5) | 0.3697 (8) | 0.0833 (5) | 0.0513 | |
C92 | 0.2534 (4) | 0.5365 (7) | 0.1593 (4) | 0.0324 | |
C102 | 0.2890 (4) | 0.6934 (7) | 0.0858 (4) | 0.0342 | |
O112 | 0.2605 (3) | 0.8723 (5) | 0.0893 (3) | 0.0483 | |
O122 | 0.3500 (3) | 0.6245 (6) | 0.0247 (3) | 0.0492 | |
O13 | 0.4923 (4) | 0.5626 (8) | 0.8312 (3) | 0.0655 | |
H111 | 0.4325 | −0.0999 | 0.9806 | 0.0574* | |
H112 | 0.4964 | −0.0368 | 0.9008 | 0.0574* | |
H113 | 0.3927 | −0.1867 | 0.8637 | 0.0574* | |
H211 | 0.3586 | 0.2121 | 0.9091 | 0.0458* | |
H212 | 0.2446 | 0.0472 | 0.8683 | 0.0458* | |
H611 | 0.2350 | 0.4805 | 0.8144 | 0.0474* | |
H612 | 0.1001 | 0.3622 | 0.7610 | 0.0474* | |
H711 | 0.0430 | 0.6528 | 0.6584 | 0.0509* | |
H712 | 0.1869 | 0.6943 | 0.6616 | 0.0509* | |
H811 | 0.0051 | 0.4133 | 0.5160 | 0.0446* | |
H812 | 0.0914 | 0.5732 | 0.4770 | 0.0446* | |
H91 | 0.1623 | 0.1947 | 0.5167 | 0.0359* | |
H121 | 0.4761 | 0.9317 | 0.4946 | 0.0526* | |
H122 | 0.3443 | 0.9974 | 0.4744 | 0.0526* | |
H123 | 0.3855 | 0.7928 | 0.5179 | 0.0526* | |
H221 | 0.3634 | 0.9267 | 0.3015 | 0.0458* | |
H222 | 0.4087 | 0.7016 | 0.3493 | 0.0458* | |
H621 | 0.0208 | 0.5085 | 0.2554 | 0.0570* | |
H622 | −0.0145 | 0.6075 | 0.1285 | 0.0570* | |
H721 | 0.1056 | 0.2255 | 0.2049 | 0.0770* | |
H722 | −0.0108 | 0.2724 | 0.0851 | 0.0770* | |
H821 | 0.1222 | 0.4189 | 0.0033 | 0.0636* | |
H822 | 0.2169 | 0.2477 | 0.0817 | 0.0636* | |
H92 | 0.3332 | 0.4734 | 0.2142 | 0.0401* | |
H131 | 0.468 (4) | 0.569 (11) | 0.7577 (10) | 0.063 (12)* | |
H132 | 0.5720 (17) | 0.535 (10) | 0.854 (3) | 0.063 (12)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N11 | 0.042 (2) | 0.034 (2) | 0.039 (2) | −0.0020 (17) | 0.0208 (18) | 0.0087 (17) |
C21 | 0.037 (2) | 0.040 (3) | 0.038 (2) | 0.008 (2) | 0.017 (2) | 0.011 (2) |
C31 | 0.039 (2) | 0.024 (2) | 0.031 (2) | −0.0047 (19) | 0.0155 (19) | 0.0002 (19) |
O41 | 0.066 (2) | 0.0355 (18) | 0.0388 (17) | 0.0153 (17) | 0.0277 (17) | 0.0031 (16) |
N51 | 0.0358 (18) | 0.0305 (19) | 0.0295 (18) | 0.0023 (16) | 0.0160 (15) | 0.0013 (16) |
C61 | 0.041 (2) | 0.038 (3) | 0.039 (2) | −0.001 (2) | 0.022 (2) | −0.006 (2) |
C71 | 0.041 (2) | 0.038 (3) | 0.048 (3) | 0.006 (2) | 0.020 (2) | 0.000 (2) |
C81 | 0.032 (2) | 0.040 (3) | 0.039 (3) | 0.003 (2) | 0.013 (2) | 0.004 (2) |
C91 | 0.030 (2) | 0.028 (2) | 0.031 (2) | −0.0039 (18) | 0.0117 (17) | 0.000 (2) |
C101 | 0.031 (2) | 0.028 (2) | 0.032 (2) | 0.0063 (19) | 0.0102 (18) | 0.006 (2) |
O111 | 0.0356 (16) | 0.0392 (18) | 0.0446 (17) | −0.0080 (15) | 0.0146 (14) | −0.0018 (17) |
O121 | 0.0510 (19) | 0.050 (2) | 0.0417 (17) | 0.0031 (17) | 0.0258 (15) | 0.0027 (18) |
N12 | 0.0358 (19) | 0.0326 (19) | 0.037 (2) | −0.0046 (17) | 0.0165 (17) | −0.0076 (17) |
C22 | 0.036 (2) | 0.047 (3) | 0.031 (2) | −0.004 (2) | 0.0179 (18) | −0.007 (2) |
C32 | 0.030 (2) | 0.033 (3) | 0.032 (2) | 0.0012 (19) | 0.0146 (18) | 0.005 (2) |
O42 | 0.0383 (17) | 0.061 (2) | 0.0488 (18) | −0.0016 (17) | 0.0287 (15) | −0.0135 (19) |
N52 | 0.0283 (18) | 0.035 (2) | 0.0357 (19) | −0.0008 (16) | 0.0154 (16) | 0.0006 (18) |
C62 | 0.037 (2) | 0.061 (3) | 0.045 (3) | −0.011 (2) | 0.019 (2) | −0.010 (3) |
C72 | 0.064 (3) | 0.056 (4) | 0.072 (4) | −0.024 (3) | 0.032 (3) | −0.011 (3) |
C82 | 0.064 (3) | 0.036 (3) | 0.058 (3) | −0.008 (2) | 0.028 (3) | −0.007 (3) |
C92 | 0.034 (2) | 0.034 (2) | 0.032 (2) | 0.007 (2) | 0.0154 (18) | 0.005 (2) |
C102 | 0.032 (2) | 0.040 (3) | 0.031 (2) | −0.004 (2) | 0.0124 (19) | 0.002 (2) |
O112 | 0.063 (2) | 0.037 (2) | 0.052 (2) | 0.0063 (17) | 0.0292 (18) | 0.0093 (17) |
O122 | 0.055 (2) | 0.057 (2) | 0.0492 (19) | 0.0046 (19) | 0.0356 (18) | 0.0030 (19) |
O13 | 0.069 (3) | 0.080 (3) | 0.047 (2) | 0.023 (3) | 0.0198 (19) | −0.016 (2) |
N11—C21 | 1.467 (6) | N12—H121 | 0.900 |
N11—H111 | 0.900 | N12—H122 | 0.900 |
N11—H112 | 0.900 | N12—H123 | 0.900 |
N11—H113 | 0.900 | C22—C32 | 1.515 (6) |
C21—C31 | 1.526 (6) | C22—H221 | 0.990 |
C21—H211 | 0.990 | C22—H222 | 0.990 |
C21—H212 | 0.990 | C32—O42 | 1.217 (5) |
C31—O41 | 1.219 (5) | C32—N52 | 1.334 (5) |
C31—N51 | 1.332 (5) | N52—C62 | 1.470 (6) |
N51—C61 | 1.474 (5) | N52—C92 | 1.467 (5) |
N51—C91 | 1.471 (5) | C62—C72 | 1.503 (9) |
C61—C71 | 1.511 (7) | C62—H621 | 0.990 |
C61—H611 | 0.990 | C62—H622 | 0.990 |
C61—H612 | 0.990 | C72—C82 | 1.521 (7) |
C71—C81 | 1.515 (7) | C72—H721 | 0.989 |
C71—H711 | 0.990 | C72—H722 | 0.990 |
C71—H712 | 0.990 | C82—C92 | 1.549 (7) |
C81—C91 | 1.538 (6) | C82—H821 | 0.990 |
C81—H811 | 0.990 | C82—H822 | 0.990 |
C81—H812 | 0.990 | C92—C102 | 1.524 (6) |
C91—C101 | 1.529 (6) | C92—H92 | 1.000 |
C91—H91 | 1.000 | C102—O112 | 1.231 (6) |
C101—O111 | 1.253 (6) | C102—O122 | 1.268 (5) |
C101—O121 | 1.253 (5) | O13—H131 | 0.852 (10) |
N12—C22 | 1.461 (5) | O13—H132 | 0.853 (10) |
C21—N11—H111 | 109.5 | C22—N12—H122 | 109.5 |
C21—N11—H112 | 109.5 | H121—N12—H122 | 109.5 |
H111—N11—H112 | 109.5 | C22—N12—H123 | 109.5 |
C21—N11—H113 | 109.5 | H121—N12—H123 | 109.5 |
H111—N11—H113 | 109.5 | H122—N12—H123 | 109.5 |
H112—N11—H113 | 109.5 | N12—C22—C32 | 110.3 (3) |
N11—C21—C31 | 108.8 (4) | N12—C22—H221 | 109.3 |
N11—C21—H211 | 109.6 | C32—C22—H221 | 109.3 |
C31—C21—H211 | 109.6 | N12—C22—H222 | 109.3 |
N11—C21—H212 | 109.6 | C32—C22—H222 | 109.3 |
C31—C21—H212 | 109.6 | H221—C22—H222 | 109.5 |
H211—C21—H212 | 109.5 | C22—C32—O42 | 119.3 (4) |
C21—C31—O41 | 120.8 (4) | C22—C32—N52 | 117.4 (4) |
C21—C31—N51 | 115.6 (4) | O42—C32—N52 | 123.3 (4) |
O41—C31—N51 | 123.6 (4) | C32—N52—C62 | 120.8 (4) |
C31—N51—C61 | 127.3 (3) | C32—N52—C92 | 127.0 (3) |
C31—N51—C91 | 119.9 (3) | C62—N52—C92 | 112.1 (4) |
C61—N51—C91 | 112.8 (3) | N52—C62—C72 | 102.3 (4) |
N51—C61—C71 | 103.3 (3) | N52—C62—H621 | 111.2 |
N51—C61—H611 | 111.0 | C72—C62—H621 | 111.2 |
C71—C61—H611 | 111.0 | N52—C62—H622 | 111.2 |
N51—C61—H612 | 111.0 | C72—C62—H622 | 111.2 |
C71—C61—H612 | 111.0 | H621—C62—H622 | 109.5 |
H611—C61—H612 | 109.5 | C62—C72—C82 | 104.2 (4) |
C61—C71—C81 | 104.0 (4) | C62—C72—H721 | 110.8 |
C61—C71—H711 | 110.8 | C82—C72—H721 | 110.8 |
C81—C71—H711 | 110.8 | C62—C72—H722 | 110.8 |
C61—C71—H712 | 110.8 | C82—C72—H722 | 110.7 |
C81—C71—H712 | 110.8 | H721—C72—H722 | 109.5 |
H711—C71—H712 | 109.5 | C72—C82—C92 | 104.3 (4) |
C71—C81—C91 | 104.5 (4) | C72—C82—H821 | 110.8 |
C71—C81—H811 | 110.7 | C92—C82—H821 | 110.7 |
C91—C81—H811 | 110.7 | C72—C82—H822 | 110.7 |
C71—C81—H812 | 110.7 | C92—C82—H822 | 110.8 |
C91—C81—H812 | 110.7 | H821—C82—H822 | 109.4 |
H811—C81—H812 | 109.5 | C82—C92—N52 | 103.5 (3) |
C81—C91—N51 | 102.1 (3) | C82—C92—C102 | 111.4 (4) |
C81—C91—C101 | 112.9 (3) | N52—C92—C102 | 113.9 (4) |
N51—C91—C101 | 111.3 (3) | C82—C92—H92 | 109.3 |
C81—C91—H91 | 110.1 | N52—C92—H92 | 109.3 |
N51—C91—H91 | 110.1 | C102—C92—H92 | 109.3 |
C101—C91—H91 | 110.1 | C92—C102—O112 | 120.6 (4) |
C91—C101—O111 | 118.3 (4) | C92—C102—O122 | 114.8 (4) |
C91—C101—O121 | 117.9 (4) | O112—C102—O122 | 124.6 (4) |
O111—C101—O121 | 123.7 (4) | H131—O13—H132 | 105.1 (10) |
C22—N12—H121 | 109.5 |
D—H···A | D—H | H···A | D···A | 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−1/2, −z+1; (ii) x, y−1, 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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