| Literature DB >> 25553003 |
Paweł Lenartowicz1, Maciej Makowski1, Bartosz Zarychta1, Krzysztof Ejsmont1.
Abstract
In the title compound, the <span class="Chemical">de-hydro-dipeptide (<class="Chemical">span class="Gene">Boc-Phe-ΔAla-OiPr, C20H28N2O5), the mol-ecule has a trans conformation of the N-methyl-amide group. The geometry of the de-hydro-alanine moiety is to some extent different from those usually found in simple peptides, indicating conjugation between the H2C=C group and the peptide bond. The bond angles around de-hydro-alanine have unusually high values due to the steric hindrance, the same inter-action influencing the slight distortion from planarity of the de-hydro-alanine. The mol-ecule is stabilized by intra-molecular inter-actions between the isopropyl group and the N atoms of the peptide main chain. In the crystal, an N-H⋯O hydrogen bond links the mol-ecules into ribbons, giving a herringbone head-to-head packing arrangement extending along the [100] direction. In the stacks, the mol-ecules are linked by weak C-H⋯O hydrogen-bonding associations.Entities:
Keywords: crystal structure; dehydro peptides; dehydroalanine; herringbone packing; α,β-dehydroamino acids
Year: 2014 PMID: 25553003 PMCID: PMC4257372 DOI: 10.1107/S1600536814025197
Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN: 1600-5368
Figure 1The molecular structure of N-(tert-butoxycarbonyl)phenylalanyldehydroalanine isopropyl ester (Boc–Phe–ΔAla–OiPr) showing 50% displacement ellipsoids. Intramolecular C—H⋯O interactions are shown as dashed lines.
Hydrogen-bond geometry (, )
|
|
| H |
|
|
|---|---|---|---|---|
| N8H8 | 0.88 | 2.21 | 2.952(2) | 141 |
| C3H3 | 0.98 | 2.51 | 3.423(3) | 155 |
| C21H21 | 0.95 | 2.27 | 2.869(3) | 120 |
| C26H26 | 0.98 | 2.52 | 3.462(3) | 162 |
Symmetry codes: (i) ; (ii) .
Figure 2The packing diagram of the title compound, viewed along the b axis, showing the intermolecular hydrogen-bonding scheme (dashed lines).
Experimental details
| Crystal data | |
| Chemical formula | C20H28N2O5 |
|
| 376.44 |
| Crystal system, space group | Orthorhombic, |
| Temperature (K) | 100 |
|
| 5.2123(2), 9.5031(3), 41.3363(17) |
|
| 2047.51(13) |
|
| 4 |
| Radiation type | Mo |
| (mm1) | 0.09 |
| Crystal size (mm) | 0.33 0.18 0.14 |
| Data collection | |
| Diffractometer | Oxford Diffraction Xcalibur CCD |
| No. of measured, independent and observed [ | 14003, 4025, 3235 |
|
| 0.046 |
| (sin /)max (1) | 0.617 |
| Refinement | |
|
| 0.046, 0.079, 0.98 |
| No. of reflections | 4025 |
| No. of parameters | 244 |
| H-atom treatment | H-atom parameters constrained |
| max, min (e 3) | 0.22, 0.22 |
| Absolute structure | Flack |
| Absolute structure parameter | 0.1(6) |
Computer programs: CrysAlis CCD and CrysAlis RED (Oxford Diffraction, 2008 ▶), SHELXL2014 and SHELXTL (Sheldrick, 2008 ▶).
| C20H28N2O5 | |
| Melting point = 367–369 K | |
| Orthorhombic, | Mo |
| Cell parameters from 4025 reflections | |
| θ = 3.3–26.0° | |
| µ = 0.09 mm−1 | |
| Irregular, colourless | |
| 0.33 × 0.18 × 0.14 mm |
| Oxford Diffraction Xcalibur CCD diffractometer | 3235 reflections with |
| Radiation source: fine-focus sealed tube | |
| Graphite monochromator | θmax = 26.0°, θmin = 3.3° |
| ω scans | |
| 14003 measured reflections | |
| 4025 independent reflections |
| Refinement on | Hydrogen site location: inferred from neighbouring sites |
| Least-squares matrix: full | H-atom parameters constrained |
| (Δ/σ)max < 0.001 | |
| Δρmax = 0.22 e Å−3 | |
| 4025 reflections | Δρmin = −0.22 e Å−3 |
| 244 parameters | Absolute structure: Flack |
| 0 restraints | Absolute structure parameter: −0.1 (6) |
| 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. |
| C1 | 1.2709 (4) | 0.0969 (2) | 0.10948 (7) | 0.0184 (6) | |
| C2 | 1.4195 (5) | 0.1063 (3) | 0.14083 (7) | 0.0249 (7) | |
| H2A | 1.5204 | 0.1933 | 0.1411 | 0.037* | |
| H2B | 1.5348 | 0.0252 | 0.1427 | 0.037* | |
| H2C | 1.2995 | 0.1065 | 0.1591 | 0.037* | |
| C3 | 1.1120 (5) | −0.0366 (3) | 0.10835 (8) | 0.0325 (7) | |
| H3A | 1.0176 | −0.0406 | 0.0879 | 0.049* | |
| H3B | 0.9903 | −0.0369 | 0.1264 | 0.049* | |
| H3C | 1.2254 | −0.1185 | 0.1100 | 0.049* | |
| C4 | 1.4374 (5) | 0.1068 (3) | 0.07954 (7) | 0.0264 (7) | |
| H4A | 1.5397 | 0.1932 | 0.0804 | 0.040* | |
| H4B | 1.3282 | 0.1085 | 0.0602 | 0.040* | |
| H4C | 1.5520 | 0.0252 | 0.0786 | 0.040* | |
| O5 | 1.0713 (3) | 0.20736 (16) | 0.10856 (4) | 0.0194 (4) | |
| C6 | 1.1322 (5) | 0.3446 (2) | 0.10987 (6) | 0.0151 (5) | |
| O7 | 1.3475 (3) | 0.39442 (16) | 0.10970 (4) | 0.0188 (4) | |
| N8 | 0.9116 (3) | 0.4203 (2) | 0.11214 (5) | 0.0148 (5) | |
| H8A | 0.7675 | 0.3751 | 0.1160 | 0.018* | |
| C9 | 0.9025 (4) | 0.5718 (2) | 0.10849 (6) | 0.0150 (5) | |
| H9A | 1.0784 | 0.6105 | 0.1122 | 0.018* | |
| C10 | 0.8141 (5) | 0.6145 (3) | 0.07443 (6) | 0.0176 (6) | |
| H10A | 0.6402 | 0.5761 | 0.0707 | 0.021* | |
| H10B | 0.8020 | 0.7184 | 0.0734 | 0.021* | |
| C11 | 0.9882 (5) | 0.5648 (3) | 0.04781 (6) | 0.0167 (6) | |
| C12 | 1.1944 (5) | 0.6462 (3) | 0.03752 (6) | 0.0231 (6) | |
| H12A | 1.2281 | 0.7335 | 0.0479 | 0.028* | |
| C13 | 1.3509 (5) | 0.6026 (3) | 0.01250 (7) | 0.0312 (7) | |
| H13A | 1.4897 | 0.6601 | 0.0056 | 0.037* | |
| C14 | 1.3057 (6) | 0.4757 (3) | −0.00244 (7) | 0.0338 (8) | |
| H14A | 1.4134 | 0.4455 | −0.0196 | 0.041* | |
| C15 | 1.1046 (5) | 0.3924 (3) | 0.00748 (7) | 0.0317 (7) | |
| H15A | 1.0739 | 0.3046 | −0.0028 | 0.038* | |
| C16 | 0.9473 (5) | 0.4367 (3) | 0.03241 (6) | 0.0244 (7) | |
| H16A | 0.8088 | 0.3787 | 0.0391 | 0.029* | |
| C17 | 0.7185 (5) | 0.6377 (3) | 0.13324 (6) | 0.0177 (6) | |
| O18 | 0.6189 (4) | 0.75177 (19) | 0.12844 (4) | 0.0266 (5) | |
| N19 | 0.6785 (4) | 0.5605 (2) | 0.16029 (5) | 0.0168 (5) | |
| H19A | 0.7841 | 0.4897 | 0.1636 | 0.020* | |
| C20 | 0.4865 (4) | 0.5814 (3) | 0.18356 (6) | 0.0163 (6) | |
| C21 | 0.3165 (5) | 0.6849 (3) | 0.18436 (6) | 0.0233 (6) | |
| H21A | 0.3171 | 0.7549 | 0.1679 | 0.028* | |
| H21B | 0.1940 | 0.6892 | 0.2013 | 0.028* | |
| C22 | 0.4947 (5) | 0.4660 (3) | 0.20809 (6) | 0.0197 (6) | |
| O23 | 0.6457 (4) | 0.36963 (19) | 0.20637 (4) | 0.0282 (5) | |
| O24 | 0.3215 (3) | 0.48235 (17) | 0.23152 (4) | 0.0232 (4) | |
| C25 | 0.3210 (5) | 0.3753 (3) | 0.25720 (6) | 0.0249 (6) | |
| H25A | 0.5018 | 0.3520 | 0.2633 | 0.030* | |
| C26 | 0.1889 (6) | 0.2446 (3) | 0.24504 (6) | 0.0274 (7) | |
| H26A | 0.2849 | 0.2060 | 0.2267 | 0.041* | |
| H26B | 0.0143 | 0.2682 | 0.2381 | 0.041* | |
| H26C | 0.1814 | 0.1746 | 0.2624 | 0.041* | |
| C27 | 0.1881 (6) | 0.4430 (3) | 0.28559 (6) | 0.0323 (7) | |
| H27A | 0.2836 | 0.5269 | 0.2923 | 0.049* | |
| H27B | 0.1807 | 0.3761 | 0.3036 | 0.049* | |
| H27C | 0.0135 | 0.4699 | 0.2793 | 0.049* |
| C1 | 0.0114 (11) | 0.0108 (13) | 0.0330 (15) | 0.0059 (10) | −0.0014 (12) | −0.0004 (12) |
| C2 | 0.0222 (14) | 0.0209 (15) | 0.0315 (16) | 0.0048 (13) | 0.0001 (13) | 0.0041 (13) |
| C3 | 0.0235 (14) | 0.0132 (13) | 0.061 (2) | 0.0028 (12) | −0.0025 (16) | 0.0000 (14) |
| C4 | 0.0188 (14) | 0.0302 (17) | 0.0301 (16) | 0.0049 (14) | −0.0019 (12) | −0.0077 (14) |
| O5 | 0.0107 (9) | 0.0111 (9) | 0.0364 (11) | 0.0019 (7) | 0.0009 (9) | −0.0001 (8) |
| C6 | 0.0163 (13) | 0.0113 (12) | 0.0177 (14) | −0.0004 (11) | −0.0003 (12) | −0.0001 (11) |
| O7 | 0.0097 (8) | 0.0159 (9) | 0.0308 (10) | −0.0025 (8) | 0.0001 (8) | 0.0022 (8) |
| N8 | 0.0084 (9) | 0.0100 (10) | 0.0261 (12) | 0.0007 (8) | 0.0041 (9) | 0.0023 (10) |
| C9 | 0.0126 (11) | 0.0106 (12) | 0.0218 (14) | −0.0004 (10) | 0.0007 (11) | 0.0011 (12) |
| C10 | 0.0163 (12) | 0.0147 (13) | 0.0218 (14) | 0.0026 (12) | −0.0026 (12) | 0.0014 (11) |
| C11 | 0.0146 (12) | 0.0189 (14) | 0.0167 (13) | 0.0044 (12) | −0.0036 (11) | 0.0053 (12) |
| C12 | 0.0219 (14) | 0.0228 (15) | 0.0246 (15) | 0.0011 (14) | −0.0054 (14) | 0.0055 (12) |
| C13 | 0.0203 (14) | 0.047 (2) | 0.0261 (16) | 0.0016 (16) | 0.0003 (14) | 0.0160 (15) |
| C14 | 0.0245 (15) | 0.056 (2) | 0.0208 (16) | 0.0117 (17) | 0.0058 (13) | 0.0011 (15) |
| C15 | 0.0312 (16) | 0.0375 (19) | 0.0265 (16) | 0.0061 (16) | 0.0001 (14) | −0.0093 (14) |
| C16 | 0.0197 (14) | 0.0281 (16) | 0.0254 (16) | −0.0011 (13) | 0.0002 (12) | 0.0002 (13) |
| C17 | 0.0154 (13) | 0.0148 (14) | 0.0228 (15) | −0.0031 (12) | −0.0022 (12) | −0.0021 (12) |
| O18 | 0.0284 (11) | 0.0159 (10) | 0.0356 (12) | 0.0083 (9) | 0.0094 (9) | 0.0026 (9) |
| N19 | 0.0135 (10) | 0.0170 (11) | 0.0198 (12) | 0.0047 (10) | 0.0000 (9) | 0.0016 (10) |
| C20 | 0.0149 (12) | 0.0171 (14) | 0.0168 (13) | −0.0033 (12) | −0.0017 (11) | −0.0029 (12) |
| C21 | 0.0232 (14) | 0.0245 (15) | 0.0221 (15) | 0.0037 (13) | 0.0067 (14) | 0.0011 (12) |
| C22 | 0.0165 (13) | 0.0235 (16) | 0.0193 (14) | −0.0037 (12) | −0.0031 (12) | 0.0003 (12) |
| O23 | 0.0242 (10) | 0.0282 (11) | 0.0322 (11) | 0.0096 (10) | 0.0027 (10) | 0.0085 (9) |
| O24 | 0.0231 (10) | 0.0256 (11) | 0.0207 (10) | 0.0009 (9) | 0.0058 (9) | 0.0035 (8) |
| C25 | 0.0228 (14) | 0.0280 (15) | 0.0238 (15) | −0.0029 (15) | 0.0007 (13) | 0.0102 (13) |
| C26 | 0.0238 (15) | 0.0253 (15) | 0.0333 (16) | 0.0004 (14) | 0.0023 (14) | 0.0057 (13) |
| C27 | 0.0368 (17) | 0.0341 (18) | 0.0262 (16) | −0.0036 (16) | 0.0039 (14) | 0.0025 (14) |
| C1—O5 | 1.478 (3) | C13—C14 | 1.375 (4) |
| C1—C2 | 1.513 (4) | C13—H13A | 0.9500 |
| C1—C4 | 1.514 (4) | C14—C15 | 1.376 (4) |
| C1—C3 | 1.516 (3) | C14—H14A | 0.9500 |
| C2—H2A | 0.9800 | C15—C16 | 1.382 (4) |
| C2—H2B | 0.9800 | C15—H15A | 0.9500 |
| C2—H2C | 0.9800 | C16—H16A | 0.9500 |
| C3—H3A | 0.9800 | C17—O18 | 1.218 (3) |
| C3—H3B | 0.9800 | C17—N19 | 1.354 (3) |
| C3—H3C | 0.9800 | N19—C20 | 1.402 (3) |
| C4—H4A | 0.9800 | N19—H19A | 0.8800 |
| C4—H4B | 0.9800 | C20—C21 | 1.324 (3) |
| C4—H4C | 0.9800 | C20—C22 | 1.494 (3) |
| O5—C6 | 1.343 (3) | C21—H21A | 0.9500 |
| C6—O7 | 1.218 (3) | C21—H21B | 0.9500 |
| C6—N8 | 1.360 (3) | C22—O23 | 1.209 (3) |
| N8—C9 | 1.448 (3) | C22—O24 | 1.333 (3) |
| N8—H8A | 0.8800 | O24—C25 | 1.470 (3) |
| C9—C10 | 1.536 (3) | C25—C26 | 1.506 (4) |
| C9—C17 | 1.536 (3) | C25—C27 | 1.507 (4) |
| C9—H9A | 1.0000 | C25—H25A | 1.0000 |
| C10—C11 | 1.503 (3) | C26—H26A | 0.9800 |
| C10—H10A | 0.9900 | C26—H26B | 0.9800 |
| C10—H10B | 0.9900 | C26—H26C | 0.9800 |
| C11—C16 | 1.390 (4) | C27—H27A | 0.9800 |
| C11—C12 | 1.391 (3) | C27—H27B | 0.9800 |
| C12—C13 | 1.381 (4) | C27—H27C | 0.9800 |
| C12—H12A | 0.9500 | ||
| O5—C1—C2 | 109.9 (2) | C11—C12—H12A | 119.4 |
| O5—C1—C4 | 109.7 (2) | C14—C13—C12 | 119.9 (3) |
| C2—C1—C4 | 113.8 (2) | C14—C13—H13A | 120.0 |
| O5—C1—C3 | 102.06 (17) | C12—C13—H13A | 120.0 |
| C2—C1—C3 | 110.8 (2) | C13—C14—C15 | 120.1 (3) |
| C4—C1—C3 | 109.9 (2) | C13—C14—H14A | 120.0 |
| C1—C2—H2A | 109.5 | C15—C14—H14A | 120.0 |
| C1—C2—H2B | 109.5 | C14—C15—C16 | 119.9 (3) |
| H2A—C2—H2B | 109.5 | C14—C15—H15A | 120.0 |
| C1—C2—H2C | 109.5 | C16—C15—H15A | 120.0 |
| H2A—C2—H2C | 109.5 | C15—C16—C11 | 121.1 (3) |
| H2B—C2—H2C | 109.5 | C15—C16—H16A | 119.4 |
| C1—C3—H3A | 109.5 | C11—C16—H16A | 119.4 |
| C1—C3—H3B | 109.5 | O18—C17—N19 | 123.5 (2) |
| H3A—C3—H3B | 109.5 | O18—C17—C9 | 121.4 (2) |
| C1—C3—H3C | 109.5 | N19—C17—C9 | 115.1 (2) |
| H3A—C3—H3C | 109.5 | C17—N19—C20 | 126.8 (2) |
| H3B—C3—H3C | 109.5 | C17—N19—H19A | 116.6 |
| C1—C4—H4A | 109.5 | C20—N19—H19A | 116.6 |
| C1—C4—H4B | 109.5 | C21—C20—N19 | 126.9 (2) |
| H4A—C4—H4B | 109.5 | C21—C20—C22 | 123.2 (2) |
| C1—C4—H4C | 109.5 | N19—C20—C22 | 109.9 (2) |
| H4A—C4—H4C | 109.5 | C20—C21—H21A | 120.0 |
| H4B—C4—H4C | 109.5 | C20—C21—H21B | 120.0 |
| C6—O5—C1 | 121.48 (18) | H21A—C21—H21B | 120.0 |
| O7—C6—O5 | 126.5 (2) | O23—C22—O24 | 124.9 (2) |
| O7—C6—N8 | 125.0 (2) | O23—C22—C20 | 122.3 (2) |
| O5—C6—N8 | 108.46 (19) | O24—C22—C20 | 112.8 (2) |
| C6—N8—C9 | 123.12 (19) | C22—O24—C25 | 116.4 (2) |
| C6—N8—H8A | 118.4 | O24—C25—C26 | 109.3 (2) |
| C9—N8—H8A | 118.4 | O24—C25—C27 | 105.5 (2) |
| N8—C9—C10 | 111.61 (19) | C26—C25—C27 | 113.7 (2) |
| N8—C9—C17 | 110.89 (19) | O24—C25—H25A | 109.4 |
| C10—C9—C17 | 108.39 (19) | C26—C25—H25A | 109.4 |
| N8—C9—H9A | 108.6 | C27—C25—H25A | 109.4 |
| C10—C9—H9A | 108.6 | C25—C26—H26A | 109.5 |
| C17—C9—H9A | 108.6 | C25—C26—H26B | 109.5 |
| C11—C10—C9 | 114.0 (2) | H26A—C26—H26B | 109.5 |
| C11—C10—H10A | 108.7 | C25—C26—H26C | 109.5 |
| C9—C10—H10A | 108.7 | H26A—C26—H26C | 109.5 |
| C11—C10—H10B | 108.7 | H26B—C26—H26C | 109.5 |
| C9—C10—H10B | 108.7 | C25—C27—H27A | 109.5 |
| H10A—C10—H10B | 107.6 | C25—C27—H27B | 109.5 |
| C16—C11—C12 | 117.8 (2) | H27A—C27—H27B | 109.5 |
| C16—C11—C10 | 121.2 (2) | C25—C27—H27C | 109.5 |
| C12—C11—C10 | 121.0 (2) | H27A—C27—H27C | 109.5 |
| C13—C12—C11 | 121.2 (3) | H27B—C27—H27C | 109.5 |
| C13—C12—H12A | 119.4 | ||
| C2—C1—O5—C6 | 60.9 (3) | C12—C11—C16—C15 | −0.6 (4) |
| C4—C1—O5—C6 | −65.0 (3) | C10—C11—C16—C15 | 178.7 (2) |
| C3—C1—O5—C6 | 178.5 (2) | N8—C9—C17—O18 | −156.2 (2) |
| C1—O5—C6—O7 | 5.3 (4) | C10—C9—C17—O18 | −33.4 (3) |
| C1—O5—C6—N8 | −173.4 (2) | N8—C9—C17—N19 | 24.2 (3) |
| O7—C6—N8—C9 | 12.2 (4) | C10—C9—C17—N19 | 147.0 (2) |
| O5—C6—N8—C9 | −169.1 (2) | O18—C17—N19—C20 | 13.5 (4) |
| C6—N8—C9—C10 | 99.5 (3) | C9—C17—N19—C20 | −166.9 (2) |
| C6—N8—C9—C17 | −139.5 (2) | C17—N19—C20—C21 | −3.8 (4) |
| N8—C9—C10—C11 | −61.4 (3) | C17—N19—C20—C22 | 175.1 (2) |
| C17—C9—C10—C11 | 176.2 (2) | C21—C20—C22—O23 | 177.4 (2) |
| C9—C10—C11—C16 | 91.7 (3) | N19—C20—C22—O23 | −1.5 (3) |
| C9—C10—C11—C12 | −89.0 (3) | C21—C20—C22—O24 | −3.0 (3) |
| C16—C11—C12—C13 | 1.0 (4) | N19—C20—C22—O24 | 178.0 (2) |
| C10—C11—C12—C13 | −178.3 (2) | O23—C22—O24—C25 | 1.1 (4) |
| C11—C12—C13—C14 | −0.7 (4) | C20—C22—O24—C25 | −178.4 (2) |
| C12—C13—C14—C15 | 0.1 (4) | C22—O24—C25—C26 | −78.0 (3) |
| C13—C14—C15—C16 | 0.3 (4) | C22—O24—C25—C27 | 159.4 (2) |
| C14—C15—C16—C11 | 0.0 (4) |
| H··· | ||||
| N8—H8 | 0.88 | 2.21 | 2.952 (2) | 141 |
| C2—H2 | 0.98 | 2.48 | 3.049 (3) | 117 |
| C3—H3 | 0.98 | 2.51 | 3.423 (3) | 155 |
| C4—H4 | 0.98 | 2.47 | 3.040 (3) | 116 |
| C21—H21 | 0.95 | 2.27 | 2.869 (3) | 120 |
| C26—H26 | 0.98 | 2.58 | 3.104 (3) | 114 |
| C26—H26 | 0.98 | 2.52 | 3.462 (3) | 162 |