| Literature DB >> 25484721 |
Naiem Ahmad Wani1, Vivek K Gupta2, Rajni Kant2, Subrayashastry Aravinda1, Rajkishor Rai1.
Abstract
N-Protected derivatives of 1-amino-cyclo-hexa-neacetic acid (β(3,3)-Ac6c), namely Valeroyl-β(3,3)-Ac6c-OH [2-(1-pentanamidocyclohexyl)acetic acid, C13H23NO3], (I), Fmoc-β(3,3)-Ac6c-OH [2-(1-{[(9H-fluoren-9-yloxy)carbonyl]amino}cyclohexyl)acetic acid, C23H25NO4], (II), and Pyr-β(3,3)-Ac6c-OH {2-[1-(pyrazine-2-amido)cyclohexyl]acetic acid, C13H17N3O3}, (III), were synthesized and their conformational properties were determined by X-ray diffraction analysis. The backbone torsion angles (ϕ, θ) for β(3,3)-Ac6c-OH are restricted to gauche conformations in all the derivatives, with a chair conformation of the cyclo-hexane ring. In the crystal structure of (I), the packing of mol-ecules shows both carb-oxy-lic acid R 2 (2)(8) O-H⋯O and centrosymmetric R (2) 2(14) N-H⋯O hydrogen-bonding inter-actions, giving rise to chains along the c-axis direction. In (II), centrosymmetric carb-oxy-lic acid R 2 (2)(8) O-H⋯O dimers are extended through N-H⋯O hydrogen bonds and together with inter-ring π-π inter-actions between Fmoc groups [ring centroid distance = 3.786 (2) Å], generate a layered structure lying parallel to (010). In the case of compound (III), carb-oxy-lic acid O-H⋯Npyrazine hydrogen bonds give rise to zigzag ribbon structures extending along the c-axis direction.Entities:
Keywords: conformation; crystal structure; disubstituted-β-amino acids; hydrogen bonds; π–π interaction
Year: 2014 PMID: 25484721 PMCID: PMC4257263 DOI: 10.1107/S1600536814020777
Source DB: PubMed Journal: Acta Crystallogr Sect E Struct Rep Online ISSN: 1600-5368
Figure 1Definition of backbone torsion angles for β-amino acids.
Figure 2ORTEP view of the molecular conformation with the atom-labelling scheme. for Valeroyl-β3,3-Ac6c-OH (I), (b) Fmoc-β3,3-Ac6c-OH (II) and (c) Pyr-β3,3-Ac6c-OH (III). The displacement ellipsoids are drawn at the 40% probability level. H atoms are shown as small spheres of arbitrary radii.
Figure 3(a) Packing of Valeroyl-β3,3-Ac6c-OH (I) down the b-axis showing the alternative hydrophilic and hydrophobic layers (b) space-filling model.
Figure 4(a) Packing of Fmoc-β3,3-Ac6c-OH (II) down the a-axis. (b) Space-filling model showing the alternative hydrophilic and hydrophobic layers (packing down the c-axis). (c) The environment of the Fmoc group showing the aromatic interaction. The centroid–centroid distances are shown.
Figure 5(a) Packing of Pyr-β3,3-Ac6c-OH (III) down the a-axis showing the ribbon structure. (b) Zigzag arrangement of the ribbons along the c-axis.
Hydrogen-bond geometry (, ) for (I)
|
|
| H |
|
|
|---|---|---|---|---|
| O2H2 | 0.87(4) | 1.74(4) | 2.599(3) | 166(4) |
| N1H1 | 0.82(3) | 2.16(3) | 2.981(3) | 172(2) |
Symmetry codes: (i) ; (ii) .
Hydrogen-bond geometry (, ) for (II)
|
|
| H |
|
|
|---|---|---|---|---|
| N1H1 | 0.86(2) | 2.35(2) | 3.182(3) | 161(2) |
| O2H2 | 0.84(3) | 1.83(3) | 2.673(3) | 177(1) |
Symmetry codes: (i) ; (ii) .
Hydrogen-bond geometry (, ) for (III)
|
|
| H |
|
|
|---|---|---|---|---|
| O2H21N2i | 0.93(4) | 1.86(4) | 2.791(3) | 177(4) |
| N1H1 | 0.79(2) | 2.34(2) | 2.729(2) | 111.3(19) |
Symmetry code: (i) .
Experimental details
| (I) | (II) | (III) | |
|---|---|---|---|
| Crystal data | |||
| Chemical formula | C13H23NO3 | C23H25NO4 | C13H17N3O3 |
|
| 241.32 | 379.44 | 263.30 |
| Crystal system, space group | Monoclinic, | Triclinic, | Orthorhombic, |
| Temperature (K) | 291 | 291 | 291 |
|
| 9.5894(5), 12.5007(7), 12.3709(8) | 6.0834(4), 12.7642(9), 12.8399(9) | 8.7135(1), 10.5321(1), 14.3907(2) |
| , , () | 90, 109.984(7), 90 | 94.018(6), 92.295(6), 100.489(6) | 90, 90, 90 |
|
| 1393.66(14) | 976.53(12) | 1320.66(3) |
|
| 4 | 2 | 4 |
| Radiation type | Mo | Mo | Mo |
| (mm1) | 0.08 | 0.09 | 0.10 |
| Crystal size (mm) | 0.30 0.08 0.08 | 0.30 0.05 0.03 | 0.25 0.25 0.25 |
| Data collection | |||
| Diffractometer | Oxford Diffraction Xcalibur, Sapphire3 CCD | Oxford Diffraction Xcalibur, Sapphire3 CCD | Oxford Difraction Xcalibur, Sapphire3 CCD |
| Absorption correction | Multi-scan ( | Multi-scan ( | Multi-scan ( |
|
| 0.797, 1.000 | 0.947, 1.000 | 0.931, 1.000 |
| No. of measured, independent and observed [ | 14087, 2737, 1717 | 7781, 4166, 2037 | 68869, 2878, 2670 |
|
| 0.047 | 0.047 | 0.034 |
| (sin /)max (1) | 0.617 | 0.639 | 0.639 |
| Refinement | |||
|
| 0.068, 0.213, 1.03 | 0.054, 0.086, 0.97 | 0.042, 0.106, 1.04 |
| No. of reflections | 2737 | 4166 | 2878 |
| No. of parameters | 162 | 353 | 240 |
| No. of restraints | 0 | 1 | 1 |
| H-atom treatment | H atoms treated by a mixture of independent and constrained refinement | All H-atom parameters refined | All H-atom parameters refined |
| max, min (e 3) | 0.36, 0.30 | 0.15, 0.20 | 0.27, 0.26 |
| Absolute structure | (Flack, 1983 | ||
| Absolute structure parameter | 0.2(14) | ||
Computer programs: CrysAlis PRO (Oxford Diffraction, 2010 ▶), SHELXS97 and SHELXL97 (Sheldrick, 2008 ▶), ORTEP-3 for Windows (Farrugia, 2012 ▶) and PLATON (Spek, 2009 ▶).
| C13H17N3O3 | |
| Orthorhombic, | Mo |
| Hall symbol: P 2c -2ac | Cell parameters from 28796 reflections |
| θ = 3.7–27.0° | |
| µ = 0.10 mm−1 | |
| Cube, colorless | |
| 0.25 × 0.25 × 0.25 mm |
| Oxford Difraction Xcalibur, Sapphire3 CCD diffractometer | 2878 independent reflections |
| Radiation source: fine-focus sealed tube | 2670 reflections with |
| Graphite monochromator | |
| Detector resolution: 16.1049 pixels mm-1 | θmax = 27.0°, θmin = 3.9° |
| ω scans | |
| Absorption correction: multi-scan ( | |
| 68869 measured reflections |
| Refinement on | Secondary atom site location: difference Fourier map |
| Least-squares matrix: full | Hydrogen site location: difference Fourier map |
| All H-atom parameters refined | |
| (Δ/σ)max = 0.032 | |
| 2878 reflections | Δρmax = 0.27 e Å−3 |
| 240 parameters | Δρmin = −0.26 e Å−3 |
| 1 restraint | Absolute structure: (Flack, 1983): 1585 Friedel pairs |
| Primary atom site location: structure-invariant direct methods | Absolute structure parameter: 0.2 (14) |
| Experimental. |
| 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 > 2sigma(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. |
| H1 | 0.902 (2) | 0.412 (2) | 1.0592 (15) | 0.030 (5)* | |
| H1B2 | 1.400 (3) | 0.435 (2) | 1.2329 (16) | 0.041 (6)* | |
| H1B5 | 1.272 (3) | 0.384 (2) | 1.4161 (18) | 0.049 (7)* | |
| H1B6 | 1.183 (3) | 0.442 (2) | 1.3342 (17) | 0.048 (6)* | |
| H1B1 | 1.499 (2) | 0.380 (2) | 1.3191 (16) | 0.033 (5)* | |
| H1D2 | 1.651 (3) | 0.100 (3) | 1.200 (2) | 0.061 (7)* | |
| H1N | 1.161 (2) | 0.172 (2) | 1.2259 (16) | 0.036 (6)* | |
| H1G1 | 1.481 (3) | 0.256 (2) | 1.1391 (19) | 0.045 (6)* | |
| H2 | 0.709 (3) | 0.107 (2) | 0.971 (2) | 0.051 (7)* | |
| H3 | 0.894 (3) | −0.021 (2) | 1.0429 (17) | 0.047 (6)* | |
| H1B4 | 1.269 (3) | 0.107 (2) | 1.3669 (17) | 0.045 (6)* | |
| H1G4 | 1.401 (3) | 0.050 (3) | 1.232 (2) | 0.061 (7)* | |
| H1G2 | 1.616 (3) | 0.323 (3) | 1.173 (2) | 0.066 (8)* | |
| H1B3 | 1.415 (3) | 0.192 (2) | 1.3989 (19) | 0.046 (6)* | |
| H1G3 | 1.502 (3) | 0.005 (3) | 1.3184 (19) | 0.065 (8)* | |
| H1D1 | 1.667 (4) | 0.176 (3) | 1.298 (2) | 0.071 (9)* | |
| H21 | 0.885 (5) | 0.352 (4) | 1.458 (3) | 0.106 (13)* | |
| C1 | 0.9028 (2) | 0.3259 (2) | 1.05370 (16) | 0.0401 (4) | |
| N2 | 0.7893 (2) | 0.27249 (19) | 1.00502 (14) | 0.0442 (4) | |
| C3 | 0.7875 (3) | 0.1459 (2) | 1.00191 (15) | 0.0433 (5) | |
| C4 | 0.8954 (3) | 0.0736 (2) | 1.04730 (16) | 0.0450 (5) | |
| N3 | 1.0074 (2) | 0.12584 (16) | 1.09722 (13) | 0.0398 (4) | |
| C6 | 1.0105 (2) | 0.25193 (18) | 1.10026 (14) | 0.0343 (4) | |
| C0 | 1.1318 (2) | 0.31669 (18) | 1.15876 (15) | 0.0382 (4) | |
| O0' | 1.1604 (2) | 0.42890 (15) | 1.14626 (15) | 0.0658 (6) | |
| N1 | 1.19610 (18) | 0.24153 (15) | 1.22264 (12) | 0.0348 (4) | |
| C1A | 1.2995 (2) | 0.28157 (17) | 1.29864 (13) | 0.0311 (4) | |
| C1B | 1.2100 (2) | 0.36660 (19) | 1.36671 (16) | 0.0381 (4) | |
| C1' | 1.0648 (2) | 0.31013 (19) | 1.40619 (15) | 0.0423 (5) | |
| O1 | 1.0357 (3) | 0.2011 (2) | 1.4129 (3) | 0.1197 (13) | |
| O2 | 0.9700 (2) | 0.39599 (18) | 1.43574 (16) | 0.0677 (6) | |
| C1B1 | 1.4369 (2) | 0.3562 (2) | 1.26078 (16) | 0.0394 (4) | |
| C1G1 | 1.5373 (3) | 0.2777 (2) | 1.19617 (18) | 0.0504 (5) | |
| C1D | 1.5948 (3) | 0.1582 (3) | 1.2448 (2) | 0.0575 (6) | |
| C1B2 | 1.3586 (2) | 0.15966 (19) | 1.34564 (14) | 0.0366 (4) | |
| C1G2 | 1.4634 (3) | 0.0817 (2) | 1.28311 (18) | 0.0483 (5) |
| C1 | 0.0386 (10) | 0.0391 (10) | 0.0428 (10) | 0.0036 (9) | −0.0049 (9) | 0.0025 (10) |
| N2 | 0.0374 (8) | 0.0538 (11) | 0.0414 (9) | 0.0036 (8) | −0.0067 (7) | 0.0039 (8) |
| C3 | 0.0402 (11) | 0.0513 (13) | 0.0386 (11) | −0.0063 (9) | −0.0045 (9) | −0.0018 (10) |
| C4 | 0.0510 (12) | 0.0399 (11) | 0.0440 (10) | −0.0049 (10) | −0.0066 (9) | −0.0016 (9) |
| N3 | 0.0445 (9) | 0.0361 (8) | 0.0389 (9) | −0.0002 (7) | −0.0048 (8) | 0.0035 (7) |
| C6 | 0.0340 (9) | 0.0368 (10) | 0.0321 (9) | 0.0012 (7) | 0.0002 (7) | 0.0023 (8) |
| C0 | 0.0388 (10) | 0.0335 (9) | 0.0422 (11) | 0.0024 (8) | −0.0048 (8) | 0.0032 (8) |
| O0' | 0.0769 (12) | 0.0360 (8) | 0.0843 (13) | −0.0095 (8) | −0.0359 (11) | 0.0160 (8) |
| N1 | 0.0365 (8) | 0.0291 (8) | 0.0388 (9) | −0.0040 (6) | −0.0074 (7) | 0.0016 (6) |
| C1A | 0.0299 (8) | 0.0305 (9) | 0.0329 (9) | −0.0015 (7) | 0.0010 (7) | −0.0030 (7) |
| C1B | 0.0352 (10) | 0.0327 (10) | 0.0464 (11) | −0.0002 (8) | 0.0058 (9) | −0.0069 (8) |
| C1' | 0.0418 (11) | 0.0358 (10) | 0.0494 (12) | −0.0009 (9) | 0.0134 (9) | −0.0037 (9) |
| O1 | 0.0886 (16) | 0.0440 (10) | 0.227 (3) | −0.0088 (10) | 0.099 (2) | −0.0111 (15) |
| O2 | 0.0533 (10) | 0.0462 (9) | 0.1035 (15) | 0.0071 (8) | 0.0373 (10) | 0.0115 (9) |
| C1B1 | 0.0322 (9) | 0.0395 (11) | 0.0464 (11) | −0.0066 (8) | 0.0044 (9) | −0.0020 (9) |
| C1G1 | 0.0453 (12) | 0.0557 (13) | 0.0500 (13) | −0.0058 (11) | 0.0180 (11) | −0.0036 (11) |
| C1D | 0.0454 (12) | 0.0660 (16) | 0.0611 (16) | 0.0172 (11) | 0.0121 (12) | −0.0050 (12) |
| C1B2 | 0.0371 (10) | 0.0398 (9) | 0.0329 (10) | 0.0042 (8) | −0.0012 (8) | 0.0026 (8) |
| C1G2 | 0.0551 (13) | 0.0404 (11) | 0.0493 (12) | 0.0171 (10) | 0.0039 (11) | −0.0012 (9) |
| C1—N2 | 1.337 (3) | C1B—H1B6 | 0.95 (3) |
| C1—C6 | 1.391 (3) | C1'—O1 | 1.180 (3) |
| C1—H1 | 0.91 (2) | C1'—O2 | 1.297 (3) |
| N2—C3 | 1.334 (3) | O2—H21 | 0.93 (5) |
| C3—C4 | 1.375 (3) | C1B1—C1G1 | 1.521 (3) |
| C3—H2 | 0.91 (3) | C1B1—H1B2 | 0.97 (2) |
| C4—N3 | 1.331 (3) | C1B1—H1B1 | 1.03 (2) |
| C4—H3 | 1.00 (3) | C1G1—C1D | 1.525 (4) |
| N3—C6 | 1.329 (3) | C1G1—H1G1 | 0.98 (3) |
| C6—C0 | 1.514 (3) | C1G1—H1G2 | 0.90 (3) |
| C0—O0' | 1.221 (2) | C1D—C1G2 | 1.505 (4) |
| C0—N1 | 1.336 (3) | C1D—H1D2 | 1.01 (3) |
| N1—C1A | 1.478 (2) | C1D—H1D1 | 1.00 (3) |
| N1—H1N | 0.79 (2) | C1B2—C1G2 | 1.523 (3) |
| C1A—C1B1 | 1.532 (3) | C1B2—H1B4 | 1.00 (2) |
| C1A—C1B | 1.539 (2) | C1B2—H1B3 | 0.97 (3) |
| C1A—C1B2 | 1.540 (3) | C1G2—H1G4 | 0.97 (3) |
| C1B—C1' | 1.509 (3) | C1G2—H1G3 | 1.01 (3) |
| C1B—H1B5 | 0.91 (3) | ||
| N2—C1—C6 | 121.03 (19) | O1—C1'—C1B | 126.5 (2) |
| N2—C1—H1 | 117.5 (14) | O2—C1'—C1B | 112.51 (18) |
| C6—C1—H1 | 121.3 (14) | C1'—O2—H21 | 106 (3) |
| C3—N2—C1 | 116.57 (18) | C1G1—C1B1—C1A | 112.85 (17) |
| N2—C3—C4 | 122.0 (2) | C1G1—C1B1—H1B2 | 113.6 (14) |
| N2—C3—H2 | 118.2 (16) | C1A—C1B1—H1B2 | 109.0 (14) |
| C4—C3—H2 | 119.8 (16) | C1G1—C1B1—H1B1 | 108.9 (12) |
| N3—C4—C3 | 121.9 (2) | C1A—C1B1—H1B1 | 104.3 (12) |
| N3—C4—H3 | 117.3 (15) | H1B2—C1B1—H1B1 | 107.7 (18) |
| C3—C4—H3 | 120.8 (15) | C1B1—C1G1—C1D | 110.9 (2) |
| C6—N3—C4 | 116.44 (19) | C1B1—C1G1—H1G1 | 110.5 (15) |
| N3—C6—C1 | 122.0 (2) | C1D—C1G1—H1G1 | 111.0 (15) |
| N3—C6—C0 | 118.85 (18) | C1B1—C1G1—H1G2 | 112.3 (19) |
| C1—C6—C0 | 119.08 (17) | C1D—C1G1—H1G2 | 111.1 (19) |
| O0'—C0—N1 | 126.08 (19) | H1G1—C1G1—H1G2 | 101 (2) |
| O0'—C0—C6 | 119.79 (18) | C1G2—C1D—C1G1 | 111.1 (2) |
| N1—C0—C6 | 114.12 (17) | C1G2—C1D—H1D2 | 106.1 (16) |
| C0—N1—C1A | 126.55 (16) | C1G1—C1D—H1D2 | 111.2 (16) |
| C0—N1—H1N | 115.3 (17) | C1G2—C1D—H1D1 | 107.4 (17) |
| C1A—N1—H1N | 116.8 (17) | C1G1—C1D—H1D1 | 113.3 (18) |
| N1—C1A—C1B1 | 111.06 (16) | H1D2—C1D—H1D1 | 107 (2) |
| N1—C1A—C1B | 109.15 (15) | C1G2—C1B2—C1A | 113.00 (17) |
| C1B1—C1A—C1B | 108.90 (15) | C1G2—C1B2—H1B4 | 110.6 (13) |
| N1—C1A—C1B2 | 106.91 (15) | C1A—C1B2—H1B4 | 109.3 (13) |
| C1B1—C1A—C1B2 | 108.81 (16) | C1G2—C1B2—H1B3 | 110.4 (15) |
| C1B—C1A—C1B2 | 112.02 (16) | C1A—C1B2—H1B3 | 102.9 (15) |
| C1'—C1B—C1A | 115.79 (16) | H1B4—C1B2—H1B3 | 110 (2) |
| C1'—C1B—H1B5 | 106.5 (16) | C1D—C1G2—C1B2 | 112.6 (2) |
| C1A—C1B—H1B5 | 108.4 (17) | C1D—C1G2—H1G4 | 109.7 (17) |
| C1'—C1B—H1B6 | 108.0 (15) | C1B2—C1G2—H1G4 | 107.0 (16) |
| C1A—C1B—H1B6 | 107.2 (15) | C1D—C1G2—H1G3 | 111.0 (17) |
| H1B5—C1B—H1B6 | 111 (2) | C1B2—C1G2—H1G3 | 109.4 (16) |
| O1—C1'—O2 | 121.0 (2) | H1G4—C1G2—H1G3 | 107 (2) |
| C6—C1—N2—C3 | −1.5 (3) | C0—N1—C1A—C1B2 | −173.2 (2) |
| C1—N2—C3—C4 | 0.8 (3) | N1—C1A—C1B—C1' | 55.0 (2) |
| N2—C3—C4—N3 | 0.3 (4) | C1B1—C1A—C1B—C1' | 176.42 (19) |
| C3—C4—N3—C6 | −0.6 (3) | C1B2—C1A—C1B—C1' | −63.2 (2) |
| C4—N3—C6—C1 | −0.2 (3) | C1A—C1B—C1'—O1 | 23.6 (4) |
| C4—N3—C6—C0 | 177.82 (19) | C1A—C1B—C1'—O2 | −157.9 (2) |
| N2—C1—C6—N3 | 1.3 (3) | N1—C1A—C1B1—C1G1 | −62.6 (2) |
| N2—C1—C6—C0 | −176.68 (19) | C1B—C1A—C1B1—C1G1 | 177.20 (19) |
| N3—C6—C0—O0' | 162.9 (2) | C1B2—C1A—C1B1—C1G1 | 54.8 (2) |
| C1—C6—C0—O0' | −19.1 (3) | C1A—C1B1—C1G1—C1D | −57.0 (3) |
| N3—C6—C0—N1 | −18.5 (3) | C1B1—C1G1—C1D—C1G2 | 55.1 (3) |
| C1—C6—C0—N1 | 159.53 (19) | N1—C1A—C1B2—C1G2 | 67.3 (2) |
| O0'—C0—N1—C1A | 8.4 (4) | C1B1—C1A—C1B2—C1G2 | −52.7 (2) |
| C6—C0—N1—C1A | −170.04 (17) | C1B—C1A—C1B2—C1G2 | −173.13 (18) |
| C0—N1—C1A—C1B1 | −54.6 (2) | C1G1—C1D—C1G2—C1B2 | −53.8 (3) |
| C0—N1—C1A—C1B | 65.5 (2) | C1A—C1B2—C1G2—C1D | 53.7 (3) |
| H··· | ||||
| O2—H21···N2i | 0.93 (4) | 1.86 (4) | 2.791 (3) | 177 (4) |
| N1—H1 | 0.79 (2) | 2.34 (2) | 2.729 (2) | 111.3 (19) |