Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S2053229615022597/lg3179sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S2053229615022597/lg3179Isup2.hkl |
CCDC reference: 1430691
The presence of Aib (α-aminoisobutyric acid) and Gly (glycine) in peptides combines the residue with the greatest conformational flexibility (Gly) with a residue, the conformational space of which is severely restricted by the second methyl group attached to the Cα atom (Aib). This space available for Aib comprises the left- and right-handed helical regions of the Ramachandran plot (Ramachandran et al., 1963). Gly is incorporated in roughly half of all known peptaibiotic (i.e. nonribosomally biosynthesized antibiotic peptides of fungal origin) sequences and frequently as the –Aib-Gly- dipeptide or as the –Aib-Gly-Aib- tripeptide unit (Stoppacher et al., 2013). On the contrary, the motifs –Gly-Aib-Gly-Aib- or –Gly-Aib-Gly- do not occur in any of the >1300 peptaibiotics known to date. Most of the crystal structures containing Aib are N-terminal protected. Deprotection of the N– or C-terminal of peptides may alter the hydrogen-bonding scheme from intra- to intermolecular hydrogen bonds, may alter the structure and may facilitate crystallization.
Z-(Gly-Aib)2—OtBu (1.40 g, 2.84 mmol; Gessmann et al., 2015) was dissolved in MeOH (20 ml) and hydrogenolysed in the presence of Pd (ca 140 mg, 5% on charcoal) by bubbling hydrogen gas through the solution. Quantitative deprotection was already completed within 1 h as revealed by thin-layer chromatography. After removal of the catalyst by filtration and evaporation of the organic phase, a colourless oil remained. The tetrapeptide was crystallized from 50% aqueous methanol by slow evaporation. Tiny crystals were detected after several weeks.
Crystal data, data collection and structure refinement details are summarized in Table 1. One single plate with the smallest dimension of about 40 µm was mounted on a cryoloop without cryoprotectant and kept in place with a minimal amount of vacuum grease. Diffraction data were collected at 100 K on the microfocus beamline I24 (Evans et al., 2011) of the Diamond Light Source in Didcot, England, using a Pilatus 6M detector (Dectris Ltd, Baden, Switzerland). A data set of 1800 images covering 360° of rotation was collected in the resolution range 26.07–0.7 Å. 54850 reflections were recorded in total, including 3303 systematic absences by space-group symmetry. Of these observed reflections, 5235 were unique including 549 systematic absences. The data were integrated using the software package XDS (Kabsch, 2010). and scaled with AIMLESS (Evans & Murshudov, 2013) implemented in the CCP4 suite (Winn et al., 2011). All non-H peptide atoms were detected by direct methods with the program SHELXS97 (Sheldrick, 2008) as the highest 25 peaks. Anisotropic refinement was performed without any constraints or restraints. All H atoms could be detected in a difference Fourier map and each one of their four parameters was freely refined. No cocrystallized solvent molecule could be detected. The hydrogen-bond distances to N atoms are in the range 0.835 (19)–1.0 (2) Å, with an average of 0.89 (2) Å, and to C atoms are in the range 0.895 (17)–1.07 (3) Å, with an average of 0.94 (2) Å.
The tetrapeptide ester H-Gly-Aib-Gly-Aib-OtBu adopts a very unusual backbone conformation (Table 2). In the molecule taken as the asymmetric unit, the torsion angles ψ (Gly1) and φ/ψ (Aib2) lie in the right-handed helical region of the Ramachandran plot. In residues Gly3 and Aib4, the conformation is turned to lie in the left-handed helical region. There exist no intramolecular hydrogen bonds, even though a hydrogen bond of type 1←4 would be possible between the C═O group of Gly1 and the N—H group of Aib4. The peptide adopts the usual trans-planar conformation, with significant deviations from planarity (ω = 180°, Table 2). The valency around the Cα atom is asymmetric for the Aib residues (Table 3). If one designates as CL and CR the atoms which occupy the same position as Cβ and α-hydrogen in L-amino acids, respectively, the bond angles N—Cα—CL and C—Cα—CL are significantly smaller than the respective N—Cα—CR and C—Cα—CR angles in Aib2, while they are significantly greater in Aib4 (Table 3). This is in excellent agreement with the findings for other Aib residues with torsion angles φ/ψ in the right-handed 310-helical regions, which is the case of Aib2 and for other Aib residues with torsion angles φ/ψ in the left-handed 310-helical regions of the Ramachabdran plot, which hold true for the Aib4 residue (Table 2) (Gessmann et al., 2014). In the crystal, there is a network of hydrogen bonds between each molecule and the six surrounding molecules, forming a total of eight hydrogen bonds (Fig. 2). The four hydrogen bonds in which the chosen central molecule acts as hydrogen-bond donor are listed in Table 4. In the other four hydrogen bonds, the central molecule is a hydrogen-bond acceptor from the molecules which are symmetry related by (x − 1/2, y, −z + 1/2), (−x + 1, y + 1/2, −z + 1/2) and (−x + 3/2, y + 1/2, z). These hydrogen bonds connect molecules of both handednesses in the a and b directions, while a pairwise connection is established in the c direction (Fig. 3), leading to hydrogen-bonded slices parallel to the ab plane which stack in the c direction via apolar contacts. The recently determined structure of Z-Gly-Aib-Gly-Aib-OtBu (Gessmann et al., 2015) possesses instead of the free N-terminus of the title compound a benzyloxycarbonyl protecting group. This difference leads to two 1←4 intramolecular hydrogen bonds, a semi-extended conformation for Gly1 and left- or right-handed 310-helical values for the Aib2, Gly3 and Aib4. Another difference between these two peptide structures is that in the case of Z-Gly-Aib-Gly-Aib-OtBu the crystallization agent, ethyl acetate, was cocrystallized along with the peptide. Among the peptide structures examined, N-terminal-unprotected Tyr-Aib-Tyr-Val (Das et al., 2005) is the only Aib-containing short peptide, which could form one intramolecular 4→1 hydrogen bond based on its length. Nevertheless, no hydrogen bond was found in this tetrapeptide.
Cell refinement: XDS (Kabsch, 2010); data reduction: AIMLESS (Evans & Murshudov, 2013); program(s) used to solve structure: SHELXS86 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: XTALVIEW (McRee, 1999) and SwissPDBViewer (Guex & Peitsch, 1997); software used to prepare material for publication: CHEMDRAW (Mills, 2006), ORTEPIII (Burnett & Johnson, 1996), ORTEP-3 for Windows (Farrugia, 2012) and POVRAY (Persistence of Vision, 2004).
C16H30N4O5 | Dx = 1.225 Mg m−3 |
Mr = 358.44 | Synchrotron radiation, λ = 0.65253 Å |
Orthorhombic, Pbca | Cell parameters from 4686 reflections |
a = 9.3500 (19) Å | θ = 1.4–27.7° |
b = 15.950 (3) Å | µ = 0.05 mm−1 |
c = 26.070 (5) Å | T = 100 K |
V = 3887.9 (14) Å3 | Plate, colourless |
Z = 8 | 0.08 × 0.07 × 0.04 mm |
F(000) = 1552 |
Synchrotron diffractometer | Rint = 0.099 |
f–scans | θmax = 27.7°, θmin = 1.4° |
51547 measured reflections | h = −11→11 |
4686 independent reflections | k = −22→21 |
4379 reflections with I > 2σ(I) | l = −36→37 |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.059 | All H-atom parameters refined |
wR(F2) = 0.151 | w = 1/[σ2(Fo2) + (0.0955P)2 + 1.0581P] where P = (Fo2 + 2Fc2)/3 |
S = 1.11 | (Δ/σ)max < 0.001 |
4686 reflections | Δρmax = 0.49 e Å−3 |
346 parameters | Δρmin = −0.51 e Å−3 |
C16H30N4O5 | V = 3887.9 (14) Å3 |
Mr = 358.44 | Z = 8 |
Orthorhombic, Pbca | Synchrotron radiation, λ = 0.65253 Å |
a = 9.3500 (19) Å | µ = 0.05 mm−1 |
b = 15.950 (3) Å | T = 100 K |
c = 26.070 (5) Å | 0.08 × 0.07 × 0.04 mm |
Synchrotron diffractometer | 4379 reflections with I > 2σ(I) |
51547 measured reflections | Rint = 0.099 |
4686 independent reflections |
R[F2 > 2σ(F2)] = 0.059 | 0 restraints |
wR(F2) = 0.151 | All H-atom parameters refined |
S = 1.11 | Δρmax = 0.49 e Å−3 |
4686 reflections | Δρmin = −0.51 e Å−3 |
346 parameters |
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. |
Refinement. One single plate with the smallest dimension of about 40 µm was mounted on a cryoloop without cryoprotectant and kept in place with a minimal amount of vacuum grease. Diffraction data were collected at 100 K on the microfocus beamline I24 (Evans et al., 2011) of the Diamond Light Source in Didcot, England, using a Pilatus 6M detector (Dectris Ltd, Baden, Switzerland). A data set of 1800 images covering 360° of rotation was collected in the resolution range 26.07–0.7 Å. 54850 reflections were recorded in total, including 3303 systematic absences by space-group symmetry. Of these observed reflections, 5235 were unique including 549 systematic absences. The data were integrated using the software package XDS (Kabsch, 2010). and scaled with AIMLESS (Evans & Murshudov, 2013) implemented in the CCP4 suite (Winn et al., 2011). All non-H peptide atoms were detected by direct methods with the program SHELXS97 (Sheldrick, 2008) as the highest 25 peaks. Anisotropic refinement was performed without any constraints or restraints. All H atoms could be detected in a difference Fourier map and each one of their four parameters was freely refined. No cocrystallized solvent molecule could be detected. The hydrogen-bond distances to N atoms are in the range 0.835 (19)–1.0 (2) Å, with an average of 0.89 (2) Å, and to C atoms are in the range 0.895 (17)–1.07 (3) Å, with an average of 0.94 (2) Å. |
x | y | z | Uiso*/Ueq | ||
N_1 | 0.61076 (13) | −0.26950 (7) | 0.20859 (5) | 0.0230 (3) | |
H1_1 | 0.591 (2) | −0.3237 (15) | 0.1909 (9) | 0.039 (5)* | |
H2_1 | 0.703 (3) | −0.2496 (15) | 0.2023 (9) | 0.046 (6)* | |
CA_1 | 0.51123 (13) | −0.20546 (8) | 0.19305 (5) | 0.0196 (3) | |
HA1_1 | 0.540 (2) | −0.1719 (12) | 0.1617 (8) | 0.027 (4)* | |
HA2_1 | 0.423 (2) | −0.2313 (13) | 0.1823 (8) | 0.029 (5)* | |
C_1 | 0.47834 (12) | −0.14172 (7) | 0.23400 (5) | 0.0156 (2) | |
O_1 | 0.40238 (9) | −0.08063 (6) | 0.22329 (4) | 0.0203 (2) | |
N_2 | 0.53398 (11) | −0.15262 (6) | 0.28108 (4) | 0.0158 (2) | |
H_2 | 0.579 (2) | −0.1977 (14) | 0.2880 (8) | 0.034 (5)* | |
CA_2 | 0.50131 (12) | −0.09512 (7) | 0.32365 (5) | 0.0151 (2) | |
CL_2 | 0.60190 (14) | −0.11646 (8) | 0.36828 (5) | 0.0205 (3) | |
HL1_2 | 0.5870 (16) | −0.0789 (10) | 0.3932 (6) | 0.012 (3)* | |
HL2_2 | 0.5806 (19) | −0.1711 (12) | 0.3834 (7) | 0.024 (4)* | |
HL3_2 | 0.702 (2) | −0.1169 (12) | 0.3564 (7) | 0.025 (4)* | |
CR_2 | 0.34621 (13) | −0.10395 (9) | 0.34067 (5) | 0.0208 (3) | |
HR1_2 | 0.3253 (18) | −0.0618 (12) | 0.3682 (7) | 0.023 (4)* | |
HR2_2 | 0.334 (2) | −0.1593 (13) | 0.3527 (7) | 0.026 (4)* | |
HR3_2 | 0.281 (2) | −0.0922 (12) | 0.3125 (7) | 0.025 (4)* | |
C_2 | 0.53213 (12) | −0.00347 (7) | 0.30872 (4) | 0.0137 (2) | |
O_2 | 0.45775 (10) | 0.05424 (6) | 0.32470 (4) | 0.0201 (2) | |
N_3 | 0.65058 (10) | 0.00881 (6) | 0.28071 (4) | 0.0150 (2) | |
H_3 | 0.7018 (19) | −0.0322 (12) | 0.2731 (7) | 0.020 (4)* | |
CA_3 | 0.70985 (13) | 0.09161 (7) | 0.27268 (5) | 0.0153 (2) | |
HA1_3 | 0.7652 (18) | 0.0899 (10) | 0.2434 (7) | 0.017 (4)* | |
HA2_3 | 0.6353 (19) | 0.1327 (11) | 0.2657 (7) | 0.019 (4)* | |
C_3 | 0.79998 (12) | 0.12386 (7) | 0.31742 (4) | 0.0145 (2) | |
O_3 | 0.80326 (10) | 0.19905 (6) | 0.32858 (4) | 0.0190 (2) | |
N_4 | 0.87403 (11) | 0.06554 (7) | 0.34303 (4) | 0.0170 (2) | |
H_4 | 0.8780 (19) | 0.0165 (13) | 0.3313 (7) | 0.021 (4)* | |
CA_4 | 0.96427 (13) | 0.08592 (8) | 0.38700 (5) | 0.0185 (3) | |
CL_4 | 1.10210 (14) | 0.12845 (11) | 0.36957 (6) | 0.0271 (3) | |
HL1_4 | 1.080 (2) | 0.1774 (15) | 0.3505 (8) | 0.036 (5)* | |
HL2_4 | 1.156 (2) | 0.0906 (13) | 0.3470 (7) | 0.028 (5)* | |
HL3_4 | 1.161 (2) | 0.1461 (14) | 0.3985 (9) | 0.043 (6)* | |
CR_4 | 0.99587 (17) | 0.00400 (10) | 0.41545 (6) | 0.0286 (3) | |
HR1_4 | 1.043 (2) | −0.0383 (15) | 0.3936 (9) | 0.039 (5)* | |
HR2_4 | 0.911 (2) | −0.0231 (13) | 0.4275 (8) | 0.031 (5)* | |
HR3_4 | 1.053 (2) | 0.0187 (15) | 0.4461 (9) | 0.043 (6)* | |
C_4 | 0.88318 (13) | 0.14365 (8) | 0.42425 (5) | 0.0188 (3) | |
O_4 | 0.94003 (11) | 0.20061 (7) | 0.44673 (4) | 0.0266 (2) | |
O_5 | 0.74945 (10) | 0.11792 (6) | 0.43058 (4) | 0.0221 (2) | |
C1_5 | 0.65102 (15) | 0.16443 (10) | 0.46480 (5) | 0.0256 (3) | |
C2_5 | 0.64146 (19) | 0.25583 (12) | 0.44851 (6) | 0.0348 (4) | |
H21_5 | 0.620 (3) | 0.2558 (16) | 0.4135 (11) | 0.051 (6)* | |
H22_5 | 0.566 (3) | 0.2812 (16) | 0.4657 (10) | 0.053 (7)* | |
H23_5 | 0.737 (3) | 0.2887 (16) | 0.4550 (9) | 0.050 (6)* | |
C3_5 | 0.69906 (19) | 0.15469 (13) | 0.51999 (6) | 0.0350 (4) | |
H31_5 | 0.708 (2) | 0.0922 (14) | 0.5293 (8) | 0.036 (5)* | |
H32_5 | 0.630 (3) | 0.1817 (16) | 0.5444 (9) | 0.047 (6)* | |
H33_5 | 0.785 (3) | 0.1844 (16) | 0.5253 (9) | 0.047 (6)* | |
C4_5 | 0.51065 (18) | 0.11932 (16) | 0.45571 (8) | 0.0458 (5) | |
H41_5 | 0.521 (3) | 0.0577 (18) | 0.4651 (10) | 0.051 (7)* | |
H42_5 | 0.483 (3) | 0.1303 (19) | 0.4164 (12) | 0.066 (8)* | |
H43_5 | 0.433 (3) | 0.1429 (18) | 0.4794 (11) | 0.059 (7)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N_1 | 0.0265 (6) | 0.0154 (5) | 0.0272 (6) | 0.0029 (4) | −0.0038 (4) | −0.0011 (5) |
CA_1 | 0.0197 (6) | 0.0158 (6) | 0.0233 (6) | −0.0007 (4) | −0.0049 (4) | −0.0001 (5) |
C_1 | 0.0117 (5) | 0.0124 (5) | 0.0226 (6) | −0.0029 (4) | −0.0011 (4) | 0.0002 (5) |
O_1 | 0.0169 (5) | 0.0195 (4) | 0.0244 (5) | 0.0031 (3) | −0.0041 (3) | 0.0025 (4) |
N_2 | 0.0154 (5) | 0.0096 (4) | 0.0224 (5) | 0.0022 (3) | −0.0017 (3) | 0.0004 (4) |
CA_2 | 0.0137 (5) | 0.0130 (5) | 0.0187 (5) | 0.0009 (4) | −0.0004 (4) | 0.0020 (5) |
CL_2 | 0.0234 (6) | 0.0182 (6) | 0.0200 (6) | 0.0008 (4) | −0.0058 (4) | 0.0031 (5) |
CR_2 | 0.0165 (6) | 0.0221 (6) | 0.0237 (6) | −0.0028 (4) | 0.0037 (4) | 0.0043 (5) |
C_2 | 0.0136 (5) | 0.0116 (5) | 0.0159 (5) | 0.0011 (4) | −0.0026 (4) | 0.0004 (4) |
O_2 | 0.0198 (4) | 0.0155 (4) | 0.0251 (5) | 0.0058 (3) | 0.0040 (3) | 0.0007 (4) |
N_3 | 0.0134 (5) | 0.0102 (4) | 0.0214 (5) | −0.0004 (3) | 0.0012 (3) | −0.0020 (4) |
CA_3 | 0.0168 (6) | 0.0121 (5) | 0.0170 (5) | −0.0023 (4) | 0.0002 (4) | 0.0006 (4) |
C_3 | 0.0136 (5) | 0.0139 (5) | 0.0161 (5) | −0.0019 (4) | 0.0037 (4) | −0.0007 (4) |
O_3 | 0.0222 (4) | 0.0123 (4) | 0.0224 (4) | −0.0018 (3) | −0.0006 (3) | −0.0011 (3) |
N_4 | 0.0186 (5) | 0.0136 (5) | 0.0187 (5) | 0.0017 (3) | −0.0013 (3) | −0.0042 (4) |
CA_4 | 0.0156 (5) | 0.0217 (6) | 0.0182 (5) | 0.0020 (4) | −0.0009 (4) | −0.0024 (5) |
CL_4 | 0.0153 (6) | 0.0370 (8) | 0.0290 (7) | −0.0017 (5) | 0.0023 (5) | −0.0064 (7) |
CR_4 | 0.0297 (7) | 0.0278 (7) | 0.0283 (7) | 0.0091 (5) | −0.0065 (5) | 0.0011 (6) |
C_4 | 0.0172 (6) | 0.0231 (6) | 0.0161 (5) | 0.0016 (4) | 0.0000 (4) | 0.0004 (5) |
O_4 | 0.0247 (5) | 0.0317 (6) | 0.0236 (5) | −0.0020 (4) | −0.0024 (4) | −0.0104 (4) |
O_5 | 0.0180 (5) | 0.0277 (5) | 0.0207 (4) | −0.0011 (3) | 0.0052 (3) | −0.0032 (4) |
C1_5 | 0.0219 (6) | 0.0356 (8) | 0.0192 (6) | 0.0052 (5) | 0.0076 (5) | 0.0000 (6) |
C2_5 | 0.0377 (9) | 0.0408 (9) | 0.0259 (7) | 0.0173 (7) | 0.0115 (6) | 0.0066 (7) |
C3_5 | 0.0386 (9) | 0.0481 (10) | 0.0185 (6) | 0.0122 (7) | 0.0061 (5) | 0.0050 (7) |
C4_5 | 0.0238 (8) | 0.0686 (14) | 0.0449 (10) | −0.0061 (7) | 0.0141 (7) | −0.0090 (10) |
N_1—CA_1 | 1.4400 (16) | C_3—N_4 | 1.3382 (16) |
N_1—H1_1 | 1.00 (2) | N_4—CA_4 | 1.4599 (16) |
N_1—H2_1 | 0.93 (2) | N_4—H_4 | 0.84 (2) |
CA_1—C_1 | 1.5060 (18) | CA_4—CR_4 | 1.5313 (19) |
CA_1—HA1_1 | 1.01 (2) | CA_4—CL_4 | 1.5256 (18) |
CA_1—HA2_1 | 0.97 (2) | CA_4—C_4 | 1.5380 (17) |
C_1—O_1 | 1.2377 (15) | CL_4—HL1_4 | 0.95 (2) |
C_1—N_2 | 1.3443 (16) | CL_4—HL2_4 | 0.98 (2) |
N_2—CA_2 | 1.4717 (16) | CL_4—HL3_4 | 0.98 (2) |
N_2—H_2 | 0.85 (2) | CR_4—HR1_4 | 0.99 (2) |
CA_2—CR_2 | 1.5231 (16) | CR_4—HR2_4 | 0.96 (2) |
CA_2—CL_2 | 1.5344 (17) | CR_4—HR3_4 | 0.99 (2) |
CA_2—C_2 | 1.5400 (16) | C_4—O_4 | 1.2048 (17) |
CL_2—HL1_2 | 0.895 (17) | C_4—O_5 | 1.3263 (16) |
CL_2—HL2_2 | 0.98 (2) | O_5—C1_5 | 1.4810 (16) |
CL_2—HL3_2 | 0.982 (19) | C1_5—C3_5 | 1.515 (2) |
CR_2—HR1_2 | 1.003 (19) | C1_5—C4_5 | 1.515 (2) |
CR_2—HR2_2 | 0.94 (2) | C1_5—C2_5 | 1.521 (2) |
CR_2—HR3_2 | 0.972 (19) | C2_5—H21_5 | 0.94 (3) |
C_2—O_2 | 1.2267 (14) | C2_5—H22_5 | 0.93 (3) |
C_2—N_3 | 1.3409 (15) | C2_5—H23_5 | 1.05 (3) |
N_3—CA_3 | 1.4475 (15) | C3_5—H31_5 | 1.03 (2) |
N_3—H_3 | 0.835 (19) | C3_5—H32_5 | 1.01 (2) |
CA_3—C_3 | 1.5280 (16) | C3_5—H33_5 | 0.94 (3) |
CA_3—HA1_3 | 0.923 (17) | C4_5—H41_5 | 1.02 (3) |
CA_3—HA2_3 | 0.974 (18) | C4_5—H42_5 | 1.07 (3) |
C_3—O_3 | 1.2343 (15) | C4_5—H43_5 | 1.02 (3) |
CA_1—N_1—H1_1 | 111.6 (13) | O_3—C_3—N_4 | 123.02 (11) |
CA_1—N_1—H2_1 | 107.8 (15) | O_3—C_3—CA_3 | 121.37 (11) |
H1_1—N_1—H2_1 | 112 (2) | N_4—C_3—CA_3 | 115.61 (10) |
N_1—CA_1—C_1 | 114.29 (11) | C_3—N_4—CA_4 | 122.41 (11) |
N_1—CA_1—HA1_1 | 115.5 (11) | C_3—N_4—H_4 | 119.2 (12) |
C_1—CA_1—HA1_1 | 105.6 (11) | CA_4—N_4—H_4 | 117.9 (12) |
N_1—CA_1—HA2_1 | 109.4 (12) | CR_4—CA_4—CL_4 | 111.14 (11) |
C_1—CA_1—HA2_1 | 108.6 (12) | N_4—CA_4—C_4 | 110.13 (10) |
HA1_1—CA_1—HA2_1 | 102.6 (16) | CA_4—CL_4—HL1_4 | 109.8 (13) |
O_1—C_1—N_2 | 122.00 (11) | CA_4—CL_4—HL2_4 | 110.0 (12) |
O_1—C_1—CA_1 | 119.25 (11) | HL1_4—CL_4—HL2_4 | 107.7 (17) |
N_2—C_1—CA_1 | 118.75 (10) | CA_4—CL_4—HL3_4 | 112.0 (14) |
C_1—N_2—CA_2 | 121.84 (10) | HL1_4—CL_4—HL3_4 | 106.9 (19) |
C_1—N_2—H_2 | 119.6 (14) | HL2_4—CL_4—HL3_4 | 110.3 (18) |
CA_2—N_2—H_2 | 117.9 (14) | CA_4—CR_4—HR1_4 | 112.9 (13) |
N_2—CA_2—CL_2 | 107.84 (10) | CA_4—CR_4—HR2_4 | 112.5 (12) |
C_2—CA_2—CL_2 | 106.71 (10) | HR1_4—CR_4—HR2_4 | 104.5 (18) |
N_4—CA_4—CL_4 | 110.70 (11) | CA_4—CR_4—HR3_4 | 107.0 (14) |
C_4—CA_4—CL_4 | 109.78 (11) | HR1_4—CR_4—HR3_4 | 112.7 (19) |
N_2—CA_2—CR_2 | 111.08 (10) | HR2_4—CR_4—HR3_4 | 107.0 (18) |
C_2—CA_2—CR_2 | 109.85 (10) | O_4—C_4—O_5 | 126.07 (12) |
N_4—CA_4—CR_4 | 107.56 (11) | O_4—C_4—CA_4 | 122.76 (11) |
C_4—CA_4—CR_4 | 107.46 (11) | O_5—C_4—CA_4 | 110.98 (11) |
CR_2—CA_2—CL_2 | 110.01 (10) | C_4—O_5—C1_5 | 120.39 (11) |
N_2—CA_2—C_2 | 111.23 (10) | O_5—C1_5—C3_5 | 109.66 (11) |
CA_2—CL_2—HL1_2 | 107.9 (10) | O_5—C1_5—C4_5 | 101.90 (12) |
CA_2—CL_2—HL2_2 | 112.3 (11) | C3_5—C1_5—C4_5 | 110.89 (14) |
HL1_2—CL_2—HL2_2 | 105.7 (15) | O_5—C1_5—C2_5 | 110.38 (11) |
CA_2—CL_2—HL3_2 | 110.2 (11) | C3_5—C1_5—C2_5 | 112.38 (14) |
HL1_2—CL_2—HL3_2 | 112.5 (15) | C4_5—C1_5—C2_5 | 111.13 (15) |
HL2_2—CL_2—HL3_2 | 108.3 (15) | C1_5—C2_5—H21_5 | 106.6 (16) |
CA_2—CR_2—HR1_2 | 109.4 (10) | C1_5—C2_5—H22_5 | 109.1 (16) |
CA_2—CR_2—HR2_2 | 107.3 (11) | H21_5—C2_5—H22_5 | 108 (2) |
HR1_2—CR_2—HR2_2 | 111.5 (16) | C1_5—C2_5—H23_5 | 112.5 (14) |
CA_2—CR_2—HR3_2 | 111.0 (11) | H21_5—C2_5—H23_5 | 110 (2) |
HR1_2—CR_2—HR3_2 | 106.8 (15) | H22_5—C2_5—H23_5 | 111 (2) |
HR2_2—CR_2—HR3_2 | 110.9 (16) | C1_5—C3_5—H31_5 | 110.2 (12) |
O_2—C_2—N_3 | 122.93 (11) | C1_5—C3_5—H32_5 | 111.4 (14) |
O_2—C_2—CA_2 | 121.36 (10) | H31_5—C3_5—H32_5 | 108.5 (18) |
N_3—C_2—CA_2 | 115.52 (10) | C1_5—C3_5—H33_5 | 109.9 (15) |
C_2—N_3—CA_3 | 121.89 (10) | H31_5—C3_5—H33_5 | 112.5 (19) |
C_2—N_3—H_3 | 119.2 (12) | H32_5—C3_5—H33_5 | 104 (2) |
CA_3—N_3—H_3 | 117.5 (12) | C1_5—C4_5—H41_5 | 109.7 (14) |
N_3—CA_3—C_3 | 114.07 (10) | C1_5—C4_5—H42_5 | 106.4 (16) |
N_3—CA_3—HA1_3 | 107.9 (10) | H41_5—C4_5—H42_5 | 114 (2) |
C_3—CA_3—HA1_3 | 109.4 (10) | C1_5—C4_5—H43_5 | 110.0 (16) |
N_3—CA_3—HA2_3 | 111.5 (10) | H41_5—C4_5—H43_5 | 106 (2) |
C_3—CA_3—HA2_3 | 108.1 (10) | H42_5—C4_5—H43_5 | 110 (2) |
HA1_3—CA_3—HA2_3 | 105.5 (15) |
D—H···A | D—H | H···A | D···A | D—H···A |
N_1—H_1···O_2i | 1.00 (2) | 2.04 (2) | 3.0111 (16) | 164 (2) |
N_2—H_2···O_3ii | 0.85 (2) | 2.25 (2) | 3.0735 (14) | 164 (2) |
N_3—H_3···O_1iii | 0.84 (2) | 2.030 (19) | 2.7548 (14) | 145 (2) |
N_4—H_4···O_1iii | 0.84 (2) | 2.12 (2) | 2.9146 (15) | 158 (2) |
Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) −x+3/2, y−1/2, z; (iii) x+1/2, y, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C16H30N4O5 |
Mr | 358.44 |
Crystal system, space group | Orthorhombic, Pbca |
Temperature (K) | 100 |
a, b, c (Å) | 9.3500 (19), 15.950 (3), 26.070 (5) |
V (Å3) | 3887.9 (14) |
Z | 8 |
Radiation type | Synchrotron, λ = 0.65253 Å |
µ (mm−1) | 0.05 |
Crystal size (mm) | 0.08 × 0.07 × 0.04 |
Data collection | |
Diffractometer | Synchrotron diffractometer |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 51547, 4686, 4379 |
Rint | 0.099 |
(sin θ/λ)max (Å−1) | 0.713 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.059, 0.151, 1.11 |
No. of reflections | 4686 |
No. of parameters | 346 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.49, −0.51 |
Computer programs: XDS (Kabsch, 2010), AIMLESS (Evans & Murshudov, 2013), SHELXS86 (Sheldrick, 2008), SHELXL2014 (Sheldrick, 2015), XTALVIEW (McRee, 1999) and SwissPDBViewer (Guex & Peitsch, 1997), CHEMDRAW (Mills, 2006), ORTEPIII (Burnett & Johnson, 1996), ORTEP-3 for Windows (Farrugia, 2012) and POVRAY (Persistence of Vision, 2004).
ψ(1) | N1—CA1—C1—N2 | -4.64 (16) |
ω(1) | CA1—C1—N2—CA2 | -177.16 (10) |
φ(2) | C1—N2—CA2—C2 | -53.40 (14) |
ψ(2) | N2—CA2—C2—N3 | -39.73 (13) |
ω(2) | CA2—C2—N3—CA3 | -167.04 (10) |
φ(3) | C2—N3—CA3—C3 | 80.62 (14) |
ψ(3) | N3—CA3—C3—N4 | 33.74 (14) |
ω(3) | CA3—C3—N4—CA4 | -179.45 (10) |
φ(4) | C3—N4—CA4—C4 | 47.00 (15) |
ψ(4) | N4—CA4—C4—O5 | 43.18 (14) |
ω(4) | C4A—C4—O5—C15 | -179.77 (10) |
N_2—CA_2—CL_2 | 107.84 (10) | N_2—CA_2—CR_2 | 111.08 (10) |
C_2—CA_2—CL_2 | 106.71 (10) | C_2—CA_2—CR_2 | 109.85 (10) |
N_4—CA_4—CL_4 | 110.70 (11) | N_4—CA_4—CR_4 | 107.56 (11) |
C_4—CA_4—CL_4 | 109.78 (11) | C_4—CA_4—CR_4 | 107.46 (11) |
D—H···A | D—H | H···A | D···A | D—H···A |
N_1—H_1···O_2i | 1.00 (2) | 2.042 (24) | 3.0111 (16) | 164 (2) |
N_2—H_2···O_3ii | 0.85 (2) | 2.245 (22) | 3.0735 (14) | 164 (2) |
N_3—H_3···O_1iii | 0.84 (2) | 2.030 (19) | 2.7548 (14) | 145 (2) |
N_4—H_4···O_1iii | 0.84 (2) | 2.116 (20) | 2.9146 (15) | 158 (2) |
Symmetry codes: (i) −x+1, y−1/2, −z+1/2; (ii) −x+3/2, y−1/2, z; (iii) x+1/2, y, −z+1/2. |