An unusually short intermolecular N—H⋯N hydrogen bond in crystals of the hemi-hydrochloride salt of 1-exo-acetamidopyrrolizidine
The title compound [systematic name: (1R*, 8S)-2-acetamidooctahydropyrrolizin-4-ium chloride–N-[(1R, 8S)-hexahydro-1H-pyrrolizin-2-yl)acetamide (1/1)], 2(C9H16N2O)·HCl or C9H17N2O+·Cl−·C9H16N2O, arose as an unexpected product when 1-exo-acetamidopyrrolizidine (AcAP; C9H16N2O) was dissolved in CHCl3. Within the AcAP pyrrolizidine group, the unsubstituted five-membered ring is disordered over two orientations in a 0.897 (5):0.103 (5) ratio. Two AcAP molecules related by a crystallographic twofold axis link to H+ and Cl− ions lying on the rotation axis, thereby forming N—H⋯N and N—H⋯Cl⋯H—N hydrogen bonds. The first of these has an unusually short N⋯N separation of 2.616 (2) Å: refinement of different models against the present data set could not distinguish between a symmetrical hydrogen bond (H atom lying on the twofold axis and equidistant from the N atoms) or static or dynamic disorder models (i.e. N—H⋯N + N⋯H—N). Computational studies suggest that the disorder model is slightly more stable, but the energy difference is very small.
In the course of our ongoing studies on the biosynthesis of loline alkaloids (Schardl et al., 2007; Pan et al., 2018), we had occasion to prepare 1-exo-acetamidopyrrolizidine (C9H16N2O; AcAP) by reduction of the corresponding oxime (Fig. 1) (Pan et al., 2014). As part of our effort to prove unambiguously that the major diastereomer obtained in this reaction was indeed the exo diastereomer, we attempted to obtain crystals of AcAP that were suitable for X-ray analysis. We obtained sufficiently high-quality crystals by recrystallization from CHCl3, but to our surprise, the analysis showed that the crystals were not AcAP, but 2AcAP·HCl, with the HCl presumably originating from amine-promoted decomposition of CHCl3. This paper describes the structure of crystalline 2AcAP·HCl, which features an unusually short +N—H⋯N interaction.
The molecular structure of AcAP recrystallized from CHCl3 is a hemi-hydrochloride, 2AcAP·HCl (Fig. 2). Within the pyrrolizidine group, the unsubstituted five-membered ring is disordered over two orientations (Fig. 3). Each five-membered ring has an envelope conformation, but since the minor component occupancy is small [i.e., 0.103 (5) versus 0.897 (5)], we restrict further comment to the major component only. The `flap' atoms, C2 and C6, for the substituted (C1–C3/N4/C8) and unsubstituted (C5–C8/N4) rings, respectively, are displaced from the mean plane of the four remaining atoms (C1/C3/N4/C8 and C7/C5/N4/C8) by 0.622(1) and 0.633(2) Å, respectively. The dihedral angle between these mean planes is 56.07 (9)°. The acetamide group is characteristically almost planar (r.m.s. deviation = 0.0181 Å), but twisted from the mean plane of C1/C8/N4/C3 by a dihedral angle of 70.56 (7)°. Aside from an unusually short N—H⋯N hydrogen bond, which will be discussed in subsequent sections, all geometrical parameters are within their expected ranges (e.g., Allen et al., 1987).
The primary structural motif within crystals of 2AcAP·HCl consists of a pair of homochiral AcAP molecules hydrogen bonded to H+ and Cl− ions about a crystallographic twofold axis of space group C2/c. Based on electron density alone, the H+ cation and Cl− anion both appear to be located on the twofold axis. As a result of the twofold symmetry axis, the hydrogen bond N4—H4N⋯N4i [symmetry code: (i) −x + 1, y, −z + ] appears to be symmetric, and since dN⋯N = 2.616 (2) Å (Table 1), it is exceptionally short (see Database survey section, below). Similarly, since the refined H+ position lies on the twofold axis and is equidistant from N4 and N4i, the refined N⋯H interatomic distance appears unusually long at 1.3080 (12) Å. The whole hydrogen-bonded ensemble makes an R33(12) supramolecular motif. For the short N4—H4N⋯N4i hydrogen bond, a difference-Fourier map (Fig. 4) clearly shows an elongated region of electron density centered on the twofold axis corresponding to the position of the refined H4N hydrogen atom. The true location of H4N, however, remains ambiguous based on X-ray data alone. Possibilities include strictly symmetric (i.e., on the twofold axis exactly halfway between N4 and N4i), statically disordered (i.e., 50% on each of N4 and N4i) or dynamically disordered (i.e., exchanging rapidly between N4 and N4i). Alternative strategies for H4N inclusion in the model refined equally well (see Refinement, below), so we settled on the simplest approach, following the recommendations of Fábry (2018). Nonetheless, the ambiguity prompted us to analyze the potential energy surface of the H4N position via computational methods for single versus double energy well character (see Computational analysis, below). In addition to the strong N—H⋯N hydrogen bond, weaker N2—H2—Cl1—H2i—N2i interactions link the twofold-related acetamide groups to the Cl− anion [N⋯Cl = 3.2263 (11) Å]. The twist of the twofold-related hydrogen-bonded pyrrolizidine moieties relative to each other, as defined by the torsion angle C8—N4⋯N4i—C8i is −69.82 (16)°. The almost planar acetamide group forms a dihedral angle with its twofold-related counterpart of 20.18 (3)°. The only other intramolecular interactions are van der Waals contacts. Estimates of the relative fractions of intermolecular contacts between individual atom types derived from a Hirshfeld-surface analysis using CrystalExplorer (Turner et al., 2017; Tan et al., 2019) are complicated by the ring disorder and by the N4—H4N⋯N4i hydrogen bond. Nevertheless, all contacts appear to involve hydrogen atoms, with the overwhelming majority being H⋯H (65.3%). The Cl− anion and the acetamide O atom each reside in pockets surrounded by hydrogen atoms, giving H⋯Cl/Cl⋯H (16.2%) and H⋯O/O⋯H (12.4%), with the remainder being N⋯H/H⋯N and C⋯H/H⋯C contacts.
A search of the Cambridge Structure Database (version 5.40, Nov. 2018; Groom et al., 2016) on the bicyclic pyrrolizidine core of AcAP yielded 584 hits. Of these, 41 are protonated at the ring N atom, but only three of those bear a substituent (other than H) at the 1-position of the pyrrolizidine ring system (assuming standard IUPAC ring numbering). CSD entry BRPYLZ (Wilson & Sawicki, 1979) is a bromide salt of a bromine derivative, and CPYRZD (Soderberg, 1971) is a zwitterion, with a carboxylate group at the 1-position and a bromo substituent at the 2-position. The relative stereochemistry of BRPYLZ and CPYRZD, however, are different from AcAP. CSD entry EDOTUP (Bhardwaj et al., 2017) was a precursor to AcAP, and is the most closely related currently deposited structure.
The most striking feature of 2AcAP·HCl is the unusually short N—H⋯N hydrogen bond. A CSD search on the fragment `C-N(X)-H-N(X)-C′, where `X′ denotes `any group', gave 45 hits. Rejection of cases where apparent close N⋯N distances were due to disorder (four entries), and those in which the N-bound H atom was missing from the model (two entries), left 39 structures, of which three were duplicates. In the remaining 36 structures the N—H⋯N hydrogen bonds are intramolecular in 22 and intermolecular in 14. The closest N⋯N separations occur in the intramolecular N—H⋯N hydrogen-bonded structures, the shortest being 2.419 Å in EBOKOV (Wilkes et al., 2000). However, in these intramolecular cases, the N⋯N separation is largely dictated by the intramolecular geometry, which effectively forces the donor and acceptor N atoms into close proximity. Of the 14 CSD entries from the search that have intermolecular N—H⋯N hydrogen bonding, the closest N⋯N separation occurs in BECHOG (Glidewell & Holden, 1982), in which a bis(4-methylpyridine)hydrogen(I) cation sits on an inversion centre, giving an apparently symmetric N—H⋯N hydrogen bond with N⋯N distance of 2.610 (15) Å, and ROHTIR (Bock et al., 1997), for which the asymmetric unit contains two separate halves of a methylammonium-methylamine cation, [CH3NH2-H-NH2CH3]+, each sitting on centres of inversion, giving N⋯N distances of 2.620 and 2.641 Å. The N⋯N separation in 2AcAP·HCl is similar, at 2.616 (2) Å, although the difference is not significant, and well within the quoted precision estimate of BECHOG and the accuracy limits imposed by the spherical-atom scattering-factor approximation (see e.g., Dawson, 1964).
A model consisting of the four 2AcAP·HCl units present in one unit cell was relaxed at the DFT level (see below for details), both with and without symmetry constraints on charge density. In the case where symmetry constraints were absent, a small displacement (0.06 Å) was applied to the hydrogen atom in the N—H⋯N hydrogen bond to break symmetry in the initial geometry. The relaxations led to two structures, one with constrained twofold symmetry (A), and one unconstrained (B). The volume difference between these theoretical models (calculations assumed absolute zero) was negligible (Avol = 1918.85 Å3 versus Bvol = 1919.63 Å3). In the symmetric model, the N—H⋯N hydrogen atom (corresponding to H4 in the crystallographic model) is equidistant between the two nitrogen atoms (N—H = 1.290 Å), whereas in model B the N—H distances differ (N—H = 1.194 and 1.406 Å). This is in agreement with the computed charge-density line profile of N—H⋯N in structure B, as shown in Fig. 5. Structure B is calculated to be slightly more stable, but the energy difference (4.7 meV per unit cell) is vanishingly small (Fig. 6). The low energy barrier suggests dynamic disorder of the N—H⋯N hydrogen atom.
Computational details: For this periodic system, density functional theory (DFT) calculations were carried out using the Vienna ab initio simulation Package (VASP) with Perdew–Burke–Ernzerhof (PBE) exchange-correlation functional (Kresse & Furthmüller, 1996a,b; Kresse et al., 1994; Perdew et al., 1996). The electron-ion interactions were described with the projector augmented-wave (PAW) method (Blöchl, 1994; Kresse & Joubert, 1999). The valence electronic wavefunctions were expanded on a plane-wave basis with a kinetic energy cutoff at 520 eV, and Gaussian smearing with a width of 0.05 eV was employed. The convergence criterion of the total energy was set to 10 −5 eV in the self-consistent field loop. The Brillouin zone was sampled with a 1×2×2 Γ-centered grid. The experimental structures were relaxed until the Hellman–Feynman forces for each site were less than 0.005 eV Å−1, and Grimme's DFT-D3 dispersion correction was applied with Becke–Johnson damping (Grimme et al., 2010, 2011).
AcAP was synthesized and purified according to the published procedure (Pan et al., 2014). Crystals of 2AcAP·HCl were obtained in the form of colorless plates by dissolving 20 mg of AcAP in 1 ml of CHCl3 in a 10 ml round-bottom flask and allowing the solution to stand in a refrigerator for about a month.
Crystal data, data collection, and structure refinement details are given in Table 2. Non-disordered carbon-bound H atoms were found in difference-Fourier maps, but subsequently included in the refinement using riding models, with constrained distances set to 0.98 Å (RCH3), 0.99 Å (R2CH2) and 1.00 Å (R3CH). Following the advice of Fábry (2018), the hydrogen atom involved in the short N—H⋯N hydrogen bond (H4N) was placed into difference-Fourier electron density and refined, albeit constrained to the twofold axis. An alternative model in which this H atom was allowed to ride at 50% occupancy on both N4 and N4i [symmetry code: (i) −x + 1, y, −z + ] refined equally well: the X-ray data alone being insufficient to establish a preference. The amide N—H hydrogen atom (H2N) was refined freely. Uiso(H) parameters for nitrogen-bound hydrogen atoms were refined, while for carbon-bound H atoms, Uiso(H) were set to values of either 1.2Ueq (R3CH, R2H2) or 1.5Ueq (RCH3) of the attached atom.
The refined displacement parameters for the Cl− anion (e.g., Figs. 2 and 4) appear a little small compared to the rest of the structure. In addition, the largest residual difference map peaks (0.67 and 0.65 e Å−3) were close (0.37 and 0.47 Å respectively) to Cl1. Refinement of the anion as mixed Cl and Br gave an occupancy ratio of 0.934 (2):0.066 (2), a lower R-value (3.02%), and a flatter difference map (Δρ = 0.29/-0.19 e Å−3). However, the reaction included no known source of Br−, so the mixed anion model was not retained.
To ensure satisfactory refinement for disordered groups in the structure, a combination of constraints and restraints were employed. The constraints (SHELXL commands EXYZ and EADP) were used to fix overlapping fragments. Restraints were used to ensure the integrity of ill-defined or disordered groups (SHELXL commands SAME, SIMU, and RIGU). An alternative model using space group Cc (50:50 inversion twinned) was considered but rejected as it required hefty restraints and did not resolve the H4N atom ambiguity.
Data collection: APEX3 (Bruker, 2016); cell refinement: APEX3 (Bruker, 2016); data reduction: APEX3 (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018/3 (Sheldrick, 2015b); molecular graphics: XP in SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELX (Sheldrick, 2008), CIFFIX (Parkin, 2013) and PLATON (Spek, 2009).
|C9H17N2O+·Cl−·C9H16N2O||F(000) = 808|
|Mr = 372.93||Dx = 1.267 Mg m−3|
|Monoclinic, C2/c||Mo Kα radiation, λ = 0.71073 Å|
|a = 20.2125 (8) Å||Cell parameters from 9978 reflections|
|b = 9.6926 (4) Å||θ = 2.3–27.5°|
|c = 10.1458 (3) Å||µ = 0.22 mm−1|
|β = 100.445 (1)°||T = 90 K|
|V = 1954.74 (13) Å3||Plate, colourless|
|Z = 4||0.40 × 0.36 × 0.04 mm|
|Bruker D8 Venture dual source |
|2235 independent reflections|
|Radiation source: microsource||2096 reflections with I > 2σ(I)|
|Detector resolution: 7.41 pixels mm-1||Rint = 0.032|
|φ and ω scans||θmax = 27.5°, θmin = 2.3°|
|Absorption correction: multi-scan |
(SADABS; Krause et al., 2015)
|h = −26→26|
|Tmin = 0.885, Tmax = 0.988||k = −12→12|
|31903 measured reflections||l = −11→13|
|Refinement on F2||Secondary atom site location: difference Fourier map|
|Least-squares matrix: full||Hydrogen site location: mixed|
|R[F2 > 2σ(F2)] = 0.037||H atoms treated by a mixture of independent and constrained refinement|
|wR(F2) = 0.096|| w = 1/[σ2(Fo2) + (0.0375P)2 + 2.4571P] |
where P = (Fo2 + 2Fc2)/3
|S = 1.12||(Δ/σ)max < 0.001|
|2235 reflections||Δρmax = 0.67 e Å−3|
|144 parameters||Δρmin = −0.22 e Å−3|
|82 restraints||Extinction correction: SHELXL-2018/3 (Sheldrick 2018), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4|
|Primary atom site location: structure-invariant direct methods||Extinction coefficient: 0.005 (1)|
Experimental. The crystal was mounted using polyisobutene oil on the tip of a fine glass fibre, which was fastened in a copper mounting pin with electrical solder. It was placed directly into the cold gas stream of a liquid-nitrogen based cryostat (Hope, 1994; Parkin & Hope, 1998).
Diffraction data were collected with the crystal at 90K, which is standard practice in this laboratory for the majority of flash-cooled crystals.
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 progress was checked using PLATON (Spek, 2009) and by an R-tensor (Parkin, 2000). The final model was further checked with the IUCr utility checkCIF.
|C1||0.63783 (6)||0.58377 (14)||0.26083 (13)||0.0182 (3)|
|C2||0.60256 (7)||0.61745 (15)||0.11816 (14)||0.0229 (3)|
|C3||0.58652 (7)||0.76915 (15)||0.12835 (14)||0.0232 (3)|
|N4||0.56555 (6)||0.78256 (11)||0.26254 (11)||0.0184 (3)|
|H4N||0.500000||0.781 (3)||0.250000||0.056 (9)*|
|C5||0.5885 (2)||0.9121 (2)||0.3373 (3)||0.0249 (7)||0.897 (5)|
|C6||0.65299 (9)||0.87111 (17)||0.43106 (16)||0.0237 (4)||0.897 (5)|
|C7||0.63499 (12)||0.7276 (2)||0.4771 (2)||0.0209 (5)||0.897 (5)|
|C8||0.59630 (6)||0.66296 (13)||0.34850 (13)||0.0178 (3)||0.897 (5)|
|C5'||0.595 (2)||0.9165 (19)||0.322 (2)||0.0249 (7)||0.103 (5)|
|C6'||0.6157 (9)||0.8793 (15)||0.4690 (15)||0.032 (3)||0.103 (5)|
|C7'||0.6489 (11)||0.739 (2)||0.458 (2)||0.030 (4)||0.103 (5)|
|C8'||0.59630 (6)||0.66296 (13)||0.34850 (13)||0.0178 (3)||0.103 (5)|
|N2||0.64091 (6)||0.43798 (12)||0.29157 (11)||0.0184 (3)|
|H2N||0.6002 (10)||0.390 (2)||0.2837 (19)||0.035 (5)*|
|C9||0.69841 (6)||0.36514 (14)||0.31606 (12)||0.0178 (3)|
|O1||0.75448 (5)||0.41694 (11)||0.32142 (11)||0.0260 (2)|
|C10||0.68897 (7)||0.21311 (14)||0.33748 (14)||0.0224 (3)|
|Cl1||0.500000||0.27309 (5)||0.250000||0.02141 (15)|
|C1||0.0169 (6)||0.0170 (6)||0.0210 (6)||−0.0016 (5)||0.0044 (5)||0.0007 (5)|
|C2||0.0266 (7)||0.0247 (7)||0.0185 (6)||−0.0007 (5)||0.0071 (5)||0.0009 (5)|
|C3||0.0240 (7)||0.0244 (7)||0.0214 (7)||−0.0021 (5)||0.0041 (5)||0.0056 (5)|
|N4||0.0201 (5)||0.0139 (5)||0.0201 (6)||−0.0016 (4)||0.0006 (4)||0.0003 (4)|
|C5||0.0284 (13)||0.0147 (7)||0.0291 (10)||−0.0044 (6)||−0.0014 (9)||−0.0013 (6)|
|C6||0.0240 (9)||0.0220 (8)||0.0234 (8)||−0.0059 (6)||0.0001 (6)||−0.0025 (6)|
|C7||0.0237 (10)||0.0206 (8)||0.0174 (9)||0.0000 (7)||0.0015 (7)||−0.0004 (7)|
|C8||0.0189 (6)||0.0154 (6)||0.0187 (6)||0.0002 (5)||0.0020 (5)||0.0012 (5)|
|C5'||0.0284 (13)||0.0147 (7)||0.0291 (10)||−0.0044 (6)||−0.0014 (9)||−0.0013 (6)|
|C6'||0.033 (7)||0.028 (5)||0.033 (5)||−0.003 (5)||−0.001 (5)||−0.008 (4)|
|C7'||0.034 (8)||0.034 (6)||0.017 (7)||0.002 (6)||−0.003 (6)||−0.006 (5)|
|C8'||0.0189 (6)||0.0154 (6)||0.0187 (6)||0.0002 (5)||0.0020 (5)||0.0012 (5)|
|N2||0.0175 (5)||0.0155 (6)||0.0228 (6)||−0.0015 (4)||0.0049 (4)||−0.0005 (4)|
|C9||0.0200 (6)||0.0191 (6)||0.0142 (6)||−0.0007 (5)||0.0028 (5)||−0.0010 (5)|
|O1||0.0179 (5)||0.0247 (5)||0.0349 (6)||−0.0010 (4)||0.0029 (4)||0.0037 (4)|
|C10||0.0246 (7)||0.0178 (7)||0.0239 (7)||0.0004 (5)||0.0022 (5)||−0.0015 (5)|
|Cl1||0.0099 (2)||0.0177 (2)||0.0354 (3)||0.000||0.00096 (16)||0.000|
|C1—C2||1.5284 (19)||C7—C8||1.529 (2)|
|C2—C3||1.513 (2)||C5'—C6'||1.521 (18)|
|C3—N4||1.5032 (18)||C6'—C7'||1.528 (17)|
|N4—H4N||1.3080 (12)||C7'—C8'||1.576 (16)|
|N4—C8'||1.5146 (16)||N2—C9||1.3439 (17)|
|N4—H4N||1.3080 (12)||N2—H2N||0.94 (2)|
|C5—C6||1.520 (4)||C9—O1||1.2317 (16)|
|N2—C1—C2||114.05 (11)||C8—C7—C6||102.97 (16)|
|C3—C2—C1||102.22 (11)||C7—C8—C1||116.80 (13)|
|C3—N4—C5'||106.2 (15)||C6'—C7'—C8'||102.6 (11)|
|C5'—N4—C8'||109.8 (9)||N4—C8'—C1||105.05 (10)|
|H4N—N4—H4N||0 (3)||N4—C8'—C7'||101.6 (8)|
|C5—N4—H4N||106.1 (12)||C1—C8'—C7'||105.9 (9)|
|C8'—N4—H4N||110.4 (12)||C9—N2—C1||123.73 (11)|
|N4—C5—C6||104.5 (2)||C9—N2—H2N||118.0 (12)|
|N2—C1—C2—C3||162.24 (11)||N2—C1—C8—C7||93.71 (16)|
|C8—C1—C2—C3||40.67 (13)||C2—C1—C8—C7||−143.19 (14)|
|C8'—C1—C2—C3||40.67 (13)||H4N—N4—C5'—C6'||97 (2)|
|C1—C2—C3—N4||−39.46 (13)||C3—N4—C5'—C6'||−142 (2)|
|C2—C3—N4—H4N||−97.5 (15)||C8'—N4—C5'—C6'||−26 (3)|
|C2—C3—N4—C5||142.30 (19)||N4—C5'—C6'—C7'||45 (3)|
|C2—C3—N4—C5'||140.9 (15)||C5'—C6'—C7'—C8'||−47 (2)|
|C2—C3—N4—C8||23.32 (13)||H4N—N4—C8'—C1||123.3 (9)|
|C2—C3—N4—C8'||23.32 (13)||C3—N4—C8'—C1||2.12 (13)|
|H4N—N4—C5—C6||141.3 (8)||C5'—N4—C8'—C1||−113 (2)|
|C3—N4—C5—C6||−95.81 (19)||H4N—N4—C8'—C7'||−126.5 (13)|
|C8—N4—C5—C6||23.5 (3)||C3—N4—C8'—C7'||112.3 (10)|
|N4—C5—C6—C7||−39.9 (3)||C5'—N4—C8'—C7'||−3 (2)|
|C5—C6—C7—C8||40.9 (2)||N2—C1—C8'—N4||−149.53 (11)|
|H4N—N4—C8—C7||−112.6 (9)||C2—C1—C8'—N4||−26.43 (13)|
|C5—N4—C8—C7||2.4 (2)||N2—C1—C8'—C7'||103.4 (9)|
|C3—N4—C8—C7||126.23 (14)||C2—C1—C8'—C7'||−133.5 (9)|
|H4N—N4—C8—C1||123.3 (9)||C6'—C7'—C8'—N4||30.6 (18)|
|C5—N4—C8—C1||−121.70 (19)||C6'—C7'—C8'—C1||140.1 (14)|
|C3—N4—C8—C1||2.12 (13)||C2—C1—N2—C9||113.29 (14)|
|C6—C7—C8—N4||−26.97 (19)||C8—C1—N2—C9||−129.88 (13)|
|C6—C7—C8—C1||89.41 (17)||C8'—C1—N2—C9||−129.88 (13)|
|N2—C1—C8—N4||−149.53 (11)||C1—N2—C9—O1||3.8 (2)|
|C2—C1—C8—N4||−26.43 (13)||C1—N2—C9—C10||−176.47 (12)|
Supercomputing resources on the Lipscomb High-Performance Computing Cluster were provided by the University of Kentucky Information Technology Department and Center for Computational Sciences (CCS).
Funding for this research was provided by: The National Science Foundation (MRI-CHE1625732 to SRP), and by the University of Kentucky. QA acknowledges the NSF under Award DMR-1627428.
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