research communications
Synthesis,
and Hirshfeld surface analysis of 2-phenyl-3-(prop-2-yn-1-yloxy)quinoxalineaLaboratory of Medicinal Chemistry, Drug Sciences Research Center, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco, bLaboratory of Heterocyclic Organic Chemistry, Faculty of Sciences, Mohammed V University, Rabat, Morocco, cDepartment of Chemistry, Tulane University, New Orleans, LA 70118, USA, dLaboratory of Medicinal Chemistry, Faculty of Clinical Pharmacy, 21 September University, Yemen, eDepartment of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran, fDepartment of Chemistry, Faculty of Science and Arts, King Khalid University, Mohail Assir, Saudi Arabia, and gMohammed VI Center for Research and Innovation (CM6), Rabat 10000, Morocco
*Correspondence e-mail: alsubaripharmaco@21umas.edu.ye, y.ramli@um5r.ac.ma
In the title compound, C17H12N2O, the quinoxaline moiety shows deviations of 0.0288 (7) to −0.0370 (7) Å from the mean plane (r.m.s. deviation of fitted atoms = 0.0223 Å). In the crystal, corrugated layers two molecules thick are formed by C—H⋯N hydrogen bonds and π-stacking interactions.
Keywords: crystal structure; quinoxaline; alkylation; hydrogen bond; π-stacking.
CCDC reference: 2142451
1. Chemical context
Quinoxaline derivatives are described extensively among the heterocycles being investigated for the discovery and development of new biologically active molecules. Numerous studies have been published regarding this class of compounds, revealing that quinoxaline is present in a number of well-established drugs with diverse therapeutic activities as well as industrial properties (e.g. Lgaz et al., 2015). In recent decades, the medicinal chemistry of quinoxaline and its derivatives have received great attention due to their wide spectrum of biological activities, in particular analgesic, anti-diabetic, antiviral, antibacterial, antioxidant, anti-inflammatory, antidepressant, and anti-tubercular (Ramli & Essassi, 2015). Our interest in quinoxalines results from their simple synthesis and the ease with which X-ray quality crystals can be grown. Following this line of research, and as a continuation of our work in this area (e.g. Missioui et al., 2022), based on the therapeutic significance of this scaffold for potential applications in medicinal chemistry, we report herein the synthesis of a new quinoxaline derivative by an alkylation reaction of 3-phenylquinoxalin-2(1H)-one using 3-bromoprop-1-yne as an alkylating reagent and potassium carbonate in the presence of tetra-n-butylammonium bromide as catalyst in (Fig. 1). A Hirshfeld surface analysis was performed to analyze the intermolecular interactions.
2. Structural commentary
In the title molecule, the fused bicyclic ring system is not entirely planar, as indicated by the dihedral angle of 2.25 (6)° between its constituent rings and by the deviations from the mean plane through the ten atoms, which range from 0.0288 (7) Å (C8) to −0.0370 (7) Å (C2) (r.m.s. deviation of fitted atoms = 0.0223 Å). The plane of the benzene ring C12–C17 is inclined to the above plane by 34.04 (4)°, while the methylene carbon of the propynyl group (C9) lies virtually in the plane of the quinoxaline unit, as indicated by the C9—O1—C7—N1 torsion angle of 0.65 (13)°. However, the propynyl group is almost perpendicular to the above plane, as indicated by the C7—O1—C9—C10 torsion angle of −87.0 (1)° (Fig. 2).
3. Supramolecular features
In the crystal, the molecules are connected into chains extending along the b-axis direction by C11—H11⋯N2 hydrogen bonds (Table 1 and Fig. 3). The chains are linked into corrugated layers two molecules thick by offset π-stacking interactions between the C1–C6 and C1/C6/N1/C7/C8/N2 rings [centroid–centroid distance = 3.6716 (8) Å; dihedral angle = 2.25 (4)°, slippage = 1.262 Å] across inversion centers (Fig. 3).
To quantify the extent of each type of intermolecular interaction in the crystal packing, a Hirshfeld surface analysis was performed using CrystalExplorer (Version 21.5; Spackman et al., 2021). Descriptions of the surfaces generated and their interpretation have been published (Tan et al., 2019). Fig. 4 shows the dnorm surface with Fig. 4a showing two neighboring molecules illustrating the C—H⋯N hydrogen bond and Fig. 4b one neighbor illustrating the π-stacking. From Fig. 4a, it is clear that the C—H⋯N hydrogen bond is the only intermolecular hydrogen bond in the structure. Fig. 5a shows the surface mapped over shape-index while Fig. 5b shows it mapped over curvature. In both of these, the characteristic features of intermolecular π-stacking interactions are quite evident. Fig. 6 presents the 2D fingerprint plots with Fig. 6a giving the total of all intermolecular interactions and Fig. 6b–6e showing those delineated into H⋯H, C⋯H/H⋯C, N⋯H/H⋯N and C⋯C interactions. These are the major interactions and contribute 42.8%, 36.8%, 8.3% and 6.3% to the total, respectively. In the absence of C—H⋯π(ring) interactions, the large contribution of C⋯H/H⋯C interactions may seem unusual, but PLATON (Spek, 2020) indicates that there are at least six and as many as ten such contacts with distances slightly shorter than to slightly longer than the sum of the respective van der Waals radii.
4. Database survey
A search of the Cambridge Structural Database (CSD, updated to January 2024; Groom et al., 2016) using fragment A (Fig. 7, R = any atom), yielded seven hits similar to the title molecule, viz. FACPEI with R = benzyl (Abad et al., 2020), 3-(2-oxo-3-phenylquinoxalin-1(2H)-yl)propyl (KOPKAF; Abad et al., 2024) and 2-(2-oxooxazolidin-3-yl)ethyl [monoclinic form (UREREP01; Daouda et al., 2020) and orthorhombic form (UREREP; Daouda et al., 2011)]. The last three are B (BZOQUX10; Oberti et al., 1978), C (YEFDUK; Moreau et al., 2012) and D (VAQNAE; Kumar et al., 2012). The quinoxaline moiety is closest to planar in BZOQUX10 [dihedral angle between constituent planes = 1.13 (1)°], while in UREREP it is furthest from planar [dihedral angle between constituent planes = 3.34 (16)°]. These two compounds also exhibit the smallest [30.60 (1)°] and largest [38.72 (16)°] angles of inclination of the phenyl group. The other structures show intermediate values for both angles, except for YEFDUK and VAQNAE where this angle is less than 5° because the phenyl ring is part of a six- or five-membered ring fused to the nitrogen-containing heterocycle.
5. Synthesis and crystallization
3-Phenylquinoxalin-2(1H)-one (1 g, 4.5 mmol), 3-bromoprop-1-yne (0.96 mL, 9 mmol), and potassium carbonate (0.931 g, 6.75 mmol) with an amount of catalytic tetra-n-butylammonium bromide (0.29 g, 0.9 mmol) were stirred in N,N-dimethylformamide (DMF) (20 mL) for 48 h (Fig. 1). The solution was filtered, and the solvent was removed under vacuum. Dichloromethane (20 mL) was added, and the solution was filtered. The residue was chromatographed on a silica gel column (hexane/ethyl acetate: 9.5/0.5, as mobile phase) to give two fractions. The first fraction was purified by recrystallization in ethanol to afford colorless crystals with a yield of 28.3% (O-alkylated isomer, title compound) while recrystallization of the second fraction gave a yellowish powder with a yield of 53.5% (N-alkylated isomer).
O-alkylated isomer: Yield: 28.3%, m.p. = 370–372 K, 1H NMR (300 MHz, CDCl3) δ ppm: 2.55 (t, 1H, CH, J = 3Hz); 5.265 (d, 2H, O—CH2, J = 3Hz); 7.55–8.20 (m, 9H, CHarom); 13C NMR (75 MHz, CDCl3) δ ppm: 53.93 (O—CH2); 74.85 (CH); 78.57 (–C); 126.85, 127.22, 128.31, 129.06, 129.75, 129.82, 129.86 (CHarom); 136.77, 139.35, 139.49, 146.29 (Cq); 154.11 (Cq—O).
N-alkylated isomer: Yield 53.5%, m.p. = 385–387 K, 1H NMR (300 MHz, CDCl3) δ ppm: 2.35 (t, H, CH, J = 3Hz); 5.155 (d, 2H, N—CH2, J = 3Hz); 7.41–8.36 (m, 9H, CHarom); 13C NMR (75 MHz, CDCl3) δ ppm: 31.69 (N—CH2); 73.19 (CH); 76.96 (–C); 114.07, 124.15, 128.13, 129.61, 130.45, 130.53, 130.63 (CHarom); 131.87, 133.31, 135.78, 153.72 (Cq); 153.98 (C=O).
6. Refinement
Crystal data, data collection and structure . Hydrogen atoms were included as riding contributions in idealized positions with isotropic displacement parameters tied to those of the attached atoms.
details are summarized in Table 2Supporting information
CCDC reference: 2142451
https://doi.org/10.1107/S2056989024002585/vm2298sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989024002585/vm2298Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989024002585/vm2298Isup3.cml
C17H12N2O | Z = 2 |
Mr = 260.29 | F(000) = 272 |
Triclinic, P1 | Dx = 1.323 Mg m−3 |
a = 8.4614 (14) Å | Mo Kα radiation, λ = 0.71073 Å |
b = 9.0947 (15) Å | Cell parameters from 6800 reflections |
c = 9.5360 (16) Å | θ = 2.2–29.1° |
α = 87.739 (2)° | µ = 0.08 mm−1 |
β = 72.963 (2)° | T = 120 K |
γ = 69.028 (2)° | Thick plate, colourless |
V = 653.39 (19) Å3 | 0.34 × 0.33 × 0.14 mm |
Bruker SMART APEX CCD diffractometer | 3456 independent reflections |
Radiation source: fine-focus sealed tube | 2869 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.026 |
Detector resolution: 8.3333 pixels mm-1 | θmax = 29.1°, θmin = 2.2° |
φ and ω scans | h = −11→11 |
Absorption correction: multi-scan (SADABS; Krause et al., 2015) | k = −12→12 |
Tmin = 0.91, Tmax = 0.99 | l = −13→12 |
12629 measured reflections |
Refinement on F2 | Primary atom site location: dual |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.044 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.139 | H-atom parameters constrained |
S = 1.17 | w = 1/[σ2(Fo2) + (0.0919P)2] where P = (Fo2 + 2Fc2)/3 |
3456 reflections | (Δ/σ)max < 0.001 |
181 parameters | Δρmax = 0.42 e Å−3 |
0 restraints | Δρmin = −0.24 e Å−3 |
Experimental. The diffraction data were obtained from 3 sets of 400 frames, each of width 0.5° in ω, colllected at φ = 0.00, 90.00 and 180.00° and 2 sets of 800 frames, each of width 0.45° in φ, collected at ω = –30.00 and 210.00°. The scan time was 10 sec/frame. |
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. H-atoms attached to carbon were placed in calculated positions (C—H = 0.95 - 1.00 Å). All were included as riding contributions with isotropic displacement parameters 1.2 - 1.5 times those of the attached atoms. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.70891 (9) | 0.56445 (8) | 0.38257 (7) | 0.02033 (18) | |
N1 | 0.46180 (11) | 0.60416 (9) | 0.30849 (8) | 0.01784 (19) | |
N2 | 0.63397 (10) | 0.29963 (9) | 0.16411 (8) | 0.01617 (19) | |
C1 | 0.46804 (12) | 0.39265 (11) | 0.15776 (10) | 0.0163 (2) | |
C2 | 0.38348 (13) | 0.33437 (11) | 0.07839 (10) | 0.0202 (2) | |
H2 | 0.443192 | 0.233469 | 0.026117 | 0.024* | |
C3 | 0.21438 (13) | 0.42397 (12) | 0.07686 (11) | 0.0221 (2) | |
H3 | 0.157226 | 0.384741 | 0.023461 | 0.027* | |
C4 | 0.12524 (13) | 0.57396 (12) | 0.15423 (11) | 0.0227 (2) | |
H4 | 0.007481 | 0.633952 | 0.154015 | 0.027* | |
C5 | 0.20634 (13) | 0.63425 (11) | 0.22970 (10) | 0.0206 (2) | |
H5 | 0.145802 | 0.736230 | 0.279815 | 0.025* | |
C6 | 0.37993 (12) | 0.54442 (11) | 0.23271 (10) | 0.0168 (2) | |
C7 | 0.61911 (12) | 0.51363 (11) | 0.31114 (9) | 0.0161 (2) | |
C8 | 0.71038 (12) | 0.35506 (10) | 0.23996 (9) | 0.0153 (2) | |
C9 | 0.62072 (14) | 0.72174 (11) | 0.45585 (10) | 0.0220 (2) | |
H9A | 0.664895 | 0.726667 | 0.540217 | 0.026* | |
H9B | 0.491675 | 0.744261 | 0.494533 | 0.026* | |
C10 | 0.65155 (13) | 0.84189 (11) | 0.35597 (10) | 0.0203 (2) | |
C11 | 0.67695 (14) | 0.94264 (12) | 0.27984 (11) | 0.0260 (2) | |
H11 | 0.697268 | 1.023246 | 0.218929 | 0.031* | |
C12 | 0.88656 (12) | 0.24852 (11) | 0.24864 (10) | 0.0164 (2) | |
C13 | 0.93639 (13) | 0.24226 (12) | 0.37693 (10) | 0.0217 (2) | |
H13 | 0.860641 | 0.313948 | 0.459583 | 0.026* | |
C14 | 1.09717 (14) | 0.13079 (12) | 0.38327 (11) | 0.0251 (2) | |
H14 | 1.129576 | 0.125487 | 0.471192 | 0.030* | |
C15 | 1.21016 (13) | 0.02769 (12) | 0.26279 (12) | 0.0259 (2) | |
H15 | 1.320346 | −0.047128 | 0.267536 | 0.031* | |
C16 | 1.16184 (13) | 0.03400 (12) | 0.13478 (11) | 0.0243 (2) | |
H16 | 1.239339 | −0.036390 | 0.051699 | 0.029* | |
C17 | 1.00061 (13) | 0.14291 (11) | 0.12807 (10) | 0.0198 (2) | |
H17 | 0.967552 | 0.145639 | 0.040722 | 0.024* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0248 (4) | 0.0157 (3) | 0.0240 (4) | −0.0084 (3) | −0.0109 (3) | 0.0001 (3) |
N1 | 0.0202 (4) | 0.0157 (4) | 0.0170 (4) | −0.0062 (3) | −0.0051 (3) | 0.0012 (3) |
N2 | 0.0171 (4) | 0.0152 (4) | 0.0165 (4) | −0.0063 (3) | −0.0050 (3) | 0.0025 (3) |
C1 | 0.0164 (4) | 0.0157 (4) | 0.0162 (4) | −0.0062 (3) | −0.0042 (3) | 0.0038 (3) |
C2 | 0.0216 (5) | 0.0182 (5) | 0.0222 (5) | −0.0084 (4) | −0.0072 (4) | 0.0013 (4) |
C3 | 0.0223 (5) | 0.0253 (5) | 0.0238 (5) | −0.0121 (4) | −0.0102 (4) | 0.0049 (4) |
C4 | 0.0170 (5) | 0.0259 (5) | 0.0234 (5) | −0.0058 (4) | −0.0069 (4) | 0.0067 (4) |
C5 | 0.0198 (5) | 0.0182 (5) | 0.0198 (4) | −0.0031 (4) | −0.0049 (4) | 0.0025 (4) |
C6 | 0.0181 (4) | 0.0165 (4) | 0.0151 (4) | −0.0062 (4) | −0.0041 (3) | 0.0024 (3) |
C7 | 0.0193 (5) | 0.0155 (4) | 0.0143 (4) | −0.0079 (4) | −0.0044 (3) | 0.0024 (3) |
C8 | 0.0171 (4) | 0.0146 (4) | 0.0144 (4) | −0.0066 (3) | −0.0041 (3) | 0.0026 (3) |
C9 | 0.0307 (5) | 0.0184 (5) | 0.0189 (4) | −0.0114 (4) | −0.0068 (4) | −0.0011 (4) |
C10 | 0.0202 (5) | 0.0182 (5) | 0.0218 (4) | −0.0055 (4) | −0.0064 (4) | −0.0028 (4) |
C11 | 0.0289 (6) | 0.0208 (5) | 0.0276 (5) | −0.0092 (4) | −0.0074 (4) | 0.0020 (4) |
C12 | 0.0170 (4) | 0.0140 (4) | 0.0203 (4) | −0.0072 (3) | −0.0066 (4) | 0.0033 (3) |
C13 | 0.0230 (5) | 0.0217 (5) | 0.0202 (4) | −0.0065 (4) | −0.0081 (4) | 0.0016 (4) |
C14 | 0.0277 (5) | 0.0247 (5) | 0.0286 (5) | −0.0095 (4) | −0.0171 (4) | 0.0056 (4) |
C15 | 0.0204 (5) | 0.0205 (5) | 0.0385 (6) | −0.0054 (4) | −0.0142 (4) | 0.0049 (4) |
C16 | 0.0203 (5) | 0.0188 (5) | 0.0292 (5) | −0.0025 (4) | −0.0064 (4) | −0.0018 (4) |
C17 | 0.0210 (5) | 0.0174 (4) | 0.0218 (4) | −0.0065 (4) | −0.0081 (4) | 0.0012 (4) |
O1—C7 | 1.3544 (11) | C8—C12 | 1.4832 (12) |
O1—C9 | 1.4493 (12) | C9—C10 | 1.4648 (13) |
N1—C7 | 1.2976 (12) | C9—H9A | 0.9900 |
N1—C6 | 1.3751 (12) | C9—H9B | 0.9900 |
N2—C8 | 1.3158 (11) | C10—C11 | 1.1874 (14) |
N2—C1 | 1.3733 (11) | C11—H11 | 0.9500 |
C1—C2 | 1.4094 (12) | C12—C17 | 1.3961 (13) |
C1—C6 | 1.4145 (13) | C12—C13 | 1.3991 (12) |
C2—C3 | 1.3741 (13) | C13—C14 | 1.3922 (14) |
C2—H2 | 0.9500 | C13—H13 | 0.9500 |
C3—C4 | 1.4110 (15) | C14—C15 | 1.3831 (16) |
C3—H3 | 0.9500 | C14—H14 | 0.9500 |
C4—C5 | 1.3709 (14) | C15—C16 | 1.3895 (14) |
C4—H4 | 0.9500 | C15—H15 | 0.9500 |
C5—C6 | 1.4105 (13) | C16—C17 | 1.3876 (13) |
C5—H5 | 0.9500 | C16—H16 | 0.9500 |
C7—C8 | 1.4525 (13) | C17—H17 | 0.9500 |
C7—O1—C9 | 117.08 (7) | O1—C9—C10 | 111.63 (8) |
C7—N1—C6 | 117.06 (8) | O1—C9—H9A | 109.3 |
C8—N2—C1 | 118.73 (8) | C10—C9—H9A | 109.3 |
N2—C1—C2 | 119.45 (8) | O1—C9—H9B | 109.3 |
N2—C1—C6 | 120.70 (8) | C10—C9—H9B | 109.3 |
C2—C1—C6 | 119.83 (8) | H9A—C9—H9B | 108.0 |
C3—C2—C1 | 119.79 (9) | C11—C10—C9 | 177.21 (10) |
C3—C2—H2 | 120.1 | C10—C11—H11 | 180.0 |
C1—C2—H2 | 120.1 | C17—C12—C13 | 119.09 (8) |
C2—C3—C4 | 120.30 (9) | C17—C12—C8 | 118.53 (8) |
C2—C3—H3 | 119.8 | C13—C12—C8 | 122.21 (8) |
C4—C3—H3 | 119.8 | C14—C13—C12 | 119.89 (9) |
C5—C4—C3 | 120.87 (9) | C14—C13—H13 | 120.1 |
C5—C4—H4 | 119.6 | C12—C13—H13 | 120.1 |
C3—C4—H4 | 119.6 | C15—C14—C13 | 120.63 (9) |
C4—C5—C6 | 119.81 (9) | C15—C14—H14 | 119.7 |
C4—C5—H5 | 120.1 | C13—C14—H14 | 119.7 |
C6—C5—H5 | 120.1 | C14—C15—C16 | 119.73 (9) |
N1—C6—C5 | 120.06 (9) | C14—C15—H15 | 120.1 |
N1—C6—C1 | 120.56 (8) | C16—C15—H15 | 120.1 |
C5—C6—C1 | 119.38 (9) | C17—C16—C15 | 120.12 (9) |
N1—C7—O1 | 120.57 (8) | C17—C16—H16 | 119.9 |
N1—C7—C8 | 123.68 (8) | C15—C16—H16 | 119.9 |
O1—C7—C8 | 115.75 (8) | C16—C17—C12 | 120.54 (8) |
N2—C8—C7 | 119.21 (8) | C16—C17—H17 | 119.7 |
N2—C8—C12 | 116.98 (8) | C12—C17—H17 | 119.7 |
C7—C8—C12 | 123.80 (8) | ||
C8—N2—C1—C2 | −179.28 (8) | C1—N2—C8—C7 | −1.53 (13) |
C8—N2—C1—C6 | −0.75 (13) | C1—N2—C8—C12 | 177.76 (7) |
N2—C1—C2—C3 | 177.16 (8) | N1—C7—C8—N2 | 2.22 (14) |
C6—C1—C2—C3 | −1.38 (14) | O1—C7—C8—N2 | −177.66 (7) |
C1—C2—C3—C4 | 0.06 (14) | N1—C7—C8—C12 | −177.02 (8) |
C2—C3—C4—C5 | 1.26 (15) | O1—C7—C8—C12 | 3.10 (13) |
C3—C4—C5—C6 | −1.21 (15) | C7—O1—C9—C10 | −87.00 (10) |
C7—N1—C6—C5 | 177.76 (7) | N2—C8—C12—C17 | 33.33 (12) |
C7—N1—C6—C1 | −1.98 (14) | C7—C8—C12—C17 | −147.42 (9) |
C4—C5—C6—N1 | −179.86 (8) | N2—C8—C12—C13 | −141.76 (9) |
C4—C5—C6—C1 | −0.13 (14) | C7—C8—C12—C13 | 37.49 (13) |
N2—C1—C6—N1 | 2.63 (14) | C17—C12—C13—C14 | −0.54 (14) |
C2—C1—C6—N1 | −178.84 (8) | C8—C12—C13—C14 | 174.53 (8) |
N2—C1—C6—C5 | −177.10 (8) | C12—C13—C14—C15 | 1.21 (15) |
C2—C1—C6—C5 | 1.42 (14) | C13—C14—C15—C16 | −0.83 (16) |
C6—N1—C7—O1 | 179.51 (7) | C14—C15—C16—C17 | −0.23 (15) |
C6—N1—C7—C8 | −0.37 (14) | C15—C16—C17—C12 | 0.90 (14) |
C9—O1—C7—N1 | 0.65 (13) | C13—C12—C17—C16 | −0.51 (14) |
C9—O1—C7—C8 | −179.47 (7) | C8—C12—C17—C16 | −175.76 (8) |
D—H···A | D—H | H···A | D···A | D—H···A |
C11—H11···N2i | 0.95 | 2.44 | 3.3164 (14) | 153 |
Symmetry code: (i) x, y+1, z. |
Acknowledgements
JTM thanks Tulane University for support of the Tulane Crystallography Laboratory.
References
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