The crystal structure of danofloxacin (DFX) as a zwitterionic dihydrate [systematic name: (1
S,4
S)-5-(3-carboxylato-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)-2-methyl-2,5-diazabicyclo[2.2.1]heptan-2-ium dihydrate], C
19H
20FN
3O
3·2H
2O, has been determined for the first time. The stability of the crystal structure is ensured by N—H
O and O—H
O hydrogen bonds, some of which are assisted by charge. The zwitterionic molecules of DFX are packed in stacks and this structural motif can be defined as a basic one from a supramolecular and energetic point of view. Hirshfeld surface analysis was used for an additional interpretation of the close contacts. The nature of the intermolecular interactions was evaluated in a pairwise manner. Destabilizing interactions were also discussed. In the context of our study on danofloxacin, we addressed the question: how common is a zwitterionic form for fluoroquinolones (FQ) in the crystalline state? A survey of the Cambridge Structural Database limited to anhydrous/hydrated/solvated forms of the most typical FQs revealed that neutral molecules are preferred, while zwitterions are less common.
Supporting information
CCDC references: 2193968; 2193967
For both structures, data collection: CrysAlis PRO (Rigaku OD, 2017); cell refinement: CrysAlis PRO (Rigaku OD, 2017); data reduction: CrysAlis PRO (Rigaku OD, 2017); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL2018 (Sheldrick, 2015b); molecular graphics: Mercury (Macrae et al., 2020); software used to prepare material for publication: publCIF (Westrip, 2010).
(1
S,4
S)-5-(3-Carboxylato-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)-2-methyl-2,5-diazabicyclo[2.2.1]heptan-2-ium dihydrate (DFX-Mo)
top
Crystal data top
C19H20FN3O3·2H2O | Dx = 1.455 Mg m−3 |
Mr = 393.41 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 3993 reflections |
a = 7.1687 (4) Å | θ = 3.5–28.2° |
b = 10.6689 (7) Å | µ = 0.11 mm−1 |
c = 23.4887 (15) Å | T = 100 K |
V = 1796.47 (19) Å3 | Needle(x)2610, colourless |
Z = 4 | 0.26 × 0.11 × 0.06 mm |
F(000) = 832 | |
Data collection top
XtaLAB Synergy, Dualflex, HyPix diffractometer | 4050 independent reflections |
Radiation source: micro-focus sealed X-ray tube, PhotonJet (Mo) X-ray Source | 3470 reflections with I > 2σ(I) |
Mirror monochromator | Rint = 0.040 |
ω scans | θmax = 28.3°, θmin = 3.4° |
Absorption correction: multi-scan (CrysAlis PRO; Rigaku OD, 2017) | h = −9→8 |
Tmin = 0.155, Tmax = 1.000 | k = −11→14 |
9878 measured reflections | l = −30→30 |
Refinement top
Refinement on F2 | Hydrogen site location: mixed |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.043 | w = 1/[σ2(Fo2) + (0.0731P)2] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.108 | (Δ/σ)max < 0.001 |
S = 1.01 | Δρmax = 0.44 e Å−3 |
4050 reflections | Δρmin = −0.25 e Å−3 |
274 parameters | Absolute structure: Flack x determined using 1169 quotients [(I+)-(I-)]/[(I+)+(I-)]
(Parsons et al., 2013) |
2 restraints | Absolute structure parameter: 0.1 (5) |
Primary atom site location: difference Fourier map | |
Special details top
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. Single-crystal X-ray diffraction data of DFX·2H2O were measured using a
Rigaku XtaLAB Synergy diffractometer at 100 K with Mo Kα radiation;
crystal data, data collection and structure refinement details are summarized
in Table 1. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.6256 (3) | 0.53197 (17) | 0.51228 (8) | 0.0141 (4) | |
C2 | 0.6177 (3) | 0.5699 (2) | 0.56708 (10) | 0.0151 (5) | |
H2 | 0.599788 | 0.656652 | 0.574276 | 0.018* | |
C3 | 0.6337 (3) | 0.4915 (2) | 0.61290 (9) | 0.0142 (5) | |
C4 | 0.6546 (3) | 0.3590 (2) | 0.60383 (10) | 0.0144 (5) | |
C5 | 0.6499 (3) | 0.3189 (2) | 0.54486 (9) | 0.0126 (5) | |
C6 | 0.6597 (3) | 0.1904 (2) | 0.53131 (10) | 0.0142 (5) | |
H6 | 0.659635 | 0.129618 | 0.560868 | 0.017* | |
C7 | 0.6690 (3) | 0.1536 (2) | 0.47649 (10) | 0.0149 (5) | |
C8 | 0.6752 (3) | 0.2385 (2) | 0.42980 (9) | 0.0134 (5) | |
C9 | 0.6590 (3) | 0.3655 (2) | 0.44321 (9) | 0.0138 (5) | |
H9 | 0.657696 | 0.425771 | 0.413432 | 0.017* | |
C10 | 0.6449 (3) | 0.4054 (2) | 0.49949 (9) | 0.0131 (5) | |
C11 | 0.6155 (4) | 0.6208 (2) | 0.46494 (10) | 0.0156 (5) | |
H11 | 0.728748 | 0.624920 | 0.440161 | 0.019* | |
C12 | 0.5106 (4) | 0.7403 (2) | 0.47132 (11) | 0.0233 (6) | |
H12A | 0.560422 | 0.815493 | 0.451842 | 0.028* | |
H12B | 0.449367 | 0.756900 | 0.508334 | 0.028* | |
C13 | 0.4327 (4) | 0.6367 (2) | 0.43489 (11) | 0.0212 (5) | |
H13A | 0.323952 | 0.589593 | 0.449588 | 0.025* | |
H13B | 0.435057 | 0.648213 | 0.393071 | 0.025* | |
N14 | 0.7093 (3) | 0.19730 (18) | 0.37566 (8) | 0.0141 (4) | |
C15 | 0.7345 (3) | 0.2851 (2) | 0.32804 (9) | 0.0140 (5) | |
H15 | 0.822428 | 0.355648 | 0.336022 | 0.017* | |
C16 | 0.7983 (3) | 0.1962 (2) | 0.28103 (9) | 0.0149 (5) | |
H16A | 0.804532 | 0.236739 | 0.243158 | 0.018* | |
H16B | 0.917492 | 0.153580 | 0.289865 | 0.018* | |
C17 | 0.6292 (3) | 0.1116 (2) | 0.28805 (10) | 0.0144 (5) | |
H17 | 0.625929 | 0.038087 | 0.261672 | 0.017* | |
C18 | 0.6375 (3) | 0.0777 (2) | 0.35133 (9) | 0.0143 (5) | |
H18A | 0.512575 | 0.056574 | 0.366538 | 0.017* | |
H18B | 0.724078 | 0.007168 | 0.358492 | 0.017* | |
C19 | 0.5439 (3) | 0.3258 (2) | 0.30579 (10) | 0.0146 (5) | |
H19A | 0.555589 | 0.391756 | 0.276379 | 0.018* | |
H19B | 0.462960 | 0.356468 | 0.336962 | 0.018* | |
N20 | 0.4696 (3) | 0.20346 (19) | 0.28052 (8) | 0.0144 (4) | |
C21 | 0.4088 (4) | 0.2173 (2) | 0.22052 (10) | 0.0194 (5) | |
H21A | 0.513152 | 0.248092 | 0.197491 | 0.029* | |
H21B | 0.305277 | 0.277177 | 0.218524 | 0.029* | |
H21C | 0.367629 | 0.135857 | 0.205893 | 0.029* | |
F22 | 0.6839 (2) | 0.02933 (12) | 0.46436 (6) | 0.0203 (3) | |
C23 | 0.6265 (3) | 0.5457 (2) | 0.67236 (9) | 0.0147 (5) | |
O24 | 0.5013 (2) | 0.62526 (18) | 0.68248 (7) | 0.0224 (4) | |
O25 | 0.7419 (3) | 0.50616 (17) | 0.70775 (7) | 0.0237 (4) | |
O26 | 0.6782 (2) | 0.28076 (16) | 0.64340 (6) | 0.0156 (4) | |
O27 | 0.6183 (3) | 0.05595 (17) | 0.70254 (8) | 0.0236 (4) | |
O28 | 0.4588 (3) | 0.8631 (3) | 0.63048 (9) | 0.0341 (5) | |
H20 | 0.372 (4) | 0.179 (2) | 0.3029 (11) | 0.008 (6)* | |
H27A | 0.621 (6) | 0.122 (2) | 0.6835 (14) | 0.060 (13)* | |
H27B | 0.571 (4) | 0.071 (3) | 0.7344 (8) | 0.018 (7)* | |
H28A | 0.475 (6) | 0.798 (5) | 0.6509 (17) | 0.055 (12)* | |
H28B | 0.503 (5) | 0.918 (4) | 0.6505 (16) | 0.039 (11)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0159 (10) | 0.0101 (9) | 0.0164 (9) | 0.0004 (8) | 0.0008 (8) | 0.0011 (7) |
C2 | 0.0122 (11) | 0.0129 (10) | 0.0201 (11) | −0.0004 (9) | 0.0006 (9) | −0.0019 (9) |
C3 | 0.0101 (11) | 0.0144 (10) | 0.0181 (11) | 0.0003 (9) | 0.0002 (9) | −0.0031 (9) |
C4 | 0.0087 (11) | 0.0156 (11) | 0.0188 (11) | −0.0003 (9) | −0.0002 (9) | −0.0005 (9) |
C5 | 0.0103 (11) | 0.0109 (10) | 0.0165 (11) | 0.0001 (9) | −0.0006 (8) | 0.0007 (8) |
C6 | 0.0128 (11) | 0.0122 (10) | 0.0177 (10) | −0.0010 (9) | −0.0006 (9) | 0.0033 (9) |
C7 | 0.0164 (12) | 0.0081 (10) | 0.0204 (11) | 0.0005 (9) | −0.0017 (9) | −0.0011 (9) |
C8 | 0.0095 (11) | 0.0140 (10) | 0.0168 (10) | −0.0005 (9) | 0.0002 (8) | −0.0015 (9) |
C9 | 0.0127 (11) | 0.0120 (10) | 0.0168 (10) | 0.0003 (9) | 0.0000 (9) | 0.0016 (9) |
C10 | 0.0108 (11) | 0.0109 (10) | 0.0176 (11) | 0.0002 (9) | 0.0006 (9) | −0.0003 (8) |
C11 | 0.0217 (12) | 0.0099 (10) | 0.0153 (10) | −0.0005 (10) | 0.0011 (9) | 0.0022 (9) |
C12 | 0.0284 (15) | 0.0142 (11) | 0.0273 (13) | 0.0053 (11) | 0.0026 (11) | 0.0021 (10) |
C13 | 0.0229 (13) | 0.0172 (12) | 0.0234 (12) | 0.0000 (10) | −0.0029 (10) | 0.0061 (10) |
N14 | 0.0159 (10) | 0.0096 (8) | 0.0169 (9) | −0.0006 (8) | 0.0001 (8) | 0.0000 (8) |
C15 | 0.0136 (11) | 0.0117 (10) | 0.0169 (11) | −0.0014 (9) | 0.0023 (9) | 0.0006 (9) |
C16 | 0.0127 (11) | 0.0145 (10) | 0.0176 (11) | −0.0013 (10) | 0.0015 (9) | −0.0009 (9) |
C17 | 0.0133 (11) | 0.0131 (10) | 0.0168 (10) | 0.0034 (9) | 0.0006 (9) | −0.0017 (9) |
C18 | 0.0154 (11) | 0.0101 (10) | 0.0175 (11) | 0.0004 (9) | 0.0006 (9) | −0.0025 (8) |
C19 | 0.0158 (12) | 0.0095 (10) | 0.0185 (11) | −0.0009 (9) | 0.0005 (9) | −0.0013 (8) |
N20 | 0.0126 (10) | 0.0133 (9) | 0.0172 (9) | −0.0008 (8) | 0.0015 (8) | −0.0005 (8) |
C21 | 0.0190 (13) | 0.0215 (12) | 0.0176 (11) | 0.0001 (10) | −0.0023 (9) | 0.0008 (10) |
F22 | 0.0325 (9) | 0.0083 (6) | 0.0202 (7) | 0.0020 (6) | −0.0012 (6) | −0.0009 (5) |
C23 | 0.0173 (12) | 0.0113 (10) | 0.0156 (10) | −0.0037 (10) | 0.0009 (9) | −0.0006 (8) |
O24 | 0.0201 (10) | 0.0218 (9) | 0.0252 (9) | 0.0074 (8) | −0.0034 (7) | −0.0073 (7) |
O25 | 0.0270 (10) | 0.0214 (9) | 0.0226 (9) | 0.0056 (8) | −0.0065 (8) | −0.0032 (8) |
O26 | 0.0160 (9) | 0.0149 (8) | 0.0158 (8) | 0.0002 (7) | −0.0015 (6) | 0.0007 (6) |
O27 | 0.0215 (10) | 0.0213 (9) | 0.0281 (10) | 0.0031 (8) | 0.0039 (8) | 0.0084 (8) |
O28 | 0.0358 (12) | 0.0338 (12) | 0.0326 (11) | −0.0035 (10) | −0.0083 (10) | 0.0065 (11) |
Geometric parameters (Å, º) top
N1—C2 | 1.350 (3) | N14—C15 | 1.470 (3) |
N1—C10 | 1.391 (3) | N14—C18 | 1.490 (3) |
N1—C11 | 1.463 (3) | C15—C19 | 1.526 (3) |
C2—C3 | 1.367 (3) | C15—C16 | 1.525 (3) |
C2—H2 | 0.9500 | C15—H15 | 1.0000 |
C3—C4 | 1.437 (3) | C16—C17 | 1.520 (3) |
C3—C23 | 1.512 (3) | C16—H16A | 0.9900 |
C4—O26 | 1.261 (3) | C16—H16B | 0.9900 |
C4—C5 | 1.450 (3) | C17—N20 | 1.516 (3) |
C5—C10 | 1.410 (3) | C17—C18 | 1.531 (3) |
C5—C6 | 1.410 (3) | C17—H17 | 1.0000 |
C6—C7 | 1.348 (3) | C18—H18A | 0.9900 |
C6—H6 | 0.9500 | C18—H18B | 0.9900 |
C7—F22 | 1.360 (2) | C19—N20 | 1.529 (3) |
C7—C8 | 1.423 (3) | C19—H19A | 0.9900 |
C8—N14 | 1.368 (3) | C19—H19B | 0.9900 |
C8—C9 | 1.396 (3) | N20—C21 | 1.483 (3) |
C9—C10 | 1.392 (3) | N20—H20 | 0.92 (3) |
C9—H9 | 0.9500 | C21—H21A | 0.9800 |
C11—C12 | 1.488 (3) | C21—H21B | 0.9800 |
C11—C13 | 1.498 (4) | C21—H21C | 0.9800 |
C11—H11 | 1.0000 | C23—O25 | 1.246 (3) |
C12—C13 | 1.505 (4) | C23—O24 | 1.259 (3) |
C12—H12A | 0.9900 | O27—H27A | 0.837 (13) |
C12—H12B | 0.9900 | O27—H27B | 0.838 (12) |
C13—H13A | 0.9900 | O28—H28A | 0.85 (5) |
C13—H13B | 0.9900 | O28—H28B | 0.81 (4) |
| | | |
C2—N1—C10 | 120.05 (18) | C8—N14—C18 | 124.76 (19) |
C2—N1—C11 | 121.92 (19) | C15—N14—C18 | 107.22 (17) |
C10—N1—C11 | 118.03 (19) | N14—C15—C19 | 109.39 (18) |
N1—C2—C3 | 124.3 (2) | N14—C15—C16 | 101.07 (18) |
N1—C2—H2 | 117.8 | C19—C15—C16 | 101.39 (18) |
C3—C2—H2 | 117.8 | N14—C15—H15 | 114.5 |
C2—C3—C4 | 119.5 (2) | C19—C15—H15 | 114.5 |
C2—C3—C23 | 119.4 (2) | C16—C15—H15 | 114.5 |
C4—C3—C23 | 121.1 (2) | C17—C16—C15 | 92.93 (17) |
O26—C4—C3 | 123.8 (2) | C17—C16—H16A | 113.1 |
O26—C4—C5 | 120.8 (2) | C15—C16—H16A | 113.1 |
C3—C4—C5 | 115.43 (19) | C17—C16—H16B | 113.1 |
C10—C5—C6 | 117.8 (2) | C15—C16—H16B | 113.1 |
C10—C5—C4 | 122.0 (2) | H16A—C16—H16B | 110.5 |
C6—C5—C4 | 120.1 (2) | N20—C17—C16 | 101.84 (18) |
C7—C6—C5 | 120.1 (2) | N20—C17—C18 | 107.18 (17) |
C7—C6—H6 | 119.9 | C16—C17—C18 | 102.40 (18) |
C5—C6—H6 | 119.9 | N20—C17—H17 | 114.6 |
C6—C7—F22 | 119.2 (2) | C16—C17—H17 | 114.6 |
C6—C7—C8 | 123.5 (2) | C18—C17—H17 | 114.6 |
F22—C7—C8 | 117.2 (2) | N14—C18—C17 | 100.57 (17) |
N14—C8—C9 | 122.4 (2) | N14—C18—H18A | 111.7 |
N14—C8—C7 | 121.2 (2) | C17—C18—H18A | 111.7 |
C9—C8—C7 | 116.2 (2) | N14—C18—H18B | 111.7 |
C10—C9—C8 | 121.1 (2) | C17—C18—H18B | 111.7 |
C10—C9—H9 | 119.4 | H18A—C18—H18B | 109.4 |
C8—C9—H9 | 119.4 | C15—C19—N20 | 101.64 (17) |
N1—C10—C9 | 120.6 (2) | C15—C19—H19A | 111.4 |
N1—C10—C5 | 118.3 (2) | N20—C19—H19A | 111.4 |
C9—C10—C5 | 121.1 (2) | C15—C19—H19B | 111.4 |
N1—C11—C12 | 120.2 (2) | N20—C19—H19B | 111.4 |
N1—C11—C13 | 118.4 (2) | H19A—C19—H19B | 109.3 |
C12—C11—C13 | 60.55 (17) | C21—N20—C17 | 113.41 (18) |
N1—C11—H11 | 115.5 | C21—N20—C19 | 112.72 (19) |
C12—C11—H11 | 115.5 | C17—N20—C19 | 104.10 (17) |
C13—C11—H11 | 115.5 | C21—N20—H20 | 110.3 (16) |
C11—C12—C13 | 60.05 (16) | C17—N20—H20 | 109.0 (17) |
C11—C12—H12A | 117.8 | C19—N20—H20 | 106.9 (16) |
C13—C12—H12A | 117.8 | N20—C21—H21A | 109.5 |
C11—C12—H12B | 117.8 | N20—C21—H21B | 109.5 |
C13—C12—H12B | 117.8 | H21A—C21—H21B | 109.5 |
H12A—C12—H12B | 114.9 | N20—C21—H21C | 109.5 |
C11—C13—C12 | 59.40 (16) | H21A—C21—H21C | 109.5 |
C11—C13—H13A | 117.8 | H21B—C21—H21C | 109.5 |
C12—C13—H13A | 117.8 | O25—C23—O24 | 125.2 (2) |
C11—C13—H13B | 117.8 | O25—C23—C3 | 117.7 (2) |
C12—C13—H13B | 117.8 | O24—C23—C3 | 117.2 (2) |
H13A—C13—H13B | 115.0 | H27A—O27—H27B | 109 (3) |
C8—N14—C15 | 121.66 (19) | H28A—O28—H28B | 102 (4) |
| | | |
C10—N1—C2—C3 | 2.3 (4) | C10—N1—C11—C12 | 151.1 (2) |
C11—N1—C2—C3 | −177.3 (2) | C2—N1—C11—C13 | −99.8 (3) |
N1—C2—C3—C4 | −2.1 (4) | C10—N1—C11—C13 | 80.5 (3) |
N1—C2—C3—C23 | 178.7 (2) | N1—C11—C12—C13 | −107.6 (2) |
C2—C3—C4—O26 | 176.9 (2) | N1—C11—C13—C12 | 110.6 (2) |
C23—C3—C4—O26 | −4.0 (4) | C9—C8—N14—C15 | 1.1 (4) |
C2—C3—C4—C5 | −2.2 (3) | C7—C8—N14—C15 | −173.8 (2) |
C23—C3—C4—C5 | 177.0 (2) | C9—C8—N14—C18 | −147.3 (2) |
O26—C4—C5—C10 | −172.7 (2) | C7—C8—N14—C18 | 37.8 (3) |
C3—C4—C5—C10 | 6.4 (3) | C8—N14—C15—C19 | −82.3 (3) |
O26—C4—C5—C6 | 4.1 (3) | C18—N14—C15—C19 | 70.9 (2) |
C3—C4—C5—C6 | −176.8 (2) | C8—N14—C15—C16 | 171.3 (2) |
C10—C5—C6—C7 | 1.8 (3) | C18—N14—C15—C16 | −35.5 (2) |
C4—C5—C6—C7 | −175.2 (2) | N14—C15—C16—C17 | 54.55 (19) |
C5—C6—C7—F22 | 178.1 (2) | C19—C15—C16—C17 | −58.06 (19) |
C5—C6—C7—C8 | 1.9 (4) | C15—C16—C17—N20 | 55.49 (18) |
C6—C7—C8—N14 | 171.3 (2) | C15—C16—C17—C18 | −55.30 (19) |
F22—C7—C8—N14 | −5.0 (3) | C8—N14—C18—C17 | 152.3 (2) |
C6—C7—C8—C9 | −3.9 (4) | C15—N14—C18—C17 | 0.2 (2) |
F22—C7—C8—C9 | 179.8 (2) | N20—C17—C18—N14 | −71.2 (2) |
N14—C8—C9—C10 | −172.8 (2) | C16—C17—C18—N14 | 35.5 (2) |
C7—C8—C9—C10 | 2.3 (4) | N14—C15—C19—N20 | −67.2 (2) |
C2—N1—C10—C9 | −178.0 (2) | C16—C15—C19—N20 | 39.0 (2) |
C11—N1—C10—C9 | 1.7 (3) | C16—C17—N20—C21 | 89.4 (2) |
C2—N1—C10—C5 | 1.9 (3) | C18—C17—N20—C21 | −163.5 (2) |
C11—N1—C10—C5 | −178.4 (2) | C16—C17—N20—C19 | −33.5 (2) |
C8—C9—C10—N1 | −178.9 (2) | C18—C17—N20—C19 | 73.7 (2) |
C8—C9—C10—C5 | 1.2 (4) | C15—C19—N20—C21 | −126.7 (2) |
C6—C5—C10—N1 | 176.8 (2) | C15—C19—N20—C17 | −3.3 (2) |
C4—C5—C10—N1 | −6.3 (3) | C2—C3—C23—O25 | −136.5 (2) |
C6—C5—C10—C9 | −3.3 (3) | C4—C3—C23—O25 | 44.4 (3) |
C4—C5—C10—C9 | 173.6 (2) | C2—C3—C23—O24 | 45.1 (3) |
C2—N1—C11—C12 | −29.2 (3) | C4—C3—C23—O24 | −134.1 (2) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N20—H20···O26i | 0.92 (3) | 1.92 (3) | 2.754 (3) | 150 (2) |
N20—H20···O25i | 0.92 (3) | 2.20 (2) | 2.782 (3) | 121 (2) |
O27—H27A···O26 | 0.84 (1) | 1.98 (2) | 2.805 (2) | 169 (4) |
O27—H27B···O24ii | 0.84 (1) | 2.10 (1) | 2.929 (3) | 170 (3) |
O28—H28A···O24 | 0.85 (5) | 1.99 (5) | 2.832 (3) | 167 (4) |
O28—H28B···O27iii | 0.81 (4) | 2.09 (4) | 2.900 (3) | 179 (4) |
Symmetry codes: (i) x−1/2, −y+1/2, −z+1; (ii) −x+1, y−1/2, −z+3/2; (iii) x, y+1, z. |
(1
S,4
S)-5-(3-Carboxylato-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinolin-7-yl)-2-methyl-2,5-diazabicyclo[2.2.1]heptan-2-ium dihydrate (DFX-Cu)
top
Crystal data top
C19H20FN3O3·2H2O | Dx = 1.449 Mg m−3 |
Mr = 393.41 | Cu Kα radiation, λ = 1.54184 Å |
Orthorhombic, P212121 | Cell parameters from 5102 reflections |
a = 7.1815 (2) Å | θ = 3.7–75.0° |
b = 10.6840 (3) Å | µ = 0.95 mm−1 |
c = 23.5104 (7) Å | T = 100 K |
V = 1803.89 (9) Å3 | Needle, colourless |
Z = 4 | 0.26 × 0.11 × 0.06 mm |
F(000) = 832 | |
Data collection top
XtaLAB Synergy, Dualflex, HyPix diffractometer | 3329 reflections with I > 2σ(I) |
Radiation source: micro-focus sealed X-ray tube, PhotonJet (Cu) X-ray Source | Rint = 0.045 |
ω scans | θmax = 77.3°, θmin = 3.8° |
Absorption correction: multi-scan (CrysAlis PRO; Rigaku OD, 2017) | h = −8→9 |
Tmin = 0.503, Tmax = 1.000 | k = −12→10 |
10288 measured reflections | l = −21→29 |
3612 independent reflections | |
Refinement top
Refinement on F2 | Hydrogen site location: mixed |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.046 | w = 1/[σ2(Fo2) + (0.0787P)2 + 0.459P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.131 | (Δ/σ)max < 0.001 |
S = 1.10 | Δρmax = 0.24 e Å−3 |
3612 reflections | Δρmin = −0.34 e Å−3 |
274 parameters | Absolute structure: Flack x determined using 1277 quotients [(I+)-(I-)]/[(I+)+(I-)]
(Parsons et al., 2013) |
0 restraints | Absolute structure parameter: 0.05 (14) |
Primary atom site location: difference Fourier map | |
Special details top
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.6254 (4) | 0.5318 (2) | 0.51230 (11) | 0.0243 (5) | |
C2 | 0.6177 (4) | 0.5694 (3) | 0.56713 (13) | 0.0254 (6) | |
H2 | 0.599820 | 0.656095 | 0.574361 | 0.030* | |
C3 | 0.6339 (4) | 0.4914 (3) | 0.61277 (12) | 0.0244 (6) | |
C4 | 0.6553 (4) | 0.3589 (3) | 0.60377 (13) | 0.0232 (6) | |
C5 | 0.6499 (4) | 0.3189 (3) | 0.54485 (12) | 0.0228 (6) | |
C6 | 0.6598 (4) | 0.1907 (3) | 0.53110 (13) | 0.0244 (6) | |
H6 | 0.659942 | 0.129849 | 0.560557 | 0.029* | |
C7 | 0.6691 (4) | 0.1543 (3) | 0.47643 (13) | 0.0240 (6) | |
C8 | 0.6756 (4) | 0.2382 (3) | 0.42988 (13) | 0.0226 (6) | |
C9 | 0.6594 (4) | 0.3655 (3) | 0.44314 (13) | 0.0252 (6) | |
H9 | 0.658102 | 0.425605 | 0.413382 | 0.030* | |
C10 | 0.6450 (4) | 0.4051 (3) | 0.49961 (13) | 0.0226 (6) | |
C11 | 0.6153 (5) | 0.6206 (3) | 0.46479 (14) | 0.0268 (6) | |
H11 | 0.728499 | 0.624941 | 0.440109 | 0.032* | |
C12 | 0.5106 (5) | 0.7397 (3) | 0.47131 (15) | 0.0332 (7) | |
H12A | 0.560349 | 0.814993 | 0.451982 | 0.040* | |
H12B | 0.449241 | 0.755999 | 0.508276 | 0.040* | |
C13 | 0.4334 (5) | 0.6367 (3) | 0.43477 (16) | 0.0327 (7) | |
H13A | 0.324828 | 0.589415 | 0.449329 | 0.039* | |
H13B | 0.435975 | 0.648430 | 0.393015 | 0.039* | |
N14 | 0.7094 (4) | 0.1973 (2) | 0.37574 (11) | 0.0238 (5) | |
C15 | 0.7342 (4) | 0.2848 (3) | 0.32816 (12) | 0.0237 (6) | |
H15 | 0.821823 | 0.355452 | 0.336088 | 0.028* | |
C16 | 0.7977 (4) | 0.1963 (3) | 0.28103 (13) | 0.0254 (6) | |
H16A | 0.803297 | 0.236896 | 0.243224 | 0.030* | |
H16B | 0.917056 | 0.153966 | 0.289689 | 0.030* | |
C17 | 0.6297 (4) | 0.1113 (3) | 0.28811 (13) | 0.0245 (6) | |
H17 | 0.626496 | 0.037881 | 0.261759 | 0.029* | |
C18 | 0.6375 (4) | 0.0781 (3) | 0.35086 (13) | 0.0249 (6) | |
H18A | 0.512655 | 0.057052 | 0.365913 | 0.030* | |
H18B | 0.723614 | 0.007506 | 0.358047 | 0.030* | |
C19 | 0.5441 (4) | 0.3249 (3) | 0.30600 (14) | 0.0255 (6) | |
H19A | 0.463229 | 0.355204 | 0.337206 | 0.031* | |
H19B | 0.555539 | 0.391210 | 0.276776 | 0.031* | |
N20 | 0.4701 (4) | 0.2039 (3) | 0.28055 (11) | 0.0247 (6) | |
C21 | 0.4083 (5) | 0.2175 (3) | 0.22046 (13) | 0.0304 (7) | |
H21A | 0.513645 | 0.244480 | 0.196981 | 0.046* | |
H21B | 0.308762 | 0.280087 | 0.218309 | 0.046* | |
H21C | 0.361719 | 0.136925 | 0.206512 | 0.046* | |
F22 | 0.6839 (3) | 0.02949 (16) | 0.46437 (8) | 0.0302 (4) | |
C23 | 0.6265 (4) | 0.5458 (3) | 0.67241 (13) | 0.0246 (6) | |
O24 | 0.5012 (3) | 0.6257 (2) | 0.68254 (9) | 0.0316 (5) | |
O25 | 0.7421 (3) | 0.5062 (2) | 0.70767 (10) | 0.0334 (5) | |
O26 | 0.6781 (3) | 0.2808 (2) | 0.64333 (9) | 0.0257 (5) | |
O27 | 0.6183 (3) | 0.0560 (2) | 0.70265 (11) | 0.0332 (5) | |
O28 | 0.4593 (4) | 0.8630 (3) | 0.63032 (12) | 0.0425 (6) | |
H20 | 0.364 (6) | 0.179 (4) | 0.3010 (16) | 0.028 (9)* | |
H27A | 0.627 (8) | 0.135 (6) | 0.683 (2) | 0.070 (17)* | |
H27B | 0.565 (6) | 0.071 (4) | 0.7371 (19) | 0.038 (11)* | |
H28A | 0.480 (7) | 0.797 (6) | 0.652 (2) | 0.057 (15)* | |
H28B | 0.517 (7) | 0.917 (5) | 0.654 (2) | 0.047 (13)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0284 (12) | 0.0184 (13) | 0.0261 (12) | 0.0002 (11) | 0.0010 (10) | 0.0010 (10) |
C2 | 0.0262 (14) | 0.0222 (15) | 0.0277 (14) | −0.0002 (12) | 0.0003 (12) | −0.0015 (12) |
C3 | 0.0257 (14) | 0.0197 (14) | 0.0277 (14) | 0.0003 (12) | 0.0019 (12) | −0.0022 (11) |
C4 | 0.0203 (13) | 0.0205 (14) | 0.0287 (14) | −0.0012 (12) | −0.0014 (11) | 0.0013 (12) |
C5 | 0.0242 (14) | 0.0190 (14) | 0.0252 (14) | −0.0005 (12) | −0.0014 (11) | 0.0002 (11) |
C6 | 0.0250 (14) | 0.0196 (14) | 0.0285 (14) | 0.0002 (12) | −0.0007 (12) | 0.0016 (12) |
C7 | 0.0268 (14) | 0.0131 (13) | 0.0322 (15) | 0.0018 (11) | −0.0030 (12) | −0.0006 (11) |
C8 | 0.0205 (13) | 0.0204 (14) | 0.0269 (14) | 0.0009 (11) | −0.0008 (11) | 0.0024 (11) |
C9 | 0.0231 (14) | 0.0232 (15) | 0.0294 (15) | −0.0002 (12) | −0.0005 (11) | 0.0003 (12) |
C10 | 0.0226 (13) | 0.0181 (14) | 0.0270 (15) | −0.0010 (11) | −0.0001 (11) | −0.0008 (11) |
C11 | 0.0349 (16) | 0.0192 (15) | 0.0264 (14) | −0.0006 (13) | 0.0009 (13) | 0.0026 (12) |
C12 | 0.0402 (18) | 0.0250 (17) | 0.0344 (16) | 0.0053 (14) | 0.0022 (15) | 0.0014 (13) |
C13 | 0.0347 (17) | 0.0246 (17) | 0.0387 (17) | −0.0009 (14) | −0.0034 (14) | 0.0056 (14) |
N14 | 0.0287 (13) | 0.0188 (12) | 0.0241 (12) | −0.0013 (10) | −0.0005 (10) | −0.0002 (10) |
C15 | 0.0263 (14) | 0.0203 (14) | 0.0244 (14) | −0.0022 (12) | 0.0006 (11) | −0.0003 (12) |
C16 | 0.0252 (14) | 0.0237 (15) | 0.0273 (15) | 0.0004 (12) | 0.0008 (11) | −0.0002 (12) |
C17 | 0.0237 (14) | 0.0188 (14) | 0.0310 (15) | 0.0014 (12) | 0.0025 (12) | −0.0035 (12) |
C18 | 0.0262 (13) | 0.0176 (15) | 0.0308 (15) | −0.0006 (12) | −0.0014 (12) | −0.0028 (11) |
C19 | 0.0273 (15) | 0.0195 (15) | 0.0299 (15) | 0.0015 (12) | 0.0030 (12) | −0.0013 (11) |
N20 | 0.0245 (13) | 0.0216 (13) | 0.0280 (13) | −0.0005 (11) | 0.0002 (10) | −0.0015 (10) |
C21 | 0.0335 (17) | 0.0288 (17) | 0.0290 (16) | −0.0004 (14) | 0.0002 (13) | −0.0006 (13) |
F22 | 0.0451 (11) | 0.0149 (9) | 0.0307 (9) | 0.0024 (8) | −0.0015 (8) | −0.0023 (7) |
C23 | 0.0263 (14) | 0.0196 (14) | 0.0279 (14) | −0.0024 (12) | 0.0000 (12) | −0.0010 (12) |
O24 | 0.0325 (12) | 0.0295 (12) | 0.0327 (11) | 0.0074 (10) | −0.0017 (9) | −0.0066 (9) |
O25 | 0.0401 (13) | 0.0294 (12) | 0.0307 (11) | 0.0069 (10) | −0.0064 (10) | −0.0032 (10) |
O26 | 0.0281 (11) | 0.0226 (11) | 0.0263 (10) | −0.0005 (9) | −0.0015 (8) | 0.0007 (8) |
O27 | 0.0344 (12) | 0.0291 (12) | 0.0360 (13) | 0.0034 (10) | 0.0023 (10) | 0.0065 (10) |
O28 | 0.0469 (15) | 0.0411 (15) | 0.0395 (14) | −0.0020 (13) | −0.0086 (12) | 0.0056 (13) |
Geometric parameters (Å, º) top
N1—C2 | 1.352 (4) | N14—C15 | 1.469 (4) |
N1—C10 | 1.393 (4) | N14—C18 | 1.493 (4) |
N1—C11 | 1.468 (4) | C15—C19 | 1.523 (4) |
C2—C3 | 1.364 (4) | C15—C16 | 1.526 (4) |
C2—H2 | 0.9500 | C15—H15 | 1.0000 |
C3—C4 | 1.440 (4) | C16—C17 | 1.519 (4) |
C3—C23 | 1.519 (4) | C16—H16A | 0.9900 |
C4—O26 | 1.260 (4) | C16—H16B | 0.9900 |
C4—C5 | 1.450 (4) | C17—C18 | 1.518 (4) |
C5—C10 | 1.407 (4) | C17—N20 | 1.524 (4) |
C5—C6 | 1.409 (4) | C17—H17 | 1.0000 |
C6—C7 | 1.345 (4) | C18—H18A | 0.9900 |
C6—H6 | 0.9500 | C18—H18B | 0.9900 |
C7—F22 | 1.367 (3) | C19—N20 | 1.521 (4) |
C7—C8 | 1.416 (4) | C19—H19A | 0.9900 |
C8—N14 | 1.368 (4) | C19—H19B | 0.9900 |
C8—C9 | 1.399 (4) | N20—C21 | 1.488 (4) |
C9—C10 | 1.397 (4) | N20—H20 | 0.94 (4) |
C9—H9 | 0.9500 | C21—H21A | 0.9800 |
C11—C12 | 1.486 (5) | C21—H21B | 0.9800 |
C11—C13 | 1.494 (5) | C21—H21C | 0.9800 |
C11—H11 | 1.0000 | C23—O25 | 1.247 (4) |
C12—C13 | 1.503 (5) | C23—O24 | 1.263 (4) |
C12—H12A | 0.9900 | O27—H27A | 0.96 (6) |
C12—H12B | 0.9900 | O27—H27B | 0.91 (5) |
C13—H13A | 0.9900 | O28—H28A | 0.87 (6) |
C13—H13B | 0.9900 | O28—H28B | 0.91 (6) |
| | | |
C2—N1—C10 | 119.9 (3) | C8—N14—C18 | 125.2 (3) |
C2—N1—C11 | 122.1 (3) | C15—N14—C18 | 106.6 (2) |
C10—N1—C11 | 118.1 (3) | N14—C15—C19 | 109.3 (2) |
N1—C2—C3 | 124.4 (3) | N14—C15—C16 | 101.2 (2) |
N1—C2—H2 | 117.8 | C19—C15—C16 | 101.2 (2) |
C3—C2—H2 | 117.8 | N14—C15—H15 | 114.5 |
C2—C3—C4 | 119.6 (3) | C19—C15—H15 | 114.5 |
C2—C3—C23 | 119.3 (3) | C16—C15—H15 | 114.5 |
C4—C3—C23 | 121.0 (3) | C17—C16—C15 | 93.1 (2) |
O26—C4—C3 | 123.8 (3) | C17—C16—H16A | 113.1 |
O26—C4—C5 | 120.9 (3) | C15—C16—H16A | 113.1 |
C3—C4—C5 | 115.3 (3) | C17—C16—H16B | 113.1 |
C10—C5—C6 | 117.6 (3) | C15—C16—H16B | 113.1 |
C10—C5—C4 | 122.0 (3) | H16A—C16—H16B | 110.5 |
C6—C5—C4 | 120.2 (3) | C18—C17—C16 | 102.5 (2) |
C7—C6—C5 | 120.2 (3) | C18—C17—N20 | 107.0 (2) |
C7—C6—H6 | 119.9 | C16—C17—N20 | 101.4 (2) |
C5—C6—H6 | 119.9 | C18—C17—H17 | 114.8 |
C6—C7—F22 | 119.0 (3) | C16—C17—H17 | 114.8 |
C6—C7—C8 | 123.8 (3) | N20—C17—H17 | 114.8 |
F22—C7—C8 | 117.1 (3) | N14—C18—C17 | 101.2 (2) |
N14—C8—C9 | 122.2 (3) | N14—C18—H18A | 111.5 |
N14—C8—C7 | 121.5 (3) | C17—C18—H18A | 111.5 |
C9—C8—C7 | 116.1 (3) | N14—C18—H18B | 111.5 |
C10—C9—C8 | 120.8 (3) | C17—C18—H18B | 111.5 |
C10—C9—H9 | 119.6 | H18A—C18—H18B | 109.3 |
C8—C9—H9 | 119.6 | N20—C19—C15 | 102.0 (2) |
N1—C10—C9 | 120.4 (3) | N20—C19—H19A | 111.4 |
N1—C10—C5 | 118.4 (3) | C15—C19—H19A | 111.4 |
C9—C10—C5 | 121.2 (3) | N20—C19—H19B | 111.4 |
N1—C11—C12 | 120.0 (3) | C15—C19—H19B | 111.4 |
N1—C11—C13 | 118.5 (3) | H19A—C19—H19B | 109.2 |
C12—C11—C13 | 60.6 (2) | C21—N20—C19 | 113.2 (3) |
N1—C11—H11 | 115.5 | C21—N20—C17 | 113.5 (2) |
C12—C11—H11 | 115.5 | C19—N20—C17 | 104.1 (2) |
C13—C11—H11 | 115.5 | C21—N20—H20 | 106 (2) |
C11—C12—C13 | 60.0 (2) | C19—N20—H20 | 109 (2) |
C11—C12—H12A | 117.8 | C17—N20—H20 | 111 (2) |
C13—C12—H12A | 117.8 | N20—C21—H21A | 109.5 |
C11—C12—H12B | 117.8 | N20—C21—H21B | 109.5 |
C13—C12—H12B | 117.8 | H21A—C21—H21B | 109.5 |
H12A—C12—H12B | 114.9 | N20—C21—H21C | 109.5 |
C11—C13—C12 | 59.4 (2) | H21A—C21—H21C | 109.5 |
C11—C13—H13A | 117.8 | H21B—C21—H21C | 109.5 |
C12—C13—H13A | 117.8 | O25—C23—O24 | 125.3 (3) |
C11—C13—H13B | 117.8 | O25—C23—C3 | 117.4 (3) |
C12—C13—H13B | 117.8 | O24—C23—C3 | 117.2 (3) |
H13A—C13—H13B | 115.0 | H27A—O27—H27B | 107 (4) |
C8—N14—C15 | 121.8 (2) | H28A—O28—H28B | 95 (5) |
| | | |
C10—N1—C2—C3 | 2.2 (5) | C10—N1—C11—C12 | 151.3 (3) |
C11—N1—C2—C3 | −177.3 (3) | C2—N1—C11—C13 | −99.8 (4) |
N1—C2—C3—C4 | −1.9 (5) | C10—N1—C11—C13 | 80.7 (4) |
N1—C2—C3—C23 | 178.8 (3) | N1—C11—C12—C13 | −107.8 (3) |
C2—C3—C4—O26 | 177.2 (3) | N1—C11—C13—C12 | 110.4 (3) |
C23—C3—C4—O26 | −3.5 (5) | C9—C8—N14—C15 | 1.1 (4) |
C2—C3—C4—C5 | −2.5 (4) | C7—C8—N14—C15 | −174.0 (3) |
C23—C3—C4—C5 | 176.7 (3) | C9—C8—N14—C18 | −147.0 (3) |
O26—C4—C5—C10 | −172.9 (3) | C7—C8—N14—C18 | 37.9 (4) |
C3—C4—C5—C10 | 6.8 (4) | C8—N14—C15—C19 | −82.5 (3) |
O26—C4—C5—C6 | 3.5 (4) | C18—N14—C15—C19 | 70.7 (3) |
C3—C4—C5—C6 | −176.7 (3) | C8—N14—C15—C16 | 171.3 (3) |
C10—C5—C6—C7 | 1.7 (4) | C18—N14—C15—C16 | −35.5 (3) |
C4—C5—C6—C7 | −174.9 (3) | N14—C15—C16—C17 | 54.4 (2) |
C5—C6—C7—F22 | 178.2 (3) | C19—C15—C16—C17 | −58.2 (3) |
C5—C6—C7—C8 | 2.1 (5) | C15—C16—C17—C18 | −54.9 (3) |
C6—C7—C8—N14 | 171.3 (3) | C15—C16—C17—N20 | 55.6 (2) |
F22—C7—C8—N14 | −4.8 (4) | C8—N14—C18—C17 | 152.5 (3) |
C6—C7—C8—C9 | −4.1 (4) | C15—N14—C18—C17 | 0.4 (3) |
F22—C7—C8—C9 | 179.8 (3) | C16—C17—C18—N14 | 35.1 (3) |
N14—C8—C9—C10 | −173.0 (3) | N20—C17—C18—N14 | −71.1 (3) |
C7—C8—C9—C10 | 2.4 (4) | N14—C15—C19—N20 | −67.5 (3) |
C2—N1—C10—C9 | −177.9 (3) | C16—C15—C19—N20 | 38.7 (3) |
C11—N1—C10—C9 | 1.6 (4) | C15—C19—N20—C21 | −126.7 (3) |
C2—N1—C10—C5 | 2.2 (4) | C15—C19—N20—C17 | −3.1 (3) |
C11—N1—C10—C5 | −178.3 (3) | C18—C17—N20—C21 | −163.3 (3) |
C8—C9—C10—N1 | −178.8 (3) | C16—C17—N20—C21 | 89.7 (3) |
C8—C9—C10—C5 | 1.2 (5) | C18—C17—N20—C19 | 73.2 (3) |
C6—C5—C10—N1 | 176.7 (3) | C16—C17—N20—C19 | −33.8 (3) |
C4—C5—C10—N1 | −6.8 (4) | C2—C3—C23—O25 | −136.5 (3) |
C6—C5—C10—C9 | −3.3 (4) | C4—C3—C23—O25 | 44.2 (4) |
C4—C5—C10—C9 | 173.3 (3) | C2—C3—C23—O24 | 44.9 (4) |
C2—N1—C11—C12 | −29.2 (4) | C4—C3—C23—O24 | −134.3 (3) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N20—H20···O26i | 0.94 (4) | 1.92 (4) | 2.761 (3) | 148 (3) |
N20—H20···O25i | 0.94 (4) | 2.17 (4) | 2.792 (4) | 123 (3) |
O27—H27A···O26 | 0.96 (6) | 1.86 (6) | 2.811 (3) | 172 (5) |
O27—H27B···O24ii | 0.91 (5) | 2.03 (5) | 2.929 (4) | 168 (4) |
O28—H28A···O24 | 0.87 (6) | 1.98 (7) | 2.833 (4) | 165 (5) |
O28—H28B···O27iii | 0.91 (6) | 2.00 (6) | 2.906 (4) | 172 (4) |
Symmetry codes: (i) x−1/2, −y+1/2, −z+1; (ii) −x+1, y−1/2, −z+3/2; (iii) x, y+1, z. |