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Acta Crystallographica Section E: Crystallographic Communications logoLink to Acta Crystallographica Section E: Crystallographic Communications
. 2023 Nov 14;79(Pt 12):1147–1150. doi: 10.1107/S205698902300974X

Synthesis and crystallographic characterization of 6-hydroxy-1,2-dihydropyridin-2-one

Sara K Phillips a, Savannah G Brancato a, Samantha N MacMillan b, Mark J Snider c, Andrew J Roering a,*, Katherine A Hicks a,*
Editor: J Reibenspiesd
PMCID: PMC10833402  PMID: 38313119

The synthesis of the title compound as a formic acid salt, rather than the standard hydro­chloride salt that is commercially available, and its spectroscopic and crystallographic characterization are described.

Keywords: crystal structure, hydrogen bonding, nicotinic acid derivative

Abstract

The title compound, C5H5NO2, is a hy­droxy­lated pyridine ring that has been studied for its involvement in microbial degradation of nicotinic acid. Here we describe its synthesis as a formic acid salt, rather than the standard hydro­chloride salt that is commercially available, and its spectroscopic and crystallographic characterization.

1. Chemical context

6-Hydroxy-1,2-dihydropyridin-2-one, more commonly known as 2,6-dihydroxypyridine (2,6-DHP), is a derivative of nicotinic acid, a common compound found within personal care products (Behrman & Stanier, 1957; Hicks et al., 2016; Nakamoto et al., 2019). Recent work has focused on the bacterial hydrolysis of nicotinic acid for use in bioremediation efforts (Bokor et al., 2022). Synthesis of 2,6-DHP can be accomplished by reaction between 2,6-di­chloro­pyridine and potassium tert-butoxide to afford 2,6-di-tert-but­oxy­pyridine (1) followed by reaction with formic acid to produce the product 2 as the pyridone tautomer (Scheme 1; Kocienski, 1994). The identification of 2 was confirmed by 1H, 13C and IR spectroscopy. The 1H NMR spectrum suggested a non-symmetric pyridone mol­ecule with an N—H proton at δ = 11.47 ppm. The aromatic region of the spectrum suggested that each of the three protons on the aromatic backbone of 2 were in different chemical environments highlighted by their different chemical shifts of δ = 7.66, 6.91 and 6.60 ppm. These shifts, along with their splitting patterns and coupling constants, are consistent with the structure of 2. IR spectroscopic data of 2 were also consistent with the overall structure of a pyridone tautomer. Crystals of 2 were grown from slow evaporation of a saturated methanol solution. The solid-state structure of 2 was consistent with the solution state as the title mol­ecule crystallized as the keto tautomer. 1.

2. Structural commentary

The structure of 2,6-di­hydroxy­pyridine (Fig. 1) shows the expected 2,6-disubstitution of the pyridine ring. The bond lengths and angles are routine for nitro­gen-containing aromatic compounds (Table 1).

Figure 1.

Figure 1

A view of 2 showing the atom-numbering scheme for one independent mol­ecule. Displacement ellipsoids are drawn at the 50% probability level.

Table 1. Selected geometric parameters (Å, °) for 2 .

O9—C21 1.2789 (12) N5—C21 1.3688 (12)
O10—C25 1.3193 (12) N5—C25 1.3557 (12)
       
C25—N5—C21 124.86 (9) N5—C21—C22 116.60 (8)
C21—N5—H5 117.3 (8) O10—C25—N5 114.23 (8)
C25—N5—H5 117.8 (8) O10—C25—C24 126.58 (9)
O9—C21—N5 117.12 (9) N5—C25—C24 119.19 (9)
O9—C21—C22 126.28 (9)    

3. Supra­molecular features

There are six independent mol­ecules in the asymmetric unit of 2; of these, two pairs of mol­ecules are each held together by O—H⋯O hydrogen bonds. In both instances, the H atoms in the hydrogen bonds are disordered over two positions with refined occupancies of 0.51 (3) and 0.49 (3) at the O6 and O7 sites, respectively, and 0.39 (3) and 0.61 (3) at the O2 and O3 sites, respectively. The mol­ecules pack together in the solid state with inter­molecular O—H⋯O and N—H⋯O inter­actions (Table 2 and Fig. 2). The crystal packing of the title compound involves no π–π ring inter­actions (Fig. 3).

Table 2. Hydrogen-bond geometry (Å, °) for 2 .

D—H⋯A D—H H⋯A DA D—H⋯A
O2—H2A⋯O3 0.84 (2) 1.60 (2) 2.4317 (10) 174 (4)
N1—H1⋯O9i 0.88 (1) 1.98 (1) 2.8606 (11) 175 (1)
O3—H3⋯O2 0.87 (2) 1.57 (2) 2.4317 (10) 176 (3)
O4—H4⋯O5ii 0.981 (14) 1.500 (14) 2.4768 (10) 173.5 (14)
N2—H2⋯O1iii 0.89 (1) 1.89 (1) 2.7554 (11) 166 (1)
O6—H6⋯O7 0.86 (1) 1.58 (1) 2.4381 (10) 177 (3)
N3—H3B⋯O11iv 0.87 (1) 1.95 (1) 2.8155 (11) 170 (1)
O7—H7A⋯O6 0.88 (2) 1.56 (2) 2.4381 (10) 179 (3)
O8—H8A⋯O9v 0.91 (1) 1.58 (1) 2.4803 (10) 175 (1)
N4—H4A⋯O10i 0.87 (1) 2.07 (1) 2.8999 (11) 161 (1)
O10—H10⋯O11iv 0.95 (1) 1.52 (1) 2.4690 (9) 176 (1)
N5—H5⋯O2i 0.88 (1) 1.90 (1) 2.7699 (11) 167 (1)
O12—H12A⋯O1iii 0.90 (1) 1.61 (1) 2.5057 (10) 178 (2)
N6—H6A⋯O5vi 0.88 (1) 1.91 (1) 2.7893 (11) 172 (1)

Symmetry codes: (i) Inline graphic ; (ii) Inline graphic ; (iii) Inline graphic ; (iv) Inline graphic ; (v) Inline graphic ; (vi) Inline graphic .

Figure 2.

Figure 2

A view of the inter­molecular inter­actions in 2.

Figure 3.

Figure 3

A view of the mol­ecular packing in 2.

4. Hirshfeld surface analysis

The Hirshfeld surface analysis of 2 was performed and the associated two-dimensional fingerprint plots were generated using Crystal Explorer 21.5 software (Spackman et al., 2021). Visualizations used a red–white–blue color scheme where red indicates shorter contacts, while blue indicates longer contacts. There are four red spots on the d norm surface (Fig. 4 a) and these spots indicate the direction and strength of the inter­molecular E—H⋯O (E = N, O). The two-dimensional fingerprint plots are shown in Fig. 4 b. The resulting fingerprint plot indicates strong O⋯H inter­actions, as shown by the two prominent spikes on either side of the diagonal. The N⋯H inter­actions are shown in the ‘wings’ of the plot and are not as prominent as the O⋯H inter­actions.

Figure 4.

Figure 4

(a) Hirshfeld surface representations of 2 with the function d norm plotted onto the surface indicating the E—H⋯O (E = N, O) inter­actions; (b) two-dimensional fingerprint plot.

5. Database survey

A search for the pyridone tautomers of relatively simple dihy­droxy-substituted pyridines in the Cambridge Structure Database (CSD version 5.44, last update April 2023; Groom et al., 2016) revealed 23 crystal structures. Nearly all these structures have N—H⋯O and O—H⋯O hydrogen-bonding motifs, similar to those observed in the title compound. The structures with dissimilar motifs involve inter­molecular inter­actions with solvent mol­ecules or intra­molecular hydrogen bonding. The closest analogues to 2 were found to be GUBKIZ and NOQGOR (Gerhardt & Bolte, 2015); these structures contain N—H⋯O and O—H⋯O(solvent) hydrogen-bonding motifs.

6. Synthesis and crystallization

1: A 100 mL round-bottom flask equipped with a stir bar was charged with 2,6-di­chloro­pyridine (1.00 g, 6.80 mmol, 1 eq) and 15 mL of mesitylene solvent. To the solution was added potassium tert-butoxide (1.52 g, 13.6 mmol, 2.1 eq). The solution was then refluxed under N2 for 18 h. A color change from colorless to deep red was observed. After 18 h, the solution was allowed to cool to room temperature and the solution was washed with water (3 × 20 mL). The organic layer was collected, dried over sodium sulfate and used without purification in step 2.

2: To the crude solution from step 1 in a 20 mL scintillation vial was added formic acid (1.00 mL, 17.8 mmol, 2.6 eq). The bi-layered solution was stirred in air at high speed for 18 h when a solid precipitate formed. The solid was collected and dried under vacuum to yield 0.180 g (17% over 2 steps).

1H NMR (300 MHz, ppm), 11.47 (bs, 1H NH), 7.68 (t, 1H), 6.91 (d, 1H), 6.60 (d, 1H). 13C NMR (75 MHz, ppm), 163.7, 147.0, 142.2, 114.9, 108.5. IR (cm−1): 1596 m, 1333 m, 825 w, 772 w, 706 s.

Crystals suitable for X-ray analysis were grown from slow evaporation of a saturated methanol solution. The melting point of 2,6-DHP was measured at 460–465 K.

7. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 3. All non-hydrogen atoms were refined anisotropically. Hydrogen atoms bonded to carbon were included in calculated positions and refined using a riding model. Hydrogen atoms bound to N and O were located in the difference-Fourier map, and refined semi-freely with the help of distance restraints.

Table 3. Experimental details.

Crystal data
Chemical formula C30H30N6O12
M r 666.60
Crystal system, space group Monoclinic, P21/n
Temperature (K) 100
a, b, c (Å) 9.58785 (4), 16.83642 (8), 19.55978 (10)
β (°) 103.7319 (5)
V3) 3067.19 (3)
Z 4
Radiation type Cu Kα
μ (mm−1) 0.97
Crystal size (mm) 0.38 × 0.12 × 0.10
 
Data collection
Diffractometer XtaLAB Synergy, Dualflex, HyPix
Absorption correction Gaussian (CrysAlis PRO; Rigaku OD, 2021)
T min, T max 0.453, 1.000
No. of measured, independent and observed [I > 2σ(I)] reflections 83138, 6554, 6155
R int 0.035
(sin θ/λ)max−1) 0.635
 
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S 0.032, 0.083, 1.02
No. of reflections 6554
No. of parameters 477
No. of restraints 14
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.19, −0.35

Computer programs: CrysAlis PRO (Rigaku OD, 2021), SHELXT2014/5 (Sheldrick, 2015a ), SHELXL2016/6 (Sheldrick, 2015b ), and OLEX2 (Dolomanov et al., 2009).

Supplementary Material

Crystal structure: contains datablock(s) I. DOI: 10.1107/S205698902300974X/jy2036sup1.cif

e-79-01147-sup1.cif (2.4MB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S205698902300974X/jy2036Isup2.hkl

e-79-01147-Isup2.hkl (521KB, hkl)

The SI contains NMR and IR spectroscopy data of the titled compound. DOI: 10.1107/S205698902300974X/jy2036sup3.docx

Supporting information file. DOI: 10.1107/S205698902300974X/jy2036sup4.mol

Supporting information file. DOI: 10.1107/S205698902300974X/jy2036Isup5.cml

CCDC reference: 2306392

Additional supporting information: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Crystal data

C30H30N6O12 F(000) = 1392
Mr = 666.60 Dx = 1.444 Mg m3
Monoclinic, P21/n Cu Kα radiation, λ = 1.54184 Å
a = 9.58785 (4) Å Cell parameters from 59431 reflections
b = 16.83642 (8) Å θ = 3.5–78.0°
c = 19.55978 (10) Å µ = 0.97 mm1
β = 103.7319 (5)° T = 100 K
V = 3067.19 (3) Å3 Block, clear colourless
Z = 4 0.38 × 0.12 × 0.10 mm

Data collection

XtaLAB Synergy, Dualflex, HyPix diffractometer 6554 independent reflections
Radiation source: micro-focus sealed X-ray tube, PhotonJet (Cu) X-ray Source 6155 reflections with I > 2σ(I)
Mirror monochromator Rint = 0.035
Detector resolution: 10.0000 pixels mm-1 θmax = 78.1°, θmin = 3.5°
ω scans h = −11→12
Absorption correction: gaussian (CrysAlisPro; Rigaku OD, 2021) k = −21→21
Tmin = 0.453, Tmax = 1.000 l = −24→24
83138 measured reflections

Refinement

Refinement on F2 Primary atom site location: dual
Least-squares matrix: full Hydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.032 H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.083 w = 1/[σ2(Fo2) + (0.0411P)2 + 1.0736P] where P = (Fo2 + 2Fc2)/3
S = 1.02 (Δ/σ)max = 0.001
6554 reflections Δρmax = 0.19 e Å3
477 parameters Δρmin = −0.35 e Å3
14 restraints

Special details

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)

x y z Uiso*/Ueq Occ. (<1)
O1 0.99326 (7) 0.14764 (4) 0.52810 (4) 0.02046 (15)
O2 0.52056 (7) 0.20046 (5) 0.45281 (4) 0.02307 (16)
H2A 0.433 (2) 0.190 (2) 0.449 (2) 0.028* 0.39 (3)
N1 0.75397 (8) 0.16938 (5) 0.49622 (4) 0.01657 (16)
H1 0.7731 (13) 0.2085 (7) 0.4701 (6) 0.020*
C1 0.86759 (10) 0.12574 (6) 0.53339 (5) 0.01703 (19)
C2 0.83551 (11) 0.06266 (6) 0.57353 (5) 0.0215 (2)
H2B 0.910124 0.031089 0.601141 0.026*
C3 0.69311 (11) 0.04690 (6) 0.57242 (6) 0.0228 (2)
H3A 0.671749 0.004190 0.599998 0.027*
C4 0.58049 (10) 0.09106 (6) 0.53259 (5) 0.0196 (2)
H4B 0.483773 0.078550 0.532377 0.024*
C5 0.61270 (10) 0.15408 (6) 0.49300 (5) 0.01704 (19)
O3 0.26881 (7) 0.17595 (5) 0.44883 (4) 0.02250 (16)
H3 0.3589 (19) 0.1824 (14) 0.4497 (13) 0.027* 0.61 (3)
O4 −0.19312 (7) 0.12596 (5) 0.35615 (4) 0.02344 (16)
H4 −0.2704 (15) 0.1017 (8) 0.3202 (7) 0.028*
N2 0.04226 (8) 0.14771 (5) 0.39488 (4) 0.01710 (16)
H2 0.0221 (13) 0.1564 (8) 0.4363 (6) 0.021*
C6 0.18169 (10) 0.15386 (6) 0.39087 (5) 0.01790 (19)
C7 0.21482 (11) 0.13432 (6) 0.32713 (6) 0.0213 (2)
H7 0.310669 0.137636 0.321914 0.026*
C8 0.10467 (11) 0.11005 (7) 0.27185 (6) 0.0239 (2)
H8 0.126899 0.095290 0.228771 0.029*
C9 −0.03761 (11) 0.10639 (6) 0.27684 (5) 0.0219 (2)
H9 −0.111893 0.090907 0.237695 0.026*
C10 −0.06756 (10) 0.12600 (6) 0.34062 (5) 0.01782 (19)
O5 1.10984 (8) 0.44209 (4) 0.77157 (4) 0.02427 (17)
O6 0.69473 (7) 0.46139 (4) 0.60703 (4) 0.02291 (16)
H6 0.633 (3) 0.4403 (16) 0.5726 (11) 0.027* 0.51 (3)
N3 0.90320 (8) 0.44362 (5) 0.68705 (4) 0.01738 (17)
H3B 0.8924 (13) 0.4921 (7) 0.7009 (7) 0.021*
C11 1.02185 (10) 0.40333 (6) 0.72324 (5) 0.01834 (19)
C12 1.03646 (12) 0.32439 (6) 0.70413 (6) 0.0254 (2)
H12 1.116169 0.293498 0.727941 0.030*
C13 0.93248 (13) 0.29207 (7) 0.64981 (6) 0.0295 (2)
H13 0.942521 0.238376 0.636833 0.035*
C14 0.81402 (11) 0.33486 (6) 0.61347 (6) 0.0240 (2)
H14 0.744993 0.311212 0.576036 0.029*
C15 0.79897 (10) 0.41320 (6) 0.63325 (5) 0.01727 (19)
O7 0.51409 (7) 0.40623 (4) 0.50930 (4) 0.02113 (15)
H7A 0.579 (3) 0.4265 (17) 0.5446 (12) 0.025* 0.49 (3)
O8 0.06505 (7) 0.32983 (5) 0.41128 (4) 0.02330 (16)
H8A −0.0264 (13) 0.3226 (8) 0.4150 (7) 0.028*
N4 0.28349 (8) 0.37226 (5) 0.46665 (4) 0.01696 (17)
H4A 0.3118 (13) 0.3515 (8) 0.4316 (6) 0.020*
C16 0.38461 (10) 0.41017 (6) 0.51679 (5) 0.01732 (19)
C17 0.33735 (11) 0.44811 (6) 0.57103 (5) 0.0218 (2)
H17 0.402967 0.476182 0.606926 0.026*
C18 0.19353 (12) 0.44388 (7) 0.57127 (6) 0.0260 (2)
H18 0.161676 0.469269 0.608196 0.031*
C19 0.09332 (11) 0.40380 (7) 0.51941 (6) 0.0239 (2)
H19 −0.004815 0.401025 0.521012 0.029*
C20 0.14144 (10) 0.36826 (6) 0.46563 (5) 0.01835 (19)
O9 0.18597 (7) 0.69692 (4) 0.58239 (4) 0.02126 (15)
O10 0.66116 (7) 0.66705 (4) 0.66883 (4) 0.01849 (15)
H10 0.7367 (13) 0.6395 (8) 0.6998 (7) 0.022*
N5 0.42153 (8) 0.67871 (5) 0.63253 (4) 0.01655 (16)
H5 0.4396 (13) 0.7114 (7) 0.6004 (6) 0.020*
C21 0.28056 (10) 0.66605 (6) 0.63264 (5) 0.01715 (19)
C22 0.25389 (10) 0.61994 (6) 0.68815 (5) 0.0203 (2)
H22 0.158220 0.610105 0.691582 0.024*
C23 0.36839 (11) 0.58916 (6) 0.73752 (6) 0.0224 (2)
H23 0.349750 0.558253 0.775009 0.027*
C24 0.51056 (11) 0.60179 (6) 0.73441 (5) 0.0203 (2)
H24 0.587906 0.579291 0.768459 0.024*
C25 0.53506 (10) 0.64807 (6) 0.68018 (5) 0.01634 (18)
O11 0.64103 (7) 0.09175 (4) 0.75468 (4) 0.01983 (15)
O12 0.20548 (7) 0.07976 (5) 0.60556 (4) 0.02324 (16)
H12A 0.1306 (14) 0.1044 (8) 0.5774 (7) 0.028*
N6 0.42400 (8) 0.09381 (5) 0.67740 (4) 0.01662 (16)
H6A 0.4165 (13) 0.0440 (7) 0.6899 (7) 0.020*
C26 0.54837 (10) 0.13190 (6) 0.70929 (5) 0.01743 (19)
C27 0.56380 (12) 0.21052 (6) 0.68974 (6) 0.0260 (2)
H27 0.649710 0.238977 0.708997 0.031*
C28 0.45219 (13) 0.24630 (7) 0.64195 (6) 0.0304 (3)
H28 0.462424 0.300102 0.629325 0.036*
C29 0.32527 (12) 0.20661 (7) 0.61155 (6) 0.0249 (2)
H29 0.249173 0.232717 0.579442 0.030*
C30 0.31366 (10) 0.12804 (6) 0.62962 (5) 0.01851 (19)

Atomic displacement parameters (Å2)

U11 U22 U33 U12 U13 U23
O1 0.0114 (3) 0.0298 (4) 0.0185 (3) 0.0016 (3) 0.0002 (2) 0.0008 (3)
O2 0.0104 (3) 0.0268 (4) 0.0301 (4) 0.0005 (3) 0.0013 (3) 0.0117 (3)
N1 0.0118 (4) 0.0194 (4) 0.0174 (4) −0.0001 (3) 0.0013 (3) 0.0032 (3)
C1 0.0133 (4) 0.0214 (5) 0.0148 (4) 0.0020 (3) 0.0000 (3) −0.0032 (3)
C2 0.0195 (5) 0.0217 (5) 0.0210 (5) 0.0054 (4) 0.0002 (4) 0.0031 (4)
C3 0.0237 (5) 0.0199 (5) 0.0244 (5) 0.0007 (4) 0.0050 (4) 0.0050 (4)
C4 0.0157 (4) 0.0202 (5) 0.0229 (5) −0.0015 (3) 0.0041 (4) 0.0014 (4)
C5 0.0127 (4) 0.0191 (4) 0.0181 (4) 0.0002 (3) 0.0013 (3) −0.0003 (4)
O3 0.0113 (3) 0.0326 (4) 0.0218 (4) −0.0029 (3) 0.0005 (3) −0.0013 (3)
O4 0.0125 (3) 0.0331 (4) 0.0237 (4) −0.0050 (3) 0.0022 (3) −0.0064 (3)
N2 0.0123 (4) 0.0207 (4) 0.0177 (4) −0.0014 (3) 0.0024 (3) −0.0020 (3)
C6 0.0127 (4) 0.0177 (4) 0.0222 (5) 0.0001 (3) 0.0019 (3) 0.0020 (4)
C7 0.0164 (4) 0.0239 (5) 0.0247 (5) 0.0015 (4) 0.0069 (4) 0.0037 (4)
C8 0.0255 (5) 0.0271 (5) 0.0205 (5) 0.0003 (4) 0.0082 (4) 0.0002 (4)
C9 0.0205 (5) 0.0246 (5) 0.0187 (5) −0.0031 (4) 0.0008 (4) −0.0023 (4)
C10 0.0144 (4) 0.0167 (4) 0.0209 (5) −0.0019 (3) 0.0011 (4) −0.0001 (4)
O5 0.0181 (3) 0.0227 (4) 0.0261 (4) 0.0047 (3) −0.0066 (3) −0.0051 (3)
O6 0.0158 (3) 0.0241 (4) 0.0241 (4) 0.0013 (3) −0.0048 (3) −0.0018 (3)
N3 0.0143 (4) 0.0166 (4) 0.0193 (4) 0.0007 (3) 0.0001 (3) −0.0023 (3)
C11 0.0146 (4) 0.0211 (5) 0.0179 (4) 0.0013 (3) 0.0010 (3) 0.0003 (4)
C12 0.0238 (5) 0.0218 (5) 0.0274 (5) 0.0069 (4) −0.0004 (4) −0.0019 (4)
C13 0.0319 (6) 0.0213 (5) 0.0319 (6) 0.0038 (4) 0.0007 (5) −0.0073 (4)
C14 0.0225 (5) 0.0238 (5) 0.0227 (5) −0.0027 (4) −0.0002 (4) −0.0059 (4)
C15 0.0133 (4) 0.0219 (5) 0.0158 (4) −0.0022 (3) 0.0019 (3) 0.0006 (4)
O7 0.0119 (3) 0.0277 (4) 0.0218 (4) −0.0025 (3) 0.0001 (3) −0.0025 (3)
O8 0.0117 (3) 0.0300 (4) 0.0265 (4) −0.0043 (3) 0.0012 (3) −0.0042 (3)
N4 0.0128 (4) 0.0200 (4) 0.0176 (4) −0.0006 (3) 0.0026 (3) −0.0009 (3)
C16 0.0146 (4) 0.0174 (4) 0.0181 (4) −0.0012 (3) 0.0001 (3) 0.0039 (3)
C17 0.0226 (5) 0.0223 (5) 0.0189 (5) −0.0026 (4) 0.0020 (4) −0.0014 (4)
C18 0.0267 (5) 0.0274 (5) 0.0261 (5) −0.0009 (4) 0.0108 (4) −0.0036 (4)
C19 0.0168 (4) 0.0271 (5) 0.0299 (5) −0.0009 (4) 0.0093 (4) −0.0003 (4)
C20 0.0134 (4) 0.0181 (4) 0.0224 (5) −0.0010 (3) 0.0020 (4) 0.0037 (4)
O9 0.0110 (3) 0.0253 (4) 0.0252 (4) −0.0008 (3) −0.0002 (3) 0.0068 (3)
O10 0.0106 (3) 0.0242 (3) 0.0193 (3) 0.0011 (3) 0.0008 (2) 0.0022 (3)
N5 0.0120 (4) 0.0197 (4) 0.0171 (4) 0.0001 (3) 0.0017 (3) 0.0038 (3)
C21 0.0126 (4) 0.0175 (4) 0.0204 (5) −0.0004 (3) 0.0020 (3) −0.0008 (4)
C22 0.0152 (4) 0.0232 (5) 0.0237 (5) −0.0004 (4) 0.0070 (4) 0.0016 (4)
C23 0.0236 (5) 0.0242 (5) 0.0207 (5) 0.0012 (4) 0.0077 (4) 0.0050 (4)
C24 0.0182 (5) 0.0231 (5) 0.0180 (5) 0.0041 (4) 0.0014 (4) 0.0036 (4)
C25 0.0132 (4) 0.0179 (4) 0.0168 (4) 0.0007 (3) 0.0013 (3) −0.0022 (3)
O11 0.0143 (3) 0.0197 (3) 0.0214 (3) −0.0014 (3) −0.0040 (3) 0.0039 (3)
O12 0.0131 (3) 0.0304 (4) 0.0222 (4) −0.0006 (3) −0.0038 (3) 0.0036 (3)
N6 0.0130 (4) 0.0185 (4) 0.0166 (4) 0.0002 (3) 0.0000 (3) 0.0022 (3)
C26 0.0146 (4) 0.0203 (5) 0.0159 (4) 0.0001 (3) 0.0008 (3) −0.0004 (4)
C27 0.0254 (5) 0.0202 (5) 0.0264 (5) −0.0045 (4) −0.0055 (4) 0.0018 (4)
C28 0.0369 (6) 0.0184 (5) 0.0291 (6) −0.0001 (4) −0.0058 (5) 0.0038 (4)
C29 0.0249 (5) 0.0234 (5) 0.0213 (5) 0.0067 (4) −0.0045 (4) 0.0021 (4)
C30 0.0138 (4) 0.0254 (5) 0.0151 (4) 0.0031 (4) 0.0010 (3) −0.0012 (4)

Geometric parameters (Å, º)

O1—C1 1.2875 (12) O7—H7A 0.879 (18)
O2—H2A 0.839 (19) O7—C16 1.2858 (12)
O2—C5 1.2956 (12) O8—H8A 0.905 (12)
N1—H1 0.880 (12) O8—C20 1.3098 (12)
N1—C1 1.3708 (12) N4—H4A 0.868 (12)
N1—C5 1.3655 (12) N4—C16 1.3630 (12)
C1—C2 1.3978 (15) N4—C20 1.3590 (12)
C2—H2B 0.9500 C16—C17 1.4026 (15)
C2—C3 1.3859 (15) C17—H17 0.9500
C3—H3A 0.9500 C17—C18 1.3819 (15)
C3—C4 1.3879 (14) C18—H18 0.9500
C4—H4B 0.9500 C18—C19 1.3946 (15)
C4—C5 1.3908 (14) C19—H19 0.9500
O3—H3 0.867 (17) C19—C20 1.3811 (15)
O3—C6 1.2928 (12) O9—C21 1.2789 (12)
O4—H4 0.981 (14) O10—H10 0.948 (11)
O4—C10 1.3096 (12) O10—C25 1.3193 (12)
N2—H2 0.888 (12) N5—H5 0.882 (12)
N2—C6 1.3616 (12) N5—C21 1.3688 (12)
N2—C10 1.3556 (12) N5—C25 1.3557 (12)
C6—C7 1.3971 (15) C21—C22 1.4067 (14)
C7—H7 0.9500 C22—H22 0.9500
C7—C8 1.3818 (15) C22—C23 1.3795 (14)
C8—H8 0.9500 C23—H23 0.9500
C8—C9 1.3919 (15) C23—C24 1.3952 (14)
C9—H9 0.9500 C24—H24 0.9500
C9—C10 1.3850 (15) C24—C25 1.3805 (14)
O5—C11 1.2856 (12) O11—C26 1.2884 (12)
O6—H6 0.861 (14) O12—H12A 0.897 (12)
O6—C15 1.2949 (12) O12—C30 1.3139 (12)
N3—H3B 0.874 (12) N6—H6A 0.881 (12)
N3—C11 1.3686 (12) N6—C26 1.3671 (12)
N3—C15 1.3672 (12) N6—C30 1.3622 (12)
C11—C12 1.3966 (14) C26—C27 1.3955 (14)
C12—H12 0.9500 C27—H27 0.9500
C12—C13 1.3843 (15) C27—C28 1.3810 (15)
C13—H13 0.9500 C28—H28 0.9500
C13—C14 1.3896 (15) C28—C29 1.3919 (16)
C14—H14 0.9500 C29—H29 0.9500
C14—C15 1.3916 (15) C29—C30 1.3805 (15)
C5—O2—H2A 117 (3) C16—O7—H7A 114.1 (19)
C1—N1—H1 117.4 (8) C20—O8—H8A 111.5 (9)
C5—N1—H1 117.1 (8) C16—N4—H4A 117.0 (8)
C5—N1—C1 125.31 (9) C20—N4—H4A 118.0 (8)
O1—C1—N1 116.42 (9) C20—N4—C16 124.96 (9)
O1—C1—C2 126.71 (9) O7—C16—N4 115.79 (9)
N1—C1—C2 116.88 (9) O7—C16—C17 127.13 (9)
C1—C2—H2B 120.5 N4—C16—C17 117.07 (9)
C3—C2—C1 118.94 (9) C16—C17—H17 120.6
C3—C2—H2B 120.5 C18—C17—C16 118.75 (9)
C2—C3—H3A 118.7 C18—C17—H17 120.6
C2—C3—C4 122.58 (9) C17—C18—H18 118.7
C4—C3—H3A 118.7 C17—C18—C19 122.56 (10)
C3—C4—H4B 120.8 C19—C18—H18 118.7
C3—C4—C5 118.37 (9) C18—C19—H19 121.1
C5—C4—H4B 120.8 C20—C19—C18 117.81 (9)
O2—C5—N1 116.12 (9) C20—C19—H19 121.1
O2—C5—C4 126.02 (9) O8—C20—N4 113.69 (9)
N1—C5—C4 117.85 (9) O8—C20—C19 127.49 (9)
C6—O3—H3 119.1 (16) N4—C20—C19 118.83 (9)
C10—O4—H4 114.4 (8) C25—O10—H10 111.5 (8)
C6—N2—H2 118.0 (8) C25—N5—C21 124.86 (9)
C10—N2—H2 117.5 (8) C21—N5—H5 117.3 (8)
C10—N2—C6 124.49 (9) C25—N5—H5 117.8 (8)
O3—C6—N2 114.22 (9) O9—C21—N5 117.12 (9)
O3—C6—C7 127.87 (9) O9—C21—C22 126.28 (9)
N2—C6—C7 117.89 (9) N5—C21—C22 116.60 (8)
C6—C7—H7 120.8 C21—C22—H22 120.4
C8—C7—C6 118.33 (9) C23—C22—C21 119.17 (9)
C8—C7—H7 120.8 C23—C22—H22 120.4
C7—C8—H8 118.7 C22—C23—H23 118.8
C7—C8—C9 122.55 (10) C22—C23—C24 122.38 (9)
C9—C8—H8 118.7 C24—C23—H23 118.8
C8—C9—H9 121.0 C23—C24—H24 121.1
C10—C9—C8 117.96 (9) C25—C24—C23 117.76 (9)
C10—C9—H9 121.0 C25—C24—H24 121.1
O4—C10—N2 113.87 (9) O10—C25—N5 114.23 (8)
O4—C10—C9 127.39 (9) O10—C25—C24 126.58 (9)
N2—C10—C9 118.74 (9) N5—C25—C24 119.19 (9)
C15—O6—H6 112.0 (19) C30—O12—H12A 112.5 (9)
C11—N3—H3B 116.6 (8) C26—N6—H6A 116.1 (8)
C15—N3—H3B 118.0 (8) C30—N6—H6A 119.5 (8)
C15—N3—C11 125.33 (9) C30—N6—C26 124.46 (9)
O5—C11—N3 116.65 (9) O11—C26—N6 116.90 (9)
O5—C11—C12 126.15 (9) O11—C26—C27 125.87 (9)
N3—C11—C12 117.21 (9) N6—C26—C27 117.24 (9)
C11—C12—H12 120.7 C26—C27—H27 120.5
C13—C12—C11 118.67 (10) C28—C27—C26 118.93 (10)
C13—C12—H12 120.7 C28—C27—H27 120.5
C12—C13—H13 118.6 C27—C28—H28 118.7
C12—C13—C14 122.76 (10) C27—C28—C29 122.56 (10)
C14—C13—H13 118.6 C29—C28—H28 118.7
C13—C14—H14 120.8 C28—C29—H29 121.1
C13—C14—C15 118.38 (9) C30—C29—C28 117.79 (9)
C15—C14—H14 120.8 C30—C29—H29 121.1
O6—C15—N3 115.11 (9) O12—C30—N6 113.73 (9)
O6—C15—C14 127.23 (9) O12—C30—C29 127.30 (9)
N3—C15—C14 117.65 (9) N6—C30—C29 118.97 (9)
O1—C1—C2—C3 −179.28 (10) O7—C16—C17—C18 −178.06 (10)
N1—C1—C2—C3 1.34 (14) N4—C16—C17—C18 1.06 (14)
C1—N1—C5—O2 −177.46 (9) C16—N4—C20—O8 178.71 (9)
C1—N1—C5—C4 2.61 (15) C16—N4—C20—C19 −1.01 (15)
C1—C2—C3—C4 0.39 (16) C16—C17—C18—C19 −0.44 (17)
C2—C3—C4—C5 −0.75 (16) C17—C18—C19—C20 −0.91 (17)
C3—C4—C5—O2 179.42 (10) C18—C19—C20—O8 −178.08 (10)
C3—C4—C5—N1 −0.66 (14) C18—C19—C20—N4 1.60 (15)
C5—N1—C1—O1 177.61 (9) C20—N4—C16—O7 178.86 (9)
C5—N1—C1—C2 −2.95 (14) C20—N4—C16—C17 −0.35 (14)
O3—C6—C7—C8 178.33 (10) O9—C21—C22—C23 178.40 (10)
N2—C6—C7—C8 0.10 (14) N5—C21—C22—C23 −1.37 (14)
C6—N2—C10—O4 −178.47 (9) C21—N5—C25—O10 178.72 (9)
C6—N2—C10—C9 1.86 (15) C21—N5—C25—C24 −1.47 (15)
C6—C7—C8—C9 1.70 (16) C21—C22—C23—C24 −0.27 (16)
C7—C8—C9—C10 −1.75 (16) C22—C23—C24—C25 1.14 (16)
C8—C9—C10—O4 −179.62 (10) C23—C24—C25—O10 179.46 (9)
C8—C9—C10—N2 0.00 (15) C23—C24—C25—N5 −0.31 (15)
C10—N2—C6—O3 179.62 (9) C25—N5—C21—O9 −177.48 (9)
C10—N2—C6—C7 −1.91 (15) C25—N5—C21—C22 2.31 (14)
O5—C11—C12—C13 −178.89 (11) O11—C26—C27—C28 −177.73 (11)
N3—C11—C12—C13 0.80 (16) N6—C26—C27—C28 2.43 (16)
C11—N3—C15—O6 179.01 (9) C26—N6—C30—O12 179.47 (9)
C11—N3—C15—C14 0.10 (15) C26—N6—C30—C29 −0.36 (15)
C11—C12—C13—C14 −0.03 (19) C26—C27—C28—C29 −1.01 (19)
C12—C13—C14—C15 −0.74 (18) C27—C28—C29—C30 −1.18 (19)
C13—C14—C15—O6 −178.07 (11) C28—C29—C30—O12 −177.96 (11)
C13—C14—C15—N3 0.70 (15) C28—C29—C30—N6 1.84 (16)
C15—N3—C11—O5 178.86 (9) C30—N6—C26—O11 178.32 (9)
C15—N3—C11—C12 −0.86 (15) C30—N6—C26—C27 −1.83 (15)

Hydrogen-bond geometry (Å, º)

D—H···A D—H H···A D···A D—H···A
O2—H2A···O3 0.84 (2) 1.60 (2) 2.4317 (10) 174 (4)
N1—H1···O9i 0.88 (1) 1.98 (1) 2.8606 (11) 175 (1)
O3—H3···O2 0.87 (2) 1.57 (2) 2.4317 (10) 176 (3)
O4—H4···O5ii 0.981 (14) 1.500 (14) 2.4768 (10) 173.5 (14)
N2—H2···O1iii 0.89 (1) 1.89 (1) 2.7554 (11) 166 (1)
O6—H6···O7 0.86 (1) 1.58 (1) 2.4381 (10) 177 (3)
N3—H3B···O11iv 0.87 (1) 1.95 (1) 2.8155 (11) 170 (1)
O7—H7A···O6 0.88 (2) 1.56 (2) 2.4381 (10) 179 (3)
O8—H8A···O9v 0.91 (1) 1.58 (1) 2.4803 (10) 175 (1)
N4—H4A···O10i 0.87 (1) 2.07 (1) 2.8999 (11) 161 (1)
O10—H10···O11iv 0.95 (1) 1.52 (1) 2.4690 (9) 176 (1)
N5—H5···O2i 0.88 (1) 1.90 (1) 2.7699 (11) 167 (1)
O12—H12A···O1iii 0.90 (1) 1.61 (1) 2.5057 (10) 178 (2)
N6—H6A···O5vi 0.88 (1) 1.91 (1) 2.7893 (11) 172 (1)

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x−3/2, −y+1/2, z−1/2; (iii) x−1, y, z; (iv) −x+3/2, y+1/2, −z+3/2; (v) −x, −y+1, −z+1; (vi) −x+3/2, y−1/2, −z+3/2.

Funding Statement

Funding for this research was provided by: National Science Foundation (MCB 1817535 to MJS and 1817633 to KAH).

References

  1. Behrman, E. J. & Stanier, R. Y. (1957). J. Biol. Chem. 228, 923–945. [PubMed]
  2. Bokor, E., Ámon, J., Varga, M., Szekeres, A., Hegedűs, Z., Jakusch, T., Szakonyi, Z., Flipphi, M., Vágvölgyi, C., Gácser, A., Scazzocchio, C. & Hamari, Z. (2022). Commun. Biol. 5, 723–734. [DOI] [PMC free article] [PubMed]
  3. Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.
  4. Gerhardt, V. & Bolte, M. (2015). Acta Cryst. C71, 19–25. [DOI] [PubMed]
  5. Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. [DOI] [PMC free article] [PubMed]
  6. Hicks, K. A., Yuen, M. E., Zhen, W. F., Gerwig, T. J., Story, R. W., Kopp, M. & Snider, M. J. (2016). Biochemistry, 55, 3432–3446. [DOI] [PubMed]
  7. Kocienski, P. J. (1994). Protecting Groups in Organic Synthesis. Stuttgart: Thieme.
  8. Nakamoto, K. D., Perkins, S. W., Campbell, R. G., Bauerle, M. R., Gerwig, T. J., Gerislioglu, S., Wesdemiotis, C., Anderson, M. A., Hicks, K. A. & Snider, M. J. (2019). Biochemistry, 58, 1751–1763. [DOI] [PubMed]
  9. Rigaku OD (2021). CrysAlis PRO. Rigaku Oxford Diffraction, Yarnton, England.
  10. Sheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.
  11. Sheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.
  12. Spackman, P. R., Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Jayatilaka, D. & Spackman, M. A. (2021). J. Appl. Cryst. 54, 1006–1011. [DOI] [PMC free article] [PubMed]

Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Supplementary Materials

Crystal structure: contains datablock(s) I. DOI: 10.1107/S205698902300974X/jy2036sup1.cif

e-79-01147-sup1.cif (2.4MB, cif)

Structure factors: contains datablock(s) I. DOI: 10.1107/S205698902300974X/jy2036Isup2.hkl

e-79-01147-Isup2.hkl (521KB, hkl)

The SI contains NMR and IR spectroscopy data of the titled compound. DOI: 10.1107/S205698902300974X/jy2036sup3.docx

Supporting information file. DOI: 10.1107/S205698902300974X/jy2036sup4.mol

Supporting information file. DOI: 10.1107/S205698902300974X/jy2036Isup5.cml

CCDC reference: 2306392

Additional supporting information: crystallographic information; 3D view; checkCIF report


Articles from Acta Crystallographica Section E: Crystallographic Communications are provided here courtesy of International Union of Crystallography

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