research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 79| Part 3| March 2023| Pages 157-162
https://doi.org/10.1107/S2056989023001056

Structures of S-(pyridin-2-yl) 4-nitro­benzo­thio­ate, S-(pyridin-2-yl) 4-methyl­benzo­thio­ate and S-(pyridin-2-yl) 4-meth­­oxy­benzo­thio­ate: building blocks for low-symmetry multifunctional tetra­pyrroles

crossmark logo
Harry C. Sample,a* Brendan Twamleyb and Mathias O. Sengea

aSchool of Chemistry, Chair of Organic Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, D02 R590, Dublin, Ireland, and bSchool of Chemistry, Trinity College Dublin, College Green, Dublin 2, Ireland
*Correspondence e-mail: sampleh@tcd.ie

Edited by C. Schulzke, Universität Greifswald, Germany (Received 10 January 2023; accepted 3 February 2023; online 9 February 2023)

The crystal structures of three S-(pyridin-2-yl) benzo­thio­esters with varying para-phenyl substituents are presented, namely, S-(pyridin-2-yl) 4-nitro­benzo­thio­ate (1, C12H8N2O3S), S-(pyridin-2-yl) 4-methyl­benzo­thio­ate (2, C13H11NO2S) and S-(pyridin-2-yl) 4-meth­oxy­benzo­thio­ate (3, C13H11NO2S). This class of compounds are used in the mono-acyl­ation of pyrrolic species to yield multifunctional tetra­pyrroles. The structures presented herein are the first of their compound class. The dominant inter­actions present in this series are π–π stacking and C—H⋯O inter­actions, and as the para-phenyl motif changes from electron withdrawing (NO2, 1) to electron donating (OCH3, 3), changes are observed in the inter­actions present in the crystal packing, from predominant π–π stacking in 1 to exclusively C—H⋯O/N inter­actions (Car­yl—H⋯Ocarbon­yl, C—H⋯Ometh­oxy and Car­yl—H⋯Npyridine) in 3.

CCDC references: 2239845; 2239844; 2239843

Similar articles

1. Chemical context

In the continual search of evermore functional tetra­pyrroles, the tedious separation of multiple regioisomeric porphyrins from mixed Adler–Longo (Adler et al., 1967[Adler, D. A., Longo, F. R., Finarelli, J. D., Goldmacher, J., Assour, J. & Korsakoff, L. (1967). J. Org. Chem. 32, 476-476.]) or Lindsey-style syntheses (Lindsey et al., 1986[Lindsey, J. S., Hsu, H. C. & Schreiman, I. C. (1986). Tetrahedron Lett. 27, 4969-4970.]) no longer suits the desires of the few in this research field. Instead, multiple elegant yet simple routes have been developed for the functionalization of the porphyrin core (Hiroto et al., 2017[Hiroto, S., Miyake, Y. & Shinokubo, H. (2017). Chem. Rev. 117, 2910-3043.]; Sample et al., 2021[Sample, H. C. & Senge, M. O. (2021). Eur. J. Org. Chem. 2021, 7-42.]), as well as from the modification of pyrrolic precursors (Lindsey, 2010[Lindsey, J. S. (2010). Acc. Chem. Res. 43, 300-311.]). One route of note is via the mono­acyl­ation of meso-substituted dipyrro­methanes (I, Fig. 1[link]). Initially reported with the use of acyl chlorides by Lindsey and coworkers (Lee et al., 1995[Lee, C.-H., Li, F., Iwamoto, K., Dadok, J., Bothner-By, A. A. & Lindsey, J. S. (1995). Tetrahedron, 51, 11645-11672.]), the procedure also yields the di­acyl­ated products in substantial yield. The same group reported the selective mono­acyl­ation of meso-aryl dipyrro­methanes through the use of S-(pyridin-2-yl) benzo­thio­esters (Rao et al., 2000[Rao, P. D., Littler, B. J., Geier, G. R. III & Lindsey, J. S. (2000). J. Org. Chem. 65, 1084-1092.]).

[Figure 1]
Figure 1
Transformation of simple meso-substituted dipyrro­methanes (I) to monoacyl-dipyrro­methanes (II) through the use of S-(pyridin-2-yl) thio­esters. A, B = aryl, R = Et, iPr, X = Br, Cl.

S-(Pyridin-2-yl)benzo­thio­esters were first synthesized for the determination of ionization constants for heterocyclic substances (Albert & Barlin, 1959[Albert, A. & Barlin, G. B. (1959). J. Chem. Soc. pp. 2384-2396.]). This methodology was later elaborated upon to generate a wide variety of alkyl, aryl and heteroaryl ketones (Araki et al., 1974[Araki, M., Sakata, S., Takei, H. & Mukaiyama, T. (1974). Bull. Chem. Soc. Jpn, 47, 1777-1780.]). These compounds were also utilized to generate 2-keto­pyrroles (Nicolau et al., 1981[Nicolaou, K. C., Claremon, D. A. & Papahatjis, D. P. (1981). Tetrahedron Lett. 22, 4647-4650.]). Their versatility was recently highlighted (Lee, 2020[Lee, J. (2020). Bull. Korean Chem. Soc. 41, 735-747.]). The developments that have led to this point now enable the generation of diverse substitution patterns for both porphyrins (Rao et al., 2000[Rao, P. D., Littler, B. J., Geier, G. R. III & Lindsey, J. S. (2000). J. Org. Chem. 65, 1084-1092.]; Senge, 2011[Senge, M. O. (2011). Chem. Commun. 47, 1943-1960.]) and chlorins (Laakso et al., 2012[Laakso, J., Rosser, G. A., Szíjjártó, C., Beeby, A. & Borbas, K. E. (2012). Inorg. Chem. 51, 10366-10374.]; Ra et al., 2015[Ra, D., Gauger, K. A., Muthukumaran, K., Balasubramanian, T., Chandrashaker, V., Taniguchi, M., Yu, Z., Talley, D. C., Ehudin, M. Ptaszek, M. & Lindsey J. S. (2015). J. Porphyrins Phthalocyanines, 19, 547-572]; Senge et al., 2021[Senge, M. O., Sergeeva, N. N. & Hale, K. J. (2021). Chem. Soc. Rev. 50, 4730-4789.]).

[Scheme 1]

2. Structural commentary

The single-crystal XRD structures of title compounds 1, 2 and 3 (Figs. 2[link]–4[link][link]), all present asymmetric units consisting of one mol­ecule of compound and no solvate. Compound 1 was found to crystallize in the ortho­rhom­bic system (Pna21, Z = 4), compound 2 was found to crystallize in the triclinic system (P[\overline{1}], Z = 2) and compound 3 was found to crystallize in the monoclinic system (P21/c, Z = 4). Each mol­ecular structure shows an S-(pyridin-2-yl) benzo­thio­ate where the para-phenyl motif is modified, from NO2 in 1, CH3 in 2, and OCH3 in 3. All of the groups utilized herein are found extensively in the field of tetra­pyrroles.

[Figure 2]
Figure 2
Mol­ecular structure of 1. Anisotropic displacement ellipsoids are drawn at the 50% probability level. Generated using OLEX2.
[Figure 3]
Figure 3
Mol­ecular structure of 2. Anisotropic displacement ellipsoids are drawn at the 50% probability level. Generated using OLEX2.
[Figure 4]
Figure 4
Mol­ecular structure of 3. Anisotropic displacement ellipsoids are drawn at the 50% probability level. Generated using OLEX2.

In all structures 1–3, the substituted phenyl moieties are all essentially planar with the pyridine ring twisted relative to this plane. This is seen in the plane normal to plane normal angle and the torsion angle described by C8—S1—C6—N1. The twist of the methane­thio­ate moiety to the phenyl ring also describes the change in the angle of the rings to each other. These values are shown in Table 1[link].

Table 1
Comparison of structural parameters (°)

  Plane|plane Torsion angle C8—S1—C6—N1 Phenyl plane|plane C8—O9—S1—C6
1 56.97 (14) 128.6 (3) 6.00 (14)
2 57.51 (6) 120.11 (14) 5.08 (6)
3 65.94 (4) 75.84 (10) 10.28 (4)
CEFMOR 51.12 (1) 122.79 (1) 10.88 (2)
In CEFMOR, the torsion angle is defined by C1—S1—C8—C13.

In compound 1 (Fig. 2[link]), the angle between the para-nitro­benzaldehyde moiety, C8–O18, and the pyridine ring is similar to the angle between the benzaldehyde moiety, C8–C16 and the pyridine ring in compound 2 (Fig. 3[link]). The phenyl plane–pyridine plane angle and C8–S1–C6–N1 torsion angle in 3 (Fig. 4[link]) are very different to those of both 1 and 2.

All three benzo­thio­esters are similar to the previously published unsubstituted S-phenyl benzo­thio­ate (refcode: CEFMOR; Belay et al., 2012[Belay, Y. H., Kinfe, H. H. & Muller, A. (2012). Acta Cryst. E68, o2825.]). An overlay of 1–3 with CEFMOR is provided as Fig. 5[link]. The bond distances are within normal ranges (Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]).

[Figure 5]
Figure 5
Overlay of 1–3 and CEFMOR showing the orientation of the pyridine ring in 3 (red) relative to the other structures. Generated using OLEX2.

3. Supra­molecular features

Of the varying para-phenyl motifs presented across the series, the NO2 group in 1 is the most electron withdrawing, according to its tabulated Hammett constant (σp = 0.78; McDaniel & Brown, 1958[McDaniel, D. H. & Brown, H. C. (1958). J. Org. Chem. 23, 420-427.]) but also observed by the differing shifts in the resonances presented for the para-substituted phenyl ring, with extensive deshielding of the respective protons (Figs. S1, S4 in the supporting information). Furthermore, considering the respective previously determined Hammett constants, it is observed that the most electron donating is the OCH3 group in 3 (σp = −0.27), with 2 (CH3) lying somewhere in between (σp = −0.17) (McDaniel & Brown, 1958[McDaniel, D. H. & Brown, H. C. (1958). J. Org. Chem. 23, 420-427.]); again, this is reflected in the 1H NMR spectra.

Compound 1 presents C—H⋯O inter­actions (Table 2[link], Fig. 6[link]) to the carbonyl O9 via C4-H and C5-H donors [D⋯A = 3.283 (4) and 3.371 (5) Å]. The pyridine N1 is also an acceptor to the phenyl C12-H [D⋯A = 3.315 (5) Å]. The nitro group is a dual acceptor with inter­actions between O18 and one pyridyl C3-H [D⋯A = 3.396 (5) Å] and also a bifurcated inter­action between O17 and phenyl C14-H and C15-H [D⋯A = 3.359 (4) and 3.312 (5) Å, respectively].

Table 2
Hydrogen-bond geometry (Å, °) for 1[link]

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C3—H3⋯O18i 0.95 2.68 3.396 (5) 133
C4—H4⋯O9ii 0.95 2.46 3.283 (4) 145
C5—H5⋯O9iii 0.95 2.56 3.371 (5) 143
C12—H12⋯N1iv 0.95 2.49 3.315 (5) 145
C14—H14⋯O17v 0.95 2.77 3.359 (4) 121
C15—H15⋯O17v 0.95 2.66 3.312 (5) 127
Symmetry codes: (i) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z+1]; (ii) [-x+1, -y+2, z+{\script{1\over 2}}]; (iii) x, y, z+1; (iv) [-x+1, -y+1, z+{\script{1\over 2}}]; (v) [-x+{\script{3\over 2}}, y+{\script{1\over 2}}, z-{\script{1\over 2}}].
[Figure 6]
Figure 6
Excerpt of the packing structure of 1 viewed in the direction of the π-stack normal. Generated using OLEX2.

Compound 2 presents C—H⋯N-paired dimers between the H6-pyridyl protons C2-H2 and N1 [D⋯A = 3.355 (2) Å; Table 3[link], Fig. 7[link]]. The carbonyl is involved in a bifurcated inter­action C3-H/C4-H⋯O9 [D⋯A = 3.278 (2) and 3.316 (2) Å, respectively] and a C16-H⋯O9 inter­action [D⋯A = 3.460 (2) Å].

Table 3
Hydrogen-bond geometry (Å, °) for 2[link]

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C2—H2⋯N1i 0.95 2.70 3.355 (2) 126
C3—H3⋯O9ii 0.95 2.67 3.278 (2) 122
C4—H4⋯O9ii 0.95 2.75 3.316 (2) 119
C16—H16B⋯O9iii 0.98 2.64 3.460 (2) 142
Symmetry codes: (i) [-x, -y+2, -z+1]; (ii) [-x, -y+1, -z+1]; (iii) x+1, y, z.
[Figure 7]
Figure 7
Hydrogen bonding, represented by dashed lines, shown in the packing structure of 2. Viewed in the normal to the b axis. The pairs of offset π-π phenyl rings are also evident. Generated using OLEX2.

Compound 3 presents a multitude of non-classical hydrogen-bonding inter­actions, of the C—H⋯Ocarbon­yl and the C—H⋯Npyrid­yl type (Table 4[link], Fig. 8[link]). The carbonyl O9 is linked by a bifurcated inter­action to C3-H and C5-H [D⋯A = 3.2566 (15) and 3.4270 (16) Å, respectively]. There is another bifurcated hydrogen-bond inter­action between the pyridine N1 and C11 and C12 [D⋯A = 3.3535 (17) and 3.4182 (16) Å, respectively], linking the mol­ecules head to tail. The meth­oxy groups form C17-H⋯O16 inter­actions [D⋯A = 3.4475 (17) Å], comprising a supra­molecular synthon linking two mol­ecules together. The meth­oxy oxygen O16 is further linked by a phenyl C14-H⋯O16 inter­action [D⋯A = 3.3340 (15) Å].

Table 4
Hydrogen-bond geometry (Å, °) for 3[link]

D—H⋯A D—H H⋯A D⋯A D—H⋯A
C3—H3⋯O9i 0.95 2.65 3.2566 (15) 122
C5—H5⋯O9ii 0.95 2.49 3.4270 (16) 170
C11—H11⋯N1iii 0.95 2.69 3.3535 (17) 128
C12—H12⋯N1iii 0.95 2.84 3.4182 (16) 120
C14—H14⋯O16iv 0.95 2.67 3.3340 (15) 127
C17—H17A⋯O16v 0.98 2.63 3.4475 (17) 141
Symmetry codes: (i) [-x+1, y-{\script{1\over 2}}, -z+{\script{3\over 2}}]; (ii) [x, y-1, z]; (iii) [x, -y+{\script{3\over 2}}, z-{\script{1\over 2}}]; (iv) [-x, y-{\script{1\over 2}}, -z+{\script{1\over 2}}]; (v) [-x, -y+1, -z].
[Figure 8]
Figure 8
Hydrogen-bonding networks represented by dotted lines shown in a excerpt of the packing structure of 3 viewed normal to the b axis. Generated using OLEX2.

π–π stacking is evident in both 1 and 2. Weak dimeric offset π–π stacking is observed in 1 with columns of anti-parallel non-inter­acting mol­ecules when viewed normal to (001) (Fig. 6[link]). The closest centroid–centroid distance in 1 (C10–C15 to C10i–C15i and N1–C6 to N1i–C6i [symmetry transformation: (i) x, y, −1 + z; x, y, 1 + z] is 3.850 (3) Å with a slippages of 1.823 and 1.856 Å, respectively, and angles between planes of 0.0 (2)°. In 2, π-stacking occurs only through phenyl ring pairs with the closest centroid–centroid distance being 3.8783 (11) Å, a slippage of 1.575 Å, and an angle between planes of 0.03 (9)°, as seen normal to the (011) plane. In 3 there is no relevant π–π stacking, with the closest centroid–centroid distance being 4.0847 (7) Å, with a slippage of 2.042 Å and an angle between the planes of 5.14 (6)°.

4. Database survey

A search in the Cambridge Structural Database (CSD, Version 5.43, update November 2022; Groom et al., 2016[Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171-179.]) shows that no pyridine-substituted benzo­thio­ester structures are in the database. The unsubstituted S-phenyl benzo­thio­ate (CEFMOR; Belay et al., 2012[Belay, Y. H., Kinfe, H. H. & Muller, A. (2012). Acta Cryst. E68, o2825.]) is similar structurally to 1 with only slight ring-twisting differences. However, the packing is quite different with only weak dimeric offset π–π stacking present in 1, with columns of anti-parallel non-inter­acting mol­ecules when viewed normal to (001). The distinct C—H⋯N inter­actions seen particularly in 3 do not exist in the phenyl homologue.

Several other phenyl benzo­thiol­ates, however, are in the database, including, (−)-S-phenyl 2-benzoyl­benzo­thio­ate (HOBREV; Takahashi et al., 1998a[Takahashi, M., Sekine, N., Fujita, T., Watanabe, S., Yamaguchi, K. & Sakamoto, M. (1998a). J. Am. Chem. Soc. 120, 12770-12776.]), (±)-S-phenyl 2-(p-tolyl­carbon­yl)benzo­thio­ate (HOBRUL; Takahashi et al., 1998a[Takahashi, M., Sekine, N., Fujita, T., Watanabe, S., Yamaguchi, K. & Sakamoto, M. (1998a). J. Am. Chem. Soc. 120, 12770-12776.]), (±)-S-phenyl 2-(p-chloro­phenyl­carbon­yl)benzo­thio­ate (HOBSAS; Takahashi et al., 1998a[Takahashi, M., Sekine, N., Fujita, T., Watanabe, S., Yamaguchi, K. & Sakamoto, M. (1998a). J. Am. Chem. Soc. 120, 12770-12776.]), S-phenyl-p-cyano­thio­benzoate (MEBDED; Ivanova et al., 2006[Ivanova, B. B., Arnaudov, M. G., Sheldrick, W. S. & Mayer-Figge, H. (2006). Acta Cryst. E62, o3-o4.]), S,S-diphenyl 2-bromo­benzene-1,3-bis­(carbo­thio­ate) (MOFQUV; Kathe­wad et al., 2014[Kathewad, N. V., Pal, S. & Khan, S. (2014). Private Communication (refcode MOFQUV). CCDC, Cambridge, England.]), S-phenyl o-chloro­thio­benzoate (PEDHOV; Jovanovski et al., 1993[Jovanovski, G., Soptrajanov, B., Kaitner, B. & Prangova, L. (1993). J. Crystallogr. Spectrosc. Res. 23, 49-53.]) and S-phenyl o-bromo­thio­benzoate (PEDHUB; Jovanovski et al., 1993[Jovanovski, G., Soptrajanov, B., Kaitner, B. & Prangova, L. (1993). J. Crystallogr. Spectrosc. Res. 23, 49-53.]), S-phenyl 4-methyl-2-benzoyl­benzo­thio­ate (PUGXEU; Takahashi et al., 1998b[Takahashi, M., Fujita, T., Watanabe, S. & Sakamoto, M. (1998b). J. Chem. Soc. Perkin Trans. 2, pp. 487-492.]; PUGXEU01; Takahashi et al., 1998a[Takahashi, M., Sekine, N., Fujita, T., Watanabe, S., Yamaguchi, K. & Sakamoto, M. (1998a). J. Am. Chem. Soc. 120, 12770-12776.]), S1,S4-diphenyl 2,5-bis­(di­phenyl­amino)­benzene-1,4-dicarbo­thio­ate (XETHAI; Shimizu et al., 2016[Shimizu, M., Fukui, H., Natakani, M. & Sakaguchi, H. (2016). Eur. J. Org. Chem. 2016, 5950-5956.]) and S-phenyl 4-meth­oxy­benzene­carbo­thio­ate (YAWYEC; El-Azab et al., 2012[El-Azab, A. S., Abdel-Aziz, A. A.-M., El-Subbagh, H. I., Chantrapromma, S. & Fun, H.-K. (2012). Acta Cryst. E68, o1074-o1075.]; YAWYEC01; El-Azab & Abdel-Aziz, 2012[El-Azab, A. S. & Abdel-Aziz, A. A.-M. (2012). Phosphorus Sulfur Silicon, 187, 1046-1055.]).

5. Synthesis and crystallization

Compounds 1, 2, and 3 were synthesized following the reported procedure (Rao et al., 2000[Rao, P. D., Littler, B. J., Geier, G. R. III & Lindsey, J. S. (2000). J. Org. Chem. 65, 1084-1092.]). Briefly, the respective acyl chloride (1 eq., ca 0.2 M) in a solution of CH2Cl2 was added dropwise over 0.5 h to a stirring solution of 2-mercapto­pyridine (1 eq., ca 0.2 M) in CH2Cl2. The solution was left to stir for a further 2 h at room temperature. Throughout the addition processes, minor exotherms were noted, particularly for 1. The solution was diluted with the same volume again of CH2Cl2, and the solution was washed with NaOH (2 M), water, brine, and the organic layer then dried (MgSO4). Excess solvent was removed under reduced pressure and the title compounds were purified in the following ways: for 1, crystals were generated via hot recrystallization from ethyl acetate, and for 2 and 3, crystals were generated via precipitation from diethyl ether and hexa­nes. Compound 1 was yielded in 69%, with yields for 2 and 3 comparable to those previously reported (Rao et al., 2000[Rao, P. D., Littler, B. J., Geier, G. R. III & Lindsey, J. S. (2000). J. Org. Chem. 65, 1084-1092.]).

1H NMR spectroscopic data matched previously reported synthesized compounds 2 and 3. Whilst the synthesis of compound 1 has been reported previously, no characterization data has been reported for it (Perrin et al., 2011[Perrin, M. L., Prins, F., Martin, C. A., Shaikh, A. J., Eelkema, R., van Esch, J. H., Briza, T., Kaplanek, R., Kral, V., van Ruitenbeek, J. M., van der Zant, H. S. J. & Dulić, D. (2011). Angew. Chem. Int. Ed. 50, 11223-11226.]). Below we present analytical data for 1, and within the supporting information we have attached the appropriate spectra, Figs. S1–S3. We also present there the NMR spectra for 2 and 3, to exhibit the electronic differences between the three compounds studied herein (Fig. S4).

Analytical data for 1:

1H NMR (298 K, 400 MHz, CDCl3) δ = 8.66–8.68 (m, 1H), 8.31 (d, J = 8.9 Hz, 2H), 8.14 (d, J = 8.9 Hz, 2H), 7.77–7.81 (m, 1H), 7.68–7.70 (m, 1H), 7.33–7.37 (m, 1H); 13C{1H} NMR (298 K, 101 MHz, CDCl3): δ = 188.3, 150.9, 150.3, 141.3, 137.7, 130.9, 128.7, 124.3, 124.2 ppm; RF = 0.58 (silica, EtOAc:C6H14 1:1, UV); m.p. = 427–429 K. Multiple attempts have been made to obtain a mol­ecular ion peak via ESI–MS and all have been unsuccessful.

6. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 5[link]. Hydrogen atoms were positioned geometrically and refined isotropically using a riding model with C—H = 0.93–0.98 Å and Uiso(H) = 1.2–1.5Ueq(C).

Table 5
Experimental details

  1 2 3
Crystal data
Chemical formula C12H8N2O3S C13H11NOS C13H11NO2S
Mr 260.26 229.29 245.29
Crystal system, space group Orthorhombic, Pna21 Triclinic, P[\overline{1}] Monoclinic, P21/c
Temperature (K) 100 100 100
a, b, c (Å) 23.0774 (11), 12.5622 (5), 3.8498 (2) 7.1775 (2), 9.1492 (3), 9.2832 (3) 16.4043 (6), 5.4939 (2), 13.0741 (4)
α, β, γ (°) 90, 90, 90 101.2966 (14), 108.4632 (13), 92.5673 (14) 90, 103.1748 (14), 90
V (Å3) 1116.07 (9) 563.28 (3) 1147.27 (7)
Z 4 2 4
Radiation type Cu Kα Cu Kα Mo Kα
μ (mm−1) 2.62 2.35 0.27
Crystal size (mm) 0.37 × 0.05 × 0.04 0.39 × 0.22 × 0.09 0.34 × 0.19 × 0.06
 
Data collection
Diffractometer Bruker APEXII Kappa Duo Bruker APEXII Kappa Duo Bruker D8 Quest ECO
Absorption correction Multi-scan (SADABS; Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.]) Multi-scan (SADABS; Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.]) Multi-scan (SADABS; Krause et al., 2015[Krause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3-10.])
Tmin, Tmax 0.596, 0.753 0.641, 0.753 0.693, 0.746
No. of measured, independent and observed [I > 2σ(I)] reflections 8764, 1870, 1759 7937, 2106, 1958 19745, 3528, 2894
Rint 0.062 0.036 0.035
(sin θ/λ)max (Å−1) 0.609 0.610 0.716
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.043, 0.122, 1.04 0.042, 0.126, 1.12 0.036, 0.089, 1.03
No. of reflections 1870 2106 3528
No. of parameters 163 146 156
No. of restraints 1 0 0
H-atom treatment H-atom parameters constrained H-atom parameters constrained H-atom parameters constrained
Δρmax, Δρmin (e Å−3) 0.45, −0.26 0.33, −0.27 0.44, −0.34
Absolute structure Flack x determined using 584 quotients [(I+)−(I−)]/[(I+)+(I−)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.]) – –
Absolute structure parameter 0.02 (3) – –
Computer programs: APEX3 (Bruker, 2017[Bruker (2017). APEX3. Bruker AXS Inc., Madison, Wisconsin, USA.]), APEX4 (Bruker, 2021[Bruker (2021). APEX4. Bruker AXS Inc., Madison, Wisconsin, USA.]), SAINT (Bruker, 2016[Bruker (2016). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.]), SHELXT (Sheldrick, 2015a[Sheldrick, G. M. (2015a). Acta Cryst. A71, 3-8.]), SHELXL (Sheldrick, 2015b[Sheldrick, G. M. (2015b). Acta Cryst. C71, 3-8.]) and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Supporting information

CCDC references: 2239845; 2239844; 2239843

Crystal structure: contains datablocks 1, 2, 3, global. DOI: https://doi.org/10.1107/S2056989023001056/yz2028sup1.cif

Structure factors: contains datablock 1. DOI: https://doi.org/10.1107/S2056989023001056/yz20281sup2.hkl

Structure factors: contains datablock 2. DOI: https://doi.org/10.1107/S2056989023001056/yz20282sup3.hkl

Structure factors: contains datablock 3. DOI: https://doi.org/10.1107/S2056989023001056/yz20283sup4.hkl

Supporting information file. DOI: https://doi.org/10.1107/S2056989023001056/yz20281sup5.cml

Supporting information file. DOI: https://doi.org/10.1107/S2056989023001056/yz20282sup6.cml

Supporting information file. DOI: https://doi.org/10.1107/S2056989023001056/yz20283sup7.cml

1H, 13C, and 1H-13C-HSQC NMR spectra of compound 1, along with overlayed aromatic regions of the 1H NMR spectra of compounds 1, 2, and 3. DOI: https://doi.org/10.1107/S2056989023001056/yz2028sup8.pdf

checkCIF report


Computing details top

Data collection: APEX3 (Bruker, 2017) for (1), (3); APEX4 (Bruker, 2021) for (2). For all structures, cell refinement: SAINT (Bruker, 2016); data reduction: SAINT (Bruker, 2016); program(s) used to solve structure: SHELXT (Sheldrick, 2015a); program(s) used to refine structure: SHELXL (Sheldrick, 2015b); molecular graphics: Olex2 (Dolomanov et al., 2009); software used to prepare material for publication: Olex2 (Dolomanov et al., 2009).

S-(Pyridin-2-yl) 4-nitrobenzothioate (1) top
Crystal data top
C12H8N2O3SDx = 1.549 Mg m−3
Mr = 260.26Cu Kα radiation, λ = 1.54178 Å
Orthorhombic, Pna21Cell parameters from 5322 reflections
a = 23.0774 (11) Åθ = 3.8–69.3°
b = 12.5622 (5) ŵ = 2.62 mm−1
c = 3.8498 (2) ÅT = 100 K
V = 1116.07 (9) Å3Needle, clear colourless
Z = 40.37 × 0.05 × 0.04 mm
F(000) = 536
Data collection top
Bruker APEXII Kappa Duo
diffractometer		1870 independent reflections
Radiation source: microfocus sealed X-ray tube, Incoatec Iµs1759 reflections with I > 2σ(I)
Mirror optics monochromatorRint = 0.062
Detector resolution: 8.33 pixels mm-1θmax = 69.8°, θmin = 3.8°
ω and φ scansh = −27→28
Absorption correction: multi-scan
(SADABS; Krause et al., 2015)		k = −15→15
Tmin = 0.596, Tmax = 0.753l = −4→4
8764 measured reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.043 w = 1/[σ2(Fo2) + (0.0767P)2 + 0.6178P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.122(Δ/σ)max < 0.001
S = 1.03Δρmax = 0.45 e Å−3
1870 reflectionsΔρmin = −0.26 e Å−3
163 parametersAbsolute structure: Flack x determined using 584 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013)
1 restraintAbsolute structure parameter: 0.02 (3)
Primary atom site location: dual
Special details top

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) top
xyzUiso*/Ueq
C20.36818 (18)0.8352 (3)0.5521 (14)0.0304 (9)
H20.3309870.8252720.4514940.037*
C30.38137 (18)0.9340 (3)0.6888 (13)0.0306 (9)
H30.3543980.9909810.6748490.037*
C40.43473 (19)0.9481 (3)0.8464 (12)0.0282 (9)
H40.4447981.0148040.9459570.034*
C50.47344 (17)0.8632 (3)0.8569 (12)0.0259 (8)
H50.5102750.8698930.9648310.031*
C60.45619 (15)0.7686 (3)0.7039 (12)0.0240 (8)
C80.56755 (16)0.7014 (3)0.5347 (11)0.0250 (9)
C100.61366 (16)0.6184 (3)0.4955 (11)0.0228 (8)
C110.60607 (17)0.5140 (3)0.6121 (11)0.0238 (8)
H110.5713830.4943570.7285170.029*
C120.64936 (16)0.4390 (3)0.5575 (12)0.0250 (8)
H120.6447360.3675670.6339140.030*
C130.69883 (17)0.4706 (3)0.3907 (12)0.0249 (8)
C140.70817 (17)0.5742 (3)0.2745 (11)0.0251 (9)
H140.7432000.5934410.1611290.030*
C150.66456 (17)0.6483 (3)0.3299 (11)0.0244 (9)
H150.6695370.7197210.2543260.029*
N10.40512 (14)0.7521 (2)0.5536 (10)0.0265 (7)
N160.74430 (14)0.3901 (2)0.3212 (10)0.0278 (8)
O90.57457 (12)0.79289 (18)0.4455 (9)0.0293 (7)
O170.73740 (13)0.3009 (2)0.4467 (10)0.0379 (8)
O180.78579 (13)0.4153 (2)0.1448 (12)0.0449 (10)
S10.50105 (4)0.65266 (6)0.7155 (4)0.0241 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C20.0261 (19)0.0317 (19)0.033 (2)0.0016 (15)0.0009 (19)0.0019 (19)
C30.036 (2)0.0242 (17)0.031 (2)0.0077 (14)0.0060 (19)0.003 (2)
C40.038 (2)0.0191 (16)0.028 (2)0.0014 (15)0.0044 (17)−0.0004 (16)
C50.030 (2)0.0210 (16)0.027 (2)−0.0019 (14)0.0007 (17)0.0000 (16)
C60.0271 (17)0.0168 (15)0.028 (2)−0.0001 (13)0.0030 (17)0.0025 (17)
C80.0270 (18)0.0194 (17)0.029 (2)−0.0038 (13)−0.0023 (17)0.0008 (16)
C100.0294 (19)0.0161 (15)0.023 (2)−0.0021 (13)−0.0042 (15)0.0006 (15)
C110.0268 (18)0.0187 (15)0.026 (2)−0.0035 (13)−0.0012 (15)0.0011 (15)
C120.0303 (19)0.0154 (15)0.029 (2)−0.0033 (13)−0.0041 (18)0.0031 (15)
C130.0268 (19)0.0189 (16)0.029 (2)0.0020 (13)−0.0041 (16)0.0007 (16)
C140.0259 (18)0.0209 (16)0.029 (2)−0.0060 (13)−0.0003 (16)−0.0007 (16)
C150.0285 (19)0.0171 (16)0.028 (2)−0.0024 (13)−0.0045 (16)0.0015 (15)
N10.0308 (16)0.0216 (14)0.0270 (19)−0.0026 (12)0.0015 (15)0.0007 (15)
N160.0279 (17)0.0229 (15)0.033 (2)0.0003 (13)−0.0030 (14)−0.0024 (15)
O90.0343 (15)0.0164 (12)0.0371 (18)−0.0024 (10)0.0016 (12)0.0055 (13)
O170.0376 (16)0.0192 (13)0.057 (2)0.0038 (10)−0.0016 (15)0.0071 (14)
O180.0337 (16)0.0310 (14)0.070 (3)0.0042 (12)0.0145 (17)0.0034 (17)
S10.0266 (5)0.0147 (4)0.0310 (5)−0.0017 (3)0.0025 (3)0.0006 (4)
Geometric parameters (Å, º) top
C2—H20.9500C10—C111.397 (5)
C2—C31.382 (6)C10—C151.388 (6)
C2—N11.348 (5)C11—H110.9500
C3—H30.9500C11—C121.389 (5)
C3—C41.384 (6)C12—H120.9500
C4—H40.9500C12—C131.369 (6)
C4—C51.392 (5)C13—C141.393 (5)
C5—H50.9500C13—N161.482 (5)
C5—C61.385 (5)C14—H140.9500
C6—N11.329 (5)C14—C151.388 (5)
C6—S11.787 (3)C15—H150.9500
C8—C101.497 (5)N16—O171.231 (4)
C8—O91.210 (4)N16—O181.215 (5)
C8—S11.793 (4)
C3—C2—H2118.1C10—C11—H11120.1
N1—C2—H2118.1C12—C11—C10119.9 (4)
N1—C2—C3123.7 (4)C12—C11—H11120.1
C2—C3—H3120.7C11—C12—H12120.9
C2—C3—C4118.5 (3)C13—C12—C11118.3 (3)
C4—C3—H3120.7C13—C12—H12120.9
C3—C4—H4120.5C12—C13—C14123.4 (3)
C3—C4—C5119.0 (4)C12—C13—N16118.5 (3)
C5—C4—H4120.5C14—C13—N16118.0 (4)
C4—C5—H5121.3C13—C14—H14121.1
C6—C5—C4117.5 (4)C15—C14—C13117.7 (4)
C6—C5—H5121.3C15—C14—H14121.1
C5—C6—S1121.5 (3)C10—C15—H15119.9
N1—C6—C5125.0 (3)C14—C15—C10120.2 (3)
N1—C6—S1113.4 (3)C14—C15—H15119.9
C10—C8—S1114.2 (3)C6—N1—C2116.2 (3)
O9—C8—C10122.5 (4)O17—N16—C13117.3 (3)
O9—C8—S1123.3 (3)O18—N16—C13118.8 (3)
C11—C10—C8122.2 (3)O18—N16—O17123.9 (3)
C15—C10—C8117.3 (3)C6—S1—C8102.01 (17)
C15—C10—C11120.5 (3)
C2—C3—C4—C51.0 (7)C12—C13—N16—O17−6.7 (6)
C3—C2—N1—C61.5 (7)C12—C13—N16—O18173.1 (4)
C3—C4—C5—C60.6 (7)C13—C14—C15—C10−0.1 (6)
C4—C5—C6—N1−1.3 (7)C14—C13—N16—O17174.9 (4)
C4—C5—C6—S1−177.6 (3)C14—C13—N16—O18−5.3 (6)
C5—C6—N1—C20.3 (7)C15—C10—C11—C12−1.0 (6)
C5—C6—S1—C8−54.6 (4)N1—C2—C3—C4−2.1 (8)
C8—C10—C11—C12177.5 (4)N1—C6—S1—C8128.6 (3)
C8—C10—C15—C14−177.7 (4)N16—C13—C14—C15177.8 (4)
C10—C8—S1—C6−177.2 (3)O9—C8—C10—C11177.3 (4)
C10—C11—C12—C130.4 (6)O9—C8—C10—C15−4.1 (6)
C11—C10—C15—C140.9 (6)O9—C8—S1—C61.5 (4)
C11—C12—C13—C140.3 (6)S1—C6—N1—C2176.9 (3)
C11—C12—C13—N16−178.0 (4)S1—C8—C10—C11−4.0 (5)
C12—C13—C14—C15−0.5 (6)S1—C8—C10—C15174.6 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C3—H3···O18i0.952.683.396 (5)133
C4—H4···O9ii0.952.463.283 (4)145
C5—H5···O9iii0.952.563.371 (5)143
C12—H12···N1iv0.952.493.315 (5)145
C14—H14···O17v0.952.773.359 (4)121
C15—H15···O17v0.952.663.312 (5)127
Symmetry codes: (i) x−1/2, −y+3/2, z+1; (ii) −x+1, −y+2, z+1/2; (iii) x, y, z+1; (iv) −x+1, −y+1, z+1/2; (v) −x+3/2, y+1/2, z−1/2.
S-(Pyridin-2-yl) 4-methylbenzothioate (2) top
Crystal data top
C13H11NOSZ = 2
Mr = 229.29F(000) = 240
Triclinic, P1Dx = 1.352 Mg m−3
a = 7.1775 (2) ÅCu Kα radiation, λ = 1.54178 Å
b = 9.1492 (3) ÅCell parameters from 5814 reflections
c = 9.2832 (3) Åθ = 5.0–70.1°
α = 101.2966 (14)°µ = 2.35 mm−1
β = 108.4632 (13)°T = 100 K
γ = 92.5673 (14)°Plate, clear colourless
V = 563.28 (3) Å30.39 × 0.22 × 0.09 mm
Data collection top
Bruker APEXII Kappa Duo
diffractometer		2106 independent reflections
Radiation source: microfocus sealed X-ray tube, Incoatec Iµs1958 reflections with I > 2σ(I)
Mirror optics monochromatorRint = 0.036
Detector resolution: 8.33 pixels mm-1θmax = 70.0°, θmin = 5.0°
ω and φ scansh = −8→8
Absorption correction: multi-scan
(SADABS; Krause et al., 2015)		k = −10→10
Tmin = 0.641, Tmax = 0.753l = −11→11
7937 measured reflections
Refinement top
Refinement on F2Primary atom site location: dual
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.042H-atom parameters constrained
wR(F2) = 0.126 w = 1/[σ2(Fo2) + (0.0776P)2 + 0.2152P]
where P = (Fo2 + 2Fc2)/3
S = 1.12(Δ/σ)max = 0.001
2106 reflectionsΔρmax = 0.33 e Å−3
146 parametersΔρmin = −0.27 e Å−3
0 restraints
Special details top

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) top
xyzUiso*/Ueq
S10.49730 (6)0.81629 (5)0.54572 (5)0.02575 (19)
N10.1173 (2)0.85006 (17)0.44707 (17)0.0239 (3)
C2−0.0761 (3)0.8008 (2)0.3793 (2)0.0250 (4)
H2−0.1678300.8729790.3685080.030*
C3−0.1488 (3)0.6502 (2)0.3242 (2)0.0245 (4)
H3−0.2869990.6204000.2781630.029*
C4−0.0162 (3)0.5439 (2)0.3376 (2)0.0241 (4)
H4−0.0615280.4399220.3004990.029*
C50.1838 (3)0.5928 (2)0.4062 (2)0.0237 (4)
H50.2790470.5232310.4161270.028*
C60.2416 (3)0.7455 (2)0.4599 (2)0.0219 (4)
C80.5659 (3)0.73280 (19)0.7124 (2)0.0216 (4)
O90.44856 (19)0.65460 (16)0.74143 (15)0.0294 (3)
C100.7791 (3)0.76691 (19)0.8087 (2)0.0218 (4)
C110.8476 (3)0.6978 (2)0.9337 (2)0.0241 (4)
H110.7578640.6346540.9573470.029*
C121.0455 (3)0.7206 (2)1.0234 (2)0.0250 (4)
H121.0902770.6728791.1083580.030*
C131.1805 (3)0.8126 (2)0.9914 (2)0.0247 (4)
C141.1111 (3)0.8823 (2)0.8667 (2)0.0255 (4)
H141.2011350.9455600.8434970.031*
C150.9125 (3)0.8605 (2)0.7760 (2)0.0229 (4)
H150.8674120.9092360.6918950.028*
C161.3959 (3)0.8344 (2)1.0883 (2)0.0313 (5)
H16A1.4339010.9394931.1444310.047*
H16B1.4753380.8083561.0204160.047*
H16C1.4187400.7696231.1632470.047*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
S10.0200 (3)0.0285 (3)0.0265 (3)−0.00191 (19)0.00180 (19)0.0118 (2)
N10.0244 (8)0.0223 (8)0.0238 (7)0.0017 (6)0.0060 (6)0.0056 (6)
C20.0217 (9)0.0264 (10)0.0276 (9)0.0063 (7)0.0068 (7)0.0090 (7)
C30.0213 (9)0.0292 (10)0.0229 (9)0.0014 (7)0.0065 (7)0.0074 (7)
C40.0274 (9)0.0224 (9)0.0199 (8)−0.0008 (7)0.0051 (7)0.0042 (7)
C50.0245 (9)0.0239 (9)0.0217 (8)0.0056 (7)0.0058 (7)0.0053 (7)
C60.0212 (8)0.0241 (9)0.0197 (8)0.0018 (7)0.0051 (7)0.0063 (7)
C80.0221 (9)0.0200 (9)0.0212 (8)0.0014 (7)0.0062 (7)0.0027 (7)
O90.0229 (7)0.0362 (8)0.0285 (7)−0.0035 (6)0.0055 (5)0.0122 (6)
C100.0217 (9)0.0201 (9)0.0216 (8)0.0020 (7)0.0061 (7)0.0019 (7)
C110.0252 (9)0.0238 (9)0.0237 (9)0.0019 (7)0.0088 (7)0.0056 (7)
C120.0259 (9)0.0269 (10)0.0217 (9)0.0051 (7)0.0060 (7)0.0070 (7)
C130.0228 (9)0.0259 (9)0.0219 (8)0.0021 (7)0.0052 (7)0.0010 (7)
C140.0233 (9)0.0248 (9)0.0265 (9)−0.0021 (7)0.0067 (7)0.0045 (7)
C150.0226 (9)0.0216 (9)0.0224 (9)0.0011 (7)0.0043 (7)0.0051 (7)
C160.0231 (10)0.0379 (11)0.0284 (10)0.0018 (8)0.0029 (8)0.0068 (8)
Geometric parameters (Å, º) top
S1—C61.7853 (18)C10—C111.394 (3)
S1—C81.7981 (18)C10—C151.398 (3)
N1—C21.344 (2)C11—H110.9500
N1—C61.333 (2)C11—C121.383 (3)
C2—H20.9500C12—H120.9500
C2—C31.387 (3)C12—C131.394 (3)
C3—H30.9500C13—C141.395 (3)
C3—C41.386 (3)C13—C161.503 (2)
C4—H40.9500C14—H140.9500
C4—C51.385 (3)C14—C151.389 (2)
C5—H50.9500C15—H150.9500
C5—C61.385 (3)C16—H16A0.9800
C8—O91.208 (2)C16—H16B0.9800
C8—C101.490 (2)C16—H16C0.9800
C6—S1—C8100.57 (8)C15—C10—C8122.97 (16)
C6—N1—C2116.56 (16)C10—C11—H11119.8
N1—C2—H2118.3C12—C11—C10120.32 (17)
N1—C2—C3123.44 (16)C12—C11—H11119.8
C3—C2—H2118.3C11—C12—H12119.5
C2—C3—H3120.6C11—C12—C13121.07 (17)
C4—C3—C2118.82 (16)C13—C12—H12119.5
C4—C3—H3120.6C12—C13—C14118.44 (17)
C3—C4—H4120.8C12—C13—C16120.50 (17)
C5—C4—C3118.49 (17)C14—C13—C16121.06 (17)
C5—C4—H4120.8C13—C14—H14119.5
C4—C5—H5120.8C15—C14—C13121.01 (17)
C6—C5—C4118.36 (16)C15—C14—H14119.5
C6—C5—H5120.8C10—C15—H15120.0
N1—C6—S1114.99 (14)C14—C15—C10119.94 (16)
N1—C6—C5124.31 (16)C14—C15—H15120.0
C5—C6—S1120.64 (14)C13—C16—H16A109.5
O9—C8—S1122.42 (14)C13—C16—H16B109.5
O9—C8—C10123.49 (16)C13—C16—H16C109.5
C10—C8—S1114.09 (12)H16A—C16—H16B109.5
C11—C10—C8117.77 (16)H16A—C16—H16C109.5
C11—C10—C15119.22 (16)H16B—C16—H16C109.5
S1—C8—C10—C11−175.48 (13)C8—S1—C6—C5−62.55 (16)
S1—C8—C10—C152.5 (2)C8—C10—C11—C12177.48 (16)
N1—C2—C3—C4−0.8 (3)C8—C10—C15—C14−177.17 (16)
C2—N1—C6—S1178.32 (12)O9—C8—C10—C113.7 (3)
C2—N1—C6—C51.1 (3)O9—C8—C10—C15−178.40 (17)
C2—C3—C4—C50.3 (3)C10—C11—C12—C130.0 (3)
C3—C4—C5—C60.8 (3)C11—C10—C15—C140.7 (3)
C4—C5—C6—S1−178.64 (13)C11—C12—C13—C140.4 (3)
C4—C5—C6—N1−1.6 (3)C11—C12—C13—C16−178.99 (17)
C6—S1—C8—O9−1.13 (17)C12—C13—C14—C15−0.2 (3)
C6—S1—C8—C10178.01 (12)C13—C14—C15—C10−0.4 (3)
C6—N1—C2—C30.1 (3)C15—C10—C11—C12−0.5 (3)
C8—S1—C6—N1120.11 (14)C16—C13—C14—C15179.19 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C2—H2···N1i0.952.703.355 (2)126
C3—H3···O9ii0.952.673.278 (2)122
C4—H4···O9ii0.952.753.316 (2)119
C16—H16B···O9iii0.982.643.460 (2)142
Symmetry codes: (i) −x, −y+2, −z+1; (ii) −x, −y+1, −z+1; (iii) x+1, y, z.
S-(Pyridin-2-yl) 4-methoxybenzothioate (3) top
Crystal data top
C13H11NO2SF(000) = 512
Mr = 245.29Dx = 1.420 Mg m−3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
a = 16.4043 (6) ÅCell parameters from 9968 reflections
b = 5.4939 (2) Åθ = 2.6–30.6°
c = 13.0741 (4) ŵ = 0.27 mm−1
β = 103.1748 (14)°T = 100 K
V = 1147.27 (7) Å3Plate, clear colourless
Z = 40.34 × 0.19 × 0.06 mm
Data collection top
Bruker D8 Quest ECO
diffractometer		3528 independent reflections
Radiation source: sealed X-ray tube, Siemens, KFF Mo 2K -90 C2894 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.035
Detector resolution: 5.12 pixels mm-1θmax = 30.6°, θmin = 2.6°
ω and φ scansh = −23→23
Absorption correction: multi-scan
(SADABS; Krause et al., 2015)		k = −7→7
Tmin = 0.693, Tmax = 0.746l = −18→18
19745 measured reflections
Refinement top
Refinement on F2Hydrogen site location: inferred from neighbouring sites
Least-squares matrix: fullH-atom parameters constrained
R[F2 > 2σ(F2)] = 0.036 w = 1/[σ2(Fo2) + (0.034P)2 + 0.7686P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.089(Δ/σ)max = 0.001
S = 1.03Δρmax = 0.44 e Å−3
3528 reflectionsΔρmin = −0.34 e Å−3
156 parametersExtinction correction: SHELXL (Sheldrick 2015b), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
0 restraintsExtinction coefficient: 0.0056 (14)
Primary atom site location: dual
Special details top

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) top
xyzUiso*/Ueq
N10.33724 (7)0.3844 (2)0.78131 (9)0.0186 (2)
C20.40114 (8)0.3820 (2)0.86600 (10)0.0191 (2)
H20.4052750.5119080.9148840.023*
C30.46148 (8)0.2013 (2)0.88640 (9)0.0175 (2)
H30.5058340.2083570.9474090.021*
C40.45592 (8)0.0107 (2)0.81631 (10)0.0186 (2)
H40.496434−0.1159160.8282120.022*
C50.38991 (8)0.0072 (2)0.72793 (10)0.0177 (2)
H50.383763−0.1220070.6784760.021*
C60.33342 (7)0.1989 (2)0.71454 (9)0.0155 (2)
S10.24650 (2)0.19535 (6)0.60431 (2)0.02004 (9)
C80.27774 (7)0.4257 (2)0.52399 (9)0.0141 (2)
O90.34259 (6)0.53792 (18)0.55168 (7)0.0197 (2)
C100.21680 (7)0.4661 (2)0.42271 (9)0.0136 (2)
C110.22903 (7)0.6656 (2)0.36245 (9)0.0158 (2)
H110.2743630.7731190.3885220.019*
C120.17643 (8)0.7112 (2)0.26502 (9)0.0166 (2)
H120.1851780.8490520.2249870.020*
C130.11069 (7)0.5514 (2)0.22707 (9)0.0147 (2)
C140.09620 (7)0.3538 (2)0.28750 (10)0.0173 (2)
H140.0501310.2485090.2619570.021*
C150.14888 (7)0.3111 (2)0.38464 (9)0.0162 (2)
H150.1389560.1761790.4256190.019*
O160.05718 (5)0.57034 (18)0.13098 (7)0.01853 (19)
C170.07223 (9)0.7626 (3)0.06401 (11)0.0237 (3)
H17A0.0317330.752011−0.0037030.036*
H17B0.1291160.7479070.0528820.036*
H17C0.0661630.9198060.0969290.036*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0185 (5)0.0166 (5)0.0193 (5)0.0021 (4)0.0014 (4)−0.0013 (4)
C20.0205 (6)0.0179 (6)0.0174 (5)0.0009 (5)0.0012 (4)−0.0041 (5)
C30.0163 (5)0.0195 (6)0.0149 (5)−0.0002 (5)−0.0002 (4)0.0020 (5)
C40.0174 (5)0.0164 (6)0.0214 (6)0.0027 (4)0.0030 (4)0.0025 (5)
C50.0200 (6)0.0157 (5)0.0172 (5)−0.0008 (5)0.0038 (4)−0.0015 (4)
C60.0151 (5)0.0162 (5)0.0140 (5)−0.0023 (4)0.0011 (4)0.0020 (4)
S10.01791 (15)0.02262 (17)0.01665 (15)−0.00707 (12)−0.00218 (10)0.00527 (12)
C80.0151 (5)0.0139 (5)0.0134 (5)0.0000 (4)0.0035 (4)−0.0013 (4)
O90.0170 (4)0.0229 (5)0.0179 (4)−0.0067 (4)0.0011 (3)−0.0003 (4)
C100.0133 (5)0.0140 (5)0.0134 (5)−0.0004 (4)0.0030 (4)−0.0009 (4)
C110.0158 (5)0.0156 (5)0.0155 (5)−0.0033 (4)0.0024 (4)−0.0016 (4)
C120.0192 (5)0.0141 (5)0.0162 (5)−0.0011 (4)0.0033 (4)0.0015 (4)
C130.0126 (5)0.0173 (6)0.0139 (5)0.0026 (4)0.0023 (4)−0.0010 (4)
C140.0136 (5)0.0205 (6)0.0168 (5)−0.0040 (4)0.0017 (4)−0.0005 (4)
C150.0159 (5)0.0172 (5)0.0151 (5)−0.0038 (4)0.0027 (4)0.0009 (4)
O160.0159 (4)0.0233 (5)0.0147 (4)0.0006 (3)−0.0002 (3)0.0026 (3)
C170.0278 (7)0.0222 (6)0.0180 (6)0.0029 (5)−0.0013 (5)0.0048 (5)
Geometric parameters (Å, º) top
N1—C21.3401 (16)C10—C151.4007 (16)
N1—C61.3342 (16)C11—H110.9500
C2—H20.9500C11—C121.3888 (16)
C2—C31.3841 (18)C12—H120.9500
C3—H30.9500C12—C131.3914 (17)
C3—C41.3810 (18)C13—C141.3943 (17)
C4—H40.9500C13—O161.3627 (14)
C4—C51.3920 (17)C14—H140.9500
C5—H50.9500C14—C151.3837 (16)
C5—C61.3873 (17)C15—H150.9500
C6—S11.7815 (12)O16—C171.4289 (16)
S1—C81.7924 (12)C17—H17A0.9800
C8—O91.2112 (14)C17—H17B0.9800
C8—C101.4828 (16)C17—H17C0.9800
C10—C111.3908 (17)
C6—N1—C2116.38 (11)C10—C11—H11119.3
N1—C2—H2118.1C12—C11—C10121.46 (11)
N1—C2—C3123.83 (12)C12—C11—H11119.3
C3—C2—H2118.1C11—C12—H12120.6
C2—C3—H3120.7C11—C12—C13118.84 (11)
C4—C3—C2118.68 (11)C13—C12—H12120.6
C4—C3—H3120.7C12—C13—C14120.49 (11)
C3—C4—H4120.6O16—C13—C12124.37 (11)
C3—C4—C5118.84 (12)O16—C13—C14115.14 (11)
C5—C4—H4120.6C13—C14—H14120.0
C4—C5—H5121.1C15—C14—C13120.05 (11)
C6—C5—C4117.73 (12)C15—C14—H14120.0
C6—C5—H5121.1C10—C15—H15119.9
N1—C6—C5124.54 (11)C14—C15—C10120.18 (11)
N1—C6—S1116.57 (9)C14—C15—H15119.9
C5—C6—S1118.83 (9)C13—O16—C17117.16 (10)
C6—S1—C8100.56 (6)O16—C17—H17A109.5
O9—C8—S1122.22 (9)O16—C17—H17B109.5
O9—C8—C10123.94 (11)O16—C17—H17C109.5
C10—C8—S1113.84 (8)H17A—C17—H17B109.5
C11—C10—C8117.96 (10)H17A—C17—H17C109.5
C11—C10—C15118.93 (11)H17B—C17—H17C109.5
C15—C10—C8123.10 (11)
N1—C2—C3—C4−0.4 (2)C8—C10—C11—C12177.74 (11)
N1—C6—S1—C875.84 (10)C8—C10—C15—C14−177.44 (12)
C2—N1—C6—C50.65 (19)O9—C8—C10—C11−9.07 (18)
C2—N1—C6—S1177.79 (10)O9—C8—C10—C15169.83 (12)
C2—C3—C4—C5−0.04 (19)C10—C11—C12—C13−0.62 (18)
C3—C4—C5—C60.72 (19)C11—C10—C15—C141.45 (18)
C4—C5—C6—N1−1.07 (19)C11—C12—C13—C142.22 (18)
C4—C5—C6—S1−178.15 (9)C11—C12—C13—O16−177.02 (11)
C5—C6—S1—C8−106.85 (11)C12—C13—C14—C15−1.98 (19)
C6—N1—C2—C30.1 (2)C12—C13—O16—C172.44 (17)
C6—S1—C8—O9−1.13 (12)C13—C14—C15—C100.12 (19)
C6—S1—C8—C10179.52 (9)C14—C13—O16—C17−176.83 (11)
S1—C8—C10—C11170.26 (9)C15—C10—C11—C12−1.20 (18)
S1—C8—C10—C15−10.84 (15)O16—C13—C14—C15177.32 (11)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
C3—H3···O9i0.952.653.2566 (15)122
C5—H5···O9ii0.952.493.4270 (16)170
C11—H11···N1iii0.952.693.3535 (17)128
C12—H12···N1iii0.952.843.4182 (16)120
C14—H14···O16iv0.952.673.3340 (15)127
C17—H17A···O16v0.982.633.4475 (17)141
Symmetry codes: (i) −x+1, y−1/2, −z+3/2; (ii) x, y−1, z; (iii) x, −y+3/2, z−1/2; (iv) −x, y−1/2, −z+1/2; (v) −x, −y+1, −z.
Comparison of structural parameters (°) top
Plane|planeTorsion angle C8—S1—C6—N1Phenyl plane|plane C8—O9—S1—C6
156.97 (14)128.6 (3)6.00 (14)
257.51 (6)120.11 (14)5.08 (6)
365.94 (4)75.84 (10)10.28 (4)
CEFMOR51.12 (1)122.79 (1)10.88 (2)
In CEFMOR, the torsion angle is defined by C1—S1—C8—C13.
 

Funding information

Funding for this research was provided by: Science Foundation Ireland (grant No. 21/FFP-A/9469 to MOS).

References

First citationAdler, D. A., Longo, F. R., Finarelli, J. D., Goldmacher, J., Assour, J. & Korsakoff, L. (1967). J. Org. Chem. 32, 476–476.  CrossRef CAS Web of Science Google Scholar
 First citationAlbert, A. & Barlin, G. B. (1959). J. Chem. Soc. pp. 2384–2396.  CrossRef Web of Science Google Scholar
 First citationAraki, M., Sakata, S., Takei, H. & Mukaiyama, T. (1974). Bull. Chem. Soc. Jpn, 47, 1777–1780.  CrossRef CAS Web of Science Google Scholar
 First citationBelay, Y. H., Kinfe, H. H. & Muller, A. (2012). Acta Cryst. E68, o2825.  CSD CrossRef IUCr Journals Google Scholar
 First citationBruker (2016). SAINT. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationBruker (2017). APEX3. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationBruker (2021). APEX4. Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
 First citationDolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339–341.  Web of Science CrossRef CAS IUCr Journals Google Scholar
 First citationEl-Azab, A. S. & Abdel-Aziz, A. A.-M. (2012). Phosphorus Sulfur Silicon, 187, 1046–1055.  CAS Google Scholar
 First citationEl-Azab, A. S., Abdel-Aziz, A. A.-M., El-Subbagh, H. I., Chantrapromma, S. & Fun, H.-K. (2012). Acta Cryst. E68, o1074–o1075.  CSD CrossRef IUCr Journals Google Scholar
 First citationGroom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179.  Web of Science CrossRef IUCr Journals Google Scholar
 First citationHiroto, S., Miyake, Y. & Shinokubo, H. (2017). Chem. Rev. 117, 2910–3043.  Web of Science CrossRef CAS PubMed Google Scholar
 First citationIvanova, B. B., Arnaudov, M. G., Sheldrick, W. S. & Mayer-Figge, H. (2006). Acta Cryst. E62, o3–o4.  Web of Science CSD CrossRef IUCr Journals Google Scholar
 First citationJovanovski, G., Soptrajanov, B., Kaitner, B. & Prangova, L. (1993). J. Crystallogr. Spectrosc. Res. 23, 49–53.  CSD CrossRef CAS Web of Science Google Scholar
 First citationKathewad, N. V., Pal, S. & Khan, S. (2014). Private Communication (refcode MOFQUV). CCDC, Cambridge, England.  Google Scholar
 First citationKrause, L., Herbst-Irmer, R., Sheldrick, G. M. & Stalke, D. (2015). J. Appl. Cryst. 48, 3–10.  Web of Science CSD CrossRef ICSD CAS IUCr Journals Google Scholar
 First citationLaakso, J., Rosser, G. A., Szíjjártó, C., Beeby, A. & Borbas, K. E. (2012). Inorg. Chem. 51, 10366–10374.  Web of Science CrossRef CAS PubMed Google Scholar
 First citationLee, C.-H., Li, F., Iwamoto, K., Dadok, J., Bothner-By, A. A. & Lindsey, J. S. (1995). Tetrahedron, 51, 11645–11672.  CrossRef CAS Web of Science Google Scholar
 First citationLee, J. (2020). Bull. Korean Chem. Soc. 41, 735–747.  Google Scholar
 First citationLindsey, J. S. (2010). Acc. Chem. Res. 43, 300–311.  Web of Science CrossRef PubMed CAS Google Scholar
 First citationLindsey, J. S., Hsu, H. C. & Schreiman, I. C. (1986). Tetrahedron Lett. 27, 4969–4970.  CrossRef CAS Web of Science Google Scholar
 First citationMcDaniel, D. H. & Brown, H. C. (1958). J. Org. Chem. 23, 420–427.  CrossRef CAS Web of Science Google Scholar
 First citationNicolaou, K. C., Claremon, D. A. & Papahatjis, D. P. (1981). Tetrahedron Lett. 22, 4647–4650.  CrossRef CAS Web of Science Google Scholar
 First citationParsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249–259.  Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
 First citationPerrin, M. L., Prins, F., Martin, C. A., Shaikh, A. J., Eelkema, R., van Esch, J. H., Briza, T., Kaplanek, R., Kral, V., van Ruitenbeek, J. M., van der Zant, H. S. J. & Dulić, D. (2011). Angew. Chem. Int. Ed. 50, 11223–11226.  Web of Science CrossRef CAS Google Scholar
 First citationRa, D., Gauger, K. A., Muthukumaran, K., Balasubramanian, T., Chandrashaker, V., Taniguchi, M., Yu, Z., Talley, D. C., Ehudin, M. Ptaszek, M. & Lindsey J. S. (2015). J. Porphyrins Phthalocyanines, 19, 547–572  Web of Science CSD CrossRef CAS Google Scholar
 First citationRao, P. D., Littler, B. J., Geier, G. R. III & Lindsey, J. S. (2000). J. Org. Chem. 65, 1084–1092.  Web of Science CrossRef PubMed CAS Google Scholar
 First citationSample, H. C. & Senge, M. O. (2021). Eur. J. Org. Chem. 2021, 7–42.  Web of Science CrossRef CAS Google Scholar
 First citationSenge, M. O. (2011). Chem. Commun. 47, 1943–1960.  Web of Science CrossRef CAS Google Scholar
 First citationSenge, M. O., Sergeeva, N. N. & Hale, K. J. (2021). Chem. Soc. Rev. 50, 4730–4789.  Web of Science CrossRef CAS PubMed Google Scholar
 First citationSheldrick, G. M. (2015a). Acta Cryst. A71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
 First citationSheldrick, G. M. (2015b). Acta Cryst. C71, 3–8.  Web of Science CrossRef IUCr Journals Google Scholar
 First citationShimizu, M., Fukui, H., Natakani, M. & Sakaguchi, H. (2016). Eur. J. Org. Chem. 2016, 5950–5956.  Web of Science CSD CrossRef CAS Google Scholar
 First citationTakahashi, M., Fujita, T., Watanabe, S. & Sakamoto, M. (1998b). J. Chem. Soc. Perkin Trans. 2, pp. 487–492.  Web of Science CSD CrossRef Google Scholar
 First citationTakahashi, M., Sekine, N., Fujita, T., Watanabe, S., Yamaguchi, K. & Sakamoto, M. (1998a). J. Am. Chem. Soc. 120, 12770–12776.  Web of Science CSD CrossRef CAS Google Scholar

This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 79| Part 3| March 2023| Pages 157-162
https://doi.org/10.1107/S2056989023001056
Follow Acta Cryst. E
Sign up for e-alerts
E-alerts
Follow Acta Cryst. on Twitter
Twitter
Follow us on facebook
Facebook
Sign up for RSS feeds
RSS