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Journal logoSTRUCTURAL
CHEMISTRY
ISSN: 2053-2296

Planarity of hetero­aryl­di­thio­carb­azic acid derivatives showing tuberculostatic activity. II. Crystal structures of 3-[amino­(pyrazin-2-yl)­methyl­­idene]-2-methyl­carbazic acid esters

aInstitute of General and Ecological Chemistry, Technical University of Łódź, Poland, and bDepartment of Organic Chemistry, Medical University of Gdańsk, Poland
*Correspondence e-mail: marekglo@p.lodz.pl

(Received 23 November 2010; accepted 29 November 2010; online 10 December 2010)

Four compounds showing moderate anti­tuberculostatic activity have been studied to test the hypothesis that the planarity of the 2-[amino­(pyrazin-2-yl)methylid­ene]­dithio­car­baz­ate fragment is crucial for activity. N′-Anilino­pyrazine-2-carbox­imid­amide, C11H11N5, D1[link], and diethyl 2,2′-[({[am­ino­(pyrazin-2-yl)methyl­idene]­hydrazinyl­idene}­methylidene)­bis­(sulfane­diyl)]­diacetate, C14H19N5O4S2, B1[link], maintain planarity due to conjugation and attractive intra­molecular hydrogen-bond contacts, while methyl 3-[amino­(pyrazin-2-yl)­methyl­idene]-2-methyldithio­­carbazate, C8H11N5S2, C1[link], and benzyl 3-[amino­(pyrazin-2-yl)­methyl­idene]-2-methyldithio­­carb­azate, C14H15N5S2, C2[link], are not planar, due to methyl­ation at one of the N atoms of the central N—N bond. The resulting twists of the two mol­ecular halves (parts) of C1[link] and C2[link] are indicated by torsion angles of 116.5 (2) and −135.9 (2)°, respectively, compared with values of about 180° in the crystal structures of nonsubstituted compounds. As the methyl­ated derivatives show similar activity against Mycobacterium tuberculosis to that of the nonsubstituted derivatives, maintaining planarity does not seem to be a prerequisite for activity.

Comment

The increasing resistance of Mycobacterium tuberculosis to existing agents and the resulting spread of the pathogen, in both developed and developing countries, makes the search for new tuberculostatics an important issue. 2-/3-/4-Pyridine­carbon­imidoyl­dithio­carbazic acid esters and N′-thio­amido-substituted pyrazine­carb­oxy­amidrazones, of which many compounds have been synthesized by Foks and Orlew­ska and tested against standard M. tuberculosis strains (Foks & Janowiec, 1979[Foks, H. & Janowiec, M. (1979). Acta Pol. Pharm. 36, 155-160.]; Foks et al., 1992[Foks, H., Orlewska, C. & Janowiec, M. (1992). Acta Pol. Pharm. Drug Res. 49, 47-50.], 2002[Foks, H., Mieczkowska, J., Janowiec, M., Zwolska, Z. & Andrzejczak, Z. (2002). Chem. Heterocycl. Compd, 38, 810-816.], 2004[Foks, H., Trapkowska, I., Janowiec, M., Zwolska, Z. & Augustynowicz-Kopeć, E. (2004). Chem. Heterocycl. Compd, 40, 1185-1193.]; Orlewska, 1996[Orlewska, C. (1996). PhD thesis, Medical University of Gdańsk, Poland.]; Orlewska et al., 1995[Orlewska, C., Foks, H., Janowiec, M. & Zwolska-Kwiek, Z. (1995). Pharmazie, 50, 565-566.], 2001[Orlewska, C., Foks, H., Sowiński, P., Martynowski, D., Olczak, A. & Główka, M. L. (2001). Pol. J. Chem. 75, 1237-1245.]), are one of the promising chemical classes showing action against tuberculosis.

[Scheme 1]

Our earlier studies of the crystal structures of the representatives of this class (A[link] in Scheme 1[link]), which all existed in a dipolar form, showed the same mol­ecular features, of which the most significant was the bifurcated intra­molecular hydrogen bond between protonated atom N3 as a donor and two acceptors, viz. the anionic S atom from the thio­acid function and the N atom at the ortho position of the pyridine or pyrazine ring (Główka et al., 2005[Główka, M. L., Martynowski, D., Olczak, A., Orlewska, C., Foks, H., Bojarska, J., Szczesio, M. & Gołka, J. (2005). J. Chem. Crystallogr. 35, 477-480.]; Olczak et al., 2007[Olczak, A., Główka, M. L., Gołka, J., Szczesio, M., Bojarska, J., Kozłowska, K., Foks, H. & Orlewska, C. (2007). J. Mol. Struct. 830, 171-175.]; Orlewska et al., 2001[Orlewska, C., Foks, H., Sowiński, P., Martynowski, D., Olczak, A. & Główka, M. L. (2001). Pol. J. Chem. 75, 1237-1245.]). A search of the Cambridge Structural Database (CSD, Version 5.31; Allen, 2002[Allen, F. H. (2002). Acta Cryst. B58, 380-388.]) succeeded in finding only two other similar structures (Bermejo et al., 2001[Bermejo, E., Castiñeiras, A., Fostiak, L. M., García, I., Llamas-Saiz, A. L., Swearingen, J. K. & West, D. X. (2001). Z. Naturforsch. Teil B, 56, 1297-1305.]; Ketcham et al., 2001[Ketcham, K. A., Swearingen, J. K., Castiñeiras, A., García, I., Bermejo, E. & West, D. X. (2001). Polyhedron, 20, 3265-3273.]) showing the features described above. The attractive intra­molecular hydrogen-bond contacts and extensive conjugation, both present in these zwitterionic structures, keep all atoms of the mol­ecules coplanar, except the terminal thio­ester or thio­amide group (A[link] in Scheme 1[link]). In addition, in two crystal structures of S,S′-diesters of pyridine­carbon­imidoyl­dithio­carbazic acid (B[link] in Scheme 1[link]) showing moderate activity against M. tuberculosis strains, coplanarity was also maintained despite the lack of an active H atom at N3 (Główka et al., 1999[Główka, M. L., Martynowski, D., Olczak, A., Kozłowska, K., Ołubek, Z., Orlewska, C. & Foks, H. (1999). Pol. J. Chem. 73, 845-851.]).

An analysis of the data available at that time suggested that planarity of the pyridin-2-yl or pyrazin-2-ylform­amide thio­semi­carbazone fragment could be a prerequisite for tuberculo­static activity (Olczak et al., 2007[Olczak, A., Główka, M. L., Gołka, J., Szczesio, M., Bojarska, J., Kozłowska, K., Foks, H. & Orlewska, C. (2007). J. Mol. Struct. 830, 171-175.]). To check the importance and generality of this observation, we have determined, and describe in this study, four crystal structures of other mono- and diesters of pyridine- or pyrazine­carbon­imidoyl­dithio­carbazic acid derivatives, namely diethyl 2,2′-[({[am­ino­(pyrazin-2-yl)methyl­idene]­hydrazinyl­idene}­methyl­idene)­bis­(sulfane­diyl)]­diacetate, B1[link], methyl 3-[amino­(pyra­zin-2-yl)­methyl­idene]-2-methyldithio­­carbazate, C1[link], benzyl 3-[amino­(pyrazin-2-yl)­methyl­idene]-2-methyldithio­­carb­azate, C2[link], and N′-anilino­pyrazine-2-carbox­imid­amide, D1[link], having the same pyridine- or pyrazine­amidine fragment but lacking protonation on atom N3 and, as a consequence, lacking crucial intra­molecular (bifurcated) hydrogen-bond contacts with N3—H as a donor.

Together with six thio­amide and thio­ester structures found in the CSD (Bermejo et al., 2004[Bermejo, E., Castiñeiras, A., García-Santos, I. & West, D. X. (2004). Z. Anorg. Allg. Chem. 630, 1096-1109.], 2005a[Bermejo, E., Castiñeiras, A., García-Santos, I. & West, D. X. (2005a). Z. Anorg. Allg. Chem. 631, 728-738.],b[Bermejo, E., Castiñeiras, A., García-Santos, I. & West, D. X. (2005b). Z. Anorg. Allg. Chem. 631, 2011-2019.]; Castiñeiras et al., 2000[Castiñeiras, A., García, I., Bermejo, E. & West, D. X. Z. (2000). Z. Naturforsch. Teil B, 55, 511-518.]; Labisbal et al., 2002[Labisbal, E., Sousa-Pedrares, A., Castiñeiras, A., Swearingen, J. K. & West, D. X. (2002). Polyhedron, 21, 1553-1559.]; West et al., 1999[West, D. X., Swearingen, J. K., Valdes-Martinez, J. & Hernandez-Ortega, S. (1999). Polyhedron, 18, 2919-2929.]), these compounds form a sufficient set for statistical analysis and verification of the hypothesis that the planarity of a whole mol­ecule is correlated with activity, especially given that, in two structures presented here (C1[link] and C2[link]), atom N2 has been substituted by a methyl group. The substitution introduces spatial repulsion between the methyl group at atom N2 and the neighbouring amine group at atom C4, and forces a twist at the N2—N3 bond (Figs. 1[link] and 2[link]), which also excludes conjugations involving that bond. As a result, we expected a significant difference in their activities.

[Scheme 2]

With the exception of the twist at the N2—N3 bond in structures C1[link] and C2[link], both halves of the mol­ecules are planar. The coplanarity of the pyrazine ring and the neighbouring imide group in all structures determined in this work, as expected on the basis of known structures (Bermejo et al., 2004[Bermejo, E., Castiñeiras, A., García-Santos, I. & West, D. X. (2004). Z. Anorg. Allg. Chem. 630, 1096-1109.], 2005a[Bermejo, E., Castiñeiras, A., García-Santos, I. & West, D. X. (2005a). Z. Anorg. Allg. Chem. 631, 728-738.],b[Bermejo, E., Castiñeiras, A., García-Santos, I. & West, D. X. (2005b). Z. Anorg. Allg. Chem. 631, 2011-2019.]; Castiñeiras et al., 2000[Castiñeiras, A., García, I., Bermejo, E. & West, D. X. Z. (2000). Z. Naturforsch. Teil B, 55, 511-518.]; Główka et al., 1999[Główka, M. L., Martynowski, D., Olczak, A., Kozłowska, K., Ołubek, Z., Orlewska, C. & Foks, H. (1999). Pol. J. Chem. 73, 845-851.]; Labisbal et al., 2002[Labisbal, E., Sousa-Pedrares, A., Castiñeiras, A., Swearingen, J. K. & West, D. X. (2002). Polyhedron, 21, 1553-1559.]; West et al., 1999[West, D. X., Swearingen, J. K., Valdes-Martinez, J. & Hernandez-Ortega, S. (1999). Polyhedron, 18, 2919-2929.]), is indicated by the C41—C4=N3—N2 torsion angles of −177.67 (12), −177.88 (13), 176.53 (12) and −178.18 (13)°, respectively, for B1[link], C1[link], C2[link] and D1[link] (Table 5[link]). The coplanarity is obviously secured by the attractive intra­molecular N5—H⋯N(pyridine) hydrogen-bond contact, characterized by H⋯N42 distances of 2.2–2.7 Å and angles at hydrogen of 101–112°, as no significant conjugation between the π systems of the pyrazine ring and imide group (Scheme 1[link]) is observed. This observation is confirmed by the lengths of the formally single bonds C4—C41 and C4—N5, in the ranges 1.473 (2)–1.493 (2) and 1.329 (2)–1.3577 (19) Å, respectively (Table 5[link]). Instead, in C1[link] and C2[link], another conjugated system (S=C1—N2) is observed, resulting in the shortening of the C1—N2 bond to about 1.34 Å (Table 5[link]), compared with 1.43–1.48 Å in similar fragments containing a tetra­hedral C atom found in the CSD. As expected, the resulting twist around the N2—N3 bond in C1[link] and C2[link] breaks the coplanarity of the pyrazinamidrazone and thio­acid fragments, which has been observed in all monoesters of heteroaryl­carbonamido­yldithio­carbazic acids studied so far by X-ray diffraction. This is evidenced in this study by the torsion angle C1—N2—N3=C4 being 116.53 (16)° in C1[link] and −135.85 (15)° in C2[link], compared with the anti­periplanar conformation observed in B1[link] and D1[link] (Figs. 3[link] and 4[link]) and 24 similar structures found in the CSD. The largest deviation of the C1—N2—N3=C4 torsion angle from 180° is 7.55 (13)° found in B1[link].

Surprisingly, as the tuberculostatic activities of the `non­planar' compounds C1[link] and C2[link] against three selected strains of Mycobacterium tuberculosis are similar to those of other tested compounds (Zwolska, 2009[Zwolska, Z. (2009). Personal communication.]), it seems that maintaining planarity of the whole mol­ecule is not important for its biological action. However, the engagement of hydro­philic H atoms in the intra­molecular hydrogen-bond contacts commonly observed in these compounds may facilitate the smooth passage of the studied mol­ecules through hydro­phobic cell membranes, which may also affect their tuberculostatic activity.

Despite the differences in the chemical structures of the type A[link], B[link], C[link] and D[link] compounds, the inter­molecular hydrogen-bond contacts observed in their crystal structures reveal a common motif, viz. a C(6) chain (Bernstein et al., 1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]) formed through an intermolecular N5—H5A⋯N45′ hydrogen bond (symmetry codes for acceptor atom N45′ are as in Tables 1[link]–4[link][link][link]). In C2[link] and B1[link], the chain runs parallel to the [010] direction, in C1[link] parallel to [100] and in D1[link] parallel to [02[\overline{1}]]. In C2[link] this is the only hydrogen-bond pattern formed (Fig. 5[link]). The same phenomenon is observed in all structures bearing appropriate functions in analogous positions of the mol­ecules (Olczak et al., 2007[Olczak, A., Główka, M. L., Gołka, J., Szczesio, M., Bojarska, J., Kozłowska, K., Foks, H. & Orlewska, C. (2007). J. Mol. Struct. 830, 171-175.]; Zhang et al., 2009[Zhang, Y.-W., Wang, J.-Q. & Cheng, L. (2009). Acta Cryst. E65, o1941.]). In C1[link], at the first level of graph-set theory, an additional motif is formed through an N5—H5B⋯S2(x, y − 1, z) inter­action (Table 2[link]), namely a C(7) chain parallel to the [010] direction (Fig. 6[link]). These two chains form a sheet parallel to the (001) plane in which (at the second level of graph-set theory) an R44(24) ring can be identified (Fig. 6[link]). In D1[link], apart from the C(6) chain common to all studied structures, a new C(4) chain parallel to the [001] direction appears through an N5—H5B⋯N3(−x + [1 \over 2], y, z − [1 \over 2]) hydrogen bond (Fig. 7[link] and Table 4). These two chains at the second level of graph-set theory cause the appearance of an R44(18) ring (Fig. 7[link]). The most complex hydrogen-bond pattern is found in B1[link] because of the existence of four different hydrogen bonds (Fig. 8[link]). At the first level there are four chains: (a) C(6) parallel to [010], (b) C(4) parallel to [001], (c) C(13) parallel to [001] and (d) C(10) parallel to [001]. At the second level, for each pair of hydrogen bonds the following rings can be identified: (ab) R33(24), (ac) R44(32), (ad) R44(30), (bc) R44(42), (bd) R44(36) and (cd) R43(32). The smallest rings observed at the third level are as follows: (abc) R55(32), (abd) R55(30), (acd) R32(7) and (bcd) R43(27). At the fourth level, R66(33) is the smallest ring which is formed in this structure.

[Figure 1]
Figure 1
The mol­ecular structure of C1[link], showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 2]
Figure 2
The mol­ecular structure of C2[link], showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 3]
Figure 3
The mol­ecular structure of B1[link], showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 4]
Figure 4
The mol­ecular structure of D1[link], showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 5]
Figure 5
The inter­molecular hydrogen bonds (dashed lines) in the crystal structure of C2[link], determining the packing of the mol­ecules. Two C(6) chains (related by a centre of symmetry) parallel to [010] run in opposite directions. Symmetry codes are as given in Table 3.
[Figure 6]
Figure 6
The inter­molecular hydrogen bonds (dashed lines) in the crystal structure of C1[link], determining the packing of the mol­ecules. Two chains, C(6) parallel to [100] and C(7) parallel to [010], form an R44(24) ring at the second level of graph-set theory. Symmetry codes are as given in Table 2.
[Figure 7]
Figure 7
The inter­molecular hydrogen bonds (dashed lines) in the crystal structure of D1[link], determining the packing of the mol­ecules. C(6) chains parallel to [02[\overline{1}]] and C(4) chains parallel to [001] form R44(18) rings at the second level of graph-set theory. [Symmetry codes: (i) −x + [1 \over 2], y, z − [1 \over 2]; (ii) −x + [1 \over 2], y + 1, z − [1 \over 2]; (iii) x, y − 1, z; (iv) −x + [1 \over 2], y − 1, z + [1 \over 2].]
[Figure 8]
Figure 8
(a) The inter­molecular hydrogen bonds (dashed lines) and (b) the packing of the mol­ecules in the crystal structure of B1[link]. The structure contains four distinct hydrogen bonds, designated a (N5—H5A⋯N45i), b (C11—H11A⋯O12iii), c (C44—H44⋯O22ii) and d (N5—H5B⋯O22iv). [Symmetry codes: (i) x, y + 1, z; (ii) x, −y, z − [{1\over 2}]; (iii) −x + [{1\over 2}], y + [{1\over 2}], −z + [{1\over 2}]; (iv) x, −y + 1, z − [{1\over 2}].]

Experimental

The syntheses of the title compounds were as described by Foks & Janowiec (1979[Foks, H. & Janowiec, M. (1979). Acta Pol. Pharm. 36, 155-160.]) for D1[link], Foks et al. (1992[Foks, H., Orlewska, C. & Janowiec, M. (1992). Acta Pol. Pharm. Drug Res. 49, 47-50.]) for B1[link], and Orlewska (1996[Orlewska, C. (1996). PhD thesis, Medical University of Gdańsk, Poland.]) for C1[link] and C2[link].

Single crystals of compounds B1[link], C1[link], C2[link] and D1[link] suitable for X-ray diffraction were obtained from chloro­form–ethanol (1:1 v/v), chloro­form–ethanol (1:1 v/v), chloro­benzene and chloro­form solutions, respectively, by slow evaporation of the solvents at room temperature.

Compound B1[link]

Crystal data
  • C14H19N5O4S2

  • Mr = 385.46

  • Monoclinic, C 2/c

  • a = 29.5249 (14) Å

  • b = 8.0969 (9) Å

  • c = 15.4717 (6) Å

  • β = 98.635 (4)°

  • V = 3656.7 (5) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.32 mm−1

  • T = 291 K

  • 0.4 × 0.3 × 0.1 mm

Data collection
  • Kuma KM-4 CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2003[Sheldrick, G. M. (2003). SADABS. Version 2.10. University of Göttingen, Germany.]) Tmin = 0.729, Tmax = 1.000

  • 21104 measured reflections

  • 3722 independent reflections

  • 3064 reflections with I > 2σ(I)

  • Rint = 0.016

Refinement
  • R[F2 > 2σ(F2)] = 0.029

  • wR(F2) = 0.092

  • S = 1.05

  • 3722 reflections

  • 227 parameters

  • H-atom parameters constrained

  • Δρmax = 0.36 e Å−3

  • Δρmin = −0.30 e Å−3

Table 1
Hydrogen-bond geometry (Å, °) for B1[link]

D—H⋯A D—H H⋯A DA D—H⋯A
N5—H5A⋯N45i 0.86 2.63 3.320 (2) 139
C44—H44⋯O22ii 0.93 2.48 3.403 (2) 174
C11—H11A⋯O12iii 0.97 2.55 3.473 (2) 159
N5—H5B⋯O22iv 0.86 2.37 3.2002 (17) 164
Symmetry codes: (i) x, y+1, z; (ii) [x, -y, z-{\script{1\over 2}}]; (iii) [-x+{\script{1\over 2}}, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (iv) [x, -y+1, z-{\script{1\over 2}}].

Compound C1[link]

Crystal data
  • C8H11N5S2

  • Mr = 241.34

  • Triclinic, [P \overline 1]

  • a = 7.7213 (1) Å

  • b = 8.1004 (1) Å

  • c = 9.3331 (1) Å

  • α = 87.9959 (11)°

  • β = 79.0802 (12)°

  • γ = 82.8402 (10)°

  • V = 568.67 (1) Å3

  • Z = 2

  • Mo Kα radiation

  • μ = 0.44 mm−1

  • T = 290 K

  • 0.3 × 0.3 × 0.3 mm

Data collection
  • Kuma KM-4 CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2003[Sheldrick, G. M. (2003). SADABS. Version 2.10. University of Göttingen, Germany.]) Tmin = 0.940, Tmax = 1.000

  • 7633 measured reflections

  • 2319 independent reflections

  • 2161 reflections with I > 2σ(I)

  • Rint = 0.009

Refinement
  • R[F2 > 2σ(F2)] = 0.032

  • wR(F2) = 0.095

  • S = 1.12

  • 2319 reflections

  • 138 parameters

  • H-atom parameters constrained

  • Δρmax = 0.36 e Å−3

  • Δρmin = −0.27 e Å−3

Table 2
Hydrogen-bond geometry (Å, °) for C1[link]

D—H⋯A D—H H⋯A DA D—H⋯A
N5—H5A⋯N45i 0.86 2.24 2.9975 (19) 147
N5—H5B⋯S2ii 0.86 2.87 3.6387 (16) 149
Symmetry codes: (i) x+1, y, z; (ii) x, y-1, z.

Compound C2[link]

Crystal data
  • C14H15N5S2

  • Mr = 317.43

  • Triclinic, [P \overline 1]

  • a = 7.2329 (1) Å

  • b = 7.9041 (1) Å

  • c = 14.0969 (2) Å

  • α = 105.717 (1)°

  • β = 91.368 (1)°

  • γ = 93.863 (1)°

  • V = 773.27 (2) Å3

  • Z = 2

  • Cu Kα radiation

  • μ = 3.12 mm−1

  • T = 290 K

  • 0.3 × 0.2 × 0.05 mm

Data collection
  • Bruker SMART APEX CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2003[Sheldrick, G. M. (2003). SADABS. Version 2.10. University of Göttingen, Germany.]) Tmin = 0.735, Tmax = 1.000

  • 8491 measured reflections

  • 2647 independent reflections

  • 2549 reflections with I > 2σ(I)

  • Rint = 0.017

Refinement
  • R[F2 > 2σ(F2)] = 0.036

  • wR(F2) = 0.098

  • S = 1.06

  • 2647 reflections

  • 191 parameters

  • H-atom parameters constrained

  • Δρmax = 0.31 e Å−3

  • Δρmin = −0.27 e Å−3

Table 3
Hydrogen-bond geometry (Å, °) for C2[link]

D—H⋯A D—H H⋯A DA D—H⋯A
N5—H5A⋯N45i 0.86 2.39 3.135 (2) 146
Symmetry code: (i) x, y+1, z.

Compound D1[link]

Crystal data
  • C11H11N5

  • Mr = 213.25

  • Orthorhombic, P c a 21

  • a = 20.7274 (6) Å

  • b = 5.7456 (1) Å

  • c = 9.1455 (3) Å

  • V = 1089.15 (5) Å3

  • Z = 4

  • Mo Kα radiation

  • μ = 0.09 mm−1

  • T = 290 K

  • 0.4 × 0.3 × 0.05 mm

Data collection
  • Kuma KM-4 CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS; Sheldrick, 2003[Sheldrick, G. M. (2003). SADABS. Version 2.10. University of Göttingen, Germany.]) Tmin = 0.728, Tmax = 1.000

  • 15567 measured reflections

  • 1415 independent reflections

  • 1055 reflections with I > 2σ(I)

  • Rint = 0.029

Refinement
  • R[F2 > 2σ(F2)] = 0.030

  • wR(F2) = 0.068

  • S = 0.90

  • 1415 reflections

  • 154 parameters

  • 1 restraint

  • H atoms treated by a mixture of independent and constrained refinement

  • Δρmax = 0.11 e Å−3

  • Δρmin = −0.12 e Å−3

Table 4
Hydrogen-bond geometry (Å, °) for D1[link]

D—H⋯A D—H H⋯A DA D—H⋯A
N5—H5B⋯N3i 0.921 (18) 2.54 (2) 3.106 (2) 119.9 (15)
N5—H5A⋯N45ii 0.894 (18) 2.135 (19) 3.005 (2) 164.1 (15)
Symmetry codes: (i) [-x+{\script{1\over 2}}, y, z-{\script{1\over 2}}]; (ii) [-x+{\script{1\over 2}}, y+1, z-{\script{1\over 2}}].

Table 5
Selected bond lengths (Å) for the title structures, compared with data from the CSD, and absolute values of selected torsion angles (°)

Structure C4—C41 C4—N5 N3—C4 N2—N3 C1(C11)—N2
B1[link] 1.486 (2) 1.3389 (19) 1.2966 (17) 1.4079 (17) 1.2803 (17)
C1[link] 1.4919 (19) 1.329 (2) 1.291 (2) 1.4215 (16) 1.334 (2)
C2[link] 1.493 (2) 1.339 (2) 1.289 (2) 1.4180 (18) 1.341 (2)
D1[link] 1.473 (2) 1.3577 (19) 1.287 (2) 1.3786 (17) 1.386 (2)
CSD 1.46–1.50 1.32–1.36 1.29–1.31 1.36–1.41 1.27–1.36
           
  N42—C—C—N5 C41—C—N—N2 C4—N—N—C1(C11) C4—N—N—Me N3—N—C—S2
B1[link] 1.8 (2) 177.67 (12) 172.45 (13)   178.75 (10)
C1[link] 27.4 (2) 177.88 (13) 116.53 (16) 78.19 (18) 168.75 (11)
C2[link] 2.1 (2) 176.52 (12) 135.85 (15) 66.56 (18) 170.04 (11)
D1[link] 5.7 (2) 178.18 (13) 174.58 (14)    

H atoms were located in difference Fourier maps and subsequently geometrically optimized and allowed for as riding atoms, with C—H = 0.95 Å for aromatic CH groups, 0.97 Å for secondary CH2 groups and 0.96 Å for methyl groups, and N—H = 0.86 Å, with Uiso(H) = 1.2Ueq(C,N). In the case of D1, the positions of all amine H atoms were refined freely. In the absence of significant anomalously scattering, atoms in the crystal of D1, Friedel pairs were merged before the final refinement and the absolute structure was assigned arbitrarily.

Data collection: CrysAlis CCD (Oxford Diffraction, 2007[Oxford Diffraction (2007). CrysAlis CCD and CrysAlis RED. Versions 1.171. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]) for B1[link], C1[link] and D1[link]; APEX2 (Bruker, 2002[Bruker (2002). APEX2. Bruker AXS Inc., Madison, Wisconsin, USA.]) for C2[link]. Cell refinement: CrysAlis RED (Oxford Diffraction, 2007[Oxford Diffraction (2007). CrysAlis CCD and CrysAlis RED. Versions 1.171. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.]) for B1[link], C1[link] and D1[link]; SAINT-Plus (Bruker, 2003[Bruker (2003). SAINT-Plus. Version 6.45. Bruker AXS Inc., Madison, Wisconsin, USA.]) for C2[link]. Data reduction: CrysAlis RED for B1[link], C1[link] and D1[link]; SAINT-Plus for C2[link]. For all compounds, program(s) used to solve structure: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXTL; molecular graphics: PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]) and Mercury (Macrae et al., 2006[Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M. & van de Streek, J. (2006). J. Appl. Cryst. 39, 453-457.]); software used to prepare material for publication: PLATON.

Supporting information


Comment top

The increasing resistance of Mycobacterium tuberculosis against existing agents and the resulting spread of the pathogen, also in developed countries, makes the search for new tuberculostatics an important issue. 2-, 3- and 4-pyridinecarbonimidoyldithiocarbazonic acid esters and N'-thioamido-substituted pyrazincarboxyamidrazones, of which many compounds have been synthesized by Foks and Orlewska and tested against standard M. tuberculosis strains (Foks & Janowiec, 1979; Foks et al., 1992, 2002, 2004; Orlewska, 1996; Orlewska et al., 1995, 2001), are one of the promising chemical classes showing action against tuberculosis.

Our earlier studies of the crystal structures of the representatives of this class (A in Scheme 1), which all existed in a dipolar form, showed the same molecular features, of which the most significant was the bifurcated intramolecular hydrogen bond between the protonated atom N3 as a donor and two acceptors, the anionic S atom from the thioacid function and the N atom at the ortho position of the pyridine or pyrazine ring (Główka et al., 2005; Olczak et al., 2007; Orlewska et al., 2001). A search of the Cambridge Structural Database (CSD, Version 5.31; Allen, 2002) succeeded in finding only two other similar structures (Bermejo et al., 2001; Ketcham et al., 2001) showing the features described above. The attractive intramolecular hydrogen-bond contacts and extensive conjugation, both present in these zwitterionic structures, keep all atoms of the molecules coplanar, except the terminal thioester or thioamide group (A in Scheme 1). In addition, in two crystal structures of S,S'-diesters of pyridinecarbonimidoyldithiocarbazonic acid (B in Scheme 1) showing moderate activity against M. tuberculosis strains, coplanarity was also maintained despite the lack of an active H atom at N3 (Główka et al., 1999).

An analysis of the data available at that time suggested that planarity of the pyridin-2-yl or pyrazin-2-yl-formamide thiosemicarbazone fragment could be a prerequisite for tuberculostatic activity (Olczak et al., 2007). To check the importance and generality of this observation, we have determined and describe in this study four crystal structures of other mono- and diesters of pyridine- or pyrazinecarbonimidoyldithiocarbazonic acid derivatives, B1, C1, C2 and D1, having the same pyridine- or pyrazineamidine fragment but lacking protonation on atom N3 and, as a consequence, lacking crucial intramolecular (bifurcated) hydrogen-bond contacts with N3—H as a donor.

Together with six thioamide and thioester structures found in the CSD (Bermejo et al., 2004, 2005a,b; Castiñeiras et al., 2000; Labisbal et al., 2002; West et al., 1999), these compounds form a sufficient set for statistical analysis and verification of the hypothesis that the planarity of a whole molecule is correlated with activity, especially given that, in two structures presented here (C1 and C2), atom N2 has been substituted by a methyl group. The substitution introduces spatial repulsion between the methyl group at atom N2 and the neighbouring amine group at atom C4, and forces a twist at the N2—N3 bond (Figs. 1 and 2), which also excludes conjugations involving that bond. As a result, we expected a significant difference in their activities.

With the exception of the twist at the N2—N3 bond in structures C1 and C2, both halves of the molecules are planar. The coplanarity of the pyrazinyl ring and the neighbouring imide group in all structures determined in this work, as expected on the basis of known structures (Bermejo et al., 2004, 2005a,b; Castiñeiras et al., 2000; Główka et al., 1999; Labisbal et al., 2002; West et al., 1999), is indicated by the C41—C4N3—N2 torsion angles of -177.67 (12), -177.88 (13), 176.53 (12) and -178.18 (13)°, respectively, for B1, C1, C2 and D1 (Table 5). The coplanarity is obviously secured by the attractive intramolecular hydrogen-bond contact N5—H···N(pyridine), characterized by H···N42 distances of 2.2–2.7 Å and angles at H of 101–112°, as no significant conjugation between the π systems of the pyrazine ring and imide group (Scheme 1) is observed. This observation is confirmed by the lengths of the formally single bonds C4—C41 and C4—N5, in the ranges 1.473–1.493 and 1.329–1.358 Å, respectively (Table 5). Instead, in C1 and C2, another conjugated system (SC1—N2) is observed, resulting in the shortening of the C1—N2 bond to about 1.34 Å (Table 5), compared with 1.43–1.48 Å in similar fragments containing a tetrahedral C atom found in the CSD. As expected, the resulting twist around the N2—N3 bond in C1 and C2 breaks the coplanarity of the pyrazinamidrazone and thioacid fragments, which has been observed in all monoesters of heteroarylcarbonamidoyldithiocarbazonic acids studied so far by X-ray diffraction. This is evidenced in this study by the torsion angle C1—N2—N3C4 being 116.5 (2)° in C1 and -135.9 (2)° in C2, compared with the antiperiplanar conformation observed in B1 and D1 (Figs. 3 and 4) and 24 similar structures found in the CSD. The largest deviation of the C1—N2—N3C4 torsion angle from 180° is 7.5° found in B1.

Surprisingly, as the tuberculostatic activities of the `non-planar' compounds C1 and C2 against three selected strains of Mycobacterium tuberculosis are similar to those of other tested compounds (Zwolska, 2009), it seems that maintaining planarity of the whole molecule is not important for its biological action. However, the engagement of hydrophilic H atoms in the intramolecular hydrogen-bond contacts commonly observed in these compounds may facilitate the smooth passage of the studied molecules through hydrophobic cell membranes, which may also affect their tuberculostatic activity.

Despite the differences in the chemical structures of the type A, B, C and D compounds, the intermolecular hydrogen-bond contacts observed in their crystal structures reveal a common motif: a C(6) chain (Bernstein et al., 1995) formed through an N5—H5A···N45 hydrogen bond (Tables 1–4). In C2 and B1, the chain runs parallel to the [010] direction, in C1 parallel to [100] and in D1 parallel to [021]. In C2 this is the only hydrogen-bond pattern formed (Fig. 5). The same phenomenon is observed in all structures bearing appropriate functions in analogous positions of the molecules (Olczak et al., 2007; Zhang et al., 2009). In C1, at the first level of graph-set theory an additional motif is formed through an N5—H5B···S2 interaction (Table 2), namely a C(7) chain parallel to the [010] direction (Fig. 6). These two chains form a sheet parallel to the (001) plane in which (at the second level of graph-set theory) an R44(24) ring can be identified (Fig. 6). In D1, apart from the C(6) chain common to all studied structures, a new C(4) chain parallel to the [001] direction appears through an N5—H5B···N3 hydrogen bond (Fig. 7). These two chains at the second level of graph-set theory cause the appearance of an R44(18) ring (Fig. 7). The most complex hydrogen-bond pattern is found in B1 because of the existence of four different hydrogen bonds (Fig. 8). At the first level there are four chains: (a) C(6) parallel to [010], (b) C(4) parallel to [001], (c) C(13) parallel to [001] and (d) C(10) parallel to [001]. At the second level, for each pair of hydrogen bonds the following rings can be identified: (ab) R33(24), (ac) R44(32), (ad) R44(30), (bc) R44(42), (bd) R44(36) and (cd) R34(32). The smallest rings observed at the third level are as follows: (abc) R55(32), (abd) R55(30), (acd) R23(7) and (bcd) R34(27). At the fourth level, R66(33) is the smallest ring which is formed in this structure.

Related literature top

For related literature, see: Allen (2002); Bermejo et al. (2001, 2004, 2005a, 2005b); Bernstein et al. (1995); Castiñeiras et al. (2000); Foks & Janowiec (1979); Foks et al. (1992, 2002, 2004); Główka et al. (1999, 2005); Ketcham et al. (2001); Labisbal et al. (2002); Olczak et al. (2007); Orlewska (1996); Orlewska et al. (1995, 2001); West et al. (1999); Zhang et al. (2009); Zwolska (2009).

Experimental top

The syntheses of the title compounds were as described by Foks & Janowiec (1979) for D1, Foks et al. (1992) for B1, and Orlewska (1996) for C1 and C2.

Single crystals of compounds B1, C1, C2 and D1 suitable for X-ray diffraction were obtained from chloroform–ethanol (Solvent ratio?), chloroform–ethanol (Solvent ratio?), chlorobenzene and chloroform solutions, respectively, by slow evaporation of the solvent at room temperature.

Refinement top

H atoms were located in difference Fourier maps and subsequently allowed for as riding atoms, with C—H = 0.95 for aromatic CH and 0.97 Å for secondary CH2 groups and N—H = 0.86 Å, and with Uiso(H) = 1.2Ueq(C,N).

Computing details top

Data collection: CrysAlis CCD (Oxford Diffraction, 2007) for B1, C1, D1; APEX2 (Bruker, 2002) for C2. Cell refinement: CrysAlis RED (Oxford Diffraction, 2007) for B1, C1, D1; SAINT-Plus (Bruker, 2003) for C2. Data reduction: CrysAlis RED (Oxford Diffraction, 2007) for B1, C1, D1; SAINT-Plus (Bruker, 2003) for C2. For all compounds, program(s) used to solve structure: SHELXTL (Sheldrick, 2008); program(s) used to refine structure: SHELXTL (Sheldrick, 2008); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2006); software used to prepare material for publication: PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of C1, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 2] Fig. 2. The molecular structure of C2, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 3] Fig. 3. The molecular structure of B1, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 4] Fig. 4. The molecular structure of D1, showing the atom-labelling scheme. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 5] Fig. 5. The intermolecular hydrogen bonds (dashed lines) in the crystal structure of C2, determining the packing of the molecules. Two C(6) chains (related by a centre of symmetry) parallel to [010] run in opposite directions.
[Figure 6] Fig. 6. The intermolecular hydrogen bonds (dashed lines) in the crystal structure of C1, determining the packing of the molecules. Two chains, C(6) parallel to [100] and C(7) parallel to [010], form an R44(24) ring at the second level of graph-set theory.
[Figure 7] Fig. 7. The intermolecular hydrogen bonds (dashed lines) in the crystal structure of D1, determining the packing of the molecules. C(6) chains parallel to [021] and C(4) chains parallel to [001] form R44(18) rings at the second level of graph-set theory.
[Figure 8] Fig. 8. (a) The intermolecular hydrogen bonds (dashed lines) and (b) the packing of the molecules in the crystal structure of B1. The structure contains four distinct hydrogen bonds, designated a (N5—H5A···N45i), b (C11—H11A···O12iii), c (C44—H44···O22ii) and d (N5—H5B···O22iv). [Symmetry codes: (i) x, y + 1, z; (ii) x, -y, z - 1/2; (iii) -x + 1/2, y + 1/2, -z + 1/2; (iv) x, -y + 1, z - 1/2.]
(B1) diethyl 2,2'-[({[amino(pyrazin-2- yl)methylidene]hydrazinylidene}methylidene)bis(sulfanediyl)]diacetate top
Crystal data top
C14H19N5O4S2F(000) = 1616
Mr = 385.46Dx = 1.400 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -C 2ycCell parameters from 12369 reflections
a = 29.5249 (14) Åθ = 2.7–28.5°
b = 8.0969 (9) ŵ = 0.32 mm1
c = 15.4717 (6) ÅT = 291 K
β = 98.635 (4)°Plate, colourless
V = 3656.7 (5) Å30.4 × 0.3 × 0.1 mm
Z = 8
Data collection top
Kuma KM-4 CCD area-detector
diffractometer
3722 independent reflections
Radiation source: fine-focus sealed tube3064 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.016
ω scansθmax = 26.4°, θmin = 2.7°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 3636
Tmin = 0.729, Tmax = 1.000k = 810
21104 measured reflectionsl = 1919
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.029H-atom parameters constrained
wR(F2) = 0.092 w = 1/[σ2(Fo2) + (0.0593P)2 + 0.6854P]
where P = (Fo2 + 2Fc2)/3
S = 1.05(Δ/σ)max < 0.001
3722 reflectionsΔρmax = 0.36 e Å3
227 parametersΔρmin = 0.30 e Å3
0 restraintsExtinction correction: SHELXTL (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0013 (2)
Crystal data top
C14H19N5O4S2V = 3656.7 (5) Å3
Mr = 385.46Z = 8
Monoclinic, C2/cMo Kα radiation
a = 29.5249 (14) ŵ = 0.32 mm1
b = 8.0969 (9) ÅT = 291 K
c = 15.4717 (6) Å0.4 × 0.3 × 0.1 mm
β = 98.635 (4)°
Data collection top
Kuma KM-4 CCD area-detector
diffractometer
3722 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
3064 reflections with I > 2σ(I)
Tmin = 0.729, Tmax = 1.000Rint = 0.016
21104 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0290 restraints
wR(F2) = 0.092H-atom parameters constrained
S = 1.05Δρmax = 0.36 e Å3
3722 reflectionsΔρmin = 0.30 e Å3
227 parameters
Special details top

Experimental. CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.32.13 (release 29–11-2007 CrysAlis171. NET) (compiled Nov 29 2007,17:23:28) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

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. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.15561 (5)0.35264 (17)0.12965 (9)0.0341 (3)
C40.10830 (5)0.23775 (18)0.07261 (8)0.0356 (3)
C110.20470 (6)0.20016 (19)0.27392 (9)0.0414 (3)
H11A0.23370.25390.27000.050*
H11B0.18630.27460.30340.050*
C120.21301 (5)0.04261 (18)0.32516 (9)0.0363 (3)
C140.24295 (6)0.05918 (18)0.46614 (9)0.0429 (4)
H14A0.26090.14060.44010.051*
H14B0.21530.11180.47940.051*
C150.26990 (7)0.0099 (2)0.54705 (11)0.0567 (5)
H15A0.25160.08870.57260.068*
H15B0.29690.06330.53280.068*
H15C0.27870.07780.58790.068*
C210.13426 (5)0.67846 (18)0.13933 (10)0.0415 (3)
H21A0.14180.78480.16670.050*
H21B0.14240.68240.08090.050*
C220.08327 (5)0.65033 (18)0.13266 (9)0.0416 (3)
C240.01131 (6)0.7266 (3)0.05408 (14)0.0791 (7)
H24A0.00150.80150.09300.095*
H24B0.00200.61510.06600.095*
C250.00556 (8)0.7709 (4)0.03911 (16)0.0989 (9)
H25A0.00070.88660.04780.119*
H25B0.03770.74640.05250.119*
H25C0.01090.70810.07690.119*
C410.09896 (5)0.08074 (18)0.12173 (9)0.0372 (3)
C430.07013 (8)0.0511 (3)0.24623 (12)0.0694 (6)
H430.05570.04900.30390.083*
C440.08200 (7)0.2004 (2)0.20854 (12)0.0604 (5)
H440.07510.29610.24100.072*
C460.11129 (6)0.0708 (2)0.08432 (11)0.0483 (4)
H460.12590.07350.02680.058*
N20.13292 (4)0.37312 (15)0.05315 (7)0.0392 (3)
N30.12640 (4)0.22133 (15)0.00863 (7)0.0400 (3)
N50.09644 (5)0.37870 (17)0.11533 (8)0.0498 (3)
H5A0.10070.47170.08850.060*
H5B0.08460.37620.16960.060*
N420.07829 (5)0.09141 (18)0.20412 (9)0.0581 (4)
N450.10316 (6)0.21282 (18)0.12694 (10)0.0586 (4)
O120.20462 (4)0.09417 (14)0.29774 (7)0.0523 (3)
O130.23145 (4)0.07862 (12)0.40646 (7)0.0462 (3)
O220.06498 (4)0.56275 (15)0.17990 (7)0.0532 (3)
O230.06124 (4)0.73868 (17)0.06809 (8)0.0621 (4)
S10.175323 (13)0.15511 (4)0.16549 (2)0.04032 (13)
S20.167798 (13)0.52195 (5)0.20082 (2)0.04149 (13)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0396 (7)0.0317 (7)0.0298 (6)0.0026 (6)0.0016 (5)0.0013 (5)
C40.0397 (7)0.0349 (8)0.0314 (7)0.0000 (6)0.0026 (5)0.0001 (6)
C110.0528 (9)0.0339 (8)0.0340 (7)0.0006 (7)0.0051 (6)0.0023 (6)
C120.0402 (7)0.0327 (8)0.0347 (7)0.0022 (6)0.0012 (6)0.0004 (6)
C140.0592 (9)0.0311 (8)0.0360 (7)0.0033 (7)0.0008 (7)0.0062 (6)
C150.0777 (12)0.0453 (9)0.0418 (9)0.0028 (9)0.0081 (8)0.0038 (7)
C210.0535 (9)0.0286 (7)0.0402 (8)0.0034 (6)0.0006 (6)0.0019 (6)
C220.0539 (9)0.0345 (8)0.0344 (7)0.0063 (7)0.0001 (6)0.0013 (6)
C240.0502 (11)0.1023 (18)0.0822 (14)0.0085 (11)0.0018 (10)0.0312 (13)
C250.0657 (14)0.133 (2)0.0912 (17)0.0060 (15)0.0089 (12)0.0316 (17)
C410.0433 (7)0.0371 (8)0.0311 (7)0.0014 (6)0.0056 (6)0.0033 (6)
C430.1009 (15)0.0554 (12)0.0450 (10)0.0038 (11)0.0120 (10)0.0166 (9)
C440.0806 (13)0.0453 (10)0.0560 (10)0.0099 (9)0.0122 (9)0.0201 (8)
C460.0676 (10)0.0376 (9)0.0395 (8)0.0002 (7)0.0068 (7)0.0012 (7)
N20.0508 (7)0.0341 (6)0.0304 (6)0.0022 (5)0.0019 (5)0.0029 (5)
N30.0539 (7)0.0332 (6)0.0305 (6)0.0031 (6)0.0018 (5)0.0036 (5)
N50.0777 (9)0.0344 (7)0.0322 (6)0.0001 (7)0.0087 (6)0.0012 (5)
N420.0846 (11)0.0448 (8)0.0381 (7)0.0019 (8)0.0128 (7)0.0070 (6)
N450.0843 (11)0.0374 (8)0.0556 (9)0.0018 (7)0.0149 (8)0.0065 (7)
O120.0722 (8)0.0335 (6)0.0457 (6)0.0007 (6)0.0087 (5)0.0013 (5)
O130.0720 (7)0.0288 (5)0.0340 (5)0.0029 (5)0.0047 (5)0.0028 (4)
O220.0606 (7)0.0528 (7)0.0453 (6)0.0011 (6)0.0053 (5)0.0123 (6)
O230.0500 (7)0.0722 (9)0.0616 (7)0.0066 (6)0.0001 (5)0.0323 (7)
S10.0564 (2)0.0309 (2)0.03109 (19)0.00535 (16)0.00190 (15)0.00167 (14)
S20.0524 (2)0.0328 (2)0.0346 (2)0.00512 (16)0.00873 (15)0.00556 (15)
Geometric parameters (Å, º) top
C1—N21.2803 (17)C21—H21B0.9700
C1—S21.7613 (14)C22—O221.2031 (19)
C1—S11.7628 (14)C22—O231.3183 (18)
C4—N31.2966 (17)C24—O231.461 (2)
C4—N51.3389 (19)C24—C251.497 (3)
C4—C411.486 (2)C24—H24A0.9700
C11—C121.5026 (19)C24—H24B0.9700
C11—S11.8062 (14)C25—H25A0.9600
C11—H11A0.9700C25—H25B0.9600
C11—H11B0.9700C25—H25C0.9600
C12—O121.1985 (18)C41—N421.3309 (18)
C12—O131.3258 (17)C41—C461.382 (2)
C14—O131.4555 (17)C43—N421.330 (2)
C14—C151.488 (2)C43—C441.365 (3)
C14—H14A0.9700C43—H430.9300
C14—H14B0.9700C44—N451.326 (2)
C15—H15A0.9600C44—H440.9300
C15—H15B0.9600C46—N451.330 (2)
C15—H15C0.9600C46—H460.9300
C21—C221.511 (2)N2—N31.4079 (17)
C21—S21.7912 (14)N5—H5A0.8600
C21—H21A0.9700N5—H5B0.8600
N2—C1—S2120.44 (11)O23—C24—C25108.02 (17)
N2—C1—S1120.70 (11)O23—C24—H24A110.1
S2—C1—S1118.86 (8)C25—C24—H24A110.1
N3—C4—N5127.24 (14)O23—C24—H24B110.1
N3—C4—C41115.22 (13)C25—C24—H24B110.1
N5—C4—C41117.53 (12)H24A—C24—H24B108.4
C12—C11—S1109.65 (10)C24—C25—H25A109.5
C12—C11—H11A109.7C24—C25—H25B109.5
S1—C11—H11A109.7H25A—C25—H25B109.5
C12—C11—H11B109.7C24—C25—H25C109.5
S1—C11—H11B109.7H25A—C25—H25C109.5
H11A—C11—H11B108.2H25B—C25—H25C109.5
O12—C12—O13124.94 (13)N42—C41—C46120.87 (14)
O12—C12—C11126.08 (13)N42—C41—C4117.24 (13)
O13—C12—C11108.98 (12)C46—C41—C4121.90 (13)
O13—C14—C15106.86 (12)N42—C43—C44122.92 (17)
O13—C14—H14A110.4N42—C43—H43118.5
C15—C14—H14A110.4C44—C43—H43118.5
O13—C14—H14B110.4N45—C44—C43121.89 (17)
C15—C14—H14B110.4N45—C44—H44119.1
H14A—C14—H14B108.6C43—C44—H44119.1
C14—C15—H15A109.5N45—C46—C41122.93 (15)
C14—C15—H15B109.5N45—C46—H46118.5
H15A—C15—H15B109.5C41—C46—H46118.5
C14—C15—H15C109.5C1—N2—N3110.69 (12)
H15A—C15—H15C109.5C4—N3—N2113.01 (12)
H15B—C15—H15C109.5C4—N5—H5A120.0
C22—C21—S2113.29 (10)C4—N5—H5B120.0
C22—C21—H21A108.9H5A—N5—H5B120.0
S2—C21—H21A108.9C43—N42—C41115.87 (16)
C22—C21—H21B108.9C44—N45—C46115.52 (16)
S2—C21—H21B108.9C12—O13—C14117.17 (11)
H21A—C21—H21B107.7C22—O23—C24116.63 (14)
O22—C22—O23124.39 (15)C1—S1—C11101.46 (7)
O22—C22—C21125.53 (14)C1—S2—C21100.01 (7)
O23—C22—C21110.07 (13)
S1—C11—C12—O124.8 (2)C46—C41—N42—C430.8 (3)
S1—C11—C12—O13175.35 (10)C4—C41—N42—C43179.58 (16)
S2—C21—C22—O2219.1 (2)C43—C44—N45—C461.0 (3)
S2—C21—C22—O23162.16 (11)C41—C46—N45—C440.3 (3)
N3—C4—C41—N42176.74 (14)O12—C12—O13—C141.1 (2)
N5—C4—C41—N421.8 (2)C11—C12—O13—C14178.77 (13)
N3—C4—C41—C463.6 (2)C15—C14—O13—C12170.58 (14)
N5—C4—C41—C46177.84 (15)O22—C22—O23—C240.3 (3)
N42—C43—C44—N450.8 (3)C21—C22—O23—C24179.12 (17)
N42—C41—C46—N450.6 (3)C25—C24—O23—C22156.0 (2)
C4—C41—C46—N45179.78 (16)N2—C1—S1—C11179.31 (12)
S2—C1—N2—N3178.75 (10)S2—C1—S1—C110.51 (11)
S1—C1—N2—N31.44 (18)C12—C11—S1—C1164.53 (11)
N5—C4—N3—N20.7 (2)N2—C1—S2—C217.65 (14)
C41—C4—N3—N2177.67 (12)S1—C1—S2—C21172.53 (9)
C1—N2—N3—C4172.45 (13)C22—C21—S2—C168.14 (12)
C44—C43—N42—C410.1 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H5A···N45i0.862.633.320 (2)139
C44—H44···O22ii0.932.483.403 (2)174
C11—H11A···O12iii0.972.553.473 (2)159
N5—H5B···O22iv0.862.373.2002 (17)164
Symmetry codes: (i) x, y+1, z; (ii) x, y, z1/2; (iii) x+1/2, y+1/2, z+1/2; (iv) x, y+1, z1/2.
(C1) methyl 3-[amino(pyrazin-2-yl)methylidene]-2-methylcarbazate top
Crystal data top
C8H11N5S2Z = 2
Mr = 241.34F(000) = 252
Triclinic, P1Dx = 1.409 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71073 Å
a = 7.7213 (1) ÅCell parameters from 6100 reflections
b = 8.1004 (1) Åθ = 2.7–31.1°
c = 9.3331 (1) ŵ = 0.44 mm1
α = 87.9959 (11)°T = 290 K
β = 79.0802 (12)°Cube, colourless
γ = 82.8402 (10)°0.3 × 0.3 × 0.3 mm
V = 568.67 (1) Å3
Data collection top
Kuma KM-4 CCD area-detector
diffractometer
2319 independent reflections
Radiation source: fine-focus sealed tube2161 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.009
ω scansθmax = 26.4°, θmin = 2.7°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 99
Tmin = 0.940, Tmax = 1.000k = 1010
7633 measured reflectionsl = 118
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.032Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.095H-atom parameters constrained
S = 1.12 w = 1/[σ2(Fo2) + (0.0476P)2 + 0.2235P]
where P = (Fo2 + 2Fc2)/3
2319 reflections(Δ/σ)max < 0.001
138 parametersΔρmax = 0.36 e Å3
0 restraintsΔρmin = 0.27 e Å3
Crystal data top
C8H11N5S2γ = 82.8402 (10)°
Mr = 241.34V = 568.67 (1) Å3
Triclinic, P1Z = 2
a = 7.7213 (1) ÅMo Kα radiation
b = 8.1004 (1) ŵ = 0.44 mm1
c = 9.3331 (1) ÅT = 290 K
α = 87.9959 (11)°0.3 × 0.3 × 0.3 mm
β = 79.0802 (12)°
Data collection top
Kuma KM-4 CCD area-detector
diffractometer
2319 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
2161 reflections with I > 2σ(I)
Tmin = 0.940, Tmax = 1.000Rint = 0.009
7633 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0320 restraints
wR(F2) = 0.095H-atom parameters constrained
S = 1.12Δρmax = 0.36 e Å3
2319 reflectionsΔρmin = 0.27 e Å3
138 parameters
Special details top

Experimental. CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.32.13 (release 29–11-2007 CrysAlis171. NET) (compiled Nov 29 2007,17:23:28) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

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. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.24407 (19)0.98717 (18)0.27399 (17)0.0307 (3)
C20.2193 (2)0.8475 (2)0.51399 (19)0.0418 (4)
H2A0.14010.77640.56960.050*
H2B0.20510.95280.56150.050*
H2C0.33970.79660.50690.050*
C40.06103 (19)0.64381 (19)0.31377 (17)0.0307 (3)
C110.2721 (3)1.1454 (3)0.0021 (2)0.0554 (5)
H11A0.24661.14560.09460.067*
H11B0.39771.11890.00220.067*
H11C0.23381.25340.04420.067*
C410.09111 (19)0.56783 (18)0.27686 (17)0.0298 (3)
C430.1821 (2)0.3755 (2)0.1478 (2)0.0472 (4)
H430.15780.28460.08610.057*
C440.3550 (2)0.4433 (2)0.1917 (2)0.0434 (4)
H440.44400.39840.15680.052*
C460.2661 (2)0.6339 (2)0.3249 (2)0.0369 (4)
H460.29080.72380.38790.044*
N20.17814 (17)0.87278 (16)0.36805 (15)0.0323 (3)
N30.02973 (17)0.80159 (16)0.33818 (17)0.0356 (3)
N50.21119 (19)0.54388 (19)0.3137 (2)0.0517 (4)
H5A0.30320.58330.33160.062*
H5B0.21640.43980.29580.062*
N420.04782 (18)0.43563 (18)0.19073 (18)0.0411 (3)
N450.39984 (18)0.57125 (19)0.28263 (18)0.0427 (4)
S10.15698 (7)0.99294 (6)0.11240 (5)0.04526 (15)
S20.39250 (6)1.10689 (6)0.30620 (5)0.04579 (15)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0290 (7)0.0263 (7)0.0386 (8)0.0043 (6)0.0089 (6)0.0060 (6)
C20.0488 (10)0.0407 (9)0.0400 (9)0.0110 (7)0.0150 (7)0.0018 (7)
C40.0248 (7)0.0309 (7)0.0382 (8)0.0075 (6)0.0073 (6)0.0013 (6)
C110.0680 (13)0.0504 (11)0.0428 (10)0.0002 (10)0.0033 (9)0.0081 (9)
C410.0274 (7)0.0264 (7)0.0378 (8)0.0091 (5)0.0085 (6)0.0014 (6)
C430.0445 (10)0.0412 (10)0.0600 (12)0.0116 (8)0.0131 (8)0.0169 (8)
C440.0378 (9)0.0422 (9)0.0575 (11)0.0185 (7)0.0182 (8)0.0009 (8)
C460.0284 (7)0.0352 (8)0.0487 (9)0.0091 (6)0.0070 (7)0.0061 (7)
N20.0309 (6)0.0294 (6)0.0415 (7)0.0107 (5)0.0140 (5)0.0011 (5)
N30.0269 (6)0.0294 (7)0.0548 (9)0.0094 (5)0.0143 (6)0.0017 (6)
N50.0294 (7)0.0345 (8)0.0967 (14)0.0027 (6)0.0235 (8)0.0163 (8)
N420.0331 (7)0.0362 (7)0.0559 (9)0.0072 (6)0.0087 (6)0.0126 (7)
N450.0274 (7)0.0423 (8)0.0616 (10)0.0112 (6)0.0108 (6)0.0040 (7)
S10.0605 (3)0.0396 (3)0.0426 (3)0.0100 (2)0.0247 (2)0.00047 (18)
S20.0454 (3)0.0432 (3)0.0559 (3)0.0244 (2)0.0150 (2)0.0019 (2)
Geometric parameters (Å, º) top
C1—N21.334 (2)C11—H11C0.9600
C1—S21.6650 (15)C41—N421.332 (2)
C1—S11.7607 (16)C41—C461.386 (2)
C2—N21.458 (2)C43—N421.330 (2)
C2—H2A0.9600C43—C441.370 (3)
C2—H2B0.9600C43—H430.9300
C2—H2C0.9600C44—N451.333 (2)
C4—N31.291 (2)C44—H440.9300
C4—N51.329 (2)C46—N451.334 (2)
C4—C411.4919 (19)C46—H460.9300
C11—S11.792 (2)N2—N31.4214 (16)
C11—H11A0.9600N5—H5A0.8600
C11—H11B0.9600N5—H5B0.8600
N2—C1—S2123.63 (12)C46—C41—C4122.18 (14)
N2—C1—S1111.64 (11)N42—C43—C44122.16 (16)
S2—C1—S1124.72 (10)N42—C43—H43118.9
N2—C2—H2A109.5C44—C43—H43118.9
N2—C2—H2B109.5N45—C44—C43122.14 (15)
H2A—C2—H2B109.5N45—C44—H44118.9
N2—C2—H2C109.5C43—C44—H44118.9
H2A—C2—H2C109.5N45—C46—C41121.34 (15)
H2B—C2—H2C109.5N45—C46—H46119.3
N3—C4—N5128.27 (14)C41—C46—H46119.3
N3—C4—C41114.71 (13)C1—N2—N3117.29 (13)
N5—C4—C41116.99 (14)C1—N2—C2123.42 (13)
S1—C11—H11A109.5N3—N2—C2117.50 (13)
S1—C11—H11B109.5C4—N3—N2113.87 (12)
H11A—C11—H11B109.5C4—N5—H5A120.0
S1—C11—H11C109.5C4—N5—H5B120.0
H11A—C11—H11C109.5H5A—N5—H5B120.0
H11B—C11—H11C109.5C43—N42—C41115.98 (14)
N42—C41—C46122.08 (14)C44—N45—C46116.21 (14)
N42—C41—C4115.71 (13)C1—S1—C11103.26 (9)
N3—C4—C41—N42150.81 (16)N5—C4—N3—N20.1 (3)
N5—C4—C41—N4227.4 (2)C41—C4—N3—N2177.88 (13)
N3—C4—C41—C4627.0 (2)C1—N2—N3—C4116.53 (16)
N5—C4—C41—C46154.72 (17)C2—N2—N3—C478.18 (18)
N42—C43—C44—N451.5 (3)C44—C43—N42—C411.2 (3)
N42—C41—C46—N452.4 (3)C46—C41—N42—C433.1 (3)
C4—C41—C46—N45175.32 (16)C4—C41—N42—C43174.76 (16)
S2—C1—N2—N3168.75 (11)C43—C44—N45—C462.3 (3)
S1—C1—N2—N312.05 (17)C41—C46—N45—C440.4 (3)
S2—C1—N2—C24.4 (2)N2—C1—S1—C11177.15 (12)
S1—C1—N2—C2176.39 (12)S2—C1—S1—C112.05 (13)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H5A···N45i0.862.242.9975 (19)147
N5—H5B···S2ii0.862.873.6387 (16)149
Symmetry codes: (i) x+1, y, z; (ii) x, y1, z.
(C2) benzyl 3-[amino(pyrazin-2-yl)methylidene]-2-methylcarbazate top
Crystal data top
C14H15N5S2Z = 2
Mr = 317.43F(000) = 332
Triclinic, P1Dx = 1.363 Mg m3
Hall symbol: -P 1Cu Kα radiation, λ = 1.54178 Å
a = 7.2329 (1) ÅCell parameters from 7068 reflections
b = 7.9041 (1) Åθ = 5.8–70.1°
c = 14.0969 (2) ŵ = 3.12 mm1
α = 105.717 (1)°T = 290 K
β = 91.368 (1)°Plate, colourless
γ = 93.863 (1)°0.3 × 0.2 × 0.05 mm
V = 773.27 (2) Å3
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer
2647 independent reflections
Radiation source: fine-focus sealed tube2549 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.017
ω scansθmax = 66.5°, θmin = 3.3°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 88
Tmin = 0.735, Tmax = 1.000k = 98
8491 measured reflectionsl = 1616
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.036Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.098H-atom parameters constrained
S = 1.06 w = 1/[σ2(Fo2) + (0.059P)2 + 0.1869P]
where P = (Fo2 + 2Fc2)/3
2647 reflections(Δ/σ)max < 0.001
191 parametersΔρmax = 0.31 e Å3
0 restraintsΔρmin = 0.27 e Å3
Crystal data top
C14H15N5S2γ = 93.863 (1)°
Mr = 317.43V = 773.27 (2) Å3
Triclinic, P1Z = 2
a = 7.2329 (1) ÅCu Kα radiation
b = 7.9041 (1) ŵ = 3.12 mm1
c = 14.0969 (2) ÅT = 290 K
α = 105.717 (1)°0.3 × 0.2 × 0.05 mm
β = 91.368 (1)°
Data collection top
Bruker SMART APEX CCD area-detector
diffractometer
2647 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
2549 reflections with I > 2σ(I)
Tmin = 0.735, Tmax = 1.000Rint = 0.017
8491 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0360 restraints
wR(F2) = 0.098H-atom parameters constrained
S = 1.06Δρmax = 0.31 e Å3
2647 reflectionsΔρmin = 0.27 e Å3
191 parameters
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. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C10.0621 (2)1.1792 (2)0.76968 (12)0.0445 (4)
C20.3422 (3)1.2506 (3)0.69269 (15)0.0585 (4)
H2A0.43601.18690.64450.070*
H2B0.29631.35480.67560.070*
H2C0.39461.28340.75650.070*
C40.22584 (19)0.92725 (19)0.54636 (11)0.0392 (3)
C110.2344 (3)1.0885 (3)0.87292 (15)0.0616 (5)
H11A0.31661.18330.86240.074*
H11B0.16751.13390.93220.074*
C120.3433 (2)0.9375 (2)0.88251 (12)0.0497 (4)
C130.2750 (3)0.8186 (3)0.93081 (14)0.0635 (5)
H130.15920.83140.95810.076*
C140.3746 (3)0.6812 (3)0.93953 (16)0.0720 (6)
H140.32580.60220.97250.086*
C150.5455 (3)0.6599 (3)0.89999 (15)0.0697 (6)
H150.61360.56770.90660.084*
C160.6147 (3)0.7747 (3)0.85095 (17)0.0717 (6)
H160.73020.76040.82350.086*
C170.5147 (3)0.9125 (3)0.84164 (15)0.0622 (5)
H170.56320.98950.80740.075*
C410.2385 (2)0.7360 (2)0.49210 (11)0.0398 (3)
C430.2553 (3)0.5263 (3)0.34587 (14)0.0617 (5)
H430.26020.49340.27730.074*
C440.2599 (3)0.3979 (2)0.39448 (14)0.0626 (5)
H440.27040.28040.35770.075*
C460.2398 (3)0.6056 (2)0.54085 (13)0.0515 (4)
H460.23360.63810.60940.062*
N20.19016 (19)1.13931 (17)0.69507 (10)0.0458 (3)
N30.21313 (19)0.95915 (17)0.64099 (10)0.0450 (3)
N50.2275 (2)1.03913 (18)0.49009 (10)0.0510 (3)
H5A0.21921.15100.51710.061*
H5B0.23680.99920.42690.061*
N420.2439 (2)0.69693 (19)0.39410 (10)0.0517 (3)
N450.2499 (3)0.43501 (19)0.49252 (12)0.0615 (4)
S10.07348 (6)1.00020 (5)0.76729 (3)0.04975 (15)
S20.03356 (7)1.37263 (6)0.85344 (4)0.06241 (17)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C10.0492 (8)0.0376 (8)0.0443 (8)0.0037 (6)0.0061 (6)0.0067 (6)
C20.0654 (11)0.0486 (10)0.0620 (11)0.0186 (8)0.0018 (8)0.0127 (8)
C40.0379 (7)0.0357 (8)0.0442 (8)0.0018 (6)0.0034 (6)0.0118 (6)
C110.0632 (11)0.0543 (11)0.0581 (10)0.0069 (8)0.0135 (8)0.0005 (8)
C120.0514 (9)0.0500 (9)0.0422 (8)0.0018 (7)0.0069 (7)0.0047 (7)
C130.0553 (10)0.0777 (14)0.0567 (11)0.0001 (9)0.0034 (8)0.0184 (10)
C140.0898 (15)0.0674 (13)0.0621 (12)0.0046 (11)0.0102 (11)0.0267 (10)
C150.0880 (15)0.0584 (12)0.0570 (11)0.0182 (10)0.0168 (10)0.0046 (9)
C160.0599 (11)0.0825 (15)0.0685 (12)0.0180 (10)0.0070 (9)0.0101 (11)
C170.0618 (11)0.0651 (12)0.0621 (11)0.0024 (9)0.0078 (9)0.0214 (9)
C410.0398 (7)0.0367 (8)0.0421 (8)0.0024 (6)0.0037 (6)0.0100 (6)
C430.0877 (14)0.0488 (10)0.0428 (9)0.0063 (9)0.0030 (9)0.0029 (8)
C440.0894 (14)0.0363 (9)0.0570 (11)0.0069 (8)0.0005 (9)0.0040 (8)
C460.0715 (11)0.0382 (8)0.0446 (8)0.0028 (7)0.0015 (7)0.0114 (7)
N20.0544 (7)0.0341 (7)0.0462 (7)0.0071 (5)0.0001 (6)0.0057 (6)
N30.0558 (8)0.0330 (7)0.0442 (7)0.0033 (5)0.0031 (6)0.0077 (5)
N50.0713 (9)0.0351 (7)0.0472 (7)0.0030 (6)0.0027 (6)0.0130 (6)
N420.0686 (9)0.0431 (8)0.0427 (7)0.0038 (6)0.0043 (6)0.0112 (6)
N450.0919 (12)0.0363 (8)0.0562 (9)0.0061 (7)0.0003 (8)0.0122 (7)
S10.0578 (3)0.0409 (2)0.0457 (2)0.00983 (18)0.00520 (17)0.00269 (17)
S20.0686 (3)0.0421 (3)0.0632 (3)0.0075 (2)0.0018 (2)0.0087 (2)
Geometric parameters (Å, º) top
C1—N21.341 (2)C14—H140.9300
C1—S21.6562 (16)C15—C161.359 (3)
C1—S11.7680 (16)C15—H150.9300
C2—N21.459 (2)C16—C171.380 (3)
C2—H2A0.9600C16—H160.9300
C2—H2B0.9600C17—H170.9300
C2—H2C0.9600C41—N421.330 (2)
C4—N31.289 (2)C41—C461.385 (2)
C4—N51.339 (2)C43—N421.332 (2)
C4—C411.493 (2)C43—C441.369 (3)
C11—C121.507 (3)C43—H430.9300
C11—S11.8176 (18)C44—N451.332 (3)
C11—H11A0.9700C44—H440.9300
C11—H11B0.9700C46—N451.332 (2)
C12—C131.376 (3)C46—H460.9300
C12—C171.383 (3)N2—N31.4180 (18)
C13—C141.374 (3)N5—H5A0.8600
C13—H130.9300N5—H5B0.8600
C14—C151.370 (3)
N2—C1—S2124.15 (12)C14—C15—H15120.3
N2—C1—S1111.71 (11)C15—C16—C17120.5 (2)
S2—C1—S1124.14 (10)C15—C16—H16119.8
N2—C2—H2A109.5C17—C16—H16119.8
N2—C2—H2B109.5C16—C17—C12120.90 (19)
H2A—C2—H2B109.5C16—C17—H17119.5
N2—C2—H2C109.5C12—C17—H17119.5
H2A—C2—H2C109.5N42—C41—C46121.46 (15)
H2B—C2—H2C109.5N42—C41—C4116.55 (13)
N3—C4—N5129.82 (15)C46—C41—C4121.98 (14)
N3—C4—C41114.44 (13)N42—C43—C44121.82 (17)
N5—C4—C41115.74 (13)N42—C43—H43119.1
C12—C11—S1106.23 (12)C44—C43—H43119.1
C12—C11—H11A110.5N45—C44—C43122.44 (17)
S1—C11—H11A110.5N45—C44—H44118.8
C12—C11—H11B110.5C43—C44—H44118.8
S1—C11—H11B110.5N45—C46—C41122.03 (16)
H11A—C11—H11B108.7N45—C46—H46119.0
C13—C12—C17117.67 (18)C41—C46—H46119.0
C13—C12—C11121.34 (17)C1—N2—N3115.55 (12)
C17—C12—C11120.98 (17)C1—N2—C2121.70 (14)
C14—C13—C12121.23 (19)N3—N2—C2118.64 (14)
C14—C13—H13119.4C4—N3—N2116.18 (13)
C12—C13—H13119.4C4—N5—H5A120.0
C15—C14—C13120.4 (2)C4—N5—H5B120.0
C15—C14—H14119.8H5A—N5—H5B120.0
C13—C14—H14119.8C41—N42—C43116.43 (15)
C16—C15—C14119.4 (2)C44—N45—C46115.78 (16)
C16—C15—H15120.3C1—S1—C11102.79 (8)
S1—C11—C12—C1383.42 (19)S2—C1—N2—N3170.04 (11)
S1—C11—C12—C1795.62 (19)S1—C1—N2—N310.27 (17)
C17—C12—C13—C141.0 (3)S2—C1—N2—C213.2 (2)
C11—C12—C13—C14179.94 (18)S1—C1—N2—C2167.12 (13)
C12—C13—C14—C150.0 (3)N5—C4—N3—N22.7 (2)
C13—C14—C15—C160.8 (3)C41—C4—N3—N2176.52 (12)
C14—C15—C16—C170.5 (3)C1—N2—N3—C4135.84 (15)
C15—C16—C17—C120.5 (3)C2—N2—N3—C466.56 (19)
C13—C12—C17—C161.3 (3)C46—C41—N42—C431.6 (2)
C11—C12—C17—C16179.64 (18)C4—C41—N42—C43179.97 (15)
N3—C4—C41—N42177.25 (14)C44—C43—N42—C410.4 (3)
N5—C4—C41—N422.1 (2)C43—C44—N45—C461.6 (3)
N3—C4—C41—C461.2 (2)C41—C46—N45—C440.5 (3)
N5—C4—C41—C46179.45 (15)N2—C1—S1—C11179.30 (13)
N42—C43—C44—N451.3 (3)S2—C1—S1—C110.39 (14)
N42—C41—C46—N451.2 (3)C12—C11—S1—C1174.38 (13)
C4—C41—C46—N45179.56 (16)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H5A···N45i0.862.393.135 (2)146
Symmetry code: (i) x, y+1, z.
(D1) N'-Anilinopyrazine-2-carboximidamide top
Crystal data top
C11H11N5F(000) = 448
Mr = 213.25Dx = 1.300 Mg m3
Orthorhombic, Pca21Mo Kα radiation, λ = 0.71073 Å
Hall symbol: p 2c -2acCell parameters from 5484 reflections
a = 20.7274 (6) Åθ = 2.9–31.6°
b = 5.7456 (1) ŵ = 0.09 mm1
c = 9.1455 (3) ÅT = 290 K
V = 1089.15 (5) Å3Plate, colourless
Z = 40.4 × 0.3 × 0.05 mm
Data collection top
Kuma KM-4 CCD area-detector
diffractometer
1415 independent reflections
Radiation source: fine-focus sealed tube1055 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.029
ω scansθmax = 28.3°, θmin = 3.0°
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
h = 2727
Tmin = 0.728, Tmax = 1.000k = 77
15567 measured reflectionsl = 912
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: inferred from neighbouring sites
R[F2 > 2σ(F2)] = 0.030H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.068 w = 1/[σ2(Fo2) + (0.0458P)2]
where P = (Fo2 + 2Fc2)/3
S = 0.90(Δ/σ)max < 0.001
1415 reflectionsΔρmax = 0.11 e Å3
154 parametersΔρmin = 0.12 e Å3
1 restraintAbsolute structure: Flack (1983), with how many Friedel pairs?
Primary atom site location: structure-invariant direct methodsAbsolute structure parameter: 0 (10)
Crystal data top
C11H11N5V = 1089.15 (5) Å3
Mr = 213.25Z = 4
Orthorhombic, Pca21Mo Kα radiation
a = 20.7274 (6) ŵ = 0.09 mm1
b = 5.7456 (1) ÅT = 290 K
c = 9.1455 (3) Å0.4 × 0.3 × 0.05 mm
Data collection top
Kuma KM-4 CCD area-detector
diffractometer
1415 independent reflections
Absorption correction: multi-scan
(SADABS; Sheldrick, 2003)
1055 reflections with I > 2σ(I)
Tmin = 0.728, Tmax = 1.000Rint = 0.029
15567 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.030H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.068Δρmax = 0.11 e Å3
S = 0.90Δρmin = 0.12 e Å3
1415 reflectionsAbsolute structure: Flack (1983), with how many Friedel pairs?
154 parametersAbsolute structure parameter: 0 (10)
1 restraint
Special details top

Experimental. CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.32.13 (release 29–11-2007 CrysAlis171. NET) (compiled Nov 29 2007,17:23:28) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

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. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R-factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
C40.25837 (8)0.8077 (2)0.02592 (15)0.0399 (3)
C110.39995 (8)1.0962 (3)0.0866 (2)0.0472 (4)
C120.42684 (7)0.9455 (3)0.1875 (2)0.0538 (4)
H120.40760.80230.20610.065*
C130.48259 (9)1.0090 (4)0.2608 (3)0.0708 (6)
H130.50050.90660.32830.085*
C140.51185 (9)1.2179 (4)0.2364 (3)0.0781 (7)
H140.54971.25690.28510.094*
C150.48431 (10)1.3700 (4)0.1385 (3)0.0801 (7)
H150.50361.51390.12230.096*
C160.42865 (9)1.3130 (3)0.0639 (2)0.0638 (6)
H160.41041.41840.00120.077*
C410.21834 (7)0.6080 (3)0.01839 (18)0.0398 (3)
C430.12908 (8)0.3876 (3)0.0203 (2)0.0576 (5)
H430.09270.35050.07530.069*
C440.14321 (9)0.2574 (3)0.1009 (2)0.0587 (5)
H440.11540.13760.12740.070*
C460.23302 (8)0.4698 (3)0.13907 (17)0.0477 (4)
H460.27060.50020.19140.057*
H20.3263 (9)1.145 (3)0.034 (2)0.057*
H5A0.2623 (8)1.040 (3)0.180 (2)0.057*
H5B0.1981 (8)0.881 (3)0.177 (2)0.057*
N20.34609 (7)1.0361 (2)0.00504 (18)0.0527 (4)
N30.31069 (6)0.8440 (2)0.04645 (14)0.0445 (3)
N50.23487 (8)0.9418 (3)0.13588 (16)0.0561 (4)
N420.16588 (6)0.5658 (2)0.06184 (15)0.0487 (4)
N450.19526 (7)0.2965 (2)0.18176 (17)0.0556 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
C40.0518 (9)0.0400 (7)0.0278 (8)0.0039 (7)0.0021 (7)0.0063 (6)
C110.0468 (9)0.0453 (8)0.0494 (10)0.0023 (7)0.0121 (8)0.0012 (7)
C120.0519 (9)0.0506 (9)0.0588 (11)0.0012 (7)0.0010 (9)0.0018 (9)
C130.0557 (11)0.0753 (13)0.0813 (15)0.0069 (10)0.0102 (11)0.0106 (12)
C140.0477 (10)0.0786 (14)0.1080 (19)0.0029 (10)0.0010 (12)0.0339 (14)
C150.0603 (12)0.0597 (11)0.120 (2)0.0180 (10)0.0247 (14)0.0216 (14)
C160.0653 (11)0.0488 (10)0.0773 (15)0.0085 (9)0.0181 (10)0.0025 (9)
C410.0464 (8)0.0438 (8)0.0292 (7)0.0028 (6)0.0016 (7)0.0042 (7)
C430.0489 (10)0.0686 (11)0.0551 (12)0.0061 (8)0.0053 (9)0.0072 (10)
C440.0548 (10)0.0586 (10)0.0626 (12)0.0106 (9)0.0064 (9)0.0112 (9)
C460.0570 (10)0.0488 (8)0.0373 (9)0.0038 (7)0.0073 (8)0.0106 (8)
N20.0609 (9)0.0472 (8)0.0499 (9)0.0078 (7)0.0024 (8)0.0170 (7)
N30.0524 (7)0.0449 (7)0.0361 (7)0.0048 (6)0.0015 (6)0.0103 (6)
N50.0702 (10)0.0576 (8)0.0404 (8)0.0095 (8)0.0114 (7)0.0191 (7)
N420.0479 (7)0.0579 (8)0.0403 (8)0.0013 (6)0.0047 (7)0.0105 (7)
N450.0651 (9)0.0529 (8)0.0488 (9)0.0062 (7)0.0006 (8)0.0169 (7)
Geometric parameters (Å, º) top
C4—N31.288 (2)C16—H160.9300
C4—N51.3573 (19)C41—N421.334 (2)
C4—C411.473 (2)C41—C461.393 (2)
C11—C121.383 (3)C43—N421.332 (2)
C11—N21.386 (2)C43—C441.369 (3)
C11—C161.396 (2)C43—H430.9300
C12—C131.385 (3)C44—N451.327 (2)
C12—H120.9300C44—H440.9300
C13—C141.363 (3)C46—N451.3253 (19)
C13—H130.9300C46—H460.9300
C14—C151.376 (3)N2—N31.3784 (18)
C14—H140.9300N2—H20.827 (18)
C15—C161.380 (3)N5—H5A0.894 (18)
C15—H150.9300N5—H5B0.921 (18)
N3—C4—N5126.24 (14)N42—C41—C46120.70 (13)
N3—C4—C41117.35 (12)N42—C41—C4116.70 (13)
N5—C4—C41116.35 (14)C46—C41—C4122.60 (14)
C12—C11—N2121.86 (14)N42—C43—C44121.89 (16)
C12—C11—C16119.09 (17)N42—C43—H43119.1
N2—C11—C16119.03 (17)C44—C43—H43119.1
C11—C12—C13119.61 (17)N45—C44—C43122.19 (16)
C11—C12—H12120.2N45—C44—H44118.9
C13—C12—H12120.2C43—C44—H44118.9
C14—C13—C12121.6 (2)N45—C46—C41122.17 (14)
C14—C13—H13119.2N45—C46—H46118.9
C12—C13—H13119.2C41—C46—H46118.9
C13—C14—C15118.77 (19)N3—N2—C11118.70 (15)
C13—C14—H14120.6N3—N2—H2117.2 (13)
C15—C14—H14120.6C11—N2—H2116.4 (13)
C14—C15—C16121.21 (18)C4—N3—N2115.90 (13)
C14—C15—H15119.4C4—N5—H5A117.4 (11)
C16—C15—H15119.4C4—N5—H5B112.6 (12)
C15—C16—C11119.6 (2)H5A—N5—H5B125.7 (18)
C15—C16—H16120.2C43—N42—C41116.70 (14)
C11—C16—H16120.2C46—N45—C44116.30 (15)
N2—C11—C12—C13176.69 (16)N42—C41—C46—N451.9 (3)
C16—C11—C12—C131.9 (3)C4—C41—C46—N45177.09 (14)
C11—C12—C13—C140.2 (3)C12—C11—N2—N313.7 (2)
C12—C13—C14—C151.2 (3)C16—C11—N2—N3167.66 (15)
C13—C14—C15—C161.0 (3)N5—C4—N3—N21.2 (2)
C14—C15—C16—C110.7 (3)C41—C4—N3—N2178.19 (13)
C12—C11—C16—C152.1 (3)C11—N2—N3—C4174.57 (14)
N2—C11—C16—C15176.50 (18)C44—C43—N42—C411.7 (2)
N3—C4—C41—N42176.93 (14)C46—C41—N42—C430.1 (2)
N5—C4—C41—N425.8 (2)C4—C41—N42—C43178.91 (15)
N3—C4—C41—C464.1 (2)C41—C46—N45—C441.6 (3)
N5—C4—C41—C46173.24 (15)C43—C44—N45—C460.2 (3)
N42—C43—C44—N452.0 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H5B···N3i0.921 (18)2.54 (2)3.106 (2)119.9 (15)
N5—H5A···N45ii0.894 (18)2.135 (19)3.005 (2)164.1 (15)
Symmetry codes: (i) x+1/2, y, z1/2; (ii) x+1/2, y+1, z1/2.

Experimental details

(B1)(C1)(C2)(D1)
Crystal data
Chemical formulaC14H19N5O4S2C8H11N5S2C14H15N5S2C11H11N5
Mr385.46241.34317.43213.25
Crystal system, space groupMonoclinic, C2/cTriclinic, P1Triclinic, P1Orthorhombic, Pca21
Temperature (K)291290290290
a, b, c (Å)29.5249 (14), 8.0969 (9), 15.4717 (6)7.7213 (1), 8.1004 (1), 9.3331 (1)7.2329 (1), 7.9041 (1), 14.0969 (2)20.7274 (6), 5.7456 (1), 9.1455 (3)
α, β, γ (°)90, 98.635 (4), 9087.9959 (11), 79.0802 (12), 82.8402 (10)105.717 (1), 91.368 (1), 93.863 (1)90, 90, 90
V3)3656.7 (5)568.67 (1)773.27 (2)1089.15 (5)
Z8224
Radiation typeMo KαMo KαCu KαMo Kα
µ (mm1)0.320.443.120.09
Crystal size (mm)0.4 × 0.3 × 0.10.3 × 0.3 × 0.30.3 × 0.2 × 0.050.4 × 0.3 × 0.05
Data collection
DiffractometerKuma KM-4 CCD area-detector
diffractometer
Kuma KM-4 CCD area-detector
diffractometer
Bruker SMART APEX CCD area-detector
diffractometer
Kuma KM-4 CCD area-detector
diffractometer
Absorption correctionMulti-scan
(SADABS; Sheldrick, 2003)
Multi-scan
(SADABS; Sheldrick, 2003)
Multi-scan
(SADABS; Sheldrick, 2003)
Multi-scan
(SADABS; Sheldrick, 2003)
Tmin, Tmax0.729, 1.0000.940, 1.0000.735, 1.0000.728, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
21104, 3722, 3064 7633, 2319, 2161 8491, 2647, 2549 15567, 1415, 1055
Rint0.0160.0090.0170.029
(sin θ/λ)max1)0.6250.6250.5950.667
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.029, 0.092, 1.05 0.032, 0.095, 1.12 0.036, 0.098, 1.06 0.030, 0.068, 0.90
No. of reflections3722231926471415
No. of parameters227138191154
No. of restraints0001
H-atom treatmentH-atom parameters constrainedH-atom parameters constrainedH-atom parameters constrainedH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.36, 0.300.36, 0.270.31, 0.270.11, 0.12
Absolute structure???Flack (1983), with how many Friedel pairs?
Absolute structure parameter???0 (10)

Computer programs: CrysAlis CCD (Oxford Diffraction, 2007), APEX2 (Bruker, 2002), CrysAlis RED (Oxford Diffraction, 2007), SAINT-Plus (Bruker, 2003), SHELXTL (Sheldrick, 2008), PLATON (Spek, 2009) and Mercury (Macrae et al., 2006), PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) for (B1) top
D—H···AD—HH···AD···AD—H···A
N5—H5A···N45i0.862.633.320 (2)138.6
C44—H44···O22ii0.932.483.403 (2)173.7
C11—H11A···O12iii0.972.553.473 (2)159.0
N5—H5B···O22iv0.862.373.2002 (17)163.7
Symmetry codes: (i) x, y+1, z; (ii) x, y, z1/2; (iii) x+1/2, y+1/2, z+1/2; (iv) x, y+1, z1/2.
Hydrogen-bond geometry (Å, º) for (C1) top
D—H···AD—HH···AD···AD—H···A
N5—H5A···N45i0.862.242.9975 (19)146.6
N5—H5B···S2ii0.862.873.6387 (16)149.4
Symmetry codes: (i) x+1, y, z; (ii) x, y1, z.
Hydrogen-bond geometry (Å, º) for (C2) top
D—H···AD—HH···AD···AD—H···A
N5—H5A···N45i0.862.393.135 (2)145.8
Symmetry code: (i) x, y+1, z.
Hydrogen-bond geometry (Å, º) for (D1) top
D—H···AD—HH···AD···AD—H···A
N5—H5B···N3i0.921 (18)2.54 (2)3.106 (2)119.9 (15)
N5—H5A···N45ii0.894 (18)2.135 (19)3.005 (2)164.1 (15)
Symmetry codes: (i) x+1/2, y, z1/2; (ii) x+1/2, y+1, z1/2.
Selected bond lengths (Å) and absolute values of selected torsion angles (°) for the title structures, compared with data from the CSD top
StructureC4—C41C4—N5N3—C4N2—N3C1(C11)—N2
B11.486 (2)1.3389 (19)1.2966 (17)1.4079 (17)1.2803 (17)
C11.4919 (19)1.329 (2)1.291 (2)1.4215 (16)1.334 (2)
C21.493 (2)1.339 (2)1.289 (2)1.4180 (18)1.341 (2)
D11.473 (2)1.3577 (19)1.287 (2)1.3786 (17)1.386 (2)
CSD1.46-1.501.32-1.361.29-1.311.36-1.411.27-1.36
N42—C—C—N5C41—C—N—N2C4—N—N—C1(C11)C4—N—N—MeN3—N—C—S2
B11.8 (2)177.67 (12)172.45 (13)178.75 (10)
C127.4 (2)177.88 (13)116.53 (16)78.19 (18)168.75 (11)
C22.1 (2)176.52 (12)135.85 (15)66.56 (18)170.04 (11)
D15.7 (2)178.18 (13)174.58 (14)
 

Footnotes

For Part I, see Olczak et al. (2007[Olczak, A., Główka, M. L., Gołka, J., Szczesio, M., Bojarska, J., Kozłowska, K., Foks, H. & Orlewska, C. (2007). J. Mol. Struct. 830, 171-175.]).

Acknowledgements

This study was supported by the Ministry of Science and Higher Education under project No. N204 111735.

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