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ISSN: 2414-3146

(5Z,7Z)-N5,N7-Bis(pyridin-2-yl)-5H-6,7-di­hydro­pyrrolo­[3,4-b]pyrazine-5,7-di­imine

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aInstitute of Chemistry, University of Neuchâtel, Av de Bellevaux 51, CH-2000 Neuchâtel, Switzerland, and bInstitute of Physics, University of Neuchâtel, rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
*Correspondence e-mail: helen.stoeckli-evans@unine.ch

Edited by J. Simpson, University of Otago, New Zealand (Received 1 May 2018; accepted 3 May 2018; online 11 May 2018)

The whole mol­ecule of the title compound, C16H11N7, is relatively planar, with an r.m.s. deviation of 0.061 Å for all 23 heteroatoms. It exhibits symmetric three-centre (bifurcated) intra­molecular hydrogen bonds. In the crystal, mol­ecules are linked by C—H⋯N hydrogen bonds, forming 31 helices propagating along the c-axis direction. Within the helices, there is evidence of offset ππ stacking being present [inter­centroid distances = 3.648 (6) and 3.832 (6) Å].

3D view (loading...)
[Scheme 3D1]
Chemical scheme
[Scheme 1]

Structure description

Symmetrical isoindolines have been synthesized to study a number of properties, such as their birefringence (Wong et al., 2012[Wong, E. W. Y., Ovens, J. S. & Leznoff, D. B. (2012). Chem. Eur. J. 18, 6781-6787.]). The isoindoline 1,3-bis­(2-pyridyl­imino)isoindoline [systematic name: (1Z,3Z)-N1,N3-bis(pyridin-2-yl)isoindoline-1,3-di­imine], possesses mirror symmetry and exhibits symmetric three-centre (bifurcated) intra­molecular hydrogen bonds (Schilf, 2004[Schilf, W. (2004). J. Mol. Struct. 691, 141-148.]). Such compounds are ideal tridentate ligands; for example, a series of six bis­(pyridyl­imino)­isoindolines with different substituents in the 4-position on the pyridine rings have been used to form homoleptic iron complexes for the study of their temperature-dependent spin and redox states (Scheja et al., 2015[Scheja, A., Baade, D., Menzel, D., Pietzonka, C., Schweyen, P. & Bröring, M. (2015). Chem. Eur. J. 21, 14196-14204.]). The title compound, the pyrazine analogue of 1,3-bis­(2-pyridyl­imino)isoindoline, was synthesized to study its coordination behaviour with transition metals (Posel, 1998[Posel, M. (1998). PhD thesis, University of Neuchâtel, Switzerland.]).

The mol­ecular structure of the title compound is illustrated in Fig. 1[link]. The mol­ecule is relatively planar (r.m.s. deviation of 0.061 Å for all 23 heteroatoms), with the two pyridine rings (N4/C6–C10) and (N7/C12–C16) being inclined to each other by 2.7 (5)° and to the central pyrrolo­pyrazine unit (N1/N2/N5/C1–C5/C11) by 4.0 (4) and 4.6 (4)°, respectively. As in 1,3-bis­(2-pyridyl­imino)isoindoline (Schilf, 2004[Schilf, W. (2004). J. Mol. Struct. 691, 141-148.]), the title compound exhibits three-centre (bifurcated) intra­molecular hydrogen bonds (Fig. 1[link] and Table 1[link]), and the configuration about the C=N bonds (C5=N3 and C11=N6) is Z.

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N5—H5N⋯N4 0.88 (6) 2.12 (7) 2.653 (11) 119 (5)
N5—H5N⋯N7 0.88 (6) 2.12 (6) 2.670 (8) 120 (5)
C2—H2⋯N2i 0.93 2.62 3.395 (11) 141
Symmetry code: (i) [-y+{\script{2\over 3}}, x-y+{\script{1\over 3}}, z+{\script{1\over 3}}].
[Figure 1]
Figure 1
The mol­ecular structure of the title compound, with the atom labelling and displacement ellipsoids drawn at the 50% probability level. The intra­molecular three-centre (bifurcated) N—H⋯N hydrogen bonds are shown as dashed lines (see Table 1[link]).

In the crystal, mol­ecules are linked by C—H⋯N hydrogen bonds, forming 31 helices propagating along the c-axis direction (Fig. 2[link] and Table 1[link]). Within the helices there is evidence of offset ππ stacking involving the pyrazine ring (N1/N2/C1–C4; centroid Cg2) and pyridine ring (N7/C12–C16; centroid Cg4), and the two pyridine rings (N4/C6–C10; centroid Cg3, and N7/C12–C16; centroid Cg4): Cg2⋯Cg4ii = 3.648 (6) Å, inter­planar distance = 3.264 (4) Å, slippage = 1.63 Å, and Cg3⋯Cg4iii = 3.832 (6) Å, inter­planar distance = 3.338 (4) Å, slippage = 1.884 Å; symmetry codes: (ii) x, xy, z + [{1\over 2}], (iii) x, xy, z − [{1\over 2}].

[Figure 2]
Figure 2
A partial view along the b axis of the crystal packing of the title compound. The intra- and inter­molecular hydrogen bonds are shown as dashed lines (see Table 1[link]; atoms H5N and H2 are shown as grey balls).

There are small channel-like cavities in the crystal, with a total potential solvent area volume of ca 72 Å3 (ca 1.1% of the unit-cell volume). They are represented in brown/yellow in Fig. 3[link]. There is no evidence of any residual electron density being present in these cavities on examination of the final difference Fourier map (see Table 2[link]).

Table 2
Experimental details

Crystal data
Chemical formula C16H11N7
Mr 301.32
Crystal system, space group Trigonal, R3c:H
Temperature (K) 293
a, c (Å) 29.781 (4), 8.3901 (14)
V3) 6444.3 (19)
Z 18
Radiation type Mo Kα
μ (mm−1) 0.09
Crystal size (mm) 0.68 × 0.19 × 0.19
 
Data collection
Diffractometer Stoe Siemens AED2 four-circle
No. of measured, independent and observed [I > 2σ(I)] reflections 7762, 2629, 1606
Rint 0.115
(sin θ/λ)max−1) 0.606
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.066, 0.147, 1.10
No. of reflections 2629
No. of parameters 213
No. of restraints 2
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.19, −0.18
Computer programs: STADI4 and X-RED (Stoe & Cie, 1997[Stoe & Cie (1997). STADI4 and X-RED. Stoe & Cie GmbH, Damstadt, Germany.]), SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]), Mercury (Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]), SHELXL2014 (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) and publCIF (Westrip, 2010[Westrip, S. P. (2010). J. Appl. Cryst. 43, 920-925.]).
[Figure 3]
Figure 3
A view along the c axis of the crystal packing of the title compound. The hydrogen bonds are shown as dashed lines (see Table 1[link]) and only H atoms H5N and H2 have been included (grey balls). The small cavities (ca 1.1% of the unit-cell volume) are represented in brown/yellow (Mercury; Macrae et al., 2008[Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.]).

Synthesis and crystallization

The title compound was synthesized by the reaction of pyrazine-2,3-dicarbo­nitrile with 2-amino­pyridine.

Synthesis of pyrazine-2,3-dicarbo­nitrile (L). 12.5 ml of deionized water in a round-bottomed flask fitted with a reflux condenser was acidified with H2SO4 (tech.) to pH = 1, then with vigorous stirring 2.7 g (0.025 mol) of 2,3-di­amino­maleo­nitrile were added. After it had dissolved (temp = 323 K), a suspension of 5.8 g (0.0 3 mol) of a 30% aqueous solution of glyoxal was added slowly dropwise. An orange precipitate was obtained and the suspension was warmed to 370 K and stirred at this temperature for 1.3 h. The suspension was then cooled to room temperature, and the orange product filtered off and washed several times with small amounts of deionized water. Immediately after, the product was purified by dissolving in a mixture of diluted oxalic acid (2–3% aqueous solution) and ethanol and heating it almost to boiling point, with the addition of active carbon; the mixture was then heated to reflux for 10 min and filtered immediately. The pale-yellow solution was left overnight in a refrigerator and the next day a white crystalline product was filtered off and washed several times with ethanol. The product was dried under vacuum in a desiccator over silica (yield 2.8 g, 86%; m.p. 404–405 K). IR (KBr pellet, cm−1): 3425, 3105, 3075, 3056, 2929, 2818, 2708, 2359, 2296, 2245, 2103, 1977, 1862, 1748, 1645, 1564, 1551, 1525, 1413, 1387, 1270, 1224, 1178, 1143, 1121, 1082, 1053, 990, 972, 876, 865, 695, 613, 574, 537, 470, 446. This compound (CAS-number 13481–25-9) is also available commercially.

Synthesis of the title compound. A round-bottomed flask was charged with 0.65 g (5 mmol) of L, 0.06 g (0.054 mmol) of anhydrous CaCl2 and 0.99 g (10.5 mmol) of 2-amino­pyridine and 25 ml of dry 1-butanol. The mixture was heated for 48 h at 333 K to give a green product. The resulting solution was evaporated to dryness under reduced pressure, and the residue was dissolved in 40 ml of deionized water. The product was extracted several times with chloro­form (4 × 100 ml), then the solution was again evaporated to dryness under reduced pressure and dried in a vacuum desiccator over silica (yield: 1.35 g, 89.6%). The pale-green–brown product was chromatographed over silica (Kieselgel 60 particle size 0.063–0.200, 70–230 Mesh ASTM, Merck) with chloro­form as eluent; the yellow fraction was collected. After evaporated to dryness under reduced pressure, the yellow product obtained was dried in a vacuum desiccator over silica (yield 0.5 g, 37%; m.p. 547–548 K). Calculated for C16H11N7 (%): C 63.78, H 3.68, N 32.54; found: C 63.69, H 3.89, N 32.40%. IR (KBr pellet, cm−1): 3443, 3057, 1706, 1641, 1607, 1581, 1554, 1477, 1458, 1435, 1378, 1354, 1296, 1261, 1249, 1203, 1166, 1139, 1091, 1053, 998, 870, 790, 736, 725, 705, 538, 484, 431, 413.

Note: Despite many crystallization attempts, it was not possible to obtain suitable crystals of the yellow product. The only crystals of the title compound, suitable for crystal structure analysis, were obtained from reactions of the title compound with metal salts.

Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. The NH hydrogen was located in a difference Fourier map and freely refined.

Structural data


Computing details top

Data collection: STADI4 (Stoe & Cie, 1997); cell refinement: STADI4 (Stoe & Cie, 1997); data reduction: X-RED (Stoe & Cie, 1997); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: PLATON (Spek, 2009) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL2014 (Sheldrick, 2015), PLATON (Spek, 2009) and publCIF (Westrip, 2010).

(5Z,7Z)-N5,N7-Bis(pyridin-2-yl)-5H-6,7-dihydropyrrolo[3,4-b]pyrazine-5,7-diimine top
Crystal data top
C16H11N7Dx = 1.398 Mg m3
Mr = 301.32Mo Kα radiation, λ = 0.71069 Å
Trigonal, R3c:HCell parameters from 17 reflections
a = 29.781 (4) Åθ = 12.8–19.2°
c = 8.3901 (14) ŵ = 0.09 mm1
V = 6444.3 (19) Å3T = 293 K
Z = 18Rod, brown
F(000) = 28080.68 × 0.19 × 0.19 mm
Data collection top
Stoe Siemens AED2 four-circle
diffractometer
Rint = 0.115
Radiation source: fine-focus sealed tubeθmax = 25.5°, θmin = 2.4°
Plane graphite monochromatorh = 3536
ω/2θ scansk = 1836
7762 measured reflectionsl = 109
2629 independent reflections3 standard reflections every 60 min
1606 reflections with I > 2σ(I) intensity decay: 2%
Refinement top
Refinement on F2Secondary atom site location: difference Fourier map
Least-squares matrix: fullHydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.066H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.147 w = 1/[σ2(Fo2) + (0.0368P)2 + 9.7595P]
where P = (Fo2 + 2Fc2)/3
S = 1.10(Δ/σ)max < 0.001
2629 reflectionsΔρmax = 0.19 e Å3
213 parametersΔρmin = 0.18 e Å3
2 restraintsExtinction correction: SHELXL2014 (Sheldrick, 2015), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4
Primary atom site location: structure-invariant direct methodsExtinction coefficient: 0.0017 (2)
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
N10.3344 (2)0.1923 (2)0.7094 (7)0.0466 (16)
N20.2900 (2)0.2525 (2)0.5971 (7)0.0469 (17)
N30.1969 (3)0.1841 (2)0.3886 (7)0.0461 (17)
N40.1451 (3)0.1023 (3)0.2631 (9)0.066 (2)
N50.2247 (2)0.1224 (2)0.4508 (7)0.0387 (15)
H5N0.201 (2)0.095 (2)0.399 (8)0.07 (3)*
N60.2733 (2)0.0847 (2)0.5673 (7)0.0405 (15)
N70.2067 (3)0.0269 (2)0.3879 (8)0.0466 (17)
C10.3524 (3)0.2415 (3)0.7485 (10)0.051 (2)
H10.38110.25730.81560.061*
C20.3310 (3)0.2710 (3)0.6946 (10)0.051 (2)
H20.34590.30530.72830.062*
C30.2718 (3)0.2029 (3)0.5587 (8)0.0383 (18)
C40.2929 (3)0.1738 (3)0.6132 (8)0.0369 (18)
C50.2269 (3)0.1699 (3)0.4560 (9)0.0412 (18)
C60.1564 (3)0.1507 (4)0.2875 (9)0.050 (2)
C70.1303 (4)0.1729 (4)0.2118 (11)0.064 (3)
H70.13910.20710.23200.077*
C80.0912 (4)0.1426 (5)0.1063 (12)0.078 (3)
H80.07340.15630.05300.093*
C90.0785 (4)0.0923 (5)0.0803 (12)0.087 (4)
H90.05190.07110.01060.105*
C100.1060 (4)0.0741 (4)0.1597 (14)0.090 (3)
H100.09750.03990.14170.108*
C110.2634 (3)0.1217 (3)0.5432 (8)0.0365 (17)
C120.2447 (3)0.0363 (3)0.4909 (9)0.0401 (17)
C130.2587 (3)0.0006 (3)0.5267 (11)0.054 (2)
H130.28540.00700.59840.065*
C140.2327 (4)0.0486 (3)0.4549 (11)0.065 (3)
H140.24110.07410.47850.078*
C150.1944 (4)0.0579 (3)0.3483 (11)0.063 (3)
H150.17670.08970.29620.075*
C160.1822 (3)0.0197 (3)0.3189 (11)0.054 (2)
H160.15570.02670.24730.064*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.043 (4)0.045 (4)0.050 (4)0.021 (3)0.007 (3)0.007 (3)
N20.057 (4)0.035 (4)0.046 (4)0.021 (3)0.005 (4)0.000 (3)
N30.054 (4)0.054 (4)0.041 (4)0.035 (4)0.002 (3)0.002 (3)
N40.058 (5)0.059 (5)0.079 (6)0.027 (4)0.018 (4)0.007 (4)
N50.040 (4)0.033 (4)0.042 (4)0.018 (3)0.008 (3)0.001 (3)
N60.042 (4)0.037 (4)0.045 (4)0.021 (3)0.002 (3)0.003 (3)
N70.050 (4)0.034 (4)0.052 (4)0.019 (3)0.003 (3)0.002 (3)
C10.047 (5)0.049 (5)0.052 (5)0.021 (4)0.003 (4)0.006 (4)
C20.057 (5)0.037 (5)0.052 (5)0.016 (4)0.001 (4)0.007 (4)
C30.046 (5)0.036 (4)0.033 (4)0.021 (4)0.002 (3)0.004 (3)
C40.037 (4)0.035 (4)0.036 (4)0.016 (4)0.007 (3)0.002 (3)
C50.046 (5)0.037 (4)0.043 (5)0.023 (4)0.008 (4)0.002 (4)
C60.048 (5)0.065 (6)0.044 (5)0.034 (5)0.006 (4)0.004 (4)
C70.068 (6)0.103 (8)0.043 (5)0.059 (6)0.003 (5)0.000 (5)
C80.075 (7)0.138 (10)0.054 (6)0.079 (8)0.001 (5)0.003 (7)
C90.061 (7)0.136 (10)0.072 (7)0.055 (7)0.022 (5)0.023 (7)
C100.074 (7)0.083 (8)0.100 (8)0.030 (6)0.034 (7)0.027 (7)
C110.037 (4)0.038 (4)0.038 (4)0.021 (4)0.006 (3)0.003 (3)
C120.045 (4)0.031 (4)0.044 (4)0.019 (4)0.010 (4)0.004 (3)
C130.062 (5)0.050 (5)0.062 (5)0.038 (5)0.001 (4)0.001 (4)
C140.087 (7)0.049 (6)0.071 (6)0.043 (6)0.012 (6)0.005 (5)
C150.079 (7)0.038 (5)0.062 (6)0.023 (5)0.012 (5)0.003 (4)
C160.056 (5)0.043 (5)0.055 (5)0.019 (4)0.006 (4)0.004 (4)
Geometric parameters (Å, º) top
N1—C11.324 (9)C3—C51.477 (10)
N1—C41.341 (9)C4—C111.472 (9)
N2—C31.335 (9)C6—C71.400 (11)
N2—C21.338 (10)C7—C81.380 (13)
N3—C51.293 (9)C7—H70.9300
N3—C61.402 (10)C8—C91.367 (14)
N4—C61.319 (11)C8—H80.9300
N4—C101.354 (11)C9—C101.362 (14)
N5—C51.384 (8)C9—H90.9300
N5—C111.397 (9)C10—H100.9300
N5—H5N0.88 (3)C12—C131.389 (10)
N6—C111.288 (9)C13—C141.378 (11)
N6—C121.410 (9)C13—H130.9300
N7—C161.335 (9)C14—C151.364 (12)
N7—C121.340 (9)C14—H140.9300
C1—C21.396 (11)C15—C161.379 (11)
C1—H10.9300C15—H150.9300
C2—H20.9300C16—H160.9300
C3—C41.377 (10)
C1—N1—C4112.6 (7)C6—C7—H7121.1
C3—N2—C2112.6 (7)C9—C8—C7120.0 (9)
C5—N3—C6121.5 (7)C9—C8—H8120.0
C6—N4—C10116.7 (8)C7—C8—H8120.0
C5—N5—C11112.3 (6)C10—C9—C8117.8 (10)
C5—N5—H5N123 (6)C10—C9—H9121.1
C11—N5—H5N124 (6)C8—C9—H9121.1
C11—N6—C12121.6 (6)N4—C10—C9124.5 (10)
C16—N7—C12117.4 (7)N4—C10—H10117.7
N1—C1—C2123.8 (8)C9—C10—H10117.7
N1—C1—H1118.1N6—C11—N5129.9 (6)
C2—C1—H1118.1N6—C11—C4124.6 (6)
N2—C2—C1123.3 (7)N5—C11—C4105.5 (6)
N2—C2—H2118.3N7—C12—C13122.2 (7)
C1—C2—H2118.3N7—C12—N6121.4 (6)
N2—C3—C4123.8 (7)C13—C12—N6116.5 (7)
N2—C3—C5127.4 (7)C14—C13—C12119.4 (8)
C4—C3—C5108.7 (6)C14—C13—H13120.3
N1—C4—C3123.9 (7)C12—C13—H13120.3
N1—C4—C11127.9 (7)C15—C14—C13118.5 (8)
C3—C4—C11108.2 (6)C15—C14—H14120.8
N3—C5—N5129.2 (7)C13—C14—H14120.8
N3—C5—C3125.5 (7)C14—C15—C16119.2 (9)
N5—C5—C3105.2 (6)C14—C15—H15120.4
N4—C6—C7123.1 (9)C16—C15—H15120.4
N4—C6—N3121.9 (7)N7—C16—C15123.4 (8)
C7—C6—N3115.0 (8)N7—C16—H16118.3
C8—C7—C6117.9 (10)C15—C16—H16118.3
C8—C7—H7121.1
C4—N1—C1—C20.4 (11)N3—C6—C7—C8177.8 (7)
C3—N2—C2—C10.6 (11)C6—C7—C8—C90.9 (13)
N1—C1—C2—N20.4 (13)C7—C8—C9—C100.8 (16)
C2—N2—C3—C40.1 (10)C6—N4—C10—C90.3 (17)
C2—N2—C3—C5179.1 (7)C8—C9—C10—N40.2 (19)
C1—N1—C4—C30.9 (10)C12—N6—C11—N52.8 (11)
C1—N1—C4—C11178.6 (7)C12—N6—C11—C4177.3 (6)
N2—C3—C4—N10.8 (11)C5—N5—C11—N6179.8 (7)
C5—C3—C4—N1179.9 (7)C5—N5—C11—C40.1 (8)
N2—C3—C4—C11178.8 (6)N1—C4—C11—N61.0 (11)
C5—C3—C4—C111.8 (7)C3—C4—C11—N6179.0 (7)
C6—N3—C5—N53.1 (12)N1—C4—C11—N5179.1 (7)
C6—N3—C5—C3177.3 (6)C3—C4—C11—N51.1 (7)
C11—N5—C5—N3178.4 (7)C16—N7—C12—C130.2 (11)
C11—N5—C5—C31.2 (8)C16—N7—C12—N6178.8 (7)
N2—C3—C5—N31.5 (12)C11—N6—C12—N71.2 (10)
C4—C3—C5—N3177.8 (7)C11—N6—C12—C13179.7 (7)
N2—C3—C5—N5178.8 (7)N7—C12—C13—C140.2 (12)
C4—C3—C5—N51.9 (8)N6—C12—C13—C14179.3 (7)
C10—N4—C6—C70.2 (13)C12—C13—C14—C151.1 (13)
C10—N4—C6—N3178.2 (8)C13—C14—C15—C161.4 (13)
C5—N3—C6—N43.7 (11)C12—N7—C16—C150.2 (12)
C5—N3—C6—C7174.4 (7)C14—C15—C16—N71.0 (13)
N4—C6—C7—C80.4 (13)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N5—H5N···N40.88 (6)2.12 (7)2.653 (11)119 (5)
N5—H5N···N70.88 (6)2.12 (6)2.670 (8)120 (5)
C2—H2···N2i0.932.623.395 (11)141
Symmetry code: (i) y+2/3, xy+1/3, z+1/3.
 

Funding information

Funding for this research was provided by: Swiss National Science Foundation; University of Neuchâtel.

References

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