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Volume 68 
Part 10 
Pages o392-o394  
October 2012  

Received 30 August 2012
Accepted 31 August 2012
Online 7 September 2012


aFacultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Casilla 233, Santiago, Chile,bDepartamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago de Chile, Chile, and cDepartamento de Física, Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, Buenos Aires, Argentina
Correspondence e-mail: aatria@ciq.uchile.cl

The title compound, C9H8N2, presents two almost identical independent molecules in the asymmetric unit, both of them exhibiting an extremely planar isoquinoline core (maximum r.m.s. deviation = 0.014 Å). The most significant deviation is found in the -NH2 groups, which present a noticeable pyramidalization around the N atom, a feature also present in related structures containing the molecule as a ligand. The supramolecular structure is based on pairs of parallel hydrogen-bonded chains formed by just one molecular type each, defined by the strongest hydrogen bonds in the structure, which are of the N-H...N type. These parallel chains are linked into pairs (or strips) via weaker C-H...N hydrogen bonds. Related strips generated by the c-glide plane define two families running along [[\overline{1}]10] and [110], giving rise to an interesting system of interwoven chains stabilized by a number of weaker contacts of the C-H...[pi] type.


We have previously reported the synthesis and structural analysis of compounds containing aromatic amines (Atria, Astete et al., 2011[Atria, A. M., Astete, A., Garland, M. T. & Baggio, R. (2011). Acta Cryst. E67, m1191-m1192.]; Atria, Garland & Baggio, 2011[Atria, A. M., Garland, M. T. & Baggio, R. (2011). Acta Cryst. C67, m275-m278.], and references therein). In most of these structures, the amine groups are in complexes with lanthanide or transition metal cations, and via their ability to promote nonbonding interactions of different types and strengths (hydrogen bonds, [pi]-[pi] interactions etc.) they end up being the vectors for, usually, highly stable three-dimensional supramolecular structures.

On rare occasions, crystals of the free ligands were serendipitously obtained in addition to (or instead of) the expected complexes, and the analyses of their crystal structures were often worth discussing, not necessarily for the extractable molecular information (which was almost predictable beforehand) but rather for the extremely interesting three-dimensional networks they gave rise to. A representative case with diaminopurine is given by Atria et al. (2010[Atria, A. M., Garland, M. T. & Baggio, R. (2010). Acta Cryst. C66, o547-o552.]).

This report presents a further example of such an unexpected situation (see Experimental for details), viz. the crystal structure of isoquinolin-5-amine, (I)[link], a very simple molecule giving rise to an unusual supramolecular arrangement. It is worth mentioning that, in spite of its simplicity, this ligand is rare from a crystallographic point of view; only one entry could be found in the Cambridge Structural Database (CSD, Version 5.33; Allen, 2002[Allen, F. H. (2002). Acta Cryst. B58, 380-388.]), in which the ligand is bonded to a ZnII nucleus {diazidobis(isoquinolin-5-amine)zinc(II), [Zn(N3)2(C9H8N2)2], (II); Miao et al., 2007[Miao, Z.-X., Shao, M. & Li, M.-X. (2007). Acta Cryst. E63, m1808.]}.

[Scheme 1]

Compound (I)[link] crystallizes in the monoclinic space group Cc with two independent molecules in the asymmetric unit (Fig. 1[link]), which we will characterize hereinafter by the trailing digit in their labels (1 or 2). As stated above, the molecular details depart neither from the usual values found in the CSD nor between the two molecules. A few comparative details between the two independent units are: (i) least-squares molecular fitting, overall r.m.s. deviation = 0.018 Å and maximum deviation (for the N21...N22 pair) = 0.036 Å; (ii) bond distances, overall r.m.s. deviation = 0.004 Å and maximum deviation (for the N2x-C6x bonds) = 0.009 Å (2[sigma]); (iii) bond angles, overall r.m.s. deviation = 0.222° and maximum deviation (for the C3x-C4x-C5x angles) = 0.44° (2[sigma]).

Both isoquinoline nuclei (1 and 2) are planar [overall r.m.s. deviation = 0.0069 Å for both molecules; maximum deviations = 0.0140 (14) Å for C21 and 0.0118 (13) Å for C22], with the amino N atoms deviating significantly from the aromatic least-squares plane [0.161 (2) Å for N21 and 0.089 (2) Å for N22]. This deviation is accompanied by a substantial (though uneven) degree of pyramidality in the arrangement around them, evidencing an N-atom hybridization with a significant sp3 contribution for N21 and a more `flattened' arrangement around atom N22, suggesting a predominant sp2 character. If pyramidality is measured by [chi](N) (the angle between the C-N vector and its projection into the NH2 plane; Allen et al., 1995[Allen, F. H., Bird, C. M., Rowland, R. S., Harris, S. E. & Schwalbe, C. H. (1995). Acta Cryst. B51, 1068-1081.]) [ideal values: [chi](N) = 0° for pure sp2 and 54.7° for pure sp3], the corresponding values for both N atoms in the case of (I)[link] are [chi](N21) = 40.5° (mostly sp3) and [chi](N22) = 28.6° (very nearly midway between sp3 and sp2). This different degree of planarity of amino groups bound to aromatic nuclei is frequently found in the literature (e.g. Atria et al., 2010[Atria, A. M., Garland, M. T. & Baggio, R. (2010). Acta Cryst. C66, o547-o552.]) and is usually ascribed to the variable ability of the delocalized [pi]-system of the ring to accommodate charge from the amino group in the extended resonance structure, a fact probably conditioned by environmental factors such as coordination to a metal centre or hydrogen bonding.

As expected, the main interest of (I)[link] is in the way in which the supramolecular structure builds up. All the responsible noncovalent interactions are of the hydrogen-bonding type, with a diversity of donors (N-H and C-H) and acceptors (N and [pi]), all of them detailed in Table 1[link].

The two conventional N-H...N hydrogen bonds, appearing as the first two entries in Table 1[link], are by far the strongest and they define the two distinct motifs in the structure (Fig. 1[link]), viz. two parallel chains, each formed by a single type of molecule (either 1 or 2). These are in turn linked by a weak nonconventional C-H...N interaction (third entry in Table 1[link]), which defines the hydrogen-bonded two-chain strips shown in Fig. 2[link] on a grey background and running along [[\overline{1}]10] (top to bottom in the figure). The H atoms involved in the main interactions (H21A and H22A) correspond to amino groups. Surprisingly, the remaining H atoms in each NH2 group are not involved in any type of hydrogen-bonding contact. This does not seem to be a particularly unusual effect; a search of the CSD showed that about 5% of the structures presenting aromatic amino units had their NH2 groups asymmetrically hydrogen bonded, as found in (I)[link].

The one-dimensional double-chain substructures are replicated by the c-glide plane into a second family of strips (Fig. 3[link]), forming an angle of 44.32 (2)° with the former ones but now running along [110] and represented in Fig. 2[link] on a white background. These chains are seen exactly in projection in the figure (with the deceptive appearance of single molecules). One of these `vertical' [110] double-chain strips has been highlighted, for clarity.

Finally, these two families are connected via C-H...[pi] intra- and inter-strip crosslinks (entries 4-6 in Table 1[link]), which in Fig. 2[link] appear as `out-of-plane' bonds with the Cg acceptors (underlined labels in the figure), which are either above or below the plane.

As a final remark, we would like to introduce here a word of caution regarding the (frequently uncritical) geometric idealization of O-H and N-H atoms, a fact which can introduce gross interpretation errors in groups like NH2. An example can be found in the related Zn complex, (II), where this simplistic assumption was made in the published results, thus making impracticable any possible comparison with our own results. Taking advantage of the fact that the data set of (II) looked fair {Rint = 0.036 and R[F2 > 2[sigma](F2)] = 0.029} and that the structure factors were available in the literature, we performed a new refinement of the structure of (II) with the amino H atoms subjected to the same restraints as we applied for (I)[link]. To our surprise, an even more enhanced pyramidalization trend was observed around the amino N atoms in the two independent isoquinolin-5-amine units, with two strongly dissimilar degrees of sp2-sp3 hybridization and a similar tendency as in (I)[link] in the corresponding C-N bond distances [[chi] = 15.9 and 40.7°; C-N = 1.358 (4) and 1.385 (3) Å]. The convenience of confirming the H-atom structure through a careful analysis of the difference maps thus becomes apparent.

[Figure 1]
Figure 1
The molecular structure of (I)[link], with displacement ellipsoids drawn at the 40% probability level. Independent (symmetry-related) atoms are shown with heavy (hollow) bonds and filled (empty) ellipsoids. Note the formation of hydrogen-bonded [[\overline{1}]10] chains. [Symmetry code: (i) x + [{1\over 2}], y - [{1\over 2}], z.]
[Figure 2]
Figure 2
A packing view of (I)[link], along the [110] direction, showing on a grey background the two independent chains running top to bottom, parallel to [[\overline{1}]10], and on a white background their c-glide symmetry-related images, perpendicular to the plane of the figure (one of these strips has been isolated on a dark triangular background). N-H...N and C-H...N interactions are represented by dashed lines and C-H...[pi] interactions are represented by thin double lines. Molecules drawn with thin lines correspond to molecule 1 and those in bold to molecule 2. Cg centroids (with underlined labels) are above or below the projection plane. [Symmetry codes: (i) x + [{1\over 2}], y - [{1\over 2}], z; (ii) x + [{1\over 2}], y + [{1\over 2}], z; (iii) x - [{1\over 2}], -y + [{3\over 2}], z + [{1\over 2}]; (iv) x - [{1\over 2}], -y + [{3\over 2}], z - [{1\over 2}].]
[Figure 3]
Figure 3
An [001] view of two c-glide symmetry-related strips, running along the [[\overline{1}]10] and [110] directions. As in Fig. 2[link], molecules drawn with thin lines correspond to molecule 1 and those in bold to molecule 2. Dashed lines represent hydrogen bonds.


Crystals of the title compound were obtained as a by-product during the synthesis of a family of lanthanide complexes with crotonic acid and isoquinolin-5-amine. To an aqueous solution (200 ml) containing the corresponding lanthanide oxide (1 mmol), an aqueous solution (20 ml) of crotonic acid (6 mmol) was added, followed by the isoquinolin-5-amine ligand (1 mmol) dissolved in ethanol (30 ml). The resulting mixture was refluxed for 8 h and filtered. The filtrate was allowed to evaporate at room temperature; in one of the attempts made, good single crystals of (I)[link] suitable for X-ray analysis were unwittingly obtained.

Crystal data
  • C9H8N2

  • Mr = 144.17

  • Monoclinic, C c

  • a = 6.0731 (15) Å

  • b = 14.921 (4) Å

  • c = 16.285 (4) Å

  • [beta] = 95.686 (4)°

  • V = 1468.5 (7) Å3

  • Z = 8

  • Mo K[alpha] radiation

  • [mu] = 0.08 mm-1

  • T = 150 K

  • 0.36 × 0.19 × 0.12 mm

Data collection
  • Bruker SMART CCD area-detector diffractometer

  • Absorption correction: multi-scan (SADABS in SAINT-NT; Bruker, 2002[Bruker (2002). SAINT-Plus (including SADABS). Bruker AXS Inc., Madison, Wisconsin, USA.]) Tmin = 0.98, Tmax = 0.99

  • 6002 measured reflections

  • 3082 independent reflections

  • 2701 reflections with I > 2[sigma](I)

  • Rint = 0.020

  • R[F2 > 2[sigma](F2)] = 0.038

  • wR(F2) = 0.090

  • S = 1.04

  • 3082 reflections

  • 215 parameters

  • 9 restraints

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

  • [Delta][rho]max = 0.15 e Å-3

  • [Delta][rho]min = -0.16 e Å-3

Table 1
Hydrogen-bond geometry (Å, °)

Cg1, Cg2 and Cg4 are the centroids of the N11/C11/C21/C71/C81/C91, C21/C31/C41/C51/C61/C71 and C22/C32/C42/C52/C62/C72 rings, respectively.

D-H...A D-H H...A D...A D-H...A
N21-H21A...N11i 0.91 (2) 2.19 (2) 3.091 (2) 179 (2)
N22-H22A...N12i 0.91 (2) 2.18 (2) 3.083 (3) 173 (2)
C91-H91...N22 0.95 2.55 3.419 (3) 152
C92-H92...Cg1ii 0.95 2.81 3.479 (2) 128
C31-H31...Cg4iii 0.95 2.63 3.423 (2) 141
C32-H32...Cg2iv 0.95 2.67 3.460 (2) 142
Symmetry codes: (i) [x+{\script{1\over 2}}, y-{\script{1\over 2}}, z]; (ii) [x+{\script{1\over 2}}, y+{\script{1\over 2}}, z]; (iii) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z+{\script{1\over 2}}]; (iv) [x-{\script{1\over 2}}, -y+{\script{3\over 2}}, z-{\script{1\over 2}}].

The absolute structure could not be determined for this light-atom structure. All H atoms were clearly seen in a difference Fourier map but were treated differently in the refinement. C-bound H atoms were repositioned at their expected locations and allowed to ride, with C-H = 0.95 Å and Uiso(H) = 1.2Ueq(C). N-bound H atoms, displaying a noticeable pyramidality, were refined isotropically with similarity restraints for the internal distances in both molecules (s.u. on N-H bonds = 0.015 Å and s.u. on H...H distances = 0.025 Å).

Data collection: SMART (Bruker, 2001[Bruker (2001). SMART. Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2002[Bruker (2002). SAINT-Plus (including SADABS). Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: SHELXTL (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); software used to prepare material for publication: SHELXTL and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supplementary data for this paper are available from the IUCr electronic archives (Reference: SK3448 ). Services for accessing these data are described at the back of the journal.


The authors acknowledge the Spanish Research Council (CSIC) for providing a free-of-charge licence to the CSD system and for funding under project FONDECYT 1110154.


Allen, F. H. (2002). Acta Cryst. B58, 380-388.  [ISI] [CrossRef] [details]
Allen, F. H., Bird, C. M., Rowland, R. S., Harris, S. E. & Schwalbe, C. H. (1995). Acta Cryst. B51, 1068-1081.
Atria, A. M., Astete, A., Garland, M. T. & Baggio, R. (2011). Acta Cryst. E67, m1191-m1192.  [CSD] [CrossRef] [details]
Atria, A. M., Garland, M. T. & Baggio, R. (2010). Acta Cryst. C66, o547-o552.  [CSD] [CrossRef] [details]
Atria, A. M., Garland, M. T. & Baggio, R. (2011). Acta Cryst. C67, m275-m278.  [CSD] [CrossRef] [details]
Bruker (2001). SMART. Bruker AXS Inc., Madison, Wisconsin, USA.
Bruker (2002). SAINT-Plus (including SADABS). Bruker AXS Inc., Madison, Wisconsin, USA.
Miao, Z.-X., Shao, M. & Li, M.-X. (2007). Acta Cryst. E63, m1808.  [CrossRef] [details]
Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.  [CrossRef] [details]
Spek, A. L. (2009). Acta Cryst. D65, 148-155.  [ISI] [CrossRef] [details]

Acta Cryst (2012). C68, o392-o394   [ doi:10.1107/S0108270112037602 ]