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ISSN: 2052-5206

Pressure-induced polymorphism in cyclo­propyl­amine

aSchool of Chemistry, The University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ, Scotland
*Correspondence e-mail: p.lozano-casal@ed.ac.uk

(Received 20 April 2005; accepted 17 August 2005)

The crystal structure of cyclopropylamine at 1.2 GPa has been determined by X-ray diffraction methods. The structure of this phase is orthorhombic, space group Pbca and the unit-cell dimensions are a =  5.0741 (10), b  =  9.7594 (10) and c  =  13.305 (2) Å. Only one of the two H atoms of the amino group actively participates in the formation of the hydrogen-bonded chains, C(2) in graph-set notation, which lie parallel to the crystallographic a axis. Additionally, the topology of the crystal packing is studied using both Voronoi–Dirichlet polyhedra and Hirshfeld surface analyses for the low-temperature and the high-pressure structures of cyclopropyl­amine and the results are compared.

1. Introduction

The main features of the hydrogen bond, which determine its strength, are the donor H atom to acceptor distance and the angle formed between them. The strength of the hydrogen bond increases as the donor H atom to acceptor distance decreases and as the angle donor—H atom—acceptor gets closer to 180°. The electronegative character of the donor and acceptor atoms plays an important role in the strength of hydrogen bonding. Thus, the more electronegative the atoms, the stronger the hydrogen bond. Typical distances for strong hydrogen bonds are between 1.2 and 1.5 Å, with angles between 170 and 180° and an example of such a bond is F—H⋯F. However, the type of hydrogen bond reported in this work is the N—H⋯N hydrogen bond, which is classified as moderate to weak (Desiraju & Steiner, 2001[Desiraju, G. & Steiner, T. (2001). The Weak Hydrogen Bond. Oxford University Press.]; Steiner, 2002[Steiner, T. (2002). Angew. Chem. Int. Ed. Engl. 41, 49-76.]), with distances between 1.5 and 2.2 Å, and angles greater than 130°. This type of hydrogen bond is commonly present in amines and their derivatives, and it is present in cyclopropyl­amine. Pressure has a significant effect not only on the hydrogen bond but on other intermolecular interactions present in the crystal structure such as van der Waals forces and steric effects. Consequently, when pressure is applied to the structure, the molecules are displaced from their equilibrium positions to form a generally more compact packing. These changes are driven by the competition between the formation of hydrogen bonding, minimizing steric effects and the necessity of achieving a maximum coordination index, and an optimum filling of space. Hydrogen-bond distances are, consequently, compressed (or expanded) as a consequence of pressure. Therefore, the study of how the properties of the hydrogen bonding are influenced by pressure might enhance our understanding of the hydrogen bond and, in turn, the crystal structures that these molecular systems adopt.

As well as inducing changes in the geometry of intermolecular interactions, pressure can also affect the crystal structures of small-molecule systems leading to the formation of previously unobserved polymorphs. We have already investigated the high-pressure polymorphism of a range of fundamental small-molecule systems including simple monoalcohols and carboxylic acids (for example, methanol, ethanol, formic acid, acetic acid and propionic acid), ketones (such as acetone) and the oxoacids (such as sulfuric acid; Allan et al., 1998[Allan, D. R., Clark, S. J., Brugmans, M. J. P., Ackland, G. J. & Vos, W. L. (1998). Phys. Rev. B, 58, R11809.]; Allan & Clark, 1999a[Allan, D. R . & Clark, S. J. (1999a). J. Phys. Rev. B, 60, 6328-6334.],b[Allan, D. R. & Clark, S. J. (1999b). J. Phys. Rev. Lett. 82, 3464-3467.]; Allan et al., 1999[Allan, D. R., Clark, S. J., Ibberson, R. M., Parsons, S., Pulham, C. R. & Sawyer, L. (1999). Chem. Commun. 8, 751-752.], 2000[Allan, D. R., Clark, S. J., Parsons, S. & Ruf, M. (2000). J. Phys. Condens. Matter, 12, L613-L618.], 2001[Allan, D. R., Parsons, S. & Teat, S. J. (2001). J. Synchrotron Rad. 8, 10-17.], 2002[Allan, D. R., Clark, S. J., Dawson, A., McGregor, P. A. & Parsons, S. (2002). Acta Cryst. B58, 1018-1024.]). We have also investigated more complex molecular materials such as pharmaceutical compounds [e.g. paracetamol (Fabbiani et al., 2003[Fabbiani, F. P. A., Allan, D. R., Dawson, A., David, W. I. F., McGregor, P. A., Oswald, I. D. H., Parsons, S. & Pulham, C. R. (2003). Chem. Commun. 24, 3004-3005.])].

We are now extending this work to include other monofunctional systems, such as the amines, and here we report a high-pressure polymorph of cyclopropylamine, whose structure has been determined at 1.2 GPa using single-crystal X-ray diffraction techniques. The new phase, phase II, crystallizes at high pressure in the orthorhombic space group Pbca, with one molecule in the asymmetric unit and eight molecules in the unit cell. The previously reported low-temperature phase I structure crystallizes in the rhombohedral space group R3c. A detailed analysis and comparison of the hydrogen bonding in both polymorphs reveals substantial differences. The mol­ecules at high pressure are no longer arranged in R33 (6) rings but, instead, they form zigzag chains of molecules along the a axis, expressed as C(2) in the graph-set notation (Berstein et al., 1995[Berstein, J., Davis, R. E., Shimoni, L. & Chang, N. L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

2. Experimental

Liquid cyclopropylamine was loaded and pressurized in a Merrill–Bassett diamond–anvil cell (DAC; Merrill & Basset, 1974[Merrill, L. & Basset, W. A. (1974). Rev. Sci. Instrum. 45, 290-294.]) that was equipped with 600 µm culet diamonds and a tungsten gasket. After the nucleation of several crystallites on pressure increase, the temperature was cycled close to the melting point in order to reduce the number of crystallites until only one crystallite remained. Finally, a single crystal was obtained at 1.2 GPa, after the cell was allowed to cool to ambient temperature.

The DAC was then mounted and centred on a Bruker SMART APEX diffractometer (graphite-monochromated Mo Kα radiation) and a sequence of eight data-collection scans was initiated, following the data-collection strategy of Dawson et al. (2004[Dawson, A., Allan, D. R., Parsons, S. & Ruf, M. (2004). J. Appl. Cryst. 37, 410-416.]). The SMART program (Bruker-AXS, 1997–2001[Bruker-AXS (1997-2001). SMART, Version 5.049-5.059. Bruker-AXS, Madison, Wisconsin, USA.], 1999[Bruker-AXS (1999). GEMINI, Version 1.01. Bruker-AXS, Madison, Wisconsin, USA.]) was used for data-collection control and, with a detector distance of 70 mm, 2θ was set at either +28° or −28° to provide maximum coverage. No beam stop was used as, with this selection of detector distance and 2θ, the primary beam does not impinge on the detector aperture. The eight scans were conducted as a sequence of 3σ frames that each had a range of 0.3° in ω and an exposure time of 30 s. The φ axis was fixed at either 90 or 270°, to ensure that the axis of the diamond-anvil cell was held parallel to the ω/2θ plane so that absorption from the pressure-cell components was minimized and the maximum possible access of reciprocal space was achieved. The overall data-collection time was 15 h. The sample reflections were identified by hand with the aid of the SMART code, and an orientation matrix was determined using the GEMINI program (Bruker-AXS, 1999[Bruker-AXS (1999). GEMINI, Version 1.01. Bruker-AXS, Madison, Wisconsin, USA.]). Data integration and global-cell refinement were performed with the program SAINT (Bruker-AXS, 2002[Bruker-AXS (2002). SAINT, Version 6. Bruker-AXS, Madison, Wisconsin, USA.]). The program ABSORB (Angel, 2004[Angel, R. J. (2004). J. Appl. Cryst. 37, 486-492.]) was used to apply a correction for the absorption caused by the DAC and gasket `shadowing', rejecting reflections for which either the incident or the diffracted beam were completely absorbed by the cell and resulted in shading of the detector. The remaining reflections were corrected for any residual absorption by the pressure-cell components with the program SORTAV (Blessing, 1995[Blessing, R. H. (1995). Acta Cryst. A51, 33-38.], 1997[Blessing, R. H. (1997). J. Appl. Cryst. 30, 421-426.]) and the transmission ranged from 1.017 to 1.273.

The structure was solved in Pbca using direct methods (SHELXTL; Sheldrick, 1997[Sheldrick, G. M. (1997a). SHELXTL. Bruker-AXS, Madison, Wisconsin, USA.]a) and subsequently refined against F2. The crystal structure is composed of eight mol­ecules in the unit cell with one in the asymmetric unit. The unit-cell parameters are a  =  5.0741 (10), b  =  9.7594 (10) and c  =  13.305 (2) Å at 1.2 GPa. One of the most serious difficulties encountered in high-pressure crystallography is the limited volume of reciprocal space that can be sampled owing to shading by the body of the pressure cell. For the Merrill–-Basset cell used in this study, the volume of accessible reciprocal space is limited to approximately 40% of what would be expected for a sample collected on a fibre at ambient conditions to the same resolution. However, the completeness of the data set collected here is 77.9% to 2θ  =  46.5°, despite the constraints of the pressure cell, owing to the relatively high symmetry of the Pbca space group and the orientation of the crystal within the cell. All the H atoms were found in the difference map. A full anisotropic refinement with independent positional parameters for each atom was performed and a common isotropic displacement parameter was also modelled for the H atoms. The structure refined to R = 0.042, Rw = 0.096 for 65 parameters and 344 data with F > 2σ(F). The final difference map extremes were 0.114 and −0.138 e Å−3 and the goodness of fit was 1.176. The refinement and experimental details are presented in Table 1[link].1

Table 1
Experimental details for the data collection of cyclopropylamine at 12 GPa

Crystal data  
Chemical formula C3H7N
Mr 57.10
Cell setting, space group Orthorhombic, Pbca
a, b, c (Å) 5.0741 (10), 9.7594 (10), 13.305 (2)
α, β, γ (°) 90.00, 90.00, 90.00
V3) 658.89 (19)
Z 8
Dx (Mg m−3) 1.151
Radiation type Mo Kα
No. of reflections for cell parameters 844
θ range (°) 2.6–23.0
μ (mm−1) 0.07
Temperature (K) 293 (2)
Crystal form, colour Block, colourless
Crystal size (mm) Not measured
   
Data collection  
Diffractometer CCD area detector
Data collection method ω scans
Absorption correction Multiscan (based on symmetry-related measurements)
Tmin 0.799
Tmax 1.000
No. of measured, independent and observed reflections 371, 371, 344
Criterion for observed reflections I > 2σ(I)
Rint 0.065
θmax (°) 23.3
Range of h, k, l −4 → h → 4
  −10 → k → 10
  −13 → l → 13
   
Refinement  
Refinement on F2
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.096, 1.18
No. of reflections 371
No. of parameters 65
H-atom treatment Mixture of independent and constrained refinement
Weighting scheme w = 1/[σ2(Fo2) + (0.0403P)2 + 0.229P], where P = (Fo2 + 2Fc2)/3
(Δ/σ)max <0.0001
Δρmax, Δρmin (e Å–3) 0.11, −0.14
Computer programs used: SMART (Bruker-AXS, 1997–2001[Bruker-AXS (1997-2001). SMART, Version 5.049-5.059. Bruker-AXS, Madison, Wisconsin, USA.]), SHELXTL (Sheldrick, 1997a[Sheldrick, G. M. (1997a). SHELXTL. Bruker-AXS, Madison, Wisconsin, USA.]), SHELXS97 (Sheldrick, 1997b[Sheldrick, G. M. (1997b). SHELXS97. University of Göttingen, Germany.]), SHELXL97 (Sheldrick, 1997c[Sheldrick, G. M. (1997c). SHELXL97. University of Göttingen, Germany.]).

3. Discussion

3.1. Low-temperature structure (phase I)

Although the low-temperature structure of cyclopropyl­amine has already been reported (de Boer et al., 1986[Boer, J. S. A. M. de, Schenk, H. & Stam, C. H. (1986). Rec. Trav. Chim. 105, 434-435.]; CSD refcode FIGYID), a complete description has not been given of how the molecules are arranged in the crystal structure or the hydrogen bonding. It is important, therefore, to describe the structure at low temperature in detail, in order to compare it to the crystal structure determined at high pressure.

Phase I of cyclopropylamine crystallizes at 170.5 K in the rhombohedral space group R3c, with 18 molecules in the unit cell and one in the asymmetric unit. The hexagonal unit-cell parameters are a  =  18.784 (2) and c  =  5.494 (2) Å. The C atoms of the molecule lie in the same plane, parallel to {[\bar1 7 \bar1]} and the N atom is rotated out of this plane by 147.3° with respect to the C atoms. There are two different N—H⋯N hydrogen-bond interactions (Table 2[link]) present in the structure, which are formed by each of the two H atoms in the amino group. What appear to be very long, and therefore very weak, N—H6⋯N interactions form three-membered rings, or trimers, stacked along the crystallographic c axis, with alternate trimers rotated by 61.8° (see Figs. 1[link] and 2[link]). This contact would be defined as R33(6) in graph-set notation, as the three-membered rings are apparently formed by three donors and three acceptors. However, the distance of this interaction is significantly longer, by ∼ 0.2 Å, than the normal range for N⋯N hydrogen bonds and, although the N—H6⋯N bond angle (150°) would be within expected linits, it is unlikely to offer a significant contribution to the overall intermolecular bonding in the structure. The trimers are bridged by shorter N—H7⋯N hydrogen bonds, which form C(2) zigzag chains of molecules along the crystallographic c direction (Fig. 3[link]).

Table 2
Selected hydrogen-bond distances (Å) and bond angles (°) for the high-pressure phase II of cyclopropylamine from the experimental studies at 12 GPa and for the low-temperature phase I of cyclopropylamine taken from the reported structure by de Boer et al. (1986[Boer, J. S. A. M. de, Schenk, H. & Stam, C. H. (1986). Rec. Trav. Chim. 105, 434-435.])

Interaction N—H⋯N (Å) N⋯N (Å) N—H⋯N (°) N⋯N—C (°)
Phase II        
N—H7⋯Ni 2.30 (3) 3.166 (3) 167 (2) 117.5
Phase I        
N—H6⋯Nii 2.711 3.541 150 130
N—H7⋯Niii 2.285 3.230 177 111
Symmetry codes: (i) −½+x, y, ½−z; (ii) −x+y, −x, z; (iii) x, xy, −½+z.
[Figure 1]
Figure 1
A view along the hydrogen-bond pattern formed by two coupled R33 (6) trimers in the low-temperature phase I of cyclopropylamine (de Boer et al., 1986[Boer, J. S. A. M. de, Schenk, H. & Stam, C. H. (1986). Rec. Trav. Chim. 105, 434-435.]). The trimers are formed by long N—H6⋯N interactions (shown by the solid lines) and alternate trimers are rotated by 61.8° with respect to its neighbours. The trimers are bridged by shorter N—H7⋯N hydrogen bonds.
[Figure 2]
Figure 2
Projection down the crystallographic c axis of the low-temperature phase I crystal structure of cyclopropylamine (de Boer et al., 1986[Boer, J. S. A. M. de, Schenk, H. & Stam, C. H. (1986). Rec. Trav. Chim. 105, 434-435.]).
[Figure 3]
Figure 3
A view of the C(2) chains, formed by the N–H7⋯N hydrogen bond, which run parallel to the c-axis direction in the low-temperature phase I crystal structure of cyclopropylamine (de Boer et al., 1986[Boer, J. S. A. M. de, Schenk, H. & Stam, C. H. (1986). Rec. Trav. Chim. 105, 434-435.]).

An alternative way of describing the crystal structure is by examining an individual molecule and its neighbouring environment. By doing so, an octahedron is formed by molecules and their closest neighbours (Fig. 4[link]). Each polyhedron is formed by six molecules and the N atom of each of the molecules has a nearest N atom at a distance of 3.230 Å, a pair of N atoms at 3.541 Å and a single N atom at 3.629 Å. The octahedra are coupled to form infinite columns along the crystallographic c direction where each of the octahedra share one face and follow an alternating sequence of parallel and perpendicular octahedra, with respect to their axial directions. Overall, each molecule is coordinated by 14 nearest neighbours.

[Figure 4]
Figure 4
Octahedron formed by the arrangement of molecules linked by the N—H⋯N hydrogen bond and the weak N—H⋯N contact in the low-temperature phase of cyclopropyl­amine (de Boer et al., 1986[Boer, J. S. A. M. de, Schenk, H. & Stam, C. H. (1986). Rec. Trav. Chim. 105, 434-435.]). Only the non-H atoms are shown. The bond distances (edges) of the polyhedron are displayed. The long (3.629 Å) N⋯N contact is omitted.

3.2. High-pressure structure (phase II)

At 1.2 GPa, the N atom is rotated 148.7° out of the plane formed by the atoms C1, C2 and C3, which form the ring of C atoms. The cyclopropylamine phase II structure at high pressure is simply formed by molecules connected in a zigzag pattern, via a cis-N—H⋯N hydrogen bond, forming sets of infinite chains [N⋯N distance 3.166 (3) Å], expressed as C(2) in graph-set notation (the repeating unit contains one hydrogen-bond donor and one acceptor). These chains lie parallel to the crystallographic a axis, as can be seen from Figs. 5[link] and 6[link]. Only one of the two H atoms, H7, from the amino group participates in the hydrogen bonding. All the molecules of cyclopropylamine lie on the same side of the plane formed by the chain of hydrogen bonds (Fig. 5[link]). From the view looking down the hydrogen bond (N—H⋯N), the dihedral angle formed by the atoms involved in its formation (C—N—N—C) is 71°, which is relatively close to the 60° required for an ideal gauche conformation. Details about the distances and angles of the hydrogen bond can be found in Table 2[link].

[Figure 5]
Figure 5
An a-axis projection of the high-pressure, Pbca, structure of cyclopropylamine at 1.2 GPa. The crystallographic b axis is horizontal while the c axis is vertical. The molecules are linked via cis hydrogen bonds.
[Figure 6]
Figure 6
One of the crystallographically C(2) unique hydrogen-bonded chains in cyclopropylamine at 1.2 GPa viewed along the b axis. The molecules adopt an alernating 1–1–1 sequence.

The packing motifs adopted by monoalcohols, ROH (Brock & Duncan, 1994[Brock, C. P. & Duncan, L. L. (1994). Chem. Mater. 6, 1307-1312.]), arise from a compromise between the packing requirements of the relatively bulky R groups present in the molecules and the necessity of the hydroxyl groups to get close enough to form the hydrogen bonding. If the R groups are relatively small, the molecules containing the hydroxyl groups will be related by translational symmetry (glide plane or 21 screw axis) forming an approximately coplanar alternating sequence about the central hydrogen-bonded core. For bulkier R groups, the molecules often cannot adopt a simple arrangement owing to steric effects and instead they form chains along three-, four- and sixfold screw axes. Finally, if the R groups occupy an even greater volume, cyclic dimer, trimer, tetramer or hexamer rings can be formed.

Thus, the structures of the two cyclopropylamine polymorphs can be compared with the structures of the monoalcohols at both low temperature and high pressure, which, in general, form molecular chains differing in the arrangement of the molecules about the chains. For example, the crystal structure of ethanol at ambient pressure (Jönsson, 1976[Jönsson, P. G. (1976). Acta Cryst. B32, 232-235.]) forms infinite chains where the molecules are connected by cis- and trans-O—H⋯O hydrogen bonds. However, at high pressure, the molecules of ethanol form linear hydrogen-bonded chains, where the molecules are linked in each chain with their methyl groups aligned in the same direction along the b axis (Allan & Clark, 1999a[Allan, D. R . & Clark, S. J. (1999a). J. Phys. Rev. B, 60, 6328-6334.]; Allan et al., 2001[Allan, D. R., Parsons, S. & Teat, S. J. (2001). J. Synchrotron Rad. 8, 10-17.]). Other similar cases are the low-temperature and high-pressure polymorphs of methanol (Tauer & Lipscomb, 1952[Tauer, K. J. & Lipscomb, W. N. (1952). Acta Cryst. 5, 606-612.]; Narten & Habenschuss, 1984[Narten, A. H. & Habenschuss, A. (1984). J. Chem. Phys. 80, 3387-3391.]; Torrie et al., 1989[Torrie, B. H., Weng, S. X. & Powell, B. M. (1989). Mol. Phys. 67, 575-581.]; Allan et al., 1998[Allan, D. R., Clark, S. J., Brugmans, M. J. P., Ackland, G. J. & Vos, W. L. (1998). Phys. Rev. B, 58, R11809.]), cyclobutanol (McGregor et al., 2005[McGregor, P. A., Allan, D. R., Parsons, S. & Pulham, C. R. (2005). Acta Cryst. B61, 449-454.]) and phenol and mono-fluorophenols, such as 2-chloro­phenol and 4-fluorophenol (Oswald et al., 2005[Oswald, I. D. H., Allan, D. R., Motherwell, S. W. D. & Parsons, S. (2005). Acta Cryst. B61, 69-79.]). All the mono-fluorophenols as well as phenol and cyclopropylamine crystallize under pressure in low-symmetry space groups with the molecules disposed about 21 screw axes. Thus, cyclopropylamine presents a polymorphism similar to that found in alcohols, where pseudo-helices and ring motifs are often observed at low temperature. However, at high pressure they tend to form hydrogen-bonded chains with a simple alternating sequence.

3.3. Comparison of the low-temperature phase I and high-pressure phase II crystal structures

3.3.1. Hirshfeld surfaces

The program Crystal Explorer (UWA Theoretical Chemistry, undated[UWA Theoretical Chemistry (undated). Crystal Explorer, Version 1.0.3, http://www.theochem.uwa.edu.au/crystal_explorer.]) makes use of Hirshfeld surfaces to partition crystal space in molecular crystals so that the packing modes and intermolecular interactions can be explored (McKinnon et al., 2004[McKinnon, J. J., Spackman, M. A. & Mitchell, A. S. (2004). Acta Cryst. B60, 627-668.]). We have used this program to visualize the packing behaviour in phase I and phase II of cyclopropylamine in order to make a more detailed com­pari­son between them.

Hirshfeld surfaces (Hirshfeld, 1977[Hirshfeld, F. L. (1977). Theor. Chim. Acta, 44, 129-138.]) for the low-temperature and high-pressure polymorphs of cyclopropylamine are shown in Fig. 7[link], with the H atoms of the amino group at the top pointing away from the viewer in each case. Only one of the two H atoms of the amino group in the high-pressure phase II polymorph actively participates in the hydrogen bond. This is shown by the red–orange region on the de surface adjacent to the N atom (where de is the distance to the nearest atom centre exterior to the surface). This situation is also observed in the even members of the diamines (e.g. 1,2-ethanediamine, 1,4-butanediamine, 1,6-hexanediamine), as was explained by McKinnon et al. (2004[McKinnon, J. J., Spackman, M. A. & Mitchell, A. S. (2004). Acta Cryst. B60, 627-668.]). Hirshfeld surfaces for the high-pressure polymorph show that there is clearly only a single interaction that could be classified as a hydrogen bond (interaction 1 in Fig. 7[link]). However, the Hirshfeld surfaces for the low-temperature polymorph show a strong contact and a weak contact (interactions 1 and 2 in Fig. 7[link]) present in the structure, which is common to the odd members of the diamines (e.g. 1,3-propanediamine and 1,5-pentanediamine).

[Figure 7]
Figure 7
Hirshfeld surfaces for the low-temperature phase I (top) and high-pressure phase II (bottom) polymorphs of cyclopropylamine. Each molecule is shown with the Hirshfeld surface mapped with curvedness (left), shape index (centre) and de (right), which is the distance to the nearest atom centre exterior to the surface [for this series mapped between 1.0 Å (red) and 2.5 Å (blue)]. The labels 1 and 2 correspond to the strong and weak hydrogen-bond interactions, respectively, present in the crystal structures of phase I and phase II. The NH2 group of the cyclopropylamine molecule for both these projections is oriented in the same way for phase I and phase II with the N atom pointing towards the viewer and the H atoms pointing away from the viewer (as can be seen from the sketch of the molecule shown beside the Hirshfeld surfaces). The H7 and H6 atoms of the low-temperature phase I are involved in the formation of a short and a long hydrogen bond, respectively, whereas the H7 atom of the high-pressure phase II is the only H atom that participates in the formation of hydrogen bonding.

The two-dimensional fingerprint plots (plot of di versus de, where di is the distance to the nearest atom centre interior to the surface) for the two polymorphs stress the systematic differences between the two structures (Fig. 8[link]). One of the main differences is that the voids (upper region of the plots in Fig. 8[link]) are more compact in the high-pressure phase II crystal structure than in the low-temperature phase I structure, indicating that the packing is more efficient. The second difference is that both structures present relatively short hydrogen bonds (the distances labelled 1 in Fig. 8[link]), one of which is slightly shorter in the case of the phase II polymorph. Finally, the phase I structure has two significant hydrogen bonds, while the high-pressure structure has only the one, short, hydrogen bond with the remaining amino H atom not involved in bonding. It can be seen that the second, longer, hydrogen bond of the low-temperature phase I polymorph is weak in nature as it does not form part of the sharp spikes in the Hirshfeld fingerprint, which represent the strong hydrogen bonds (the distance labelled 2 in Fig. 8[link]).

[Figure 8]
Figure 8
Two-dimensional fingerprint plots for the low-temperature (left) and high-pressure (right) polymorphs of cyclopropylamine. The labels 1 and 2 correspond to the strong and weak hydrogen-bond interactions, respectively, present in the crystal structures of phase I and phase II. de and di are the distances to the nearest atom centre exterior and interior to the surface, respectively.
3.3.2. Topological analysis

Topological analyses of phase I and phase II can be useful to rationalize the more significant structural changes caused by pressure. Voronoi–Dirichlet polyhedra (VDPs) were used to analyse the molecular structure of the two polymorphs of cyclopropylamine (Blatov, 2004[Blatov, V. A. (2004). Crystallogr. Rev. 10, 249-318.]).

The calculation of molecular coordination numbers, and topological and geometrical analysis of the environment of the two different polymorphs of cyclopropylamine were carried out by using the TOPOS4.0 program suite (Blatov et al., 1999[Blatov, V. A., Shevchenko, A. P. & Serezhkin, V. N. (1999). Russ. J. Coord. Chem. 25, 453-465.]). Adjacent matrices were calculated using the AUTOCN program using the method of spherical sectors; the minimum solid angle of a Voronoi–Dirichlet polyhedron (VDP) face corresponding to an intermolecular contact was set to zero. Analyses of the VDPs were carried out with the program ADS, with the geometrical centres of the molecules (as opposed to their centres of gravity) as reference points. Coordination sequences were calculated out to three coordination spheres. The results of the topological analysis of cyclopropylamine polymorphs are presented in Fig. 9[link]. The coordination sequences are 14–54–122 and 14–53–120 for the phase I and phase II crystal structures, respectively. Consequently, it can be seen that the structure of phase II is closer to a perfect body-centred cubic structure (14–50–110) than that of phase I. Nevertheless, both structures are significantly distorted from body-centred cubic.

[Figure 9]
Figure 9
Lattice Voronoi–Dirichlet polyhedra in: (a) the low-temperature polymorph and (b) the high-pressure polymorph of cyclopropylamine and (c) for perfect body-centred cubic packing. Combinatorial types (Peresypkina & Blatov, 2000[Peresypkina, E. V. & Blatov, V. A. (2000). Acta Cryst. B56, 501-511.]) can be written as f/vn, where f is the number of faces and v is the number of vertices; n is just an ordinal number to distinguish different VDPs where f and v are equal. These are: (a) 14/21–1, (b) 14/24–1 and (c) 14/24–1. The combinatorial types for (b) and (c) are therefore equivalent.

4. Conclusions

We have determined the high-pressure crystal structure of cyclopropylamine at 1.2 GPa. All the atomic positions were found, including those of the H atoms. Therefore, as the H-atom positions were determined completely, it can be demonstrated directly, and without resorting to purely geometrical considerations, that only one of the H atoms of the amino group is involved in the hydrogen bonding. As both H atoms appear to be involved in the hydrogen bonding in the crystal structure of phase I, this represents a significant difference between the two polymorphs. This change in bonding was also observed in the differences between the Hirshfeld surfaces and fingerprint plots for the two different polymorphs of cyclopropylamine. Finally, the molecular packing environments were studied for the low-temperature and the high-pressure phases I and II of cyclopropylamine and compared with that for perfect body-centred cubic. The molecular environment at 1.2 GPa was found to be less distorted from ideal body-centred cubic packing than that at low temperature.

Supporting information


Computing details top

Program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997).

Figures top
[Figure 1]
[Figure 2]
[Figure 3]
[Figure 4]
[Figure 5]
[Figure 6]
[Figure 7]
[Figure 8]
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(comb) top
Crystal data top
C3H7NF(000) = 256
Mr = 57.10Dx = 1.151 Mg m3
Orthorhombic, PbcaMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ac 2abCell parameters from 844 reflections
a = 5.0741 (10) Åθ = 2.6–23.0°
b = 9.7594 (10) ŵ = 0.07 mm1
c = 13.305 (2) ÅT = 293 K
V = 658.89 (19) Å3Block, colourless
Z = 8 × × mm
Data collection top
CCD area detector
diffractometer
371 independent reflections
Radiation source: fine-focus sealed tube344 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.065
ω scansθmax = 23.3°, θmin = 4.2°
Absorption correction: multi-scan
SORTAV
h = 44
Tmin = 0.799, Tmax = 1.000k = 1010
371 measured reflectionsl = 1313
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)] = 0.042Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.096H atoms treated by a mixture of independent and constrained refinement
S = 1.18 w = 1/[σ2(Fo2) + (0.0403P)2 + 0.229P]
where P = (Fo2 + 2Fc2)/3
371 reflections(Δ/σ)max < 0.001
65 parametersΔρmax = 0.11 e Å3
0 restraintsΔρmin = 0.14 e Å3
Crystal data top
C3H7NV = 658.89 (19) Å3
Mr = 57.10Z = 8
Orthorhombic, PbcaMo Kα radiation
a = 5.0741 (10) ŵ = 0.07 mm1
b = 9.7594 (10) ÅT = 293 K
c = 13.305 (2) Å × × mm
Data collection top
CCD area detector
diffractometer
371 independent reflections
Absorption correction: multi-scan
SORTAV
344 reflections with I > 2σ(I)
Tmin = 0.799, Tmax = 1.000Rint = 0.065
371 measured reflectionsθmax = 23.3°
Refinement top
R[F2 > 2σ(F2)] = 0.0420 restraints
wR(F2) = 0.096H atoms treated by a mixture of independent and constrained refinement
S = 1.18Δρmax = 0.11 e Å3
371 reflectionsΔρmin = 0.14 e Å3
65 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. 022_ALERT_3_A Ratio Unique / Expected Reflections too Low.. 0.78 029_ALERT_3_A _diffrn_measured_fraction_theta_full Low ···.. 0.78 088_ALERT_3_A Poor Data / Parameter Ratio ·················· 5.71 023_ALERT_3_B Resolution (too) Low [sin(th)/Lambda < 0.6]··· 23.26 Deg. The ratio of expected to reported Tmax/Tmin(RR') is < 0.90 T min and Tmax reported: 0.799 1.000 Tmin' and Tmax expected: 1.000 1.000 RR' = 0.799 Please check that your absorption correction is appropriate.

This is due to the fact that the quality of the data is low.

REFLT03_ALERT_3_A Reflection count < 85% complete (theta max?) From the CIF: _diffrn_reflns_theta_max 23.26 From the CIF: _diffrn_reflns_theta_full 23.26 From the CIF: _reflns_number_total 371 TEST2: Reflns within _diffrn_reflns_theta_max Count of symmetry unique reflns 476 Completeness (_total/calc) 77.94% REFNR01_ALERT_3_A Ratio of reflections to parameters is < 6 for a centrosymmetric structure sine(theta)/lambda 0.5556 Proportion of unique data used 1.0000 Ratio reflections to parameters 5.7077

These alerts are due to restrictions of the high-pressure cell.

053_ALERT_1_A Minimum Crystal Dimension Missing (or Error). ? 054_ALERT_1_A Medium Crystal Dimension Missing (or Error). ? 055_ALERT_1_A Maximum Crystal Dimension Missing (or Error). ?

The crystal dimensions were not measured.

PLAT199_ALERT_1_C Check the Reported cell_measurement_temperature 293 PLAT200_ALERT_1_C Check the Reported cell_ambient_temperature ···. 293

The data collection was performed at ambient temperature.

420_ALERT_2_C D—H Without Acceptor N1 - H6 ?

Only one of the hydrogen bonds is involved in hydrogen bonding.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
N10.0207 (4)0.27144 (17)0.17881 (15)0.0381 (6)
C10.0020 (5)0.16221 (19)0.10728 (17)0.0349 (6)
C20.0896 (5)0.0273 (2)0.1476 (2)0.0406 (7)
C30.2726 (5)0.1120 (2)0.0844 (2)0.0416 (7)
H10.126 (5)0.1575 (17)0.0543 (18)0.031 (5)*
H30.124 (5)0.021 (2)0.215 (2)0.046 (7)*
H40.313 (5)0.0826 (19)0.0175 (19)0.045 (6)*
H70.176 (6)0.2696 (19)0.2092 (19)0.038 (7)*
H20.025 (5)0.054 (2)0.1185 (19)0.049 (6)*
H50.407 (6)0.157 (2)0.119 (2)0.052 (7)*
H60.002 (5)0.352 (3)0.152 (2)0.058 (8)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
N10.0362 (16)0.0344 (11)0.0438 (14)0.0011 (8)0.0033 (9)0.0003 (8)
C10.0297 (19)0.0371 (11)0.0377 (18)0.0014 (8)0.0032 (9)0.0006 (9)
C20.0431 (19)0.0335 (11)0.0452 (19)0.0006 (9)0.0005 (10)0.0031 (10)
C30.040 (2)0.0469 (12)0.0376 (18)0.0009 (11)0.0068 (10)0.0028 (10)
Geometric parameters (Å, º) top
N1—C11.434 (3)C2—C31.500 (3)
N1—H70.88 (3)C2—H30.91 (3)
N1—H60.87 (3)C2—H20.94 (2)
C1—C31.489 (4)C3—H40.96 (2)
C1—C21.490 (3)C3—H50.93 (3)
C1—H10.96 (2)
C1—N1—H7111.1 (14)C3—C2—H3117.8 (14)
C1—N1—H6113.0 (18)C1—C2—H2119.4 (14)
H7—N1—H6109 (2)C3—C2—H2116.7 (15)
N1—C1—C3117.0 (2)H3—C2—H2114 (2)
N1—C1—C2116.2 (2)C1—C3—C259.78 (15)
C3—C1—C260.48 (15)C1—C3—H4119.0 (14)
N1—C1—H1117.9 (12)C2—C3—H4119.2 (12)
C3—C1—H1117.4 (15)C1—C3—H5114.9 (16)
C2—C1—H1115.1 (10)C2—C3—H5116.1 (17)
C1—C2—C359.75 (16)H4—C3—H5116 (2)
C1—C2—H3118.1 (13)

Experimental details

Crystal data
Chemical formulaC3H7N
Mr57.10
Crystal system, space groupOrthorhombic, Pbca
Temperature (K)293
a, b, c (Å)5.0741 (10), 9.7594 (10), 13.305 (2)
V3)658.89 (19)
Z8
Radiation typeMo Kα
µ (mm1)0.07
Crystal size (mm) × ×
Data collection
DiffractometerCCD area detector
diffractometer
Absorption correctionMulti-scan
SORTAV
Tmin, Tmax0.799, 1.000
No. of measured, independent and
observed [I > 2σ(I)] reflections
371, 371, 344
Rint0.065
θmax (°)23.3
(sin θ/λ)max1)0.556
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.042, 0.096, 1.18
No. of reflections371
No. of parameters65
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.11, 0.14

Computer programs: SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997).

 

Footnotes

1Supplementary data for this paper are available from the IUCr electronic archives (Reference: WS5029 ). Services for accessing these data are described at the back of the journal.

Acknowledgements

We thank the Engineering and Physical Sciences Research Council of the UK for funding PLC's PhD studentship and DRA's EPSRC Advanced Research Fellowship.

References

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