organic compounds\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

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ISSN: 2056-9890

5-Amino­pentan-1-ol

aNelson Mandela Metropolitan University, Summerstrand Campus, Department of Chemistry, University Way, Summerstrand, PO Box 77000, Port Elizabeth 6031, South Africa
*Correspondence e-mail: richard.betz@webmail.co.za

(Received 2 June 2011; accepted 23 June 2011; online 30 June 2011)

The title compound, C5H13NO, is an aliphatic amino­alcohol with both functional groups residing on terminal C atoms. Apart from the hy­droxy group, all non-H atoms are nearly co-planar, the maximum deviation of an atom taking part in the least-squares plane defined by the mentioned non-H atoms being 0.029 (1) Å. In the crystal, O—H⋯N and N—H⋯O hydrogen bonds connect the mol­ecules, forming a three-dimensional network.

Related literature

For the crystal structure of 5-amino­valeric acid, see: Honda et al. (1990[Honda, K., Goto, M. & Kurahashi, M. (1990). Chem. Lett. pp. 13-16.]). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990[Etter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256-262.]); Bernstein et al. (1995[Bernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555-1573.]).

[Scheme 1]

Experimental

Crystal data
  • C5H13NO

  • Mr = 103.16

  • Orthorhombic, P c c n

  • a = 10.0973 (2) Å

  • b = 17.4145 (4) Å

  • c = 7.0564 (1) Å

  • V = 1240.79 (4) Å3

  • Z = 8

  • Mo Kα radiation

  • μ = 0.08 mm−1

  • T = 100 K

  • 0.57 × 0.54 × 0.51 mm

Data collection
  • Bruker APEXII CCD diffractometer

  • 10385 measured reflections

  • 1530 independent reflections

  • 1422 reflections with I > 2σ(I)

  • Rint = 0.030

Refinement
  • R[F2 > 2σ(F2)] = 0.032

  • wR(F2) = 0.089

  • S = 1.06

  • 1530 reflections

  • 76 parameters

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

  • Δρmax = 0.38 e Å−3

  • Δρmin = −0.18 e Å−3

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
O1—H81⋯N1i 0.879 (14) 1.851 (14) 2.7284 (8) 176.5 (12)
N1—H71⋯O1ii 0.886 (13) 2.225 (13) 3.0768 (9) 161.3 (10)
N1—H72⋯O1iii 0.881 (12) 2.248 (12) 3.0954 (8) 161.2 (9)
Symmetry codes: (i) [-x+1, y+{\script{1\over 2}}, -z+{\script{1\over 2}}]; (ii) -x+1, -y, -z; (iii) [x-{\script{1\over 2}}, -y, -z+{\script{1\over 2}}].

Data collection: APEX2 (Bruker, 2010[Bruker (2010). APEX2 and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.]); cell refinement: SAINT (Bruker, 2010[Bruker (2010). APEX2 and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.]); data reduction: SAINT; program(s) used to solve structure: SIR97 (Altomare et al., 1999[Altomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115-119.]); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]); molecular graphics: ORTEP-3 (Farrugia, 1997[Farrugia, L. J. (1997). J. Appl. Cryst. 30, 565.]) and 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.]); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2009[Spek, A. L. (2009). Acta Cryst. D65, 148-155.]).

Supporting information


Comment top

Multidentate ligands are versatile complexation agents for a variety of main group elements as well as transition metals. The possible formation of chelate compounds, in this aspect, is – as a rule of thumb – more likely for smaller chelate ring sizes with four-, five- and six-membered ring systems while the formation of bigger rings is comparatively hampered. As a consequence, the knowledge about the properties of such compounds is limited and precludes a thorough assessment of their properties. In our continuous efforts to elucidate the rules guiding the formation of coordination compounds with chelate ligands featuring a N/O-set of donor atoms, we determined the crystal structure of the title compound to allow for comparative studies with envisioned coordination compounds. The crystal structure of the oxidation product of the title compound, 5-aminovaleric acid, is apparent in the literature (Honda et al., 1990).

The molecule is a primary alcohol and primary amine at the same time. The molecule adopts a zigzag-chain conformation. Apart from the hydroxy group, all non-hydrogen atoms are in-plane. The OH group encloses a dihedral angle of 62.86 (8) ° with the atoms of the carbon chain (Fig. 1 and Fig. 2).

In the molecule, hydrogen bonds between the hydroxy group as well as the amino groups give rise to a three-dimensional network. While a set of cooperative hydrogen bonds (alternating between hydroxy groups and amino groups) connects the molecules to discrete tetrameric units (Fig. 3), the remaining hydrogen atom of the amino group gives rise to centrosymmetric dimers upon interaction with the hydroxy group. In terms of graph-set analysis (Etter et al., 1990; Bernstein et al., 1995), the hydrogen bonding system requires a C11(8)C11(8)C11(8) descriptor on the unitary level. A description of the cooperative set of hydrogen bonds is possible on the binary level with a R44(8) descriptor while the centrosymmetric dimers necessitate a R22(16) descriptor on the unitary level (Fig. 4).

The packing of the compound in the crystal is shown in Figure 5.

Related literature top

For the crystal structure of 5-aminovaleric acid, see: Honda et al. (1990). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990); Bernstein et al. (1995).

Experimental top

The compound was obtained commercially (Aldrich). Crystals suitable for the X-ray diffraction study were taken directly from the provided compound.

Refinement top

Carbon-bound H atoms were placed in calculated positions (C—H 0.99 °) and were included in the refinement in the riding model approximation, with U(H) set to 1.2Ueq(C). The hydrogen atoms of the hydroxy as well as the amino group were located on a difference Fourier map and refined freely.

Computing details top

Data collection: APEX2 (Bruker, 2010); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT (Bruker, 2010); program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2008); software used to prepare material for publication: SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Figures top
[Figure 1] Fig. 1. The molecular structure of the title compound, with atom labels and anisotropic displacement ellipsoids (drawn at 50% probability level).
[Figure 2] Fig. 2. Selected Newman projections and dihedral angles in the title compound.
[Figure 3] Fig. 3. Tetrameric units formed by cooperative hydrogen bonding (indicated by dashed lines), viewed along [0 0 - 1]. Symmetry operators: i x - 1/2, -y, -z + 1/2; ii -x + 1, y - 1/2, -z + 1/2.
[Figure 4] Fig. 4. Intermolecular contacts (indicated by dashed lines), viewed approximately along [0 0 - 1]. Symmetry operators: i -x + 1, y - 1/2, -z + 1/2; ii -x + 1, -y, -z; iii x - 1/2, -y, -z + 1/2; iv x + 1/2, -y, -z + 1/2; v -x + 1, y + 1/2, -z + 1/2.
[Figure 5] Fig. 5. Molecular packing of the title compound, viewed along [0 0 - 1] (anisotropic displacement ellipsoids drawn at 50% probability level).
5-Aminopentan-1-ol top
Crystal data top
C5H13NODx = 1.105 Mg m3
Mr = 103.16Melting point = 308–310 K
Orthorhombic, PccnMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ab 2acCell parameters from 8278 reflections
a = 10.0973 (2) Åθ = 2.3–28.2°
b = 17.4145 (4) ŵ = 0.08 mm1
c = 7.0564 (1) ÅT = 100 K
V = 1240.79 (4) Å3Block, colourless
Z = 80.57 × 0.54 × 0.51 mm
F(000) = 464
Data collection top
Bruker APEXII CCD
diffractometer
1422 reflections with I > 2σ(I)
Radiation source: fine-focus sealed tubeRint = 0.030
Graphite monochromatorθmax = 28.3°, θmin = 2.3°
ϕ and ω scansh = 1313
10385 measured reflectionsk = 1923
1530 independent reflectionsl = 99
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) = 0.089H atoms treated by a mixture of independent and constrained refinement
S = 1.06 w = 1/[σ2(Fo2) + (0.0468P)2 + 0.2724P]
where P = (Fo2 + 2Fc2)/3
1530 reflections(Δ/σ)max < 0.001
76 parametersΔρmax = 0.38 e Å3
0 restraintsΔρmin = 0.18 e Å3
Crystal data top
C5H13NOV = 1240.79 (4) Å3
Mr = 103.16Z = 8
Orthorhombic, PccnMo Kα radiation
a = 10.0973 (2) ŵ = 0.08 mm1
b = 17.4145 (4) ÅT = 100 K
c = 7.0564 (1) Å0.57 × 0.54 × 0.51 mm
Data collection top
Bruker APEXII CCD
diffractometer
1422 reflections with I > 2σ(I)
10385 measured reflectionsRint = 0.030
1530 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0320 restraints
wR(F2) = 0.089H atoms treated by a mixture of independent and constrained refinement
S = 1.06Δρmax = 0.38 e Å3
1530 reflectionsΔρmin = 0.18 e Å3
76 parameters
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.55733 (5)0.19608 (3)0.27542 (8)0.01969 (16)
H810.5858 (12)0.2427 (8)0.3007 (16)0.040 (3)*
N10.35089 (6)0.16146 (3)0.13148 (9)0.01779 (16)
H710.3718 (11)0.1601 (6)0.0096 (19)0.031 (3)*
H720.2639 (12)0.1619 (6)0.1406 (15)0.027 (3)*
C10.42120 (7)0.19396 (4)0.32624 (11)0.01792 (17)
H110.37810.24300.29080.022*
H120.41240.18720.46500.022*
C20.35429 (7)0.12773 (4)0.22406 (10)0.01683 (17)
H210.36520.13470.08570.020*
H220.25830.12880.25240.020*
C30.41026 (7)0.04968 (4)0.28073 (9)0.01553 (17)
H310.39530.04180.41800.019*
H320.50710.04980.25870.019*
C40.34889 (7)0.01724 (4)0.17219 (10)0.01532 (17)
H410.25200.01730.19340.018*
H420.36460.00980.03490.018*
C50.40539 (7)0.09476 (4)0.23205 (10)0.01638 (17)
H510.50250.09380.21240.020*
H520.38940.10160.36940.020*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0152 (3)0.0157 (3)0.0281 (3)0.00153 (18)0.00239 (19)0.0044 (2)
N10.0173 (3)0.0145 (3)0.0216 (3)0.0007 (2)0.0004 (2)0.0005 (2)
C10.0162 (3)0.0153 (3)0.0223 (4)0.0007 (2)0.0022 (3)0.0023 (3)
C20.0152 (3)0.0152 (3)0.0200 (3)0.0005 (2)0.0014 (2)0.0004 (2)
C30.0157 (3)0.0143 (3)0.0165 (3)0.0006 (2)0.0012 (2)0.0003 (2)
C40.0153 (3)0.0142 (3)0.0165 (3)0.0003 (2)0.0009 (2)0.0000 (2)
C50.0164 (3)0.0146 (3)0.0181 (3)0.0001 (2)0.0013 (2)0.0007 (2)
Geometric parameters (Å, º) top
O1—C11.4210 (8)C2—H220.9900
O1—H810.879 (14)C3—C41.5260 (9)
N1—C51.4682 (9)C3—H310.9900
N1—H710.886 (13)C3—H320.9900
N1—H720.881 (12)C4—C51.5252 (9)
C1—C21.5188 (9)C4—H410.9900
C1—H110.9900C4—H420.9900
C1—H120.9900C5—H510.9900
C2—C31.5253 (9)C5—H520.9900
C2—H210.9900
C1—O1—H81106.8 (8)C2—C3—H31108.9
C5—N1—H71111.1 (7)C4—C3—H31108.9
C5—N1—H72110.2 (7)C2—C3—H32108.9
H71—N1—H72108.0 (10)C4—C3—H32108.9
O1—C1—C2109.28 (6)H31—C3—H32107.7
O1—C1—H11109.8C5—C4—C3112.65 (6)
C2—C1—H11109.8C5—C4—H41109.1
O1—C1—H12109.8C3—C4—H41109.1
C2—C1—H12109.8C5—C4—H42109.1
H11—C1—H12108.3C3—C4—H42109.1
C1—C2—C3112.80 (6)H41—C4—H42107.8
C1—C2—H21109.0N1—C5—C4115.23 (6)
C3—C2—H21109.0N1—C5—H51108.5
C1—C2—H22109.0C4—C5—H51108.5
C3—C2—H22109.0N1—C5—H52108.5
H21—C2—H22107.8C4—C5—H52108.5
C2—C3—C4113.48 (6)H51—C5—H52107.5
O1—C1—C2—C362.86 (8)C2—C3—C4—C5179.54 (6)
C1—C2—C3—C4177.13 (6)C3—C4—C5—N1179.56 (6)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H81···N1i0.879 (14)1.851 (14)2.7284 (8)176.5 (12)
N1—H71···O1ii0.886 (13)2.225 (13)3.0768 (9)161.3 (10)
N1—H72···O1iii0.881 (12)2.248 (12)3.0954 (8)161.2 (9)
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x+1, y, z; (iii) x1/2, y, z+1/2.

Experimental details

Crystal data
Chemical formulaC5H13NO
Mr103.16
Crystal system, space groupOrthorhombic, Pccn
Temperature (K)100
a, b, c (Å)10.0973 (2), 17.4145 (4), 7.0564 (1)
V3)1240.79 (4)
Z8
Radiation typeMo Kα
µ (mm1)0.08
Crystal size (mm)0.57 × 0.54 × 0.51
Data collection
DiffractometerBruker APEXII CCD
diffractometer
Absorption correction
No. of measured, independent and
observed [I > 2σ(I)] reflections
10385, 1530, 1422
Rint0.030
(sin θ/λ)max1)0.666
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.032, 0.089, 1.06
No. of reflections1530
No. of parameters76
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.38, 0.18

Computer programs: APEX2 (Bruker, 2010), SAINT (Bruker, 2010), SIR97 (Altomare et al., 1999), ORTEP-3 (Farrugia, 1997) and Mercury (Macrae et al., 2008), SHELXL97 (Sheldrick, 2008) and PLATON (Spek, 2009).

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H81···N1i0.879 (14)1.851 (14)2.7284 (8)176.5 (12)
N1—H71···O1ii0.886 (13)2.225 (13)3.0768 (9)161.3 (10)
N1—H72···O1iii0.881 (12)2.248 (12)3.0954 (8)161.2 (9)
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x+1, y, z; (iii) x1/2, y, z+1/2.
 

Acknowledgements

The authors thank Mr Nicholas Mackay for helpful discussions.

References

First citationAltomare, A., Burla, M. C., Camalli, M., Cascarano, G. L., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Polidori, G. & Spagna, R. (1999). J. Appl. Cryst. 32, 115–119.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationBernstein, J., Davis, R. E., Shimoni, L. & Chang, N.-L. (1995). Angew. Chem. Int. Ed. Engl. 34, 1555–1573.  CrossRef CAS Web of Science Google Scholar
First citationBruker (2010). APEX2 and SAINT Bruker AXS Inc., Madison, Wisconsin, USA.  Google Scholar
First citationEtter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256–262.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationFarrugia, L. J. (1997). J. Appl. Cryst. 30, 565.  CrossRef IUCr Journals Google Scholar
First citationHonda, K., Goto, M. & Kurahashi, M. (1990). Chem. Lett. pp. 13–16.  CrossRef Google Scholar
First citationMacrae, 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.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSheldrick, G. M. (2008). Acta Cryst. A64, 112–122.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSpek, A. L. (2009). Acta Cryst. D65, 148–155.  Web of Science CrossRef CAS IUCr Journals Google Scholar

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