5-Amino­pentan-1-ol

Betz, R.; Gerber, T.; Schalekamp, H.

doi:10.1107/S1600536811024731

organic compounds

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ISSN: 2056-9890

Volume 67| Part 7| July 2011| Page o1841

doi:10.1107/S1600536811024731

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5-Aminopentan-1-ol

Richard Betz,^a ^* Thomas Gerber ^a and Henk Schalekamp ^a

^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 ). For graph-set analysis of hydrogen bonds, see: Etter et al. (1990 ); Bernstein et al. (1995 ).

Experimental

Crystal data

C₅H₁₃NO
M_r = 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)
R_int = 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
Δρ_max = 0.38 e Å⁻³
Δρ_min = −0.18 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	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 ); cell refinement: SAINT (Bruker, 2010); data reduction: SAINT; 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 and PLATON (Spek, 2009 ).

Supporting information

Crystal structure: contains datablocks I, global. DOI: 10.1107/S1600536811024731/ez2250sup1.cif

Supporting information file. DOI: 10.1107/S1600536811024731/ez2250Isup2.cdx

Structure factors: contains datablock I. DOI: 10.1107/S1600536811024731/ez2250Isup3.hkl

Supporting information file. DOI: 10.1107/S1600536811024731/ez2250Isup4.cml

checkCIF report

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.

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

	Fig. 1. The molecular structure of the title compound, with atom labels and anisotropic displacement ellipsoids (drawn at 50% probability level).
	Fig. 2. Selected Newman projections and dihedral angles in the title compound.
	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.
	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.
	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

C₅H₁₃NO	D_x = 1.105 Mg m⁻³
M_r = 103.16	Melting point = 308–310 K
Orthorhombic, Pccn	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ab 2ac	Cell parameters from 8278 reflections
a = 10.0973 (2) Å	θ = 2.3–28.2°
b = 17.4145 (4) Å	µ = 0.08 mm⁻¹
c = 7.0564 (1) Å	T = 100 K
V = 1240.79 (4) Å³	Block, colourless
Z = 8	0.57 × 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 tube	R_int = 0.030
Graphite monochromator	θ_max = 28.3°, θ_min = 2.3°
ϕ and ω scans	h = −13→13
10385 measured reflections	k = −19→23
1530 independent reflections	l = −9→9

Refinement top

Refinement on F²	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F² > 2σ(F²)] = 0.032	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.089	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	w = 1/[σ²(F_o²) + (0.0468P)² + 0.2724P] where P = (F_o² + 2F_c²)/3
1530 reflections	(Δ/σ)_max < 0.001
76 parameters	Δρ_max = 0.38 e Å⁻³
0 restraints	Δρ_min = −0.18 e Å⁻³

Crystal data top

C₅H₁₃NO	V = 1240.79 (4) Å³
M_r = 103.16	Z = 8
Orthorhombic, Pccn	Mo Kα radiation
a = 10.0973 (2) Å	µ = 0.08 mm⁻¹
b = 17.4145 (4) Å	T = 100 K
c = 7.0564 (1) Å	0.57 × 0.54 × 0.51 mm

Data collection top

Bruker APEXII CCD diffractometer	1422 reflections with I > 2σ(I)
10385 measured reflections	R_int = 0.030
1530 independent reflections

Refinement top

R[F² > 2σ(F²)] = 0.032	0 restraints
wR(F²) = 0.089	H atoms treated by a mixture of independent and constrained refinement
S = 1.06	Δρ_max = 0.38 e Å⁻³
1530 reflections	Δρ_min = −0.18 e Å⁻³
76 parameters

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å²) top

	x	y	z	U_iso*/U_eq
O1	0.55733 (5)	0.19608 (3)	0.27542 (8)	0.01969 (16)
H81	0.5858 (12)	0.2427 (8)	0.3007 (16)	0.040 (3)*
N1	0.35089 (6)	−0.16146 (3)	0.13148 (9)	0.01779 (16)
H71	0.3718 (11)	−0.1601 (6)	0.0096 (19)	0.031 (3)*
H72	0.2639 (12)	−0.1619 (6)	0.1406 (15)	0.027 (3)*
C1	0.42120 (7)	0.19396 (4)	0.32624 (11)	0.01792 (17)
H11	0.3781	0.2430	0.2908	0.022*
H12	0.4124	0.1872	0.4650	0.022*
C2	0.35429 (7)	0.12773 (4)	0.22406 (10)	0.01683 (17)
H21	0.3652	0.1347	0.0857	0.020*
H22	0.2583	0.1288	0.2524	0.020*
C3	0.41026 (7)	0.04968 (4)	0.28073 (9)	0.01553 (17)
H31	0.3953	0.0418	0.4180	0.019*
H32	0.5071	0.0498	0.2587	0.019*
C4	0.34889 (7)	−0.01724 (4)	0.17219 (10)	0.01532 (17)
H41	0.2520	−0.0173	0.1934	0.018*
H42	0.3646	−0.0098	0.0349	0.018*
C5	0.40539 (7)	−0.09476 (4)	0.23205 (10)	0.01638 (17)
H51	0.5025	−0.0938	0.2124	0.020*
H52	0.3894	−0.1016	0.3694	0.020*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0152 (3)	0.0157 (3)	0.0281 (3)	−0.00153 (18)	0.00239 (19)	−0.0044 (2)
N1	0.0173 (3)	0.0145 (3)	0.0216 (3)	−0.0007 (2)	0.0004 (2)	−0.0005 (2)
C1	0.0162 (3)	0.0153 (3)	0.0223 (4)	0.0007 (2)	0.0022 (3)	−0.0023 (3)
C2	0.0152 (3)	0.0152 (3)	0.0200 (3)	0.0005 (2)	−0.0014 (2)	0.0004 (2)
C3	0.0157 (3)	0.0143 (3)	0.0165 (3)	−0.0006 (2)	−0.0012 (2)	−0.0003 (2)
C4	0.0153 (3)	0.0142 (3)	0.0165 (3)	−0.0003 (2)	−0.0009 (2)	0.0000 (2)
C5	0.0164 (3)	0.0146 (3)	0.0181 (3)	0.0001 (2)	−0.0013 (2)	0.0007 (2)

Geometric parameters (Å, º) top

O1—C1	1.4210 (8)	C2—H22	0.9900
O1—H81	0.879 (14)	C3—C4	1.5260 (9)
N1—C5	1.4682 (9)	C3—H31	0.9900
N1—H71	0.886 (13)	C3—H32	0.9900
N1—H72	0.881 (12)	C4—C5	1.5252 (9)
C1—C2	1.5188 (9)	C4—H41	0.9900
C1—H11	0.9900	C4—H42	0.9900
C1—H12	0.9900	C5—H51	0.9900
C2—C3	1.5253 (9)	C5—H52	0.9900
C2—H21	0.9900

C1—O1—H81	106.8 (8)	C2—C3—H31	108.9
C5—N1—H71	111.1 (7)	C4—C3—H31	108.9
C5—N1—H72	110.2 (7)	C2—C3—H32	108.9
H71—N1—H72	108.0 (10)	C4—C3—H32	108.9
O1—C1—C2	109.28 (6)	H31—C3—H32	107.7
O1—C1—H11	109.8	C5—C4—C3	112.65 (6)
C2—C1—H11	109.8	C5—C4—H41	109.1
O1—C1—H12	109.8	C3—C4—H41	109.1
C2—C1—H12	109.8	C5—C4—H42	109.1
H11—C1—H12	108.3	C3—C4—H42	109.1
C1—C2—C3	112.80 (6)	H41—C4—H42	107.8
C1—C2—H21	109.0	N1—C5—C4	115.23 (6)
C3—C2—H21	109.0	N1—C5—H51	108.5
C1—C2—H22	109.0	C4—C5—H51	108.5
C3—C2—H22	109.0	N1—C5—H52	108.5
H21—C2—H22	107.8	C4—C5—H52	108.5
C2—C3—C4	113.48 (6)	H51—C5—H52	107.5

O1—C1—C2—C3	62.86 (8)	C2—C3—C4—C5	−179.54 (6)
C1—C2—C3—C4	−177.13 (6)	C3—C4—C5—N1	−179.56 (6)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	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+1/2, −z+1/2; (ii) −x+1, −y, −z; (iii) x−1/2, −y, −z+1/2.

Experimental details

Crystal data
Chemical formula	C₅H₁₃NO
M_r	103.16
Crystal system, space group	Orthorhombic, Pccn
Temperature (K)	100
a, b, c (Å)	10.0973 (2), 17.4145 (4), 7.0564 (1)
V (Å³)	1240.79 (4)
Z	8
Radiation type	Mo Kα
µ (mm⁻¹)	0.08
Crystal size (mm)	0.57 × 0.54 × 0.51

Data collection
Diffractometer	Bruker APEXII CCD diffractometer
Absorption correction	–
No. of measured, independent and observed [I > 2σ(I)] reflections	10385, 1530, 1422
R_int	0.030
(sin θ/λ)_max (Å⁻¹)	0.666

Refinement
R[F² > 2σ(F²)], wR(F²), S	0.032, 0.089, 1.06
No. of reflections	1530
No. of parameters	76
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρ_max, Δρ_min (e Å⁻³)	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···A	D—H	H···A	D···A	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+1/2, −z+1/2; (ii) −x+1, −y, −z; (iii) x−1/2, −y, −z+1/2.

Acknowledgements

The authors thank Mr Nicholas Mackay for helpful discussions.

References

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