Cylopentyl­amine monohydrate

Allan, D.R.

doi:10.1107/S1600536806005198

organic compounds

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ISSN: 2056-9890

Volume 62| Part 3| March 2006| Pages o1064-o1066

https://doi.org/10.1107/S1600536806005198

Cylopentylamine monohydrate

D. R. Allan ^a ^*

^aSchool of Chemistry, The University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3JJ, Scotland
^*Correspondence e-mail: d.r.allan@ed.ac.uk

(Received 25 January 2006; accepted 13 February 2006; online 17 February 2006)

The crystal structure of cylopentylamine monohydrate, C₅H₁₁N·H₂O, is composed of molecular chains of alternating cyclopentylamine and water molecules which are linked by O—H⋯O and O—H⋯N hydrogen bonds. These chains are parallel to the monoclinic b axis and they are bridged by weaker O⋯H—N contacts, forming hydrogen-bonded layers of molecules parallel to (100).

Comment

The crystal structure of cylopentylamine monohydrate, (I), was determined at 205 K (just below the ∼215 K melting point) as part of a series of studies on the structural behaviour of prototypical hydrogen-bonded molecular systems at conditions of either non-ambient temperature or pressure. It crystallizes in the monoclinic space group P2₁/c with one cyclopentylamine molecule and a single water molecule in the asymmetric unit (Fig. 1).

The water molecules are linked by O—H⋯O hydrogen bonds, forming the backbone of molecular chains which run parallel to the b axis, while O—H⋯N hydrogen bonds link the cyclopentylamine molecules to this backbone in an alternating sequence (Fig. 2 and Table 1). The lengths of these hydrogen bonds are fairly similar, while the weaker O—H⋯N hydrogen bond is correspondingly less linear. Significantly weaker O⋯H—N contacts bridge neighbouring molecular chains, forming slabs of molecules parallel to (100) (Fig. 3). One of these O⋯N distances is marginal.

Figure 1
The asymmetric unit of (I)

, showing 30% probability displacement ellipsoids.

Figure 2
The hydrogen-bonded molecular chains of (I)

, viewed perpendicular to (101). The O—H⋯O and O—H⋯N hydrogen bonds are shown as light dotted lines and heavy dashed lines, respectively.

Figure 3
The packing of (I)

, viewed along the b axis. The O—H⋯O and O—H⋯N hydrogen bonds are shown as dashed lines.

Experimental

The sample of cyclopentylamine monohydrate was prepared from anhydrous starting material (of 99% purity, as received from Aldrich) and placed in a sealed glass capillary tube with an internal diameter of ca 0.2 mm. The sample was cooled using an Oxford Cryosystems low-temperature device (Cosier & Glazer, 1986 ) until crystallization was observed. The temperature was then cycled between 180 and 215 K, and the capillary successively translated through the gas stream, so that the sample was partially remelted and the number of crystallites reduced. The final sample, at 205 K, was composed of a small number of crystals and the reflections from the largest of these were indexed and their intensities subsequently used for structure solution.

Crystal data

C₅H₁₁N·H₂O
M_r = 103.16
Monoclinic, P 2₁ /c
a = 12.969 (4) Å
b = 4.7125 (13) Å
c = 11.005 (3) Å
β = 102.614 (17)°
V = 656.4 (3) Å³
Z = 4
D_x = 1.044 Mg m⁻³
Synchrotron radiation
λ = 0.6813 Å
Cell parameters from 445 reflections
θ = 8–43°
μ = 0.07 mm⁻¹
T = 205 K
Cylinder, colourless
0.20 × 0.10 (radius) mm

Data collection

Bruker SMART diffractometer
φ and ω scans
Absorption correction: multi-scan(SADABS; Sheldrick, 2004 )T_min = 0.35, T_max = 0.99
5211 measured reflections
1573 independent reflections
875 reflections with I > 2σ(I)
R_int = 0.051
θ_max = 27.5°
h = −17 → 17
k = −6 → 6
l = −14 → 14

Refinement

Refinement on F
R[F² > 2σ(F²)] = 0.056
wR(F²) = 0.054
S = 1.13
875 reflections
76 parameters
H atoms treated by a mixture of independent and constrained refinement
Modified Chebychev polynomial (Watkin, 1994 ; Prince, 1982 ) with the coefficients 2.88, −1.06, 1.90
(Δ/σ)_max = 0.001
Δρ_max = 0.25 e Å⁻³
Δρ_min = −0.16 e Å⁻³

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
O1—H1⋯N1	0.82 (1)	2.01 (1)	2.821 (2)	172 (2)
O1—H2⋯O1ⁱ	0.82 (1)	2.00 (1)	2.820 (1)	178 (3)
N1—H11⋯O1ⁱⁱ	0.89 (1)	2.35 (1)	3.137 (2)	148 (2)
N1—H12⋯O1ⁱⁱⁱ	0.89 (1)	2.55 (1)	3.426 (2)	166 (2)
Symmetry codes: (i) $[-x+2, y+{\script{1\over 2}}, -z+{\script{3\over 2}}]$ ; (ii) -x+2, -y, -z+2; (iii) -x+2, -y+1, -z+2.

H atoms attached to C atoms were placed in idealized positions (C—H = 0.96–1.00 Å) and allowed to ride on their parent atoms. H atoms attached to N and O atoms were located in a difference map and restrained to idealized distances and angles [N—H = 0.90 (1) Å, O—H = 0.82 (1) Å and O—H—O = 104 (1)°]. All H atoms were constrained so that U_iso(H) values were equal to 1.2U_eq of their respective parent atoms.

Data collection: SMART (Bruker, 2001 ); cell refinement: SAINT; data reduction: SAINT (Bruker, 2003 ); program(s) used to solve structure: SIR92 (Altomare et al., 1994 ); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003 ); molecular graphics: CAMERON (Watkin et al., 1996 ); software used to prepare material for publication: CRYSTALS and PLATON (Spek, 2003 ).

Supporting information

Crystal structure: contains datablocks global, I. DOI: https://doi.org/10.1107/S1600536806005198/jh6043sup1.cif

Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S1600536806005198/jh6043Isup2.hkl

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SAINT; data reduction: SAINT (Bruker, 2003); program(s) used to solve structure: SIR92 (Altomare et al., 1994); program(s) used to refine structure: CRYSTALS (Betteridge et al., 2003); molecular graphics: CAMERON (Watkin et al., 1996); software used to prepare material for publication: CRYSTALS and PLATON (Spek, 2003).

Cylopentylamine monohydrate top

Crystal data top

C₅H₁₁N·H₂O	F(000) = 232
M_r = 103.16	D_x = 1.044 Mg m⁻³
Monoclinic, P2₁/c	Synchrotron radiation, λ = 0.68130 Å
Hall symbol: -P 2ybc	Cell parameters from 445 reflections
a = 12.969 (4) Å	θ = 8–43°
b = 4.7125 (13) Å	µ = 0.07 mm⁻¹
c = 11.005 (3) Å	T = 205 K
β = 102.614 (17)°	Cylinder, colourless
V = 656.4 (3) Å³	0.20 × 0.10 × 0.10 × 0.10 (radius) mm
Z = 4

Data collection top

Bruker SMART diffractometer	875 reflections with I > 2σ(I)
Curved silicon monochromator	R_int = 0.051
φ and ω scans	θ_max = 27.5°, θ_min = 4.3°
Absorption correction: multi-scan (SADABS; Sheldrick, 2004)	h = −17→17
T_min = 0.35, T_max = 0.99	k = −6→6
5211 measured reflections	l = −14→14
1573 independent reflections

Refinement top

Refinement on F	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Hydrogen site location: inferred from neighbouring sites
R[F² > 2σ(F²)] = 0.056	H atoms treated by a mixture of independent and constrained refinement
wR(F²) = 0.054	Modified Chebychev polynomial (Watkin, 1994; Prince, 1982) with the coefficients 2.88, -1.06, 1.90
S = 1.13	(Δ/σ)_max = 0.001
875 reflections	Δρ_max = 0.25 e Å⁻³
76 parameters	Δρ_min = −0.16 e Å⁻³
5 restraints

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

	x	y	z	U_iso*/U_eq
O1	1.01039 (11)	0.1644 (3)	0.82203 (12)	0.0497
N1	0.87797 (12)	0.2930 (4)	0.98670 (14)	0.0473
C2	0.76853 (14)	0.3412 (4)	0.92430 (17)	0.0473
C3	0.75593 (15)	0.5310 (5)	0.81296 (17)	0.0552
C6	0.69733 (15)	0.4823 (6)	1.00014 (19)	0.0638
C4	0.63976 (15)	0.6122 (6)	0.78280 (19)	0.0630
C5	0.60449 (16)	0.5968 (6)	0.9053 (2)	0.0678
H21	0.7390	0.1534	0.8947	0.0574*
H32	0.7998	0.7044	0.8354	0.0677*
H31	0.7771	0.4371	0.7433	0.0675*
H62	0.7337	0.6375	1.0504	0.0798*
H61	0.6744	0.3489	1.0547	0.0796*
H42	0.6295	0.8019	0.7461	0.0731*
H41	0.5999	0.4774	0.7238	0.0730*
H52	0.5840	0.7785	0.9321	0.0824*
H51	0.5454	0.4708	0.9009	0.0827*
H1	0.9678 (15)	0.188 (5)	0.8667 (18)	0.0777*
H12	0.9016 (16)	0.454 (3)	1.0256 (19)	0.0630*
H2	1.0062 (19)	0.311 (3)	0.7810 (19)	0.0780*
H11	0.8823 (17)	0.155 (4)	1.0422 (16)	0.0627*

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
O1	0.0579 (8)	0.0455 (8)	0.0482 (8)	0.0092 (7)	0.0172 (6)	0.0043 (6)
N1	0.0446 (9)	0.0530 (11)	0.0420 (8)	0.0072 (8)	0.0044 (7)	0.0023 (8)
C2	0.0442 (10)	0.0479 (11)	0.0474 (10)	0.0012 (9)	0.0046 (8)	−0.0010 (9)
C3	0.0486 (10)	0.0762 (15)	0.0403 (10)	0.0097 (11)	0.0089 (8)	0.0055 (10)
C6	0.0542 (12)	0.0909 (17)	0.0500 (11)	0.0145 (12)	0.0194 (9)	0.0110 (12)
C4	0.0465 (11)	0.0831 (17)	0.0536 (12)	0.0070 (11)	−0.0021 (9)	0.0056 (11)
C5	0.0438 (11)	0.0847 (17)	0.0756 (15)	0.0073 (11)	0.0148 (10)	0.0102 (13)

Geometric parameters (Å, º) top

O1—H1	0.823 (9)	C3—H31	0.975
O1—H2	0.822 (9)	C6—C5	1.510 (3)
N1—C2	1.453 (2)	C6—H62	0.975
N1—H12	0.894 (9)	C6—H61	0.960
N1—H11	0.887 (9)	C4—C5	1.517 (3)
C2—C3	1.497 (3)	C4—H42	0.978
C2—C6	1.526 (3)	C4—H41	0.973
C2—H21	0.991	C5—H52	0.961
C3—C4	1.519 (3)	C5—H51	0.962
C3—H32	0.995

H1—O1—H2	103.9 (9)	C2—C6—H62	111.3
C2—N1—H12	106.9 (14)	C5—C6—H62	109.7
C2—N1—H11	110.4 (14)	C2—C6—H61	111.4
H12—N1—H11	109.4 (19)	C5—C6—H61	110.9
N1—C2—C3	113.65 (16)	H62—C6—H61	108.3
N1—C2—C6	117.06 (16)	C3—C4—C5	105.72 (16)
C3—C2—C6	102.50 (17)	C3—C4—H42	111.0
N1—C2—H21	106.4	C5—C4—H42	111.8
C3—C2—H21	107.4	C3—C4—H41	109.8
C6—C2—H21	109.4	C5—C4—H41	110.0
C2—C3—C4	104.77 (17)	H42—C4—H41	108.4
C2—C3—H32	109.5	C4—C5—C6	106.34 (16)
C4—C3—H32	109.5	C4—C5—H52	112.7
C2—C3—H31	111.9	C6—C5—H52	109.8
C4—C3—H31	112.3	C4—C5—H51	112.1
H32—C3—H31	108.9	C6—C5—H51	108.7
C2—C6—C5	105.32 (17)	H52—C5—H51	107.2

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O1—H1···N1	0.82 (1)	2.01 (1)	2.821 (2)	172 (2)
O1—H2···O1ⁱ	0.82 (1)	2.00 (1)	2.820 (1)	178 (3)
N1—H11···O1ⁱⁱ	0.89 (1)	2.35 (1)	3.137 (2)	148 (2)
N1—H12···O1ⁱⁱⁱ	0.89 (1)	2.55 (1)	3.426 (2)	166 (2)

Symmetry codes: (i) −x+2, y+1/2, −z+3/2; (ii) −x+2, −y, −z+2; (iii) −x+2, −y+1, −z+2.

Acknowledgements

We thank Dr T. Prior of Daresbury Laboratory for his help during the experiment on station 9.8 at SRS. We also thank the EPSRC for funding both this project and DRA's Advanced Research Fellowship.

References

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