organic compounds
Methyl 6-amino-6-oxohexanoate
aChemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, England, and bChemical Crystallography, Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, England
*Correspondence e-mail: amber.thompson@chem.ox.ac.uk
The title compound, C7H13NO3, adopts an approximately planar conformation. The torsion angles in the aliphatic chain between the carbonyl group C atoms range from 172.97 (14) to 179.38 (14)° and the r.m.s. deviation of all non-H atoms is 0.059 Å. The crystal packing is dominated by two strong N—H⋯O hydrogen bonds involving the amide groups and forming R22(8) rings and C(4) chains. Overall, a two-dimensional network parallel to (100) is formed. A weak intermolecular C—H⋯O interaction is also present.
Related literature
For the synthesis of the title compound, see: Kulikova et al. (1960); Nishitani et al. (1982); Micovic et al. (1988). For information on the solid-state characteristics of different polymorphs of adipic acid, see: Fun & Chantrapromma (2009); Ranganathan et al. (2003); Srinivasa Gopalan et al. (1999, 2000); Pfefer & Boistelle (2000); Housty & Hospital (1965); Arevalo & Canut (1961); Hirokawa (1950); Morrison & Robertson (1949); MacGillavry (1941). For details on co-crystals of the title compound, see: Goswami et al. (2010); Delori et al. (2008); Bucar et al. (2007); Childs & Hardcastle (2007); Duan et al. (2005); Li et al. (2001); Urbanczyk-Lipkowska & Gluzinski (1996). For other reports of adipic acid derivatives, see: Li & Goddard (2002); Seaton & Tremayne (2002); Hospital & Housty (1966). For uses of the title compound in heterocycle synthesis, see: Jungheim et al. (2005); Fukumoto et al. (2007). For hydrogen-bond motifs, see: Bernstein et al. (1995). For details of the H-atom treatment, see: Cooper et al. (2010).
Experimental
Crystal data
|
Refinement
|
Data collection: CrysAlis PRO (Agilent, 2010); cell CrysAlis PRO; data reduction: CrysAlis PRO; 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, 2009).
Supporting information
10.1107/S1600536812003303/lh5383sup1.cif
contains datablocks global, I. DOI:Supporting information file. DOI: 10.1107/S1600536812003303/lh5383Isup2.cdx
Structure factors: contains datablock I. DOI: 10.1107/S1600536812003303/lh5383Isup3.hkl
Supporting information file. DOI: 10.1107/S1600536812003303/lh5383Isup4.cml
The title compound was recovered as a side product in 0.5% yield from the
reaction of amino pimelic acid methylester in p-cymene via a redox process (Nishitani et al., 1982). Crystals suitable for X-ray diffraction were obtained by slow evaporation of a solution of the compound in methanol.Alternatively, the title compound can also preprared by reaction of the respective acid chloride with ammonia (Micovic et al., 1988) and the partial hydrolysis of the corresponding nitrile (Kulikova et al., 1960).
The structure was refined by full-matrix least-squares. H atoms were treated in the usual manner: positioned geometrically (aliphatic) or located in the difference map (amide) and refined prior to inclusion in the model using riding constraints (Cooper et al., 2010).
Dihedral angles were calculated with PLATON (Spek, 2009); all other standard uncertainties calculated from the full variance co-variance matrix within CRYSTALS (Betteridge et al., 2003).
Data collection: CrysAlis PRO (Agilent, 2010); cell
CrysAlis PRO (Agilent, 2010); data reduction: CrysAlis PRO (Agilent, 2010); 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 (Betteridge et al., 2003) and PLATON (Spek, 2009).C7H13NO3 | F(000) = 344 |
Mr = 159.19 | Dx = 1.230 Mg m−3 |
Monoclinic, P21/c | Melting point: not measured K |
Hall symbol: -P 2ybc | Cu Kα radiation, λ = 1.54184 Å |
a = 12.896 (3) Å | Cell parameters from 2081 reflections |
b = 7.2143 (8) Å | θ = 4–76° |
c = 9.6324 (12) Å | µ = 0.80 mm−1 |
β = 106.474 (17)° | T = 150 K |
V = 859.4 (2) Å3 | Lath, clear_pale_colourless |
Z = 4 | 0.18 × 0.12 × 0.02 mm |
Agilent SuperNova Dual (Cu at zero) diffractometer with an Atlas detector | 1426 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.035 |
ω scans | θmax = 76.0°, θmin = 3.6° |
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010) | h = −16→15 |
Tmin = 0.48, Tmax = 0.98 | k = −9→7 |
7240 measured reflections | l = −12→11 |
1771 independent reflections |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.044 | H-atom parameters constrained |
wR(F2) = 0.128 | Method = Modified Sheldrick w = 1/[σ2(F2) + ( 0.07P)2 + 0.22P], where P = (max(Fo2,0) + 2Fc2)/3 |
S = 1.00 | (Δ/σ)max = 0.001 |
1770 reflections | Δρmax = 0.24 e Å−3 |
100 parameters | Δρmin = −0.24 e Å−3 |
0 restraints |
C7H13NO3 | V = 859.4 (2) Å3 |
Mr = 159.19 | Z = 4 |
Monoclinic, P21/c | Cu Kα radiation |
a = 12.896 (3) Å | µ = 0.80 mm−1 |
b = 7.2143 (8) Å | T = 150 K |
c = 9.6324 (12) Å | 0.18 × 0.12 × 0.02 mm |
β = 106.474 (17)° |
Agilent SuperNova Dual (Cu at zero) diffractometer with an Atlas detector | 1771 independent reflections |
Absorption correction: multi-scan (CrysAlis PRO; Agilent, 2010) | 1426 reflections with I > 2σ(I) |
Tmin = 0.48, Tmax = 0.98 | Rint = 0.035 |
7240 measured reflections |
R[F2 > 2σ(F2)] = 0.044 | 0 restraints |
wR(F2) = 0.128 | H-atom parameters constrained |
S = 1.00 | Δρmax = 0.24 e Å−3 |
1770 reflections | Δρmin = −0.24 e Å−3 |
100 parameters |
Experimental. Agilent Technologies (2010). CrysAlisPro. Version 1.171.35.4 (release 09-12-2010 CrysAlis171 .NET) (compiled Dec 9 2010,10:47:41) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.07129 (11) | 1.29877 (15) | 0.44865 (11) | 0.0413 | |
C2 | 0.09105 (12) | 1.2640 (2) | 0.58008 (14) | 0.0323 | |
N3 | 0.05751 (12) | 1.37331 (17) | 0.66941 (12) | 0.0372 | |
H31 | 0.0242 | 1.4758 | 0.6389 | 0.0445* | |
H32 | 0.0717 | 1.3426 | 0.7589 | 0.0449* | |
C4 | 0.15519 (14) | 1.0967 (2) | 0.64774 (15) | 0.0380 | |
C5 | 0.18119 (13) | 0.9615 (2) | 0.54141 (15) | 0.0339 | |
C6 | 0.24703 (14) | 0.7987 (2) | 0.62007 (15) | 0.0373 | |
C7 | 0.27433 (15) | 0.6613 (2) | 0.51664 (17) | 0.0417 | |
C8 | 0.34505 (14) | 0.5046 (2) | 0.59123 (17) | 0.0411 | |
O9 | 0.36947 (12) | 0.39151 (19) | 0.49492 (14) | 0.0571 | |
C10 | 0.43990 (18) | 0.2384 (3) | 0.5546 (2) | 0.0604 | |
H101 | 0.4474 | 0.1631 | 0.4773 | 0.0899* | |
H103 | 0.5097 | 0.2837 | 0.6123 | 0.0882* | |
H102 | 0.4069 | 0.1646 | 0.6164 | 0.0903* | |
O11 | 0.37696 (14) | 0.48159 (19) | 0.71881 (14) | 0.0605 | |
H71 | 0.3122 | 0.7249 | 0.4570 | 0.0507* | |
H72 | 0.2080 | 0.6062 | 0.4549 | 0.0501* | |
H62 | 0.3138 | 0.8436 | 0.6854 | 0.0443* | |
H61 | 0.2066 | 0.7354 | 0.6763 | 0.0458* | |
H52 | 0.2233 | 1.0258 | 0.4878 | 0.0396* | |
H51 | 0.1133 | 0.9163 | 0.4743 | 0.0412* | |
H41 | 0.2227 | 1.1408 | 0.7133 | 0.0470* | |
H42 | 0.1152 | 1.0285 | 0.7024 | 0.0471* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0675 (8) | 0.0363 (6) | 0.0230 (5) | 0.0117 (5) | 0.0176 (5) | 0.0041 (4) |
C2 | 0.0438 (8) | 0.0298 (7) | 0.0251 (6) | −0.0007 (6) | 0.0126 (6) | 0.0004 (5) |
N3 | 0.0586 (8) | 0.0333 (6) | 0.0223 (5) | 0.0073 (6) | 0.0154 (5) | 0.0023 (4) |
C4 | 0.0549 (9) | 0.0355 (8) | 0.0247 (6) | 0.0069 (7) | 0.0133 (6) | 0.0033 (5) |
C5 | 0.0441 (8) | 0.0312 (7) | 0.0269 (6) | 0.0011 (6) | 0.0109 (5) | −0.0001 (5) |
C6 | 0.0521 (9) | 0.0317 (7) | 0.0281 (7) | 0.0030 (6) | 0.0112 (6) | 0.0006 (5) |
C7 | 0.0532 (9) | 0.0378 (8) | 0.0327 (7) | 0.0066 (7) | 0.0100 (7) | −0.0031 (6) |
C8 | 0.0461 (9) | 0.0330 (8) | 0.0408 (8) | −0.0015 (6) | 0.0070 (7) | −0.0036 (6) |
O9 | 0.0645 (8) | 0.0499 (7) | 0.0489 (7) | 0.0206 (6) | 0.0031 (6) | −0.0128 (5) |
C10 | 0.0552 (11) | 0.0471 (10) | 0.0707 (13) | 0.0130 (9) | 0.0046 (9) | −0.0113 (9) |
O11 | 0.0857 (10) | 0.0492 (7) | 0.0424 (7) | 0.0185 (7) | 0.0111 (7) | 0.0068 (5) |
O1—C2 | 1.2441 (18) | C6—H62 | 0.967 |
C2—N3 | 1.3269 (19) | C6—H61 | 0.966 |
C2—C4 | 1.503 (2) | C7—C8 | 1.501 (2) |
N3—H31 | 0.864 | C7—H71 | 0.969 |
N3—H32 | 0.858 | C7—H72 | 0.977 |
C4—C5 | 1.5193 (19) | C8—O9 | 1.338 (2) |
C4—H41 | 0.972 | C8—O11 | 1.192 (2) |
C4—H42 | 0.970 | O9—C10 | 1.442 (2) |
C5—C6 | 1.520 (2) | C10—H101 | 0.949 |
C5—H52 | 0.967 | C10—H103 | 0.971 |
C5—H51 | 0.984 | C10—H102 | 0.981 |
C6—C7 | 1.516 (2) | ||
O1—C2—N3 | 121.98 (13) | C7—C6—H62 | 108.5 |
O1—C2—C4 | 122.14 (13) | C5—C6—H61 | 109.3 |
N3—C2—C4 | 115.88 (12) | C7—C6—H61 | 108.8 |
C2—N3—H31 | 120.7 | H62—C6—H61 | 108.4 |
C2—N3—H32 | 118.8 | C6—C7—C8 | 113.61 (13) |
H31—N3—H32 | 120.4 | C6—C7—H71 | 109.3 |
C2—C4—C5 | 115.01 (11) | C8—C7—H71 | 107.5 |
C2—C4—H41 | 107.5 | C6—C7—H72 | 109.9 |
C5—C4—H41 | 108.7 | C8—C7—H72 | 107.0 |
C2—C4—H42 | 109.3 | H71—C7—H72 | 109.5 |
C5—C4—H42 | 107.1 | C7—C8—O9 | 110.96 (14) |
H41—C4—H42 | 109.2 | C7—C8—O11 | 125.70 (15) |
C4—C5—C6 | 111.05 (12) | O9—C8—O11 | 123.34 (16) |
C4—C5—H52 | 108.5 | C8—O9—C10 | 115.85 (15) |
C6—C5—H52 | 108.5 | O9—C10—H101 | 108.6 |
C4—C5—H51 | 109.3 | O9—C10—H103 | 110.4 |
C6—C5—H51 | 109.8 | H101—C10—H103 | 110.9 |
H52—C5—H51 | 109.7 | O9—C10—H102 | 109.0 |
C5—C6—C7 | 112.25 (12) | H101—C10—H102 | 108.9 |
C5—C6—H62 | 109.5 | H103—C10—H102 | 109.1 |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H31···O1i | 0.86 | 2.07 | 2.929 (2) | 173 (1) |
N3—H32···O1ii | 0.86 | 2.09 | 2.922 (2) | 162 (1) |
C10—H101···O11iii | 0.95 | 2.61 | 3.486 (3) | 153 (1) |
Symmetry codes: (i) −x, −y+3, −z+1; (ii) x, −y+5/2, z+1/2; (iii) x, −y+1/2, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | C7H13NO3 |
Mr | 159.19 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 150 |
a, b, c (Å) | 12.896 (3), 7.2143 (8), 9.6324 (12) |
β (°) | 106.474 (17) |
V (Å3) | 859.4 (2) |
Z | 4 |
Radiation type | Cu Kα |
µ (mm−1) | 0.80 |
Crystal size (mm) | 0.18 × 0.12 × 0.02 |
Data collection | |
Diffractometer | Agilent SuperNova Dual (Cu at zero) diffractometer with an Atlas detector |
Absorption correction | Multi-scan (CrysAlis PRO; Agilent, 2010) |
Tmin, Tmax | 0.48, 0.98 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 7240, 1771, 1426 |
Rint | 0.035 |
(sin θ/λ)max (Å−1) | 0.629 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.044, 0.128, 1.00 |
No. of reflections | 1770 |
No. of parameters | 100 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.24, −0.24 |
Computer programs: CrysAlis PRO (Agilent, 2010), SIR92 (Altomare et al., 1994), CAMERON (Watkin et al., 1996), CRYSTALS (Betteridge et al., 2003) and PLATON (Spek, 2009).
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H31···O1i | 0.86366 | 2.069 | 2.929 (2) | 172.95 (5) |
N3—H32···O1ii | 0.85792 | 2.094 | 2.922 (2) | 161.75 (5) |
C10—H101···O11iii | 0.94863 | 2.614 | 3.486 (3) | 153.02 (6) |
Symmetry codes: (i) −x, −y+3, −z+1; (ii) x, −y+5/2, z+1/2; (iii) x, −y+1/2, z−1/2. |
Footnotes
‡Present address: Institut für Organische Chemie, TU Braunschweig, Hagenring 30, D-38106 Braunschweig, Germany.
Acknowledgements
TG thanks Deutsche Forschungsgemeinschaft (DFG), Germany, for generous funding (GR 3693/1–1:1).
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This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
Adipic acid has importance in various industrial applications including the production of polyamides and polyurethanes. The solid state characteristics of different polymorphs of adipic acid have already been investigated intensively (Fun & Chantrapromma, 2009; Ranganathan et al., 2003; Srinivasa Gopalan et al., 2000; Pfefer & Boistelle, 2000; Srinivasa Gopalan et al., 1999; Housty & Hospital, 1965; Arevalo & Canut, 1961; Hirokawa, 1950; Morrison & Robertson, 1949; MacGillavry, 1941), as have adipic acid co-crystals (Goswami et al., 2010; Delori et al., 2008; Bucar et al., 2007; Childs & Hardcastle, 2007; Duan et al., 2005, Li et al., 2001; Urbanczyk-Lipkowska & Gluzinski, 1996). Reports on single-crystal X-ray structures of adipic acid derivatives have focused on the important nylon-based materials (Li & Goddard, 2002). Here we describe the structure of a simple adipic acid derivative, viz. methyl 6-amino-6-oxohexanoate (I), an approved starting material for heterocyclic synthesis (Jungheim et al., 2005; Fukumoto et al., 2007).
Methyl 6-amino-6-oxohexanoate (I) crystallizes from methanol as colourless crystals in the monoclinic space group P21/c (Fig. 1). The molecule is approximately planar; the largest deviation from the mean plane defined by the non-hydrogen atoms is 0.116 Å for carbonyl oxygen O1 and the aliphatic chain between the carbonyl carbons is only slightly twisted with torsion angles ranging from 172.97 (14) to 179.38 (14)°. The crystal packing is dominated by two strong N—H···O hydrogen bonds (see Table 1), similar to those seen in the two polymorphs of adipamide (monoclinic: Hospital & Housty, 1966; triclinic: Seaton & Tremayne, 2002). In (I), the the amide nitrogen in serves as a double intermolecular hydrogen donor: N3—H31···O1i forms an R22(8) amide dimer around an inversion centre, while N3—H32···O1ii connects pairs of dimers to form C(4) chains parallel to the c axis. The combination of the C(4) and R22(8) motifs generates a secondary network of R106(24) as described for related compounds including benzamide etc. (Bernstein et al. (1995); Fig. 2).
Notably, the methyl ester carbonyl group is not involved in hydrogen bonding, however, it is in a suitable position to engage in a weak C—H···O intermolecular interaction with an ester methyl group [d(H···O) = 2.614 (3) Å].
In conclusion, the structure of (I), together with those similar and previously reported, suggest that the variation in the carbonyl substituent at adipic acid does not cause substantial changes to the conformation of the molecule.