research communications\(\def\hfill{\hskip 5em}\def\hfil{\hskip 3em}\def\eqno#1{\hfil {#1}}\)

Journal logoCRYSTALLOGRAPHIC
COMMUNICATIONS
ISSN: 2056-9890
Volume 72| Part 2| February 2016| Pages 136-139

Crystal structure of N-(3-oxo­butano­yl)-L-homoserine lactone

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aDepartment of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA, and bDepartment of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI, 53706, USA
*Correspondence e-mail: rtraines@wisc.edu

Edited by S. V. Lindeman, Marquette University, USA (Received 12 December 2015; accepted 29 December 2015; online 9 January 2016)

The structure and absolute configuration of the title compound, C8H11NO4, which is a known quorum-sensing modulator, have been determined. The mol­ecule exhibits signs of an intra­molecular attractive carbon­yl–carbonyl nπ* inter­action between the amide and lactone ester groups, specifically – a short contact of 2.709 (2) Å between the amide oxygen atom and ester carbon atom, approach of the amide oxygen atom to the ester carbonyl group along the Bürgi–Dunitz trajectory, at 99.1 (1)°, and pyramidalization of the ester carbonyl group by 1.1 (1)°. Moreover, a similar nπ* inter­action is observed for the amide carbonyl group approached by the ketone oxygen donor. These inter­actions apparently affect the conformation of the uncomplexed mol­ecule, which adopts a different shape when bound to protein receptors. In the crystal, the mol­ecules form translational chains along the a axis via N—H⋯O hydrogen bonds.

1. Chemical context

N-Acyl homoserine lactones (AHLs) mediate quorum sensing in Gram-negative bacteria (Miller & Bassler, 2001[Miller, M. B. & Bassler, B. L. (2001). Annu. Rev. Microbiol. 55, 165-199.]; Waters & Bassler, 2005[Waters, C. M. & Bassler, B. L. (2005). Annu. Rev. Cell Dev. Biol. 21, 319-346.]). We have previously shown that AHLs engage in nπ* inter­actions between the acyl and lactone ester carbonyl groups (Newberry & Raines, 2014[Newberry, R. W. & Raines, R. T. (2014). ACS Chem. Biol. 9, 880-883.]). These inter­actions cause attraction through donation of oxygen lone pair (n) electron density into the π* anti­bonding orbital of an acceptor carbonyl group (Hinderaker & Raines, 2003[Hinderaker, M. P. & Raines, R. T. (2003). Protein Sci. 12, 1188-1194.]). This inter­action is observed in the free mol­ecule but not in structures of these compounds bound to their protein receptors, implicating these inter­actions in the potency of AHLs and their analogs. Background to carbon­yl–carbonyl inter­actions is given by Bretscher et al. (2001[Bretscher, L. E., Jenkins, C. L., Taylor, K. M., DeRider, M. L. & Raines, R. T. (2001). J. Am. Chem. Soc. 123, 777-778.]), DeRider et al. (2002[DeRider, M. L., Wilkens, S. J., Waddell, M. J., Bretscher, L. E., Weinhold, F., Raines, R. T. & Markley, J. L. (2002). J. Am. Chem. Soc. 124, 2497-2505.]), Hinderaker & Raines (2003[Hinderaker, M. P. & Raines, R. T. (2003). Protein Sci. 12, 1188-1194.]), and Bartlett et al. (2010[Bartlett, G. J., Choudhary, A., Raines, R. T. & Woolfson, D. N. (2010). Nat. Chem. Biol. 6, 615-620.]). Our previous studies were restricted to AHLs with simple acyl appendages, but natural AHLs are also often oxidized at the 3-position to yield β-keto acyl groups, such as that reported here.

[Scheme 1]

2. Structural commentary and NBO analysis

This is, to our knowledge, the first report of the structure of a free 3-oxo AHL (Fig. 1[link]). Individual mol­ecules pack in linear arrays thanks to inter­molecular hydrogen bonds between amide groups (Fig. 2[link]). The mol­ecule crystallizes as the keto tautomer, consistent with other β-keto amides (Allen, 2002[Allen, F. H. (2002). Acta Cryst. B58, 380-388.]). Like unoxidized AHLs, it displays the hallmark features of an attractive nπ* inter­action between the amide and ester carbonyl groups (Fig. 3[link]). Specifically, the donor oxygen atom makes a sub-van der Waals contact of 2.709 (2) Å with the acceptor carbonyl group, with an angle of approach of 99.1 (1)°, characteristic of the Bürgi–Dunitz trajectory for nucleophilic addition (Bürgi et al., 1973[Bürgi, H. B., Dunitz, J. D. & Shefter, E. (1973). J. Am. Chem. Soc. 95, 5065-5067.], 1974[Bürgi, H. B., Dunitz, J. D. & Shefter, E. (1974). Acta Cryst. B30, 1517-1527.]). This geometry enables electron donation that, in turn, causes a characteristic pyramidalization of the acceptor carbonyl group. We observe that the carbonyl carbon atom rises 0.016 (1) Å out of the plane of its substituents, creating a distortion angle θ (see Fig. 3[link]) of 1.1 (1)°. This signature has been used to diagnose the presence of these inter­actions in many mol­ecules (Choudhary et al., 2009[Choudhary, A., Gandla, D., Krow, G. R. & Raines, R. T. (2009). J. Am. Chem. Soc. 131, 7244-7246.], 2014[Choudhary, A., Newberry, R. W. & Raines, R. T. (2014). Org. Lett. 16, 3421-3423.]; Choudhary & Raines, 2011[Choudhary, A. & Raines, R. T. (2011). Protein Sci. 20, 1077-1081.]; Newberry et al., 2013[Newberry, R. W., VanVeller, B., Guzei, I. A. & Raines, R. T. (2013). J. Am. Chem. Soc. 135, 7843-7846.]), including polymers (Newberry & Raines, 2013[Newberry, R. W. & Raines, R. T. (2013). Chem. Commun. 49, 7699-7701.]) and proteins (Newberry et al., 2014[Newberry, R. W., Bartlett, G. J., VanVeller, B., Woolfson, D. N. & Raines, R. T. (2014). Protein Sci. 23, 284-288.]). Consistent with these observations, natural bond orbital (NBO) analysis (Reed et al., 1988[Reed, A. E., Curtiss, L. A. & Weinhold, F. (1988). Chem. Rev. 88, 899-926.]; Glendening et al., 2012[Glendening, E. D., Badenhoop, J. K., Reed, A. E., Carpenter, J. E., Bohmann, J. A., Morales, C. M. & Weinhold, F. (2012). NBO 5.9.]) of the crystal structure at the B3LYP/6-311+G(2d,p) level of theory predicts the release of 2.67 kcal mol−1 of energy due to the nπ* inter­action, indicating a significant contribution of this inter­action to the conformation of this mol­ecule (Fig. 4[link]).

[Figure 1]
Figure 1
Mol­ecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level.
[Figure 2]
Figure 2
Packing of the title compound.
[Figure 3]
Figure 3
Structural parameters describing an nπ* inter­action
[Figure 4]
Figure 4
Overlap of amide lone pair (n) and ester π* orbitals.

Inter­estingly, a short contact is also observed between the ketone oxygen and amide carbonyl groups. In this case, the donor oxygen atom makes a 2.746 (2) Å contact at 107.5 (1)° to the amide carbonyl group. This contact causes the amide carbonyl group to distort 0.008 (1) Å out of plane, corresponding to a distortion angle Θ of 0.59 (6)°. The pyramidalization of the amide carbonyl group indicates a weaker nπ* inter­action from the ketone to the amide than from the amide to the ester, as would be expected for the enclosing of a four-membered ring relative to the enclosing of a five-membered ring, respectively. Indeed, NBO analysis predicts release of 1.42 kcal mol−1 of energy due to the nπ* inter­action between the ketone and amide (Fig. 5[link]), which is nevertheless a significant contribution that likely biases the conformation of this mol­ecule.

[Figure 5]
Figure 5
Overlap of ketone lone pair (n) and amide π* orbitals.

Based on the specific geometric parameters measured in this crystal structure, we conclude that the structure of unbound oxo-AHLs are influenced by nπ* inter­actions, similarly to simple AHLs. Moreover, an additional nπ* inter­action specific to oxo-AHLs might bias their conformation further and thus affect their binding to protein receptors.

3. Supra­molecular features

In the crystal, the mol­ecules form translational chains along the a axis via N—H⋯O hydrogen bonds (Table 1[link] and Fig. 2[link]).

Table 1
Hydrogen-bond geometry (Å, °)

D—H⋯A D—H H⋯A DA D—H⋯A
N1—H1⋯O2i 0.83 (2) 2.05 (2) 2.7973 (19) 149 (2)
Symmetry code: (i) x+1, y, z.

4. Synthesis and crystallization

The title compound was prepared as reported previously (Eberhard & Schineller, 2000[Eberhard, A. & Schineller, J. B. (2000). Methods in Enzymology, Vol. 305, Bioluminescence and Chemiluminescence, Part C, edited by Miriam M. Ziegler & Thomas O. Baldwin, pp. 301-315. New York: Academic Press.]). A small amount of solid product was dissolved in hexa­nes with a minimal amount of di­chloro­methane. Slow evaporation afforded high-quality crystals after 4 days.

5. Refinement

Crystal data, data collection and structure refinement details are summarized in Table 2[link]. Except for hydrogen-bond donors and terminal methyl groups, all H atoms were placed in idealized locations and refined as riding with appropriate thermal displacement coefficients Uiso(H) = 1.2 or 1.5 times Ueq(bearing atom).

Table 2
Experimental details

Crystal data
Chemical formula C8H11NO4
Mr 185.18
Crystal system, space group Orthorhombic, P212121
Temperature (K) 100
a, b, c (Å) 5.0215 (4), 9.8852 (10), 17.7668 (14)
V3) 881.91 (14)
Z 4
Radiation type Cu Kα
μ (mm−1) 0.96
Crystal size (mm) 0.23 × 0.13 × 0.04
 
Data collection
Diffractometer Bruker APEXII CCD
Absorption correction Multi-scan (SADABS; Bruker, 2014/5[Bruker (2014/5). SADABS. Buker AXS, Inc., Madison, Wisconsin, USA.])
Tmin, Tmax 0.785, 0.841
No. of measured, independent and observed [I > 2σ(I)] reflections 11955, 1755, 1702
Rint 0.028
(sin θ/λ)max−1) 0.621
 
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.026, 0.067, 1.04
No. of reflections 1755
No. of parameters 134
H-atom treatment H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3) 0.22, −0.15
Absolute structure Flack x determined using 657 quotients [(I+)−(I)]/[(I+)+(I)] (Parsons et al., 2013[Parsons, S., Flack, H. D. & Wagner, T. (2013). Acta Cryst. B69, 249-259.]).
Absolute structure parameter −0.01 (8)
Computer programs: APEX2 (Bruker, 2012[Bruker (2012). APEX2. Buker AXS, Inc., Madison, Wisconsin, USA.]), SAINT (Bruker, 2013[Bruker (2013). SAINT. Buker AXS, Inc., Madison, Wisconsin, USA.]), SHELXS (Sheldrick, 2008[Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122.]), SHELXL (Sheldrick, 2015[Sheldrick, G. M. (2015). Acta Cryst. C71, 3-8.]) and OLEX2 (Dolomanov et al., 2009[Dolomanov, O. V., Bourhis, L. J., Gildea, R. J., Howard, J. A. K. & Puschmann, H. (2009). J. Appl. Cryst. 42, 339-341.]).

Supporting information


Chemical context top

N-Acyl homoserine lactones (AHLs) mediate quorum sensing in Gram-negative bacteria (Miller & Bassler, 2001; Waters & Bassler, 2005). We have previously shown that AHLs engage in nπ* inter­actions between the acyl and lactone ester carbonyl groups (Newberry & Raines, 2014). These inter­actions cause attraction through donation of oxygen lone pair (n) electron density into the π* anti­bonding orbital of an acceptor carbonyl group (Hinderaker & Raines, 2003). This inter­action is observed in the free molecule but not in structures of these compounds bound to their protein receptors, implicating these inter­actions in the potency of AHLs and their analogs. Background to carbonyl–carbonyl inter­actions is given by Bretscher et al. (2001), DeRider et al. (2002), Hinderaker & Raines (2003), and Bartlett et al. (2010). Our previous studies were restricted to AHLs with simple acyl appendages, but natural AHLs are also often oxidized at the 3-position to yield β-keto acyl groups, such as that reported here.

Structural commentary and NBO analysis top

This is, to our knowledge, the first report of the structure of a free 3-oxo AHL (Fig. 1). Individual molecules pack in linear arrays thanks to inter­molecular hydrogen bonds between amide groups (Fig. 2). The molecule crystallizes as the keto tautomer, consistent with other β-keto amides (Allen, 2002). Like unoxidized AHLs, it displays the hallmark features of an attractive nπ* inter­action between the amide and ester carbonyl groups (Fig. 3). Specifically, the donor oxygen makes a sub-van der Waals contact of 2.709 (2) Å with the acceptor carbonyl group, with an angle of approach of 99.1 (1)°, characteristic of the Bürgi–Dunitz trajectory for nucleophilic addition (Bürgi et al., 1973, 1974). This geometry enables electron donation that, in turn, causes a characteristic pyramidalization of the acceptor carbonyl group. We observe that the carbonyl carbon rises 0.016 (1) Å out of the plane of its substituents, creating a distortion angle Θ of 1.1 (1)°. This signature has been used to diagnose the presence of these inter­actions in many molecules (Choudhary et al., 2009, 2014; Choudhary & Raines, 2011; Newberry et al., 2013), including polymers (Newberry & Raines, 2013) and proteins (Newberry et al., 2014). Consistent with these observations, natural bond orbital (NBO) analysis (Reed et al., 1988; Glendening et al., 2012) of the crystal structure at the B3LYP/6–311+G(2 d,p) level of theory predicts the release of 2.67 kcal mol−1 of energy due to the nπ* inter­action, indicating a significant contribution of this inter­action to the conformation of this molecule (Fig. 4).

Inter­estingly, a short contact is also observed between the ketone oxygen and amide carbonyl groups. In this case, the donor oxygen makes a 2.746 (2) Å contact at 107.5 (1)° to the amide carbonyl group. This contact causes the amide carbonyl group to distort 0.008 (1) Å out of plane, corresponding to a distortion angle Θ of 0.59 (6)°. The pyramidalization of the amide carbonyl group indicates a weaker nπ* inter­action from the ketone to the amide than from the amide to the ester, as would be expected for the enclosing of a four-membered ring relative to the enclosing of a five-membered ring, respectively. Indeed, NBO analysis predicts release of 1.42 kcal mol−1 of energy due to the nπ* inter­action between the ketone and amide (Fig. 5), which is nevertheless a significant contribution that likely biases the conformation of this molecule.

Based on the specific geometric parameters measured in this crystal structure, we conclude that the structure of unbound oxo-AHLs are influenced by nπ* inter­actions, similarly to simple AHLs. Moreover, an additional nπ* inter­action specific to oxo-AHLs might bias their conformation further and thus affect their binding to protein receptors.

Supra­molecular features top

In the crystal, the molecules form translational chains along the a axis via N—H···O hydrogen bonds (Table 1 and Fig. 2).

Synthesis and crystallization top

The title compound was prepared as reported previously (Eberhard & Schineller, 2000). A small amount of solid product was dissolved in hexanes with a minimal amount of di­chloro­methane. Slow evaporation afforded high-quality crystals after ~4 days.

Refinement top

Crystal data, data collection and structure refinement details are summarized in Table 2. Except for hydrogen-bond donors and terminal methyl groups, all H atoms were placed in idealized locations and refined as riding with appropriate thermal displacement coefficients Uiso(H) = 1.2 or 1.5 times Ueq(bearing atom).

Related literature top

For background on the biological relevance of homoserine lactones see: Miller & Bassler (2001) and Waters & Bassler (2005). For previous examination of the solid-state structures of homoserine lactones see Newberry & Raines (2014). For background on carbonyl–carbonyl interactions see: Bretscher et al. (2001), DeRider et al. (2002), Hinderaker & Raines (2003), and Bartlett et al. (2010). For background on natural bond orbital analysis see Reed et al. (1988) and Glendening et al. (2012). For Gaussian software, see Frisch et al. (2009).

Structure description top

N-Acyl homoserine lactones (AHLs) mediate quorum sensing in Gram-negative bacteria (Miller & Bassler, 2001; Waters & Bassler, 2005). We have previously shown that AHLs engage in nπ* inter­actions between the acyl and lactone ester carbonyl groups (Newberry & Raines, 2014). These inter­actions cause attraction through donation of oxygen lone pair (n) electron density into the π* anti­bonding orbital of an acceptor carbonyl group (Hinderaker & Raines, 2003). This inter­action is observed in the free molecule but not in structures of these compounds bound to their protein receptors, implicating these inter­actions in the potency of AHLs and their analogs. Background to carbonyl–carbonyl inter­actions is given by Bretscher et al. (2001), DeRider et al. (2002), Hinderaker & Raines (2003), and Bartlett et al. (2010). Our previous studies were restricted to AHLs with simple acyl appendages, but natural AHLs are also often oxidized at the 3-position to yield β-keto acyl groups, such as that reported here.

This is, to our knowledge, the first report of the structure of a free 3-oxo AHL (Fig. 1). Individual molecules pack in linear arrays thanks to inter­molecular hydrogen bonds between amide groups (Fig. 2). The molecule crystallizes as the keto tautomer, consistent with other β-keto amides (Allen, 2002). Like unoxidized AHLs, it displays the hallmark features of an attractive nπ* inter­action between the amide and ester carbonyl groups (Fig. 3). Specifically, the donor oxygen makes a sub-van der Waals contact of 2.709 (2) Å with the acceptor carbonyl group, with an angle of approach of 99.1 (1)°, characteristic of the Bürgi–Dunitz trajectory for nucleophilic addition (Bürgi et al., 1973, 1974). This geometry enables electron donation that, in turn, causes a characteristic pyramidalization of the acceptor carbonyl group. We observe that the carbonyl carbon rises 0.016 (1) Å out of the plane of its substituents, creating a distortion angle Θ of 1.1 (1)°. This signature has been used to diagnose the presence of these inter­actions in many molecules (Choudhary et al., 2009, 2014; Choudhary & Raines, 2011; Newberry et al., 2013), including polymers (Newberry & Raines, 2013) and proteins (Newberry et al., 2014). Consistent with these observations, natural bond orbital (NBO) analysis (Reed et al., 1988; Glendening et al., 2012) of the crystal structure at the B3LYP/6–311+G(2 d,p) level of theory predicts the release of 2.67 kcal mol−1 of energy due to the nπ* inter­action, indicating a significant contribution of this inter­action to the conformation of this molecule (Fig. 4).

Inter­estingly, a short contact is also observed between the ketone oxygen and amide carbonyl groups. In this case, the donor oxygen makes a 2.746 (2) Å contact at 107.5 (1)° to the amide carbonyl group. This contact causes the amide carbonyl group to distort 0.008 (1) Å out of plane, corresponding to a distortion angle Θ of 0.59 (6)°. The pyramidalization of the amide carbonyl group indicates a weaker nπ* inter­action from the ketone to the amide than from the amide to the ester, as would be expected for the enclosing of a four-membered ring relative to the enclosing of a five-membered ring, respectively. Indeed, NBO analysis predicts release of 1.42 kcal mol−1 of energy due to the nπ* inter­action between the ketone and amide (Fig. 5), which is nevertheless a significant contribution that likely biases the conformation of this molecule.

Based on the specific geometric parameters measured in this crystal structure, we conclude that the structure of unbound oxo-AHLs are influenced by nπ* inter­actions, similarly to simple AHLs. Moreover, an additional nπ* inter­action specific to oxo-AHLs might bias their conformation further and thus affect their binding to protein receptors.

In the crystal, the molecules form translational chains along the a axis via N—H···O hydrogen bonds (Table 1 and Fig. 2).

For background on the biological relevance of homoserine lactones see: Miller & Bassler (2001) and Waters & Bassler (2005). For previous examination of the solid-state structures of homoserine lactones see Newberry & Raines (2014). For background on carbonyl–carbonyl interactions see: Bretscher et al. (2001), DeRider et al. (2002), Hinderaker & Raines (2003), and Bartlett et al. (2010). For background on natural bond orbital analysis see Reed et al. (1988) and Glendening et al. (2012). For Gaussian software, see Frisch et al. (2009).

Synthesis and crystallization top

The title compound was prepared as reported previously (Eberhard & Schineller, 2000). A small amount of solid product was dissolved in hexanes with a minimal amount of di­chloro­methane. Slow evaporation afforded high-quality crystals after ~4 days.

Refinement details top

Crystal data, data collection and structure refinement details are summarized in Table 2. Except for hydrogen-bond donors and terminal methyl groups, all H atoms were placed in idealized locations and refined as riding with appropriate thermal displacement coefficients Uiso(H) = 1.2 or 1.5 times Ueq(bearing atom).

Computing details top

Data collection: APEX2 (Bruker, 2012); cell refinement: SAINT (Bruker, 2013); data reduction: SAINT (Bruker, 2013); program(s) used to solve structure: SHELXS (Sheldrick, 2008); program(s) used to refine structure: SHELXL (Sheldrick, 2015); molecular graphics: OLEX2 (Dolomanov et al., 2009); software used to prepare material for publication: OLEX2 (Dolomanov et al., 2009).

Figures top
[Figure 1] Fig. 1. Molecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level.
[Figure 2] Fig. 2. Packing of the title compound.
[Figure 3] Fig. 3. Structural parameters describing an nπ* interaction
[Figure 4] Fig. 4. Overlap of amide lone pair (n) and ester π* orbitals.
[Figure 5] Fig. 5. Overlap of ketone lone pair (n) and amide π* orbitals.
N-(3-Oxobutanoyl)-L-homoserine lactone top
Crystal data top
C8H11NO4Dx = 1.395 Mg m3
Mr = 185.18Cu Kα radiation, λ = 1.54178 Å
Orthorhombic, P212121Cell parameters from 6262 reflections
a = 5.0215 (4) Åθ = 5.0–73.3°
b = 9.8852 (10) ŵ = 0.96 mm1
c = 17.7668 (14) ÅT = 100 K
V = 881.91 (14) Å3Block, colourless
Z = 40.23 × 0.13 × 0.04 mm
F(000) = 392
Data collection top
Bruker APEXII CCD
diffractometer
1702 reflections with I > 2σ(I)
φ and ω scansRint = 0.028
Absorption correction: multi-scan
(SADABS; Bruker, 2014/5)
θmax = 73.3°, θmin = 5.0°
Tmin = 0.785, Tmax = 0.841h = 66
11955 measured reflectionsk = 1211
1755 independent reflectionsl = 2221
Refinement top
Refinement on F2Hydrogen site location: mixed
Least-squares matrix: fullH atoms treated by a mixture of independent and constrained refinement
R[F2 > 2σ(F2)] = 0.026 w = 1/[σ2(Fo2) + (0.0377P)2 + 0.2168P]
where P = (Fo2 + 2Fc2)/3
wR(F2) = 0.067(Δ/σ)max < 0.001
S = 1.04Δρmax = 0.22 e Å3
1755 reflectionsΔρmin = 0.15 e Å3
134 parametersAbsolute structure: Flack x determined using 657 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013).
0 restraintsAbsolute structure parameter: 0.01 (8)
Crystal data top
C8H11NO4V = 881.91 (14) Å3
Mr = 185.18Z = 4
Orthorhombic, P212121Cu Kα radiation
a = 5.0215 (4) ŵ = 0.96 mm1
b = 9.8852 (10) ÅT = 100 K
c = 17.7668 (14) Å0.23 × 0.13 × 0.04 mm
Data collection top
Bruker APEXII CCD
diffractometer
1755 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2014/5)
1702 reflections with I > 2σ(I)
Tmin = 0.785, Tmax = 0.841Rint = 0.028
11955 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.026H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.067Δρmax = 0.22 e Å3
S = 1.04Δρmin = 0.15 e Å3
1755 reflectionsAbsolute structure: Flack x determined using 657 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013).
134 parametersAbsolute structure parameter: 0.01 (8)
0 restraints
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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.1639 (3)0.52850 (12)0.55760 (7)0.0190 (3)
O20.0589 (2)0.37968 (12)0.41512 (7)0.0189 (3)
N10.3857 (3)0.39964 (14)0.42086 (8)0.0156 (3)
O30.0157 (2)0.68079 (12)0.47556 (7)0.0164 (3)
O40.2366 (3)0.25259 (13)0.26283 (7)0.0253 (3)
C40.0901 (4)0.73341 (18)0.40163 (10)0.0189 (4)
H4A0.18550.82060.40690.023*
H4B0.07030.74800.37030.023*
C70.2289 (3)0.15843 (17)0.30622 (9)0.0166 (3)
C10.1762 (3)0.57897 (16)0.49600 (9)0.0141 (3)
C80.2475 (5)0.01346 (18)0.28126 (11)0.0230 (4)
C50.1638 (3)0.32746 (17)0.41024 (9)0.0142 (3)
C60.2005 (3)0.17999 (16)0.39064 (9)0.0161 (3)
H6A0.04540.12790.40920.019*
H6B0.36150.14510.41630.019*
C20.3719 (3)0.54444 (16)0.43286 (10)0.0158 (3)
H20.55280.57800.44720.019*
C30.2703 (4)0.62767 (17)0.36590 (10)0.0200 (4)
H3A0.41990.67100.33870.024*
H3B0.16960.57010.33030.024*
H10.534 (5)0.363 (2)0.4159 (12)0.018 (5)*
H8A0.389 (5)0.031 (3)0.3095 (14)0.030 (6)*
H8B0.073 (6)0.032 (3)0.2945 (15)0.044 (8)*
H8C0.272 (6)0.006 (3)0.2277 (15)0.034 (6)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0201 (6)0.0182 (6)0.0187 (6)0.0031 (5)0.0022 (5)0.0006 (5)
O20.0105 (5)0.0182 (6)0.0279 (6)0.0009 (5)0.0000 (5)0.0035 (5)
N10.0093 (6)0.0163 (7)0.0213 (7)0.0032 (6)0.0009 (5)0.0034 (6)
O30.0141 (5)0.0160 (6)0.0192 (6)0.0013 (5)0.0027 (5)0.0007 (5)
O40.0359 (8)0.0200 (6)0.0201 (6)0.0004 (6)0.0007 (6)0.0030 (5)
C40.0192 (8)0.0199 (8)0.0176 (8)0.0009 (7)0.0012 (7)0.0018 (7)
C70.0131 (7)0.0182 (8)0.0185 (8)0.0006 (7)0.0008 (6)0.0003 (6)
C10.0107 (7)0.0125 (7)0.0191 (8)0.0046 (6)0.0004 (6)0.0033 (6)
C80.0316 (10)0.0185 (8)0.0190 (8)0.0005 (8)0.0004 (8)0.0024 (7)
C50.0125 (7)0.0170 (7)0.0132 (7)0.0016 (7)0.0000 (6)0.0009 (6)
C60.0158 (8)0.0145 (7)0.0180 (8)0.0011 (7)0.0001 (6)0.0005 (6)
C20.0121 (7)0.0155 (8)0.0196 (8)0.0013 (6)0.0021 (6)0.0028 (6)
C30.0205 (8)0.0202 (8)0.0193 (8)0.0001 (8)0.0037 (7)0.0012 (6)
Geometric parameters (Å, º) top
O1—C11.204 (2)C2—C31.534 (2)
O2—C51.235 (2)C2—H21.000
N1—C51.337 (2)C3—H3a0.990
N1—C21.449 (2)C3—H3b0.990
O3—C41.461 (2)C4—H4a0.990
O3—C11.340 (2)C4—H4b0.990
O4—C71.209 (2)N1—H10.83 (2)
C4—C31.521 (2)C6—H6a0.990
C7—C81.503 (2)C6—H6b0.990
C7—C61.522 (2)C8—H8a0.98 (3)
C1—C21.530 (2)C8—H8b1.01 (3)
C5—C61.510 (2)C8—H8c0.96 (3)
C5—N1—C2120.55 (14)C4—C3—H3a111.0
C1—O3—C4110.93 (13)C4—C3—H3b111.0
O3—C4—C3106.42 (13)H3a—C3—H3b109.0
O4—C7—C8122.95 (15)C3—C4—H4a110.4
O4—C7—C6121.57 (15)C3—C4—H4b110.4
C8—C7—C6115.48 (14)O3—C4—H4a110.4
O1—C1—O3121.79 (15)O3—C4—H4b110.4
O1—C1—C2127.35 (15)H4a—C4—H4b108.6
O3—C1—C2110.82 (14)C2—N1—H1119.2 (15)
O2—C5—N1121.47 (15)C5—N1—H1119.9 (15)
O2—C5—C6122.02 (15)C5—C6—H6a109.2
N1—C5—C6116.50 (14)C5—C6—H6b109.2
C5—C6—C7111.96 (13)C7—C6—H6a109.2
N1—C2—C1111.04 (13)C7—C6—H6b109.2
N1—C2—C3115.58 (15)H6a—C6—H6b107.9
C1—C2—C3103.61 (14)C7—C8—H8a108.9 (17)
C4—C3—C2104.05 (14)C7—C8—H8b107.5 (17)
C1—C2—H2108.8C7—C8—H8c111.9 (18)
N1—C2—H2108.8H8a—C8—H8b108 (2)
C3—C2—H2108.8H8b—C8—H8c108 (2)
C2—C3—H3a111.0H8c—C8—H8a112 (2)
C2—C3—H3b111.0
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.83 (2)2.05 (2)2.7973 (19)149 (2)
Symmetry code: (i) x+1, y, z.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.83 (2)2.05 (2)2.7973 (19)149 (2)
Symmetry code: (i) x+1, y, z.

Experimental details

Crystal data
Chemical formulaC8H11NO4
Mr185.18
Crystal system, space groupOrthorhombic, P212121
Temperature (K)100
a, b, c (Å)5.0215 (4), 9.8852 (10), 17.7668 (14)
V3)881.91 (14)
Z4
Radiation typeCu Kα
µ (mm1)0.96
Crystal size (mm)0.23 × 0.13 × 0.04
Data collection
DiffractometerBruker APEXII CCD
Absorption correctionMulti-scan
(SADABS; Bruker, 2014/5)
Tmin, Tmax0.785, 0.841
No. of measured, independent and
observed [I > 2σ(I)] reflections
11955, 1755, 1702
Rint0.028
(sin θ/λ)max1)0.621
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.026, 0.067, 1.04
No. of reflections1755
No. of parameters134
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.22, 0.15
Absolute structureFlack x determined using 657 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013).
Absolute structure parameter0.01 (8)

Computer programs: APEX2 (Bruker, 2012), SAINT (Bruker, 2013), SHELXS (Sheldrick, 2008), SHELXL (Sheldrick, 2015), OLEX2 (Dolomanov et al., 2009).

 

Acknowledgements

We thank I. A. Guzei and the Mol­ecular Structure Laboratory at UW–Madison for assistance with the data collection. This work was funded by grants CHE-1124944 (NSF) and R01 AR044276 (NIH). RWN was supported by NIH Biotechnology Training Grant T32 GM008349 and by an ACS Division of Organic Chemistry Graduate Fellowship.

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Volume 72| Part 2| February 2016| Pages 136-139
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