research communications
N-(3-oxobutanoyl)-L-homoserine lactone
ofaDepartment 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
The structure and 8H11NO4, which is a known quorum-sensing modulator, have been determined. The molecule exhibits signs of an intramolecular attractive carbonyl–carbonyl n→π* 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 n→π* 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.
of the title compound, CKeywords: crystal structure; homoserine lactone; carbonyl interaction; NBO analysis; hydrogen bonding.
CCDC reference: 1444720
1. Chemical context
N-Acyl homoserine (AHLs) mediate quorum sensing in Gram-negative bacteria (Miller & Bassler, 2001; Waters & Bassler, 2005). We have previously shown that AHLs engage in n→π* 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 such as that reported here.
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). 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 (Allen, 2002). Like unoxidized AHLs, it displays the hallmark features of an attractive n→π* interaction between the amide and ester carbonyl groups (Fig. 3). 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, 1974). 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) 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 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 n→π* 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 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 n→π* 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 n→π* 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 n→π* interactions, similarly to simple AHLs. Moreover, an additional n→π* interaction specific to oxo-AHLs might bias their conformation further and thus affect their binding to protein receptors.
we conclude that the structure of unbound oxo-AHLs are influenced by3. Supramolecular features
In the crystal, the molecules form translational chains along the a axis via N—H⋯O hydrogen bonds (Table 1 and Fig. 2).
4. Synthesis and crystallization
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.
5. Refinement
Crystal data, data collection and structure . 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).
details are summarized in Table 2Supporting information
CCDC reference: 1444720
10.1107/S2056989015024913/ld2139sup1.cif
contains datablock I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S2056989015024913/ld2139Isup3.hkl
N-Acyl homoserine →π* 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 such as that reported here.
(AHLs) mediate quorum sensing in Gram-negative bacteria (Miller & Bassler, 2001; Waters & Bassler, 2005). We have previously shown that AHLs engage in nThis 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 (Allen, 2002). Like unoxidized AHLs, it displays the hallmark features of an attractive n→π* 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 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 n→π* 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 n→π* 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 n→π* 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 →π* interactions, similarly to simple AHLs. Moreover, an additional n→π* interaction specific to oxo-AHLs might bias their conformation further and thus affect their binding to protein receptors.
we conclude that the structure of unbound oxo-AHLs are influenced by nIn the crystal, the molecules form translational chains along the a axis via N—H···O hydrogen bonds (Table 1 and Fig. 2).
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.
Crystal data, data collection and structure
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).N-Acyl homoserine →π* 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 such as that reported here.
(AHLs) mediate quorum sensing in Gram-negative bacteria (Miller & Bassler, 2001; Waters & Bassler, 2005). We have previously shown that AHLs engage in nThis 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 (Allen, 2002). Like unoxidized AHLs, it displays the hallmark features of an attractive n→π* 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 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 n→π* 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 n→π* 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 n→π* 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 →π* interactions, similarly to simple AHLs. Moreover, an additional n→π* interaction specific to oxo-AHLs might bias their conformation further and thus affect their binding to protein receptors.
we conclude that the structure of unbound oxo-AHLs are influenced by nIn 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
see: Miller & Bassler (2001) and Waters & Bassler (2005). For previous examination of the solid-state structures of homoserine 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).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.
detailsCrystal data, data collection and structure
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).Data collection: APEX2 (Bruker, 2012); cell
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).Fig. 1. Molecular structure of the title compound with displacement ellipsoids drawn at the 50% probability level. | |
Fig. 2. Packing of the title compound. | |
Fig. 3. Structural parameters describing an n→π* interaction | |
Fig. 4. Overlap of amide lone pair (n) and ester π* orbitals. | |
Fig. 5. Overlap of ketone lone pair (n) and amide π* orbitals. |
C8H11NO4 | Dx = 1.395 Mg m−3 |
Mr = 185.18 | Cu Kα radiation, λ = 1.54178 Å |
Orthorhombic, P212121 | Cell parameters from 6262 reflections |
a = 5.0215 (4) Å | θ = 5.0–73.3° |
b = 9.8852 (10) Å | µ = 0.96 mm−1 |
c = 17.7668 (14) Å | T = 100 K |
V = 881.91 (14) Å3 | Block, colourless |
Z = 4 | 0.23 × 0.13 × 0.04 mm |
F(000) = 392 |
Bruker APEXII CCD diffractometer | 1702 reflections with I > 2σ(I) |
φ and ω scans | Rint = 0.028 |
Absorption correction: multi-scan (SADABS; Bruker, 2014/5) | θmax = 73.3°, θmin = 5.0° |
Tmin = 0.785, Tmax = 0.841 | h = −6→6 |
11955 measured reflections | k = −12→11 |
1755 independent reflections | l = −22→21 |
Refinement on F2 | Hydrogen site location: mixed |
Least-squares matrix: full | H 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 = 1.04 | Δρmax = 0.22 e Å−3 |
1755 reflections | Δρmin = −0.15 e Å−3 |
134 parameters | Absolute structure: Flack x determined using 657 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013). |
0 restraints | Absolute structure parameter: −0.01 (8) |
C8H11NO4 | V = 881.91 (14) Å3 |
Mr = 185.18 | Z = 4 |
Orthorhombic, P212121 | Cu Kα radiation |
a = 5.0215 (4) Å | µ = 0.96 mm−1 |
b = 9.8852 (10) Å | T = 100 K |
c = 17.7668 (14) Å | 0.23 × 0.13 × 0.04 mm |
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 = 0.841 | Rint = 0.028 |
11955 measured reflections |
R[F2 > 2σ(F2)] = 0.026 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.067 | Δρmax = 0.22 e Å−3 |
S = 1.04 | Δρmin = −0.15 e Å−3 |
1755 reflections | Absolute structure: Flack x determined using 657 quotients [(I+)-(I-)]/[(I+)+(I-)] (Parsons et al., 2013). |
134 parameters | Absolute structure parameter: −0.01 (8) |
0 restraints |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.1639 (3) | 0.52850 (12) | 0.55760 (7) | 0.0190 (3) | |
O2 | −0.0589 (2) | 0.37968 (12) | 0.41512 (7) | 0.0189 (3) | |
N1 | 0.3857 (3) | 0.39964 (14) | 0.42086 (8) | 0.0156 (3) | |
O3 | 0.0157 (2) | 0.68079 (12) | 0.47556 (7) | 0.0164 (3) | |
O4 | 0.2366 (3) | 0.25259 (13) | 0.26283 (7) | 0.0253 (3) | |
C4 | 0.0901 (4) | 0.73341 (18) | 0.40163 (10) | 0.0189 (4) | |
H4A | 0.1855 | 0.8206 | 0.4069 | 0.023* | |
H4B | −0.0703 | 0.7480 | 0.3703 | 0.023* | |
C7 | 0.2289 (3) | 0.15843 (17) | 0.30622 (9) | 0.0166 (3) | |
C1 | 0.1762 (3) | 0.57897 (16) | 0.49600 (9) | 0.0141 (3) | |
C8 | 0.2475 (5) | 0.01346 (18) | 0.28126 (11) | 0.0230 (4) | |
C5 | 0.1638 (3) | 0.32746 (17) | 0.41024 (9) | 0.0142 (3) | |
C6 | 0.2005 (3) | 0.17999 (16) | 0.39064 (9) | 0.0161 (3) | |
H6A | 0.0454 | 0.1279 | 0.4092 | 0.019* | |
H6B | 0.3615 | 0.1451 | 0.4163 | 0.019* | |
C2 | 0.3719 (3) | 0.54444 (16) | 0.43286 (10) | 0.0158 (3) | |
H2 | 0.5528 | 0.5780 | 0.4472 | 0.019* | |
C3 | 0.2703 (4) | 0.62767 (17) | 0.36590 (10) | 0.0200 (4) | |
H3A | 0.4199 | 0.6710 | 0.3387 | 0.024* | |
H3B | 0.1696 | 0.5701 | 0.3303 | 0.024* | |
H1 | 0.534 (5) | 0.363 (2) | 0.4159 (12) | 0.018 (5)* | |
H8A | 0.389 (5) | −0.031 (3) | 0.3095 (14) | 0.030 (6)* | |
H8B | 0.073 (6) | −0.032 (3) | 0.2945 (15) | 0.044 (8)* | |
H8C | 0.272 (6) | 0.006 (3) | 0.2277 (15) | 0.034 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0201 (6) | 0.0182 (6) | 0.0187 (6) | −0.0031 (5) | 0.0022 (5) | 0.0006 (5) |
O2 | 0.0105 (5) | 0.0182 (6) | 0.0279 (6) | 0.0009 (5) | 0.0000 (5) | −0.0035 (5) |
N1 | 0.0093 (6) | 0.0163 (7) | 0.0213 (7) | 0.0032 (6) | 0.0009 (5) | −0.0034 (6) |
O3 | 0.0141 (5) | 0.0160 (6) | 0.0192 (6) | 0.0013 (5) | 0.0027 (5) | −0.0007 (5) |
O4 | 0.0359 (8) | 0.0200 (6) | 0.0201 (6) | 0.0004 (6) | 0.0007 (6) | 0.0030 (5) |
C4 | 0.0192 (8) | 0.0199 (8) | 0.0176 (8) | 0.0009 (7) | −0.0012 (7) | 0.0018 (7) |
C7 | 0.0131 (7) | 0.0182 (8) | 0.0185 (8) | −0.0006 (7) | −0.0008 (6) | 0.0003 (6) |
C1 | 0.0107 (7) | 0.0125 (7) | 0.0191 (8) | −0.0046 (6) | 0.0004 (6) | −0.0033 (6) |
C8 | 0.0316 (10) | 0.0185 (8) | 0.0190 (8) | 0.0005 (8) | −0.0004 (8) | −0.0024 (7) |
C5 | 0.0125 (7) | 0.0170 (7) | 0.0132 (7) | 0.0016 (7) | 0.0000 (6) | 0.0009 (6) |
C6 | 0.0158 (8) | 0.0145 (7) | 0.0180 (8) | 0.0011 (7) | −0.0001 (6) | 0.0005 (6) |
C2 | 0.0121 (7) | 0.0155 (8) | 0.0196 (8) | −0.0013 (6) | 0.0021 (6) | −0.0028 (6) |
C3 | 0.0205 (8) | 0.0202 (8) | 0.0193 (8) | −0.0001 (8) | 0.0037 (7) | 0.0012 (6) |
O1—C1 | 1.204 (2) | C2—C3 | 1.534 (2) |
O2—C5 | 1.235 (2) | C2—H2 | 1.000 |
N1—C5 | 1.337 (2) | C3—H3a | 0.990 |
N1—C2 | 1.449 (2) | C3—H3b | 0.990 |
O3—C4 | 1.461 (2) | C4—H4a | 0.990 |
O3—C1 | 1.340 (2) | C4—H4b | 0.990 |
O4—C7 | 1.209 (2) | N1—H1 | 0.83 (2) |
C4—C3 | 1.521 (2) | C6—H6a | 0.990 |
C7—C8 | 1.503 (2) | C6—H6b | 0.990 |
C7—C6 | 1.522 (2) | C8—H8a | 0.98 (3) |
C1—C2 | 1.530 (2) | C8—H8b | 1.01 (3) |
C5—C6 | 1.510 (2) | C8—H8c | 0.96 (3) |
C5—N1—C2 | 120.55 (14) | C4—C3—H3a | 111.0 |
C1—O3—C4 | 110.93 (13) | C4—C3—H3b | 111.0 |
O3—C4—C3 | 106.42 (13) | H3a—C3—H3b | 109.0 |
O4—C7—C8 | 122.95 (15) | C3—C4—H4a | 110.4 |
O4—C7—C6 | 121.57 (15) | C3—C4—H4b | 110.4 |
C8—C7—C6 | 115.48 (14) | O3—C4—H4a | 110.4 |
O1—C1—O3 | 121.79 (15) | O3—C4—H4b | 110.4 |
O1—C1—C2 | 127.35 (15) | H4a—C4—H4b | 108.6 |
O3—C1—C2 | 110.82 (14) | C2—N1—H1 | 119.2 (15) |
O2—C5—N1 | 121.47 (15) | C5—N1—H1 | 119.9 (15) |
O2—C5—C6 | 122.02 (15) | C5—C6—H6a | 109.2 |
N1—C5—C6 | 116.50 (14) | C5—C6—H6b | 109.2 |
C5—C6—C7 | 111.96 (13) | C7—C6—H6a | 109.2 |
N1—C2—C1 | 111.04 (13) | C7—C6—H6b | 109.2 |
N1—C2—C3 | 115.58 (15) | H6a—C6—H6b | 107.9 |
C1—C2—C3 | 103.61 (14) | C7—C8—H8a | 108.9 (17) |
C4—C3—C2 | 104.05 (14) | C7—C8—H8b | 107.5 (17) |
C1—C2—H2 | 108.8 | C7—C8—H8c | 111.9 (18) |
N1—C2—H2 | 108.8 | H8a—C8—H8b | 108 (2) |
C3—C2—H2 | 108.8 | H8b—C8—H8c | 108 (2) |
C2—C3—H3a | 111.0 | H8c—C8—H8a | 112 (2) |
C2—C3—H3b | 111.0 |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2i | 0.83 (2) | 2.05 (2) | 2.7973 (19) | 149 (2) |
Symmetry code: (i) x+1, y, z. |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1···O2i | 0.83 (2) | 2.05 (2) | 2.7973 (19) | 149 (2) |
Symmetry code: (i) x+1, y, z. |
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) |
V (Å3) | 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) |
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 (Å−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). |
Absolute structure parameter | −0.01 (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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