Dominik Heger1,2, Alexis J Eugene1, Sean R Parkin1, Marcelo I Guzman1. 1. Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, USA. 2. Department of Chemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
Abstract
The structure of zymonic acid (systematic name: 4-hy-droxy-2-methyl-5-oxo-2,5-di-hydro-furan-2-carb-oxy-lic acid), C6H6O5, which had previously eluded crystallographic determination, is presented here for the first time. It forms by intra-molecular condensation of parapyruvic acid, which is the product of aldol condensation of pyruvic acid. A redetermination of the crystal structure of pyruvic acid (systematic name: 2-oxo-propanoic acid), C3H4O3, at low temperature (90 K) and with increased precision, is also presented [for the previous structure, see: Harata et al. (1977 ▸). Acta Cryst. B33, 210-212]. In zymonic acid, the hy-droxy-lactone ring is close to planar (r.m.s. deviation = 0.0108 Å) and the dihedral angle between the ring and the plane formed by the bonds of the methyl and carb-oxy-lic acid carbon atoms to the ring is 88.68 (7)°. The torsion angle of the carb-oxy-lic acid group relative to the ring is 12.04 (16)°. The pyruvic acid mol-ecule is almost planar, having a dihedral angle between the carb-oxy-lic acid and methyl-ketone groups of 3.95 (6)°. Inter-molecular inter-actions in both crystal structures are dominated by hydrogen bonding. The common R 2 2(8) hydrogen-bonding motif links carb-oxy-lic acid groups on adjacent mol-ecules in both structures. In zymonic acid, this results in dimers about a crystallographic twofold of space group C2/c, which forces the carb-oxy-lic acid group to be disordered exactly 50:50, which scrambles the carbonyl and hydroxyl groups and gives an apparent equalization of the C-O bond lengths [1.2568 (16) and 1.2602 (16) Å]. The other hydrogen bonds in zymonic acid (O-H⋯O and weak C-H⋯O), link mol-ecules across a 21-screw axis, and generate an R 2 2(9) motif. These hydrogen-bonding inter-actions propagate to form extended pleated sheets in the ab plane. Stacking of these zigzag sheets along c involves only van der Waals contacts. In pyruvic acid, inversion-related mol-ecules are linked into R 2 2(8) dimers, with van der Waals inter-actions between dimers as the only other inter-molecular contacts.
The structure of zymonic acid (systematic name: 4-hy-droxy-2-methyl-5-oxo-2,5-di-hydro-furan-2-carb-oxy-lic acid), C6H6O5, which had previously eluded crystallographic determination, is presented here for the first time. It forms by intra-molecular condensation of parapyruvic acid, which is the product of aldol condensation of pyruvic acid. A redetermination of the crystal structure of pyruvic acid (systematic name: 2-oxo-propanoic acid), C3H4O3, at low temperature (90 K) and with increased precision, is also presented [for the previous structure, see: Harata et al. (1977 ▸). Acta Cryst. B33, 210-212]. In zymonic acid, the hy-droxy-lactone ring is close to planar (r.m.s. deviation = 0.0108 Å) and the dihedral angle between the ring and the plane formed by the bonds of the methyl andcarb-oxy-lic acidcarbon atoms to the ring is 88.68 (7)°. The torsion angle of the carb-oxy-lic acid group relative to the ring is 12.04 (16)°. The pyruvic acid mol-ecule is almost planar, having a dihedral angle between the carb-oxy-lic acid and methyl-ketone groups of 3.95 (6)°. Inter-molecular inter-actions in both crystal structures are dominated by hydrogen bonding. The common R 2 2(8) hydrogen-bonding motif links carb-oxy-lic acid groups on adjacent mol-ecules in both structures. In zymonic acid, this results in dimers about a crystallographic twofold of space group C2/c, which forces the carb-oxy-lic acid group to be disordered exactly 50:50, which scrambles the carbonyl and hydroxyl groups and gives an apparent equalization of the C-O bond lengths [1.2568 (16) and 1.2602 (16) Å]. The other hydrogen bonds in zymonic acid (O-H⋯O and weak C-H⋯O), link mol-ecules across a 21-screw axis, and generate an R 2 2(9) motif. These hydrogen-bonding inter-actions propagate to form extended pleated sheets in the ab plane. Stacking of these zigzag sheets along c involves only van der Waals contacts. In pyruvic acid, inversion-related mol-ecules are linked into R 2 2(8) dimers, with van der Waals inter-actions between dimers as the only other inter-molecular contacts.
The Human Metabolome Database (Wishart et al., 2007 ▸, 2009 ▸, 2013 ▸, 2018 ▸) lists the compound 4-hydroxy-2-methyl-5-oxofuran-2-carboxylic acid (C6H6O5), commonly named zymonic acid, with the metabocard HMDB0031210. Zymonic acid is used as a flavor constituent for confectionery and tobacco products (Yannai, 2004 ▸). The generation of zymonic acid can proceed by condensation of parapyruvic acid, which itself forms by aldol condensation of pyruvic acid (IUPAC name 2-oxopropanoic acid, C3H4O3; Bloomer et al., 1970 ▸). Therefore, zymonic acid is directly derived from pyruvic acid, and is thus related to the compounds present in the tricarboxylic acid (Krebs) cycle (Nelson & Cox, 2004 ▸) and its reductive version (Guzman, 2011 ▸; Guzman & Martin, 2008 ▸; Zhou & Guzman, 2016 ▸). As an intermediate in central metabolism, zymonic acid is produced in the cytoplasm at very low concentration, from where it can be excreted to the extracellular region.The electron-impact mass spectrum (MS) and electrospray ionization fragmentation of zymonic acid following gas and liquid chromatography, respectively, have been reported (Allen et al., 2015 ▸, 2016 ▸). The use of 13C-zymonic acid has enabled mapping of pH changes, independently of concentration, in mammalian organs and tumors via hyperpolarized magnetic resonance (Düwel et al., 2017 ▸). Thus, zymonic acid is a non-invasive extracellular imaging sensor to localize and quantify pH in vivo (Düwel et al., 2017 ▸; Hundshammer et al., 2017 ▸), with many possible applications in medical diagnosis (Schilling et al., 2016 ▸). As part of the process resulting in the aforementioned invention, the detailed 1H and 13C NMR spectra of pure zymonic acid have been reported (Hundshammer et al., 2017 ▸). Herein, we contribute new information to characterize zymonic acid by reporting for the first time its crystal structure, along with a low-temperature redetermination of pyruvic acid.
Structural commentary
Aside from the effects on the geometry of the carboxylic acid group in zymonic acid that stem from disorder about the twofold axis (see below), there are no unusual bond lengths or angles in either compound.In zymonic acid (Fig. 1 ▸), the hydroxylactone ring is essentially planar (r.m.s. deviation = 0.0108 Å), with the largest deviation from planarity [0.0171 (8) Å] for the ring oxygen atom, O3. The plane defined by the ring carbon atom C4, the methyl carbon atom C6, and the carboxylic acid carbon atom C5, is almost perpendicular to the mean plane of the ring atoms [dihedral angle = 88.68 (7)°]. Lastly, the orientation of the carboxylic acid group relative to the ring, as defined by the torsion angle O4—C5—C4—O3, is 12.04 (16)°. For the carboxylic acid group, disorder about the crystallographic twofold axis effectively averages the C=O double and C—O single bonds, rendering them equivalent [the C5—O4 and C5—O5 distances are 1.2568 (16) and 1.2602 (16) Å, respectively], and requires modeling of half-occupancy hydrogens (H4O and H5O) on each.
Figure 1
The molecular structure of zymonic acid, with displacement ellipsoids drawn at the 50% probability level.
In spite of increased precision resulting from much lower temperature (90 K versus 266 K) and data collection on modern equipment, the redetermined structure of pyruvic acid (Fig. 2 ▸) is largely unchanged from that reported by Harata et al. (1977 ▸). For example, the dihedral angle between the planes defined by atoms C1/C2/C3/O3 and C1/C2/O1/O2 is 3.95 (6)° at 90.00 (2) K versus 3.5° at 266 (1) K.
Figure 2
The molecular structure of pyruvic acid, with displacement ellipsoids drawn at the 50% probability level.
Supramolecular features
The main intermolecular interactions in the crystals of both zymonic and pyruvic acids are hydrogen bonds. In zymonic acid, the carboxylic acid groups of adjacent molecules are related by a crystallographic twofold axis to form hydrogen bonds [O4—H4O⋯O4ii and O5—H5O⋯O5ii; symmetry code: (ii) 1 − x, y, − z] giving (8) dimer motifs (Table 1 ▸). This common supramolecular construct in carboxylic acids usually occurs between inversion-related or symmetry-independent molecules. Here, the orientation of the dimer relative to the crystallographic twofold axis forces the average structure to be statistically disordered (Fig. 3 ▸). Another pair of hydrogen bonds [O2—H2⋯O1i and C3—H3⋯O2i; symmetry code: (i) − x, + y, − z], link molecules related by a 21-screw axis, into (9) motifs (Fig. 4 ▸). These hydrogen-bonding interactions combine to form extended pleated sheets that propagate in the ab plane (Fig. 5 ▸), which in turn, stack along the c-axis direction. In pyruvic acid, inversion-related molecules form the common (8) dimer motif (Fig. 6 ▸, Table 2 ▸). In accordance with the work of Harata et al. (1977 ▸), there are no other noteworthy intermolecular interactions.
Table 1
Hydrogen-bond geometry (Å, °) for zymonic acid
D—H⋯A
D—H
H⋯A
D⋯A
D—H⋯A
O2—H2⋯O1i
0.84
1.96
2.7103 (14)
148
C3—H3⋯O2i
0.95
2.48
3.0720 (16)
120
O4—H4O⋯O4ii
1.09
1.52
2.607 (2)
176
O5—H5O⋯O5ii
0.99
1.63
2.624 (2)
179
Symmetry codes: (i) ; (ii) .
Figure 3
The (8) dimer of zymonic acid. Unlabeled atoms are related to their labeled counterparts by a crystallographic twofold axis (1 − x, y, − z). This uncommon symmetry [for an (8) dimer] forces the O—H⋯O hydrogen bonds involved to be 50:50 disordered about the twofold axis.
Figure 4
The (9) dimer of zymonic acid. Unlabeled atoms are related to their labeled counterparts by a crystallographic 21-screw axis ( − x, + y, − z). Disorder of the carboxylic acid H atoms is omitted to enhance clarity.
Figure 5
A packing plot of zymonic acid viewed down the b axis, showing the stacking along c of zigzag pleated assemblies of molecules. Disorder of the carboxylic acid hydrogen atoms is omitted to enhance clarity.
Figure 6
The (8) dimer of pyruvic acid. Unlabeled atoms are related to their labeled counterparts by crystallographic inversion symmetry (1 − x, 1 − y, 1 − z).
Table 2
Hydrogen-bond geometry (Å, °) for pyruvic acid
D—H⋯A
D—H
H⋯A
D⋯A
D—H⋯A
O1—H1⋯O2i
0.913 (14)
1.742 (14)
2.6536 (8)
175.5 (12)
Symmetry code: (i) .
Database survey
A search of the Cambridge Crystal Structure Database (Version 5.40, Nov. 2018; Groom et al., 2016 ▸) for zymonic acid gave no hits for searches on either ‘zymonic’ or on the structural formula. A search on the structural formula of pyruvic acid gave two hits. CSD entry PRUVAC (Harata et al., 1977 ▸) describes the pure compound at 266 K, and is similar to the present pyruvic acid structure (after transformation to a common cell setting). CSD entry FAFGUR (Prohens et al., 2016 ▸) describes a co-crystal of pyruvic acid with the drug agomelatine. The CSD does contain structures for derivatives of both zymonic and pyruvic acids, but none of these have features that are especially relevant to the current work.
Synthesis and crystallization
Vacuum distillation of pyruvic acid (Sigma–Aldrich, 98.5%) was used for purification (Eugene & Guzman, 2017a
▸,b
▸). Freshly distilled pyruvic acid was crystallized in a closed vial in a freezer at 253 K. The tail of this distillation, a viscous yellowish residue enriched in parapyruvic and zymonic acids, was isolated in a vial, and the headspace filled with N2(g) before sealing it with a cap. Crystals of zymonic acid were produced slowly from this isolated residue kept at 275 K inside a refrigerator. The easily identifiable transparent crystals of zymonic acid appear above the level of the viscous solution within two weeks. Pyruvic acid crystals are deliquescent in air, even at 263 K (Harata et al., 1977 ▸), so they had to be kept cold, with minimal exposure to ambient air. Thus, throughout all experimental stages from initial inspection through data collection, special techniques for crystal handling at low temperature (Parkin & Hope, 1998 ▸) were employed.
Refinement
Crystal data, data collection, and structure refinement details are summarized in Table 3 ▸. Non-disordered hydrogen atoms were found in difference Fourier maps. For pyruvic acid, the hydroxyl hydrogen-atom coordinates were refined freely, while methyl hydrogenC—H distances used a riding model that allowed the C—H distance to refine. For zymonic acid, riding models were used for all hydrogen atoms apart from those disordered about the twofold axis, which were modeled in accordance with the recommendations of Fábry (2018 ▸). U
iso(H) parameters of non-disorderedhydrogens were set to either 1.2U
eq or 1.5U
eq (for the methyl and hydroxyl groups, respectively) of the attached atom. To ensure stable refinement of disordered groups in the zymonic acid structure, constraints (SHELXL command EADP) were used to equalize displacement parameters of superimposed atoms.
Table 3
Experimental details
zymonic acid
pyruvic acid
Crystal data
Chemical formula
C6H6O5
C3H4O3
Mr
158.11
88.06
Crystal system, space group
Monoclinic, C2/c
Monoclinic, P21/c
Temperature (K)
90
90
a, b, c (Å)
24.145 (3), 6.6523 (7), 8.6201 (7)
10.7486 (3), 5.1925 (2), 6.8302 (2)
β (°)
95.169 (4)
99.063 (1)
V (Å3)
1378.9 (3)
376.45 (2)
Z
8
4
Radiation type
Mo Kα
Mo Kα
μ (mm−1)
0.14
0.14
Crystal size (mm)
0.30 × 0.25 × 0.02
0.26 × 0.22 × 0.18
Data collection
Diffractometer
Bruker D8 Venture dual source
Bruker D8 Venture dual source
Absorption correction
Multi-scan (SADABS; Krause et al., 2015 ▸)
Multi-scan (SADABS; Krause et al., 2015 ▸)
Tmin, Tmax
0.721, 0.959
0.890, 0.971
No. of measured, independent and observed [I > 2σ(I)] reflections
18595, 1586, 1392
10479, 1425, 1242
Rint
0.062
0.025
(sin θ/λ)max (Å−1)
0.650
0.796
Refinement
R[F2 > 2σ(F2)], wR(F2), S
0.037, 0.100, 1.09
0.031, 0.082, 1.08
No. of reflections
1586
1425
No. of parameters
104
60
H-atom treatment
H atoms treated by a mixture of independent and constrained refinement
H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)
0.36, −0.24
0.40, −0.21
Computer programs: APEX3 (Bruker, 2016 ▸), SHELXT (Sheldrick, 2015a
▸), SHELXL2018/3 (Sheldrick, 2015b
▸), XP in (Sheldrick, 2008 ▸), and CIFFIX (Parkin, 2013 ▸).
Crystal structure: contains datablock(s) global, pyruvic, zymonic. DOI: 10.1107/S2056989019007072/hb7818sup1.cifStructure factors: contains datablock(s) zymonic. DOI: 10.1107/S2056989019007072/hb7818zymonicsup2.hklStructure factors: contains datablock(s) pyruvic. DOI: 10.1107/S2056989019007072/hb7818pyruvicsup3.hklClick here for additional data file.Supporting information file. DOI: 10.1107/S2056989019007072/hb7818zymonicsup4.cmlClick here for additional data file.Supporting information file. DOI: 10.1107/S2056989019007072/hb7818pyruvicsup5.cmlCCDC references: 1916323, 1916322Additional supporting information: crystallographic information; 3D view; checkCIF report
C6H6O5
F(000) = 656
Mr = 158.11
Dx = 1.523 Mg m−3
Monoclinic, C2/c
Mo Kα radiation, λ = 0.71073 Å
a = 24.145 (3) Å
Cell parameters from 9925 reflections
b = 6.6523 (7) Å
θ = 3.2–27.5°
c = 8.6201 (7) Å
µ = 0.14 mm−1
β = 95.169 (4)°
T = 90 K
V = 1378.9 (3) Å3
Thin plate, colourless
Z = 8
0.30 × 0.25 × 0.02 mm
Bruker D8 Venture dual source diffractometer
1586 independent reflections
Radiation source: microsource
1392 reflections with I > 2σ(I)
Detector resolution: 5.6 pixels mm-1
Rint = 0.062
φ and ω scans
θmax = 27.5°, θmin = 3.2°
Absorption correction: multi-scan (SADABS; Krause et al., 2015)
h = −31→31
Tmin = 0.721, Tmax = 0.959
k = −8→8
18595 measured reflections
l = −11→10
Refinement on F2
Secondary atom site location: difference Fourier map
Least-squares matrix: full
Hydrogen site location: mixed
R[F2 > 2σ(F2)] = 0.037
H atoms treated by a mixture of independent and constrained refinement
wR(F2) = 0.100
w = 1/[σ2(Fo2) + (0.0428P)2 + 1.4377P] where P = (Fo2 + 2Fc2)/3
Primary atom site location: structure-invariant direct methods
Extinction coefficient: 0.0057 (13)
Experimental. The crystal was mounted using polyisobutene oil on the tip of a fine glass
fibre, which was fastened in a copper mounting pin with electrical solder.
It was placed directly into the cold gas stream of a liquid-nitrogen based
cryostat (Hope, 1994; Parkin & Hope, 1998). Diffraction data were collected with the crystal at 90K, which is standard
practice in this laboratory for the majority of flash-cooled crystals.
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes.
Refinement. Refinement progress was checked using Platon (Spek, 2009) and by
an R-tensor (Parkin, 2000). The final model was further checked
with the IUCr utility checkCIF.
x
y
z
Uiso*/Ueq
Occ. (<1)
C1
0.67036 (5)
0.40914 (19)
0.56905 (14)
0.0170 (3)
O1
0.68738 (4)
0.24154 (14)
0.54864 (11)
0.0209 (2)
C2
0.69378 (5)
0.5659 (2)
0.67706 (14)
0.0178 (3)
O2
0.74026 (4)
0.51656 (15)
0.76588 (12)
0.0240 (3)
H2
0.752557
0.618162
0.815574
0.036*
C3
0.66149 (5)
0.7275 (2)
0.66335 (15)
0.0182 (3)
H3
0.667502
0.849554
0.719574
0.022*
O3
0.62412 (4)
0.48283 (13)
0.48901 (11)
0.0188 (2)
C4
0.61371 (5)
0.68442 (19)
0.54353 (15)
0.0186 (3)
O4
0.54061 (4)
0.51162 (15)
0.66013 (12)
0.0249 (3)
H4O
0.507244
0.517998
0.736346
0.109 (14)*
0.5
O5
0.54177 (4)
0.84824 (16)
0.66262 (14)
0.0303 (3)
H5O
0.509866
0.849228
0.727610
0.109 (14)*
0.5
C5
0.56056 (5)
0.67919 (19)
0.62725 (15)
0.0188 (3)
C6
0.60945 (7)
0.8285 (2)
0.40645 (17)
0.0257 (3)
H6A
0.644218
0.825746
0.355945
0.039*
H6B
0.602833
0.964985
0.443442
0.039*
H6C
0.578557
0.787894
0.331471
0.039*
U11
U22
U33
U12
U13
U23
C1
0.0184 (6)
0.0180 (6)
0.0151 (6)
−0.0007 (5)
0.0038 (5)
0.0010 (5)
O1
0.0238 (5)
0.0173 (5)
0.0213 (5)
0.0015 (4)
0.0010 (4)
−0.0013 (4)
C2
0.0165 (6)
0.0204 (6)
0.0165 (6)
−0.0023 (5)
0.0016 (5)
−0.0020 (5)
O2
0.0186 (5)
0.0249 (5)
0.0274 (5)
0.0035 (4)
−0.0050 (4)
−0.0073 (4)
C3
0.0168 (6)
0.0190 (6)
0.0190 (6)
−0.0032 (5)
0.0020 (5)
−0.0036 (5)
O3
0.0213 (5)
0.0155 (5)
0.0192 (5)
0.0003 (3)
−0.0013 (4)
−0.0027 (3)
C4
0.0205 (6)
0.0135 (6)
0.0212 (6)
−0.0007 (5)
−0.0012 (5)
−0.0018 (5)
O4
0.0225 (5)
0.0207 (5)
0.0314 (6)
−0.0031 (4)
0.0027 (4)
0.0013 (4)
O5
0.0252 (5)
0.0209 (5)
0.0457 (7)
0.0027 (4)
0.0074 (5)
−0.0040 (4)
C5
0.0165 (6)
0.0171 (6)
0.0217 (6)
0.0004 (5)
−0.0042 (5)
−0.0001 (5)
C6
0.0351 (8)
0.0192 (7)
0.0223 (7)
−0.0013 (6)
−0.0008 (6)
0.0026 (5)
C1—O1
1.2067 (16)
C4—C6
1.5179 (19)
C1—O3
1.3505 (15)
C4—C5
1.5282 (19)
C1—C2
1.4763 (18)
O4—C5
1.2568 (16)
C2—C3
1.3268 (18)
O4—H4O
1.0854
C2—O2
1.3411 (16)
O5—C5
1.2602 (16)
O2—H2
0.8400
O5—H5O
0.9926
C3—C4
1.5051 (17)
C6—H6A
0.9800
C3—H3
0.9500
C6—H6B
0.9800
O3—C4
1.4505 (15)
C6—H6C
0.9800
O1—C1—O3
122.52 (12)
O3—C4—C5
108.03 (10)
O1—C1—C2
128.95 (12)
C3—C4—C5
107.73 (11)
O3—C1—C2
108.53 (11)
C6—C4—C5
112.41 (11)
C3—C2—O2
134.75 (12)
C5—O4—H4O
115.0
C3—C2—C1
109.12 (11)
C5—O5—H5O
117.2
O2—C2—C1
116.12 (11)
O4—C5—O5
125.69 (13)
C2—O2—H2
109.5
O4—C5—C4
118.80 (11)
C2—C3—C4
108.35 (11)
O5—C5—C4
115.45 (11)
C2—C3—H3
125.8
C4—C6—H6A
109.5
C4—C3—H3
125.8
C4—C6—H6B
109.5
C1—O3—C4
109.24 (10)
H6A—C6—H6B
109.5
O3—C4—C3
104.7 (1)
C4—C6—H6C
109.5
O3—C4—C6
109.47 (11)
H6A—C6—H6C
109.5
C3—C4—C6
114.07 (11)
H6B—C6—H6C
109.5
O1—C1—C2—C3
−179.25 (13)
C1—O3—C4—C5
−112.19 (11)
O3—C1—C2—C3
1.17 (15)
C2—C3—C4—O3
−1.69 (14)
O1—C1—C2—O2
−0.3 (2)
C2—C3—C4—C6
−121.33 (13)
O3—C1—C2—O2
−179.92 (10)
C2—C3—C4—C5
113.14 (12)
O2—C2—C3—C4
−178.23 (14)
O3—C4—C5—O4
12.04 (16)
C1—C2—C3—C4
0.39 (15)
C3—C4—C5—O4
−100.56 (13)
O1—C1—O3—C4
178.13 (12)
C6—C4—C5—O4
132.92 (13)
C2—C1—O3—C4
−2.26 (13)
O3—C4—C5—O5
−170.61 (11)
C1—O3—C4—C3
2.43 (13)
C3—C4—C5—O5
76.79 (14)
C1—O3—C4—C6
125.11 (12)
C6—C4—C5—O5
−49.72 (16)
D—H···A
D—H
H···A
D···A
D—H···A
O2—H2···O1i
0.84
1.96
2.7103 (14)
148
C3—H3···O2i
0.95
2.48
3.0720 (16)
120
O4—H4O···O4ii
1.09
1.52
2.607 (2)
176
O5—H5O···O5ii
0.99
1.63
2.624 (2)
179
C3H4O3
F(000) = 184
Mr = 88.06
Dx = 1.554 Mg m−3
Monoclinic, P21/c
Mo Kα radiation, λ = 0.71073 Å
a = 10.7486 (3) Å
Cell parameters from 6955 reflections
b = 5.1925 (2) Å
θ = 3.8–34.3°
c = 6.8302 (2) Å
µ = 0.14 mm−1
β = 99.063 (1)°
T = 90 K
V = 376.45 (2) Å3
Well-facetted block, colourless
Z = 4
0.26 × 0.22 × 0.18 mm
Bruker D8 Venture dual source diffractometer
1425 independent reflections
Radiation source: microsource
1242 reflections with I > 2σ(I)
Detector resolution: 5.6 pixels mm-1
Rint = 0.025
φ and ω scans
θmax = 34.5°, θmin = 3.8°
Absorption correction: multi-scan (SADABS; Krause et al., 2015)
h = −16→16
Tmin = 0.890, Tmax = 0.971
k = −7→8
10479 measured reflections
l = −10→10
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)] = 0.031
Hydrogen site location: mixed
wR(F2) = 0.082
H atoms treated by a mixture of independent and constrained refinement
S = 1.08
w = 1/[σ2(Fo2) + (0.0299P)2 + 0.1264P] where P = (Fo2 + 2Fc2)/3
1425 reflections
(Δ/σ)max < 0.001
60 parameters
Δρmax = 0.40 e Å−3
0 restraints
Δρmin = −0.21 e Å−3
Experimental. The crystal was mounted using polyisobutene oil on the tip of a fine glass
fibre, which was fastened in a copper mounting pin with electrical solder.
It was placed directly into the cold gas stream of a liquid-nitrogen based
cryostat (Parkin & Hope, 1998). Diffraction data were collected with the crystal at 90K, which is standard
practice in this laboratory for the majority of flash-cooled crystals.
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes.
Refinement. Refinement progress was checked using Platon (Spek, 2009) and by
an R-tensor (Parkin, 2000). The final model was further checked
with the IUCr utility checkCIF.
Authors: David S Wishart; Dan Tzur; Craig Knox; Roman Eisner; An Chi Guo; Nelson Young; Dean Cheng; Kevin Jewell; David Arndt; Summit Sawhney; Chris Fung; Lisa Nikolai; Mike Lewis; Marie-Aude Coutouly; Ian Forsythe; Peter Tang; Savita Shrivastava; Kevin Jeroncic; Paul Stothard; Godwin Amegbey; David Block; David D Hau; James Wagner; Jessica Miniaci; Melisa Clements; Mulu Gebremedhin; Natalie Guo; Ying Zhang; Gavin E Duggan; Glen D Macinnis; Alim M Weljie; Reza Dowlatabadi; Fiona Bamforth; Derrick Clive; Russ Greiner; Liang Li; Tom Marrie; Brian D Sykes; Hans J Vogel; Lori Querengesser Journal: Nucleic Acids Res Date: 2007-01 Impact factor: 16.971
Authors: David S Wishart; Craig Knox; An Chi Guo; Roman Eisner; Nelson Young; Bijaya Gautam; David D Hau; Nick Psychogios; Edison Dong; Souhaila Bouatra; Rupasri Mandal; Igor Sinelnikov; Jianguo Xia; Leslie Jia; Joseph A Cruz; Emilia Lim; Constance A Sobsey; Savita Shrivastava; Paul Huang; Philip Liu; Lydia Fang; Jun Peng; Ryan Fradette; Dean Cheng; Dan Tzur; Melisa Clements; Avalyn Lewis; Andrea De Souza; Azaret Zuniga; Margot Dawe; Yeping Xiong; Derrick Clive; Russ Greiner; Alsu Nazyrova; Rustem Shaykhutdinov; Liang Li; Hans J Vogel; Ian Forsythe Journal: Nucleic Acids Res Date: 2008-10-25 Impact factor: 16.971