research papers
Accurate molecular structures and hydrogen bonding in two polymorphs of ortho-acetamidobenzamide by single-crystal neutron diffraction
aISIS Facility, CCLRC Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, England, bDepartment of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, England, and cWestCHEM, Department of Chemistry, University of Glasgow, Glasgow G12 8QQ, Scotland
*Correspondence e-mail: c.k.leech@rl.ac.uk
The structures of both known forms of the polymorphic material ortho-acetamidobenzamide, C9H10N2O2, have been determined by low-temperature neutron single-crystal diffraction. Neutron diffraction allows the full description of the H-atom positions in this molecular material, which is vital in benchmarking related crystal-structure predictions. Significant conformational differences are indicated by a number of the torsion angles involving H atoms when compared with previous X-ray studies. A comprehensive description of the hydrogen-bonding scheme in both polymorphs is given.
Keywords: single-crystal neutron diffraction; accurate molecular structures; hydrogen bonding; polymorphism.
1. Introduction
Computational methods of crystal-structure prediction for flexible molecules can only be successful if they can accurately model the energy changes involved in conformational ; Bernstein, 2002). A molecule can change its conformation, giving rise to an intramolecular energy penalty, if it thereby improves its interactions with other molecules such that the lower intermolecular lattice energy more than compensates for the increase due to the conformational change. The balance of these interactions is very sensitive to the positions of the protons involved in hydrogen-bonding interactions, and computationally optimizing the geometries of amide groups can have a marked effect on the calculated relative stability of crystal structures (Karamertzanis & Price, 2006). The two polymorphs of ortho-acetamidobenzamide (I) provide a particularly stringent test (Buttar et al., 1998) of whether computational methods can model the balance between intermolecular and intramolecular forces sufficiently adequately to allow realistic crystal-structure prediction studies.
(Nowell & Price, 2005The α-form of the title compound (I) exhibits an intramolecular hydrogen bond between the O atom of the amide group and the N—H of the acetamido group, whereas the β form has a more twisted geometry and no intramolecular hydrogen bond (Errede et al., 1981; Etter, 1983). The total energy difference between the two forms has been calculated as ca 20 kJ mol−1 (Buttar et al., 1998; Day, 2002) and is considerably larger than expected for polymorphs of the same compound (ca 4 kJ mol−1: Bernstein, 2002). Thus, the structure of the less stable β form would be rejected if generated during a crystal-structure prediction study (Buttar et al., 1998). The exact energy difference, defined as the difference between the conformational energies plus the difference between the intermolecular lattice energies, is highly dependent on:
et al. (1981) for the α and β forms, but both Buttar et al. and Day emphasize the influence that small deviations from expected bond lengths and angles (especially those involving H atoms) can have on the calculated energies. `Standardization' of C—H and N—H bond lengths to 1.08 and 1.01 Å, respectively, while effective in correcting errors in X-ray determined H-atom positions, does not alter errors in bond angles and bond torsions, nor does it address the possibility of the geometry of the NH2 group being affected by crystal packing (Day, 2002). Thus, accurate determinations of the full molecular structures of (I) in its two polymorphs are essential for the development of methods for calculating the relative stability of conformational polymorphs that differ so markedly in their hydrogen-bonding motifs. This work sets out to provide such accurate starting models for the α and β forms of (I) by employing single-crystal neutron diffraction (where the atomic positions of H atoms, as defined by the position of the nucleus of the atom, are typically obtained with greater accuracy and precision than from corresponding X-ray experiments) at a time-of-flight neutron source.2. Experimental
ortho-Acetamidobenzamide (C9H10N2O2) was prepared according to the literature method of Baker & Almaula (1962). All starting chemicals were purchased from the Aldrich Chemical Company and were used without further purification. The yield was 82% and microanalysis showed excellent agreement between found (C 61.0, H 5.7, N 15.7) and calculated (C 60.7, H 5.7, N 15.7) percentages. X-ray powder diffraction confirmed the product to be the α form.
Crystals of the α form, suitable for single-crystal neutron diffraction, were obtained relatively easily by slow evaporation from a of (I) in methanol. The single crystals of the β form of (I) were produced in the same way, but only after some partially deuterated polycrystalline acetamidobenzamide (shown to be the β form by X-ray powder diffraction) had been prepared in the laboratory.
Neutron diffraction data were collected from crystals of the β form (dimensions 3.5 × 1.5 × 1.0 mm3) and the α form (dimensions 5.0 × 2.0 × 1.0 mm3); each crystal was mounted on a closed-cycle refrigerator on a vertically mounted ω-orienter. Data were collected on the SXD instrument (Wilson, 1990; Keen & Wilson, 1996; Keen et al., 2006) at the ISIS spallation neutron source, using the time-of-flight Laue diffraction method. This method uses a wavelength-sorted white neutron beam, along with 11 large area position-sensitive detectors, to allow a large volume of to be measured in a single-crystal setting (a `frame'). The full data collection comprises a series of such frames, each collected with a stationary crystal-detector arrangement.
For both crystals the temperature was held at 30 ± 5 K throughout the experiment. A total of six frames, each containing information from 11 detectors, was collected, with a typical exposure time of 8 h (1300 μA h) for each frame for the β form crystal and 4 h (700 μA h) for each frame for the α-form crystal. The difference in exposure time required was a result of the difference in crystal size and diffraction quality.
Reflection intensities were extracted and reduced to structure factors using standard SXD procedures, as implemented in the computer program SXD2001 (Gutmann, 2005). A total of 11 488 reflections were collected for the β form and 5267 reflections for the α form. Crystal data and details are given in Table 1.1 Refinements were carried out using SHELXL97 (Sheldrick, 1997a) using anisotropic displacement parameters for all atoms, including the H atoms. The resulting molecular structures are shown in Fig. 1, with the bond lengths involving H atoms detailed in Table 2.
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3. Results and discussion
Unsurprisingly, with respect to the non-H atoms, the molecular and crystal structures obtained show good agreement with previously published X-ray structures. The r.m.s. difference between the non-H atoms of the neutron derived structure (30 K) and the corresponding non-H atoms of the published X-ray structures (room temperature) was 0.027 Å for α-AABA and 0.030 Å for β-AABA. Equally unsurprisingly, the differences with respect to the H atoms are substantial and these are summarized in Tables 2 and 3. In Table 2 those bond lengths and angles involving H atoms are compared for the models derived from the neutron data and the published X-ray structures. Differences in bond lengths are as expected, with the X-ray distances being systematically shorter than their neutron counterparts. For the NH2 groups, the X-ray structures give H atoms in the correct general locations, but there are significant differences in the angles. The pyramidalization of the NH2 groups in the neutron structures (as defined by the distance d of the nitrogen N1 from the C7—H1A—H1B plane) is almost identical to that found in the X-ray structures: dneutron = +0.113 (3) Å, dX-ray = +0.112 Å for the α form; dneutron = + 0.060 (1) Å, dX-ray = + 0.041 Å for the β form.
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The intermolecular interactions present in the two polymorphic forms are summarized in Figs. 2(a) and (b) and in Table 4. Both forms exhibit the same number of short hydrogen bonds, those interactions occurring between the same chemical groups in each polymorph. These short hydrogen bonds are numbered 1–3 in the diagrams and tables. The main difference in the hydrogen-bonding patterns of the two polymorphs is that the O1⋯H2—N2 hydrogen bond (1) is intra-molecular in the α form and inter-molecular in the β form. In terms of graph-set notation (Etter, 1990), the hydrogen bond 1 has the motif S(6) in the α form and C(6) in the β form, with the same six atoms being involved in each polymorph. Both forms exhibit the same dimer (hydrogen bond 2 O1⋯H1B—N1) and C(8) chain (hydrogen bond 3 O2⋯H1A—N1) motifs that link the molecules into sheets. However, as can be seen from Figs. 2(a) and (b), the appearance of these sheets is very different. In the α form the molecules lie approximately planar within the sheet and the dimers are arranged in a herringbone arrangement with adjacent dimers linked by hydrogen bond 3. In the β form, the plane of the molecules lies approximately normal to the plane of the sheet, and hydrogen bonds 1 and 3 are involved in linking adjacent dimers. In addition to the hydrogen bonds discussed above, there are a further two long hydrogen bonds (4 and 5) that occur only in the β form of (I).
Lattice-energy minimizations were performed in order to ascertain whether the differences between the neutron and X-ray molecular structures have a significant effect on computational modelling of this system. Comparison of the lattice parameters and lattice energies (approximately −0.4 and +0.7 kJ mol−1 for the α and β forms, respectively) obtained by the static rigid-molecule lattice-energy minimization (Table 5) reveals that the differences are small but significant. In particular, they are significant:
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‡For the room-temperature X-ray structures, the corresponding wavefunctions were calculated using C—H and N—H bond lengths elongated to the standard neutron values of 1.08 and 1.01 Å, respectively (Allen et al., 1987). §ΔE is the difference between the lattice energies of the α and β polymorphs. |
The more accurate neutron-derived model does reduce the difference in the lattice energy of the two forms by ca 1 kJ mol−1.
4. Conclusions
The crystal structures presented here represent a significant improvement upon existing X-ray derived structures and as such have removed a great deal of structural uncertainty, particularly with respect to the H-atom positions and atomic displacement parameters. The improved starting models yield small but significant improvements in the lattice-energy calculations, resulting in a slight reduction in the large (ca 20 kJ mol−1) lattice stabilization that results from the additional intermolecular hydrogen bond present in the β form. The structures thus provide a reliable starting point for future computational studies that seek to provide more reliable estimates of the relative stability of the two forms of (I).
Supporting information
10.1107/S0108768106025821/bm5034sup1.cif
contains datablocks aaba_alpha_30K, aaba_beta_30K, global. DOI:Structure factors: contains datablock aaba_alpha. DOI: 10.1107/S0108768106025821/bm5034aaba_alpha_30Ksup2.hkl
Structure factors: contains datablock aaba_beta. DOI: 10.1107/S0108768106025821/bm5034aaba_beta_30Ksup3.hkl
Data collection: SXD-2001 (Gutmann, 2005) for aaba_alpha_30K; SXD-2001 for aaba_beta_30K. Cell
SXD-2001 (Gutmann, 2005) for aaba_alpha_30K; SXD-2001 for aaba_beta_30K. Data reduction: SXD-2001 (Gutmann, 2005) for aaba_alpha_30K; SXD-2001 for aaba_beta_30K. For both compounds, program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.C9H10N2O2 | F(000) = 213 |
Mr = 178.19 | Dx = 1.382 Mg m−3 |
Monoclinic, P21/n | Neutron radiation, λ = 0.5-7.0 Å |
a = 4.8591 (12) Å | Cell parameters from 330 reflections |
b = 14.395 (3) Å | µ = 0.00 mm−1 |
c = 12.250 (3) Å | T = 30 K |
β = 92.151 (16)° | Block, colourless |
V = 856.3 (3) Å3 | 5.0 × 2.0 × 1.0 mm |
Z = 4 |
SXD diffractometer | Rint = 0.000 |
Radiation source: ISIS spallation source | θmax = 81.7°, θmin = 8.7° |
time–of–flight LAUE diffraction scans | h = −7→3 |
5267 measured reflections | k = −31→36 |
5267 independent reflections | l = −29→28 |
5267 reflections with I > 2σ(I) |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.057 | All H-atom parameters refined |
wR(F2) = 0.128 | w = 1/[σ2(Fo2) + (0.0826P)2] where P = (Fo2 + 2Fc2)/3 |
S = 1.04 | (Δ/σ)max < 0.001 |
5267 reflections | Δρmax = 2.00 e Å−3 |
274 parameters | Δρmin = −1.49 e Å−3 |
0 restraints | Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.00129 (6) |
C9H10N2O2 | V = 856.3 (3) Å3 |
Mr = 178.19 | Z = 4 |
Monoclinic, P21/n | Neutron radiation, λ = 0.5-7.0 Å |
a = 4.8591 (12) Å | µ = 0.00 mm−1 |
b = 14.395 (3) Å | T = 30 K |
c = 12.250 (3) Å | 5.0 × 2.0 × 1.0 mm |
β = 92.151 (16)° |
SXD diffractometer | 5267 reflections with I > 2σ(I) |
5267 measured reflections | Rint = 0.000 |
5267 independent reflections |
R[F2 > 2σ(F2)] = 0.057 | 0 restraints |
wR(F2) = 0.128 | All H-atom parameters refined |
S = 1.04 | Δρmax = 2.00 e Å−3 |
5267 reflections | Δρmin = −1.49 e Å−3 |
274 parameters |
Experimental. For peak integration a local UB matrix refined for each frame, using approximately 30 reflections from each of the 11 detectors. Hence _cell_measurement_reflns_used 330 For final cell dimensions a weighted average of all local cells was calculated Because of the nature of the experiment, it is not possible to give values of theta_min and theta_max for the cell determination. The same applies for the wavelength used for the experiment. The range of wavelengths used was 0.48–7.0 Angstroms, BUT the bulk of the diffraction information is obtained from wavelengths in the range 0.7–2.5 Angstroms. The data collection procedures on the SXD instrument used for the single-crystal neutron data collection are most recently summarized in the Appendix to the following paper Wilson, C·C. (1997). J. Mol. Struct. 405, 207–217 |
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. |
Refinement. The variable wavelength nature of the data collection procedure means that sensible values of _diffrn_reflns_theta_min & _diffrn_reflns_theta_max cannot be given instead the following limits are given _diffrn_reflns_sin(theta)/lambda_min 0.05 _diffrn_reflns_sin(theta)/lambda_max 1.31 _refine_diff_density_max/min is given in Fermi per per angstrom cubed not electons per angstrom cubed. Another way to consider the _refine_diff_density_ is as a percentage of the diffracted intensity of a given atom: _refine_diff_density_max = 5% of Carbon _refine_diff_density_min = −4% of Carbon Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | ||
O1 | −0.3257 (5) | 0.11090 (10) | 0.00091 (10) | 0.0083 (5) | |
O2 | −0.2943 (6) | 0.42403 (10) | 0.16253 (11) | 0.0102 (5) | |
N1 | −0.2414 (3) | −0.01111 (7) | 0.11383 (7) | 0.0096 (3) | |
N2 | −0.2672 (3) | 0.27463 (6) | 0.09767 (7) | 0.0075 (3) | |
C1 | −0.0625 (5) | 0.23375 (9) | 0.16623 (9) | 0.0046 (4) | |
C2 | −0.0229 (5) | 0.13613 (9) | 0.15779 (9) | 0.0053 (4) | |
C3 | 0.1868 (5) | 0.09345 (8) | 0.22104 (10) | 0.0067 (4) | |
C4 | 0.3557 (5) | 0.14459 (9) | 0.29321 (9) | 0.0065 (4) | |
C5 | 0.3090 (5) | 0.23967 (9) | 0.30440 (9) | 0.0070 (4) | |
C6 | 0.1029 (5) | 0.28459 (9) | 0.24204 (10) | 0.0066 (4) | |
C7 | −0.2071 (4) | 0.07776 (9) | 0.08497 (9) | 0.0053 (4) | |
C8 | −0.3744 (5) | 0.36174 (9) | 0.09990 (9) | 0.0066 (4) | |
C9 | −0.6077 (5) | 0.37851 (9) | 0.01622 (10) | 0.0080 (4) | |
H6 | 0.0699 (11) | 0.3586 (2) | 0.2504 (3) | 0.0205 (10) | |
H1B | −0.3817 (11) | −0.0498 (2) | 0.0687 (2) | 0.0210 (10) | |
H2 | −0.3478 (10) | 0.2288 (2) | 0.0410 (2) | 0.0183 (9) | |
H3 | 0.2219 (12) | 0.0192 (2) | 0.2119 (3) | 0.0234 (11) | |
H1A | −0.1833 (11) | −0.0332 (2) | 0.1899 (2) | 0.0203 (10) | |
H5 | 0.4365 (11) | 0.2813 (2) | 0.3620 (2) | 0.0227 (10) | |
H4 | 0.5204 (11) | 0.1095 (2) | 0.3401 (3) | 0.0218 (10) | |
H9C | −0.6831 (13) | 0.3139 (2) | −0.0197 (3) | 0.0337 (14) | |
H9B | −0.5367 (13) | 0.4225 (3) | −0.0481 (3) | 0.0335 (13) | |
H9A | −0.7695 (13) | 0.4152 (3) | 0.0554 (3) | 0.0352 (14) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0148 (17) | 0.0045 (5) | 0.0055 (4) | −0.0011 (7) | −0.0029 (6) | 0.0005 (4) |
O2 | 0.0182 (16) | 0.0052 (5) | 0.0069 (5) | 0.0011 (8) | −0.0021 (7) | −0.0030 (4) |
N1 | 0.0164 (10) | 0.0062 (3) | 0.0062 (3) | −0.0018 (5) | −0.0016 (4) | 0.0009 (2) |
N2 | 0.0112 (9) | 0.0051 (3) | 0.0060 (3) | 0.0008 (5) | −0.0014 (4) | −0.0008 (2) |
C1 | 0.0055 (12) | 0.0039 (5) | 0.0043 (4) | 0.0011 (6) | −0.0003 (5) | 0.0005 (3) |
C2 | 0.0078 (13) | 0.0038 (4) | 0.0041 (4) | 0.0002 (6) | −0.0003 (5) | 0.0002 (3) |
C3 | 0.0088 (13) | 0.0048 (5) | 0.0063 (4) | −0.0006 (7) | −0.0012 (6) | −0.0001 (3) |
C4 | 0.0057 (14) | 0.0081 (5) | 0.0055 (4) | 0.0005 (6) | −0.0014 (6) | 0.0004 (4) |
C5 | 0.0073 (13) | 0.0085 (5) | 0.0051 (4) | −0.0015 (7) | −0.0012 (6) | −0.0005 (3) |
C6 | 0.0083 (13) | 0.0058 (5) | 0.0056 (4) | 0.0006 (6) | −0.0020 (5) | −0.0006 (3) |
C7 | 0.0087 (13) | 0.0037 (4) | 0.0035 (4) | −0.0005 (6) | −0.0012 (5) | −0.0005 (3) |
C8 | 0.0118 (13) | 0.0047 (5) | 0.0034 (4) | 0.0000 (6) | 0.0004 (5) | −0.0003 (3) |
C9 | 0.0092 (14) | 0.0078 (5) | 0.0068 (4) | 0.0012 (6) | −0.0009 (6) | 0.0008 (3) |
H6 | 0.024 (3) | 0.0103 (11) | 0.0266 (13) | 0.0029 (16) | −0.0047 (16) | −0.0032 (9) |
H1B | 0.028 (3) | 0.0161 (12) | 0.0181 (11) | −0.0101 (17) | −0.0044 (15) | −0.0013 (9) |
H2 | 0.022 (3) | 0.0155 (12) | 0.0168 (11) | −0.0002 (17) | −0.0103 (13) | −0.0034 (9) |
H3 | 0.032 (4) | 0.0106 (11) | 0.0272 (13) | 0.0007 (17) | −0.0037 (17) | −0.0011 (10) |
H1A | 0.026 (3) | 0.0201 (13) | 0.0147 (11) | 0.0012 (17) | −0.0068 (14) | 0.0058 (9) |
H5 | 0.024 (3) | 0.0228 (14) | 0.0206 (12) | −0.0059 (18) | −0.0104 (15) | −0.0049 (10) |
H4 | 0.016 (3) | 0.0240 (15) | 0.0242 (13) | 0.0083 (19) | −0.0121 (15) | 0.0014 (11) |
H9C | 0.045 (4) | 0.0150 (13) | 0.0391 (18) | 0.000 (2) | −0.019 (2) | −0.0036 (13) |
H9B | 0.037 (4) | 0.041 (2) | 0.0220 (14) | −0.002 (2) | 0.0002 (18) | 0.0173 (13) |
H9A | 0.033 (4) | 0.045 (2) | 0.0286 (16) | 0.017 (3) | 0.007 (2) | −0.0043 (15) |
O1—C7 | 1.255 (2) | C3—C4 | 1.393 (3) |
O2—C8 | 1.234 (2) | C3—H3 | 1.088 (3) |
N1—C7 | 1.3394 (16) | C4—C5 | 1.395 (2) |
N1—H1B | 1.026 (4) | C4—H4 | 1.092 (5) |
N1—H1A | 1.015 (3) | C5—C6 | 1.396 (3) |
N2—C8 | 1.3586 (18) | C5—H5 | 1.099 (4) |
N2—C1 | 1.406 (2) | C6—H6 | 1.082 (3) |
N2—H2 | 1.025 (3) | C8—C9 | 1.519 (3) |
C1—C6 | 1.410 (3) | C9—H9C | 1.087 (4) |
C1—C2 | 1.4226 (18) | C9—H9B | 1.078 (4) |
C2—C3 | 1.399 (3) | C9—H9A | 1.076 (5) |
C2—C7 | 1.498 (2) | ||
C7—N1—H1B | 117.6 (2) | C4—C5—C6 | 121.11 (16) |
C7—N1—H1A | 120.6 (2) | C4—C5—H5 | 120.6 (3) |
H1B—N1—H1A | 118.8 (3) | C6—C5—H5 | 118.3 (3) |
C8—N2—C1 | 129.60 (12) | C5—C6—C1 | 119.98 (13) |
C8—N2—H2 | 118.1 (3) | C5—C6—H6 | 120.6 (3) |
C1—N2—H2 | 112.3 (2) | C1—C6—H6 | 119.4 (3) |
N2—C1—C6 | 123.29 (12) | O1—C7—N1 | 121.45 (16) |
N2—C1—C2 | 117.68 (14) | O1—C7—C2 | 121.42 (13) |
C6—C1—C2 | 119.03 (17) | N1—C7—C2 | 117.13 (13) |
C3—C2—C1 | 119.42 (16) | O2—C8—N2 | 124.83 (19) |
C3—C2—C7 | 119.35 (13) | O2—C8—C9 | 120.95 (15) |
C1—C2—C7 | 121.20 (17) | N2—C8—C9 | 114.22 (12) |
C4—C3—C2 | 121.24 (13) | C8—C9—H9C | 111.7 (3) |
C4—C3—H3 | 119.6 (3) | C8—C9—H9B | 109.6 (4) |
C2—C3—H3 | 119.2 (3) | H9C—C9—H9B | 108.6 (3) |
C3—C4—C5 | 119.13 (17) | C8—C9—H9A | 108.5 (3) |
C3—C4—H4 | 119.5 (2) | H9C—C9—H9A | 111.1 (5) |
C5—C4—H4 | 121.4 (2) | H9B—C9—H9A | 107.2 (4) |
C9H10N2O2 | Z = 4 |
Mr = 178.19 | F(000) = 211 |
Monoclinic, P21/c | Dx = 1.376 Mg m−3 |
a = 7.788 (1) Å | Neutron radiation, λ = 0.69-5.9 Å |
b = 8.972 (2) Å | Cell parameters from 400 reflections |
c = 12.547 (2) Å | T = 30 K |
β = 101.12 (1)° | Block, colourless |
V = 860.2 (3) Å3 | 3.5 × 1.5 × 1.5 mm |
SXD diffractometer | 11484 reflections with I > 2σ(I) |
Radiation source: ISIS spallation source | Rint = 0.000 |
time–of–flight LAUE diffraction scans | θmax = 82.5°, θmin = 8.2° |
Absorption correction: gaussian Gaussian intigration method applied thought SXD-2001 program | h = −21→16 |
Tmin = ?, Tmax = ? | k = −15→19 |
11484 measured reflections | l = −33→27 |
11484 independent reflections |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.058 | All H-atom parameters refined |
wR(F2) = 0.148 | w = 1/[σ2(Fo2) + (0.0926P)2 + 11.2116P] where P = (Fo2 + 2Fc2)/3 |
S = 1.03 | (Δ/σ)max < 0.001 |
11484 reflections | Δρmax = 2.35 e Å−3 |
274 parameters | Δρmin = −2.38 e Å−3 |
0 restraints | Extinction correction: SHELXL, Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.0450 (7) |
C9H10N2O2 | β = 101.12 (1)° |
Mr = 178.19 | V = 860.2 (3) Å3 |
Monoclinic, P21/c | Z = 4 |
a = 7.788 (1) Å | Neutron radiation, λ = 0.69-5.9 Å |
b = 8.972 (2) Å | T = 30 K |
c = 12.547 (2) Å | 3.5 × 1.5 × 1.5 mm |
SXD diffractometer | 11484 independent reflections |
Absorption correction: gaussian Gaussian intigration method applied thought SXD-2001 program | 11484 reflections with I > 2σ(I) |
Tmin = ?, Tmax = ? | Rint = 0.000 |
11484 measured reflections |
R[F2 > 2σ(F2)] = 0.058 | 0 restraints |
wR(F2) = 0.148 | All H-atom parameters refined |
S = 1.03 | w = 1/[σ2(Fo2) + (0.0926P)2 + 11.2116P] where P = (Fo2 + 2Fc2)/3 |
11484 reflections | Δρmax = 2.35 e Å−3 |
274 parameters | Δρmin = −2.38 e Å−3 |
Experimental. For peak integration a local UB matrix refined for each frame, using approximately 35–40 reflections from each of the 11 detectors. Hence _cell_measurement_reflns_used 400 For final cell dimensions a weighted average of all local cells was calculated Because of the nature of the experiment, it is not possible to give values of theta_min and theta_max for the cell determination. The same applies for the wavelength used for the experiment. The range of wavelengths used was 0.69–5.9 Angstroms, BUT the bulk of the diffraction information is obtained from wavelengths in the range 0.7–2.5 Angstroms. The data collection procedures on the SXD instrument used for the single-crystal neutron data collection are most recently summarized in the Appendix to the following paper Wilson, C·C. (1997). J. Mol. Struct. 405, 207–217. |
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. |
Refinement. The variable wavelength nature of the data collection procedure means that sensible values of _diffrn_reflns_theta_min & _diffrn_reflns_theta_max cannot be given instead the following limits are given _diffrn_reflns_sin(theta)/lambda_min 0.06 _diffrn_reflns_sin(theta)/lambda_max 1.37 _refine_diff_density_max/min is given in Fermi per per angstrom cubed not electons per angstrom cubed. Another way to consider the _refine_diff_density_ is as a percentage of the diffracted intensity of a given atom: _refine_diff_density_max = 3% of Carbon _refine_diff_density_min = −3% of Carbon Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.30407 (8) | 0.45434 (11) | 0.06498 (5) | 0.00571 (13) | |
O2 | 0.45233 (9) | 0.44751 (12) | 0.32723 (6) | 0.00736 (13) | |
N1 | 0.49421 (5) | 0.64900 (7) | 0.09770 (3) | 0.00633 (9) | |
N2 | 0.46827 (5) | 0.69965 (7) | 0.33038 (3) | 0.00516 (8) | |
C1 | 0.29204 (7) | 0.72026 (9) | 0.27464 (4) | 0.00442 (11) | |
C2 | 0.23108 (7) | 0.65871 (9) | 0.17126 (4) | 0.00428 (10) | |
C3 | 0.05534 (7) | 0.67694 (10) | 0.12146 (5) | 0.00569 (12) | |
C4 | −0.05798 (7) | 0.75886 (10) | 0.17259 (5) | 0.00678 (12) | |
C5 | 0.00313 (8) | 0.82164 (10) | 0.27477 (5) | 0.00708 (12) | |
C6 | 0.17756 (7) | 0.80121 (10) | 0.32588 (5) | 0.00657 (12) | |
C7 | 0.34806 (7) | 0.57761 (9) | 0.10839 (4) | 0.00400 (10) | |
C8 | 0.53825 (7) | 0.56233 (9) | 0.35385 (4) | 0.00510 (11) | |
C9 | 0.72597 (8) | 0.55796 (11) | 0.41339 (5) | 0.00847 (13) | |
H2 | 0.5428 (2) | 0.7909 (3) | 0.35617 (16) | 0.0200 (4) | |
H1B | 0.5733 (2) | 0.6050 (3) | 0.04917 (15) | 0.0196 (4) | |
H3 | 0.0071 (2) | 0.6274 (3) | 0.04198 (13) | 0.0201 (4) | |
H1A | 0.5146 (2) | 0.7555 (3) | 0.12716 (15) | 0.0191 (4) | |
H6 | 0.2260 (2) | 0.8474 (3) | 0.40600 (13) | 0.0226 (5) | |
H4 | −0.19351 (19) | 0.7759 (3) | 0.13325 (15) | 0.0224 (4) | |
H5 | −0.0857 (2) | 0.8848 (3) | 0.31499 (15) | 0.0233 (5) | |
H9C | 0.7817 (3) | 0.6684 (3) | 0.4312 (2) | 0.0295 (5) | |
H9B | 0.8041 (3) | 0.4982 (5) | 0.3639 (2) | 0.0379 (8) | |
H9A | 0.7330 (3) | 0.4966 (4) | 0.48892 (18) | 0.0376 (8) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.00659 (18) | 0.0037 (4) | 0.00728 (19) | −0.0009 (2) | 0.00238 (16) | −0.00190 (19) |
O2 | 0.0077 (2) | 0.0026 (4) | 0.0109 (2) | −0.0003 (2) | −0.00037 (18) | −0.0003 (2) |
N1 | 0.00616 (12) | 0.0052 (3) | 0.00854 (14) | −0.00169 (13) | 0.00359 (10) | −0.00214 (13) |
N2 | 0.00535 (11) | 0.0034 (2) | 0.00629 (12) | −0.00002 (12) | 0.00012 (10) | −0.00020 (12) |
C1 | 0.00465 (15) | 0.0037 (3) | 0.00495 (16) | 0.00035 (16) | 0.00107 (13) | −0.00051 (15) |
C2 | 0.00377 (14) | 0.0043 (3) | 0.00481 (16) | 0.00002 (16) | 0.00082 (12) | −0.00085 (15) |
C3 | 0.00390 (15) | 0.0060 (4) | 0.00698 (17) | 0.00037 (16) | 0.00043 (13) | −0.00132 (17) |
C4 | 0.00438 (16) | 0.0071 (4) | 0.00897 (19) | 0.00099 (18) | 0.00144 (14) | −0.00128 (18) |
C5 | 0.00594 (16) | 0.0064 (4) | 0.00921 (19) | 0.00153 (19) | 0.00230 (14) | −0.00176 (18) |
C6 | 0.00627 (16) | 0.0074 (4) | 0.00629 (17) | 0.00132 (18) | 0.00184 (14) | −0.00220 (17) |
C7 | 0.00433 (14) | 0.0031 (3) | 0.00484 (15) | 0.00012 (16) | 0.00142 (12) | −0.00076 (15) |
C8 | 0.00522 (15) | 0.0038 (3) | 0.00590 (16) | 0.00030 (17) | 0.00018 (13) | 0.00009 (16) |
C9 | 0.00635 (17) | 0.0080 (4) | 0.00988 (19) | 0.00101 (19) | −0.00125 (15) | −0.0001 (2) |
H2 | 0.0171 (5) | 0.0125 (10) | 0.0280 (7) | −0.0038 (6) | −0.0013 (5) | −0.0021 (7) |
H1B | 0.0182 (5) | 0.0198 (13) | 0.0239 (6) | −0.0004 (6) | 0.0121 (5) | −0.0068 (6) |
H3 | 0.0179 (5) | 0.0254 (13) | 0.0153 (5) | 0.0003 (6) | −0.0007 (4) | −0.0070 (6) |
H1A | 0.0209 (6) | 0.0130 (11) | 0.0244 (6) | −0.0056 (6) | 0.0071 (5) | −0.0065 (6) |
H6 | 0.0232 (6) | 0.0286 (15) | 0.0148 (5) | 0.0029 (7) | 0.0008 (5) | −0.0093 (6) |
H4 | 0.0100 (4) | 0.0301 (14) | 0.0252 (7) | 0.0041 (6) | −0.0012 (4) | −0.0028 (7) |
H5 | 0.0180 (6) | 0.0277 (15) | 0.0254 (7) | 0.0076 (7) | 0.0075 (5) | −0.0085 (7) |
H9C | 0.0222 (7) | 0.0171 (14) | 0.0444 (11) | −0.0047 (8) | −0.0057 (7) | −0.0049 (10) |
H9B | 0.0194 (7) | 0.053 (3) | 0.0415 (11) | 0.0091 (9) | 0.0056 (7) | −0.0212 (12) |
H9A | 0.0301 (9) | 0.050 (2) | 0.0278 (9) | −0.0049 (11) | −0.0060 (7) | 0.0216 (11) |
O1—C7 | 1.2511 (12) | C3—C4 | 1.3960 (10) |
O2—C8 | 1.2387 (12) | C3—H3 | 1.0902 (17) |
N1—C7 | 1.3351 (8) | C4—C5 | 1.3972 (9) |
N1—H1B | 1.0249 (17) | C4—H4 | 1.0863 (15) |
N1—H1A | 1.025 (2) | C5—C6 | 1.3979 (8) |
N2—C8 | 1.3564 (10) | C5—H5 | 1.090 (2) |
N2—C1 | 1.4272 (7) | C6—H6 | 1.0856 (17) |
N2—H2 | 1.020 (2) | C8—C9 | 1.5085 (8) |
C1—C6 | 1.3988 (9) | C9—H9C | 1.087 (3) |
C1—C2 | 1.4055 (8) | C9—H9B | 1.090 (3) |
C2—C3 | 1.4002 (7) | C9—H9A | 1.088 (2) |
C2—C7 | 1.5029 (9) | ||
C7—N1—H1B | 119.78 (14) | C4—C5—C6 | 119.80 (6) |
C7—N1—H1A | 119.09 (11) | C4—C5—H5 | 120.00 (11) |
H1B—N1—H1A | 120.25 (18) | C6—C5—H5 | 120.19 (11) |
C8—N2—C1 | 122.16 (6) | C5—C6—C1 | 120.42 (6) |
C8—N2—H2 | 118.71 (12) | C5—C6—H6 | 120.54 (12) |
C1—N2—H2 | 119.08 (13) | C1—C6—H6 | 119.04 (12) |
C6—C1—C2 | 119.76 (5) | O1—C7—N1 | 123.20 (6) |
C6—C1—N2 | 118.68 (5) | O1—C7—C2 | 120.91 (6) |
C2—C1—N2 | 121.55 (6) | N1—C7—C2 | 115.80 (7) |
C3—C2—C1 | 119.55 (6) | O2—C8—N2 | 121.55 (6) |
C3—C2—C7 | 117.49 (5) | O2—C8—C9 | 122.24 (8) |
C1—C2—C7 | 122.93 (5) | N2—C8—C9 | 116.20 (7) |
C4—C3—C2 | 120.43 (6) | C8—C9—H9C | 112.85 (14) |
C4—C3—H3 | 119.88 (11) | C8—C9—H9B | 108.97 (13) |
C2—C3—H3 | 119.69 (11) | H9C—C9—H9B | 108.7 (3) |
C3—C4—C5 | 120.02 (5) | C8—C9—H9A | 109.01 (14) |
C3—C4—H4 | 120.67 (13) | H9C—C9—H9A | 109.3 (2) |
C5—C4—H4 | 119.31 (13) | H9B—C9—H9A | 107.9 (3) |
Experimental details
(aaba_alpha_30K) | (aaba_beta_30K) | |
Crystal data | ||
Chemical formula | C9H10N2O2 | C9H10N2O2 |
Mr | 178.19 | 178.19 |
Crystal system, space group | Monoclinic, P21/n | Monoclinic, P21/c |
Temperature (K) | 30 | 30 |
a, b, c (Å) | 4.8591 (12), 14.395 (3), 12.250 (3) | 7.788 (1), 8.972 (2), 12.547 (2) |
β (°) | 92.151 (16) | 101.12 (1) |
V (Å3) | 856.3 (3) | 860.2 (3) |
Z | 4 | 4 |
Radiation type | Neutron, λ = 0.5-7.0 Å | Neutron, λ = 0.69-5.9 Å |
µ (mm−1) | 0.00 | ? |
Crystal size (mm) | 5.0 × 2.0 × 1.0 | 3.5 × 1.5 × 1.5 |
Data collection | ||
Diffractometer | SXD diffractometer | SXD diffractometer |
Absorption correction | – | Gaussian Gaussian intigration method applied thought SXD-2001 program |
No. of measured, independent and observed [I > 2σ(I)] reflections | 5267, 5267, 5267 | 11484, 11484, 11484 |
Rint | 0.000 | 0.000 |
Refinement | ||
R[F2 > 2σ(F2)], wR(F2), S | 0.057, 0.128, 1.04 | 0.058, 0.148, 1.03 |
No. of reflections | 5267 | 11484 |
No. of parameters | 274 | 274 |
H-atom treatment | All H-atom parameters refined | All H-atom parameters refined |
w = 1/[σ2(Fo2) + (0.0826P)2] where P = (Fo2 + 2Fc2)/3 | w = 1/[σ2(Fo2) + (0.0926P)2 + 11.2116P] where P = (Fo2 + 2Fc2)/3 | |
Δρmax, Δρmin (e Å−3) | 2.00, −1.49 | 2.35, −2.38 |
Computer programs: SXD-2001 (Gutmann, 2005), SXD-2001, SHELXS97 (Sheldrick, 1990), SHELXL97 (Sheldrick, 1997), SHELXTL.
Acknowledgements
This work was funded by RCUK through the Control and Prediction of the Organic Solid State (CPOSS) project (GR/S24114/01, https://www.cposs.org.uk ). Neutron beamtime on SXD at ISIS was provided by CCLRC (Council for the Central Laboratory of the Research Councils). The authors would like to thank Professor S. L. Price for helpful discussions on the lattice-energy minimization work.
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