Buy article online - an online subscription or single-article purchase is required to access this article.
X-ray diffraction experiments at very low temperatures require samples to be isolated from atmospheric conditions and held under vacuum. These conditions are usually maintained via the use of beryllium chambers, which also scatter X-rays, causing unwanted contamination of the sample's diffraction pattern. The removal of this contamination requires novel data-collection and processing procedures to be employed. Herein a new approach is described, which utilizes the differences in origin of scattering vectors from the sample and the beryllium to eliminate non-sample scattering. The program Masquerade has been written to remove contaminated regions of the diffraction data from the processing programs. Coupled with experiments at different detector distances, it allows for the acquisition of decontaminated data. Studies of several single crystals have shown that this approach increases data quality, highlighted by the improvement in internal agreement factor with the test case of cytidine presented herein.
Supporting information
CCDC reference: 873872
Data collection: Apex II (Bruker, 2010); cell refinement: Apex II (Bruker, 2010); data reduction: SAINT (Bruker, 2009); program(s) used to solve structure: XS, G.M. Sheldrick, Acta Cryst.
(2008). A64, 112-122; program(s) used to refine structure: XL, G.M. Sheldrick, Acta Cryst.
(2008). A64, 112-122; molecular graphics: O. V. Dolomanov, L. J. Bourhis, R. J. Gildea, J. A. K. Howard and H. Puschmann,
OLEX2: a complete structure solution, refinement and analysis program.
J. Appl. Cryst. (2009). 42, 339-341.; software used to prepare material for publication: O. V. Dolomanov, L. J. Bourhis, R. J. Gildea, J. A. K. Howard and H. Puschmann,
OLEX2: a complete structure solution, refinement and analysis program.
J. Appl. Cryst. (2009). 42, 339-341..
Crystal data top
C9H13N3O5 | F(000) = 512 |
Mr = 243.22 | Dx = 1.556 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
a = 5.0784 (3) Å | µ = 0.13 mm−1 |
b = 13.9046 (10) Å | T = 2 K |
c = 14.6992 (10) Å | Needle, clear colourless |
V = 1037.96 (12) Å3 | 0.26 × 0.05 × 0.05 mm |
Z = 4 | |
Data collection top
Bruker APEX-II CCD diffractometer | 2456 independent reflections |
Radiation source: Bruker TXS with Helios Optics, Rotating Anode | 1916 reflections with I > 2σ(I) |
Multilayer optics monochromator | Rint = 0.052 |
Detector resolution: 8.3333 pixels mm-1 | θmax = 29.5°, θmin = 2.0° |
φ scans | h = −6→5 |
Absorption correction: multi-scan SADABS2008/1 (Bruker,2008) was used for absorption correction.
R(int) was 0.0761 before and 0.0570 after correction.
The Ratio of minimum to maximum transmission is 0.8445.
The λ/2 correction factor is 0.0015. | k = −19→19 |
Tmin = 0.365, Tmax = 0.432 | l = −20→20 |
9630 measured reflections | |
Refinement top
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.046 | H-atom parameters constrained |
wR(F2) = 0.090 | w = 1/[σ2(Fo2) + (0.0431P)2 + 0.0504P] where P = (Fo2 + 2Fc2)/3 |
S = 1.03 | (Δ/σ)max < 0.001 |
2456 reflections | Δρmax = 0.29 e Å−3 |
157 parameters | Δρmin = −0.24 e Å−3 |
0 restraints | Absolute structure: Not refined as all light-atom structure |
Primary atom site location: structure-invariant direct methods | |
Crystal data top
C9H13N3O5 | V = 1037.96 (12) Å3 |
Mr = 243.22 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 5.0784 (3) Å | µ = 0.13 mm−1 |
b = 13.9046 (10) Å | T = 2 K |
c = 14.6992 (10) Å | 0.26 × 0.05 × 0.05 mm |
Data collection top
Bruker APEX-II CCD diffractometer | 2456 independent reflections |
Absorption correction: multi-scan SADABS2008/1 (Bruker,2008) was used for absorption correction.
R(int) was 0.0761 before and 0.0570 after correction.
The Ratio of minimum to maximum transmission is 0.8445.
The λ/2 correction factor is 0.0015. | 1916 reflections with I > 2σ(I) |
Tmin = 0.365, Tmax = 0.432 | Rint = 0.052 |
9630 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.046 | 0 restraints |
wR(F2) = 0.090 | H-atom parameters constrained |
S = 1.03 | Δρmax = 0.29 e Å−3 |
2456 reflections | Δρmin = −0.24 e Å−3 |
157 parameters | Absolute structure: Not refined as all light-atom structure |
Special details top
Experimental. Data were collected using φ scans of 0.5 degree width at 20 second exposures.
Data were collected at 2 Kelvin, resulting in the Alert C in the CIF report. |
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. 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. Completeness value resulting in Alert A is due to constraints on the
experimental data collection parameters, the reduction in data completeness
forms a significant result in the paper and is highlighted therein |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O4 | 0.0496 (4) | 0.67555 (11) | 0.44839 (8) | 0.0117 (4) | |
H4 | 0.0239 | 0.6560 | 0.3950 | 0.018* | |
N1 | 0.1182 (4) | 0.46426 (12) | 0.67742 (10) | 0.0082 (4) | |
O5 | −0.1453 (3) | 0.41486 (10) | 0.42909 (9) | 0.0121 (4) | |
H5 | −0.0444 | 0.4305 | 0.3863 | 0.018* | |
N2 | 0.4615 (4) | 0.40068 (13) | 0.76938 (10) | 0.0093 (4) | |
O3 | −0.0475 (3) | 0.71677 (10) | 0.63188 (8) | 0.0109 (4) | |
H3 | −0.1203 | 0.7403 | 0.5857 | 0.016* | |
C5 | −0.0654 (5) | 0.54615 (15) | 0.66010 (12) | 0.0089 (5) | |
H5A | −0.1363 | 0.5708 | 0.7191 | 0.011* | |
O2 | −0.2749 (3) | 0.51363 (10) | 0.60459 (8) | 0.0091 (3) | |
N3 | 0.6470 (4) | 0.25597 (13) | 0.73486 (10) | 0.0123 (4) | |
H3A | 0.7533 | 0.2638 | 0.7816 | 0.015* | |
H3B | 0.6586 | 0.2038 | 0.7012 | 0.015* | |
O1 | 0.2930 (3) | 0.54968 (10) | 0.79465 (8) | 0.0103 (3) | |
C1 | 0.2956 (5) | 0.47393 (15) | 0.74938 (12) | 0.0095 (5) | |
C2 | 0.4694 (5) | 0.32267 (15) | 0.71530 (12) | 0.0100 (5) | |
C8 | −0.2618 (5) | 0.55944 (14) | 0.51559 (12) | 0.0088 (5) | |
H8 | −0.3876 | 0.6147 | 0.5141 | 0.011* | |
C9 | −0.3374 (5) | 0.48805 (15) | 0.44212 (12) | 0.0103 (5) | |
H9A | −0.5072 | 0.4577 | 0.4586 | 0.012* | |
H9B | −0.3630 | 0.5230 | 0.3841 | 0.012* | |
C7 | 0.0187 (5) | 0.59789 (15) | 0.51006 (12) | 0.0090 (5) | |
H7 | 0.1406 | 0.5445 | 0.4926 | 0.011* | |
C4 | 0.1191 (5) | 0.38328 (15) | 0.62465 (12) | 0.0103 (5) | |
H4A | −0.0035 | 0.3775 | 0.5761 | 0.012* | |
C3 | 0.2917 (5) | 0.31144 (15) | 0.64051 (12) | 0.0115 (5) | |
H3C | 0.2950 | 0.2555 | 0.6034 | 0.014* | |
C6 | 0.0735 (5) | 0.62804 (14) | 0.60846 (12) | 0.0093 (5) | |
H6 | 0.2667 | 0.6291 | 0.6216 | 0.011* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O4 | 0.0160 (10) | 0.0124 (8) | 0.0067 (6) | −0.0011 (7) | 0.0004 (6) | 0.0010 (5) |
N1 | 0.0072 (12) | 0.0076 (9) | 0.0098 (7) | 0.0009 (7) | −0.0004 (7) | 0.0014 (6) |
O5 | 0.0141 (11) | 0.0108 (8) | 0.0115 (6) | 0.0008 (7) | 0.0036 (6) | −0.0003 (5) |
N2 | 0.0098 (12) | 0.0095 (9) | 0.0085 (7) | 0.0001 (8) | 0.0004 (7) | −0.0002 (6) |
O3 | 0.0142 (11) | 0.0089 (7) | 0.0094 (6) | 0.0031 (7) | −0.0015 (6) | −0.0003 (5) |
C5 | 0.0068 (14) | 0.0105 (11) | 0.0094 (8) | 0.0003 (8) | −0.0006 (8) | −0.0006 (7) |
O2 | 0.0072 (10) | 0.0120 (7) | 0.0082 (6) | −0.0013 (6) | −0.0004 (6) | 0.0023 (5) |
N3 | 0.0165 (14) | 0.0100 (9) | 0.0105 (7) | 0.0026 (8) | −0.0007 (7) | −0.0008 (6) |
O1 | 0.0116 (10) | 0.0099 (8) | 0.0095 (6) | 0.0004 (6) | −0.0012 (6) | −0.0017 (5) |
C1 | 0.0085 (15) | 0.0126 (11) | 0.0074 (8) | −0.0015 (9) | 0.0033 (8) | 0.0023 (7) |
C2 | 0.0100 (15) | 0.0100 (11) | 0.0100 (8) | −0.0044 (9) | 0.0021 (8) | 0.0037 (7) |
C8 | 0.0095 (14) | 0.0090 (10) | 0.0078 (7) | 0.0005 (9) | 0.0008 (8) | 0.0019 (7) |
C9 | 0.0103 (15) | 0.0121 (11) | 0.0086 (8) | −0.0008 (9) | 0.0011 (9) | −0.0001 (7) |
C7 | 0.0119 (15) | 0.0075 (10) | 0.0076 (8) | −0.0001 (9) | 0.0010 (8) | −0.0008 (7) |
C4 | 0.0100 (14) | 0.0126 (11) | 0.0082 (8) | −0.0029 (8) | −0.0005 (8) | 0.0004 (7) |
C3 | 0.0157 (16) | 0.0094 (11) | 0.0096 (8) | −0.0023 (9) | −0.0010 (8) | −0.0007 (7) |
C6 | 0.0105 (14) | 0.0089 (11) | 0.0084 (8) | 0.0010 (8) | −0.0001 (8) | −0.0015 (7) |
Geometric parameters (Å, º) top
O4—C7 | 1.419 (2) | C5—C6 | 1.540 (3) |
N1—C5 | 1.493 (3) | O2—C8 | 1.456 (2) |
N1—C1 | 1.396 (3) | N3—C2 | 1.325 (3) |
N1—C4 | 1.367 (2) | O1—C1 | 1.246 (2) |
O5—C9 | 1.423 (3) | C2—C3 | 1.431 (3) |
N2—C1 | 1.354 (3) | C8—C9 | 1.516 (3) |
N2—C2 | 1.345 (3) | C8—C7 | 1.524 (3) |
O3—C6 | 1.421 (3) | C7—C6 | 1.531 (2) |
C5—O2 | 1.415 (3) | C4—C3 | 1.349 (3) |
| | | |
C1—N1—C5 | 117.29 (15) | N3—C2—C3 | 121.31 (19) |
C4—N1—C5 | 122.24 (17) | O2—C8—C9 | 110.00 (15) |
C4—N1—C1 | 120.46 (18) | O2—C8—C7 | 104.13 (16) |
C2—N2—C1 | 119.77 (18) | C9—C8—C7 | 115.36 (17) |
N1—C5—C6 | 111.22 (18) | O5—C9—C8 | 113.00 (19) |
O2—C5—N1 | 108.91 (16) | O4—C7—C8 | 113.87 (17) |
O2—C5—C6 | 107.25 (15) | O4—C7—C6 | 112.03 (16) |
C5—O2—C8 | 110.11 (15) | C8—C7—C6 | 102.46 (16) |
N2—C1—N1 | 119.59 (17) | C3—C4—N1 | 120.9 (2) |
O1—C1—N1 | 118.64 (18) | C4—C3—C2 | 117.49 (19) |
O1—C1—N2 | 121.76 (18) | O3—C6—C5 | 108.94 (18) |
N2—C2—C3 | 121.5 (2) | O3—C6—C7 | 112.82 (17) |
N3—C2—N2 | 117.15 (19) | C7—C6—C5 | 100.36 (16) |
Experimental details
Crystal data |
Chemical formula | C9H13N3O5 |
Mr | 243.22 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 2 |
a, b, c (Å) | 5.0784 (3), 13.9046 (10), 14.6992 (10) |
V (Å3) | 1037.96 (12) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.13 |
Crystal size (mm) | 0.26 × 0.05 × 0.05 |
|
Data collection |
Diffractometer | Bruker APEX-II CCD diffractometer |
Absorption correction | Multi-scan SADABS2008/1 (Bruker,2008) was used for absorption correction.
R(int) was 0.0761 before and 0.0570 after correction.
The Ratio of minimum to maximum transmission is 0.8445.
The λ/2 correction factor is 0.0015. |
Tmin, Tmax | 0.365, 0.432 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 9630, 2456, 1916 |
Rint | 0.052 |
(sin θ/λ)max (Å−1) | 0.694 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.046, 0.090, 1.03 |
No. of reflections | 2456 |
No. of parameters | 157 |
H-atom treatment | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.29, −0.24 |
Absolute structure | Not refined as all light-atom structure |
Subscribe to Journal of Applied Crystallography
The full text of this article is available to subscribers to the journal.
If you have already registered and are using a computer listed in your registration details, please email
support@iucr.org for assistance.