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From a high-resolution X-ray data set (sin θ/λ = 1.1 Å−1) measured at 20 K the electron-density distribution of the nucleoside thymidine was derived by a classical multipole refinement and by application of the invariom formalism. Owing to the presence of the heteroaromatic thymine ring system two invariom models were compared which considered the nearest and next-nearest neighbors for the invariom assignments. Differences between the two invariom models were small for the bond topological and atomic properties – about five times smaller than differences with the classical multipole refinement. Even the latter differences are in the uncertainty ranges which are commonly observed in experimental charge-density work and were found in molecular regions involved in intermolecular contacts. The application of the constrained wavefunction-fitting approach allowed the electron localization function (ELF) to be obtained from the experimental X-ray data, which was graphically represented and topologically analyzed. ELF basin populations were derived from experiment for the first time. The electron populations in the disynaptic valence basins were related quantitatively to bond orders.
Supporting information
 | Crystallographic Information File (CIF) https://doi.org/10.1107/S0108768108005776/sn5064sup1.cif |
 | Structure factor file (CIF format) https://doi.org/10.1107/S0108768108005776/sn5064sup2.fcf |
CCDC reference: 652771
Computing details top
Data collection: SMART (Bruker, 1997-2003); cell refinement: SAINT (Bruker, 1997-2003); data reduction: SAINT (Bruker, 1997-2003); program(s) used to solve structure: SHELXS97 (Sheldrick, (1997)); program(s) used to refine structure: Volkov et al., (2006); molecular graphics: Volkov et al., (2006); software used to prepare material for publication: Volkov et al., (2006).
![[Figure 1]](https://journals.iucr.org/b/issues/2008/03/00/sn5064/sn5064fig1thm.gif)
![[Figure 2]](https://journals.iucr.org/b/issues/2008/03/00/sn5064/sn5064fig2thm.gif)
![[Figure 3]](https://journals.iucr.org/b/issues/2008/03/00/sn5064/sn5064fig3thm.gif)
![[Figure 4]](https://journals.iucr.org/b/issues/2008/03/00/sn5064/sn5064fig4thm.gif)
![[Figure 5]](https://journals.iucr.org/b/issues/2008/03/00/sn5064/sn5064fig5thm.gif)
![[Figure 6]](https://journals.iucr.org/b/issues/2008/03/00/sn5064/sn5064fig6thm.gif)
![[Figure 7]](https://journals.iucr.org/b/issues/2008/03/00/sn5064/sn5064fig7thm.gif)
![[Figure 8]](https://journals.iucr.org/b/issues/2008/03/00/sn5064/sn5064fig8thm.gif)
![[Figure 9]](https://journals.iucr.org/b/issues/2008/03/00/sn5064/sn5064fig9thm.gif)
![[Figure 10]](https://journals.iucr.org/b/issues/2008/03/00/sn5064/sn5064fig10thm.gif)
(I) top
Crystal data top
| C10H14N2O5 | F(000) = 512 |
| Mr = 242.23 | Dx = 1.464 Mg m−3 |
| Orthorhombic, P212121 | Mo Kα radiation, λ = 0.7107 Å |
| Hall symbol: P 2ac 2ab | Cell parameters from 61343 reflections |
| a = 4.8462 (19) Å | θ = 1.9–51.7° |
| b = 13.901 (6) Å | µ = 0.12 mm−1 |
| c = 16.316 (7) Å | T = 20 K |
| V = 1099.2 (8) Å3 | Block, colorless |
| Z = 4 | 0.5 × 0.3 × 0.2 mm |
Data collection top
| Bruker SMART Apex CCD Detector
on Huber four circle diffractometer | Rint = 0.039 |
| ϕ scans | θmax = 51.7° |
| 61343 measured reflections | h = −5→9 |
| 6295 independent reflections | k = −30→30 |
| 5638 reflections with I > 3 σ(I) | l = −35→36 |
Refinement top
| Refinement on F | 396 parameters |
| Least-squares matrix: full | 0 restraints |
| R[F2 > 2σ(F2)] = 0.016 | w1 = 1/[s2(Fo)] |
| wR(F2) = 0.019 | (Δ/σ)max < 0.001 |
| S = 0.94 | Δρmax = 0.16 e Å−3 |
| 5638 reflections | Δρmin = −0.17 e Å−3 |
Crystal data top
| C10H14N2O5 | V = 1099.2 (8) Å3 |
| Mr = 242.23 | Z = 4 |
| Orthorhombic, P212121 | Mo Kα radiation |
| a = 4.8462 (19) Å | µ = 0.12 mm−1 |
| b = 13.901 (6) Å | T = 20 K |
| c = 16.316 (7) Å | 0.5 × 0.3 × 0.2 mm |
Data collection top
| Bruker SMART Apex CCD Detector
on Huber four circle diffractometer | 5638 reflections with I > 3 σ(I) |
| 61343 measured reflections | Rint = 0.039 |
| 6295 independent reflections |
Refinement top
| R[F2 > 2σ(F2)] = 0.016 | 396 parameters |
| wR(F2) = 0.019 | 0 restraints |
| S = 0.94 | Δρmax = 0.16 e Å−3 |
| 5638 reflections | Δρmin = −0.17 e Å−3 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
| x | y | z | Uiso*/Ueq | ||
| O(1) | −0.27392 (8) | 0.48974 (2) | 0.82551 (2) | 0.009 | |
| O(2) | 0.38731 (8) | 0.27278 (2) | 0.90436 (2) | 0.008 | |
| O(3) | −0.23933 (6) | 0.39971 (2) | 0.592764 (15) | 0.006 | |
| O(4) | −0.40009 (7) | 0.59172 (2) | 0.528361 (17) | 0.007 | |
| O(5) | 0.08021 (8) | 0.29452 (2) | 0.48150 (2) | 0.009 | |
| N(1) | −0.03020 (7) | 0.41050 (2) | 0.723762 (19) | 0.006 | |
| N(2) | 0.05672 (9) | 0.37898 (3) | 0.86211 (2) | 0.007 | |
| C(1) | −0.09517 (8) | 0.43070 (2) | 0.805028 (19) | 0.006 | |
| C(2) | 0.26413 (8) | 0.31199 (2) | 0.84618 (2) | 0.006 | |
| C(3) | 0.31971 (8) | 0.29240 (2) | 0.75978 (2) | 0.006 | |
| C(4) | 0.17086 (8) | 0.34299 (2) | 0.70320 (2) | 0.006 | |
| C(5) | 0.53292 (9) | 0.21722 (3) | 0.73673 (2) | 0.008 | |
| C(6) | −0.18386 (8) | 0.46365 (2) | 0.65926 (2) | 0.005 | |
| C(7) | −0.02388 (8) | 0.55037 (2) | 0.62331 (2) | 0.006 | |
| C(8) | −0.12530 (8) | 0.55170 (2) | 0.53411 (2) | 0.006 | |
| C(9) | −0.14973 (7) | 0.44302 (2) | 0.51572 (2) | 0.005 | |
| C(10) | 0.12031 (8) | 0.39716 (2) | 0.48636 (2) | 0.007 | |
| H(1) | 0.004915 | 0.388833 | 0.921571 | 0.026 (4) | |
| H(2) | 0.190298 | 0.331268 | 0.637766 | 0.018 (4) | |
| H(3) | 0.720792 | 0.224306 | 0.773073 | 0.031 (4) | |
| H(4) | 0.462523 | 0.143649 | 0.747114 | 0.032 (4) | |
| H(5) | 0.593879 | 0.223907 | 0.672583 | 0.033 (4) | |
| H(6) | −0.378024 | 0.484223 | 0.68889 | 0.003 (3) | |
| H(7) | −0.058568 | 0.616685 | 0.657871 | 0.027 (3) | |
| H(8) | 0.197551 | 0.535326 | 0.624391 | 0.029 (3) | |
| H(9) | 0.018372 | 0.589037 | 0.4929 | 0.023 (3) | |
| H(10) | −0.310487 | 0.426945 | 0.470309 | 0.023 (3) | |
| H(11) | 0.166064 | 0.427624 | 0.425908 | 0.017 (3) | |
| H(12) | 0.290519 | 0.416683 | 0.527354 | 0.026 (3) | |
| H(13) | −0.402784 | 0.654913 | 0.552208 | 0.007 (3) | |
| H(14) | 0.250273 | 0.259976 | 0.488676 | 0.016 (4) |
Atomic displacement parameters (Å2) top
| U11 | U22 | U33 | U12 | U13 | U23 | |
| O(1) | 0.01075 (12) | 0.00982 (9) | 0.00608 (11) | 0.00505 (10) | 0.00070 (9) | −0.00076 (8) |
| O(2) | 0.01005 (11) | 0.00733 (8) | 0.00591 (10) | 0.00133 (10) | −0.00194 (9) | 0.00126 (7) |
| O(3) | 0.00760 (11) | 0.00546 (8) | 0.00442 (8) | −0.00123 (8) | −0.00004 (7) | 0.00008 (5) |
| O(4) | 0.00741 (11) | 0.00606 (8) | 0.00694 (8) | 0.00171 (7) | −0.00120 (7) | −0.00076 (6) |
| O(5) | 0.00778 (12) | 0.00555 (8) | 0.01275 (11) | 0.00093 (7) | 0.00120 (8) | −0.00080 (7) |
| N(1) | 0.00687 (10) | 0.00652 (8) | 0.00399 (8) | 0.00183 (7) | −0.00010 (7) | 0.00035 (7) |
| N(2) | 0.00823 (13) | 0.00756 (9) | 0.00415 (9) | 0.00218 (9) | 0.00022 (9) | 0.00023 (8) |
| C(1) | 0.00724 (12) | 0.00630 (8) | 0.00425 (9) | 0.00164 (9) | 0.00012 (8) | −0.00000 (7) |
| C(2) | 0.00682 (12) | 0.00562 (8) | 0.00483 (9) | 0.00064 (8) | −0.00042 (9) | 0.00046 (7) |
| C(3) | 0.00675 (11) | 0.00620 (9) | 0.00504 (9) | 0.00168 (9) | −0.00009 (9) | 0.00021 (7) |
| C(4) | 0.00696 (12) | 0.00679 (9) | 0.00481 (10) | 0.00199 (9) | 0.00000 (9) | 0.00020 (7) |
| C(5) | 0.00823 (12) | 0.00752 (9) | 0.00867 (11) | 0.00228 (9) | 0.00046 (9) | −0.00009 (8) |
| C(6) | 0.00633 (12) | 0.00571 (9) | 0.00443 (9) | 0.00042 (8) | −0.00024 (9) | 0.00018 (7) |
| C(7) | 0.00771 (12) | 0.00571 (8) | 0.00604 (9) | −0.00068 (8) | −0.00154 (8) | 0.00015 (7) |
| C(8) | 0.00658 (11) | 0.00505 (8) | 0.00518 (9) | 0.00009 (7) | −0.00027 (8) | 0.00048 (7) |
| C(9) | 0.00584 (11) | 0.00520 (8) | 0.00474 (8) | 0.00024 (7) | 0.00003 (8) | −0.00014 (7) |
| C(10) | 0.00617 (12) | 0.00610 (9) | 0.00754 (10) | 0.00042 (8) | 0.00099 (9) | −0.00001 (7) |
Geometric parameters (Å, º) top
| O(1)—C(1) | 1.2389 (6) | C(4)—H(2) | 1.0841 (4) |
| O(2)—C(2) | 1.2467 (5) | C(5)—H(3) | 1.0914 (4) |
| O(3)—C(6) | 1.4280 (5) | C(5)—H(4) | 1.0914 (4) |
| O(4)—H(13) | 0.9607 (3) | C(5)—H(5) | 1.0914 (4) |
| O(5)—H(14) | 0.9607 (4) | C(6)—H(6) | 1.0958 (4) |
| N(1)—C(1) | 1.3916 (5) | C(7)—C(8) | 1.5362 (5) |
| N(1)—C(4) | 1.3941 (5) | C(7)—H(7) | 1.0937 (4) |
| N(2)—C(1) | 1.3877 (5) | C(7)—H(8) | 1.0937 (4) |
| N(2)—C(2) | 1.3946 (5) | C(8)—H(9) | 1.0982 (4) |
| N(2)—H(1) | 1.0117 (4) | C(9)—C(10) | 1.5320 (5) |
| C(2)—C(3) | 1.4610 (5) | C(9)—H(10) | 1.0982 (4) |
| C(3)—C(4) | 1.3660 (5) | C(10)—H(11) | 1.0962 (4) |
| C(3)—C(5) | 1.5167 (6) | C(10)—H(12) | 1.0963 (4) |
| C(1)—N(1)—C(4) | 121.55 (3) | C(3)—C(5)—H(3) | 111.80 (3) |
| C(1)—N(2)—C(2) | 127.11 (4) | C(3)—C(5)—H(4) | 113.24 (4) |
| C(1)—N(2)—H(1) | 116.24 (4) | C(3)—C(5)—H(5) | 111.34 (3) |
| C(2)—N(2)—H(1) | 116.58 (4) | H(3)—C(5)—H(4) | 105.10 (3) |
| O(1)—C(1)—N(1) | 123.30 (4) | H(3)—C(5)—H(5) | 106.69 (4) |
| O(1)—C(1)—N(2) | 122.18 (4) | H(4)—C(5)—H(5) | 108.26 (3) |
| N(1)—C(1)—N(2) | 114.51 (3) | O(3)—C(6)—H(6) | 109.65 (3) |
| O(2)—C(2)—N(2) | 119.70 (4) | C(8)—C(7)—H(7) | 115.42 (3) |
| O(2)—C(2)—C(3) | 124.38 (4) | C(8)—C(7)—H(8) | 109.36 (3) |
| N(2)—C(2)—C(3) | 115.91 (3) | H(7)—C(7)—H(8) | 107.66 (3) |
| C(2)—C(3)—C(4) | 117.31 (3) | C(7)—C(8)—H(9) | 112.52 (3) |
| C(2)—C(3)—C(5) | 119.57 (3) | C(10)—C(9)—H(10) | 108.08 (3) |
| C(4)—C(3)—C(5) | 123.12 (3) | C(9)—C(10)—H(11) | 107.06 (3) |
| N(1)—C(4)—C(3) | 123.57 (3) | C(9)—C(10)—H(12) | 110.43 (3) |
| N(1)—C(4)—H(2) | 113.47 (3) | H(11)—C(10)—H(12) | 107.51 (3) |
| C(3)—C(4)—H(2) | 122.87 (4) |
Experimental details
| Crystal data | |
| Chemical formula | C10H14N2O5 |
| Mr | 242.23 |
| Crystal system, space group | Orthorhombic, P212121 |
| Temperature (K) | 20 |
| a, b, c (Å) | 4.8462 (19), 13.901 (6), 16.316 (7) |
| V (Å3) | 1099.2 (8) |
| Z | 4 |
| Radiation type | Mo Kα |
| µ (mm−1) | 0.12 |
| Crystal size (mm) | 0.5 × 0.3 × 0.2 |
| Data collection | |
| Diffractometer | Bruker SMART Apex CCD Detector
on Huber four circle diffractometer |
| Absorption correction | – |
| No. of measured, independent and observed [I > 3 σ(I)] reflections | 61343, 6295, 5638 |
| Rint | 0.039 |
| (sin θ/λ)max (Å−1) | 1.104 |
| Refinement | |
| R[F2 > 2σ(F2)], wR(F2), S | 0.016, 0.019, 0.94 |
| No. of reflections | 5638 |
| No. of parameters | 396 |
| Δρmax, Δρmin (e Å−3) | 0.16, −0.17 |
Computer programs: SMART (Bruker, 1997-2003), SAINT (Bruker, 1997-2003), SHELXS97 (Sheldrick, (1997)), Volkov et al., (2006).
Selected geometric parameters (Å, º) top
| O(1)—C(1) | 1.2389 (6) | C(4)—H(2) | 1.0841 (4) |
| O(2)—C(2) | 1.2467 (5) | C(5)—H(3) | 1.0914 (4) |
| O(3)—C(6) | 1.4280 (5) | C(5)—H(4) | 1.0914 (4) |
| O(4)—H(13) | 0.9607 (3) | C(5)—H(5) | 1.0914 (4) |
| O(5)—H(14) | 0.9607 (4) | C(6)—H(6) | 1.0958 (4) |
| N(1)—C(1) | 1.3916 (5) | C(7)—C(8) | 1.5362 (5) |
| N(1)—C(4) | 1.3941 (5) | C(7)—H(7) | 1.0937 (4) |
| N(2)—C(1) | 1.3877 (5) | C(7)—H(8) | 1.0937 (4) |
| N(2)—C(2) | 1.3946 (5) | C(8)—H(9) | 1.0982 (4) |
| N(2)—H(1) | 1.0117 (4) | C(9)—C(10) | 1.5320 (5) |
| C(2)—C(3) | 1.4610 (5) | C(9)—H(10) | 1.0982 (4) |
| C(3)—C(4) | 1.3660 (5) | C(10)—H(11) | 1.0962 (4) |
| C(3)—C(5) | 1.5167 (6) | C(10)—H(12) | 1.0963 (4) |
| C(1)—N(1)—C(4) | 121.55 (3) | C(3)—C(5)—H(3) | 111.80 (3) |
| C(1)—N(2)—C(2) | 127.11 (4) | C(3)—C(5)—H(4) | 113.24 (4) |
| C(1)—N(2)—H(1) | 116.24 (4) | C(3)—C(5)—H(5) | 111.34 (3) |
| C(2)—N(2)—H(1) | 116.58 (4) | H(3)—C(5)—H(4) | 105.10 (3) |
| O(1)—C(1)—N(1) | 123.30 (4) | H(3)—C(5)—H(5) | 106.69 (4) |
| O(1)—C(1)—N(2) | 122.18 (4) | H(4)—C(5)—H(5) | 108.26 (3) |
| N(1)—C(1)—N(2) | 114.51 (3) | O(3)—C(6)—H(6) | 109.65 (3) |
| O(2)—C(2)—N(2) | 119.70 (4) | C(8)—C(7)—H(7) | 115.42 (3) |
| O(2)—C(2)—C(3) | 124.38 (4) | C(8)—C(7)—H(8) | 109.36 (3) |
| N(2)—C(2)—C(3) | 115.91 (3) | H(7)—C(7)—H(8) | 107.66 (3) |
| C(2)—C(3)—C(4) | 117.31 (3) | C(7)—C(8)—H(9) | 112.52 (3) |
| C(2)—C(3)—C(5) | 119.57 (3) | C(10)—C(9)—H(10) | 108.08 (3) |
| C(4)—C(3)—C(5) | 123.12 (3) | C(9)—C(10)—H(11) | 107.06 (3) |
| N(1)—C(4)—C(3) | 123.57 (3) | C(9)—C(10)—H(12) | 110.43 (3) |
| N(1)—C(4)—H(2) | 113.47 (3) | H(11)—C(10)—H(12) | 107.51 (3) |
| C(3)—C(4)—H(2) | 122.87 (4) |
