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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

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108768108005776/sn5064sup1.cif
Contains datablock I

fcf

Structure factor file (CIF format) https://doi.org/10.1107/S0108768108005776/sn5064sup2.fcf
Contains datablock I

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).

Figures top
[Figure 1]
[Figure 2]
[Figure 3]
[Figure 4]
[Figure 5]
[Figure 6]
[Figure 7]
[Figure 8]
[Figure 9]
[Figure 10]
(I) top
Crystal data top
C10H14N2O5F(000) = 512
Mr = 242.23Dx = 1.464 Mg m3
Orthorhombic, P212121Mo Kα radiation, λ = 0.7107 Å
Hall symbol: P 2ac 2abCell parameters from 61343 reflections
a = 4.8462 (19) Åθ = 1.9–51.7°
b = 13.901 (6) ŵ = 0.12 mm1
c = 16.316 (7) ÅT = 20 K
V = 1099.2 (8) Å3Block, colorless
Z = 40.5 × 0.3 × 0.2 mm
Data collection top
Bruker SMART Apex CCD Detector on Huber four circle
diffractometer
Rint = 0.039
ϕ scansθmax = 51.7°
61343 measured reflectionsh = 59
6295 independent reflectionsk = 3030
5638 reflections with I > 3 σ(I)l = 3536
Refinement top
Refinement on F396 parameters
Least-squares matrix: full0 restraints
R[F2 > 2σ(F2)] = 0.016 w1 = 1/[s2(Fo)]
wR(F2) = 0.019(Δ/σ)max < 0.001
S = 0.94Δρmax = 0.16 e Å3
5638 reflectionsΔρmin = 0.17 e Å3
Crystal data top
C10H14N2O5V = 1099.2 (8) Å3
Mr = 242.23Z = 4
Orthorhombic, P212121Mo Kα radiation
a = 4.8462 (19) ŵ = 0.12 mm1
b = 13.901 (6) ÅT = 20 K
c = 16.316 (7) Å0.5 × 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 reflectionsRint = 0.039
6295 independent reflections
Refinement top
R[F2 > 2σ(F2)] = 0.016396 parameters
wR(F2) = 0.0190 restraints
S = 0.94Δρmax = 0.16 e Å3
5638 reflectionsΔρmin = 0.17 e Å3
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/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)0.0049150.3888330.9215710.026 (4)
H(2)0.1902980.3312680.6377660.018 (4)
H(3)0.7207920.2243060.7730730.031 (4)
H(4)0.4625230.1436490.7471140.032 (4)
H(5)0.5938790.2239070.6725830.033 (4)
H(6)0.3780240.4842230.688890.003 (3)
H(7)0.0585680.6166850.6578710.027 (3)
H(8)0.1975510.5353260.6243910.029 (3)
H(9)0.0183720.5890370.49290.023 (3)
H(10)0.3104870.4269450.4703090.023 (3)
H(11)0.1660640.4276240.4259080.017 (3)
H(12)0.2905190.4166830.5273540.026 (3)
H(13)0.4027840.6549130.5522080.007 (3)
H(14)0.2502730.2599760.4886760.016 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
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 formulaC10H14N2O5
Mr242.23
Crystal system, space groupOrthorhombic, P212121
Temperature (K)20
a, b, c (Å)4.8462 (19), 13.901 (6), 16.316 (7)
V3)1099.2 (8)
Z4
Radiation typeMo Kα
µ (mm1)0.12
Crystal size (mm)0.5 × 0.3 × 0.2
Data collection
DiffractometerBruker 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
Rint0.039
(sin θ/λ)max1)1.104
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.016, 0.019, 0.94
No. of reflections5638
No. of parameters396
Δρmax, Δρmin (e Å3)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)
 

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