Comparative experimental electron density and electron localization function study of thymidine based on 20 K X-ray diffraction data

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.

Computing details

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

(I)

Crystal data

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) Å^3	Block, colorless
Z = 4	0.5 × 0.3 × 0.2 mm

Data collection

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

Refinement on F	396 parameters
Least-squares matrix: full	0 restraints
R[F^2 > 2σ(F^2)] = 0.016	w1 = 1/[s^2(Fo)]
wR(F^2) = 0.019	(Δ/σ)max < 0.001
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 (Ų)

	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 (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
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)

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)