organic papers
o1488
Ding, Liu, Xiao and Hu C19H18N2O2 DOI: 10.1107/S160053680301986X Acta Cryst.(2003). E59, o1488±o1489 Acta Crystallographica Section EStructure Reports Online
ISSN 1600-5368
1,3-Dibenzylthymine
Jin-Chang Ding,* Miao-Chang Liu, Hong-Ping Xiao and Mao-Lin Hu
Department of Chemistry and Material Science, Wenzhou Normal College, Wenzhou, 325027, People's Republic of China
Correspondence e-mail: [email protected]
Key indicators
Single-crystal X-ray study
T= 273 K
Mean(C±C) = 0.003 AÊ
Rfactor = 0.039
wRfactor = 0.098
Data-to-parameter ratio = 16.7
For details of how these key indicators were automatically derived from the article, see http://journals.iucr.org/e.
#2003 International Union of Crystallography Printed in Great Britain ± all rights reserved
In the title compound, C19H18N2O2, the two phenyl rings are
located on the same side of the thymine ring, resembling the two front claws of a crab. The crystal structure involves some weak CÐH O interactions.
Comment
Nucleobases are important in biology, being responsible for a wide range of biochemical processes, such as complementary base pairing in genetic information storage and transfer, molecular recognition and some enzymatic reactions (Bazzi-calupiet al., 2001). As a result, considerable efforts have been made to investigate thymine and its derivatives. These studies include the crystal structure and theoretical investigation of the electronic properties ofcis -5-hydroperoxy-6-hydroxy-5,6-dihydrothymine (Jolibois et al., 1998); the low-frequency vibrational spectrum of 1-methylthymine (Kirinet al., 1975); the synthesis, cation reporter properties and recognition of 1-methylthymine by a macrocyclic zinc(II) complex (Koikeet al., 1998).
In an earlier study, we reported the synthesis and crystal structure of 1-benzylthymine (Dinget al., 2002). Since then, a new thymine derivative, 1,3-dibenzylthymine, (I), has been obtained and its crystal structure is reported here.
The title compound contains two phenyl rings and one heterocyclic ring (Fig. 1). The two phenyl rings, (C1±C6) and (C14±C19) are each essentially planar, with average deviations from planarity of 0.007 and 0.008 AÊ, respectively. The atoms of the thymine ring (C8, C9, C11, C12, N1, N2) are coplanar, with an average deviation of 0.013 AÊ; the value in 1-benzylthymine is very similar,viz. 0.010 AÊ.
The two phenyl rings are located on the same side of the thymine ring, resembling the two front claws of a crab. The dihedral angles between the mean planes of the thymine ring and the phenyl rings are 81.7 (2) (phenyl ring C1±C6) and
67.4 (2)(phenyl ring C14±C19).
Moreover, the non-bonded interactions are also different in 1,3-dibenzylthymine and in 1-benzylthymine. In the former, there are only weak CÐH O interactions C7Ð
H7B O1(xÿ1
2, 52ÿy, ÿz) and C18ÐH18 O2(1 +x, y, z)
with C O distances of 3.391 (2) and 3.481 (2) AÊ, respec-tively; the angles at H7Band H18 are 151 and 169,
respec-tively. On the other hand, in 1-benzylthymine, there are strong NÐH O hydrogen bond interactions with N O distances of 2.872 (5) AÊ and 2.834 (5) AÊ and signi®cant interac-tions between neighboring phenyl rings separated by 3.46 AÊ.
Experimental
The title compound was synthesized through the benzylation of 0.25 g thymine with 0.54 ml benzyl bromide by neutralization of 2.00 g potassium carbonate, and catalysis of 0.10 g tetrabutylammonium bromide in the mixed solventsN,N0-dimethylacetamide and
diethyl-ene glycol (v/v = 1:10); the reaction time was ®ve minutes in a National NN-S568WFS 900 W microwave oven. Single crystals suitable for X-ray data collection were obtained by recrystallization from a mixture of of ethanol and dichloromethane.
Crystal data C19H18N2O2
Mr= 306.35
Orthorhombic,P212121
a= 8.7466 (10) AÊ
b= 8.8637 (10) AÊ
c= 20.720 (3) AÊ
V= 1606.3 (3) AÊ3
Z= 4
Dx= 1.267 Mg mÿ3
MoKradiation Cell parameters from 599
re¯ections
= 2.3±18.0
= 0.08 mmÿ1
T= 273 (2) K Block, colorless 0.450.280.25 mm
Data collection
Bruker SMART CCD area-detector diffractometer
'and!scans
Absorption correction: none 7934 measured re¯ections 3508 independent re¯ections
2618 re¯ections withI> 2(I)
Rint= 0.026
max= 27.0
h=ÿ10!11
k=ÿ11!7
l=ÿ20!26
Re®nement Re®nement onF2
R[F2> 2(F2)] = 0.039
wR(F2) = 0.098
S= 0.97 3508 re¯ections 210 parameters
H-atoms parameters constrained
w= 1/[2(F
o2) + (0.0549P)2] whereP= (Fo2+ 2Fc2)/3 (/)max< 0.001
max= 0.12 e AÊÿ3
min=ÿ0.12 e AÊÿ3
Extinction correction:SHELXL
Extinction coef®cient: 0.16(SU?)
Table 1
Selected geometric parameters (AÊ,).
O1ÐC12 1.2168 (18) O2ÐC11 1.2206 (19) N1ÐC12 1.373 (2) N1ÐC8 1.376 (2) N1ÐC7 1.470 (2) N2ÐC12 1.385 (2) N2ÐC11 1.4047 (19) N2ÐC13 1.4819 (19) C1ÐC6 1.356 (3) C1ÐC2 1.361 (3) C2ÐC3 1.377 (3) C3ÐC4 1.367 (2) C4ÐC5 1.371 (2)
C4ÐC7 1.507 (2) C5ÐC6 1.381 (3) C8ÐC9 1.327 (2) C9ÐC11 1.441 (2) C9ÐC10 1.503 (2) C13ÐC14 1.510 (3) C14ÐC19 1.377 (2) C14ÐC15 1.377 (3) C15ÐC16 1.375 (3) C16ÐC17 1.366 (3) C17ÐC18 1.368 (3) C18ÐC19 1.380 (3)
N1ÐC7ÐC4 114.68 (13) N2ÐC13ÐC14 112.84 (13)
In the absence of signi®cant anomalous dispersion effects, the 1480 Friedel pairs were merged and the absolute con®guration can not be determined from the crystallographic experiment.
All H atoms were positioned geometrically and allowed to ride on their parent atoms at distances of 0.93 AÊ for Csp2ÐH, 0.96 AÊ for
C(methyl)ÐH and 0.97 AÊ for C(methylene)ÐH. Isotropic displace-ment parameters were set to 1.5Ueq(methylene and methyl) and
1.2Ueq(other H atoms) of the carrier atom.
Data collection:SMART(Bruker, 2000); cell re®nement:SMART; data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXTL (Bruker, 2000); program(s) used to re®ne structure:SHELXTL; molecular graphics:SHELXTL; software used to prepare material for publication:SHELXTL.
We acknowledge ®nancial support by the Zhejiang Provincial Natural Science Foundation of China (No. 202137).
References
Bazzicalupi, C., Bencini, A., Berni, E., Ciattini, S., Bianchi, A., Giorgi, C., Paoletti, P., Valtancoli, B. (2001).Inorg. Chim. Acta,317, 259±267. Bruker (2000).SMART, SAINTandSHELXTL.Bruker AXS Inc., Madison,
Wisconsin, USA.
Ding, J. C., Liu, M. C., Zhao, Y. J. & Hu, M. L. (2002).Z. Kristallogr. New Cryst. Struct.217, 499±500.
Jolibois, F., D'Ham, C., Grand, A., Subra, R., Cadet, J. (1998).J. Mol. Struct.
(Theochem),427, 143±155.
Kirin, D., Colombo, L., Furic, K. & Meier, W. (1975).Spectrochim. Acta,31A, 1721±1727.
Koike, T., Gotoh, T., Aoki, S., Kimura, E., Shiro, M. (1998).Inorg. Chim. Acta,
270, 424±432.
Figure 1
supporting information
sup-1
Acta Cryst. (2003). E59, o1488–o1489
supporting information
Acta Cryst. (2003). E59, o1488–o1489 [https://doi.org/10.1107/S160053680301986X]
1,3-Dibenzylthymine
Jin-Chang Ding, Miao-Chang Liu, Hong-Ping Xiao and Mao-Lin Hu
1,3-dibenzylthymine
Crystal data C19H18N2O2
Mr = 306.35
Orthorhombic, P212121
Hall symbol: P 2ac 2ab a = 8.7466 (10) Å b = 8.8637 (10) Å c = 20.720 (3) Å V = 1606.3 (3) Å3
Z = 4
F(000) = 648 Dx = 1.267 Mg m−3
Mo Kα radiation, λ = 0.71073 Å Cell parameters from 599 reflections θ = 2.3–18.0°
µ = 0.08 mm−1
T = 273 K Block, colorless 0.45 × 0.28 × 0.25 mm
Data collection
Bruker SMART CCD area-detector diffractometer
Radiation source: fine-focus sealed tube Graphite monochromator
φ and ω scans
7934 measured reflections 3508 independent reflections
2618 reflections with I > 2σ(I) Rint = 0.026
θmax = 27.0°, θmin = 2.0°
h = −10→11 k = −11→7 l = −20→26
Refinement Refinement on F2
Least-squares matrix: full R[F2 > 2σ(F2)] = 0.039
wR(F2) = 0.098
S = 0.97 3508 reflections 210 parameters 0 restraints
Primary atom site location: structure-invariant direct methods
Secondary atom site location: difference Fourier map
Hydrogen site location: inferred from neighbouring sites
H atoms treated by a mixture of independent and constrained refinement
w = 1/[σ2(F
o2) + (0.0549P)2]
where P = (Fo2 + 2Fc2)/3
(Δ/σ)max < 0.001
Δρmax = 0.12 e Å−3
Δρmin = −0.12 e Å−3
Extinction correction: SHELXL Extinction coefficient: 0.16
Special details
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.
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2)
x y z Uiso*/Ueq
O1 0.40423 (13) 1.19121 (14) 0.07784 (6) 0.0749 (4)
O2 0.06716 (14) 0.81307 (15) 0.12073 (6) 0.0734 (4)
N1 0.22761 (14) 1.13075 (15) 0.00165 (7) 0.0567 (3)
N2 0.23650 (13) 1.00069 (16) 0.09917 (6) 0.0541 (3)
C1 0.5975 (3) 1.1347 (2) −0.18855 (11) 0.0841 (6)
H1 0.6670 1.1090 −0.2207 0.101*
C2 0.5984 (3) 1.0608 (3) −0.13095 (11) 0.0951 (7)
H2 0.6702 0.9854 −0.1235 0.114*
C3 0.4940 (2) 1.0965 (2) −0.08357 (10) 0.0768 (5)
H3 0.4951 1.0435 −0.0448 0.092*
C4 0.38888 (17) 1.20868 (17) −0.09264 (8) 0.0544 (4)
C5 0.3904 (2) 1.2829 (2) −0.15068 (9) 0.0788 (6)
H5 0.3202 1.3598 −0.1580 0.095*
C6 0.4940 (2) 1.2461 (3) −0.19847 (9) 0.0873 (6)
H6 0.4927 1.2979 −0.2375 0.105*
C7 0.27772 (18) 1.2545 (2) −0.04062 (8) 0.0624 (4)
H7A 0.3250 1.3319 −0.0142 0.075*
H7B 0.1883 1.2986 −0.0609 0.075*
C8 0.11132 (18) 1.03707 (18) −0.01822 (8) 0.0549 (4)
H8 0.0709 1.0513 −0.0593 0.066*
C9 0.05374 (17) 0.92755 (18) 0.01805 (7) 0.0543 (4)
C10 −0.0742 (2) 0.8272 (2) −0.00439 (10) 0.0770 (5)
H10A −0.1652 0.8498 0.0197 0.115*
H10B −0.0465 0.7236 0.0023 0.115*
H10C −0.0927 0.8442 −0.0495 0.115*
C11 0.11435 (17) 0.90589 (18) 0.08204 (8) 0.0543 (4)
C12 0.29712 (18) 1.11346 (19) 0.06058 (8) 0.0563 (4)
C13 0.30099 (19) 0.9825 (2) 0.16485 (7) 0.0638 (5)
H13A 0.2189 0.9588 0.1946 0.077*
H13B 0.3461 1.0774 0.1784 0.077*
C14 0.42074 (17) 0.8601 (2) 0.16851 (7) 0.0572 (4)
C15 0.3854 (2) 0.7192 (2) 0.19221 (8) 0.0690 (5)
H15 0.2864 0.6995 0.2063 0.083*
C16 0.4938 (2) 0.6071 (3) 0.19541 (10) 0.0835 (6)
H16 0.4670 0.5120 0.2106 0.100*
C17 0.6406 (2) 0.6348 (3) 0.17636 (9) 0.0826 (6)
H17 0.7141 0.5592 0.1790 0.099*
C18 0.6787 (2) 0.7746 (3) 0.15341 (9) 0.0847 (6)
H18 0.7785 0.7944 0.1405 0.102*
supporting information
sup-3
Acta Cryst. (2003). E59, o1488–o1489
H19 0.5960 0.9807 0.1335 0.087*
Atomic displacement parameters (Å2)
U11 U22 U33 U12 U13 U23
O1 0.0592 (7) 0.0808 (8) 0.0849 (9) −0.0192 (7) −0.0082 (6) 0.0006 (7)
O2 0.0626 (7) 0.0884 (9) 0.0692 (8) −0.0146 (7) −0.0023 (6) 0.0170 (6)
N1 0.0488 (7) 0.0600 (8) 0.0614 (8) −0.0021 (6) 0.0022 (6) 0.0036 (6)
N2 0.0460 (7) 0.0658 (8) 0.0505 (7) −0.0039 (6) −0.0008 (6) −0.0022 (6)
C1 0.0851 (13) 0.0910 (14) 0.0761 (13) 0.0019 (13) 0.0188 (11) −0.0025 (11)
C2 0.0985 (16) 0.0872 (14) 0.0998 (17) 0.0318 (13) 0.0265 (14) 0.0129 (12)
C3 0.0836 (12) 0.0690 (11) 0.0778 (13) 0.0193 (10) 0.0164 (10) 0.0191 (9)
C4 0.0469 (8) 0.0532 (9) 0.0632 (10) −0.0047 (7) −0.0042 (7) 0.0055 (8)
C5 0.0654 (10) 0.0919 (13) 0.0791 (13) 0.0156 (11) −0.0026 (10) 0.0261 (11)
C6 0.0792 (13) 0.1188 (17) 0.0638 (12) 0.0002 (14) 0.0010 (10) 0.0235 (12)
C7 0.0558 (9) 0.0571 (10) 0.0743 (11) 0.0024 (8) 0.0011 (8) 0.0107 (9)
C8 0.0485 (8) 0.0641 (9) 0.0521 (9) 0.0055 (8) −0.0026 (7) −0.0028 (8)
C9 0.0481 (8) 0.0612 (10) 0.0537 (9) 0.0011 (7) 0.0000 (7) −0.0033 (8)
C10 0.0733 (11) 0.0854 (12) 0.0724 (12) −0.0198 (10) −0.0133 (10) −0.0014 (10)
C11 0.0437 (7) 0.0601 (9) 0.0592 (10) 0.0009 (7) 0.0036 (7) −0.0025 (8)
C12 0.0460 (8) 0.0625 (10) 0.0605 (10) 0.0001 (8) 0.0008 (7) −0.0036 (8)
C13 0.0589 (9) 0.0817 (12) 0.0508 (9) −0.0054 (9) −0.0030 (8) −0.0071 (8)
C14 0.0514 (9) 0.0812 (11) 0.0389 (8) −0.0110 (9) −0.0031 (7) −0.0012 (7)
C15 0.0567 (9) 0.0964 (14) 0.0538 (9) −0.0101 (10) −0.0041 (8) 0.0159 (10)
C16 0.0820 (14) 0.0949 (15) 0.0736 (13) −0.0004 (12) −0.0157 (11) 0.0245 (11) C17 0.0782 (14) 0.1089 (17) 0.0607 (11) 0.0217 (13) −0.0155 (10) 0.0053 (11)
C18 0.0510 (9) 0.141 (2) 0.0624 (12) 0.0013 (12) −0.0001 (9) 0.0048 (13)
C19 0.0536 (10) 0.0939 (13) 0.0691 (11) −0.0123 (10) 0.0005 (8) 0.0125 (10)
Geometric parameters (Å, º)
O1—C12 1.2168 (18) C8—C9 1.327 (2)
O2—C11 1.2206 (19) C8—H8 0.9300
N1—C12 1.373 (2) C9—C11 1.441 (2)
N1—C8 1.376 (2) C9—C10 1.503 (2)
N1—C7 1.470 (2) C10—H10A 0.9600
N2—C12 1.385 (2) C10—H10B 0.9600
N2—C11 1.4047 (19) C10—H10C 0.9600
N2—C13 1.4819 (19) C13—C14 1.510 (3)
C1—C6 1.356 (3) C13—H13A 0.9700
C1—C2 1.361 (3) C13—H13B 0.9700
C1—H1 0.9300 C14—C19 1.377 (2)
C2—C3 1.377 (3) C14—C15 1.377 (3)
C2—H2 0.9300 C15—C16 1.375 (3)
C3—C4 1.367 (2) C15—H15 0.9300
C3—H3 0.9300 C16—C17 1.366 (3)
C4—C5 1.371 (2) C16—H16 0.9300
C5—C6 1.381 (3) C17—H17 0.9300
C5—H5 0.9300 C18—C19 1.380 (3)
C6—H6 0.9300 C18—H18 0.9300
C7—H7A 0.9700 C19—H19 0.9300
C7—H7B 0.9700
C12—N1—C8 121.75 (14) C9—C10—H10A 109.5
C12—N1—C7 118.76 (14) C9—C10—H10B 109.5
C8—N1—C7 119.48 (14) H10A—C10—H10B 109.5
C12—N2—C11 125.23 (13) C9—C10—H10C 109.5
C12—N2—C13 117.55 (13) H10A—C10—H10C 109.5
C11—N2—C13 117.16 (13) H10B—C10—H10C 109.5
C6—C1—C2 119.16 (19) O2—C11—N2 119.63 (15)
C6—C1—H1 120.4 O2—C11—C9 124.73 (15)
C2—C1—H1 120.4 N2—C11—C9 115.63 (14)
C1—C2—C3 120.7 (2) O1—C12—N1 122.63 (15)
C1—C2—H2 119.6 O1—C12—N2 122.26 (15)
C3—C2—H2 119.6 N1—C12—N2 115.11 (14)
C4—C3—C2 120.99 (18) N2—C13—C14 112.84 (13)
C4—C3—H3 119.5 N2—C13—H13A 109.0
C2—C3—H3 119.5 C14—C13—H13A 109.0
C3—C4—C5 117.57 (16) N2—C13—H13B 109.0
C3—C4—C7 122.10 (15) C14—C13—H13B 109.0
C5—C4—C7 120.30 (15) H13A—C13—H13B 107.8
C4—C5—C6 121.48 (17) C19—C14—C15 117.81 (18)
C4—C5—H5 119.3 C19—C14—C13 121.25 (17)
C6—C5—H5 119.3 C15—C14—C13 120.93 (15)
C1—C6—C5 120.08 (18) C16—C15—C14 121.19 (17)
C1—C6—H6 120.0 C16—C15—H15 119.4
C5—C6—H6 120.0 C14—C15—H15 119.4
N1—C7—C4 114.68 (13) C17—C16—C15 120.3 (2)
N1—C7—H7A 108.6 C17—C16—H16 119.9
C4—C7—H7A 108.6 C15—C16—H16 119.9
N1—C7—H7B 108.6 C16—C17—C18 119.5 (2)
C4—C7—H7B 108.6 C16—C17—H17 120.3
H7A—C7—H7B 107.6 C18—C17—H17 120.3
C9—C8—N1 123.54 (16) C17—C18—C19 120.10 (18)
C9—C8—H8 118.2 C17—C18—H18 120.0
N1—C8—H8 118.2 C19—C18—H18 120.0
C8—C9—C11 118.62 (15) C14—C19—C18 121.11 (19)
C8—C9—C10 122.70 (15) C14—C19—H19 119.4