TTF-cytosine dyad as an electron-donor molecule having proton-accepting ability: Formation of hemiprotonated cytosine Dimer in i3- salt

Article abstract of DOI:10.1246/cl.2007.1102

A tetrathiafulvalene (TTF) derivative with a cytosine moiety was designed and synthesized as a bi-functional molecule with both electron-donating and proton-accepting abilities. In the crystal of I₃^- salt, TTF-cytosine dyad formed a

Full text of DOI:10.1246/cl.2007.1102

1102
Chemistry Letters Vol.36, No.9 (2007)
TTF–Cytosine Dyad as an Electron-donor Molecule Having ProtoÀn-accepting Ability:
Formation of Hemiprotonated Cytosine Dimer in I3 Salt
Eigo Miyazaki,1 Yasushi Morita,ꢀ1;2 Yumi Yakiyama,1 Suguru Maki,1 Yoshikazu Umemoto,1
Makoto Ohmoto,1 and Kazuhiro Nakasujiꢀ3
1Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043
2PRESTO, Japan Science and Technology (JST), 4-1-8 Hon-cho, Kawaguchi 332-0012
3Fukui University of Technology, 3-6-1 Gakuen, Fukui 910-8105
(Received June 15, 2007; CL-070650; E-mail: morita@chem.sci.osaka-u.ac.jp)
Ar
N
O
A tetrathiafulvalene (TTF) derivative with a cytosine moiety
was designed and synthesized as a bi-functional molecule
with both electron-donating and proton-accepting abilities. In
the crystal of I3 salt, TTF–cytosine dyad formed a hemiproto-
nated dimer through triple hydrogen-bonds with radical cationic
state of the TTF moieties.
SnBu3
NBu
S
S
S
S
i
ii
S
S
S
S
TTF
ꢁ
1
2
iii
H
N
O
O
NBu
S
S
S
iv
An attractive application based on the bio-molecule inspired
functional molecular systems are rapidly spread in the field of
materials science.1 Cytosine possesses a self-assembling nature
to form a hydrogen-bonded (H-bonded) dimer having double
N–HꢂꢂꢂN interactions under neutral condition.2 Interestingly,
due to a proton-accepting ability, two cytosine molecules catch
one proton under acidic condition, forming a hemiprotonated
cytosine dimer with triple H-bonds (Chart 1).3 This unique
self-assembling ability was utilized in charge-transfer (CT) salt
of pristine cytosine with TCNQ derivative, in which the dimer
acted as cationic part in the salt.4 Our previous study on H-bond-
ed CT complex of TTF–imidazole (D) with p-chloranil (A)
revealed the new role of H-bond to control electronic structure
by regulating electron-accepting ability of p-chloranil and the
donor/acceptor ratio by forming a D–A–D triad.5 In order to
expand examples involving these new roles of H-bonds, recent
our attention is concentrating on nucleobase systems with TTF
moieties, i.e. TTF-U (Scheme 1).6 Focusing on the hemiproto-
nated cytosine dimer, we have designed a novel TTF–cytosine
dyad (TTF-C) in this study (Chart 1). Here, we report the synthe-
ses and crystal structures of TTF-C and a hemiprotonated
TTF-C
S
TTF-U
Scheme 1. Reagents and conditions: i) n-BuLi then Bu3SnCl,
ꢁ78 ꢃC, ii) 1-n-butyl-5-iodo-4-(o-nitrophenoxy)pyrimidin-2-
one, Pd(PPh3)4, Ar = o-nitrophenoxy, iii) aqueous NH3 solu-
tion, THF, rt, iv) 2-mesitylenesulfonyl chloride, dimethylamino-
pyridine, and triethylamine, rt, then aqueous NH3 solution.
TTF-C. Notably, this molecule possesses a reasonable solubility
toward common organic solvents in spite of a cytosine deriva-
tive. Cyclic voltammetry (CV) measurement of TTF-C in a DMF
solution showed two-stage one-electron oxidation waves (see
Supporting Information).8 The first oxidation potential exhibited
a positive shift (0.06 V) compared with that of TTF, indicating
that the cytosine moiety worked as a weak electron-withdrawing
group.
.
Single crystals of TTF-C containing crystal water, TTF-C
H2O, were obtained as orange blocks by vapor-diffusion method
using hexane–CH2Cl2.9 Dihedral angle between TTF and cyto-
sine moieties is 31.8ꢃ. TTF-C forms complementary quadruple
H-bonds, two of which are direct N–HꢂꢂꢂN bonds (2.98 A) and
˚
ꢁ
cytosine dimer in its I3 salt, demonstrating a high potential of
TTF-C for H-bonded electron-donor molecule in a complemen-
tary triple H-bonded cationic dimer.
the other two bonds are through water molecules (Figure 1).
The H-bonded dimer was connected by intermolecular OꢂꢂꢂS
contacts and ꢀꢂꢂꢂꢀ interactions, resulting in the formation of a
two-dimensional network.8 In the IR spectrum measured by
KBr pellet, the absorption band of 1674 cmꢁ1 is attributed to
C=O stretching mode.8 The broad N–H stetching absorptions
are observed around 3080 cmꢁ1 due to N–HꢂꢂꢂN and N–HꢂꢂꢂO
H-bonds. IR data and H-bonding distances of the cytosine moie-
TTF-C was obtained as an orange powder by the Stille
cross-coupling reaction of SnBu3-substituted TTF 1 with iodo
derivative of 1-n-butylpyrimidin-2-one followed by treatment
of aqueous NH3 solution (Scheme 1).7 As an alternative method,
a transformation of TTF-U6a by two steps (mesitylenesulfonyla-
tion and substitution by ammonia) also gave an effective way to
.
ty of TTF-C H2O are similar to those reported for 1-methylcy-
tosine.8,10
A I3 salt of TTF-C was obtained as black platelets by
the diffusion method using TTF-C and I2 in 1,2-dichloroethane
solution.11 This I3 salt was composed of crystallographically
equivalent two TTF þ-C, and three I3 as determined by X-ray
structure analysis (Figure 2).8,12 Furthermore, considering the
total balance of charge, a proton with 0.5 of site occupancy
factor was disordered into two cytosine moieties. This proton
might be derived from HI which was generated from contami-
H
ꢁ
N
H
H
O
N
N
H2N
O
N
NH
+
ꢁ
N
NBu
S
S
S
S
ꢄ
ꢁ
HN
O
H
H
TTF-C
hemiprotonated cytosine dimer
Chart 1.
Copyright Ó 2007 The Chemical Society of Japan

Chemistry Letters Vol.36, No.9 (2007)
1103
features, TTF and cytosine moieties adoptedꢁthe radical cationic
state and the hemiprotonated dimer in the I3 salt, respectively.
These results open a new possibility for preparing a highly
conductive CT complex having a partial CT state of TTF moiety
in the hemiprotonated cytosine dimer motif by using an appro-
priate electron-acceptor molecule. Current studies are carried
out in this direction.
This work was partially supported by PRESTO-JST, Grant-
in-Aid for Scientific Research (No. 16350074) from the Ministry
of Education, Culture, Sports, Science and Technology, Japan,
and by grants of the Asahi Glass Foundation and CASIO Science
Promotion Foundation.
.
Figure 1. Crystal structure of TTF-C H2O. H-bonded dimer
structure through complementary quadruple H-bonds including
H2O molecules. Hydrogen atoms are omitted for clarity.
References and Notes
1
2
3
For example, see E. Katz, I. Willner, Angew. Chem., Int. Ed. 2004,
43, 6042.
a) F. S. Mathews, A. Rich, Nature 1964, 201, 179. b) G. A. Jeffrey,
Y. Kinoshita, Acta Cryst. 1963, 16, 20.
a) T. J. Kistenmacher, M. Rossi, L. G. Marzilli, Biopolymers 1978,
´
17, 2581. b) K. Gehring, J.-L. Leroy, M. Gueron, Nature 1993,
363, 561. c) D. Armentano, G. D. Munno, R. Rossi, New J. Chem.
2006, 30, 13.
4
a) G. G. Sheina, E. D. Radchenko, I. P. Blagoi, B. I. Verkin, Dokl.
Akad. Nauk SSSR 1978, 240, 463. b) T. Murata, G. Saito, Chem. Lett.
2006, 35, 1342. c) T. Murata, K. Nishimura, G. Saito, Mol. Cryst.
Liq. Cryst. 2007, 466, 101.
5
6
T. Murata, Y. Morita, K. Fukui, K. Sato, D. Shiomi, T. Takui,
M. Maesato, H. Yamochi, G. Saito, K. Nakasuji, Angew. Chem.,
Int. Ed. 2004, 43, 6343.
a) Y. Morita, S. Maki, M. Ohmoto, H. Kitagawa, T. Okubo, T.
Mitani, K. Nakasuji, Org. Lett. 2002, 4, 2185. b) E. Miyazaki, Y.
Morita, Y. Umemoto, K. Fukui, K. Nakasuji, Chem. Lett. 2005,
34, 1326. c) Y. Morita, E. Miyazaki, Y. Umemoto, K. Nakasuji,
J. Org. Chem. 2006, 71, 5631.
7
Selected physical data of TTF-C: mp 169–170 ꢃC (dec). 1H NMR
(270 MHz, DMSO-d6): ꢁ 0.88 (t, J ¼ 7:4 Hz, 3H), 1.17–1.31 (m,
2H), 1.49–1.60 (m, 2H), 3.85 (t, J ¼ 7:2 Hz, 2H), 6.68 (s, 1H),
ꢄ
Figure 2. Crystal structure of (TTF þ-C)2
(I3ꢁ)3. (a) Hem-
þ
.H .
iprotonated dimer through complementary triple H-bonds. (b)
Two-dimensional network through the IꢂꢂꢂS contacts (red color
line) and H-bonds (blue color line). Hydrogen atoms (a and b)
and the n-butyl group of the cytosine moiety (b) are omitted
for clarity.
6.73 (s, 2H), 7.85 (s, 1H). Anal. Calcd for (C14H15N3OS4)(H2O)0:5
:
C, 44.42; H, 4.26; N, 11.10%. Found: C, 44.36; H, 3.90; N, 10.98%.
Supporting Information is electronically available on the CSJ-Jour-
nal Web site, http://www.csj.jp/journals/chem-lett/index.html.
8
9
.
Crystal data for TTF-C H2O: C14H17N3O2S4, fw 387.55, monoclin-
ic, space group, P21=c (no. 14), a ¼ 11:7943ð9Þ, b ¼ 5:6155ð3Þ,
nated H2O and decomposed I2. Consequently, the molecular for-
ꢁ
ꢃ
3
˚
˚
c ¼ 26:1325ð16Þ A, ꢂ ¼ 100:683ð2Þ , V ¼ 1700:78ð19Þ A , Z ¼ 4,
ꢄ
mula of the I3 salt was determined as (TTF þ-C)2
(I3ꢁ)3,
þ
.H .
Dcalcd ¼ 1:506 g/cmꢁ3
,
ꢃ(Mo Kꢄ) = 5.70 cmꢁ1
,
T ¼ 200ð2Þ K,
confirming a formation of the hemiprotonated cytosine dimer
through complementary triple H-bonds (Figure 2a). The N–
HꢂꢂꢂO and N–HꢂꢂꢂN distances between the cytosine moieties
3902 unique reflections (Rint ¼ 0:128). The structure was refined to
R1 ¼ 0:079, wR2 ¼ 0:190 for 2305 reflections with I > 2ꢅðIÞ and
224 parameters, goodness-of-fit = 1.02. The data was deposited in
Cambridge Crystallographic Data Centre (CCDC-652831).
˚
were 2.79 and 2.83 A, respectively, which are almost the same
10 In the case of 1-methylcytosine, complementary double H-bonds
of N–HꢂꢂꢂN were formed.2a
as those of the known hemiprotonated cytosine dimers.8,13 The
IR spectrum in KBr also corroborated the formation of this dimer
structure: The absorption band attributed to C=O stretching
mode was observed in 1733 cmꢁ1. This data was similar to
that of reported hemiprotonated cytosine dimers.8,13 The radical
cationic state of TTF-C may influence the molecular structure:
The larger dihedral angle of 131ꢃ between TTF and cytosine
ꢄ
þ
.H .
11 Selected physical data of (TTF þ-C)2
(I3ꢁ)3: mp 182–183 ꢃC
(dec); Anal. Calcd for (C14H15N3OS4)2(H)(I3)3: C, 17.87; H, 1.66;
N, 4.46%. Found: C, 18.25; H, 1.63; N, 4.66%.
12 Bond lengths analyses indicate TTF moieties are oxidized to be +1.
ꢄ
þ
Crystal data for (TTF-C þ
(I3ꢁ)3: C14H15:5N3OS4I4:5, fw
) .H .
2
ꢀ
941.11, triclinic, space group, P1 (no. 2), a ¼ 7:83ð1Þ, b ¼ 8:11ð1Þ,
ꢃ
˚
c ¼ 20:42ð3Þ A, ꢄ ¼ 80:71ð4Þ, ꢂ ¼ 78:70ð4Þ, ꢆ ¼ 84:43ð5Þ , V ¼
.
1252ð2Þ A , Z ¼ 2, Dcalcd ¼ 2:496 g/cmꢁ3
,
ꢃ
(Mo Kꢄ) =
3
moieties than that of neutral TTF-C H2O indicates the effect
˚
59.41 cmꢁ1, T ¼ 200:2 K; 5305 unique reflections (Rint ¼ 0:040).
The structure was refined to R1 ¼ 0:044, wR2 ¼ 0:082 for 2145
reflections with I > 1ꢅðIÞ and 241 parameters, goodness-of-fit =
0.92. CCDC-652830.
of electrostatic repulsion between the TTF radical cation and
the cationic hemiprotonated cytosine dimer. In the crystal struc-
˚
ture, there were some IꢂꢂꢂS contacts of 3.55–3.75 A between
TTFꢄþ-C and I3ꢁ, resulting in the construction of a two-dimen-
13 In the hemiprotonated cytosine dimer of the reported com-
pounds,3c,4b N–HꢂꢂꢂO and N–HꢂꢂꢂN distances were determined to
sional network (Figure 2b).8
˚
In summary, TTF-C was newly synthesized as an electron-
donor molecule with proton-accepting ability. Reflecting such
be 2.78–2.84 A, and C=O stretching absorptions in the IR spectra
.
were observed in 1725 and 1731 cmꢁ1
Published on the web (Advance View) July 28, 2007; doi:10.1246/cl.2007.1102