Macrocycles from pentafluoropyridine and tetrafluoropyrimidine

Article abstract of DOI:10.1016/j.jfluchem.2008.01.009

Macrocycles were synthesised by sequential nucleophilic aromatic substitution processes involving pentafluoropyridine and tetrafluoropyrimidine and various diamines as the structural components.

Full text of DOI:10.1016/j.jfluchem.2008.01.009

Available online at www.sciencedirect.com
Journal of Fluorine Chemistry 129 (2008) 307–313
www.elsevier.com/locate/fluor
Macrocycles from pentafluoropyridine and tetrafluoropyrimidine
b
b
Reza Ranjbar-Karimi c, Graham Sandford a, , Dmitrii S. Yufit , Judith A.K. Howard
*
a Department of Chemistry, University of Durham, South Road, Durham DH1 3LE, UK
b Chemical Crystallography Group, Department of Chemistry, University of Durham, South Road, Durham DH1 3LE, UK
c Department of Chemistry, Vali-e-Asr University of Rafsanjan, Rafsanjan 77176, Iran
Received 27 November 2007; received in revised form 11 January 2008; accepted 17 January 2008
Available online 26 January 2008
Abstract
Macrocycles were synthesised by sequential nucleophilic aromatic substitution processes involving pentafluoropyridine and tetrafluoropyr-
imidine and various diamines as the structural components.
# 2008 Elsevier B.V. All rights reserved.
Keywords: Macrocycles; Heterocyclic; Perfluoroheterocycle; Pentafluoropyridine
1. Introduction
groups’ at the 2- and 6-positions of the pyridine unit to give the
corresponding ‘bridged compounds’ 3 and, ultimately, macro-
cycles 4. This versatile sequential methodology allows a variety
of bridging units (Nuc2–Nuc2) to be used for a range of
cryptand and crown ether syntheses and, in all preparations
carried out following Route a, the nitrogen atoms of the
pyridine ring form part of the macrocyclic ring.
The field of macrocyclic synthesis [1–3] and, more
generally, supramolecular chemistry [4] has attracted great
interest over recent years and as a result macrocyclic systems
are now used in various applications [3] as, for example, sensors
and contrast imaging agents [4]. The synthesis of many
macrocyclic derivatives relies upon nucleophilic substitution
processes at saturated sites (e.g. many crown ether and cryptand
syntheses [5]) or addition–elimination reactions involving
carbonyl systems (e.g. calixarenes [6]) in the ring closing steps.
In contrast, synthetic approaches that involve nucleophilic
aromatic substitution processes in the macrocyclic ring forming
step are far less common [7] because, in part, only a limited
number of suitably activated aromatic building blocks, such as
chlorinated triazines [8,9], tetrachloropyridine [10], chloropyr-
imidine derivatives [11] or difluorodinitrobenzene [12,13] are
available for successful macrocyclic ring closure to occur. In
this context, we have recently described [14–16] the synthesis
of novel macrocyclic systems starting from pentafluoropyridine
1 via various tetrafluoropyridine systems 2 by a strategy
outlined in Scheme 1 (Route a).
In this paper, we adapt our synthetic methodology to the
synthesis of macrocyclic systems 6 that are formed from
reaction of the 2- and 4-positions of the pyridine sub-units
(Route b, Scheme 1) via a different structural class of bridging
unit 5. This strategy will enable access to macrocycles with
different structural features such as macrocycles in which the
pyridine nitrogen atoms are not part of the macrocyclic ring
and fluorine atoms that are located at active sites that are
outside the ring cavity and may be further functionalised if
required, for example, for the attachment of a porphyrin-based
sensor unit [12]. We also extend this methodology to the
incorporation of pyrimidine units by utilising tetrafluoropyr-
imidine 7 as the starting material in macrocyclic synthesis for
the first time.
This strategy involves firstly ‘blocking’ the most reactive 4-
position of pentafluoropyridine to give tetrafluoropyridine
derivatives 2 that react with suitable difunctional ‘bridging
2. Results and discussion
Reaction of an excess of pentafluoropyridine 1 and diamines
8a and 8b gave the corresponding bis-pyridyl bridged
compounds 9a and 9b in 76% and 88% yield, respectively
after heating together at reflux temperature in THF (Scheme 2).
* Corresponding author. Tel.: +44 191 334 2039; fax: +44 191 384 4737.
E-mail address: Graham.Sandford@durham.ac.uk (G. Sandford).
0022-1139/$ – see front matter # 2008 Elsevier B.V. All rights reserved.
doi:10.1016/j.jfluchem.2008.01.009

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Scheme 1. Synthetic strategies for the construction of macrocycles from pentafluoropyridine.
Subsequent attempts to form macrocycles from 9a and 9b upon
reaction with N,N0-dimethylethylene diamine 10 were unsuc-
cessful due to competing side product formation. However, we
found that methylation of the NH groups by reaction of 9a and
9b with methyl iodide to give 11a and 11b, respectively was
necessary before cyclization to macrocycles 12a and 12b could
be effected using diamine 10 in high dilution conditions. By a
similar process tetrafluoropyrimidine 7 gave bridged compound
13 upon reaction with diamine 10 and this subsequently formed
macrocycle 14 upon reaction with a further equivalent of 10 in
high dilution conditions in acetonitrile.
In all reactions, the nucleophilic aromatic substitution
processes are regioselective, following established principles
[17,18]. For example, reaction of pentafluorinated aromatic
Scheme 2. Synthesis of macrocycles. Reagents and conditions: (i) C5F5N 1, THF, reflux, 12 h; (ii) MeI, K2CO3, MeCN, reflux, 12 h; (iii) 10, MeCN, reflux 3 d; (iv)
THF, reflux 12 h.

R. Ranjbar-Karimi et al. / Journal of Fluorine Chemistry 129 (2008) 307–313
309
systems such as pentafluoroiodobenzene occur selectively at
4. Reactions of diamines with perfluoroheteroaromatic
systems
sites para to the substituent [18], reaction of pentafluoropyr-
idine with nucleophiles occurs at the most activated 4-position
[17,18] and reaction of 4-amino tetrafluoropyridine systems
with nucleophiles was established recently [19] to occur at the
2-position.
4.1. General procedure
Diamine was added to a solution of the perfluoroheterocycle
in dry THF (70 mL) and heated to reflux temperature for 12 h
under an atmosphere of dry nitrogen. After cooling to room
temperature, dil. sodium hydrogen carbonate solution (20 mL)
was added. The organic products were extracted into
dichloromethane (2ꢁ 30 mL), dried (MgSO4) and evaporated
to give the product which was purified by recrystalisation from
ethyl acetate/n-hexane.
The structures of compounds 9b, 11a, 13 and 14 were
confirmed by X-ray crystallography (Fig. 1a–d) and by
comparison of NMR spectroscopic data. Structure 9b contains
two independent molecules with different conformations which
are quite different from the conformation of the closely related
molecule 11a, reflecting the conformational lability of these
molecules.
In previous papers [19–21] we noted the importance of
stacking interaction between aromatic rings in the crystal
packing of compounds containing fluorinated heterocycles. In
these cases, the compounds also exhibit pꢀ ꢀ ꢀp interactions
which determine not only the packing of the molecules in the
crystals but also molecular conformation. The comparison of
the molecular conformation of 13 with its Ph-analogues [22]
shows the drastic change of shape of the molecule from
extended to angular. There is a number of C–Hꢀ ꢀ ꢀN and C–
Hꢀ ꢀ ꢀp interactions in the structure of the Ph-analogue, but no
stacking interactions were observed. At the same time the
packing of the molecules in the structure 13 is determined by
interactions between planar aromatic fragments (Fig. 2).
Similar overlapping of the aromatic systems is also present
in the crystal structures of 9b, 11a and 14. The hydrogen bonds
of the N–Hꢀ ꢀ ꢀO type link molecules in zigzag chains in the
structure of 9b. The significance of pꢀ ꢀ ꢀp interactions between
aromatic systems for crystal packing and their influence on the
conformation of molecules is well known and has been a
subject of several reviews [23].
4.1.1. N,N0-Bis-(2,3,5,6-tetrafluoro-pyridin-4-yl)-4,40-
diaminodiphenyl-ether 9a
Pentafluoropyridine 1 (1.60 g, 9.3 mmol) and 4,40-diami-
nodiphenyl ether 8a (0.94 g, 4.7 mmol) gave N,N0-bis-(2,3,5,6-
tetrafluoro-pyridin-4-yl)-4,40-diaminodiphenyl
ether
9a
(1.77 g, 76%) as a white crystalline solid; mp 117–119 8C
(found: C, 52.9; H, 2.3; N, 10.9. C22H10F8N4O requires C, 53.0;
H, 2.0; N, 11.2%); dH 6.29 (2H, br s, NH), 7.07 (8H, m, aryl-H);
dC 119.5 (s, C-20), 124.7 (s, C-30), 132.4 (dm, 1JCF 253.6, C-3),
133.8 (s, C–NH), 134.9 (m, C-4), 144.4 (dm, 1JCF 241.1, C-2),
155.2 (s, C–O); dF ꢂ92. 9 (2F, m, F-2), ꢂ157.2 (2F, m, F-3); m/z
(EI+) 498 ([M]+, 38%), 257 (52), 229 (20).
4.1.2. N,N0-Bis-(2,3,5,6-tetrafluoro-pyridin-4-yl)-
diphenylmethane 4,40-diamine 9b
Pentafluoropyridine 1 (1.42 g, 8.4 mmol) and 4,40-diami-
nodiphenylmethane 8b (0.83 g, 4.2 mmol) gave N,N0-bis-
(2,3,5,6-tetrafluoro-pyridin-4-yl)-diphenylmethane 4,40-dia-
mine 9b (1.83 g, 88%); mp 89–92 8C (found: C, 55.4; H,
2.4; N, 11.1. C23H12F8N4 requires C, 55.65; H, 2.4; N, 11.3%);
dH 3.98 (2H, s, CH2), 6.45 (2H, br s, NH), 7.04–7.18 (8H, m,
aryl-H); dC 40.9 (s, CH2), 122.5 (s, C-20), 129.7 (s, C-30), 132.6
(dm, 1JCF 253.8, C-3), 134.6 (m, C-4), 136.6 (s, C–CH2), 138.5
In summary, macrocycles may be synthesised by reaction of
pentafluoropyridine and tetrafluoropyrimidine by linking
positions most reactive towards nucleophilic attack by various
diamine-bridging units. The range of macrocyclic structures
with differing architectures that may be accessed using this
SNAr ring-closing methodology is, therefore, expanded
considerably.
1
(s, C–N), 144.4 (dm, JCF 239.4, C-2); dF ꢂ93.1 (2F, m, F-2),
ꢂ156.3 (2F, m, F-3); m/z (EI+) 496 ([M]+, 88%), 330 (93), 254
(64), 164 (100).
3. Experimental
All starting materials were obtained commercially. All
solvents were dried using literature procedures. NMR spectra
were recorded in deuteriochloroform, unless otherwise stated,
on a spectrometer operating at 500 MHz (1H NMR), 376 MHz
(19F NMR) and 100 MHz (13C NMR) with tetramethylsilane
and trichlorofluoromethane as internal standards. Mass spectra
were recorded on a VG 7070E spectrometer coupled with a
Hewlett Packard 5890 series II gas chromatograph. Elemental
analyses were obtained on an Exeter Analytical CE-440
elemental analyser. Melting points and boiling points were
recorded at atmospheric pressure unless otherwise stated and
are uncorrected. The progress of reactions was monitored by
19F NMR and column chromatography was carried out on silica
gel.
4.1.3. N,N0-Dimethyl-N,N0-bis-(2,5,6-trifluoro-pyrimidin-4-
yl)-ethane-1,2-diamine 13
Tetrafluoropyrimidine 7 (1.32 g, 8.5 mmol) and N,N0-
dimethylethylene diamine 10 (0.38 g, 4.3 mmol) gave N,N0-
dimethyl-N,N0-bis-(2,5,6-trifluoro-pyrimidin-4-yl)-ethane-1,2-
diamine 13 (1.4 g, 93%); mp 100–102 8C (found: C, 40.7; H,
2.8; N, 23.6. C12H10F6N6 requires C, 40.9; H, 2.9; N, 23.9); dH
3.24 (3H, s, CH3), 3.87 (2H, m, CH2); dC 38.6 (s, CH3), 49.7 (s,
CH2), 130.7 (ddd, 1JCF 234, 2JCF 15, 4JCF 9, C-5), 154.7 (ddd,
1JCF 178, 3JCF 21, 3JCF 3, C-6), 155.6 (dt, 2JCF 19, 3JCF 5, C-4),
160.1 (ddd, 1JCF 241, 3JCF 21, 4JCF 9, C-2); dF ꢂ48.8 (1F, d, 3JFF
25, F-5), ꢂ87.7 (1F, d, 4JFF 16, F-2), ꢂ174.1 (1F, dd, 3JFF 25,
4JFF 16, F-6); m/z (EI+) 352 ([M]+, 2%), 180 (5), 178 (100), 165
(12), 131 (12), 40 (22).

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5. Methylation of diamines 9
of dry nitrogen. Methyl iodide was added to the
reaction mixture which was heated to reflux temperature
for a further 12 h. After cooling to RT, the organic
products were extracted into dichloromethane (2ꢁ
30 mL), dried (MgSO4) and the solvent evaporated.
Recrystalisation from dichloromethane/light petroleum gave
pure product 11.
5.1. General procedure
Potassium carbonate was added to a solution of
bridged compound 9 in dry acetonitrile (70 mL) and
heated to reflux temperature for 1 h under an atmosphere
Fig. 1. (a) Molecular structure of 9b, (b) molecular structure of 11a, (c) molecular structure of 13, and (d) molecular structure of 14.

R. Ranjbar-Karimi et al. / Journal of Fluorine Chemistry 129 (2008) 307–313
311
aryl-H); dC 41.3 (t, 4JCF 4.4, CH3), 119.8 (s, C-20), 121.2 (s, C-
30), 136.8 (ddd, 1JCF 256.9, 2JCF 22.7, 3JCF 4.7, C-3) 138.3 (m,
1
2
3
C-4), 142.0 (s, C–N), 144.9 (ddd, JCF 241.3, JCF 16.3, JCF
3.2, C-2), 153.7 (s, C–O); dF ꢂ92.3 (2F, m, F-2), ꢂ149.2 (2F, m,
F-3); m/z (EI+) 526 ([M]+, 100%), 497 (100), 255 (62).
5.1.2. N,N0-Dimethyl-N,N0-bis-(2,3,5,6-tetrafluoro-pyridin-
4-yl)-diphenylmethane 4,40-diamine 11b
Methyl iodide (0.84 g, 5.8 mmol) and 9b (1.45 g, 2.9 mmol)
gave
N,N0-dimethyl-N,N0-bis-(2,3,5,6-tetrafluoro-pyridin-4-
yl)-diphenylmethane 4,40-diamine 11b (1.43 g, 92%); mp
93–96 8C (found: C, 57.0; H, 2.9; N, 10.6. C25H16F8N4
requires C, 57.3; H, 3.1; N, 10.7%); dH 3.47 (6H, m, CH3), 3.93
(2H, s, CH2), 6.92 (4H, m, aryl-H), 7.12 (4H, m, aryl-H); dC
40.5 (s, CH2), 40.7 (t, 4JCF 4.1, CH3), 119.0 (s, C-20), 130.0 (s,
C-30), 137.2 (ddd, 1JCF 256, 2JCF 22, 3JCF 5.76, C-3), 136.3 (s,
C–CH2), 138.1 (m, C-4), 144.3 (s, C–N), 144.9 (ddd, 1JCF 243,
2JCF 16.6, 3JCF 3.1, C-2); dF ꢂ93.2 (2F, m, F-2), ꢂ148.1 (2F, m,
F-3); m/z (EI+) 524 ([M]+, 100%), 345 (70), 269 (62), 164 (60).
6. Synthesis of macrocycles
6.1. General procedure
Fig. 1. (Continued).
Sodium hydrogen carbonate was added to a solution of
bridged compounds 11 or 13 and diamine in dry acetonitrile
(200 mL) under an atmosphere of dry nitrogen. The reaction
mixture was heated to reflux temperature for 72 h. After
cooling, solvent was evaporated, the organic products were
extracted into dichloromethane (3ꢁ 30 mL), dried (MgSO4)
and the solvent evaporated. The crude product was purified by
column chromatography using ethyl acetate/n-hexane (1:3) and
recrystalisation.
5.1.1. N,N0-Dimethyl-N,N0-bis-(2,3,5,6-tetrafluoro-pyridin-
4-yl)-4,40-diaminodiphenyl ether 11a
Methyl iodide (0.84 g, 5.8 mmol) and 9a (1.47 g, 2.9 mmol)
gave
N,N0-dimethyl-N,N0-bis-(2,3,5,6-tetrafluoro-pyridin-4-
yl)-4,40-diaminodiphenyl ether 11a (1.38 g, 89%); mp 87–
89 8C (found: C, 54.6; H, 2.4; N, 10.5. C24H14F8N4O requires
C, 54.8; H, 2.7; N, 10.6%); dH 3.50 (6H, m, CH3), 6.98 (8H, m,
Fig. 2. Packing in a crystal of 13.

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6.2. Macrocycle 12a
Crystal data for 9b: 2(C23H12F8N4)ꢀCH2Cl2, M = 1077.66,
monoclinic, space group P21/c, a = 25.9093(7), b = 7.4516(2),
3
˚
˚
Sodium hydrogen carbonate (0.35 g, 5 mmol), 11a (1.31 g,
2.5 mmol) and N,N0-dimethylethylene diamine 10 (0.22 g,
2.5 mmol) gave macrocycle 12a (0.43 g, 30%) as a white solid;
mp 161–163 8C (found: C, 58.4; H, 4.2; N, 14.5%.
C28H24F6N6O requires C, 58.5; H, 4.2; N 14.6%); dH 3.29
(6H, s, CH3), 3.40 (4H, s, CH2), 3.45 (6H, s, CH3), 6.82–6.92
(8H, m, aryl-H); dF ꢂ93.0 (1F, m, F-2), ꢂ141.0 (1F, m, F-5),
ꢂ158.6 (1F, m, F-3); m/z (EI+) 574 ([M]+, 10%), 489 (37), 349
(100), 226 (21).
c = 26.3977(7) A, ( = 116.29(1)8, U = 4569.3(2) A , F(0 0 0)
= 2168, Z = 4, Dc = 1.567 mg mꢂ3, ( = 0.253 mmꢂ1. 50402
reflections collected; 12727 unique data (Rmerg = 0.046). Final
wR2(F2) = 0.1395 for all data (758 refined parameters),
conventional R(F) = 0.0469 for 10,075 reflections with
I ꢃ 2(, GOF = 1.032.
Crystal data for 11a: C24H14F8N4O, M = 526.39, mono-
clinic, space group P21/c, a = 14.5346(4), b = 7.8419(2),
3
˚
˚
c = 19.3663(6) A, ( = 102.15(1)8, U = 2157.9(1) A , F(0 0 0)
= 1064, Z = 4, Dc = 1.620 mg mꢂ3, ( = 0.150 mmꢂ1, 27,215
reflections collected; 5998 unique data (Rmerg = 0.095). Final
wR2(F2) = 0.1355 for all data (390 refined parameters),
conventional R(F) = 0.0394 for 5007 reflections with I ꢃ 2(,
GOF = 1.076.
6.3. Macrocycle 12b
Sodium hydrogen carbonate (0.35 g, 5 mmol), 11b (1.31 g,
2.5 mmol) and N,N0-dimethylethylene diamine 10 (0.22 g,
2.5 mmol) gave macrocycle 12b (0.48 g, 34%) as a white solid;
mp 152–154 8C (found: C, 60.7; H, 4.5; N, 14.6. C29H26F6N6
requires C, 60.9; H, 4.6; N 14.7%); dH 3.06 (6H, s, CH3), 3.31
(6H, s, CH3), 3.51 (4H, s, CH2), 3.87 (2H, s, CH2), 6.77 (4H, m,
aryl-H), 7.02 (4H, m, aryl-H); dF ꢂ94.1 (1F, m, F-2), ꢂ141.5
(1F, m, F-5), ꢂ161.4 (1F, m, F-3); m/z (EI+) 572 ([M]+, 5%),
331 (17), 330 (100).
Crystal data for 13: C12H10F6N6, M = 352.26, monoclinic,
group
space
C2/c,
a = 11.4620(3),
b = 12.2442(4),
3
˚
˚
c = 9.9728(3) A, ( = 90.45(1)8, U = 1399.69(7) A , F(0 0 0)
= 712, Z = 4, Dc = 1.672 mg mꢂ3, ( = 0.163 mmꢂ1, 8624
reflections collected; 1871 unique data (Rmerg = 0.067). Final
wR2(F2) = 0.1350 for all data (133 refined parameters),
conventional R(F) = 0.0429 for 1514 reflections with I ꢃ 2(,
GOF = 1.079. Molecule is located on the twofold axis.
Crystal data for 14: C16H20F4N8, M = 400.40, monoclinic,
space
group
P21/c,
a = 8.7586(2),
b = 11.4815(3),
3
6.4. Macrocycle 14
˚
˚
c = 8.4589(2) A, ( = 93.07(1)8, U = 849.42(4) A , F(0 0 0) =
416, Z = 2, Dc = 1.565 mg mꢂ3
, , 10,668
( = 0.132 mmꢂ1
Sodium hydrogen carbonate (0.35 g, 5 mmol), 13 (0.6 g,
1.7 mmol) and N,N0-dimethylethylene diamine 10 (0.14 g,
1.7 mmol) gave macrocycle 14 (0.35 g, 54%); mp 134–136 8C
(found: C, 47.9; H, 5.0; N, 27. 9%. C16H20F4N8 requires C,
48.0; H, 5.0; N 28.0%); dH 3.09 (6H, s, CH3), 3.12 (4H, m,
reflections collected; 2360 unique data (Rmerg = 0.044). Final
wR2(F2) = 0.1366 for all data (167 refined parameters),
conventional R(F) = 0.0381 for 2133 reflections with I ꢃ 2(,
GOF = 1.185.
1
CH2); dC 38.6 (s, CH3), 49.7 (s, CH2), 130.8 (dd, JCF 236.6,
4JCF 4.5, C-5), 153.84 (m, C-4), 155.2 (dd, 1JCF 204.3, 4JCF 4.1,
C-2); dF ꢂ51.3 (2F, d, 5JFF 11.8, F-2), ꢂ89.65 (2F, d, 5JFF 11.8,
F-5); m/z (EI+) 400 ([M]+, 20%), 226 (30), 200 (75), 186 (100).
Acknowledgement
We thank the Iranian Government for a travel grant (to RK).
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