Energy Harvesting in a Bodipy-Functionalized Rotaxane

Article abstract of DOI:10.1021/acs.joc.8b01928

A rotaxane composed of two separate Bodipy-functionalized units can be synthesized with a high yield. The resulting structure shows a very efficient through-space energy transfer (FRET), acting as an energy funnel. Thus, maximum solar output in the visibl

Full text of DOI:10.1021/acs.joc.8b01928

Subscriber access provided by UNIV OF NEWCASTLE
Article
Energy Harvesting in a Bodipy-Functionalized Rotaxane
Nisa YESILGUL, Ozlem Seven, Ruslan Guliyev, and Engin Umut Akkaya
J. Org. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.joc.8b01928 • Publication Date (Web): 03 Oct 2018
Downloaded from http://pubs.acs.org on October 3, 2018
Just Accepted
“Just Accepted” manuscripts have been peer-reviewed and accepted for publication. They are posted
online prior to technical editing, formatting for publication and author proofing. The American Chemical
Society provides “Just Accepted” as a service to the research community to expedite the dissemination
of scientific material as soon as possible after acceptance. “Just Accepted” manuscripts appear in
full in PDF format accompanied by an HTML abstract. “Just Accepted” manuscripts have been fully
peer reviewed, but should not be considered the official version of record. They are citable by the
Digital Object Identifier (DOI®). “Just Accepted” is an optional service offered to authors. Therefore,
the “Just Accepted” Web site may not include all articles that will be published in the journal. After
a manuscript is technically edited and formatted, it will be removed from the “Just Accepted” Web
site and published as an ASAP article. Note that technical editing may introduce minor changes
to the manuscript text and/or graphics which could affect content, and all legal disclaimers and
ethical guidelines that apply to the journal pertain. ACS cannot be held responsible for errors or
consequences arising from the use of information contained in these “Just Accepted” manuscripts.
is published by the American Chemical Society. 1155 Sixteenth Street N.W.,
Washington, DC 20036
Published by American Chemical Society. Copyright © American Chemical Society.
However, no copyright claim is made to original U.S. Government works, or works
produced by employees of any Commonwealth realm Crown government in the course
of their duties.

Page 1 of 15
The Journal of Organic Chemistry
1
2
3
4
5
Energy Harvesting in a Bodipy-Functionalized Rotaxane
6
7
8
9
Nisa Yesilgul,§ Ozlem Seven,¶ Ruslan Guliyev¶ and Engin U. Akkaya§,¶,*
§Department of Chemistry, Bilkent University, 06800 Ankara, Turkey.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
¶UNAM-National Nanotechnology Research Center, Bilkent University, 06800 Ankara, Turkey.
ABSTRACT: A rotaxane composed of two separate Bodipy-functionalized units, can be synthesized
with high yield. The resulting structure shows a very efficient through-space energy transfer (FRET),
acting as an energy funnel. Thus, maximum solar output in the visible region can be collected and
converted into red light, which can be transformed efficiently with a fine tuned photovoltaic device.
The versatility of the synthetic pathway demonstrates the potential utility of rotaxane-based energy
harvesting supramolecules assemblies.
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 2 of 15
1
2
3
4
5
6
7
8
9
INTRODUCTION
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Organic solar concentrators continue to attract attention.1 Dendritic energy funnels with two or
more distinct chromophores is an established approach2 for obtaining a molecular solar concentrator
producing a monochromic emission, which could then be coupled to high-end photovoltaic device for
enhanced efficiency. A promising alternative is to make use of mechanical interlocking3, thus quickly
assembling multiple chromophores in close proximity for through space energy transfer.4
Bodipy dyes on the other hand, proved themselves to be very attractive chromophores in very
diverse fields of applications5 due to their high photostability and chemical stability coupled with
large extinction coefficients in the visible region and impressive quantum yields. Not surprizingly,
they attracted attention in various solar cell designs, as well.6 Bodipy dyes are also very amenable to
modification,7 yielding dyes with absorbance peaks covering essentially the entire visible spectrum,
and even near IR. Our goal in this work, was to assemble a [2]rotaxane making use of dibenzo-fused
[24]-crown-8, and dibenzyl ammonium modules. The affinity of this crown unit and the dibenzyl
ammonium cation is well established in the literature.8
RESULTS AND DISCUSSION
Our synthesis of the energy funnel-rotaxane starts with tosylation of the commercially available
oligoethyleneglycol 1, followed by the closure of the crown ring, yielding formyl substituted dibenzo
fused 24-crown-8 (3, Scheme 1). Then, meso substituted Bodipy (4) was synthesized by a well
established protocol in Bodipy synthesis.9 Next step is the transformation of the green emitting light
into a red emitting dye (5) by a reaction with p-methoxybenzaldehyde under conditions optimized in
our laboratory.10 The synthesis of the axle component of the rotaxane starts with p-
ACS Paragon Plus Environment

Page 3 of 15
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
9
hydroxybenzaldehyde (6); which can easily be reacted with propargyl bromide. Reductive amination
using compound 8 in methanol yields dibenzylamine derivative 9 in high yield. Protonation is
followed by ion exchange with NH4PF6 which yields organic soluble ammonium salt 10. Green
emitting absorbing Bodipy modules were synthesized starting from previously reported10b
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
o
compound 11, its reaction with sodium azide in DMSO at 100 C yields Bodipy compound 12. The
final assembly reaction of the rotaxane makes use of the affinity of dibenzylammonium cation for
dibenzo-fused [24]-crown-8, which is followed by the click attachment of the chromophore/stoppers
yielding the target supramolecular assembly 13 (Scheme 1 and Figure 1).
Scheme 1. Synthesis of the rotaxane-based energy funnel 13.
In order to assess energy transfer characteristics of the rotaxane, we acquired absorption spectra
of the rotaxane and the related modules separately, and as a mixture.
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 4 of 15
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Figure 1. Structure of the target [2]-rotaxane 13 and the direction of energy transfer and conversion.
In the absorbance spectrum, the changes are relatively minor (Figure 2). More revealing is the
emission spectra of the [2]-rotaxane 13, and the modules 5 and 12 separately and as a mixture, Figure
3. Green emission module is highly fluorescent either alone (12), or in the mixture. However, in the
mixture, excitation at 500 nm yields no detectable emission at 675 nm. The energy funneling rotaxane
however, at the same concentrations, yields a very minor peak around 530 nm while most of the
emission is centered around 675 nm when excited at 500 nm. This is a very clear evidence for energy
transfer in rotaxane 13. An excitation spectrum was also acquired Figure 4. As expected it shows two
peaks when the emission is collected at 673 nm. Energy transfer efficiencies are often reported with
large over estimations11 based on the decrease in the quantum yield of the donor chromophore. Thus,
change in the quantum yields of the donor suggest an efficiency of 97 %, but a more reliable estimate
ACS Paragon Plus Environment

Page 5 of 15
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
of energy transfer as a function of wavelength can be obtained by normalizing absorption spectrum
and excitation spectrum of the energy transfer cassette, at the peak of the acceptor absorption.12 This
yields an approximate energy transfer of 40-50 % between 475 and 550 nm.
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Figure 2. The absorption spectra of [2]rotaxane 13 (1.0x10-6 M), compound 5 (1.0x10-6 M), compound 12
(2.0x10-6 M), and mixture M (a mixture of 5 and 12 in a molar ratio of 1:2) in chloroform.
Figure 3. The emission spectra of [2]rotaxane 13 (1.0x10-6 M), compound 5 (1.0x10-6 M), compound 12
(2.0x10-6 M), and mixture M (a mixture of 5 and 12 in a molar ratio of 1:2) in chloroform. The excitation
wavelength of the fluorescent spectra is 500 nm.
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 6 of 15
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Figure 4. Percent energy transfer efficiency of 13 (solid line) as a function of wavelength of excitation.
Excitation spectrum of 13 (dotted line) and absorption spectrum of 13 (dash-dotted line), normalized at 660
nm. (Emission data were collected at 673 nm).
Modular synthesis of energy funneling supramolecular systems is likely to find practical
applications in organic solar concentrators. In this work, we presented a concise approach for the
assembly of a trichromophoric system however the idea presented here is fully transferable to more
elaborate multi chromophoric assembly, with higher conversion efficiencies. Our work towards that
goal is in progress.
EXPERIMENTAL SECTION
General Procedures. 1H NMR and 13C NMR spectra were recorded on Bruker DPX-400 (operating
1
at 400 MHz for H NMR and 100 MHz for 13C NMR) in CDCl3 with tetramethylsilane as internal
o
standard. All spectra were recorded at 25 C and coupling constants (J values) were given in Hz.
Chemical shifts were given in parts per million (ppm). Splitting patterns are designated as s (singlet),
13
d (doublet), t (triplet), q (quartet), m (multiplet), and p (pentet). All the C spectra were recorded
with simultaneous decoupling of proton nuclei. Melting points were determined with Electrochemical
9100. Mass spectra were recorded on Agilent Technologies 6530 Accurate-Mass Q-TOF LC/MS.
Absorption spectra were performed by using a Varian Cary-100 spectrophotometer. Fluorescence
ACS Paragon Plus Environment

Page 7 of 15
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
9
measurements were conducted on a Varian Eclipse spectrofluometer. Reactions were monitored by
thin layer chromatography using Merck TLC Silica gel 60 F254. Silica gel column chromatography was
performed over Merck Silica gel 60 (particle size: 0.040-0.063 mm, 230-400 mesh ASTM). All other
reagents and solvents were purchased from Aldrich and used without further purification.
Compounds 113 and 88b were synthesized according to literature.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Synthesis of Compound 2. Compound 1 (5.6 g, 15 mmol), triethylamine (8.7 mL, 62 mmol) and 4-
o
dimethylamino pyridine (10 mg, 0.15 mmol) were mixed in DCM (60 mL) at 0 C in ice bath. 4-
toluenesulfonyl chloride (7.2 g, 38 mmol) dissolved in DCM (150 mL) was added dropwise to the
reaction mixture with vigorously stirring. After keeping at 0 oC for 1 h, the ice bath was removed. The
reaction mixture was stirred at room temperature overnight. The reaction mixture was washed with
0.1 M HCl (twice) and saturated NaCl solutions (twice). The organic layer was dried over Na2SO4 and
concentrated by evaporation. The crude product was purified by column chromatography (Silica gel,
1
EtOAc/Hexane: 1/6 (v/v)). Compound 2 was obtained as colorless oil (6.68 g, 65%) . H NMR (400
MHz, CDCl3): δ; 7.81 (d, J= 8.0 Hz, 4H), 7.34 (d, J=8.0 Hz, 4H), 6.93 (s, 4H), 4.18-4.14 (q, J=4.0 Hz, 8H),
3.84 (t, J= 4.0 Hz, 4H), 3.72-3.68 (m, 8H), 3.64-3.61 (m, 4H), 2.45 (s, 6H). 13C NMR (100 MHz, CDCl3) δ;
149.0, 144.8, 133.1, 129.8, 128.0, 121.7, 115.0, 70.8, 70.8, 69.8, 69.3, 68. 9, 68.7, 21.6 ppm. HRMS (ESI-
TOF) m/z: [M + Na]+ Calcd for C32H42O12S2Na 705.2010 ; Found 705.1977.
Synthesis of Compound 3. Under argon atmosphere, 3,4-dihydroxybenzaldehyde (1.38 g, 10
mmol), K2CO3 (16.3 g, 50 mmol) were mixed in THF (300 mL). The mixture was heated under reflux
for 1 h, then compound 2 (6.83 g, 10 mmol) in THF (100 mL) was added. The reaction mixture was
heated under reflux for 24 h. After cooling to room temperature the solvent was removed by
evaporation. The residue was dissolved in DCM (200 mL) and washed with 1 M HCl and saturated
NaCl aqueous solutions. The organic layer was dried over Na2SO4 and concentrated by evaporation.
The crude product was purified by column chromatography (Silica gel, EtOAC/MeOH: 10/1).
o
Compound 3 was obtained as off-white solid (2.88 g, 60%). mp 95.0-97.0 C. 1H NMR (400 MHz,
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 8 of 15
1
2
3
4
5
6
7
8
9
CDCl3): δ; 9.77 (s, 1H), 7.40-7.33 (m, 2H), 6.92 -6.82 (m, 5H), 4.19-4.11 (m, 8H), 3.92-3.78 (m, 16H).
13C NMR (100 MHz, CDCl3) δ; 190.8, 154.3, 149.2, 148.9, 148.9, 130.2, 126.7, 121.4, 121.4, 114.1, 112.0,
111.2, 71.5, 71.4, 71.3, 69.9, 69.7, 69.5, 69.4, 69.4, 69.3 ppm. HRMS (ESI-TOF) m/z: [M + Na]+ Calcd
for C25H32O9Na 499.1939; Found 499.1922.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Synthesis of Dibenzocrown-substituted Bodipy 4. CH2Cl2 (300 mL) was purged with Argon for 30
min. Compound 3 (500 mg, 1.04 mmol) and 3-ethyl-2,4-dimethyl pyrrole (0.33 mL, 2.41 mmol) were
added. The color of the solution turned into red after the addition of 2 drops of trifluoroacetic acid.
The reaction mixture was stirred at room temperature overnight. Then, p-chloranil (283mg, 1.15
mmol) was added and the reaction mixture was stirred at room temperature for 2 h. Then triethyl
amine (1.3 mL) and boron trifluoride diethyl etherate (1.3 mL) were added sequentially. After stirring
at room temperature for 30 min, the reaction mixture was extracted with water. Organic layer was
dried over Na2SO4 and concentrated by evaporation. The crude product was purified by column
chromatography (Silica gel, EtOAC/Hexane: 2/1 (v/v)). Compound 4 was obtained as red vax (0.33 g,
44%). 1H NMR (400 MHz, CDCl3): δ; 6.98-6.90 (m, 5H), 6.82 (d, J=8.0 Hz, 2H), 4.24-4.17 (m, 6H), 4.15-
4.11 (m, 2H), 3.87- 4.02 (m, 16H), 2.54 (s, 6H), 2.32 (q, J= 8.0 Hz, 4H), 1.38 (s, 6H), 1.00 (t, J= 8.0 Hz,
6H). 13C NMR (100 MHz, CDCl3) δ: 153.6, 149.6, 149.3, 149.0, 139.9, 138.4, 132.7, 131.0, 128.5, 121.5,
121.4, 114.2, 114.1, 113.9, 71.5, 71.4, 71.3, 69.98, 69.91, 69.87, 69.6, 69.5, 69.4, 69.3, 17.1, 14.6, 12.5,
11.8 ppm. HRMS (ESI-TOF) m/z: [M + Na]+ Calcd for C41H53BF2N2O8Na 772.3792; Found 772.3793.
Extended-conjugation chromophore 5. Compound 4 (259 mg, 0.345 mmol) and 4-methoxy
benzaldehyde (105 µL, 0.862 mmol) were dissolved in benzene (40 mL). Piperidine (0.32 mL) and
acetic acid (0.32 mL) were added to the reaction mixture. The reaction mixture was refluxed using
Dean Stark apparatus until all aldehyde was consumed. After the reaction was completed, it was
extracted with DCM and water. Organic layer was dried over Na2SO4 and concentrated by evaporation.
The crude product was purified by silica gel column chromatography (first DCM/ MeOH: 95/5 then
EtOAC/Hexane: 2/1 (v/v)). Compound 5 was obtained as green solid (0.18 g, 54%). mp 212.2-214.1
ACS Paragon Plus Environment

Page 9 of 15
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
9
1
oC (decomp). H NMR (400 MHz, CDCl3): δ; 7.68 (d, J=16.8 Hz, 2H), 7.59 (d, J= 7.6 Hz, 4 H), 7.23 (d, J=
16.0 Hz, 2H), 7.01-7.91 (m, 9 H), 6.85 (d, J=10.0 Hz, 2 H), 4.29-4.12 (m, 10H), 4.01-3.91 (m, 14H), 3.88
(s, 6H), 4.02 (q, J=8.0 Hz, 4H), 1.43 (s, 6H), 1.18 (t, J= 8.0 Hz, 6H). 13C NMR (100 MHz, CDCl3) δ: 160.2,
150.4, 149.6, 149.4, 138.8, 137.7, 135.3, 133.5, 130.4, 128.8, 121.5,121.5, 118.2, 114.2, 71.5, 71.4, 71.3,
71.3, 70.0, 69.9, 69.9, 69.6, 69.5, 69.4, 69.4, 55.4, 29.7, 18.4, 14.0, 11.6 ppm. HRMS (ESI-TOF) m/z: [M
+ K]+ Calcd for C57H65BF2N2O10K 1024.4368; Found 1024.4389.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Synthesis of 4-propargyloxybenzaldehyde 7. To a solution of K2CO3 (1.50 g, 7.3 mmol) in
acetonitrile (100 ml), 4-hydroxybenzaldehyde (0.1 g, 0.82 mmol) and propargyl bromide (0.11 g, 0.90
mmol) was added and the mixture was refluxed for 2 d under argon atmosphere, then, the reaction
mixture was cooled and concentrated under reduced pressure. The residue was dissolved in CH2Cl2
(100 ml) and filtrated, then, washed with water (100 mL) three times. The organic phase was dried
with Na2SO4 and concentrated under reduced pressure. The crude product was purified by column
o
1
chromatography (eluent: CHCl3) to afford white solid (0.98 g, 74%). mp 82.0-84.0 C. H NMR (400
MHz, CDCl3) δ; 9.90 (s, 1H), 7.85 (d, J = 8.5 Hz, 2H), 7.09 (d, J = 8.5 Hz, 2H), 4.78 (s, 2H), 2.59 (s, 1H).
13C NMR (100 MHz, CDCl3) δ; 190.6, 162.4, 132.3, 130.59, 115.16, 77.58, 76.40, 56.11. HRMS (ESI-TOF)
m/z: [M + H]+ Calcd for C10H9O2 161.0597; Found 161.0569.
Synthesis of the Dibenzylamine-compound 9. Compound 7 (0.43 g, 2.67 mmol) and compound 8
(0.43 g, 2.67 mmol) were mixed in methanol (20 mL) and refluxed for 24 h, then, the reaction mixture
was cooled to 0oC and NaBH4 (1.0 g, 26.4 mmol) was added portion wise. The reaction mixture was
stirred at room temperature for 24 h. Water was added to the reaction and the mixture was
concentrated under vacuum pressure. The residue was dissolved in CH2Cl2 (100 mL) and was washed
with water (100 mL) three times. The organic phase was dried with Na2SO4 and concentrated under
reduced pressure. The crude product was purified by column chromatography (eluent: 100:1
DCM/MeOH ) to afford yellow oil (0.50 g, 61%). 1H NMR (400 MHz, CDCl3) δ; 7.30 (d, J = 8.4 Hz, 4H),
6.97 (d, J = 8.5 Hz, 4H), 4.69 (d, J = 2.3 Hz, 4H), 3.76 (s, 4H), 2.56 (t, J = 2.3 Hz, 2H). 13C NMR (100 MHz,
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 10 of 15
1
2
3
4
CDCl3) δ; 156.7, 133.4, 129.4, 114.9, 78.8, 75.65, 55.9, 52.4. HRMS (ESI-TOF) m/z: [M + H]+ Calcd for
5
6
C20H20NO2 306.1489; Found 306.1517.
7
8
9
Synthesis of Compound 10. Compound 9 (0.50 g, 1.61 mmol) was dissolved in methanol (15 mL)
and concentrated HCl was added to adjust pH lower than 2, then, the solvent was removed in vacuo.
The reaction residue was dissolved in acetone (15 mL) and a saturated solution of NH4PF6 was added
drop wise until the reaction mixture became clear. The solvent was removed under reduced pressure
and water was added to the residue. The resulting mixture was filtered and washed with water
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
o
1
several times and dried to give white solid (0.68 g, 94%). mp 238.0-240.0 C. H NMR (400 MHz,
MeOD) δ; 7.44 (d, J = 8.7 Hz, 4H), 7.07 (d, J = 8.8 Hz, 4H), 4.77 (d, J = 2.4 Hz, 4H), 4.18 (s, 4H), 2.95 (t, J
13
= 2.4 Hz, 2H). C NMR (100 MHz, MeOD) δ; 158.6, 131.2, 123.7, 115.2, 78.1, 75.7, 55.3, 50.0. HRMS
(ESI-TOF) m/z: [M–PF6]+ Calcd for C20H20NO2 306.1494; Found 306.1510.
Synthesis of Compound 12. Compound 11 (0.40 g, 0.72 mmol) and NaN3 (0.12 g, 1.79 mmol) were
dissolved in DMSO (20 mL) and the reaction mixture was heated to 100 oC for 2 h. The reaction was
controlled by TLC. When the reaction was complete, it was cooled to room temperature and CHCl3
(100 mL) was added and washed with water (100 mL) six times. The organic layer was dried with
Na2SO4 and concentrated under reduced pressure. The crude product was used without further
o
1
purification. Dark red solid (0.35 g, 97%) was afforded. mp 102.0-103.0 C (decomp). H NMR (400
MHz, CDCl3) δ; 7.17 (d, J = 8.4 Hz, 2H), 7.01 (d, J = 8.4 Hz, 2H), 4.04 (t, J = 6.4 Hz, 2H), 3.32 (t, J = 6.8 Hz,
2H), 2.55 (s, 6H), 2.32 (q, J = 7.5 Hz, 4H), 1.94 – 1.80 (m, 2H), 1.71-1.64 (m, 2H), 1.61 – 1.49 (m, 4H),
13
1.36 (s, 6H), 1.00 (t, J = 7.5 Hz, 6H). C NMR (100 MHz, CDCl3) δ; 159.5, 153.5, 140.4, 138.4, 132.6,
131.2, 129.4, 127.8, 115.0, 67.9, 51.4, 29.1, 28.8, 26.6, 25.7, 17.1, 14.6, 12.5, 11.8. HRMS (ESI-TOF)
m/z: [M+Na]+ Calcd for C29H38BF2N5ONa 543.3066; Found 543.3039.
Synthesis of Rotaxane 13. A solution of compound 5 (326 mg, 0.33 mmol) and compound 10 (100
mg, 0.22 mmol) was dissolved in degassed DCM (15 mL) and stirred at room temperature for 4 hours.
ACS Paragon Plus Environment

Page 11 of 15
The Journal of Organic Chemistry
1
2
3
4
5
6
7
8
9
Then, compound 12 (252 mg, 0.48 mmol) in 5 mL of DCM and Cu(CH3CN)4PF6 (74 mg, 0.20 mmol)
and 2,6-lutidine (5 μL, 0.107 mmol) were added. The resulting mixture was stirred at room
temperature for 1 day. After 1 day, DCM (25 mL) was added to reaction mixture and it was washed
with water (30 mL). The organic layer was dried with Na2SO4 and concentrated under reduced
pressure. The crude product was purified with column chromatography over silica gel (9:1
DCM/MeOH). Compound 13 was afforded as dark purple solid (175 mg, 32%) was afforded. mp
204.0-206.0 oC (decomp). 1H NMR (400 MHz, CDCl3): δH 7,83 (s, 2H), 7.66 (d, J=16.8 Hz, 2H), 7.58 (d,
J=8.8 Hz, 4H), 7.38 (, J=1.2 Hz, 4H), 7.25 (d, J= 8. 0 Hz, 2H), 7.15 (d, J=8.4 Hz, 4H), 7.05 (d, J=8.0 Hz, 2H),
7 (s, 2H), 6.97 (d, J= 4.8 Hz, 4H), 6.94 (d, J= 4.8 Hz, 4H), 6.90 (d, J=8.0 Hz, 4H), 6.82 (s, 1H), 6.78-6.73
(m, 2H), 5.19(s, 4H) 4.50 (m, 2H), 4.41 (t, J= 7.2 Hz), 4.31-4.26 (m, 2H), 4.19-4.16 (m, 2H), 4.11-4.10
(m 2H), 4.05-4.04 (m, 2H), 4.01 (t, J= 6.4 Hz, 4H), 3.95-3.93 (m, 2H), 3.90-3.88 (m, 2H), 3.87 (s, 6H, Ar-
OCH3), 3.73-3.69 (m, 2H), 3.67-364 (m, 2H), 3.52 -3.42 (m, 6H), 3.37-3.34 (m,2H), 2.54 (s, 12H), 2.31
(q, J1= 7.2 Hz, J2=7.6 Hz, 10 H), 2.04-1.95 (m, 6H), 1.88-1.80 (m, 6H), 1.47-1.44 (m, 4H), 1.35 (s, 12H),
1.25 (s, 6H), 1.13 (t, J=7.2 Hz, 6H), 1.00 (t, J=7.2 Hz, 12H). 13C NMR (100 MHz, CDCl3) δ; 160.3, 159.5,
159.0, 153.4, 150.6, 148.5, 148.4, 147.2, 143.2, 140.4, 138.5, 138.3, 135.6, 133.7, 132.6, 130.7, 130.2,
129.4, 128.8, 128.3, 127.7, 123.9, 123.5, 121.9, 118.0, 115.1, 114.9, 114.3, 70.7, 67.8, 61.6, 55.4, 52.01,
50.3, 30.2, 29.7, 29.7, 29.1, 26.3, 25.6, 22.7, 18.4, 17.1, 14.6, 14.0, 12.49, 12.46, 12.44, 11.9, 11.4. HRMS
(ESI-TOF) m/z: [M–PF6]+ Calcd for C135H161B3F6N13O14 2333.2651; Found 2333.2310.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
ASSOCIATED CONTENT
Supporting Information
The Supporting Information is available free of charge on the ACS Publications website at DOI:
Spectral data, copies of 1H, and 13C spectra for new compounds (PDF).
AUTHOR INFORMATION
*Corresponding Author
*E-mail: eua@fen.bilkent.edu.tr
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 12 of 15
1
2
3
4
Notes
5
6
7
8
The authors declare no competing financial interest.
ORCID
9
Engin U. Akkaya: 0000-0003-4720-7554
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
ACKNOWLEDGMENT
We gratefully acknowledge support from Bilkent University.
REFERENCES
(1) Chemisana, D. Building Integrated Concentrating Photovoltaics. Renew. Sustain. Energy Rev. 2011,
15, 603-611.
(2) Mirloup, A.; Retailleau, P.; Ziessel, R. Luminescent molecular solar concentrators made of multi-
Bodipy dyes. Tetrahedron Lett. 2013, 54, 4456-4462.
(3) (a) Saha, S.; Stoddart, J. F. Photo-driven molecular devices. Chem. Soc. Rev. 2007, 36, 77-92. (b)
Crowley, J. D.; Leigh, D. A.; Lusby, P. J.; McBurney, R. T.; Perret-Aebi, L.-E.; Petzold, C.; Slawin, A. M. Z.;
Symes, M. D. A. A Switchable Palladium-Complexed Molecular Shuttle and Its Metastable Positional
Isomers. J. Am. Chem. Soc. 2007, 129, 15085-15090. (c) Harada, A.; Hashidzume, A.; Yamaguchi, H.;
Takashima, Y. Polymeric Rotaxanes. Chem. Rev. 2009, 109, 5974-6073. (d) Zhang, Z.-J.; Zhang, Y.-M.;
Liu, Y. Controlled Molecular Self-Assembly Behaviors between Cucurbituril and Bispyridinium
Derivatives. J. Org. Chem. 2011, 76, 4682-4685. (e) Kobr, L.; Zhao, K.; Shen, Y.; Comotti, A.; Bracco, S.;
Shoemaker, R. K.; Sozzani, P.; Clark, N. A.; Price, J. C.; Rogers, C. T.; Michl, J. Inclusion Compound Based
Approach to Arrays of Artificial Dipolar Molecular Rotors. A Surface Inclusion. J. Am. Chem. Soc. 2012,
134, 10122-10131. (f) Gallina, M. E.; Baytekin, B.; Schalley, C.; Ceroni, P. Light-harvesting in
multichromophoric rotaxanes. Chem. – A Eur. J. 2012, 18, 1528-1535. (g) Arumugaperumal, R.;
–
Srinivasadesikan, V.; Raju, M. V. R.; Lin, M.-C.; Shukla,T.; Singh, R.; Lin, H.-C. Acid/Base and H2PO4
ACS Paragon Plus Environment

Page 13 of 15
The Journal of Organic Chemistry
1
2
3
4
5
6
Controllable High-Contrast Optical Molecular Switches with a Novel BODIPY Functionalized
[2]Rotaxane. ACS Appl. Mater. Interfaces, 2015, 7, 26491-26503.
7
8
9
(4) (a) Devadoss, C.; Bharathi, P.; Moore, J. S. Energy Transfer in Dendritic Macromolecules:ꢀ Molecular
Size Effects and the Role of an Energy Gradient. J. Am. Chem. Soc. 1996, 118, 9635-9644. (b) Hiratani,
K.; Kaneyama, M.; Nagawa, Y.; Koyama, E.; Kanesato, M. Synthesis of [1]Rotaxane via Covalent Bond
Formation and Its Unique Fluorescent Response by Energy Transfer in the Presence of Lithium Ion.
J. Am. Chem. Soc. 2004, 126, 13568-13569. (c) Onagi, H.; Rebek, J. Fluorescence resonance energy
transfer across a mechanical bond of a rotaxane. Chem. Commun. 2005, 4604-4606.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
(5) (a) Ziessel, R.; Ulrich, G.; Haefele, A.; Harriman, A. An Artificial Light-Harvesting Array Constructed
from Multiple Bodipy Dyes. J. Am. Chem. Soc. 2013, 135, 11330-11344. (b) Wang, J.; Wu, Q.; Wang, S.;
Yu, C.; Li, J.; Hao, E.; Wei, Y.; Mu, X.; Jiao, L. Conformation-Restricted Partially and Fully Fused BODIPY
Dimers as Highly Stable Near-Infrared Fluorescent Dyes. Org. Lett. 2015, 17, 5360-5363.
(6) (a) Liao, J.; Zhao, H.; Xu, Y.; Zhou, W.; Peng, F.; Wang, Y.; Fang, Y. Novel BODIPY dyes with electron
donor variety for dye-sensitized solar cells. RSC Adv. 2017, 7, 33975-33985. (b) Klfout, H.; Stewart, A.;
Elkhalifa, M.; He, H. BODIPYs for Dye-Sensitized Solar Cells. ACS Appl. Mater. Interfaces 2017, 9,
39873-39889.
(7) (a) Killoran, J.; Allen, L.; Gallagher, J. F.; Gallagher, W. M.; O’Shea, D. F. Synthesis of BF2 chelates of
tetraarylazadipyrromethenes and evidence for their photodynamic therapeutic behaviour. Chem.
Commun. 2002, 1862-1863. (b) Jiao, L.; Yu, C.; Uppal, T.; Liu, M.; Li, Y.; Zhou, Y.; Hao, E.; Hu, X.; Vicente,
M. G. H. Long wavelength red fluorescent dyes from 3,5-diiodo-BODIPYs. Org. Biomol. Chem. 2010, 8,
2517-2519. (c) Isaad, J.; El Achari, A. A water soluble fluorescent BODIPY dye with azathia-crown ether
functionality for mercury chemosensing in environmental media. Analyst 2013, 138, 3809-3819. (d)
Salim, M. M.; Owens, E. A.; Gao, T.; Lee, J. H.; Hyun, H.; Choi, H. S.; Henary, M. Hydroxylated near-infrared
BODIPY fluorophores as intracellular pH sensors. Analyst 2014, 139, 4862-4873. (e) Kilic, B.; Yesilgul,
N.; Polat, V.; Gercek, Z.; Akkaya, E. U. Bodipy-based photosensitizers with long alkyl tails at
ACS Paragon Plus Environment

The Journal of Organic Chemistry
Page 14 of 15
1
2
3
4
5
6
the meso position: efficient singlet oxygen generation in Cremophor-EL micelles. Tetrahedron Lett.
2015, 57, 1317-1320.
7
8
9
(8) (a) Ashton, P. R.; Bartsch, R. A.; Cantrill, S. J.; Hanes, R. E.; Hickingbottom, S. K.; Lowe, J. N.; Preece,
J. A.; Stoddart, J. F.; Talanov, V. S.; Wang, Z. H. Secondary dibenzylammonium ion binding by
[24]crown-8 and [25]crown-8 macrocycle. Tetrahedron Lett. 1999, 40, 3661-3664. (b) Zhang, Z. J.;
Zhang, H. Y.; Wang, H.; Liu, Y. A Twin-Axial Hetero[7]rotaxane. Angew. Chemie - Int. Ed. 2011, 50,
10834-10838.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
(9) (a) Ulrich, G.; Ziessel, R.; Harriman, A. The Chemistry of Fluorescent Bodipy Dyes: Versatility
Unsurpassed. Angew. Chem. Int. Ed. 2008, 47, 1184-1201. (b)Bozdemir, Ö. A.; Büyükcakir, O.; Akkaya,
E. U. Novel Molecular Building Blocks Based on the Boradiazaindacene Chromophore: Applications in
Fluorescent Metallosupramolecular Coordination Polymers. Chem. – A Eur. J. 2009, 15, 3830-3838.
(10) (a) Buyukcakir, O.; Bozdemir, O. A.; Kolemen, S.; Erbas, S.; Akkaya, E. U. Tetrastyryl-Bodipy Dyes:
Convenient Synthesis and Characterization of Elusive Near IR Fluorophores. Org. Lett. 2009, 11,
4644-4647. (b) Kostereli, Z.; Ozdemir, T.; Buyukcakir, O.; Akkaya, E. U. Tetrastyryl-BODIPY-Based
Dendritic Light Harvester and Estimation of Energy Transfer Efficiency. Org. Lett. 2012, 14, 3636–
3639.
(11) (a) Hawker, C. J.; Frechet, J. M. J. Preparation of polymers with controlled molecular architecture.
A new convergent approach to dendritic macromolecules. J. Am. Chem. Soc. 1990, 112, 7638-7647. (b)
Hawker, C. J.; Frechet, J. M. J. A new convergent approach to monodisperse dendritic macromolecules. J.
Chem. Soc., Chem. Commun. 1990, 1010-1013. (c) Li, F.; Yang, S. I.; Ciringh, Y.; Seth, J.; Martin, C. H.;
Singh, D. L.; Kim, D.; Birge, R. R.; Bocian, D. F.; Holten, D.; Lindsey, J. L. Design, Synthesis, and
Photodynamics of Light-Harvesting Arrays Comprised of a Porphyrin and One, Two, or Eight Boron-
Dipyrrin Accessory Pigments. J. Am. Chem. Soc. 1998, 120, 10001-10017. (d) Adronov, A.; Frechet, J.
M. J. Light-harvesting dendrimers. Chem. Commun. 2000, 1701-1710. (e) Dichtel, W. R.; Hecht, S.;
Frechet, J. M. J. Functionally Layered Dendrimers:ꢀ A New Building Block and Its Application to the
ACS Paragon Plus Environment

Page 15 of 15
The Journal of Organic Chemistry
1
2
3
4
Synthesis of Multichromophoric Light-Harvesting Systems. Org. Lett. 2005, 7, 4451-4454. (f)
5
6
Bozdemir, O. A.; Yilmaz, M. D.; Buyukcakir, O.; Siemiarczuk, A.; Tutas, M.; Akkaya, E. U. Convergent
7
8
synthesis
and light
harvesting properties
of
dendritic boradiazaindacene (BODIPY)
9
appended perylenediimide dyes. New J. Chem. 2010, 34, 151-155. (g) Ziessel, R.; Harriman, A. Artificial
light-harvesting antennae: electronic energy transfer by way of molecular funnels. Chem. Commun. 2011,
47, 611-631.
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
(12) Roberts, D. V.; Wittmershaus, B. P.; Zhang, Y.-Z.; Swan, S.; Klinosky, M. P. Efficient excitation
energy transfer among multiple dyes in polystyrene microspheres. J. Lumin. 1998, 79, 225–231.
(13) Liu, D.; Wang, D.; Wang, M.; Zheng, Y.; Koynov, K.; Auernhammer, G. K.; Butt, H-J.; Ikeda, T.
Supramolecular Organogel Based on Crown Ether and Secondary Ammoniumion Functionalized
Glycidyl Triazole Polymers. Macromolecules, 2013, 46, 4617-4625.
ACS Paragon Plus Environment