Stable Near-IR Dyes
FULL PAPER
rial, and the resulting crude product was subjected to chromatography by
using a silica column and a mixture of methanol/chloroform (1:19) as the
eluent.
to ride on the positions of the parent atoms. All non-hydrogen atoms
were refined with parameters for anisotropic thermal motion. There were
no significant peaks in the final difference map; the largest peak=
À3
0.26 eÀ3. The deepest hole was of similar magnitude, 0.25 e
.
Rotaxane 2a:[7a] Yield 30%; TLC: Rf =0.5 (methanol/chloroform 1:19);
1H NMR (500 MHz, CDCl3, TMS): d=4.38 (d, J=5 Hz, 8H; -Ph-CH2
(wheel)), 4.79 (s, 8H; -Ph-CH2 (thread)), 6.47 (d, J=9 Hz, 4H; thread),
6.66 (s, 8H; wheel), 7.16 (d, J=8 Hz, 8H; thread), 7.37 (t, J=7 Hz, 4H;
thread), 7.41 (t, J=8 Hz, 8H; thread), 7.51 (t, J=8 Hz, 2H; wheel), 7.69
(d, J=10 Hz, 4H; thread), 8.06 (t, J=10 Hz, 4H; -NH), 8.20 (d, J=
10 Hz, 4H; wheel), 9.22 ppm (s, 2H; wheel); 13C NMR (125 MHz,
CDCl3, TMS): d=44.1, 54.6, 113.2, 118.7, 124.5, 126.4, 128.2, 129.1, 129.2,
129.3, 131.6, 133.1, 133.9, 135.2, 136.4, 155.3, 166.0, 183.1, 184.9; FAB-MS
(NBA matrix): m/z: 1158 [M+H]+.
CCDC-297976 (3) contains the supplementary crystallographic data for
this paper. This data can be obtained free of charge from the Cambridge
Acknowledgements
This work was supported by the National Institutes of Health (USA),
Philip Morris USA Inc., and Philip Morris International. The X-ray dif-
fraction instrumentation was supported by NSF award CHE-0443233.
Rotaxane 2b: Yield 34%; TLC: Rf =0.3 (methanol/chloroform 1:19);
1H NMR (300 MHz, CDCl3, TMS): d=3.37 (s, 12H; -OCH3), 3.55 (t, J=
4.4 Hz, 8H; -OCH2), 3.64–3.75 (m, 24H; -OCH2), 3.89 (t, J=4.8 Hz, 8H;
-OCH2), 4.17 (t, J=4.8 Hz, 8H; -OCH2), 4.50 (d, J=5.7 Hz, 8H; -Ph-
CH2 (wheel)), 4.56 (s, 8H; -Ph-CH2 (thread)), 6.28 (d, J=9.6 Hz, 4H;
thread), 6.56 (s, 8H; wheel), 6.92 (d, J=9 Hz, 8H; thread), 6.99 (d, J=
8.7 Hz, 8H; thread), 8.02 (t, J=7.8 Hz, 2H; wheel), 8.07 (d, J=9.3 Hz
4H; thread), 8.40 (d, J=8.1 Hz, 4H; wheel), 9.89 ppm (t, J=5.9 Hz, 4H;
-NH); 13C NMR (150 MHz, CDCl3, TMS): d=43.2, 53.4, 59.0, 67.5, 69.7,
70.5, 70.6, 70.8, 71.9, 112.5, 115.1, 119.6, 125.1, 127.5, 127.8, 128.9, 133.5,
136.6, 138.6, 149.3, 154.8, 158.5, 163.4, 184.9, 185.5 ppm; FAB-MS (NBA
matrix): m/z: 1810 [M+H]+.
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Rotaxane 2c:[7a] Yield 30%; TLC: Rf =0.5 (methanol/chloroform 1:19);
1H NMR (500 MHz, CDCl3, TMS): d=4.50 (d, J=6 Hz, 8H; -Ph-CH2
(wheel)), 4.67 (s, 8H; -Ph-CH2 (thread)), 6.26 (d, J=9 Hz, 4H; thread),
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(125 MHz, CDCl3, TMS): d=43.4, 54.5, 112.7, 120.0, 125.3, 126.6, 128.2,
129.0, 129.4, 133.8, 135.7, 136.9, 138.7, 149.4, 155.1, 163.6, 185.0, 186.3;
FAB-MS (NBA matrix): m/z: 1159 [M+H]+.
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Rotaxane 3: Yield 9%; TLC: Rf =0.5 (methanol/chloroform 1:19);
1H NMR (800 MHz, DMSO, TMS): d=4.43 (d, J=5.6 Hz, 8H; -Ph-CH2
(wheel)), 4.80 (s, 8H; -Ph-CH2 (thread)), 6.23 (d, J=8.8 Hz; 4H, thread),
6.93 (s, 8H; wheel), 6.97 (t, J=7.6 Hz, 2H; wheel), 7.2 (d, J=8 Hz, 4H;
wheel), 7.24–7.26 (m, 12H; thread), 7.35 (t, J=7.2 Hz, 4H; thread), 7.43
(t, J=7.6 Hz, 4H; thread), 7.7 (s, 2H; wheel), 8.28 ppm (t, J=6 Hz, 4H;
-NH); 13C NMR data were not acquired because of poor solubility; FAB-
MS (NBA matrix): m/z: 1158 [M+H]+.
X-ray crystallographic structure determinations
Rotaxane 3: Crystallization was carried out in dimethylformamide
(DMF)/diisopropyl ether (1:1). Molecular formula=C88H92N10O10; Mr =
1449.72; crystal size=0.430.110.06 mm3; monoclinic; space group
P21/c; translucent blue needles; a=9.8115(4), b=16.4125(6), c=
24.0231(10) ;
b=99.994(3)8;
V=3809.8(3) 3;
Z=2;
1calcd =
1.264 mgmÀ3. Crystals were examined under a light hydrocarbon oil. The
crystal was affixed to a thin glass fiber mounted atop a tapered copper
mounting pin and transferred to the 100 K nitrogen stream of a Bruker
APEX diffractometer equipped with an Oxford Cryosystems 700 series
low-temperature apparatus. Cell parameters were determined with Cell_-
Now by using reflections harvested from three sets of twenty 0.38 w
scans. The orientation matrix derived from this was passed to COSMO to
determine the optimum data-collection strategy. Average fourfold redun-
dancy was achieved by using four w scan series. Data were measured to
0.80 . Cell parameters were refined by using 5480 reflections with I=
10s(I) and 2.128=s=23.128 harvested from the entire data collection. In
total, 70216 reflections were measured, 12323 unique, 7395 observed, I>
2s(I). All data were corrected for Lorentz and polarization effects and
runs were scaled by using TWINABS. The structure was solved by using
data from the dominant component and refined against data from all
three components. The scale factors for the second and third components
are 0.3274(14) and 0.1938(14), respectively. The asymmetric unit contains
1
a = molecule each of the squaraine and macrocycle. In addition, there
2
are two molecules of DMF. The complete structure is generated by inver-
sion. Hydrogen atoms were placed at calculated geometries and allowed
Chem. Eur. J. 2006, 12, 4684 – 4690
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