Stereochemistry of samarcandin-type sesquiterpenoid coumarins. Crystal structures of feshurin and nevskin

2 
 
4 
Î4–Í…Î2 
Î5–Í…Î1 
Î4–Í…Î5 
Î5–Í…Î2 
0.88 (4) 
0.91 (5) 
1.01 (3) 
0.97 (3) 
2.36 (5) 
2.48 (5) 
1.93 (3) 
1.87 (3) 
3.206 (4) 
3.265 (4) 
2.795 (3) 
2.817 (3) 
160 (3) 
145 (3) 
142 (2) 
165 (2) 
1-x,-1/2+y,1/2-z 
-1/2+x,1/2-y,1-z 
-2-x,-1/2+y,-1/2-z 
-1/5-x,-1-y,-1/2+z 
Fig. 1. Molecular structures and atomic numbering for 2 and 4.
C11
c
C5
c
O5
C6
c
C7
c
C8
c
C15
c
C9
c
C10
c
C4
c
C3
c
C2
c
C4
c
O4
C1
c
C13
c
O3
C7
C6
C5
C8
C10
C9
O1
C2
O2
C3
C4
C11
c
C5
c
O5
C6
c
C7
c
C8
c
C15
c
C9
c
C10
c
C4
c
C3
c
C2
c
C4
c
O4
C1
c
C13
c
O3
C7
C6
C5
C8
C10
C9
O1
C2
O2
C3
C4
C12
c
C12
c
2
4

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244
The H-bonds in the crystal of 4 formed channel-type cavities that were directed along the crystallographic a axis.
Figure 2 illustrates the cavities. Calculations indicated that the channel had approximate dimensions 10.2 
u 8.1 A
°
. The cavity
volume was 1097 A
°
3
and occupied 35.4% of the unit-cell volume. The anomalous calculated density d
calcd
= 0.857 g/cm
3
from the XSA (without considering molecules of crystallization) also indicated that the crystal of 4 had cavities although the
density of 2 (d
calcd
= 1.277 g/cm
3
) and other crystals of organic compounds usually vary in the range 1.1–1.3 g/cm
3
.
Traces of solvates were observed in the cavities. Their atoms were disordered over eight positions with occupancies
from 0.3 to 0.9. Together they formed a discrete cluster that was not bonded by H-bonds or other weak intermolecular
interactions to the crystal framework formed by nevskin molecules or other solvate clusters (Fig. 3). We hypothesized that this
could be either water (involved in nevskin isolation) or EtOAc, from which the crystals were grown (see Experimental).
EtOAc was the favored choice of the two possible solvates entrained in the crystal because there were no H-bonds between
clusters and with the framework walls. However, the experimental positions were highly disordered so that a geometrically
reasonable EtOAc molecule could not be recognized in a difference electron-density synthesis.
Thermogravimetric analysis did not provide clarity to this issue. Figure 4 shows thermogravimetric (TG) and differential
scanning calorimetric (DSC) curves for nevskin crystals.
TABLE 2. Principal Crystallographic Parameters and X-ray Structure Characteristics for 2 and 4
Parameter 
2 4 
Molecular formula 
MW, g/mol 
System 
Space group 
Z 
a, A
°
b, A
°
 
c, A
°
 
V, A
°
3
U, g/cm
3
Crystal size, mm 
Scan range 
P
exp
, cm
–1
Number of reflections 
Number of reflections with I > 2
V (I) 
R
1
(I > 2
V (I) and total) 
WR
2
GOOF 
Electron-density difference peaks, e A
°
–3
CCDC 
C
24
Í
32
Î
5
400.50 
Orthorhombic 
P 2
1
2
1
2
1
4 
6.0412 (3) 
18.0135 (9) 
19.1359 (9) 
2082.4 (2) 
1.277 
0.5 
u 0.25 u 0.15 
3.37 
d T d 76.09q 
0.710 
4299 
3140 
0.0647 (0.0853) 
0.1474 (0.1599) 
0.979 
0.16 and –0.22 
1029087
C
24
Í
32
Î
5
·Ñ
4
Í
8
Î
2
481.56 
Orthorhombic 
P 2
1
2
1
2
1
4 
6.2360 (1) 
16.3709 (5) 
30.4025 (7) 
3103.76 (13) 
1.030 
0.6 
u 0.3 u 0.15 
5.40 
d T d 75.98q 
0.477 
6323 
4656 
0.0477 (0.0645) 
0.1196 (0.1278) 
0.957 
0.16 and –0.17 
1029086
0
a
b
c
0
a
c
b
Fig. 2. Packing of 4 projected on the bc axis Fig. 3. Packing of water clusters in the crystal structure of 4.
(solvate molecules in cavities not shown).

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245
It can be seen from Fig. 4 that a mass loss of 12.83% occurred in the range 140–150°C. This corresponded to release
from the crystal structure of solvate molecules (3.8 molecules of H
2
O or 0.7 molecules of EtOAc). The crystal itself melted at
185°C. It was noteworthy that the temperature (140°C) at which the guest molecules vacated the crystal structure was
considerably greater than the boiling points of H
2
O (100°C) and EtOAc (77°C). Although the solvate molecules were not
H-bonded to the nevskin crystal framework, they were rather strongly held in its crystal structure.
Refinement of the crystal structure by least-squares methods (LS) including the eight strongest residual electron-
density peaks as isolated O (or C) atoms with varying occupancies gave the best R-factor (4.8%) and residual electron density
(0.16; –0.17 e 
˜ A
°
3
). The total populations of all positions were approximated using FVAR and gave values of 4.4 and 1.1 for
H
2
O and EtOAc, respectively. These results did not agree completely with the TG data. The explanation for this discrepancy
could be the fact that the disordered molecules entrained in the crystal structure were not H-bonded to nevskin molecules.
Therefore, they could partially vacate the crystal cavity even during preparation for the TG-DSC experiment. The stoichiometries
of their inclusion in the crystal cavity could also differ.
Thus, routine XSA and TG-DSC analyses did not define unambiguously the nature of the solvate molecules entrained
in the nevskin crystal cavity. Additional crystal-chemical research is required to answer this question.