Crystalline molecular gyroscopes: The effects of subtle molecular differences on the crystal packing of triphenylmethyl and triphenylsilyl stators

Article abstract of DOI:10.1080/15421400600788757

Single crystals of molecular gyroscopes, 1,4-bis(3,3,3-triphenylpropynyl) benzene and 1,4-bis(triphenyl-silanylethynyl)-benzene were studied by single crystal X-ray diffraction (XRD) analysis and their packing tendencies were compared to those of analogou

Full text of DOI:10.1080/15421400600788757

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Crystalline Molecular
Gyroscopes: The Effects of
Subtle Molecular Differences
on the Crystal Packing
of Triphenylmethyl and
Triphenylsilyl Stators
a
a
Steven D. Karlen , Saeed I. Khan & Miguel A.
a
Garcia-Garibay
a
Department of Chemistry and Biochemistry ,
University of California , Los Angeles, California
Published online: 21 Dec 2006.
To cite this article: Steven D. Karlen , Saeed I. Khan & Miguel A. Garcia-Garibay
(2006) Crystalline Molecular Gyroscopes: The Effects of Subtle Molecular Differences
on the Crystal Packing of Triphenylmethyl and Triphenylsilyl Stators, Molecular
Crystals and Liquid Crystals, 456:1, 221-230, DOI: 10.1080/15421400600788757
To link to this article: http://dx.doi.org/10.1080/15421400600788757
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Mol. Cryst. Liq. Cryst., Vol. 456, pp. 221–230, 2006
Copyright # Taylor & Francis Group, LLC
ISSN: 1542-1406 print=1563-5287 online
DOI: 10.1080/15421400600788757
Crystalline Molecular Gyroscopes: The Effects of Subtle
Molecular Differences on the Crystal Packing of
Triphenylmethyl and Triphenylsilyl Stators
Steven D. Karlen
Saeed I. Khan
Miguel A. Garcia-Garibay
Department of Chemistry and Biochemistry, University of California,
Los Angeles, California
Single crystals of molecular gyroscopes, 1,4-bis(3,3,3-triphenylpropynyl)benzene
and 1,4-bis(triphenyl-silanylethynyl)-benzene were studied by single crystal
X-ray diffraction (XRD) analysis and their packing tendencies were compared to
those of analogous structures without the central phenylene rotator.
Keywords: crystal engineering; molecular gyroscopes; six-fold phenyl embrace; X-ray
diffraction
INTRODUCTION
Packing forces in molecular crystals are determined by a large number
of weak, attractive and repulsive, equilibrating interactions, including
p-p stacking, dipole-dipole and van der Waals interactions. The
strength of these interactions depends on their nature, the compo-
sition of the groups involved, and the distances and geometries over
which they occur. In general, there is an inverse relationship between
the distance and strength of the interaction, which may be given as a
x
function of 1=r , where r is the distance between the atoms involved,
with x varying from 2 for Coulombic interactions, up to 6 and 12 for
van der Waals forces [1]. With such strong distance dependence, it is
This work was supported by the National Science Foundation through grants
DGE-0114443 (NSF IGERT: Materials Creation Training Program (MCTP)) and
DMR03070288
Address correspondence to Miguel A. Garcia-Garibay, Department of Chemistry and
Biochemistry, 607 Charles E. Young Dr. East, University of California, Los Angeles,
California 90095-1569, USA. E-mail: mgg@chem.ucla.edu
221

2
22
S. D. Karlen et al.
FIGURE 1 Toy gyroscopes have a rigid outer frame encasing a mass, which
rotates around an ideally frictionless axis. Molecular analogs of gyroscopes
should possess the same three components.
not surprising that any small change in molecular structure has the
potential of creating considerable changes in the molecular packing.
The purpose of this paper is to investigate how a very small change in
the structure of a molecular gyroscope may affects its crystal packing.
Macroscopic toy gyroscopes have a rigid outer frame (stator) encas-
ing a mass (rotator), which rotates around an ideally frictionless axle
(
Fig. 1). Molecular analogs to toy gyroscopes should possess the same
three components: a stator, a rotator, and an axle [2]. Through molecu-
lar engineering, we have designed a family of molecular gyroscopes
ꢀ
that exhibit rapid 180 phenylene rotation (flipping) in the solid state
[
3]. The simplest of these molecules (molecular gyroscopes 1) consists
of a bis-triphenylmethyl (trityl) stator, a dialkynyl axle, and a para-
phenylene rotator (Fig. 1). At room temperature, the phenylene of 1
ꢀ
exhibits 180 flipping motions with an average correlation time of
0
.9 ms (ꢁ1100 flips per second) and a barrier to rotation of
1
1.6 kcal=mol [4]. To determine the effects of a minor perturbation
on the structure, in this paper we will compare the crystal packing
of molecular gyroscope 1 to that of an analogous molecular gyroscope
2
, which has a bis-triphenylsilyl stator in place of the triphenylmethyl
stator in 1 (Scheme 1). The suggested substitution should create small
changes in the structure. In addition to the obvious replacement of
3
carbon by silicon, the bond lengths between the sp hybridized atom
˚
and the four substituents should be around 0.4 A longer for the silane
[
5]. Due to the larger size of the silicon atom and the longer bond
length, the three phenyls are expected to extend farther apart from
the center of the molecule. This expansion should result in lower steric
crowding and increased flexibility of the three aromatic groups

Crystalline Molecular Gyroscopes
223
attached to the silane center. These small differences have the poten-
tial of dramatically changing the packing structure and dynamic
properties of molecular gyroscope 2 as compared to those of molecular
gyroscope 1.
EXPERIMENTAL
Molecular gyroscope 1 can be made by Sonogashira coupling of 3,3,3-tri-
phenylpropyne and diiodobenzene (Scheme 1) [4]. In the presence of
oxygen, this reaction will also lead to the dimerization of the terminal
alkyne forming 1,1,1,6,6,6-hexaphenyl-2,4-hexadiyne, 3 (Scheme 1).
Large amounts of pure diyne 3 can be prepared using standard
Glaser coupling of 3,3,3-triphenylpropyne in the presence of copper
(
I) chloride and oxygen [6].
Molecular gyroscope 2 and bis-(triphenylsilanyl)-1,4-butadiyne (4)
can be prepared by substituting triphenylsilylacetylene for the 3,3,3-
triphenylpropyne in the reaction used to prepare 1 and 3, respectively.
Compounds 2 and 4 were noticeably more soluble than the carbon ana-
logs 1 and 3 in common organic solvents, such as dichloromethane,
acetone, benzene, toluene, and chloroform.
Single crystal X-ray diffraction analysis of compounds 1, 2, and 3
were performed on a Bruker SMART 1000 CCD-based X-ray diffract-
˚
ometer system equipped with a Mo-target X-ray tube (l ¼ 0.71073 A)
operated at 2250 watts power. The detector was placed at a distance
of 4.986 cm from the crystal. The frames were integrated with the
Bruker SAINT software package using a narrow-frame integration
algorithm. The structure was refined using the Bruker SHELXTL
(
Version 6.12) Software Package.
SCHEME 1

2
24
S. D. Karlen et al.
RESULTS AND DISCUSSION
Crystal Structure Analysis
As it was recently reported, the alkynyl dimer (3) crystallizes from
many different solvents (dichloromethane, chloroform, acetone, ben-
zene, toluene, para-diflourobenzene, and 2,6-dimethylnitrobenzene)
in a solvent-free structure [7]. The structure was solved in a Rhombo-
hedral crystal system in the space group R-3. There are 12 molecules
per unit cell, of which three are unique (A, B, C) (Figure 2). With axi-
ally chiral triphenylmethyl groups, molecules A and C are meso and
molecule B occurs in D, L forms. The packing structure is character-
ized by head-to-tail chains along the c-axis in the repeat pattern
ACA’B, with A and A’ representing molecules of opposite chirality.
These chains come together to form a close packed hexagonal array
in which six chains surround a seventh chain.
The trityl groups are arranged in what is known as a six-fold phenyl
embrace (6PE) [8]. The 6PE is characterized by a cyclic arrangement of
complementary edge-to-face interaction between adjacent Ph X
3
groups (XPh ----Ph X). In this structure, the distance over which the
3
3
˚
trityl embrace occurs is very different for molecules A and B (6.15 A),
˚
as compared to that for molecules A and C (6.94 A). This distances are
measured from the methane carbon of one trityl group to the methane
carbon of the other one (Table 1). The difference between the two 6PE’s
can also be seen by the presence of short (less than the sum of van der
Waals radii) contacts between the phenyl rings of molecules A and B,
while there are no close contacts between molecules A and C. The
three molecules A, B, and C have a distance between the two methane
˚
carbons that is 6.735(15) A long.
FIGURE 2 Left: Ortep diagram of the trityl dimer, showing the three unique
molecules. Right: packing diagram with the three unique molecules in a repeat
pattern of ACA’B.

Crystalline Molecular Gyroscopes
225
TABLE 1 Length of the Phenyl Embrace in Molecules 1–4,
as Measured from the Central X Nuclei of the Two Ph X
3
Groups, where X ¼ C or Si
˚
Molecules
Distance (A)-XPh
3
3
—Ph X-
1
2
3
3
4
4
4
4
4
4
4
–1
7.56
6.46
6.15
6.94
6.83
6.29
6.88
6.05
6.44
6.95
5.84
A–3B
A–3C
A–4B
A–4C
B–4B
C–4D
(1)–4(2)
(2)–4(3)
(3)–4(3)
The triphenylsilylacetylene dimer 4 crystallizes in two polymorphs,
one polymorph occurs in the rhombohedral crystal system in the space
group R-3 and the other in the triclinic crystal system and the space
group P-1 (Figure 3) [9]. The molecules in the R-3 structure are packed
in a very similar arrangement as that previously seen in the crystal
structure of compound 3. In the unit cell of the R-3 structure of 4 there
are 21 molecules, four of which are unique (A, B, C, D). The repeat pat-
tern of the four unique molecules is ABB’A’CDC’, where A’, B’, and C’
are of the opposite chirality of molecules A, B, and C. The ‘trityl’
˚
embrace distances present in this structure range from 6.05–6.88 A,
which are similar to those seen for compound 3. The Si—Si distances
˚
˚
are 7.45(2) A long, which is 0.75 A longer than those of compound 3, as
expected for the longer C-Si bonds.
The P-1 structure of the triphenylsilyl acetylene dimer 4 is very
similar to the higher symmetry R-3 structures, with the head-to-tail
alignment of the molecules, the presence of the ‘trityl’ embrace, and
several unique molecules per asymmetric unit. In this structure there
are five molecules in the unit cell, three of which are unique (1, 2, 3).
The repeat pattern of the three unique molecules is 1233’2, where 3’ is
the opposite chirality of molecule 3. The ‘trityl’ embraces are slightly
offset resulting is a subtle tilt of each molecular with respect to the
˚
long head-to-tail chain. The trityl embraces are 5.84–6.95 A long,
˚
and the molecules are 7.47(1) A long.
Molecular gyroscope 1, with
a triphenylmethyl stator and
phenylene rotator forms a solvent-free crystal structure from acetone,
chloroform, dichloromethane, and diethyl ether. This structure is in a

2
26
S. D. Karlen et al.
FIGURE 3 Top: Packing diagram of the triphenylsilyl dimer (3) in space
group R-3 with the four unique molecules in the repeat pattern of ABB’A’CDC’.
Bottom: Packing diagram of the second polymorph of 3 in the space group P-1
with the three unique molecules in the repeat pattern 1233’2’.
triclinic crystal system with the space group P-1 (Figure 4). Molecular
gyroscope 1 also crystallizes as a clathrate from several aromatic
solvents such as benzene, fluorobenzene, and pyridine. It also forms
ꢀ
a clathrate with chloroform at ꢂ78 C. The unit cell of the solvent free
crystal contains one molecule, and half of it represents the asymmetric
unit as the molecule sits in an inversion center, which makes the two
FIGURE 4 Left: Ortep diagram of the trityl phenylene rotor. Right: Packing
diagrams looking at the side of the phenylene rotator and at the top of the
rotator.

Crystalline Molecular Gyroscopes
227
FIGURE 5 Left: Ortep diagram of the triphenylsilanyl phenylene rotor. Note
the disorder in all three phenyl rings of the end groups. Right: packing dia-
grams looking at the side of the phenylene rotator and at the top of the rotator,
only one orientation of each phenyl ring is shown for clarity.
chiral trityl groups enantiomeric. The packing of the molecules 1 is
very similar to that of the P-1 structure of compound 4. Long chains
of molecular gyroscopes aligned in a head-to-tail manner with slightly
˚
offset molecular axes, and a long phenyl embrace distance of 7.56 A
(
Fig. 2, Table 1). Interdigitation of phenyl rings of adjacent molecules
between the trityl groups form a pocket around the phenylene rotator,
which allow for the flipping of the phenylene ring to occur with an
energy barrier of ca. 11–14 kcal=mol [4].
Molecular gyroscope 2, with a triphenylsilyl stator and a phenylene
rotator, has similar crystallization characteristics as 1. Compound 2
forms a solvent free structure from dichloromethane, chloroform,
and acetone and it forms a solvent clathrate with benzene. The solvent
free structure occurs in the triclinic crystal system in the space group
P-1 (Figure 5) [10]. There is one molecule per unit cell and half of it
accounts for the crystal asymmetric unit. As with compound 1, the
molecule sits on an inversion center making the two trityl groups
enantiomeric. One notable change is the disorder in the phenyl rings.
In fact, this is the first structure in this family of compounds to show
disorder in the stator. Despite this disorder, the two trityl groups
experience a phenyl embrace. However, with their long molecular axis
offset in the lattice, the embrace is not a perfect 6PE. The phenyl
˚
embrace distance in the structure is 6.46 A, and Si—Si distance is
˚
1
1.73 A.
DISCUSSION
The substitution of a silicon atom for the methane carbon in elongates
˚
the structure of 1 and 3 by ca. 0.7 A (Table 2). The geometry around

2
28
S. D. Karlen et al.
TABLE 2 Distance Between the two X Nuclei in
Ph
3
XCC(C
6
H
4
)
n
CCXPh
3
, where n ¼ 1 for Compounds 1
and 2, n ¼ 0 for Compounds 3 and 4
˚
Molecule
Molecular Length (A)
1
2
11.02
11.73
6.75
6.72
6.72
7.43
7.45
7.47
7.43
7.48
7.46
7.46
3
3
3
4
4
4
4
4
4
4
A
B
C
A
B
C
D
(1)
(2)
(3)
3
the sp hybridized X nucleus in the Ph X-CC groups for all molecules
3
1
–4 is slightly flattened from the standard tetrahedral geometry
ꢀ
ꢀ
(
109.5 ). This may be seen by an average value of 107.8–108.1 for
the C-(alkyne)-C(methane)-C(ipso) bond angle in the structures of
the four compounds (Table 3). Notably, this bond angle has much more
variability in the two triphenylsilyl compounds 2 and 4 than in their
trityl counterparts (1 and 3). The increased variability is also apparent
in the torsion angles describing the orientation of the aromatic rings in
the trityl groups of the two compounds (Table 3).
The substitution of the methane carbon in compounds 1 and 3 with
a silicon atom to form compounds 2 and 4 changes the molecular
length, provides increased variability in the bond angles, and
improves the solubility in many common organic solvents. Yet, the
TABLE 3 Selected Bond Angles (CXCipso) and Torsion Angles (CXCipso
for Molecules 1–4, where X ¼ C or Si
ortho
C )
ꢀ
ꢀ
Bond Angle ( )
Torsion Angle ( )
Molecule
Space Group)
Atoms Involved:
CXCipso
Atoms Involved:
(
CXCipso C
ortho
1
2
3
4
4
(P-1)
(P-1)
(R-3)
(R-3)
(P-1)
CCCipso
106.5–110.0
101.8–110.5
107.7–108.5
106.5–109.7
104.6–113.3
CCCipso
C
C
ortho
122.8–161.5
109.1–179.7
131.7–147.1
127.0–156.2
109.1–164.6
CSiCipso
CCCipso
CSiCipso
CSiCipso
CSiCipso
ortho
CCCipso
CSiCipso
CSiCipso
C
ortho
C
C
ortho
ortho

Crystalline Molecular Gyroscopes
229
molecules are similar enough to retain the same packing structure
with parallel rows of structures aligned in head-to-tail chains.
Interestingly, of all these structures only compound 2 shows disorder
in the six phenyl rings, possibly attributed to the larger range of bond
angles and dihedral angles that the molecules can tolerate.
CONCLUSIONS
Small changes in molecular structure have the possibility of creating
significant changes in molecular packing. The crystal structures of
two very similar molecular gyroscopes were studied. One has a bis-
triphenylmethyl stator (1) and the other has a bis-triphenylsilanyl
analog (2). In addition, a structural analysis of the dimers of 3,3,3-tri-
phenylpropyne (3) and triphenylsilylacetylene (4) was performed. The
substitution of silicon for carbon increases the core molecular length
˚
by ca. 0.7 A and allows for more flexibility of the bond angle and tor-
3
sion angle around the sp hybridized atom. Even with some relaxed
geometric restrictions on the molecular angles and increased molecu-
lar length, the molecular packing of compounds 2 and 4 are very simi-
lar to those of 1 and 3. Their packing structures retain the six-fold
trityl embrace between head-to-tail parallel molecular chains. The tri-
phenylsilyl derivatives seem to posses a slightly greater tendency for
disorder, as demonstrated by the structure of 2 and the presence a
large number of unique molecules in the structures of the two poly-
morphs of compound 4. Solid state rotational dynamics studies of com-
pound 2 are currently under way, preliminary results reveal that
compound 2 has a significantly lower barrier for phenylene flipping
than compound 1 [11].
REFERENCES
[
1] (a) Kitaigorodskii, A. I. (1973). Molecular Crystals and Molecules, Academic Press:
New York; (b) Bernstein, J. (2002). Polymorphism in Organic Chemistry, Oxford
University Press: Oxford.
[
[
2] Kottas, G. S., Clarke, L. I., Horinek, D., & Michl, J. (2005). Chem. Rev., 105, 1281–
1
376.
3] Karlen, S. D. & Garcia-Garibay, M. A. (2005). Amphidynamic crystals: Structural
blueprints for molecular machines. In Molecular Machines, Kelly, T. R. (Ed.),
Topics in Current Chemistry: Springer, Vol. 262, 179–227.
[
4] (a) Dominguez, Z., Dang, H., Strouse, M. J., & Garcia-Garibay, M. A. (2002). J. Am.
Chem. Soc., 124, 2398–2399; (b) Dominguez, Z., Dang, H., Strouse, M. J., & Garcia-
Garibay, M. A. (2002). J. Am. Chem. Soc., 124, 7719–7727.
[
[
5] CRC Handbook of Chemistry and Physics, 84 ed.
6] (a) Glaser, C. (1869). Ber., 2, 422; (b) Menger, F. M., Y., C. X., Brocchini, S.,
Hopkins, H. P., & Hamilton, D. (1993). J. Am. Chem. Soc., 115, 6600–6608.

2
30
S. D. Karlen et al.
[
[
7] Karlen, S. D., Khan, S. I., & Garcia-Garibay, M. A. (2005). Crys. Growth & Design,
5
, 53–55.
8] (a) Scudder, M. & Dance, I. (1998). J. Chem. Soc. Dalton Trans., 329–344; (b) Scud-
der, M. & Dance, I. (2000). Dalton, 2909–2915; (c) Dance, I. & Scudder, M. (1998).
New Journal of Chemistry, 22, 481–492; (d) Lacour, J., Bernardinelli, G., Russell,
V., & Dance, I. (2002). Cryst Eng Comm., 4, 165–170.
[
9] Carr e´ , F., Devylder, N., Dutremez, S. G., Gu e´ rin, C., Henner, B. J. L., Jolivet, A.,
Tomberli, V., & Dahan, F. (2003). Organometallics, 22, 2014–2033.
[
10] Selected crystallographic information for compound 2: C46
H
34Si
˚
2
, MW ¼ 642.91,
˚
˚
triclinic, space group P-1, a ¼ 8.9594(19) A, b ¼ 9.003(2) A, c ¼ 12.198(3) A,
ꢀ
ꢀ
ꢀ
˚
3
a ¼ 99.492(4) , b ¼ 98.721(4) , c ¼ 111.133(4) , V ¼ 881.0(3) A , Z ¼ 1,
q
cald
¼
3
˚
ꢂ1
1
.212 Mg=m , F(000) ¼ 338, k ¼ 0.71073 A, l(Mo K
a
) ¼ 0.067 mm , T ¼ 100(2) K,
6926 reflections collected
3
crystal
(
size ¼ 0.6 ꢃ 0.3 ꢃ 0.03 mm ,
of
the
ꢀ
2.50 ꢄ h ꢄ 27.08 ), 3978 [R(int) ¼ 0.0327] were independent reflections; max=min
˚
ꢂ3
residual electron density 0.529 and ꢂ0.458 e A , R1 ¼ 0.0788 (I > 2r(I)) and
wR2 ¼ 0.2227 (all data).
[11] Karlen, S. D. & Garcia-Garibay, M. A. Unpublished data.