Twisting of Alkynes towards a Carbon Double Helix

Article abstract of DOI:10.1002/chem.201701096

The carbon allotrope exhibiting only one-dimensional sp-hybridized carbon atoms is called carbyne. However, its existence is very controversial. Studies on model compounds for carbyne revealed that many oligoalkynes show not a straight, but a bent structu

Full text of DOI:10.1002/chem.201701096

A Journal of
Accepted Article
Title: Twisting of Alkynes Towards a Carbon Double Helix
Authors: Abdulselam Adam and Gebhard Haberhauer
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10.1002/chem.201701096
Chemistry - A European Journal
Twisting of Alkynes Towards a Carbon Double Helix
Abdulselam Adam† and Gebhard Haberhauer*†
† Institut für Organische Chemie, Universität Duisburg-Essen, Universitätsstr. 7, D-45117
Essen, Germany
Email address: gebhard.haberhauer@uni-due.de
ABSTRACT:
The carbon allotrope exhibiting only one-dimensional sp-hybridized carbon atoms is called
carbyne. However, its existence is very controversially discussed. Studies regarding model
compounds for carbyne revealed that many oligoalkynes show not a straight, but a bent
structure of the carbon chain. Here we deal with the question whether it would also be
possible to get a more complex structure from carbyne like a dimeric double helix. By means
of quantum chemical calculations we were able to show that only a small energetic expense
is needed for the formation of a double helix starting from oligoalkyne chains. In some cases
the double helix-like conformation is more stable than the corresponding conformation with a
parallel arrangement of the acetylene chains. Furthermore, model systems, in which two
diphenyl oligoalkyne chains are fixed and twisted by a chiral imidazole-containing clamp,
were synthesized. The structural investigation of these model systems were performed by
UV and CD spectroscopy and quantum chemical calculations. The observed twisting in these
model systems can be regarded as the first small step towards an imaginable carbon double
helix.
Table of Contents graphic:
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Introduction
Pure carbon can exist in various allotrope modifications. The most famous forms, which have
also been used by mankind for thousands of years, are diamond and graphite.[1] In chemical
terms, diamond consists of three-dimensional sp3-hybridized carbon atoms, whereby each
carbon atom shows four covalent bonds (Figure 1). In the meantime, further carbon
allotropes have been discovered, which feature sp3-hybridized carbon atoms; these are
lonsdaleite[2] and C8 . Graphite consists of two-dimensional sp2-hybridized carbon atoms
[3]
which form two-dimensional layers. The latter are held together by non-covalent interactions
(Figure 1). In addition to graphite, there are also graphene[4], fullerenes[5] and carbon
nanotubes[6], which are also composed of sp2-hybridized carbon atoms. In the case of
fullerenes and carbon nanotubes, a bending – i.e. a slight deviation from the ideal sp2 hybrid
– results in the formation of three-dimensional structures (spheres and tubes) from a two-
dimensional basic unit.
Figure 1. Schematic representation of the three types of hybridization of carbon atom and
the resulting carbon allotropes. The existence of carbyne remains controversial. Here, we
discuss the principle of a carbon double helix, a dimeric derivative of carbyne.
Carbon allotropes exhibiting only one-dimensional sp-hybridized carbon atoms are
cyclo[n]carbons[7] and carbyne (Figure 1). However, the existence of the latter is very
controversial.[8] Astrophysicists proposed that it might exist in meteorites[9] or as a by-product
of shock-fused graphite.[10] The synthesis of a series of conjugated polyynes as carbyne
models[11] has shown that they become more unstable with increasing number of acetylene
units.[12] The synthesis of polyynes with more than ten acetylene units is only possible if very
bulky groups are attached to the terminal carbon atoms.[11a,13] With increasing number of
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acetylene units, the absorption maximum is also shifted to the long-wave range; e.g. a
polyyne having 22 acetylene units is intensely red-orange colored.[11a] The maximum
wavelength for a carbyne was extrapolated to ca. 485 nm (green color).[11a] Recently, the
synthesis of a polyyne moiety with more than 6000 conjugated sp carbon atoms was
achieved by covering the reactive polyacetylene in carbon nanotubes.[14] The recently
published report about a solid carbyne[15] has been largely refuted.[16] Thus, the preparation
of carbyne remained unsuccessful. A possible decomposition reaction of carbyne could be
the dimerization of two acetylene units into a diradical:[17] The higher the number of acetylene
units in the molecule, the lower is the corresponding activation energy[18], whereby the most
reactive units in an acetylene chain are the carbon atoms C(2) and C(ω-1).[18] With increasing
number of acetylene units, the bending of the oligoalkynes usually also increases.[19] The
bent structures were proven both in the solid state and in solution.[20] The reason for this is
the low energy required for deformation.[21] Already for the decapentayne the lowest energy
deformation mode amounts to only 0.13 kcal/mol (44 cm-1).[22]
In view of the easy way of bending carbyne, the question arises whether it would also be
possible to get more complex structures from carbyne. One of these would be a carbon
double helix; i.e. a dimer of carbyne (Figure 1). Here, we describe quantum chemical
investigations regarding the twisting behavior of oligoynes and their behavior for forming a
double helix. Furthermore, we synthesized model compounds in order to examine if a double
helix-like structure of oligoynes can be achieved by incorporation of two twisted clamps.
Results and Discussion
a) Quantum Chemical Investigations on the Double Helix Formation of Hexaynes and
Longer Oligoynes
First we wanted to examine by means of quantum chemical calculations, how much energy
is required to achieve the twisting of two oligoalkyne chains towards a carbon double helix.
The structures of the model systems were optimized by using the DFT potential B3LYP[23]
with the additional empirical dispersion correction D3[24]. Unless otherwise noticed, the basis
set def2-TZVP[25] was employed. We used hexayne as a model system: this is the first
oligoalkyne with a lowest energy deformation mode of less than 200 cm-1 (0.57 kcal/mol)[22]
and its derivatives, which do not show bulky groups at the terminal sp carbon atoms, are
relatively stable. A problem in the study of two hexaynes forming a double helix-like structure
is the fact, that without external influence the double helix-like structure does not represent a
minimum on the potential hypersurface. In order to check the energetic requirement for the
formation of a double helix, it is therefore necessary to define parameters and keep them
partly constant in the calculation. For our model we have defined the following three
parameters: the distance a between the ends of the alkyne chains, the height of the chain d
3
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and the dihedral angle θ (see Figure 2a). The dihedral angle θ is defined as the angle
between the centers C1-M1-M12-C12 and can be viewed as a degree for the twisting. The
center M1 (M12) is defined as the middle point between the atoms C1 and C1' (M12 and
M12'; see Figure 2a). For further simplification, the angle α(C1-C1'-C12') was fixed to 90°;
this means that the two carbon chains start at the same level; i.e. there is no relative
displacement of the chains to each other.
Figure 2. Dimers of hexayne (1) as a model system and definition of the parameters a, d and
θ.
The dimer 1(0) was used as reference system: Here, the value 0 in brackets means that θ is
fixed to an angle of 0°. Considering that the angle α(C1-C1'-C12') is fixed to 90°, 1(0)
corresponds to a dimer showing the point group D2h. Accordingly, 1(0) can be completely
optimized within this point group. For the optimized dimer 1(0), the distance a amounts to
4.05 Å and the distance d is 14.02 Å. It should be noted that 1(D2h) is not the dimer with the
lowest energy. Dimer 1(C1), in which the chains are displaced against each other and in
which the angle α(C1-C1'-C12') has a value of 107°, has the minimum energy of the pair of
strands (Figure 2c). Dimer 1(C1) is 1.7 kcal/mol more stable than 1(D2h).
The dimers 1(θ = 90°, 180° and 270°) were calculated as model systems for helix formation.
The computation of these systems was carried out as following: The dihedral angles θ were
fixed at the values 90°, 180° and 270°, respectively. Furthermore, the angle α(C1-C1'-C12')
was fixed to 90° and for the distance a, the optimized value of 1(D2h) was used (4.05 Å). It
can be assumed that the distance between the oligoalkyne chains will not be significantly
changed by helix formation. Therefore, it should be reasonable to use the optimized value of
1(D2h) also for the dimers 1(θ = 90°, 180° and 270°). All other parameters, including distance
d were optimized.
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1(0)
1(90)
1.6
1(180)
1(270)
2(360)
1.7
5.1
25.5
11.1 kcal/mol
3(360)
4.8 kcal/mol
Figure 3. Molecular structures of the model compounds 1(θ = 0°, 90°, 180° and 270°), 2(360)
and 3(360) calculated by means of B3LYP-D3. The relative energies with respect to the C1-
symmetric isomers are also given.
The optimized structures obtained for 1(θ = 90°, 180° and 270°) are depicted in Figure 3. It
can be seen at first glance that increase of the twisting (dihedral angle θ) results in a
decrease of the height d of the chain. For example, d is 14.02 Å in 1(0), 13.75 Å in 1(90),
12.75 Å in 1(180) and 11.50 Å in 1(270). This behavior was anticipated. The energy
distribution of the conformers is remarkable: relative to 1(C1) the dimer 1(270) shows an
energy of 25.5 kcal/mol, dimer 1(180) has a relative energy of only 5.1 kcal/mol (0.43
kcal/mol per acetylene unit) and dimer 1(90) is destabilized by only 1.6 kcal/mol compared to
1(C1). Please note that 1(0) is destabilized by 1.7 kcal/mol relative to 1(C1), and accordingly
1(90) is energetic more favorable than 1(0) (= 1(D2h)). These values show that even with low
energy effort dimeric oligoalkynes can form double helix-like structures. However, with
increasing twisting the energetic destabilization increases strongly.
The curvature of a double helix can also be expressed by the pitch. Thus, 1(90) is a model
for a carbyne double helix, which undergoes a total turn of 360° after 24 acetylene units.
Dimer 1(180) is a model for a carbyne double helix with a pitch of 12 acetylene units. In order
to examine whether the results of the dimers 1 can be extended to higher oligoalkynes, the
dimers 2(C1) and 2(θ = 0° and 360°) as well as the dimers 3(C1) and 3(θ = 0° and 360°) were
optimized in analogy to the above mentioned procedure (Figure 3). The dimers 2(C1) and
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3(C1) have the minimum energies of the pair of strands. The dimers 2 consist of two
dodecayne units and the dimers 3 of two tetracosayne units. Compounds 2(360) and 3(360)
show one complete turn of 360° and are essentially a doubling of 1(180) and a
quadruplication of 1(90), respectively. In the case of 3 the structures were optimized by using
the def-SV(P) basis set.[26] A comparison of the relative energies shows that dimer 2(360) is
compared to 2(C1) energetically disfavored by 11.1 kcal/mol. For dimer 3(360), the energy
difference to 3(C1) amounts to only 4.8 kcal/mol. Please note that 3(360) is energetic more
favorable than 3(0), which exhibits a parallel arrangement of the acetylene chains, by a value
of 1.6 kcal/mol. This behavior is analogous to that found for 1(90) and 1(0). Therefore, it is
justified to extrapolate the predications made for model system 1(θ) to the dimers of carbyne:
The formation of a double helix with a high pitch is possible without large energy effort.
b) Twisted systems for the investigation of Carbon Double Helix
The quantum chemical study mentioned above shows that no high energy effort is needed to
obtain a double helix from two oligoalkyne chains. However, the helix formation won't
proceed spontaneously, especially not with short chains and/or strong twisting.
Thus, a dilemma exists for the synthesis of model compounds with double helix-like
oligoacetylene structures: on the one hand, many acetylene units are required to obtain an
energetically favorable twisting. On the other hand, the synthesis of oligoalkynes with non-
bulky substituents at the terminal carbon atoms leads to unstable compounds. If shorter
model compounds are used, the double helix formation is only weakly pronounced. In order
to solve this problem, we intended to use a system which fixes the ends of the oligoacetylene
chains and at the same time twists them through its scaffold. Systems which should meet
these requirements are imidazole-containing clamps,[27] which have been successfully used
to fix a conformation in flexible systems by chiral induction.[28] In a first step, the oligoalkyne
building blocks were prepared for the synthesis of the model compounds (Scheme 1). We
used diphenyl polyynes as oligoalkynes because of two reasons: first, these compounds can
be easily attached to the imidazole-containing clamps via the phenyl groups[29] and secondly
the diphenyl polyynes show characteristic bands in the UV spectra[30] which should allow the
identification of the twisting by means of CD spectroscopy. After synthesis of the already
known dibromides 6[31] and 7[32], the dibromides 10 and 13 were obtained from the TIPS-
protected alkynes 9 and 12 via a Sonogashira coupling[33] with simultaneous TIPS
deprotection[34] followed by a bromination (Scheme 1). Due to the instability of the
oligoalkynes, it was necessary to use the TIPS group instead of a TMS protective group. The
bromide 14 was synthesized from the benzyl alcohol 12 by a simple bromination reaction. To
our best knowledge the dibromide 13 is up to now the longest isolated oligoalkyne with a
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reactive benzylic or propargylic bromide group. The longest oligoalkyne with a reactive
benzylic or propargylic bromide group was a tetrayne.[35]
Scheme 1. Synthesis of the dibromides 6, 7, 10 and 13. Reaction conditions: i) Et3N, CuI,
PdCl2(PPh3)2, HC≡C-SiMe3, ∆, 99%; ii) 4, Et3N, CuI, PdCl2(PPh3)2, n-Bu4NF×3 H2O, ∆, 66%;
iii) DCM, PBr3, 52%; iv) DMF, CuCl, ∆, 86%; v) Et2O, PBr3, 50%; vi) acetone, AgNO3, N-
bromosuccinimide, 74%; vii) n-BuNH2, H2O, CuCl, [NH3OH]Cl, HC≡C-SiiPr3, 75%; viii)
Cu(OAc)2×H2O, pyridine, Et2O, n-Bu4NF×3 H2O, THF, 96%; ix) DCM, acetone, PBr3, 72%; x)
CH3CN, N-bromosuccinimide, AgF, 97%; xi) n-BuNH2, H2O, CH3OH, CuCl, [NH3OH]Cl,
HC≡C-SiiPr3, 53%; xii) Cu(OAc)2×H2O, pyridine, Et2O, n-Bu4NF×3 H2O, THF; xiii) Et2O, PBr3,
50% (over 2 steps); xiv) DCM, PBr3, 71%.
The dibromides 10 and 13 were prepared in an analogous dimerization; however, due to the
instability of the oligoalkynes, it was necessary to use the TIPS group instead of a TMS
protective group. The bromide 14 was synthesized from the benzyl alcohol 12 by a simple
bromination reaction. To our best knowledge the dibromide 13 is up to now the longest
isolated oligoalkyne with a reactive benzylic or propargylic bromide group. The longest
oligoalkyne with a reactive benzylic or propargylic bromide group was a tetrayne.[35]
The next step was the treatment of the dibromides 6, 7, 10 and 13 in the presence of a base
with the chiral imidazole clamp 16[27] in acetonitrile as solvent. By means of this nucleophilic
substitution of the secondary nitrogen atom at the imidazole, the model compounds 18(1),
18(2) and 18(4) were obtained in 20-44% yields, which is quite good for a
cyclotetramerization reaction (Scheme 2). All model compounds were identified by NMR and
high-resolution mass spectrometry. The analogous synthesis of 18(6) was not successful.
Also a variation of the reaction conditions did not lead to the desired product 18(6). This is
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probably due to the fact that the dibromide 13 tends to decompose under basic conditions
even at room temperature. For this reason, an alternative reaction was carried out via a
dimerization. For this purpose, the oligoalkyne 19, which already contains the imidazole
clamp was prepared and then reacted under the already proven conditions of alkyne
dimerization.[34] Unfortunately, we could not isolate any product. In addition to the model
compounds 18(1), 18(2) and 18(4), the bis(diphenyl) system 17, which possesses no
acetylene units between the phenyl rings, was also prepared.
Scheme 2. a) Synthesis of the clamp-containing systems 17, 18(n) and 19. Reaction
conditions: i) CH3CN, Cs2CO3, ∆, 36%; ii) 18(1): 6, CH3CN, Cs2CO3, ∆, 44%; 18(2): 7,
CH3CN, Cs2CO3, ∆, 33%; 18(4): 10, CH3CN, Cs2CO3, 20%; iii) 14, CH3CN, Cs2CO3, 72%. b)
Definition of the dihedral angles θ1 and θα.
To investigate the structure and to interpret the experimentally determined UV and CD
spectra, 17 and the model compounds 18(n = 1, 2, 4, 6 and 8) were calculated by means of
quantum chemical calculations. The structures were optimized using B3LYP-D3[24,23] and the
basis set def-SV(P)[26]. Subsequently, the UV and CD spectra were simulated using TD-
DFT[36]. The potential PBE0[37] and the basis set 6-31G*[38] were employed.
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17
18(1)
18(2)
18(4)
18(8)
θ1 = -94°
θα = ---
-107°
-16°
-152°
-59°
-173°
-94°
-212°
-140°
Figure 4. Molecular structures and dihedral angles θ1 and θα of 17 and 18(n) (n = 1, 2, 4 and
8) calculated by means of B3LYP-D3/def-SV(P). Below the entire molecules, the extracted
structures of the diphenyl polyyne units shown along the helical axis are depicted. For
definition of θ1 and θα see Scheme 2b.
In Figure 4 the molecular structures of 17 and 18(n) (n = 1, 2, 4 and 8) calculated by means
of B3LYP-D3/def-SV(P) are depicted. The perspective is perpendicular to the helix axis. In
addition to the entire molecules, the extracted structures of the diphenyl polyyne units along
the helical axis are also shown. In the structures of the entire molecules, the imidazole
clamps at the bottoms are arranged in the same orientation. By comparison of the imidazole
clamp positions at the tops, it become obviously that with increasing number of acetylene
units the position of the upper clamps is twisted related to the lower ones. It should be
mentioned that in the case of 17 (without an acetylene unit), the two clamps are almost in
identical positions. The extracted structures of the diphenyl polyyne units illustrate the double
helix formation in the model compounds. To quantify the twisting of the model compounds,
we introduced the dihedral angles θα and θ1 (for definition see Scheme 2). The first
parameter describes the twisting of the pure oligoalkyne chain (θα), the second one (θ1)
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represents the twisting of the entire conjugated diphenyl oligoyne system. For 18(1) a θα
value of -16° and a θ1 value of -107° are found; for 18(8), the θα value is -140° and the θ1
value amounts to -212°. Thus, with increasing number of acetylene units the twist develops.
The driving force for the twist is attractive dispersion interaction which increases with
increasing twisting due to an enlargement of the contact surface between the two strands. In
order to obtain an energy gain for the twisting, we calculated compound 18(8; θα = -22°) in
which the dihedral angle θα was fixed to a value of -22°, whereas all other parameters were
optimized within the point group C1. The energy difference between 18(8; θα = -22°) and
18(8), which shows a θα angle of -140°, amounts to 4.8 kcal/mol. This value can be
considered as extent for the twisting power in 18(8). This result demonstrates that the
concept of twisting towards the formation of double helix-like structures by the imidazole
clamps works.
6.0
4.0
2.0
6.0
4.0
2.0
ε
ε
ε
ε
0.0
8.0
0.0
8.0
6.0
4.0
2.0
6.0
4.0
2.0
ε
0.0
8.0
0.0
8.0
6.0
4.0
2.0
6.0
4.0
2.0
ε
0.0
8.0
0.0
8.0
6.0
4.0
2.0
0.0
6.0
4.0
2.0
0.0
ε
ε
200
300
λ / nm
400
500
200
300
λ / nm
400
500
Figure 5. Measured (left) and calculated (right) UV spectra of 17 and 18(n) (n = 1, 2 and 4).
The calculated UV spectra were simulated by means of TD-B3LYP/6-31G*. The bands A and
B, as well as the vibronic fine structures are also indicated.
The agreement between the calculated structures and the structures in solution can be easily
checked by comparing the measured and calculated CD spectra. CD spectroscopy is very
suitable for the interpretation of twisted structures.[39] In Figure 5 the measured and
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calculated (TD-B3LYP/6-31G*) UV spectra and in Figure 6 the measured and calculated
(TD-B3LYP/6-31G*) CD spectra of 17, 18(1), 18(2) and 18(4) are shown. In addition, the
calculated (TD-B3LYP/6-31G*) UV and CD spectra of 18(6) and 18(8) are depicted in
Figures S3 and S4. As expected, the long-wave range of the model compounds 18(n) is
dominated by the absorption bands of the diphenyl oligoynes. The UV spectra of diphenyl
oligoynes show two significant bands which are indicated in the following as A and B.[40] In
the case of pure diphenyl oligoynes (D2h symmetry), these bands are caused by the
electronic transitions S0 → 1B1u (A band) and S0 → 2B1u (B band).[40] In the one-electron
view, band A corresponds to the transition from HOMO to LUMO. Both HOMO and LUMO
belong to the π system, which is in-plane with the π system of the phenyl units; in the
following this system will be classified as πx. Since the HOMO-LUMO gap decreases with
increasing number of alkyne units, the band underlies a bathochromic shift. The second band
(B) arises from a one-electron transition from the highest occupied molecular orbital of the πy
system (HOMOπy), which lies perpendicular to the π system of the phenyl units, into the
lowest unoccupied molecular orbital of the πy system (LUMOπy). Since the HOMOπy-LUMOπy
gap decreases even more with increasing number of alkyne units, the band is shifted to
higher wavelength with an increasing number of acetylene units.[41,40] The intensity of band B
growths whereas the intensity of band A band diminishes with increasing number of
acetylene units.
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150
100
50
150
100
50
0
0
ε
ε
ε
ε
200
300
400
500
200
300
400
500
-50
-50
-100
100
λ / nm
λ / nm
λ / nm
λ / nm
-100
100
λ / nm
λ / nm
λ / nm
λ / nm
50
0
50
0
200
300
400
500
200
300
400
500
ε
ε
ε
-50
-50
-100
200
-100
200
100
0
100
0
200
300
400
500
200
300
400
500
-100
-100
-200
100
-200
100
0
-100
-200
0
-100
-200
200
300
400
500
200
300
400
500
ε
Figure 6. Measured (left) and calculated (right) CD spectra of 17 and 18(n) (n = 1, 2 and 4).
The calculated CD spectra were simulated by means of TD-B3LYP/6-31G*. The bands A
and B and the vibronic fine structures are also indicated.
The two diphenyl oligoynes in the model systems 18(n) are not conjugated to each other and
are located ca. 4 Å apart from each other. Therefore, we expect only a small splitting of the
chromophore units in the UV and CD spectra.[39] With other words, the same assignment
(band A and B) as for the pure diphenyl oligoynes can be used in the model systems 18(n).
A comparison of the UV spectra of 17 and 18(n) (n = 1, 2 and 4) reveals (Figure 5) that
experiment and simulation match very well. The most obvious difference between the
experimentally determined and the simulated spectra is the vibronic fine structures in the
experimental spectra of 18(n). This vibration with ca. 1950-2100 cm-1 can be assigned to the
C≡C stretching mode.[40] A glance at the CD spectra of 17 and 18(n) (n = 1, 2 and 4) confirms
the agreement of experiment and calculation; only the vibronic fine structure (ca. 2000-2100
cm-1 caused by the C≡C stretching vibration mode) is not taken into account in the simulated
spectra (Figure 6). In contrast to 17, all three model compounds 18(1), 18(2) and 18(4) show
a pattern with a positive Cotton effect followed by a negative one at ca. 300 nm. Please note
that the clamp 16 shows only a negative Cotton effect at 260 nm and a positive one at 240
nm, whereby ∆ε ranges around 20 M-1cm-1.[42] The analysis of the absorption bands shows
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that the pattern with a positive Cotton effect followed by a negative one at ca. 300 nm stems
from band A in the case of 18(1) and 18(2); in the case of 18(4) this pattern is caused by
band B. Band A of the model compound 18(4) shoes only a positive cotton effect at 401 nm.
This matches very well with the calculated spectra (Figure 6). The bands in the CD spectrum
of 18(4) are relatively independent on the solvent and of the temperature (Figures S1 and
S2).
S0 → 2A
S0 → 2B
S0 → 8A
S0 → 8B
Figure 7. Transfer of the electron during the excitation from the ground state to the excited
states 2A, 2B, 8A and 8B which dominate the UV and CD spectra of 18(4) computed by
means of TD-DFT/6-31G*. In all representations the isovalues for the surfaces have the
same amount. The cyan-colored (violet-colored) areas represent the regions where the
electron density is reduced (increased) upon excitation. The excitations S0 → 2A and S0 →
2B represent band A, whereas the excitations S0 → 8A and S0 → 8B represent band B in the
UV and CD spectra of 18(4).
An analysis of electronic excitations of 18(4) shows, that band A is dominated by the
transitions S0 → 2A and S0 → 2B, while band B arises from the transitions S0 → 8A and S0
→ 8B. In the one-electron view, the transitions S0 → 2A and S0 → 2B are electron excitations
within the πx system, while the transitions S0 → 8A and S0 → 8B occur within the πy system.
Accordingly, both transitions are allowed. In Figure 7, the transfer of the electron during the
excitation from the ground state to the excited states 2A, 2B, 8A and 8B of 18(4) computed
by means of TD-DFT/6-31G* is depicted. Based on these it is easy to see that the transition
takes place only within the oligoalkyne chain. Accordingly, the chiral arrangement and the
twisting of the chains can be directly derived from the observed Cotton effects.
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10.1002/chem.201701096
Chemistry - A European Journal
a)
160
80
0
180
280
380
480
ε
-80
-160
λ / nm
b)
160
80
0
180
280
380
480
ε
-80
-160
λ / nm
Figure 8. CD spectra computed by means of TD-DFT/6-31G*, formulas and molecular
structures (viewed from two different sides) of the reference systems I (a) and II (b).
A further hint that the diphenyl oligoalkyne units in 18(4) form a helix-like structure can be
found by comparing the two reference systems I and II (Figure 8). The reference system I
represents the extracted diphenyl oligoalkyne of the B3LYP-D3-optimized structure 18(4).
The unsaturated valences were saturated by hydrogen atoms. The reference system II was
constructed from two diphenyl oligoalkyne units, whereby the distance between the units and
the angle between them are fixed at identical values found in the reference system I. The
difference in the two reference systems is therefore only the twisting of the diphenyl
oligoalkyne units in space: In the reference system I, they are twisted into a helix and in the
reference system II they are only rotated to each other. These different arrangements of the
diphenyl oligoalkyne units in space are noticeable in the CD spectra. The reference system I
exhibits, like the model compound 18(4) from which it is cut out, only a positive Cotton effect
of band A. In the case of reference system II, a pattern with a positive Cotton effect followed
by a negative one is found for band A. This underlines that the diphenyl oligoalkyne units in
18(4) are helically twisted in solution, as also only a positive Cotton effect for band A can be
observed.
Conclusion
Many oligoalkynes are known to have curved structures both in solution and in the solid state
as deformation from a linear geometry costs very little in energy. Here, we were able to show
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10.1002/chem.201701096
Chemistry - A European Journal
by means of quantum chemical calculations that also only a small energetic expense is
needed for the formation of a three-dimensional double helix starting from linear oligoalkyne
chains. The higher the pitch of the double helix, the higher is the required energy input. It is
of interest that in some cases the double helix-like conformation is more stable than the
corresponding conformation with a parallel arrangement of the acetylene chains.
Furthermore, we were able to synthesize model compounds with double helix-like
oligoacetylene structures. In these systems, the two diphenyl oligoalkyne chains were fixed
by a chiral imidazole-containing clamp. The scaffold of the latter also guarantees the twisting
of the oligoalkyne chains. The structural investigation of the chiral model systems were
conducted by UV and CD spectroscopy. Quantum chemical calculations support the
prediction that the diphenyl oligoalkyne units in the chiral model systems are helically twisted
in solution. The observed twisting in these model systems is the first small step towards an
imaginable carbon double helix.
Computational Details
All calculations were performed by using the program packages TURBOMOLE[43] and
Gaussian 09[44]. The geometrical parameters of the stationary points were optimized by
means of B3LYP[23] with the additional empirical dispersion correction D3[24]. In the case of
the dimers 1 and 2, the basis set def2-TZVP[25] was employed. For the dimer 3, the model
systems 17 and 18(n) (n = 1, 2, 4, 6 and 8), the basis set def-SV(P)[26] was used. The dimers
1(C1), 2(C1) and 3(C1) were fully optimized without symmetry restriction. A subsequent
frequency analysis revealed that 1(C1), 2(C1) and 3(C1) do not have negative frequencies.
The dimers 1(0), 2(0) and 3(0) were fully optimized within in the point ground D2h. In the case
of the dimers 1(θ = 90°, 180° and 270°), 2(θ = 360°) and 3(θ = 360°), the dihedral angle θ,
the angle α(C1-C1'-C12') (90°) and distance a (4.05 Å) were fixed, whereas all other
parameters, including distance d were optimized. The optimization of the latter one was
achieved in a step wise way. The optimization of the model systems 17 and 18(n) (n = 1, 2,
4, 6 and 8) was performed within point group C2. A subsequent frequency analysis showed
that the compounds 17, 18(1), 18(2) and 18(8) do not have negative frequencies. In the
compounds 18(4) and 18(6) two weakly negative frequencies are found. However, all of them
have modes below 4.5 cm-1 and belong to the symmetry group a. That means that an
optimization without symmetry restriction would make no difference. Indeed, further
calculations using no symmetry and/or with other starting geometry leads to no improvement
concerning the weakly negative frequencies. For the optimization of compound 18(8; θα = -
22) the dihedral angle θα was fixed to a value of -22°, whereas all other parameters were
optimized within the point group C1. The CD and UV spectra of 17 and of the model
compounds 18(n = 1, 2, 4, 6 and 8) were simulated with time-dependent density functional
15
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10.1002/chem.201701096
Chemistry - A European Journal
theory (TD-DFT)[36], using the potential PBE0[37] and the basis set 6-31G*[38]. The energy,
oscillator strength, and rotatory strength were calculated for each of the 50 lowest singlet
excitations.
Supporting Information
Synthesis of the compounds, CD spectra, cartesian coordinates and absolute energies of all
calculated compounds as well as 1H NMR and 13C NMR spectra of the compounds.
Acknowledgments
This work was generously supported by the Professor Werdelmann-Stiftung
(T167/23664/2013). The authors thank Sven Fabig for helpful support.
References
[1]
(a) E. H. L. Falcao, F. Wudl, J. Chem. Technol. Biotechnol. 2007, 82, 524-531. (b) H.
O. Pierson, Handbook of Carbon, Graphite, Diamond and Fullerenes - Properties,
Processing and Applications, Noyes Publications, Park Ridge, New Jersey, 1993.
C. Frondel, U. B. Marvin, Nature 1967, 214, 587-589.
[2]
[3]
[4]
P. Liu, H. Cui, G. W. Yang, Cryst. Growth Des. 2008, 8, 581-586.
(a) A. K. Geim, K. S. Novoselov, Nat. Mater. 2007, 6, 183-191. (b) K. S. Novoselov, A.
K. Geim, S. V. Morozov, D. Jiang, Y. Zhang, S. V. Dubonos, I. V. Grigorieva, A. A.
Firsov, Science 2004, 306, 666-669.
[5]
H. W. Kroto, J. R. Heath, S. C. O'Brien, R. F. Curl, R. E. Smalley, Nature 1985, 318,
162-163.
[6]
[7]
S. Iijima, Nature 1991, 354, 56-58.
(a) U. H. F. Bunz, Angew. Chem. 1994, 106, 1127-1131; Angew. Chem., Int. Ed.
Engl. 1994, 33, 1073-1076. (b) F. Diederich, Y. Rubin, Angew. Chem. 1992, 104,
1123-1146; Angew. Chem., Int. Ed. Engl. 1992, 31, 1101-1123.
P. P. K. Smith, P. R. Buseck, Science 1982, 216, 984-986.
[8]
[9]
A. G. Whittaker, E. J. Watts, R. S. Lewis, E. Anders, Science 1980, 209, 1512-1514.
A. El Goresy, G. Donnay, Science 1968, 161, 363-364.
[10]
[11]
(a) W. A. Chalifoux, R. R. Tykwinski, Nature Chem. 2010, 2, 967-971. (b) M. M.
Haley, Nature Chem. 2010, 2, 912-913.
[12]
(a) R. Gleiter, G. Haberhauer, Aromaticity and Other Conjugation Effects, Wiley-VCH,
Weinheim, 2012. (b) Carbon-Rich Compounds, Eds.: M. M. Haley, R. R. Tykwinski,
Wiley-VCH, Weinheim, 2006. (c) Modern Acetylene Chemistry, Eds.: P. J. Stang, F.
Diederich, Wiley-VCH, Weinheim, 1995.
16
This article is protected by copyright. All rights reserved.

10.1002/chem.201701096
Chemistry - A European Journal
[13]
[14]
(a) Q. Zheng, J. C. Bohling, T. B. Peters, A. C. Frisch, F. Hampel, J. A. Gladysz,
Chem. Eur. J. 2006, 12, 6486-6505. (b) R. Eastmond, T. R. Johnson, D. R. M.
Walton, Tetrahedron 1972, 28, 4601-4616.
L. Shi, P. Rohringer, K. Suenaga, Y. Niimi, J. Kotakoski, J. C. Meyer, H. Peterlik, M.
Wanko, S. Cahangirov, A. Rubio, Z. J. Lapin, L. Novotny, P. Ayala, T. Pichler, Nat.
Mater. 2016, 15, 634-639.
[15]
[16]
[17]
[18]
[19]
B. Pan, J. Xiao, J. Li, P. Liu, C. Wang, G. Yang, Sci. Adv. 2015, 1, e1500857.
P. Tarakeshwar, P. R. Buseck, H. W. Kroto, J. Phys. Chem. Lett. 2016, 7, 1675-1681.
S. Fabig, G. Haberhauer, R. Gleiter, J. Am. Chem. Soc. 2015, 137, 1833-1843.
G. Haberhauer, R. Gleiter, S. Fabig, J. Org. Chem. 2015, 80, 5077-5083.
(a) S. Szafert, J. A. Gladysz, Chem. Rev. 2006, 106, PR1-PR33. (b) S. Szafert, J. A.
Gladysz, Chem. Rev. 2003, 103, 4175-4206.
[20]
(a) A. Lucotti, M. Tommasini, W. A. Chalifoux, D. Fazzi, G. Zerbi, R. R. Tykwinski, J.
Raman Spectrosc. 2012, 43, 95-101. (b) A. Lucotti, M. Tommasini, D. Fazzi, M. Del
Zoppo, W. A. Chalifoux, M. J. Ferguson, G. Zerbi, R. R. Tykwinski, J. Am. Chem. Soc.
2009, 131, 4239-4244.
[21]
(a) W. A. Chalifoux, R. McDonald, M. J. Ferguson, R. R. Tykwinski, Angew. Chem.
2009, 121, 8056-8060; Angew. Chem., Int. Ed. 2009, 48, 7915-7919. (b) S. Eisler, A.
D. Slepkov, E. Elliott, T. Luu, R. McDonald, F. A. Hegmann, R. R. Tykwinski, J. Am.
Chem. Soc. 2005, 127, 2666-2676.
[22]
[23]
R. Zahradník, L. Šroubková, Helv. Chim. Acta 2003, 86, 979-1000.
(a) B. Miehlich, A. Savin, H. Stoll, H. Preuss, Chem. Phys. Lett. 1989, 157, 200-206.
(b) A. D. Becke, Phys. Rev. A 1988, 38, 3098-3100. (c) C. Lee, W. Yang, R. G. Parr,
Phys. Rev. B 1988, 37, 785-789.
[24]
[25]
(a) S. Grimme, Chem. Eur. J. 2012, 18, 9955-9964. (b) S. Grimme, J. Antony, S.
Ehrlich, H. Krieg, J. Chem. Phys. 2010, 132, 154104.
(a) F. Weigend, R. Ahlrichs, Phys. Chem. Chem. Phys. 2005, 7, 3297-3305. (b) A.
Schäfer, C. Huber, R. Ahlrichs, J. Chem. Phys. 1994, 100, 5829-5835.
A. Schäfer, H. Horn, R. Ahlrichs, J. Chem. Phys. 1992, 97, 2571-2577.
G. Haberhauer, Angew. Chem. 2007, 119, 4476-4479; Angew. Chem., Int. Ed. 2007,
46, 4397-4399.
[26]
[27]
[28]
(a) A. Adam, G. Haberhauer, Chem. Eur. J. 2015, 21, 4333-4339. (b) G. Haberhauer,
Angew. Chem. 2010, 122, 9474-9477; Angew. Chem., Int. Ed. 2010, 49, 9286-9289.
(c) G. Haberhauer, C. Kallweit, Angew. Chem. 2010, 122, 2468-2471; Angew. Chem.,
Int. Ed. 2010, 49, 2418-2421. (d) G. Haberhauer, Angew. Chem. 2008, 120, 3691-
3694; Angew. Chem., Int. Ed. 2008, 47, 3635-3638.
[29]
G. Haberhauer, T. Oeser, F. Rominger, Chem. Eur. J. 2005, 11, 6718-6726.
17
This article is protected by copyright. All rights reserved.

10.1002/chem.201701096
Chemistry - A European Journal
[30]
[31]
T. Luu, E. Elliott, A. D. Slepkov, S. Eisler, R. McDonald, F. A. Hegmann, R. R.
Tykwinski, Org. Lett. 2005, 7, 51-54.
K. N. Houk, S. Menzer, S. P. Newton, F. M. Raymo, J. F. Stoddart, D. J. Williams, J.
Am. Chem. Soc. 1999, 121, 1479-1487.
[32]
[33]
[34]
[35]
[36]
[37]
[38]
B. J. Kim, D. K. Oh, J. Y. Chang, Macromol. Res. 2008, 16, 103-107.
K. Sonogashira, Y. Tohda, N. Hagihara, Tetrahedron Lett. 1975, 16, 4467-4470.
M. A. Heuft, S. K. Collins, G. P. A. Yap, A. G. Fallis, Org. Lett. 2001, 3, 2883-2886.
F. Bohlmann, K. Kieslich, Chem. Ber. 1954, 87, 1363-1372.
F. Furche, R. Ahlrichs, J. Chem. Phys. 2002, 117, 7433-7447.
C. Adamo, V. Barone, J. Chem. Phys. 1999, 110, 6158-6170.
(a) W. J. Hehre, R. Ditchfield, J. A. Pople, J. Chem. Phys. 1972, 56, 2257-2261. (b) R.
Ditchfield, W. J. Hehre, J. A. Pople, J. Chem. Phys. 1971, 54, 724-728.
N. Berova, K. Nakanishi, R. W. Woody in Circular Dichroism: Principles and
Applications, 2nd Edition, Vol. John Wiley & Sons, New York, 2000.
Y. Nagano, T. Ikoma, K. Akiyama, S. Tero-Kubota, J. Am. Chem. Soc. 2003, 125,
14103-14112.
[39]
[40]
[41]
[42]
[43]
E. Fazio, L. D’Urso, G. Consiglio, A. Giuffrida, G. Compagnini, O. Puglisi, S. Patane,
F. Neri, G. Forte, J. Phys. Chem. C 2014, 118, 28812-28819.
Á. Pintér, G. Haberhauer, Modeling of Molecular Properties, Ed.: P. Comba, Wiley-
VCH, Weinheim, 2011.
TURBOMOLE V6.3 2011, A development of University of Karlsruhe and
Forschungszentrum Karlsruhe GmbH, 1989-2007, TURBOMOLE GmbH, since 2007,
available from http://www.turbomole.com, 2011.
[44]
M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R.
Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M.
Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L.
Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T.
Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery Jr., J. E.
Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N.
Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S.
S. Iyengar, J. Tomasi, M. Cossi, N. Rega, N. J. Millam, M. Klene, J. E. Knox, J. B.
Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev,
A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G.
Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, Ö.
Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian 09, Revision
A.02, Gaussien, Inc., Wallingford CT, 2009.
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