Crystal Engineering of 1-Halopolyynes by End-Group Manipulation

Article abstract of DOI:10.1021/acs.cgd.9b00987

Polyynes are compounds with two or more conjugated carbon-carbon triple bonds. Such molecules are usually regarded as models of carbyne- A hypothetical one-dimensional allotropic form of carbon. 1-Halopolyynes are rare representatives of such species, but few interesting crystal-to-crystal reactions have been recently reported for them. Herein, we present 11 new X-ray structures of 1-halopolyynes, nearly doubling the number of such compounds characterized with the use of single-crystal X-ray diffraction. The influence of an end-group on packing motifs in crystal structures of the 1-halopolyynes were thoroughly examined. Especially the strength of halogen bond as a function of polyyne chain length was analyzed with the support of theoretical calculations. Moreover, the compound CNC₈I is the longest 1-halopolyyne characterized to date with the use of rentgenostructural analysis. In addition to that, the compounds NO₂C₆Br and MeC(O)C₆Br are the first 1-bromohexatriynes characterized by means of X-ray single-crystal diffraction.

Full text of DOI:10.1021/acs.cgd.9b00987

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Article
Crystal Engineering of 1-Halopolyynes by End-Group Manipulation
Bart#omiej Pigulski, Nurbey Gulia, Patrycja M#cik, Robert Wieczorek, Agata Arendt, and Slawomir Szafert
Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.9b00987 • Publication Date (Web): 18 Sep 2019
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Crystal Engineering of 1-Halopolyynes by End-
Group Manipulation
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AUTHOR NAMES Bartłomiej Pigulski,* Nurbey Gulia, Patrycja Męcik, Robert Wieczorek,
Agata Arendt, Sławomir Szafert*
AUTHOR ADDRESS Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie, 50-
383 Wrocław, Poland
KEYWORDS polyynes, halogen bond, alkynes, X-ray crystallography
ABSTRACT
Polyynes are compounds with two or more conjugated carbon-carbon triple bonds. Such
molecules are usually regarded as models of carbyne – hypothetical one-dimensional
allotropic form of carbon. 1-Halopolyynes are rare representatives of such species but few
interesting crystal-to-crystal reactions have been lately reported for them. Herein, we present
11 new X-ray structures of 1-halopolyynes nearly doubling the number of such compounds
characterized with the use of single crystal X-ray diffraction. The influence of an end-group
on packing motifs in crystal structures of the 1-halopolyynes were thoroughly examined.
Especially the strength of halogen bond as a function of polyyne chain length was analyzed
with the support of theoretical calculations. Moreover, compound CNC8I is the longest 1-
halopolyyne characterized to date with the use of rentgenostructural analysis. In addition to
that, compounds NO2C6Br and MeC(O)C6Br are the first 1-bromohexatriynes characterized
by means of X-ray single crystal diffraction.
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INTRODUCTION
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The synthesis and properties of polyynic compounds – exciting linear carbon rods – have
been attracting an interest of scientific community for a long time.1-4 Polyynes are usually
regarded as mimics of hypothetical linear allotropic form of carbon – carbyne. This makes the
exploration of spectroscopic and structural properties of such carbon rods a very attractive
task. Crystallographic studies of longer polyynes gives very valuable insight into possible
structure of carbyne.5-6 For instance, Tykwinski and co-workers reported a significant
reduction in the bond length alternation as a function of the polyyne length and such trend
seems to be saturated before cumulenic structure is achieved.7 Moreover, polyynes might be
used as valuable precursors in various chemical transformation.8 They also possess a
significant potential as molecular wires and switches,9-13 NLO (nonlinear optics) materials,14-
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or even in live-cells imaging and sorting.21 It is worth to note that such unusual structural
motif may be found in many natural products.22 Theoretical calculations reported by
Yakobson and co-workers suggest that carbyne might be about twice as stiff as the stiffest
known materials.23 Isolation of exceptionally long carbon chains encapsulated in double-
walled carbon nanotubes (polyynes@DWCNTs) was recently reported and it gives hope that
bulk carbyne might be accessible someday.24 Moreover, the formation of polyynes induced by
atomic manipulation of their dibromoolefin precursors has been reported very recently.25
Our recent research has been focused on 1-halopolyynes i.e. polyynes that contain at least
one halogen end-group. Such compounds exhibit unusual reactivity in for instance
mechanoactivated coupling with pyrroles,26-27 allow for the formation of amine end-capped
polyynes28-31 or might be used in the synthesis of fluorescent dyes.32 Moreover, 1-
halopolyynes are versatile substrates for palladium(II)33-34 or iridium(III) end-capped
polyynes.35 Examples of X-ray structures of 1-halopolyynes, especially homologs longer than
butadiyne, are rather sparse. According to the CSD,36 for now only one structure containing
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(CC)2Cl structural motif37 and four structures containing (CC)2Br38-40 motif are known.
Moreover, 11 structures with (CC)2I motif37,41-46 and 3 with (CC)3I42,47 motif were reported.
Except for one 1-iodobutadiyne structure37 all the others are different cocrystals of I(CC)nI
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(n = 2, 3). Structures of pure I(CC)nI compounds are not known due to the fact that they
form needle-like crystals that are disordered along one axis.43 Despite the rarity of 1-
halopolyynes, some interesting crystal-to-crystal transformations of such compounds have
been reported. For instance, Frauenrath and co-workers discovered unprecedented crystal-to-
crystal dimerization of 1-bromobutadiyne that involves unusually large atom displacements
associated with bond cleavage and formation of new bonds (Scheme 1, upper left part).38 It is
noteworthy, that it was possible to measure X-ray single crystal structure before and after the
reaction. Similar reaction was carried out for 1-bromohexatriyne but only microcrystalline
samples were obtained (Scheme 1, upper right part).
Halogen bond is an extremely powerful tool that may be used in crystal engineering.48
Goroff and co-workers reported topochemical polymerization of diiododiacetylene templated
by Lewis base host molecules (Scheme 1, down).43,49 Strong halogen bond between
diiodobutadiyne and the host molecules forced butadiyne molecules to adopt geometry
appropriate for such polymerization. As a result, poly(diiododiacetylene) (PIDA) was
obtained. The same strategy was next used for more unstable dibromodiacetylene.39
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a)
HO
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Ph3
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Br
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b)
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O
Scheme 1. Crystal-to-crystal reactions of 1-halopolyynes: a) dimerization of 1-
bromobutadiyne and 1-bromohexatriyne; b) polymerization of diiododiacetylene templated by
Lewis base host molecule.
The abovementioned examples of an extraordinary crystal-to-crystal reactivity of 1-
halopolyynes makes an understanding of factors that allow to control packing motifs of such
molecules what is very valuable in a context of crystal engineering.
Herein we report 11 new structures of 1-halopolyynes nearly doubling the number of such
compounds characterized with the use of single crystal X-ray diffraction. The use of one non-
halogen end-group allowed to obtain crystal structures of pure 1-halopolyynes to be compared
with the X(CC)nX series. Moreover, structure of CNC8I is the only known structure of 1-
halooctatetrayne. In addition to that, thorough analysis of packing motifs and intermolecular
interactions was performed. Especially an influence of linear carbon chain on C-X bond as
well as on intermolecular halogen bonds was investigated.
EXPERIMENTAL SECTION
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General. All reactions were conducted under N2 with the use of standard Schlenk
techniques. Glassware was pre-dried at 120 C. Solvents were treated as follows: hexane was
distilled from Na, THF was distilled from Na/benzophenone, CH2Cl2 was distilled from P2O5,
and CH3CN (HPLC grade) was used as received. Known 1-halopolyynes27,33-34,50 and 1-
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haloalkynes
(1-(bromoethynyl)-4-fluorobenzene
and
1,2,3,4,5-pentafluoro-6-
(iodoethynyl)benzene51-52 were obtained according to the known procedures. CuI (Aldrich,
99%), Pd(PPh3)2Cl2 (Aldrich, 98%), diisopropylamine (Aldrich, 99.5%), AgF (Alfa Aesar,
98%), NIS (N-iodosuccinimide, Alfa Aesar, 97%), trimethylsilylacetylene (Fluorochem, 98%)
were used as received.
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1H, C and F NMR spectra were recorded on a Bruker Avance 500 spectrometer. For all
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the H NMR spectra, the chemical shifts are given in ppm relative to the solvent residual
peaks. For 13C NMR spectra, the chemical shifts are given in ppm relative to the solvent peaks
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(CDCl3, H: 7.26 ppm, C: 77.2 ppm,). For the F NMR spectra, hexafluorobenzene was
used as an internal standard (-165 ppm). Coupling constants are given in Hz. HRMS spectra
were recorded using Bruker apex ultra FT-ICR and MicOTOF-Q spectrometers with ESI ion
source. IR spectra were recorded using a Bruker 66/s FTIR spectrometer. Microanalyses were
conducted with an Elementar CHNS Vario EL III analyzer.
X-ray single crystal diffraction.
The structurally analyzed compounds were crystallized from their hexane or hexane/CH2Cl2
solutions. X-ray diffraction data were collected with a Kuma KM4 CCD of Xcalibur Onyx (
scan technique) diffractometers. The space groups were determined from systematic absences
and subsequent least-squares refinement. Lorentz and polarization corrections were applied.
The structures were solved by direct methods and refined by full-matrix, least-squares on F2
by use of SHELXTL package.53 Non-hydrogen atoms were refined with anisotropic thermal
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parameters. Hydrogen atom positions were calculated and added to the structure factor
calculations, but were not refined. Absorption corrections were applied with the use of
CrysAlisPRO.54 Mercury 3 software was used for crystal and molecular structures plots.55
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Computational details.
The molecular orbital studies on isolated molecules of MeC(O)C4Cl, MeC(O)C4Br,
MeC(O)C6Br, CNC4I, CNC6I, CNC8I, NO2C4I, NO2C4Br, NO2C6Br, C6F5C6I and FC4I
compounds have been performed at the DFT level of theory. Gaussian 09 C.0156 suite of
programs using the B97X-D57 long-range corrected hybrid density functional with damped
atom-atom dispersion corrections was used with DGDZVP for Cl, Br, I and 6-311G(2d,2p)
for N, O, C, H atoms basis set. All presented structures are fully optimized with tight (as
defined in Gaussian) convergence criteria. All isolated molecules are thermodynamically
stable. The atomic charges have been calculated on the base of full NBO analysis, the
CHELPG (Charges from Electrostatic Potentials using a Grid based method) with scheme by
Merz, Singh and Kollman58-59 with fitting atom radii using Universal Force Field.60 The
molecular electrostatic potential (MEP) as a predictive reactivity factor of the molecule has
been presented on isosurface of the total electron density 0.0004 e/au3 using the GaussView
5.08 software.61
Hirshfeld Surface Analysis. Hirshfeld surfaces and the fingerprint plots were generated
using CrystalExplorer,62 which utilizes a structure input file in CIF format. The distance from
the Hirshfeld surface to the nearest atoms outside and inside the surface are characterized by
the de (external) and di (internal) values, respectively. The normalized contact distance based
on these values is dnorm= (di − rivdW)/rivdW + (de − revdW)/revdW, where rivdW and revdW
are the van der Waals radii of the external and internal atoms. The dnorm is encoded on
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Hirshfeld surface with colors: red – the highest value, blue – the lowest value. The 2D
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histograms, with fingerprints, plot de versus di.
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Syntheses.
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((4-Fluorophenyl)buta-1,3-diyn-1-yl)trimethylsilane (FC4TMS)
1-(Bromoethynyl)-4-fluorobenzene (0.769 g, 3.86 mmol) was dissolved in 40 mL of dry and
oxygen-free THF and then ethynyltrimethylsilane (0.82 mL, 5.7 mmol), CuI (0.029 g, 0.15
mmol), and Pd(PPh3)2Cl2 (0.055 g, 0.31 mmol) were added. Next diisopropylamine (1.37 mL,
9.66 mmol) was added dropwise and then the mixture was stirred for 3.5 h under N2. The
solvent was removed under reduced pressure and the residue was purified by silica gel
chromatography (hexanes) yielding 0.279 g (1.29 mmol) of white solid. Yield 33%. 1H NMR
(500 MHz, CDCl3): δ = 7.49 – 7.45 (m, 2H , HAr), 7.04 – 6.98 (m, 2H, HAr), 0.23 (s, 9H,
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Si(CH3)3); C NMR (126 MHz, CDCl3): δ = 163.3 (d, JCF = 251.8 Hz), 134.9 (d, JCF = 8.6
Hz), 117.6 (d, JCF = 3.6 Hz), 116.0 (d, JCF = 22.2 Hz), 90.9 (s), 87.8 (s), 75.8 (s), 74.1 (d, , JCF
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= 1.6 Hz), -0.3 (s); F NMR (471 MHz, CDCl3): δ = -111.5 (m, C-F); FTIR (cm-1, KBr
pellet): 2208(C≡C), 2102(C≡C); Elemental analysis: Calcd for C13H13FSi: C 72.18%, H
6.06%, found: C 72.13%, H 6.34%.
Trimethyl((perfluorophenyl)hexa-1,3,5-triyn-1-yl)silane (C6F5C6TMS)
1,2,3,4,5-Pentafluoro-6-(iodoethynyl)benzene (0.873 g, 2.751 mmol) was dissolved in 10 mL
of dry and oxygen-free THF and then buta-1,3-diyn-1-yltrimethylsilane (0.403 g, 3.301
mmol), CuI (0.021 g, 0.110 mmol), and Pd(PPh3)2Cl2 (0.039 g, 0.055 mmol) were added.
Next diisopropylamine (0.97 mL, 6.86 mmol) was added dropwise and then the mixture was
stirred for 1.5 h under N2. The solvent was removed under reduced pressure and the residue
was purified by silica gel chromatography (hexanes) yielding 0.199 g (0.637 mmol) of white
solid. Yield 23%. 1H NMR (500 MHz, CDCl3): δ = 0.24 (s, SiMe3, 9H); 19F NMR (471 MHz,
CDCl3): δ = -137.2 – -137.3 (m, 2F), -152.4 (tt, J = 20.7, 2.6 Hz, 1F), -163.8 – -163.9 (m, 2F);
13C NMR (126 MHz, CDCl3): δ = 150.4 – 147.9 (m), 144.1 – 141.4 (m), 139.1 – 136.6 (m),
99.0 – 98.6 (m), 92.1 (s), 87.4 (s), 85.60 (q, J = 3.5 Hz), 70.4 (s), 60.1 (q, J = 3.9 Hz), 60.1
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(s), -0.5 (s); IR (cm-1 nujol mull): 2047 (C≡C), 2077 (C≡C); Elemental analysis: Calcd for
,
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C15H9F5Si: C 57.69%, H 2.90%, found: C 57.77%, H 2.52%.
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1-Fluoro-4-(iodobuta-1,3-diyn-1-yl)benzene (FC4I)
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((4-Fluorophenyl)buta-1,3-diyn-1-yl)trimethylsilane (0.079 g, 0.370 mmol) was dissolved in
10 mL of acetonitrile and next H2O (13 μL) and AgF (0.046 g, 0.370 mmol) and NIS (0.102
g, 0.438 mmol) were added. The flask was wrapped in aluminum foil and the mixture was
stirred for 2 h at room temperature. The solvent was removed under reduced pressure and the
residue was purified by passing the mixture through the silica gel (hexanes:CH2Cl2; v/v; 1/1)
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yielding 0.096 g (0.35 mmol) of white solid. Yield 97%. H NMR (500 MHz, CDCl3): δ =
7.50 – 7.45 (m, 2H , HAr), 7.04 – 6.99 (m, 2H, HAr); 13C NMR (126 MHz, CDCl3): δ = 163.4
(d, JCF = 252.0 Hz), 135.3 (d, JCF = 8.6 Hz), 117.1 (d, JCF = 3.6 Hz), 116.7 (d, JCF = 22.3 Hz),
78.3 (s), 74.9 (d, JCF = 1.6 Hz), 72.9 (s), 2.7 (s); 19F NMR (471 MHz, CDCl3): δ = -111.2 (m,
C-F); FTIR (cm-1, KBr pellet): 2208(C≡C), 2112(C≡C); Elemental analysis: Calcd for
C10H4FI: C 44.48%, H 1.49%, found: C 44.72%, H 1.50%.
1,2,3,4,5-Pentafluoro-6-(iodohexa-1,3,5-triyn-1-yl)benzene (C6F5C6I)
Trimethyl((perfluorophenyl)hexa-1,3,5-triyn-1-yl)silane (C6F5C6TMS, 0.061 g, 0.196 mmol)
was dissolved in 7 mL of acetonitrile and next H2O (7 μL), AgF (0.025 g, 0.196 mmol) and
NIS (0.055 g, 0.235 mmol) were added. The flask was wrapped in aluminum foil and the
mixture was stirred for 1 h at room temperature. The solvent was removed under reduced
pressure and the residue was purified by elution through silica gel (hexanes) yielding 0.042 g
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(0.115 mmol) of yellow solid. Yield 58%. F NMR (471 MHz, CDCl3): δ = -137.11 – -
137.23 (m, 2F), -152.12 (tt, J = 20.6, 2.7 Hz, 1F), -163.68 – -163.81 (m, 2F); 13C NMR (126
MHz, CDCl3): δ = 150.5 – 148.0 (m), 144.1 – 141.6 (m), 139.2 – 136.6 (m), 98.8 – 98.4 (m),
85.1 (q, J = 3.6 Hz), 78.7 (s), 71.1 (s), 59.4 (q, J = 3.8 Hz), 57.3 (s), 5.6 (s); IR (cm-1 nujol
,
mull): 2080 (C≡C), 2166 (C≡C); HRMS(ESI): m/z calcd for C12HF5I: 366.9043 [M+H+];
found: 366.9037.
RESULTS AND DISCUSSION
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First, we have decided to obtain a series of 1-halopolyynes with one non-halogen end group
in order to be able to crystallize them without a necessity of using host molecules. That was
not possible for previously reported symmetrical X(CC)nX molecules. Moreover,
unsymmetrical 1-halopolyynes are far more stable than dihalopolyynes34 so the synthesis and
crystallization of longer 1-halopolyynes were possible. The new 1-halopolyynes FC4I and
C6F5C6I were obtained according to standard Cadiot-Chodkiewicz/halogenation procedure.
Other polyynes were known and we have reported their syntheses in recent years.27,33-34,50 In
order to investigate an impact of an end-group on a crystal structure of 1-halogenopolyynes,
11 compounds with different substituents on aryl end-group were obtained in crystalline form
(Figure 1). Most of the analyzed compounds possess one end-group that is halogen bond
acceptor and CCX end-group that is strong halogen bond donor. Thus they may be regarded
as linear carbon rod-linked XB donor-acceptor molecules. Only compounds FC4I and
C6F5C6I possess fluorinated phenyl end-groups that are not able to act as halogen bond
acceptors. Another target was to determine whether the length of the polyyne chain may have
an impact on the strength of halogen bond and on the packing motifs in general. The CNCnI
series is the most valuable here especially due to the fact that crystal structure of para-
NCC6H4CCI (CNC2I) was already reported and could be included in such analysis.51
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NO2
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NO2
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Cl
MeC(O)C4Cl
Br
Br
MeC(O)C4Br
Br
Br
NO2C6Br
MeC(O)C6Br
NO2C4Br
N
N
F
N
F
F
F
NO2
F
F
I
I
I
I
I
I
CNC4I
CNC6I
C6F5C6I
CNC8I
NO2C4I
FC4I
Figure 1. 1-Halopolyynes used in this study.
Molecular structure plots of all analyzed 1-halopolyynes are presented in the Supporting
Information (Figures S1-S12). Summarized bond lengths in the polyyne chain are presented in
the Table 1 and the contraction coefficients are presented in the Table 2. Due to resonance
effect, triple bonds in such carbon rods are longer than typical “isolated” triple bond whereas
single bonds are significantly shorter. This effect is observed due to some contribution of
cumulene resonance form in the structure of polyynes.5-6 Generally, longer carbon chain
means longer triple bonds and shorter single bonds and it seems that this trend is saturated
since certain point.7 Moreover, longer polyynes are quite flexible systems and sp-carbon chain
is very often substantially distorted.5-6
Contraction coefficient is a useful parameter that is used for measuring a distortion of
polyyne chains (Table 2).5-6 Such parameter may be calculated with (chain from X to CAr) or
without (chain form C1-CAr-1) first atoms of end-groups (where CAr-1 is the closest sp carbon
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to phenyl ring, and CAr the first carbon of phenyl ring). Generally, longer polyyne chain
usually means higher deformation. In the presented structures, most polyynes are almost
linear (contraction coefficients in the 0.02-0.05 or 0.02-0.09% range). However, the
compound FC4I is rather highly distorted (contraction coefficients: 0.11% and 0.25%,
respectively) despite its short butadiyne chain. Also hexatriynes C6F5C6I (contraction
coefficients: 0.09% and 0.16%, respectively) and NO2C6Br (contraction coefficients: 0.08%
and 0.12%, respectively) are quite distorted. It is not surprising that the longest polyyne
CNC8I is the most distorted one with contraction coefficients 0.55% and 0.60%.
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The CNCnI series may be also used to investigate the influence of carbon chain length on
the C-X distance (Table 1). Longer sp-carbon chain starts to be more and more electron
deficient what may impact the C-I bond. Hence, known compound CNC2I51 compared with
longer homologues has visibly longer C-I bond length (2.009(2) Å) and this trend seems to be
present along the whole series (2.002(3) Å for CNC4I, 1.991(2) Å for CNC6I, 1.989(5) Å for
CNC8I). However, for longer compounds the differences are similar to standard deviations so
we decided to perform theoretical calculations to confirm that trend. Selected calculated bond
lengths for all 1-halopolyynes are in the Supporting Information (Tables S4-S7). Calculated
C-I bond lengths for CNCnI series are 1.999 Å for CNC2I, 1.994 Å for CNC4I, 1.992 Å for
CNC6I and 1.992 Å for CNC8I. Thus theoretical calculations suggests that this trend is
already saturated for CNC8I. Such changes in C1-X bond length are consistent with C1
13
carbon chemical shift in C NMR. Shorter C-I bond should cause stronger shielding and
lower chemical shift. Indeed, 13C NMR chemical shifts for C-I are: 13.1 ppm for CNC2I,51 6.4
ppm for CNC4I,33 4.2 ppm for CNC6I34 and 3.7 ppm for CNC8I.34 Opposite trend could be
observed for C1-C2 bond. Shortening of C1-I bond for longer polyyne chain is associated
with an elongation of C1-C2 bond. That all may be an effect of increasing contribution of
cumulene resonance form in the structure of polyyne (Scheme 2). The fact of growing
contribution of cumulenic resonance form along with carbon chain elongation is known and
well documented.5-7
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Table 1. Bond lengths in polyyne chains.
5
6
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X
C1 C2 C3 C4 C5 C6 C7 C8
R
8
9
C5-C6 - only for hexatriynes and octatetrayne
C7-C8 - only for octatetrayne
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Compound
Bond length [Å]
C1-X
C1—C2
C2—C3
C3—C4
C4—C5 C5—C6 C6—C7 C7—C8
CAr-1—
CAr
1.431 (4)
MeC(O)C4Cl
NO2C4Br
1.649(3)
1.794(1)
1.792(3)
1.782(3)
1.796(3)
1.194(5)
1.198(2)
1.198(4)
1.375(4)
1.371(2)
1.377(4)
1.205(5)
1.209(2)
1.201(4)
1.425 (2)
1.428 (4)
1.429 (4)
1.424 (4)
MeC(O)C4Br
NO2C6Br
1.186(4) 1.382 (4) 1.200 (4) 1.370 (4) 1.200 (4)
1.199(4) 1.372 (4) 1.212 (4) 1.376 (4) 1.207 (4)
MeC(O)C6Br
Aa
MeC(O)C6Br
1.787(3)
1.202(4) 1.368 (4) 1.209 (4) 1.379 (4) 1.200 (4)
1.193(3)
1.429 (4)
Ba
CNC2I25a
2.009(2)
2.002(3)
2.022(3)
1.996(4)
1.991(2)
1.985(3)
1.989(5)
1.438(3)
1.426 (4)
1.425 (4)
1.437(5)
1.431 (2)
1.424 (4)
CNC4I
NO2C4I
FC4I
1.203(4)
1.162(4)
1.211(6)
1.377(4)
1.398(4)
1.362(6)
1.205(4)
1.200(4)
1.202(6)
CNC6I
C6F5C6I
CNC8I
1.210(2) 1.364 (2) 1.217 (2) 1.369 (2) 1.200 (2)
1.199(4) 1.374 (4) 1.207 (4) 1.365 (4) 1.207 (4)
1.209(6) 1.367 (7) 1.214 (7) 1.394 (7) 1.174 (7) 1.362 (7) 1.213 (7) 1.426 (6)
aTwo molecules in the asymmetric unit.
I
•
•
•
•
N
I
N
n-1
n-1
Scheme 2. Polyynic and one of the possible cumulenic resonance forms for CNCnI series.
Table 2. Contraction coefficients.
C1-CAr-1a [%]
X-CArb [%]
0
CNC4I
FC4I
0
0.11
0.05
0.05
0.02
0.05
0.25
MeC(O)C4Br
MeC(O)C4Cl
NO2C4Br
NO2C4I
0.09
0.07
0.03
0.04
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C6F5C6I
CNC6I
0.09
0.03
0.03
0.02
0.08
0.55
0.16
0.02
0.05
0.02
0.12
0.60
MeC(O)C6Br Ac
MeC(O)C6Br Bc
NO2C6Br
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CNC8I
aContraction C1-CAr-1 = ((C1-CAr-1-sum of bond lengths−C1-CAr-1 distance)/C1-CAr-1 sum of
bond lengths)×100ꢀ%; bContraction X-CAr = ((X-CAr sum of bond lengths−X-CAr distance)/X-
CAr sum of bond lengths)×100ꢀ%; cTwo molecules in the asymmetric unit.
Packing Analysis.
If substituent on an aryl group may form halogen bond with CCX moiety then packing
motif of the crystal structure is quite predictable. The use of MeC(O)-, O2N- or NC- group
usually results in rather similar arrangements. In the crystal structures for MeC(O)C4Cl,
NO2C4Br, MeC(O)C4Br, MeC(O)C6Br, CNC4I, NO2C4I, CNC6I and CNC8I
intermolecular CCX∙∙∙A halogen bond is the strongest intermolecular interaction (Figure 2).
Linear 1-halopolyyne molecules form one-dimensional chains due to those interactions. Then,
such chains are grouped into layers because of C-H∙∙∙π(polyyne) interactions (Figure 2).
Those layers interact with each other by stacking π∙∙∙π interactions to give formally 3D-
structures. A little different situation is for NO2C6Br. Here, also strong CBr∙∙∙O interactions
might be observed (Figure 3) but 1-halopolyyne molecules form zig-zag chains that are also
grouped into layers due to C-H∙∙∙π(polyyne) interactions.
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Figure 2. Crystal structures of MeC(O)C4Cl, NO2C4Br, MeC(O)C4Br, MeC(O)C6Br,
CNC4I, NO2C4I, CNC6I and CNC8I.
Figure 3. Crystal structure of NO2C6Br.
If there is no end-group that is halogen bond acceptor then other interactions start to play a
crucial role. For instance, in the crystal structure of FC4I, I∙∙∙I interactions (3.741 Å) are
present (Figure 4). Such interactions are slightly shorter than sum of van der Waals radii (3.98
Å) and facilitate formation of I∙∙∙I bonded belts.
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Figure 4. Crystal structure of FC4I.
Different situation is observed in C6F5C6I crystal structure (Figure 5), where there are no
I∙∙∙I contacts. Instead, strong π∙∙∙π intractions between perfluorinated phenyl rings and polyyne
chains are observed. Such contacts might be regarded as analogues of C6H6/C6F6 strong
interactions63-64 which are useful tool in crystal engineering.65 CHELPG electrostatic potential
calculations are in accordance with that (see Theoretical Calculations) and polyyne chain is
electron deficient whereas there is a positive electrostatic potential on perfluorinated phenyl
ring.
Figure 5. Crystal structure of C6F5C6I.
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Halogen bond plays a crucial role in intermolecular interactions in most of the structures. It
is known that the polarizing effect of sp-carbon in combination with electron-withdrawing
effect of phenyl ring substituent should lead to highly electrophilic halogen atoms and thus
strong halogen bonds.66-68 The geometrical parameters of the CCX∙∙∙D interactions are
summarized in the Table 3. The Cl∙∙∙O halogen bond in the structure of 1-chlorobutadiyne
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(RXD = 0.94) is significantly weaker than Br∙∙∙O interaction in the 1-bromopolyynes (RXD
=
0.83-0.86). Since iodine forms stronger halogen bonds than bromine or chlorine it is not
surprising that I∙∙∙O and I∙∙∙N interactions in the structures of 1-iodopolyynes are even
stronger. Comparing to the literature such halogen bonds should be regarded as very strong.69
Inspired by the fact that the length of C-I bond is influenced by the length of polyyne chain
we decided to investigate an impact of chain length on I∙∙∙N distance for CNCnI series. The
packing motif of CNC2I crystal structure is similar to its longer homologues thus it was
included in this analysis. The difference between I∙∙∙N distance in CNC2I (2.962(3) Å) and in
the crystal structures for longer CNCnI homologs (n = 4, 2.883(3) Å; n = 6, 2.881(2) Å; n = 8,
2.888(5) Å) is significant but this trend seems to be quickly saturated. Moreover, the
shortening of Br∙∙∙O interaction is observed for NO2C4Br and NO2C6Br pair (2.915 Å and
2.880 Å, respectively). The trend in Br∙∙∙O interactions for MeC(O)C4Br and MeC(O)C6Br
crystal structures is not so clear. The Br∙∙∙O distance for MeC(O)C4Br is 2.880(3) Å whereas
in the crystal structure of MeC(O)C6Br - where there are two molecules in two asymmetric
unit - it is 2.815(2) Å or 2.894(2) Å.
Table 3. Geometrical parameters of halogen bonds in structures of 1-halopolyynes.
Compound
X∙∙∙D
sym.
X∙∙∙D [Å]
RXD
[%]
0.94
0.86
∠(CXD) [deg]
Equivalence
1+x,y,1+z
-1+x,y,1+z
MeC(O)C4Cl
NO2C4Br
Cl∙∙∙O
Br∙∙∙O
3.062(3)
2.915(2)
173.07(13)
174.10(5)
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MeC(O)C4Br
NO2C6Br
Br∙∙∙O
Br∙∙∙O
1+x,y,1+z
1-x,-1/2+y,3/2-z 2.880(3)
2-x,1-y,-z 2.815(2)
-x,-1/2+y,1/2-z 2.894(2)
2.880(3)
175.44(11)
173.31(12)
179.89(10)
173.14(10)
175.17(2)
176.96(11)
176.90(10)
178.11(7)
178.45(18)
0.85
0.85
0.83
0.86
0.84
0.82
0.84
0.82
0.82
MeC(O)C6Bra Br∙∙∙O
MeC(O)C6Bra Br∙∙∙O
CNC2I25a
CNC4I
NO2C4I
CNC6I
CNC8I
I∙∙∙N
I∙∙∙N
I∙∙∙O
I∙∙∙N
I∙∙∙N
-1+x, y, 1+z
1+x,y,-1+z
1+x,y,-1+z
2+x,y,-1+z
2.962(3)
2.883(3)
2.935(3)
2.881(2)
2.888(5)
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aTwo molecules in the asymmetric unit; RXD = (X∙∙∙D)/(rX + rD) where rX and rD are the van
b
der Waals radii.70
Theoretical Calculations.
We decided to calculate CHELPG electrostatic potentials (Charges from Electrostatic
Potentials using a Grid based method) in order to investigate the ability for halogen bond
formation for all 1-halopolyynes. Especially an impact of carbon chain length on electrostatic
potential on halogen atom was interesting. Higher electrostatic potential should lead to
stronger halogen bond with the same electron pair donor. CHELPG potentials are summarized
in the Table 4, whereas electron density isosurface plots are shown in Figure 6. The
experimental trend in the length of I∙∙∙N interaction for CNCnI series seems to be consistent
with calculated CHELPG values. CHELPG value on iodine atom for CNC2I is 0.163 whereas
for longer analogues it is significantly higher (0.207, 0.210, 0.213 for n = 4, 6 and 8,
respectively). This quick saturation of the trend is consistent with halogen bond lengths for
this series of 1-halopolyynes (Table 4). An increase of electrostatic potential on halogen
atoms with increasing carbon chain length is also observed for MeC(O)C4Br and
MeC(O)C4Br pair (CHELPG = 0.159 and 0.175) as well as for NO2C4Br and NO2C6Br pair
(CHELPG = 0.172 and 0.185). The NBO (Natural Bond Orbital) values are consistent with
CHELPG values and the same trends are observed.
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Table 4. The NBO (Natural Bond Orbital) charges and charges from electrostatic potentials
(CHELPG) of halogen atoms.
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Compound
MeC(O)C4Cl
MeC(O)C4Br
MeC(O)C6Br
CNC2I
NBO [e]
0.139
0.225
0.232
0.344
0.360
0.367
0.371
0.129
0.231
0.237
0.349
0.369
CHELPG [e]
0.109
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0.159
0.175
0.163
CNC4I
0.207
CNC6I
0.210
CNC8I
0.213
NO2C4I
0.361
NO2C4Br
NO2C6Br
FC4I
0.172
0.185
0.179
C6F5C6I
0.221
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Figure 6. The charges from electrostatic potentials (CHELP) of 1-halopolyynes. The red color
on electron density isosurface indicates maximum of negative values of electrostatic potential
and the blue color indicates the maximum of positive electrostatic potential.
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Hirshfeld Surface Analysis
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The intermolecular contacts in the crystal structures of all 1-halopolyynes were analyzed by
Hirshfeld surface studies using CrystalExplorer software.71 The shape and size of Hirshfeld
surface is related to the intermolecular contacts between atoms and in addition to that some
properties (like curvature) may be encoded with the use of colors.72 This analysis may be also
visualized as two-dimensional (di, de) fingerprint graph.73 Such graph brings more information
than simple measurements of distances between atoms and is a perfect way to visualize
various intermolecular interactions. Here dnorm values are encoded with colors: red – the
highest value, blue – the lowest value.
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The packing motifs of all 1-halopolyynes that have strong electron pair donor end-
group (MeC(O)C4Cl, NO2C4Br, MeC(O)C4Br, NO2C6Br, MeC(O)C6Br, CNC4I, NO2C4I,
CNC6I and CNC8I) are quite similar and their interactions are visible due to Hirshfeld surface
analysis as well as related fingerprint plots are rather analogous. As an example, more
detailed analysis was conducted here for CNC8I. Hirshfeld surface plots and fingerprint
graphs of all 1-halopolyynes are in the Supporting Information (Figures S13-S24).
Fingerprints and Hirshfeld surface for CNC8I are shown in Figure 7 (top). Main features of
the fingerprint may be assigned to strong interactions. Strong C-I∙∙∙N halogen bond is clearly
visible on fingerprint plot as sharp spikes denoted with letter a. Moreover, weaker Csp2-
H∙∙∙π(polyyne) interactions are visible as more blurred shapes that are denoted with letter b.
Flat shape of molecule facilitates π∙∙∙π interactions between polyyne systems that might be
also visible on fingerprint plot (Figure 7, down).
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Figure 7. a) Fingerprint plot (upper, left) and Hirshfeld surface of CNC8I (upper, right); b)
fingerprint plot (lower, left)) and Hirshfeld surface of CNC8I (lower, right) with π∙∙π
interaction underlined (down).
Intermolecular interactions in the structure of FC4I are different than in structures with the
presence of X∙∙∙O or X∙∙∙N halogen bonds. Significant I∙∙∙I interactions a are visible as sharp
needles on fingerprint plot (Figure 8). Also some alkyne π∙∙∙H-C interactions might be
observed as more blurred shapes b. Moreover, numerous weaker π∙∙∙π stacking interactions
are present in the crystal structure and are denoted with the letter c.
Figure 8. Fingerprint plot and Hirshfeld surface of FC4I.
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The situation is different when there is no possibility of halogen bond formation and other
interactions start to play more important role. Fingerprint plot and Hirshfeld surface of
C6F5C6I are shown in Figure 9. The C-F∙∙∙I interactions are clearly visible as sharp spike on
fingerprint plot and are denoted with the letter a. In addition to that few F∙∙∙F interactions may
be observed (b). In this case the flat shape of the molecule as well as high affinity of C6F5
moiety to electron poor polyyne chains also facilitates close and strong π∙∙∙π contacts denoted
here with letter c. The strongest π∙∙∙π interactions are observed between C6F5 moiety and the
electron poor polyyne chain of the other molecule. Moreover, some C-F∙∙∙π contacts may be
observed (d).
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Figure 9. Fingerprint plot and Hirshfeld surface of C6F5C6I.
CONCLUSIONS
We have reported 11 new crystal structures of 1-halopolyynes greatly increasing the
number of such compounds characterized by X-ray single crystal diffraction. Compound
CNC8I is the longest known 1-halopolyyne characterized with the use of such method to date.
Moreover, the first two crystal structures of 1-bromohexatriynes were reported herein. The
impact of an end-group on packing was analyzed and if halogen bond acceptor end-group is
used then crystal structure might be predicted with good accuracy. In other cases halogen-
halogen or π-π interactions may start to play more crucial role. An influence of the length of
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sp-hybridized carbon chain on the C-X bond distance was analyzed. Longer polyyne chain
means stronger halogen bond formed by 1-halopolyyne. However, this trend seems to be quite
quickly saturated and the biggest difference is between simple 1-haloalkyne and 1-
halobutadiyne. This might be important information in future prediction of crystal structures
for new 1-halopolyynes.
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ASSOCIATED CONTENT
The Supporting Information is available free of charge on the ACS Publications website at
DOI: .
X-ray crystallography details, molecular structures of 1-halopolyynes, Hirshfeld surfaces,
calculated bond lengths, and NMR spectra of all new compounds (PDF)
Accession Codes CCDC 1866791-1866801 contain the supplementary crystallographic data
for
this
paper.
These
data
can
be
obtained
free
of
charge
via
www.ccdc.cam.ac.uk/data_request/cif, or by emailing data_request@ccdc.cam.ac.uk, or by
contacting The Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2
1EZ, UK; fax: +44 1223 336033.
AUTHOR INFORMATION
Corresponding Authors
*(S.S.) E-mail: slawomir.szafert@chem.uni.wroc.pl
*(B.P.) E-mail: bartlomiej.pigulski@chem.uni.wroc.pl
ORCID
Bartłomiej Pigulski: 0000-0002-9925-2878
Sławomir Szafert: 0000-0002-0570-884
Author Contributions
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The manuscript was written through contributions of all authors. All authors have given
approval to the final version of the manuscript.
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ACKNOWLEDGMENT
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The authors would like to thank the National Science Centre Poland (Grants UMO-
2015/19/B/ST5/02917 and UMO-2017/25/N/ST5/01062) and the National Centre for
Research and Development (Grant TANGO1/266660/NCBR/2015) for support of this
research.
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