Crystal structures of fluorinated aryl biscarbonates and a biscarbamate: A counterpoise between weak intermolecular interactions and molecular symmetry

Article abstract of DOI:10.1039/c0ce00537a

Conformational features and supramolecular structural organization in three aryl biscarbonates and an aryl biscarbamate with rigid acetylenic unit providing variable spacer lengths have been probed to gain insights into the packing features associated wit

Full text of DOI:10.1039/c0ce00537a

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Crystal structures of fluorinated aryl biscarbonates and a biscarbamate:
a counterpoise between weak intermolecular interactions and molecular
symmetry†
a
Amol G. Dikundwar, Ch. Venkateswarlu, Ross O. Piltz, Srinivasan Chandrasekaran and
b
c
b
*
a
*
Tayur N. Guru Row
Received 14th August 2010, Accepted 12th October 2010
DOI: 10.1039/c0ce00537a
Conformational features and supramolecular structural organization in three aryl biscarbonates and an
aryl biscarbamate with rigid acetylenic unit providing variable spacer lengths have been probed to gain
insights into the packing features associated with molecular symmetry and the intermolecular
interactions involving ‘organic’ fluorine. Four structures but-2-yne-1,4-diyl bis(2,3,4,5,6-
pentafluorophenylcarbonate), 1; but-2-yne-1,4-diyl bis(4-fluorophenylcarbonate), 2; but-2-yne-1,4-diyl
bis(2,3,4,5,6-pentafluorophenylcarbamate), 3 and hexa-2,4-diyne-1,6-diyl bis(2,3,4,5,6-
pentafluorophenylcarbonate), 4 have been analyzed in this context. Compound 1 adopts a non-
centrosymmetric ‘‘twisted’’ (syn) conformation, whereas 2, 3 and 4 acquire a centrosymmetric
‘‘extended’’ (anti) conformation. Weak intermolecular interactions and in particular those involving
fluorine are found to dictate this conformational variation in the crystal structure of 1. A single-crystal
neutron diffraction study at 90 K was performed on 1 to obtain further insights into these interactions
involving ‘organic’ fluorine.
pentafluorophenyl prop-2-ynyl carbonate,5 Csp3–H/F–C
Introduction
hydrogen bonds get the preference over the possibility of
relatively stronger and more likely C^C–H/O]C hydrogen
bond.
The presence of fluorine invokes a variety of intra- and inter-
molecular interactions in organic compounds. However, the high
electronegativity associated with the fluorine atom and its
reluctance to readily form hydrogen bonds has been a subject of
debate over the last few years. In this context, compounds con-
taining fluorine have received special attention in material
science and biology.1 The importance of fluorine in organic
compounds, particularly in pharmaceuticals (15% of all phar-
maceuticals contain at least one F atom)2 have evoked consid-
erable interest in recent times mainly in terms of forming weak
but highly directional interactions. Indeed, a number of reports
in early literature3 indicated that organic fluorine does not
contribute to crystal packing. However, in recent times the
ubiquitous occurrence of C–H/F interactions4a along with the
occasional occurrence of F/F and C–F/p interactions4b,c in
a large number of crystal structures have indicated that these
interactions could serve as motifs to build supramolecular
assemblies. We have shown recently that in the structure of
Supramolecular organization in the molecular crystals
involves the considerations of molecular shape, size and
peripheral functionalities along with the molecular symmetry,
repetition and space filling.6,7 Centrosymmetric molecules,
usually occupy inversion centres in the unit cell with the
molecular centre of inversion coinciding the crystallographic
inversion centre leading to the fractional Z0 values as analyzed
by Brock and Dunitz.7 However, there are several reports
where the molecule does not adopt
a centrosymmetric
conformation or even if it does so, the molecular inversion
centre does not coincide with the crystallographic centre of
inversion.8,9 The deviations have been attributed to the reasons
such as psuedo-symmetry,9a frustration and disorder (leading to
high Z0 structures)8b and conformational flexibility of the
molecule.8c
In fact, the conformation of large organic molecules, partic-
ularly in folded form are considered unusual and explained to be
due to ‘‘the steric effect’’.10 However, it has been realized by
Nishio and co-workers11 that unusual conformations result more
as a consequence of weak intermolecular interactions rather than
depend on the contents of the molecule. This feature has been
demonstrated in our earlier work involving specifically C–H/F
interactions.12 The present study is designed to ascertain the
influence of weak intermolecular interactions involving fluorine
in the presence of restrictions induced by the simultaneous
occurrence of molecular and crystallographic symmetry on
conformational control. Scheme 1 lists the four test cases
analyzed in this context, compounds 1, 2 and 4 are aryl biscar-
bonates and 3 is an aryl biscarbamate.
aSolid State and Structural Chemistry Unit, Indian Institute of Science,
Bangalore, 560012 Karnataka, India. E-mail: ssctng@sscu.iisc.ernet.in;
Fax: +91-080-23601310; Tel: +91-080-22932796
bDepartment of Organic Chemistry, Indian Institute of Science, Bangalore,
560012 Karnataka, India. E-mail: scn@orgchem.iisc.ernet.in; Fax: +91 80
23600529; Tel: +91-80-22932404
cBragg Institute, Australian Nuclear Science and Technology Organisation
PMB 1, Menai, NSW, 2234, Australia
† Electronic supplementary information (ESI) available: Fig. S1 and S2,
details of the cohesive energy calculations using CRYSTAL09 package,
Synthesis and characterization details of the compound
but-2-yne-1,4-diyl bisphenylcarbonate. CCDC reference numbers
784067–784071. For ESI and crystallographic data in CIF or other
electronic format see DOI: 10.1039/c0ce00537a
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Experimental
Synthesis and characterization
All reagents and solvents were purchased from Sigma-Aldrich,
Lancaster or Fisher and were used as supplied unless otherwise
stated. All reactions were performed in oven dried apparatus and
were stirred magnetically. Infrared spectra were recorded using
a JASCO FT-IR instrument and the frequencies are reported in
wave numbers (cmꢀ1) and intensities of the peaks are denoted as s
1
(strong), w (weak), m (medium). H and 13C NMR spectra were
recorded on Jeol 300 MHz (75 MHz, 13C) or 400 MHz (100 MHz
13C) NMR spectrometer and calibrated using residual undeu-
terated solvent as an internal reference. 19F NMR spectra were
recorded on a Bruker 400 MHz (376 MHz, 19F) spectrometer and
calibrated using trichlorofluoromethane as an external reference.
Chemical shifts are reported in parts per million and multiplicity
is indicated using the following abbreviations: s (singlet),
d (doublet), t (triplet), q (quartet), m (multiplet), sb (broad
singlet) and db (broad doublet). Mass spectra were recorded on
a Q-TOF electrospray instrument.
Scheme 2 Synthetic schemes for molecules 1, 2, 3 and 4.
Synthetic procedures for compounds 1, 2 and 4
5.99 mmol, 2.2 equiv.) was added and stirred for 10 min. But-
2-yne-1,4-bisoxycarbonylchloride (Bbc-Cl)13 (0.58 g, 2.72 mmol,
1 equiv.) was added over a period of 10 min. The reaction was
followed by TLC till the disappearance of starting material (4 h)
(Scheme 2). The reaction mixture was diluted with dichloro-
methane (30 mL) and water (2 ꢂ 15 mL). The organic layer was
extracted and washed with brine solution (15 mL) and dried over
anhydrous Na2SO4. The crude product was purified carefully by
column chromatography on silica gel (230–400 mesh), eluting
with hexane. Recrystallisation with DCM and pet-ether afforded
3 as a white crystalline solid.
To a solution of pentafluorophenol [or p-fluorophenol for 2] (2
ꢁ
equiv.) in anhydrous dichloromethane (20 mL) at ꢀ10 C, trie-
thylamine (0.83 mL, 5.99 mmol, 2.2 equiv.) was added dropwise.
The solution was stirred for 10 min and but-2-yne-1,4-bisoxy-
carbonylchloride (Bbc-Cl)13 (0.58 g, 2.72 mmol, 1 equiv.) was
added over a period of 10 min and stirred at this temperature for
1 h. The reaction mixture (Scheme 2) was allowed to attain room
temperature. After 4 h, the reaction mixture was diluted with
dichloromethane (30 mL), water (2 ꢂ 15 mL) and brine solution
(15 mL). The organic layer was dried over anhydrous Na2SO4
and the product 1 [or 2] was purified by column chromatography
on silica gel (100–200 mesh), eluting with solution of 5% ethyl
acetate in hexane. Recrystallisation with DCM and pet-ether
afforded the products as white crystalline solids.
Compound 1. Melting point: 113 ꢁC; FTIR (KBr): 1790 (s),
1522 (s), 1231 (s), 966 (s); 1H NMR (300 MHz, CDCl3): d 4.99 (s);
13C NMR (75 MHz, CDCl3): d 150.8, 80.9. 57.4; 19F NMR (376
MHz, CDCl3): d ꢀ152.84 (d, 2F), ꢀ156.77 (t, 1F), 161.63 (t, 2F);
High resolution ESMS (m/z): Found. 528.9758 (calculated for
C18H4O6F10 + Na: 528.9746).
A similar procedure was followed for the synthesis of 4, except
that the starting materials were hex-2,4-diyne-1,6-bisoxy-
carbonyl chloride (Hbc-Cl)14 and pentafluorophenol (2 equiv.)
(Scheme 2).
Compound 2. Melting point: 111 ꢁC; FTIR (KBr): 1752 (s),
1504 (s), 1383 (m), 1272 (s), 972 (s), 783 (m); 1H NMR (300 MHz,
CDCl3): d 7.15 (d, J ¼ 6.8 Hz, 2H), 7.07 (d, J ¼ 6.8 Hz, 2H), 4.90
(s, 2H); 13C NMR: d 161.6, 153.0, 146.82, 122.3, 116.3, 81.0, 56.0;
19F NMR (376 MHz, CDCl3): d ꢀ116.1 (s, 1F); High resolution
ESMS (m/z): Found. 385.0500 (calculated for C18H12F2O6 + Na:
385.0496).
Synthetic procedure for compound 3
To a solution of pentafluoroaniline (2 equiv.) in anhydrous
dichloromethane (20 mL) at ꢀ10 ꢁC, sodium bicarbonate (0.5 g,
ꢁ
Compound 3. Melting point: 178–180 C; FTIR (KBr): 3329
(s), 1722 (s), 1522 (s), 852 (m); 1H NMR (400 MHz, D6DMSO):
d 8.54 (bs, 1H), 4.85 (s, 2H); 13C NMR (400 MHz, D6DMSO):
d 153.0, 87.1, 55.0; 19F NMR (376 MHz, D6DMSO): d ꢀ146.46
(d, 2F), ꢀ159.17 (t, 1F), ꢀ163.96 (t, 2F); High resolution ESMS
(m/z): Found. 527.0060 (calculated for C18H6F10N2 O4 + Na:
527.0066).
Compound 4. Melting point: 85–86 ꢁC; FTIR (KBr): 1798 (s),
1524 (s), 1222 (s), 980 (s); 1H NMR (300 MHz, CDCl3): d 4.99 (s);
Scheme 1 Chemical structures of 1, 2, 3 and 4.
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13C NMR (75 MHz, CDCl3): d 150.8, 72.3, 72.0, 57.7; 19F NMR
(376 MHz. CDCl3): d ꢀ146.46 (d, 2F), ꢀ159.17 (t, 1F), ꢀ163.96
(t, 2F); High resolution ESMS (m/z): Found. 552.9746 (calcu-
lated for C20H4F10 O6 + Na: 552.9741).
ARGONNE BOXES25 software. Merging of intensities and
corrections for detector efficiency, wavelength, secondary
extinction, and time dependent effects were performed using the
Bragg Institute software LAUE4. 6192 integrated intensities
were merged by LAUE4 to 870 symmetry independent intensities
with weighted merging R factor of 6.2%. The refinement of the
structure was done by using the WinGX18 suite of programs by
using initial coordinates of the atomic positions of non-hydrogen
atoms from the X-ray study. After successful refinement of this
model, all hydrogen atoms were located from difference maps
and were introduced into the model. Subsequent refinement of
the positional and anisotropic displacement parameters for all
atoms of the structure led to a final R(obs) of 3.2% for 789
independent reflections with I >2s(I) [Table 1].
Crystallography
X-Ray diffraction datasets were collected on an Oxford Xcalibur
(Mova) diffractometer15 equipped with a EOS CCD detector
ꢀ
using Mo-Ka radiation (l ¼ 0.71073 A). The crystal was main-
tained at the desired temperature during data collection using the
Oxford instruments Cryojet-HT controller.16 All structures were
solved by direct methods using SHELXS-97 and refined against
F2 using SHELXL-97.17 H-atoms were located on the difference
map and refined isotropically. The WinGX package18 was used
for refinement and production of data tables, and ORTEP-319 for
structure visualisation. All ORTEP representations were made
using POV-Ray20 showing ellipsoids at the 50% probability level.
Analysis of the H-bonded and p-interactions was carried out
using PLATON21 for all the structures. Packing diagrams were
generated by using CAMERON.22
Results
But-2-yne-1,4-diyl bis(pentafluorophenylcarbonate), 1
Compound 1 crystallizes in an orthorhombic system, space
group Aba2 with Z ¼ 4, resulting in the molecular axis coinciding
with the crystallographic 2-fold axis (Table 1). The crystal
structure of 1 has a molecule with its pentafluorophenyl
carbonate moieties adopting a ‘‘cisoid’’ position relative to each
other, with the torsion angle, f(O1–C2–C20–O20) being 93.75ꢁ
(Fig. 1(a)). Fig. 1(b) shows the packing features which are
essentially built from C–H/p interactions running along the
b- axis and with C–H/F hydrogen bonds aligned along the
2 fold axis (Table 2). It is noteworthy that the expected ‘‘trans’’
Neutron diffraction experiment was carried out on 1, a crystal
suitable for neutron diffraction was wrapped in aluminium foil
and mounted in the helium flow cryostat of the instrument
KOALA23 at the Bragg Institute, ANSTO, Australia. 12 Laue
images were recorded from the stationary crystal at a tempera-
ture of 90 K with an exposure of 1 h per image. Integrated
intensities were obtained using the LAUEGEN24 and
Table 1 Crystallographic details of compounds 1, 2, 3 and 4
1
DATA
X-Ray
Neutron
2
3
4
CCDC number
Formula
Formula weight
Colour
Crystal morphology
Crystal size/mm
T/K
Radiation
ꢀ
l/A
784067
C18H4O6F10
506.2
Colourless
Block
784068
C18H4O6F10
506.2
Colourless
Block
784069
C18H12O6F2
362.3
Colourless
Needle
784070
C18H4N2O4F10
504.2
Colourless
Plate
784071
C20H4O6F10
530.2
Colourless
Needle
0.2 ꢂ 0.2 ꢂ 0.25
1.20 ꢂ 1.24 ꢂ 1.30
0.15 ꢂ 0.12 ꢂ 0.4
0.1 ꢂ 0.3 ꢂ 0.35
0.12 ꢂ 0.12 ꢂ 0.3
90
90
Neutron
0.7–1.8
150
150
150
Mo-Ka
0.71073
Orthorhombic
Aba2
16.3233(5)
9.9385(4)
10.9883(4)
90
1782.62(1)
4
1.89
0.206
999.9
2.5, 53.7
10 628
162
ꢀ32, 37
ꢀ22, 19
ꢀ24, 24
0.051, 0.113
0.040, 0.105
ꢀ0.281, 0.672
1.053
Mo-Ka
0.71073
Monoclinic
P21/c
14.2326(14)
4.0156(5)
13.8877(12)
98.500(9)
784.99(11)
2
1.53
0.131
372.0
2.9, 26
1530
142
Mo-Ka
0.71073
Monoclinic
P21/c
6.8592(5)
4.8508(3)
27.2014(22)
102.247(6)
884.46(12)
2
1.89
0.202
499.9
3, 26
1731
166
Mo-Ka
0.71073
Monoclinic
P21/c
5.8951(9)
10.1943(16)
17.2447(24)
108.115(5)
984.98(17)
2
Crystal system
Space group
Orthorhombic
Aba2
16.3233(5)
9.9385(4)
10.9883(4)
90
1782.62(1)
4
1.89
0.031
784.1
ꢀ
a/A
ꢀ
b/A
ꢀ
c/A
b/ꢁ
ꢀ
V/A
3
Z
Dcalcd/g mLꢀ1
m/mmꢀ1
F(000)
1.79
0.191
523.9
2.3, 26
1937
171
ꢀ7, 7
q (min, max)
No. unique reflections
No. of parameters
hmin,max
kmin,max
lmin,max
Rall, wR2all
Robs, wR2obs
Drmin, Drmax/e A
4.7, 26.3
870
172
ꢀ15, 15
ꢀ12, 12
ꢀ8, 13
ꢀ17, 17
ꢀ8, 8
ꢀ4, 4
ꢀ5, 5
ꢀ12, 12
ꢀ21, 21
0.067, 0.120
0.050, 0.114
ꢀ0.182, 0.268
1.152
ꢀ17, 17
0.048, 0.090
0.034, 0.086
ꢀ0.189, 0.193
1.053
ꢀ33, 33
0.054, 0.084
0.034, 0.080
ꢀ0.236, 0.199
1.002
0.042, 0.062
0.032, 0.059
ꢀ0.336, 0.361
1.096
ꢀ3
ꢀ
GOF
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conformation got side lined and instead a dissymmetric chiral
H-bonding. Both carbonyl groups point towards the interior of
the molecule and hence offer a sterically hindered accessibly for
the incoming methylene protons thus allowing the C–H/F
hydrogen bond the required priority. It needs to be pointed out
that, amongst the peripheral fluorine atoms, only fluorine atoms
at para position are exclusively involved in the hydrogen bonded
interactions.
conformation gets preferred. The significantly short C–H/ꢁF
ꢀ
hydrogen bond [C(2)–H(2a)/F(3)–C(7); 2.25(1) A, 154(1) ,
Fig. 1(c)] involving a methylene H-atom (H2a) and a fluorine
atom at para position (F3) of the pentafluorophenyl ring appears
to be the main cause for the ‘‘cisoid’’ conformation adopted by
the molecule in the crystal structure. An enhanced acidity of the
methylene protons (NMR chemical shift, d ¼ 4.99), because of
the presence of electron withdrawing pentafluorophenyl
carbonate groups, is yet another significant factor contributing
to the C–H/F hydrogen bond. A close inspection of the struc-
ture (Fig. 1(a)) enumerates the unfavourable orientation of the
carbonyl (C]O) acceptors to participate in the intermolecular
A single crystal neutron diffraction experiment at 90 K was
performed to evaluate the significance of this rather short C–H/
F hydrogen bond. It is imperative that this hydrogen bond is
a root cause for the molecule to adopt the observed conforma-
tion in the crystal structure. Analysis of the neutron diffraction
data, in particular the location of the hydrogen atoms supports
the formation of short C–H/F hydrogen bond. Indeed the H/
ꢀ
F distance from the neutron data is 2.162(8) A as against 2.25(1)
ꢀ
A observed in X-ray diffraction analysis and the corresponding
ꢀ
ꢀ
C–H distance is 1.093(7) A and 0.98(1) A, respectively (Table 2,
Fig. 1(c)). It is of interest to note that this C–H/F interaction
distance is one of the shortest intermolecular C–H/F contact
distances reported till date.
But-2-yne-1,4-diyl bis(4-fluorophenylcarbonate), 2
In an effort to evaluate the nature of organic fluorine and in
particular to check the propensity of formation of C–H/F
hydrogen bond, like the one observed in structure 1 above,
compound 2 was synthesized. It needs to be pointed out that the
peripheral fluorine atoms have been replaced by hydrogen atoms
except for the ones at para position which were involved in short
C–H/F interactions in case of 1. This substitution does not
significantly alter the steric features of the molecule from that
found in structure 1, however it is expected to result in a differ-
ently polarized molecule.26 Further, it will also test the hypothesis
of Nishio and co-workers11 that weak intermolecular interactions
guide unusual conformational features of molecules in crystal
structures.
The compound crystallizes in a monoclinic, centrosymmetric
space group P21/c with Z ¼ 2 (Table 1). The ORTEP and the
packing diagrams are shown in Fig. 2(a) and 2(b), respectively.
Remarkably, the conformation of the molecule is anti [f(O1–
C2–C20–O10) ¼ 180ꢁ] and the structure is devoid of the short
intermolecular C–H/F hydrogen bond observed in 1. The main
stabilizing interaction is a well defined C–H/O hydrogen bond
involving the methylene hydrogen and the oxygen O(1)
(Fig. 2(b)). The F-atom at the para position is now involved in
weak interactions with the aromatic protons. The structure is
further stabilized by the weak C–H/O interactions involving the
carbonyl group (Table 2, Fig. S1, ESI†).
But-2-yne-1,4-diyl bis(pentafluorophenylcarbamate), 3
Based on the nature of the packing motif in structure 2, where
a C–H/O interaction holds the molecules together in anti
fashion (Fig. 2b), it was conjectured that inclusion of a N–H
substitution at the phenolate oxygen position would ensure the
formation of strong N–H/O]C hydrogen bonds which would
stabilize the ensuing crystal structure keeping molecules in anti
form. The compound, 3 was thus synthesized. The phenyl rings
were decorated with fluorine substitution as in compound 1 to
Fig. 1 (a) Molecular structure of 1 (ORTEP diagram drawn with 50%
probability displacement ellipsoids). (b) Packing diagram of 1 showing
intermolecular C–H/F and C–H/p interactions [‘g’ represents a centre
of gravity of the pentafluorophenyl ring]. (c) Molecuꢁlar chain formed via
ꢀ
short C–H/F hydrogen bonds [2.162(8) A, 153.8(5) from neutron data
ꢁ
ꢀ
and 2.25(1) A, 154(1) from X-ray data].
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Table 2 Intermolecular interactions in crystal structures of 1, 2, 3 and 4a
D–H/A
:D–H/A/ꢁ
Symmetry
ꢀ
ꢀ
r(D–A)/A
ꢀ
r(D–H)/A
r(H/A)/A
1 (Both X-ray and neutron data at 90 K)
C2–H2B/F3
X-Ray
0.98(1)
1.093(7)
0.99(2)
1.081(7)
3.174(1)
3.179(5)
3.549(1)
3.551(3)
2.25(1)
2.162(8)
2.75(1)
2.669(7)
154(1)
x, y, z ꢀ 1
Neutron
X-Ray
Neutron
153.8(5)
137(1)
138.5(5)
x, y, z ꢀ 1
C2–H2A/Cg1
1 ꢀ x, ½ ꢀ y, ꢀ1/2 + z
1 ꢀ x, ½ ꢀ y, ꢀ1/2 + z
2 (X-Ray data at 150 K)
C2–H2B/O1
C8–H7/O3
C5–H5/F1
C8–H7/O1
C6–H6/F1
C2–H2A/O2
C9–H8/O2
0.95(2)
0.94(3)
0.94(4)
0.94(3)
0.92(2)
1.01(1)
0.94(1)
3.540(2)
3.784(2)
3.466(2)
3.499(3)
3.542(2)
3.183(2)
3.456(2)
2.64(1)
2.86(2)
2.60(2)
2.68(3)
2.71(3)
2.42(1)
2.76(2)
156(2)
164(3)
151(2)
144(1)
150(2)
130(2)
131(3)
x, y + 1, z
x,ꢀy ꢀ 1/2, z + 1/2
x, ꢀy + 1/2, z ꢀ 1/2
x, ꢀy ꢀ 1/2, z + 1/2
ꢀx, ꢀy + 1, ꢀz + 1
ꢀx + 1, y ꢀ 1/2, ꢀz + 1/2
x, y ꢀ 1, z
3 (X-Ray data at 150 K)
N1–H1N/O2
C2–H2A/O2
C2–H2B/F5
0.76(1)
0.94(2)
0.94(2)
2.857(2)
3.650(3)
3.369(3)
2.10(2)
2.73(2)
2.50(3)
170(3)
163(2)
152(2)
x, y + 1, z
ꢀx, ꢀy, ꢀz
x ꢀ 1, y ꢀ 1, z
4 (X-Ray data at 150 K)
C3–H2A
0.99(3)
3.435(3)
2.49(2)
157(4)
x + 1, y, z
a
Hydrogen atoms in all the structures were located from the difference maps; hydrogen bonds with :D–H/A $ 130ꢁ are shown in the table; Cg1 is the
centre of gravity of the ring formed by the atoms C4–C9.
evaluate the formation of C–H/F hydrogen bond in the pres-
ence of strong N–H/O hydrogen bond.
the torsion angle f(O1–C2–C20–O10) is 180ꢁ. The molecules are
linked together via strong N–H/O hydrogen bonds forming
a molecular chain along the b axis. The weak C–H/F hydrogen
bonds involving the methylene hydrogen and the fluorine atom at
ortho position and the C–H/O hydrogen bonds involving
carbonyl oxygen add further stability to the structure (Table 2;
Fig S2, ESI†).
Compound 3 crystallizes in a monoclinic centrosymmetric
space group, P21/c with Z ¼ 2 (Table 1). Fig. 3(a) and 3(b) show
the molecular structure and the packing features, respectively.
Molecular conformation shows that the pentafluorophenyl
carbamate moieties are ‘‘transoid’’ with respect to each other and
Fig. 2 (a) ORTEP diagram of 2 drawn with 50% probability displacement ellipsoids. (b) Packing diagram showing C–H/O hydrogen bonds along the
b axis.
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Fig. 3 (a) ORTEP diagram of 3 drawn with 50% probability displacement ellipsoids. (b) Packing diagram showing N–H/O]C hydrogen bonds along
b axis.
Hexa-2,4-diyne-1,6-diyl bis(pentafluorophenylcarbonate), 4
anti conformation which can be expected a priori in this family of
compounds.
In order to evaluate the propensity of participation of methylenic
protons in hydrogen bond generation, it was decided to extend
the spacer length by an additional acetylenic unit. Compound 4
was synthesized, wherein the two methylene groups are spaced by
a diacetylenic spacer.
Discussion
There are several issues which have been addressed in the crystal
structure analysis of compounds 1–4. The observation that C–
H/F interaction was preferred over a stronger C–H/O]C
hydrogen bond in the structure of pentafluorophenyl prop-2-ynyl
carbonate,5 opens up an argument regarding the preferences of
interactions formed by fluorine. Structure 1 was contemplated to
possess essentially C–H/F interactions as primary structure
building blocks with no other strong hydrogen bonding potential
that can be associated with the system based on the earlier
structural motif.5 This logic was extended in case of 2 and 4 as
well. Compound 3 provides the evaluation of the propensity of
The crystal structure belongs to a monoclinic, centrosym-
metric space group, P21/c with Z ¼ 2 (Table 1). The conforma-
tion of the molecule is once again anti [f(O1–C3–C30–O10) ¼
180ꢁ; Fig. 4(a)]. Fig. 4(b) shows the packing diagram depicting
the formation of well defined C–H/O]C hydrogen bonds
involving the carbonyl oxygen atom O(2) with methylene
hydrogen, H(2a), forming the molecular chains along a-axis. In
this case, the peripheral fluorine atoms were not found to involve
in any significant hydrogen bonding interactions. Compound 4
thus provides an idealized packing holding the molecules in an
Fig. 4 (a) Molecular structure of 4. (b) Packing diagram showing the C–H/O intermolecular interactions in molecule 4.
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What is revealing is the fact that all the molecules adopt an anti
conformation except for compound 1. The exclusive occurrence
of C–H/F and C–H/p interactions in structure 1 steers the
unusual ‘‘cisoid’’ conformation of the molecule.11 The anti
molecular conformations in structures 2, 3 and 4 show clearly
that due to the absence of C–H/F and C–H/p interactions,
other intermolecular contacts (C–H/O in 2 and 4; N–H/O in
3) take prominence in the packing characteristics.
Cohesive energy calculations27 for compounds 1, 2 and 3
clearly show that structure 1 is stabilized to a greater extent
compared to structure 2 due to the presence of short C–H/F
and C–H/p interactions, whereas structure 3 shows maximum
cohesive energy because of the presence of stronger N–H/O
interactions. In addition, a non-fluoro analogue, but-2-yne-1,4-
diyl bisphenylcarbonate,28 of molecule 1 is a liquid at ambient
conditions exemplifying the role of fluorine atoms in the solid
state packing arrangements of molecules 1 and 2.
It is important to note that, all the structures have Z0 ¼ 1/2
keeping the requirement of molecular symmetry intact. The
appearance of the non-centrosymmetric space group Aba2 for
structure 1 puts the molecular centre at the two-fold symmetry
position whereas, in structures 2–4 (space group P21/c), the
molecular centre coincides with the crystallographic inversion
centre.
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Conclusion
The importance of the interactions involving ‘organic’ fluorine as
a structure directing tool has been demonstrated and its influence
on the conformational control of a flexible molecule has been
investigated. Compounds 1, 2 and 4 provide a clear picture of the
variability in the conformational features depending on the
nature of the weak hydrogen bonds while compound 3 brings out
the robustness of a strong N–H/O]C hydrogen bond.
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14 Hbc-Cl was prepared by the reaction of Hex-2,4-diyne-1,6-diol with
triphosgene; for synthesis of diol see: Y. Weiyan, H. Chuan,
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15 Oxford Diffraction (2009). CrysAlis PRO CCD and CrysAlis PRO
RED. Oxford Diffraction Ltd, Yarnton, England.
Acknowledgements
We thank the DST, India, for the funding under DST-FIST
(Level II) for the X-ray diffraction facility at SSCU, IISc,
Bangalore and Ms. Rumpa Pal for the assistance in theoretical
calculations. Single-crystal neutron diffraction experiment was
carried out at the neutron beam facility of OPAL research
reactor of the Bragg Institute, ANSTO, Australia. AGD thanks
CSIR, New Delhi for a fellowship and the DST for a travel grant
to Australia. CVR thanks CSIR for a Shyama Prasad Mukherjee
fellowship.
16 Oxford instruments, Cryojet XL/HT controller, Oxford Diffraction
Ltd, Yarnton, England.
Notes and references
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27 All the calculations were performed using CRYSTAL09 package at
HF/6-31G** level by using the coordinates obtained from the
experimental structures determined at 90 K (compound 1) and 150
K
(compounds 2 and 3), further details are given in the
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28 Synthetic procedure and characterization details of the compound
but-2-yne-1,4-diyl bisphenylcarbonate are provided in the ESI†.
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