An Organic Receptor Isolated in an Unusual Intermediate Conformation: Computation, Crystallography, and Hirshfeld Surface Analysis

Article abstract of DOI:10.1021/acs.jpca.7b00091

1,1″-1,4-Phenylene-bis(methylene)bis-4,4′-bipyridinium cation [C₂₈H₂₄N₄]²⁺ (c), an organic receptor that generally crystallizes in its anti conformation, has recently been shown to be isolated in its syn conform

Full text of DOI:10.1021/acs.jpca.7b00091

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Article
An Organic Receptor Isolated in an Unusual Intermediate Conformation:
Computation, Crystallography and Hirshfeld Surface Analysis
Indravath Krishna Naik, Rudraditya Sarkar, Vedichi Madhu,
Ramababu Bolligarla, Ravada Kishore, and Samar Kumar Das
J. Phys. Chem. A, Just Accepted Manuscript • DOI: 10.1021/acs.jpca.7b00091 • Publication Date (Web): 06 Apr 2017
Downloaded from http://pubs.acs.org on April 11, 2017
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An Organic Receptor Isolated in an Unusual Intermediate
Conformation: Computation, Crystallography and Hirshfeld
Surface Analysis
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Indravath Krishna Naik, Rudraditya Sarkar, Vedichi Madhu, Ramababu Bolligarla,
Ravada Kishore and Samar K. Das*
School of Chemistry, University of Hyderabad, Hyderabad 500 046, India
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ABSTRACT: 1,1"ꢀ1,4ꢀphenyleneꢀbis(methylene)bisꢀ4,4'ꢀbipyridinium cation [C H N ] (c),
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an organic receptor that generally crystallizes in its antiꢀconformation, has recently been shown
to be isolated in its synꢀconformation in an ion paired compound [C H N ][Zn(dmit) ] ⋅ 2DMF
2
8
24
4
2
2‒
(
dmit = 1,3ꢀdithioleꢀ2ꢀthioneꢀ4,5ꢀdithiolate). In this article, we have demonstrated that the same
2
+
receptor [C H N ] (c) can also be stabilized in an unusual intermediate conformation (neither
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‒
syn nor anti) with PF6 anion in compound [C H N ](PF ) ⋅(1,4ꢀdioxane) (1·(1,4ꢀdioxane)).
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6 2
The energetically favored anti conformation has been described in its nitrate salt
C H N ](NO ) ⋅2H O (2·2H O). Compounds 1·(1,4ꢀdioxane) and 2·2H O, crystallizing in
[
2
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3 2
2
2
2
triclinic and monoclinic systems with space groups Pꢀ1 and P2 /n respectively, have additionally
1
been characterized by Hirshfeld surface analysis. The density functional theory calculations are
performed to understand the internal mechanism of the stability of various conformers of
cationic receptor c, compound 1 and compound 2. In conjunction with the electronic stability of
the conformers, the natural bond orbital analysis and conformational equilibrium constants at
different temperatures are also calculated to find out the sources of the different stability of the
various conformers of experimentally synthesized compounds.
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■
INTRODUCTION
Intermolecular interactions in the solid state continue to be a topic of great interest in the field of
supramolecular as well as materials chemistry because of its fundamental importance for the
formation of higher organized chemical systems that result from the association of two or more
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chemical species. Depending upon the function and need of selectivity in the molecular
assembly processes, several types of weak but specific (mostly noncovalent) intermolecular
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4
interactions are involved that include ion pairing, hydrogen bonding, areneꢀarene (πꢀπ)
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ꢀ7
8ꢀ10
stacking interactions etc. The biological processes,
that encounter such nonꢀcovalent
interactions, are substrateꢀenzyme complex formation, the protein folding, the formation of
membranes, antiportation of neutral and ionic species through membranes etc. In these
intermolecular interactions, particularly between substrate and receptor (e.g., the active site of
the enzyme), the receptor is generally flexible to undergo conformational changes to
1
1
accommodate the substrate in an optimal geometry, comparable to ‘lockꢀandꢀkey fit’ situation.
Mimicking such conformational change using a specific substance is a great challenge to
modern chemistry researchers. Many captivating, structurally diverse receptors (hosts) have been
designed and synthesized for the purpose of studying the interactions between the receptor (host)
1
2
and substrate (guest). Besides wellꢀcharacterized macrocycles (hosts), e.g., cyclophanes,
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cyclodextrins, cryptophanes, cucurbiturils, carcerands, supramolecular capsules etc.,
acyclic compounds with cavities of flexible size, that are generally termed as molecular tweezers
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and clefts, proved to be effective synthetic receptors. A molecular tweezer is defined as a
synthetic receptor that contains two aromatic (complexing) chromophores connected by a single
spacer. A cleft is nothing but a molecular tweezer having converged functional groups
(receptors) that are separated by 10ꢀ12 Å (with the help of the spacer) to create a cavity for
1
9
guest/substrate binding. We report here an organic acyclic receptor cation having two aromatic
sideꢀarms (4,4’ꢀbipyridines) connected by a single spacer (1,4ꢀphenyleneꢀbis(methylene)),
2
+
namely, 1,1"ꢀ1,4ꢀphenyleneꢀbis(methylene)bisꢀ4,4'ꢀbipyridinium cation [C H N ] (c), which
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4
can interconvert between its synꢀ / (cleftꢀlike) and antiꢀ conformations as shown in Scheme 1
left and right respectively). The receptor cation c can also be isolated in an unusual intermediate
(
conformation (Scheme 1, middle). In this contribution, we have described synthesis and crystal
structures of [C H N ](PF ) ⋅(1,4ꢀdioxane) (1·(1,4ꢀdioxane)) and [C H N ](NO ) ⋅ 2H O
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6 2
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3 2
2
(2·2H O) having an intermediate and antiꢀconformation respectively. The hexafluorophosphate
2
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–
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(
PF ) salts of the same cation c have been reported earlier: in one of these, c is in antiꢀform
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and in other salt, c has a similar conformation, found in 1·(1,4ꢀdioxane). However, both
reports focused only on their respective crystal structures of the concerned hexafluorophosphate
–
(
PF ) salts including their supramolecular sturctures. We have undertaken this work to compare
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the synꢀ and antiꢀconformations of c in 1·(1,4ꢀdioxane) and 2·2H O respectively emphasizing
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the role of hydrogen bonding of surrounding anions. We have also performed Hirshfeld surface
analyses on the crystal structues of 1·(1,4ꢀdioxane) and 2·2H O to rationalize the molecular
2
conformations of c in their respective salts.
In order to understand the unusual conformation of the cation c in compound 1·(1,4ꢀ
dioxane), we performed quantum mechanical calculations using density functional theory and
we tried to understand internal mechanism of the stability of different conformers of the cationic
receptor c, compound 1 and compound 2. The electronic stability of the conformers were
analyzed by considering isodesmic reaction between the cationic receptor c and donor anions,
–
–
PF6 and NO , following the principles of thermodynamics. The different conformational
3
analyses of the compound 1 have been performed by fixing the 1Nꢀ24Cꢀ52Cꢀ29N dihedral angle
at different values (see in the text for details). On the other hand, stability of these compounds on
excitation is also measured by evaluating the energy gap between highest occupied molecular
orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) at the electronic ground state
of the respective compounds. The possible interactions between the occupied donor orbitals and
unoccupied acceptor orbitals in these compounds are also calculated by using secondꢀorder
perturbation theory as implemented in natural bond orbital analysis (NBO). As a result of these
analyses, the sources of the different stabilities of the various conformers of the respective
compounds can be accounted and results are discussed in details in the text. At last, we
calculated the equilibrium constants of various conformational equilibria among the different
conformers of the respective compounds to confirm the results of the above analyses by taking
the experimental conformational equilibrium constant values between the cisꢀ2ꢀbutene and transꢀ
2ꢀbutene at different temperature as a reference.
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Scheme 1
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Syn- / Cleftꢀlike
Intermediate
Anti-
■
EXPERIMENTAL, PHYSICAL AND THEORETICAL METHODS
Physical measurements. All reagents and solvents were commercially available and used
without further purification. Elemental analysis (C, H and N) were obtained with a FLASH EA
–
1
1112 Series CHNS analyser. FTꢀIR spectra were recorded in the range 400ꢀ4000 cm with a
1
JASCO FT/IRꢀ5300 spectrometer using KBr pellet. H NMR spectra were recorded on Bruker
DRXꢀ 400 spectrometer using Si(CH ) as an internal standard.
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Synthesis of compound [C H N ](PF ) ⋅(1,4ꢀdioxane) (1⋅(1,4ꢀdioxane)). 150 mg (0.568
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6 2
mmol) of 1,4ꢀbis(bromomethyl)benzene, dissolved in 10 mL of dry acetonitrile, were added
dropwise to a refluxing solution of 4,4'−bipyridine (500 mg, 3.2 mmol) in 10 mL of acetonitrile.
The reaction mixture was then refluxed for additional 2 h. The [C H N ]Br salt came out as
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2
insoluble white solid. The precipitate was washed with acetonitrile and dried in vacuum. This
product was then dissolved in warm water and subsequently, it was treated with NH PF . This
4
6
'
'
results in the precipitation of [C H N ](PF ) (1,1–1,4ꢀphenyleneꢀbis(methylene)bis–4,4ꢀ
2
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6 2
bipyridinium–bis(hexafluorophosphate). Yield: 0.276 g (~70%). This can be described as crude
PF salt of c, [C H N ](PF ) . This crude product was recrystallized by the vapor diffusion of
6
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6 2
diethylether into a solution of [C H N ](PF ) in a mixed solvents of DMF:1,4ꢀdioxane (1:3)
2
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6 2
into the single crystals of [C H N ](PF ) ⋅(1,4ꢀdioxane) (1·(1,4ꢀdioxane)). Anal. Calcd. for
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6 2
(C H F N O P ): C, 48.37; H, 4.06; N, 7.05. Found: C, 48.26; H, 4.11; N, 7.12. IR (KBr
3
2
32 12
4
2 2
ꢀ
1
pellet) (υ/cm ) :3134s, 3074w, 2150w, 1699m, 1639s, 1502m, 1460s, 1421m, 1215s, 1184m,
1
1010m, 835s, 557s, 515w. H NMR (DMSOꢀd ): δ 9.28(d, J=6.647, 4H); 8.81(d, J=6.51, 4H);
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.62(d, J=6.48, 4H); 7.97(d, J=6.491, 4H); 7.66(S, 4H); 5.89(S, 4H).
Synthesis of compound [C H N ](NO ) ⋅2H O (2⋅2H O). Compound 2⋅2H O was
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synthesized by an ion exchange method as follows: 0.07 g (0.1 mmol) of [C H N ](PF ) was
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taken in a 10mL round bottom flask and 0.034 g (0.2 mmol) of AgNO was taken in an another
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0mL round bottom flask.Then the two round bottom flasks were fitted into two terminals of a λꢀ
shaped glass tube. Then the whole λ tube was filled by CH CN solution keeping the whole
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system closed. After two weeks, colorless needleꢀshaped crystals of [C H N ](NO ) ⋅ 2H O
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(2⋅2H O) were deposited on the top of the λ tube. Yield: 0.048 g (84%). Anal. Calcd. for
2
(C H N O ): C, 58.33; H, 4.89; N, 14.58. Found: C, 58.26; H, 4.95; N, 14.49. IR (KBr pellet)
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8
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6
8
ꢀ1
ꢀ
(υ/cm ) for 2⋅2H O: 3323m, 3107w, 3020w, 1633s, 1593w, 1545m, 1523m, 1493m, 1350 (NO
2
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)s, 1211w, 1161m, 1070w, 895w, 823s, 771s, 727m, 513m, 478w.
Xꢀray crystallography. [C H N ](PF ) ⋅(1,4ꢀdioxane) (1⋅(1,4ꢀdioxane)) was measured at
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100 K and [C H N ](NO ) ⋅ 2H O (2⋅2H O) was measured at 298 K on a Bruker SMART
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2
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APEX CCD area detector system [λ(MoꢀKα) = 0.71073 Å] with a graphite monochromator.
o
2400 frames were recorded with an ω scan width of 0.3 , each for 8 s. Crystalꢀdetector distance
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was 60 mm with a collimator of 0.5 mm. The SMART software was used for intensity data
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acquisition and the SAINTPLUS software was used for data extraction. Absorption correction
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was performed with the help of SADABS program. Programs of SHELXꢀ97 were used for
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structure solution by direct methods and leastꢀsquare refinement on F . All nonꢀhydrogen atoms
were refined anisotropically. Hydrogen atoms on aromatic ring were introduced on calculated
positions and included in the refinement riding on their respective parent atoms. We tried to
locate the hydrogen atoms of solvent water molecules in the crystal structure of compound
2
⋅2H O through differential Fourier maps, but could not succeed. Therefore the O–H···O
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hydrogen bonding distances in the supramolecular structure of water in compound 2⋅2H O have
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been described as O···O separations (taking O···O distance in the range of 2.395 Å to 2.950
Å). Detailed information about crystal data and structure determination are summarized in Table
1.
Computational methods. Computational simulations of the different conformers of
cationic receptor c, compound 1 and compound 2 were performed with density functional theory
2
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(DFT) as implemented in Gaussian 09 suite programming package. Computational data
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25ꢀ29
evaluation through out the present study were performed with B3LYP hybrid functional,
which includes HartreeꢀFock (HF) exchange as well as DFT exchange correlations. The nonꢀ
local correlations part is taken care by Lee, Yang and Parr (LYP) functional. All calculations
were performed using Pople’s 6ꢀ31G(d,p) basis set. The calculations of minimum energy
conformers of the cationic receptor c, compound 1 and compound 2 were confirmed by
subsequent frequency calculations of the optimized geometry at the ground state of the
respective conformers. We note that no imaginary frequency was found at the optimized
geometry of the conformers. The first thirtyꢀfour lowest frequencies of each conformer are given
in Table S1 in the supporting information.
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Natural bond orbital (NBO) analysis was performed to find out the different intra
molecular interactions in cationic receptor c, compound 1 and compound 2 The possible
interaction between the filled donor orbital (i) and vaccent acceptor orbital (j) was accounted in
(2)
the NBO analysis. The stabilization energy of the donorꢀacceptor interaction [E (i,j)] was
(2)
calculated by secondꢀorder perturbation theory. The stabilization energy [E (i,j)] associated
with the electron delocalization between the donor (i) and acceptor (j) orbitals can be expressed
as:
(1)
Where, q is the orbital occupancy, E , E are diagonal elements and F are the offꢀ
i
i
j
i,j
diagonal elements of the NBO Fock matrix.
Equilibrium constant (K) between the different conformers of cationic receptor c and
compound 1 were calculated by considering the ratio of number of reactant (r, more stable
25ꢀ29
conformer) and product (p, less stable conformer) molecules at equilibrium.
and p can be expressed as:
The ratio of r
(2)
Where, N , N are the number of product and reactant molecules at equilibrium. The partition
p
r
functions of the product and reactant are designated as q , q , respectively. ∆E is the total energy
p
r
difference between the reactant and product and R is the universal gas constant. T represents the
temperature in Kelvin. So the equilibrium constant of these conformers can be expressed as:
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(3)
or,
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vib
rot
vib
rot
Where qp , qp , qr and qr are the vibrational and rotational partition functions of the
product and reactant, respectively. The translational partition functions of reactant and product
are equal and hence cancel out. The electronic ground states of product and reactant are nonꢀ
degenerate; hence electronic partition function is unity. To validate the above Eq. (4), we
calculated the equilibrium constants (K) between cisꢀ2ꢀbutene and transꢀ2ꢀbutene, conformers of
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2ꢀbutene at different temperatures and compared with the available experimental values. The
calculated rotational constants, symmetry numbers of these conformers are given in Table S2 in
the Supporting information. The rotational and vibrational partition functions of these
conformers at different temperature are given in Table S3 in the Supporting information. This
comparison between the experimental and theoretical K values of cisꢀ2ꢀbutene ⇌ transꢀ2ꢀbutene
equilibrium at different temperatures is given in Table S4 in the Supporting information. It is
found that theoretically evaluated K values between cisꢀ2ꢀbutene and transꢀ2ꢀbutene equilibrium
30
are in good accord with the experimental values. The values of rotational constants, symmetry
rot
vib
number, q and q of the conformers of cationic receptor, compound 1 and compound 2 are
also given in the Tables S2 and S3 in the Supporting information to make the theoretical analysis
more easier in latter sections.
■
RESULTS AND DISCUSSION
Synthesis. The crude [C H N ](PF ) is synthesized from 1,4ꢀbis(bromomethyl)benzene
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6 2
and 4,4'−bipyridine (Scheme 2). This crude solid is then crystallized from DMFꢀ1,4ꢀdioxane to
obtain the single crystals of compound [C H N ](PF ) ⋅(1,4ꢀdioxane) (1⋅(1,4ꢀdioxane)). The
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nitrate salt (compound 2⋅2H2O) could not be synthesized from a direct method, but this can be
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Scheme 2
+
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Reflux
2PF6ꢀ
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N
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Scheme 3
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CH CN
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PF6-
2NO3-
AgNO3
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N
N
prepared from the crude PF ꢀsalt of compound 1.(1,4ꢀdioxane) by an ion exchange method with
6
1
silver nitrate (Scheme 3). Compounds 1 and 2 have been characterized by IR spectral studies, H
NMR studies including elemental analyses and finally unambiguously by single crystal Xꢀray
crystallography.
Crystal structure description and discussion. The bromide salt of the title cationic
2+
receptor [C H N ] (c), [C H N ]Br was structurally characterized and the usual antiꢀ
2
8
24
4
28 24
4
2
conformation of the cation c (Scheme 1, right) is found in the crystal structure of
21
[
C H N ]Br . When these offꢀwhite crystals of [C H N ]Br are suspended in MeCN
28 24 4 2 28 24 4 2
solvent with few drops of DMF ([c]Br crystals are not soluble in this medium) dissolving an
2
excess amount of [Bu N] [Zn(dmit) ] and stirred for about an week, the offꢀwhite solid of
4
2
2
[C H N ]Br becomes dark brown with the conversion of [C H N ][Zn(dmit) ]⋅in a solidꢀ
2
8
24
4
2
28 24
4
2
liquid interface crystalline state reaction. In the redꢀbrown solid of compound
2
+
[
C H N ][Zn(dmit) ], the cationic receptor [C H N ] (c) has synꢀconformation (Scheme 1,
28 24 4 2 28 24 4
31
left), as observed in the crystal structure of [C H N ][Zn(dmit) ]⋅ 2DMF. By exploiting the
2
8
24
4
2
2+
flexible nature of this acyclic cationic receptor [C H N ] (c), we could demonstrate the
28
24
4
reversible synꢀanti conformational change of c in solid to solid antiformations (equation 1). We
2
+
wanted to exploit further the flexible nature of [C H N ]
2
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[
C H N ][Zn(dmit) ]⋅ 2DMF (solid phase) + [Bu N]Br (soln. Phase)
2
8
24
4
2
4
⇌ [C H N ]Br (solid phase) + [Bu N] [Zn(dmit) ] (soln. Phase) (equation 1)
2
8
24
4
2
4
2
2
(c)
by crystallizing this cation with diverse anions and we synthesized compound
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‒
[
C H N ](PF ) ⋅(1,4ꢀdioxane) (1⋅(1,4ꢀdioxane)) (with PF6
anion) and compound
28 24
4
6 2
‒
3
[
C H N ](NO ) ⋅ 2H O (2⋅2H O) (with NO anion).
28 24
4
3 2
2
2
Compound C H N ](PF ) ⋅(1,4ꢀdioxane) (1⋅(1,4ꢀdoxane)) crystallizes in the triclinic
28
24
4
6 2
system with space group Pꢀ1 and concerned single crystal Xꢀray data parameters, obtained at 100
K, are described in Table 1. The thermal ellipsoidal plot of the compound 1⋅(1,4ꢀdioxane) is
displayed in Figure 1 and the relevant selected bond lengths and angles are described in Table
2. Interestingly, the cation c, observed in the crystal structure of C H N ](PF ) ⋅(1,4ꢀdioxane)
2
8
24
4
6 2
(
1⋅(1,4ꢀdioxane)) adopts an intermediate conformation which is inꢀbetween synꢀ and antiꢀ
2+
Figure 1
[
Thermal ellipsoidal plot (30 % probability) of organic receptor [C H N ] in compound
28 24 4
C H N ](PF ) ⋅(1,4ꢀdioxane) (1.(1,4ꢀdioxane)); anions, solvent molecules and hydrogens are omitted for clarity.
28
24
4
6 2
conformations (Scheme 1, middle and Figure 1). We believe that interꢀcationꢀanion hydrogen
bonding interactions (mostly C‒H···F hydrogen bonds) between the cation receptor c and anion
‒
PF6 are responsible for this unusual intermediate conformation of c in the crystal struture of
‒
compound 1⋅(1,4ꢀdioxane). The C‒H···F hydrogen bonding environment around the PF anion
6
is given in Figure 2. The relevant hydrogen bonding parameters are presented in Table 3. In other
words, in the crystal structure, the stability of intermediate conformation (between syn and anti)
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Figure 2. CꢀH···F hydrogen bonding environment around a PF anion in [C H N ](PF ) ⋅(1,4ꢀdioxane) (1 (1,4ꢀ
dioxane)).
⋅
6
28 24
4
6 2
2+
of the organic receptor [C H N ] (c) in compound [C H N ](PF ) ⋅(1,4ꢀdioxane) (1⋅(1,4ꢀ
28 24
4
28 24
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6 2
dioxane)) can be rationalized by its strong hydrogen bonding interactions with surrounding PF6−
anions resulting in a threeꢀdimensional supramolecular network that have wellꢀdefined void
spaces, occupied by the solvent 1,4ꢀdioxane molecules as shown in Figure 3. We have also
performed density functional theory (DFT) calculations to understand this intermediate
conformation of c in compound 1⋅(1,4ꢀdioxane) (vide infra).
Figure 3. View (wireꢀframe representation) of the molecular packing of [C H N ](PF ) ⋅(1,4ꢀdioxane) (1 (1,4ꢀ
⋅
2
8
24
4
6 2
dioxane)) (4×4) cells; color code: F, green; P, purple; C, gray; N, blue; O, red; H, medium gray.
Compound [C H N ](NO ) ⋅ 2H O (2⋅2H O) crystallizes in monoclinic system with
28 24
4
3 2
2
2
space group P2 /n. The Xꢀray analysis of a single crystal of compound 2.2H O reveals that the
1
2
2+
dication [C H N ] (c) adopts an usual antiꢀconformation with respect to the two bipyridine
28
24
4
units of the paraꢀxylene ring as shown in Figure 4. In the asymmetric unit of the concerned
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crystal structure, one lattice water molecule (O4, located in a general position) exists with half of
the cationic receptor (c) and one nitrate anion. Thus the molecular formula of compound 2⋅2H O
2
consists of a full molecule of cationic receptor, two nitrate anions and two lattice water
molecules.
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Figure 4. Thermal ellipsoidal plot of the asymmetric unit of compound [C H N ](NO ) ⋅2H O (2 2H2O),
⋅
2
8
24
4
3 2
2
hydrogen atoms are not shown for clarity (50% probability).
Interestingly, the solvent water molecule (O4) arranges in the form of a water chain (a
centroꢀsymmetric array) with two different hydrogen bonding distances (2.395 Å and 2.678 Å).
A small fragment of the chain is formed by the hydrogen bonding interaction (2.395 Å) between
O4 and O4(a) (Figure 5a, left). These fragments are connected further by a relatively larger Hꢀ
bond distance (2.678 Å) to form the water chain (Figure 5a, right).
(a)
(b)
Figure 5. (a) left: Supramolecular water dimer and right: its oneꢀdimensional chainꢀlike arrangement formed
from hydrogen bonding interactions of O4 and O4(a), that are related by a symmetry operation: a, 2ꢀx, 1ꢀy, ꢀz.(b)
Extended water structure formed from the solvent water molecule (O4), showing its hydrogen bonding interactions
with its surrounding nitrate anions.
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Each water molecule of this water chain is further hydrogen bonded (2.912 Å) to an oxygen atom
(O2) of the surrounding nitrate anion (Figure 5(b)). In the crystal structure of compound
2+
[C H N ](NO ) ⋅2H O (2⋅2H O), the stairꢀcaseꢀlike (antiꢀconformation) dications [C H N ]
2
8
24
4
3 2
2
2
28 24
4
(c) pack to form zigꢀzag arrays with two nitrate anions and two crystal water molecules, inserted
in between the dications as shown in Figure 6(a). The corresponding space filling plot (without
nitrate anions and lattice water molecules) is shown in Figure 6(b).
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+
−
Figure 6. (a) Packing diagram consisting of the dication [C H N ] , NO anion and crystal water molecules in
2
8
24
4
3
2 2H O. Hydrogen atoms are not shown for clarity. (b) View (face filling representation) of the molecular packing
⋅
2
2
+
of [C H N ] cations in the [C H N ][NO ] ⋅2H O (2
⋅
2H2O) (3×3) cells. Color code: N, blue; C, gray; O, red.
2
8
24
4
28 24
4
3 2
2
The hydrogen atoms, nitrate anions and water molecules are not shown for clarity
2
+
Organic receptor [C H N ] (c) take up its usual antiꢀconformation in compound
2
8
24
4
2
⋅2H O (nitrate salt) and is stabilized in an unusual intermediateꢀconformation in
2
compound 1⋅(1,4ꢀdioxane) (PF salt)! Why is it so? A supramolecular analysis from
6
respective crystal structures.
2+
The usual energetically favored conformation of the cationic receptor [C H N ] (c) is anti,
2
8
24
4
observed in the crystal structure of compound [C H N ](NO ) ⋅ 2H O (2.2H O).
The
28
24
4
3 2
2
2
deviation from this usual antiꢀconformation of c can be explained by considering supramolecular
‒
hydrogen bonding interactions of this dication (c) with its surrounding anions (PF anion in case
6
‒
of compound 1⋅(1,4ꢀdioxane) and NO3 anion in the case of compound 2⋅2H O). The
2
supramolecular hydrogen bonding interactions around the cationic receptor (c) can be ‘balanced’
as well as ‘unbalanced’. The receptor c is flexible and it can undergo conformational change
from anti (Scheme 1, right) to an intermediate (Scheme 1, middle) through syn (Scheme 1, left).
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However, this movement (conformational change) can be restricted by the number of
supramolecular interactions with its surrounding anions. As shown in Figure 7(a), there are unꢀ
balanced supramolecular Hꢀbonding interactions around the diꢀcation c; the unbalanced
supramolecular interactions mean unꢀequivalent interactions with respect to the central part of
the molecule. This diꢀcation has two bipyridine side arms with respect to the central phenylene
ring. In the case of compound 1⋅(1,4ꢀdioxane), one side arm is involved with five C‒H···F
hydrogen bonds and the other side arm is involved in six C‒H···F hydrogen bonds as shown in
Figure 7(a). These unꢀequivalent supramolecular hydrogen bonding interactions, called
unbalanced supramolecular interactions, around c enable this system to adopt an unusual
intermediate conformation (Scheme 1, middle). The supramolecular hydrogen bonding
interactions around c in compound [C H N ](NO ) ⋅ 2H O (2·2H O) is shown in Figure 7(b).
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3 2
2
2
In the crystal structure of compound 2·2H O, there are balanced/equivalent C‒H···O hydrogen
2
bonding interactions around c with respect to the central phenylene ring (Figure 7(b)). Both side
‒
arms of c are hydrogen bonded with its surrounding NO3 anions in such a way that hydrogen
bonding force of one arm would cancel that of other arm. Thus there is an equivalent force along
2
+
all the sides of cationic receptor [C H N ] (c), which implies that there is no more distortion
28
24
4
from its usual antiꢀconformation. This justifies the antiꢀconformation of c in compound 2.2H O.
2
The antiꢀconformation of c in compound 2·2H O and an intermediate conformation of c in
2
compound 1 can also be corroborated by DFT calculations, Hirshfeld surface analysis and 2D
finger plots, described in the succeeding sections.
Figure 7. (a) Unbalanced/unsymmetrical C−H···F hydrogen bonding interactions around the cationic receptor
2
+
[
C H N ] , observed in the crystal structure of compound [C H N ](PF ) ⋅(1,4ꢀdioxane) (1·(1,4ꢀdioxane)). (b)
28 24
4
28 24
4
6 2
2+
Balanced/symmetrical C–H···O hydrogen bonding interactions around C H N ] , found in the crystal of
28 24
4
compound [C H N ](NO ) ⋅2H O (2·2H O)
28 24
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3 2
2
2
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Hirshfeld Surface Analysis. The hydrogenꢀbonding supramolecular interactions around
2
+
the cationic receptor [C H N ] (c) with surrounding associated anions are further analyzed
28
24
4
with the Hirshfeld Surfaces (HSs) and 2D fingerprint plots (FPs), which are generated by using
3
2,33
the software Crystal explorer 3.1.
based on the pertinent CIF files. Hirshfeld surfaces
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mapped with different properties e.g., d dnorm, shape index, curvedness, have been proven to be
e,
an useful visualization tool for the analysis of supramolecular intermolecular interactions and
3
4,35
crystal packing behavior of molecules.
The 3D Hirshfeld surfaces offer more insight into
longꢀ and shortꢀrange interactions, experienced by the relevant molecules, and 2D finger plots,
derived from the HSs provide the nature, type and relative contribution of the intermolecular
2+
interactions. The HSs of the present cationic receptor [C H N ] (c) experiences unbalanced
2
8
24
4
Figure 8. Hirshfeld surfaces mapped with (a) dnorm ranging from ‒0.376 (red) to 1.441 (blue), (b) 2D finger print
plots with d and d ranging from 1.0 to 2.8 Å, (c) H···F interactions (left) and percentage contribution of all other
i
e
interactions around the cation (right) in compound 1·(1,4ꢀdioxane).
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Figure 9. Hirshfeld surfaces mapped with (a) dnorm ranging from ꢀ0.179 (red) to 1.360 (blue), (b) 2D finger print
º
plots with d and d ranging from 1.0 to 2.8 A , (c) percentage of contributions from all other interactions around
i
e
the cation (left ) and H···O interactions (right) in compound 2·2H O.
2
‒
‒
and balanced hydrogen bonding interactions with PF6 and NO3 anions in compound 1·(1,4ꢀ
dioxane) and compound 2·2H O respectively, that have been mapped over dnorm (‒0.3 to 1.45
2
Å in compound 1·(1,4ꢀdioxane) and ‒0.1 to 1.4 Å in compound 2·2H O as shown in Figures 8
2
and 9 respectively (see also Figures S2 and S3 of SI for HSs mapped with the shape index and
curvedness). All are the deep red spots, seen in the dnorm surface, represent the interactions,
whereas the blue spots indicate the areas without close contacts. The intensity of the red spots on
the Hirshfeld Surfaces of the cationic receptor c in compounds 1· (1,4ꢀdioxane) and 2·2H O
2
clearly indicate that it has been experiencing unbalanced and balanced hydrogen bonding
‒
6
‒
3
inteactions with PF and NO anions respectively (compare Figures 8a and 9a respectively).
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Among
noncovalent contacts, experienced by the cationic receptor c in compound
[
C H N ](PF ) ⋅(1,4ꢀdioxane) (1·(1,4ꢀdioxane)), the major interactions are H···F (30.4%) and
2
8
24
4
6 2
H···H (28.2 %) as shown in Figure 8c (right). The relative contributions from other different
interactions are calculated and given in Figure 8c (left). In the case of [C H N ](NO ) ⋅2H O
2
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3 2
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(
2·2H O), and dominating H···O (basically C‒H···O hydrogen bonds) and H···H interactions
2
are nearly 31.3% and 28.5% respectively among all other interactions as shown in Figure 9c
left).
(
2
+
Computational studies on different conformers of cationic receptor [C H N ] (c),
compound [C H N ](PF ) (1), and compound [C H N ](NO ) (2).
2
8
24
4
28
24
4
6 2
28 24
4
3 2
In continuation of experimental work on cationic receptor c, we also performed the theoretical
calculations to find out its conformational structures as such c and in compounds 1 and 2
including the stability of those conformers in gas phase. It is found that its antiꢀconformer (Eelec
= ‒1299.97188 a.u.) is more stable by ~1.65 kcal/mol than its syn conformer (Eelec
1299.96926 a.u.). The atom numbering is shown to the respective figures to facilitate the
discussion. The conformers of the compounds and the atom numbering are made by GaussView5
=
‒
3
6
software. The x,y,z coordinates of the anti and syn conformers of the cationic receptor c at its
ground state energy minimized structure are given in Table S5 and S6 in the section of
Supporting Information. The structures of the other conformers of c around the 1Nꢀ24Cꢀ52Cꢀ
29N dihedral angle are shown in Figure 10. The energy profile diagram corresponding to these
different dihedral angles is shown in Figure 11. The structures of different conformers are
o
optimized at the interval of 20 dihedral angle. It is found that antiꢀconformer with 1Nꢀ24Cꢀ52Cꢀ
o
29N dihedral angle of ‒180 is the most stable conformer than the other conformers, whereas syn
conformer is the least stable conformer. Energy of the intermediate conformers rises very
o
o
o
o
steeply between, ‒180 to ‒240 and ‒180 to ‒120 , 1Nꢀ24Cꢀ52Cꢀ29N dihedral angle,
whereas the steepness of the curve decreases in the both sides, after the above mentioned range
of dihedral angle (cf. Figure 11). Analysis of the energy profile diagram (cf. Figure 11) provides
the energy difference between the most stable and least stable structure, which is ~3 kcal/mol.
2+
Thus, this cationic receptor [C H N ] (c) is flexible to form ion pair complexes with diverse
28
24
4
anions in a wide range of 1Nꢀ24Cꢀ52Cꢀ29N dihedral angles. We have chosen two different
‒
‒
3
anions PF and NO in this study to obtain the ion pair compounds [C H N ](PF ) ] (1) and
6
28 24
4
6 2
[C H N ](NO ) ] (2) respectively; the preferable conformations of c (cationic receptor) in
2
8
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4
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presence PF anion (compound 1) and NO anion (compound 2) are discussed here. It is found
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3
that the compound 2 always prefers to form an antiꢀconformation of c with 1Nꢀ24Cꢀ52Cꢀ29N
o
dihedral angle of ~167 . But in the case of compound 1, both anti (with1Nꢀ24Cꢀ52Cꢀ29N
o
o
dihedral angle of ~180 ) and syn (1Nꢀ24Cꢀ52Cꢀ29N dihedral angle of ~8 ) conformers of c are
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Figure 10. Energy minimized structures of different conformers of cationic receptor c.
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-815744.71
-
815745
-360 -320 -280 -240 -200 -160 -120
-80
-40
0
1N-24C-52C-29N Dihedral Angle (degree)
Figure 11. Potential energy analysis at different 1Nꢀ24Cꢀ52Cꢀ29N dihedral angles of cationic receptor c.
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formed with different stabilization energy. The optimized structures of these preferred
conformers in compound 2 and in compound 1 with the Hꢀbond indication are shown in panels
(a) ‒ (f) of Figure 12. Panel (a) is the anti conformer of c in compound 2 and panels (b) ‒ (f) are
different conformers of c in compound 1. The stabilization energy of the antiꢀconformer of
compound 2 is ~229 kcal/mol, whereas the same for the antiꢀ and synꢀconformers of compound 1
are ~215 kcal/mol and ~230 kcal/mol, respectively. Thus, the calculations of
0
1
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(
a)
(d)
1N-24C-52C-29N
Eelec= -1861.0078 a.u.
Eelec= -3181.6055 a.u.
dihedral angle (degree)
(a) = -180.0
(b)= -180.0
(c) = -120.0
(d)= -90.0
(
(
e) = -60.0
f) = 0.0
(
e)
(
b)
Eelec= -3181.6114 a.u.
Eelec= -3181.6007 a.u.
(
c)
(f)
Eelec= -3181.5985 a.u.
Eelec= -3181.6245 a.u.
Figure 12. Energy minimized structures of antiꢀconformer in compound 2 (panel (a)) and various conformers in
compound 1. (panels (b) ‒ (f)).
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Stabilization energy indicate that the syn conformer of compound 1. is more preferable than its
antiꢀconformer. The stabilization energies of the intermediate conformers of c in compound 1 are
also calculated to obtain more detailed conformational analysis of compound 1.
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60
The calculated stabilization energies of the intermediates with 1Nꢀ24Cꢀ52Cꢀ29N dihedral
o
o
o
angles of ‒120 , ‒90 and ‒60 are ~214 kcal/mol, ~215 kcal/mol, ~222 kcal/mol respectively.
The optimized structures of these intermediates with Hꢀbond indication are shown in panels (c),
(
d) and (e) of Figure 12, respectively. A graphical representation of the stabilization energies of
various conformers of c in compound 1 with different 1Nꢀ24Cꢀ52Cꢀ29N dihedral angles is
shown in Figure 13. It is seen from Figure 13 that the stabilization energy of the
225
223.62
223.62
222.49
222.48
221.04
221.03
220
219.57
219.56
218.02
218.01
215.24
215.24
214.87
2
15
2
14.61
214.61
2
13.97
213.97
213.75
213.74
-
360 -320 -280 -240 -200 -160 -120
-80
-40
0
1N-24C-52C-29N Dihedral Angle (degree)
Figure 13. A diagram of stabilization energies at various 1Nꢀ24Cꢀ52Cꢀ29N dihedral angles in c in compound 1.
o
o
o
conformers is decreased in comparison to antiꢀconformer (‒180 ) to ‒120 (‒240 ) 1Nꢀ24Cꢀ
52Cꢀ29N dihedral angle. Whereas an increment of stabilization energy is observed in different
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o
o
intermediate conformers in compound 1 in the range of ‒100 to 0 1Nꢀ24Cꢀ52Cꢀ29N dihedral
angle. It is noted that the stabilization energies of the conformers of Figure 13 should be differed
from the actual stabilization energies calculated for ꢀ180˚, ꢀ120˚, ꢀ90˚, ꢀ60˚ and 0˚ 1Nꢀ24Cꢀ52Cꢀ
2
9N dihedral angles, as the parameter 1Nꢀ24Cꢀ52Cꢀ29N dihedral angle of these conformers (cf.
0
1
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1
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0
Figure 13) is not optimized. The above discussion on stabilization energies of different
conformers of c in compound 1 indicates that the energy difference between the different
o
o
conformers in the ‒100 to 0 1Nꢀ24Cꢀ52Cꢀ29N dihedral angle range is a small amount. Thus
‒
according to this calculation, the anion PF6 prefers to form the ion pair complex either with syn
conformer of c or with an intermediate conformer of c (cationic receptor). A similar
conformation of c, found in the crystal structure of 1·(1,4ꢀdioxane), has also been observed in
2
1
the crystal structure of c.2PF by KomꢀBei Shiu and coꢀworkers as far as relevant NꢀꢀꢀCꢀꢀꢀCꢀꢀꢀ
6
o
o
N torsion angles are concerned [98.08 for 1·(1,4ꢀdioxane) and 97.28 for c.2PF ].
6
The HOMO and LUMO diagrams of the conformers of cationic receptor c, compound 1
and compound 2 are shown in Figure 14 [panels (a) and (b) for cationic receptor c; panel (c) for
compound 2; panels (d) and (e) for compound 1]. Figure 14 shows that the HOMOs of synꢀ
cationic receptor as such (Figure 14a), antiꢀcationic receptor as such (Figure 14b), compound 2
(
Figure 14c), antiꢀconformer of compound 1 (Figure 14d) and synꢀconformer of compound 1
(
Figure 14e) are stabilized by ~75, ~73, ~47, ~95 and ~97 kcal/mol, respectively compared to
their respective LUMOs. These data indicate that the HOMOꢀLUMO stabilization is increased
‒
during the ion pair complex formation of cationic receptor (c) with PF anion, whereas the same
6
‒
is decreased during the ion pair complex formation of cationic receptor (c) with NO anion.
3
Natural bond orbital (NBO) analysis. In order to have more insight into the stabilization of
compounds 1 and 2 with respect to the conformations of receptor cation c, we performed the
NBO analysis of the different conformers of these compounds. The results of the donorꢀacceptor
interactions of different conformers of compound 1 and compound 2 are given in Table 6. The
donor orbital (i), acceptor orbital (j), calculated secondꢀorder interaction energies between the
2
donorꢀacceptor orbitals [E (i,j)] and Hꢀbond distances in compound 2 and that in different
conformers of compound 1 are given in this table. NBO analysis of compound 2 indicates that ~
6
0 kcal/mol stabilization energy is acquired due to the Hꢀbond formation between the oxygen
–
(O) lone pairs (LP) and σ* C–H bonds. It is found that both the NO3 anions interact
symmetrically through Hꢀbonds with the two bipyridine sides of the cationic receptor c (Figure
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2a; see also Figure 7b, the experimental crystallographic evidence). That is why, c in compound
2
prefers anti conformation. A minute inspection of the Figure 12a and its NBO analysis indicate
that the Hꢀbond interaction between LP of 64 O and σ* of 37C–38H on the
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59
60
LUMO (-0.29648 a.u.)
LUMO (-0.12540 a.u.)
HOMO (-0.41637 a.u.)
a)
(
HOMO (-0.27742 a.u.)
d)
(
LUMO (-0.29337 a.u.)
HOMO (-0.41287 a.u.)
(
b)
LUMO (-0.10989 a.u.)
LUMO (-0.12023 a.u.)
HOMO (-0.26585 a.u.)
e)
(
HOMO (-0.41637 a.u.)
(
c)
Figure 14. HOMOꢀLUMO diagrams of (a) synꢀ conformer of cationic receptor, (b) antiꢀ conformer of cationic
receptor, (c) antiꢀ conformer of compound 2, (d) antiꢀ conformer of compound 1 and (e) synꢀ conformer of
compound 1..
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one bipyridine side of the cationic receptor (c) stabilizes the compound 2 by ~14 kcal/mol with
1.943 Å Hꢀbond distance. On the other hand, Hꢀbond between LP of 58 O and σ* of 9C–10H on
the other bipyridine side of the cationic receptor (c) gives the compound 2 more stability by ~ 21
kcal/mol with 1.833 Å Hꢀbond distance. These two marginally different symmetric Hꢀbonding
interactions of the two opposite bipyridine sides of the cationic receptor (c) makes the compound
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2
somewhat different orientation from the actual antiꢀconformation. Thus, the compound 2
o
prefers a predominantly antiꢀorientation with 1Nꢀ24Cꢀ52Cꢀ29N dihedral angle of ~167 (not
o
exactly 180 ) as shown in Figure 12a. On the other hand, the different conformational
o
o
o
o
o
orientations with 1Nꢀ24Cꢀ52Cꢀ29N dihedral angles of ꢀ180 , ꢀ120 , ꢀ90 , ꢀ60 and ꢀ8 of
compound 1 show ~22, ~26, ~32, ~36 and ~32 kcal/mol stability, respectively, on Hꢀbonding
interactions between the LPs of different F atoms and different σ* C–H bonds in compound 1.
Therefore, this result (consistent with energy minimized calculations, vide supra) also suggests
–
o
o
that PF anion prefers to form an ion pair complex either with intermediate (ꢀ90 , ꢀ60 ) or syn
6
o
orientation (ꢀ8 ) of the cationic receptor c. A symmetric Hꢀbond formation around c with respect
to its two bipyridine sides is observed (Figure 12b). This can be also encountered from the data
given in Table 6. The Hꢀbonding interaction between the LP of 64F and σ* 9C‒10H bond on the
one bipyridine side and the Hꢀbond between LP of 69F σ* 37C‒38H bond on the other
bipyridine side provide similar ~6 kcal/mol of stabilization. Similarly, the LP of 59F and σ*
9C‒10H bond on the one bipyridine side and the LP of 67F σ* 37C‒38H bond on the other
bipyridine side provide similar ~3 kcal/mol of stabilization. These symmetric Hꢀbonding
interactions give the proper antiꢀorientation conformer of compound 1 as shown in Figure 12b.
This type of symmetric Hꢀbonding interactions are absent in other conformers of compound 1 as
shown in Figures 12c, 12d and 12e. In the case of syn conformer of compound 1 (Figure 12f),
an unbalanced symmetric Hꢀbonding interaction is observed between the LP of 62 F and σ* of
37C‒38H bond and LP of 66 F and σ* of 9C‒10H bond. Both the Hꢀbonding interaction stabilize
the molecule by ~5 kcal/mol and has the bond distance of 2.18 A˚ . The same is observed in the
Hꢀbond, initiated by LPs of 58F, 70F, 60F and 69F atoms. These are the forces behind the
stability and syn orientation of the conformer of compound 1 (Figure 12f). The NBO analysis
shows that the overall Hꢀbonding stability is highest in the conformer of compound 1 with the
o
o
1Nꢀ24Cꢀ52Cꢀ29N dihedral of ꢀ60 , an intermediate one (not ꢀ8 , syn conformer). Thus, this study
‒
6
also indicates that PF anion prefers to form an unusual intermediate conformation of c or its
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syn conformation, whereas NO anion prefers to form normal anti conformation of c, cationic
3
receptor.
In order to validate the above discussion, we performed the equilibrium constant
calculations between different conformers of cationic receptor c and the compound 1. The
calculated values of equilibrium constant at different temperature (T, Kelvin) are given in Table
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43
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52
53
54
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58
59
60
7
. It is found that anti conformer of cationic receptor c is dominant than syn conformer of it at
the equilibrium in the temperature range of 100ꢀ800 K. The percentage of syn conformer is
increased with the temperature. The syn conformer of cationic receptor c occupies only 1.16% at
the room temperature (300K). Similar analysis of the conformers of compound 1 shows that syn
conformer is dominant than anti conformer at their equilibrium at different temperatures (Table
7
). Even at room temperature (300K), the conversion of syn to anti is not expected to be
achievable. An increment of this conversion is observed from 650 K temperature. So it is
expected that the barrier of synꢀanti conversion of compound 1 can be overcome at higher
temperature. Similar analysis of two intermediate conformers with 1Nꢀ24Cꢀ52Cꢀ29N dihedral
o
o
angle of ꢀ90 and ꢀ60 indicates that these two conformers are dominant than antiꢀconformer of
compound 1 in the respective equilibrium. The increment of this conversion with temperature is
higher than the synꢀanti conversion of compound 1. An opposite scenario is observed
considering the intermediate conformer with 1Nꢀ24Cꢀ52Cꢀ29N dihedral angle of ꢀ120˚ and antiꢀ
conformer equilibrium of compound 1. In this case, antiꢀconformer is found as a dominant in the
equilibrium. So the calculations of equilibrium constant between different conformers of
‒
compound 1 also suggest that the PF anion prefers to form complex with cationic receptor c at
6
its syn or intermediate (ꢀ90˚ and ꢀ60˚) orientations.
■
SUMMARY
An organic
C H N ] (c) was known to be isolated as its antiꢀ as well as its synꢀconformations. In the
receptor,
1,1"ꢀ1,4ꢀphenyleneꢀbis(methylene)bisꢀ4,4'ꢀbipyridinium
cation
2+
[
2
8
24
4
present work, we have isolated this cationic receptor as an unusual intermediate conformation
‒
(neither syn nor anti) with PF6 anion in compound [C H N ](PF ) ⋅(1,4ꢀdioxane) (1·(1,4ꢀ
28
24
4
6 2
dioxane)). The energetically favored anti conformation of this organic cation has been described
in its nitrate salt [C H N ](NO ) ⋅2H O (2·2H O). Both compounds are characterized by single
2
8
24
4
3 2
2
2
crystal Xꢀray crystallography. We have a given rationale of why an atypical intermediate
‒
conformer of the title receptor is stabilized with PF6 anion and a typical antiꢀform of this
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receptor is isolated with nitrate anion, with the help of supramolecular hydrogen bonding
interactions and Hirshfeld surface analysis.
A detailed theoretical account of the stability of the various conformers of the cationic
2
+
receptor [C H N ] (c), compound [C H N ](PF ) (1) and compound [C H N ](NO ) (2)
28 24
4
28 24
4
6 2
28 24
4
3 2
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0
has been discussed in this study by calculating their electronic stability, HOMO‒LUMO
stabilization and NBO analysis. Final conclusion of their stability is obtained by calculation of
conformational equilibrium constants at different temperatures between the conformers of the
cationic receptor c and compound 1. It is found that anti form of the cationic receptor c is more
‒
stable than its syn orientation, whereas, in presence of PF6 anion, it prefers syn or an
o
o
intermediate (with 1Nꢀ24Cꢀ52Cꢀ29N dihedral angles of ꢀ60 and ꢀ90 ) conformers. An opposite
scenario of usual anti orientation of the cationic recepector c with little deviation is observed,
‒
when the cationic receptor c binds with NO anion. A symmetric interaction through Hꢀbonds
3
‒
between the two bipyridine sides of the cationic receptor c and two NO3 anions is the main
cause behind the antiꢀorientation of the compound 2, whereas, an unbalanced symmetric Hꢀ
ꢀ
bonding interactions between the LP of F atoms (PF anion) and σ* of CꢀH bonds (cationic
6
receptor c) give the compound 2 unusual syn or intermediate orientation.
■
S ASSOCIATED CONTENT
Supporting Information
Elemental analyses plots; Hirshfeld Surface Analysis plots; First lowest thirty four vibrational
ꢀ1
frequencies (in cm ) of the optimized structures of anti and syn cationic receptor c conformers and
different conformers of compound 2 (in a tabular form); Rotational constant values (A, B, C in GHz) and
symmetry numbers for different conformers of 2ꢀbutene, cationic receptor c and compound 1 (in a
rot
vib
tabular form); rotational (q ) and vibrational (q ) partition functions values of different
conformers of 2ꢀbutene, cationic receptor c and compound 1 at different temperature (in a tabular
form); calculated and experimental equilibrium constants (K) at different temperatures (in
kelvin) between cisꢀ2ꢀbutene and transꢀ2ꢀbutene (in a tabular form). The x, y, z coordinates of
the ground state energy minimized structure of the different conformers of the cationic receptor
c, compound 1 and compound 2 are also given in Tables S5ꢀS9, in the supporting information.
The conformational analysis of the cationic receptor c and compound 1 with respect to benzene
torsional angle are also discussed in the Supporting information. CCDC 1525549 and CCDC
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1
023590 contains the supplementary crystallographic data for compounds 1·(1,4ꢀdioxane) and
2
·2H O respectively. Relevant crystal data can be obtained free of charge via
2
http://www.ccdc.cam.atc.uk/conts/retrieving.html, or from the Cambridge Crystallographic Data
Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: (+44) 1223−336− 033; or eꢀmail:
deposit@ccdc.cam.ac.uk.
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■
S AUTHOR INFORMATION
Corresponding Author
Phone +91ꢀ40 – 2313ꢀ4853; email skdas@uohyd.ac.in (SKD)
*
Notes
The authors declare no competing financial interest.
■
ACKNOWLEDGMENTS
We thank SERB, DST, Government of India, for financial support (Project No. SB/S1/ICꢀ
4/2013). We are grateful to UGC, New Delhi, for UPEꢀII grant. R.S. acknowledges UGC, New
3
Delhi, India, for his doctoral fellowship. Our special thanks to Professor S. Mahapatra, School of
Chemistry, University of Hyderabad for his help in theoretical calculations and CMSD for
computational facility.
■
REFERENCES
(
1) Klärner, F.ꢀG.; Kahlert, B. Molecular Tweezers and Clips as Synthetic Receptors.
Molecular Recognition and Dynamics in Receptor−Substrate Complexes. Acc. Chem. Res. 2003,
6, 919ꢀ932.
2) Lehn. J. – M. Supramolecular Chemistry. Concepts and Perspectives, VCH, Weinheim,
3
(
1995.
(3) Gallivan, J. P.; Dougherty, D. A. A Computational Study of Cation−π Interactions vs Salt
Bridges in Aqueous Media:ꢁ Implications for Protein Engineering. J. Am. Chem. Soc. 2000, 122,
870ꢀ874.
(4) Prins, L. J.; Reinhoudt, D. N.; Timmerman, P. Noncovalent Synthesis Using Hydrogen
Bonding. Angew. Chem. Int. Ed. 2001, 40, 2382ꢀ2426.
(5) Sinnokrot, M. O.; Valeev, E. F.; Sherrill, C. D. Estimates of the Ab Initio Limit for π−π
Interactions:ꢁ the Benzene Dimer. J. Am. Chem. Soc. 2002, 124, 10887ꢀ10893.
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(
6) Sokolov, A. N.; Friščić, T.; MacGillivray, L. R. Enforced FaceꢀtoꢀFace Stacking of Organic
Semiconductor Building Blocks within HydrogenꢀBonded Molecular Cocrystals. J. Am. Chem.
Soc. 2006, 128, 2806ꢀ2807.
(7) Nohra, B.; Graule, S.; Lescop, C.; Réau, R. Mimicking [2,2]ꢀParacyclophane Topology:
Molecular Clips for the CoordinationꢀDriven Cofacial Assembly of πꢀConjugated systems. J.
Am. Chem. Soc. 2006, 128, 3520ꢀ3521.
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J.; CregoꢀCalama, M.; Reinhoudt, D. N. Assembly of a Supramolecular Capsule on a Molecular
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19) Klärner, F.ꢀG.; Panitzky, J.; Bläser, D.; Boese, R. Synthesis and Supramolecular Structures
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Superstructures Generated using AreneꢀArene Interactions. New. J. Chem. 1998, 155ꢀ157.
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Table 1. Crystallographic data and structure refinement for compound 1.(1,4ꢀdioxane) and
2
.2H O
2
1·(1,4ꢀdioxane)
C H F N O P
2·2H O
2
Empirical formula
Formula weight
Temperature (K)
Crystal size (mm)
Crystal system
space group
C H N O
32 32 12
4
2
2
28 28
576.56
298 K
6
8
794.56
100(2) K
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
1
2
3
4
5
6
7
8
9
0
0.20x0.16x0.06
0.21x0.17x0.14
Monoclinic
p21/n
Triclinic
Pꢀ1
Z
2
2
Wavelength(A)
Unit cell dimensions
0.71073
0.71073
ͦ
a [A]
9.2462(7)
11.7988(9)
16.7537(13)
106.49(10)
103.76(10)
98.33(10)
1657.3(2)
1.592
4.5103(9)
19.774(4)
15.054(3)
90
ͦ
b [A]
ͦ
c [A]
α [º]
β [º]
γ [º]
97.786(4)
90
ͦ
3
Volume [A ]
1331.2(5)
1.428
ꢀ3
Calculated density (Mg/m )
Reflections collected/ unique
R(int)
15442/4749
0.0408
15147/3145
0.0604
F(000)
812
604
Max. and min. antimission
Theta range for data collection
0.985 and 0.954
1.33 to 25.07
0.956 and 0.989
0.956 to 28.23
(deg.)
2
2
Refinement method
Fullꢀmatrix leastꢀsquare on F
5829/0/469
Fullꢀmatrix leastꢀsquare on F
3145/0/190
Data/restrains/parameters
2
Goodnessꢀofꢀfit on F
1.198
1.003
R /wR [I>2sigma(I)]
0.0713/0.1378
0.0900/0.1452
0.0915/0/0.264
0.142/0.304
1
2
R /WR (all data)
1
2
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ͦ
ꢀ3
ͦ
ꢀ3
Largest diff. peak and hole
0.501 and ꢀ0.270 e.A
0.487 and ꢀ0.284 e.A
Table 2. Complete list of bond lengths [Å] and angles [deg] for C H N ](PF ) ⋅(1,4ꢀdioxane)
2
8
24
4
6 2
(1·(1,4ꢀdioxane))
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C(7)ꢀN(3)
1.474(5)
1.343(5)
1.393(5)
1.361(5)
1.193(5)
C(18)ꢀN(1)
C(26)ꢀN(2)
C(29)ꢀC(30)#1
C(32)ꢀC(31)#2
F(1)ꢀP(1)
1.347(4)
1.333(5)
1.492(6)
1.485(6)
1.594(2)
C(8)ꢀN(3)
C(9)ꢀC(10)
C(11)ꢀC(12)
C(13)ꢀC(17)
O(1)ꢀC(29)ꢀC(30)#1 109.8(3)
O(2)ꢀC(31)ꢀC(32)#2 111.3(3)
F(4)ꢀP(1)ꢀF(2)
F(7)ꢀP(2)ꢀF(9)
179.85(18)
89.71(13)
123.8(4)
125.0(4)
121.6(3)
C(23)ꢀN(1)ꢀC(19)
C(19)ꢀN(1)ꢀC(18)
C(30)ꢀO(1)ꢀC(29)
120.6(3)
118.2(3)
108.7(3)
N(2)ꢀC(26)ꢀC(25)
N(4)ꢀC(16)ꢀC(17)
N(1)ꢀC(23)ꢀC(22)
Symmetry antiformations used to generate equivalent atoms#1ꢀx+2,ꢀy+1,ꢀz #2 ꢀx+1,ꢀy+1,ꢀz+2
Table 3. Hydrogen bonds for compound 1·(1,4ꢀdioxane) [ Å and °].
DꢀH...A
d(DꢀH)
0.95
0.95
0.95
0.95
0.99
0.99
0.95
0.95
0.99
0.95
d(H...A)
2.42
2.65
2.42
2.30
2.42
2.54
2.59
2.43
2.37
2.58
d(D...A)
3.308(5)
3.482(5)
3.302(5)
3.156(4)
3.411(4)
3.422(4)
3.509(4)
3.286(4)
3.304(4)
3.524(4)
<(DHA)
155.9
146.3
154.0
149.4
178.2
149.1
161.7
150.5
157.8
170.3
C(22)ꢀH(22)...N(4)#3
C(28)ꢀH(28)...N(4)#3
C(9)ꢀH(9)...N(2)#4
C(8)ꢀH(8)...F(1)#5
C(7)ꢀH(7A)...F(6)#5
C(7)ꢀH(7B)...F(7)#6
C(2)ꢀH(2)...F(6)#7
C(23)ꢀH(23)...F(9)#8
C(18)ꢀH(18A)...F(9)#8
C(11)ꢀH(11)...F(3)
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