Designed Synthesis and Crystallization of Isomorphic Molecular Gyroscopes with Cell-like Bilayer Self-Assemblies

Article abstract of DOI:10.1021/acs.cgd.7b01542

Two molecular rotors featuring pyridine and fluorobenzene rings as polar rotators and 9-octylfluorenyl stators were synthesized. Their crystal structures were established through SXRD techniques, crystallizing in the monoclinic chiral P2₁ space group. The supramolecular assemblies of both isomorphs showed an orientation of static dipoles through the crystal lattice and the formation of intriguing 2D layers that resemble cell membranes, a typical example of an amphidynamic system. Small activation energies and the modulation of the first-order hyperpolarizabilities of these compounds as a function of rotational dynamics were revealed through DFT computations at the CAM-B3LYP/M06-2X/cc-pVDZ level of theory and correlated with a potential use of these materials as photonic switches.

Full text of DOI:10.1021/acs.cgd.7b01542

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Designed synthesis and crystallization of isomorphic
molecular gyroscopes with cell-like bilayer self-assemblies.
Ma. Eugenia Ochoa, Pablo Labra-Vázquez, Norberto Farfan, and Rosa Santillan
Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.7b01542 • Publication Date (Web): 05 Apr 2018
Downloaded from http://pubs.acs.org on April 6, 2018
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Designed synthesis and crystallization of isomorphic
molecular gyroscopes with cellꢀlike bilayer selfꢀ
assemblies.
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Ma. Eugenia Ochoa,a Pablo Labra-Vázquez,b Norberto Farfán,b Rosa Santillan,a*
a Departamento de Química, Centro de Investigación y de Estudios Avanzados del IPN, Apdo.
Postal 14ꢀ740, 07000, México
b Facultad de Química, Departamento de Química Orgánica, Universidad Nacional Autónoma de
México, 04510 México D.F., México.
ABSTRACT
Two molecular rotors featuring pyridine and fluorobenzene rings as polar rotators and 9ꢀ
octylfluorenyl stators were synthesized. Their crystal structures were established through SXRD
techniques, crystallizing in the monoclinic chiral P21 space group. The supramolecular
assemblies of both isomorphs showed an orientation of static dipoles through the crystal lattice
and the formation of intriguing 2D layers that resemble cell membranes, a typical example of an
amphidynamic system. Small activation energies and the modulation of the firstꢀorder
hyperpolarizabilities of these compounds as a function of rotational dynamics were revealed
through DFT computations at the CAMꢀB3LYP/M06ꢀ2X/ccꢀpVDZ level of theory and
correlated with a potential use of these materials as photonic switches.
1. INTRODUCTION
Amphidynamic systems, defined as 3D molecular arrays that despite their long range phase order
also display fast molecular dynamics, have the potential to act as molecular rotors, i.e. crystalline
molecular machines that, when properly engineered, may display efficient rotational work such
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as that of macroscopic gyroscopes or compasses.1 These crystal systems, expected to display
interesting properties like dichroism and birefringence,2 usually incorporate a 1,4ꢀ
diethynylphenylene ring linked at both ends to rigid frameworks that provide the supramolecular
information that dictates the crystal packing.
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Our group of work has put intense collaborative efforts in studying the rotational dynamics of
molecular rotors possessing diverse rigid steroidal frameworks linked through acetylenic axles to
1,4ꢀphenylene stators.3ꢀ5 During the course of these investigations, the possibility of controlling
the rotational dynamics of these molecular compasses like systems using a magnetic stimulus
became appealing.
Herein we describe the synthesis and supramolecular structure of molecular rotors featuring
9,9ꢀdioctylfluorene groups as stators and pyridine and fluorobenzene rings as polar rotators. The
static dipolar moments present in these molecules are intended to facilitate control of rotational
dynamics upon application of an external magnetic field. Through SXRD analysis of these
systems, we found that they present peculiar solidꢀstate selfꢀassemblies that resemble closely cell
membranes, as well as other supramolecular features that make these crystalline isomorphs
interesting systems to be studied as molecular gyroscopes.
2. EXPERIMENTAL
General experimental considerations
Materials
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All starting materials were purchased from SigmaꢀAldrich and used without further
purification. Solvents were purified by distillation over appropriate drying agents. Compounds
2–4 were obtained following reported methodologies;6ꢀ8 spectroscopic data is in good agreement.
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Instrumentation
NMR spectra were recorded on Jeol ECA 500 and Jeol 270 MHz spectrometers using
deuterated solvents; chemical shifts for H and 13C NMR data are relative to the residual
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nondeuterated solvent signal, fixed at δ = 7.26 ppm for HꢀNMR and δ = 77.00 ppm for Cꢀ
NMR. Infrared spectra were registered on a FTꢀIR Varian ATR spectrometer. HRMS data was
acquired using an Agilent G1969A MS TOF spectrometer. Elemental Analysis for MR2 was
determined on a Thermofinnigan Flash 1112 equipment (CHONS). Absorption spectra were
obtained in chloroform solutions using a Perkin Elmer Lambda 2S UV/Vis spectrophotometer.
Synthetic procedures
Synthesis of molecular rotors
2,5-bis((9,9-dioctyl-fluoren-2-yl)ethynyl)pyridine (MR1). 2ꢀethynylꢀ9,9ꢀdioctylfluorene (4)
(0.20 g, 0.48 mmol), 2,5ꢀdibromopyridine (5) (0.06 g, 0.25 mmol), Pd(PPh3)2Cl2 (0.02 g, 0.028
mmol) and CuI (0.009 g, 0.03 mmol) were placed in a dried round bottom flask followed by the
addition of diisopropylamine (1 mL) and freshly distilled THF (25 mL) under nitrogen
atmosphere. The mixture was refluxed 8 h, allowed to cool to room temperature, quenched with
a saturated solution of ammonium chloride (25 mL), extracted with ethyl acetate (3x25 mL),
dried over Na2SO4, evaporated to dryness and chromatographed on silica gel (70ꢀ230 Mesh)
using hexanes. The brown solid thus obtained was recrystallized from deuterated chloroform and
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acetonitrile to yield 80 mg (37 %) of MR1 as a yellow solid. M.P. 78ꢀ79 °C. FTIR (ATR cmꢀ1):
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ν 3268, 2923, 2875, 2316, 1467, 843, 827, 737, 571, 555. H-NMR (CDCl3, 500 MHz) δ 8.82
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(d, J = 1.9 Hz, 1H, Hꢀ24), 7.84 (dd, J = 8.1, 1.9 Hz, 1H, Hꢀ22), 7.72 – 7.68 (m, 4H, Hꢀ4/Hꢀ4’/Hꢀ
5/Hꢀ5’), 7.62 – 7.58 (m, 2H, Hꢀ1/Hꢀ3), 7.56 – 7.52 (m, 3H, Hꢀ1’/Hꢀ2’/Hꢀ3’), 7.36 – 7.32 (m, 6H,
Hꢀ6/Hꢀ6’/Hꢀ7/Hꢀ7’/Hꢀ8/Hꢀ8’), 1.97 (q, J = 7.7 Hz, 8H, Hꢀ10/Hꢀ10’), 1.23 – 1.17 (m, 8H, Hꢀ
16/Hꢀ16’), 1.15 – 1.02 (m, 32H, Hꢀ12/Hꢀ12’/Hꢀ13/Hꢀ13’/Hꢀ15/Hꢀ15’), 0.82 (t, J = 7.2 Hz, 12H,
Hꢀ17/Hꢀ17’), 0.61 (br s, 8H, Hꢀ11/Hꢀ11’). 13C-NMR (CDCl3,125 MHz) δ 152.47 (Cꢀ24), 151.18
(Cꢀ9a’), 151.07 (Cꢀ9a), 150.88 (C9b’), 150.78 (Cꢀ9b), 142.32 (Cꢀ4a), 142.13 (Cꢀ4a’), 141.92 (Cꢀ
20), 140.19 (Cꢀ4b/Cꢀ4b’), 138.30 (Cꢀ22), 130.73 (Cꢀ3’), 127.76 (Cꢀ7), 127.74 (Cꢀ7’), 126.92 (Cꢀ
6’), 126.90 (Cꢀ6), 126.71 (Cꢀ1), 126.22 (Cꢀ1’), 126.02 (Cꢀ21), 122.90 (Cꢀ8/Cꢀ8’), 120.43 (Cꢀ2’),
120.14 (Cꢀ5), 120.11 (Cꢀ5’), 120.07 (Cꢀ2), 119.74 (Cꢀ4), 119.68 (Cꢀ4’), 119.44 (Cꢀ23), 95.58 (Cꢀ
18’), 92.52 (Cꢀ18), 88.70 (Cꢀ19), 86.05 (Cꢀ19’), 55.17 (Cꢀ9’), 55.14 (Cꢀ9), 40.31 (Cꢀ10/Cꢀ10’),
31.76 (Cꢀ15/Cꢀ15’), 30.00 (Cꢀ14), 29.98 (Cꢀ14’), 29.21 (Cꢀ13/Cꢀ13’), 29.20 (Cꢀ12/Cꢀ12’), 23.72
(Cꢀ11’), 23.69 (Cꢀ11), 22.57 (Cꢀ16/Cꢀ16’), 14.06 (Cꢀ17/Cꢀ17’). HRMS (APCIꢀTOF+) m/z:
[M+H]+ Observed: 904.6755, required for C67H86N: 904.6754, error: 0.23 ppm
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2,5-bis(9,9-dioctyl-2-ethynyl-fluoren)fluorobenzene (MR2). Synthesized as described above
for MR1, from 2ꢀethynylꢀ9,9ꢀdioctylfluorene (4) (0.15 g, 0.36 mmol) and 1,4ꢀdibromoꢀ2ꢀ
fluorobenzene (6) (0.05 g, 0.18 mmol). The procedure yielded 92 mg (56 %) of MR2 as a pale
yellow solid (92 mg, 56 %). M.P. 116 ꢀ 117 °C. FTIR (ATR, cmꢀ1) 3063, 2925, 2853, 1467,
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1451, 828, 737, 721. H-NMR (CDCl3, 500 MHz) δ 7.72 – 7.69 (m, 4H, Hꢀ4/Hꢀ4’/Hꢀ5/Hꢀ5’),
7.57 – 7.51 (m, 5H, Hꢀ1/Hꢀ1’/Hꢀ3/Hꢀ3’/Hꢀ21), 7.37 – 7.32 (m, 8H, Hꢀ6/Hꢀ6’/Hꢀ7/Hꢀ7’/Hꢀ8/Hꢀ
8’/Hꢀ22/Hꢀ24), 1.98 (t, J = 8.3 Hz, 8H, Hꢀ10/Hꢀ10’), 1.26 – 1.19 (m, 8H, Hꢀ16/Hꢀ16’), 1.15 –
1.05 (m, 32H, Hꢀ12/Hꢀ12’/Hꢀ13/Hꢀ13’/Hꢀ14/Hꢀ14’/Hꢀ15/Hꢀ15’), 0.82 (t, J = 7.2 Hz, 12H, Hꢀ
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17/Hꢀ17’), 0.65 – 0.59 (m, 8H, Hꢀ11/Hꢀ11’). C-NMR (CDCl3, 125 MHz) δ 162.09 (d, JCꢀF
=
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141.95 (Cꢀ4a), 140.29 (Cꢀ4b), 140.25 (Cꢀ4b’), 133.18 (d, JCꢀF = 2.2 Hz, Cꢀ21), 130.78 (Cꢀ3’),
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130.71 (Cꢀ3), 127.68 (Cꢀ7’), 127.64 (Cꢀ7), 127.30 (d, JCꢀF = 3.4 Hz, Cꢀ22), 126.90 (Cꢀ6’),
126.88 (Cꢀ6), 126.03 (Cꢀ1), 126.01 (Cꢀ1’), 124.88 (Cꢀ20), 123.01 (Cꢀ8), 123.01 (Cꢀ8’), 120.80
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(Cꢀ2), 120.66 (Cꢀ2’), 120.07 (Cꢀ5/Cꢀ5’), 119.68 (d, JCꢀF = 5.0 Hz, Cꢀ24), 118.39 (Cꢀ4), 118.30
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(d, JCꢀF = 22.6 Hz, Cꢀ23), 118.21 (Cꢀ4’), 97.36 (Cꢀ18), 93.34 (Cꢀ18’), 88.10 (Cꢀ19’), 82.57 (Cꢀ
19), 55.16 (Cꢀ9’), 55.14 (Cꢀ9), 40.33 (Cꢀ10/Cꢀ10’), 31.78 (Cꢀ15/Cꢀ15’), 30.00 (Cꢀ14/Cꢀ14’),
29.22 (Cꢀ12/Cꢀ12’/Cꢀ13/Cꢀ13’), 23.70 (Cꢀ11/Cꢀ11’), 22.59 (Cꢀ16/Cꢀ16’) 14.07 (Cꢀ17/Cꢀ17’).
Anal. Calcd. for C68H85F: C, 88.64; H, 9.30. Found: C, 88.36; H, 9.62.
Single X-Ray Diffraction studies
Crystals of MR1 and MR2 suitable for singleꢀcrystal Xꢀray diffraction studies were obtained by
room temperature evaporation of a saturated solution of the analytes in a chloroform/acetonitrile
mixture.
The intensity data were collected on EnrafNonius Kappa diffractometer with a CCD area
detector (λMoKα = 0.71073 A˚, monochromator: graphite) and Bruker D8 Venture CMOS
diffractometer at 173 K. The crystals were mounted on conventional MicroLoops.™ All heavier
atoms were found by Fourier map difference and refined anisotropically. All reflection data set
were corrected for Lorentz and polarization effects. The first structure solution was obtained
using the SHELXSꢀ2017 program and the SHELXLꢀ2017 was applied for refinement and output
data.9 All software manipulations were done under the WinGX environment program set. The
programs Mercury 3.7 and ORTEPꢀ3 were used to prepare artwork representations.10, 11 Free
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volumes around the rotators were approximated to the space confined by a hypothetical prism
with two edges defined with the distances shown in Figure 3 (~8 and ~10 Å) and the third edge
taken as the C2ꢀC2’ distance (~11 Å).
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CCDC 1582960 and CCDC 1582963 contain the supplementary crystallographic data for this
paper. These data can be obtained free of charge via https://summary.ccdc.cam.ac.uk/structureꢀ
summaryꢀform (or from the Cambridge Crystallographic Data Centre, 12, Union Road,
Cambridge CB2 1EZ, UK; fax: +44 1223 336033).
Theoretical methods
Gas phase geometries were computed within the framework of the Density Functional
Theory using the Gaussian 09W software package,12 from the crystal structures of MR1 and
MR2. Both equilibrium geometries were obtained using the doubleꢀζ 6ꢀ31G(d,p) polarized basis
set with different hybrid functionals: B3LYP, PBE0 and the longꢀrange corrected CAMꢀB3LYP
and M06ꢀ2X. In either case a former optimization at the HF/6ꢀ31G(d,p) was required. These
relaxed conformers were confirmed as energetic local minima through analytical inspection of
their vibrational frequencies and were further optimized using the integral equation formalism of
the Polarizable Continuum Model (IFPCM) with chloroform as solvent. The resulting geometries
were subjected to a TDꢀDFT computation of the vertical excitation energies for MR1 and MR2,
which were compared to the experimental electronic spectra. From all the methods, only the
CAMꢀB3LYP and M06ꢀ2X functional were found to predict these energies accurately, with
differences between the experimental and computed excitations below the usually accepted
threshold of 0.3 eV (Figure S8). These functionals were consequently employed with Dunning’s
ccꢀpVDZ basis set in the computation of firstꢀorder hyperpolarizabilities (β), as the use of such
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larger atomic functions has proved effective in predicting this optical parameter.13 For
consistency reasons, the same method was applied in the computation of rotational activation
energies (Ea) and static molecular dipoles (ꢀ0). It should be remarked that throughout the entire
set of computations, the CAMꢀB3LYP/ccꢀpVDZ was unambiguously found as the better DFT
method both in terms of accuracy and computational expense. Also, the use of a smaller basis set
such as the doubleꢀζ 6ꢀ31G** basis set behaved catastrophically, particularly at predicting
electronic parameters such as electronic excitation energies and should therefore be avoided
when computing NLO parameters of molecules with similar quadrupolar architectures as the
rotors herein studied.
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Evaluation of the modulation of ꢀ0 and β as functions of the orientation of the pyridine and
fluorobenzene rotators, was carried out by varying their relative positions from the coꢀplanar
(equilibrium) geometries. Singleꢀpoint energy calculations were then performed for conformers
with successive 15° increments in the dihedral angle formed between the plane containing the
rotator and that of the 9ꢀoctylꢀfluorenyl stators, i.e. the [C1ꢀC2ꢀC20ꢀC21] torsion angle.
In order to confirm or correct the NMR assignments, a Gaussian Invariant Atomic Orbital
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(GIAO) computation of the isotropic magnetic shieldings of C nuclei was performed. These
calculations were conducted at the PBE0/6ꢀ31G(d,p) level of theory rather than with the M06ꢀ
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2X/ccꢀpVDZ approach, as it was unexpectedly found that the former predicted the desired C
chemical shifts with better accuracy and performance, as reflected in lower Mean Unsigned
Errors (MUE, Table S1) obtained for both MR1 and MR2. Although the methodology employed
provides absolute chemical shifts, for clarity they are herein reported as scaled with respect to an
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external tetramethylsilane (TMS) reference computed at the B3LYP/6ꢀ311+G(2d,p) level of
theory.
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3. RESULTS AND DISCUSSION
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3.1. Synthesis and Molecular Characterization
Sonogashira double crossꢀcoupling reaction between 2ꢀethynylꢀ9,9ꢀdioctylfluorene (4) and either
2,5ꢀdibromopyridine (5) or 1,4ꢀdibromoꢀ2ꢀfluorobenzene (6) allowed access to unsymmetrical
molecular rotors MR1 and MR2 in moderate yields (Scheme 1).
Scheme 1. Synthesis and numbering for molecular rotors MR1 and MR2. Displayed in color
code are the 9ꢀoctylfluorenyl stators (blue), the polarizable rotators (red) and the acetylenic axles
(black). Reagents and conditions: i) 1ꢀBromooctane, KOH, DMSO, ii) Ethynyltrimethylsilane,
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Pd(PPh3)2Cl2, CuI, DIPA, reflux, iii) K2CO3, MeOH/ether. rt. iv) Pd(PPh3)2Cl2, CuI, DIPA, THF,
reflux.
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In the HꢀNMR spectrum of MR1, two spin systems could be readily identified through
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homonuclear COSY (1Hꢀ1H) 2DꢀNMR spectroscopy. The first coupled nuclei was ascribed to the
pyridine ring, with the characteristic resonance of Hꢀ24 appearing as a highly unshielded doublet
at δ = 8.82 ppm. Aromatic hydrogens from the fluorene submolecular fragments appeared as
multiplets, with magnetic inequivalences between the Hꢀ1/Hꢀ1’ and Hꢀ3/Hꢀ3’ nuclei from both
fluorenyl stators. Nonetheless, their signals were successfully assigned owing to their marked
longꢀrange scalar couplings.
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Most C nuclei were also found to be magnetically nonꢀequivalent in solution, which was
observed as a ubiquitous splitting of the signals in the 13CꢀNMR spectra of both MR1 and MR2,
with chemical shift differences even below 0.05 ppm. Ambiguity found in the assignment of
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these resonances was thus circumvented employing APT and 2D (1Hꢀ1H, Hꢀ13C) NMR
techniques and a Gaussian Invariant Atomic Orbital (GIAO) calculation of the isotropic 13C
chemical shifts for both molecular rotors at the PBE0/6ꢀ31G(d,p) level of theory (For details, see
Supplementary Table S1 and Figures S9 and S10).
3.2. X-Ray Diffraction Studies
Crystals of compounds MR1 and MR2 suitable for SXRD experiments were grown in
chloroform/acetonitrile at room temperature (Figure 1). Interestingly, despite the replacement of
the pyridine nitrogen in MR1 for a CꢀF moiety in MR2, both compounds crystalized without
solvent in the monoclinic P 21 space group, with 2 molecules per unit cell and with nearly the
same cell constants (Table 1). Also, both showed an anti conformation for the two fluorenyl
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stators, which lie in close orthogonality to the plane containing the rotator and the acetylenic
axles as evidenced by the values for the [C1ꢀC2ꢀC20ꢀC21] dihedral angle of 84.6 and 86.2 ° for
MR1 and MR2, respectively. To further evidence the likenesses of these isomorphic crystals, a
comparison between their calculated PXRD patterns is depicted in Figure 2.
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Table 1. Crystal structure and refinement data.
Compound
Empirical formula
Formula weight
Temperature
Crystal system
Space group
a (Å)
MR1
C67H85N
904.42
MR2
C68H85F
921.36
173 K
173 K
Monoclinic
P21
Monoclinic
P21
12.610(16)
14.291(18)
16.78 (2)
90
12.48(5)
14.11(4)
16.49(5)
90
b (Å)
c (Å)
α (°)
104.07 (4)
90
103.2(2)
90
β (°)
γ (°)
Volume (Å)3
2933(6)
2
2825(16)
2
Z
Density (g⋅cmꢀ3)
Crystal size (mm)
θ Range (°)
1.024
1.083
0.1 x 0.1 x 0.2
2.19 to 28.28
0.32 x 0.069 x 0.04
2.70 to 26.71
ꢀ16 ≤ h ≤ 16, ꢀ19 ≤ k
≤ 19, ꢀ22≤ l ≤ 22
ꢀ15 ≤ h ≤ 15, ꢀ17 ≤ k ≤
17, ꢀ20≤ l ≤ 20
Index ranges
Nref
14556
10915
R (reflections)
0.0537 (8423)
0.0575 (7766)
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0.1385 (14374)
0.1167 (10915)
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Figure 1. Crystal structure of (a) MR1 and (b) MR2 with the thermal ellipsoids drawn at 50%
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probability for every atom other than hydrogen.
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Figure 2. Calculated PXRD patterns for MR1 (top) and MR2 (bottom).
Remarkably, in spite of the presence of the polar pyridine and fluorobenzene rotators, the
crystal packing of both MR1 and MR2 is dominated exclusively by weak nonꢀpolar contacts
among the alkyl chains of the fluorene stators (For details, see Supplementary Figure S10). It is
worth noting that such absence of intermolecular interactions involving the rotators may
facilitate their rotational dynamics.
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Further analysis of the crystalline structure of these compounds revealed that a given rotator
has 3.8ꢀ5.2 Å of distance from the ring centroid to the closest atoms within the crystal lattice of
MR1 and MR2 (see Figure 3), conferring a free volume of ca. 796 and 854 Å3 around the
pyridine and fluorobenzene rotators, respectively, which may be enough to allow the rotational
dynamics of these molecules.3 However, the distances between the centroids of two adjacent
rotators are of 11.0 and 10.8 Å for MR1 and MR2 respectively, which may limit correlation of
internal rotational motion. Nonetheless, cooperative effects arising by the alignment of molecular
dipoles throughout the crystallographic c axis (vide infra) of these crystal arrays may help
overcome this limitation.
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Figure 3. Distances (Å) from a rotator centroid to the closest atoms within the crystal packing of
(a) MR1 and (b) MR2.
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Both MR1 and MR2 crystal structures exhibited intriguing 2D layers that resemble the lipidic
bilayers that constitute cell membranes (Figure 4). This peculiar selfꢀassembly, which spreads
along the crystallographic c axis, is of relevance within the study of solidꢀstate molecular rotors
due to the need (of that particular type of molecular machines) of having an amphidynamic
character, i.e. to display fast molecular dynamics while maintaining a highly ordered phase, such
as that offered by a crystalline array. The similarity of the crystal packing of these studied
molecular rotors with the lipidic bilayers in cell membranes is thus of importance due to the fact
that cell membranes constitute an archetypical example of an amphidynamic system, given that
they are wellꢀknown to present both phase order and fast molecular dynamics.14
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Figure 4. Schematic representation of 2D layers formed within the crystal packing of
compounds MR1 (top) and MR2 (bottom). The crystal structures are viewed along the
crystallographic b axis and the rotators are in space fill representation for clarity.
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As depicted in Figure 5, both MR1 and MR2 showed a peculiar orientation of molecular
dipoles throughout the crystallographic b axis. We expect that given the free space that the
rotators display and the low rotational energetic barriers provided by the acetylenic axles, the
orientation of these microscopic molecular dipoles might change with the presence of an applied
magnetic field, yielding these crystalline systems as molecular analogues of macroscopic
compasses.
Figure 5. Orientation of static molecular dipoles along the crystallographic b axis for MR1 (left)
and MR2 (right).
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It is worth noting that because of their chiral selfꢀassembly, these isomorphic crystals are also
of particular interest for nonlinear optical (NLO) applications, where nonꢀcentrosymmetric
arrangements are required for solidꢀstate applications, such as the second (or higher order)
harmonic generation. Moreover, due to the alignment of molecular dipoles within the crystals,
these materials are expected to display enhanced NLO properties due to cooperative effects
among the static dipoles aligned throughout the crystal lattice.
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3.3. Theoretical studies
The molecular structure of rotors MR1 and MR2 was studied through DFT computations using
the ccꢀpVDZ basis set with the hybrid longꢀrange corrected M06ꢀ2X and CAMꢀB3LYP
functionals. Negligible geometrical differences between the gasꢀphase geometries were found
between both methods. When compared to the solidꢀstate conformers, the main geometrical
difference is that the former are predicted to have coꢀplanarity among the pyridine (MR1) or
fluorobenzene (MR2) rotators and the fluorenyl stators (Figure 6). Such conformations may
reasonably be preferred due to a better stabilization of the static molecular dipoles (ꢀ0) in these
planar geometries. This was confirmed through singleꢀpoint energy computation at the same
level of theory for both conformers, showing changes in molecular dipoles (ꢁꢀ0) of ca. 0.25 and
0.05 Debye for MR1 and MR2, respectively, favoring the planar conformations.
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Figure 6. Superposed equilibrium (M06ꢀ2X/ccꢀpVDZ) and solidꢀstate (blue) geometries for
MR1 (top) and MR2 (bottom).
In order to estimate how free the pyridine and fluorobenzene rotators are to perform the
rotational work, the energy profiles of both MR1 and MR2 were computed for conformers with
incremental 15 ° deviations from the equilibrium (planar) geometries, allowing us to predict very
small activation energies (Ea) for both rotors (2.5 ꢀ 4.5 kcal/mol), mainly accounted for the loss
of πꢀconjugation and aromaticity of these molecules as they deviate from coꢀplanarity (Figure 7).
It is worth noting that even considering that the nonꢀplanar solidꢀstate conformers should have
been observed due to potential CꢀHꢁꢁꢁπ contacts involving the rotators, these weak (~1.5
kcal/mol)15 interactions should not constrain rotational motion in the solid state, as efficient
dynamics have been observed with even higher energetic thresholds.5
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Figure 7. Energy profiles for the [C1ꢀC2ꢀC20ꢀC21] dihedral angle in MR1 (top) and MR2
(bottom), respectively, using the ccꢀpVDZ basis set with the CAMꢀB3LYP (blue) and M06ꢀ2X
(red) functionals.
As mentioned earlier, prospective applications of molecular rotors include their use as
microscopic analogues of compasses, with conformational changes effectively induced by a
magnetic stimulus. Due to the absence of inversion symmetry in the crystal packing of MR1 and
MR2, a pulsed laser could be used to induce not only the conformational change but also an
associated evenꢀorder nonlinear optical (NLO) response, such as the Second Harmonic
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Generation (SHG). These optical phenomena may arise from a crystal as its molecules polarize
due to the appliance of an external magnetic field, following:16
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ꢂ ꢄ
ꢀ ꢃ = ꢅꢁꢆꢃ + ꢇꢁꢆꢈꢃ ꢃꢈ + ⋯
(1)
ꢁ
ꢆ
ꢆ
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Where P(E) is the molecular polarization induced by the electric field (E),
α
and
β
are the
molecular polarizability and firstꢀorder hyperpolarizability, respectively, and i,j,k refer to the
molecular coordinate system.
The SHG response in crystals is restricted to nonꢀcentrosymmetric space groups, as the presence
of inversion symmetry within the molecule yields
expected in centrosymmetric supramolecular arrangements. In nonꢀcentrosymmetric media, the
magnitude of greatly influences the strength of the SHG signal. This leads to the possibility of
developing photonic switches from MR1 and MR2 where, as consequence of an induced
reorientation of the rotator, a modulation of and thus of the SHG response could be achieved. It
should be noted that because of the quasiꢀcentrosymmetric quadrupolar (DꢀπꢀAꢀπꢀD) topology of
these molecules, small (but nonꢀzero) values of are expected in the coplanar conformations.
Nonetheless, should be modified as the rotators deviate from coplanarity, as this process
interrupts πꢀconjugation and consequently alters the molecular topology, leading to an “OFF”
state (i.e. the conformer with the lowest ) which could be switched to an “ON” state as
β = 0 and a cancelation of resonant dipoles is
β
β
β
β
β
molecular dipoles are reꢀoriented due to the application of an external magnetic field, as
successfully described by our group for analogous systems.17
The results of a DFT computation of the modulation of ꢀ0 and β as functions of the orientation of
the fluorobenzene and pyridine rotators are depicted in Figure 8. Surprisingly, while the variation
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of ꢀ0 followed the same trend in both rotors (increasing as the molecule deviates from coꢀ
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planarity and thus of centrosymmetry), opposite behaviors were found for the modulation of
β.
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In the case of MR1, has a minimum value at a dihedral angle of 0 ° (i.e. in the coplanar
β
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conformer) and a maximum near 90 °, as expected for the change in topology previously
explained. Strikingly, both DFT methods employed predicted the exact opposite trend for MR2
with a maximum value of
approaches 90 °.
β at coplanarity, which markedly decreases as the dihedral angle
Figure 8. Modulation of the static dipole moment (ꢀ0, dotted lines) and the firstꢀorder
hyperpolarizability (β, solid lines) as a function of the [C1ꢀC2ꢀC20ꢀC21] dihedral angle for MR1
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(top) and MR2 (bottom) using the ccꢀpVDZ basis set with the CAMꢀB3LYP (blue) and M06ꢀ2X
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(red) functionals.
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The rationale behind this divergent behavior is far from trivial and out of the scope of this paper.
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Further studies should deal with computing the involved excited states, since the value of
β,
commonly assumed by a twoꢀstate model,18 depends not only on the herein studied ground state
dipole (ꢀg) but also on the change in dipole moment between the involved eigenstates (ꢁꢀge) and
on the energy (Ege) and oscillator strength (fge) for the transition, following:
ꢍ
∆ꢉ
ꢌ
ꢊꢋ ꢊꢋ
ꢇ ∝
(2)
ꢍ
ꢎ
ꢊꢋ
Despite the different behaviors of both molecular rotors, ON/OFF ratios of 2.6ꢀ2.9 for MR1 and
1.3ꢀ1.4 for MR2 are expected, according to DFT computations. While the computed values are
not particularly appealing at the molecular level, an enhancement in the NLO response in these
crystals may occur due to cooperative effects caused by the crystal packing as mentioned earlier
(vide supra).
4. CONCLUSIONS
Two molecular rotors featuring 9ꢀoctylfluorenyl stators with pyridine or fluorobenzene rings as
rotators were successfully obtained employing a Sonogashira double crossꢀcoupling reaction as
the key synthetic step. The crystal structure of these compounds formed 2D layers that highly
resemble cell membranes, which suggests these crystals may also display a dynamic behavior
within a highly ordered phase. Free volumes of ca. 796 ꢀ 854 Å3 were estimated around the
rotators, potentially allowing their rotational dynamics in the solid state, which may occur at
room temperature according to DFT computations. Moreover, both their chiral crystal packing
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and the modulation of the firstꢀorder hyperpolarizabilites (β) with the orientation of the rotators,
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make these compounds particularly appealing as photonic switches, which may reorientate upon
the appliance of a magnetic field, potentially displaying rotational work such as that of a
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gyroscope. In silico evaluation of the modulation of
β as a function of the rotational dynamics
showed ON/OFF ratios of ~2.7 and ~1.3, further confirming a prospective application as
photonic switches. The experimental evaluation of the solid state rotational dynamics of
deuterated isotopologues, as well as the study of the nonlinear optical behavior of these materials
is ongoing.
AUTHOR INFORMATION
* Corresponding author: rsantill@cinvestav.mx
ACKNOWLEDGEMENTS
The authors acknowledge support from PAPIIT (INꢀ216616) and CONACYT for a doctoral
scholarship for P.L.ꢀV (337958). Marco A. Leyva, Geiser Cuellar and Teresa CortezꢀPicasso
(CINVESTAVꢀIPN) are gratefully acknowledged for Xꢀray structure determinations, HRMS
analyses and NMR experiments, correspondingly. We would like to express our gratitude to
Prof. Pascal G. Lacroix (CNRS) for his valuable comments on this work.
ASSOCIATED CONTENT
1
13
Supporting Information Available: Synthesis of starting materials, H, C NMR and HRMS
spectra, elemental analyses, crystal packing, optimized geometries and Gaussian Invariant
13
Atomic Orbital C chemical shifts plots (DFT), as well as crystal packing of MR1 and MR2.
This material is available free of charge via the Internet at http://pubs.acs.org.
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Designed synthesis and crystallization of isomorphic molecular gyroscopes with cell-like
bilayer self-assemblies.
Ma. Eugenia Ochoa,a Pablo LabraꢀVázquez,b Norberto Farfán,b Rosa Santillan,a*
Two molecular rotors featuring pyridine and fluorobenzene rings as polar rotators and 9ꢀ
octylfluorenyl stators were synthesized. Their crystal structures were established through SXRD
techniques, crystallizing in the monoclinic chiral P21 space group. The supramolecular
assemblies of both isomorphs showed an orientation of static dipoles through the crystal lattice
and the formation of intriguing 2D layers that resemble cell membranes, a typical example of an
amphidynamic system. Small activation energies and the modulation of the firstꢀorder
hyperpolarizabilities of these compounds as a function of rotational dynamics were revealed
through DFT computations at the CAMꢀB3LYP/M06ꢀ2X/ccꢀpVDZ level of theory and
correlated with a potential use of these materials as photonic switches.
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