Determination of the absolute stereostructure of a cyclic
azobenzene from the crystal structure of the precursor
containing a heavy element
Reji Thomas1,2 and Nobuyuki Tamaoki*1

Full Research Paper
Address:
1Research Institute for Electronic for Science, Hokkaido University,
Kita-ku, N 20, W 10, Sapporo-001-0020, Japan and 2Postgraduate
and Research Department of Chemistry, Farook College, Farook
College P. O., Kozhikode, 673632, Kerala, India
Email:
Nobuyuki Tamaoki* - Tamaoki@es.hokudai.ac.jp

Open Access
Beilstein J. Org. Chem. 2016, 12, 2211–2215.
doi:10.3762/bjoc.12.212
Received: 15 August 2016
Accepted: 07 October 2016
Published: 19 October 2016
This article is part of the Thematic Series "Strategies in asymmetriccatalysis".

* Corresponding author
Guest Editor: T. P. Yoon
Keywords:
azobenzene; cyclic compound; enantiomer; stereostructure; X-ray
crystal analysis© 2016 Thomas and Tamaoki; licensee Beilstein-Institut.
License and terms: see end of document.

Abstract
Single crystal X-ray diffraction has been used as one of the common methods for the unambiguous determination of the absolutestereostructure of chiral molecules. However, this method is limited to molecules containing heavy atoms or to molecules with thepossibility of functionalization with heavy elements or chiral internal references. Herein, we report the determination of theabsolute stereostructure of the enantiomers of molecule (E)-2, which lacks the possibility of functionalization, using a reverse
method, i.e., defunctionalization of its precursor of known stereostructure with bromine substitution (S-(−)-(E)-1). A reductive
debromination of S-(−)-(E)-1 results in formation of one of the enantiomers of (E)-2. Using a combination of HPLC and CD spectroscopy we could safely assign the stereostructure of one of the enantiomers of (E)-2, the reduced product R-(−)-(E)-1.

Introduction
Chirality is a topic of fundamental importance in several
branches of science [1-5]. Homochirality in nature was one of
the most important challenges for researchers and the origin isstill unsolved [6-8]. It is well known that biological functions ofmost living systems are determined by the stereostructure of
biologically active molecules [9]. Beyond the academic interest,
the synthesis and separation of chiral molecules plays a key rolein chemical industry, particularly as catalysts [10] and pharmaceutical ingredients [11]. In addition to the special interest inmolecular chirality in diverse fields of biology and pharmaceu-

tical chemistry, several chiral molecules have been synthesised
and studied for their stereostructure-dependent physical properties such as optical activity [12-22] and magnetic properties[23-25]. Hence, the chiral separation and the determination ofabsolute stereostructure are important aspects of stereochemistry for the complete understanding of the role of chiral structures in various physical and biological functions.
Until date there have been several spectroscopic, diffraction
methods developed to determine the absolute stereostructure of2211

Beilstein J. Org. Chem. 2016, 12, 2211–2215.

chiral molecules [26-35]. The non-empirical methods employed to determine the absolute configuration of a molecule
include circular dichroism, exciton chirality methods [28,29],
NMR spectroscopy [30-32], X-ray diffraction [33-35], etc. In
addition to these methods, many researchers explored a combination of vibrational circular dichroism and quantum mechanical calculations to determine the absolute stereostructures [3638]. Among various methods used for determining the absolutestereostructure of the molecules, the X-ray diffraction methods
obtained more credibility, especially the method using a single
parameter viz. ‘Flack Parameter’ [33-35] which clearly identifies the absolute structure rather than measuring the intensity of
the Bijvoet pairs [39]. However, the requirement of heavy
atoms for the better anomalous dispersion, limits the usage of
X-ray diffraction in determining the absolute stereostructure. In
many of the molecules, the requirement of a heavy atom leads
either to functionalization of the molecules with groups containing an heavy atom [40-44] or the relative position of the chiral
centre is estimated in relation to an internal reference of known
chirality [26]. Nevertheless, this approach can be applicable
only to the molecules with easily functionalizable groups.
Hence, it is important to provide an alternative method for thedetermination of the absolute stereostructure of a molecule
without the possibility of functionalization.

the molecules are of three categories (i) achiral (irrespective of
the isomerized state of the azobenzene, i.e., E or Z), (ii) chiral inE-state and achiral in Z-state of azobenzene, (iii) chiral in bothstates of the azobenzene unit. We have explored the property ofplanar chirality of these molecules and carried out the opticalresolution to demonstrate various properties such as molecularbrakes, chiroptical switches and chirality sensors for light andsolvent etc. [45-50]. Although we could separate the enantiomers of all these chiral cyclic azobenzenes, the experimental determination of the absolute stereostructure by X-ray diffraction
was difficult due to the lack of heavy elements.
In the present study, we demonstrate the determination of theabsolute stereostructure of a molecule without any functionalgroups for the introduction of heavy atoms. We used a reverse
reaction, i.e., not a reaction to add a heavy atom auxiliary to thechiral cyclic azobenzene but a reaction to remove the heavy
atom from the precursor molecule with known chirality toobtain the target molecule. We could determine the stereostructure of the cyclic azobenzene by comparing the HPLC data obtained with a chiral column and the circular dichroism (CD)
spectra of the product obtained by reduction of the enantiopure
precursor and the target molecule.

Results and Discussion
Recently our group reported the synthesis of several cyclic
azobenzene molecules and their properties [45-50]. All thesemolecules share a comparable cyclic structure, with a photoisomerizable azobenzene unit linked to a substituted or unsubstituted aromatic unit such as naphthalene or benzene. Generally

Figure 1 shows the schematic representation of experiments
involved in the separation and reductive debromination of theenantiomer (E)-1B. The enantiomers of molecules (E)-1 and(E)-2 are previously reported as photocontrolled chiropticalswitches for various nematic liquid crystalline hosts for tuning

Figure 1: Schematic representation of the steps to enantiomer (E)-2A.

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the reflection colors through the entire visible region [45,46].
The molecule (E)-1 has been also used to demonstrate the completely photocontrolled rotation of the micro glass rods on thechiral nematic liquid crystalline films induced by the rotational
reorganization of the polygonal finger print texture [45]. Molecule (E)-1 contains a 2,6-dibromo-1,5-dihydroxynaphthalene
part linked to an azobenzene unit through bismethylene spacers.
The constricted rotation of the naphthalene unit in the cyclic
structure gives planar chirality to this molecule with separable
enantiomers. The presence of the bromine substitution in thenaphthalene unit gives an added advantage in determining theabsolute stereostructure of the separated enantiomers. The determination of the absolute stereostructure of one of the enantiomers of (E)-1 by X-ray diffraction has been presented in ourprevious report [45]. In this study, we employ this enantiomer
as a precursor for the determination of the absolute configuration of its reduced product, which is expected as one of the enantiomers of (E)-2.
In order to characterize the reduced product we have carried out
the 1H NMR spectroscopy of the compound and found that the
spectrum completely matches with the previously reported compound (E)-2 [46]. To confirm the formation of compound (E)-2
we have carried out chiral HPLC studies on a Chiralpak IA
column using a mixture of ethyl acetate and hexane (10:90) as
the eluent to characterize the nature of the enantiomer formedby the reductive debromination. In the previous study with the
combination of density functional theoretical calculations(DFT) and electronic circular dichroism (ECD), we haveassigned the first and second eluted enantiomers of (E)-2 as
R-(−)-(E)-2 and S-(+)-(E)-2, respectively, on a chiralpak IA
column using hexane and ethyl acetate as eluent [46]. Figure 2ashows the chromatogram obtained for the racemic (E)-1 withtwo peaks corresponding to the first (14.6 min) and second(15.9 min) eluted trans enantiomers, R-(+)-(E)-1 and
S-(−)-(E)-1, respectively. Whereas, Figure 2b shows the chromatogram recorded for the crystalline sample of S-(−)-(E)-1
which is used for the reductive debromination. The chromatogram shows a single peak at 15.9 min ascertaining theenantiomeric purity of the sample. After reduction of
S-(−)-(E)-1 we have carried out the HPLC of the reduced sample where the chromatogram shows a single peak with aretention time of 11.9 min (Figure 2c). In order to obtainan idea about the enantiomeric nature of the reduced product wehave recorded the chromatogram for the pure racemic sample of(E)-2. The chromatogram shows two peaks corresponding tofirst and second eluted enantiomers, respectively with the retention time of 11.9 and 13.5 min (Figure 2d). Comparing the chromatograms of the reduced product and the racemic mixture, it isclear that the reduced product is the first eluted enantiomer of(E)-2.

Figure 2: Chromatogram (Chiral HPLC) obtained for (a) racemic mixture of (E)-1 (b) sample used for reductive debromination (second
eluted enantiomer S-(−)-(E)-1) (c) recorded after the LiAlH4 reductionof S-(−)-(E)-1 and (d) the chromatogram of racemic (E)-2. (Column:
Chiralpak IA, eluent: ethyl acetate/hexane (10:90), Flow rate:
3 mL/min)To further confirm the formation of (E)-2 A we studied thechiroptical properties of the product obtained by reductive
debromination. Figure 3 shows the circular dichroism spectra of
the reduced product along with that of S-(−)-(E)-1. From thespectral features and band intensity ratios, it is clear that the
reduced product shows completely different cotton bands withthat of S-(−)-(E)-1. We compared the spectra of the reduced
product with that of the previously reported spectra of the enantiomers of (E)-2 and found that the spectra matches the CD
spectra of (E)-2A [46]. Thus from the HPLC and CD data it isclear that the reduced product of S-(−)-(E)-1 gives the firsteluted enantiomer of (E)-2.

Figure 3: CD spectra recorded for solutions in THF for S-(−)-(E)-1 (redcurve) and for the reduced product of S-(−)-E-1, i.e., R-(−)-(E)-2 (black
curve).

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According to the Cahn–Ingold–Prelog (CIP) priority rules [51],the absolute configuration of the reduced product should be ‘R’.
The priorities of the functional groups on the reduced productreverse on removal of the bromine atom from the parent structure. Comparing the HPLC and CD data with structural data of
S-(−)-(E)-1 the absolute stereostructure of its reduced product isdetermined as R-(−)-(E)-2. The experimentally derived stereostructure completely matches with the absolute structure previously predicted from theoretical calculations.

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In summary, we demonstrated the determination of the absoluteconfiguration of the enantiomers of a molecule from its precursor with known stereostructure. More importantly, this method
can be used for the determination of stereostructures of molecules without functional groups for the functionalization withheavy elements or chiral internal references.

Experimental
All solvents and chemicals were obtained from commercial
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