Computational and crystallographic examination of naphthoquinone based diarylethene photochromes

Article abstract of DOI:10.3390/molecules25112630

Photochromic compounds have a lengthy history of study and a profusion of applications that stand to gain from these studies. Among the classes of photochromic compounds, diarylethenes show desirable properties including high fatigue resistance and thermal stability, thus meeting some of the most important criteria necessary to enter the realm of practical applications. Recently, photochromic diarylethenes containing quinone functionalities have demonstrated interesting optical and solid-state properties. When properly interfaced with suitable electron withdrawing groups on the aryl component, both the ring-opening and ring-closing reactions can be achieved with visible light; this is in contrast to most other diarylethenes where UV light is required for ring closure. Unfortunately, quantitative conversion from open to closed forms is not possible. In this work, we examine the relative energies of conformations of solid-state structures observed by X-ray crystallography and evaluate their thermal stabilities based on density functional theory (DFT) calculations. Time-dependent DFT (TD-DFT) is used to model the UV-vis absorption spectra of these quinone diarylethenes. We show that spectral overlap between open and closed forms is a major hindrance to full photoconversion.

Full text of DOI:10.3390/molecules25112630

molecules
Article
Computational and Crystallographic Examination of
Naphthoquinone Based Diarylethene Photochromes
1
,
2,
3
, Ian M. Walton 3,
Dinesh G. Patel * , Martial Boggio-Pasqua * , Travis B. Mitchell
William R. Quigley 1 and Frank A. Novak 1
1
Department of Chemistry, the Pennsylvania State University at Hazleton, Hazleton, PA 18202, USA;
wrq5004@psu.edu (W.R.Q.); fxn449@gmail.com (F.A.N.)
Laboratoire de Chimie et Physique Quantiques, CNRS/Université Paul Sabatier, 31062 Toulouse, France
Department of Chemistry, the State University of New York at Buffalo, Buffalo, NY 14260-3000, USA;
travismi@buffalo.edu (T.B.M.); ian.walton@chbe.gatech.edu (I.M.W.)
2
3
*
Correspondence: dgp15@psu.edu (D.G.P.); martial.boggio@irsamc.ups-tlse.fr (M.B.-P.)
ꢀ
ꢁꢂꢀꢃꢄꢅꢆꢇ
ꢀ
ꢁꢂꢃꢄꢅꢆ
Received: 8 May 2020; Accepted: 1 June 2020; Published: 5 June 2020
Abstract: Photochromic compounds have a lengthy history of study and a profusion of applications
that stand to gain from these studies. Among the classes of photochromic compounds, diarylethenes
show desirable properties including high fatigue resistance and thermal stability, thus meeting
some of the most important criteria necessary to enter the realm of practical applications. Recently,
photochromic diarylethenes containing quinone functionalities have demonstrated interesting optical
and solid-state properties. When properly interfaced with suitable electron withdrawing groups
on the aryl component, both the ring-opening and ring-closing reactions can be achieved with
visible light; this is in contrast to most other diarylethenes where UV light is required for ring
closure. Unfortunately, quantitative conversion from open to closed forms is not possible. In this
work, we examine the relative energies of conformations of solid-state structures observed by X-ray
crystallography and evaluate their thermal stabilities based on density functional theory (DFT)
calculations. Time-dependent DFT (TD–DFT) is used to model the UV-vis absorption spectra of these
quinone diarylethenes. We show that spectral overlap between open and closed forms is a major
hindrance to full photoconversion.
Keywords: diarylethenes; photochromes; quinones; TD–DFT computations
1
. Introduction
Photochromic molecules [1,2], described as reversible dyes under photochemical control [1],
have proven themselves attractive as molecular scale switches with the means to optically control
or gain information about systems of interest. Isomerization between two unique optical states is
achieved by light of different wavelengths, though thermally induced isomerization can occur in
some cases. These isomers, in addition to having different light absorption profiles, possess different
electronic properties and molecular structures. Initially finding practical applications in ophthalmic
lenses, specialty inks and in novelty items, potential applications for photochromic molecules have
greatly increased in recent years. Taking advantages of these photonically reversible changes,
researchers have demonstrated the use of photochromes in sensors [
magnetic switches [ 10], data storage [11 14] and photomechanical materials [15
applications [22,23], transistor behavior [24–26] and digital processing [27] have been examined.
3
–
7
] including dosimetery [
8],
9,
–
–
21]. Even biological
Molecules 2020, 25, 2630; doi:10.3390/molecules25112630
www.mdpi.com/journal/molecules

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The most cited classes of organic photochromes and their means of isomerization (optical and/or
thermal) are shown in Figure 1. Spiropyrans, spirooxazines, azobenzenes and diarylethenes units
constitute some of the most studied compounds as determined by prevalence in the literature. Among
the compounds in Figure 1, diarylethenes and fulgides are notable as their thermal isomerization
pathways are restricted through careful molecular design. Between the two classes, however, it can be
argued that diarylethenes have received greater attention.
Figure 1. Classes of organic photochromic compounds.
Diarylethene photoisomerization is typically driven by UV light for ring closure, while ring
opening is facilitated by visible light (Figure 1). Given the limitations inherent to using UV-light for
materials of practical utility, much research lately has been directed towards achieving photoswitching
that is affected by visible light in both directions. This would increase the applicability and appeal of
the diarylethene class of photochromes [28
have emerged as compliments to the better-known hexafluorocyclopentene based diarylethenes [33
–
32]. Quinone based diarylethene photochromes (qDAEs)
34
,
]
and similar scaffolds. Fortuitously these quinone containing diarylethenes possess highly desirable
photoisomerization driven by visible light in both the ring closing and ring opening directions [35].
Unfortunately, unlike hexafluorocyclopentene and similar diarylethenes, qDAEs have shown only
5–30% photoconversion [36] as opposed to the near quantitative conversion that can be found in other
DAEs that photoswitch with UV light [ ]. This inability to achieve close to 100% conversion from ring
1
open to ring closed isomers has largely precluded a complete understanding of the electronics of the
closed form. A greater understanding of the electronic and structural limitations of current qDAEs is
essential to the molecular design of more effective qDAEs in the future.
DAEs have been the subject of many theoretical studies [37] aimed at understanding their thermal
biostability and optical properties but also their photoswitching and photodegradations mechanisms,
highlighting the critical role of extended conical intersection seams [38,39]. To our knowledge, only
one report exists of the computational analysis of a qDAE [40]. Herein we examine the structural
and electronic restrictions of qDAEs that lead to the observed reduced photoconversion. This study
involves a series of photochromic 2,3-bisthienyl-1,4-naphthoquinone diarylethenes (nqDAEs, Figure 2).
The selected thiophenes are diester substituted (compounds
compound ) or dibromide substituted (compound ), all of which have some degree of electron
withdrawing character present on the molecule. Bisphenyl substituted 1,4-naphthoquinone compound
was also synthesized and has recently been reported [41] by a different synthetic route than reported
1 and 2), dicarboxylic acid substituted
(
3
4
5
here (Scheme 1). These diarylethene molecules were selected partly because the electronic structure of
the quinone-DAE system results in a donor-acceptor system [42] that effectively lowers the electronic
energy gap into the range of visible light.

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Figure 2. Structures of 4-naphthoquinone diarylethenes (nqDAEs)
well as the structure of phenyl nqDAE 5.
1–4 in the open and closed forms as
Scheme 1. Synthetic routes to the compounds in this study. Reagents used: (i) CsF, PEPPSI-IPr,
dimethoxyethane, (ii) K PO , Pd(OAc) , H O/dioxane.
3
4
2
2
2
. Results and Discussion
2
.1. Synthesis and Characterization
The realization of functionally diverse photochromic qDAEs has proven a synthetic challenge in
that Stille coupling reactions have, until recently, been exclusively employed to couple halogenated
quinones to stanyllated thiophenes [36 40 43 44]. Harsh conditions are required to install the necessary
,
,
,
trialkyl tin coupling partner, and this concomitantly restricts molecules to possessing only functional
groups that can tolerate the organolithium promoted stannylation step. As the variety of functional
groups is limited, so are the potential applications of qDAEs. The use of milder Suzuki methods,
for example transition metal catalyzed installation of boronic acids and esters without the need for
organolithium reagents [45,46], allows the inclusion of nucleophile sensitive functional groups.
We have previously reported the synthesis and characterization data of compounds 1–4 [35].
Briefly, in our original synthesis 2,3-dibromo-1,4-naphthoquinone is coupled, via a Suzuki reaction,
to the boronic acid of 5-methyl-2-thiophene carboxylic acid methyl ester or the analogous t-butyl
ester (Scheme 1). Loss of the t-butyl group and subsequent bromination of the resulting acid lead
to compounds
under the most common Suzuki conditions. Anhydrous conditions were employed to prevent the
naphthoquinone coupling partner from decomposing under aqueous conditions [47 48]. To synthesize
compound , similar conditions were used with the commercially available phenyl boronic acid.
During the preparation of this manuscript, compound was reported by Migulin [41], who synthesized
3 and 4, respectively. As we have noted, this reaction does not appear to proceed
,
5
5
and used the more reactive 2,3-diiodo-1,4-naphthoquinone with a traditional aqueous Suzuki coupling
scheme. We have used this as the basis for our synthesis of 2 in this study.
Purification of
eluent system. Curiously, the ring-closed forms of
405–410 nm) the impure compound band immediately after beginning chromatography leads to a
1–
5
is achieved by column chromatography using a hexanes/ethyl acetate gradient
1
and have higher R values, thus irradiating
2
f
(
green band that is easily isolable. By using this technique, we isolated a miniscule amount of pure
closed form 1b with crystals grown by slow evaporation of the chromatographed fractions. The crystals
attained were not enough for nuclear magnetic resonance spectroscopy (NMR) or UV-Vis experiments
but it was possible to select a single crystal and an X-ray structure was acquired.

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2
.2. Optical Studies and Photochromic Properties
Within the context of quinone based diarylethenes, Deng and Liebeskind [36] reported that
complete conversion between open and closed forms is not possible. The reason for this inability
to quantitatively photoisomerize was not discussed, nor has its origins been probed since. We, too,
1
report the same observation with methyl ester substituted
NMR sample [35]. The UV-Vis spectra of and
Despite being synthesized previously, the UV-Vis spectrum of both compounds has not been examined
in DCM. As expected, compound is not photochromic but compound shows new peaks at 612 nm
and 440 nm following irradiation with 405–410 nm light.
1
as evidenced by irradiation of an H
1
5 in dichloromethane (DCM) are presented in Figure 3.
5
1
Figure 3. Experimental UV-Vis spectra of pure 1a, a solution of 1a after irradiation with 405–410 nm
−5
wavelength light and
a after irradiation contains a mixture of 1a and 1b.
5 in dichloromethane. Concentrations are on the order of 10 M. The solution of
1
2
.3. X-Ray Crystallography
In our initial attempts at understanding the behavior of these photochromes we turned to structural
analysis through single crystal X-ray diffraction techniques. We found it difficult to grow crystals
of most of our compounds, though fortuitously, crystals of 1b and are easily obtained by slow
5
evaporation of solvent from hexane/ethyl acetate chromatographic fractions. Crystals of 1b were
grown with the exclusion of light. Efforts at growing crystals of 1a and 2a gave amorphous solids;
attainment of crystals of 4 has not yet been attempted.
2
.3.1. Compound 5
Yellow prism-shaped crystals of
5 crystallize in the centrosymmetric space group P1 with an
asymmetric unit comprising two crystallographically unique phenyl nqDAE molecules (Figure 4).
Both unique molecules in assume the anti-parallel conformation with active C—C separation distances
of 3.209(2) Å (C16···C22) and 3.256(2) Å (C38···C44). The two unique molecules form dimers through a
slipped stacking mode in which both the quinoid (Cg1, yellow) and benzenoid ring (Cg2, magenta)
of one unique molecule interact with the benzenoid ring (Cg4, cyan) of the other unique molecule
Supporting Information, Figure S5). Additionally, the dimers are stabilized by two sets of hydrogen
bonding (Supporting Information, Figure S5) between a quinoid oxygen atom of one molecule and
5
π-π
(

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a phenyl hydrogen atom of the other molecule and an electrostatic intreaction between a quinoidal
oxygen on one molecule and a carbonyl carbon of the other molecule (C23···O1=3.128(1) Å) [49].
Further, the dimers interact with neighboring dimers through an extensive hydrogen-bonding network,
which acts as a stabilizing force for the lattice (Supporting Information, Figure S7 and Table S3). Finally,
it is worth mentioning that the quinoid ring Cg4 is non-planar while the quinoid ring Cg1 is planar.
While interesting, the nature and consequences of this observation is beyond the scope of this paper.
Figure 4. Molecular structure of the phenyl nqDAE 5 asymmetric unit with thermal ellipsoids drawn
at the 50% probability level. Hydrogen atoms are omitted for clarity.
2
.3.2. Closed form 1b
The closed nqDAE isomer 1b, gained by brief irradiation during column chromatography, was
crystallized by slow evaporation of a hexanes/ethyl acetate chromatographic fraction. The resulting
dark green crystals were found to be suitable for analysis by single-crystal X-ray diffraction (SCXRD).
Compound 1b crystallizes in the P2 /c space group (crystallographic details are provided in the
1
Supporting Information). Analysis of the crystal structure found that there were two crystallographically
distinct molecules in the asymmetric unit (Figure 5). The two distinct molecules stack with overlap of
the quinone backbone and one of the thiophene methyl ester groups. The stacking of the aromatic
portion of the quinone backbone is similar to the classic π-π slip stacking model [50,51]. The phenyl
rings of the naphthoquinone backbones have a centroid to centroid distance of 3.5517(12) Å with a shift
of 1.210(3) Å. Additionally, the distance from the quinone centroid to the phenyl centroid is 3.708(11)
Å with a 1.610(3) Å offset. Orientation of the two crystallographically distinct naphthylquinone
backbones position one of the quinone oxygens 3.3437(16) Å from the centroid of the other quinone
ring. The specific interactions are shown in the Supporting Information, Figure S6. When viewed
down the a-axis, the role of the quinone π-π slip stacking becomes more apparent (Figure 5).
Each stacked column of quinone-DAE runs parallel to the a-axis, however the plane of the
quinone backbone does not lie parallel to the b-c plane (Supporting Information, Figure S6).
Each column interacts with neighboring columns through the overlap of exterior methyl ester
groups. Each neighboring column has the opposite tilt of the planar backbone from the b-c plane.
The angle of the quinone backbone within the stack and the position of the neighboring quinone results
in a slip stacking of the phenyl region. Aromatic slip stacking has been found to be a preferred energetic
minimum and is often present in crystal structures of aromatic molecules [50
is also an overlap of carbonyl groups of the methyl ester groups between stacks. The orientation
of the overlap is suggestive of some level of interaction and electrostatic interactions between
,51]. Interestingly there
π-π
opposing carbonyl carbons and oxygens, though further studies would be needed to confirm specific
stabilizing interactions.

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Figure 5. Molecular structure of the two crystallographically unique molecules of phenyl nqDAE
5
with thermal ellipsoids drawn at the 50% probability level. Hydrogen atoms are omitted for clarity.
Transparent dashed lines and atoms represent modeled disorder. Gray: Carbon, Red: Oxygen;
Yellow: Sulfur.
2
.4. Computations
2
.4.1. Conformational Analysis and Thermal Stability of Compound 1
X-ray analysis of 1b (Figure 5) shows two distinct isomers present in the crystal structure. We label
these isomers based on their symmetry (Figure 6). The conformers, C1-closed and C2-closed differ only
in the relative orientations of the methyl ester groups due to free rotation about the thiophene-ester
bond. In C1-closed the ester carbonyl groups adopt a “transoid” type geometry while in C2-closed
these groups adopt a “cisoid” type geometry. Given the ratio of C1-closed and C2-closed in the
crystal structure, we surmise that these two forms are close in energy. As part of our computational
analysis, however, we also examined the analogous open form conformers C1-open and C2-open
.
Other potential conformers were not examined.
Figure 6. Conformations for compound 1 with symmetry given.
Geometry optimizations of open- and closed-ring isomers in the gas phase and in DCM were
performed using density functional theory (DFT). The geometry optimization results obtained for
examining the various conformers is presented in Table 1. All energies are relative to C1-open
(1a,
C ). From the data, it is evident that the conformers C1-open
(
1a, C ) and C2-open
(
1a, C ) are
1
1
2
−1
−1
near identical in energy with differences of 0.8 kJ
·
mol and 0.4 kJ
·
mol in the gas phase and in
DCM, respectively. When examining closed forms C1-closed
(
1b, C ) and C2-closed
(
1b, C ), we
1
2
−1
see differences of 0.3 kJ
·
mol both in the gas phase and in DCM. Considering that the C1 and C2
conformers are quasi-isoenergetic, we will only discuss results on the C1 conformers of compound
1 in
the following.

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Table 1. Relative Conformer Energies for compound 1.
Symmetry
Geometry
Open
∆E (gas Φ) kJ/mol
∆E (in DCM) kJ/mol
C1
C2
C1
C2
0.0
0.8
0.0
0.4
Open
Closed
Closed
43.6
43.9
49.9
50.2
−
−1
The energy difference between the open and closed form is estimated at 44 kJ
·
mol 1 and 50 kJ·mol
in the gas phase and in DCM, respectively. The activation energy for the cyclization is calculated in
−1
−1
DCM at 174 kJ
·
mol while that for the reverse reaction is found to be 124 kJ mol . These results
·
indicate that compound 1 should exhibit good thermal bistability.
2
.4.2. Computed Spectra and Molecular Orbital Analysis for Compound 1
Figure 7 shows the computed UV-vis absorption spectra for the C conformer of 1a and 1b
1
at the TD-DFT level along with the molecular orbitals involved in the main electronic transitions.
The spectrum of 1a has the correct line shape compared to the experimental spectrum (Figure 3)
with the first maximum predicted at 401 nm, close to the experimental value of 406 nm. While the
experimental spectrum for the pure closed-form 1b was not obtained, as the photostationary state is a
mixture of 1a and 1b, the computed spectrum of 1b is consistent with the line shape of the experimental
spectrum shown in Figure 3. The simulated spectrum presents two maxima at 597 and 426 nm, in good
agreement with the two absorption bands appearing at 612 nm and 441 nm upon irradiation of 1a
.
Note that the absorption maxima are slightly blue-shifted in the calculated spectra but that this shift
(<0.2 eV) is well within the typical margin of error for such methods.
Figure 7. Computed spectrum of 1a and 1b in dichloromethane at time-dependent density functional
theory (TD–DFT) level and molecular orbitals (H: HOMO, L: LUMO, isocontour: 0.02) involved in the
main electronic transitions.
2
.4.3. Modeling of the Ratio of Open and Closed Forms of 1b
Experimentally, upon irradiation we see a new absorption band appear in the region of 600 nm,
attributed to the closed form 1b. In our previous experiments [35], we irradiated dilute solutions

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~10 5 M) for 20 s with 405–410 nm light to reach the photostationary state. We then turned to H NMR
spectroscopy to obtain the ratio of 1a 1b after irradiation. Given that the NMR data [35] showed only
22% photoconversion, using that number we modeled the expected spectra in this work. Further,
−
1
(
:
~
for this work we examined various irradiation times and find that the photostationary state, using our
setup [35], is reached upon 10 s. In the supporting information, video files of concentrated solutions
are provided illustrating these conversions. Given the higher sample concentrations needed for easily
observed color changes, however, longer and arbitrary irradiation times were used.
In order to model the spectrum of the photostationary state observed experimentally, we have
simulated the absorption spectrum of a mixture made of 78% of 1a and 22% of 1b, as deduced from
NMR data [35]. The result is shown in Figure 8 in comparison with the experimental spectrum (inset).
A very nice agreement is obtained with the appearance of a broad band centered around 600 nm and
the rise of sharper and more intense band in the 400 nm region.
Figure 8. Computed spectrum of the photostationary state obtained upon irradiation of 1a in
dichloromethane at TD-DFT level, along with the computed spectrum of 1a and pure 1b given as a
reference. The photostationary state assumes a 78/22 ratio of 1a:1b. The inset shows the obtained
experimental data.
2
.4.4. Thermal Stability, Computed Spectra and Molecular Orbital Analysis for Compound 3
The dicarboxylic acid nqDAE presents similar ground-state energetic properties as the diester
derivatives and . The closed-ring isomer 3b is computed at 48 kJ
open-ring isomer 3a in the gas phase and in DCM, respectively. The energy barriers for the cyclization
3
−
1
−1
1
2
·
mol and 54 kJ mol above the
·
−
1
−1
and cycloreversion reactions are 174 kJ
similar to the diester nqDAEs within a few kJ
of compounds.
·
mol and 120 kJ
·
mol in DCM, respectively. These results are
−1
·
mol , indicating similar thermal stabilities this series
Figure 9 illustrates the comparison between the simulated UV-vis absorption spectra of the open
and closed forms of compounds and . It clearly appears that the acid derivative displays very similar
1
3
spectra to the methyl ester derivative with both the band positions and intensities being unchanged.
We thus also expect a similar photochromic behavior for the dicarboxylic acid nqDAE compared to the
diester nqDAEs.
2
.4.5. Conformational Analysis and Thermal Stability of Compound 4
Bromine qDAE compound presents only the C conformer for the open and closed forms
due to symmetry. Unlike the diester and dicarboxylic acid nqDAEs, which present very similar
4
2

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thermal stabilities and optical properties, the bromide nqDAE
4
presents some differences with these
derivatives. First, the thermal stability is predicted to be improved for compound
The closed-ring isomer 4a is found at a very similar energy to the open-ring form, only 5 kJ
4 by the calculations.
−1
·
mol and
mol above it in the gas phase and in DCM, respectively. This is a drastic reduction of the energy
gap between these two isomers compared to the diester and dicarboxylic acid nqDAEs. In addition,
−
1
1
2 kJ
·
−1
while the energy barrier for the cyclization computed at 173 kJ
, that of the cycloreversion is largely increased as it is computed at 161 kJ
improved thermal bistability for the bromide nqDAE.
·
mol remains similar to derivatives
−1
1
–
3
·mol , suggesting an
Figure 9. Computed spectrum of 3a and 3b in dichloromethane at TD-DFT level and molecular orbitals
H: HOMO, L: LUMO, isocontour: 0.02) involved in the main electronic transitions. The computed
(
spectra for 1a and 1b are shown for comparison.
2
.4.6. Computed Spectra and Molecular Orbital Analysis for Compound 4
The calculated and experimental optical properties of compound
Figure 10a shows the comparison between the simulated UV-Vis absorption spectra of
Substantial differences between and can be observed. On the one hand, the absorption band of the
4
are illustrated in Figure 10.
1
with
4.
1
4
open-ring isomer 4a in the 400 nm region is substantially red shifted compared to 1a. The maximum of
this absorption band is computed at 431 nm compared to 401 nm in 1a. This represents a bathochromic
–1
shift of 1736 cm . On the other hand, the absorption of the closed-ring isomer 4b becomes blue
shifted compared to 1b. In particular, the maximum of the first absorption band is moved from 597 nm
–1
to 520 nm, corresponding to a hypsochromic shift of 2480 cm . The intensities of these bands are
comparable between compounds and . Note, however, that despite these substantial shifts in the
4
1
absorption, there is still a strong overlap of the first absorption band of the open-ring isomer 4a with
the second absorption band of the more intense closed-ring isomer 4b in the 400 nm region. This is
probably the main reason for the inefficient photocyclization reaction in these nqDAEs.
Experimentally, this absorption band shifts from 427 nm before irradiation to 404 nm after
irradiation (Figure 10b). In the previous report of irradiation of 4, 405–410 nm light was used. Here,
we employed a 430 nm diode as the irradiation source to better overlap with the absorption band of 4a
;
however, we do not see an increase in the long wavelength absorption band due to the closed form.

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(
a)
(b)
Figure 10. (a) Computed spectrum of 4a and 4b in dichloromethane at TD-DFT level and molecular
orbitals (H: HOMO, L: LUMO, isocontour: 0.02) involved in the main electronic transitions.
The computed spectra of 1a and 1b are shown for comparison. ( ) Experimental spectrum of 4a
b
and the spectrum obtained after irradiation of 4a with 430 nm wavelength light.
3
. Materials and Methods
3
.1. General
Experimental UV-Vis spectra were obtained in dichloromethane (DCM) for 1, 2, 4 and 5 or acetone
for
3 using a Shimadzu UV-1800 spectrometer. Irradiation was achieved using a home-built light
source [35]. All irradiation experiments were conducted using a 405–410 nm light emitting diode with
the exception of the irradiation of
4
, which was conducted using a 430 nm light emitting diode. NMR
1
spectra were recorded on a Bruker AVIII-500 spectrometer operating at 500 MHz for H and 125 MHZ
13
for C. As this data has been previously presented for 1–4 [35] and 5 [41], it is not included here.
Tetrahydrofuran (THF) and dioxane were dried over sodium/benzophenone and stored over
4
9
Å molecular sieves. All other reagents, including palladium catalyst PEPPSI-IPr (CAS Number:
05459-27-0), were obtained from commercial suppliers and used as received. Flash column
chromatography was accomplished using silica gel obtained from Fisher Scientific (230–400 mesh).
3
.2. Synthesis
The syntheses of
1, 3 and 4 have been previously been reported and the molecules characterized by
1H NMR, 13C NMR and high resolution mass spectrometry. Our synthetic routes and characterization
matched that in the literature [35].
Given the new synthetic approach by Migulin
compound through the use 2,3-diiodo-1,4-naphthoquinone under aqueous conditions.
Briefly, (5-(tert-Butoxycarbonyl)-2-methylthiophen-3-yl)boronic acid (1.949 g, 8.05 mmol),
,3-diiodo1,4-naphthoquinone (1.500 g, 3.66 mmol), potassium phosphate (4.660 g, 21.95 g), water
15 mL), dioxane (45 mL) and palladium acetate (0.016 g, 0.07 mmol) were added to a 100 mL Schlenk
[41
]
we opted to synthesize
2
2
(
flask. The mixture was degassed by three freeze-pump-thaw cycles, then backfilled with nitrogen and
allowed to stir until starting the quinone and monocoupled product were no longer visible by thin layer
chromatography (silica plate, 15% ethyl acetate in hexanes). The reaction was then diluted with ethyl
acetate (150 mL) and washed with water (3
×
50 mL) and brine (50 mL). The organic phase was dried
over magnesium sulfate, then adsorbed onto silica. The crude product was chromatographed using a
silica column eluting with 100% hexanes to 20% acetone in hexanes. The pure fractions were collected
affording a yellow solid upon removal of solvent. The yellow solid slowly turned dark green upon
exposure to room light (1.280 g, 64%). Characterization data matched that of compound
2 obtained by

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our previous synthetic route [35]. While the yield was comparable to that reported using anhydrous
Suzuki methodology, the chromatography was much cleaner.
Compound
5
. In a 100 mL Schlenk tube was placed KF 2H O (1.788 g, 18.99 mmol) followed by
·
2
◦
heating to ~120 C for 30 min while under high vacuum. Upon cooling and backfilling with nitrogen,
,3-dibromo-1,4-naphthoquinone (1.000 g, 3.17 mmol), phenylboronic acid (1.158 g, 9.50 mmol),
8-crown-6 ether (0084 g, 0.32 mmol), PEPPSI (0.043 g, 0.06 mmol) and anhydrous THF (15 mL) were
2
1
added under a stream of nitrogen. The yellow reaction mixture was subjected to three freeze-pump-thaw
cycles, backfilled with nitrogen and refluxed overnight (15 h). The yellow-brown mixture obtained was
diluted with ethyl acetate (100 mL) and washed with water (3
×
20 mL) and brine (20 mL). The organic
phase was dried over magnesium sulfate, filtered and solvent removed under reduced pressure to give
a yellow solid. The solid was adsorbed onto silica and chromatographed on silica eluting with 100%
hexanes to 9:1 hexanes/ethyl acetate. Upon standing, some crystals formed and were saved for X-ray
crystallographic analysis. The remainder of the product was collected by removal of solvent to yield a
yellow solid (0.549 g, 56%). Characterization data matched that in the literature [41].
3
.3. Computational
DFT has been used to perform geometry optimizations of the nqDAEs 1–4 in their ground
electronic state. These calculations were performed in the gas phase and in dichloromethane using the
polarizable continuum model (PCM). The optimizations were carried out for the open- and closed-ring
isomers of these compounds and for the transition states connecting them. Harmonic frequency
analysis was performed on the optimized structures to verify the nature of the stationary points (minima
or transition states) on the potential energy surface. These transition states correspond to open-shell
singlet (diradical) species and were computed using broken-symmetry DFT calculations. To account for
the spin contamination, spin-projected energies were computed with an approximate spin-correction
procedure proposed by Yamaguchi and coworkers [52,53]. All these geometry optimizations were
performed with the B3LYP functional [54] and the 6-31G(d) basis set [55,56].
The UV-vis absorption spectra were simulated at the TD-DFT level using the long-range corrected
CAM-B3LYP functional [57] along with the 6-311+G(d,p) basis set [58,59]. The use of a range-separated
functional was necessary in order to describe the electronic transitions to charge transfer states
accurately. All absorption spectra were computed using PCM to describe the dichloromethane solvent
The convoluted spectra were obtained using a phenomenological Gaussian broadening characterized
by a half-width at half-height of 2000 cm–1 for each vertical transition. The effect of the functional and
basis set on these spectra is presented in Supporting Information.
All the calculations were performed with the Gaussian 09 series of programs [60].
3
.4. X-ray Crystallographic Data Collection and Refinement
Parameters for the crystal structures of 1b and are shown in the supporting information (Table S1).
Single crystals of 1b and suitable for X-ray diffraction were mounted on the tip of a glass
fiber using Paratone oil under atmospheric conditions and placed on a Bruker SMART APEX II CCD
diffractometer installed on a rotating anode source (Mo-K radiation, = 0.71073 Å) with a detector
5
5
α
λ
distance of 40.00 mm from the crystal. During the data collection, the crystals were cooled to 90(1) K
using an Oxford Cryosystem (Cryostream 700) nitrogen gas-flow apparatus. Frames were collected for
◦ ◦ ◦ ◦
ω-scans (0.5 scan width) at different ϕ-angles (ϕ = 0 to 72 at 72 increments) and
1
b
using two 180
stopped halfway through run two for a total of 540 frames, nominally covering complete reciprocal
space. Frames were collected for using the same data acquisition strategy except that five 180 -scans
0.5 scan width) were used with = 0 to 288 at 72 increments for a total of 1800 frames, nominally
5
ω
◦
◦
(
ϕ
covering complete reciprocal space. Data reduction was completed using SAINT version 8.40A and
a multi-scan absorption correction was applied using SADABS version 2016 included in the Bruker
APEX3 software suite [61]. Space-group determination was performed using XPREP utility included
in the SHELXTL software package [62]. The structures were solved with ShelXT [63] using intrinsic

Molecules 2020, 25, 2630
12 of 16
phasing and refined with ShelXL [64] using least-squares minimization (full-matrix least-squares on
2
F ). Non-hydrogen atoms were refined anisotropically and hydrogen atoms were placed at calculated
idealized position and refined using a riding model.
Disorder of the cyclized thiophene rings for 1b was resolved through the free refinement of the
disordered atoms (bridging thiophene carbons and inner methyl groups), with the corresponding
atoms split between major and minor location. Free refinement of the disordered atoms suggests a 70/30
ratio between molecular orientation in each of the distinct orientations in each crystallographically
distinct molecule. Examination of the packing shows why the disorder between the two orientations
of the thiophenes does not disrupt the packing. The methyl groups reside in nearly the exact same
location, regardless of orientation and the difference in the bridging thiophene carbon is less than 1 Å.
4
. Conclusions
Previously, qDAE and nqDAE closed forms were obtained only upon treatment of open forms with
strong Lewis acids [36 40]. Here we have shown that closed forms can be obtained by irradiation of an
,
impure sample during chromatography with the closed form eluting faster than the corresponding open
form. Specifically, this allowed for the isolation of 1b, giving single crystals upon slow evaporation of
solvent and facilitating a greater investigation of the ring-closed isomer. Crystals of 1b and
obtained and examined by single crystal X-ray diffraction. To our knowledge, this is the first report of
a closed form qDAE crystal structure. To obtain and in this study, we employed anhydrous Suzuki
5 were
1
5
conditions; using Migulin’s newly reported synthesis of 2,3,-diiodonaphthoquinone [41] and employing
this highly reactive compound, we were able to obtain 2 under typical Suzuki coupling conditions.
Compounds 1–4 were subjected to computational analysis at the TD-CAM-B3LYP/6-311+G(d,p)
level of theory. The simulated UV-vis absorption spectra closely match the experimental spectral data,
most notably for systems containing a mix of ring open and ring closed isomers and suggest that
these computations would be useful for modeling other similar systems that achieve a photostationary
equilibrium in solution. Importantly, the relatively low photoswitching efficiency of these nqDAEs
compared to other DAEs is explained by the overlap of absorption bands between the open and
closed forms leading to incomplete conversion from the open- to the closed-ring isomer. Additionally,
the obtained data suggests a high thermal biostability for these compounds. The thermal stability
and unique electronic structures of quinone DAEs make this class of DAE a very promising subclass
of photochromes.
Supplementary Materials: Figure S1: Computed UV-Vis spectra of the conformers for open form isomer 1a in
DCM and in the gas phase at TD-B3LYP/6-31G*, Figure S2: Computed UV-Vis spectra of the conformers for
closed form isomer 1b in dichloromethane and in the gas phase at TD-B3LYP/6-31G* level, Figure S3: Computed
spectrum of the C conformers of 1a and 1b in DCM at TD-CAM-B3LYP/6-31G* level, Figure S4: A comparison of
1
TD-CAM-B3LYP/6-31G* and TD-CAM-B3LYP/6-311+G** simulated spectra for the C conformers of 1a and 1b
,
1
Figure S5: Computed UV-Vis spectra of 2a and 2b in dichloromethane, Figure S6: ORTEP of phenyl nqDAE
illustrating the dimer formation through stacking, hydrogen bonding and electrostatic interactions, Figure S7:
Interactions of the naphthoquinone backbone facilitating the stacking observed in the crystal structure of 1b
Figure S8: Extensive hydrogen-bonding network of viewed down the crystallographic a-axis, Figure S9:
Comparison of the planar and non-planar naphthoquinone regions of compound , Table S1: Crystal data and
structure refinement for Compound and Compound 1b, Table S2: interactions in the lattice of Compound
and Compound 1b, Table S3: Hydrogen Bond Geometry for , Tables S4–S17: Optimized B3LYP/6-31G* Cartesian
5
π-π
,
5
5
5
π
-
π
5
5
coordinates for compounds in this study, Video S1: Photoisomerization of 1a to 1b, Video S2: Photoisomerization
of 1b to 1a. CCDC 2002586 and 2002587 contain the supplementary crystallographic data in CIF format and this
data can be obtained free of charge at http://www.ccdc.cam.ac.uk/structures.
Author Contributions: Conceptualization of this study, D.G.P. and M.B.-P.; computations, M.B.-P.; X-ray
crystallography, I.M.W. and T.B.M.; synthesis and characterization, D.G.P. and W.R.Q.; acquisition of experimental
UV-vis spectra, D.G.P. and W.R.Q.; construction of the light source used in this study, F.A.N.; writing, review
and editing, D.G.P., M.B.-P., I.M.W. and T.B.M. All authors have read and agreed to the published version of
the manuscript.

Molecules 2020, 25, 2630
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Funding: D.G.P. and W.R.Q. thank Penn State Hazleton for funding in the form of a Research Development Grant.
Work by I.M.W. and T.B.M. was supported by the National Science Foundation under grant no. DMR-1455039.
Acknowledgments: The authors thank Tatiana Laremore for help with sample preparation, data interpretation
and providing access to the Pennsylvania State University mass spectrometry facility. Carlos Pacheco and Tapas
Mal are acknowledged for assistance in the acquisition of NMR data. This work was granted access to the HPC
resources of CALMIP supercomputing center under the allocation 2019-[12158].
Conflicts of Interest: The authors declare no conflict of interest.
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Sample Availability: Samples of compound 1 are available from the authors.
©
2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access
article distributed under the terms and conditions of the Creative Commons Attribution
(CC BY) license (http://creativecommons.org/licenses/by/4.0/).