A rotaxane mimic of the photoactive yellow protein chromophore environment: Effects of hydrogen bonding and mechanical interlocking on a coumaric amide derivative

Article abstract of DOI:10.1039/b618781a

Hydrogen bonding in a [2]rotaxane is shown to stabilise the phenolate anion of a coumaric amide chromophore by almost 3 pK_a units; however, the effect on the UV spectral shift in the anion is small and, significantly given the photochemistry of

Full text of DOI:10.1039/b618781a

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A rotaxane mimic of the photoactive yellow protein chromophore
environment: effects of hydrogen bonding and mechanical interlocking
on a coumaric amide derivative{
Jose´ Berna´,b Albert M. Brouwer,*a Sandro M. Fazio,a Natalia Haraszkiewicz,a David A. Leigh*b and
Claire M. Lennon (nee´ Keaveney)b
Received (in Cambridge, UK) 2nd January 2007, Accepted 22nd January 2007
First published as an Advance Article on the web 15th February 2007
DOI: 10.1039/b618781a
Hydrogen bonding in a [2]rotaxane is shown to stabilise the
phenolate anion of a coumaric amide chromophore by almost
3 pKa units; however, the effect on the UV spectral shift in the
anion is small and, significantly given the photochemistry of
PYP, despite the hydrogen bonding olefin photoisomerisation
in the anionic rotaxane remains heavily suppressed.
In biological photoreceptors, the protein environment often leads
to considerable changes of the spectroscopic and photochemical
properties of embedded chromophores. Well known examples
include the retinal chromophore, where the absorption spectrum is
red-shifted to different extents in the different protein complexes
involved in vision,1 and the coumaric thioester chromophore in the
Photoactive Yellow Protein (PYP) of Halorhodospira halophila.2–4
In the latter case, the large red shift of the absorption is partly
due to deprotonation of the phenolic OH-group, which is
considerably more acidic in the protein environment than in
water. The extent to which hydrogen bonding contributes to the
red shift is unclear.3–5
Mechanically interlocked architectures, such as catenanes and
rotaxanes, offer an attractive approach to the study of relatively
weak intermolecular interactions without the complications of
dissociation of the assemblies in solution. Rotaxanes have been
reported in which chromophores were surrounded by a macro-
cyclic ring, which affects the spectral properties and stabilises the
chromophore.6–8 In the present work we describe how hydrogen
bonding and mechanical interlocking in a rotaxane architecture
affect the pKa and the spectral and photochemical properties of the
Scheme 1 Synthesis of 3-alkoxycoumaric amide thread 4 and rotaxane 5.
coumaric amide chromophore,9 which is structurally and photo-
chemically similar to the coumaric thioester present in PYP.
Rotaxane 1 was synthesized by a five component clipping
reaction10 in which a benzylic amide macrocycle is assembled
around the SEM ether-protected thread 2 (Scheme 1). In this case
a single amide group directs the ring closure rather than the more
established fumaramide, succinamide or peptide templates,11 hence
the modest yield (14%) of the protected rotaxane 1. In order to
prevent the ring dissociating from the thread, a side chain was
required on the aromatic ring. The protected thread 2 was
prepared from a Wadsworth–Emmons condensation of aldehyde 3
and the masked phenolic groups of thread 2 and rotaxane 1
subsequently liberated with Bu4NF to yield 4 and 5, respectively
(Scheme 1). Compounds 4 and 5 are related to ferulic acid
(3-methoxycoumaric acid), which can replace the coumaric unit in
PYP without compromising the photochemical cycle.12
aVan ’t Hoff Institute for Molecular Sciences, University of Amsterdam,
Nieuwe Achtergracht 129, 1018 WS, Amsterdam, The Netherlands.
E-mail:a.m.brouwer@uva.nl;Fax:+31205255680;Tel:+31205255491
bSchool of Chemistry, University of Edinburgh, The King’s Buildings,
West Mains Road, Edinburgh, United Kingdom EH9 3JJ.
E-mail: David.Leigh@ed.ac.uk; Fax: +44 131 667 9085;
Tel: +44 131 650 4730
In the neutral form of rotaxane 5 (i.e. the phenol in 5 is not
deprotonated), the macrocycle is hydrogen bonded to the amide
group in apolar environments. This results in a shielding of the
1
protons of the double bond in the H NMR spectrum of 5 in
CDCl3 by 1.03 ppm (olefin proton adjacent to benzene ring) and
1.46 ppm (olefin proton adjacent to carbonyl group).{ Molecular
modeling (Macromodel 8, AMBER force field, GBSA solvent
model for CHCl3) revealed a number of low-energy conformations
{ Electronic supplementary information (ESI) available: Details of
synthesis and structural characterization; NMR spectra of photostationary
mixtures; determination of pKa. See DOI: 10.1039/b618781a
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intense and somewhat blue-shifted. One reason for the predomi-
nance of the Z-isomer in the photostationary state is its lower
absorption coefficient at 313 nm. The quantum yields of the
isomerisation have not been determined, but the ratio of the
quantum yields WEAZ/WZAE can be derived from the photosta-
tionary state composition and the absorption coefficients at the
excitation wavelength. For thread 4 this ratio was found to be 0.57.
In other words, the efficiency of the Z A E isomerisation is almost
twice that of the E A Z reaction. In the case of rotaxane 5, less
than 10% of the Z-isomer was found in the photostationary state
at 313 nm. This precluded a reliable estimation of the spectrum of
Z-5, but there is no reason to suspect that this will be dramatically
different from that of Z-4. Thus, the ratio of the quantum yields
WEAZ/WZAE in the rotaxane 5 is even smaller than that in thread 4.
Both 4 and 5 show very weak and short-lived fluorescence at
Fig. 1 Computationally determined low-energy structure of rotaxane 5
in its protonated form. Macromodel 8, AMBER* force field, GBSA
solvent model for CHCl3.
room temperature. The excited state lifetime is of the order of a
few picoseconds, as found for other related chromophores.14–20 At
lower temperatures, the decay times and intensities increase.21
In the protein environment of PYP, the coumaric thioester unit
has a much lower pKa than in solution.12 A similar effect was
found when comparing the ‘naked’ thread 4 to the ‘encapsulated’
situation in rotaxane 5. In mixtures of methanol and water (3 : 2)
the apparent pKa of 4 was found to be 9.3, which is a normal value
for a phenol substituted with an electron withdrawing group.4 For
rotaxane 5, on the other hand, a pKa value of 6.7 was found under
the same conditions. Thus, the macrocycle decreases the pKa of the
coumaric amide unit by almost 3 units. Most likely the macrocycle
forms strong hydrogen bonds with the ArO2 group, as illustrated
in the calculated energy minimised structure shown in Fig. 3.
Deprotonation of the coumaric unit leads to red shifts of the
absorption bands (Fig. 4) of 3900 cm21 for 4 (320 A 366 nm) and
4400 cm21 for 5 (322 A 375 nm). These shifts are similar to those
reported for hybrid PYP’s.12 The interaction between the
macrocycle and the ArO2 group contributes slightly to the red
shift in the absorption spectrum. Given the fact that phenols are
more acidic in the excited state than in the ground state, a stronger
hydrogen bonding would be expected in the ground state, resulting
in a blue shift of the absorption band. In agreement with this
notion, a computational study of PYP chromophores concluded
that the hydrogen bonding interaction of the deprotonated
chromophore indeed has a negative contribution to the observed
overall red shift of the chromophore in the protein.3 The
electrochromic contribution due to charged amino groups in the
protein plays a major role in the spectral tuning of the coumaric
which support this structural assignment. A typical low energy
conformation is shown in Fig. 1. The oxygen atom of the carbonyl
group is involved in a bifurcated hydrogen bond, which is a
recurring theme in the X-ray crystal structures of rotaxanes based
on the same macrocycle, and the NH of the amide is bonded to a
CLO group of the ring, which is twisted inward.13
The UV absorption spectra of 4 and 5 in dichloromethane are
shown in Fig. 2A. The absorption bands .300 nm can be
attributed to p–p* transitions of the ferulic amide chromophore.
Absorption due to the macrocycle occurs at shorter wavelengths.
Some interaction between the ring and the thread in rotaxane 5 is
apparent from the small red shift of the positions of the absorption
maxima (322 vs. 317 nm).
Irradiation of dichloromethane solutions of thread 4 and
rotaxane 5 at 313 nm leads to clear changes in the UV-absorption
1
spectra (Fig. 2B and 2C). According to H NMR analysis, the
photostationary state of 4 at 313 nm consists of 63% of the
Z-isomer. Using this information the spectrum of the photosta-
tionary state can be deconvoluted into contributions from the two
olefin isomers (Fig. 2D). The spectrum of the Z isomer is less
Fig. 2 A. UV absorption spectra of thread 4 and rotaxane 5 in CH2Cl2
at RT. B. Spectral changes during photoisomerisation of 4. C. Spectral
changes during photoisomerisation of 5. D. Comparison of spectra of the
isomers of 4.
Fig. 3 Computationally generated low-energy structure of rotaxane 5 in
deprotonated (ArO2) form.
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Notes and references
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Fig. 4 UV-Vis absorption spectra of protonated and deprotonated
forms of 4 and 5 in methanol : water, 3 : 2.
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We thank the Netherlands Foundation for Scientific Research
(NWO), the Netherlands Research School Combination Catalysis,
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helpful discussions. DAL is an EPSRC Senior Research Fellow
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