Self-trapped vibrational states in synthetic β-sheet helices

Article abstract of DOI:10.1039/b907830d

Femtosecond vibrational pump-probe spectroscopy on β-helical polyisocyanopeptides reveals vibrational self-trapping in the well-defined hydrogen-bonded side groups that is absent when non-hydrogen bonded monomers are mixed in. The Royal Society of Chemist

Full text of DOI:10.1039/b907830d

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Self-trapped vibrational states in synthetic b-sheet helicesw
Erik Schwartz,a Pavol Bodis,b Matthieu Koepf,a Jeroen J. L. M. Cornelissen,*a
Alan E. Rowan,*a Sander Woutersen*b and Roeland J. M. Nolte*a
Received (in Cambridge, UK) 20th April 2009, Accepted 3rd June 2009
First published as an Advance Article on the web 23rd June 2009
DOI: 10.1039/b907830d
Femtosecond vibrational pump–probe spectroscopy on b-helical
polyisocyanopeptides reveals vibrational self-trapping in the
well-defined hydrogen-bonded side groups that is absent when
non-hydrogen bonded monomers are mixed in.
Here, we investigate whether NH-stretch self-trapping can
also occur in b-sheet structures.5 To this purpose, we study the
self-trapped vibrational states in synthetic b-sheet helices, i.e.
polyisocyanopeptides. These helical polymers possess peptide
side chains that form well-defined NHÁ Á ÁOC hydrogen-bonded
networks, which are arranged in the form of four b-sheet type
arrays along the polymer backbone. By engineering the
structure of this polymer, i.e. by the inclusion of side arms
without amide functions, the hydrogen-bonded NHÁ Á ÁOC
chain in which the self-trapping occurs can be readily modified
without significantly changing the secondary structure allow-
ing the self-trapping process to be more easily quantified.
Polyisocyanides can be readily prepared by nickel(II) induced
polymerisation of isocyanide monomers to give helical
In 1973 Davydov hypothesised that the energy-transport
mechanism in proteins and enzymes, which remains to this
date largely unknown, may actually occur by a vibrational
soliton mechanism.1,2 It was suggested that in an a-helix,
coupling between the amide I (CO-stretching) mode of the
amide units and the NHÁ Á ÁOC hydrogen bonds can lead to
localisation (self-trapping) of vibrational energy. The vibra-
tional excitation would then be accompanied by a local
contraction of the hydrogen-bonded chain. This self-trapping
makes it possible to transport the vibrational energy along the
hydrogen-bonded chain in the form of a dispersionless wave
packet, which would be spread out over only a few consecutive
amide units in the hydrogen-bonded chain. As a consequence,
the energy generated at one site of the protein could thus be
transported to another site without any dispersion of the
energy packet.1,3
macromolecules.6 The introduction of
a chiral peptide
substituent (e.g., L or D-alanine) as side chain both stabilises
the helix and induces a preferred helix handedness (Fig. 1).7
Dipeptide derived polyisocyanides have a typical MW of
106 g molÀ1 as analyzed by AFM7 and possess a highly defined
rigid (persistent length of 76 nm)8 secondary structure in which
the side arms form the above-mentioned b-sheet-like arrays of
hydrogen bonds.
In order to verify the soliton concept the amide I vibrational
self-trapping has been extensively studied over the last decades
in particular in crystalline acetanilide, a solid compound with
a well-defined array of hydrogen bonds, often used as a model
for a-helices.4 Despite this considerable interest, to date only
Hamm and co-workers have reported a direct observation of
self-trapped vibrational states in an a-helix.2 They observed
self-trapping of the NH-stretch (rather than the amide I) mode
in poly-g-benzyl-L-glutamate. Using femtosecond infrared
pump–probe spectroscopy Edler et al. could directly monitor
the self-trapped vibrational states through their anharmonicity.2
Upon excitation of the NH-stretching mode, two positive
excited-state bands in the pump–probe response were
observed, which were attributed to self-trapped NH-stretch
excitations. Interestingly, the NH-stretch mode has an energy
approximately equal to that of ATP - ADP conversion,
relating it to the transport of energy in biological systems.
The resulting polymers are extremely stable and remain
ordered even in competitive hydrogen-bonding solvents such
Fig. 1 (a) Molecular structure of poly-(L-isocyanolalanyl-D-alanine
methyl ester) (LD-PIAA, 1)7 and the random copolymer 2 synthesised
by random polymerisation of D-isocyanolalanyl-L-alanine methyl ester
(DL-IAA, 4)7 and monomer 3 (see Scheme 1) used in this study.
(b) Schematic drawing of the vibrational self-trapping process. An
ultrashort (100 fs) infrared pulse is used to resonantly excite an
NH bond in the hydrogen-bonded chain to the n = 1 state. This
causes contraction of the hydrogen bonds attached to the amide
group, which in turn causes a lowering of the stretching frequency
of the excited NH bond. The excited NH-group is thus no longer in
resonance with its neighbouring NH-groups. This prevents delocalisation
of (hence ‘traps’) the vibrational excitation.
a Institute for Molecules and Materials, Radboud University Nijmegen,
Toernooiveld 1, 6525 ED Nijmegen, The Netherlands.
E-mail: r.nolte@science.ru.nl, j.cornelissen@science.ru.nl,
a.rowan@science.ru.nl
b Van ’t Hoff Institute for Molecular Sciences, University of
Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam,
The Netherlands. E-mail: s.woutersen@uva.nl
w Electronic supplementary information (ESI) available: Full experi-
mental description of the femtosecond pump–probe experiments and
characterisation of the monomers and polymers used in this work. See
DOI: 10.1039/b907830d
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Fig. 2 Transient absorption change of LD-PIAA 1 upon NH-stretch
excitation, at three delay times (see below). The thin curve represents
the steady-state absorption spectrum. The inset shows the time
dependence of the absorption change for three probing frequencies,
together with least-squares-fitted exponential decays with time
constants of 0.80 Æ 0.04 ps (3258 cmÀ1), 0.78 Æ 0.11 ps (3121 cmÀ1),
and 0.73 Æ 0.05 ps (2986 cmÀ1).
NH-group (TVBS-I) and on nearest-neighbouring NH-groups
(TVBS-II), respectively.2
To investigate if we could modify or change the self-
trapping behaviour without influencing the secondary structure,
the transient absorption change of the random copolymers
was also measured. It was presumed that the hydrogen-bonding
network in the latter polyisocyanopeptide side chains will
be partially interrupted, which should lead to isolated
NH moieties and consequently a low chance of two neigh-
bouring NH-groups interacting with each other. We chose
to incorporate a non-hydrogen bonding isocyanide (with
similarities to the bis-alanine derived isocyanide) instead of
denaturing the secondary structure (by acid or high temperature)2,
as the latter method would change the overall conformation
of the polymer and lead to a complex, inhomogeneously
broadened infrared spectrum. To disrupt the one-dimensional
hydrogen-bonding network in the side chain initial focus was
directed to the incorporation of an N-methylated alanine unit
in the isocyanopeptide, but this however proved to be un-
successful due to cyclisation of the N-methylated monomer
into a diketopiperazine (Scheme 1 and ESIw). As a con-
sequence focus was directed to replace an amide moiety with
an ester functionality, as illustrated in monomer 3 (Scheme 1
and ESIw). In short, Boc-L-Ala-OH was first coupled, using
carbodiimide chemistry, to methyl (R)-(+)-lactate methyl
ester. Liberation of the free amine of the ‘dipeptide’ with acid
followed by refluxing in ethyl formate in the presence of
sodium formate generated, after column chromatography, the
formamide ((S)-((R)-1-methoxy-1-oxopropan-2-yl)2-formamido-
propanoate) derivative. Dehydration of the N-formyl moiety
with diphosgene and N-methylmorpholine resulted in the iso-
cyanide derivative 3 which could be subsequently copolymerised.
1H NMR spectroscopy (Fig. S1 and S2, ESIw), however,
revealed complete epimerisation of the first ‘amino acid’
residue, as also indicated by the doubling of the signals in
the 13C NMR spectrum. The formamide was optically pure as
evidenced by the comparison of the optical rotation of the
formamide precursor of 3 ([a]D = +17 (c 1.2, CHCl3)) with
the enantiomer of the formamide ([a]D = À17 (c 1.2, CHCl3),
Scheme 1 Synthesis of compounds 2–4 and the formation of the
diketopiperazine. Reagents and reaction conditions: (i) EtOAcÁHCl or
in the case of the tert-butyl ester Pd/H2, MeOH; (ii) HCO2Et,
NaHCO2, various conditions/2,4,5-trichlorophenyl formate, DIPEA,
CH2Cl2; (iii) diphosgene, N-methylmorpholine, CH2Cl2, À30 1C;
(iv) 0.03 equivalents Ni(ClO4)2Á6H2O, CH2Cl2 with a monomer feed
ratio of 15 (3) to 1 (4).
as methanol and DMSO. Disruption of the b-sheet network of
the polymer is only possible by the addition of strong acids,
such as trifluoroacetic acid. This well-defined hydrogen-bonding
network and stiffness makes the helical polyisocyanopeptide 1
ideal for the study of the NH-stretched self-trapped states in
amino acid hydrogen bonding using femtosecond vibrational
pump–probe spectroscopy.9 In order to further quantify the
self-trapping states the random copolymer 2 consisting of
monomers 3 and 4 (DL-IAA)7 (Scheme 1) has also been
studied in which the hydrogen-bonding chain is interrupted.10
Changing the NH : O fraction in the copolymer allows
one to manipulate the degree of connectivity of the hydrogen-
bonded chain of NH moieties without changing the secondary
structure.
The NH-stretch vibrational self-trapping was followed
using femtosecond vibrational pump–probe spectroscopy.
Upon excitation of the NH-stretch mode with a short
(100 fs) infrared pulse (centre frequency 3260 cmÀ1), the
optical response can be observed using a time-delayed probing
pulse which is detected in a frequency dispersed manner.11 The
result is shown in Fig. 2. The identical delay (see inset) and
polarisation9 dependence implies that the two excited-state
absorption peaks are both due to the NH-stretching mode
(Fig. 2). This anomalous response (for normal vibrational
excitations only a single excited-state absorption peak is
observed12) is very similar to the one observed by Hamm
and co-workers for self-trapped states in a-helices.2 The two
peaks represent absorptions of two-vibron bound states
(TVBS) in which the vibrational energy is localised on a single
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excellent model systems for the study of vibrational
self-trapping and energy transport in b-sheet-like structures.
Erik Schwartz would like to thank Nico Veling for providing
the schematic drawing in Fig. 1. The Technology Foundation
STW, NanoNed, The Council for the Chemical Sciences of the
Netherlands Organisation for Scientific Research, and the
Royal Academy for Arts and Sciences are acknowledged for
financial support.
Notes and references
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2 J. Edler, R. Pfister, V. Pouthier, C. Falvo and P. Hamm, Phys. Rev.
Lett., 2004, 93, 106405.
Fig. 3 Absorption change upon NH-stretch excitation of LD-PIAA
and of random copolymer 2 (red line 1 : 15 NH : O). Disruption
of the hydrogen-bond network completely eliminates vibrational
self-trapping.
3 For a reference to the involvement of H-bonding in electron
transfer processes in peptides, see: Y. T. Long, E. Abu-Rhayem
and H. B. Kraatz, Chem.–Eur. J., 2005, 11, 5186–5194.
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see ESIw). Epimerisation was further confirmed by chiral
HPLC, which showed two retention times for the isocyanide
(7.32 min and 8.29 min) (Fig. S3, ESIw). In spite of the
epimerisation behaviour of monomer 3, which would result
in two helices of opposite handedness, the self-trapping could
still be studied since the hydrogen-bonding network would
be identical. Therefore, a random copolymerisation based
on isocyanides 3 and DL-IAA (4) (with a 15 : 1 ratio of
3
:
4)7,10 was carried out at room temperature with
Ni(ClO4)2Á6H2O as a catalyst. The resulting polymer 2 was
precipitated from diethyl ether, obtained as powder,
a
characterised by H and 13C NMR and IR spectroscopy and
1
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The pump–probe signals of the NH : O random copolymer
2 (Fig. 3), when compared to those of the regular b-sheet helix,
reveal that disruption of the hydrogen-bonded NHÁ Á ÁOC
chains in the b-sheet structure leads to a dramatic change in
the vibrational response. Upon disturbance of the hydrogen-
bond structure the NH-stretch vibrational response becomes
completely regular (exhibiting a single excited-state absorption
peak) and shows no evidence of self-trapping.
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Our studies show that NH-stretch vibrational self-trapping
occurs not only in a-helices but also in synthetic b-sheet helical
polymers. This implies that delocalisation (spreading out) of
the vibrational excitation can be eliminated, which is one
of the requirements for vibrational energy transport by means of
Davydov solitons.1,2 At present, the role of Davydov solitons
in energy transport in proteins is still under debate, and
needs further investigations. The high persistence length of
peptide-based polyisocyanides, combined with their structural
integrity, allows one to further tailor their hydrogen-bonding
structure, making these synthetically well-accessible polymers
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Chem. Commun., 2009, 4675–4677 | 4677