Diene conformation in the naturally occurring tricarboxylic acid, telfairic acid, by Raman spectroscopy

Article abstract of DOI:10.1016/j.molstruc.2005.12.012

The conformational geometry of the two C{double bond, short}C bonds in a naturally occurring dienetricarboxylic acid, telfairic acid, isolated from Xylaria telfairii, has been determined by Raman spectroscopy. This application of analytical Raman spectroscopy is important because infrared, UV and NMR spectroscopic techniques have failed to provide sufficient information for the determination of the diene geometry. Several specially synthesised model dienecarboxylic acids with known diene conformations were used to calibrate the Raman data. The natural extract from X. telfairii was shown to be a mixture of both cis (Z) and trans (E) forms whereas the purified extract was predominantly the trans isomer. Raman data also suggest that the established method for the preparation of a trans-trans sorbic acid is open to debate. Further applications of the Raman technique for the determination of diene conformation of fungal metabolite extracts are proposed.

Full text of DOI:10.1016/j.molstruc.2005.12.012

Journal of Molecular Structure 789 (2006) 24–29
www.elsevier.com/locate/molstruc
Diene conformation in the naturally occurring tricarboxylic acid,
telfairic acid, by Raman spectroscopy
*
Howell G.M. Edwards , Raymond L. Edwards, Melanie J. Hartley, Michael Quinn
Chemical and Forensic Sciences, University of Bradford, Richmond Road, Bradford, West Yorkshire BD7 1DP, UK
Received 9 November 2005; received in revised form 6 December 2005; accepted 6 December 2005
Available online 9 February 2006
Abstract
The conformational geometry of the two CaC bonds in a naturally occurring dienetricarboxylic acid, telfairic acid, isolated from Xylaria
telfairii, has been determined by Raman spectroscopy. This application of analytical Raman spectroscopy is important because infrared, UV and
NMR spectroscopic techniques have failed to provide sufficient information for the determination of the diene geometry. Several specially
synthesised model dienecarboxylic acids with known diene conformations were used to calibrate the Raman data. The natural extract from
X. telfairii was shown to be a mixture of both cis (Z) and trans (E) forms whereas the purified extract was predominantly the trans isomer. Raman
data also suggest that the established method for the preparation of a trans–trans sorbic acid is open to debate. Further applications of the Raman
technique for the determination of diene conformation of fungal metabolite extracts are proposed.
q 2006 Elsevier B.V. All rights reserved.
Keywords: Raman spectroscopy; Dienecarboxylic acids; Telfairic acid; Diene conformation
1. Introduction
noted for the simplicity of the quantitative assessment and the
ability to record the Raman data directly from the solid
polymer specimens without prior mechanical or chemical
treatment. In addition, the NMR spectroscopic differentiation
[5] between the cis and trans diene conformations was
achieved by the observation of their coupling constants J,
namely 6–15 and 11–18 Hz , respectively, for the cis and trans
forms. However, a requirement for the NMR analysis of these
coupling constants is the presence of adjacent C–H bonds at
carbons 1–4 of the –CaC–CaC– unit.
Ultraviolet spectroscopic absorptions of dienecarboxylic
acids are also not sufficiently discriminating for the identifi-
cation of the cis and trans geometric isomers since, the cis–cis,
cis–trans and trans–trans forms all absorb at 262G3 nm with
extinction coefficients in the range 24,000–36,000.
Previous vibrational spectroscopic work on the confor-
mational geometry of CaC bonds in polybutadienes has
demonstrated the application of Raman spectroscopy in
particular for the qualitative and quantitative estimation of
(1,4)-cis and (1,4)-trans structures and of the presence of (1,2)-
pendant vinyl units in the polymer skeletal structure [1,2].
Whereas, all three conformers exhibit Raman spectroscopic
activity in the 1600–1700 cmK1 region of the spectrum, the
situation is very different for infrared spectroscopy since the
(1,4)-trans conformer has no dipole moment and is therefore
infrared inactive in this region [3]. In a critical comparison of
infrared, Raman and NMR structural analyses of polybutadiene
conformers synthesised using anionic polymerisation methods
[4], the infrared inactivity of the trans component resulted in a
significant dissimilarity being observed between the infrared
data from conformational mixtures and Raman and NMR data
from the same systems. The advantage of Raman techniques
over NMR spectroscopy for the rapid analysis of confor-
mational diene compositions of the polybutadienes was further
Following the recent isolation [6] of telfairic acid, a new
unsaturated diene tricarboxylic acid from Xylaria telfairii, an
interesting structural problem has been realised; because of the
absence of a proton on carbon 4 of the (1,4)-diene system the
NMR spectra cannot provide values of the J coupling constants
for the (3,4)-unsaturation on –CaC–, although that of the
corresponding (1,2)-alkene moiety is still accessible. Since, the
infrared spectral activity of a trans-conformational geometry at
this (3,4)-CaC– unit is also forbidden by the selection rules, it
appears that Raman spectroscopy could uniquely afford the
opportunity to determine unequivocally the molecular
*
Corresponding author. Tel.: C44 1274 233787; fax: C44 1274 235350.
E-mail address: h.g.m.edwards@bradford.ac.uk (H.G.M. Edwards).
0022-2860/$ - see front matter q 2006 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2005.12.012

H.G.M. Edwards et al. / Journal of Molecular Structure 789 (2006) 24–29
25
conformational structure of the geometry of the substituted
alkene at this location in the diene.
molecular structures of telfairic acid and of the selected
diene carboxylic acids are given below.
To demonstrate the reliability and potential effectiveness of
the Raman spectroscopic analytical approach for this novel
natural product, several model compounds of (1,2) and (3,4)
unsaturated dienecarboxylic acids of reliably known alkene
bond conformational geometries were studied. From these
results, it was possible to monitor and evaluate the analytical
Raman spectroscopic data and to determine for the first time
the conformational geometry of the naturally occurring diene
tricarboxylic acid, telfairic acid.
2.1.1. Buta-1,3-diene-1,4-dioic acid (muconic acid)
CH(COOH)aCHCHaCH(COOH)
Cis–cis muconic acid, 2(Z), 4(Z)-muconic acid, was
prepared by the oxidation of phenol with peracetic acid
under carefully controlled conditions, avoiding the use of heat
and maintaining the reactants in a darkened environment [7,8].
The cis–cis acid crystallised from boiling ethanol and remained
unaffected during subsequent acidification and isolation from
solution. The solid cis–cis acid was stable for several hours at
100 8C and was unchanged on exposure to daylight for up to
5 h. However, exposure of the ethanolic solution of the cis–cis
acid resulted in conversion into the trans–trans isomer.
2. Experimental
2.1. Specimens
2.1.2. Buta-1,3-diene-1,4-dimethyl-1,4-dioic acid
(dimethylmuconic acid)
CH3C(COOH)aCHCHaC(CH3)COOH
A similar synthetic procedure to that outlined above was
undertaken using 2,5-dimethyl phenol (para-xylenol) and
peracetic acid at room temperature for several days followed
by recrystallisation from ethanol produced a specimen of cis–
cis dimethylmuconic acid.
X. telfairii is a tropical fungus species which is found
growing on dead wood; the specimens for the current analyses
were collected in Fazenda Intervales, Sao Paulo State, Brazil,
from dead dicot wood and were cultured for 8 weeks on a 3%
malt extract medium in Thompson bottles (2 L!20), each
containing 1 L of culture medium [6]. The fungus produced a
thick white mycelium supporting small white stromata,
approximately 3 mm long. Twenty litres of medium was
extracted three times with ethyl acetate; the extracts were them
dried and solidified to yield some 2.9 g of crude material.
Following trituration with ethyl acetate, 0.8 g of a colourless
solid was recrystallised from nitromethane and ethyl acetate to
give 0.58 g of telfairic acid, 127–134 8C.
2.1.3. Hexadieneoic acid (sorbic acid)
CH3CHaCHCHaCHCOOH
Sorbic acid was amongst the first diene carboxylic acids to
be isolated, obtained by Hofmann [9] by the action of alkalis or
mineral acids on rowanberry oil. The synthesis of sorbic acid
from the ring opening of a methyl pentenyl lactone with boiling
aqueous sodium hydroxide solution or methanolic sodium
methoxide which produced the cis–cis and cis–trans isomers,
respectively. Here, a classic Doebner [10] reaction between
crotonaldehyde and malonic acid in dry pyridine, refluxed on a
steam bath for 3 h followed by recrystallisation from boiling
water gave colourless crystals of the trans–trans sorbic acid.
A work-up of the filtrate from the isolation of the telfairic
acid produced above by evaporation to dryness, extraction with
toluene/ethyl acetate/acetic acid (50/49/1) and elution on a
silica gel column gave two fractions, one of which was
identified as a 2,3-didehydrotelfairic acid and the other a
colourless solid which on recrystallisation from ethyl acetate
gave identical infrared and UV spectra to the telfairic acid
isolated above, indicating that they were both telfairic acid [6].
1
Small changes in the 13C and H NMR spectra of the two
isolates confirmed that they were both telfairic acid, but with
the threo-and erythro- conformations, a and b, respectively, as
shown below.
2.1.4. 5-Phenylpentadienoic acid
C6H5CHaCHCHaCHCOOH
Decarboxylation of a phenyl divinylmalonic acid,
2-carboxy-5-phenylpentadienoic acid (cinnamylidenemalonic
acid), in pyridine solution [11] produced the cis–cis dienoic
acid; sustained heating of the acid in quinoline at 130 8C for
several hours produced isomerisation to the cis–trans isomer,
specifically the 2(Z) 4(E) geometric isomer. Further thermo-
lysis gave a mixture of the 2(Z) 4(E) and 2(E) 4(E) forms in
approximately a 60:40 ratio, from which the 2(E) 4(E) isomer
is obtained preferentially by recrystallisation.
The significant difference between these two telfairic acids
is the conformation at the optically active site at carbon atom 2;
this has no effect on the IR and UV spectra but does produce
subtle changes in the NMR spectra as indicated above. It is
clear, however, that the local conformation of the diene units
have not been derived in the analyses, and this forms the
objective of the current study.
Samples of telfairic acid, isolated from cultures of
X. telfairii as described previously [6], including the sample
which has been recrystallised from ethyl acetate, and having
the proposed molecular structure shown in a above were
analysed using FT-Raman spectroscopy. Model compounds
based on a diene carboxylic acid system and having known
structural CaC conformational geometries were also prepared
according to literature methods as described below. The
2.1.5. Telfairic acid
CH3CH2C(COOH)aCHCHaC(COOH)CH(CH3)COOH
The specimens of telfairic acid subjected to analysis were
obtained from cultures [6] of X. telfairii, with a sample that had
been recrystallised from ethyl acetate.

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H.G.M. Edwards et al. / Journal of Molecular Structure 789 (2006) 24–29
2.2. Raman spectroscopy
Fourier transform Raman spectra of telfairic acid and the
model diene carboxylic acids were obtained using a Bruker
IFS66/FRA 106 spectrometer with Nd3C/YAG laser excitation
at 1064 nm and a liquid nitrogen cooled InGaAs detector.
Spectra were recorded in a macroscopic mode with a spectral
footprint of 100 microns using a spectral resolution of 4 cmK1
over a wavenumber range of 100–3750 cmK1; this range
covered the skeletal modes of the diene as well as the CH
stretching and bending modes. Spectral accumulation of 500
scans over a time of about 10 min was necessary to achieve
improved signal-to-noise ratios for spectral comparisons
between the extracts and the model compounds. Strong,
sharp spectral bands were accurate to better than G1 cmK1
.
The spectra shown in the figures have not been subjected to
smoothing.
3. Results and discussion
Previous Raman spectroscopic studies [1,2,4] of polybuta-
dienes revealed that the three possible diene geometrical
confirmations, namely (1,4)-trans, (1,4)-cis and (1,2)-vinyl
pendant, were identified through characteristic bands at 1655,
1640 and 1624 cmK1, respectively. From controlled anionic
polymerisation syntheses of di-block copolymers involving
two or more of the conformers, it was demonstrated [2]
conclusively that the diene geometrical conformers could be
estimated quantitatively with a precision of about 1%.
Fig. 1. FT-Raman spectrum, 1064 nm excitation, of trans–trans-muconic acid,
with
a . Spectrum (a),
CaC stretching wavenumber of 1641 cmK1
100–3400 cmK1. Spectrum (b), 1575–1700 cmK1, showing the singlet
Raman band characteristic of the all -trans diene conformation.
deformations in the range 1350–1460 cmK1 and C–C bond
In Fig. 1a, the FT-Raman spectrum of the muconic acid
specimen synthesised in the present work is shown over the
whole wavenumber range for CaC characterisation, 100–
3600 cmK1.A single symmetric Raman band at 1642 cmK1
(Fig. 1b) confirms the exclusively trans–trans (2Z, 4Z)
geometrical arrangement of the diene double bonds in this
compound.
stretching at 780 cmK1
.
Fig. 3a shows the Raman spectrum of the sorbic acid
specimen synthesised according to the definitive literature
recipe in this work; however, the Raman spectrum of the
1580–1700 cmK1 region (Fig. 3b) which is definitive for the
CaC stretching conformation geometry reveals that
the specimen has two bands, at 1627 and 1641 cmK1, which
is indicative of both cis and trans components being present. It
is not clear from the data whether the sample is a cis–trans
(2E, 4Z) or a mixture of cis–cis (2E, 4E) and trans –trans (2Z,
4Z) isomers. Nevertheless, it appears that the literature
experiment for the preparation of a pure trans –trans specimen
Fig. 2 shows the Raman spectrum of the specimen of
dimethylmuconic acid, which again exhibits a single strong
band in the diene stretching region at 1625 cmK1; this is
characteristic of a cis–cis conformational arrangement of the
two CaC bonds. In both Figs. 1 and 2, there is no evidence for
the presence of a cis or a trans conformer, respectively, in the
predominantly trans–trans and cis–cis structures. Fig. 2 is also
interesting in that the large molecular scattering cross-section
of the CaC moiety is seen; the CaC is clearly the strongest
band in the Raman spectrum and previous quantitative
measurements of CaC conformational composition in dienes
can be made to 1% or better. The CaC band is 500% stronger
in intensity than the group of bands characteristic of CH
stretching near 3000 cmK1.The acid CaO functionality,
which occurs strongly in the infrared and which can interfere
with the determination of the infrared active diene modes is
not visible at all in the Raman spectrum of the dienedioic
acid in Fig. 2. There are other subsidiary features in the
Raman spectra which are indicative of the additional methyl
groups in the dimethyl muconic acid such as the more
complex CH stretching region near 2950 cmK1, CH
Fig. 2. FT-Raman spectrum, 1064 nm excitation, of dimethylmuconic acid with
a cis–cis-diene conformational arrangement and a CaC stretching wavenumber
of 1625 cmK1, wavenumber region 100–3400 cmK1
.

H.G.M. Edwards et al. / Journal of Molecular Structure 789 (2006) 24–29
27
Fig. 4. Detail of the 1580–1650 cmK1 region of the FT-Raman spectrum of
phenylpentadienoic acid, showing the presence of an all trans–trans
conformational arrangement of the CaC bonds with a characteristic stretching
mode at 1629 cmK1, with the quadrant CCH aromatic ring stretching band at
1595 cmK1
.
the aromatic ring substituent in the dieneoic acid is mirrored in
styrene monomer, a trans-alkene, where the Raman bands
occur in this region at 1631 and 1604 cmK1
.
The Raman spectra of the isolated specimens of telfairic
acid, namely the crude extract from X. telfairii (a, upper
spectrum) and a recrystallised compound (b, lower spectrum)
are shown in Figs. 6 and 7 where the two wavenumber regions
2500–3400 cmK1 and 100–1800 cmK1, respectively, are
presented; the former indicates the CH stretching region with
a CaCH band at 3020 cmK1 and saturated aliphatic CH
stretching below 3000 cmK1. The latter region shows the CaC
stretching activity for the crude extract is based on a mixture of
Fig. 3. FT-Raman spectrum, 1064 nm excitation, of an apparently cis–cis-diene
conformationspecimen of sorbic acid; (a), wavenumberrange, 100–3400 cmK1
showing a doublet band in the CaC stretching region, 1600–1650 cmK1; (b),
wavenumber range, 1580–1700 cmK1, confirming the presence of both cis and
trans conformational components at 1627 and 1641 cmK1, respectively.
,
of sorbic acid needs to be questioned on the evidence of our
Raman data. It is possible that there is some dependence on
recrystallisation temperature or time that has not been realised
hitherto but this can only be checked by an exhaustive range of
repetitive experiments.
cis and trans geometries with bands at 1627 and 1642 cmK1
,
respectively, whereas the recrystallised compound obtained
from boiling ethyl acetate has just one band at 1642 cmK1
indicative of the trans component solely. There is a slight
asymmetry noted on the low wavenumber side of the
1642 cmK1 band in the lower spectrum which could indicate
the presence of a small amount of residual cis isomer.
In the preceding Raman spectra, it has been noted that the
trans and cis wavenumbers are at about 1642 and 1627 cmK1
,
respectively, which are displaced some K13 cmK1 from their
analogous positions in the unsubstituted butadienes [1,2,4]; this
can be attributed to the influence of the electron-withdrawing
carboxylic acid groups attached to the CaC units in the diene
dicarboxylic acids.
In common with the literature preparations of trans
carboxylic acids from cis–cis and cis–trans isomers, the heating
effected (and possible increased exposure to light) during the
This electron-withdrawing effect is even greater for the
phenyl-substituted diene carboxylic acid specimen and Fig. 4
shows the Raman spectrum of the trans–trans isomer with two
bands at 1629 and 1595 cmK1; the former is the CaC
stretching band of the trans–trans diene unit and the latter is
the quadrant CCH stretching mode of the aromatic ring. In
contrast, the specimen of 5-phenylpentadienoic acid which
gave the Raman spectrum in Fig. 5 shows three bands at 1629,
1615 and 1595 cmK1; here, the additional band at 1615 cmK1
is now assigned to the cis geometric isomer, but it is not
possible to say that this originates from a cis–cis or a cis–trans
moiety in this compound or a mixture of these isomers. It is
clear from the bands shown in Figs. 4 and 5 that the further
reduction in band wavenumber caused by the presence of the
phenyl group substituent in this dienoic acid is about
K24 cmK1 based on the unsubstituted dienes. The effect of
Fig. 5. Detail of the 1580–1650 cmK1 region of the FT-Raman spectrum of a
phenylpantadienoic acid specimen which shows a cis–trans-conformational
arrangement with CaC bands at 1629 and 1615 cmK1, respectively, for the cis
and trans CaC components. The quadrant CChH aromatic ring stretching band
occurs at 1595 cmK1
.

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H.G.M. Edwards et al. / Journal of Molecular Structure 789 (2006) 24–29
obtained from a variety of other analytical techniques [2,3].
The assumption made in the previous Raman spectroscopic
work that the molar scattering coefficients for the cis-,
trans- and pendant vinyl components in butadienes was the
same therefore seemed to be correct to within 1%.
† The presence of cis–cis, cis–trans and trans–trans
geometric structures in our specimens are not completely
differentiable in the Raman spectra. Hence, although it is
clear that it is possible to discriminate unequivocally
between a totally cis and a totally trans component in a
mixture, the influence of the mixed cis–trans component in
the same molecular structure has not been defined. A
possible test of this would be effected if the Raman
spectrum of a well-characterised cis–trans molecule could
be obtained. The doubt already cast upon apparently well-
established literature methods of preparation of these
materials by the work carried out here means that the
selection of such an apparently well-defined molecular
geometry is not simple.
Fig. 6. FT-Raman spectral stackplot of (a), telfairic acid specimen extracted
from Xylaria telfairii, and (b), specimen recrystallised from boiling ethyl
acetate; 1064 nm excitation, wavenumber region, 250–3400 cmK1
.
recrystallisation process has converted the cis–trans mixture
almost completely to an all-trans isomeric arrangement.
This is the first time that a definitive statement can be made
concerning the geometric arrangement of the diene CaC bonds
in this natural product.
We believe that the band intensity differences between the
Raman spectra of the geometric isomers studied here
represents a real indicator of contributions from mixed
component species rather that a fundamental difference
between the molar scattering coefficients of the individual
isomeric molecular forms which is not displayed elsewhere. On
the basis of the assumption of similar molar scattering
coefficients for the cis–cis, cis–trans and trans–trans isomers
and the spectra recorded here, we can state that a 20% cis-
isomer excess initially created from the extraction of telfairic
acid from X. telfairii is reduced upon recystallisation from
boiling ethyl actetate solution to a predominantly trans-isomer
with perhaps only a residual content of about 3% cis-
component, i.e. the recrystallisation has resulted in the
production of a 97% geometric isomeric purification into the
trans–trans form.
3.1. Raman band intensities
Throughout this current study, it is apparent that the Raman
bands which are characteristics of the cis and trans diene
isomeric arrangements do not have the same intensities and it is
important to attempt an explanation of this. There are
essentially two possible factors that could contribute to the
different band intensities observed for the cis and trans CaC
modes in these Raman spectra:
† The molar scattering coefficients of the cis and trans
isomers are not identical; this is not the case for
unsubstituted butadienes reported in the literature, where
Raman band intensities of the three isomeric components
were used to derive estimates of specimen composition
which were accurate to about 1% when correlated with data
4. Conclusions
The results of this study demonstrate the viability of Raman
spectroscopy for the determination and identification of the
diene geometries in a natural product dienetricarboxylic acid,
telfairic acid. The opportunities for using Raman spectroscopy
for monitoring the production of dienecarboxylic acids in
biotechnological processes is also now presented, for example
the ortho-cleavage of para-xylene by Nocardia corallina
results in good yields of alpha, alpha-dimethyl-muconic acid
which is believed to be the cis–cis form [12]. Benzene can be
oxidised microbiologically (Pseudomonas sp.) to catechol and
hence to cis–cis- muconic acid [13,14], which is one of the
model type compounds used in the present analyses.
Stanier[15] has stated that the production bacterially of cis–
trans geometric isomers of substituted muconic acids from
benzene derivatives needs to be considered. Evidence is also
now being presented for the production of difunctionalised
dienes [16], including dienoic acids, from enzymatic degra-
dation of chlorophenyl aromatic compounds. As the scope for
Fig. 7. FT-Raman spectral stackplot of (a), telfairic acid specimen extracted
from Xylaria telfairii, and (b), specimen recrystallised from boiling ethyl
acetate; 1064 nm excitation, wavenumber region, 100–1800 cmK1
.

H.G.M. Edwards et al. / Journal of Molecular Structure 789 (2006) 24–29
29
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which can define the geometric structures of isomers is a real
requirement and the present study addresses this.
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