Synthesis of DIBAC analogues with excellent SPAAC rate constants

Article abstract of DOI:10.1039/c4ob00694a

In search for increased reactivity in strain-promoted azide alkyne cycloadditions (SPAAC), the synthesis of new and more reactive cyclooctynes is of pivotal importance. To identify cyclooctynes with enhanced reactivity, without loss of stability, the synthesis and kinetic analysis of new dibenzoazacyclooctyne (DIBAC) analogues were conducted. Starting from iodobenzyl alcohol analogues and ortho-ethynylaniline various substituted dihydrodibenzo[b,f]azocines were produced. Subsequent bromination and elimination proved to be difficult depending on the aromatic substitution pattern, yielding chloro-, bromo-, and methoxy-substituted DIBACs in moderate yield. In the elimination reaction towards nitro- and Br,Cl-DIBAC, the corresponding cyclooctene was obtained instead of the cyclooctyne. Additionally, a dimethoxy-substituted DIBAC analogue was prepared following an alternative route involving light-induced deprotection of a cyclopropenone derivative. In total, four DIBAC analogues were successfully prepared showing excellent rate constants in the SPAAC reaction ranging from 0.45 to 0.9 M^-1 s ^-1, which makes them comparable to the fastest cyclooctynes currently known. This journal is the Partner Organisations 2014.

Full text of DOI:10.1039/c4ob00694a

View Article Online
View Journal
Organic &
Biomolecular
Chemistry
Accepted Manuscript
This article can be cited before page numbers have been issued, to do this please use: M. Debets, J.
Prins, D. Merkx, S. S. van Berkel, F. L. van Delft, J. C. M. van Hest and F. P. Rutjes, Org. Biomol. Chem.,
2014, DOI: 10.1039/C4OB00694A.
This is an Accepted Manuscript, which has been through the
Royal Society of Chemistry peer review process and has been
accepted for publication.
Accepted Manuscripts are published online shortly after
acceptance, before technical editing, formatting and proof reading.
Using this free service, authors can make their results available
to the community, in citable form, before we publish the edited
article. We will replace this Accepted Manuscript with the edited
and formatted Advance Article as soon as it is available.
You can find more information about Accepted Manuscripts in the
Information for Authors.
Please note that technical editing may introduce minor changes
to the text and/or graphics, which may alter content. The journal’s
standard Terms & Conditions and the Ethical guidelines still
apply. In no event shall the Royal Society of Chemistry be held
responsible for any errors or omissions in this Accepted Manuscript
or any consequences arising from the use of any information it
contains.
www.rsc.org/obc

Page 1 of 8
Organic & Biomolecular Chemistry
View Article Online
DOI: 10.1039/C4OB00694A
Journal Name
RSCPublishing
Graphical Abstract
Four new DIBAC analogues showed excellent SPAAC rate
constants making them comparable to the fastest cyclooctynes
currently known.
This journal is © The Royal Society of Chemistry 2013
J. Name., 2013, 00, 1-3 | 1

Organic & Biomolecular Chemistry
Page 2 of 8
View Article Online
DOI: 10.1039/C4OB00694A
Journal Name
RSCPublishing
ARTICLE
Synthesis of DIBAC analogues with excellent SPAAC
rate constants
Cite this: DOI: 10.1039/x0xx00000x
Marjoke F. Debetsa, Jasper S. Prinsa, Donny Merkxa, Sander S. van Berkela, Floris
L. van Delfta, Jan C. M. van Hesta and Floris P. J. T. Rutjesa,*
Received 00th January 2012,
Accepted 00th January 2012
In search for increased reactivity in strain-promoted azide alkyne cycloadditions (SPAAC), the
synthesis of new and more reactive cyclooctynes is of pivotal importance. To identify
cyclooctynes with enhanced reactivity, without loss of stability, the synthesis and kinetic
analysis of new dibenzoazacyclooctyne (DIBAC) analogues were conducted. Starting from
DOI: 10.1039/x0xx00000x
www.rsc.org/
iodobenzyl
alcohol
analogues
and
ortho-ethynylaniline
various
substituted
dihydrodibenzo[b,f]azocines were produced. Subsequent bromination and elimination proved
to be difficult depending on the aromatic substitution pattern, yielding chloro-, bromo-, and
methoxy-substituted DIBACs in moderate yield. In the elimination reaction towards nitro- and
Br,Cl-DIBAC, the corresponding cyclooctene was obtained instead of the cyclooctyne.
Additionally, a dimethoxy-substituted DIBAC analogue was prepared following an alternative
route involving light-induced deprotection of a cyclopropenone derivative. In total, four
DIBAC analogues were successfully prepared showing excellent rate constants in the SPAAC
reaction ranging from 0.45 to 0.9 M-1s-1, which makes them comparable to the fastest
cyclooctynes currently known.
disadvantage that it is susceptible to Michael addition by
Introduction
thiols.10 Another interesting cyclooctyne is DIBAC ( )9 (also
1
referred to as ADIBO18 or Aza-DBCO),19 designed in analogy
to DIBO,20 displaying a rate constant of 0.3 + 0.1 M-1s-1. Unlike
BARAC, DIBAC shows no Michael addition product when
reacted with glutathione, even at elevated temperatures. In
addition, DIBAC showed complete shelf-stability when stored
in neat form at –20 ºC, and was stored in aqueous solution for
over a year at 4 ºC without noticeable loss of reactivity.
Presumably, it is this optimal combination of reactivity and
stability which has made DIBAC the most commonly used
cyclooctyne for SPAAC applications.
Selective bioorthogonal ligation strategies for the investigation
of biological processes and biomolecule modification have
become increasingly important in the last decade. Currently, the
azide function is the most commonly applied reactive group in
bioorthogonal chemistry being utilised in the Staudinger
ligation,1 the Cu(I)-catalysed azide–alkyne cycloaddition
(CuAAC),2,3
and
the
strain-promoted
azide–alkyne
cycloaddition (SPAAC).4,5 The advantages of SPAAC over the
Staudinger ligation include, depending on the cyclooctyne used,
an increased reactivity and, as opposed to phosphines, the
stability under ambient conditions. Unlike CuAAC, SPAAC
avoids the use of a toxic Cu(I)-catalyst.
We envisioned that the addition of substituents on the aromatic
rings of DIBAC would lead to an increase in reactivity while
retaining stability. Based on previous studies,17,21 we
anticipated that electron-withdrawing groups could have a
substantial positive effect on the reactivity. In addition, we
expected a change in reactivity based on the positioning of
substituents on the aromatic rings. To investigate these
hypotheses we aimed to prepare a series of DIBAC analogues
Since the first application of SPAAC in a biological system,6 a
wide range of cyclooctynes and dibenzocyclooctynes has been
developed.5,7,8 Each cyclooctyne displays specific advantageous
characteristics, e.g. excellent rate constant,9-11 good water
solubility,12,13 synthetic ease,14 and/or fluorogenic properties,
but nevertheless requires improvement.15,16 In particular
hydrophilicity, reactivity, stability, and selectivity are key
aspects for a wider applicability of the strained alkynes in a
biological context.
(
3a-f, Figure 1) following a previously reported synthetic route9
and investigate the rate constants in SPAAC reactions with
benzyl azide.
The fastest dibenzocyclooctyne currently known is BARAC (2)
with a rate constant of 0.9 M-1s-1. It was recently shown that the
reactivity of BARAC could be tuned by the introduction of
substituents on the aromatic rings.17 BARAC, however, has the
This journal is © The Royal Society of Chemistry 2013
J. Name., 2013, 00, 1‐3 | 1

Page 3 of 8
ARTICLE
Organic & Biomolecular Chemistry
View Article Online
Journal Name
DOI: 10.1039/C4OB00694A
R1
R2
I
R1
R2
NH2
R1
R2
N2
i
CO2H
CO2H
CO2H
9
8
R1
R2
I
iii
ii
R1
R2
NHR3
HO
OH
6
R3 = H (10)
3 = Boc (11)
iv
HO
R
BocHN
v
vi
a: R1 = Cl, R2 = H
b: R1 = Cl, R2 = Br
c: R1 = H, R2 = Br
d: R1 = H, R2 = NO2
Figure 1. DIBAC (1), BARAC (2) and target DIBAC-analogues 3a-f.
R1
O
R2
5
Retrosynthesis of the proposed DIBAC analogues 3a
involved acylation of dihydrodibenzoazocine , bromination
and subsequent elimination (Scheme 1). The key intermediate
was envisaged to be prepared from Z-olefin in two steps,
which in turn was prepared from 2-ethynylaniline ( ) and
. A different
-e
4
e: R1 = OMe, R2 = H
BocHN
H
4
vii
5
7
substituted iodobenzyl alcohol derivatives
6
R1
R1
R2
12
strategy was envisaged for DIBAC analogue 3f
.
R1
R2
R2
N
viii
O
O
HN
OMe
4
13
Scheme 2. Synthesis of dihydroazocines 13a-e
H2SO4, NaNO2, DMSO; 2) KI, H2O; (ii) 1) ClCO2Et, NEt3, CH2Cl2; 2)
NaBH4, H2O; (iii) 2-ethynylaniline ( ), PdCl2(PPh3)2, CuI, Et3N, THF,
. Reagents: (i) 1) 30%
7
N2/H2-atmosphere; (iv) Boc2O, THF, 70 ºC; (v) 10% Pd/BaSO4,
quinoline, H2-gas, MeOH; (vi) Dess-Martin periodinane, NaHCO3,
CH2Cl2; (vii) 1)
2 M HCl in EtOAc; 2) NaBH4, H2O; (viii)
ClCO2C3H6CO2Me, NEt3, CH2Cl2.
Acetylenes 10a-e were Boc-protected yielding compounds 11
(Scheme 2), which proceeded smoothly except for analogues
containing strongly electron-withdrawing substituents (i.e. 10b
Scheme 1. Retrosynthetic analysis of the synthesis of DIBAC
analogues 3a-e
and
triple bond was in order. For compounds 11a
hydrogenation gave excellent yields, while for compounds 11d
and full reduction to the alkane was observed indicating a
d
, Table 1). Next, partial Z-selective hydrogenation of the
.
-c
the
Synthesis of cyclooctene intermediates. The synthesis
commenced with the readily available anthranilic acids
which were transformed into the aryl iodides via the
corresponding diazonium salts (Scheme 2). Subsequently, the
e
8
,
strong effect of the electron-withdrawing and electron-donating
groups on the hydrogenation rate. Fortunately, compounds 5d
9
and
of quinoline (0.5 and 5 equivalents for the conversion of 11d
and respectively). Subsequent steps towards
dihydrodibenzoazocines included Dess-Martin oxidation,
yielding 12, Boc-deprotection, and ring-closing reductive
amination. For almost all substrates, these reactions proceeded
in good to excellent yields (Table 1). Only in case of compound
4b, reductive amination was troublesome, since the reduction of
the imine went sluggishly and resulted in side product
formation.
e could be obtained in high yields by increasing the amount
carboxylic acids were reduced to the corresponding alcohols
which underwent Sonogashira coupling with ortho
ethynylaniline (
6
-
,
e
,
7
) to produce the chloro-, bromo-, nitro- and
4
methoxy-substituted iodobenzyl alcohols 10a, c-e in excellent
yields (89-100%, Table 1).9 The para-bromo derivative 10b
was obtained via a similar pathway after bromination of 4-
chloroanthranilic acid 8a
.
In our previously reported DIBAC synthesis, we observed that
acyl protection of the ring-nitrogen prior to formation of the
alkyne was required, either using a protecting group or a
suitable linker. Attempts to form DIBAC with an unprotected
nitrogen resulted in indole formation.9 Linker attachment to
compound
4 proceeded swiftly, producing 13b-c, and e in good
yields (Table 1). Linker attachment to compounds 4a and 4d
2 | J. Name., 2012, 00, 1‐3
This journal is © The Royal Society of Chemistry 2012

Organic & Biomolecular Chemistry
Page 4 of 8
View ArticAle ROnTliInCeLE
Journal Name
DOI: 10.1039/C4OB00694A
led to the formation of side products, resulting in relatively low
yields (46 and 36%, respectively).
Table 1. Results for the synthesis of dihydroazocines 13a-e
.
Entry R1
R2
H
6
a
b
c
d
e
(%) 10 (%) 11 (%)
5
a
b
c
d
e
(%) 12 (%)
4
a
b
c
d
e
(%) 13 (%)
1
Cl
Cl
H
H
(75)
(46)
(54)
(55)
(54)
a
b
c
d
e
(95)
(94)
(100)
(89)
(91)
a
b
c
d
e
(81)
(57)b
(88)
(51)b
(80)
(97)
(100)
(90)
(78)
(90)
a
b
c
d
e
(94)
(88)
(86)
(86)
(78)
(95)
(50)
(91)
(100)
(87)
a
b
c
d
e
(46)
(82)
(90)
(37)
(76)
2a
3
Br
Br
NO2
H
4
5
a
OMe
Substrate 6b was prepared from 6a using Br2 in AcOH, resulting in a
mixture of two products, which could be separated at the iodobenzyl
b
alcohol stage. The crude yield was 81%. For 9b, 87% based on
c
recovered starting material (b.r.s.m.), for 9d, 91% b.r.s.m. Yield
starting from compound 6a
.
Bromination yields cis- and trans-isomers. Crucial steps in
the formation of the substituted cyclooctynes are bromination
and subsequent double elimination. Bromination of 13 to form
dibromides 14 generally proceeded rapidly and in good yields
with the bromination of compound 13e being the only
exception.
o
Figure 2. Diastereoisomers
X (marked with *) and Y (marked with )
of dibromides 14a-e and 15. The ratio as observed in the displayed
spectra is not always representative for the ratio of the isolated isomers.
Table 2. Overview of synthesis of dibromides 14
.
Entry
Starting
Material
13a
13b
13c
R1
R2
Product
(%)
Ratio
1:0.8
X:
Ya
Cl
Cl
H
H
H
14a (71)
14b (96)
14c (80)
14d (84)
14e (39)
1
2
3
4
Br
Br
NO2
H
0.32:1
1:0.47
0.42:1
1:0.2
13d
OMe
5
13e
a
For the non-substituted dibromide (15), the ratio between
X:Y was
1:0.18.
Remarkably, while applying the bromination/elimination
methodology this observation has largely been ignored by
various groups constructing DIBAC.18,19 Recently, Schubert
and co-workers described in their synthesis of DIBAC, utilising
a Hiyama-Heck coupling to form the dibenzo[b,f]azocine core
structure, the formation of two conformers upon bromination.22
This effect was ascribed to the cisoid/transoid interconversion
of the exocyclic amide bond. Our results, however, suggest that
the observed peaks in 1H-NMR are the result of different
diastereoisomers, namely the cis- and trans-isomer, being
formed. Consequently we set out to identify the different,
isolated isomers of the bromination reaction. Focussing on the
differences in NMR, the most notable dissimilarity is the
difference in chemical shift of one of the benzylic protons (H2,
Scheme 3. Bromination of dihydroazocines 13 yielding dibromides 14
Reagents: (i) Br2, CH2Cl2.
.
Surprisingly, bromination led to two diastereoisomers (
X and
Y
), being the corresponding cis- and trans-isomers. The ratio
between the two isomers changed depending on the substituents
on the aromatic ring and was determined either by separation
by column chromatography or by comparing the signals
1
originating from one of the two benzylic protons in the H-
NMR spectra of the crude reaction mixtures (assigned with
*
vs. o, Figure 2), possibly caused by the shielding of H2 by one
o
either
*
or
in Figure 2). This phenomenon was already
) showing a ratio of
). While synthesising the DIBAC analogues, we
of the bromides. In addition, the coupling constants for H3 and
observed in the synthesis of DIBAC (
1:0.18 (
1
H4 are different for the cis- and trans-isomer for all analogues
X
:Y
(
J
= 10 Hz (for
X) vs. J = 9.4 Hz (for Y)), indicative of a
noted that electron-withdrawing groups on the aromatic ring
significantly changed the ratio between the two isomers. For
example, in case of Br,Cl-compound 14b and nitro-compound
difference in dihedral angle between the two protons.
14d isomer
Y was obtained as the major isomer (Table 2,
entries 2 and 4, and Figure 2).
Figure 3. The trans
- and cis-isomers obtained by cyclooctene
bromination.
To determine the distance between the bromides and H2 and the
dihedral angle between H3 and H4, the trans- and cis
-
This journal is © The Royal Society of Chemistry 2012
J. Name., 2012, 00, 1‐3 | 3

Page 5 of 8
ARTICLE
Organic & Biomolecular Chemistry
View Article Online
Journal Name
DOI: 10.1039/C4OB00694A
compounds (Figure 3) were modelled using ChemBio3D with
MOPAC interface. The results of these structure minimisations
are depicted in Figure 4. For the trans-conformer (–146.8
kcal/mol), one bromide atom is in close proximity of H2 (2.8
Å), while for the cis-conformers two energy minima were
obtained (–89.3 kcal/mol and –90.6 kcal/mol) which showed a
distance between H2 and the closest bromide atom equals either
4.4 Å or 2.8 Å (cis-1 and cis-2, respectively). The average
distance between a bromide atom and H2 is smaller for the
trans-isomer compared to the cis-isomer, suggesting that for
this isomer H2 is more shielded, and hence shows a smaller
chemical shift, thus suggesting that conformer
X corresponds to
the trans-isomer.
An additional support for this assignment was obtained by
comparing the dihedral angle between H3 and H4 (highlighted
in yellow in Figure 4) for the cis- and trans-isomers (113.2º,
and 19º, respectively). According to the Karplus curve coupling
constants become larger with increasing deviation from the 90º
dihedral angle. Since the trans-isomer shows a larger coupling
constant, this is yet another strong indication for
X being the
trans-isomer.
Scheme 4. Tentative mechanism for formation of cis-isomer
bromonium ion
V from
I
.
Bromide elimination. The last step in the synthesis of the
DIBAC analogues involved double elimination of the two
bromides. Optimisation performed for DIBAC (1) had shown
Figure 4. 3D models of energy-minimised structures of the cis- and
trans-isomers of compound 15. For the cis-isomer, two energy minima
were observed. To clarify the atoms used for distance measurements in
all models, H2 and one bromide are highlighted in green, H3 and H4 are
highlighted in yellow.
that elimination proceeds smoothly using slightly more than
two equivalents of a 1 M KOtBu solution in THF. To
investigate whether the elimination would proceed differently
for the two stereoisomers of 14a, elimination was performed
with one of the isomers and compared to the outcome of the
elimination on a 1:1 mixture (only the major isomer could be
obtained in pure form). Upon reaction with KOtBu, the major
isomer was successfully converted into alkyne 3a (yield 35%)
with only slight contamination of alkene 13a (2%), whereas for
the 1:1 mixture alkyne 3a was obtained with a 20%
contamination of alkene 13a. The latter indicated that the minor
diastereoisomer had yielded 24% of alkene and 76% of alkyne.
Notably, the isomer giving the best conversion to the alkyne,
was the major isomer for compound 14 (see also Table 2).
Treatment of the anti-isomer of 14c and 14e with KOtBu
successfully yielded cyclooctynes 3c and 3e in moderate yields
(35 and 34%, respectively) with little to no alkene formation (2
and 0%, respectively). In contrast, double elimination of
analogues 14b and 14d (isomer mixtures) mainly resulted in
alkene formation, while no alkyne was observed (Table 3). In
both cases, alkene product formation was confirmed by mass
analysis and 1H NMR spectroscopy (see: Supporting
Information Figure S1).
In addition, we observed that
Y
slowly isomerises to
X in
solution, which also indicates that
X
is the trans-isomer, as this
is the thermodynamically more stable isomer. Summarising, we
conclude that the trans-isomer is the main product for
dibromides 15
, 14a, 14c, and 14e, while the cis-isomer is the
main product for dibromides 14b and 14d
.
The rationale for the formation of the unexpected cis-isomer
most likely involves neighbouring group participation.23
Scheme 4 depicts the possible resonance structures II and III of
bromonium ion I, which are both stabilised by the aromatic
rings. However, with electron-withdrawing groups on one of
the rings, a (partial) positive charge (II) is significantly
destabilised, compared to III. Possibly, when structure III is
favoured, neighbouring group attack is more likely compared to
bromide attack, forming intermediate IV as shown in Scheme
4. Attack of the bromide anion on this intermediate structure
would then lead to cis-isomer
V.
4 | J. Name., 2012, 00, 1‐3
This journal is © The Royal Society of Chemistry 2012

Organic & Biomolecular Chemistry
Page 6 of 8
View ArticAle ROnTliInCeLE
Journal Name
DOI: 10.1039/C4OB00694A
azide) of two orders of magnitude.31 This decrease in reactivity
was most likely caused by steric hindrance of the methoxy
group positioned at the ortho-position relative to the alkyne. It
has been shown that ortho-substituents cause a significant
decrease in reactivity for BARAC, while para-substitution did
not show this effect.17 In order to increase reactivity, while
retaining the beneficial hydrophilicity increase by the methoxy-
groups we aimed for synthesis of compound 3f
.
The synthesis of 3f started with a reductive amination of 3-
methoxybenzaldehyde with 3-methoxyaniline, yielding amine
16 in good yield (98%). Next, a functionalisable linker was
attached, giving rise to compound 17 in 54% yield. Compound
17 was subjected to a double Friedel-Crafts alkylation (Scheme
6), providing cyclopropenone 18 in a moderate yield (30%).
This low yield was mainly caused by the formation of side
products as a result of poor regioselectivity of the double
Friedel-Crafts alkylation. In the final step, cyclopropenone 18
was subjected to UV light irradiation (320-500 nm, absorption
spectrum shown in Supporting Information) to produce alkyne
Scheme 5. Elimination of dibromides 14a-e, yielding alkynes
3 and/or
alkenes 13.
Reagents: (a) 1 M KOtBu in THF.
1
3f. While clean and full conversion was observed by H-NMR,
product isolation by column chromatography only yielded 35%
of the desired product. This indicates poor silica stability of the
product and hence explains the one-pot procedure described in
literature, i.e. alkyne formation and subsequent cycloaddition.30
Although this route involves significantly less steps, overall
yields are comparable to the aforementioned route.
Disadvantage of the cyclopropenone route is that electron-
donating substituents are required to direct the Friedel-Craft
reaction, thus limiting the scope of this route.
Table 3. Products obtained after elimination of compounds 14
.
Entry
R1
Cl
R2
H
3
a
b
c
d
e
(%)
(35)
(0)
(35)
(0)
13 (%)
14
a
b
c
d
e
a
b
c
(2)
1
2
3
4
5
Cl
H
H
OMe
Br
Br
NO2
H
(n.d.a)
(2)
d
e
(n.d.a)
(0)
(34)
a Yield was not determined (n.d.)
In literature, the elimination of vicinal halogen atoms to give
the corresponding alkene has been described for dihalides of
stilbenes.24 In addition, when the acetylene is extremely hard to
form via dibromide elimination, alkene formation has been
previously observed.25,26 Furthermore, a potential mechanism
for alkene formation using alkoxides was proposed by Ramazan
and Osman in 2004.27 In an attempt to obtain Br,Cl-DIBAC
(3b) and NO2-DIBAC (3d) via bromination and subsequent
elimination, screening of different bases was performed. Bases
which had already proven unsuccessful in the synthesis of
DIBAC were LDA, aqueous NaOH and nBuLi.9 In addition, we
tried NaH,28,29 KH, DBU, Verkade’s base and NaHMDS,
however, none of them was successful (Supporting
Information, Table S1). As an alternative, we envisioned that
the alkyne could also be obtained via dihydroxylation of the
alkene (13b or
d), followed by triflation and elimination.
Unfortunately, double hydroxylation was not successful in our
hands. Mono-hydroxylation, followed by oxidation and
formation of the enol triflate did not result in formation of the
desired product either.
In conclusion, Cl-DIBAC (3a), Br-DIBAC (3c), and MeO-
DIBAC (3e) were obtained in moderate yields over 10 steps (6,
7, and 2.5%, respectively). In addition, Cl-DIBAC (3a) was
stored at –20 ºC for two years without detectable degradation or
loss of activity.
Scheme 6. Synthesis of DIBAC-analogue 3f. Reagents and conditions:
(i) 1) dry MeOH, r.t., 1.5 h; 2) NaBH4, r.t., 30 min (98%); (ii)
ClCO2C3H6CO2Me, Et3N, CH2Cl2, 0 ºC, 1.5 h (54%); (iii) 1) AlCl3,
perchlorocycloprop-1-ene, CH2Cl2, -78 ºC to r.t., o.n.; 2) 1M HCl, r.t., 5
min; (30%); (iv) MeCN, UV-light (320-500 nm), r.t. 65 min (35%).
DIBAC analogue via a cyclopropenone. The aforementioned
results demonstrated that alkyne formation is the limiting step
in the synthesis of DIBAC derivatives. To prepare additional
DIBAC analogues, an alternative strategy was pursued based
on the work described by Popik et al. involving a method to
Kinetics of DIBAC analogues. With various DIBAC
analogues in hand, we set out to determine the influence of the
different substitutions on the reaction rate of cycloaddition. All
DIBAC derivatives were reacted with benzyl azide in
deuterated methanol, as depicted in Scheme 7.
prepare dibenzocyclooctynes via the formation of
a
cyclopropenone ring, followed by UV irradiation.13, 30
Pietzsch et al. utilised this method for the preparation of a
DIBAC analogue containing four methoxy groups which,
however, showed a drop in reaction rate (SPAAC with benzyl
This journal is © The Royal Society of Chemistry 2012
J. Name., 2012, 00, 1‐3 | 5

Page 7 of 8
ARTICLE
Organic & Biomolecular Chemistry
View Article Online
Journal Name
DOI: 10.1039/C4OB00694A
can possibly be explained by the larger electron-withdrawing
effect of the chloride compared to the bromide. Interestingly,
substituents on DIBAC appear to have a larger effect on the
rate than observed for BARAC. For example, a fluoride
substituent on the meta-position of BARAC relative to the
alkyne, resulted in a 1.1 to 1.3-fold rate enhancement, while a
meta-chloride substituent on DIBAC, being less electron-
withdrawing than a fluoride, resulted in a 2.2 fold rate
enhancement. A similar pattern was observed for substituents
on the para-position.
X
Y
R = C(O)C3H6CO2Me
Z
1, 19, 21: X = Y = Z = H
a: X = Cl, Y, Z = H
c: X = H, Y, Z = Br
e: X = OMe, Y, Z = H
f: Y, Z = OMe, X = H
N
R
1, 3a,c,e-f
BnN3
N
N
Bn
Bn
N
N
N
N
Conclusions
X
Y
X
Y
In conclusion, substituted DIBAC analogues have been
successfully prepared following our previously reported route
for DIBAC (1). Until the synthesis of the intermediate
Z
Z
N
N
R
R
cyclooctenes, the individual steps proceeded virtually identical
to non-substituted DIBAC, proving the envisioned versatility of
the route. Dibromination of these cyclooctenes proceeded in
moderate to good yields, whereby it was noted that not only the
expected trans-isomer was obtained, but also the cis-isomer.
Depending on the substitution pattern on the aromatic rings, the
19, 20a,c,e-f
21, 22a,c,e-f
Scheme 7. Cycloaddition of DIBAC (
, and )) with benzyl azide, yielding both regioisomers.
1) and DIBAC analogues (3a, c,
e
f
To increase the comparability of the kinetics for
, the same stock solution of benzyl azide in deuterated
1, 3a, c, e, and
cis/trans ratio varied; the amount of cis-isomer increased with
f
an increasing number of electron-withdrawing groups on the
aromatic ring. The identity of the cis- and trans-isomers was
confirmed by NMR spectroscopy in combination with
modelling studies.
methanol was used for all experiments. The rate constants
obtained are depicted in Figure 5. The results show that having
substituents on the DIBAC core structure gave rise to an
increase of the rate constant, corresponding to the observations
made for BARAC analogues.17 The electron-withdrawing effect
of the halogens (i.e. 3a and 3c) proved to have the largest
influence on the rate of the cycloaddition. Comparing the rate
constants for MeO-DIBAC (3e) and (MeO)2-DIBAC (3f) we
The alkyne formation appeared the most troublesome step for
all analogues in the cyclooctyne synthesis. Cl-DIBAC, Br-
DIBAC, and MeO-DIBAC were obtained in moderate yields
with little or no cyclooctene contamination. Inversely, despite
extensive elimination attempts to produce Cl,Br-DIBAC and
NO2-DIBAC, the corresponding cyclooctenes were formed
instead. To avoid the troublesome bromide elimination, a
different route towards the diMeO-DIBAC analogue was
successfully pursued, forming the cyclooctyne by UV-
irradiation of a cyclopropenone precursor, following previously
published precedent.30
found a rate constant for 3e comparable to DIBAC (
3f reacted notably faster than DIBAC ( ). The DIBAC
1), whereas
1
analogue as reported by Pietzsch showed a rate constant which
was two orders of magnitude smaller (0.8 × 10-2 M-1s-1).
Finally, the rate constants of the 1,3-dipolar cycloaddition with
benzyl azide were determined for all four new DIBAC
derivatives showing increased rate constants (0.9 (Cl), 0.8 (Br),
0.45 (MeO), and 0.62 (MeO)2 M-1s-1) compared to the rate
constant of DIBAC (0.4 M-1s-1). Gratifyingly, the rate constant
of Cl-DIBAC is competitive with the rate constant of BARAC,
while the stability of Cl-DIBAC is significantly higher, thus
making this an unparalleled cyclooctyne.
Notes and references
a
Radboud University Nijmegen, Institute for Molecules and Materials,
Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands, Fax: (+)31-
(0)24 365 3393, E-mail: F.Rutjes@science.ru.nl
Electronic Supplementary Information (ESI) available: experimental
procedures, spectroscopic characterization, 1H and 13C NMR spectra of all
compounds. See DOI: 10.1039/b000000x/
Figure 5. Rate constants for DIBAC and DIBAC-analogues. Standard
errors are calculated based on the average of two to five measurements.
1
2
E. Saxon and C. R. Bertozzi, Science, 2000, 287, 2007-2010.
V. V. Rostovtsev, L. G. Green, V. V. Fokin and K. B. Sharpless,
Angew. Chem. Int. Ed., 2002, 41, 2596-2599.
C. W. Tornøe, C. Christensen and M. Meldal, J. Org. Chem., 2002,
67, 3057-3064.
Examining the effect of the halogen substitution of DIBAC
derivatives 3a and 3c on the rate constant, a two-fold increase
in reaction rate compared to DIBAC was observed (0.9 and 0.8
M-1s-1, respectively). These rate constants are comparable to
BARAC (2), the fastest non-substituted cyclooctyne currently
known. It seems that the chloride substituent has a slightly
larger positive effect on the rate constant than the bromide. This
3
4
E. M. Sletten and C. R. Bertozzi, Acc. Chem. Res., 2011, 44, 666-
676.
6 | J. Name., 2012, 00, 1‐3
This journal is © The Royal Society of Chemistry 2012

Organic & Biomolecular Chemistry
Page 8 of 8
Journal Name
View ArticAle ROnTliInCeLE
DOI: 10.1039/C4OB00694A
5
6
7
M. F. Debets, S. S. van Berkel, J. Dommerholt, A. J. Dirks, F. P. J. T.
Rutjes and F. L. van Delft, Acc. Chem. Res., 2011, 44, 805-815.
N. J. Agard, J. A. Prescher and C. R. Bertozzi, J. Am. Chem. Soc.
2004, 126, 15046-15047.
,
M. F. Debets, C. W. J. van der Doelen, F. P. J. T. Rutjes and F. L.
van Delft, ChemBioChem, 2010, 11, 1168-1184.
8
9
J. C. Jewett and C. R. Bertozzi, Chem. Soc. Rev., 2010, 39, 1272.
M. F. Debets, S. S. van Berkel, S. Schoffelen, F. P. J. T. Rutjes, J. C.
M. van Hest and F. L. van Delft, Chem. Commun., 2010, 46, 97-99.
10 J. C. Jewett, E. M. Sletten and C. R. Bertozzi, J. Am. Chem. Soc.
2010, 132, 3688-3690.
,
11 B. R. Varga, M. Kállay, K. Hegyi, S. Béni and P. Kele, Chem. Eur.
J., 2012, 18, 822-828.
12 E. M. Sletten and C. R. Bertozzi, Org. Lett., 2008, 10, 3097-3099.
13 F. Friscourt, P. A. Ledin, N. E. Mbua, H. R. Flanagan-Steet, M. A.
Wolfert, R. Steet and G.-J. Boons, J. Am. Chem. Soc., 2012, 134
,
5381-5389.
14 J. Dommerholt, S. Schmidt, R. P. Temming, L. J. A. Hendriks, F. P.
J. T. Rutjes, J. C. M. van Hest, D. J. Lefeber, P. Friedl and F. L. van
Delft, Angew. Chem. Int. Ed., 2010, 49, 9422-9425.
15 F. Friscourt, C. J. Fahrni and G.-J. Boons, J. Am. Chem. Soc., 2012,
134, 18809-18815.
16 J. C. Jewett and C. R. Bertozzi, Org. Lett., 2011, 13, 3097-3099.
17 C. G. Gordon, J. L. Mackey, J. C. Jewett, E. M. Sletten, K. N. Houk
and C. R. Bertozzi, J. Am. Chem. Soc., 2012, 134, 9199-9208.
18 A. Kuzmin, A. A. Poloukhtine, M. A. Wolfert and V. V. Popik,
Bioconjugate Chem., 2010, 21, 2076-2085.
19 L. S. Campbell-Verduyn, L. Mirfeizi, A. K. Schoonen, R. A.
Dierckx, P. H. Elsinga and B. L. Feringa, Angew. Chem. Int. Ed.
2011, 50, 11117-11120.
,
20 X. Ning, J. Guo, M. A. Wolfert and G.-J. Boons, Angew. Chem. Int.
Ed., 2008, 47, 2253-2255.
21 J. M. Baskin, J. A. Prescher, S. T. Laughlin, N. J. Agard, P. V.
Chang, I. A. Miller, A. Lo, J. A. Codelli and C. R. Bertozzi, Proc.
Natl. Acad. Sci. U. S. A., 2007, 104, 16793-16797.
22 M. Jager, H. Gorls, W. Gunther and U. S. Schubert, Chem. Eur. J.
2013, 19, 2150-2157.
,
23 G. Bellucci, R. Bianchini and S. Vecchiani, J. Org. Chem., 1987, 52
3355-3362.
,
24 T. L. Jacobs, Organic Reactions, John Wiley & Sons , Inc., New
York, 4 edn., 1949.
25 C. Harries and H. von Splawa-Neyman, Ber. Dtsch. Chem. Ges.
1909, 42, 693-698.
,
26 C. Harries, Ber. Dtsch. Chem. Ges., 1912, 45, 809-816.
27 E. Ramazan and C. Osman, J. Chem. Res., 2004, 566-569.
28 I. Singh and F. Heaney, Chem. Commun., 2011, 47, 2706-2708.
29 C. Joce, J. Caryl, P. G. Stockley, S. Warriner and A. Nelson, Org.
Biomol. Chem., 2009, , 635-638.
7
30 A. A. Poloukhtine, N. E. Mbua, M. A. Wolfert, G.-J. Boons and V.
V. Popik, J. Am. Chem. Soc., 2009, 131, 15769-15776.
31. F. Starke, M. Walther and H.-J. Pietzsch, ARKIVOC, 2010, 350-359
(xi).
This journal is © The Royal Society of Chemistry 2012
J. Name., 2012, 00, 1‐3 | 7