Clues to a Pd/C catalyst’s efficiency can be found on its surface: Identification
of an efficient catalyst for the global hydrogenolysis of ether protecting groups
Conor J. Crawford,1,4 Yan Qiao,2,3,4 Yequn Liu,2,3 Dongmei Huang,2,3 Wenjun Yan,2,3
and Stefan Oscarson1,* Shuai Chen,3,*
1Centre
for Synthesis and Chemical Biology, University College Dublin, Belfield, Dublin, Ireland.
of Materials Science and Optoelectronics Engineering, University of Chinese Academy of
Sciences, Beijing 100049, People’s Republic of China.
3State Key Laboratory of Coal Conversion, Institute of Coal Chemistry, Chinese Academy of Sciences,
Taiyuan 030001, People’s Republic of China.
2Center
4C.J.C
and Y.Q contributed equally to this work
*Corresponding authors, email: chenshuai@sxicc.ac.cn, stefan.oscarson@ucd.ie, qiaoy@sxicc.ac.cn
Abstract
We report insights into our observations of the wide variability in quality of palladium catalyst from
different suppliers, finding the fundamental differences can be rationalized through a combination of
XRD, XPS, and TEM analysis, offering the possibility to predict a catalysts performance prior to the use
of valuable synthetic material and save time consuming efforts to identify high quality palladium on
carbon catalysts. The synthetic glycan accessed in this study will allow further steps towards the
development of semisynthetic vaccines against cryptococcal infections.
Introduction
A major bottleneck we have encountered in accessing pure synthetic glycans is in the final palladium
catalyzed hydrogenolysis or global deprotection reactions, where we experienced long reaction times,
poor yields, and saturation of aromatic protecting groups to their corresponding ethers. 1 This was
especially prominent in our synthesis of glycans related to structures from C. neoformans,2 which we
carry out in order to develop vaccine candidates. The glucuronoxylomannan (GXM) from native sources
is highly heterogenous and large components of the biosynthesis are unknown, meaning synthetic
glycans are currently the only viable means to access structures in any meaningful purity.3 To overcome
this we recently reported a catalyst pre-tuning methodology that increases catalyst selectivity towards
hydrogenolysis and inhibits these unwanted saturation by-products.1 We also experienced a wide
variability in catalyst quality from different manufactures, forcing extensive testing with complex material
in order to identify an efficient catalyst, as defined under the parameters of short reaction times, high
isolated yields, and its selectivity towards hydrogenolysis over hydrogenation. In order to further
advance our understanding and possibly predict a palladium on carbons efficiency prior to use of
valuable synthetic material we sought to characterize to the physical properties of the catalysts.
Therefore, we demonstrate clues to a palladium catalysts efficiency can be found by studying
the surface chemistry of the catalysts using a combination of high-resolution TEM (HRTEM), X-ray
photoelectron spectroscopy (XPS), and X-ray diffractometer (XRD) analysis. Which could prove useful
as standards to quickly assess the quality of a catalyst at hand and circumvent the need for extensive
optimization experiments with valuable materials from total synthesis. Finally, we prove the analysis of
the palladium catalysts completed is useful and mirrors the observed activity during reactions by
comparing the activity of these catalysts for deprotecting a serotype A decasaccharide which is currently
a candidate for semi-synthetic vaccine development.4
Results and Discussion
Total Synthesis of Serotype A Decasaccharide
To complete the total synthesis of the serotype A decasaccharide we followed a convergent building
block approach, utilizing di- and tetrasaccharide thioglycoside building blocks.5 The synthesis of which
has reported previously,4 the use of a convergent synthesis is attractive for several reasons; as it allows
quick assembly of the target GXM glycans in minimal steps; the 6-O-acetylation along the mannose
backbone is preinstalled; and glycan branching is formed at an early stage, specifically the β-1,2 xylose
branches and β-1,2 glucuronic acid branches.
Palladium Catalyst Analysis
To allow comparison we performed a hydrogenolysis reaction optimisation study using a synthetic
serotype A decasaccharide 1, which when deprotected, we have recently identified as a good antigen
to be tested as part of a semi-synthetic vaccine candidate against C. neoformans infections (Scheme
1, Table 1).4 Using either a Pearman’s catalyst (20% Pd[OH]2/C, Sigma-Aldrich) or a 10% Pd/C (SigmaAldrich) both led to exceedingly long reaction times (5-6 days), this was in spite of using our optimised
pre-tuning conditions (Table 1 Entry 1 & 2). While, in keeping with our previous observations the 5%
Pd/C Evonik Noblyst® from Strem Chemicals allowed access to the desired decasaccharide 2 in the
shortest reaction times, highest yields, and no aromatic protecting group related saturation when using
our pre-tuning methodology (Figure 2, Table 1 Entry 3).1
While pleased with our findings, we sought to further push our understanding in relation to the
wide variability experienced when using different palladium on carbon catalysts. To do so we sought to
characterize the catalysts with a range of spectroscopic and imaging techniques. We chose to
characterise the three different Pd/C catalysts used in this study to allow direct comparison between
the isolated yields and reaction times with the direct analysis of the catalysts surface properties. We
envisaged that then in the future we could possibly predict a catalysts activity through analysis without
the need for extensive optimisation reactions using precious synthetic material.
X-ray diffraction (XRD) analysis of the 5% Pd/C from Strem Chemicals (Figure 1A) obtained
diffraction peaks of at 2θ of 33.3°, 34.4°,42.9 and 55.3° are assigned to the (002), (101), (110) and
(112) facets of tetragonal PdO (powder diffraction file, PDF No. 88-2434),6,7 the existence of palladium
was confirmed by the peaks at 2θ of 40.1°, 46.7° and 68.1°, which are correspondent to the (111), (200)
and (220) planes of cubic Pd (PDF No. 05-0681) respectively.8–10 The broadening and low intensities of
the diffraction peaks characteristic of the 5% Pd/C (Strem Chemicals) indicate that the particles are
very small. The XRD pattern for the two Sigma-Aldrich catalysts shows clear peaks at 33.3°, 34.4°,42.9°
and 55.3° for crystalline tetragonal PdO, matching well with PDF No. 88-2434. The corresponding XRD
peaks intensity from the Sigma-Aldrich catalysts show a significant increase, compared to those of the
5% Pd/C (Strem Chemicals), confirming the size of particle of PdO is larger in the Sigma-Aldrich
catalysts, which is consistent with the TEM image results (Figure 1C). All of the samples show a very
broad peak located at 2θ of ~25o, which assigns to the (002) diffraction planes of graphite microcrystals
in the disordered carbon.10,11
TEM images were taken of each catalyst and enabled visualisation of the morphology and size
distribution of the catalysts (Figure 1C). The 5% Pd/C (Strem Chemicals) indicated that Pd and PdO
nanoparticles are uniformly dispersed on carbon black with the mean size of ~4 nm. The existence of
large numbers of active sites in the corners and edges of small-sized nanoparticles, is consistent with
the observation of a more favourable catalytic performance during the global hydrogenolysis reactions
(Table 1 Entry 3 & 4). The high-resolution TEM (HRTEM) image of the 5% Pd/C (Strem Chemicals)
(Figure 1C) reveals three lattice fringes with space of 0.224 nm and 0.207 nm, which are corresponding
to the (111) crystalline plane of Pd and (110) crystalline plane of PdO, respectively. This indicates the
coexistence of Pd, and PdO in the 5% Pd/C (Strem Chemicals). Conversely, the catalysts from SigmaAldrich exhibit large particle size and poor size distribution, which is not favourable for catalytic process
and corresponds to the lower isolated yields and longer reactions times experienced when using these
catalysts (Table 1 Entry 1 & 2). The HRTEM image of the catalysts from Sigma-Aldrich indicate that the
lattice spacing of ~ 0.208 nm corresponding to the (110) crystal plane of PdO.
The elemental constituents and states of the catalysts were analysed using XPS analysis,
showing high-resolution XPS spectra of Pd 3d (Figure 1B). The binding energies of 337.5 and 342.8
eV were observed in the all catalysts were ascribed to Pd2+ 3d5/2 and 3d3/2 split orbitals of PdO,
respectively. Additionally, in the 5% Pd/C (Strem Chemicals) another two lower binding energies of
336.0 and 341.1 eV are assigned to 3d5/2 and 3d3/2 levels of metallic Pd (Pd0), respectively,12–14 again
confirming that PdO and Pd exist in the 5% Pd/C (Strem Chemicals) but not in the other two catalysts.
Conclusions
We completed the analysis of three palladium on carbon catalysts physical and chemical properties,
finding this can be used to predict a catalysts efficiency prior to the use of precious synthetic materials,
as our analysis is consistent with the results of the global deprotections of serotype A decasaccharide
in terms of overall reaction efficiency (isolated yields and reaction times). These findings are particularly
relevant for complex total synthesis where often access to only minute quantities of material is possible.
Experimental Section
General Notes
Silica gel flash chromatography was carried out using automated flash chromatography systems, Buchi
Reveleris® X2 (UV 200-500 nm and ELSD detection, Reveleris® silica cartiges 40 μm, BÜCHI
Labortechnik AG). Size-exclusion chromatography was performed on Bio-Gel® P-2 (Bio-Rad
Laboratories Inc.) using isocratic elution (H 2O:tBuOH, 99:1, v/v). Instrumentation: peristaltic pump P-3
(Pharmacia Fine Chemicals), refractive index detector Iota 2 (Precision Instruments), PrepFC fraction
collector (Gilson Inc.). Software: Trilution® LC (version 1.4, Gilson Inc.). All chemicals for the synthesis
were purchased from commercial suppliers (Acros, Carbosynth Ltd, Fisher Scientific Ltd, A/S, Merck,
Sigma-Aldrich, VWR, Strem Chemicals and AlfaAesar) and used without purification. Dry Solvents were
obtained from a PureSolv-ENTM solvent purification system (Innovative Technology Inc.). All other
anhydrous solvents were used as purchased from Sigma-Aldrich in AcroSeal® bottles.
Procedure for Catalyst Pre-treatment1
500 mg Pd/C (any commercial catalyst), was suspended in 1 mL DMF:H2O mixture (80:20 v/v), and the
solution was made acidic by the addition of 200 µL HCl (ACS Reagent, 37%, pH 2-3), with or without
an atmosphere of hydrogen gas for about 20 minutes. The presence of dimethylamine was confirmed
via ninhydrin staining. The treated Pd/C catalysts was re-isolated though filtration. The moistened
catalyst was then be used directly in the hydrogenolysis reaction.
General Procedure for Hydrogenolysis Batch Reaction 1
The treated catalyst (0.2-0.5 molar eq. of palladium per benzyl group) was added to a solution of
oligosaccharide (1 eq.) dissolved in THF:tert-butyl alcohol:PBS (100 mM, pH 4) (60:10:30, v/v/v). The
reaction was placed in a high pressure reactor at 10 bar and was monitored via normal phase TLC
(MeCN:H2O mixtures) and MALDI-TOF mass spectrometry Once complete the reaction mixture was
filtered through a plug of Ceilte® and then concentrated in vacuo. The residue was then re-dissolved in
a minimal amount of sterile water and purified with a Bio-gel P2 Column, after lyophilization to yield the
desired product.
Palladium on Carbon Characterization
A transmission electron microscope (JEOL JEM-2100F) was used to obtain transmission electron
microscopy (TEM) images, high-resolution TEM (HRTEM) images at an acceleration voltage of 200 kV.
An X-ray diffractometer (XRD, Bruker D8 Advance) with Cu-Kα radiation was used for analyzing the
crystallographic structure of the as-prepared samples from 5°~90° with a scanning step of 0.02°. The
surface elemental composition and chemical state of the as-prepared samples were collected from an
X-ray photoelectron spectra spectrometer (XPS, Kratos AXIS ULTRA DLD), in which a monochromatic
Al Kα source (hν = 1486.6 eV) was applied. All binding energies were calibrated using the C 1s
hydrocarbon peak at 284.60 eV.
Acknowledgements
We thank Dr Yannick Ortin and Dr Jimmy Muldoon for NMR and MS support. C.J.C. was funded by
Irish Research Council postgraduate award (GOIPG/2016/998). S.O was supported by Science
Foundation Ireland Award 13/IA/1959.
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Scheme 1. Global Deprotection of Serotype A Decasaccharide
RO
RO
O
RO
RO
RO
R 2O
O
O
RO
RO
O
O
AcO
RO
O
RO
RO
O RO
OR
O
O
O
AcO
RO
O
OR
O
RO
RO
RO
RO
O
1: R1 = Bn; R2 = NAP; R3 = N3
2: R1 = H; R2 = H; R3 = NH2
O
5% Pd/C,
THF:tBuOH:PBS
(100 mM pH 4)
O
OR
O
O
RO
RO
O
AcO
RO
O
OR
O
O
R3
Table 1. Global Deprotection of GXM Glycans a
Entry
Substrate
Catalyst
Supplier
Time (d)
1
1
20%Pd[OH]2
Sigma-Aldrich
6
76
2
1
10% Pd/C
Sigma-Aldrich
5
58
3
1
5% Pd/C
Strem Chemicals
1.5
88
a Preconditioned
catalyst (see protocol), THF:tBuOH:PBS (100 mM pH 4) (60:10:30 v/v/v).
% Yield
Figure 1. Characterization of Palladium on Carbon Catalysts. Pd/C STREM Chemicals (#1), Pd/C
Sigma-Aldrich (#2), and Pd[OH]2/C Sigma-Aldrich (3#). A. XRD patterns of the Pd/C. B. XPS for Pd
3d electrons. C. TEM and HRTEM of catalyst. Scale inset.
Figure 2. 1H NMR Spectrum of Serotype A Decasaccharide.