A modular strategy toward the synthesis of heparin-like oligosaccharides using monomeric building blocks in a sequential glycosylation strategy

A novel flexible assembly strategy is described for the modular synthesis of heparin and heparan sulfates. The reported strategy uses monomeric building blocks to construct the oligosaccharide chain to attain a maximum degree of flexibility. In the assembly, 1-hydroxyl glucosazido- and 1-thio uronic acid donors are combined in a sequential glycosylation protocol using sulfonium triflate activator systems. The key 1-thio uronic acids were obtained in an efficient manner from diacetone glucose employing a chemo- and regioselective oxidation of partially protected glucose and idose thioglycosides.     

A unified orbital model of delocalised and localised currents in monocycles, from annulenes to azabora-heterocycles

Why are some (4n+2)π systems aromatic, and some not? The ipsocentric approach to the calculation of the current density induced in a molecule by an external magnetic field predicts a four‐electron diatropic (aromatic) ring current for (4n+2)π carbocycles and a two‐electron paratropic (antiaromatic) current for (4n)π carbocycles. With the inclusion of an electronegativity parameter, an ipsocentric frontier‐orbital model also predicts the transition from delocalised currents in carbocycles to nitrogen‐localised currents in alternating azabora‐heterocycles, which rationalises the differences in (magnetic) aromaticity between these isoelectronic π‐conjugated systems. Ab initio valence‐bond calculations confirm the localisation predicted by the naïve model, and coupled‐Hartree–Fock calculations give current‐density maps that exhibit the predicted delocalised‐to‐localised/carbocycle–heterocycle transition.     

Quantum Chemistry-based Molecular Dynamics Simulations as a Tool for the Assignment of ESI-MS/MS Spectra of Drug Molecules

In organic mass spectrometry, fragment ions provide important information on the analyte as a central part of its structure elucidation. With increasing molecular size and possible protonation sites, the potential energy surface (PES) of the analyte can become very complex, which results in a large number of possible fragmentation patterns. Quantum chemical (QC) calculations can help here, enabling the fast calculation of the PES and thus enhancing the mass spectrometry-based structure elucidation processes. In this work, the previously unknown fragmentation pathways of the two drug molecules Nateglinide (45 atoms) and Zopiclone (51 atoms) were investigated using a combination of generic formalisms and calculations conducted with the Quantum Chemical Mass Spectrometry (QCxMS) program. The computations of the de novo fragment spectra were conducted with the semi-empirical GFNn-xTB (n=1, 2) methods and compared against Orbitrap measured electrospray ionization (ESI) spectra in positive ion mode. It was found that the unbiased QC calculations are particularly suitable to predict non-evident fragment ion structures, sometimes contrasting the accepted generic formulation of fragment ion structures from electron migration rules, where the “true” ion fragment structures are approximated. For the first time, all fragment and intermediate structures of these large-sized molecules could be elucidated completely and routinely using this merger of methods, finding new undocumented mechanisms, that are not considered in common rules published so far. Given the importance of ESI for medicinal chemistry, pharmacokinetics, and metabolomics, this approach can significantly enhance the mass spectrometry-based structure elucidation processes and contribute to the understanding of previously unknown fragmentation pathways.     

Rational Tuning of the Reactivity of Three-Membered Heterocycle Ring Openings via SN2 Reactions

The development of small-molecule covalent inhibitors and probes continuously pushes the rapidly evolving field of chemical biology forward. A key element in these molecular tool compounds is the “electrophilic trap” that allows a covalent linkage with the target enzyme. The reactivity of this entity needs to be well balanced to effectively trap the desired enzyme, while not being attacked by off-target nucleophiles. Here we investigate the intrinsic reactivity of substrates containing a class of widely used electrophilic traps, the three-membered heterocycles with a nitrogen (aziridine), phosphorus (phosphirane), oxygen (epoxide) or sulfur atom (thiirane) as heteroatom. Using quantum chemical approaches, we studied the conformational flexibility and nucleophilic ring opening of a series of model substrates, in which these electrophilic traps are mounted on a cyclohexene scaffold (C₆H₁₀Y with Y=NH, PH, O, S). It was revealed that the activation energy of the ring opening does not necessarily follow the trend that is expected from C−Y leaving-group bond strength, but steeply decreases from Y=NH, to PH, to O, to S. We illustrate that the HOMO_Nu–LUMO_Substrate interaction is an all-important factor for the observed reactivity. In addition, we show that the activation energy of aziridines and phosphiranes can be tuned far below that of the corresponding epoxides and thiiranes by the addition of proper electron-withdrawing ring substituents. Our results provide mechanistic insights to rationally tune the reactivity of this class of popular electrophilic traps and can guide the experimental design of covalent inhibitors and probes for enzymatic activity.     

Amylose and Amylopectin Hybrid Materials via Enzymatic Pathways

Summary: Oligo- and polysaccharides are important macromolecules in living systems, showing their multifunctional characteristics in the construction of cell walls, energy storage, cell recognition and their immune response. Saccharides as organic raw materials can open new perspectives on the way to new biocompatible and biodegradable products which could help to overcome the problems resulting from the upcoming restrictions of petrochemical resources. Construction of well-defined carbohydrate polymer backbones is very challenging as it is difficult to realize complete regio and stereo-control of the glycosylating process. Most synthetic approaches are therefore based on the modification or degradation of naturally occurring polysaccharides resulting in less then perfect products. Enzymes have several remarkable catalytic properties compared with other types of catalysts in terms of their selectivity, high catalytic activity, lack of undesirable side reactions and operation under mild conditions. A biocatalytic pathway to synthesize saccharides is therefore very attractive as it results in well-defined polysaccharides avoiding the above drawbacks. When biogenic polysaccharides are combined with synthetic macromolecules, surfaces etc. materials with new interesting properties arise and the processability of the designed hybrid materials is facilitated. Amylose and amylopectin hybrid materials can be synthesized via enzymatic polymerization routes utilizing transferases. This approach opens access to well-defined hybrid structures bearing amylase or amylopectin moieties that cannot be synthesized by any other means.     

Capillary electrophoresis-high resolution sector field inductively coupled plasma mass spectrometry

The background and applications of high resolution sector field inductively coupled plasma mass spectrometry (HR-ICP-MS) as a detector for capillary (CE) and gel electrophoretic separations are reviewed. Notable progress has been made in the fields of bioinorganic and environmental (geo-) chemistry. Metallomics, the study of metal species interactions and functions in biological systems, puts substantial technical demands on speciation analysis. The combination of high species resolving power (CE) and high sensitivity-high mass resolving power (HR-ICP-MS) provides a solid base to meet such demands.     

Nanoscale organization of the pathogen receptor DC-SIGN mapped by single-molecule high-resolution fluorescence microscopy.

DC-SIGN, a C-type lectin exclusively expressed on dendritic cells (DCs), plays an important role in pathogen recognition by binding with high affinity to a large variety of microorganisms. Recent experimental evidence points to a direct relation between the function of DC-SIGN as a viral receptor and its spatial arrangement on the plasma membrane. We have investigated the nanoscale organization of fluorescently labeled DC-SIGN on intact isolated DCs by means of near-field scanning optical microscopy (NSOM) combined with single-molecule detection. Fluorescence spots of different intensity and size have been directly visualized by optical means with a spatial resolution of less than 100 nm. Intensity- and size-distribution histograms of the DC-SIGN fluorescent spots confirm that approximately 80 % of the receptors are organized in nanosized domains randomly distributed on the cell membrane. Intensity-size correlation analysis revealed remarkable heterogeneity in the molecular packing density of the domains. Furthermore, we have mapped the intermolecular organization within a dense cluster by means of sequential NSOM imaging combined with discrete single-molecule photobleaching. In this way we have determined the spatial coordinates of 13 different individual dyes, with a localization accuracy of 6 nm. Our experimental observations are all consistent with an arrangement of DC-SIGN designed to maximize its chances of binding to a wide range of microorganisms. Our data also illustrate the potential of NSOM as an ultrasensitive, high-resolution technique to probe nanometer-scale organization of molecules on the cell membrane.     

Iterative tandem catalysis of secondary diols and diesters to chiral polyesters

The well-known dynamic kinetic resolution of secondary alcohols and esters was extended to secondary diols and diesters to afford chiral polyesters. This process is an example of iterative tandem catalysis (ITC), a polymerization method where the concurrent action of two fundamentally different catalysts is required to achieve chain growth. In order to procure chiral polyesters of high enantiomeric excess value (ee) and good molecular weight, the catalysts employed need to be complementary and compatible during the polymerization reaction. We here show that Shvo's catalyst and Novozym 435 fulfil these requirements. The optimal polymerization conditions of 1,1'-(1,3-phenylene) diethanol (1,3-diol) and diisopropyl adipate required 2 mol% Shvo's catalyst and 12 mg Novozym 435 per mmol alcohol group in the presence of 0.5 M 2,4-dimethyl-3-pentanol as the hydrogen donor. With these conditions, chiral polyesters were obtained with peak molecular weights up to 15 kDa, an ee value up to 99% and with 1-3 % ketone end groups. Also with the structural isomer, 1,4-diol, a chiral polyester was obtained, albeit with lower molecular weight (8.3 kDa) and slightly lower ee (94%). Aliphatic secondary diols also resulted in enantio-enriched polymers but at most an ee of 46 % was obtained with molecular weights in the range of 3.3-3.7 kDa. This low ee originates from the intrinsic low enantioselectivity of Novozym 435 for this type of secondary aliphatic diols. The results presented here show that ITC can be applied to procure chiral polyesters with good molecular weight and high ee from optically inactive AA-BB type monomers.     

Investigations of a highly crowded phosphino-substituted biphenyl: A precursor for a λ3, λ5-diphosphaphenanthrene

The synthesis of 2,2′-bis(bis(dimethylamino)-phosphino)-3,3′5,5′-tetra-tert-butylbiphennyl ( 5 ) is described. It was extensively studied by ¹H, ¹³C, and ³¹P NMR spectroscopy. Furthermore, the X-ray analysis of 5 is reported. Crystals of 5 are tetragonal, space group P¯42₁c, a = b = 24.770 (3) Å, c = 12.658 (4) Å, Z = 8. The surprising reaction of 5 with proton acids leading to the formation of various phosphorus containing five- and six-membered ring compounds is discussed. On reaction of one of the six-membered ring compounds ( 9 ) with magnesium in THF, a λ³, λ⁵-diphosphaphenanthrene ( 19 ) was obtained.     

Using Terpene Synthase Plasticity in Catalysis: On the Enzymatic Conversion of Synthetic Farnesyl Diphosphate Analogues

Four synthetic farnesyl diphosphate analogues were enzymatically converted with three bacterial sesquiterpene synthases, including β-himachalene synthase (HcS) and (Z)-γ-bisabolene synthase (BbS) from Cryptosporangium arvum, and germacrene A synthase (SmTS6) from Streptomyces mobaraensis. These enzyme reactions not only yielded several previously unknown compounds, showing that this approach opened the door to a new chemical space, but substrates with blocked or altered reactivities also gave interesting insights into the cyclisation mechanisms and the potential to catalyse reactions with different initial cyclisation modes.