Synthesis of an elongated linear oligo(phenylene ethynylene)-based building block for application in DNA-programmed assembly

The synthesis of an elongated linear oligonucleotide-functionalised module (ELOM) is described. The ELOM structure is based on an oligo(phenylene ethynylene) backbone substituted with two decyloxy groups. The two termini constitute two salicylaldehyde moieties acting as chemical cross-linkers. Before incorporation into an oligonucleotide sequence the organic part of the module, the elongated linear module (ELM), is functionalised with a dimethoxytrityl group and a phosphoramidite group. This enables incorporation into the middle of 30-mer oligonucleotide sequences by automated DNA synthesis. The obtained ELOMs were characterised by polyacrylamide gel electrophoresis and MALDI-TOF mass spectrometry. In analogy with previously reported LOM and TOM structures the coupling reactions of the ELOM modules were tested.     

Modular DNA-programmed assembly of linear and branched conjugated nanostructures

A new strategy for self-assembly and covalent coupling of encoded molecular modules into nanostructures with predetermined connectivity has been developed. The method uses DNA-functionalized oligo(phenylene ethynylene)-derived organic modules for controlling the assembly and covalent coupling of multiple modules. Rigid linear modules (LM) and tripoidal modules (TM) were functionalized with short oligonucleotides at each terminus. They can hybridize and thereby link up modules containing complementary sequences. Each terminus of the oligo(phenylene ethynylene) modules also consists of a salicylaldehyde moiety, which can form metal-salen complexes with other modules. The salicylaldehyde groups of two modules are brought in proximity when their adjoining DNA sequences are complementary, and they selectively form a manganese-salen complex in the presence of ethylenediamine and manganese acetate. The resulting structures consist of a matrix of linear and branched oligo(phenylene ethynylene)s which are linked by conjugated and rigid manganese-salen complexes. These nanostructures are potential conductors for applications in molecular electronics.     

Synthesis of branched oligonucleotides with three different sequences using an oxidatively removable tritylthio group

We synthesized a three-way branched oligodeoxynucleotide (ODN) 30-mer using a new branch unit with acid-labile DMTr and oxidatively cleavable TrS groups as orthogonal protecting groups. The branched ODN was successfully synthesized using 5-[3,5-bis(trifluoromethyl)phenyl]-1H-tetrazole and (2R,8aS)-(+)-(camphorylsulfonyl)oxaziridine as the activator of phosphoramidite units and the oxidizing reagent, respectively. We also found that the TrS group was orthogonal to the Lev, TBDMS, and Fmoc groups. These results indicate the possibility of the synthesis of more complex four- and five-way branched ODNs by the combined use of DMTr, TrS, Lev, TBDMS, and Fmoc groups.     

Elaboration of corona functionalized regular unimolecular hyperbranched polystyrene nanoparticles

Functional arborescent graft polystyrenes prepared by the “graft-on-graft” technique, involving the iterative grafting of end functional polymer chains onto reactive polymer backbones were synthesized. The zero-generation comb polymers and then the first generation hyperbranched structures were obtained by the coupling reaction of living α-acetal polystyryllithium onto linear or comb chains of poly(chloroethyl vinyl ether) (PCEVE) of controlled D̄P̄_n and structure. Both the PS grafts and the PCEVE reactive backbones were synthesized individually by living polymerization techniques. Initiation of styrene polymerization from acetal functionalized lithium derivatives yield the ω-functionalization of all external polystyrene branches. Derivatization of these acetal branch termini allowed the generation of aldehyde, hydroxyl and carboxyl groups as well as the introduction of functional organic molecules at the periphery of the nanoparticles.     

Synthesis of a protected ribonucleoside phosphoramidite-linked spin label via an alkynyl chain at the 5′ position of uridine

New, spin-labeled nucleosides, and an efficient synthetic route for a modified uridine amidite, were developed. The spin-labeled part was the 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) group, which was linked via an alkynyl chain at the 5 position of uridine. Three typical protecting groups, the t-butyldimethylsilyl (TBDMS) group at 2′, the dimethoxytrityl (DMTr) group at 5′, and the phosphoramidite group at 3′, were introduced to produce an automated nucleic acid synthesizer. The TEMPO group at the 5 position in the uridine structure affected introduction of bulky protecting groups, such as the DMTr group at the 5′ position and the TBDMS group at the 2′ position. The electron paramagnetic resonance (EPR) data revealed a nitroxyl radical in the structure of synthetic nucleoside compounds; however, RNA produced by automated synthesis using a TEMPO-linked uridine phosphoramidite building block was EPR silent.     

Solid-phase synthesis of oligonucleotide glycoconjugates bearing three different glycosyl groups: orthogonally protected bis(hydroxymethyl)-N,N'-bis(3-hydroxypropyl)malondiamide phosphoramidite as key building block

Diethyl O,O'-(methoxymethylene)bis(hydroxymethyl)malonate (3) was observed to undergo a stepwise aminolysis when treated with 3-aminopropanol. This allowed convenient preparation of bis(hydroxymethyl)-N,N'-bis(3-hydroxypropyl)malondiamide bearing orthogonal levulinyl (Lev) and tert-butyldiphenylsilyl (TBDPS) protections at the two N-hydroxypropyl groups (8). One of the hydroxylmethyl functions was then protected with a 4,4'-dimethoxytrityl (DMTr) group, and the other one was phosphitylated to obtain a methyl N,N-diisopropylphosphoramidite (1). This building block was used for the synthesis of oligonucleotide glycoconjugates (25 and 26) carrying three different sugar units. After conventional phosphoramidite chain assembly of the sequence containing 1, the 5'-terminal DMTr group was removed and an appropriate glycosyl 6-O-phosphoramidite was coupled. The remaining protections of the branching unit were removed in the order of Lev and TBDPS, and the exposed hydroxyl functions were reacted one after another with the desired glycosyl 6-O-phosphoramidites. Global deprotection and cleavage of the conjugate from the support were achieved by conventional ammonolysis.     

Porous organic alloys

Another brick in the wall: Porous ternary cocrystals were prepared by chiral recognition between organic cage modules. One module, CC1, is ordered on 50?% of the lattice positions with respect to two other modules, CC3 and CC4, that are disordered across the other 50?% of sites (see picture). There is a linear relationship between relative module composition and the cocrystal lattice parameters.     

Synthesis of the ribosomal P-site substrate CCA-pcb

[reaction: see text] CCA-pcb (cytidylyl-(3'5')-cytidylyl-(3'5')-3'(2')-O-(N-(6-D-(+)-biotinoylaminohexanoyl)-L-phenylalanyl)adenosine), a ribosomal P-site substrate, was synthesized by phosphoramidite chemistry in 26 steps with an overall yield of 18%, starting from biotin. The synthesis relies on the judicious selection of orthogonal silyl protecting groups for the 5'-hydroxyls and acid-labile protecting groups (DMTr, AcE, and MeE) at other reactive sites to ensure the intactness of the labile ester. Both 3'-esterification and nucleotide coupling were accomplished by in situ activation with imidazolium ions.     

Cellulose Oligomers: Preparation from Cellulose Triacetate, Chemical Transformations and Reactions

Cellulose oligomers obtained by a new degradation method (pivaloylysis) are used as starting materials in organic synthesis. On the one hand these oligomers are functionalized to potent glycosyl donors, on the other hand several methods are shown to generate different types of hydroxy compounds (glycosyl acceptors). Glycosidation reactions performed with these two types of building blocks allow an access to linear products (unidisperse celluloses) as well as to new branched cellulose units.     

Two Aluminophosphate Molecular Sieves Built from Pairs of Enantiomeric Structural Building Units

Herein we report the synthesis and structures of two new small‐pore aluminophosphate molecular sieves PST‐13 and PST‐14 with mutually connected 8‐ring channels. The structure of PST‐13, synthesized using diethylamine as an organic structure‐directing agent, contains penta‐coordinated framework Al atoms bridged by hydroxy groups and thus edge‐sharing 3‐ and 5‐rings. Upon calcination, PST‐13 undergoes a transformation to PST‐14 with loss of bridging hydroxy groups and occluded organic species. The structures of both materials consist “nonjointly” of pairs of previously undiscovered 1,5‐ and 1,6‐open double 4‐rings (d4rs) which are mirror images of each other. We also present a series of novel chemically feasible hypothetical structures built from 1‐open d4r (sti) or 1,3‐open d4r (nsc) units, as well as from these two enantiomeric structural building units.     

Oligonucleotide-directed assembly of materials: defined oligomers.

A nano-architectural system that has high variability while maintaining component specificity is described. Tetraphenylcyclobutadiene(cyclopentadienyl)cobalt complexes and phenyleneethynylene trimers were synthesized and subsequently modified with oligonucleotides utilizing standard phosphoramidite chemistry. The resulting oligonucleotide modified organics (OMOs) were characterized by UV-vis spectroscopy, fluorescence spectroscopy, and phosphate analysis. Hybridization of these OMOs resulted in a series of self-assembled oligomeric hybrids of varying length and topology. These hybrids were characterized by melting temperature, polyacrylamide gel electrophoresis, and fluorescence spectroscopy. This model system demonstrates the power of DNA to self-assemble modules of interest-independent of the module itself.     

Synthesis of oligo(α-D-glycosyl phosphate) derivatives by a phosphoramidite method via boranophosphate intermediates

An efficient method for the synthesis of short oligo(α-D-glycosyl boranophosphate) derivatives by using an α-D-glycosyl phosphoramidite as a monomer unit was developed. The synthesis of oligomers was carried out by repeating a cycle consisting of the condensation of the monomer unit with a terminal hydroxy group of carbohydrates, boronation of the resultant phosphite intermediates, and terminal deprotection. The phosphoramidite monomer unit was synthesized from the corresponding glycosyl iodide and methyl N,N-diisopropylphosphonamidate in a highly α-selective manner. Di- and tri(α-D-glycosyl boranophosphate) derivatives obtained by the synthetic cycle were converted into the corresponding H-phosphonate diester derivatives, which were then used to synthesize di- and tri(α-D-glycosyl phosphate) derivatives including a fragment of Leishmania glycocalyx lipophosphoglycans.     

Efficient conjugation of peptides to oligonucleotides by "native ligation"

A new strategy has been developed for conjugation of peptides to oligonucleotides. The method is based on the "native ligation" of an N-terminal thioester-functionalized peptide to a 5'-cysteinyl oligonucleotide. Two new reagents were synthesized for use in solid-phase peptide and oligonucleotide synthesis, respectively. Pentafluorophenyl S-benzylthiosuccinate was used in the final coupling step in standard Fmoc-based solid-phase peptide assembly. Deprotection with trifluoracetic acid generated in solution peptides substituted with an N-terminal S-benzylthiosuccinyl moiety. O-trans-4-(N-alpha-Fmoc-S-tert-butylsulfenyl-L-cysteinyl)aminoc yclohe xyl O-2-cyanoethyl-N,N-diisopropylphosphoramidite was used in the final coupling step in standard phosphoramidite solid-phase oligonucleotide assembly. Deprotection with aqueous ammonia solution generated in solution 5'-S-tert-butylsulfenyl-L-cysteinyl functionalized oligonucleotides. Functionalized peptides and oligonucleotides were used without purification in native ligation conjugation reactions in aqueous/organic solution using tris-(2-carboxyethyl)phosphine to remove the tert-butylsulfenyl group in situ and thiophenol as a conjugation enhancer. A range of peptide-oligonucleotide conjugates were prepared by this route and purified by reversed-phase HPLC.     

Total synthesis of the polyene-polyol macrolide RK-397, featuring cross-couplings of alkynylepoxide modules

The total synthesis of the natural product RK-397 is based on a new synthetic strategy for assembling polyacetate structures, by efficient cross-coupling of nucleophilic terminal alkyne modules with electrophilic epoxides bearing another alkyne at the opposite terminus. The natural product is constructed from four principal modules: a polyene precursor for carbons 3-9, and three alkyne-terminated modules for carbons 10-16, 17-22, and 23-33. Each module is prepared with control of all stereochemical elements, and the alkynyl alcohols obtained from alkyne-epoxide couplings are converted into 1,3-diols by a sequence of hydroxyl-directed hydrosilylation, C-Si bond oxidation, and stereoselective ketone reduction with induction from the beta-hydroxyl group. The highly convergent nature of our synthetic pathway and the flexibility of the modular synthesis strategy for virtually any stereoisomer can provide access to other members of the polyene-polyol macrolides, including stereoisomers of RK-397.     

Star/Linear Polymer Topology Transformation Facilitated by Mechanical Linking of Polymer Chains

Topology transformation of a star polymer to a linear polymer is demonstrated for the first time. A three‐armed star polymer possessing a mechanical linking of two polymer chains was synthesized by the living ring‐opening polymerization of δ‐valerolactone initiated by a pseudo[2]rotaxane having three hydroxy groups as the initiator sites on the wheel component and at both axle termini. The polymerization was followed by the propagation end‐capping reaction with a bulky isocyanate not only to prevent the wheel component deslippage but also to introduce the urethane moiety at the axle terminal. The resulting rotaxane‐linked star polymer with a fixed rotaxane linkage based on the ammonium/crown ether interaction was subjected to N‐acetylation of the ammonium moiety, which liberated the components from the interaction to move the wheel component to the urethane terminal as the interaction site, eventually affording the linear polymer. The physical property change caused by the present topology transformation was confirmed by the hydrodynamic volume and viscosity.     

Post‐polymerization modification of branched polyglycidol with N‐Hydroxy phthalimide to give ratio‐controlled amino‐oxy functionalized species

Ratio‐controlled amino‐oxy functionalized, branched polyglycidols are prepared by a post‐polymerizaton modification using and optimizing the Mitsunobu reaction for this purpose. The hydroxyl side‐groups are functionalized with N‐hydroxy phthalimide and the hydrazinolysis of this group furnishes a new class of branched polyglycidols with pendant amino‐oxy groups. Reproducible functionalization degrees of 17, 33, 43, and 63% of the hydroxyl groups are obtained via the presented developed methodology. MTT assays demonstrate the biocompatibility of amino‐oxy functionalized materials. With this, the prepared structural motifs are valuable precursors for the synthesis of biomaterials, bioconjugates and hydrogels in which orthogonal strategies are desired. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 2820–2825     

Hydrophilic quaternary ammonium type ionic liquids. Systematic study of the relationship among molecular structures, osmotic pressures, and water-solubility

This Letter examines the relationship between the structures of ionic liquids and their water-solubility or osmotic pressure with a number of synthesized quaternary ammonium type ionic liquids and organic salts containing a hydroxyl group as hydrophilic substituted groups on ammonium group cations, and bromide or methylsulfonate as anions. The study found a linear relation between the amount and osmotic pressure of the water-soluble ionic liquids synthesized here, strongly indicating that these water-soluble ionic liquids are perfectly ionized in water like inorganic salts with small diameter ions.     

γ-Lactam-containing peptidomimetics

Protected diaminoalcohols obtained through allyl addition to α-amino acid-derived imines and subsequent hydroboration were used for the preparation of pyrrolidinones and pyrrolidines. Pyrrolidinones were synthesized with moderate yields by oxidation of the hydroxy function with tetrapropylammonium perruthenate/N-methylmorpholine-N-oxide and concomitant cyclization while pyrrolidines were synthesized in good yields by tosylation of the hydroxy group and subsequent intramolecular nucleophilic substitution. Thus accessible substrates were transferred into peptidomimetics by attachment of amino acid moieties at both termini using conventional peptide coupling strategies. Molecular mechanics optimizations suggest that these substrates preferentially adopt a turn conformation.     

Ceric ammonium nitrate on silica gel for efficient and selective removal of trityl and silyl groups

Silica gel-supported ceric ammonium nitrate (CAN-SiO2) was found effective for rapid and selective cleavage of trityl (Tr), monomethoxytrityl (MMTr), and dimethoxytrityl (DMTr) groups from protected nucleosides and nucleotides under mild conditions. Efficiency of deprotections depended upon the stability of the resultant carbocationic species: DMTr+ > MMTr+ > Tr+. Use of a catalytic amount of this solid-supported reagent can also efficiently and selectively remove the tert-butyldimethylsilyl or the triisopropylsilyl group from a primary hydroxyl functionality in di- or trisilyl ethers of ribonucleosides. A comparative study of deprotection reactions by utilization of CAN alone or CAN-SiO2 indicates a remarkable increase in the rate of the reactions involving a solid support. The mechanism of electron-transfer processes is proposed for the use of CAN-SiO2 in the removal of these protective groups from organic molecules.     

Asymmetric baker’s yeast reductions of bridgehead-substituted bicyclo[2.2.2]octane-2,6-dione derivatives followed by conversion into catalytically active BODOLs for the diethylzinc addition to benzaldehyde

4-Substituted bicyclo[2.2.2]octane-2,6-diones have been synthesized and tested as substrates in the enantioselective reduction with baker’s yeast to give the corresponding hydroxy ketones. It was found that the derivative bearing a TIPSO group at the 4-position was not reduced at all while that with a TBDMSO group gave 87% yield and 46% ee. Other 4-oxy functionalized derivatives were reduced with varying yields (36–87%) and ees (10–82%). The best result was obtained for the 4-Oallyl derivative (80% yield, 82% ee). The hydroxy ketones carrying the benzyloxy and allyloxy groups at the 4-position were converted into the corresponding BODOLs, which were tested as catalysts in the diethylzinc addition to benzaldehyde. In this reaction the ees were 90% and 89%, respectively, which showed that BODOLs substituted at the 4-position are essentially as good catalysts in this reaction as those bearing a hydrogen.