Conception and Evaluation of a Library of Cleavable Mass Tags for Digital Polymers Sequencing.

A library of phosphoramidite monomers containing a main-chain cleavable alkoxyamine and a side-chain substituent of variable molar mass (i.e. mass tag) was prepared in this work. These monomers can be used in automated solid-phase phosphoramidite chemistry and therefore incorporated periodically as spacers inside digitally-encoded poly(phosphodiester) chains. Consequently, the formed polymers contain tagged cleavable sites that guide their fragmentation in mass spectrometry sequencing and enhance their digital readability. The spacers were all prepared via a seven steps synthetic procedure. They were afterwards tested for the synthesis and sequencing of model digital polymers. Uniform digitally-encoded polymers were obtained as major species in all cases, even though some minor defects were sometimes detected. Furthermore, the polymers were decoded in pseudo-MS3 conditions, thus confirming the reliability and versatility of the spacers library.

Chain Entropy Beats Hydrogen Bonds to Unfold and Thread Dialcohol Phosphates inside Cyanostar Macrocycles To Form [3]Pseudorotaxanes.

The recognition of substituted phosphates underpins many processes including DNA binding, enantioselective catalysis, and recently template-directed rotaxane synthesis. Beyond ATP and a few commercial substrates, however, little is known about how substituents effect organophosphate recognition. Here, we examined alcohol substituents and their impact on recognition by cyanostar macrocycles. The organophosphates were disubstituted by alcohols of various chain lengths, dipropanol, dihexanol, and didecanol phosphate, each accessed using modular solid-phases syntheses. Based on the known size-selective binding of phosphates by π-stacked dimers of cyanostars, threaded [3]pseudorotaxanes were anticipated. While seen with butyl substituents, pseudorotaxane formation was disrupted by competitive OH···O- hydrogen bonding between both terminal hydroxyls and the anionic phosphate unit. Crystallography also showed formation of a backfolded propanol conformation resulting in an 8-membered ring and a perched cyanostar assembly. Motivated by established entropic penalties accompanying ring formation, we reinstated [3]pseudorotaxanes by extending the size of the substituent to hexanol and decanol. Chain entropy overcomes the enthalpically favored OH···O- contacts to favor random-coil conformations required for seamless, high-fidelity threading of dihexanol and didecanol phosphates inside cyanostars. These studies highlight how chain length and functional groups on phosphate's substituents can be powerful design tools to regulate binding and control assembly formation during phosphate recognition.

Precise Alkoxyamine Design to Enable Automated Tandem Mass Spectrometry Sequencing of Digital Poly(phosphodiester)s.

A major step towards reliable reading of information coded in the sequence of long poly(phosphodiester)s was previously achieved by introducing an alkoxyamine spacer between information sub-segments. However, MS/MS decoding had to be performed manually to safely identify useful fragments of low abundance compared to side-products from the amide-based alkoxyamine used. Here, alternative alkoxyamines were designed to prevent side-reactions and enable automated MS/MS sequencing. Different styryl-TEMPO spacers were prepared to increase radical delocalization and stiffness of the structure. Their dissociation behavior was investigated by EPR and best results were obtained with spacers containing in-chain benzyl ring, with no side-reaction during synthesis or sequencing. Automated decoding of these polymers was performed using the MS-DECODER software, which interprets fragmentation data recorded for each sub-segment and re-align them in their original order based on location tags.

Revealing Data Encrypted in Sequence-Controlled Poly(Alkoxyamine Phosphodiester)s by Combining Ion Mobility with Tandem Mass Spectrometry.

The defined sequence of two comonomers in sequence-controlled macromolecules can be used to store binary information which is further decoded by MS/MS sequencing. In order to achieve the full sequence coverage requested for reliable decoding, the structure of these polymers can be optimized to minimize their dissociation extent, as shown for poly(alkoxyamine phosphodiester)s (PAPs) where weak alkoxyamine bonds were introduced in each repeating unit to make all phosphate groups MS/MS silent. However, for secret communications, a too high MS/MS readability could be a drawback. In this context, the design of PAPs was further optimized in this work to also include a decrypting key based on slight variation of a fragment collision cross section. This was achieved by employing two different nitroxides to build the alkoxyamine moiety, each containing a coding alkyl segment of the same mass but different architectures. As a result, the digital sequence determined from primary fragments observed in MS/MS had to be decrypted according to appropriate rules that depend on the drift times measured by ion mobility spectrometry for repeating units released as secondary product ions.

A Simple Post-Polymerization Modification Method for Controlling Side-Chain Information in Digital Polymers.

A three-step post-polymerization modification method was developed for the design of digitally encoded poly(phosphodiester)s with controllable side groups. Sequence-defined precursors were synthesized, either manually on polystyrene resins or automatically on controlled pore glass supports, using two phosphoramidite monomers containing either terminal alkynes or triisopropylsilyl (TIPS) protected alkyne side groups. Afterwards, these polymers were modified by stepwise copper-catalyzed azide-alkyne cycloaddition (CuAAC). The terminal alkynes were first reacted with a model azide compound, and after removal of the TIPS groups, the remaining alkynes were reacted with another organic azide. This simple method allows for quantitative side-chain modification, thus opening up interesting avenues for the preparation of a wide variety of digital polymers.

Orthogonal Synthesis of "Easy-to-Read" Information-Containing Polymers Using Phosphoramidite and Radical Coupling Steps.

A new orthogonal solid-phase iterative strategy is proposed for the synthesis of sequence-coded polymers. This approach relies on the use of two successive chemoselective steps: (i) phosphoramidite coupling, and (ii) radical-radical coupling. These repeated steps can be performed using two different types of building blocks, i.e. a phosphoramidite monomer that also contains an alkyl bromide and a hydroxy-functionalized nitroxide. The phosphoramidite and the hydroxy group are reacted in step (i), thus leading to a phosphite that is oxidized in situ into a phosphate bond. The alkyl bromide is activated by copper bromide in step (ii) to afford a carbon-centered radical that is spin-trapped in situ by the nitroxide. The iterative repetition of these steps allow synthesis of uniform polymers, as evidenced by high-resolution electrospray mass spectrometry. Moreover, binary information could be easily implemented in the polymers using different types of phosphoramidite monomers in step (i). Interestingly, it was found that the formed information-containing polymers are very easy to sequence by tandem mass spectrometry due to the presence of easily cleavable alkoxyamine bonds formed in step (ii).

Optimal ATRP-Made Soluble Polymer Supports for Phosphoramidite Chemistry.

Soluble polystyrene supports with optimal molecular structures for iterative phosphoramidite chemistry were prepared by atom-transfer radical polymerization (ATRP) and subsequent chain-end modification steps. The controlled radical polymerization of styrene was first performed in the presence of an 9-fluorenylmethoxycarbonyl (Fmoc)-protected amino-functional ATRP initiator. Soluble supports of different molecular weight were prepared. Size-exclusion chromatography and NMR analysis indicated formation of well-defined polymers with controlled chain lengths and narrow dispersity. After synthesis, the bromo ω end group of the ATRP polymer was removed by dehalogenation in the presence of tributyltin hydride, and the Fmoc protecting group of the α moiety was subsequently cleaved with piperidine. The resulting α-primary amine was afterwards treated with a linker containing a carboxyl group, a cleavable ester site, and a dimethoxytrityl-protected hydroxyl group to afford ideal soluble supports for phosphoramidite chemistry. NMR analysis indicated that these chain-end modifications were quantitative. The supports were tested for the synthesis of a non-natural sequence-defined oligophosphates. High-resolution ESI-MS analysis of the cleaved oligomers indicated formation of uniform species, and thus confirmed the efficiency of the ATRP-made soluble polymer supports. In addition, the synthesis of a thymidine-loaded soluble support was achieved.

Orthogonal Synthesis of Xeno Nucleic Acids.

Sequence-defined peptide triazole nucleic acids (PTzNA) were synthesized by means of a solid-phase orthogonal "AB+CD" iterative strategy. In this approach, AB and CD building blocks containing carboxylic acid (A), azide (B), alkyne (C), and primary amine (D) functions are assembled together by successive copper-catalyzed azide-alkyne cycloaddition (CuAAC) and acid-amine coupling steps. Different PTzNA genetic sequences were prepared using a library of eight building blocks (i.e., four AB and four CD building blocks).

Hybrid Fibrillar Xerogels with Unusual Magnetic Properties.

We report on the preparation of a hybrid nanomaterial made up of 1D filaments of an antiferromagnetic self-assembling bicopper complex encapsulated in polymer nanofibrils. The encapsulation process is achieved through the heterogeneous nucleation of the growth of polymer fibrils obtained by thermoreversible gelation as shown by calorimetry experiments. Neutron scattering experiments confirm that the filaments of a bicopper complex retain their 1D character after encapsulation in the fibrils. Superconducting quantum interference device experiments show that the bicopper complex, originally in the gapped spin state in the 3D bulk mesophase, displays a gapless behavior once encapsulated. Extended absorption fine structure and infrared results further highlight the difference in the molecular arrangement of the bicopper complex between the bulk mesophase and the encapsulated state, which may account for the magnetic behavior. This material, which is largely disordered, differs totally from the usual magnetic systems where this effect is observed only on highly crystalline systems with long-range order. Also, this hybrid material is very easy to prepare from its basic constituents and can be further processed in many ways.

Origin of Invariant Gel Melting Temperatures in the c-T Phase Diagram of an Organogel.

Binary c-T phase diagrams of organogelators in solvent are frequently simplified to two domains, gel and sol, even when the melting temperatures display two distinct regimes, an increase with T and a plateau. Herein, the c-T phase diagram of an organogelator in solvent is elucidated by rheology, DSC, optical microscopy, and transmitted light intensity measurements. We evidence a miscibility gap between the organogelator and the solvent above a threshold concentration, cL. In this domain the melting or the formation of the gel becomes a monotectic transformation, which explains why the corresponding temperatures are nonvariant above cL. As shown by further studies by variable temperature FTIR and NMR, different types of H-bonds drive both the liquid-liquid phase separation and the gelation.

Synthesis of non-natural sequence-encoded polymers using phosphoramidite chemistry.

Sequence-defined non-natural polyphosphates were prepared using iterative phosphoramidite protocols on a polystyrene solid support. Three monomers were used in this work: 2-cyanoethyl (3-dimethoxytrityloxy-propyl) diisopropylphosphoramidite (0), 2-cyanoethyl (3-dimethoxytrityloxy-2,2-dimethyl-propyl) diisopropylphosphoramidite (1), and 2-cyanoethyl (3-dimethoxytrityloxy-2,2-dipropargyl-propyl) diisopropylphosphoramidite (1'). Phosphoramidite coupling steps allowed rapid synthesis of homopolymers and copolymers. In particular, the comonomers (0, 1), (0, 1'), and (1, 1') were used to synthesize sequence-encoded copolymers. It was found that long encoded sequences could be easily built using phosphoramidite chemistry. ESI-HRMS, MALDI-HRMS, NMR, and size exclusion chromatography analyses indicated the formation of monodisperse polymers with controlled comonomer sequences. The polymers obtained with the comonomers (0, 1') and (1, 1') were also modified by copper-catalyzed azide-alkyne cycloaddition with a model azide compound, namely 11-azido-3,6,9-trioxaundecan-1-amine. (1)H and (13)C NMR analysis evidenced quantitative modification of the alkyne side-chains of the monodisperse copolymers. Thus, the molecular structure of the coding monomer units can be easily varied after polymerization. Altogether, the present results open up interesting avenues for the design of information-containing macromolecules.

Design of Nanohybrid Systems from a Partially Fluorinated Organogelator and Syndiotactic Polystyrene Thermoreversible Gel.

Nanohybrid systems are prepared from organogels of a partially fluorinated molecule and from thermoreversible gels of syndiotactic polystyrene. The thermodynamic behavior, morphology, and structure are investigated by using differential scanning calorimetry, atomic force microscopy, small-angle X-ray scattering (SAXS), and small-angle neutron scattering (SANS). The outcomes of these investigations suggest that the fibrils of the organogel coil around the sPS fibrils, probably through a heterogeneous nucleation process. These systems therefore differ from previously investigated sPS/OPV systems (oligo vinylene phenylene) where OPV fibrils pervade the sPS network.

Experimental and theoretical study of the n-doped successive polyanions of oligocruciform molecular wires: up to five units of charge.

The electronic structure of polyanions of sterically encumbered triisopropylsilyl-substituted linear and cyclic oligo(phenyleneethynylene)s (Monomer, Trimer, Pentamer, and Triangle) is investigated by electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and UV/Vis-near-infrared (NIR) spectroscopies, cyclic voltammetry, and theoretical calculations (DFT). Increasing anion orders are generated sequentially in vacuo at room temperature by chemical reaction with potassium metal up to the pentaanion. The relevance of these compounds acting as electron reservoirs is thus demonstrated. Even-order anions are EPR silent, whereas the odd species exhibit different signatures, which are identified after comparison of the measured hyperfine couplings by ENDOR spectroscopy with those predicted by DFT calculations. With increasing size of the oligomers the electron spin density is first distributed over the backbone carbon atoms for the monoanions, and then further localized at the outer phenyl rings for the trianion species. Examination of the UV/Vis-NIR spectra indicates that the monoanions (T(.-) , P(.-) ) exhibit two transitions in the Vis-NIR region, whereas a strong absorption in the IR region is solely observed for higher reduced states. Electronic transitions of the neutral monoanions and trianions are redshifted with increasing oligomer size, whereas for a given oligomer a blueshift is observed upon increasing the charge, which suggests a localization of the spin density.

Electronic, spectroscopic, and ion-sensing properties of a dehydro[m]pyrido[14]- and [15]annulene isomer library.

An isomeric series of dehydro[m]pyrido[n]annulenes incorporating strained 1,4-buta-1,3-diyne units have been synthesized, where m = 2, n = 14 (1a-d); m = 2, n = 15 (2a,b); and m = 3, n = 15 (3). The number of pyridine rings and annulene ring π-electrons are denoted by m and n, respectively. The X-ray crystal structures of 1b and 1c confirmed their cyclic formulation. All macrocycles were found to be luminescent chromophores with differing isomer-dependent proton and metal ion-sensory emission responses, which appear collectively as analyte-specific color patterns. Within the series studied, 1a was singular in displaying the highest luminescence quantum yield and sharing the strongest emission energy and molar absorption changes upon protonation and Hg(II) binding. Spectroscopic and electrochemical results were supported by density functional theory calculations in showing 1a, 2a, and 3 to be low bandgap materials with lowest unoccupied molecular orbitals delocalized over the 1,4-di(pyridin-4-yl)buta-1,3-diyne bridges that provide a pathway for electronic communication between the nitrogens. Overall, the investigations suggest that 1a, 2a, and 3 would be excellent ligands for the construction of novel conjugated hybrid metallosupramolecular nanostructures, polymers, and ion-sensory systems.

Aerolysin nanopores decode digital information stored in tailored macromolecular analytes.

Digital data storage is a growing need for our society and finding alternative solutions than those based on silicon or magnetic tapes is a challenge in the era of "big data." The recent development of polymers that can store information at the molecular level has opened up new opportunities for ultrahigh density data storage, long-term archival, anticounterfeiting systems, and molecular cryptography. However, synthetic informational polymers are so far only deciphered by tandem mass spectrometry. In comparison, nanopore technology can be faster, cheaper, nondestructive and provide detection at the single-molecule level; moreover, it can be massively parallelized and miniaturized in portable devices. Here, we demonstrate the ability of engineered aerolysin nanopores to accurately read, with single-bit resolution, the digital information encoded in tailored informational polymers alone and in mixed samples, without compromising information density. These findings open promising possibilities to develop writing-reading technologies to process digital data using a biological-inspired platform.

Synthesis and properties of oligo[n]cruciforms: nanosized sterically encumbered tetraethynylphenyl-homologated fluorophores.

A series of nanosized phenyleneethynylenes have been prepared which are sterically insulated from the surrounding environment by multiple functionalization with triisopropylsilyl (TIPS) substituents. The phenyleneethynylenes comprise oligo[n]cruciforms 1-4 (n = 3-5) and a dehydrotribenzo[12]annulene 5, the former of which possess para-acyclic and the latter ortho-cyclic electronic conjugation pathways. All compounds were characterized by (1)H and (13)C NMR, IR, and mass spectroscopic techniques. The X-ray crystal structure of 1 confirmed the sterically isolating properties of the TIPS substituents. A comparison of the physical properties of these electronically differing systems revealed that they were all luminescent upon UV irradiation displayed negligible aggregation in dilute solution and that particular members of the series studied were electrochemically active, undergoing facile reversible reductions. The phenyleneethynylenes also exhibited significantly enhanced thermal stability by virtue of the presence of the TIPS substituents. The properties of 1-5 suggest that they are promising building blocks for the construction of materials for novel molecular electronics applications.

Photo-editable macromolecular information.

Light-induced alteration of macromolecular information plays a central role in biology and is known to influence health, aging and Darwinian evolution. Here, we report that light can also trigger sequence variations in abiotic information-containing polymers. Sequence-coded poly(phosphodiester)s were synthesized using four phosphoramidite monomers containing either photo-sensitive or photo-inert substituents. These monomers allow different sequence manipulations. For instance, using two light-cleavable monomers containing o-nitrobenzyl ether and o-nitroveratryl ether motifs, photo-erasable digital polymers were prepared. These polymers can be decoded by tandem mass spectrometry but become unreadable after UVA exposure. The opposite behavior, i.e. photo-revealable sequences, was obtained with polymers made of two isobaric monomers containing light-cleavable o-nitrobenzyl ether and light-inert p-nitrobenzyl ether substituents. Furthermore, when the latter two monomers were used in conjunction with a third monomer bearing a light-inert OH group, site-directed photo-mutations were induced in synthetic polymers. This was used herein to change the meaning of binary sequences.

Mass spectrometry sequencing of long digital polymers facilitated by programmed inter-byte fragmentation.

In the context of data storage miniaturization, it was recently shown that digital information can be stored in the monomer sequences of non-natural macromolecules. However, the sequencing of such digital polymers is currently limited to short chains. Here, we report that intact multi-byte digital polymers can be sequenced in a moderate resolution mass spectrometer and that full sequence coverage can be attained without requiring pre-analysis digestion or the help of sequence databases. In order to do so, the polymers are designed to undergo controlled fragmentations in collision-induced dissociation conditions. Each byte of the sequence is labeled by an identification tag and a weak alkoxyamine group is placed between 2 bytes. As a consequence of this design, the NO-C bonds break first upon collisional activation, thus leading to a pattern of mass tag-shifted intact bytes. Afterwards, each byte is individually sequenced in pseudo-MS3 conditions and the whole sequence is found.Digital information can be stored in monomer sequences of non-natural macromolecules, but only short chains can be read. Here the authors show long multi-byte digital polymers sequenced in a moderate resolution mass spectrometer. Full sequence coverage can be attained without pre-analysis digestion or the help from sequence databases.

Synthesis of Monodisperse Sequence-Coded Polymers with Chain Lengths above DP100.

Non-natural, sequence-encoded polyphosphates were prepared using the phosphoramidite approach on a DNA synthesizer. Two phosphoramidite monomers, namely, 2-cyanoethyl (3-dimethoxytrityloxy-propyl) diisopropylphosphoramidite (0) and 2-cyanoethyl (3-dimethoxytrityloxy-2,2-dimethyl-propyl) diisopropylphosphoramidite (1), were used in this approach to form binary-coded sequences. Using 1000 Å controlled pore glass as a support and a large excess of monomers at each step, it was possible to synthesize homopolymers and sequence-coded copolymers of high chain-length. For instance, monodisperse polymers containing 16, 24, 56, and 104 coded monomer units were synthesized and characterized in this work. These results indicate that highly efficient phosphoramidite steps are suitable for the synthesis of long non-natural information-containing macromolecules.

Extended supramolecular organization of π-systems using yet unexplored simultaneous intra- and inter-molecular H-bonding motifs of 1,3-dihydroxy derivatives.

Unique H-bonding motifs of 1,3-dihydroxyl derivatives involving simultaneous intra- and inter-molecular H-bonding results in extended organization of pendant chromophores with a spatial distance suitable for π-π interaction. A preformed assembly with appended acceptor units exhibits host-guest interaction with specific donors by charge-transfer complex formation.