Using ion mobility spectrometry to understand signal dilution during tandem mass spectrometry sequencing of digital polymers: Experimental evidence of intramolecular cyclization.

RATIONALE: Optimizing the structure of digital polymers is an efficient strategy to ensure their tandem mass spectrometry (MS/MS) readability. In block-truncated poly(phosphodiester)s, homolysis of C-ON bonds in long chains permits the release of smaller blocks amenable to sequencing. Yet the dissociation behavior of diradical blocks was observed to strongly depend on their charge state. METHODS: Polymers were ionized in negative mode electrospray and activated in-source so that blocks released as primary fragments can be investigated using ion mobility spectrometry (IMS) or sequenced in the post-IMS collision cell. Collision cross sections (CCS) were derived from arrival times using a calibration procedure developed for polyanions using the IMSCal software. A multistep protocol based on quantum methods and classical molecular dynamics was implemented for molecular modeling and calculation of theoretical CCS. RESULTS: Unlike their triply charged homologues, dissociation of diradical blocks at the 2- charge state produces additional fragments, with +1 m/z shift for those holding the nitroxide α-termination and -1 m/z for those containing the carbon-centered radical ω-end. These results suggest cyclization of these diradical species, followed by H• transfer on activated reopening of this cycle. This assumption was validated using IMS resolution of the cyclic/linear isomers and supported by molecular modeling. CONCLUSIONS: Combining IMS with molecular modeling provided new insights into how the charge state of digital blocks influences their dissociation. These results permit to define new guidelines to improve either ionization conditions or the structural design of these digital polymers for best MS/MS readability.

Mass spectrometry of dendrimers.

Mass spectrometry (MS) has become an essential technique to characterize dendrimers as it proved efficient at tackling analytical challenges raised by their peculiar onion-like structure. Owing to their chemical diversity, this review covers benefits of MS methods as a function of dendrimer classes, discussing advantages and limitations of ionization techniques, tandem mass spectrometry (MS/MS) strategies to determine the structure of defective species, as well as most recently demonstrated capabilities of ion mobility spectrometry (IMS) in the field. Complementarily, the well-defined structure of these macromolecules offers major advantages in the development of MS-based method, as reported in a second section reviewing uses of dendrimers as MS and IMS calibration standards and as multifunctional charge inversion reagents in gas phase ion/ion reactions.

Desorption electrospray ionization mass spectrometry imaging of latent fingerprints revealed by Oil Red O.

Mass spectrometry imaging (MSI) is increasingly used to produce chemical images of latent fingerprints. Yet, the actual benefits of MSI for real case studies have to be assessed for fingerprints previously processed by forensic techniques. Here, we have evaluated the compatibility of desorption electrospray ionization (DESI) with the fingerprint enhancement technique involving Oil Red O (ORO). METHODS: To optimize the ionization step independently from surface extraction, the ORO reagent and its mixture with model compounds (triolein and linoleic acid) were first studied in solution using high-resolution electrospray ionization tandem mass spectrometry (ESI-MS/MS). Then, DESI-MSI experiments were performed in both polarity modes for ORO-processed fingermarks deposited on pieces of paper used as porous substrates. RESULTS: ESI-MS of ORO reveals a complex mixture of azo dyes. Two main impurities detected beside the targeted species were characterized using MS/MS and then were usefully employed to produce DESI-MS images of fingermarks, decreasing the scanning rate to get sufficient ion abundance from natural fingerprints. ORO did not prevent chemical profiling, and one major added value of this pink dye was to produce MS images with contrast that cannot be obtained optically for some colored substrates. CONCLUSIONS: DESI-MS has demonstrated imaging compatibility with the application of ORO used to enhance latent fingerprints on paper and could also enable chemical profiling in natural fingermarks. In addition, MS images of ORO impurities were of higher quality than optical ones for fingerprints revealed on colored paper.

Using Nitroxides To Model the Ion Mobility Behavior of Nitroxide-Ended Oligomers: A Bottom-up Approach To Predict Mobility Separation.

Block-truncated poly(phosphodiester)s are digital macromolecules storing binary information that can be decoded by MS/MS sequencing of individual blocks released as primary fragments of the entire polymer. As such, they are ideal species for the serial sequencing methodology enabled by MS-(CID)-IMS-(CID)-MS coupling, where two activation stages are combined in-line with ion mobility spectrometry (IMS) separation. Yet, implementation of this coupling still requires efforts to achieve IMS resolution of inner blocks, that can be considered as small oligomers with α termination composed of one nitroxide decorated with a different tag. As shown by molecular dynamics simulation, these oligomers adopt a conformation where the tag points out of the coil formed by the chain. Accordingly, the sole nitroxide termination was investigated here as a model to reduce the cost of calculation aimed at predicting the shift of collision cross-section (CCS) induced by new tag candidates and extrapolate this effect to nitroxide-terminated oligomers. A library of 10 nitroxides and 7 oligomers was used to validate our calculation methods by comparison with experimental IMS data as well as our working assumption. Based on conformation predicted by theoretical calculation, three new tag candidates could be proposed to achieve the +40 Å2 CCS shift required to ensure IMS separation of oligomers regardless of their coded sequence.

Internal Dynamics and Modular Peripheral Binding in Stimuli-Responsive 3 : 2 Host:Guest Complexes.

Now that the chemistry of 1 : 1 host:guest complexes is well-established, it is surprising to note that higher stoichiometry (oligomeric) complexes, especially those with excess host, remain largely unexplored. Yet, proteins tend to oligomerize, affording new functions for cell machinery. Here, we show that cucurbit[n]uril (CB[n]) macrocycles combined with symmetric, linear di-viologens form unusual 3 : 2 host:guest complexes exhibiting remarkable dynamic properties, host self-sorting, and external ring-translocation. These results highlight the structural tunability of cucurbit[8]uril (CB[8]) based 3 : 2 host:guest complexes in water and their responsiveness toward several stimuli (chemicals, pH, redox).

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.

Preparation and In Vitro Validation of a Cucurbit[7]uril-Peptide Conjugate Targeting the LDL Receptor.

Here we report the coupling of a cyclic peptide (VH4127) targeting the low density lipoprotein (LDL) receptor (LDLR) noncompetitively to cucurbit[7]uril (CB[7]) to develop a new kind of drug delivery system (DDS), namely, CB[7]-VH4127, with maintained binding affinity to the LDLR. To evaluate the uptake potential of this bismacrocyclic compound, another conjugate was prepared comprising a high-affinity group for CB[7] (adamantyl(Ada)-amine) coupled to the fluorescent tracker Alexa680 (A680). The resulting A680-Ada·CB[7]-VH4127 supramolecular complex demonstrated conserved LDLR-binding potential and improved LDLR-mediated endocytosis and intracellular accumulation potential in LDLR-expressing cells. The combination of two technologies, namely, monofunctionalized CB[7] and the VH4127 LDLR-targeting peptide, opens new avenues in terms of targeting and intracellular delivery to LDLR-expressing tissues or tumors. The versatile transport capacity of CB[7], known to bind a large spectrum of bioactive or functional compounds, makes this new DDS suitable for a wide range of therapeutic or imaging applications.

Sequential Formation of Heteroternary Cucurbit[10]uril (CB[10]) Complexes.

The globular and monocationic guest molecule trimethyl-azaphosphatrane (AZAP, a protonated Verkade superbase) was shown to form a host:guest 1 : 1 complex with the cucurbit[10]uril (CB[10]) macrocycle in water. Molecular dynamics calculations showed that CB[10] adopts an 8-shape with AZAP occupying the majority of the internal space, CB[10] contracting around AZAP and leaving a significant part of the cavity unoccupied. This residual space was used to co-include planar and monocationic co-guest (CG) molecules, affording heteroternary CB[10]⋅AZAP⋅CG complexes potentially opening new perspectives in supramolecular chemistry.

Covalent Attachment and Detachment by Reactive DESI of Sequence-Coded Polymer Taggants.

The use of sequence-defined polymers is an interesting emerging solution for materials identification and traceability. Indeed, a very large amount of identification sequences can be created using a limited alphabet of coded monomers. However, in all reported studies, sequence-defined taggants are usually included in a host material by noncovalent adsorption or entrapment, which may lead to leakage, aggregation, or degradation. To avoid these problems, sequence-defined polymers are covalently attached in the present work to the mesh of model materials, namely acrylamide hydrogels. To do so, sequence-coded polyurethanes containing a disulfide linker and a terminal methacrylamide moiety are synthesized by stepwise solid-phase synthesis. These methacrylamide macromonomers are afterward copolymerized with acrylamide and bisacrylamide in order to achieve cross-linked hydrogels containing covalently-bound polyurethane taggants. It is shown herein that these taggants can be selectively detached from the hydrogel mesh by reactive desorption electrospray ionization. Using dithiothreitol the disulfide linker that links the taggant to the gel can be selectively cleaved. Ultimately, the released taggants can be decoded by tandem mass spectrometry.

Enantioselective Synthesis of Acyclic Stereotriads Featuring Fluorinated Tetrasubstituted Stereocenters.

Elaboration of enantioenriched complex acyclic stereotriads represents a challenge for modern synthesis even more when fluorinated tetrasubstituted stereocenters are targeted. We have been able to develop a simple strategy in a sequence of two unprecedented steps combining a diastereoselective aldol-Tishchenko reaction and an enantioselective organocatalyzed kinetic resolution. The aldol-Tishchenko reaction directly generates a large panel of acyclic 1,3-diols possessing a fluorinated tetrasubstituted stereocenter by condensation of fluorinated ketones with aldehydes under very mild basic conditions. The anti 1,3-diols featuring three contiguous stereogenic centers are generated with excellent diastereocontrol (typically >99 : 1 dr). Depending upon the precursors both diastereomers of stereotriads are accessible through this flexible reaction. Furthermore, from the obtained racemic scaffolds, development of an organocatalyzed kinetic resolution enabled to generate the desired enantioenriched stereotriads with excellent selectivity (typically er >95 : 5).

Design of Experiments for Matrix-Assisted Laser Desorption/Ionization of Amphiphilic Poly(Ethylene Oxide)-b-Polystyrene Block Copolymers.

Matrix-assisted laser/desorption ionization (MALDI) has become a very popular ionization technique for mass spectrometry of synthetic polymers because it allows high throughput analysis of low amounts of sample while avoiding the complexity introduced by extensive multiple charging of electrospray ionization. Yet, fundamental mechanisms underlying this ionization process are not fully understood, so development of sample preparation methods remains empirical. Reliable prediction for the optimal matrix/analyte/salt system is indeed still not possible for homopolymers and it becomes even more challenging in the case of amphiphilic block copolymers where conditions dictated by one block are not compatible with MALDI requirements of the second block. In order to perform MALDI of copolymers composed of poly (ethylene oxide) (PEO) and polystyrene (PS) blocks, it was postulated here that experimental conditions suitable for both species would also be successful for PEO-b-PS. Accordingly, designs of experiments based on Quantitative Structure Activity Relationship (QSAR) analysis were first implemented, studying the influence of 19 matrices and 26 salts on the laser fluence requested for successful MALDI. This analysis first permitted to highlight correlations between the investigated 10 descriptors of matrices and salts and the analytical response, and then to construct models that permits reliable predictions of matrix/salt couples to be used for one or the other homopolymer. Selected couples were then used for MALDI of a PEO-b-PS copolymer but no general trend was observed: experimental conditions expected to work often failed whereas ionic adducts of the copolymer were clearly detected with some matrix/salt systems that were shown to badly perform for constituting homopolymers. Overall, this rules out the working assumption stating that the MALDI behavior of chains composed of PEO and PS segments should combine the behavior of the two polymeric species. Yet, although requiring a dedicated design of experiments, MALDI of the amphiphilic PEO-b-PS copolymer was achieved for the first time.

Reactive Desorption Electrospray Ionization Mass Spectrometry To Determine Intrinsic Degradability of Poly(lactic-co-glycolic acid) Chains.

Because of its speed, sensitivity, and ability to scrutinize individual species, mass spectrometry (MS) has become an essential tool in analytical strategies aimed at studying the degradation behavior of polyesters. MS analyses can be performed prior to the degradation event for structural characterization of initial substrates or after it has occurred to measure the decreasing size of products as a function of time. Here, we show that MS can also be usefully employed during the degradation process by online monitoring the chain solvolysis induced by reactive desorption electrospray ionization (DESI). Cleavage of ester bonds in random copolymers of lactic acid (LA) and glycolic acid (GA) was achieved by electrospraying methanol-containing NaOH onto the substrates. Experimental conditions were optimized to generate methanolysis products of high abundance so that mass spectra can be conveniently processed using Kendrick-based approaches. The same reactive-DESI performance was demonstrated for two sample preparations, solvent casting for soluble samples or pressed pellets for highly crystalline substrates, permitting to compare polymers with LA/GA ratios ranging from 100/0 to 5/95. Analysis of sample fractions collected by size exclusion chromatography showed that methanolysis occurs independently of the original chain size, so data recorded for poly(LA-co-GA) (PLAGA) copolymers with the average molecular weight ranging from 10 to 180 kDa could be safely compared. The average mass of methanolysis products was observed to decrease linearly (R2 = 0.9900) as the GA content increases in PLAGA substrates, consistent with the susceptibility of ester bonds toward solvolysis being higher in GA than in LA. Because DESI only explores the surface of solids, these data do not reflect bulk degradability of the copolymers but, instead, their relative degradability at the molecular level. Based on a "reactive-DESI degradability scale" such as that established here for PLAGA, the proposed method offers interesting perspectives to qualify intrinsic degradability of different polyesters and evaluate their erosion susceptibility or to determine the degradability of those polymers known to degrade via erosion only.

Switching from Single to Simultaneous Free-Radical and Anionic Polymerization with Enamine-Based Organic Electron Donors.

Although most monomers can polymerize through different propagation pathways, polymerization-initiating systems that can switch from one mode to another are rare. In this study, we demonstrate that enamine-based organic electron donors (OEDs) constitute the first systems able to initiate either free-radical or anionic polymerization under simple, mild, and safe conditions. While direct electron-transfer reduction of monomers by OEDs results in the initiation of anionic chain-growth polymerization, introduction of a competing oxidant with a higher reduction potential than the monomer switches the former anionic propagation to a clean radical-propagation process. The benefit of this dual-mode activator is highlighted in the synthesis of an interpenetrating polymer network through simultaneous initiation of radical and anionic propagation processes.

Indirect Tertiary Alcohol Enantiocontrol by Acylative Organocatalytic Kinetic Resolution.

The stereocontrol of tertiary alcohols represents a recurrent challenge in organic synthesis. In the present paper, we describe a simple, efficient, and indirect method to enantioselectively prepare tertiary alcohols through a chiral isothiourea catalyzed selective acylation of adjacent secondary alcohols. This transformation enables the kinetic resolution (KR) of easily prepared racemic diastereoenriched secondary/tertiary diols providing both monoesters and starting diols in highly enantioenriched forms (s-value >200).

Triple Stack of a Viologen Derivative in a CB[10] Pair.

A viologen-phenylene-imidazole (VPI) conjugate, previously shown to be singly complexed by CB[7] and doubly bound by CB[8], is herein shown to form antiparallel triple stacks in water with cucurbit[10]uril (CB[10]), pairwise complexing the guest trimer. The quinary host:guest 2:3 complex showed features assignable to charge-transfer interactions. Under reductive conditions, CB[10] could solubilize a VPI radical, even though CB[10] and reduced VPI are almost insoluble, thereby illustrating a possible new application for CB[10].

Design of Abiological Digital Poly(phosphodiester)s.

In biological systems, the storage and transfer of genetic information rely on sequence-controlled nucleic acids such as DNA and RNA. It has been realized for quite some time that this property is not only crucial for life but could also be very useful in human applications. For instance, DNA has been actively investigated as a digital storage medium over the past decade. Indeed, the "hard-disk of life" is an obvious choice and a highly optimized material for storing data. Through decades of nucleic acids research, technological tools for parallel synthesis and sequencing of DNA have been readily available. Consequently, it has already been demonstrated that different types of documents (e.g., texts, images, videos, and industrial data) can be stored in chemically synthesized DNA libraries. However, DNA is subject to biological constraints, and its molecular structure cannot be easily varied to match technological needs. In fact, DNA is not the only macromolecule that enables data storage. In recent years, it has been demonstrated that a wide variety of synthetic polymers can also be used for such a purpose. Indeed, modern polymer synthesis allows the preparation of synthetic macromolecules with precisely controlled monomer sequences. Altogether, about a dozens of synthetic digital polymers have already been described, and many more can be foreseen. Among them, sequence-defined poly(phosphodiester)s are one of the most promising options. These polymers are prepared by stepwise phosphoramidite chemistry like chemically synthesized oligonucleotides. However, they are constructed with non-natural building blocks and therefore share almost no structural characteristics with nucleic acids, except phosphate repeat units. Still, they contain readable digital messages that can be deciphered by nanopore sequencing or mass spectrometry sequencing. In this Account, we describe our recent research efforts in synthesizing and sequencing optimal abiological digital poly(phosphodiester)s. A major advantage of these polymers over DNA is that their molecular structure can easily be varied to tune their properties. During the last 5 years, we have engineered the molecular structure of these polymers to adjust crucial parameters such as the storage density, storage capacity, erasability, and readability. Consequently, high-capacity PPDE chains, containing hundreds of bits per chains, can now be synthesized and efficiently sequenced using a routine mass spectrometer. Furthermore, sequencing data can be automatically decrypted with the help of decoding software. This new type of coded matter can also be edited using practical physical triggers such as light and organized in space by programmed self-assembly. All of these recent improvements are summarized and discussed herein.

Precisely Defined Aptamer-b-Poly(phosphodiester) Conjugates Prepared by Phosphoramidite Polymer Chemistry.

Uniform conjugates combining a DNA aptamer (either anti-MUC1 or ATP aptamer) and a synthetic polymer segment were synthesized by automated phosphoramidite chemistry. This multistep growth polymer chemistry enables the use of both natural (i.e., nucleoside phosphoramidites) and non-natural monomers (e.g., alkyl- and oligo(ethylene glycol)-phosphoramidites). Thus, in the present work, six different aptamer-polymer conjugates were synthesized and characterized by ion-exchange HPLC, circular dichroism spectroscopy, and electrospray mass spectrometry. All these methods evidenced the formation of uniform molecules with precisely controlled chain-length and monomer sequences. Furthermore, aptamer folding was not affected by polymer bioconjugation. The method described herein is straightforward and allows covalent attachment of homopolymers and copolymers to biofunctional DNA aptamers.

Guest Exchange by a Partial Energy Ratchet in Water.

Molecular machines are ubiquitous in nature and function away from equilibrium by consuming fuels to produce appropriate work. Chemists have recently excelled at mimicking the fantastic job performed by natural molecular machines with synthetic systems soluble in organic solvents. In efforts toward analogous systems working in water, we show that guest molecules can be exchanged in the synthetic macrocycle cucurbit[7]uril by involving kinetic traps, and in such a way as modulating energy wells and kinetic barriers using pH, light, and redox stimuli. Ditolyl-viologen can also be exchanged using the best kinetic trap and interfaced with alginate, thus affording pH-responsive blue, fluorescent hydrogels. With tunable rate and binding constants toward relevant guests, cucurbiturils may become excellent ring molecules for the construction of advanced molecular machines working in water.

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.

Using solid-state nuclear magnetic resonance to rationalize best efficiency of 2,6-dihydroxybenzoic acid over other 2,X-dihydroxybenzoic acid isomers in solvent-free matrix-assisted laser desorption/ionization of poly(ethylene glycol).

RATIONALE: Among isomers of dihydroxybenzoic acid (DHB), 2,5-DHB is often the most efficient matrix in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for a great variety of compounds. Yet, when performing solvent-free MALDI, 2,6-DHB yields better results for poly(ethylene glycol [PEG]). This intriguing feature is explored here using solid-state nuclear magnetic resonance (NMR). METHODS: Ternary mixtures were prepared by grinding 2,X-DHB (X = 3-6), poly(ethylene glycol) (Mn = 2000 g mol-1 ) and lithium fluoride (LiF) in a matrix/analyte/salt molar ratio of 50/1/10 for 16 min under a controlled atmosphere. After mixing, a few grains were applied to the MALDI target for MS analysis, whereas the major part of the ground sample was transferred into rotors to perform 13 C, 7 Li, and 19 F NMR experiments. RESULTS: Lithiated PEG chains are mainly formed with 2,6-DHB in solvent-free MALDI, but their abundance increases with 2,3-DHB and 2,4-DHB when water uptake is favored by a humid atmosphere. Solid-state NMR shows that grinding 2,6-DHB-based samples in atmospheric conditions leads to a solid phase in which the matrix, PEG, and salt molecules exhibit a high mobility compared with systems involving other 2,X-DHB isomers. This mobile environment would favor (as a solvent) LiF dissociation and best promote PEG cationization. CONCLUSIONS: Complementary data in 13 C, 7 Li, and 19 F NMR spectra are consistent with the formation of a solid phase of high mobility composed of 2,6-DHB, PEG, and the two salt components that ultimately favor the production of lithiated PEG chains.