Controlling the structure of sequence‐defined poly(phosphodiester)s for optimal MS/MS reading of digital information

Digital polymers are monodisperse chains with a controlled sequence of co‐monomers, defined as letters of an alphabet, and are used to store information at the molecular level. Reading such messages is hence a sequencing task that can be efficiently achieved by tandem mass spectrometry. To improve their readability, structure of sequence‐controlled synthetic polymers can be optimized, based on considerations regarding their fragmentation behavior. This strategy is described here for poly(phosphodiester)s, which were synthesized as monodisperse chains with more than 100 units but exhibited extremely complex dissociation spectra. In these polymers, two repeating units that differ by a simple H/CH₃ variation were defined as the 0 and 1 bit of the ASCII code and spaced by a phosphate moiety. They were readily ionized in negative ion mode electrospray but dissociated via cleavage at all phosphate bonds upon collisional activation. Although allowing a complete sequence coverage of digital poly(phosphodiester)s, this fragmentation behavior was not efficient for macromolecules with more than 50 co‐monomers, and data interpretation was very tedious. The structure of these polymers was then modified by introducing alkoxyamine linkages at appropriate location throughout the chain. A first design consisted of placing these low dissociation energy bonds between each monomeric bit: while cleavage of this sole bond greatly simplified MS/MS spectra, efficient sequencing was limited to chains with up to about 50 units. In contrast, introduction of alkoxyamine bonds between each byte (i.e. a set of eight co‐monomers) was a more successful strategy. Long messages (so far, up to 8 bytes) could be read in MS³ experiments, where single‐byte containing fragments released during the first activation stage were further dissociated for sequencing. The whole sequence of such byte‐truncated poly(phosphodiester)s could be easily re‐constructed based on a mass tagging system which permits to determine the original location of each byte in the chain. Copyright © 2017 John Wiley & Sons, Ltd.     

Kinetic analysis of the cross reaction between dithioester and alkoxyamine by a Monte Carlo simulation

A model reaction of dithioester and alkoxyamine is proposed to probe the reversible addition–fragmentation chain transfer (RAFT) process. The kinetics of the model reaction is analyzed and compared with that of pure alkoxyamine homolysis with a Monte Carlo simulation. Although the pure alkoxyamine obeys the law of persistent radical effect, the model reaction results in higher concentration of the persistent radical during the main period of the reaction. However, for a very fast RAFT process or a very low addition rate constant, the time dependence of the persistent radical concentration is quite close to that of pure alkoxyamine. Furthermore, the cross termination between the intermediate and alkyl radicals causes a retardation effect for the model reaction when the intermediate is relatively long‐lived. The Monte Carlo simulation indicates that it is feasible to measure the individual rate constants of the RAFT process, such as the rate constant of addition, with a large excess of alkoxyamine. In addition, the special feature of the system with different leaving groups in the alkoxyamine and dithioester is also discussed. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 374–387, 2007     

Preparation of poly(ethylene oxide)‐block‐poly(isoprene) by nitroxide‐mediated free radical polymerization from PEO macroinitiators

Amphiphilic poly(ethylene oxide)‐block‐poly(isoprene) (PEO‐b‐PI) diblock copolymers were prepared by nitroxide‐mediated polymerization of isoprene from alkoxyamine‐terminal poly(ethylene oxide) (PEO). PEO monomethyl ether (M_n ≈ 5200 g/mol) was functionalized by esterification with 2‐bromopropionyl bromide with subsequent copper‐mediated replacement of the terminal bromine with 2,2,5‐trimethyl‐4‐phenyl‐3‐azahexane‐3‐nitroxide. The resulting PEO‐alkoxyamine macroinitiator was used to initiate polymerization of isoprene in bulk and in solution at 125 °C to yield PEO‐b‐PI block copolymers with narrow molecular weight distributions (M_w/M_n ≤ 1.1). Polymerizations were first order in isoprene through 35% conversion. Micellar aggregates of PEO‐b‐PI in aqueous solution were crosslinked by treatment with a water‐soluble redox initiating system, and persistent micellar structures were observed in the dry state by AFM. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2977–2984, 2005     

Cyclic alkoxyamines for nitroxide‐mediated radical polymerization

A 5‐membered cyclic alkoxyamine and a 17‐membered cyclic alkoxyamine were synthesized and used in the polymerization of styrene. Polymerizations using the 5‐membered cyclic alkoxyamine resulted in polymers with uncontrolled molecular weights and high polydispersities. Polymerizations using the 17‐membered cyclic alkoxyamine produced oligomeric polymers in which multiple polymer chains are linked through NO‐C bonds. EPR homolysis experiments revealed that the 5‐membered cyclic alkoxyamine does not dissociate to form a nitroxide species, even at temperatures as high as 403 K. In contrast, the 17‐membered cyclic alkoxyamine does dissociate to form nitroxide, but the rate of dissociation is slower than that of parent acyclic alkoxyamine 2,2,5‐trimethyl‐3‐(1‐phenylethoxy)‐4‐phenyl‐3‐azahexane. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 8049–8069, 2008     

Synthesis of Poly （styrene-b-isoprene-b-styrene） via Nitroxide-mediated Radical Polymerization by a Novel Alkoxyamine

Bifunctional alkoxyamine bis-TIPNO derived from 2,2,5-trimethyl-4-phenyl-3-azahexane-3-oxyl （TIPNO） and α, ω-alkyl bromide by atom transfer radical addition（ATRA） was employed as “biradical initiator” for nitroxide-mediated radical polymerization（NMRP） of isoprene and styrene. The kinetics study for the polymerization of styrene at different time showed living features. The poly（styrene-b-isoprene-b-styrene） （SIS） copolymers have two glass transition temperatures, indicating the immiscibility of the corresponding blocks.     

Kinetic study of H‐atom transfer in imidazoline‐, imidazolidine‐, and pyrrolidine‐based alkoxyamines: Consequences for nitroxide‐mediated polymerization

The H‐atom transfer reaction was studied for a series of imidazoline, imidazolidine, and pyrrolidine‐based alkoxyamines containing either isobutyrate‐2‐yl or 1‐phenylethyl alkyl fragments. The C O bond homolysis rate constants and activation energies were determined by ¹H NMR product analysis as a function of temperature. Inter‐ and intramolecular H‐atom transfer reactions were distinguished by examination of alkoxyamine thermolysis products in the absence and in the presence of a radical scavenger (thiophenol or deuterated styrene). A correlation between the structure of the nitroxyl fragment of alkoxyamine and the H‐transfer reaction was found. The high steric demands of the substituents on the nitroxyl part of the isobutyrate‐2‐yl alkoxyamine decrease both types of reaction. For alkoxyamines containing the 1‐phenylethoxyamines, neither inter‐ nor intramolecular H‐atom transfer was observed. Controlled polymerization of methylmethacrylate initiated with imidazoline‐based alkoxyamine was observed, although the polymer obtained was not living. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 6579–6595, 2009     

End‐Group Characterization of Poly(acrylic acid) Prepared by Nitroxide‐Mediated Controlled Free‐Radical Polymerization

Summary: A low‐molar‐mass poly(acrylic acid) with a narrow molar‐mass distribution, prepared by SG1 nitroxide‐mediated controlled free‐radical polymerization, was subjected to end‐group analysis to confirm its living nature. ¹H and ³¹P NMR spectroscopy confirmed the presence of the SG1‐based alkoxyamine end group. Furthermore, chain extension with styrene and n‐butyl acrylate demonstrated the ability of the homopolymer to initiate the polymerization of a second block. These results open the door to the synthesis of poly(acrylic acid)‐based block copolymers by direct nitroxide‐mediated polymerization of acrylic acid.

Acrylic acid polymerization using an alkoxyamine initiator based on SG1 (N‐tert‐butyl‐N‐(1‐diethyl phosphono‐2,2‐dimethylpropyl) nitroxide resulting in a homopolymer capable of initiating the polymerization of a second block.     

15N NMR spectroscopy of labeled alkoxyamines. 15N-labeled model compounds for nitroxide-trapping studies in free-radical (Co)polymerization

Eight (15)N-labeled derivatives of 1-ethoxy-2,2,6,6-tetramethylpiperidine were synthesized in order to investigate the effects of their structural units on (15)N NMR spectra. A single peak is found for each alkoxyamine. The chemical shift depends extensively on the nature of the alpha carbon atom of the alkoxy group. The remote functional group attached to position 4 of the piperidine ring has a smaller but still significant effect. The results of the (15)N NMR measurements are supported by the detection of the N-H and N-C spin-spin coupling from the (1)H and (13)C NMR. The investigated alkoxyamines are model compounds for the radical-trapping products of styryl, methyl methacryloyl, alpha-methylstyryl, and methyl acryloyl radicals by (15)N-labeled nitroxides. The potential of (15)N NMR spectroscopy to analyze such products is discussed. In addition, it is shown that the (13)C chemical shifts of the alpha carbon atom of the alkoxy group fall in an empty part of the (13)C NMR spectrum, which allows the identification of trapped (macro)radicals via natural abundance (13)C NMR.     

End group effect on the thermo‐sensitive properties of well‐defined water‐soluble polystyrenics with short pendant oligo(ethylene glycol) groups synthesized by nitroxide‐mediated radical polymerization

The effects of hydrophobic chain end groups on the cloud points of thermo‐sensitive water‐soluble polystyrenics were investigated. Well‐defined poly (4‐vinylbenzyl methoxytris(oxyethylene) ether) (PTEGSt) and poly(α‐hydro‐ω‐(4‐vinylbenzyl)tetrakis(oxyethylene)) (PHTrEGSt) were prepared by nitroxide‐mediated radical polymerization using α‐hydrido alkoxyamine initiators including two monomer‐based initiators. The polymers were reduced with (n‐Bu)₃SnH to replace the alkoxyamine end group with hydrogen. In the studied molecular weight range (M_n,GPC = 3000 to 28,000 g/mol), we found that the hydrophobic end groups decreased the cloud point by 1–20 °C depending on the molecular weight and the largest depression was observed at the lowest molar mass. The cloud points of PTEGSt and PHTrEGSt with two hydrophobic end groups, phenylethyl and alkoxyamine, exhibited a monotonic increase with the increase of molecular weight. For polymers with only one hydrophobic end group, either phenylethyl or alkoxyamine, the cloud point initially increased with the increase of molecular weight but leveled off/decreased slightly with further increasing molar mass. For polymers with essentially no end groups, the cloud point decreased with the increase of chain length, which represents the “true” molecular weight dependence of the cloud point. The observed molecular weight dependences of the cloud points of polystyrenics with hydrophobic end group(s) are believed to result from the combined end group effect and “true” molecular weight effect. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 3707–3721, 2007     

The kinetics of living free-radical polymerization of styrene in the presence of alkoxyamine: Interpretation within the framework of secondary inhibition hypothesis

The kinetics of the free-radical polymerization of styrene at 120°C in the presence of alkoxyamine as a living polymerization agent has been studied. The alkoxyamine forms in situ with a 100-fold variation in the initial concentration of 2,2,6,6-tetramethyl-1-piperidinyloxy. The rate of the process at the stationary stage decreases with an increase in the initial concentration of 2,2,6,6-tetramethyl-1-piperidinyloxy. The computer simulation of the kinetic features of the process under study demonstrates that this tendency is related to the possible secondary inhibition of the process by alkoxyamine and/or hydroxylamine arising in the system in the course of polymerization.     

Nitroxide‐mediated living free‐radical polymerization of styrene: A systematic study of the variation of the alkoxyamine concentration

The effect of the variation of the alkoxyamine concentration on the conversion and polydispersity of the nitroxide‐mediated living free‐radical polymerization of styrene is discussed. Four different alkoxyamines ( 1 – 4 ) have been used for these studies. For an alkoxyamine with a small equilibrium rate constant (K), such as styryl–TEMPO 2 , the conversion is governed by the autopolymerization of styrene. For efficient alkoxyamines 1 , 3 , and 4 , the conversion at high alkoxyamine concentrations is higher than the conversion obtained by autopolymerization. At high alkoxyamine concentrations, the conversions vary to a small extent for all the alkoxyamines studied. As long as the conversion remains high, the polydispersity index is small. In addition, simulations of polymerizations with a program for modeling nonlinear dynamics are discussed. Polymerizations with efficient alkoxyamines at high alkoxyamine concentrations are well described by the kinetic scheme applied. K for alkoxyamines 1 and 4 has been estimated with the simulations. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 3342–3351, 2004     

Nitroxide mediated styrene radical polymerization using a fluorescence marked mediator

Polystyrenes containing fluorescence end-groups were prepared by nitroxide-mediated radical polymerization. Combined molar mass regulator contained besides alkoxyamine part the structure of fluorescence mark. Stable nitroxyl radical represented 2,2,6,6-tetramethylpiperidine-Noxyl and covalently bonded fluorescence mark was benzothioxanthene. A fluorescence method as well as UV absorption was employed for measuring the concentration of nitroxyl-terminated chains in polystyrene samples. Theoretical molar masses of polystyrenes were calculated from these concentrations on the assumption that all polystyrene chains are terminated by alkoxyamine dormant end-functionality bearing fluorescence probe. Comparisons of these data with the molar masses from GPC gave us the range of the marked active polymer chain ends. Fractions of active polymer chain ends depended on the conversion. With increased conversion the fraction of polystyrene chains terminated by alkoxyamine was decreased. From this follows that the “livingness” of polymerization process decreased with the increasing of conversion. It should result in higher extent of termination and subsequently in the increasing of polydispersity with increased conversion. Despite this the observed polydispersity was the same for all conversion and reached the value ca. 1.3. The changing viscosity is responsible for the constant polydispersity.     

Synthesis of NMP/RAFT inifers and preparation of block copolymers

Two different initiator/transfer agents (inifers) containing an alkoxyamine and a dithiobenzoate were synthetized and used to trigger out either reversible addition‐fragmentation chain transfer (RAFT) polymerization or nitroxide‐mediated polymerization (NMP). α‐Dithiobenzoate‐ω‐alkoxyamine‐difunctional polymers were produced in both cases which were subsequently used as precursors in the formation of block copolymers. This synthetic approach was applied to N‐isopropylacrylamide (NIPAM) or polyethylene oxide methacrylate (EOMA) to form α,ω‐heterodifunctional homopolymers via RAFT at 60°C which were chain extended with styrene by activating the alkoxyamine moiety at 120°C. Under such temperature conditions, it is proposed that a tandem NMP/RAFT polymerization is initiated producing a simultaneous growth of polystyrene blocks at both chain‐ends. Self‐assembled nanostructures of these amphiphilic block copolymers were evidenced by scanning electron microscopy. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Direct functionalization of labile alkoxyamines

Direct esterification of a labile alkoxyamine R¹R²NOR³, which was previously reported as unsuccessful, is achieved by a Mitsunobu reaction or a nucleophilic substitution. Ester derivatives are obtained under smooth conditions and easily purified. Macrocyclization attempts on ester derivatives were successful for five-membered ring lactones and unsuccessful for 13-membered ring lactones. Moreover, the success of the cyclization was dramatically dependent on the quality of the solution degassing. Poor degassing led to unexpected carbonate alkoxyamine.     

Tin-free radical alkoxyamine addition and isomerization reactions by using the persistent radical effect: variation of the alkoxyamine structure

Various C-centered radicals can efficiently be generated through thermal C-O-bond homolysis of alkoxyamines. This method is used to perform environmentally benign radical cyclization and intermolecular addition reactions. These alkoxyamine isomerizations and intermolecular carboaminoxylations are mediated by the persistent radical effect (PRE). In the paper, the effect of the variation of the alkoxyamine structure--in particular steric effects in the nitroxide moiety--on the outcome of the PRE mediated radical reactions will be discussed. Fourteen different nitroxides were used in the studies. It will be shown that reaction times can be shortened about 100 times upon careful tuning of the alkoxyamine structure. Activation energies for the C-O-bond homolysis of the various alkoxyamines are provided. The kinetic data are used to explain the reaction outcome of the PRE-mediated processes.     

A bidirectional ATRP‐NMRP initiator: The effect of nitroxide size on the rate of nitroxide‐mediated polymerization

An N‐alkoxyamine macroinitiator bearing a polymeric nitroxide cap was synthesized and used to investigate the effect of nitroxide size on the rate of nitroxide‐mediated radical polymerization (NMRP). This macroinitiator was prepared from asymmetric double‐headed initiator 9 , which contains both an α‐bromoester and an N‐alkoxyamine functionality. Poly(methyl methacrylate) was grown by atom transfer radical polymerization from the α‐bromoester end of this initiator, resulting in a macroinitiator (M_n = 31,000; PDI = 1.34) bearing a nitroxide cap permanently attached to a polymer chain. The polymerization kinetics of this macroinitiator in NMRP were compared with known N‐alkoxyamine initiator 1 . It was found that the rate of polymerization was unaffected by the size of the macromolecular nitroxide cap. It was confirmed that NMRP using this macroinitiator is a “living” process. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 2015–2025, 2007     

Kinetic study of the nitroxide‐mediated controlled free‐radical polymerization of n‐butyl acrylate in aqueous miniemulsions

The controlled free‐radical homopolymerization of n‐butyl acrylate was studied in aqueous miniemulsions at 112 and 125 °C with a low molar mass alkoxyamine unimolecular initiator and an acyclic β‐phosphonylated nitroxide mediator, N‐tert‐butyl‐N‐(1‐diethylphosphono‐2,2‐dimethylpropyl) nitroxide, also called SG1. The polymerizations led to stable latices with 20 wt % solids and were obtained with neither coagulation during synthesis nor destabilization over time. However, in contrast to latices obtained via classical free‐radical polymerization, the average particle size of the final latices was large, with broad particle size distributions. The initial [SG1]₀/[alkoxyamine]₀ molar ratio was shown to control the rate of polymerization. The fraction of SG1 released upon macroradical self‐termination was small with respect to the initial alkoxyamine concentration, indicating a very low fraction of dead chains. Average molar masses were controlled by the initial concentration of alkoxyamine and increased linearly with monomer conversion. The molar mass distribution was narrow, depending on the initial concentration of free nitroxide in the system. The initiator efficiency was lower than 1 at 112 °C but was very significantly improved when either a macroinitiator was used at 112 °C or the polymerization temperature was raised to 125 °C. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4410–4420, 2002     

Role of the alkyl fragment of initiating alkoxyamine in nitroxide mediated polymerization of styrene

The role of the alkyl fragment of alkoxyamine initiating the homopolymerization of styrene is experimentally and theoretically studied in the case of 2,2,6,6-tetramethylpiperidine-1-oxyl derivatives. The rate constants of homolysis and recombination are measured for the alkoxyamines under study. The characteristics of polymerization initiated by these compounds are experimentally examined. The kinetics of polymerization is theoretically calculated with allowance for the measured kinetic parameters and the experimentally detected side reaction of hydrogen-atom transfer to the nitroxide radical during the thermolysis of alkoxyamine 2-cyano-2-isopropyl-TEMPO.     

Factors influencing the C?ON bond strength of the alkoxyamines in the styrene–acrylonitrile–TEMPO copolymerization system

Homolytic bond dissociation energy (BDE) of the (C? ON) bond for several N‐alkoxyamines derived from 2,2,6,6‐tetramethylpiperidine‐1‐oxyl (TEMPO) and the corresponding (C? H) bonds were determined from quantum‐mechanical calculations including the B3‐LYP6‐31G(d), B3‐LYP/6‐311++G(2df,p), UB3‐LYP/6‐311+G(3df,2p), and integrated IMOMO (G3:ROMP2/6‐31G(d)) method. The investigated N‐alkoxyamines were considered as models for dormant forms of propagating chains in the radical copolymerization process of styrene with acrylonitrile in the presence of TEMPO according to the terminal and penultimate model. The substituent effect on BDE was investigated. Radical stabilization energies (RSE) for radicals created from homolysis of the investigated N‐alkoxyamines were calculated according to Rüchardt's method. Polar, steric, and stabilization effects on C? ON alkoxyamine bond homolysis were studied. A dramatically weakened C? ON bond in the alkoxyamine‐containing two consecutive styrene units in the propagating chain was ascribed to geometric parameters characterizing energetically unfavorable conformation of the substituents. These phenomena can be regarded as the penultimate effect in the radical living/controlled copolymerization system of styrene with acrylonitrile. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1165–1177, 2008     

Kinetics of Nitroxide Mediated Radical Polymerization of Styrene with Unimolecular Initiators

Summary: This study examined the kinetics of nitroxide-mediated radical polymerization of styrene with unimolecular (alkoxyamine) initiators. Control of polymerization rate and polymer molecular weight in unimolecular nitroxide-mediated radical polymerization was studied by looking at the effects of the three main factors: initiator concentration, temperature, and initiator molecular weight on polymerization rate, molecular weight and polydispersity. In addition, the behavior of the unimolecular initiating systems was compared to that of the corresponding bimolecular system. The effective TEMPO concentration and degree of self-initiation of styrene were proved to be significant in dictating magnitudes of molecular weight averages and widths of molecular weight distribution.