Monomer Backbone Research Articles

Unified understanding of the impact of semiflexibility, concentration, and molecular weight on macromolecular-scale ring diffusion

Conformationally fluctuating, globally compact macromolecules such as polymeric rings, single-chain nanoparticles, microgels, and many-arm stars display complex dynamic behaviors due to their rich topological structure and intermolecular organization. Synthetic rings are hybrid objects with conformations that display both ideal random walk and compact globular features, which can serve as models of genomic DNA. To date, emphasis has been placed on the effect of ring molecular weight on their unusual behaviors. Here, we combine simulations and a microscopic force-level theory to build a unified understanding for how key aspects of ring dynamics depend on different tunable molecular properties including backbone rigidity, monomer concentration, degree of traditional entanglement, and molecular weight. Our large-scale molecular dynamics simulations of ring melts with very different backbone stiffnesses reveal unanticipated behaviors which agree well with our generalized theory. This includes a universal master curve for center-of-mass diffusion constants as a function of molecular weight scaled by a chemistry and thermodynamic state-dependent critical molecular weight that generalizes the concept of an entanglement cross-over for linear chains. The key physics is how backbone rigidity and monomer concentration induced changes of the entanglement length, interring packing, degree of interpenetration, and liquid compressibility slow down space-time dynamic-force correlations on macromolecular scales. A power law decay of the center-of-mass diffusion constant with inverse molecular weight squared is the first consequence, followed by an ultraslow activated hopping transport regime. Our results set the stage to address slow dynamics and kinetic arrest in different families of compact synthetic and biological polymeric systems.

Functionalised carbon nanotube thin film nanocomposite membranes: A comparison study on the role of backbone monomers and hydraulic pressure on membrane's performance and fouling

Thin film nanocomposite (TFN) reverse osmosis (RO) and nanofiltration (NF) membranes have attracted considerable attention for industrial applications in recent years. Among recent nanomaterials used in the fabrication of TFN membranes, carbon nanotubes (CNTs) have gained significant interest due to their unique structure (e.g., tubular shape, mechanical strength, porosity, etc.). Here, the effects of multi-walled carbon nanotubes (MWCNTs) with different functional groups as one of the well proven nanchannel structures and their interaction with two typical monomers, MPD and PIP, were thoroughly investigated. All fabricated membranes were analysed using SEM, FTIR, AFM and contact angle analyzer. Pressure variation significantly affected the performance of membranes over 24 hours of testing. The membranes incorporated with polypyrrole (PPy) modified MWCNTs showed promising results with nearly 37 % and 99 % water flux improvement for the TFN-RO and NF membranes, respectively, compared to the bare (unmodified) TFC RO/NF membranes. Specifically, the water flux of the RO OX-MWCNTs-PPy membrane increased from 18.9 to 25.5 L.m−2.h−1, while the NF OX-MWCNTs-PPy membrane's water flux rose from 45.2 to 90.1 L.m−2.h−1. The salt rejection of RO and NF remained relatively high, with over 90 % salt rejection against NaCl and Na2SO4 for RO and NF membranes. The NF OX-MWCNTs-PPy membrane exhibited a 98.2 % rejection rate for Na2SO4, and the RO OX-MWCNTs-PPy membrane showed around a 98.8 % rejection rate for NaCl. The TFN membranes showed less fouling tendency compared to the TFC membranes. In general, the integration of MWCNTs with various functional groups significantly enhanced the water flux and salt rejection properties of these membranes. Specifically, the modified membranes showed considerable improvements in water flux and maintained high salt rejection rates. Additionally, the interaction between MWCNTs and PIP monomers in TFN-NF membranes exhibited a stronger affinity compared to MPD monomers in TFN-RO membranes, indicating a more promising performance for NF applications. The findings suggest that TFN-NF membranes incorporating MWCNTs hold great promise for future industrial use, offering enhanced performance and reduced fouling rates.

Challenges in photocatalysis using covalent organic frameworks

Photocatalysis is an attractive, energy-efficient technology for organic transformations, polymer synthesis, and degradation of environmental pollutants. There is a need for new photocatalysts stable in different media and that can be tailored for specific applications. Covalent organic frameworks (COF) are crystalline, nanoporous materials with π-conjugated backbone monomers, representing versatile platforms as heterogeneous, metal-free photocatalysts. The backbone structure can be tailored to achieve desired photocatalytic properties, side-chains can mediate adsorption, and the nanoporous structure provides large surface area for molecular adsorption. While these properties make COFs attractive as photocatalysts, several fundamental questions remain regarding mechanisms for different photocatalytic transformations, reactant transport into porous COF structures, and both structural and chemical stability in various environments. In this perspective, we provide a brief overview of COF photocatalysts and identify challenges that should be addressed in future research seeking to employ COFs as photocatalysts. We close with an outlook and perspective on future research directions in the area of COF photocatalysts.

Strengthening Near‐Infrared Photon Harvesting in Semi‐Transparent All‐Polymer Solar Cells through the Synergy of Fluorination on the Selenide Monomer Backbone

AbstractAll‐polymer solar cells (all‐PSCs) offer promising potential for large‐scale manufacturing due to their remarkable mechanical and thermal stability. However, the limited capacity of polymer acceptors for near‐infrared (NIR) photon harvesting has impeded their progress in semi‐transparent (ST) all‐PSCs. Here, the study develops a pair of new NIR polymer acceptors, named PYSeF‐T and PYSe2F‐T, with mono‐/di‐fluorinated end groups capped to the selenide monomer backbone, respectively. Owing to the stronger intermolecular interaction and intramolecular charge transfer effect of the di‐fluorinated end groups with the selenide backbone, PYSe2F‐T exhibits a stronger crystallinity and a more bathochromic absorption to 1000 nm. When blended with the donor, PM6, the PY2SeF‐T‐based all‐PSC demonstrates a higher efficiency of 16.73% with a remarkable short‐circuit current (JSC) of 27.7 mA cm−2, which is the highest JSC for all‐PSCs. Based on these, the ST device based on PM6:PYSe2F‐T demonstrates a superior efficiency of 12.52% with an average visible transmittance of 26.2% and a light utilization efficiency of 3.28%, outperforming the mono‐fluorinated counterpart. The work provides an in‐depth understanding of the above synergistic effects to develop NIR polymer acceptors and establishes a solid foundation for future investigations into large‐area and flexible ST all‐PSCs.

Incorporation of Multiple β2-Hydroxy Acids into a Protein In Vivo Using an Orthogonal Aminoacyl-tRNA Synthetase.

The programmed synthesis of sequence-defined biomaterials whose monomer backbones diverge from those of canonical α-amino acids represents the next frontier in protein and biomaterial evolution. Such next-generation molecules provide otherwise nonexistent opportunities to develop improved biologic therapies, bioremediation tools, and biodegradable plastic-like materials. One monomer family of particular interest for biomaterials includes β-hydroxy acids. Many natural products contain isolated β-hydroxy acid monomers, and polymers of β-hydroxy acids (β-esters) are found in polyhydroxyalkanoate (PHA) polyesters under development as bioplastics and drug encapsulation/delivery systems. Here we report that β2-hydroxy acids possessing both (R) and (S) absolute configuration are substrates for pyrrolysyl-tRNA synthetase (PylRS) enzymes in vitro and that (S)-β2-hydroxy acids are substrates in cellulo. Using the orthogonal MaPylRS/MatRNAPyl synthetase/tRNA pair, in conjunction with wild-type E. coli ribosomes and EF-Tu, we report the cellular synthesis of model proteins containing two (S)-β2-hydroxy acid residues at internal positions. Metadynamics simulations provide a rationale for the observed preference for the (S)-β2-hydroxy acid and provide mechanistic insights that inform future engineering efforts. As far as we know, this finding represents the first example of an orthogonal synthetase that acylates tRNA with a β2-hydroxy acid substrate and the first example of a protein hetero-oligomer containing multiple expanded-backbone monomers produced in cellulo.

All-Atom Molecular Dynamics Simulations of Uncharged Linear Polymer Bottlebrushes: Effect of the Brush Sizes and the Number of Side-Chain Monomers.

Bottlebrush polymers (BBPs), characterized by grafted polymer side chains on linear backbone polymer chain, have emerged as a unique and versatile class of macromolecules with extensive applications in the fields of material science, electronics, battery materials, self-healing technology, etc. In this paper, we employ all-atom molecular dynamics (MD) simulations to present a comprehensive study of poly(methyl methacrylate)-g-poly(2-ethyl-2-oxazoline) (PMMA-g-PEtOx) BBP and its structural and hydration properties for varying number of backbone monomers (NBB) and side chain monomers (NSC), as well as properties of water molecules supported by the BBP. We find that the radius of gyration follows a scaling of Rg ∼NSC0.36 for smaller grafts and Rg ∼ NSC0.52-0.58 for longer grafts. We also find that the overall shape of the bottlebrush goes from a rod to sphere-like shape with the increase in NSC. Both the hydration per side chain monomer and hydrogen bonds (HBs) per oxygen and nitrogen of the side chain monomer reduce with an increase in NSC, caused by a corresponding enhancement in localization of the side chain monomers in the interior of the BBP. Furthermore, steric influences ensure the number of water-oxygen HBs is much more than the number of water-nitrogen HBs (with oxygen and nitrogen atoms belonging to the monomer side chains). Also, the BBP-supported water molecules demonstrate two distinctly ordered domains with one more structured and one less structured. The more structured domain disappears with an increase in NSC that causes more side chain monomers to localize in the interior of the BBPs. Finally, we observe that despite the highly negative partial charges of the oxygen and nitrogen atoms (of the side chain monomers), the dipole orientation distributions of water molecules around these atoms exhibit the presence of a neutral environment rather than an anionic environment. Overall, we anticipate that our study will generate significant interest in probing the various BBP systems in greater atomistic detail.

Impact of Protein Corona Formation on the Thermoresponsive Behavior of Acrylamide-Based Nanogels.

The ability to fine-tune the volume phase transition temperature (VPTT) of thermoresponsive nanoparticles is essential to their successful application in drug delivery. The rational design of these materials is limited by our understanding of the impact that nanoparticle-protein interactions have on their thermoresponsive behavior. In this work, we demonstrate how the formation of protein corona impacts the transition temperature values of acrylamide-based nanogels and their reversibility characteristics, in the presence of lysozyme, given its relevance for the ocular and intranasal administration route. Nanogels were synthesized with N-isopropylacrylamide or N-n-propylacrylamide as backbone monomers, methylenebis(acrylamide) (2.5-20 molar %) as a cross-linker, and functionalized with negatively charged monomers 2-acrylamido-2-methylpropanesulfonic acid, N-acryloyl-l-proline, or acrylic acid; characterization showed comparable particle diameter (c.a.10 nm), but formulation-dependent thermoresponsive properties, in the range 28-54 °C. Lysozyme was shown to form a complex with the negatively charged nanogels, lowering their VPTT values; the hydrophilic nature of the charged comonomer controlled the drop in VPTT upon complex formation, while matrix rigidity only had a small, yet significant effect. The cross-linker content was found to play a major role in determining the reversibility of the temperature-dependent transition of the complexes, with only 20 molar % cross-linked-nanogels displaying a fully reversible transition. These results demonstrate the importance of evaluating protein corona formation in the development of drug delivery systems based on thermoresponsive nanoparticles.

A novel phosphorylated hyper-crosslinked porous polymer for efficient uranium adsorption in water

As the nuclear resource industry rapidly progresses, efficient adsorbents play a vital role in separating and eliminating uranium from aqueous solutions. Herein, 9,9-dimethyl-fluorenylphosphonic acid was designed as a phosphate functional monomer and the triptycene as a rigid backbone monomer. Through the “knitting” strategy, a novel triptycene-based phosphorylated hyper-crosslinked porous polymer (TPP-DFP) was obtained by the above monomers. The resulted polymer TPP-DFP has a high BET surface area of 1397.62 m2/g with a rich porosity. The porous polymer TPP-DFP was the first time used for uranium adsorption from water and showed outstanding adsorption performance. The maximum uranium adsorption capacity of TPP-DFP was 414.26 mg/g, which was higher than that of most of other porous adsorbents. In the presence of impurity ions such as Ca2+, Mg2+, Al3+, Co2+, Ni2+, V5+, NO3−, CO32− etc., TPP-DFP exhibited high selectivity (Su up to 99%) for uranium. In addition, TPP-DFP has excellent reusability, and the removal percentage of uranium can reach more than 95% after 5 adsorption–desorption cycles. According to the XPS experiment, the mechanism of interaction between TPP-DFP and U(VI) was mainly due to the complex formed by the phosphate functional groups and U(VI). The theory DFT calculation indicated a 1:2 ratio of U(VI) and phosphate functional group on the two-distinct graft chain, which was consistent with the experimental results. Accordingly, the “knitting” polymerization technique showed potential for preparation effective adsorbents for uranium extraction from water.

Response surface methodology-based modeling and optimization of fenugreek gum-based hydrogel for efficient removal of malachite green dye

This research work describes the synthesis of a fenugreek gum (FG)-based hydrogel (FG-g-poly(AAm)) via free radical polymerization for the removal of malachite green (MG) dye from an aqueous solution. The effects of various parameters such as backbone amount, initiator, monomer, cross-linker, and solvent on the percentage swelling were investigated using a 2-level-5-factor central composite half fraction design as an experimental design for response surface methodology. The model was found to be significant with a maximum percentage swelling of 1360%. The formation of a crosslinked network was validated by FTIR, TGA, XRD, BET, and FE-SEM characterization techniques. The surface area and average pore radius of the prepared FG-g-poly(AAm) were found to be 0.695 m2/g and 18.124 Å, respectively. The synthesized FG-g-poly(AAm) hydrogel was examined for the adsorption of MG dye from an aqueous solution as a function of time, pH, adsorbent dose, initial dye concentration, and temperature. The prepared hydrogel showed a maximum sorption capacity of 585 mg/g, as confirmed by pseudo-2nd-order kinetic and Langmuir adsorption models, revealing adsorption's chemisorption nature. The positive values of ΔHo and ΔSo showed that an endothermic process accompanied the adsorption process and had an affinity for dye molecules. The synthesized hydrogel can be used as a candidate for cationic dye removal.

Early bird gets the network: The relative importance of reactivity ratios, Ψ parameter, and crosslinker level on gel formation in FRP

AbstractNetwork topology is manipulated in free‐radical copolymerization via proper selection of crosslinker type and its respective properties when paired with specific monomers. Our prior work has focused on the impact of the reduced reactivity parameter Ψ applied to a pendent vinyl, characteristic for each monomer/crosslinker pair, yet here we assess the relative importance of the comonomer reactivity ratios to see whether one factor can counterbalance the other. The traditional reactivity ratio determines when the crosslinker molecule is incorporated into the polymer backbone, while the reduced reactivity Ψ parameter relates to the efficiency of the resulting pendent side chain vinyl being utilized to form a crosslink node at some later point during the polymerization. Both factors are then contrasted with simply the overall loading of crosslinker. Either n‐butyl methacrylate (n‐BMA) or styrene (STY) was chosen as a primary backbone monomer to copolymerize with one of three crosslinkers: 1,4‐butanediol dimethacylate (BDDMA), 1,4‐butanediol diacrylate (BDDA), or divinylbenzene (DVB). Both kinetics and gel can be most dramatically boosted when a crosslinker is applied having a reactivity ratio favouring early insertion. This in turn leads to an earlier onset of gel formation, which ultimately results in greater final gel content. This amplification of both kinetics and gel can overcome an otherwise small Ψ due to crosslinker or main monomer choice. This reactivity ratio effect was further confirmed by Monte Carlo simulations. By whatever mechanism (higher Ψ, lower rA, or higher crosslinker level), earlier onset of gelation produces more gel overall and a tighter network topology.

Molecular Weight Distribution of Branched Polymers: Comparison between Monte Carlo Simulation and Flory-Stockmayer Theory.

It is challenging to predict the molecular weight distribution (MWD) for a polymer with a branched architecture, though such information will significantly benefit the design and development of branched polymers with desired properties and functions. A Monte Carlo (MC) simulation method based on the Gillespie algorithm is developed to quickly compute the MWD of branched polymers formed through step-growth polymerization, with a branched polyetherimide from two backbone monomers (4,4'-bisphenol A dianhydride and m-phenylenediamine), a chain terminator (phthalic anhydride), and a branching agent (tris[4-(4-aminophenoxy)phenyl] ethane) as an example. This polymerization involves four reactions that can be all reduced to a condensation reaction between an amine group and a carboxylic anhydride group. A comparison between the MC simulation results and the predictions of the Flory-Stockmayer theory on MWD shows that the rates of the reactions are determined by the concentrations of the functional groups on the monomers involved in each reaction. It further shows that the Flory-Stockmayer theory predicts MWD well for systems below the gel point but starts to fail for systems around or above the gel point. However, for all the systems, the MC method can be used to reliably predict MWD no matter if they are below or above the gel point. Even for a macroscopic system, a converging distribution can be quickly obtained through MC simulations on a system of only a few hundred to a few thousand monomers that have the same molar ratios as in the macroscopic system.

Unexpected Solvent Effect Leading to Interface Segregation of Single-Chain Nanoparticles in All-Polymer Nanocomposite Films upon Solvent Evaporation

In athermal all-polymer nanocomposites (all-PNCs), single-chain nanoparticles (SCNPs) are often considered to be well miscible with polymer matrixes due to their similarity in chemical compositions. However, internal cross-linking units of SCNPs must have different chemistries from the backbone monomers and, therefore, also from matrix chains. Here, we use large-scale molecular dynamics simulations to study the influence of solvent selectivity, particularly to internal cross-linkers in SCNPs, on dispersion state of SCNPs in all-PNC films upon solvent evaporation. Surprisingly, we find distinct dispersion states of SCNPs in drying films with different solvent selectivities. When the solvent is both good for cross-linkers and backbone/matrix monomers, SCNPs can be uniformly dispersed. However, when the backbone/matrix monomers have better solvophilicity than the cross-linkers and the solvophilicity of the latter is weak enough, we find segregation of SCNPs in surface regions. Such phenomena can be attributed to the intrinsic difference in the solvent density at an interface region from that in the bulk, which eventually results in the aggregation of SCNPs at the interface region where the solvent particles are much less than in the bulk. At the interface region, cross-linkers in the SCNPs will have less contact with the solvent and, therefore, less enthalpy penalty than being located in the bulk region of the film. The results demonstrate that solvent selectivity has a non-negligible effect on the structure of the composite film, which will inevitably have impacts on macroscopic properties of the film.

Charge‐Transfer Polymeric Hydrogels with Self‐Healing, Injectable, Thermosensitive, Adhesive, and Antibacterial Properties for Diabetic Wound Healing

AbstractCharge transfer (CT) complexes are self‐assembled structures with a variety of attractive properties, but little is known about their performance in the construction of polymeric hydrogels. Herein, a series of hydrogels (CT‐hydrogels) with CT complex are designed and synthesized. The CT complex, consisting of pyranine derivative (sodium 8‐((4‐vinylbenzyl)oxy)pyrene‐1,3,6‐trisulfonate, VB‐HPTS) and viologen derivative (1‐methyl‐1′‐(4‐vinylbenzyl)‐[4,4′‐bipyridine]‐1,1′‐diium chloride iodide, VB‐MV), serves as the cross‐linker, and N‐(2‐hydroxyethyl)acrylamide is used as the backbone monomer. The CT complex allows CT‐hydrogels to have rapid self‐healing property, injectability, thermosensitivity, good adhesive strength on skin, and excellent antibacterial performance against both Gram‐negative and Gram‐positive bacteria. In addition, they have good biocompatibility and long‐term stability in both ambient and aqueous environments, showing potential application as wound dressing. Their performance in diabetic wound healing displays high wound healing rate, effectively inhibits inflammatory infiltration, and promotes neovascularization as compared with commercial wound dressings. The results of this study suggest that the multifunctional CT‐hydrogels are of great value in wound healing, and show a promising future to design hydrogels with CT complexes.

Influence of the photopolymerization matrix on the indicator response of optical fiber pH sensors

Optical fiber pH sensors work by observing a change in the indicator’s optical signal caused by variations in pH and these indicators can be immobilized onto the surface of an optical fiber using a polymer matrix. How the composition of the polymer matrix changes pH detection range using the indicator (5(6)-carboxynaphthofluorescein (CNF)) has not been studied. Here we show that the composition of the polymer matrix affects the working pH ranges of optical fiber CNF sensors. We used acrylamide (AAm) or N-isopropylacrylamide (NIPAM) as the backbone monomer, and N, N’-methylenebisacrylamide (BIS) as the crosslinker for the polymer matrix. We found that AAm-based pH sensors showed rapid response over the pH range 6.6 – 8.0, while the dynamic ranges of NIPAM-based sensors shifted to basic pH compared with AAm-based pH sensors. Furthermore, we found that an increased ratio of the backbone monomer, NIPAM, over the crosslinker, BIS, significantly shifted the working range to more basic pH values, covering a pH range of 8.1 – 10.3. Our results demonstrate that the polymer matrix can be a powerful means to control the indicator response of optical pH sensors.

Hyperbranched Poly(β-amino ester)s (HPAEs) Structure Optimisation for Enhanced Gene Delivery: Non-Ideal Termination Elimination

Many polymeric gene delivery nano-vectors with hyperbranched structures have been demonstrated to be superior to their linear counterparts. The higher delivery efficacy is commonly attributed to the abundant terminal groups of branched polymers, which play critical roles in cargo entrapment, material-cell interaction, and endosome escape. Hyperbranched poly(β-amino ester)s (HPAEs) have developed as a class of safe and efficient gene delivery vectors. Although numerous research has been conducted to optimise the HPAE structure for gene delivery, the effect of the secondary amine residue on its backbone monomer, which is considered the non-ideal termination, has never been optimised. In this work, the effect of the non-ideal termination was carefully evaluated. Moreover, a series of HPAEs with only ideal terminations were synthesised by adjusting the backbone synthesis strategy to further explore the merits of hyperbranched structures. The HPAE obtained from modified synthesis methods exhibited more than twice the amounts of the ideal terminal groups compared to the conventional ones, determined by NMR. Their transfection performance enhanced significantly, where the optimal HPAE candidates developed in this study outperformed leading commercial benchmarks for DNA delivery, including Lipofectamine 3000, jetPEI, and jetOPTIMUS.

FP.02 Mutation in KBTBD13 causes stiffening of thin filaments in skeletal muscle

Nemaline myopathy is caused by mutations in genes encoding thin filament proteins. Nemaline myopathy-type 6 (NEM6) is caused by mutations in <i>KBTBD13</i>. NEM6 patients display muscle weakness and slow kinetics of muscle relaxation. Whether KBTBD13 plays a role in thin filament structure/function, and whether such role can explain the NEM6 phenotype, is incompletely understood. Therefore, we developed a KBTBD13R408C–knockin (KI) mouse model. In line with the patients' phenotype, KI mice exhibit nemaline rods and slow relaxation kinetics. We used low-angle x-ray diffraction to study whether structural changes in the myofilaments can explain the contractile phenotype of KI mice. Intact soleus and extensor digitorum longus muscles (EDL) were dissected from wt and KI mice. Low angle x-ray diffraction experiments were conducted at the BioCAT beamline, Argonne National Laboratories. Muscles were mounted between a force transducer and a fixed hook, exposed to the x-ray beam during relaxed and maximal tetanic conditions. Images were recorded with 15ms acquisition time using a Pilatus 3xM1 detector set at 1.26 meter distance from the muscle. Results show that in relaxed soleus muscles the actin monomer spacing (27A) and myosin backbone spacing (28A) are shorter in KI compared to wt mice (2.7329 vs 2.7343nm; 2.8764nm vs 2.8797nm). Upon maximal tetanic activation, which was comparable between KI and wt muscles, the 27A spacing increased less in KI compared to wt muscles, indicating increased stiffness. Upon maximal tetanic activation, the 28A spacing increased in wt muscles, but this increase was comparable to that in KI mice. EDL muscle of KI mice showed no differences in actin monomer or myosin backbone spacings. Results indicate that thin filament stiffness, but not thick filament stiffness, is increased in KI mice, and that this increase is muscle-type specific. Sarcomere modeling shows that the increased stiffness of thin filaments contributes to slow relaxation kinetics.

Evaluating the Conformations and Dynamics of Peptoid Macrocycles.

Peptoid macrocycles are versatile and chemically diverse peptidomimetic oligomers. However, the conformations and dynamics of these macrocycles have not been evaluated comprehensively and require extensive further investigation. Recent studies indicate that two degrees of freedom, and four distinct conformations, adequately describe the behavior of each monomer backbone unit in most peptoid oligomers. On the basis of this insight, we conducted molecular dynamics simulations of model macrocycles using an exhaustive set of idealized possible starting conformations. Simulations of various sizes of peptoid macrocycles yielded a limited set of populated conformations. In addition to reproducing all relevant experimentally determined conformations, the simulations accurately predicted a cyclo-octamer conformation for which we now present the first experimental observation. Sets of three adjacent dihedral angles (ϕi, ψi, ωi+1) exhibited correlated crankshaft motions over the course of simulation for peptoid macrocycles of six residues and larger. These correlated motions may occur in the form of an inversion of one amide bond and the concerted rotation of the preceding ϕ and ψ angles to their mirror-image conformation, a variation on "crankshaft flip" motions studied in polymers and peptides. The energy landscape of these peptoid macrocycles can be described as a network of conformations interconnected by transformations of individual crankshaft flips. For macrocycles of up to eight residues, our mapping of the landscape is essentially complete.

Synthesis and characterization of nitrogen-rich polybenzoxazines for energetic applications

In a vision to develop new synthetic routes for the preparation of energetic materials, two new energetic benzoxazine monomers were synthesized via a two-step Mannich reaction process involving the incorporation of nitrogen–nitrogen bonds and explosophore groups (NO2) into the monomer backbone. The molecular structures of the synthesized monomers were confirmed by 1H NMR, Fourier transform infrared and elemental analysis techniques. The curing behavior and the degradation phenomena were evaluated by differential scanning calorimetry-thermogravimetric analysis analyses. The two monomers showed two distinct exothermic peaks related to the polymerization and degradation phases. The energetic performances were evaluated by determining the heat of combustion and formation using a bomb calorimeter, in an oxygen atmosphere. The results indicated that the 2,4 dinitrophenylhydrazine–based benzoxazine has better energetic properties than the phenylsemicarbazide-based benzoxazine, and the two developed polymers showed comparable performances with nitrocellulose and glycid azide polymer. Overall, this study has demonstrated that the ease of synthesis of the benzoxazine resins via Mannich reaction can be further extended to the energetic field and further research is undergoing to fully unravel the potential of these exceptional materials.

MP-NeRF: A massively parallel method for accelerating protein structure reconstruction from internal coordinates.

The conversion of proteins between internal and cartesian coordinates is a limiting step in many pipelines, such as molecular dynamics simulations and machine learning models. This conversion is typically carried out by sequential or parallel applications of the Natural extension of Reference Frame (NeRF) algorithm. This work proposes a massively parallel NeRF implementation which, depending on the polymer length, achieves speedups between 400 and 1200× over the previous state-of-the-art. It accomplishes this by dividing the conversion into three main phases: parallel composition of the monomer backbone, assembly of backbone subunits, and parallel elongation of sidechains; and by batching these computations into a minimal number of efficient matrix operations. Special emphasis is placed on reusability and ease of use. We open source the code (available at https://github.com/EleutherAI/mp_nerf) and provide a corresponding python package.

Mannich reaction as an interesting synthetic route for the development of energetic benzoxazine polymers

In this study, three new energetic benzoxazine monomers were synthesized via a one-step Mannich reaction process involving the incorporation of explosophore nitro groups (NO2) in different positions (ortho, meta and para) into the monomer backbone. The molecular structures of the synthesized monomers were confirmed by FTIR, 1H and 13CNMR techniques. The curing behavior, thermomechanical properties and the thermal stability were assessed by DSC-TGA analyses. All monomers displayed two exothermic peaks related to the polymerization and degradation steps except 4-NBZ that present the polymerization and the degradation phenomena through one unique exotherm pic. The energetic performances were evaluated by the determination of the heat of combustion using a bomb calorimeter in an oxygen atmosphere. The results indicated that the para position provided the benzoxazine monomers with a high calorific value comparable to that of the nitrocellulose (about 10.401 kJ/g). Meanwhile, the aforementioned monomer was found to ignite at a temperature of about 267 °C. Overall, this study showed that the ease of synthesis of the benzoxazine resins via Mannich reaction can be further extended the energetic field and further researches are undergoing to fully unravel the potential of these exceptional materials.