Monomer Sequence Research Articles

Large language models design sequence-defined macromolecules via evolutionary optimization

We demonstrate the ability of a large language model to perform evolutionary optimization for materials discovery. Anthropic’s Claude 3.5 model outperforms an active learning scheme with handcrafted surrogate models and an evolutionary algorithm in selecting monomer sequences to produce targeted morphologies in macromolecular self-assembly. Utilizing pre-trained language models can potentially reduce the need for hyperparameter tuning while offering new capabilities such as self-reflection. The model performs this task effectively with or without context about the task itself, but domain-specific context sometimes results in faster convergence to good solutions. Furthermore, when this context is withheld, the model infers an approximate notion of the task (e.g., calling it a protein folding problem). This work provides evidence of Claude 3.5’s ability to act as an evolutionary optimizer, a recently discovered emergent behavior of large language models, and demonstrates a practical use case in the study and design of soft materials.

Structural transitions of a semi-flexible polyampholyte.

Polyampholytes (PAs) are charged polymers composed of positively and negatively charged monomers along their backbone. The sequence of the charged monomers and the bending of the chain significantly influence the conformation and dynamical behavior of the PA. Using coarse-grained molecular dynamics simulations, we comprehensively study the structural and dynamical properties of flexible and semi-flexible PAs. The simulation results demonstrate a flexible PA chain, displaying a transition from a coil to a globule in the parameter space of the charge sequence. In addition, the behavior of the mean-square displacement (MSD), denoted as ⟨(Δr(t))2⟩, reveals distinct dynamics, specifically for the alternating and charge-segregated sequences. The MSD follows a power-law behavior, where ⟨(Δr(t))2⟩ ∼ tβ, with β ≈ 3/5 and β ≈ 1/2 for the alternating sequence and the charge-segregated sequence in the absence of hydrodynamic interactions, respectively. However, when hydrodynamic interactions are incorporated, the exponent β shifts to ∼3/5 for the charge-segregated sequence and 2/3 for the well-mixed alternating sequence. For a semi-flexible PA chain, varying the bending rigidity and electrostatic interaction strength (Γe) leads to distinct, fascinating conformational states, including globule, bundle, and torus-like conformations. We show that PAs acquire circular and hairpin-like conformations in the intermediate bending regime. The transition between various conformations is identified in terms of the shape factor estimated from the ratios of eigenvalues of the gyration tensor.

Toward Fully Controllable Monomers Sequence: Binary Organocatalyzed Polymerization from Epoxide/Aziridine/Cyclic Anhydride Monomer Mixture.

The sequence of monomers within a polymer chain plays a pivotal role in determining the physicochemical properties of the polymer. In the copolymerization of two or more monomers, the arrangement of monomers within the resulting polymer is primarily dictated by the intrinsic reactivity of the monomers. Precisely controlling the monomer sequence in copolymerization, particularly through the manipulation of catalysts, is a subject of intense interest and poses significant challenges. In this study, we report the catalyst-controlled copolymerization of epoxides, N-tosyl aziridine (TAz), and cyclic anhydrides. To achieve this, a binary catalyst system comprising a Lewis acid, triethylborane, and Brønsted base, t-BuP1, was utilized. This system was utilized to regulate the selectivity between two catalytic reactions: ring-opening alternating copolymerization (ROAC) of epoxides/cyclic anhydrides and ROAC of TAz/cyclic anhydrides. Changing the catalyst ratio made it possible to continuously modulate the resulting poly(ester-amide ester) from ABA-type real block copolymers to gradient, random-like, reversed gradient, and reversed BAB-type block-like copolymers. A range of epoxides and anhydrides was investigated, demonstrating the versatility of this polymerization system. Additionally, density functional theory calculations were conducted to enhance our mechanistic understanding of the process. This synthetic method not only provides a versatile means for producing copolymers with comparable chemical compositions but also facilitates the exploration of the intricate relationship between monomer sequences and the resultant polymer properties, offering valuable insights for advancements in polymer science.

CROSSLINK DENSITY AND ITS DISTRIBUTION IN HEAT AND OIL RESISTANT ELASTOMERS BY DOUBLE QUANTUM NUCLEAR MAGNETIC RESONANCE

ABSTRACT Double quantum (DQ) nuclear magnetic resonance (NMR) was used to characterize the crosslink density, crosslink density distribution, and defect level in a series of heat and oil resistant elastomers. A wide range of defect levels, crosslink densities, and crosslink density distributions was measured, and results depended on elastomer type and compound formulations, including the vulcanization system. The sol fraction defect level generally correlated with the concentration of added plasticizer in the formulation. The presence of polar side chains appeared to cause additional dynamic contributions to the dangling chain end fraction. The large differences in elastomer composition and rubber formulations prevented meaningful correlation of the measured crosslink densities with the low strain modulus. Fast Tikhonov regularization and log normalization fitting of the corrected DQ build-up curve was extremely useful to provide insight into the modality and widths of the crosslink density distributions. A high degree of heterogeneity of the crosslink network of heat and oil resistant elastomers was found. Crosslink density distributions were explained in terms of the polymer chain structure comprised of monomer sequencing coupled with the position of the crosslinking sites. The type of vulcanization system had a lesser effect of the nature of the crosslink density distribution. The primary polymer chain crosslinking sites may become segregated from the continuous phase due to polarity differences seen in the microstructure of oil and heat resistance elastomers. The development of such micromorphologies can favor curative partitioning. The sole use of DQ NMR can provide valuable insight into the nature of the polymer chain structure and crosslink network in rubber.

A novel model for tracking copolymerization kinetics: Sequence structure quality evaluation

AbstractPrecise control over sequence structure in copolymers is essential for chemical product engineering. The complexity of sequence structures results in the challenging characterization of monomer sequences. Herein, a chemical composition model (CD model) is developed to record the distribution density of monomers in the chain segment, where the deviation of the chemical composition function between a copolymer and its ideal sequence structure can directly map the sequence structure quality. The application of the CD model in randomly generated virtual copolymers demonstrates that the model has great sensitivity and discrimination to evaluate sequence structures accurately. Furthermore, the CD model is combined with the kinetic Monte Carlo algorithm to explicitly track the evolution of sequence structure quality in the copolymerization process. The CD model provides an insight into the evolution of sequence structure, which is conducive to building the bridge between molecular structure and properties for the development of chemical product engineering.

Exo-chirality of the α-helix

The structure of helical polymers is dictated by the molecular chirality of their monomer units. Particularly, macromolecular helices with monomer sequence control have the potential to generate chiral topologies. In α-helical folded peptides, the sequential repetition of amino acids generates a chiral layer defined by the amino acid side chains projected outside the amide backbone. Despite being closely related to peptides’ structural and functional properties, to the best of our knowledge, a general exo-helical symmetry model has not been yet described for the α-helix. Here, we perform the theoretical, computational, and spectroscopic elucidation of the α-helix principal exo-helical topologies. Non-canonical labeled amino acids are employed to spectroscopically characterize the different exo-helical topologies in solution, which precisely match the theorical prediction. Backbone-to-chromophore distance also shows the expected impact in the exo-helices’ geometry and spectroscopic fingerprint. Theoretical prediction and spectroscopic validation of this exo-helical topological model provides robust experimental evidence of the chiral potential on the surface of helical peptides and outlines an entirely new structural scenario for the α-helix.

Sequence of Monomers and Position of Stereocenters Matter for Thermal Properties of Stereocontrolled Oligourethanes.

Polyurethanes are commodity materials used for multiple applications. In recent years, a new category of polyurethane material has emerged, characterized by the lack of polymer molar mass dispersity, control of the monomer arrangement in the chain, and even full stereocontrol. Various multistep synthesis strategies have been developed to fabricate sequence-defined polyurethanes. However, synthesizing stereocontrolled polyurethanes with a controlled sequence is still a challenge. Polyurethanes with structural precision, as represented by biopolymers, i. e. proteins or nucleic acids, have opened new application directions for these groups of materials. It has been shown that polyurethanes can be used as biomimetics, information carriers, molecular tags, and materials with strictly controlled properties. Precise synthesis of macromolecules allows us to fine-tune the properties of polymers to specific needs. Therefore, it is essential to collect information on the sequence-structure relationship of polymers. In our work, we present synthetic pathways to make sequence and stereo-defined oligourethanes. We demonstrate that structural details, i. e., the monomer sequences and position of the stereocenter, have a tremendous effect on the thermal properties of model oligourethanes. We show that the introduction of chirality by constitutional isomerization can be used to program the thermal characteristics of polymers, which are key features for material applications.

Sequence-encoded bioactive protein-multiblock polymer conjugates via quantitative one-pot iterative living polymerization

Protein therapeutics are essential in treating various diseases, but their inherent biological instability and short circulatory half-lives in vivo pose challenges. Herein, a quantitative one-pot iterative living polymerization technique is reported towards precision control over the molecular structure and monomer sequence of protein-polymer conjugates, aiming to maximize physicochemical properties and biological functions of proteins. Using this quantitative one-pot iterative living polymerization technique, we successfully develop a series of sequence-controlled protein-multiblock polymer conjugates, enhancing their biostability, pharmacokinetics, cellular uptake, and in vivo biodistribution. All-atom molecular dynamics simulations are performed to disclose the definite sequence-function relationship of the bioconjugates, further demonstrating their sequence-encoded cellular uptake behavior and in vivo biodistribution in mice. Overall, this work provides a robust approach for creating precision protein-polymer conjugates with defined sequences and advanced functions as a promising candidate in disease treatment.

Advanced Synthesis, Structural Characterization, and Functional Applications of Precision Polymers.

In the realm of biological macromolecules, entities such as nucleic acids and proteins are distinguished by their homochirality, consistently defined chain lengths, and integral sequence-dependent functionalities. Historically, these refined attributes have eluded traditional synthetic polymers, which often exhibit wide variabilities in chain lengths, limited batch-to-batch reproducibility, and stochastic monomer arrangements. Bridging this divide represents a pivotal challenge within the domain of polymer science - a challenge that the burgeoning discipline of precision polymer chemistry is poised to address. Recent advancements have yielded precision polymers that boast prescribed monomer sequences and narrow molecular weight distributions, heralding a new era for developing model systems to decipher structure-property correlations within functional polymers, analogous to those within biological matrices. This review discusses the innovative liquid-phase and solid-phase synthesis techniques for creating precision polymers and the advanced characterization tools essential for dissecting their structure and properties. We highlight potential applications in self-assembly, catalysis, data storage, imaging, and therapy, and provide insights into the future challenges and directions of precision polymers.

Polypeptoid Monomer Sequence and Chemical Composition as Independent Controls of Interfacial Tension and Elasticity at Air/Fluid Interfaces.

We use sequence-specific polypeptoids to characterize the impact of the monomer sequence on the adsorption of surface-active polymers at fluid/fluid interfaces. Sets of 36 repeat unit polypeptoids with identical chemical composition, but different sequences of hydrophobic moieties along the oligomer chain (taper, inverse taper, blocky, and evenly distributed), are designed and characterized at air/water interfaces. Polypeptoids are driven to the interfaces by decreasing the solvent quality of the aqueous solution. In situ processing of the adsorbed layers causes a collapse of polypeptoids and the formation of irreversibly adsorbed, solvent-avoiding layers at interfaces. Differences in thermodynamic properties, driven by solubility, between the collapsed structures at interfaces are studied with measurements of interfacial tension. The dilatational modulus of polypeptoid-coated interfaces is used as a proxy to probe the extent of the coil-globule collapse at the interface. The role of hydrophobicity is investigated by comparing four sequences of polypeptoids with an increased size of the hydrophilic side chains. In each set of polypeptoids, the composition of molecules, not the sequence, controls the surface concentration. The molecules are described in terms of the distribution of the hydrophobic monomers on the backbone of the polymer. Inverse taper (IT) and blocky (B) sequences of hydrophobic moieties favor the formation of highly elastic interfaces after processing, while taper (T) and distributed (D) showed lower elasticity after processing, which is achieved by replacing good solvent with poor solvent and then nonsolvent. These structures allow for the study of the impact of the chemical composition and sequence of monomers on the properties of polymer-coated interfaces.

Expression, characterization, and application of human-like recombinant gelatin

Gelatin is a product obtained through partial hydrolysis and thermal denaturation of collagen, belonging to natural biopeptides. With irreplaceable biological functions in the field of biomedical science and tissue engineering, it has been widely applied. The amino acid sequence of recombinant human-like gelatin was constructed through a newly designed hexamer composed of six protein monomer sequences in series, with the minimum repeating unit being the characteristic Gly-X-Y sequence found in type III human collagen α1 chain. The nucleotide sequence was subsequently inserted into the genome of Pichia pastoris to enable soluble secretion expression of recombinant gelatin. At the shake flask fermentation level, the yield of recombinant gelatin is up to 0.057 g/L, and its purity can rise up to 95% through affinity purification. It was confirmed in the molecular weight determination and amino acid analysis that the amino acid composition of the obtained recombinant gelatin is identical to that of the theoretically designed. Furthermore, scanning electron microscopy revealed that the freeze-dried recombinant gelatin hydrogel exhibited a porous structure. After culturing cells continuously within these gelatin microspheres for two days followed by fluorescence staining and observation through confocal laser scanning microscopy, it was observed that cells clustered together within the gelatin matrix, exhibiting three-dimensional growth characteristics while maintaining good viability. This research presents promising prospects for developing recombinant gelatin as a biomedical material.

Modulating the Thermoresponsive Characteristics of PLGA-PEG-PLGA Hydrogels via Manipulation of PLGA Monomer Sequences.

Hydrogels are promising materials for biomedical applications, particularly in drug delivery and tissue engineering. This study highlights thermoresponsive hydrogels, specifically poly(lactic-co-glycolic acid) (PLGA)-poly(ethylene glycol) (PEG)-PLGA triblock copolymers, and introduces a feed rate-controlled polymerization (FRCP) method. By utilizing an organic catalyst and regulating the monomer feed rate, the sequence distribution of PLGA within the triblock copolymer is controlled. Various analyses, including 13C NMR and rheological measurements, were conducted to investigate the impact of sequence distribution. Results show that altering sequence distribution significantly influences the sol-gel transition, hydrophobicity-hydrophilicity balance, and drug release profile. Increased sequence uniformity lowers the glass transition temperature, raises the sol-gel transition temperature due to enhanced hydrophilicity, and promotes a more uniform drug (curcumin) distribution within the PLGA domain, resulting in a slower release rate. This study emphasizes the importance of PLGA sequence distribution in biomedical applications and the potential of FRCP to tailor thermoresponsive hydrogels for biomedical advancements.

Monomer sequence segregation in the liquid crystalline phase of thermotropic copolyester amide. In-situ X-ray scattering

In-situ wide-angle X-ray scattering of a sheared thermotropic random copolyester amide revealed monomeric sequence segregation in the liquid crystalline phase. The copolyester amide is based on 60 mol% 2,6-hydroxynaphthoic acid, 20 mol% terephthalic acid and 20 mol% amino phenol (designated N-T-AP). The solid phase exhibits unusual crystallinity and the fiber X-ray diffraction exhibits aperiodic meridional reflections consistent with sequence segregation along the chain. In the liquid crystalline phase at 305 °C polarized optical microscopy showed a “worm” texture, and X-ray scattering showed an amorphous halo denoting no preferred macromolecular orientation. Upon application of shear the X-ray pattern became anisotropic with an increase of intensity on the equatorial axis consistent with the macromolecules being aligned along the flow axis. Strikingly, the X-ray pattern also exhibited a meridional reflection in the melt indicative of spatial monomer register along chains axes. Increasing the shear rate increased the equatorial intensity and reduced the azimuthal spread of the meridional reflection corresponding to an increase of longitudinal monomer register. The monomer register was preserved over a range of temperatures and upon quenching the polymer under shear. Therefore, the unusual crystallinity in solid state would be explained by the existence of monomer sequence segregation already present in the melt.

Effect of Different Monomer Sequence of Polyacrylate Copolymers with Coumarin Moieties on their Photodimerization Reaction

Effect of Different Monomer Sequence of Polyacrylate Copolymers with Coumarin Moieties on their Photodimerization Reaction

Metal-Free, Photoinitiated Cationic Terpolymerization of Vinyl Ethers, Oxiranes, and Ketones: Simultaneous Control of Monomer Sequence and Molecular Weight by the Formation of Long-Lived Propagating Species

Metal-Free, Photoinitiated Cationic Terpolymerization of Vinyl Ethers, Oxiranes, and Ketones: Simultaneous Control of Monomer Sequence and Molecular Weight by the Formation of Long-Lived Propagating Species

Synthesis and characterization of statistical and block copolymers of n‐hexyl isocyanate and 2‐chloroethyl isocyanate via coordination polymerization

AbstractStatistical and block copolymers of n‐hexyl isocyanate (HIC) and 2‐chloroethyl isocyanate (ClEtIC) were synthesized via cοοrdination polymerization employing the half‐titanocene complex [(η5‐C5H5)((S)‐2‐Bu‐O)TiCl2] as initiator. The complex, bearing a chiral substituent, led to optically active products, as confirmed by circular dichroism measurements. The molecular characterization of all products was carried out by NMR and IR spectroscopy and size exclusion chromatography (SEC), while their thermal stability was investigated through differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), and differential thermogravimetry (DTG). The reactivity ratios of the two monomers were determined using various graphical methods, as well as the COPOINT program, according to the terminal copolymerization model. Structural parameters, such as the dyad monomer sequences and the mean sequence lengths were calculated as well. In addition, the kinetics of the thermal degradation of the statistical copolymers was studied, and the activation energies of the thermal degradation were calculated employing the Kissinger, Ozawa–Flynn–Wall (OFW), and Kissinger–Akahira–Sunose (KAS) methods. The block copolymers were synthesized by sequential addition of monomers starting from the polymerization of HIC. Well‐defined products were obtained in a controlled way as revealed by SEC, IR, and NMR measurements.

Nanopatterned Monolayers of Bioinspired, Sequence-Defined Polypeptoid Brushes for Semiconductor/Bio Interfaces.

The ability to control and manipulate semiconductor/bio interfaces is essential to enable biological nanofabrication pathways and bioelectronic devices. Traditional surface functionalization methods, such as self-assembled monolayers (SAMs), provide limited customization for these interfaces. Polymer brushes offer a wider range of chemistries, but choices that maintain compatibility with both lithographic patterning and biological systems are scarce. Here, we developed a class of bioinspired, sequence-defined polymers, i.e., polypeptoids, as tailored polymer brushes for surface modification of semiconductor substrates. Polypeptoids featuring a terminal hydroxyl (-OH) group are designed and synthesized for efficient melt grafting onto the native oxide layer of Si substrates, forming ultrathin (∼1 nm) monolayers. By programming monomer chemistry, our polypeptoid brush platform offers versatile surface modification, including adjustments to surface energy, passivation, preferential biomolecule attachment, and specific biomolecule binding. Importantly, the polypeptoid brush monolayers remain compatible with electron-beam lithographic patterning and retain their chemical characteristics even under harsh lithographic conditions. Electron-beam lithography is used over polypeptoid brushes to generate highly precise, binary nanoscale patterns with localized functionality for the selective immobilization (or passivation) of biomacromolecules, such as DNA origami or streptavidin, onto addressable arrays. This surface modification strategy with bioinspired, sequence-defined polypeptoid brushes enables monomer-level control over surface properties with a large parameter space of monomer chemistry and sequence and therefore is a highly versatile platform to precisely engineer semiconductor/bio interfaces for bioelectronics applications.

Dynamic Interfaces in Self-Healable Polymers.

It is well-established that interfaces play critical roles in biological and synthetic processes. Aside from significant practical applications, the most accessible and measurable quantity is interfacial tension, which represents a measure of the energy required to create or rejoin two surfaces. Owing to the fact that interfacial processes are critical in polymeric materials, this review outlines recent advances in dynamic interfacial processes involving physics and chemistry targeting self-healing. Entropic interfacial energies stored during damage participate in the recovery, and self-healing depends upon copolymer composition and monomer sequence, monomer molar ratios, molecular weight, and polymer dispersity. These properties ultimately impact chain flexibility, shape-memory recovery, and interfacial interactions. Self-healing is a localized process with global implications on mechanical and other properties. Selected examples driven by interfacial flow and shape memory effects are discussed in the context of covalent and supramolecular rebonding targeting self-healable materials development.

Control over Conformational Landscapes of Polypeptoids by Monomer Sequence Patterning

Control over Conformational Landscapes of Polypeptoids by Monomer Sequence Patterning

Cyclic and Linear Tetrablock Copolymers Synthesized at Speed and Scale by Lewis Pair Polymerization of a One-Pot (Meth)acrylic Mixture and Characterized at Multiple Levels.

Cyclic block copolymers (cBCP) are fundamentally intriguing materials, but their synthetic challenges that demand precision in controlling both the monomer sequence and polymer topology limit access to AB and ABC block architectures. Here, we show that cyclic ABAB tetra-BCPs (cABAB) and their linear counterpart (lABAB) can be readily obtained at a speed and scale from one-pot (meth)acrylic monomer mixtures, through coupling the Lewis pair polymerization's unique compounded-sequence control with its precision in topology control. This approach achieves fast (<15 min) and quantitative (>99%) conversion to tetra-BCPs of predesignated linear or cyclic topology at scale (40 g) in a one-pot procedure, precluding the needs for repeated chain extensions, stoichiometric addition steps, dilute conditions, and postsynthetic modifications, and/or postsynthetic ring-closure steps. The resulting lABAB and cABAB have essentially identical molecular weights (Mn = 165-168 kg mol-1) and block degrees/symmetry, allowing for direct behavioral comparisons in solution (hydrodynamic volume, intrinsic viscosity, elution time, and refractive indices), bulk (thermal transitions), and film (thermomechanical and rheometric properties and X-ray scattering patterns) states. To further the morphological characterizations, allylic side-chain functionality is exploited via the thiol-ene click chemistry to install crystalline octadecane side chains and promote phase separation between the A and B blocks, allowing visualization of microdomain formation.