From Sequence Definition to Structure-Property Relationships in Discrete Synthetic Macromolecules: Insights from Molecular Modeling

Inspired by the exquisite properties emerging from the sequence order in nucleic acids and proteins, researchers are increasingly considering synthetic sequence-defined macromolecules (SDMs) to reach precise functions, e.g. for catalysis, data storage, energy, and health. Although researchers develop iterative techniques permitting the synthesis of perfectly defined sequences, there is still an important gap to achieve the desired properties leading to their utilization as materials. This arises from the fact that the effect of the sequence order on the 3D structure is unknown for most current synthetic SDMs. Although the Protein Data Bank gathers hundreds of thousands of elucidated 3D structures of proteins, and many more computed (using, e.g., AlphaFold), extended information on sequence-structure relationships does not exist yet for synthetic SDMs. To tackle this problem for relatively flexible synthetic macromolecules, one can nowadays utilize the existing tools of molecular modeling simulations. In this review, we report an advanced practice to reveal the 3D structures and the interactions, through the combination of all-atom molecular dynamics simulations and network analysis applied to different types of SDMs. By combining the computational results to the experimental ones, we show the potential of this approach for an in-depth understanding of the sequence-structure-property relationships in discrete macromolecular systems, toward guiding their rational design for specific functions.

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.

Revealing the Effect of Stereocontrol on Intermolecular Interactions between Abiotic, Sequence-Defined Polyurethanes and a Ligand

The development of precision polymer synthesis has facilitated access to a diverse library of abiotic structures wherein chiral monomers are positioned at specific locations within macromolecular chains. These structures are anticipated to exhibit folding characteristics similar to those of biotic macromolecules and possess comparable functionalities. However, the extensive sequence space and numerous variables make selecting a sequence with the desired function challenging. Therefore, revealing sequence-function dependencies and developing practical tools are necessary to analyze their conformations and molecular interactions. In this study, we investigate the effect of stereochemistry, which dictates the spatial location of backbone and pendant groups, on the interaction between sequence-defined oligourethanes and bisphenol A ligands. Various methods are explored to analyze the receptor-like properties of model oligomers and the ligand. The accuracy of molecular dynamics simulations and experimental techniques is assessed to uncover the impact of discrete changes in stereochemical arrangements on the structures of the resulting complexes and their binding strengths. Detailed computational investigations providing atomistic details show that the formed complexes demonstrate significant structural diversity depending on the sequence of stereocenters, thus affecting the oligomer-ligand binding strength. Among the tested techniques, the fluorescence spectroscopy data, fitted to the Stern-Volmer equation, are consistently aligned with the calculations, thus validating the developed simulation methodology. The developed methodology opens a way to engineer the structure of sequence-defined oligomers with receptor-like functionality to explore their practical applications, e.g., as sensory materials.

Telechelic sequence-defined oligoamides: their step-economical synthesis, depolymerization and use in polymer networks

The application of sequence-defined macromolecules in material science remains largely unexplored due to their challenging, low yielding and time-consuming synthesis. This work first describes a step-economical method for synthesizing unnatural sequence-defined oligoamides through fluorenylmethyloxycarbonyl chemistry. The use of a monodisperse soluble support enables homogeneous reactions at elevated temperature (up to 65 °C), leading to rapid coupling times (<10 min) and improved synthesis protocols. Moreover, a one-pot procedure for the two involved iterative steps is demonstrated via an intermediate quenching step, eliminating the need for in-between purification. The protocol is optimized using γ-aminobutyric acid (GABA) as initial amino acid, and the unique ability of the resulting oligomers to depolymerize, with the formation of cyclic γ-butyrolactame, is evidenced. Furthermore, in order to demonstrate the versatility of the present protocol, a library of 17 unnatural amino acid monomers is synthesized, starting from the readily available GABA-derivative 4-amino-2-hydroxybutanoic acid, and then used to create multifunctional tetramers. Notably, the obtained tetramers show higher thermal stability than a similar thiolactone-based sequence-defined macromolecule, which enables its exploration within a material context. To that end, a bidirectional growth approach is proposed as a greener alternative that reduces the number of synthetic steps to obtain telechelic sequence-defined oligoamides. The latter are finally used as macromers for the preparation of polymer networks. We expect this strategy to pave the way for the further exploration of sequence-defined macromolecules in material science.

Unveiling the Configurational Landscape of Carbamate: Paving the Way for Designing Functional Sequence-Defined Polymers

Carbamate is an emerging class of a polymer backbone for constructing sequence-defined, abiotic polymers. It is expected that new functional materials can be de novo designed by controlling the primary polycarbamate sequence. While amino acids have been actively studied as building blocks for protein folding and peptide self-assembly, carbamates have not been widely investigated from this perspective. Here, we combined infrared (IR), vibrational circular dichroism (VCD), and nuclear magnetic resonance (NMR) spectroscopy with density functional theory (DFT) calculations to understand the conformation of carbamate monomer units in a nonpolar, aprotic environment (chloroform). Compared with amino acid building blocks, carbamates are more rigid, presumably due to the extended delocalization of π-electrons on the backbones. Cis configurations of the amide bond can be energetically stable in carbamates, whereas peptides often assume trans configurations at low energies. This study lays an essential foundation for future developments of carbamate-based sequence-defined polymer material design.

Macromolecular Engineering: From Precise Macromolecular Inks to 3D Printed Microstructures

Macromolecules with complex, defined structures exist in nature but rarely is this degree of control afforded in synthetic macromolecules. Sequence-defined approaches provide a solution for precise control of the primary macromolecular structure. Despite a growing interest, very few examples for applications of sequence-defined macromolecules exist. In particular, the use of sequence-defined macromolecules as printable materials remains unexplored. Herein, the rational design of precise macromolecular inks for 3D microprinting is investigated for the first time. Specifically, three printable oligomers are synthesized, consisting of eight units, either crosslinkable (C) or non-functional (B) with varied sequence (BCBCBCBC, alternating; BBCCCBB, triblock; and BBBBCCCC, block). The oligomers are printed using two-photon laser printing and characterized. It is clearly demonstrated that the macromolecular sequence, specifically the positioning of the crosslinkable group, plays a critical role in both the printability and final properties of the printed material. Thus, through precise design and printability of sequence-defined macromolecules, an exciting avenue for the next generation of functional materials for 3D printing is created.

Uniform soluble support for the large-scale synthesis of sequence-defined macromolecules

A monodisperse soluble support is used as an effective tool for the large-scale, liquid-phase synthesis of sequence-defined macromolecules. This uniform support allows for direct characterisation and leads to a single peak in mass spectrometry.

Discrete, self-immolative N-substituted oligourethanes and their use as molecular tags

The depolymerization of N-substituted oligourethanes via an intramolecular cyclization event was studied in-depth, while the applicability of these macromolecules as anti-counterfeiting tags was demonstrated by labeling a polyurethane material.