Triazine-based sequence-defined polymers have recently been developed that are biomimetic and robust. In molecular dynamics (MD) simulations, the triazine polymers were shown to form linear nanorod foldamers through hydrogen bonding and π-π interactions. The nanorod foldamers have motifs resembling those of DNA, α-helices, and β-sheets and have potential to be useful building blocks for new macromolecules and materials. To understand the formation of nanorod foldamers, we investigate how linker structures in the middle of the triazine polymers lead to folding using MD simulations. We found that a variety of linkers can participate in folding but that specific linker structures are more favorable than others, depending on the polymer length. Folding of hexamers into well-defined nanorod foldamers was most favorable with pentanediamine and ortho-xylenediamine linkers in the center of the polymers. Foldamers with ortho-xylenediamine linkers in the center were investigated for longer polymers, i.e., octamers and decamers, using two different enhanced sampling methods, since regular MD simulations had failed to show any folding for these longer polymers. In particular, the recently developed concurrent adaptive sampling (CAS) algorithm and replica exchange molecular dynamics (REMD) were used. We found that the two enhanced sampling methods did lead to the observation of foldamers and that REMD revealed new foldamer architectures where cis-trans isomerizations had occurred. Foldamer formation, diversity, and the strengths and limitations of simulation techniques are discussed. These findings provide new insights into the diversity of foldamer architectures for a new type of biomimetic synthetic polymer.

Grate and co-workers at Pacific Northwest National Laboratory recently developed high information content triazine-based sequence-defined polymers that are robust by not having hydrolyzable bonds and can encode structure and functionality by having various side chains. Through molecular dynamics (MD) simulations, the triazine polymers have been shown to form particular sequential stacks, have stable backbone-backbone interactions through hydrogen bonding and π-π interactions, and conserve their cis/trans conformations throughout the simulation. However, we do not know the effects of having different side chains and backbone structures on the entire conformation and whether the cis or trans conformation is more stable for the triazine polymers. For this reason, we investigate the role of non-covalent interactions for different side chains and backbone structures on the conformation and assembly of triazine polymers in MD simulations. Since there is a high energy barrier associated with the cis-trans isomerization, we use replica exchange molecular dynamics (REMD) to sample various conformations of triazine hexamers. To obtain rates and intermediate conformations, we use the recently developed concurrent adaptive sampling (CAS) algorithm for dimers of triazine trimers. We found that the hydrogen bonding ability of the backbone structure is critical for the triazine polymers to self-assemble into nanorod-like structures, rather than that of the side chains, which can help researchers design more robust materials.

In our publication, 1 when producing the free energy landscapes for the replica exchange molecular dynamics (REMD) simulations, 2 the multistate Bennett acceptance ratio (MBAR), specifically the Python implementation by Shirts and Chodera, was used.3 The incorrect input file (replica-temp.xvg instead of replica-index.xvg from GROMACS4) was used for MBAR which produced an incorrect free energy landscape and an incorrect most stable conformation for each triazine hexamer and one triazine trimer. Figures 6-10 show the correct free energy landscape and the most stable conformation obtained for the trimer with S-ethyl side chains (2 hydrogen bonds and 3 trans bonds), the hexamer with S-ethyl side chains (6 hydrogen bonds and 3 trans bonds), the hexamer with amino-ethyl-sulfide side chains (4 hydrogen bonds and 6 trans bonds), the hexamer with amino-ethyl side chains (5 hydrogen bonds and 7 trans bonds), and the hexamer with amino side chains (7 hydrogen bonds and 8 trans bonds), respectively. Since the correct most stable conformation for the hexamer with amino-ethyl-sulfide side chains was also the nanorod structure but with a different number of trans bonds than previously stated (6 instead of 3), a more thorough search for nanorod structures was conducted. The nanorod structures are the same as previously stated, but three out of the four hexamers can take various numbers of hydrogen bonds and trans bonds than previously stated to form the nanorod structure. Specifically, the hexamer with amino-ethyl-sulfide side chains is the nanorod structure when it has 4 hydrogen bonds and 3-6 trans bonds; the hexamer with aminoethyl side chains is the nanorod structure when it has 4, 6 hydrogen bonds and 5, 7 trans bonds (previously stated as 6 hydrogen bonds and 6 trans bonds but should be 6 hydrogen bonds and 5 trans bonds); the hexamer with amino side chains is the nanorod structure when it has 4 hydrogen bonds and 3, 5 trans bonds or 6 hydrogen bonds and 5, 7 trans bonds. This erratum does not change the rest of the results and any of the conclusions and discussions in our publication. The correct input file (replica-temp.xvg) was used to calculate the average number of round trips in a given observation time τ= 10 ns, so the REMD simulations remain as converged simulations. (Figure Presented). In the supplementary material, the figure numbers correspond to the figures in the original article. Corrected PSE files for the triazine trimer and all of the triazine hexamers are available. The files can be viewed using Pymol.

Molecular dynamics simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules, but they are limited by the time scale barrier. That is, we may not obtain properties' efficiently because we need to run microseconds or longer simulations using femtosecond time steps. To overcome this time scale barrier, we can use the weighted ensemble (WE) method, a powerful enhanced sampling method that efficiently samples thermodynamic and kinetic properties. However, the WE method requires an appropriate partitioning of phase space into discrete macrostates, which can be problematic when we have a high-dimensional collective space or when little is known a priori about the molecular system. Hence, we developed a new WE-based method, called the "Concurrent Adaptive Sampling (CAS) algorithm," to tackle these issues. The CAS algorithm is not constrained to use only one or two collective variables, unlike most reaction coordinate-dependent methods. Instead, it can use a large number of collective variables and adaptive macrostates to enhance the sampling in the high-dimensional space. This is especially useful for systems in which we do not know what the right reaction coordinates are, in which case we can use many collective variables to sample conformations and pathways. In addition, a clustering technique based on the committor function is used to accelerate sampling the slowest process in the molecular system. In this paper, we introduce the new method and show results from two-dimensional models and bio-molecules, specifically penta-alanine and a triazine trimer.

We recently demonstrated Solvent Immersion Imprint Lithography (SIIL), a rapid benchtop microsystem prototyping technique, including polymer functionalization, imprinting and bonding. Here, we focus on the realization of planar polymer sensors using SIIL through simple solvent immersion without imprinting. We describe SIIL's impregnation characteristics, including an inherent mechanism that not only achieves practical doping concentrations, but their unexpected 2-fold enhancement compared to the immersion solution. Subsequently, we developed and characterized optical sensors for detecting molecular O₂. To this end, a substantially high dynamic range is reported, including its control through the immersion duration, a manifestation of SIIL's modularity. Overall, SIIL exhibits the potential of improving the operating characteristics of polymer sensors, while significantly accelerating their prototyping, as it requires a few seconds of processing and no need for substrates or dedicated instrumentation. These are critical for O₂ sensing as probed by way of example here, as well as any polymer permeable reactant.

Solid sampling and analysis methods, such as laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), are challenged by matrix effects and calibration difficulties. Matrix-matched standards for external calibration are seldom available and it is difficult to distribute spikes evenly into a solid matrix as internal standards. While isotopic ratios of the same element can be measured to high precision, matrix-dependent effects in the sampling and analysis process frustrate accurate quantification and elemental ratio determinations. Here we introduce a potentially general solid matrix transformation approach entailing chemical reactions in molten ammonium bifluoride (ABF) salt that enables the introduction of spikes as tracers or internal standards. Proof of principle experiments show that the decomposition of uranium ore in sealed PFA fluoropolymer vials at 230 °C yields, after cooling, new solids suitable for direct solid sampling by LA. When spikes are included in the molten salt reaction, subsequent LA-ICP-MS sampling at several spots indicate that the spikes are evenly distributed, and that U-235 tracer dramatically improves reproducibility in U-238 analysis. Precisions improved from 17% relative standard deviation for U-238 signals to 0.1% for the ratio of sample U-238 to spiked U-235, a factor of over two orders of magnitude. These results introduce the concept of solid matrix transformation (SMT) using ABF, and provide proof of principle for a new method of incorporating internal standards into a solid for LA-ICP-MS. This new approach, SMT-LA-ICP-MS, provides opportunities to improve calibration and quantification in solids based analysis. Looking forward, tracer addition to transformed solids opens up LA-based methods to analytical methodologies such as standard addition, isotope dilution, preparation of matrix-matched solid standards, external calibration, and monitoring instrument drift against external calibration standards.