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Pfaendtner, Jim

Publications and source records attributed to Pfaendtner, Jim.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Toward Computation-Guided Design of Tunable Organic-Inorganic CdS Quantum Dot Binary Superlattices

Combining the advantages of structural programmability in sequence-defined biomimetic molecules and the controllable packing geometry in nanoparticle superlattices, we demonstrate a self-assembled organic-inorganic superlattice whose structure can be altered with the slightest change in the sequence of the organic counterpart. Here, oleate-coated CdS quantum dots (QDs) form a square-packed superlattice with a 1:1 molar equivalence of a di-block amphiphilic peptoid (Nbrpe6Dig) in chloroform. In contrast, no apparent structure is observed in the organic solvent alone. Based on theoretical evidence, we show that the assembly is a binary superlattice where both the CdS QDs and the peptoids serve as building blocks and further predict a correlation between the superlattice structure and the peptoid sequence. The computationally guided prediction is validated by experiments where superlattice transformation is observed with modified peptoids. The mechanism identified in our work inspires new ways to control and tune organic-inorganic hybrid nanomaterial self-assembly.

Qi, Xin↗
DOE OSTI2024

Exploration of Tertiary Structure in Sequence-Defined Polymers Using Molecular Dynamics Simulations

Peptoids are a class of sequence-defined biomimetic polymers with peptide-like backbones and side chains located on backbone nitrogens rather than alpha carbons. These materials demonstrate a strong ability for precise control of single-chain structure, multiunit self-assembly, and macromolecular assembly through careful tuning of sequence due to the diversity of available side chains, although the driving forces behind these assemblies are often not understood. Prior experimental work has shown that linked 15mer peptoids can mimic the protein helical hairpin structure by leveraging the chirality-inducing nature of bulky side chains and hydrophobicity, but there are still gaps in our understanding of the relationship between sequence, stability, and particular secondary or tertiary structure. Here, we present a molecular dynamics (MD) study on the folding behavior of these polymers into hairpins, discussing the differences in structure from sequences with various characteristics in water and acetonitrile, and then compare the handedness preference of common helical motifs between solvents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Two-dimensional silk

Despite the promise of silk-based devices, the inherent disorder of native silk limits performance. Here, we report highly ordered two-dimensional silk fibroin (SF) films grown epitaxially on van der Waals (vdW) substrates. Using atomic force microscopy, nano–Fourier transform infrared spectroscopy, and molecular dynamics, we show that the films consist of lamellae of SF molecules that exhibit the same secondary structure as the nanocrystallites of native silk. Increasing the SF concentration results in multilayers that grow either by direct assembly of SF molecules into the lamellae or, at high concentrations, along a two-step pathway beginning with a disordered monolayer that then crystallizes. Scanning Kelvin probe measurements show that these films substantially alter the surface potential; thus, they provide a platform for silk-based electronics on vdW solids.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Chemical recycling of post-consumer polyester wastes using a tertiary amine organocatalyst

Recycling diverse waste plastics poses challenges due to complex sorting and processing, resulting in high costs and inefficiency. To tackle this, we present a metal-free catalytic sorting method for targeted deconstruction of polyester from post-consumer plastic waste, encompassing textiles, plastic mixtures, and multilayer packaging materials. This method employs N-methylpiperidine, a tertiary amine catalyst in methanol, to depolymerize polyethylene terephthalate (PET). Operating under these conditions (160°C, 1 h), we achieve 100% yields of dimethyl terephthalate and ethylene glycol. This technique also effectively breaks down other polyesters, including polylactic acid, polycarbonate, and polybutylene terephthalate, yielding high-yield monomers at relatively low temperatures. Through comprehensive nuclear magnetic resonance (NMR) analysis, we propose that N-methylpiperidine’s role is in enhancing methanol nucleophilicity and activating PET’s ester bond. Our insights advance the chemical recycling of post-consumer plastic waste, offering a potentially simple and efficient path to closing the polyester production loop.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Identifying Performance Advantaged Biobased Chemicals Utilizing Bioprivileged Molecules

Two technology areas were advanced; a) novel molecules with improved performance in the end use application of organic corrosion inhibitors and flame retardant nylon polymers and b) development of a systematic process for identifying biomass-derived molecules with improved performance in end use applications. In total 17 novel organic corrosion inhibitors were identified that had significantly better performance than the commercial reference organic corrosion inhibitor and 7 novel nylons were synthesized with improved flame retardant properties relative to standard nylon-6,6. While an end-to-end systematic process for identifying biomass-derived molecules with improved end use performance was not completed, important progress was made computational tools for mining chemical structures from the literature and databases as well as establishing reaction network generation algorithms to aid in the discovery of novel molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Thermodynamic Analysis of Silk Fibroin–Graphite Hybrid Materials and Their Morphology

Silk fibroin (SF) is a β-sheet-rich protein that is responsible for the remarkable tensile strength of silk. In addition to its mechanical properties, SF is biocompatible and biodegradable, making it an attractive candidate for use in biotic/abiotic hybrid materials. A pairing of particular interest is the use of SF with graphene-based nanomaterials (GBNs). The properties of this interface drive the formation of well-ordered nanostructures and can improve the electronic properties of the resulting hybrid. It was previously demonstrated that SF can form lamellar nanostructures in the presence of graphite; however, the equilibrium morphology and associated driving interactions are not fully understood. Here, in this study, we characterize these interactions between SF and SF lamellar with graphite using molecular dynamics (MD) simulations and umbrella sampling (US). We find that SF lamellar nanostructures have strong orientational and spatial preferences on graphite that are driven by the hydrophobic effect, destabilizing solvent–protein interactions and stabilizing protein–protein and protein–graphite interactions. Finally, we show how careful consideration of these underlying interactions can be applied to rationally modify the nanostructure morphology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Early Career Researcher Support for Foundations of Molecular Modeling and Simulation Conference

This project enabled 14 early career researchers, including graduate students and postdocs, to attend the 8th triennial conference on Foundations of Molecular Modeling and Simulation (FOMMS 2022), which took place in Delavan, WI (Lake Geneva area), from July 17 to 21, 2022. Molecular-level modeling and simulation, which serve as critical tools for advancing science and engineering in a myriad of applications, were at the forefront of discussions. These ranged from the design of new materials for various energy applications to insights into the interaction between drug molecules and protein receptors within the body.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Rational Design of Novel Biomimetic Sequence-Defined Polymers for Mineralization Applications

Silica biomineralization is a naturally occurring process, wherein organisms use proteins and other biological structures to direct the formation of complex, hierarchical nanostructures. Discovery and characterization of such proteins and their underlying mechanisms spurred significant efforts to identify routes for biomimetic mineralization that reproduce the exquisite shapes and size selectivities found in nature. A common strategy has been the use of short peptide sequences with chemistry mimicking those found in natural systems, such as the use of the silaffin-derived R5 peptide. While progress has been made using this approach, there are many limitations that have prevented breakthroughs in biomimicry. To advance our ability to use charged macromolecules for silica formation, we propose to use sequence-defined synthetic polymers known as peptoids, or N-substituted polyglycines, which present significant capability for the precise tuning of sequence and structure beyond what can often be achieved with peptides alone. This study presents a computationally predicted design of these polymers that leads to the controlled formation of silica nanomaterials. We investigate surface adsorption and the mineralization process through analysis of binding mechanisms and energetics of the R5 system. Next, we synthesized two R5-inspired peptoids and validated our prediction in the design of mineralization polymers through characterization using surface plasmon resonance and electron microscopy. Here, this computationally guided study holds great promise for designing new sequences with unprecedented control of the placement of chemical functional groups, thus allowing for further unraveling of silicification mechanisms and the eventual design of sequence-defined synthetic polymers leading to the predictive synthesis of nanostructured functional materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Role of Surface Features on the Initial Dissolution of CH 3 NH 3 PbI 3 Perovskite in Liquid Water: An Ab Initio Molecular Dynamics Study

In this study, the degradation of CH 3 NH 3 PbI 3 (MAPbI 3 ) hybrid organic inorganic perovskite (HOIP) by water has been the major issue hampering its use in commercial perovskites solar cells (PSCs) as MAPbI 3 HOIP have been known to easily degrade in the presence of water molecules. However, even though there have been numerous studies investigating this phenomenon, there is still no consensus on the mechanisms of initial stages of dissolution. Here, we attempt to consolidate differing mechanistic interpretations previously reported in the literature through the use of the first-principles constrained ab-initio molecular dynamics (AIMD) to study the mechanisms, kinetics, and thermodynamics that accompany the degradation of MAPbI 3 HOIP in liquid water. We consider not only the dissolution of the species found on the pristine MAPbI 3 HOIP surfaces, but also the dissolution from defect sites to imitate the successive degradation steps, and propose a sequence of events in the initial phase of MAPbI 3 HOIP dissolution. By comparing the dissolution free energy barrier between surface species of different surficial types, we find that the dominant dissolution mechanisms of surface species varies widely based on the specific surface features adjacent to the dissolving ion. The high sensitivity of dissolution mechanism to surface features has contributed to the many dissolution mechanisms proposed in the literature. In contrast, the dissolution free energy barriers are mainly determined by the dissolving species rather than the type of surfaces, and the type of surfaces the ions are dissolving from are inconsequential toward the dissolution free energy barrier. However, the presence of surface defects such as vacancy sites are found to significantly lower the dissolution free energy barriers. Based on the estimated dissolution free energy barriers from different types of surfaces that we investigated in this study, we proposed that the dissolution of MAPbI 3 HOIP in liquid water originates from surface defect sites that propagate laterally along the surface layer of the MAPbI 3 HOIP crystal.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Identifying Performance Advantaged Biobased Chemicals Utilizing Bioprivileged Molecules (Final Report)

Two technology areas were advanced; a) novel molecules with improved performance in the end use application of organic corrosion inhibitors and flame retardant nylon polymers and b) development of a systematic process for identifying biomass-derived molecules with improved performance in end use applications. In total 17 novel organic corrosion inhibitors were identified that had significantly better performance than the commercial reference organic corrosion inhibitor and 7 novel nylons were synthesized with improved flame retardant properties relative to standard nylon-6,6. While an end-to-end systematic process for identifying biomass-derived molecules with improved end use performance was not completed, important progress was made computational tools for mining chemical structures from the literature and databases as well as establishing reaction network generation algorithms to aid in the discovery of novel molecules.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Efficient 3D Molecular Design with an E(3) Invariant Transformer VAE

This work introduces a three-dimensional (3D) invariant graph-to-string transformer variational autoencoders (VAE) (Vagrant) for generating molecules with accurate density functional theory (DFT)-level properties. Vagrant learns to model the joint probability distribution of a 3D molecular structure and its properties by encoding molecular structures into a 3D-aware latent space. Directed navigation through this latent space implicitly optimizes the 3D structure of a molecule, and the latent embedding can be used to condition a generative transformer to predict the candidate structure as a one-dimensional (1D) sequence. Additionally, we introduce two novel sampling methods that exploit the latent characteristics of a VAE to improve performance. Here, we show that our method outperforms comparable 3D autoregressive and diffusion methods for predicting quantum chemical property values of novel molecules in terms of both sample quality and computational efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains

Peptoids are a class of highly customizable biomimetic foldamers that retain properties from both proteins and polymers. It has been shown that peptoids can adopt peptide-like secondary structures through the careful selection of sidechain chemistries, but the underlying conformational landscapes that drive these assemblies at the molecular level remain poorly understood. Given the high flexibility of the peptoid backbone, it is essential that methods applied to study peptoid secondary structure formation possess the requisite sensitivity to discriminate between structurally similar yet energetically distinct microstates. In this work, a generalizable simulation scheme is used to robustly sample the complex folding landscape of various 12mer polypeptoids, resulting in a predictive model that links sidechain chemistry with preferential assembly into one of 12 accessible backbone motifs. Using a variant of the metadynamics sampling method, four peptoid dodecamers are simulated in water: sarcosine, N-(1-phenylmethyl)glycine (Npm), (S)-N-(1-phenylethyl)glycine (Nspe), and (R)-N-(1-phenylethyl)glycine (Nrpe)–to determine the underlying entropic and energetic impacts of hydrophobic and chiral peptoid sidechains on secondary structure formation. Our results indicate that the driving forces to assemble Nrpe and Nspe sequences into polyproline type-I helices in water are found to be enthalpically driven, with small benefits from an entropic gain for isomerization and steric strain due to the presence of the chiral center. The minor entropic gains from bulky chiral sidechains in Nrpe- and Nspe-containing peptoids can be explained through increased configurational entropy in the cis state. However, overall assembly into a helix is found to be overall entropically unfavorable. Furthermore, these results highlight the importance of considering the many various competing interactions in the rational design of peptoid secondary structure building blocks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N -1-Phenylethyl Sidechains

N-substituted glycines (polypeptoids) containing chiral hydrophobic sidechains are known to fold into biomimetic alpha helices. These helix formers often produce conformationally heterogeneous structures and are difficult to characterize at a sub-nanometer resolution. Previously, peptoid N-1-phenylethyl (S)-enantiomer sidechains (Nspe) were inferred from various experiments to form right-handed helices and (R)-enantiomers (Nrpe), left-handed helices. Prior computational work for N(s/r)pe oligomers has struggled to reproduce this trend. Herein, quantum mechanics calculations and molecular dynamics simulations are used to understand the origins of this discrepancy. Results from DFT and molecular mechanics calculations on a variety of Nspe and Nrpe oligomers as a function of chain length are in agreement, showing that Nspe and Nrpe prefer left- and right-handed helices, respectively. Additional metadynamics simulations are used to study Nrpe and Nspe oligomers folding in water. These results show that the free-energy driving forces for assembly into a helical backbone configuration are very small (within ~k B T). Lastly, we compare DFT calculations for other experimentally characterized peptoid sidechains, N(r/s)sb, N(r/s)tbe, and N(r/s)npe. In this analysis, we show that peptoid sidechains determined to be more robust experimentally (tbe and npe) have helical preferences opposite the trend seen in less robust assemblies formed by N(r/s)pe and N(r/s)sb chemistries. Furthermore, the more robust tbe and nnpe favor the (S)-enantiomer to right-handed and the (R)-enantiomers to left-handed helices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Computational and Experimental Determination of the Properties, Structure, and Stability of Peptoid Nanosheets and Nanotubes

Peptoids (N-substituted glycines) are a group of highly controllable peptidomimetic polymers. Amphiphilic diblock peptoids have been engineered to assemble crystalline nanospheres, nanofibrils, nanosheets, and nanotubes with biochemical, biomedical, and bioengineering applications. The mechanical properties of peptoid nanoaggregates and their relationship to the emergent self-assembled morphologies have been relatively unexplored and are critical for the rational design of peptoid nanomaterials. In this work, we consider a family of amphiphilic diblock peptoids consisting of a prototypical tube-former (Nbrpm6Nc6, a NH 2 -capped hydrophobic block of six N-((4-bromophenyl)methyl)glycine residues conjugated to a polar NH 3 (CH 2 ) 5 CO tail), a prototypical sheet-former (Nbrpe6Nc6, where the hydrophobic block comprises six N-((4-bromophenyl)ethyl)glycine residues), and an intermediate sequence that forms mixed structures ((NbrpeNbrpm)3Nc6). We combine all-atom molecular dynamics simulations and atomic force microscopy to determine the mechanical properties of the self-assembled 2D crystalline nanosheets and relate these properties to the observed self-assembled morphologies. We find good agreement between our computational predictions and experimental measurements of Young’s modulus of crystalline nanosheets. A computational analysis of the bending modulus along the two axes of the planar crystalline nanosheets reveals bending to be more favorable along the axis in which the peptoids stack by interdigitation of the side chains compared to that in which they form columnar crystals with π-stacked side chains. Here, we construct molecular models of nanotubes of the Nbrpm6Nc6 tube-forming peptoid and predict a stability optimum in good agreement with experimental measurements. A theoretical model of nanotube stability suggests that this optimum is a free energy minimum corresponding to a “Goldilocks” tube radius at which capillary wave fluctuations in the tube wall are minimized.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Discrete Orientations of Interfacial Waters Direct Crystallization of Mica-Binding Proteins

Understanding the basis of templated molecular assembly on a solid surface requires a fundamental comprehension of both short- and long-range aqueous response to the surface under a variety of solution conditions. Herein we provide a detailed picture of how the molecular-scale response to different mica surfaces yields distinct solvent orientations that produce quasi-static directional potentials onto which macromolecules can adsorb. We connect this directionality to observed (a)symmetric epitaxial alignment of designed proteins onto these surfaces, corroborate our findings with 3D atomic force microscopy experiments, and identify slight differences in surface structure as the origin of this effect. Furthermore, our work provides a detailed picture of the intrinsic electrolyte response in the vicinity of mineral interfaces, with clear predictions for experiment, and highlights the role of solvent on the predictive assembly of hierarchical materials on mineral surfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Designing sequence-defined peptoids for fibrillar self-assembly and silicification

In the biological environment, mineral crystals exquisitely controlled by biomacromolecules often show intricate hierarchical structures and superior mechanical properties. Among these biominerals, spicules, hybrid silica/protein superstructures serving as skeletal elements in demosponges, represent an excellent example for motivating the synthesis of silica materials. Herein, by designing sequence-defined peptoids containing side chains with a strong binding to silica, we demonstrated that self-assembly of these peptoids into fiber structures enables the mimicking of both biocatalytic and templating functions of silicatein filaments for the formation of silica fibers at near-neutral pH and ambient temperature. We further showed that the presence of amino groups is significant for the nucleation of silica on self-assembled peptoid nanofibers. Molecular dynamics simulation further confirmed that having silica-binding of amino side chains is critical for self-assembled peptoid fibers in triggering silica formation. Here, we demonstrated that tuning inter-peptoid interactions by varying carboxyl and amino side chains significantly influences the assembly kinetics and final morphologies of peptoid assemblies as scaffolds for directing silica mineralization to form silica spheres, fibers, and sheets. The formation of silica shell on peptoid fibers increased the mechanical property of peptoid hydrogel materials by nearly 1000-fold, highlighting the great potential of using silicification to enhance the mechanical property of hydrogel materials for applications including tissue engineering. Since peptoids are highly robust and programmable, we expect that self-assembly of peptoids containing solid-binding side chains into hierarchical materials opens new opportunities in the design and synthesis of highly tunable scaffolds that direct the formation of composite nanomaterials.

59 BASIC BIOLOGICAL SCIENCES↗