Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “backbone”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Spectroscopic Investigation into P(NDI2OD-T2) Charge Localization

P(NDI2OD-T2), commonly referred to as N2200, stands out as a promising electron-transporting (n-type) polymer for low-cost, flexible (photo)electrochemical applications due to its reversible two-electron reduction and high electron mobility. UV–vis spectroelectrochemistry in the tetrabutyl ammonium hexafluorophosphate/acetonitrile electrolyte shows two sets of chemically reversible redox signals in the cyclic voltammetry corresponding to the reduction of the neutral polymer film to polaronic and bipolaronic species. These electrochemical signatures suggest a distinct electronic reorganization upon reduction (polaron/bipolaron formation), highlighting the need for molecular-level insights into how charges are accommodated within the polymer backbone. While it has been previously hypothesized that charge predominantly localizes on the naphthalene diimide (NDI) unit during reductive charging, specific changes in atomic environments that confirm this localization have not been characterized in n-type polymers. Herein, we use near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to probe electronic transitions in an electrochemically charged polymer to deduce charge localization. The O K-edge (1s) spectra exhibit two distinct π* peaks; the intensity of the lower-energy π* a peak that corresponds to an excitation to a largely localized carbonyl state decreases with reductive potentials relative to the higher-energy π* b peak. We corroborate this with Raman spectroscopy at different potentials, which shows a decrease in intensity on the C–C/C═C and C═O stretching bands of NDI as well as a red shift of the carbonyl band due to the formation of a polaron on the NDI. Additionally, new Raman active NDI signals associated with elongated C═O and C═C bonds are observed at lower energy during the formation of charged states. Together with theoretical calculations, these findings show that the injected charge spatially localizes on the NDI units and is dominantly distributed on the carbonyl groups. In conclusion, the combination of NEXAFS, optical and vibrational spectroscopies, and theoretical calculations is generalizable to other pi-conjugated polymers and can identify charge localization for the further development of organic semiconductors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Probing the Mechanism of Cadmium Sulfide Cluster Nucleation and Growth via Sequential Infiltration Synthesis

Few-atom metal chalcogenide clusters may be realized through the sequential infiltration of metal–organic precursors in polymer films. However, the underlying nucleation and growth mechanisms that allow for cluster synthesis with near atomic-scale precision are not fully resolved. The kinetics of the sequential infiltration synthesis (SIS) method that control the nucleation and growth mechanisms of primarily Cd 4 S 4 -core clusters within a poly­(4-vinylpyridine) (P4VP) matrix are probed with in situ UV–visible absorbance spectroscopy. Density functional theory (DFT) calculations that allow simulation of the optical properties of cluster fragments further reveal the thermodynamics that guide cluster growth within the P4VP matrix. Here, we conclude that a reactive capture mechanism for cluster nucleation and growth is dominant, although transient dimethyl cadmium adduction to the polymer backbone may contribute to cluster nucleation under shorter metal–organic purge process conditions. Grazing incidence X-ray diffraction (GI-XRD) and X-ray absorption spectroscopy (XAS) analyses further corroborate the cluster size and atom connectivity throughout the stepwise synthesis.

Jayaweera, Nuwanthaka P. [Argonne National Laborat↗
DOE OSTI2019

Toward Long-Life, Ultrahigh-Nickel Layered Oxide Cathodes for Lithium-Ion Batteries: Optimizing the Interphase Chemistry with a Dual-Functional Polymer

Boosting the Ni content in LiMO 2 (M = Ni, Co, Mn, etc.) layered oxides is a promising way to establish high-energydensity, low-cost cathodes, but the poor cathode surface stability is a daunting challenge for their practical viability. Herein, by constructing a dual-functional binder framework with a conductive polymer - polyaniline (PANI), the ultrahigh-Ni layered oxide cathode (LiNi 0.94 Co 0.06 O 2 ) exhibits significantly improved cyclability, with a capacity retention greatly increased from 47% to 81% over 1,000 cycles in full cells. It is demonstrated that the acidic species (e.g. HF) in the electrolyte can be efficiently scavenged through a protonation process of PANI, hence the cathode surface reactivity is greatly suppressed and the rock-salt phase propagation into bulk structure is considerably alleviated. Furthermore, the PANI binder system effectively prevents both the cathode-electrolyte interphase (CEI) and anode-electrolyte interphase (AEI) from degrading to a thick “triple-layer” architecture upon extensive cycling, resulting in more robust, thinner CEI and AEI with regulated interphasial chemistry. Moreover, the delocalized π-conjugated electrons along the backbone of PANI facilitate fast electron transfer and promote rate capability even at low temperatures (-20 °C). Finally, this work sheds light on rational binder engineering for developing high-energy-density lithium-ion batteries with acceptable cycle life.

25 ENERGY STORAGE↗
DOE OSTI2024

Catalytic Upcycling of Polyolefins

The large production volumes of commodity polyolefins (specifically, polyethylene, polypropylene, polystyrene, and poly(vinyl chloride)), in conjunction with their low unit values and multitude of short-term uses, have resulted in a significant and pressing waste management challenge. Only a small fraction of these polyolefins is currently mechanically recycled, with the rest being incinerated, accumulating in landfills, or leaking into the natural environment. Since polyolefins are energy-rich materials, there is considerable interest in recouping some of their chemical value while simultaneously motivating more responsible end-of-life management. An emerging strategy is catalytic depolymerization, in which a portion of the C–C bonds in the polyolefin backbone is broken with the assistance of a catalyst and, in some cases, additional small molecule reagents. When the products are small molecules or materials with higher value in their own right, or as chemical feedstocks, the process is called upcycling. This review summarizes recent progress for four major catalytic upcycling strategies: hydrogenolysis, (hydro)cracking, tandem processes involving metathesis, and selective oxidation. Key considerations include macromolecular reaction mechanisms relative to small molecule mechanisms, catalyst design for macromolecular transformations, and the effect of process conditions on product selectivity. Metrics for describing polyolefin upcycling are critically evaluated, and an outlook for future advances is described.

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

Molecular Design of Functional Polymers for Silica Scale Inhibition

Silica polymerization, which involves the condensation reaction of silicic acid, is a fundamental process with wide-ranging implications in biological systems, material synthesis, and scale formation. The formation of a silica-based scale poses significant technological challenges to energy-efficient operations in various industrial processes, including heat exchangers and water treatment membranes. Despite the common strategy of applying functional polymers for inhibiting silica polymerization, the underlying mechanisms of inhibition remain elusive. In this study, we synthesized a series of nitrogen-containing polymers as silica inhibitors and elucidated the role of their molecular structures in stabilizing silicic acids. Polymers with both charged amine and uncharged amide groups in their backbones exhibit superior inhibition performance, retaining up to 430 ppm of reactive silica intact for 8 h under neutral pH conditions. In contrast, monomers of these amine/amide-containing polymers as well as polymers containing only amine or amide functionalities present insignificant inhibition. Molecular dynamics simulations reveal strong binding between the deprotonated silicic acid and a polymer when the amine groups in the polymer are protonated. Notably, an extended chain conformation of the polymer is crucial to prevent proximity between the interacting monomeric silica species, thereby facilitating effective silica inhibition. Furthermore, the hydrophobic nature of alkyl segments in polymer chains disrupts the hydration shell around the polymer, resulting in enhanced binding with ionized silicic acid precursors compared to monomers. Finally, our findings provide novel mechanistic insights into the stabilization of silicic acids with functional polymers, highlighting the molecular design principles of effective inhibitors for silica polymerization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Influence of the Cubic Sublattice on Magnetic Coupling between the Tetrahedral Sites of Garnet

Here, we present a study on the nuclear and magnetic structures of two iron-based garnets with magnetic cations isolated on tetrahedral sites. Ca 2 YZr 2 Fe 3 O 12 and Ca 2 LaZr 2 Fe 3 O 12 offer an interesting comparison for examining the effect of increasing cation size within the diamagnetic backbone of the garnet crystal structure, and how such changes affect the magnetic order. Despite both systems exhibiting well-pronounced magnetic transitions at low temperatures, we also find evidence for diffuse magnetic scattering due to a competition between the nearest-neighbor, next nearest-neighbor, and so on, within the tetrahedral sites. This competition results in a complex noncollinear magnetic structure on the tetrahedral sublattice creating a mixture of ferro- and antiferromagnetic interactions above the long-range ordering temperature near 20 K and suggests that the cubic site of the garnet plays a significant role in mediating the superexchange interactions between tetrahedral cations.

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

Chelating Rare-Earth Metals (Ln 3+ ) and 225 Ac 3+ with the Dual-Size-Selective Macrocyclic Ligand Py 2 -Macrodipa

Radioisotopes of metallic elements, or radiometals, are widely employed in both therapeutic and diagnostic nuclear medicine. For this application, chelators that efficiently bind the radiometal of interest and form a stable metal–ligand complex with it are required. Toward the development of new chelators for nuclear medicine, we recently reported a novel class of 18-membered macrocyclic chelators that is characterized by their ability to form stable complexes with both large and small rare-earth metals (Ln 3+ ), a property referred to as dual size selectivity. A specific chelator in this class called py-macrodipa, which contains one pyridyl group within its macrocyclic core, was established as a promising candidate for 135 La 3+ , 213 Bi 3+ , and 44 Sc 3+ chelation. Building upon this prior work, here we report the synthesis and characterization of a new chelator called py 2 -macrodipa with two pyridyl units fused into the macrocyclic backbone. Its coordination chemistry with the Ln 3+ series was investigated by NMR spectroscopy, X-ray crystallography, density functional theory (DFT) calculations, analytical titrations, and transchelation assays. These studies reveal that py 2 -macrodipa retains the expected dual size selectivity and possesses an enhanced thermodynamic affinity for all Ln 3+ compared to py-macrodipa. By contrast, the kinetic stability of Ln 3+ complexes with py 2 -macrodipa is only improved for the light, large Ln 3+ ions. Based upon these observations, we further assessed the suitability of py 2 -macrodipa for use with 225 Ac 3+ , a large radiometal with valuable properties for targeted α therapy. Radiolabeling and stability studies revealed py 2 -macrodipa to efficiently incorporate 225 Ac 3+ and to form a complex that is inert in human serum over 3 weeks. Although py 2 -macrodipa does not surpass the state-of-the-art chelator macropa for 225 Ac 3+ chelation, it does provide another effective 225 Ac 3+ chelator. Furthermore, these studies shed light on the fundamental coordination chemistry of the Ln 3+ series and may inspire future chelator design efforts.

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

Sulfur-Ligated [2Fe-2C] Clusters as Synthetic Model Systems for Nitrogenase

Metal clusters featuring carbon and sulfur donors have coordination environments comparable to the active site of nitrogenase enzymes. Here, we report a series of di-iron clusters supported by the dianionic yldiide ligands, in which the Fe sites are bridged by two μ 2 -C atoms and four pendant S donors. The [L 2 Fe 2 ] (L = {[Ph 2 P(S)] 2 C} 2– ) cluster is isolable in two oxidation levels, all-ferrous Fe 2 II and mixed-valence Fe II Fe III . The mixed-valence cluster displays two peaks in the Mössbauer spectra, indicating slow electron transfer between the two sites. The addition of the Lewis base 4-dimethylaminopyridine to the Fe2 II cluster results in coordination with only one of the two Fe sites, even in the presence of an excess base. Conversely, the cluster reacts with 8 equiv of isocyanide t BuNC to give a monometallic complex featuring a new C–C bond between the ligand backbone and the isocyanide. The electronic structure descriptions of these complexes are further supported by X-ray absorption and resonant X-ray emission spectroscopies.

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

Lewis Acids and Electron-Withdrawing Ligands Accelerate CO Coordination to Dinuclear Cu I Compounds

A series of dinuclear molecular copper complexes were prepared and used to model the binding and Lewis acid stabilization of CO in heterogeneous copper CO 2 reduction electrocatalysts. Experimental studies (including measurement of rate and equilibrium constants) and electronic structure calculations suggest that the key kinetic barrier for CO binding may be a σ-interaction between CuI and the incoming CO ligand. The rate of CO coordination can be increased upon the addition of Lewis acids or electron-withdrawing substituents on the ligand backbone. Conversely, K eq for CO coordination can be increased by adding electron density to the metal centers of the compound, consistent with stronger π-backbonding. Lastly, the electrochemically measured kinetic results were mapped onto an electrochemical zone diagram to illustrate how these system changes enabled access to each zone.

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

Ligand Noninnocence in β-Diketiminate and β-Diketimine Copper Complexes

Metal–ligand cooperative systems have a long precedent in catalysis, with the classification depending on the site of substrate bond cleavage and formation and on redox state changes. Recently, our group reported the participation of a β-diketiminate ligand in chemical bonding to heterocumulenes such as CO 2 and CS 2 by tricopper complexes, leading to cooperative catalysis. Herein, we report the reactivity of these copper clusters, [Cu 3 EL] – (E = S, Se; L = tris(β-diketiminate) cyclophane ligand), toward other electrophiles, viz. alkyl halides and Brønsted acids. We identified a family of ligand-functionalized complexes, Cu 3 EL (R) (R = primary alkyls), and a series of disubstituted products, Cu 3 EL (R) 2 , through single-crystal X-ray diffraction, mass spectrometry, and infrared and UV–visible spectroscopy. Furthermore, as part of mechanistic studies on these alkylation reactions, we evaluated the acid–base reactivity of these complexes and the influence of the backbone substitution on the reduction potential. Implications of these findings for ligand noninnocence and the relevance of the metal core as a cofactor for the ligand’s reactivity are discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

Coarse-grained modeling can be used to explore general theories that are independent of specific chemical detail. In this paper, we present cg_openmm, a Python-based simulation framework for modeling coarse-grained hetero-oligomers and screening them for structural and thermodynamic characteristics of cooperative secondary structures. cg_openmm facilitates the building of coarse-grained topology and random starting configurations, setup of GPU-accelerated replica exchange molecular dynamics simulations with the OpenMM software package, and features a suite of postprocessing thermodynamic and structural analysis tools. In particular, native contact analysis, heat capacity calculations, and free energy of folding calculations are used to identify and characterize cooperative folding transitions and stable secondary structures. In this work, we demonstrate the capabilities of cg_openmm on a simple 1–1 Lennard-Jones coarse-grained model, in which each residue contains 1 backbone and 1 side-chain bead. By scanning both nonbonded and bonded force-field parameter spaces at the coarse-grained level, we identify and characterize sets of parameters which result in the formation of stable helices through cooperative folding transitions. Furthermore, we show that the geometries and stabilities of these helices can be tuned by manipulating the force-field parameters.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Low-Lying Excited States of Linear All- Trans Polyenes: Insights from Analytic Gradient and Nonadiabatic Coupling Calculations Based on Multireference Configuration Interaction

Polyenes serve as a rigorous test for theoretical models and electronic structure methods, playing a key role in advancing computational and theoretical chemistry. Here, we present a high-level theoretical investigation of linear, all-trans polyenes using energy gradients and nonadiabatic coupling vectors based on an MR-CISD wave function to describe electronic transitions involving the ground state (1 1 A g – ) and three low-lying excited states (2 1 A g – , 1 1 B u + , and 2 1 B u – ) of hexatriene, octatetraene, and decapentaene. This approach enables accurate evaluation of both adiabatic and vertical excitation and emission energies, yielding results in excellent agreement with experiment, as well as locating minima on the crossing seam between adiabatic states. Our results show that vertical excitation energies to the 1 1 B u + state are blue-shifted by 0.2–0.3 eV relative to the experimental absorption maximum, whereas the vertical emission energy from the 2 1 A g – state is red-shifted by ∼0.2 eV relative to the experimental emission maximum. Upon relaxation from the Franck–Condon geometry, the 2 1 A g – state stabilizes by around 1 eV, compared to 0.2–0.3 eV for the 1 1 B u + state. An analysis of the S 1 /S 0 crossing seam in hexatriene shows that its minimum involves asymmetric backbone deformations and provides an efficient channel for ultrafast internal conversion to the ground state, consistent with the absence of detectable fluorescence in this molecule. These results demonstrate the power of analytic gradients and nonadiabatic coupling vectors based on an MR-CISD wave function for accurately characterizing the electronic structure and photophysics of polyenes.

Excited states↗
DOE OSTI2022

Substituent Effects on the Electronic Spectroscopy of Four-Carbon Criegee Intermediates

Atmospheric ozonolysis of biogenic and anthropogenic alkenes generates zwitterionic carbonyl oxide intermediates (R 1 R 2 C=O + O – ), known as Criegee intermediates, with different structural motifs and conformations. This study reports a systematic laboratory study of substituent effects on the electronic spectroscopy of four-carbon Criegee intermediates (CIs) with methyl–ethyl (MECI) and isopropyl (IPCI) groups, which are isomers produced in ozonolysis of asymmetric branched alkenes. The four-carbon CIs are separately generated by an alternative synthetic route, and spectroscopically characterized on the strong π* ← π transition associated with the carbonyl oxide group in a pulsed supersonic expansion with VUV photoionization at 118 nm and UV-induced depletion of the m/z 88 signal. The resultant broad and unstructured UV spectral features for MECI and IPCI are peaked at ca. 320 and 330 nm, respectively, with large absorption cross-sections of ca. 10 –17 cm 2 . Comparisons are made with the four-carbon CIs formed in isoprene ozonolysis, methyl vinyl ketone oxide (MVK-oxide) and methacrolein oxide (MACR-oxide), which have the same backbone connectivity as MECI and IPCI but have extended conjugation across the vinyl and carbonyl groups. A remarkable 50 nm shift of the peak absorption to longer wavelength is observed for MVK-oxide and MACR-oxide compared to MECI and IPCI, respectively. Furthermore, vertical excitation energies computed theoretically agree well with the experimental findings, confirming that the spectral shifts are caused by the extended π conjugation in the isoprene-derived Criegee intermediates.

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

High-Accuracy Heats of Formation for Alkane Oxidation: From Small to Large via the Automated CBH-ANL Method

It is generally challenging to obtain high-accuracy predictions for the heat of formation for species with more than a handful of heavy atoms, such as those of importance in standard combustion mechanisms. To this end, we construct the CBH-ANL approach and illustrate that, for a set of 194 alkane oxidation species, it can be used to produce ΔH f (o K) values with 2σ uncertainties of 0.2-0.5 kcal mol -1 . This set includes the alkanes, hydroperoxides, and alkyl, peroxy, and hydroperoxyalkyl radicals for 17 representative hydrocarbon fuels containing up to 10 heavy atoms with various degrees of branching in the alkane backbone. The CBH-ANL approach, automated in the QTC and AutoMech software suites, builds balanced chemical equations for the calculation of ΔH f (o K), in which the reference species may be up to five heavy atoms. The high-level ANLo and ANL1 reference ΔH f (o K) values are further refined for even the largest of these reference species with a novel laddering approach. We perform a comprehensive quantification of the uncertainties for both the individual reference species (the largest of which is 0.15 kcal mol -1 ) and the propagation of those uncertainties when used in the calculation of ΔH f (o K) for the 194 target species. Here we examine the sensitivity of the predicted ΔH f (o K) values to (i) electronic energies from various methods, including ωB97X-D/cc-pVTZ, B2PLYP-D3/cc-pVTZ, CCSD(T)-F12b/cc-pVDZ-F12//B2PLYP-D3/cc-pVTZ, and CCSD(T)-F12b/cc-pVTZ-F12//B2PLYP-D3/cc-pVTZ; (ii) the zero-point vibrational energies (ZPVEs), where we consider harmonic ZPVEs as well as two scaling-based estimates of the anharmonic ZPVEs, all implemented for both ωB97X-D/cc-pVTZ and B2PLYP-D3/cc-pVTZ calculations; (iii) the particular CBH-ANL scheme employed; and (iv) the procedure for choosing the reference conformer for the analyses. The discussion concludes with a summary of the estimated overall uncertainty in the predictions and a validation of the predictions for the alkane subset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Formation of 1 H -Phenalene (C 13 H 10 ) in the Taurus Molecular Cloud via Methylidyne Addition-Cyclization-Aromatization (MACA)

The formation of 1H-phenalene (C 13 H 10 ) in cold molecular clouds, such as the Taurus Molecular Cloud-1 (TMC-1), presents a significant challenge to traditional astrochemical models, which predominantly suggest high-temperature pathways for polycyclic aromatic hydrocarbon (PAH) formation. In this study, we explore computationally the Methylidyne Addition-Cyclization-Aromatization (MACA) mechanism as a viable, barrierless pathway for phenalene synthesis under low-temperature conditions. Through electronic structure calculations and Rice–Ramsperger–Kassel–Marcus (RRKM) statistical methods, we demonstrate that the reaction of 1-vinylnaphthalene (C 10 H 7 C 2 H 3 ) with the methylidyne radical (CH) leads to the formation of 1H-phenalene via a bimolecular reaction, a process that is exoergic and without entrance barrier. The MACA mechanism facilitates the growth of the aromatic carbon backbone via a [5 + 1] ring annulation, providing a new insight into PAH formation in cold molecular clouds. Notably, the MACA mechanism has previously been shown to form indene (C9H8), which was detected in TMC-1 as well, via a [4 + 1] annulation, demonstrating its potential to produce a variety of complex PAHs by addition of a five- and six-membered ring to a benzene moiety via [4 + 1] and [5 + 1] annulation, respectively. As a result, this work highlights the importance of barrierless, exoergic reactions involving MACA in the synthesis of complex aromatic molecules in space, expanding our physicochemical understanding of carbon-rich chemistry in cold molecular clouds.

Aromatic compounds↗
DOE OSTI2020

N-Terminal Decarboxylation as a Probe for Intramolecular Contact Formation in $γ$-Glu-(Pro) n -Met Peptides

The kinetics of intramolecular-contact formation between remote functional groups in peptides with restricted conformational flexibility were examined using designed peptides with variable-length proline bridges. As probes for this motion, free radicals were produced using the • OH-induced oxidation at the C-terminal methionine residue of γ-Glu-(Pro) n -Met peptides ( n = 0–3). The progress of the radicals’ motion along the proline bridges was monitored as the radicals underwent reactions along the peptides’ backbones. Of particular interest was the reaction between the sulfur atom located in the side chain of the oxidized Met residue and the unprotonated amino group of the glutamic acid moiety. Interactions between them were probed by the radiation-chemical yields (expressed as G values) of the formation of C-centered, α-aminoalkyl radicals (αN) on the Glu residue. These radicals were monitored directly or via their reaction with p -nitroacetophenone (PNAP) to generate the optically detected PNAP •– radical anions. The yields of these αN radicals were found to be linearly dependent on the number of Pro residues. A constant decrease by 0.09 μM J –1 per spacing Pro residue of the radiation-chemical yields of G (αN) was observed. Previous reports support the conclusion that the αN radicals in these cases would have to result from (S$\therefore$N) + -bonded cyclic radical cations that arose as a result from direct contact between the ends of the peptides. Furthermore, by analogy with the rate constants for the formation of intramolecularly (S$\therefore$S) + -bonded radical cations in Met-(Pro) n -Met peptides ( J. Phys. Chem. B 2016 , 120 , 9732), the rate constants for the formation of intramolecularly (S$\therefore$N) + -bonded radical cations are activated to the same extent for all of the γ-Glu-(Pro) n -Met peptides. Thus, the continuous decrease of G (αN) with the number of Pro residues (from 0 to 3) suggests that the formation of a contact between the S-atom in the C-terminal Met residue and the N-atom of a deprotonated N-terminal amino group of Glu is controlled in peptides with 0 to 3 Pro residues by the relative diffusion of the S •+ and unoxidized N-atom. The overall rate constants of cyclization to form the (S$\therefore$N)-bonded radical cations were estimated to be 3.8 × 10 6 , 1.8 × 10 6 , and 8.1 × 10 5 s –1 for peptides with n = 0, 1, and 2 Pro residues, respectively. If activation is the same for all of the peptides, then these rate constants are a direct indication for the end-to-end dynamics along the chain.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids

Peptoids (poly-N-substituted glycines) are a class of synthetic polymers that are regioisomers of peptides (poly-C-substituted glycines), in which the point of side-chain connectivity is shifted from the backbone C to the N atom. Peptoids have found diverse applications as peptidomimetic drugs, protein mimetic polymers, surfactants, and catalysts. Computational modeling is valuable in the understanding and design of peptoid-based nanomaterials. In this work, we report the bottom-up parameterization of coarse-grained peptoid force fields based on the MARTINI peptide force field against all-atom peptoid simulation data. Our parameterization pipeline iteratively refits coarse-grained bonded interactions using iterative Boltzmann inversion and nonbonded interactions by matching the potential of mean force for chain extension. We assure good sampling of the amide bond cis/trans isomerizations in the all-atom simulation data using parallel bias metadynamics. We develop coarse-grained models for two representative peptoids—polysarcosine (poly(N-methyl glycine)) and poly(N-((4-bromophenyl)ethyl)glycine)—and show their structural and thermodynamic properties to be in excellent accord with all-atom calculations but up to 25-fold more efficient and compatible with MARTINI force fields. Here, this work establishes a new rigorously parameterized coarse-grained peptoid force field for the understanding and design of peptoid nanomaterials at length and time scales inaccessible to all-atom calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗