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DOE OSTI2017

Effect of Autohydrolysis Pretreatment Conditions on Sugarcane Bagasse Structures and Product Distribution Resulting from Pyrolysis

Pyrolysis has been increasingly perceived as a promising technology to produce biofuel precursors (bio-oil) from agricultural residuals; however, there is a significant quality gap between a bio-oil and the fuels used for transportation. In this paper, we autohydrolyzed pretreated sugarcane bagasse at three different conditions (180 °C–10 min, 180 °C–40 min, 200 °C–40 min), then we investigated the effect of this pretreatment on a subsequent pyrolysis stage. High-pressure ion-exchange chromatography (HPIC) and the 13 C cross-polarization/magic angle spinning (CP/MAS) solid-state nuclear magnetic resonance (NMR) revealed that the autohydrolysis pretreatment significantly disrupted the hemicellulose fractions in the sugarcane bagasse and caused the breakage of lignin ether linkages in the sugarcane bagasse feedstocks. As the 31 P NMR results indicated, the autohydrolysis pretreatment removed carboxylic acid groups up to 66.7 %, which could significantly address the corrosion problem of bio-oils. Heteronuclear single quantum correlation (HSQC) analysis suggested that the autohydrolysis pretreatment effectively lowered the presence of the oxygenated aromatic compounds in the bio-oils. Finally, gel permeation chromatography (GPC) analysis of the bio-oils indicated that the oils from severely pretreated sugarcane bagasse pyrolyzed at a low temperature (i.e., 400 °C) contained lower-molecular-weight components similar to those present gasoline products.

09 BIOMASS FUELS↗

DOE OSTI2016

Going with the Electron Flow: Heme Electronic Structure and Electron Transfer in Cytochrome c

Heme is an essential and functionally versatile cofactor. Our understanding of how the environment of a heme in a protein tunes its function has benefited from spectroscopic and functional investigations of heme proteins and their variants with altered heme environments. Two properties of current interest are the conformation of the heme and hydrogen bonding to heme propionates. By combining nuclear magnetic resonance experiments and density functional theory calculations, both of these characteristics have been shown to influence the distribution of the singly occupied molecular orbital on the heme of ferricytochrome c, which affects coupling to redox partners and electron-transfer rates. In addition, heme conformation has been shown to tune reduction potential. These results reveal that subtle variations in heme conformation and in interactions with its propionates can have significant impacts on electron-transfer activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

An insight into microscopy and analytical techniques for morphological, structural, chemical, and thermal characterization of cellulose

Cellulose obtained from plants is a bio-polysaccharide and the most abundant organic polymer on earth that has immense household and industrial applications. Hence, the characterization of cellulose is important for determining its appropriate applications. In this article, we review the characterization of cellulose morphology, surface topography using microscopic techniques including optical microscopy, transmission electron microscopy, scanning electron microscopy, and atomic force microscopy. Additionally, other physicochemical characteristics like crystallinity, chemical composition, and thermal properties are studied using techniques including X-ray diffraction, Fourier transform infrared, Raman spectroscopy, nuclear magnetic resonance, differential scanning calorimetry, and thermogravimetric analysis. This review may contribute to the development of using cellulose as a low-cost raw material with anticipated physicochemical properties.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

27 Al NMR diffusometry of Al 13 Keggin nanoclusters

Although nanometer-sized aluminum hydroxide clusters (i.e., ϵ-Al 13 , [Al 13 O 4 (OH) 24 (H 2 O) 12 ] 7+ ) command a central role in aluminum ion speciation and transformations between minerals, measurement of their translational diffusion is often limited to indirect methods. Here, in this work, 27 Al pulsed field gradient stimulated echo nuclear magnetic resonance (PFGSTE NMR) spectroscopy has been applied to the AlO 4 core of the ϵ-Al 13 cluster with complementary theoretical simulations of the diffusion coefficient and corresponding hydrodynamic radii from a boundary element-based calculation. The tetrahedral AlO 4 center of the ϵ-Al 13 cluster is symmetric and exhibits only weak quadrupolar coupling, which results in favorable T 1 and T 2 27 Al NMR relaxation coefficients for 27 Al PFGSTE NMR studies. Stokes–Einstein relationship was used to relate the 27 Al diffusion coefficient of the ϵ-Al 13 cluster to the hydrodynamic radius for comparison with theoretical simulations, dynamic light scattering from literature, and previously published 1 H PFGSTE NMR studies of chelated Keggin clusters. This first-of-its-kind observation proves that 27 Al PFGSTE NMR diffusometry can probe symmetric Al environments in polynuclear clusters of greater molecular weight than previously considered.

27Al↗

DOE OSTI2019

Coupling of NMR to ACOMP for Terpolymerization Monitoring and Control

Abstract Monitoring and control of free radical copolymerization using automatic continuous online monitoring of polymerization reactions (ACOMP) with UV detection has been recently achieved. It is difficult, however, to achieve spectral separation of similar monomers with UV alone. Here, nuclear magnetic resonance (NMR) is coupled to ACOMP for the first time and terpolymerization reactions involving acrylamide (Am), sodium acrylate (Ac), and styrene sulfonate (SS) are monitored, and a first attempt at active composition control is made. The NMR resolves the concentrations of Am and Ac, while the UV resolves SS and the sum of Am and Ac. NMR analysis is performed in water, using signal suppression, to eliminate the need for deuterated solvents. From this, instantaneous fractions of each comonomer in the terpolymer are continuously known, along with weight average molecular weight and intrinsic viscosity, IV. Am and Ac have similar reactivities, whereas the reactivity ratio of SS is much larger. Hence, there is high composition drift in batch polymerization and SS is rapidly consumed, leaving a final copolymer of Am and SS to form. Maintaining constant terpolymer composition is taken as a first step toward active control.

McAfee, Terry↗

DOE OSTI2017

Highly efficient reversible addition-fragmentation chain-transfer polymerization in ethanol/water via flow chemistry

Here, utilization of a flow reactor under high pressure allows highly efficient polymer synthesis via reversible addition–fragmentation chain-transfer (RAFT) polymerization in an aqueous system. Compared with the batch reaction, the flow reactor allows the RAFT polymerization to be performed in a high-efficiency manner at the same temperature. The adjustable pressure of the system allows further elevation of the reaction temperature and hence faster polymerization. Other reaction parameters, such as flow rate and initiator concentration, were also well studied to tune the monomer conversion and the molar mass dispersity (Ð) of the obtained polymers. Gel permeation chromatography, nuclear magnetic resonance (NMR), and Fourier transform infrared spectroscopies (FTIR) were utilized to monitor the polymerization process. With the initiator concentration of 0.15 mmol L –1 , polymerization of poly(ethylene glycol) methyl ethermethacrylate with monomer conversion of 52% at 100 °C under 73 bar can be achieved within 40 min with narrow molar mass dispersity (D) Ð (<1.25). The strategy developed here provides a method to produce well-defined polymers via RAFT polymerization with high efficiency in a continuous manner.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

Untargeted metabolomic profiling of Sphagnum fallax reveals novel antimicrobial metabolites

Abstract Sphagnum mosses dominate peatlands by employing harsh ecosystem tactics to prevent vascular plant growth and microbial degradation of these large carbon stores. Knowledge about Sphagnum ‐produced metabolites, their structure and their function, is important to better understand the mechanisms, underlying this carbon sequestration phenomenon in the face of climate variability. It is currently unclear which compounds are responsible for inhibition of organic matter decomposition and the mechanisms by which this inhibition occurs. Metabolite profiling of Sphagnum fallax was performed using two types of mass spectrometry (MS) systems and 1 H nuclear magnetic resonance spectroscopy ( 1 H NMR). Lipidome profiling was performed using LC‐MS/MS. A total of 655 metabolites, including one hundred fifty‐two lipids, were detected by NMR and LC‐MS/MS—329 of which were novel metabolites (31 unknown lipids). Sphagum fallax metabolite profile was composed mainly of acid‐like and flavonoid glycoside compounds, that could be acting as potent antimicrobial compounds, allowing Sphagnum to control its environment. Sphagnum fallax metabolite composition comparison against previously known antimicrobial plant metabolites confirmed this trend, with seventeen antimicrobial compounds discovered to be present in Sphagnum fallax , the majority of which were acids and glycosides. Biological activity of these compounds needs to be further tested to confirm antimicrobial qualities. Three fungal metabolites were identified providing insights into fungal colonization that may benefit Sphagnum . Characterizing the metabolite profile of Sphagnum fallax provided a baseline to understand the mechanisms in which Sphagnum fallax acts on its environment, its relation to carbon sequestration in peatlands, and provide key biomarkers to predict peatland C store changes (sequestration, emissions) as climate shifts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Chain extension epoxide polymerization to well‐defined block polymers using a N‐Al Lewis pair catalyst

Block polyethers comprised of poly(propylene oxide) (PPO) and poly(ethylene oxide) (PEG or PEO) segments form the basis of ABA-type PEO-b-PPO-b-PEO poloxamer materials. The inverse architecture with an internal hydrophilic PEO segment flanked by hydrophobic blocks can be difficult to prepare with control of architecture by use of traditional anionic polymerization. These oxyanionic polymerizations are plagued by chain-transfer-to-monomer side reactions that occur with substituted epoxides such as propylene oxide (PO). Herein, we report a new method for the preparation of block polymers through a controlled polymerization involving a N-Al Lewis adduct catalyst and an aluminum alkoxide macroinitiator. The Lewis pair catalyst was able to chain-extend commercial PEO macroinitiators to prepare di-, tri-, and pentablock polyethers with low dispersity and reasonable monomer tolerance. Chain extension was confirmed using size exclusion chromatography and diffusion ordered nuclear magnetic resonance spectroscopy. In conclusion, the resulting block polymers were additionally analyzed with small-angle X-ray scattering to correlate the morphology to molecular architecture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Comparing linear and cyclic synthetic homopolypeptides: Synthesis and molecular characterization

We report the synthesis and molecular characterization of a linear and a cyclic homopolypeptide of protected l-tyrosine. The successful synthesis of polypeptides exhibiting the desired linear and cyclic structures through various characterization methods such as high temperature gel permeation chromatography, Fourier transform infrared spectroscopy, proton and carbon nuclear magnetic resonance spectroscopy, mass spectrometry, dynamic light scattering, differential scanning calorimetry, and thermogravimetric analysis was verified in this work. Our results are very promising especially if such cyclic materials will be potentially used as carriers for drug delivery, either through conjugation with specific ligands or directly through the functional hydroxyl groups of the monomeric units of poly(l-Tyr) after deprotection.

36 MATERIALS SCIENCE↗

DOE OSTI2015

Fundamental investigations into the free‐radical copolymerization of N ‐phenylmaleimide and norbornene

ABSTRACT A fundamental investigation into the copolymerization of N ‐phenylmaleimide and norbornene via conventional free‐radical polymerization techniques was conducted. Reaction conditions were optimized for molecular weight and percent yield by tuning overall concentration and initiator loading. The copolymerization kinetics were monitored using in‐situ , variable temperature nuclear magnetic resonance and first‐order behavior was observed with respect to each monomer. Although the related copolymerization of norbornene and maleic anhydride was well‐known to proceed in a perfectly alternating manner, the copolymerization of norbornene and N ‐phenylmaleimide was found to deviate from strictly alternating copolymerization behavior, producing significant amounts of sequentially enchained N ‐phenylmaleimide units within the polymeric backbone. This deviation from perfectly alternating behavior was confirmed by analysis of individual monomer conversion rates and by measurement of monomer reactivity ratios using the Mayo–Lewis graphical analysis method. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54 , 985–991

Gmernicki, Kevin R.↗

DOE OSTI2026

Energetic Copolymers From LLM-105 and Aliphatic Isocyanates

Energetic polymers typically feature fuel-rich backbones with pendant oxidizing explosophores, which are used to modify pressure and temperature characteristics in energetic formulations. However, these pendant explosophores generally increase sensitivity and decrease the thermal stability of the polymer in the condensed phase. Direct polymerization of insensitive high explosives (IHEs) bearing polymerizable functionalities, such as amines, provides a synthetic platform for deriving tunable energetic materials. Here, this work demonstrates the first direct polymerization of the IHE 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) with aliphatic isocyanate comonomers to yield an energetic copolyurea (PUa1) and an energetic copolyurea network (PUa2). 1 H and 13 C nuclear magnetic resonance (NMR) and Fourier transform infrared spectroscopy (FTIR) confirm copolyurea synthesis. PUa1 exhibited branching reactions commonly found in polyurea syntheses, and these side reactions were suppressed in PUa2 through use of a polyfunctional isocyanate. Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) demonstrate the energetic IHE based polyurea preserves the energetic decomposition of the parent monomer LLM-105 in PUa1 (1203 J g −1 ) and PUa2 (687 J g −1 ), albeit with reduced thermal stability with peak decomposition temperatures of 235°C and 233°C, respectively. This work presents a new approach for generating energetic polymers from IHE cores with tunable energetic, thermal, and structural characteristics.

Chemistry↗

DOE OSTI2014

Characterization of Free Surface-Bound and Entrapped Water Environments in Poly(N-Isopropyl Acrylamide) Hydrogels via 1H HRMAS PFG NMR Spectroscopy

We found that different water environments in poly(N-isopropyl acrylamide) (PNIPAAm) hydrogels are identified and characterized using 1 H high resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR). Local water environments corresponding to a “free” highly mobile species, along with waters showing restricted dynamics are resolved in these swollen hydro-gels. For photo-initiated polymerized PNIPAAm gels, an additional entrapped water species is observed. Spin–spin R 2 relaxation experiments support the argument of reduced mobility in the restricted and entrapped water species. Furthermore, by combining pulse field gradient techniques with HRMAS NMR it is possible to directly measure the self-diffusion rate for these different water environments. The behavior of the heterogeneous water environments through the lower critical solution temperature transition is described.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Hydrophilic domain structure in polymer exchange membranes: Simulations of NMR spin diffusion experiments to address ability for model discrimination

Here, we detail the development of a flexible simulation program (NMR_DIFFSIM) that solves the nuclear magnetic resonance (NMR) spin diffusion equation for arbitrary polymer architectures. The program was used to explore the proton ( 1 H) NMR spin diffusion behavior predicted for a range of geometrical models describing polymer exchange membranes. These results were also directly compared with the NMR spin diffusion behavior predicted for more complex domain structures obtained from molecular dynamics (MD) simulations. The numerical implementation and capabilities of NMR_DIFFSIM were demonstrated by evaluating the experimental NMR spin diffusion behavior for the hydrophilic domain structure in sulfonated Diels-Alder Poly(Phenylene) (SDAPP) polymer membranes. The impact of morphology variations as a function of sulfonation and hydration level on the resulting NMR spin diffusion behavior were determined. These simulations allowed us to critically address the ability of NMR spin diffusion to discriminate between different structural models, and to highlight the extremely high fidelity experimental data required to accomplish this. A direct comparison of experimental double-quantum-filtered 1 H NMR spin diffusion in SDAPP membranes to the spin diffusion behavior predicted for MD-proposed morphologies revealed excellent agreement, providing experimental support for the MD structures at low to moderate hydration levels.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Syntheses and characterization of isotopically labeled 1,3,5-triamino-2,4,6-trinitrobenzene (TATB)

Synthesis and characterization of chemical analogues of TATB, where specific atoms in the structure have been isotopically substituted, are reported. 15 N, 2 H, and 18 O have replaced the naturally occurring isotope distributions in the amino and/or the nitro attendant sites and 13 C has replaced the carbon in the ring structure. A modified wet-amination method was used to produce the analogues, and the isotopic replacements were performed by selective choice of labeled precursors. Four 15 N-labeled compounds (N replaced in the amino and nitro positions), two deuterium-labeled compounds (hydrogens replaced on the amino groups), and one 13 C-labeled compound (C in the ring substituted) were synthesized of high isotopic and chemical purity. One partially labeled 18 O-labeled compound (O in the nitro position) was a result of incomplete labeling due to exchange reactions during synthesis. The compounds were characterized by various spectroscopic methods – mass spectrometry (MS), solid-state nuclear magnetic resonance (SS-NMR), infrared (FTIR), powder x-ray diffraction (PXRD), and differential scanning calorimetry (DSC), depending upon the substitution. In conclusion, these compounds have been critical to the efforts in understanding the decomposition pathways of TATB when exposed to abnormal thermal environments.

36 MATERIALS SCIENCE↗

DOE OSTI2014

The dynamics of interleukin-8 and its interaction with human CXC receptor I peptide

Interleukin-8 (CXCL8, IL-8) is a pro-inflammatory chemokine important for the regulation of inflammatory and immune responses via its interaction with G-protein coupled receptors, including CXC receptor 1 (CXCR1). CXCL8 exists as both a monomer and as a dimer at physiological concentrations, yet the molecular basis of CXCL8 interaction with its receptor as well as the importance of CXCL8 dimer formation remain poorly characterized. Although several biological studies have indicated that both the CXCL8 monomer and dimer are active, biophysical studies have reported conflicting results regarding the binding of CXCL8 to CXCR1. To clarify this problem, we expressed and purified a peptide (hCXCR1pep) corresponding to the N-terminal region of human CXCR1 (hCXCR1) and utilized nuclear magnetic resonance (NMR) spectroscopy to interrogate the binding of wild-type CXCL8 and a previously reported mutant (CXCL8M) that stabilizes the monomeric form. Our data reveal that CXCL8M engages hCXCR1pep with a slightly higher affinity than CXCL8, and that CXCL8 does not dissociate upon binding hCXCR1pep. These investigations also indicate that CXCL8 exhibits inherent flexibility within its receptor-binding site on multiple timescales, which may help explain the versatility in this interleukin for engaging its target receptors.

dimer↗

DOE OSTI2018

Cytosolic expression, solution structures, and molecular dynamics simulation of genetically encodable disulfide‐rich de novo designed peptides

Abstract Disulfide‐rich peptides represent an important protein family with broad pharmacological potential. Recent advances in computational methods have made it possible to design new peptides which adopt a stable conformation de novo. Here, we describe a system to produce disulfide‐rich de novo peptides using Escherichia coli as the expression host. The advantage of this system is that it enables production of uniformly 13 C‐ and 15 N‐labeled peptides for solution nuclear magnetic resonance (NMR) studies. This expression system was used to isotopically label two previously reported de novo designed peptides, and to determine their solution structures using NMR. The ensemble of NMR structures calculated for both peptides agreed well with the design models, further confirming the accuracy of the design protocol. Collection of NMR data on the peptides under reducing conditions revealed a dependency on disulfide bonds to maintain stability. Furthermore, we performed long‐time molecular dynamics (MD) simulations with tempering to assess the stability of two families of de novo designed peptides. Initial designs which exhibited a stable structure during simulations were more likely to adopt a stable structure in vitro , but attempts to utilize this method to redesign unstable peptides to fold into a stable state were unsuccessful. Further work is therefore needed to assess the utility of MD simulation techniques for de novo protein design.

Buchko, Garry W.↗

DOE OSTI2021

PDB ‐101: Educational resources supporting molecular explorations through biology and medicine

Abstract The Protein Data Bank (PDB) archive is a rich source of information in the form of atomic‐level three‐dimensional (3D) structures of biomolecules experimentally determined using macromolecular crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy (3DEM). Originally established in 1971 as a resource for protein crystallographers to freely exchange data, today PDB data drive research and education across scientific disciplines. In 2011, the online portal PDB‐101 was launched to support teachers, students, and the general public in PDB archive exploration ( pdb101.rcsb.org ). Maintained by the Research Collaboratory for Structural Bioinformatics PDB, PDB‐101 aims to help train the next generation of PDB users and to promote the overall importance of structural biology and protein science to nonexperts. Regularly published features include the highly popular Molecule of the Month series, 3D model activities, molecular animation videos, and educational curricula. Materials are organized into various categories (Health and Disease, Molecules of Life, Biotech and Nanotech, and Structures and Structure Determination) and searchable by keyword. A biennial health focus frames new resource creation and provides topics for annual video challenges for high school students. Web analytics document that PDB‐101 materials relating to fundamental topics (e.g., hemoglobin, catalase) are highly accessed year‐on‐year. In addition, PDB‐101 materials created in response to topical health matters (e.g., Zika, measles, coronavirus) are well received. PDB‐101 shows how learning about the diverse shapes and functions of PDB structures promotes understanding of all aspects of biology, from the central dogma of biology to health and disease to biological energy.

Zardecki, Christine↗

DOE OSTI2021

RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

We report the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.

59 BASIC BIOLOGICAL SCIENCES↗