Synthesis of Perdeuterated Alkyl Amines/Amides with Pt/C as Catalyst under Mild Conditions.

A convenient method for the synthesis of perdeuterated alkyl amides/amines is disclosed. Perdeuterated acetyl amides can be achieved by a hydrogen-deuterium (H/D) exchange protocol with Pt/C as a catalyst and D2O as a deuterium source under mild conditions. After removal or reduction of the acetyl group, this protocol can provide perdeuterated primary, secondary, and tertiary amines, which are difficult to achieve via other methods.

Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors.

The effect of mutations of the catalytic dyad residues of SARS-CoV-2 main protease (MProWT) on the thermodynamics of binding of covalent inhibitors comprising nitrile [nirmatrelvir (NMV), NBH2], aldehyde (GC373), and ketone (BBH1) warheads to MPro is examined together with room temperature X-ray crystallography. When lacking the nucleophilic C145, NMV binding is ∼400-fold weaker corresponding to 3.5 kcal/mol and 13.3 °C decrease in free energy (ΔG) and thermal stability (Tm), respectively, relative to MProWT. The H41A mutation results in a 20-fold increase in the dissociation constant (Kd), and 1.7 kcal/mol and 1.4 °C decreases in ΔG and Tm, respectively. Increasing the pH from 7.2 to 8.2 enhances NMV binding to MProH41A, whereas no significant change is observed in binding to MProWT. Structures of the four inhibitor complexes with MPro1-304/C145A show that the active site geometries of the complexes are nearly identical to that of MProWT with the nucleophilic sulfur of C145 positioned to react with the nitrile or the carbonyl carbon. These results support a two-step mechanism for the formation of the covalent complex involving an initial non-covalent binding followed by a nucleophilic attack by the thiolate anion of C145 on the warhead carbon. Noncovalent inhibitor ensitrelvir (ESV) exhibits a binding affinity to MProWT that is similar to NMV but differs in its thermodynamic signature from NMV. The binding of ESV to MProC145A also results in a significant, but smaller, increase in Kd and decrease in ΔG and Tm, relative to NMV.

Covalent narlaprevir- and boceprevir-derived hybrid inhibitors of SARS-CoV-2 main protease.

Emerging SARS-CoV-2 variants continue to threaten the effectiveness of COVID-19 vaccines, and small-molecule antivirals can provide an important therapeutic treatment option. The viral main protease (Mpro) is critical for virus replication and thus is considered an attractive drug target. We performed the design and characterization of three covalent hybrid inhibitors BBH-1, BBH-2 and NBH-2 created by splicing components of hepatitis C protease inhibitors boceprevir and narlaprevir, and known SARS-CoV-1 protease inhibitors. A joint X-ray/neutron structure of the Mpro/BBH-1 complex demonstrates that a Cys145 thiolate reaction with the inhibitor's keto-warhead creates a negatively charged oxyanion. Protonation states of the ionizable residues in the Mpro active site adapt to the inhibitor, which appears to be an intrinsic property of Mpro. Structural comparisons of the hybrid inhibitors with PF-07321332 reveal unconventional F···O interactions of PF-07321332 with Mpro which may explain its more favorable enthalpy of binding. BBH-1, BBH-2 and NBH-2 exhibit comparable antiviral properties in vitro relative to PF-07321332, making them good candidates for further design of improved antivirals.

Structural, Electronic, and Electrostatic Determinants for Inhibitor Binding to Subsites S1 and S2 in SARS-CoV-2 Main Protease.

Creating small-molecule antivirals specific for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteins is crucial to battle coronavirus disease 2019 (COVID-19). SARS-CoV-2 main protease (Mpro) is an established drug target for the design of protease inhibitors. We performed a structure-activity relationship (SAR) study of noncovalent compounds that bind in the enzyme's substrate-binding subsites S1 and S2, revealing structural, electronic, and electrostatic determinants of these sites. The study was guided by the X-ray/neutron structure of Mpro complexed with Mcule-5948770040 (compound 1), in which protonation states were directly visualized. Virtual reality-assisted structure analysis and small-molecule building were employed to generate analogues of 1. In vitro enzyme inhibition assays and room-temperature X-ray structures demonstrated the effect of chemical modifications on Mpro inhibition, showing that (1) maintaining correct geometry of an inhibitor's P1 group is essential to preserve the hydrogen bond with the protonated His163; (2) a positively charged linker is preferred; and (3) subsite S2 prefers nonbulky modestly electronegative groups.

Biosynthesis and characterization of deuterated chitosan in filamentous fungus and yeast.

Deuterated chitosan was produced from the filamentous fungus Rhizopus oryzae, cultivated with deuterated glucose in H2O medium, without the need for conventional chemical deacetylation. After extraction and purification, the chemical composition and structure were determined by Fourier-transform infrared spectroscopy (FTIR), nuclear magnetic resonance (NMR), and small-angle neutron scattering (SANS). 13C NMR experiments provided additional information about the position of the deuterons in the glucoseamine backbone. The NMR spectra indicated that the deuterium incorporation at the non-exchangeable hydrogen positions of the aminoglucopyranosyl ring in the C3 - C5 positions was at least 60-80 %. However, the C2 position was deuterated at a much lower level (6%). Also, SANS showed that the structure of deuterated chitosan was very similar compared to the non-deuterated counterpart. The most abundant radii of the protiated and deuterated chitosan fibers were 54 Å and 60 Å, respectively, but there is a broader distribution of fiber radii in the protiated chitosan sample. The highly deuterated, soluble fungal chitosan described here can be used as a model material for studying chitosan-enzyme complexes for future neutron scattering studies. Because the physical behavior of non-deuterated fungal chitosan mimicked that of shrimp shell chitosan, the methods presented here represent a new approach to producing a high quality deuterated non-animal-derived aminopolysaccharide for studying the structure-function association of biocomposite materials in drug delivery, tissue engineering and other bioactive chitosan-based composites.

On-surface cyclodehydrogenation reaction pathway determined by selective molecular deuterations.

Understanding the reaction mechanisms of dehydrogenative Caryl-Caryl coupling is the key to directed formation of π-extended polycyclic aromatic hydrocarbons. Here we utilize isotopic labeling to identify the exact pathway of cyclodehydrogenation reaction in the on-surface synthesis of model atomically precise graphene nanoribbons (GNRs). Using selectively deuterated molecular precursors, we grow seven-atom-wide armchair GNRs on a Au(111) surface that display a specific hydrogen/deuterium (H/D) pattern with characteristic Raman modes. A distinct hydrogen shift across the fjord of Caryl-Caryl coupling is revealed by monitoring the ratios of gas-phase by-products of H2, HD, and D2 with in situ mass spectrometry. The identified reaction pathway consists of a conrotatory electrocyclization and a distinct [1,9]-sigmatropic D shift followed by H/D eliminations, which is further substantiated by nudged elastic band simulations. Our results not only clarify the cyclodehydrogenation process in GNR synthesis but also present a rational strategy for designing on-surface reactions towards nanographene structures with precise hydrogen/deuterium isotope labeling patterns.

Fractionation of Lignin for Selective Shape Memory Effects at Elevated Temperatures.

We report a facile approach to control the shape memory effects and thermomechanical characteristics of a lignin-based multiphase polymer. Solvent fractionation of a syringylpropane-rich technical organosolv lignin resulted in selective lignin structures having excellent thermal stability coupled with high stiffness and melt-flow resistance. The fractionated lignins were reacted with rubber in melt-phase to form partially networked elastomer enabling selective programmability of the material shape either at 70 °C, a temperature that is high enough for rubbery matrix materials, or at an extremely high temperature, 150 °C. Utilizing appropriate functionalities in fractionated lignins, tunable shape fixity with high strain and stress recovery, particularly high-stress tolerance were maintained. Detailed studies of lignin structures and chemistries were correlated to molecular rigidity, morphology, and stress relaxation, as well as shape memory effects of the materials. The fractionation of lignin enabled enrichment of specific lignin properties for efficient shape memory effects that broaden the materials' application window. Electron microscopy, melt-rheology, dynamic mechanical analysis and ultra-small angle neutron scattering were conducted to establish morphology of acrylonitrile butadiene rubber (NBR)-lignin elastomers from solvent fractionated lignins.

A physical catalyst for the electrolysis of nitrogen to ammonia.

Ammonia synthesis consumes 3 to 5% of the world's natural gas, making it a significant contributor to greenhouse gas emissions. Strategies for synthesizing ammonia that are not dependent on the energy-intensive and methane-based Haber-Bosch process are critically important for reducing global energy consumption and minimizing climate change. Motivated by a need to investigate novel nitrogen fixation mechanisms, we herein describe a highly textured physical catalyst, composed of N-doped carbon nanospikes, that electrochemically reduces dissolved N2 gas to ammonia in an aqueous electrolyte under ambient conditions. The Faradaic efficiency (FE) achieves 11.56 ± 0.85% at -1.19 V versus the reversible hydrogen electrode, and the maximum production rate is 97.18 ± 7.13 µg hour-1 cm-2. The catalyst contains no noble or rare metals but rather has a surface composed of sharp spikes, which concentrates the electric field at the tips, thereby promoting the electroreduction of dissolved N2 molecules near the electrode. The choice of electrolyte is also critically important because the reaction rate is dependent on the counterion type, suggesting a role in enhancing the electric field at the sharp spikes and increasing N2 concentration within the Stern layer. The energy efficiency of the reaction is estimated to be 5.25% at the current FE of 11.56%.

Recycling Waste Polyester via Modification with a Renewable Fatty Acid for Enhanced Processability.

Polyethylene terephthalate (PET) waste often contains a large amount of thermally unstable contaminants and additives that negatively impacts processing. A reduced processing temperature is desired. In this work, we report using a renewably sourced tall oil fatty acid (TOFA) as a modifier for recycled PET. To that end, PET was compounded with TOFA at different concentrations and extruded at 240 °C. Phase transition behaviors characterized by thermal and dynamic mechanical analyses exhibit shifts in the melting and recrystallization temperatures of PET to lower temperatures and depression of glass transition temperature from 91 to 65 °C. Addition of TOFA also creates crystal-phase imperfection that slows recrystallization, an important processing parameter. Changes in the morphology of plasticized PET reduces and stabilizes the melt viscosity at 240 and 250 °C. Melt-spun, undrawn continuous filaments of diameter 36-46 µm made from these low-melting PET exhibit 29-38 MPa tensile strength, 2.7-2.8 GPa tensile modulus, and 20-36% elongation. These results suggest a potential path for reusing waste PET as high-performance polymeric fibers.

Rigid Oligomer from Lignin in Designing of Tough, Self-Healing Elastomers.

Converting lignin into well-defined compounds is often challenged by structural complexation and inorganic contamination induced by the pulping process. In this report, instead of breaking down lignin into small molecules, we extracted a uniform and rigid oligomer from the lignin waste stream. The multifunctional polyphenol oligomer containing carboxylic acid, alcohol, and phenol groups is highly reactive and brings stiffness into the material matrix. Tough and self-healing elastomers are economically prepared from this oligomer by a reaction with epoxy-terminated polyethylene glycol, without needing any solvent. Specifically, the polyaromatic backbone's rigidity enhances the elastomer's toughness, and the multiple polar substituents form a network of hydrogen bonding that heals the elastomer. Many other applications, including adhesives, hydrogels, coating, and metal scavengers, are envisioned based on this oligomer's unique properties.

Reduction-Triggered Self-Assembly of Nanoscale Molybdenum Oxide Molecular Clusters.

Understanding the formation mechanism of giant molecular clusters is essential for rational design and synthesis of cluster-based nanomaterials with required morphologies and functionalities. Here, typical synthetic reactions of a 2.9 nm spherical molybdenum oxide cluster, {Mo132} (formula: [Mo(VI)72Mo(V)60O372(CH3COO)30(H2O)72](42-)), with systematically varied reaction parameters have been fully explored to determine the morphologies and concentration of products, reduction of metal centers, and chemical environments of the organic ligands. The growth of these clusters shows a typical sigmoid curve, suggesting a general multistep self-assembly mechanism for the formation of giant molecular clusters. The reaction starts with a lag phase period when partial Mo(VI) centers of molybdate precursors are reduced to form {Mo(V)2(acetate)} structures under the coordination effect of the acetate groups. Once the concentration of {Mo(V)2(acetate)} reaches a critical value, it triggers the co-assembly of Mo(V) and Mo(VI) species into the giant clusters.

Nanoconfinement Inside Molecular Metal Oxide Clusters: Dynamics and Modified Encapsulation Behavior.

Encapsulation behavior, as well as the presence of internal catalytically active sites, has been spurring the applications of a 3 nm hollow spherical metal oxide cluster {Mo132 } as an encapsulation host and a nanoreactor. Due to its well-defined and tunable cluster structures, and nanoscaled internal void space comparable to the volumes of small molecules, this cluster provides a good model to study the dynamics of materials under nanoconfinement. Neutron scattering studies suggest that bulky internal ligands inside the cluster show slower and limited dynamics compared to their counterparts in the bulk state, revealing the rigid nature of the skeleton of the internal ligands. NMR studies indicate that the rigid internal ligands that partially cover the interfacial pore on the molybdenum oxide shells are able to block some large guest molecules from going inside the capsule cluster, which provides a convincing protocol for size-selective encapsulation and separation.

X-ray and Neutron Scattering Study of the Formation of Core-Shell-Type Polyoxometalates.

A typical type of core-shell polyoxometalates can be obtained through the Keggin-type polyoxometalate-templated growth of a layer of spherical shell structure of {Mo72Fe30}. Small-angle X-ray scattering is used to study the structural features and stability of the core-shell structures in aqueous solutions. Time-resolved small-angle X-ray scattering is applied to monitor the synthetic reactions, and a three-stage formation mechanism is proposed to describe the synthesis of the core-shell polyoxometalates based on the monitoring results. New protocols have been developed by fitting the X-ray data with custom physical models, which provide more convincing, objective, and completed data interpretation. Quasi-elastic and inelastic neutron scattering are used to probe the dynamics of water molecules in the core-shell structures, and two different types of water molecules, the confined and structured water, are observed. These water molecules play an important role in bridging core and shell structures and stabilizing the cluster structures.

Supramolecular polymerization of a prebiotic nucleoside provides insights into the creation of sequence-controlled polymers.

Self-assembly of a nucleoside on Au(111) was studied to ascertain whether polymerization on well-defined substrates constitutes a promising approach for making sequence-controlled polymers. Scanning tunneling microscopy and density functional theory were used to investigate the self-assembly on Au(111) of (RS)-N(9)-(2,3-dihydroxypropyl)adenine (DHPA), a plausibly prebiotic nucleoside analog of adenosine. It is found that DHPA molecules self-assemble into a hydrogen-bonded polymer that grows almost exclusively along the herringbone reconstruction pattern, has a two component sequence that is repeated over hundreds of nanometers, and is erasable with electron-induced excitation. Although the sequence is simple, more complicated ones are envisioned if two or more nucleoside types are combined. Because polymerization occurs on a substrate in a dry environment, the success of each combination can be gauged with high-resolution imaging and accurate modeling techniques. These characteristics make nucleoside self-assembly on a substrate an attractive approach for designing sequence-controlled polymers. Further, by choosing plausibly prebiotic nucleosides, insights may be provided into how nature created the first sequence-controlled polymers capable of storing information. Such insights, in turn, can inspire new ways of synthesizing sequence-controlled polymers.

Development of in situ Electrochemical Small-Angle Neutron Scattering (eSANS) for Simultaneous Structure and Redox Characterization of Nanoparticles.

An in situ electrochemical small-angle neutron scattering (eSANS) method was developed to measure simultaneously the redox properties and size, shape and interactions of solution-dispersed nanomaterials. By combining multi-step potentials and chronocoulometry readout with SANS, the structure and redox properties of engineered nanomaterials are followed in one experiment. Specifically, ZnO nanoparticles were examined as dilute dispersions in pH buffered deuterium oxide solutions under negative electrode potentials. The ZnO disk-shaped nanoparticles undergo an irreversible size transformation upon reduction at the vitreous carbon electrode. The decrease in average nanoparticle size near a current maximum shows the reduction reaction from ZnO to Zn occurs. The eSANS method provides nanometer scale sensitivity to nanoparticle size and shape changes due to an electrochemical reaction that is crucial to understand in energy, healthcare, and other applications.

Selectivity control in synergistic liquid-liquid anion exchange of univalent anions via structure-specific cooperativity between quaternary ammonium cations and anion receptors.

Two anion receptors enhance liquid-liquid anion exchange when added to quaternary alkylammonium chloride anion exchangers, but with a striking dependence on the structure of the alkylammonium cation that suggests a supramolecular cooperative effect. Two anion receptors were investigated, meso-octamethylcalix[4]pyrrole (C4P) and the bisthiourea tweezer 1,1'-(propane-1,3-diyl)bis(3-(4-sec-butylphenyl)thiourea (BTU). Whereas synergism is comparatively weak when either methyltri(C(8,10))alkylammonium chloride (Aliquat 336) or tetraheptylammonium chloride is used with the BTU receptor, synergism between C4P and Aliquat 336 is so pronounced that anion exchange prefers chloride over more extractable nitrate and trifluoroacetate, effectively overcoming the ubiquitous Hofmeister bias. A thermochemical analysis of synergistic anion exchange has been provided for the first time, resulting in the estimation of binding constants for C4P with the ion pairs of A336(+) with Cl(-), Br(-), OAc(F3)(-), NO(3)(-), and I(-).

Ion-pair triple helicates and mesocates self-assembled from ditopic 2,2'-bipyridine-bis(urea) ligands and Ni(II) or Fe(II) sulfate salts.

NiSO(4) and FeSO(4) self-assemble with heteroditopic ligands (L) comprising 2,2'-bipyridine and o-phenylene-(bis)urea cation- and anion-binding sites, respectively, into [ML(3)SO(4)] (M = Ni(2+), Fe(2+)) triple-stranded ion-pair helicates and mesocates.

Neutron reflectivity characterization of the photoacid reaction-diffusion latent and developed images of molecular resists for extreme ultraviolet lithography.

Lithographic feature size requirements have approached a few radius of gyration of photoresist polymers used in thin-film patterning. Furthermore, the feature dimensions are commensurate with the photoacid diffusion length that defines the underlying latent image. Smaller imaging building blocks may enable reduced feature sizes; however, resolution limits are also dependent upon the spatial extent of the photoacid-catalyzed reaction diffusion front and subsequent dissolution mechanism. The reaction-diffusion front was characterized by neutron reflectivity for ccc stereoisomer-purified, deuterium-labeled tert-butoxycarbonyloxy calix[4]resorcinarene molecular resists. The spatial extent of the reaction front exceeds the size of the molecular resist with an effective diffusion constant of (0.13 ± 0.06) nm(2)/s for reaction times longer than 60 s, with the maximum at shorter times. Comparison to a mean-field reaction-diffusion model shows that a photoacid trapping process provides bounds to the spatial and extent of reaction via a reaction-limited mechanism whereas the ratio of the reaction rate to trapping rate constants recovers the effective diffusion peak. Under the ideal step-exposure conditions, surface roughness was observed after either positive- or negative-tone development. However, negative-tone development follows a surface-restructuring mechanism rather than etch-like dissolution in positive-tone development.

Urea-functionalized M4L6 cage receptors: anion-templated self-assembly and selective guest exchange in aqueous solutions.

We present an extensive study of a novel class of de novo designed tetrahedral M(4)L(6) (M = Ni, Zn) cage receptors, wherein internal decoration of the cage cavities with urea anion-binding groups, via functionalization of the organic components L, led to selective encapsulation of tetrahedral oxoanions EO(4)(n-) (E = S, Se, Cr, Mo, W, n = 2; E = P, n = 3) from aqueous solutions, based on shape, size, and charge recognition. External functionalization with tBu groups led to enhanced solubility of the cages in aqueous methanol solutions, thereby allowing for their thorough characterization by multinuclear ((1)H, (13)C, (77)Se) and diffusion NMR spectroscopies. Additional experimental characterization by electrospray ionization mass spectrometry, UV-vis spectroscopy, and single-crystal X-ray diffraction, as well as theoretical calculations, led to a detailed understanding of the cage structures, self-assembly, and anion encapsulation. We found that the cage self-assembly is templated by EO(4)(n-) oxoanions (n ≥ 2), and upon removal of the templating anion the tetrahedral M(4)L(6) cages rearrange into different coordination assemblies. The exchange selectivity among EO(4)(n-) oxoanions has been investigated with (77)Se NMR spectroscopy using (77)SeO(4)(2-) as an anionic probe, which found the following selectivity trend: PO(4)(3-) ≫ CrO(4)(2-) > SO(4)(2-) > SeO(4)(2-) > MoO(4)(2-) > WO(4)(2-). In addition to the complementarity and flexibility of the cage receptor, a combination of factors have been found to contribute to the observed anion selectivity, including the anions' charge, size, hydration, basicity, and hydrogen-bond acceptor abilities.

Seven-coordinate anion complex with a tren-based urea: binding discrepancy of hydrogen sulfate in solid and solution states.

Structural characterization of a hydrogen sulfate complex with a tren-based urea suggests that the anion is coordinated with six NH···O bonds (d(N···O) = 2.857 (3) to 3.092 (3) Å) and one OH···O bond (d(O···O) = 2.57 (2) Å) from three receptors; however, in solution the anion is bound within the pseudo-cavity of one receptor.