Solid-Phase-Supported Chemoenzymatic Synthesis and Analysis of Chondroitin Sulfate Proteoglycan Glycopeptides.

Proteoglycans (PGs), consisting of glycosaminoglycans (GAGs) linked with the core protein through a tetrasaccharide linkage region, play roles in many important biological events. The chemical synthesis of PG glycopeptides is extremely challenging. In this work, the enzymes required for synthesis of chondroitin sulfate (CS) PG (CSPG) have been expressed and the suitable sequence of enzymatic reactions has been established. To expedite CSPG synthesis, the peptide acceptor was immobilized on solid phase and the glycan units were directly installed enzymatically onto the peptide. Subsequent enzymatic chain elongation and sulfation led to the successful synthesis of CSPG glycopeptides. The CS dodecasaccharide glycopeptide was the longest homogeneous CS glycopeptide synthesized to date. The enzymatic synthesis was much more efficient than the chemical synthesis of the corresponding CS glycopeptides, which could reduce the total number of synthetic steps by 80%. The structures of the CS glycopeptides were confirmed by mass spectrometry analysis and NMR studies. In addition, the interactions between the CS glycopeptides and cathepsin G were studied. The sulfation of glycan chain was found to be important for binding with cathepsin G. This efficient chemoenzymatic strategy opens new avenues to investigate the structures and functions of PGs.

Chemistry and Dynamics of Supercritical Carbon Dioxide and Methane in the Slit Pores of Layered Silicates.

ConspectusIn the mid 2010s, high-pressure diffraction and spectroscopic tools opened a window into the molecular-scale behavior of fluids under the conditions of many CO2 sequestration and shale/tight gas reservoirs, conditions where CO2 and CH4 are present as variably wet supercritical fluids. Integrating high-pressure spectroscopy and diffraction with molecular modeling has revealed much about the ways that supercritical CO2 and CH4 behave in reservoir components, particularly in the slit-shaped micro- and mesopores of layered silicates (phyllosilicates) abundant in caprocks and shales. This Account summarizes how supercritical CO2 and CH4 behave in the slit pores of swelling phyllosilicates as functions of the H2O activity, framework structural features, and charge-balancing cation properties at 90 bar and 323 K, conditions similar to a reservoir at ∼1 km depth. Slit pores containing cations with large radii, low hydration energy, and large polarizability readily interact with CO2, allowing CO2 and H2O to adsorb and coexist in these interlayer pores over a wide range of fluid humidities. In contrast, cations with small radii, high hydration energy, and low polarizability weakly interact with CO2, leading to reduced CO2 uptake and a tendency to exclude CO2 from interlayers when H2O is abundant. The reorientation dynamics of confined CO2 depends on the interlayer pore height, which is strongly influenced by the cation properties, framework properties, and fluid humidity. The silicate structural framework also influences CO2 uptake and behavior; for example, smectites with increasing F-for-OH substitution in the framework take up greater quantities of CO2. Reactions that trap CO2 in carbonate phases have been observed in thin H2O films near smectite surfaces, including a dissolution-reprecipitation mechanism when the edge surface area is large and an ion exchange-precipitation mechanism when the interlayer cation can form a highly insoluble carbonate. In contrast, supercritical CH4 does not readily associate with cations, does not react with smectites, and is only incorporated into interlayer slit mesopores when (i) the pore has a z-dimension large enough to accommodate CH4, (ii) the smectite has low charge, and (iii) the H2O activity is low. The adsorption and displacement of CH4 by CO2 and vice versa have been studied on the molecular scale in one shale, but opportunities remain to examine behavioral details in this more complicated, slit-pore inclusive system.

Thermochemistry of per- and polyfluoroalkyl substances.

The determination of gas phase thermochemical properties of per- and polyfluoroalkyl substances (PFAS) is central to understanding the long-range transport behavior of PFAS in the atmosphere. Prior gas-phase studies have reported the properties of perfluorinated sulfonic acid (PFOS) and perfluorinated octanoic acid (PFOA). Here, this study reports the gas phase enthalpies of formation of short- and long-chain PFAS and their precursor molecules determined using density functional theory (DFT) and ab initio approaches. Two density functionals, two ab initio methods and an empirical method were used to compute enthalpies of formation with the total atomization approach and an isogyric reaction. The performance of the computational methods employed in this work were validated against the experimental enthalpies of linear alkanoic acids and perfluoroalkanes. The gas-phase determinations will be useful for future studies of PFAS in the atmosphere, and the methodological choices will be helpful in the study of other PFAS.

Adsorption, Structure, and Dynamics of Short- and Long-Chain PFAS Molecules in Kaolinite: Molecular-Level Insights.

The ubiquitous presence of poly- and perfluoroalkyl substances (PFAS) in different natural settings poses a serious threat to environmental and human health. Soils and sediments represent one of the important exposure pathways of PFAS for humans and animals. With increasing bioaccumulation and mobility, it is extremely important to understand the interactions of PFAS molecules with the dominant constituents of soils such as clay minerals. This study reports for the first time the fundamental molecular-level insights into the adsorption, interfacial structure, and dynamics of short- and long-chain PFAS molecules at the water-saturated mesopores of kaolinite clay using classical molecular dynamics (MD) simulations. At environmental conditions, all the PFAS molecules are exclusively adsorbed near the hydroxyl surface of the kaolinite, irrespective of the terminal functional groups and metal cations. The interfacial adsorption structures and coordination environments of PFAS are strongly dependent on the nature of the functional groups and their hydrophobic chain length. The formation of large, aggregated clusters of long-chain PFAS at the hydroxyl surface of kaolinite is responsible for their restricted dynamics in comparison to short-chain PFAS molecules. Such comprehensive knowledge of PFAS at the clay mineral interface is critical to developing novel site-specific degradation and mitigation strategies.

A Mechanistic Exploration of Natural Organic Matter Aggregation and Surface Complexation in Smectite Mesopores.

Soil minerals and organic matter play critical roles in nutrient cycling and other life-essential biogeochemical processes, yet the structural and dynamical details of natural organic matter (NOM) film formation on smectites are not fully understood on the molecular scale. XRD of Suwannee River NOM-hectorite (a smectite clay) complexes shows that the humic and fulvic components of NOM bind predominantly at the external surfaces of packets of smectite platelets rather than in the interlayer slit pores, suggesting that the key behavior governing smectite-NOM interactions takes place in mesopores between smectite particles. New molecular dynamics modeling of a ∼110 ŠH2O-saturated smectite mesopore at near-neutral pH shows that model NOM molecules initially form small clusters of 2-3 NOM molecules near the center of the pore fluid. Formation of these clusters is driven by the hydrophobic mechanism, where aromatic/aliphatic regions associate with one another to minimize their interactions with H2O, and charge-balancing cations associated with the deprotonated carboxylate sites are located only at the outer surface of these clusters. Despite hydrophobicity driving the initial clustering, NOM clusters are formed more quickly when high-charge-density cations like Ca2+ are present vs low-charge-density cations like Cs+, as the former cations more effectively minimize the electrostatic repulsions between the negatively charged NOM molecules. Once the small hydrophobicity-driven NOM clusters form, the simulations show that Ca2+ promotes the aggregation of NOM clusters through tetradentate Ca2+ bridges involving carboxylate groups on two different NOM clusters. Importantly, our studies indicate that Ca2+ plays a crucial role in binding the NOM clusters to the smectite surface, which occurs through multiple quaternary complexes (Ob)-H2O-Ca2+-COO-NOM. In contrast, Cs+ never forms any coordination or acts like bridges between NOM molecules nor as ion bridges to the smectite surface. Additionally, we observe the formation of a metastable superaggregate involving all 16 NOM molecules several times in a Ca2+-bearing mesopore fluid. Superaggregates are never observed in the simulations involving Cs+. The modeling results are fully consistent with helium ion microscope images of NOM-hectorite complexes suggesting that NOM surface films develop when preformed NOM clusters interact with smectite surfaces. Overall, the binding of NOM clusters to the outer surfaces of smectite particles and the formation of large NOM aggregates at neutral pH occur through cation bridging, and cation bridging only occurs when high-charge-density cations like Ca2+ are present.

Understanding methane/carbon dioxide partitioning in clay nano- and meso-pores with constant reservoir composition molecular dynamics modeling.

The interactions among fluid species such as H2O, CO2, and CH4 confined in nano- and meso-pores in shales and other rocks is of central concern to understanding the chemical behavior and transport properties of these species in the earth's subsurface and is of special concern to geological C-sequestration and enhanced production of oil and natural gas. The behavior of CO2, and CH4 is less well understood than that of H2O. This paper presents the results of a computational modeling study of the partitioning of CO2 and CH4 between bulk fluid and nano- and meso-pores bounded by the common clay mineral montmorillonite. The calculations were done at 323 K and a total fluid pressure of 124 bars using a novel approach (constant reservoir composition molecular dynamics, CRC-MD) that uses bias forces to maintain a constant composition in the fluid external to the pore. This purely MD approach overcomes the difficulties in making stochastic particle insertion-deletion moves in dense fluids encountered in grand canonical Monte Carlo and related hybrid approaches. The results show that both the basal siloxane surfaces and protonated broken edge surfaces of montmorillonite both prefer CO2 relative to CH4 suggesting that methods of enhanced oil and gas production using CO2 will readily displace CH4 from such pores. This preference for CO2 is due to its preferred interaction with the surfaces and extends to approximately 20 Å from them.

Temperature dependent structure and dynamics in smectite interlayers: 23Na MAS NMR spectroscopy of Na-hectorite.

23Na MAS NMR spectroscopy of the smectite mineral hectorite acquired at temperatures from -120 °C to 40 °C in combination with the results from computational molecular dynamics (MD) simulations show the presence of complex dynamical processes in the interlayer galleries that depend significantly on their hydration state. The results indicate that site exchange occurs within individual interlayers that contain coexisting 1 and 2 water layer hydrates in different places. We suggest that the observed dynamical averaging may be due to motion of water volumes comparable to the dripplons recently proposed to occur in hydrated graphene interlayers (Yoshida et al. Nat. Commun., 2018, 9, 1496). Such motion would cause rippling of the T-O-T structure of the clay layers at frequencies greater than ∼25 kHz. For samples exposed to 0% relative humidity (R.H.), the 23Na spectra show the presence of two Na+ sites (probably 6 and 9 coordinated by basal oxygen atoms) that do not undergo dynamical averaging at any temperature from -120 °C to 40 °C. For samples exposed to R.H.s from 29% to 100% the spectra show the presence of three hydrated Na+ sites that undergo dynamical averaging beginning at -60 °C. These sites have different numbers of H2O molecules coordinating the Na+, and diffusion calculations indicate that they probably occur within the same individual interlayer. The average hydration state of Na+ increases with increasing R.H. and water content of the clay.

Tipping Point for Expansion of Layered Aluminosilicates in Weakly Polar Solvents: Supercritical CO2.

Layered aluminosilicates play a dominant role in the mechanical and gas storage properties of the subsurface, are used in diverse industrial applications, and serve as model materials for understanding solvent-ion-support systems. Although expansion in the presence of H2O is well-known to be systematically correlated with the hydration free energy of the interlayer cation, particularly in environments dominated by nonpolar solvents (i.e., CO2), uptake into the interlayer is not well-understood. Using novel high-pressure capabilities, we investigated the interaction of dry supercritical CO2 with Na-, NH4-, and Cs-saturated montmorillonite, comparing results with predictions from molecular dynamics simulations. Despite the known trend in H2O and that cation solvation energies in CO2 suggest a stronger interaction with Na, both the NH4- and Cs-clays readily absorbed CO2 and expanded, while the Na-clay did not. The apparent inertness of the Na-clay was not due to kinetics, as experiments seeking a stable expanded state showed that none exists. Molecular dynamics simulations revealed a large endothermicity to CO2 intercalation in the Na-clay but little or no energy barrier for the NH4- and Cs-clays. Indeed, the combination of experiment and theory clearly demonstrate that CO2 intercalation of Na-montmorillonite clays is prohibited in the absence of H2O. Consequently, we have shown for the first time that in the presence of a low dielectric constant, gas swelling depends more on the strength of the interaction between the interlayer cation and aluminosilicate sheets and less on that with solvent. The finding suggests a distinct regime in layered aluminosilicate swelling behavior triggered by low solvent polarizability, with important implications in geomechanics, storage, and retention of volatile gases, and across industrial uses in gelling, decoloring, heterogeneous catalysis, and semipermeable reactive barriers.