Combining Rosetta Sequence Design with Protein Language Model Predictions Using Evolutionary Scale Modeling (ESM) as Restraint

Computational protein sequence design has the ambitious goal of modifying existing or creating new proteins; however, designing stable and functional proteins is challenging without predictability of protein dynamics and allostery. Informing protein design methods with evolutionary information limits the mutational space to more native-like sequences and results in increased stability while maintaining functions. Recently, language models, trained on millions of protein sequences, have shown impressive performance in predicting the effects of mutations. Assessing Rosetta-designed sequences with a language model showed scores that were worse than those of their original sequence. To inform Rosetta design protocols with language model predictions, we added a new metric to restrain the energy function during design using the Evolutionary Scale Modeling (ESM) model. The resulting sequences have better language model scores and similar sequence recovery, with only a minor decrease in the fitness as assessed by Rosetta energy. In conclusion, our work combines the strength of recent machine learning approaches with the Rosetta protein design toolbox.

Screening Efficient C-N Coupling Catalysts for Electrosynthesis of Acetamide and Output Ammonia through a Cascade Strategy of Electrochemical CO2 and N2 Reduction Using Cu-Based Nitrogen-Carbon Nanosheets

Due to the limitation of the high-value-added products obtained from electrocatalytic CO2 reduction within an acid environment, introducing additional elements can expand the diversity of the products obtained during the CO2 reduction reaction (CO2RR) and nitrogen reduction reaction (NRR). Thus, coelectroreduction of CO2 and N2 is a new strategy for producing acetamide (CH3CONH2) via both C-C and C-N bond coupling using Cu-based nitrogen-carbon nanosheets. CO2 can reduce to CO, and a key ketene (*C═C═O) can be generated from *CO*CO dimerization; this ketene is postulated as an intermediate in the formation of acetamide. However, most studies focus on promoting the C-C bond formation. Here, we propose that C-N bond coupling can form acetamide through the interaction of *C═C═O with NH3. The acetamide is formed via a nucleophilic attack between *NH3 and the *C═C═O intermediate. The C-N coupling mechanism was successfully applied to expand the variety of nitrogen-containing products obtained from CO2 and N2 coreduction. Thus, we successfully screened Cu2-based graphite and Cu-based C3N4 as catalysts that can produce C2+ compounds by integrating CO dimerization with acetamide synthesis. In addition, we observed that Cu2-based C2N and Cu-based C3N4 catalysts are suitable for the NRR. Cu-based C3N4 showed high CO2RR and NRR activities with small negative limiting potential (UL) values of -0.83 and -0.58 V compared to those of other candidates, respectively. The formation of *COHCOH from *COHCO was considered the rate-determining step (RDS) during acetamide electrosynthesis. The limiting potential value of Cu2-based C2N was only -0.46 V for NH3 synthesis, and the formation of *NNH was via the RDS via an alternating path. The adsorption energy difference analysis both CO2 and N2 compare with the hydrogen evolution reaction (HER), suggesting that Cu2-based C2N exhibited the highest CO2RR and NRR selectivity among the 13 analyzed catalysts. The results of this study provide innovative insights into the design principle of Cu-based nitrogen-carbon electrocatalysts for generating highly efficient C-N coupling products.

The stability of oxygen-centered radicals and its response to hydrogen bonding interactions

The stability of various alkoxy/aryloxy/peroxy radicals, as well as TEMPO and triplet dioxygen (3 O2 ) has been explored at a variety of theoretical levels. Good correlations between RSEtheor and RSEexp are found for hybrid DFT methods, for compound schemes such as G3B3-D3, and also for DLPNO-CCSD(T) calculations. The effects of hydrogen bonding interactions on the stability of oxygen-centered radicals have been probed by addition of a single solvating water molecule. While this water molecule always acts as a H-bond donor to the oxygen-centered radical itself, it can act as a H-bond donor or acceptor to the respective closed-shell parent.

Infrastructure in the Age of Pandemics: Utilizing Polypropylene-Based Mask Waste for Durable and Sustainable Road Pavements

When navigating the environmental exigencies precipitated by global pandemics, the escalation of mask waste presents a multifaceted dilemma. In this avant-garde research, we unveil a novel approach: harnessing the sterilized shredded mask residues (SMRs), predominantly composed of 100 wt. % polypropylene, as pioneering modifiers for asphalt. Distinct proportions of SMR (e.g., 3, 6, and 9 wt. %) were judiciously integrated with fresh-virgin base AP-5 asphalt and subjected to an extensive suite of state-of-the-art examinations, encompassing thin-layer chromatography-flame ionization detection (TLC-FID), Fourier-transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and specific rheological metrics. The TLC-FID diagnostic trajectories highlighted the nuanced rejuvenating influence of SMR on the binder, a facet reinforced by a pronounced elevation in the thermodynamic stability index (IC). The FT-IR spectra elucidated SMR's preeminent role as a filler, negating notions of chemical reactivity. The TGA analyses unveiled an elevated thermal onset of degradation, signposting enhanced thermal resilience, whereas the DSC readings illuminated a superior thermal comportment at lower extremities. The SEM evaluations rendered a clearer panorama: there was heightened textural perturbation at escalated SMR incorporations, yet the 3 wt. % concoction showcased an optimal, coherent microtexture symbiosis with asphalt. The rheological scrutinies revealed a systematic trajectory: a diminishing penetration and ductility countered by ascending softening points and viscosity metrics. The coup de maître stemmed from the DSR analyses, unequivocally validating SMR's unparalleled prowess in curtailing rutting distress. This seminal inquiry not only posits a blueprint for refined pavement longevity but also champions a sustainable countermeasure to pandemic-propelled waste, epitomizing the confluence of environmental prudence an d infrastructural fortitude.

Characterization and Antifungal Activity of Lemongrass Essential Oil-Loaded Nanoemulsion Stabilized by Carboxylated Cellulose Nanofibrils and Surfactant

Nanocellulose is an emerging green, biodegradable and biocompatible nanomaterial with negligible toxicities. In this study, a carboxylated nanocellulose (i.e., 2,2,6,6-tetramethylpiperidin-1-oxyl (TEMPO)-oxidized cellulose nanofibril (TEMPO-CNF)) was prepared from corn stover and characterized by X-ray diffraction (XRD), Fourier Transform Infrared Spectroscopy (FTIR) and differential scanning calorimetry (DSC)/thermogravimetric analysis (TGA). Corn stover-derived TEMPO-CNF was explored as an emulsion co-stabilizer together with Tween 80 for lemongrass essential oil-loaded emulsions. Droplet size, phase behavior and thermodynamic stability of oil-in-water emulsions stabilized by Tween 80 and TEMPO-CNF were investigated. The optimal nanoemulsion stabilized by this binary stabilizer could achieve a mean particle size of 19 nm, and it did not form any phase separation against centrifugal forces, freeze-thaw cycles and at least 30 days of room temperature storage. The nanoencapsulated essential oil had better inhibition activity against the mycelial growth of Aspergillus flavus than pure essential oil. Results from this study demonstrate the potential of using agricultural byproduct-derived nanomaterial as nanoemulsion stabilizers for essential oils with good emulsion thermodynamic stability as well as enhanced antifungal activities.

Structural Transformation of Unconventional-Phase Materials

The structural transformation of materials, which involves the evolution of different structural features, including phase, composition, morphology, etc., under external conditions, represents an important fundamental phenomenon and has drawn substantial research interest. Recently, materials with unconventional phases that are different from their thermodynamically stable ones have been demonstrated to possess distinct properties and compelling functions and can further serve as starting materials for structural transformation studies. The identification and mechanism study of the structural transformation process of unconventional-phase starting materials can not only provide deep insights into their thermodynamic stability in potential applications but also offer effective approaches for the synthesis of other unconventional structures. Here, we briefly summarize the recent research progress on the structural transformation of some typical starting materials with various unconventional phases, including the metastable crystalline phase, amorphous phase, and heterophase, induced by different approaches. The importance of unconventional-phase starting materials in the structural modulation of resultant intermediates and products will be highlighted. The employment of diverse in situ/operando characterization techniques and theoretical simulations in studying the mechanism of the structural transformation process will also be introduced. Finally, we discuss the existing challenges in this emerging research field and provide some future research directions.

Not all 2',4'-bridged modifications stabilize DNA/RNA duplexes

2',4'-Bridged modifications such as 2'-O,4'-C-methylene-bridged nucleotides (LNAs) and 2'-O,4'-C-ethylene-bridged nucleotides (ENAs) provide high binding affinity for duplex formation. Stabilization by the introduction of the bridged nucleic acids is considered to be due to pre-organization. In this study, we found that the introduction of 2',4'-C-bridged 2'-deoxynucleotides (CRNs; Conformationally Restricted Nucleotides) into DNA/RNA duplexes leads to destabilization, as opposed to the previously accepted notion that 2',4'-bridged modifications always lead to stabilization.

Key Allosteric and Active Site Residues of SARS-CoV-2 3CLpro Are Promising Drug Targets

The main protease of SARS-CoV-2, 3-chymotrypsin-like protease (3CLpro), is a prominent target for antiviral development due to its essential role in the viral life cycle. Research has largely focused on competitive inhibitors of 3CLpro that target the active site. However, allosteric sites distal to the peptide substrate-binding region are also potential targets for the design of reversible noncompetitive inhibitors. Computational analyses have examined the importance of key contacts at allosteric sites of 3CLpro, but these contacts have not been validated experimentally. In this work, four druggable pockets spanning the surface of SARS-CoV-2 3CLpro were predicted: pocket 1 is the active site, whereas pockets 2, 3, and 4 are located away from the active site at the interface of domains II and III. Site-directed alanine mutagenesis of selected residues with important structural interactions revealed that 7 of 13 active site residues (N28, R40, Y54, S147, Y161, D187 and Q192) and 7 of 12 allosteric site residues (T111, R131, N133, D197, N203, D289 and D295) are essential for maintaining catalytically active and thermodynamically stable 3CLpro. Alanine substitution at these key amino acid residues inactivated or reduced the activity of 3CLpro. In addition, the thermodynamic stability of 3CLpro decreased in the presence of some of these mutations. This work provides experimental validation of essential contacts in the active and allosteric sites of 3CLpro that could be targeted with competitive and noncompetitive inhibitors as new therapeutics against COVID-19.

Adsorption Characteristics between Ti Atoms of TiO2(100) and Corrosive Species of CO2-H2S-Cl- System in Oil and Gas Fields

The service environment of OCTG (Oil Country Tubular Goods) in oil and gas fields is becoming more and more severe due to the strong affinity between ions or atoms of corrosive species coming from solutions and metal ions or atoms on metals. While it is difficult for traditional technologies to accurately analyze the corrosion characteristics of OCTG in CO₂-H₂S-Cl^- systems, it is necessary to study the corrosion-resistant behavior of TC4 (Ti-6Al-4V) alloys based on an atomic or molecular scale. In this paper, the thermodynamic characteristics of the TiO₂(100) surface of TC4 alloys in the CO₂-H₂S-Cl^- system were simulated and analyzed by first principles, and the corrosion electrochemical technologies were used to verify the simulation results. The results indicated that all of the best adsorption positions of corrosive ions (Cl^-, HS^-, S^2-, HCO₃^-, and CO₃^2-) on TiO₂(100) surfaces were bridge sites. A forceful charge interaction existed between Cl, S, and O atoms in Cl^-, HS^-, S^2-, HCO₃^-, CO₃^2-, and Ti atoms in TiO₂(100) surfaces after adsorption in a stable state. The charge was transferred from near Ti atoms in TiO₂ to near Cl, S, and O atoms in Cl^-, HS^-, S^2-, HCO₃^-, and CO₃^2-. Electronic orbital hybridization occurred between 3p⁵ of Cl, 3p⁴ of S, 2p⁴ of O, and 3d² of Ti, which was chemical adsorption. The effect strength of five corrosive ions on the stability of TiO₂ passivation film was S^2- > CO₃^2- > Cl^- > HS^- > HCO₃^-. In addition, the corrosion current density of TC4 alloy in different solutions containing saturated CO₂ was as follows: NaCl + Na₂S + Na₂CO₃ > NaCl + Na₂S > NaCl + Na₂CO₃ > NaCl. At the same time, the trends of R_s (solution transfer resistance), R_ct (charge transfer resistance), and R_c (ion adsorption double layer resistance) were opposite to the corrosion current density. The corrosion resistance of TiO₂ passivation film to corrosive species was weakened owing to the synergistic effect of corrosive species. Severe corrosion resulted, especially pitting corrosion, which further proved the simulation results mentioned above. Thus, this outcome provides the theoretical support to reveal the corrosion resistance mechanism of OCTG and to develop novel corrosion inhibitors in CO₂-H₂S-Cl^- environments.

Nano-Gels: Recent Advancement in Fabrication Methods for Mitigation of Skin Cancer

In the 21st century, melanoma and non-melanoma skin cancers have become an epidemic outbreak worldwide. Therefore, the exploration of all potential preventative and therapeutic measures based on either physical or bio-chemical mechanisms is essential via understanding precise pathophysiological pathways (Mitogen-activated protein kinase, Phosphatidylinositol 3-kinase Pathway, and Notch signaling pathway) and other aspects of such skin malignancies. Nano-gel, a three-dimensional polymeric cross-linked porous hydrogel having a diameter of 20-200 nm, possesses dual properties of both hydrogel and nanoparticle. The capacity of high drug entrapment efficiency with greater thermodynamic stability, remarkable solubilization potential, and swelling behavior of nano-gel becomes a promising candidate as a targeted drug delivery system in the treatment of skin cancer. Nano-gel can be either synthetically or architectonically modified for responding to either internal or external stimuli, including radiation, ultrasound, enzyme, magnetic, pH, temperature, and oxidation-reduction to achieve controlled release of pharmaceuticals and several bio-active molecules such as proteins, peptides, genes via amplifying drug aggregation in the active targeted tissue and reducing adverse pharmacological effects. Several drugs, such as anti-neoplastic biomolecules having short biological half-lives and prompt enzyme degradability capacity, must be appropriate for administration employing either chemically bridged or physically constructed nano-gel frameworks. The comprehensive review summarizes the advancement in the preparation and characterization methods of targeted nano-gel with enhanced pharmacological potential and preserved intracellular safety limits for the mitigation of skin malignancies with a special emphasize on skin cancer inducing pathophysiological pathways and prospective research opportunities for skin malignancy targeted nano-gels.

High-Temperature Mechanical and Dynamical Properties of γ-(U,Zr) Alloys

High-temperature body-centered cubic (BCC) γ-U is effectively stablized by γ-(U,Zr) alloys that also make it feasible to use it as a nuclear fuel. However, relatively little research has focused on γ-(U,Zr) alloys due to their instability at room temperature. The effect of Zr composition on its mechanical properties is not clear yet. Herein, we perform molecular dynamics simulations to investigate the mechanical and dynamical stabilities of γ-(U,Zr) alloys under high temperatures, and we calculate the corresponding lattice constants, various elastic moduli, Vickers hardness, Debye temperature, and dynamical structure factor. The results showed that γ-U, β-Zr, and γ-(U,Zr) are all mechanically and dynamically stable at 1200 K, which is in good agreement with the previously reported high-temperature phase diagram of U-Zr alloys. We found that the alloying treatment on γ-U with Zr can effectively improve its mechanical strength and melting points, such as Vickers hardness and Debye temperature, making it more suitable for nuclear reactors. Furthermore, the Zr concentrations in γ-(U,Zr) alloys have an excellent effect on these properties. In addition, the dynamical structure factor reveals that γ-U shows different structural features after alloying with Zr. The present simulation data and insights could be significant for understanding the structures and properties of UZr alloy under high temperatures.

Equiatomic binary phases of Copper-Rare Earth Elements. An overview of monocuprides from first-principles calculations

Equiatomic binary phases of copper with rare earth (RE) elements exhibit either primitive cubic ( P m 3 ‾ m ${Pm\bar 3m}$ ) or orthorhombic (Pnma) structures and in some cases both. By using density functional theory (DFT), we calculated the enthalpies of formation along the series of RE elements combined equimolarly with copper. For RE from Sc to Lu, the calculated enthalpies of formation fall in the range -49.8 kJ/mol for LuCu to -9.1 kJ/mol for the least thermodynamically stable CeCu. Except NdCu, all the other cubic or orthorhombic compounds exhibit lattice stability. Either forms of NdCu indicated lattice instability. Along the Sc-group, the hypothetical primitive cubic and orthorhombic forms of LuCu are found thermodynamically and mechanically stable. The overall trend of the formation enthalpies as a function of the Meyer Periodic Number is consistent with the energy trend of the 4 f-orbital filling as moving from Sc to Lu monocuprides. In addition, the calculated Gibbs free energies indicate that the thermodynamic stability is largely due to the entropic contributions. All standard DFT calculations were also repeated with DFT+U to better describe the correlation between the 5d-4f and 3d shells of RECu compounds. It has been found that DFT+U slightly affects the enthalpies of formation of RECu binaries. Moreover, DFT+U shifts up the f-band energies of RECu with light RE elements (such as La, Ce and Pr) and in contrast lowers them in the case of RECu with heavy RE elements from Nd to Lu.

Thermodynamic stability of human lipocalin-type prostaglandin D synthase under various pH conditions

Lipocalin-type prostaglandin D synthase (L-PGDS) binds various hydrophobic small molecules. Since we aim to use human L-PGDS as a carrier in a drug delivery system (DDS) for poorly water-soluble drugs, quality control of the protein is indispensable. In this study, we investigated the thermodynamic stability of human L-PGDS under various pH conditions. Differential scanning calorimetry revealed that the thermal unfolding of L-PGDS was an almost-reversible two-state transition between the native and unfolded states over the pH range from 2.5 to 7.4. The linear relationship of ΔH(Tm) to Tm in this pH range gave a heat capacity change (ΔCp) of 4.76 kJ/(K·mol), which was small compared to those commonly found in globular proteins. The temperature-dependent free energy of unfolding, ΔG(T), specified by Tm, ΔH(Tm), and ΔCp, showed a pH dependence with the highest value at pH 7.4 closest to the isoelectric point of 8.3. The small value of Cp resulted in a large value of ΔG(T), which contributed to the stability of the protein. Taken together, these results demonstrated that human L-PGDS is sufficiently thermostable for storage and practical use and can be useful as a delivery vehicle of protein-based DDS.

Symplectic Geometry Aspects of the Parametrically-Dependent Kardar-Parisi-Zhang Equation of Spin Glasses Theory, Its Integrability and Related Thermodynamic Stability

A thermodynamically unstable spin glass growth model described by means of the parametrically-dependent Kardar-Parisi-Zhang equation is analyzed within the symplectic geometry-based gradient-holonomic and optimal control motivated algorithms. The finitely-parametric functional extensions of the model are studied, and the existence of conservation laws and the related Hamiltonian structure is stated. A relationship of the Kardar-Parisi-Zhang equation to a so called dark type class of integrable dynamical systems, on functional manifolds with hidden symmetries, is stated.

Stability and Strength of Monolayer Polymeric C60

Two-dimensional fullerene networks have been synthesized in several forms, and it is unknown which monolayer form is stable under ambient conditions. Using first-principles calculations, I show that the believed stability of the quasi-tetragonal phases is challenged by mechanical, dynamic, or thermodynamic stability. For all temperatures, the quasi-hexagonal phase is thermodynamically the least stable. However, the relatively high dynamic and mechanical stabilities suggest that the quasi-hexagonal phase is intrinsically stronger than the other phases under various strains. The origin of the high stability and strength of the quasi-hexagonal phase can be attributed to the strong covalent C-C bonds that strongly hold the linked C₆₀ clusters together, enabling the closely packed hexagonal network. These results rationalize the experimental observations that so far only the quasi-hexagonal phase has been exfoliated experimentally as monolayers.

On the Chemical Origin of Biological Cognition

One of life's most striking characteristics is its mental dimension, one whose very existence within a material system has long been a deep scientific mystery. Given the current scientific view that life emerged from non-life, how was it possible for 'dead' matter to have taken on mental capabilities? In this Perspective we describe the existence of a recently discovered non-equilibrium state of matter, an energized dynamic kinetic state, and demonstrate how particular chemical systems once activated into that kinetic state could manifest rudimentary cognitive behavior. Thus, contrary to a common view that biology is not reducible to physics and chemistry, recent findings in both chemistry and biology suggest that life's mental state is an outcome of its physical state, and therefore may be explicable in physical/chemical terms. Such understanding offers added insight into the physico-chemical process by which life was able to emerge from non-life and the perennial 'what is life?' question. Most remarkably, it appears that Darwin, through his deep understanding of the evolutionary process, already sensed the existence of a connection between life's physical and mental states.

Biochemical and biophysical properties of an unreported T96R mutation causing transthyretin cardiac amyloidosis

OBJECTIVES

We presented an unreported T96R mutation induced transthyretin cardiac amyloidosis (ATTR). The biochemical and biophysical properties were explored to support its pathogenicity.

BACKGROUND

Understanding the biochemical and biophysical nature of genetically mutated transthyretin (TTR) proteins is key to provide precise medical cares for ATTR patients.

RESULTS

Genetic testing showed heterozygosity for the T96R pathogenic variant c.347C > G (ATTR p.T116R) after myocardial biopsy confirmed amyloid deposition. Biochemical characterizations revealed slight perturbation of its thermodynamic stability (C_m=3.7 M for T96R, 3.4 M for WT and 2.3 M for L55P (commonly studied TTR mutant)) and kinetic stability (t_1/2=39.8 h for T96R, 42 h for WT and 4.4 h in L55P). Crosslinking experiment demonstrated heterozygous subunit exchange between wild-type and TTR T96R protein destabilized the tetramer. Inhibitory effect of tafamidis and diflunisal on TTR T96R fibril formation was slightly less effective compared to WT and L55P.

CONCLUSIONS

A novel T96R mutation was identified for TTR protein. Biochemical and biophysical analyses revealed slightly destabilized kinetic stability. T96R mutation destabilized heterozygous protein but not proteolytic degradation, explaining its pathogenicity. Inhibitory effect of small molecule drugs on T96R mutation was different, suggesting personalized treatment may be required.

Charge-Compensated N-Doped π-Conjugated Polymers: Toward both Thermodynamic Stability of N-Doped States in Water and High Electron Conductivity

The understanding and applications of electron-conducting π-conjugated polymers with naphtalene diimide (NDI) blocks show remarkable progress in recent years. Such polymers demonstrate a facilitated n-doping due to the strong electron deficiency of the main polymer chain and the presence of the positively charged side groups stabilizing a negative charge of the n-doped backbone. Here, the n-type conducting NDI polymer with enhanced stability of its n-doped states for prospective "in-water" applications is developed. A combined experimental-theoretical approach is used to identify critical features and parameters that control the doping and electron transport process. The facilitated polymer reduction ability and the thermodynamic stability in water are confirmed by electrochemical measurements and doping studies. This material also demonstrates a high conductivity of 10^-2  S cm^-1  under ambient conditions and 10^-1  S cm^-1  in vacuum. The modeling explains the stabilizing effects  for various dopants. The simulations show a significant doping-induced "collapse" of the positively charged side chains on the core bearing a partial negative charge. This explains a decrease in the lamellar spacing observed in experiments. This study fundamentally enables a novel pathway for achieving both thermodynamic stability of the n-doped states in water and the high electron conductivity of polymers.

New evaluation of the thermodynamics stability for bcc-Fe

The thermodynamic properties for bcc-Fe were predicted by combination of the first-principles calculations, the quasiharmonic approximation, the CALPHAD method and the Weiss molecular field theory. The hybrid method considers the effects of the lattice vibration, electron, intrinsic magnetism and external magnetic fields on the thermodynamic properties at finite temperature. Combined with experimental data, the calculated heat capacity without external magnetic fields was used to verify the validity of the hybrid method. Close to the Fermi level the high electronic density of states leads to a significant electronic contribution to free energy. Near the Curie temperature lattice vibrations dominant the Gibbs free energy. The order of the other three excitation contributions to Gibbs free energy from high to low is: intrinsic magnetism > electron > external magnetic fields. The investigation suggests that all the excitation contributions to Gibbs free energy are not negligible which provides a correct direction for tuning the thermodynamic properties for Fe-based alloy.

Impact of the PEG length and PEGylation site on the structural, thermodynamic, thermal, and proteolytic stability of mono-PEGylated alpha-1 antitrypsin

Conjugation to polyethylene glycol (PEG) is a widely used approach to improve the therapeutic value of proteins essentially by prolonging their body residence time. PEGylation may however induce changes in the structure and/or the stability of proteins and thus on their function(s). The effects of PEGylation on the thermodynamic stability can either be positive (stabilization), negative (destabilization), or neutral (no effect). Moreover, various factors such as the PEG length and PEGylation site can influence the consequences of PEGylation on the structure and stability of proteins. In this study, the effects of PEGylation on the structure, stability, and polymerization of alpha1-antitrypsin (AAT) were investigated, using PEGs with different lengths, different structures (linear or 2-armed) and different linking chemistries (via amine or thiol) at two distinct positions of the sequence. The results show that whatever the size, position, and structure of PEG chains, PEGylation (a) does not induce significant changes in AAT structure (either at the secondary or tertiary level); (b) does not alter the stability of the native protein upon both chemical- and heat-induced denaturation; and (c) does not prevent AAT to fully refold and recover its activity following chemical denaturation. However, the propensity of AAT to aggregate upon heat treatment was significantly decreased by PEGylation, although PEGylation did not prevent the irreversible inactivation of the enzyme. Moreover, conjugation to PEG, especially 2-armed 40 kDa PEG, greatly improved the proteolytic resistance of AAT. PEGylation of AAT could be a promising strategy to prolong its half-life after infusion in AAT-deficient patients and thereby decrease the frequency of infusions.

Unraveling Thermodynamic and Kinetic Contributions to the Stability of Doped Nanocrystalline Alloys using Nanometallic Multilayers

Targeted doping of grain boundaries is widely pursued as a pathway for combating thermal instabilities in nanocrystalline metals. However, certain dopants predicted to produce grain-boundary-segregated nanocrystalline configurations instead form small nanoprecipitates at elevated temperatures that act to kinetically inhibit grain growth. Here, thermodynamic modeling is implemented to select the Mo-Au system for exploring the interplay between thermodynamic and kinetic contributions to nanostructure stability. Using nanoscale multilayers and in situ transmission electron microscopy thermal aging, evolving segregation states and the corresponding phase transitions are mapped with temperature. The microstructure is shown to evolve through a transformation at lower homologous temperatures (<600 °C) where solute atoms cluster and segregate to the grain boundaries, consistent with predictions from thermodynamic models. An increase in temperature to 800 °C is accompanied by coarsening of the grain structure via grain boundary migration but with multiple pinning events uncovered between migrating segments of the grain boundary and local solute clustering. Direct comparison between the thermodynamic predictions and experimental observations of microstructure evolution thus demonstrates a transition from thermodynamically preferred to kinetically inhibited nanocrystalline stability and provides a general framework for decoupling contributions to complex stability transitions while simultaneously targeting a dominant thermal stability regime.

Key dimer interface residues impact the catalytic activity of 3CLpro, the main protease of SARS-CoV-2

3C-like protease (3CLpro) is one of two proteases that process and liberate functional viral proteins essential for the maturation and infectivity of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19. It has been suggested that 3CLpro is catalytically active as a dimer, making the dimerization interface a target for antiviral development. Guided by structural analysis, here we introduced single amino acid substitutions at nine residues at three key sites of the dimer interface to assess their impact on dimerization and activity. We show that at site 1, alanine substitution of S1 or E166 increased by 2-fold or reduced relative activity, respectively. At site 2, alanine substitution of S10 or E14 eliminated activity, whereas K12A exhibited ∼60% relative activity. At site 3, alanine substitution of R4, E290, or Q299 eliminated activity, whereas S139A exhibited 46% relative activity. We further found the oligomerization states of the dimer interface mutants varied; the inactive mutants R4A, R4Q, S10A/C, E14A/D/Q/S, E290A, and Q299A/E were present as dimers, demonstrating that dimerization is not an indication of catalytically active 3CLpro. In addition, present mostly as monomers, K12A displayed residual activity, which could be attributed to the conspicuous amount of dimer present. Finally, differential scanning calorimetry did not reveal a direct relationship between the thermodynamic stability of mutants with oligomerization or catalytic activity. These results provide insights on two allosteric sites, R4/E290 and S10/E14, that may promote the design of antiviral compounds that target the dimer interface rather than the active site of SARS-CoV-2 3CLpro.

Lornoxicam-Loaded Chitosan-Decorated Nanoemulsion: Preparation and In Vitro Evaluation for Enhanced Transdermal Delivery

Nanoemulsions are promising drug delivery systems for the administration of poorly soluble drugs like lornoxicam (LRX) by oral or parenteral routes. Such formulations work perfectly for transdermal delivery of lornoxicam-type drugs. It has also been established that formulating such a delivery system is highly dependent on the presence, type, and concentration of excipients taking part in the formulation. The inherent characteristics of nanoemulsion (NE), i.e., smaller globule size and excipient nature, facilitate the drug's passage through skin. The current study was aimed at the development of an NE-based formulation of LRX to improve the drug solubility in vitro as well as to enhance drug skin permeation to promote therapeutic outcome in appropriate time. Spontaneous self-emulsification technique was utilized to develop optimized LRX-encapsulated NE-based formulations. ATR-FTIR spectra of the pure drug and various formulations did not show any interaction between the drug and various formulation excipients showing compatibility. Globule size for stable formulations ranged between 63-168 nm. These formulations were characterized for viscosity, surface tension, pH, drug encapsulation efficiency, in vitro drug release, and drug skin permeation studies. Chitosan-decorated optimized NE formulation of LRX showed about 58.82% cumulative drug release, showing an anomalous non-Fickian diffusion mechanism of drug release. Drug encapsulation efficiency, in vitro drug release, and skin permeation studies exhibited promising results. An appreciable drug entrapment efficiency was exhibited by optimized NE formulations LRX-6, 71.91 ± 3.17% and C-LRX, 65.25 ± 4.89%. Permeability parameters like enhancement ratio (Er), permeability constant (Kp), and steady state flux (Jss) showed higher values and exhibited good results based on formulation type. The selected promising formulation type "LRX-6" showed significantly different results as compared to other formulations (LRX-4, 5, and 7). The skin permeation property of the LRX-6 formulation was compared to similar chitosan-based formulations and was found to have better skin permeation results than chitosan-based formulations. This study clearly exhibited that an LRX-containing NE-based formulation can be formulated to form a stable drug delivery system. Such formulations are promising in terms of physicochemical characteristics, improved solubility, and high skin permeation potential.

Remarked suppression of Aβ42 protomer-protomer dissociation reaction elucidated by molecular dynamics simulation

Multimeric protein complexes are molecular apparatuses to regulate biological systems and often determine their fate. Among proteins forming such molecular assemblies, amyloid proteins have drawn attention over a half-century since amyloid fibril formation of these proteins is supposed to be a common pathogenic cause for neurodegenerative diseases. This process is triggered by the accumulation of fibril-like aggregates, while the microscopic mechanisms are mostly elusive due to technical limitation of experimental methodologies in individually observing each of diverse aggregate species in the aqueous solution. We then addressed this problem by employing atomistic molecular dynamics simulations for the paradigmatic amyloid protein, amyloid-β (Aβ₄₂ ). Seven different dimeric forms of oligomeric Aβ₄₂ fibril-like aggregate in aqueous solution, ranging from tetramer to decamer, were considered. We found additive effects of the size of these fibril-like aggregates on their thermodynamic stability and have clarified kinetic suppression of protomer-protomer dissociation reactions at and beyond the point of pentamer dimer formation. This observation was obtained from the specific combination of the Aβ₄₂ protomer structure and the physicochemical condition that we here examined, while it is worthwhile to recall that several amyloid fibrils take dimeric forms of their protomers. We could thus conclude that the stable formation of fibril-like protomer dimer should be involved in a turning point where rapid growth of amyloid fibrils is triggered.

How the Chemical Properties of GBCAs Influence Their Safety Profiles In Vivo

The extracellular class of gadolinium-based contrast agents (GBCAs) is an essential tool for clinical diagnosis and disease management. In order to better understand the issues associated with GBCA administration and gadolinium retention and deposition in the human brain, the chemical properties of GBCAs such as relative thermodynamic and kinetic stabilities and their likelihood of forming gadolinium deposits in vivo will be reviewed. The chemical form of gadolinium causing the hyperintensity is an open question. On the basis of estimates of total gadolinium concentration present, it is highly unlikely that the intact chelate is causing the T₁ hyperintensities observed in the human brain. Although it is possible that there is a water-soluble form of gadolinium that has high relaxitvity present, our experience indicates that the insoluble gadolinium-based agents/salts could have high relaxivities on the surface of the solid due to higher water access. This review assesses the safety of GBCAs from a chemical point of view based on their thermodynamic and kinetic properties, discusses how these properties influence in vivo behavior, and highlights some clinical implications regarding the development of future imaging agents.

Thermodynamic Stability of Fenclorim and Clopyralid

The present work reports an experimental thermodynamic study of two nitrogen heterocyclic organic compounds, fenclorim and clopyralid, that have been used as herbicides. The sublimation vapor pressures of fenclorim (4,6-dichloro-2-phenylpyrimidine) and of clopyralid (3,6-dichloro-2-pyridinecarboxylic acid) were measured, at different temperatures, using a Knudsen mass-loss effusion technique. The vapor pressures of both crystalline and liquid (including supercooled liquid) phases of fenclorim were also determined using a static method based on capacitance diaphragm manometers. The experimental results enabled accurate determination of the standard molar enthalpies, entropies and Gibbs energies of sublimation for both compounds and of vaporization for fenclorim, allowing a phase diagram representation of the (p,T) results, in the neighborhood of the triple point of this compound. The temperatures and molar enthalpies of fusion of the two compounds studied were determined using differential scanning calorimetry. The standard isobaric molar heat capacities of the two crystalline compounds were determined at 298.15 K, using drop calorimetry. The gas phase thermodynamic properties of the two compounds were estimated through ab initio calculations, at the G3(MP2)//B3LYP level, and their thermodynamic stability was evaluated in the gaseous and crystalline phases, considering the calculated values of the standard Gibbs energies of formation, at 298.15 K. All these data, together with other physical and chemical properties, will be useful to predict the mobility and environmental distribution of these two compounds.

Expanding the toolbox for predictive parameters describing antibody stability considering thermodynamic and kinetic determinants

PURPOSE

Introduction of the activation energy (E_a) as a kinetic parameter to describe and discriminate monoclonal antibody (mAb) stability.

METHODS

E_a is derived from intrinsic fluorescence (IF) unfolding thermograms. An apparent irreversible three-state fit model based on the Arrhenius integral is developed to determine E_a of respective unfolding transitions. These activation energies are compared to the thermodynamic parameter of van´t Hoff enthalpies (∆H_vh). Using a set of 34 mAbs formulated in four different formulations, both the apparent thermodynamic and kinetic parameters together with apparent melting temperatures are correlated collectively with each other to storage stabilities to evaluate its predictive power with respect to long-term effects potentially reflected in shelf-life.

RESULTS

E_a allows for the discrimination of (i) different parent mAbs, (ii) different variants that originate from parent mAbs, and (iii) different formulations. Interestingly, we observed that the E_a of the CH₂ unfolding transition shows strongest correlations with monomer and aggregate content after storage at accelerated and stress conditions when collectively compared to ∆H_vh and T_m of the CH₂ transition. Moreover, the predictive parameters determined for the CH₂ domain show generally stronger correlations with monomer and aggregate content than those derived for the Fab. Qualitative assessment by ranking E_a of the Fab domain showed good agreement with monomer content in storage stabilities of individual mAb sub-sets.

CONCLUSION

E_a from IF unfolding transitions can be used in addition to other commonly used thermodynamic predictive parameters to discriminate and characterize thermal stability of different mAbs in different formulations. Hence, it shows great potential for antibody engineering and formulation scientists.

Strain tailored thermodynamic stability, electronic transitions, and optoelectronic properties of III (In, Ga and Al)-nitride monolayers

The thermodynamic stability of III-nitride monolayers is calculated using the phonon band structure. Electronic properties are computed using the generalized gradient approximation-Perdew-Burke-Ernzerhof exchange-correlation potentials, which show the semiconducting behavior with bandgap 0.59 eV, 2.034 eV, and 2.906 eV for InN, GaN, and AlN monolayers, respectively. The biaxial tensile and compressive strains are used as external stimuli to understand their impact on the optoelectronic properties of these monolayers. The thermodynamic stability of strained monolayers is investigated to explore the maximum possible strains, i.e. flexibility limit, these monolayers can sustain. These monolayers are more sensitive to compressive strains, showing thermodynamic instability even at 1% compressive strain for all the considered monolayers. Further, the III-nitride monolayers are more robust with the tensile strain. InN, GaN, and AlN monolayers can sustain up to 4%, 16%, and 18% tensile strain, respectively. More interestingly, the electronic transitions, such as direct to indirect and semiconducting to metallic, are noticed with strain in the considered monolayers. The optical properties also exhibit strong strain dependency at the different transition points.

Semi-Rigid (Aminomethyl) Piperidine-Based Pentadentate Ligands for Mn(II) Complexation

Two pentadentate ligands built on the 2-aminomethylpiperidine structure and bearing two tertiary amino and three oxygen donors (three carboxylates in the case of AMPTA and two carboxylates and one phenolate for AMPDA-HB) were developed for Mn(II) complexation. Equilibrium studies on the ligands and the Mn(II) complexes were carried out using pH potentiometry, ¹H-NMR spectroscopy and UV-vis spectrophotometry. The Mn complexes that were formed by the two ligands were more stable than the Mn complexes of other pentadentate ligands but with a lower pMn than Mn(EDTA) and Mn(CDTA) (pMn for Mn(AMPTA) = 7.89 and for Mn(AMPDA-HB) = 7.07). ¹H and ¹⁷O-NMR relaxometric studies showed that the two Mn-complexes were q = 1 with a relaxivity value of 3.3 mM⁻¹ s⁻¹ for Mn(AMPTA) and 3.4 mM⁻¹ s⁻¹ for Mn(AMPDA-HB) at 20 MHz and 298 K. Finally, the geometries of the two complexes were optimized at the DFT level, finding an octahedral coordination environment around the Mn²⁺ ion, and MD simulations were performed to monitor the distance between the Mn²⁺ ion and the oxygen of the coordinated water molecule to estimate its residence time, which was in good agreement with that determined using the ¹⁷O NMR data.

Entropy Landscaping of High-Entropy Carbides

The entropy landscape of high-entropy carbides can be used to understand and predict their structure, properties, and stability. Using first principles calculations, the individual and temperature-dependent contributions of vibrational, electronic, and configurational entropies are analyzed, and compare them qualitatively to the enthalpies of mixing. As an experimental complement, high-entropy carbide thin films are synthesized with high power impulse magnetron sputtering to assess structure and properties. All compositions can be stabilized in the single-phase state despite finite positive, and in some cases substantial, enthalpies of mixing. Density functional theory calculations reveal that configurational entropy dominates the free energy landscape and compensates for the enthalpic penalty, whereas the vibrational and electronic entropies offer negligible contributions. The calculations predict that in many compositions, the single-phase state becomes stable at extremely high temperatures (>3000 K). Consequently, rapid quenching rates are needed to preserve solubility at room temperature and facilitate physical characterization. Physical vapor deposition provides this experimental validation opportunity. The computation/experimental data set generated in this work identifies "valence electron concentration" as an effective descriptor to predict structural and thermodynamic properties of multicomponent carbides and educate new formulation selections.

Annealing-Induced Off-Stoichiometric and Structural Alterations in Ca2+- and Y3+-Stabilized Zirconia Ceramics

In the current study, high-temperature stability was investigated in two types of zirconia ceramics stabilized with two different additives, namely, calcia and yttria. The evolutions of structure and oxygen-vacancy-related defects upon annealing in air were investigated as a function of temperature by combining X-ray diffractometry with Raman, X-ray photoelectron and cathodoluminescence spectroscopies. We systematically characterized variations in the concentration of oxygen vacancies and hydroxyl groups during thermal treatments and linked them to structural alterations and polymorphic transformation. With this approach, we clarified how the combined effects of different dopants and temperature impacted on structural development and on the thermal stability of the oxygen-vacancy-related defect complex.

Dimethyl sulfoxide reduces the stability but enhances catalytic activity of the main SARS-CoV-2 protease 3CLpro

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is responsible for coronavirus disease 2019 (COVID‐19), one of the most challenging global pandemics of the modern era. Potential treatment strategies against COVID‐19 are yet to be devised. It is crucial that antivirals that interfere with the SARS‐CoV‐2 life cycle be identified and developed. 3‐Chymotrypsin‐like protease (3CLpro) is an attractive antiviral drug target against SARS‐CoV‐2, and coronaviruses in general, because of its role in the processing of viral polyproteins. Inhibitors of 3CLpro activity are screened in enzyme assays before further development of the most promising leads. Dimethyl sulfoxide (DMSO) is a common additive used in such assays and enhances the solubility of assay components. However, it may also potentially affect the stability and efficiency of 3CLpro but, to date, this effect had not been analyzed in detail. Here, we investigated the effect of DMSO on 3CLpro‐catalyzed reaction. While DMSO (5%‐20%) decreased the optimum temperature of catalysis and thermodynamic stability of 3CLpro, it only marginally affected the kinetic stability of the enzyme. Increasing the DMSO concentration up to 20% improved the catalytic efficiency and peptide‐binding affinity of 3CLpro. At such high DMSO concentration, the solubility and stability of peptide substrate were improved because of reduced aggregation. In conclusion, we recommend 20% DMSO as the minimum concentration to be used in screens of 3CLpro inhibitors as lead compounds for the development of antiviral drugs against COVID‐19.

Structural and Genomic Insights Into Pyrazinamide Resistance in Mycobacterium tuberculosis Underlie Differences Between Ancient and Modern Lineages

Resistance to drugs used to treat tuberculosis disease (TB) continues to remain a public health burden, with missense point mutations in the underlying Mycobacterium tuberculosis bacteria described for nearly all anti-TB drugs. The post-genomics era along with advances in computational and structural biology provide opportunities to understand the interrelationships between the genetic basis and the structural consequences of M. tuberculosis mutations linked to drug resistance. Pyrazinamide (PZA) is a crucial first line antibiotic currently used in TB treatment regimens. The mutational promiscuity exhibited by the pncA gene (target for PZA) necessitates computational approaches to investigate the genetic and structural basis for PZA resistance development. We analysed 424 missense point mutations linked to PZA resistance derived from ∼35K M. tuberculosis clinical isolates sourced globally, which comprised the four main M. tuberculosis lineages (Lineage 1-4). Mutations were annotated to reflect their association with PZA resistance. Genomic measures (minor allele frequency and odds ratio), structural features (surface area, residue depth and hydrophobicity) and biophysical effects (change in stability and ligand affinity) of point mutations on pncA protein stability and ligand affinity were assessed. Missense point mutations within pncA were distributed throughout the gene, with the majority (>80%) of mutations with a destabilising effect on protomer stability and on ligand affinity. Active site residues involved in PZA binding were associated with multiple point mutations highlighting mutational diversity due to selection pressures at these functionally important sites. There were weak associations between genomic measures and biophysical effect of mutations. However, mutations associated with PZA resistance showed statistically significant differences between structural features (surface area and residue depth), but not hydrophobicity score for mutational sites. Most interestingly M. tuberculosis lineage 1 (ancient lineage) exhibited a distinct protein stability profile for mutations associated with PZA resistance, compared to modern lineages.

Variations in the Abortive HIV-1 RNA Hairpin Do Not Impede Viral Sensing and Innate Immune Responses

The highly conserved trans-acting response element (TAR) present in the RNA genome of human immunodeficiency virus 1 (HIV-1) is a stably folded hairpin structure involved in viral replication. However, TAR is also sensed by viral sensors, leading to antiviral immunity. While high variation in the TAR RNA structure renders the virus replication-incompetent, effects on viral sensing remain unclear. Here, we investigated the role of TAR RNA structure and stability on viral sensing. TAR mutants with deletions in the TAR hairpin that enhanced thermodynamic stability increased antiviral responses. Strikingly, TAR mutants with lower stability due to destabilization of the TAR hairpin also increased antiviral responses without affecting pro-inflammatory responses. Moreover, mutations that affected the TAR RNA sequence also enhanced specific antiviral responses. Our data suggest that mutations in TAR of replication-incompetent viruses can still induce immune responses via viral sensors, hereby underscoring the robustness of HIV-1 RNA sensing mechanisms.

Physical, chemical, and biological characterization of ginsenoside F1 incorporated in nanostructured lipid carrier

This study was aimed to determine the physical property and thermodynamic stability of nanostructured lipid carrier suspension incorporating ginsenoside F1 (GF1_NLC), and to evaluate its transport and antioxidant properties. GF1_NLC suspension possessed spherical particles with an average size of 98.9 nm, and the encapsulation efficiency reached approximately 90%. There was a good compatibility between ginsenoside F1 (GF1) and the nanostructured lipid carrier (NLC) formulation, giving no contribution to the changes in the structural organization and crystallization behavior of lipid particles. However, the incorporation of GF1 reduced the thermodynamic stability of the lipid particles. The permeability of GF1_NLC (39.2%) across Caco-2 cell monolayer was higher than that of free GF1 (26.0%); however, no significant differences were observed in the radical scavenging activity (84.1% and 85.5%, respectively). In conclusion, NLC could be a potential candidate for the delivery of GF1 into the living body due to its small particle size, high encapsulation efficiency, and improved permeability. PRACTICAL APPLICATIONS: Poor water solubility in an aqueous solution and low absorption rate of ginsenoside F1 in the intestinal track limit its practical application in food systems. In this study, ginsenoside F1 was encapsulated in nanostructured lipid carrier to enhance its water solubility and absorption rate. The results of the encapsulated ginsenoside F1 showed high encapsulation efficiency of 90% with fine particle size of 98.9 nm that could correspond to the enhancement of water solubility in an aqueous solution and permeability across Caco-2 cell monolayer. The results may encourage the food industry to utilize this encapsulation technique for the enhancement of the functional properties of poorly water-soluble bioactive compounds.

Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR

Multidimensional NMR intrinsically provides multiple probes that can be used for deciphering the folding pathways of proteins: NH amide and CαHα groups are strategically located on the backbone of the protein, while CH₃ groups, on the side-chain of methylated residues, are involved in important stabilizing interactions in the hydrophobic core. Combined with high hydrostatic pressure, these observables provide a powerful tool to explore the conformational landscapes of proteins. In the present study, we made a comparative assessment of the NH, CαHα, and CH₃ groups for analyzing the unfolding pathway of ∆+PHS Staphylococcal Nuclease. These probes yield a similar description of the folding pathway, with virtually identical thermodynamic parameters for the unfolding reaction, despite some notable differences. Thus, if partial unfolding begins at identical pressure for these observables (especially in the case of backbone probes) and concerns similar regions of the molecule, the residues involved in contact losses are not necessarily the same. In addition, an unexpected slight shift toward higher pressure was observed in the sequence of the scenario of unfolding with CαHα when compared to amide groups.

Catalytic Dyad Residues His41 and Cys145 Impact the Catalytic Activity and Overall Conformational Fold of the Main SARS-CoV-2 Protease 3-Chymotrypsin-Like Protease

Coronaviruses are responsible for multiple pandemics and millions of deaths globally, including the current pandemic of coronavirus disease 2019 (COVID-19). Development of antivirals against coronaviruses, including the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) responsible for COVID-19, is essential for containing the current and future coronavirus outbreaks. SARS-CoV-2 proteases represent important targets for the development of antivirals because of their role in the processing of viral polyproteins. 3-Chymotrypsin-like protease (3CLpro) is one such protease. The cleavage of SARS-CoV-2 polyproteins by 3CLpro is facilitated by a Cys145–His41 catalytic dyad. We here characterized the catalytic roles of the cysteine–histidine pair for improved understanding of the 3CLpro reaction mechanism, to inform the development of more effective antivirals against Sars-CoV-2. The catalytic dyad residues were substituted by site-directed mutagenesis. All substitutions tested (H41A, H41D, H41E, C145A, and C145S) resulted in a complete inactivation of 3CLpro, even when amino acids with a similar catalytic function to that of the original residues were used. The integrity of the structural fold of enzyme variants was investigated by circular dichroism spectroscopy to test if the catalytic inactivation of 3CLpro was caused by gross changes in the enzyme secondary structure. C145A, but not the other substitutions, shifted the oligomeric state of the enzyme from dimeric to a higher oligomeric state. Finally, the thermodynamic stability of 3CLpro H41A, H41D, and C145S variants was reduced relative the wild-type enzyme, with a similar stability of the H41E and C145A variants. Collectively, the above observations confirm the roles of His41 and Cys145 in the catalytic activity and the overall conformational fold of 3CLpro SARS-CoV-2. We conclude that the cysteine–histidine pair should be targeted for inhibition of 3CLpro and development of antiviral against COVID-19 and coronaviruses.

Steering the Catalytic Properties of Intermetallic Compounds and Alloys in Reforming Reactions by Controlled in Situ Decomposition and Self-Activation

Based on the increasing importance of intermetallic compounds and alloys in heterogeneous catalysis, we explore the possibilities of using selected intermetallic compounds and alloy structures and phases as catalyst precursors to prepare highly active and CO2-selective methanol steam reforming (MSR) as well as dry reforming of methane (DRM) catalyst entities by controlled in situ decomposition and self-activation. The exemplary discussed examples (Cu51Zr14, CuZn, Pd2Zr, GaPd2, Cu2In, ZnPd, and InPd) show both the advantages and pitfalls of this approach and how the concept can be generalized to encompass a wider set of intermetallic compounds and alloy structures. Despite the common feature of all systems being the more or less pronounced decomposition of the intermetallic compound surface and bulk structure and the in situ formation of much more complex catalyst entities, differences arise due to the oxidation propensity and general thermodynamic stability of the chosen intermetallic compound/alloy and their constituents. The metastability and intrinsic reactivity of the evolving oxide polymorph introduced upon decomposition and the surface and bulk reactivity of carbon, governed by the nature of the metal/intermetallic compound-oxide interfacial sites, are of equal importance. Structural and chemical rearrangements, dictating the catalytic performance of the resulting entity, are present in the form of a complete destruction of the intermetallic compound bulk structure (Cu51Zr14) and the formation of an metal/oxide (Cu51Zr14, InPd) or intermetallic compound/oxide (ZnPd, Cu2In, CuZn) interface or the intertranformation of intermetallic compounds with varying composition (Pd2Zr) before the formation of Pd/ZrO2. In this Perspective, the prerequisites to obtain a leading theme for pronounced CO2 selectivity and high activity will be reviewed. Special focus will be put on raising awareness of the intrinsic properties of the discussed catalyst systems that need to be controlled to obtain catalytically prospective materials. The use of model systems to bridge the material's gap in catalysis will also be highlighted for selected examples.

Biogenic Selenium Nanoparticles: A Fine Characterization to Unveil Their Thermodynamic Stability

Among the plethora of available metal(loid) nanomaterials (NMs), those containing selenium are interesting from an applicative perspective, due to their high biocompatibility. Microorganisms capable of coping with toxic Se-oxyanions generate mostly Se nanoparticles (SeNPs), representing an ideal and green alternative over the chemogenic synthesis to obtain thermodynamically stable NMs. However, their structural characterization, in terms of biomolecules and interactions stabilizing the biogenic colloidal solution, is still a black hole that impairs the exploitation of biogenic SeNP full potential. Here, spherical and thermodynamically stable SeNPs were produced by a metal(loid) tolerant Micrococcus sp. Structural characterization obtained by Scanning Electron Microscopy (SEM) revealed that these SeNPs were surrounded by an organic material that contributed the most to their electrosteric stabilization, as indicated by Zeta (ζ) potential measurements. Proteins were strongly adsorbed on the SeNP surface, while lipids, polysaccharides, and nucleic acids more loosely interacted with SeNMs as highlighted by Fourier Transform Infrared Spectroscopy (FTIR) and overall supported by multivariate statistical analysis. Nevertheless, all these contributors were fundamental to maintain SeNPs stable, as, upon washing, the NM-containing extract showed the arising of aggregated SeNPs alongside Se nanorods (SeNRs). Besides, Density Functional Theory (DFT) calculation unveiled how thiol-containing molecules appeared to play a role in SeO₃²⁻ bioreduction, stress oxidative response, and SeNP stabilization.

Pressure and Chemical Unfolding of an α-Helical Bundle Protein: The GH2 Domain of the Protein Adaptor GIPC1

When combined with NMR spectroscopy, high hydrostatic pressure is an alternative perturbation method used to destabilize globular proteins that has proven to be particularly well suited for exploring the unfolding energy landscape of small single-domain proteins. To date, investigations of the unfolding landscape of all-β or mixed-α/β protein scaffolds are well documented, whereas such data are lacking for all-α protein domains. Here we report the NMR study of the unfolding pathways of GIPC1-GH2, a small α-helical bundle domain made of four antiparallel α-helices. High-pressure perturbation was combined with NMR spectroscopy to unravel the unfolding landscape at three different temperatures. The results were compared to those obtained from classical chemical denaturation. Whatever the perturbation used, the loss of secondary and tertiary contacts within the protein scaffold is almost simultaneous. The unfolding transition appeared very cooperative when using high pressure at high temperature, as was the case for chemical denaturation, whereas it was found more progressive at low temperature, suggesting the existence of a complex folding pathway.

The thermodynamic stability and mechanical properties of TiCxN1-x(0x⩽ 1) compounds by cluster expansion method and first-principles calculations

The thermodynamic stability and mechanical properties of titanium carbonitrides TiC_xN_1-x(0 ⩽x⩽ 1) are investigated by a combination of the universal cluster expansion method and the first-principles calculations. By considering the ordering of the N/C distributions on the anion sublattice sites of TiC_xN_1-x, a binary diagram of the heat of formation is constructed, and seven kinds of ground-state structures are predicted in the whole range of 0 ⩽x⩽ 1. These predicted ground-state TiC_xN_1-xstructures are further proved to be dynamically and mechanically stable by examining their phonon dispersion spectra and elastic constants. Further studies indicate that the mechanical and thermodynamic properties of the ternary TiC_xN_1-xstructures are generally better than those of the binary TiC or TiN, while the differences within the ternary systems are insignificant. The possible origin of the enhancement of the mechanical and thermodynamic properties of the predicted ground-state TiC_xN_1-xare discussed together with the electronic structures.

KRAS Promoter G-Quadruplexes from Sequences of Different Length: A Physicochemical Study

DNA G-quadruplexes (G4s) form in relevant genomic regions and intervene in several biological processes, including the modulation of oncogenes expression, and are potential anticancer drug targets. The human KRAS proto-oncogene promoter region contains guanine-rich sequences able to fold into G4 structures. Here, by using circular dichroism and differential scanning calorimetry as complementary physicochemical methodologies, we compared the thermodynamic stability of the G4s formed by a shorter and a longer version of the KRAS promoter sequence, namely 5′-AGGGCGGTGTGGGAATAGGGAA-3′ (KRAS 22RT) and 5′-AGGGCGGTGTGGGAAGAGGGAAGAGGGGGAGG-3′ (KRAS 32R). Our results show that the unfolding mechanism of KRAS 32R is more complex than that of KRAS 22RT. The different thermodynamic stability is discussed based on the recently determined NMR structures. The binding properties of TMPyP4 and BRACO-19, two well-known G4-targeting anticancer compounds, to the KRAS G4s were also investigated. The present physicochemical study aims to help in choosing the best G4 target for potential anticancer drugs.

Heme-iron ligand (M80-Fe) in cytochrome c is destabilizing: combined in vitro and in silico approaches to monitor changes in structure, stability and dynamics of the protein on mutation

Structure, stability and dynamics properties of horse cytochrome c (cyt c) and its genetically engineered M80G mutant have been investigated. The nature of the Met80 axial ligation to heme iron is believed to be the major determinant of the oxidation-reduction reactions inside and outside the cell of a particular cytochrome. This ligation has played an important role in the studies of protein structure, stability and protein folding/unfolding. To understand this ligation better, Met80 of horse cyt c has been mutated to Gly that is unable to bind to the heme iron. We have examined the effect of the M80G mutation on the structure and stability of the WT (wild type) protein by using absorbance spectroscopy, far-UV, near-UV and Soret circular dichroism, fluorescence spectroscopy and differential scanning calorimetry. We have observed that mutation caused a partial loss of secondary and tertiary structure with slightly increased overall stability of the protein. We have also measured the dynamic behavior of WT cyt c and its M80G mutant in the oxidized form (Fe³⁺) using the essential dynamics (ED) method. A 400 ns MD simulations were run for WT cyt c and its mutant M80G in water using GROMOS96 force field. MD results revealed that the stability and flexibility increased in mutant M80G (Fe…S (Met80) bond removed). Essential dynamics analysis revealed that the first five eigenvectors were mainly involved in overall motions of WT cyt c and its M80G mutant but the amplitude of concerted motions decreased in M80G mutant relative to WT cyt c.Communicated by Ramaswamy H. Sarma.

Greigite (Fe3S4) is thermodynamically stable: Implications for its terrestrial and planetary occurrence

Iron sulfide minerals are widespread on Earth and likely in planetary bodies in and beyond our solar system. Using measured enthalpies of formation for three magnetic iron sulfide phases: bulk and nanophase Fe₃S₄ spinel (greigite), and its high-pressure monoclinic phase, we show that greigite is a stable phase in the Fe-S phase diagram at ambient temperature. The thermodynamic stability and low surface energy of greigite supports the common occurrence of fine-grained Fe₃S₄ in many anoxic terrestrial settings. The high-pressure monoclinic phase, thermodynamically metastable below about 3 GPa, shows a calculated negative P-T slope for its formation from the spinel. The stability of these three phases suggests their potential existence on Mercury and their magnetism may contribute to its present magnetic field.

Computationally Predicted High-Throughput Free-Energy Phase Diagrams for the Discovery of Solid-State Hydrogen Storage Reactions

The design of multinary solid-state material systems that undergo reversible phase changes via changes in temperature and pressure provides a potential means of safely storing hydrogen. However, fully mapping the stabilities of known or newly targeted compounds relative to competing phases at reaction conditions has previously required many stringent experiments or computationally demanding calculations of each compound's change in Gibbs energy with respect to temperature, G(T). In this work, we have extended the approach of constructing chemical potential phase diagrams based on ΔG_f(T) to enable the analysis of phase stability at non-zero temperatures. We first performed density functional theory calculations to compute the formation enthalpies of binary, ternary, and quaternary compounds within several compositional spaces of current interest for solid-state hydrogen storage. Temperature effects on solid compound stability were then accounted for using our recently introduced machine learned descriptor for the temperature-dependent contribution G^δ(T) to the Gibbs energy G(T). From these Gibbs energies, we evaluated each compound's stability relative to competing compounds over a wide range of conditions and show using chemical potential and composition phase diagrams that the predicted stable phases and H₂ release reactions are consistent with experimental observations. This demonstrates that our approach rapidly computes the thermochemistry of hydrogen release reactions for compounds at sufficiently high accuracy relative to experiment to provide a powerful framework for analyzing hydrogen storage materials. This framework based on G(T) enables the accelerated discovery of active materials for a variety of technologies that rely on solid-state reactions involving these materials.

In Situ Dispersion of Palladium on TiO2 During Reverse Water-Gas Shift Reaction: Formation of Atomically Dispersed Palladium

The application of single-atom catalysts (SACs) to high-temperature hydrogenation requires materials that thermodynamically favor metal atom isolation over cluster formation. We demonstrate that Pd can be predominantly dispersed as isolated atoms onto TiO₂ during the reverse water-gas shift (rWGS) reaction at 400 °C. Achieving atomic dispersion requires an artificial increase of the absolute TiO₂ surface area by an order of magnitude and can be accomplished by physically mixing a precatalyst (Pd/TiO₂ ) with neat TiO₂ prior to the rWGS reaction. The in situ dispersion of Pd was reflected through a continuous increase of rWGS activity over 92 h and supported by kinetic analysis, infrared and X-ray absorption spectroscopies and scanning transmission electron microscopy. The thermodynamic stability of Pd under high-temperature rWGS conditions is associated with Pd-Ti coordination, which manifests upon O-vacancy formation, and the artificial increase in TiO₂ surface area.

Programming Biomimetically Confined Aptamers with DNA Frameworks

Active sites of proteins are generally encapsulated within three-dimensional peptide scaffolds that provide the molecular-scale confinement microenvironment. Nevertheless, the ability to tune thermodynamic stability in biomimetic molecular confinement relies on the macromolecular crowding effect of lack of stoichiometry and reconfigurability. Here, we report a framework nucleic acid (FNA)-based strategy to increase thermodynamic stability of aptamers. We demonstrate that the molecular-scale confinement increases the thermodynamic stability of aptamers via facilitated folding kinetics, which is confirmed by the single-molecule FRET (smFRET). Unfavorable conformations of aptamers are restricted as revealed by the Monte Carlo simulation. The binding affinity of the DNA framework-confined aptamer is improved by ∼3-fold. With a similar strategy we improve the catalytic activity of hemin-binding aptamer. Our approach thus shows high potential for designing protein-mimicking DNA nanostructures with enhanced binding affinity and catalytic activity for biosensing and biomedical engineering.

Rapid Prediction of Bimetallic Mixing Behavior at the Nanoscale

The nanoparticle (NP) design space allows for variations in size, shape, composition, and chemical ordering. In the search for low-energy structures, this results in an extremely large search space which cannot be screened by brute force methods. In this work, we develop a genetic algorithm to predict stable bimetallic NPs of any size, shape, and metal composition. Our method predicts nanostructures in agreement with experimental trends and it captures the detailed chemical ordering of an experimental 23,196-atom FePt NP with nearly atom-by-atom accuracy. Our developed screening process is extremely fast, allowing us to generate and analyze a database of 5454 low-energy bimetallic NPs. By identifying thermodynamically stable NPs, we rationalize bimetallic mixing at the nanoscale and reveal metal-, size-, and temperature-dependent mixing behavior. Importantly, our method is applicable to any bimetallic NP size, bridging the materials gap in nanoscale simulations, and guides experimentation in the lab by elucidating stability, mixing, and detailed chemical ordering behavior of bimetallic NPs.

Cs4 PbI6 -Mediated Synthesis of Thermodynamically Stable FA0.15 Cs0.85 PbI3 Perovskite Solar Cells

The stability issue is still one of the main limitations of the commercialization of perovskite photovoltaics. The mixed cation FA_x Cs_{1 -x} PbI₃ has shown great promise owing to its improved thermal and moisture stability. However, the study of FA_x Cs_{1 -x} PbI₃ is concentrated on formamidine (FA)-rich perovskite, whereas cesium (Cs)-rich FA_x Cs_{1 -x} PbI₃ perovskites are barely studied due to the inevitable phase separation when Cs > 30 mol%. Here, a Cs₄ PbI₆ -mediated method is developed to synthesize Cs-rich FA_x Cs_{1 -x} PbI₃ perovskites. It is demonstrated that Cs₄ PbI₆ intermediate phase has a low Cs cation diffusion barrier and therefore offers a fast ion exchange with the preformed FA-rich perovskite phase to finally form the Cs-rich FA_x Cs_{1 -x} PbI₃ perovskite. The results indicate that ≈15% alloying with organic FA cations can sufficiently stabilize the perovskite phase with excellent phase and UV-irradiation stability. The FA_0.15 Cs_0.85 PbI₃ perovskite solar cells achieve a champion power conversion efficiency of 17.5%, showing the great potential of Cs-based perovskites for efficient and stable solar cells.

Predicting the stability of mutant proteins by computational approaches: an overview

A very large number of computational methods to predict the change in thermodynamic stability of proteins due to mutations have been developed during the last 30 years, and many different web servers are currently available. Nevertheless, most of them suffer from severe drawbacks that decrease their general reliability and, consequently, their applicability to different goals such as protein engineering or the predictions of the effects of mutations in genetic diseases. In this review, we have summarized all the main approaches used to develop these tools, with a survey of the web servers currently available. Moreover, we have also reviewed the different assessments made during the years, in order to allow the reader to check directly the different performances of these tools, to select the one that best fits his/her needs, and to help naïve users in finding the best option for their needs.