Porous and Meltable Metal-Organic Polyhedra for the Generation and Shaping of Porous Mixed-Matrix Composites.

Here, we report the synthesis of BCN-93, a meltable, functionalized, and permanently porous metal-organic polyhedron (MOP) and its subsequent transformation into amorphous or crystalline, shaped, self-standing, transparent porous films via melting and subsequent cooling. The synthesis entails the outer functionalization of a MOP with meltable polymer chains: in our model case, we functionalized a Rh(II)-based cuboctahedral MOP with poly(ethylene glycol). Finally, we demonstrate that once melted, BCN-93 can serve as a porous matrix into which other materials or molecules can be dispersed to form mixed-matrix composites. To illustrate this, we combined BCN-93 with one of various additives (either two MOF crystals, a porous cage, or a linear polymer) to generate a series of mixed-matrix films, each of which exhibited greater CO2 uptake relative to the parent film.

In silico design of a lipid-like compound targeting KRAS4B-G12D through non-covalent bonds.

One of the most common drivers in human cancer is the peripheral membrane protein KRAS4B, able to promote oncogenic signalling. To signal, oncogenic KRAS4B not only requires a sufficient nucleotide exchange, but also needs to recruit effectors by exposing its effector-binding sites while anchoring to the phospholipid bilayer where KRAS4B-mediated signalling events occur. The enzyme phosphodiesterase-δ plays an important role in sequestering KRAS4B from the cytoplasm and targeting it to cellular membranes of different cell species. In this work, we present an in silico design of a lipid-like compound that has the remarkable feature of being able to target both an oncogenic KRAS4B-G12D mutant and the phosphodiesterase-δ enzyme. This double action is accomplished by adding a lipid tail (analogous to the farnesyl group of the KRAS4B protein) to an previously known active compound (2H-1,2,4-benzothiadiazine, 3,4-dihydro-,1,1-dioxide). The proposed lipid-like molecule was found to lock KRAS4B-G12D in its GDP-bound state by adjusting the effector-binding domain to be blocked by the interface of the lipid bilayer. Meanwhile, it can tune GTP-bound KRAS4B-G12D to shift from the active orientation state to the inactive state. The proposed compound is also observed to stably accommodate itself in the prenyl-binding pocket of phosphodiesterase-δ, which impairs KRAS4B enrichment at the lipid bilayer, potentially reducing the proliferation of KRAS4B inside the cytoplasm and its anchoring at the bilayer. In conclusion, we report a potential inhibitor of KRAS4B-G12D with a lipid tail attached to a specific warhead, a compound which has not yet been considered for drugs targeting RAS mutants. Our work provides new ways to target KRAS4B-G12D and can also foster drug discovery efforts for the targeting of oncogenes of the RAS family and beyond.

How a few help all: cooperative crossing of lipid membranes by COSAN anions.

Experimental results show that the presence of a concentration gradient of certain nano-ions (most notably cobaltabisdicarbollide ([o-COSAN]- anions), induce a current across intact artificial phospholipid bilayers in spite of the high Born free energy estimated for these ions. The mechanism underlying this observed translocation of nano-anions across membranes has yet to be determined. Here we show, using molecular dynamics simulations, that the permeation of [o-COSAN]- anions across a lipid bilayer proceeds in a cooperative manner. Single nano-ions can enter the bilayer but permeation is hampered by a free energy barrier of about 8kBT. The interaction between these nano-ions inside a leaflet induces a flip-flop translocation mechanism with the formation of transient, elongated structure inside the membrane. This cooperative flip-flop allows an efficient distribution of [o-COSAN]- anions in both leaflets of the bilayer. These results suggest the existence of a new mechanism for permeation of nano-ions across lipid membranes, relevant for those that have the appropriate self-assembly character.

(Bio)Functionalisation of Metal-Organic Polyhedra by Using Click Chemistry.

The surface chemistry of Metal-Organic Polyhedra (MOPs) is crucial to their physicochemical properties because it governs how they interact with external substances such as solvents, synthetic organic molecules, metal ions, and even biomolecules. Consequently, the advancement of synthetic methods that facilitate the incorporation of diverse functional groups onto MOP surfaces will significantly broaden the range of properties and potential applications for MOPs. This study describes the use of copper(I)-catalysed, azide-alkyne cycloaddition (CuAAC) click reactions to post-synthetically modify the surface of alkyne-functionalised cuboctahedral MOPs. To this end, a novel Rh(II)-based MOP with 24 available surface alkyne groups was synthesised. Each of the 24 alkyne groups on the surface of the "clickable" Rh-MOP can react with azide-containing molecules at room temperature, without compromising the integrity of the MOP. The wide substrate catalogue and orthogonal nature of CuAAC click chemistry was exploited to densely functionalise MOPs with diverse functional groups, including polymers, carboxylic and phosphonic acids, and even biotin moieties, which retained their recognition capabilities once anchored onto the surface of the MOP.

Interaction-Limited Aggregation: Fine-Tuning the Size of pNIPAM Particles by Association with Hydrophobic Ions.

We have investigated the formation of stable clusters of poly(N-isopropylacrylamide) (pNIPAM) chains in water at temperatures above the lower critical solution temperature (LCST), induced by the presence of sodium tetraphenylborate, NaPh4B. The hydrophobic Ph4B- ions interact strongly with the pNIPAM chains, providing them with a net effective negative charge, which leads to the stabilization of pNIPAM clusters for temperatures above the LCST, with a mean cluster size that depends non-monotonically on salt concentration. Combining experiments with physical modeling at the mesoscopic level and atomistic molecular dynamic simulations, we show that this effect is caused by the interplay between the hydrophobic attraction between pNIPAM chains and the electrostatic repulsion induced by the associated Ph4B- ions. These results provide insight on the significance of weak associative anion-polymer interaction driven by hydrophobic interaction and how this anionic binding can prevent macroscopic phase separation. Harvesting the competition between attractive hydrophobic and repulsive electrostatic interaction opens avenues for the dynamic control of the formation of well-calibrated polymer microparticles.

Effect of surfactants on SARS-CoV-2: Molecular dynamics simulations.

Surfactants are commonly used as disinfection agents in personal care products against bacteria and viruses, including SARS-CoV-2. However, there is a lack of understanding of the molecular mechanisms of the inactivation of viruses by surfactants. Here, we employ coarse grain (CG) and all-atom (AA) molecular dynamics simulations to investigate the interaction between general families of surfactants and the SARS-CoV-2 virus. To this end, we considered a CG model of a full virion. Overall, we found that surfactants have only a small impact on the virus envelope, being inserted into the envelope without dissolving it or generating pores, at the conditions considered here. However, we found that surfactants may induce a deep impact on the spike protein of the virus (responsible for its infectivity), easily covering it and inducing its collapse over the envelope surface of the virus. AA simulations confirmed that both negatively and positively charged surfactants are able to extensively adsorb over the spike protein and get inserted into the virus envelope. Our results suggest that the best strategy for the design of surfactants as virucidal agents will be to focus on those strongly interacting with the spike protein.

Ammonia Capture in Rhodium(II)-Based Metal-Organic Polyhedra via Synergistic Coordinative and H-Bonding Interactions.

Ammonia (NH3) is among the world's most widely produced bulk chemicals, given its extensive use in diverse sectors such as agriculture; however, it poses environmental and health risks at low concentrations. Therefore, there is a need for developing new technologies and materials to capture and store ammonia safely. Herein, we report for the first time the use of metal-organic polyhedra (MOPs) as ammonia adsorbents. We evaluated three different rhodium-based MOPs: [Rh2(bdc)2]12 (where bdc is 1,3-benzene dicarboxylate); one functionalized with hydroxyl groups at its outer surface [Rh2(OH-bdc)2]12 (where OH-bdc is 5-hydroxy-1,3-benzene dicarboxylate); and one decorated with aliphatic alkoxide chains at its outer surface [Rh2(C12O-bdc)2]12 (where C12O-bdc is 5-dodecoxybenzene-1,3-benzene dicarboxylate). Ammonia-adsorption experiments revealed that all three Rh-MOPs strongly interact with ammonia, with uptake capacities exceeding 10 mmol/gMOP. Furthermore, computational and experimental data showed that the mechanism of the interaction between Rh-MOPs and ammonia proceeds through a first step of coordination of NH3 to the axial site of the Rh(II) paddlewheel cluster, which triggers the adsorption of additional NH3 molecules through H-bonding interaction. This unique mechanism creates H-bonded clusters of NH3 on each Rh(II) axial site, which accounts for the high NH3 uptake capacity of Rh-MOPs. Rh-MOPs can be regenerated through their immersion in acidic water, and upon activation, their ammonia uptake can be recovered for at least three cycles. Our findings demonstrate that MOPs can be used as porous hosts to capture corrosive molecules like ammonia, and that their surface functionalization can enhance the ammonia uptake performance.

Stable nanovesicles formed by intrinsically planar bilayers.

HYPOTHESIS: Quatsome nanovesicles, formed through the self-assembly of cholesterol (CHOL) and cetyltrimethylammonium bromide (CTAB) in water, have shown long-term stability in terms of size and morphology, while at the same time exhibiting high CHOL-CTAB intermolecular binding energies. We hypothesize that CHOL/CTAB quatsomes are indeed thermodynamically stable nanovesicles, and investigate the mechanism underlying their formation. EXPERIMENTS: A systematic study was performed to determine whether CHOL/CTAB quatsomes satisfy the experimental requisites of thermodynamically stable vesicles. Coarse-grain molecular dynamics simulations were used to investigate the molecular organization in the vesicle membrane, and the characteristics of the simulated vesicle were corroborated with experimental data obtained by cryo-electron microscopy, small- and wide-angle X-ray scattering, and multi-angle static light scattering. FINDINGS: CHOL/CTAB quatsomes fulfill the requisites of thermodynamically stable nanovesicles, but they do not exhibit the classical membrane curvature induced by a composition asymmetry between the bilayer leaflets, like catanionic nanovesicles. Instead, CHOL/CTAB quatsomes are formed through the association of intrinsically planar bilayers in a faceted vesicle with defects, indicating that distortions in the organization and orientation of molecules can play a major role in the formation of thermodynamically stable nanovesicles.

Computer Simulation of the Interaction between SARS-CoV-2 Spike Protein and the Surface of Coinage Metals.

A prominent feature of the SARS-CoV-2 virus is the presence of a large glycoprotein spike protruding from the virus envelope. The spike determines the interaction of the virus with the environment and the host. Here, we used an all-atom molecular dynamics simulation method to investigate the interaction of up- and down-conformations of the S1 subunit of the SARS-CoV-2 spike with the (100) surface of Au, Ag, and Cu. Our results revealed that the spike protein is adsorbed onto the surface of these metals, with Cu being the metal with the highest interaction with the spike. In our simulations, we considered the spike protein in both its up-conformation Sup (one receptor binding domain exposed) and down-conformation Sdown (no exposed receptor binding domain). We found that the affinity of the metals for the up-conformation was higher than their affinity for the down-conformation. The structural changes in the spike in the up-conformation were also larger than the changes in the down-conformation. Comparing the present results for metals with those obtained in our previous MD simulations of Sup with other materials (cellulose, graphite, and human skin models), we see that Au induces the highest structural change in Sup, larger than those obtained in our previous studies.

Ultrabright Föster Resonance Energy Transfer Nanovesicles: The Role of Dye Diffusion.

The development of contrast agents based on fluorescent nanoparticles with high brightness and stability is a key factor to improve the resolution and signal-to-noise ratio of current fluorescence imaging techniques. However, the design of bright fluorescent nanoparticles remains challenging due to fluorescence self-quenching at high concentrations. Developing bright nanoparticles showing FRET emission adds several advantages to the system, including an amplified Stokes shift, the possibility of ratiometric measurements, and of verifying the nanoparticle stability. Herein, we have developed Förster resonance energy transfer (FRET)-based nanovesicles at different dye loadings and investigated them through complementary experimental techniques, including conventional fluorescence spectroscopy and super-resolution microscopy supported by molecular dynamics calculations. We show that the optical properties can be modulated by dye loading at the nanoscopic level due to the dye's molecular diffusion in fluid-like membranes. This work shows the first proof of a FRET pair dye's dynamism in liquid-like membranes, resulting in optimized nanoprobes that are 120-fold brighter than QDot 605 and exhibit >80% FRET efficiency with vesicle-to-vesicle variations that are mostly below 10%.

Multicomponent, Functionalized HKUST-1 Analogues Assembled via Reticulation of Prefabricated Metal-Organic Polyhedral Cavities.

Metal-organic frameworks (MOFs) assembled from multiple building blocks exhibit greater chemical complexity and superior functionality in practical applications. Herein, we report a new approach based on using prefabricated cavities to design isoreticular multicomponent MOFs from a known parent MOF. We demonstrate this concept with the formation of multicomponent HKUST-1 analogues, using a prefabricated cavity that comprises a cuboctahedral Rh(II) metal-organic polyhedron functionalized with 24 carboxylic acid groups. The cavities are reticulated in three dimensions via Cu(II)-paddlewheel clusters and (functionalized) 1,3,5-benzenetricarboxylate linkers to form three- and four-component HKUST-1 analogues.

Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface.

A prominent feature of coronaviruses is the presence of a large glycoprotein spike (S) protruding from the viral particle. The specific interactions of a material with S determine key aspects such as its possible role for indirect transmission or its suitability as a virucidal material. Here, we consider all-atom molecular dynamics simulations of the interaction between a polymer surface (polystyrene) and S in its up and down conformations. Polystyrene is a commonly used plastic found in electronics, toys, and many other common objects. Also, previous atomic force microscopy (AFM) experiments showed substantial adhesion of S over polystyrene, stronger than in other common materials. Our results show that the main driving forces for the adsorption of the S protein over polystyrene were hydrophobic and π-π interactions with S amino acids and glycans. The interaction was stronger for the case of S in the up conformation, which exposes one highly flexible receptor binding domain (RBD) that adjusts its conformation to interact with the polymer surface. In this case, the interaction has similar contributions from the RBD and glycans. In the case of S in the down conformation, the interaction with the polystyrene surface was weaker and it was dominated by glycans located near the RBD. We do not find significant structural changes in the conformation of S, a result which is in deep contrast to our previous results with another hydrophobic surface (graphite). Our results suggest that SARS-CoV-2 virions may adsorb strongly over plastic surfaces without significantly affecting their infectivity.

Real-Space Image of Charged Patches in Tunable-Size Nanocrystals.

The remarkable dual nature of faceted-charge patchy metal fluoride nanocrystals arises from the spontaneous selective coordination of anionic and cationic ligands on the different facets of the nanocrystals. In previous studies, the identification and origin of the charge at the patches were obtained by combining computer simulations with indirect experimental evidence. Taking a step further, we report herein the first direct real-space identification by Kelvin probe force microscopy of the predicted faceted-charge patchy behavior, allowing the image of the dual faceted-charge surfaces. High-resolution transmission electron microscopy reveals the detailed nanocrystal faceting and allows unambiguously inferring the hydrophilic or hydrophobic role of each facet from the identification of the surface atoms exposed at the respective crystallographic planes. The success of the study lies in a foresighted synthesis methodology designed to tune the nanocrystal size to be suitable for microscopy studies and demanding applications.

Interaction between SARS-CoV-2 spike glycoprotein and human skin models: a molecular dynamics study.

The possibility of contamination of human skin by infectious virions plays an important role in indirect transmission of respiratory viruses but little is known about the fundamental physico-chemical aspects of the virus-skin interactions. In the case of coronaviruses, the interaction with surfaces (including the skin surface) is mediated by their large glycoprotein spikes that protrude from (and cover) the viral envelope. Here, we perform all atomic simulations between the SARS-CoV-2 spike glycoprotein and human skin models. We consider an "oily" skin covered by sebum and a "clean" skin exposing the stratum corneum. The simulations show that the spike tries to maximize the contacts with stratum corneum lipids, particularly ceramides, with substantial hydrogen bonding. In the case of "oily" skin, the spike is able to retain its structure, orientation and hydration over sebum with little interaction with sebum components. Comparison of these results with our previous simulations of the interaction of SARS-CoV-2 spike with hydrophilic and hydrophobic solid surfaces, suggests that the "soft" or "hard" nature of the surface plays an essential role in the interaction of the spike protein with materials.

Steric Hindrance in Metal Coordination Drives the Separation of Pyridine Regioisomers Using Rhodium(II)-Based Metal-Organic Polyhedra.

The physicochemical similarity of isomers makes their chemical separation through conventional techniques energy intensive. Herein, we report that, instead of using traditional encapsulation-driven processes, steric hindrance in metal coordination on the outer surface of RhII -based metal-organic polyhedra (Rh-MOPs) can be used to separate pyridine-based regioisomers via liquid-liquid extraction. Through molecular dynamics simulations and wet experiments, we discovered that the capacity of pyridines to coordinatively bind to Rh-MOPs is determined by the positions of the pyridine substituents relative to the pyridine nitrogen and is influenced by steric hindrance. Thus, we exploited the differential solubility of bound and non-bound pyridine regioisomers to engineer liquid-liquid self-sorting systems. As a proof of concept, we separated four different equimolecular mixtures of regioisomers, including a mixture of the industrially relevant compounds 2-chloropyridine and 3-chloropyridine, isolating highly pure compounds in all cases.

Computer simulations of the interaction between SARS-CoV-2 spike glycoprotein and different surfaces.

A prominent feature of coronaviruses is the presence of a large glycoprotein spike protruding from a lipidic membrane. This glycoprotein spike determines the interaction of coronaviruses with the environment and the host. In this paper, we perform all atomic molecular dynamics simulations of the interaction between the SARS-CoV-2 trimeric glycoprotein spike and surfaces of materials. We considered a material with high hydrogen bonding capacity (cellulose) and a material capable of strong hydrophobic interactions (graphite). Initially, the spike adsorbs to both surfaces through essentially the same residues belonging to the receptor binding subunit of its three monomers. Adsorption onto cellulose stabilizes in this configuration, with the help of a large number of hydrogen bonds developed between cellulose and the three receptor-binding domains of the glycoprotein spike. In the case of adsorption onto graphite, the initial adsorption configuration is not stable and the surface induces a substantial deformation of the glycoprotein spike with a large number of adsorbed residues not pertaining to the binding subunits of the spike monomers.

Unified View of Magnetic Nanoparticle Separation under Magnetophoresis.

The migration process of magnetic nanoparticles and colloids in solution under the influence of magnetic field gradients, which is also known as magnetophoresis, is an essential step in the separation technology used in various biomedical and engineering applications. Many works have demonstrated that in specific situations, separation can be performed easily with the weak magnetic field gradients created by permanent magnets, a process known as low-gradient magnetic separation (LGMS). Due to the level of complexity involved, it is not possible to understand the observed kinetics of LGMS within the classical view of magnetophoresis. Our experimental and theoretical investigations in the last years unravelled the existence of two novel physical effects that speed up the magnetophoresis kinetics and explain the observed feasibility of LGMS. Those two effects are (i) cooperative magnetophoresis (due to the cooperative motion of strongly interacting particles) and (ii) magnetophoresis-induced convection (fluid dynamics instability originating from inhomogeneous magnetic gradients). In this feature article, we present a unified view of magnetophoresis based on the extensive research done on these effects. We present the physical basis of each effect and also propose a classification of magnetophoresis into four distinct regimes. This classification is based on the range of values of two dimensionless quantities, namely, aggregation parameter N* and magnetic Grashof number Grm, which include all of the dependency of LGMS on various physical parameters (such as particle properties, thermodynamic parameters, fluid properties, and magnetic field properties). This analysis provides a holistic view of the classification of transport mechanisms in LGMS, which could be particularly useful in the design of magnetic separators for engineering applications.

Surface specificity and mechanistic pathway of de-fluorination of C60F48 on coinage metals.

We provide experimental and theoretical understanding on fundamental processes taking place at room temperature when a fluorinated fullerene dopant gets close to a metal surface. By employing scanning tunneling microscopy and photoelectron spectroscopies, we demonstrate that the on-surface integrity of C60F48 depends on the interaction with the particular metal it approaches. Whereas on Au(111) the molecule preserves its chemical structure, on more reactive surfaces such as Cu(111) and Ni(111), molecules interacting with the bare metal surface lose the halogen atoms and transform to C60. Though fluorine-metal bonding can be detected depending on the molecular surface density, no ordered fluorine structures are observed. We show the implications of the metal-dependent de-fluorination in the electronic structure of the molecules and the energy alignment at the molecule-metal interface. Molecular dynamics simulations with ReaxFF reactive force field corroborate the experimental facts and provide a detailed mechanistic picture of the surface-induced de-fluorination, which involves the rotation of the molecule on the surface. Outstandingly, a thermodynamic analysis indicates that the effect of the metal surface is lowering and diminishing the energy barrier for C-F cleave, demonstrating the catalytic role of the surface. The present study contributes to in-depth knowledge of the mechanisms that affect the degree of stability of chemical species on surfaces, which is essential to advance our understanding of the chemical reactivity of metals and their role in on-surface chemical reactions.

Atomistic Simulations of COSAN: Amphiphiles without a Head-and-Tail Design Display "Head and Tail" Surfactant Behavior.

Cobaltabisdicarbollide (COSAN) anions have an unexpectedly rich self-assembly behavior, which can lead to vesicles and micelles without having a classical surfactant molecular architecture. This was rationalized by the introduction of new terminology and novel driving forces. A key aspect in the interpretation of COSAN behavior is the assumption that the most stable form of these ions is the transoid rotamer, which lacks a "hydrophilic head" and a "hydrophobic tail". Using implicit solvent DFT calculations and MD simulations we show that in water, 1) the cisoid rotamer is the most stable form of COSAN and 2) this cisoid rotamer has a well-defined hydrophilic polar region ("head") and a hydrophobic apolar region ("tail"). In addition, our simulations show that the properties of this rotamer in water (interfacial affinity, micellization) match those expected for a classical surfactant. Therefore, we conclude that the experimental results for the COSAN ions can now be understood in terms of its amphiphilic molecular architecture.