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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.

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.

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.

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.

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.

Coordinates (input files and equilibrated structures) corresponding to the MD simulations reported in Sahihi and Faraudo, J. Chem. Inf. Model. 2022, 62, 16, 3814–3824 https://doi.org/10.1021/acs.jcim.2c00562 . Please cite this publication and the dataset in any use of the data. The coordinate files in pdb format include fully glycosylated structures of the S1 subunit of SARS-CoV-2 spike protein (up and down confirmations) and a polystyrene slab.

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%.

Coinage metals like silver, gold and copper are historically known as materials with anti-infective properties; but the mechanism behind these properties is not yet clear, and several features seem to be effective in this regard. 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 protein with the (100) surface of Au, Ag and Cu. Our results revealed that spike protein is adsorbed onto the surface of these metals, being the Cu-metal with the highest interaction with the spike and Au, the metal which induces bigger structural changes in the spike. In our simulations, we considered the spike protein in both its up and down conformations. We found that the affinity of the metals for the up-conformation was higher than their affinity for the down conformation of the spike protein due to the interactions with the receptor binding domain that is exposed in the up conformation but hidden in the down conformation. Comparing the present results for metals with those obtained in our previous MD simulations with other materials (cellulose, graphite, and human skin models), we see that Au induces the highest structural change in the spike, larger than those obtained in our previous studies.

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.

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.

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 over 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.

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.

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.

Industries, governments and consumers increasingly request sustainable resources and greener routes for the integration of advanced functional nanocomposites in products and devices. Among renewable biopolymers, cellulose deserves special consideration since it is the most abundant one. While inorganic nanoparticles add functional properties to a nanocomposite, a flexible and porous cellulosic support will facilitate the interaction of the nanoparticles with the surroundings, their handling and recycling. A significant challenge is to develop high strength, flexible nanobiocomposites controlling the nanoparticle properties, their volume fraction and their topographic distribution within the scaffold. A new concept is presented here for multifunctional laminates where layers consist of bacterial cellulose fibrils decorated by inorganic nanoparticles. Each layer can provide a specific function using a different nanoparticle. As model systems, we have selected two metals (Au, Ag) and two semiconductors (TiO2 and Fe2O3). Energy-efficient microwave-assisted synthetic routes have been used to in situ nucleate and grow the inorganic nanocrystals on the cellulose fibrils. Then, functionalized bacterial cellulose films can be arranged as laminates in a millefeuille construct simply by layering and drying the wet films at 60 °C. After drying, they perform as a single integrated and thicker film. Structural, functional and mechanical integrity of the laminates have been investigated. Molecular dynamics simulations were used to compute the surface adhesion energy between two cellulose fibrils and the results are discussed in light of the experimental peel-off data for the separation of the layers in the laminate.