The Role of Lysozyme in the Formation of Bioinspired Silicon Dioxide.

Several organisms are able to polycondensate tetraoxosilicic(IV) acid to form silicon (IV) dioxide using polycationic molecules. According to an earlier mechanistic proposal, these molecules undergo a phase-separation and recent experimental evidence appears to confirm this model. At the same time, polycationic proteins like lysozyme can also promote polycondensation of silicon (IV) dioxide, and they do so under conditions that are not compatible with liquid-liquid phase separation. In this manuscript we investigate this conundrum by molecular simulations. Several organisms are able to polycondensate tetraoxosilicic(IV) acid to form silicon (IV) dioxide using polycationic molecules. According to an earlier mechanistic proposal, these molecules undergo a phase-separation and recent experimental evidence appears to confirm this model. At the same time, polycationic proteins like lysozyme can also promote polycondensation of silicon (IV) dioxide, and they do so under conditions that are not compatible with liquid-liquid phase separation. In this manuscript we investigate this conundrum by molecular simulations.

Exploring High-Pressure Polymorphism in Carbonic Acid through Direct Synthesis from Carbon Dioxide Clathrate Hydrate.

Carbon dioxide (CO2) is widespread in astrochemically relevant environments, often coexisting with water (H2O) ices and thus triggering a great interest regarding the possible formation of their adducts under various thermodynamic conditions. Amongst them, solid carbonic acid (H2CO3) remains elusive, yet being widely studied. Synthetic routes followed for its production have always been characterised by drastic irradiation on solid ice mixtures or complex procedures on fluid samples (such as laser heating at moderate to high pressures). Here we report about a simpler yet effective synthetic route to obtain two diverse carbonic acid crystal structures from the fast, cold compression of pristine clathrate hydrate samples. The two distinct polymorphs we obtained, differing in the water content, have been deeply characterised via spectroscopic and structural techniques to assess their composition and their astonishing pressure stability, checked up to half a megabar, also highlighting the complex correlations between them so to compile a detailed phase diagram of this system. These results may have a profound impact on the prediction and modelisation of the complex chemistry which characterises many icy bodies of our Solar System.

Photosensitizers Based on Bichromophoric Dyads Combining Ru(II)-Polypyridyl Complexes and Dissymmetric Perylene Monoimide Derivatives: The Nontrivial Role of Ligand Substitution.

The covalent modification of Ru(II) polypyridyl complexes (RPCs) with organic chromophores is a powerful strategy to obtain metal-based photosensitizer agents (PSs) with improved performance for application in photodynamic therapy (PDT). In this respect, perylene-imides are of particular interest due to their rich chemical-physical repertoire, and it is therefore quite surprising that their combination with RPCs has been poorly considered so far. Herein, we report on the photophysical behavior of two newly synthesized RPCs bearing a perylene monoimide appendant (PMI-Ad). Differently from the majority of RPCs-perylene-imides dyads, these chromophores are dissymmetric and are tethered to the metal centers through a single C-C bond in the 3- or 5-position of 1,10-phenanthroline (Ru-3PMI-Ad and Ru-5PMI-Ad). Both compounds show excellent singlet oxygen photosensitizing activity, with quantum yields reaching >90% in the case of Ru-3PMI-Ad. A combined spectroscopic and theoretical analysis, also involving transient absorption and luminescence lifetime measurements, demonstrates that both compounds undergo intersystem crossing on a very fast time scale (tens of picoseconds) and with high efficiency. Our results further demonstrate that the increased electron delocalization between the metal center and the PMI-Ad chromophore observed for Ru-3PMI-Ad additionally contributes to increase the singlet oxygen quantum yields by prolonging the lifetime of the triplet state.

Upgrading of the general AMBER force field 2 for fluorinated alcohol biosolvents: A validation for water solutions and melittin solvation.

The standard GAFF2 force field parameterization has been refined for the fluorinated alcohols 2,2,2-trifluoroethanol (TFE), 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), and 1,1,1,3,3,3-hexafluoropropan-2-one (HFA), which are commonly used to study proteins and peptides in biomimetic media. The structural and dynamic properties of both proteins and peptides are significantly influenced by the biomimetic environment created by the presence of these cosolvents in aqueous solutions. Quantum mechanical calculations on stable conformers were used to parameterize the atomic charges. Different systems, such as pure liquids, aqueous solutions, and systems formed by melittin protein and cosolvent/water solutions, have been used to validate the new models. The calculated macroscopic and structural properties are in agreement with experimental findings, supporting the validity of the newly proposed models.

Concerted versus stepwise proton transfer reactions in the [2, 2'-bipyridyl]-3-3'-diol molecule: A static and dynamic ab-initio investigation.

The double proton transfer (PT) reaction has been investigated in the [2,2'-bipyridyl]-3-3'-diol, a complex molecule where the proton movements is coupled to significant rearrangement of the electronic structure. Moreover, the reaction could be concerted, that is the two protons are exchanged simultaneously, or stepwise, where the two protons are transferred sequentially. To this end, a static exploration of the potential energy surface (PES) was carried together with the analysis of the free-energy surface (FES), both surfaces being evaluated at density functional theory level and different exchange-correlation functionals. While the concerted mechanism has been clearly discharged, the characteristics of the stepwise PT significantly depends on the chosen functionals, some suggesting a clear stepwise mechanism characterized by a stable reaction intermediates and two transitions states, whereas other approaches propend for a asynchronous PT, with a single TS. These features appear on both PES and FES, albeit some differences appears due to their different nature.

Crystal engineering of high explosives through lone pair-π interactions: Insights for improving thermal safety.

In this high-risk/high-reward study, we prepared complexes of a high explosive anion (picrate) with potentially explosive s-tetrazine-based ligands with the sole purpose of advancing the understanding of one of the weakest supramolecular forces: the lone pair-π interaction. This is a proof-of-concept study showing how lone pair-π contacts can be effectively used in crystal engineering, even of high explosives, and how the supramolecular architecture of the resulting crystalline phases influences their experimental thermokinetic properties. Herein we present XRD structures of 4 novel detonating compounds, all showcasing lone pair-π interactions, their thermal characterization (DSC, TGA), including the correlation of experimental thermokinetic parameters with crystal packing, and in silico explosion properties. This last aspect is relevant for improving the safety of high-energy materials.

The Smart Drifter Cluster: Monitoring Sea Currents and Marine Litter Transport Using Consumer IoT Technologies.

The study of marine Lagrangian transport holds significant importance from a scientific perspective as well as for practical applications such as environmental-pollution responses and prevention (e.g., oil spills, dispersion/accumulation of plastic debris, etc.). In this regard, this concept paper introduces the Smart Drifter Cluster: an innovative approach that leverages modern "consumer" IoT technologies and notions. This approach enables the remote acquisition of information on Lagrangian transport and important ocean variables, similar to standard drifters. However, it offers potential benefits such as reduced hardware costs, minimal maintenance expenses, and significantly lower power consumption compared to systems relying on independent drifters with satellite communication. By combining low power consumption with an optimized, compact integrated marine photovoltaic system, the drifters achieve unlimited operational autonomy. With the introduction of these new characteristics, the Smart Drifter Cluster goes beyond its primary function of mesoscale monitoring of marine currents. It becomes readily applicable to numerous civil applications, including recovering individuals and materials at sea, addressing pollutant spills, and tracking the dispersion of marine litter. An additional advantage of this remote monitoring and sensing system is its open-source hardware and software architecture. This fosters a citizen-science approach, enabling citizens to replicate, utilize, and contribute to the improvement of the system. Thus, within certain constraints of procedures and protocols, citizens can actively contribute to the generation of valuable data in this critical field.

Ruthenium(II) Polypyridyl Complexes and Metronidazole Derivatives: A Powerful Combination in the Design of Photoresponsive Antibacterial Agents Effective under Hypoxic Conditions.

Ruthenium(II) polypyridyl complexes (RPCs) are gaining momentum in photoactivated chemotherapy (PACT), thanks to the possibility of overcoming the classical reliance on molecular oxygen of photodynamic therapy while preserving the selective drug activation by using light. However, notwithstanding the intriguing perspectives, the translation of such an approach in the development of new antimicrobials has been only barely considered. Herein, MTZH-1 and MTZH-2, two novel analogues of metronidazole (MTZ), a mainstay drug in the treatment of anaerobic bacterial infections, were designed and inserted in the strained ruthenium complexes [Ru(tpy)(dmp)(MTZ-1)]PF6 (Ru2) and [Ru(tpy)(dmp)(MTZ-2)]PF6 (Ru3) (tpy = terpyridine, dmp = 2,9-dimethyl-1,10-phenanthroline) (Chart 1). Analogously to the parental compound [Ru(tpy)(dmp)(5NIM)]PF6 (Ru1) (5-nitroimidazolate), the Ru(II)-imidazolate coordination of MTZ derivatives resulted in promising Ru(II) photocages, capable to easily unleash the bioactive ligands upon light irradiation and increase the antibacterial activity against Bacillus subtilis, which was chosen as a model of Gram-positive bacteria. The photoreleased 5-nitroimidazole-based ligands led to remarkable phototoxicities under hypoxic conditions (<1% O2), with the lead compound Ru3 that exhibited the highest potency across the series, being comparable to the one of the clinical drug MTZ. Besides, the chemical architectures of MTZ derivatives made their interaction with NimAunfavorable, being NimA a model of reductases responsible for bacterial resistance against 5-nitroimidazole-based antibiotics, thus hinting at their possible use to combat antimicrobial resistance. This work may therefore provide fundamental knowledge in the design of novel photoresponsive tools to be used in the fight against infectious diseases. For the first time, the effectiveness of the "photorelease antimicrobial therapy" under therapeutically relevant hypoxic conditions was demonstrated.

A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data.

Classical molecular dynamics (MD) simulations are widely used to inspect the behavior of zinc(II)-proteins at the atomic level, hence the need to properly model the zinc(II) ion and the interaction with its ligands. Different approaches have been developed to represent zinc(II) sites, with the bonded and nonbonded models being the most used. In the present work, we tested the well-known zinc AMBER force field (ZAFF) and a recently developed nonbonded force field (NBFF) to assess how accurately they reproduce the dynamic behavior of zinc(II)-proteins. For this, we selected as benchmark six zinc-fingers. This superfamily is extremely heterogenous in terms of architecture, binding mode, function, and reactivity. From repeated MD simulations, we computed the order parameter (S2) of all backbone N-H bond vectors in each system. These data were superimposed to heteronuclear Overhauser effect measurements taken by NMR spectroscopy. This provides a quantitative estimate of the accuracy of the FFs in reproducing protein dynamics, leveraging the information about the protein backbone mobility contained in the NMR data. The correlation between the MD-computed S2 and the experimental data indicated that both tested FFs reproduce well the dynamic behavior of zinc(II)-proteins, with comparable accuracy. Thus, along with ZAFF, NBFF represents a useful tool to simulate metalloproteins with the advantage of being extensible to diverse systems such as those bearing dinuclear metal sites.

NE-RDFE: A protocol and toolkit for computing relative dissociation free energies with GROMACS between dissimilar molecules using bidirectional nonequilibrium dual topology schemes.

We describe a step-by-step protocol and toolkit for the computation of the relative dissociation free energy (RDFE) with the GROMACS molecular dynamics package, based on a novel bidirectional nonequilibrium alchemical approach. The proposed methodology does not require any intervention on the code and allows computing with good accuracy the RDFE between small molecules with arbitrary differences in volume, charge, and chemical topology. The procedure is illustrated for the challenging SAMPL9 batch of host-guest pairs. The article is supplemented by a detailed online tutorial, available at https://procacci.github.io/vdssb_gromacs/NE-RDFE and by a public Zenodo repository available at https://zenodo.org/record/6982932.

Characterization of a Ruthenium(II) Complex in Singlet Oxygen-Mediated Photoelectrochemical Sensing.

A water-soluble ruthenium(II) complex (L), capable of producing singlet oxygen (1O2) when irradiated with visible light, was used to modify the surface of an indium-tin oxide (ITO) electrode decorated with a nanostructured layer of TiO2 (TiO2/ITO). Singlet oxygen triggers the appearance of a cathodic photocurrent when the electrode is illuminated and biased at a proper reduction potential value. The L/TiO2/ITO electrode was first characterized with cyclic voltammetry, impedance spectroscopy, NMR, and Raman spectroscopy. The rate constant of singlet oxygen production was evaluated by spectrophotometric measurements. Taking advantage of the oxidative process initiated by 1O2, the analysis of phenolic compounds was accomplished. Particularly, the 1O2-driven oxidation of hydroquinone (HQ) produced quinone moieties, which could be reduced back at the electrode surface, biased at -0.3 V vs Ag/AgCl. Such a light-actuated redox cycle produced a photocurrent dependent on the concentration of HQ in solution, exhibiting a limit of detection (LOD) of 0.3 µmol dm-3. The L/TiO2/ITO platform was also evaluated for the analysis of p-aminophenol, a commonly used reagent in affinity sensing based on alkaline phosphatase.

Rider Variables Affecting the Stirrup Directional Force Asymmetry during Simulated Riding Trot.

Riders' asymmetry may cause back pain in both human and equine athletes. This pilot study aimed at documenting in a simple and quick way asymmetry in riders during a simulation of three different riding positions on wooden horseback using load cells applied on the stirrup leathers and identifying possible associations between riders' asymmetry and their gender, age, level of riding ability, years of riding experience, riding style, motivation of riding, primary discipline and handedness. After completing an interview to obtain the previously mentioned information, 147 riders performed a standardized test on a saddle fixed on a wooden horseback-shaped model. The riding simulation was split into three phases of 1 min each: (1) sit in the saddle, (2) standing in the stirrups and (3) rising trot. The directional force on the left and the right stirrup leathers was recorded every 0.2 s. A paired t-test was performed on the recorded data to test the difference (i.e., asymmetry) in each phase. In phases 1, 2 and 3, 99.3% (53.4% heavier on the right (R)), 98% (52.8% heavier on the left (L)) and 46.3% (51.5% heavier on the left (L)) of the riders were asymmetrical, respectively. Chi-square tests showed a significant association between riding ability and riding experience, but no significant association between reported handedness and calculated leg-sidedness (p > 0.05). Univariate logistic (1: asymmetry, 0: symmetry) regression analysis was performed only on the phase 3 data. One-hand riders were found twice more likely to be asymmetrical than two-hand riders (Odds Ratio (OR): 2.18, Confidence Interval (CI): 1.1−4.29; p = 0.024). This preliminary study confirmed that the majority of the riders are asymmetrical in load distribution on stirrups and suggested the riding style as a possible risk factor for asymmetry.

Absorption Spectra of Flexible Fluorescent Probes by a Combined Computational Approach: Molecular Dynamics Simulations and Time-Dependent Density Functional Theory.

A detailed understanding and interpretation of absorption spectra of molecular systems, especially in condensed phases, requires computational models that allow their structural and electronic features to be connected to the observed macroscopic spectra. This work is focused on modeling the electronic absorption spectrum of a fluorescent probe, namely, the 9-(4-((bis(2-((2-(ethylthio)ethyl)thio)ethyl)amino)methyl)phenyl)-6-(pyrrolidin-1-yl)-3H-xanthen-3-one molecule, depicted by a combined classical-quantum chemical approach. Particularly, first classical molecular dynamics (MD) has been used to explore the configurational space, and next, the absorption spectrum has been reconstructed by averaging the results of time-dependent density functional theory (TD-DFT) calculations performed on equispaced molecular conformations extracted from MD to properly sample the configurational space explored at finite temperature. To verify the effect of molecular conformation on the spectral profile, the generated electronic absorption spectra were compared with those obtained considering a single structure corresponding to the optimized one, an approach also referred to as static. This comparison allows one to highlight a sizable though small shift between the maxima of the corresponding reconstructed absorption spectra, highlighting the importance of conformational sampling in the case of this rather flexible molecule. Four different exchange and correlation functionals (PBE, BLYP, PBE0, B3LYP) were considered to compute vertical transition via TD-DFT calculations. From the results obtained in gas and in condensed, here solution, phases, it appears that the magnitude of the shift is actually more affected by the phase in which the system is found than by the functional used. This fact underlines the central importance of conformational mobility, that is flexibility, of this molecule. From a more quantitative point of view, a comparison with available experimental data shows that hybrid functionals, such as PBE0 and B3LYP, enable one to faithfully reproduce the observed absorption maxima.

2-Butanol Aqueous Solutions: A Combined Molecular Dynamics and Small/Wide-Angle X-ray Scattering Study.

Structural properties of 2-butanol aqueous solutions at different concentrations have been studied using small- and wide-angle X-ray scattering and molecular dynamics simulations. The experimental structure factors have been accurately reproduced by the simulations, allowing one to explain their variation with concentration and to achieve a detailed description of the structural and dynamic properties of the studied systems. The analysis of experimental and computational data has shown that 2-butanol, the simplest aliphatic chiral alcohol, tends to form aggregates at a concentration above 1 M, affecting also both the structural and dynamic properties of the solvent.

Ethanol electro-oxidation reaction on the Pd(111) surface in alkaline media: insights from quantum and molecular mechanics.

The ethanol electro-oxidation catalyzed by Pd in an alkaline environment involves several intermediate reaction steps promoted by the hydroxyl radical, OH. In this work, we report on the dynamical paths of the first step of this oxidation reaction, namely the hydrogen atom abstraction CH3CH2OH + OH → CH3CHOH + H2O, occurring at the Pd(111) surface and address the thermodynamic stability of the adsorbed reactants by means of quantum and molecular mechanics calculations, with special focus on the effect of the solvent. We have found that the impact of the solvent is significant for both ethanol and OH, contributing to a decrease in their adsorption free energies by a few dozen kcal mol-1 with respect to the adsorption energy under vacuum. Furthermore, we observe that hydrogen atom abstraction is enhanced for those simulation paths featuring large surface-reactant distances, namely, when the reactants weakly interact with the catalyst. The picture emerging from our study is therefore that of a catalyst whose coverage in an aqueous environment is largely dominated by OH with respect to ethanol. Nevertheless, only a small amount of them, specifically those weakly bound to the catalyst, is really active in the ethanol electro-oxidation reaction. These results open the idea of a rational design of co-catalysts based on the tuning of surface chemical properties to eventually enhance exchange current density.

Development, Validation, and Pilot Application of a Generalized Fluctuating Charge Model for Computational Spectroscopy in Solution.

A general approach enforcing nonperiodic boundary conditions for the computation of spectroscopic properties in solution has been improved including an effective description of charge-transfer contributions and coordination number adjustment for explicit solvent molecules. Both contributions are obtained from a continuous description of intermolecular hydrogen bonds, which has been employed also for an effective clustering of molecular dynamics trajectories. Fine tuning of the model has been performed for several water clusters, and then its efficiency and reliability have been demonstrated by computing the absorption spectra of different creatinine tautomers in aqueous solution.

Characterization of the non-covalent interaction between the PF-07321332 inhibitor and the SARS-CoV-2 main protease.

We have studied the non-covalent interaction between PF-07321332 and SARS-CoV-2 main protease at the atomic level using a computational approach based on extensive molecular dynamics simulations with explicit solvent. PF-07321332, whose chemical structure has been recently disclosed, is a promising oral antiviral clinical candidate with well-established anti-SARS-CoV-2 activity in vitro. The drug, currently in phase III clinical trials in combination with ritonavir, relies on the electrophilic attack of a nitrile warhead to the catalytic cysteine of the protease. Nonbonded interaction between the inhibitor and the residues of the binding pocket, as well as with water molecules on the protein surface, have been characterized using two different force fields and the two possible protonation states of the main protease catalytic dyad HIS41-CYS145. When the catalytic dyad is in the neutral state, the non-covalent binding is likely to be stronger. Molecular dynamics simulations seems to lend support for an inhibitory mechanism in two steps: a first non-covalent addition with the dyad in neutral form and then the formation of the thiolate-imidazolium ion pair and the ligand relocation for finalising the electrophilic attack.

Exploring the effect of Mg2+ substitution on amorphous calcium phosphate nanoparticles.

HYPOTHESIS: The study of Amorphous Calcium Phosphate (ACP) has become a hot topic due to its relevance in living organisms and as a material for biomedical applications. The preparation and characterization of Mg-substituted ACP nanoparticles (AMCP) with tunable Ca/Mg ratio is reported in the present study to address the effect of Mg2+ on their structure and stability. EXPERIMENTS: AMCPs particles were synthesized by precipitation of the precursors from aqueous solutions. The particles were analyzed in terms of morphology, crystallinity, and thermal stability, to get a complete overview of their physico-chemical characteristics. Computational methods were also employed to simulate the structure of ACP clusters at different levels of Mg2+ substitution. FINDINGS: Our results demonstrate that AMCP particles with tunable composition and crystallinity can be obtained. The analysis of the heat-induced crystallization of AMCP shows that particles' stability depends on the degree of Mg2+ substitution in the cluster, as confirmed by computational analyses. The presented results shed light on the effect of Mg2+ on ACP features at different structural levels and may be useful guidelines for the preparation and design of AMCP particles with a specific Ca/Mg ratio.

Nitroimidazole-Based Ruthenium(II) Complexes: Playing with Structural Parameters to Design Photostable and Light-Responsive Antibacterial Agents.

5-Nitroimidazole (5NIMH), chosen as a molecular model of nitroimidazole derivatives, which represent a broad-spectrum class of antimicrobials, was incorporated into the ruthenium complexes [Ru(tpy)(phen)(5NIM)]PF6 (1) and [Ru(tpy)(dmp)(5NIM)]PF6 (2) (tpy = terpyridine, phen = phenanthroline, dmp = 2,9-dimethyl-1,10-phenanthroline). Besides the uncommon metal coordination of 5-nitroimidazole in its imidazolate form (5NIM), the different architectures of the spectator ligands (phen and dmp) were exploited to tune the "mode of action" of the resulting complexes, passing from a photostable compound where the redox properties of 5NIMH are preserved (1) to one suitable for the nitroimidazole phototriggered release (2) and whose antibacterial activity against B. subtilis, chosen as cellular model, is effectively improved upon light exposure. This study may provide a fundamental knowledge on the use of Ru(II)-polypyridyl complexes to incorporate and/or photorelease biologically relevant nitroimidazole derivatives in the design of a novel class of antimicrobials.

Wearable Robots: An Original Mechatronic Design of a Hand Exoskeleton for Assistive and Rehabilitative Purposes.

Robotic devices are being employed in more and more sectors to enhance, streamline, and augment the outcomes of a wide variety of human activities. Wearable robots arise indeed as of-vital-importance tools for telerehabilitation or home assistance targeting people affected by motor disabilities. In particular, the field of "Robotics for Medicine and Healthcare" is attracting growing interest. The development of such devices is a primarily addressed topic since the increasing number of people in need of rehabilitation or assistive therapies (due to population aging) growingly weighs on the healthcare systems of the nation. Besides, the necessity to move to clinics represents an additional logistic burden for patients and their families. Among the various body parts, the hand is specially investigated since it most ensures the independence of an individual, and thus, the restoration of its dexterity is considered a high priority. In this study, the authors present the development of a fully wearable, portable, and tailor-made hand exoskeleton designed for both home assistance and telerehabilitation. Its purpose is either to assist patients during activities of daily living by running a real-time intention detection algorithm or to be used for remotely supervised or unsupervised rehabilitation sessions by performing exercises preset by therapists. Throughout the mechatronic design process, special attention has been paid to the complete wearability and comfort of the system to produce a user-friendly device capable of assisting people in their daily life or enabling recorded home rehabilitation sessions allowing the therapist to monitor the state evolution of the patient. Such a hand exoskeleton system has been designed, manufactured, and preliminarily tested on a subject affected by spinal muscular atrophy, and some results are reported at the end of the article.