Modulating Efficiency and Color of Thermally Activated Delayed Fluorescence by Rationalizing the Substitution Effect.

Thermally activated delayed fluorescence (TADF) constitutes the process by which third-generation organic light-emitting diodes (OLEDs) are being designed and produced. Despite several years of trial-and-error attempts, mainly driven by chemical intuition about how to improve a certain aspect of the process, few studies focused on the in-depth description of its two key properties: efficiency of the T1 → S1 intersystem crossing and further S1 → S0 emission. Here, by means of a newly developed theoretical formalism, we propose a systematic rationalization of the substituent effect in a paradigmatic class of OLED compounds, based on phenothiazine-dibenzothiophene-S,S-dioxide, known as PTZ-DBTO2. Our methodology allows to discern among geometrical and electronic effects induced by the substituent, deeply understanding the relationships existing between charge transfer, spin density, geometrical deformations, and energy modulations between electronic states. By our results, we can finally elucidate, depending on the substituent, the fate of the overall TADF process, quantitatively assessing its efficiency and predicting the color emission. Moreover, the general terms by which this methodology was developed allow its application to any chromophore of interest.

Electro- and photochemical H2 generation by Co(ii) polypyridyl-based catalysts bearing ortho-substituted pyridines.

Cobalt(ii) complexes featuring hexadentate amino-pyridyl ligands have been recently discovered as highly active catalysts for the Hydrogen Evolution Reaction (HER), whose high performance arises from the possibility of assisting proton transfer processes via intramolecular routes involving detached pyridine units. With the aim of gaining insights into such catalytic routes, three new proton reduction catalysts based on amino-polypyridyl ligands are reported, focusing on substitution of the pyridine ortho-position. Specifically, a carboxylate (C2) and two hydroxyl substituted pyridyl moieties (C3, C4) are introduced with the aim of promoting intramolecular proton transfer which possibly enhances the efficiency of the catalysts. Foot-of-the-wave and catalytic Tafel plot analyses have been utilized to benchmark the catalytic performances under electrochemical conditions in acetonitrile using trifluoroacetic acid as the proton source. In this respect, the cobalt complex C3 turns out to be the fastest catalyst in the series, with a maximum turnover frequency (TOF) of 1.6 (±0.5) × 105 s-1, but at the expense of large overpotentials. Mechanistic investigations by means of Density Functional Theory (DFT) suggest a typical ECEC mechanism (i.e. a sequence of reduction - E - and protonation - C - events) for all the catalysts, as previously envisioned for the parent unsubstituted complex C1. Interestingly, in the case of complex C2, the catalytic route is triggered by initial protonation of the carboxylate group resulting in a less common (C)ECEC mechanism. The pivotal role of the hexadentate chelating ligand in providing internal proton relays to assist hydrogen elimination is further confirmed within this novel class of molecular catalysts, thus highlighting the relevance of a flexible polypyridine ligand in the design of efficient cobalt complexes for the HER. Photochemical studies in aqueous solution using [Ru(bpy)3]2+ (where bpy = 2,2'-bipyridine) as the sensitizer and ascorbate as the sacrificial electron donor support the superior performance of C3.

Binding of Nitriles and Isonitriles to V(III) and Mo(III) Complexes: Ligand vs Metal Controlled Mechanism.

The synthesis and structures of nitrile complexes of V(N[tBu]Ar)3, 2 (Ar = 3,5-Me2C6H3), are described. Thermochemical and kinetic data for their formation were determined by variable temperature Fourier transform infrared (FTIR), calorimetry, and stopped-flow techniques. The extent of back-bonding from metal to coordinated nitrile indicates that electron donation from the metal to the nitrile plays a less prominent role for 2 than for the related complex Mo(N[tBu]Ar)3, 1. Kinetic studies reveal similar rate constants for nitrile binding to 2, but the activation parameters depend critically on the nature of R in RCN. Activation enthalpies range from 2.9 to 7.2 kcal·mol-1, and activation entropies from -9 to -28 cal·mol-1·K-1 in an opposing manner. Density functional theory (DFT) calculations provide a plausible explanation supporting the formation of a π-stacking interaction between a pendant arene of the metal anilide of 2 and the arene substituent on the incoming nitrile in favorable cases. Data for ligand binding to 1 do not exhibit this range of activation parameters and are clustered in a small area centered at ΔH‡ = 5.0 kcal·mol-1 and ΔS‡ = -26 cal·mol-1·K-1. Computational studies are in agreement with the experimental data and indicate a stronger dependence on electronic factors associated with the change in spin state upon ligand binding to 1.

Production of Dihydrogen Using Ammonia Borane as Reagent and Pyrazole as Catalyst.

Theoretical chemistry (DLPNO-CCSD(T)/def2-TZVP//M06-2x/aug-cc-pVDZ) was used to design a system based on ammonia boranes catalyzed by pyrazoles with the aim of producing dihydrogen, nowadays of high interest as clean fuel. The reactivity of ammonia borane and cyclotriborazane were investigated, including catalytic activation through 1H-pyrazole, 4-methoxy-1H-pyrazole, and 4-nitro-1H-pyrazole. The results point toward a catalytic cycle by which, at the same time, ammonia borane can initially store and then, through catalysis, produce dihydrogen and amino borane. Subsequently, amino borane can trimerize to form cyclotriborazane that, in presence of the same catalyst, can also produce dihydrogen. This study proposes therefore a consistent progress in using environmentally sustainable (metal free) catalysts to efficiently extract dihydrogen from small B-N bonded molecules.

Taking up the quest for novel molecular solar thermal systems: Pros and cons of storing energy with cubane and cubadiene.

Molecular solar thermal (MOST) systems are working their way as a possible technology to store solar light and release it when necessary. Such systems could, in principle, constitute a solution to the energy storage problem characteristic of solar cells and are conceived, at a first instance, as simple molecular photoswitches. Nevertheless, the optimization of their different required properties is presently limiting their technological scale up. From the chemical perspective, we need to design a novel MOST system based on unconventional photoswitches. Here, by applying multi-configurational quantum chemistry methods, we unravel the potentialities of ad hoc-designed molecular photoswitches, which aim to photoproduce cubane or cubadiene as high-energy isomers that can be thermally (or eventually catalytically) reverted to the initial structure, releasing their stored energy. Specifically, while cubane can be photoproduced via different paths depending on the reactant tricycle diene conformation, an undesired bicyclic by-product limits its application to MOST systems. An evolution of this starting design toward cubadiene formation is therefore proposed, avoiding conformational equilibria and by-products, considerably red shifting the absorption to reach the visible portion of the solar spectrum and maintaining an estimated storage density that is expected to overcome the current MOST reference system (norbornadiene/quadricyclane), although consistently increasing the photoisomerization energy barrier.

Revealing the Molecular Interactions between Human ACE2 and the Receptor Binding Domain of the SARS-CoV-2 Wild-Type, Alpha and Delta Variants.

After a sudden and first spread of the pandemic caused by the novel SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus 2) wild-type strain, mutants have emerged which have been associated with increased infectivity, inducing surges in the contagions. The first of the so-called variants of concerns, was firstly isolated in the United Kingdom and later renamed Alpha variant. Afterwards, in the middle of 2021, a new variant appeared called Delta. The latter is characterized by the presence of point mutations in the Spike protein of SARS-CoV-2, especially in the Receptor Binding Domain (RBD). When in its active conformation, the RBD can interact with the human receptor Angiotensin-Converting Enzyme 2 (ACE2) to allow the entry of the virions into cells. In this contribution, by using extended all-atom molecular dynamic simulations, complemented with machine learning post-processing, we analyze the changes in the molecular interaction network induced by these different strains in comparison with the wild-type. On one hand, although relevant variations are evidenced, only limited changes in the global stability indicators and in the flexibility profiles have been observed. On the other hand, key differences were obtained by tracking hydrophilic and hydrophobic molecular interactions, concerning both positioning at the ACE2/RBD interface and formation/disruption dynamic behavior.

Autophagy and evasion of the immune system by SARS-CoV-2. Structural features of the non-structural protein 6 from wild type and Omicron viral strains interacting with a model lipid bilayer.

The viral cycle of SARS-CoV-2 is based on a complex interplay with the cellular machinery, which is mediated by specific proteins eluding or hijacking the cellular defense mechanisms. Among the complex pathways induced by the viral infection, autophagy is particularly crucial and is strongly influenced by the action of the non-structural protein 6 (Nsp6) interacting with the endoplasmic reticulum membrane. Importantly, differently from other non-structural proteins, Nsp6 is mutated in the recently emerged Omicron variant, suggesting a possible different role of autophagy. In this contribution we explore, for the first time, the structural properties of Nsp6 thanks to long-timescale molecular dynamics simulations and machine learning analysis, identifying the interaction patterns with the lipid membrane. We also show how the mutation brought by the Omicron variant may indeed modify some of the specific interactions, and more particularly help anchor the viral protein to the lipid bilayer interface.

Specific Recognition of the 5'-Untranslated Region of West Nile Virus Genome by Human Innate Immune System.

In the last few years, the sudden outbreak of COVID-19 caused by SARS-CoV-2 proved the crucial importance of understanding how emerging viruses work and proliferate, in order to avoid the repetition of such a dramatic sanitary situation with unprecedented social and economic costs. West Nile Virus is a mosquito-borne pathogen that can spread to humans and induce severe neurological problems. This RNA virus caused recent remarkable outbreaks, notably in Europe, highlighting the need to investigate the molecular mechanisms of its infection process in order to design and propose efficient antivirals. Here, we resort to all-atom Molecular Dynamics simulations to characterize the structure of the 5'-untranslated region of the West Nile Virus genome and its specific recognition by the human innate immune system via oligoadenylate synthetase. Our simulations allowed us to map the interaction network between the viral RNA and the host protein, which drives its specific recognition and triggers the host immune response. These results may provide fundamental knowledge that can assist further antivirals' design, including therapeutic RNA strategies.

Atomistic-Level Description of the Covalent Inhibition of SARS-CoV-2 Papain-like Protease.

Inhibition of the papain-like protease (PLpro) of SARS-CoV-2 has been demonstrated to be a successful target to prevent the spreading of the coronavirus in the infected body. In this regard, covalent inhibitors, such as the recently proposed VIR251 ligand, can irreversibly inactivate PLpro by forming a covalent bond with a specific residue of the catalytic site (Cys111), through a Michael addition reaction. An inhibition mechanism can therefore be proposed, including four steps: (i) ligand entry into the protease pocket; (ii) Cys111 deprotonation of the thiol group by a Brønsted-Lowry base; (iii) Cys111-S- addition to the ligand; and (iv) proton transfer from the protonated base to the covalently bound ligand. Evaluating the energetics and PLpro conformational changes at each of these steps could aid the design of more efficient and selective covalent inhibitors. For this aim, we have studied by means of MD simulations and QM/MM calculations the whole mechanism. Regarding the first step, we show that the inhibitor entry in the PLpro pocket is thermodynamically favorable only when considering the neutral Cys111, that is, prior to the Cys111 deprotonation. For the second step, MD simulations revealed that His272 would deprotonate Cys111 after overcoming an energy barrier of ca. 32 kcal/mol (at the QM/MM level), but implying a decrease of the inhibitor stability inside the protease pocket. This information points to a reversible Cys111 deprotonation, whose equilibrium is largely shifted toward the neutral Cys111 form. Although thermodynamically disfavored, if Cys111 is deprotonated in close proximity to the vinylic carbon of the ligand, then covalent binding takes place in an irreversible way (third step) to form the enolate intermediate. Finally, due to Cys111-S- negative charge redistribution over the bound ligand, proton transfer from the initially protonated His272 is favored, finally leading to an irreversibly modified Cys111 and a restored His272. These results elucidate the selectivity of Cys111 to enable formation of a covalent bond, even if a weak proton acceptor is available, as His272.

Controlling Antimicrobial Activity of Quinolones Using Visible/NIR Light-Activated BODIPY Photocages.

Controlling the activity of a pharmaceutical agent using light offers improved selectivity, reduction of adverse effects, and decreased environmental build-up. These benefits are especially attractive for antibiotics. Herein, we report a series of photoreleasable quinolones, which can be activated using visible/NIR light (520-800 nm). We have used BODIPY photocages with strong absorption in the visible to protect two different quinolone-based compounds and deactivate their antimicrobial properties. This activity could be recovered upon green or red light irradiation. A comprehensive computational study provides new insight into the reaction mechanism, revealing the relevance of considering explicit solvent molecules. The triplet excited state is populated and the photodissociation is assisted by the solvent. The light-controlled activity of these compounds has been assessed on a quinolone-susceptible E. coli strain. Up to a 32-fold change in the antimicrobial activity was measured.

Hijacking of Cellular Functions by Severe Acute Respiratory Syndrome Coronavirus-2. Permeabilization and Polarization of the Host Lipid Membrane by Viroporins.

Like all viral infections, SARS-CoV-2 acts at multiple levels, hijacking fundamental cellular functions and assuring its replication and immune system evasion. In particular, the viral 3' Open Reading Frame (ORF3a) codes for a hydrophobic protein, which embeds in the cellular membrane, where it acts as an ion viroporin and is related to strong inflammatory response. Here we report equilibrium and enhanced sampling molecular dynamic simulation of the SARS-CoV-2 ORF3a in a model lipid bilayer, showing how the protein permeabilizes the lipid membrane, via the formation of a water channel, which in turn assures ion transport. We report the free energy profile for both K+ and Cl- transfer from the cytosol to the extracellular domain. The important role of ORF3a in the viral cycle and its high conservation among coronaviruses may also make it a target of choice for future antiviral development, further justifying the elucidation of its mechanism at the atomistic level.

Interaction of a 1,3-Dicarbonyl Toxin with Ru(II)-Biimidazole Complexes for Luminescence Sensing: A Spectroscopic and Photochemical Experimental Study Rationalized by Time-Dependent Density Functional Theory Calculations.

A family of ruthenium(II) complexes containing one 2,2'-biimidazole (bim) ligand and two polypyridyl (NN) ligands has been prepared and their photophysical and photochemical features have been tested in the presence of tenuazonic acid (TeA), a widespread food and feed mycotoxin of current concern. While not tested in in vivo studies, TeA and other secondary metabolites of Alternaria fungi are suspected to exert adverse effects on the human health, so sensors and rapid analytical procedures are required. It is well-known that 1,3-dicarbonyl compounds such as TeA are relatively easy to deprotonate (the pKa of TeA is 3.5), yielding an enolate anion stabilized by resonance. The chelating and hydrogen-donor features of bim allow simultaneous binding to the metal core and to the target ß-diketonate delocalized anion. Such a binding induces changes in the blue absorption (40 nm bathochromic shift), red luminescence intensity (>75% quenching), and triplet lifetime (0.2 µs decrease) of the Ru(NN)2(bim)2+ luminophore. Moreover, we have computationally rationalized, by time-dependent density functional theory, the structure of the different adducts of Ru-bim complexes with TeA and the electronic nature of the spectral absorption bands and their change upon the addition of TeA.

E/Z Molecular Photoswitches Activated by Two-Photon Absorption: Comparison between Different Families.

Nonlinear optical techniques as two-photon absorption (TPA) have raised relevant interest within the last years due to the capability to excite chromophores with photons of wavelength equal to only half of the corresponding one-photon absorption energy. At the same time, its probability being proportional to the square of the light source intensity, it allows a better spatial control of the light-induced phenomenon. Although a consistent number of experimental studies focus on increasing the TPA cross section, very few of them are devoted to the study of photochemical phenomena induced by TPA. Here, we show a design strategy to find suitable E/Z photoswitches that can be activated by TPA. A theoretical approach is followed to predict the TPA cross sections related to different excited states of various photoswitches' families, finally concluding that protonated Schiff-bases (retinal)-like photoswitches outperform compared to the others. The donor-acceptor substitution effect is therefore rationalized for the successful TPA activatable photoswitch, in order to maximize its properties, finally also forecasting a possible application in optogenetics. Some experimental measurements are also carried out to support our conclusions.

Structure and Dynamics of RNA Guanine Quadruplexes in SARS-CoV-2 Genome. Original Strategies against Emerging Viruses.

Guanine quadruplex (G4) structures in the viral genome have a key role in modulating viruses' biological activity. While several DNA G4 structures have been experimentally resolved, RNA G4s are definitely less explored. We report the first calculated G4 structure of the RG-1 RNA sequence of SARS-CoV-2 genome, obtained by using a multiscale approach combining quantum and classical molecular modeling and corroborated by the excellent agreement between the corresponding calculated and experimental circular dichroism spectra. We prove the stability of the RG-1 G4 arrangement as well as its interaction with G4 ligands potentially inhibiting viral protein translation.

Microscopic interactions between ivermectin and key human and viral proteins involved in SARS-CoV-2 infection.

The identification of chemical compounds able to bind specific sites of the human/viral proteins involved in the SARS-CoV-2 infection cycle is a prerequisite to design effective antiviral drugs. Here we conduct a molecular dynamics study with the aim to assess the interactions of ivermectin, an antiparasitic drug with broad-spectrum antiviral activity, with the human Angiotensin-Converting Enzyme 2 (ACE2), the viral 3CLpro and PLpro proteases, and the viral SARS Unique Domain (SUD). The drug/target interactions have been characterized in silico by describing the nature of the non-covalent interactions found and by measuring the extent of their time duration along the MD simulation. Results reveal that the ACE2 protein and the ACE2/RBD aggregates form the most persistent interactions with ivermectin, while the binding with the remaining viral proteins is more limited and unspecific.

Thermal and Mechanochemical Tuning of the Porphyrin Singlet-Triplet Gap for Selective Energy Transfer Processes: A Molecular Dynamics Approach.

Molecular dynamics simulations provide fundamental knowledge on the reaction mechanism of a given simulated molecular process. Nevertheless, other methodologies based on the "static" exploration of potential energy surfaces are usually employed to firmly provide the reaction coordinate directly related to the reaction mechanism, as is the case in intrinsic reaction coordinates for thermally activated reactions. Photoinduced processes in molecular systems can also be studied with these two strategies, as is the case in the triplet energy transfer process. Triplet energy transfer is a fundamental photophysical process in photochemistry and photobiology, being for instance involved in photodynamic therapy, when generating the highly reactive singlet oxygen species. Here, we study the triplet energy transfer process between porphyrin, a prototypical energy transfer donor, and different biologically relevant acceptors, including molecular oxygen, carotenoids, and rhodopsin. The results obtained by means of nanosecond time-scale molecular dynamics simulations are compared to the "static" determination of the reaction coordinate for such a thermal process, leading to the distortions determining an effective energy transfer. This knowledge was finally applied to propose porphyrin derivatives for producing the required structural modifications in order to tune their singlet-triplet energy gap, thus introducing a mechanochemical description of the mechanism.

Rationalizing Photo-Triggered Hydrogen Evolution Using Polypyridine Cobalt Complexes: Substituent Effects on Hexadentate Chelating Ligands.

Four novel polypyridine cobalt(II) complexes were developed based on a hexadentate ligand scaffold bearing either electron-withdrawing (-CF3 ) or electron-donating (-OCH3 ) groups in different positions of the ligand. Experiments and theoretical calculations were combined to perform a systematic investigation of the effect of the ligand modification on the hydrogen evolution reaction. The results indicated that the position, rather than the type of substituent, was the dominating factor in promoting catalysis. The best performances were observed upon introduction of substituents on the pyridine moiety of the hexadentate ligand, which promoted the formation of the Co(II)H intermediate via intramolecular proton transfer reactions with low activation energy. Quantum yields of 11.3 and 10.1 %, maximum turnover frequencies of 86.1 and 76.6 min-1 , and maximum turnover numbers of 5520 and 4043 were obtained, respectively, with a -OCH3 and a -CF3 substituent.

π-Bridge Substitution in DASAs: The Subtle Equilibrium between Photochemical Improvements and Thermal Control*.

Donor-acceptor Stenhouse adducts (DASAs) are playing an outstanding role as innovative and versatile photoswitches. Until now, all the efforts have been spent on modifying the donor and acceptor moieties to modulate the absorption energy and improve the cyclization and reversion kinetics. However, there is a strong dependence on specific structural modifications and a lack of predictive behavior, mostly owing to the complex photoswitching mechanism. Here, by means of a combined experimental and theoretical study, the effect of chemical modification of the π-bridge linking the donor and acceptor moieties is systematically explored, revealing the significant impact on the absorption, photocyclization, and relative stability of the open form. In particular, a position along the π-bridge is found to be the most suited to redshift the absorption while preserving the cyclization. However, thermal back-reaction to the initial isomer is blocked. These effects are explained in terms of an increased acceptor capability offered by the π-bridge substituent that can be modulated. This strategy opens the path toward derivatives with infra-red absorption and a potential anchoring point for further functionalization.

The role of CO2 detachment in fungal bioluminescence: thermally vs. excited state induced pathways.

Different fungi lineages are known to emit light on Earth, mainly in tropical climates. Although the preparation of bioluminescent cell-free extracts allowed one to characterize the enzymatic requirements, the molecular mechanism underlying luminescence is still largely unknown and is based on the experimental putative assumption that a high-energy intermediate should be formed by reaction with O2 and formation of an endoperoxide. Here, we aim at determining, through state-of-the-art multiconfigurational quantum chemistry, the full mechanistic landscape leading from the endoperoxide to the emitting species, envisaging different possible pathways and proposing their viability. Especially, thermal CO2 detachment followed by excited-state peroxide opening (thermal-chemiluminescence) can compete with a parallel pathway, i.e., first excited-state endoperoxide opening, followed by CO2 detachment on the same excited-state (excited state-chemiluminescence). Clear differences in the energy supplies, as well as the possibility to directly populate the emitting species from the intersection seam between ground and excited states, land credence to a kinetically efficient thermal-chemiluminescent pathway, establishing for the first time a detailed description of fungal bioluminescence.

Molecular Basis of SARS-CoV-2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches.

The emergence in late 2019 of the coronavirus SARS-CoV-2 has resulted in the breakthrough of the COVID-19 pandemic that is presently affecting a growing number of countries. The development of the pandemic has also prompted an unprecedented effort of the scientific community to understand the molecular bases of the virus infection and to propose rational drug design strategies able to alleviate the serious COVID-19 morbidity. In this context, a strong synergy between the structural biophysics and molecular modeling and simulation communities has emerged, resolving at the atomistic level the crucial protein apparatus of the virus and revealing the dynamic aspects of key viral processes. In this Review, we focus on how in silico studies have contributed to the understanding of the SARS-CoV-2 infection mechanism and the proposal of novel and original agents to inhibit the viral key functioning. This Review deals with the SARS-CoV-2 spike protein, including the mode of action that this structural protein uses to entry human cells, as well as with nonstructural viral proteins, focusing the attention on the most studied proteases and also proposing alternative mechanisms involving some of its domains, such as the SARS unique domain. We demonstrate that molecular modeling and simulation represent an effective approach to gather information on key biological processes and thus guide rational molecular design strategies.