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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 β-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.

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 3CL^pro and PL^pro 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.

Thermodynamics of the Interaction between the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus-2 and the Receptor of Human Angiotensin-Converting Enzyme 2. Effects of Possible Ligands

Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 1000000 deaths all over the world and still lacks a medical treatment despite the attention of the whole scientific community. Human angiotensin-converting enzyme 2 (ACE2) was recently recognized as the transmembrane protein that serves as the point of entry of SARS-CoV-2 into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the protein complex. Moreover, the free energy of binding between ACE2 and the active receptor binding domain of the SARS-CoV-2 spike protein is evaluated quantitatively, providing for the first time the thermodynamics of virus-receptor recognition. Furthermore, the action of different ACE2 ligands is also examined in particular in their capacity to disrupt SARS-CoV-2 recognition, also providing via a free energy profile the quantification of the ligand-induced decreased affinity. These results improve our knowledge on molecular grounds of the SARS-CoV-2 infection and allow us to suggest rationales that could be useful for the subsequent wise molecular design for the treatment of COVID-19 cases.

Fat Injection for Cases of Severe Burn Outcomes: A New Perspective of Scar Remodeling and Reduction

BACKGROUND

Despite civilization and progress, burns occur frequently in the world. Remarkable discoveries of wound healing mechanisms have been reported. On the other hand, long-term outcomes from burn injuries represent a barrier to improvement of patients' social, functional, and psychological condition. Lipofilling, described since the 1980s, currently is used for several clinical applications. This study aimed to verify whether lipofilling could ameliorate scar remodeling in three clinical cases.

METHODS

Three adult patients with hemifacial hypertrophic scars and keloids resulting from severe burns 2 to 13 years previously were selected. The patients were treated by injection of adipose tissue harvested from abdominal subcutaneous fat and processed according to Coleman's technique. Two injections (with a 13-month interval between) were administered at the dermohypodermal junction. Histologic examination of scar tissue punch biopsies (hematoxylin-eosin staining) before and after the treatment was performed as well as magnetic resonance scan with contrast.

RESULTS

The clinical appearance and subjective patient feelings after a 6-month follow-up period suggest considerable improvement in the mimic features, skin texture, and thickness. Histologic examination shows patterns of new collagen deposition, local hypervascularity, and dermal hyperplasia in the context of new tissue, with high correspondence to the original.

CONCLUSIONS

The preliminary results show that lipofilling improves scar quality and suggest a tissue regeneration enhancing process.

Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses

Coronaviruses may produce severe acute respiratory syndrome (SARS). As a matter of fact, a new SARS-type virus, SARS-CoV-2, is responsible for the global pandemic in 2020 with unprecedented sanitary and economic consequences for most countries. In the present contribution we study, by all-atom equilibrium and enhanced sampling molecular dynamics simulations, the interaction between the SARS Unique Domain and RNA guanine quadruplexes, a process involved in eluding the defensive response of the host thus favoring viral infection of human cells. Our results evidence two stable binding modes involving an interaction site spanning either the protein dimer interface or only one monomer. The free energy profile unequivocally points to the dimer mode as the thermodynamically favored one. The effect of these binding modes in stabilizing the protein dimer was also assessed, being related to its biological role in assisting the SARS viruses to bypass the host protective response. This work also constitutes a first step in the possible rational design of efficient therapeutic agents aiming at perturbing the interaction between SARS Unique Domain and guanine quadruplexes, hence enhancing the host defenses against the virus.

Competing ultrafast photoinduced electron transfer and intersystem crossing of [Re(CO) 3 (Dmp)(His124)(Trp122)] + in Pseudomonas aeruginosa azurin: a nonadiabatic dynamics study

We present a computational study of sub-picosecond nonadiabatic dynamics in a rhenium complex coupled electronically to a tryptophan (Trp) side chain of Pseudomonas aeruginosa azurin, a prototypical protein used in the study of electron transfer in proteins. To gain a comprehensive understanding of the photoinduced processes in this system, we have carried out vertical excitation calculations at the TDDFT level of theory as well as nonadiabatic dynamics simulations using the surface hopping including arbitrary couplings (SHARC) method coupled to potential energy surfaces represented with a linear vibronic coupling model. The results show that the initial photoexcitation populates both singlet metal-to-ligand charge transfer (MLCT) and singlet charge-separated (CS) states, where in the latter an electron was transferred from the Trp amino acid to the complex. Subsequently, a complex mechanism of simultaneous intersystem crossing and electron transfer leads to the sub-picosecond population of triplet MLCT and triplet CS states. These results confirm the assignment of the sub-ps time constants of previous experimental studies and constitute the first computational evidence for the ultrafast formation of the charge-separated states in Re-sensitized azurin.

Trans-to-cis photoisomerization of cyclocurcumin in different environments rationalized by computational photochemistry

Cyclocurcumin is a turmeric component that has attracted much less attention compared to the well-known curcumin. In spite of the less deep characterization of its properties, cyclocurcumin has shown promising anticancer effects when used in combination with curcumin. Especially, due to its peculiar molecular structure, cyclocurcumin can be regarded as an almost ideal photoswitch, whose capabilities can also be exploited for relevant biological applications. Here, by means of state-of-the-art computational methods for electronic excited-state calculations (TD-DFT, MS-CASPT2, and XMS-CASPT2), we analyze in detail the absorption and photoisomerization pathways leading from the more stable trans isomer to the cis one. The different molecular surroundings, taken into account by means of the electrostatic solvent effect and compared with available experimental data, have been found to be critical in describing the fate of irradiated cyclocurcumin: when in non-polar environments, an excited state barrier prevents photoisomerization and favours fluorescence, whereas in polar solvents, an almost barrierless path results in a striking decrease of fluorescence, opening the way toward a crossing region with the ground state and thus funneling the photoproduction of the cis isomer.

First-principles characterization of the singlet excited state manifold in DNA/RNA nucleobases

TD-DFT characterization of the high-energy singlet excited state manifold of the canonical DNA/RNA nucleobasesin vacuumis assessed against RASPT2 reference computations for reliable simulations of linear and non-linear electronic spectra.

Allyl amino-thioxanthone derivatives as highly efficient visible light H-donors and co-polymerizable photoinitiators

Allyl-amino thioxanthone derivatives as new visible-light photoinitiators for efficient free-radical, cationic and thiol–ene polymerizations.

Induced Night Vision by Singlet-Oxygen-Mediated Activation of Rhodopsin

In humans, vision is limited to a small fraction of the whole electromagnetic spectrum. One possible strategy for enhancing vision in deep-red or poor-light conditions consists of recruiting chlorophyll derivatives in the rod photoreceptor cells of the eye, as suggested in the case of some deep-sea fish. Here, we employ all-atom molecular simulations and high-level quantum chemistry calculations to rationalize how chlorin e6 (Ce6), widely used in photodynamic therapy although accompanied by enhanced visual sensitivity, mediates vision in the dark, shining light on a fascinating but largely unknown molecular mechanism. First, we identify persistent interaction sites between Ce6 and the extracellular loops of rhodopsin, the transmembrane photoreceptor protein responsible for the first steps in vision. Triggered by Ce6 deep-red light absorption, the retinal within rhodopsin can be isomerized thus starting the visual phototransduction cascade. Our data largely exclude previously hypothesized energy-transfer mechanisms while clearly lending credence to a retinal isomerization indirectly triggered by singlet oxygen, proposing an alternative mechanism to rationalize photosensitizer-mediated night vision.

Far Red Fluorescent Proteins: Where Is the Limit of the Acylimine Chromophore?

The search for new near-infrared probes for fluorescence imaging applications is a rapidly growing field of research. Monomeric fluorescent proteins that autocatalyze their chromophore are the most versatile markers for in vivo applications, but the development of bright far-red fluorescent proteins (RFPs) has proven difficult. In this contribution, we search for the theoretical limit of the red shift and how it can be reached without sacrificing the fluorescence quantum yield. Through extensive excited-state pathway calculations, molecular dynamics sampling, and statistical modeling using QM/MM schemes, we provide a new understanding of the chromophore's photophysics including the role of its acylimine extension, which is the main difference from other families of fluorescent proteins. The excited-state dynamics of the mPlum RFP and its mutants provide an ideal basis due to mPlum's flexible binding pocket and extended dynamic Stokes shift. We found a large number of structural species with red-shifted emission that differ in rotamer states and H-bonds between key amino acid residues in the binding pocket. By analyzing their spectral and structural features, we derive guidelines for future rational genetic design strategies.

Correction: Different hydrogen bonding environments of the retinal protonated Schiff base control the photoisomerization in channelrhodopsin-2

Correction for 'Different hydrogen bonding environments of the retinal protonated Schiff base control the photoisomerization in channelrhodopsin-2' by Yanan Guo et al., Phys. Chem. Chem. Phys., 2018, 20, 27501-27509.

Charge-Transfer versus Charge-Separated Triplet Excited States of [ReI (dmp)(CO)3 (His124)(Trp122)]+ in Water and in Modified Pseudomonas aeruginosa Azurin Protein

A computational investigation of the triplet excited states of a rhenium complex electronically coupled with a tryptophan side chain and bound to an azurin protein is presented. In particular, by using high-level molecular modeling, evidence is provided for how the electronic properties of the excited-state manifolds strongly depend on coupling with the environment. Indeed, only upon explicitly taking into account the protein environment can two stable triplet states of metal-to-ligand charge transfer or charge-separated nature be recovered. In addition, it is also demonstrated how the rhenium complex plus tryptophan system in an aqueous environment experiences too much flexibility, which prevents the two chromophores from being electronically coupled. This occurrence disables the formation of a charge-separated state. The successful strategy requires a multiscale approach of combining molecular dynamics and quantum chemistry. In this context, the strategy used to parameterize the force fields for the electronic triplet states of the metal complex is also presented.

Ultrafast dynamics in polycyclic aromatic hydrocarbons: the key case of conical intersections at higher excited states and their role in the photophysics of phenanthrene monomer

Proper interpretation of phenanthrene's and similar PAHs’ photocycle relies on two higher excited state relaxations due to the simultaneous presence of non-adiabatic and adiabatic transitions.

Dynamics of the excited-state hydrogen transfer in a (dG)·(dC) homopolymer: intrinsic photostability of DNA

The intrinsic photostability of nucleic acids is intimately related to evolution of life, while its understanding at the molecular and electronic levels remains a challenge for modern science. Among the different decay pathways proposed in the last two decades, the excited-state hydrogen transfer between guanine-cytosine base pairs has been identified as an efficient non-reactive channel to dissipate the excess of energy provided by light absorption. The present work studies the dynamics of such phenomena taking place in a (dG)·(dC) B-DNA homopolymer in water solution using state-of-the-art molecular modelling and simulation methods. A dynamic effect that boosts the photostability of the inter-strand hydrogen atom transfers, inherent to the Watson-Crick base pairing, is unveiled and ascribed to the energy released during the proton transfer step. Our results also reveal a novel mechanism of DNA decay named four proton transfer (FPT), in which two protons of two adjacent G-C base pairs are transferred to form a biradical zwitterionic intermediate. Decay of the latter intermediate to the ground state triggers the transfer of the protons back to the guanine molecules recovering the Watson-Crick structure of the tetramer. This FPT process is activated by the close interaction of a nearby Na+ counterion with the oxygen atoms of the guanine nucleobases and hence represents a photostable channel operative in natural nucleic acids.

Steady-State Linear and Non-linear Optical Spectroscopy of Organic Chromophores and Bio-macromolecules

Bio-macromolecules as DNA, lipid membranes and (poly)peptides are essential compounds at the core of biological systems. The development of techniques and methodologies for their characterization is therefore necessary and of utmost interest, even though difficulties can be experienced due to their intrinsic complex nature. Among these methods, spectroscopies, relying on optical properties are especially important to determine their macromolecular structures and behaviors, as well as the possible interactions and reactivity with external dyes—often drugs or pollutants—that can (photo)sensitize the bio-macromolecule leading to eventual chemical modifications, thus damages. In this review, we will focus on the theoretical simulation of electronic spectroscopies of bio-macromolecules, considering their secondary structure and including their interaction with different kind of (photo)sensitizers. Namely, absorption, emission and electronic circular dichroism (CD) spectra are calculated and compared with the available experimental data. Non-linear properties will be also taken into account by two-photon absorption, a highly promising technique (i) to enhance absorption in the red and infra-red windows and (ii) to enhance spatial resolution. Methodologically, the implications of using implicit and explicit solvent, coupled to quantum and thermal samplings of the phase space, will be addressed. Especially, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are explored for a comparison with solely QM methods, in order to address the necessity to consider an accurate description of environmental effects on spectroscopic properties of biological systems.

The effect of solvent relaxation in the ultrafast time-resolved spectroscopy of solvated benzophenone

Modeling time-resolved spectra to unravel ultra fast solvent reorganization.

Different hydrogen bonding environments of the retinal protonated Schiff base control the photoisomerization in channelrhodopsin-2

The first event of the channelrhodopsin-2 (ChR2) photocycle, i.e. trans-to-cis photoisomerization, is studied by means of quantum mechanics/molecular mechanics, taking into account the flexible retinal environment in the ground state.

Level of Theory and Solvent Effects on DASA Absorption Properties Prediction: Comparing TD-DFT, CASPT2 and NEVPT2

Donor-acceptor Stenhouse adducts (DASAs) are a very recent class of organic photoswitches that combine excellent properties, such as color and polarity change, a large structural modification, and excellent fatigue resistance. Despite their potential applications in different fields, very few studies have focused on rationalizing their electronic structure properties. Here, by means of different state-of-the-art theoretical methods, including solvent and vibrational effects, we show that while time dependent-density functional theory (TD-DFT) can qualitatively describe DASAs' excited states, multiconfigurational quantum chemistry methods along with dynamic electron correlation (CASPT2, NEVPT2) are required for a quantitative agreement with the experiment. This finding is reasoned based on the different charge transfer characteristics observed. Moreover, the TD-DFT computed two-photon absorption properties are reported and suggested to red-shift the absorption band, as required for biological applications.

Ibuprofen and ketoprofen potentiate UVA-induced cell death by a photosensitization process

Nonsteroidal 2-arylproprionic acids are widely used, over-the-counter, anti-inflammatory drugs. Photosensitivity is a commonly overlooked adverse effect of these drugs. Based on the combined use of cell viability assays and molecular modeling, we prove and rationalize the photochemical pathways triggering photosensitization for two drugs, ibuprofen and ketoprofen. As its parent compound benzophenone, ketoprofen produces singlet oxygen, upon triplet manifold population. However, ibuprofen and ketoprofen photodissociate and hence may generate two highly reactive radicals. The formation of metastable aggregates between the two drugs and B-DNA is also directly probed by molecular dynamics. Our approach characterizes the coupled influence of the drug's intrinsic photochemistry and the interaction pattern with DNA. The photosensitization activity of nonsteroidal 2-arylproprionic acids, being added to gels and creams for topical use, should be crucially analyzed and rationalized to enact the proper preventive measures.

When combined X-ray and polarized neutron diffraction data challenge high-level calculations: spin-resolved electron density of an organic radical

Joint refinement of X-ray and polarized neutron diffraction data has been carried out in order to determine charge and spin density distributions simultaneously in the nitronyl nitroxide (NN) free radical Nit(SMe)Ph. For comparison purposes, density functional theory (DFT) and complete active-space self-consistent field (CASSCF) theoretical calculations were also performed. Experimentally derived charge and spin densities show significant differences between the two NO groups of the NN function that are not observed from DFT theoretical calculations. On the contrary, CASSCF calculations exhibit the same fine details as observed in spin-resolved joint refinement and a clear asymmetry between the two NO groups.