Exploring electron donor and acceptor effects: DFT analysis of ESIPT/GSIPT in 2-(oxazolinyl)-phenols for photophysical and luminophore enhancement.

Understanding excited-state intramolecular proton transfer (ESIPT) is essential for designing organic molecules to enhance photophysical and luminophore properties in the development of optoelectronic devices. In this context, an attempt has been made to understand the impact of substituents on the ESIPT process of 2-(oxazolinyl)-phenol. Electron donating (EDG: -NH2, -OCH3, and -CH3) and electron withdrawing (EWG: -Cl, -Br, -COOH, -CF3, -CN, and -NO2) substitutions have been computationally designed and screened through density functional theory (DFT) and time-dependent density-functional theory (TDDFT) calculations. Furthermore, the ground state intramolecular proton transfer and ESIPT mechanisms of these designed luminophores are explored using the transition state theory. The results reveal that molecules with EDG show higher absorption and emission peaks than molecules with EWG and also indicate that the mobility of charge carriers in 2-(oxazolinyl)-phenol derivatives is significantly influenced by substituents. We found that the EWGs decrease the reorganization energy and increase the vertical ionization potential and electron affinity values, as well as the highest occupied molecular orbital-lowest unoccupied molecular orbital gap, compared to the EDG substituted molecules. Significantly, the excited state (S1) of the keto emission (K) form shows notably larger values for the EDG substitutions. The intersystem crossing pathway efficiency weakens with reduced spin-orbit coupling matrix element in the enol form with electron-donating substituents and vice versa in the keto form during S1-T3 transitions. Our research links intramolecular proton transfers and triplet generation, making these substituted molecules appealing for optoelectronic devices. Introducing EDGs, such as -NH2, boosts the ESIPT reaction in 2-(oxazolinyl)-phenol. This study guides designing ESIPT emitters with unique photophysical properties.

A theoretical study on radical scavenging activity of phenolic derivatives naturally found within Alternaria alternata extract.

The increasing oxidative stress demands potential chemical compounds derived from natural resources with good antioxidant activity to overcome adverse health issues. In this context, we investigated the antioxidant properties of four dibenzopyrone phenolic compounds obtained from the endophytic fungus Alternaria alternata: altenusin, altenusin B, alterlactone, and dehydroaltenusin using DFT calculations. Our investigation focused on understanding the structure-antioxidant property relationship. It delved into probing the activity by modelling the antioxidant mechanisms. The computed transition states and thermochemical parameters, along with the structural attributes, indicate that altenusin B has good antioxidant efficacy among the four compounds, and it follows the HAT mechanism in an aqueous phase. Remarkably, our findings indicate that altenusin B exhibits potent HOO˙ radical scavenging properties, characterized by the computed high rate constant. The molecular docking studies of these compounds with the pro-oxidant enzyme xanthine oxidase (XO) gave insights into the binding modes of the compounds in the protein environment. Furthermore, molecular dynamics (MD) simulations were employed to study the interaction and stability of the compounds inside the XO enzyme. Our exploration sheds light on the radical scavenging potential of the -OH sites and the underlying antioxidant mechanisms that underpin the compounds' effective antioxidant potential.

The Surface of Ionic Liquids in Water: From an Ionic Tug of War to a Quasi-Ordered Two-Dimensional Layer.

The sustainable development encompasses the search for new materials for energy storage, gas capture, separation, and solvents in industrial processes that can substitute conventional ones in an efficient and clean manner. Ionic liquids (ILs) emerged and have been advanced as alternative materials for such applications, but an obstacle is their hygroscopicity and the effects on their physical properties in the presence of humidity. Several industrial processes depend on the aqueous interfacial properties, and the main focus of this work is the water/IL interface. The behavior of the aqueous ionic liquids at the water-vacuum interface is representative for their water interfacial properties. Using X-ray photoelectron spectroscopy in combination with molecular dynamics simulations we investigate four aqueous IL systems, and provide molecular level insight on the interfacial behaviour of the ionic liquids, such as ion-pair formation, orientation and surface concentration. We find that ionic liquids containing a chloride anion have a lowered surface enrichment due to the low surface propensity of chloride. In contrast, the ionic liquids containing a bistriflimide anion are extremely surface-enriched due to cooperative surface propensity between the cations and anions, forming a two-dimensional ionic liquid on the water surface at low concentrations.

Strain induced electrochemical behaviors of ionic liquid electrolytes in an electrochemical double layer capacitor: Insights from molecular dynamics simulations.

Electrochemical Double Layer Capacitors (EDLCs) with ionic liquid electrolytes outperform conventional ones using aqueous and organic electrolytes in energy density and safety. However, understanding the electrochemical behaviors of ionic liquid electrolytes under compressive/tensile strain is essential for the design of flexible EDLCs as well as normal EDLCs, which are subject to external forces during assembly. Despite many experimental studies, the compression/stretching effects on the performance of ionic liquid EDLCs remain inconclusive and controversial. In addition, there is hardly any evidence of prior theoretical work done in this area, which makes the literature on this topic scarce. Herein, for the first time, we developed an atomistic model to study the processes underlying the electrochemical behaviors of ionic liquids in an EDLC under strain. Constant potential non-equilibrium molecular dynamics simulations are conducted for EMIM BF4 placed between two graphene walls as electrodes. Compared to zero strain, low compression of the EDLC resulted in compromised performance as the electrode charge density dropped by 29%, and the performance reduction deteriorated significantly with a further increase in compression. In contrast, stretching is found to enhance the performance by increasing the charge storage in the electrodes by 7%. The performance changes with compression and stretching are due to changes in the double-layer structure. In addition, an increase in the value of the applied potential during the application of strain leads to capacity retention with compression revealed by the newly performed simulations.

Zn-doping and oxygen vacancy effects on the reactivity and properties of monoclinic and tetragonal ZrO2: a DFT study.

Zirconia oxide (ZrO2) is a material that has aroused great interest in the scientific community for its general use in various technological applications, such as fuel cells, solar cells, electronic devices, catalysis, dental biomaterial and ceramics. When it is applied as a catalyst, the doping and vacancy effects of their crystalline phases are important properties to guide new developments. This work investigates tetragonal and monoclinic crystalline phases of the Zn-doped ZrO2 by periodic density functional calculations. Changes in the electronic and acid-basic properties were performed by Bader charge analysis, the density of states calculations (DOS) and the projected density of states (PDOS). The formation of oxygen vacancies was also evaluated. The calculated oxygen vacancy formation energies indicate that it is much easier to generate oxygen vacancy in the Zn-doped ZrO2 than in the pure material; in addition, oxygen vacancy formation is favored in the monoclinic phase. Bader charge analyses and projected density of states indicated that the doping of ZrO2 with Zn creates more basic and acid sites. The most stable material is the Zn-doped 3-fold coordinated Zr atom of the m-ZrO2, which can be used for future developments and applications.

Theoretical study of keto-enol tautomerism in 7-epi-clusianone by quantum chemical calculations of NMR chemical shifts.

Plants from the Garcinia genus have been used worldwide due to their therapeutic properties. Among the various metabolites isolated from this genus, 7-epi-clusianone, a tetraprenylated benzophenone, stands out for its wide range of identified biological activities. This benzophenone can exist in five tautomeric forms, although the benzene-d6 and chloroform-d3 solution nuclear magnetic resonance (NMR) spectra revealed only two tautomeric forms (B and C) in equilibrium, with concentration ratio depending on the solvent in which the spectrum was obtained. Calculated energy values suggested that tautomeric forms B and E would be prevalent in benzene-d6 solution, in contrast to the experimental data. Considering this conflicting result, we employed the statistical DP4 + method based on 13C and 1H NMR chemical shift calculations, in the gas phase and in benzene-d6 solution, to confirm that the B and C tautomeric forms of 7-epi-clusianone are the most prevalent in the experimental conditions.

Potential colchicine binding site inhibitors unraveled by virtual screening, molecular dynamics and MM/PBSA.

Microtubules have been widely studied in recent decades as an important pharmacological target for the treatment of cancer especially due to its key role in the mitosis process. Among the constituents of the microtubules, αß-tubulin dimers stand out in view of their four distinct interaction sites, including the so-called colchicine binding site (CBS) - a promising target for the development of new tubulin modulators. When compared to other tubulin sites, targeting the CBS is advantageous because this site is able to host ligands with lower molecular volume and lipophilicity, thus reducing the chances of entailing the phenomenon of multiple drug resistance (MDR) - one of the main reasons of failure in chemotherapy. However, colchicine, the first ligand ever discovered with affinity towards the CBS, despite modulating the action of microtubules, has shown toxicity in clinical studies. Therefore, in order to expand the known chemical space of scaffolds capable of interacting with CBS and to design non-toxic colchicine binding site inhibitors, we conducted a robust virtual screening pipeline. This has been rigorously validated and consisted of ligand- and structure-based methodologies, which allowed us to select four promising CBS inhibitors called tubLCQF1-4. These four compounds were also evaluated with long trajectories molecular dynamics simulations and respective results were used for the theoretical determination of the free energy released in the formation of the complexes, using the Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) methodology.

The structure of CO2 and CH4 at the interface of a poly(urethane urea) oligomer model from the microscopic point of view.

The world desperately needs new technologies and solutions for gas capture and separation. To make this possible, molecular modeling is applied here to investigate the structural, thermodynamic, and dynamical properties of a model for the poly(urethane urea) (PUU) oligomer model to selectively capture CO2 in the presence of CH4. In this work, we applied a well-known approach to derive atomic partial charges for atoms in a polymer chain based on self-consistent sampling using quantum chemistry and stochastic dynamics. The interactions of the gases with the PUU model were studied in a pure gas based system as well as in a gas mixture. A detailed structure characterization revealed high interaction of CO2 molecules with the hard segments of the PUU. Therefore, the structural and energy properties explain the reasons for the greater CO2 sorption than CH4. We find that the CO2 sorption is higher than the CH4 with a selectivity of 7.5 at 298 K for the gas mixture. We characterized the Gibbs dividing surface for each system, and the CO2 is confined for a long time at the gas-oligomer model interface. The simulated oligomer model showed performance above the 2008 Robeson's upper bound and may be a potential material for CO2/CH4 separation. Further computational and experimental studies are needed to evaluate the material.

Understanding carbon dioxide capture on metal-organic frameworks from first-principles theory: The case of MIL-53(X), with X = Fe3+, Al3+, and Cu2.

Metal-organic frameworks (MOFs) constitute a class of three-dimensional porous materials that have shown applicability for carbon dioxide capture at low pressures, which is particularly advantageous in dealing with the well-known environmental problem related to the carbon dioxide emissions into the atmosphere. In this work, the effect of changing the metallic center in the inorganic counterpart of MIL-53 (X), where X = Fe3+, Al3+, and Cu2+, has been assessed over the ability of the porous material to adsorb carbon dioxide by means of first-principles theory. In general, the non-spin polarized computational method has led to adsorption energies in fair agreement with the experimental outcomes, where the carbon dioxide stabilizes at the pore center through long-range interactions via oxygen atoms with the axial hydroxyl groups in the inorganic counterpart. However, spin-polarization effects in connection with the Hubbard corrections, on Fe 3d and Cu 3d states, were needed to properly describe the metal orbital occupancy in the open-shell systems (Fe- and Cu-based MOFs). This methodology gave rise to a coherent high-spin configuration, with five unpaired electrons, for Fe atoms leading to a better agreement with the experimental results. Within the GGA+U level of theory, the binding energy for the Cu-based MOF is found to be Eb = -35.85 kJ/mol, which is within the desirable values for gas capture applications. Moreover, it has been verified that the adsorption energetics is dominated by the gas-framework and internal weak interactions.

Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening.

Herein, molecular modeling techniques were used with the main goal to obtain candidates from a drug database as potential targets to be used against SARS-CoV-2. This novel coronavirus, responsible by the COVID-19 outbreak since the end of 2019, became a challenge since there is not vaccine for this disease. The first step in this investigation was to solvate the isolated S-protein in water for molecular dynamics (MD) simulation, being observed a transition from "up" to "down" conformation of receptor-binding domain (RBD) of the S-protein with angle of 54.3 and 43.0 degrees, respectively. The RBD region was more exposed to the solvent and to the possible drugs due to its enhanced surface area. From the equilibrated MD structure, virtual screening by docking calculations were performed using a library contained 9091 FDA approved drugs. Among them, 24 best-scored ligands (14 traditional herbal isolate and 10 approved drugs) with the binding energy below -8.1 kcal/mol were selected as potential candidates to inhibit the SARS-CoV-2 S-protein, preventing the human cell infection and their replication. For instance, the ivermectin drug (present in our list of promise candidates) was recently used successful to control viral replication in vitro. MD simulations were performed for the three best ligands@S-protein complexes and the binding energies were calculated using the MM/PBSA approach. Overall, it is highlighted an important strategy, some key residues, and chemical groups which may be considered on clinical trials for COVID-19 outbreak. [Formula: see text]Communicated by Ramaswamy H. Sarma.

A potential for molecular simulation of compounds with linear moieties.

The harmonic angle bending potential is used in many force fields for (bio)molecular simulation. The force associated with this potential is discontinuous at angles close to 180°, which can lead to numeric instabilities. Angle bending of linear groups, such as alkynes or nitriles, or linear molecules, such as carbon dioxide, can be treated by a simple harmonic potential if we describe the fluctuations as a deviation from a reference position of the central atom, the position of which is determined by the flanking atoms. The force constant for the linear angle potential can be derived analytically from the corresponding force constant in the traditional potential. The new potential is tested on the properties of alkynes, nitriles, and carbon dioxide. We find that the angles of the linear groups remain about 2° closer to 180° using the new potential. The bond and angle force constants for carbon dioxide were tuned to reproduce the experimentally determined frequencies. An interesting finding was that simulations of liquid carbon dioxide under pressure with the new flexible model were stable only when explicitly modeling the long-range Lennard-Jones (LJ) interactions due to the very long-range nature of the LJ interactions (>1.7 nm). In the other tested liquids, we find that a Lennard-Jones cutoff of 1.1 nm yields similar results as the particle mesh Ewald algorithm for LJ interactions. Algorithmic factors influencing the stability of liquid simulations are discussed as well. Finally, we demonstrate that the linear angle potential can be used in free energy perturbation calculations.

Interfacial Structures in Ionic Liquid-Based Ternary Electrolytes for Lithium-Metal Batteries: A Molecular Dynamics Study.

Lithium-metal batteries are promising candidates to fulfill the future performance requirements for energy storage applications. However, the tendency to form metallic dendrites and the undesirable side reactions between the electrolyte and the Li electrode lead to poor performance and safety issues in these batteries. Therefore, understanding the interfacial properties and the Li-metal surface/electrolyte interactions is crucial to resolve the remaining obstacles and make these devices feasible. Here, we report a computational study on the interface effects in ternary polymer electrolytes composed by poly(ethylene oxide) (PEO), lithium salts, and different ionic liquids (ILs) confined between two Li-metal slabs. Atomistic simulations are used to characterize the local environment of the Li+ ions and the transport properties in the bulk and at the interface regions. Aggregation of ions at the metal surface is seen in all investigated systems; the structure and composition are directly correlated to the IL components. The strong interactions between the electrolyte species and the Li-metal atoms result in the structuring of the electrolyte at the interface region, in which comparatively small and flat ions result in a well-defined region with extensive Li+ populations and high self-diffusion coefficients. In contrast, large ions such as [P222mom]+ increase the PEO density in the bulk due to large steric effects at the interface. Therefore, the choice of specific ILs in ternary polymer electrolytes can tune the structure-dynamic properties at the Li-metal surface/electrolyte interface, controlling the SEI formation at the electrode surface, and thereby improve battery performance.

Restricted Ion Transport by Plasticizing Side Chains in Polycarbonate-Based Solid Electrolytes.

Increasing the ionic conductivity has for decades been an overriding goal in the development of solid polymer electrolytes. According to fundamental theories on ion transport mechanisms in polymers, the ionic conductivity is strongly correlated to free volume and segmental mobility of the polymer for the conventional transport processes. Therefore, incorporating plasticizing side chains onto the main chain of the polymer host often appears as a clear-cut strategy to improve the ionic conductivity of the system through lowering of the glass transition temperature (T g). This intended correlation between T g and ionic conductivity is, however, not consistently observed in practice. The aim of this study is therefore to elucidate this interplay between segmental mobility and polymer structure in polymer electrolyte systems comprising plasticizing side chains. To this end, we utilize the synthetic versatility of the ion-conductive poly(trimethylene carbonate) (PTMC) platform. Two types of host polymers with side chains added to a PTMC backbone are employed, and the resulting electrolytes are investigated together with the side chain-free analogue both by experiment and with molecular dynamics (MD) simulations. The results show that while added side chains do indeed lead to a lower T g, the total ionic conductivity is highest in the host matrix without side chains. It was seen in the MD simulations that while side chains promote ionic mobility associated with the polymer chain, the more efficient interchain hopping transport mechanism occurs with a higher probability in the system without side chains. This is connected to a significantly higher solvation site diversity for the Li+ ions in the side-chain-free system, providing better conduction paths. These results strongly indicate that the side chains in fact restrict the mobility of the Li+ ions in the polymer hosts.

Identification of novel αß-tubulin modulators with antiproliferative activity directed to cancer therapy using ligand and structure-based virtual screening.

Among several strategies related to cancer therapy targeting the modulation of αß-tubulin has shown encouraging findings, more specifically when this is achieved by inhibitors located at the colchicine binding site. In this work, we aim to fish new αß-tubulin modulators through a diverse and rational VS study, and thus, exhibiting the development of two VS pipelines. This allowed us to identify two compounds 5 and 9 that showed IC50 values of 19.69 and 21.97 µM, respectively, towards possible modulation of αß-tubulin, such as assessed by in vitro assays in C6 glioma and HEPG2 cell lines. We also evaluated possible mechanisms of action of obtained hits towards the colchicine binding site of αß-tubulin by using docking approaches. In addition, assessment of the stability of the active (5 and 9) and inactive compounds (3 and 13) within the colchicine binding site was carried out by molecular dynamics (MD) simulations, highlighting the solvent effect and revealing the compound 5 as the most stable in the complex. At last, deep analysis of these results provided some valuable insights on the importance of using mixed ligand- and structure-based strategies in VS campaigns, in order to achieve higher chemical diversity and biological effect as well.

X-ray Photoelectron Fingerprints of High-Valence Ruthenium-Oxo Complexes along the Oxidation Reaction Pathway in an Aqueous Environment.

Recent advances in operando-synchrotron-based X-ray techniques are making it possible to address fundamental questions related to complex proton-coupled electron transfer reactions, for instance, the electrocatalytic water splitting process. However, it is still a grand challenge to assess the ability of the different techniques to characterize the relevant intermediates, with minimal interference on the reaction mechanism. To this end, we have developed a novel methodology employing X-ray photoelectron spectroscopy (XPS) in connection with the liquid-jet approach to probe the electrochemical properties of a model electrocatalyst, [RuII(bpy)2(py)(OH2)]2+, in an aqueous environment. There is a unique fingerprint of the extremely important higher-valence ruthenium-oxo species in the XPS spectra along the oxidation reaction pathway. Furthermore, a sequential method combining quantum mechanics and molecular mechanics is used to illuminate the underlying physical chemistry of such systems. This study provides the basis for the future development of in-operando XPS techniques for water oxidation reactions.

Structure and bonding in triorganotin chlorides: a perspective from energy decomposition analysis.

The Sn-Cl chemical bond of four organotin halides (Me3SnCl, Et3SnCl, Bu3SnCl, and Ph3SnCl) was studied by using relativistic density functional theory in combination with a quantitative energy decomposition analysis to explain the formation of charged species. The σ orbital is the dominant contributor to the stabilization of the Sn-Cl bond, and the π-orbital interactions also have a significant contribution to the stabilization of Ph3Sn+ cation when the aromatic groups are bonded to the tin atom. The aromaticity of the phenyl groups delocalizes the positive charge, donating electrons to tin atom by conjugation. Although Me3SnCl and Ph3SnCl are constituted by groups which the size of the substituents is different, the interaction energies obtained with the energy decomposition analysis present similar values, which also occur with the thermodynamic parameters. Graphical abstract Organotin compounds have widely studied as a potential antitumoral agent. The mechanism in triorganotin compounds includes the formation of cation species, R3Sn+. This article studies the influence of the R groups on the rupture of Sn-Cl bond using the fragment analysis and quantitative energy decomposition analysis.

Solvation Structure and Dynamics of Li+ in Ternary Ionic Liquid-Lithium Salt Electrolytes.

The structural and dynamical changes in the solvation shell surrounding Li+ in a multianion environment are studied by Raman spectroscopy and molecular dynamics (MD) simulations. The ternary electrolyte is composed of a mixture of two ionic liquids (ILs), n-methyl- n-propylpyrrolidinium bis(trifluoromethanesulfonyl)imide ([PYR13][TFSI]) and 1-ethyl-3-methylimidazolium dicyanamide ([EMIM][DCA]), and a lithium bis(trifluoromethanesulfonyl)imide ([Li][TFSI]) salt (0-1 M). A 1:9 volumetric mixture of [PYR13][TFSI]/[EMIM][DCA] formed an eutectic that exhibited a lower melting point than that of either parent IL. The local structure of Li+ in this eutectic is found to be heterogenous and preferentially solvated by [DCA], which is the smaller and more abundant anion. Whereas [TFSI] is able to bridge multiple Li+ at high salt concentrations and form both monodentate and bidentate conformations through its oxygen atoms, [DCA] is capable of forming only monodentate coordination with Li+ through either of its end nitrogen atoms. The Raman and MD analyses suggest a wide distribution of solvation structures in the form of [Li(TFSI) m(DCA) n]( m+ n-1)- where m = 0-1 and n = 3-4. The computations showed increased ion pair lifetime for Li+-[DCA] and decreased lifetimes for Li+-[TFSI] in the ternary mixture with the increase in the [Li][TFSI] concentration. These results show that the solvation and transport properties of charge carriers in ILs can be modified via the presence of multiple ions with varying degree of coordination, which provides an approach to impact the performance in electrochemical processes.

Encapsulation of the Sulfur Compounds by Cucurbit[7]uril: A Quantum Chemistry Study.

Benzothiophene (BT) and dibenzothiophene (DT) are the most important contaminants in the petroleum derivatives responsible for serious environmental and health problems. Therefore, we have investigated the absorption of these compounds for the first time by considering cucurbit[7]uril (CB[7]) as the host molecule and using the theoretical levels of density functional theory//B3LYP-D3/6-31G(d). BT and DT absorbed into CB[7] do not undergo a significant structural change in the CB[7] structure. The energy gap of the S-compounds@CB[7] in water and hexane solvents was approximately 5 eV, and this large value implies that the complexes have high chemical stability. Moreover, the absorption of the BT and DT into CB[7] in the water and hexane solvents is a favorable process, whereas the lowest binding energy was observed between the dibenzothiophene and CB[7] in the DT@CB[7] complex. The solvation enthalpy shows a preferential solvation of the complexes in water than in hexane solvent. This trend is confirmed by the AIM analysis that shows the highest stability for the DT@CB[7] system with the contribution of cooperative hydrogen bonding. The transfer free energy of S-compounds@CB[7] complexes from hexane to water are -66.12 and -59.56 kcal/mol for BT@CB[7] and DT@CB[7], respectively, implying the spontaneous transference of these complexes from hexane to water solvent. Overall, our results show that the cucurbiturils can be a new class of host molecules to be used in the removal of S-compounds from petroleum derivatives. Finally, a schematic flow diagram of the desulfurization process by cucurbiturils was proposed.

A molecular dynamics study of lithium-containing aprotic heterocyclic ionic liquid electrolytes.

Classical molecular dynamics simulations were performed on twelve different ionic liquids containing aprotic heterocyclic anions doped with Li+. These ionic liquids have been shown to be promising electrolytes for lithium ion batteries. Self-diffusivities, lithium transference numbers, densities, and free volumes were computed as a function of lithium concentration. The dynamics and free volume decreased with increasing lithium concentration, and the trends were rationalized by examining the changes to the liquid structure. Of those examined in the present work, it was found that (methyloxymethyl)triethylphosphonium triazolide ionic liquids have the overall best performance.