Molecular Modeling Insights on the Pharmaceuticals and Hypotheses of Alzheimer's Disease.

Alzheimer's disease (AD) stands as the predominant contributor to dementia cases. The ongoing developments in our understanding of its pathogenesis have sparked the interest of researchers, driving them to explore innovative treatment approaches. Existing therapies incorporating cholinesterase inhibitors and/or NMDA antagonists have shown limited improvement in alleviating symptoms. This, in turn, highlights the urgency for the pursuit of more effective therapeutic options. Given the annual rise in the number of individuals affected by dementia, it is imperative to allocate resources and efforts towards the exploration of novel therapeutic options. This review aims to provide a comprehensive overview of the AD-related hypotheses, along with the computational approaches employed in research within each hypothesis. In this comprehensive review, the authors shed light on using various computational tools, including diverse case studies, in the pursuit of finding efficacious treatments for AD. The development of more sophisticated diagnostic techniques is crucial, enabling early detection and intervention in the battle against this challenging condition. The potential treatments investigated in this analysis are poised to assume ever more significant functions in both preventing and treating AD, ultimately enhancing the management of the condition and the overall well-being of individuals affected by AD.

Chemiluminescence of a Firefly Luciferin Analogue Reveals that Formation of the Key Intermediate Responsible for Excited State Generation Occurs on a Fully Concerted Step.

The chemiluminescence (CL) reaction of eight different 2-(4-hydroxyphenyl)-4,5-dihydrothiazole-4-carboxylate esters with an organic superbase and oxygen was investigated through a kinetic and computational study. These esters are all analogues to the luciferin substrate involved in efficient firefly bioluminescence. The kinetic data obtained from CL emission and light absorption assays were used in the context of linear free energy relationships (LFER); we obtained the Hammett reaction constant ρ = +1.62 ± 0.09 and the Brønsted constant ßlg = -0.39 ± 0.04. These observations from LFER, together with activation parameters obtained from Arrhenius plots, suggest that the formation of the high-energy intermediate (HEI) 1,2-dioxetanone occurs via a concerted mechanism during the rate-determining step of the reaction. Calculations performed using density functional theory support a late transition state for HEI formation within the reaction mechanism pathway, which was described considering geometric parameters, Wiberg bond indices from natural bond order analysis, and the atomic charges derived from the electrostatic potential.

Synergistic Interaction of Hyperbranched Polyglycerols and Cetyltrimethylammonium Bromide for Oil/Water Interfacial Tension Reduction: A Molecular Dynamics Study.

Applying surfactants to reduce the interfacial tension (IFT) on water/oil interfaces is a proven technique. The search for new surfactants and delivery strategies is an ongoing research area with applications in many fields such as drug delivery through nanoemulsions and enhanced oil recovery. Experimentally, the combination of hyperbranched polyglycerol (HPG) with cetyltrimethylammonium bromide (CTAB) substantially reduced the observed IFT of oil/water interface, 0.9 mN/m, while HPG alone was 5.80 mN/m and CTAB alone IFT was 8.08 mN/m. Previous simulations in an aqueous solution showed that HPG is a surfactant carrier. Complementarily, in this work, we performed classical molecular dynamics simulations on combinations of CTAB and HPG with one aliphatic chain to investigate further the interaction of this pair in oil interfaces and propose the mechanism of IFT decrease. Basically, from our results, one can observe that the IFT reduction comes from a combination of effects that have not been observed for other dual systems: (i) Due to the CTAB-HPG strong interaction, a weakening of their specific and isolated interactions with the water and oil phases occurs. (ii) Aggregates enlarge the interfacial area, turning it into a less ordered interface. (iii) The spread of individual molecules charge profiles leads to the much lower interfacial tension observed with the CTAB+HPG systems.

Diving into the optoelectronic properties of Cu(II) and Zn(II) curcumin complexes: a DFT and wavefunction benchmark.

CONTEXT: Curcumin is a popular food additive around the world whose medicinal properties have been known since ancient times. The literature has recently highlighted several biological properties, but besides the health-related usages, its natural yellowish color may also be helpful for light-harvesting applications. This research aims to close a knowledge gap regarding the photophysical description of curcumin and its metallic complexes. METHODS: We conducted benchmark experiments comparing NEVPT calculations with several DFT functionals (B3LYP, M06-L, M06-2X, CAM-B3LYP, and ωB97X-D) for describing the UV spectra of curcumin and its metallo-derivative, curcumin-copper(II). Once we determined the most suitable functional, we performed tests with different basis sets and conditions, such as solvation and redox state, to identify their impact on excited state properties. These results are also reported for the curcumin-zinc(II) derivative. We found that the accuracy of DFT functionals depends strongly on the nature of curcumin's excitations. Intra-ligand transitions dominate the absorption spectra of the complexes. Curcumin absorption is marginally affected by solvation and chelation, but when combined with redox processes, they may result in significant modifications. This is because copper cation changes its coordination geometry in response to redox conditions, changing the spectrum. We found that, compared to a NEVPT reference, B3LYP is the best functional for a general description of the compounds, despite not being appropriate for charge transfer transitions. M06-L was the best for LMCT transitions. However, compared with NEVPT2 and PNO-LCCSD(T)-F12 results, no functional achieved acceptable accuracy for MLCT transitions.

Mechanisms for the Deactivation of the Electronic Excited States of α-(2-Hydroxyphenyl)-N-phenylnitrone: From Intramolecular Proton and Charge Transfer to Structure Twisting and Aggregation.

The search for new prominent chemosensors is significantly related to the rationalization of possible multiple pathways of excited-state deactivation. We have prepared and studied compound α-(2-hydroxyphenyl)-N-phenylnitrone (Nit-OH), observing that Nit-OH is stable in acetonitrile solution under UV-vis light. The experimentally observed 540 nm fluorescence for Nit-OH was shown to be related to excitation at 360 nm from the highest occupied molecular orbital to the lowest unoccupied molecular orbital (HOMO-LUMO transition). Potential energy curves (PECs) for the S1 state of Nit-OH did show that there are structures associated with excited-state intramolecular proton transfer (ESIPT), and the existence of an intramolecular H-bonding was confirmed using X-ray powder diffraction (XRD). Twisted intramolecular charge transfer (TICT) took place following ESIPT, and a nonradiative deactivation at the S1/S0 conical intersection occurred; aggregation-induced emission was observed at 540 nm associated with the formation of a stacked dimer. Anti-Kasha emission from the S2 was proposed based on the dependence of the fluorescence excitation wavelength on Nit-OH concentration. From the calculation of the PEC for the S2 state, we obtained radiative transitions at 379 and 432 nm, similar to the obtained experimental values of 383 and 453 nm. We proposed a Jablonski-like diagram that depicts all experimental and theoretical electronic transitions for Nit-OH, summarizing the unique intricate photophysical behavior of this nitrone derivative.

Photochemical and photophysical properties of tetracarboxylic acid phthalocyanines from glycolic and lactic acids in homogeneous and micro heterogeneous media.

Glycolic acid and lactic acid substituted zinc phthalocyanines were studied concerning their photophysical and photochemical properties in eight organic solvents (homogeneous medium) and in aqueous media with the presence of CTAB and PVP 360 surfactants. Solvent effects were investigated according to several physical solvent parameters, including studies that used more than one parameter at a time, such as the ET(30) scale and the Lippet-Mataga equation. Computational studies were realized and was found in good agreement with experimental data indicating J-type dimers' formation through hydrogen bonds, which may not affect the spectroscopic properties. Fluorescence lifetimes were recorded using a time-correlated single-photon counting setup (TCSPC) technique. The direct method (analyzing the phosphorescence decay curves of singlet oxygen at 1270 nm) was employed to study singlet oxygen quantum yields. Phthalocyanine macrocycle with lactic acid substituent showed better solvation arrangement than the glycolic derivative, which can be explained based on the presence of the methyl group bonded to the chain. The water solvation of Pc's in the presence of cationic surfactant (CTAB) and biocompatible polymer PVP 360 increses the importance of this study for appliance in photodynamic therapy (PDT).

Metal-Cocatalyst Interaction Governs the Catalytic Activity of MII-Porphyrazines for Chemical Fixation of CO2.

Chemical fixation of CO2 to produce cyclic carbonates can be a green and atomic efficient process. In this work, a series of porphyrazines (Pzs) containing electron-withdrawing groups and central MII ions (where M = Mg, Zn, Cu, and Co) were synthesized and investigated as catalysts for the cycloaddition of CO2 to epoxides. Then, the efficiency of the Pzs was tested by varying cocatalyst type and concentration, epoxide, temperature, and pressure. MgIIPz bearing trifluoromethyl groups (1) showed the best conversion, producing, selectively, 78% of propylene cyclic carbonate (PCC), indicating that a harder and stronger Lewis acid is more effective for epoxide activation. Moreover, cocatalyst variation showed a notable effect on the reaction yields. Spectrophotometric titrations, MALDI-TOF mass spectra, and theoretical calculations suggest poisoning of the catalyst when tetrabutylammonium chloride (TBAC) and large amounts of tetrabutylammonium bromide (TBAB) were used in the system. The same was not observed for tetrabutylammonium iodide (TBAI), indicating that the metal-cocatalyst interaction may govern the reaction rate. In addition, two rare examples of crystalline structures were obtained, proving the distorted square pyramidal geometry with water molecule as axial ligand. This is one of the first studies reporting Pzs as catalysts for the chemical fixation of CO2, and we believe that the intricate balance between cocatalyst concentration and conversion efficiency shown here may aid future studies in the area.

Can one use the electronic absorption spectra of metalloporphyrins to benchmark electronic structure methods? A case study on the cobalt porphyrin.

In this article, we describe calculations on the absorption spectrum of cobalt(ii) porphyrin, using density functional (DFT) and multireference n-electron valence perturbation (NEVPT) theories. With these calculations, we describe the lowest-energy states of doublet and quartet spin multiplicities, the excited states that originate the Q and B bands of porphyrins, some higher-energy π-π* excitations and charge-transfer states, HOMO-LUMO gaps, and ionisation potentials. Results undoubtedly show that the position of B band is essentially independent on the DFT functional, while the Q band is better described by pure functionals, and these bands do not depend on the initial state of the transition (whether doublet or quartet) as well. However, other excitation energies, orbital energies, and ionisation potentials strongly depend on the functional, in some cases varying more than 2 eV. Based on these results we conclude that one should not use the UV-Vis spectrum of metalloporphyrins to benchmark density functionals, mainly those properties related to coordination with the metallic ion. Furthermore, the results show that functionals that yield correct spectra may be based on an incorrect ground state description. Moreover, we reinforce that one must be skeptical about the reference chosen to benchmark electronic structure calculations, such as DFT functionals and active spaces for multireference calculations.

Competition Between Phenothiazines and BH3 Peptide for the Binding Site of the Antiapoptotic BCL-2 Protein.

The study of proteins and mechanisms involved in the apoptosis and new knowledge about cancer's biology are essential for planning new drugs. Tumor cells develop several strategies to gain proliferative advantages, including molecular alterations to evade from apoptosis. Failures in apoptosis could contribute to cancer pathogenesis, since these defects can cause the accumulation of dividing cells and do not remove genetic variants that have malignant potential. The apoptosis mechanism is composed by proteins that are members of BCL-2 and cysteine-protease families. BH3-only peptides are the "natural" intracellular ligands of BCL-2 family proteins. On the other hand, studies have proved that phenothiazine compounds influence the induction of cellular death. To understand the characteristics of phenothiazines and their effects on tumoral cells and organelles involved in the apoptosis, as well as evaluating their pharmacologic potential, we have carried out computational simulation with the purpose of relating the structures of the phenothiazines with their biological activity. Since the tridimensional (3D) structure of the target protein is known, we have employed the molecular docking approach to study the interactions between compounds and the protein's active site. Hereafter, the molecular dynamics technique was used to verify the temporal evolution of the BCL-2 complexes with phenothiazinic compounds and the BH3 peptide, the stability and the mobility of these molecules in the BCL-2 binding site. From these results, the calculation of binding free energy between the compounds and the biological target was carried out. Thus, it was possible to verify that thioridazine and trifluoperazine tend to increase the stability of the BCL-2 protein and can compete for the binding site with the BH3 peptide.

Photobleaching Efficiency Parallels the Enhancement of Membrane Damage for Porphyrazine Photosensitizers.

Photostability is considered a key asset for photosensitizers (PS) used in medical applications as well as for those used in energy conversion devices. In light-mediated medical treatments, which are based on PS-induced harm to diseased tissues, the photoinduced cycle of singlet oxygen generation has always been considered to correlate with PS efficiency. However, recent evidence points to the fundamental role of contact-dependent reactions, which usually cause PS photobleaching. Therefore, it seems reasonable to challenge the paradigm of photostability versus PS efficiency in medical applications. We have prepared a series of Mg(II) porphyrazines (MgPzs) having similar singlet oxygen quantum yields and side groups with different electron-withdrawing strengths that fine-tune their redox properties. A detailed investigation of the photobleaching mechanism of these porphyrazines revealed that it is independent of singlet oxygen, occurring mainly via photoinduced electron abstraction of surrounding electron rich molecules (solvents or lipids), as revealed by the formation of an air-stable radical anion intermediate. When incorporated into phospholipid membranes, photobleaching of MgPzs correlates with the degree of lipid unsaturation, indicating that it is caused by an electron abstraction from the lipid double bond. Interestingly, upon comparing the efficiency of membrane photodamage between two of these MgPzs (with the highest and the lowest photobleaching efficiencies), we found that the higher the rate of PS photobleaching the faster the leakage induced in the membranes. Our results therefore indicate that photobleaching is a necessary step toward inflicting irreversible biological damage. We propose that the design of more efficient PS for medical applications should contemplate contact-dependent reactions as well as strategies for PS regeneration.

Density Functional Theory Applied to Excited State Intramolecular Proton Transfer in Imidazole-, Oxazole-, and Thiazole-Based Systems.

Excited state intramolecular proton transfer (ESIPT) is a photoinduced process strongly associated to hydrogen bonding within a molecular framework. In this manuscript, we computed potential energy data using Time Dependent Density Functional Theory (TDDFT) for triphenyl-substituted heterocycles, which evidenced an energetically favorable proton transfer on the excited state (i.e., ESIPT) but not on the ground state. Moreover, we describe how changes on heterocyclic functionalities, based on imidazole, oxazole, and thiazole systems, affect the ESIPT process that converts an enolic species to a ketonic one through photon-induced proton transfer. Structural and photophysical data were obtained theoretically by means of density functional theory (DFT) calculations and contrasted for the three heterocyclics. Different functionals were used, but B3LYP was the one that adequately predicted absorption data. It was observed that the intramolecular hydrogen bond is strengthened in the excited state, supporting the occurrence of ESIPT. Finally, it was observed that, with the formation of the excited state, there is a decrease in electronic density at the oxygen atom that acts as proton donor, while there is a substantial increase in the corresponding density at the nitrogen atom that serves as proton acceptor, thus, indicating that proton transfer is indeed favored after photon absorption.

Mechanistic model for the firefly luciferin regeneration in biomimetic conditions: a model for the in vivo process?

The emission of light by fireflies involves the enzymatic oxidation of firefly luciferin and ends up in the formation of 2-cyano-6-hydroxybenzothiazole, and this is recycled back to luciferin by condensation with cysteine. In this work, we suggest a mechanism for this transformation that operates under mild conditions that are similar to in vivo environments (i.e. biomimetic); the rate-determining step consists of an intermolecular nucleophilic attack from the cysteine thiolate on the nitrile, catalysed by a specific base, followed by a complex sequence of intramolecular reactions which are highly dependent on the medium pH.

Quantum-chemistry descriptors for photosensitizers based on macrocycles.

Phthalocyanines, porphyrins, and chlorins have been widely studied as photosensitizers. Both experimental and computational strategies are employed in order to propose new and more active molecules derived from those macrocycles. In this context, there are two main strategies used: (i) the addition of different substituents and (ii) the complexation of the macrocycle with different metallic ions. In this work, we present selected descriptors based on quantum chemistry calculations for forty macrocycles, including some approved drugs. We have found that density functional theory is a suitable methodology to study the large sets of molecules when applying the B3LYP/LanL2DZ methodology for geometry optimization and TD-OLYP/6-31G(d) for absorption spectrum. The inclusion of solvent effects by means of continuum model is important in order to obtain the accurate electronic data. We have verified that by bonding charged or polar substituents to the macrocycle, it is possible to enhance water solvation as well as to improve spectroscopic properties because molecular orbital contributions for Q band can be affected by some substituents. Selected descriptors, electronic and steric, were pointed out as important to propose the new photosensitizers.

Morphological dependence of silver electrodeposits investigated by changing the ionic liquid solvent and the deposition parameters.

The low toxicity and environmentally compatible ionic liquids (ILs) are alternatives to the toxic and harmful cyanide-based baths used in industrial silver electrodeposition. Here, we report the successful galvanostatic electrodeposition of silver films using the air and water stable ILs 1-ethyl-3-methylimidazolium trifluoromethylsulfonate ([EMIM]TfO) and 1-H-3-methylimidazolium hydrogen sulphate ([HMIM(+)][HSO4(-)]) as solvents and AgTfO as the source of silver. The electrochemical deposition parameters were thoughtfully studied by cyclic voltammetry before deposition. The electrodeposits were characterized by scanning electron microscopy coupled with X-ray energy dispersive spectroscopy and X-ray diffraction. Molecular dynamics (MD) simulations were used to investigate the structural dynamic and energetic properties of AgTfO in both ILs. Cyclic voltammetry experiments revealed that the reduction of silver is a diffusion-controlled process. The morphology of the silver coatings obtained in [EMIM]TfO is independent of the applied current density, resulting in nodular electrodeposits grouped as crystalline clusters. However, the current density significantly influences the morphology of silver electrodeposits obtained in [HMIM(+)][HSO4(-)], thus evolving from dendrites at 15 mA cm(-2) to the coexistence of dendrites and columnar shapes at 30 mA cm(-2). These differences are probably due to the greater interaction of Ag(+) with [HSO4(-)] than with TfO(-), as indicated by the MD simulations. The morphology of Ag deposits is independent of the electrodeposition temperature for both ILs, but higher values of temperature promoted increased cluster sizes. Pure face-centred cubic polycrystalline Ag was deposited on the films with crystallite sizes on the nanometre scale. The morphological dependence of Ag electrodeposits obtained in the [HMIM(+)][HSO4(-)] IL on the current density applied opens up the opportunity to produce different and predetermined Ag deposits.

Riboflavin-photosensitized oxidation is enhanced by conjugation in unsaturated lipids.

Methyl esters of polyunsaturated fatty acids were found to quench triplet-excited riboflavin ((3)Rib) in efficient bimolecular reactions with rate constants, as determined by laser flash photolysis, linearly depending upon the number of bis-allylic methylene (from 1 to 5). Deactivation of (3)Rib is predicted by combining the experimental second-order rate constants k2 determined for acetonitrile/water (8:2, v/v) at 25 °C with density functional theory (DFT) calculations of bond dissociation energy to have an upper limiting value of 1.22 × 10(7) L mol(-1) s(-1) for hydrogen abstraction from bis-allylic methylene groups in unsaturated lipid by (3)Rib. Still, ergosterol was found to deactivate (3)Rib with k2 = 6.2 × 10(8) L mol(-1) s(-1), which is more efficient than cholesterol, with 6.9 × 10(7) L mol(-1) s(-1). Likewise conjugated (9E,11E) methyl linoleate (CLA) reacts with 3.3 × 10(7) L mol(-1) s(-1), 30 times more efficient than previously found for methyl α-linolenate. Conjugation as in CLA and ergosterol is concluded to enhance (3)Rib deactivation, and dietary plant sterols and CLA may accordingly be important macronutrients for eye and skin health, protecting against light exposure through efficient deactivation of (3)Rib.

Copper(II) complexation to 1-octarepeat peptide from a prion protein: insights from theoretical and experimental UV-visible studies.

The octarepeat domain in cellular prion protein (PrP(C)) has attracted much attention over the last 10 years because of its importance in the complexation of copper with PrP(C). The aim of this research was to study the UV-vis spectra of a peptide similar to the 1-repeat of the octarepeat region in PrP(C) using experimental and theoretical approaches and to gain insight into the complexation of the PrP(C) octarepeat domain with copper(II) ions in solution. We found that the copper atom was responsible for the peptide conformation, which allows for charge transfers between its two terminal residues.

The interaction of an azo compound with a surfactant and ion pair adsorption to solid phases.

The adsorption of SPADNS (trisodium salt of 2-(p-sulfophenylazo)-1,8-dihydroxynaphthalene-3,6-disulfonic acid) onto resins XAD 2, XAD 7 and silica gel was studied in the presence and in the absence of the cationic surfactant CTAB (cetyl trimethylammonium bromide). At a ratio of 2.5 CTAB to 1 SPADNS, the surfactant caused a marked increase in SPADNS adsorption. The experimental results for adsorption versus time were applied on the basis of three kinetic models (pseudo-first-order Lagergren, pseudo-second-order, and intraparticle diffusion). The interaction between CTAB and SPADNS was investigated using spectrophotometric, conductometric, and computational techniques. Theoretical results point to the formation of an ion pair between CTAB and SPADNS that influences the solution spectra, in agreement with conductometric and spectrophotometric data.

Reactivity of beer bitter acids toward the 1-hydroxyethyl radical as probed by spin-trapping electron paramagnetic resonance (EPR) and electrospray ionization-tandem mass spectrometry (ESI-MS/MS).

The iso-α-acids or isohumulones are the major contributors to the bitter taste of beer, and it is well-recognized that they are degraded during beer aging. In particular, the trans-isohumulones seem to be less stable than the cis-isohumulones. The major radical identified in beer is the 1-hydroxyethyl radical; however, the reactivity between this radical and the isohumulones has not been reported until now. Therefore, we studied the reactivity of isohumulones toward the 1-hydroxyethyl radical through a competitive kinetic approach. It was observed that both cis- and trans-isohumulones and dihydroisohumulones are decomposed in the presence of 1-hydroxyethyl radicals, while the reactivities are comparable. On the other hand, the tetrahydroisohumulones did not react with 1-hydroxyethyl radicals. The apparent second-order rate constants for the reactions between the 1-hydroxyethyl radical and these compounds were determined by electron paramagnetic resonance (EPR) spectroscopy and electrospray ionization-tandem mass spectrometry [ESI(+)-MS/MS]. It follows that degradation of beer bitter acids is highly influenced by the presence of 1-hydroxyethyl radicals. The reaction products were detected by liquid chromatography-electrospray ionization-ion trap-tandem mass spectrometry (LC-ESI-IT-MS/MS), and the formation of oxidized derivatives of the isohumulones was confirmed. These data help to understand the mechanism of beer degradation upon aging.

Role of physicochemical properties in the activation of peroxisome proliferator-activated receptor δ.

Current researches on treatments for metabolic diseases involve a class of biological receptors called peroxisome proliferator-activated receptors (PPARs), which control the metabolism of carbohydrates and lipids. A subclass of these receptors, PPARδ, regulates several metabolic processes, and the substances that activate them are being studied as new drug candidates for the treatment of diabetes mellitus and metabolic syndrome. In this study, several PPARδ agonists with experimental biological activity were selected for a structural and chemical study. Electronic, stereochemical, lipophilic and topological descriptors were calculated for the selected compounds using various theoretical methods, such as density functional theory (DFT). Fisher's weight and principal components analysis (PCA) methods were employed to select the most relevant variables for this study. The partial least squares (PLS) method was used to construct the multivariate statistical model, and the best model obtained had 4 PCs, q ( 2 ) = 0.80 and r ( 2 ) = 0.90, indicating a good internal consistency. The prediction residues calculated for the compounds in the test set had low values, indicating the good predictive capability of our PLS model. The model obtained in this study is reliable and can be used to predict the biological activity of new untested compounds. Docking studies have also confirmed the importance of the molecular descriptors selected for this system.

Theoretical study on the molecular and electronic properties of some substances used for diabetes mellitus treatment.

Diabetes mellitus (DM) is a disease that affects a large number of people, and the number of problems associated with the disease has been increasing in the past few decades. These problems include cardiovascular disorders, blindness and the eventual need to amputate limbs. Therefore, the quality of life for people living with DM is less than it is for healthy people. In several cases, metabolic syndrome (MS), which can be considered a disturbance of the lipid metabolism, is associated with DM. In this work, two drugs used to treat DM, pioglitazone and rosiglitazone, were studied using theoretical methods, and their molecular properties were related to the biological activity of these drugs. From the results, it was possible to correlate the properties of each substance - particularly electronic properties - with the biological interactions that are linked to their pharmacological effects. These results suggest that there are future prospects for designing or developing new drugs based on the correlation between theoretical and experimental properties.