Revisiting the Sweet Taste Receptor T1R2-T1R3 through Molecular Dynamics Simulations Coupled with a Noncovalent Interactions Analysis.

It is nowadays widely accepted that sweet taste perception is elicited by the activation of the heterodimeric complex T1R2-T1R3, customarily known as sweet taste receptor (STR). However, the interplay between STR and sweeteners has not yet been fully clarified. Here through a methodology coupling molecular dynamics and the independent gradient model (igm) approach we determine the main interacting signatures of the closed (active) conformation of the T1R2 Venus flytrap domain (VFD) toward aspartame. The igm methodology provides a rapid and reliable quantification of noncovalent interactions through a score (Δginter) based on the attenuation of the electronic density gradient when two molecular fragments approach each other. Herein, this approach is coupled to a 100 ns molecular dynamics simulation (MD-igm) to explore the ligand-cavity contacts on a per-residue basis as well as a series of key inter-residue interactions that stabilize the closed form of VFD. We also apply an atomic decomposition scheme of noncovalent interactions to quantify the contribution of the ligand segments to the noncovalent interplay. Finally, a series of structural modification on aspartame are conducted in order to obtain guidelines for the rational design of novel sweeteners. Given that innovative methodologies to reliably quantify the extent of ligand-protein coupling are strongly demanded, this approach combining a noncovalent analysis and MD simulations represents a valuable contribution, that can be easily applied to other relevant biomolecular systems.

Hierarchical Porous Carbon-PtPd Catalysts and Their Activity toward Oxygen Reduction Reaction.

PtPd bimetallic catalysts supported on hierarchical porous carbon (HPC) with different porous sizes were developed for the oxygen reduction reaction (ORR) toward fuel cell applications. The HPC pore size was controlled by using SiO2 nanoparticles as a template with different sizes, 287, 371, and 425 nm, to obtain three HPC materials denoted as HPC-1, HPC-2, and HPC-3, respectively. PtPd/HPC catalysts were characterized by scanning electron microscopy, X-ray photoelectron spectroscopy, X-ray diffraction, and high-resolution transmission electron microscopy. The electrochemical performance was examined by cyclic voltammetry and linear sweep voltammetry. PtPd/HPC-2 turned out to be the most optimal catalyst with an electroactive surface area (ESA) of 40.2 m2 g-1 and a current density for ORR of -1285 A g-1 at 2 mV s-1 and 1600 rpm. In addition, we conducted a density functional theory computational study to examine the interactions between a PtPd cluster and a graphitic domain of HPC, as well as the interaction between the catalyst and the oxygen molecule. These results reveal the strong influence of the porous size (in HPC) and ESA values (in PtPd nanoparticles) in the mass transport process which rules the electrochemical performance.

Pyridazinone derivatives as potential anti-inflammatory agents: synthesis and biological evaluation as PDE4 inhibitors.

Cyclic nucleotide phosphodiesterase type 4 (PDE4), which controls the intracellular level of cyclic adenosine monophosphate (cAMP), has aroused scientific attention as a suitable target for anti-inflammatory therapy of respiratory diseases. This work describes the development and characterization of pyridazinone derivatives bearing an indole moiety as potential PDE4 inhibitors and their evaluation as anti-inflammatory agents. Among these derivatives, 4-(5-methoxy-1H-indol-3-yl)-6-methylpyridazin-3(2H)-one possesses promising activity, and selectivity towards PDE4B isoenzymes and is able to regulate potent pro-inflammatory cytokine and chemokine production by human primary macrophages.

Highly Porous Reduced Graphene Oxide-Coated Carbonized Cotton Fibers as Supercapacitor Electrodes.

High-surface-area carbon-based capacitors exhibit significant advantages relative to conventional graphite-based systems, such as high power density, low weight, and mechanical flexibility. In this work, novel porous carbon-based electrodes were obtained from commercial cotton fibers (CFs) impregnated with graphene oxide (GO) at different dipping times. A subsequent thermal treatment under inert atmosphere conditions enables the synthesis of electrodes based on reduced GO (RGO) supported on carbon fibers. Those synthetized with 15 min and 30 min of dipping time displayed high specific capacitance given their optimal micro-/ mesoporosity ratio. Particularly, the RGO/CCF15A supercapacitor reports a remarkable specific capacitance of 74.1 F g-1 at 0.2 A g-1 and a high cycling stability with a 97.7% capacitive retention, making this electrode a promising candidate for supercapacitor design. Finally, we conducted a density functional theory study to obtain deeper information about the driving forces leading to the GO/CF structures.

Novel approach to accurately predict bond strength and ligand lability in platinum-based anticancer drugs.

Prompted by the antineoplastic properties of cisplatin, a plethora of platinum(ii)-based complexes have been synthesized in the past decades. At present, their rational design is based on a number of structure-activity relationships involving the nature of the ligands initially coordinated to platinum(ii): either non-labile (acting as a carrier) or labile (undergoing substitution). The coordinate bond strength of the labile ligand plays a key role in the first step of the drug mechanism of action, i.e., the hydrolysis process, which is associated to the retention time of the medicine in the body. Therefore, an accurate determination of the metal-ligand bond strength becomes highly relevant as it will help the rational design of novel chemotherapeutic agents. Herein, we challenge the recently developed intrinsic bond strength index (IBSI) as a rapid and practical tool to assess the ligand lability in Pt(ii) complexes. In a first stage, given the importance of the trans-effect in synthetic strategies of cisplatin-based drugs, the effect of eleven trans-directing ligands T is quantified in two sets of complexes [Pt(NH3)2(H2O)T]n+ and [PtCl2(NH3)T]m+ where T = H2O, F-, NH3, Cl-, Br-, I-, SO32-, CH3-, CN-, CO, and H-. An essential outcome of this work is a novel index IBSItrans = IBSIσ + IBSIπ able to rank the directing ligands by their trans-effect according to their σ-donation and π-backbonding electronic contributions. In a second stage, we apply the IBSI score to a panel of eleven case studies, comprising mostly antineoplastic agents, such as cisplatin, carboplatin, lobaplatin etc., in order to quantify the coordinate bond strength of the ligands, providing insights about the hydrolysis process. The obtained results, in good agreement with experimental data and reported theoretical studies, demonstrate that the IBSI score is able to deliver a rapid and reliable picture of the coordinate bond strength, representing a chemically intuitive tool helpful for the development of novel anticancer agents prior to synthetic efforts.

Mechanistic insights into Smiles rearrangement. Focus on π-π stacking interactions along the radical cascade.

The synthesis of new arene and heteroarene scaffolds of therapeutic interest has generated a renewed interest in the domino radical cyclisation-Smiles. In this work we present a detailed mechanistic investigation of the radical version of a cascade involving a desulfonative Smiles rearrangement on an aromatic ring bearing a sulfonamide linker. Competing routes have been explored to characterize the molecular mechanism of the studied reaction. The knowledge gained from previous experimental observations is explained through the energy profile obtained by means of quantum mechanical calculations. This study answers questions about the rate determining step and the type of mechanism involved (two-step or concerted). Supplementary rate constant calculations as well as quantum molecular dynamics support experimental observations. An IGM-δg analysis performed along the reaction path unveils and quantifies an intramolecular π-π stacking interaction accelerating the reaction. This novel post processing IGM-δg tool based on the electron density, turns out to be useful to monitor and quantify specific intramolecular weak interactions along a reaction path from wave functions. From this mechanistic investigation it turns out that Smiles rearrangement here takes place in two steps rather than in a direct intramolecular radical substitution. Furthermore, we show that chain length effects must be taken into account in the functionalization of new sulfonylated derivatives subjected to this radical cascade, given their influence in the reaction rate.

Atomic Decomposition Scheme of Noncovalent Interactions Applied to Host-Guest Assemblies.

The design of novel stimuli-responsive supramolecular systems based on host-guest chemistry implies a thorough understanding of the noncovalent interactions involved. In this regard, some computational tools enabling the extraction of the noncovalent signatures from local descriptors based on the electron density have been previously proposed. Although very useful to detect the existence of such interactions, these analyses provide only a semi-quantitative description, which represents a limitation. In this work, we present a novel computational tool based on the local atomic descriptor IGM-δginter/At, which is able to decompose the fragment interaction into atomic contributions. Then, the role played by each atom in the formation of the host-guest assembly is quantified by an integrated Δginter/At score. Herein, we apply the IGM-Δginter/At approach to some challenging systems, including multimetallic arrays, buckycatchers, and organic assemblies. These systems exhibit unique structural features that make it difficult to determine the host/guest atoms that contribute the most to the guest encapsulation. Here, the Δginter/At score proves to be an appealing tool to shed light on the guest accommodation on a per-atom basis and could be useful in the rational design of more selective target agents. We strongly believe that this novel approach will be useful for experimental teams devoted to the synthesis of supramolecular systems based on host-guest chemistry.

Dibenzyl Disulfide Adsorption on Cationic Exchanged Faujasites: A DFT Study.

Although dibenzyl disulfide (DBDS) is used as a mineral oil stabilizer, its presence in electrical transformer oil is associated as one of the major causes of copper corrosion and subsequent formation of copper sulfide. In order to prevent these undesirable processes, MY zeolites (with M = Li, Na, K, Cs, Cu or Ag) are proposed to adsorb molecularly DBDS. In this study, different MY zeolites are investigated at the DFT+D level in order to assess their ability in DBDS adsorption. It was found that CsY, AgY and CuY exhibit the best compromise between high interaction energies and limited S-S bond activation, thus emerging as optimal adsorbents for DBDS.

The role of solvation models on the computed absorption and emission spectra: the case of fireflies oxyluciferin.

Surrounding effects are crucial to successfully simulate the absorption and emission spectra of molecular systems. In this work we test different solvation models to compute transition energies and to simulate the spectra of oxyluciferin responsible for the light emission in fireflies and its derivatives. We demonstrate that, within the PCM model, the IBSF formalism is suitable for computing the transition energies of the oxyluciferin chemical forms characterized by a charge transfer character. On the other hand, the LR approach could be used for the chemical forms where an almost negligible charge transfer takes place. Moreover, we demonstrate that explicit solvation models, applied by QM/MM calculations, are needed to accurately reproduce the experimental shape of the spectra. Finally, the vibrationally resolved spectra using a solvation model (implicit or microsolvation) is computed. Some noticeable differences arise when considering the implicit solvation with respect to gas phase vibrational spectra, while small changes were found when explicit water molecules within a microsolvated model are considered.

Nature of cucurbituril-halogen encapsulation. Structural and interaction energy consideration in the X2@CB[n] (X = Cl, Br, I, n = 6, 7, 8) from relativistic DFT calculations.

The formation of host-guest species is a relevant issue in the obtaining of supramolecular arrays. In this work, the encapsulation of dihalogen molecules into different cucurbituril hosts allows further evaluation of the role of size and interaction energy for the stabilization of host-guest species. Our results for the X2@CB[n] (X = Cl, Br, I, n = 6, 7, 8) series, allow exploration of the hosts providing increasing cavity sizes, resulting in different host-guest scenarios. It is found that the interaction is mostly given by London type interactions (59% to 65%), followed by the electrostatic character of the interaction (31-27%). For species with a packing coefficient (PC) within the suggested favorable range (PC = 55-68%), and lower, the strength of the stabilizing electrostatic interaction and covalent character, and the repulsive Pauli term, remain similar. Moreover, the dispersion term varies to a large extent, owing to its relation to the available interacting internal face of CB[n], which is less in n = 7 and 8 counterparts. Hence, greater host flexibility is able to maximize the host-guest interactions, where this feature can be viewed as an interesting characteristic towards molecular recognition capabilities, which can be further studied in other related species such as cyclodextrins, pillararenes and other supramolecular hosts.

Design of a multifunctionalizable BODIPY platform for the facile elaboration of a large series of gold(i)-based optical theranostics.

A simple trifunctional BODIPY platform was designed. The high potential of this platform was validated via the elaboration of twelve optical theranostics. More specifically, we reported on the synthesis, the characterization, the photophysical properties, and the evaluation of the hydrophilicity properties of the different BODIPY derivatives, as well as a theoretical rationalization of the intriguing chemical behavior of some of them. The antiproliferative evaluation and confocal imaging of the different compounds in three human and murine cancer cell lines were performed and analysed, along with the measurement of gold(i) uptake in one cancer cell line via ICP-MS.

Rationalisation of the optical signatures of nor-dihydroxanthene-hemicyanine fused near-infrared fluorophores by first-principle tools.

Using a computational approach combining the Time-Dependent Density Functional Theory (TD-DFT) and the second-order Coupled Cluster (CC2) approaches, we investigate the spectral properties of a large panel of nor-dihydroxanthene (DHX)-hemicyanine fused dyes. First we compare the theoretical and experimental 0-0 energies for a set of 14 known synthetic compounds and show that a remarkable agreement between theory and experiment is obtained when a suitable environmental model is selected. In addition, we obtain vibrationally-resolved spectra for several compounds and theory also accurately reproduces the experimental band shapes. We show that the electronic transitions in nor-DHX-based fluorophores are associated with small variations of the dipole moments but large oscillator strengths. Using various chemical strategies, we design a series of compounds with red-shifted 0-0 energies.

Combined TD-DFT-SOS-CIS(D) Study of BOPHY Derivatives with Potential Application in Biosensing.

A set of 13 bis(difluoroboron)-1,2-bis((pyrrol-2-yl)methylene)hydrazine (BOPHY) dyes is studied through a hybrid time-dependent density functional theory (TD-DFT)-scaled opposite spin-configuration interaction singles with a double correction [SOS-CIS(D)] approach accounting for solvent effects, to shed light onto the structure-property relationships of these recently developed chromophores. In the first step, we calculate the absorption-fluorescence crossing points with refined TD-DFT models considering the influences of both vibrational and solvent contributions. We found that the systematic overestimation of the 0-0 energies is effectively reduced by combining polarizable continuum model-TD-DFT with a scaled opposite spin-configuration interaction singles with a double correction [SOS-CIS(D)]. Next, for a representative system, the vibrationally resolved spectrum within the harmonic approximation is computed on the basis of TD-DFT vibrational signatures and an excellent match with experiment is found. Finally, the influence of different lateral groups on the spectroscopic properties is rationalized by investigating charge transfer parameters and examining electronic density difference maps. It is found that one can tune the position of the absorption/emission maxima by a judicious choice of the lateral substituents or by using π-extended segments. The largest absorption and emission wavelengths as well as the largest Stokes shifts are obtained for BOPHYs containing strong electron-donor dimethylaminophenyl groups attached to the α-positions of the pyrrole units through vinyl linkers, making these chromophores promising candidates for bioluminescence applications.

Boron Difluoride Curcuminoid Fluorophores with Enhanced Two-Photon Excited Fluorescence Emission and Versatile Living-Cell Imaging Properties.

The synthesis of boron difluoride complexes of a series of curcuminoid derivatives containing various donor end groups is described. Time-dependent (TD)-DFT calculations confirm the charge-transfer character of the second lowest-energy transition band and ascribe the lowest energy band to a "cyanine-like" transition. Photophysical studies reveal that tuning the donor strength of the end groups allows covering a broad spectral range, from the visible to the NIR region, of the UV-visible absorption and fluorescence spectra. Two-photon-excited fluorescence and Z-scan techniques prove that an increase in the donor strength or in the rigidity of the backbone results in a considerable increase in the two-photon cross section, reaching 5000 GM, with predominant two-photon absorption from the S0-S2 charge-transfer transition. Direct comparisons with the hemicurcuminoid derivatives show that the two-photon active band for the curcuminoid derivatives has the same intramolecular charge-transfer character and therefore arises from a dipolar structure. Overall, this structure-relationship study allows the optimization of the two-photon brightness (i.e., 400-900 GM) with one dye that emits in the NIR region of the spectrum. In addition, these dyes demonstrate high intracellular uptake efficiency in Cos7 cells with emission in the visible region, which is further improved by using porous silica nanoparticles as dye vehicles for the imaging of two mammalian carcinoma cells type based on NIR fluorescence emission.

Borondifluoride complexes of hemicurcuminoids as bio-inspired push-pull dyes for bioimaging.

Hemicurcuminoids are based on half of the π-conjugated backbone of curcuminoids. The synthesis of a series of such systems and their borondifluoride complexes is described. The electrochemical and photophysical properties of difluorodioxaborine species were investigated as a function of the nature of electron donor and acceptor groups appended at either terminal positions of the molecular backbone. The emissive character of these dipolar dyes was attributed to an intraligand charge transfer process, leading to fluorescence emission that is strongly dependent on solvent polarity. Quasi-quantitative quenching of fluorescence in high polarity solvents was attributed to photoinduced electron transfer. These dyes were shown to behave as versatile fluorophores. Indeed, they display efficient two-photon excited fluorescence emission leading to high two-photon brightness values. Furthermore, they form nanoparticles in water whose fluorescence emission quantum yield is less than that of the dye in solution, owing to aggregation-induced fluorescence quenching. When cos7 living cells were exposed to these weakly-emitting nanoparticles, one- and two-photon excited fluorescence spectra showed a strong emission within the cytoplasm that originated from the individual molecules. Dye uptake thus involved a disaggregation mechanism at the cell membrane which restored fluorescence emission. This off-on fluorescence switching allows a selective optical monitoring of those molecules that do enter the cell, which offers improved sensitivity and selectivity of detection for bioimaging purposes.

Metal containing cryptands as hosts for anions: evaluation of Cu(I)···X and π···X interactions in halide-tricopper(I) complexes through relativistic DFT calculations.

More selective than crown ethers, cryptands arise as suitable hosts for several ions, with the size of the cavity and the behavior of the atoms belonging to the structure being the main factors governing their selectivity. Similar to metallacrowns, inorganic counterparts of crown ethers, the presence of metal centers in cryptands can offer significant advantages in terms of ion recognition as they provide positively charged sites, which allow them to encapsulate anions. Here, through density functional methodologies, we evaluate the preference of a tricopper(I) cryptand host toward a series of halide ions ranging from the hard fluoride to the soft iodide, where the more intense interactions are established with the hardest one, and the electrostatic term is the more relevant contributor to total interaction energy. Upon exploration of this electrostatic contribution in more detail, it is observed that as the guest becomes softer, the increase of higher order Coulombic terms, such as dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole, acquires more relevance on going from 9.22% to 41.25%, denoting the key role and variation of such forces in inclusion systems with metal-containing hosts.

A study on the versatility of metallacycles in host-guest chemistry: interactions in halide-centered hexanuclear copper(II) pyrazolate complexes.

Hexanuclear copper(II) pyrazolate complexes have shown the ability to encapsulate different halide ions, leading to [trans-Cu6{µ-3,5-(CF3)2pz}6(µ-OH)6X](-) (X = F, Cl, Br, I). They offer an interesting case study for variation in local properties at host binding sites, due to the presence of a six membered ring involving Cu(II) centers considered as the borderline Lewis acid according to the Pearson Hard and Soft Acids and Bases (HSAB) principle. Here, we describe the host-guest interactions via relativistic density functional calculations, involving the graphical description of local dipole and quadrupole moments, energy decomposition analysis, non-covalent indices, and magnetic behavior. The observed variation in the copper local dipole and quadrupole moments suggests that a metallacycle host offers great advantages in comparison to their organic counterparts, prompted by the versatility of the metallic centers to modulate the surrounding electron density accordingly. According to our results, the contribution of ion-dipole forces in the halide-centered series decreases from 95.0% to 77.0% from the fluoride to the iodide complex, whereas the contribution of higher order interactions such as quadrupole-dipole and quadrupole-quadrupole, goes from 5.0% to 23.0% towards a softer guest. In addition, the through-the-space magnetic response of trans-Cu6{µ-3,5-(CF3)2pz}6(µ-OH)6, reveals a noteworthy aromatic structure, which is driven by the superexchange through the ligands leading to a singlet ground state.