Closed-shell d10-d10 mechanochromic [AuPh(CNPh)]n complex: quantum chemistry electronic and optical properties

The electronic structure, spectroscopic properties, and solid state chemistry of monomer and dimers of [AuPh(CNPh)] complex were studied at post-Hartree-Fock (MP2, SCS-MP2, and CC2) and density functional theory levels. The absorption spectra of these complexes were calculated using single excitation time-dependent (TD) methods at DFT, CC2, and SCS-CC2 levels. The influences of the bulk are accounted for at the PBE-D3 level, incorporating dispersion effects. The calculated values agree with the experimental range, where absorption and emission energies reproduce experimental trends with large Stokes shifts. The aurophilic interaction is identified as a key factor influencing the spectroscopic and structural properties of these complexes. The intermetallic interactions were found as the main factor responsible for MMCT electronic transitions in the models studied.

Is there a Covalent Au(I)-Au(I) Bond in the trans-(AuX)2 (X = F, Cl, Br, I) Structure? A Post-Hartree-Fock and Density Functional Theory Study

We present an exhaustive exploration of the driving forces dominating the interaction between gold atoms in the trans-(AuX)2, where X is a halogen ligand. This work provides insights into the nature of the gold-gold contact in the trans-(AuX)2. The geometries and energies were calculated at the MP2, CCSD(T), and DFT-D3(BJ) (B3LYP, PBE, and TPSS) levels of theory. The results show a short Au-Au distance, typical of a covalent bond, but with a weak interaction energy associated with noncovalent interactions. It is established that the physical contributions from polarization and the electronic correlation forces are the most relevant at the post-Hartree-Fock level of theory. Also, the electrostatic term is attractive but with low contribution. Finally, the Wiberg indices and NBO analysis exposed a small covalent character between the gold atoms, revealing that this contribution is insufficient to explain the stability of the dimers. It is concluded that a sum of contributions makes it possible to establish an attraction between the gold atoms in the dimers studied beyond a classical aurophilic interaction.

Unveiling the tartrazine binding mode with ds-DNA by UV-visible spectroscopy, electrochemical, and QM/MM methods

Here, we studied the interaction between the food colorant tartrazine (TZ) and double stranded DNA (dsDNA), using spectroscopic, electrochemical, and computational methods such as QM/MM combined with TD-DFT. Despite the UV-vis spectroscopy is widely used to study the interaction between molecules, for the case of TZ there are discrepancies in the analyses presented in the literature available, presenting both hyperchromic and hypochromic effects and consequently different rationalizations for their results. Herein we propose the combination of UV-vis experiments with the design of high-level computational models capable of reproducing the experimental behavior to finally define the proper binding mode at the molecular scale together with the rationalization of the experimental optical response due to the complex formation. To complement the UV-vis experiments, we propose the use of electrochemical measurements, to support the results obtained through UV-vis spectroscopy, as it has been successfully used for the determination of interaction modes between small molecules and biomolecules in any condition. Our UV-vis spectroscopy experiments showed only a hypochromic effect of the absorption spectra of TZ after interaction with DNA, indicative of TZ being deeply buried in the DNA structure. The effect of ionic strength in the experimental procedures led to the dissociation of TZ, thus indicating that the interaction mode was groove binding. On the other hand, the electrochemical studies showed an irreversible reduction peak of TZ, which after the interaction with DNA exhibited a positive shift in potential that can be attributed to groove binding. The binding constant for TZ-DNA was calculated as 4.45x10⁴M^-1 (UV-vis) and 5.75x10⁴M^-1 (electrochemistry), in line with other groove binder azo dyes. Finally, through the QM/MM calculations we found that the minor-groove binding mode interacting in zones rich in adenine and thymine was the model best suited to reproduce the experimental UV-vis response.

The interaction mechanism of polystyrene microplastics with pharmaceuticals and personal care products

Microplastics (MPs) have been detected in the hydrosphere, with hazardous implications in transporting coexisting water pollutants. Our knowledge about the interaction mechanisms that MPs establish with organic pollutants are still growing, which is essential to understand the adsorption properties of MPs and their relative stability with adsorbates. Here, we used classical (force field methods) and ab-initio (density functional theory) computational chemistry tools to characterize the interaction mechanisms between Polystyrene-MPs (PS-MPs) and pharmaceuticals/personal care products (PPCPs). Adsorption conformations and energies, thermochemistry, binding, and energy decomposition analyses were performed to obtain the quantitative mechanistic information. Our results show that PS-MPs have permanent dipoles, increasing the interaction with neutral PPCPs while repelling the charged pollutants; in all cases, a stable physisorption takes place. Moreover, PS-MPs increase their solubility upon pollutant adsorption due to an increase in the dipole moment, increasing their co-transport ability in aqueous environments. The stability of the PS-MPs/PPCPs complexes is further confirmed by thermochemical and molecular dynamics trajectory analysis as a function of temperature and pressure. The interaction mechanism of high pKa pollutants (pKa > 5) is due to a balanced contribution of electrostatic and dispersion forces, while the adsorption of low pKa pollutants (pKa < 5) maximizes the electrostatic forces, and steric repulsion effects explain their relative lower adsorption stability. In this regard, several pairwise intermolecular interactions are recognized as a source of stabilization in the PS-MPs/PPCPs binding: hydrogen bonding, π-π, OH⋯π, and CH⋯π, CCl⋯CH and CH⋯CH interactions. The ionic strength in solution slightly affects the adsorption stability of neutral PPCPs, while the sorption of charged pollutants is enhanced. This mechanistic information provides quantitative data for a better understanding of the interactions between organic pollutants and MPs, serving as valuable information for sorption/kinetic studies.

Mechanistic insights into the adsorption of endocrine disruptors onto polystyrene microplastics in water

Microplastics and endocrine disruptors (EDs) are contaminants of emerging concerns and ubiquitously present in aquatic ecosystems, establishing interactions that still are the subject of investigation due to their implications in the cotransport of pollutants. Then, we conducted mechanistic studies based on state-of-art computational chemistry methods to quantitatively understand the interaction mechanisms whereby polystyrene micro or nanoplastics (PS-MPs) interact with representative classes of EDs in water (Ethynylestradiol, Estradiol, and Bisphenol A). The results showed that PS-MPs increase their charge distribution when forming microparticles in water, giving a permanent dipole that explains their increasing solubility in aqueous conditions. In agreement with experimental assessments, the PS-MPs favorably adsorb EDs with adsorption energies larger than 15 kcal/mol, even with comparable stability to nanostructured materials for adsorption, removal, and/or analysis of pollutants. The adsorption occurs via physisorption without covalent binding, bond breaking, or structural preparation energies, where the molecular structure of EDs can favor inner or outer surface adsorption depending on the molecular structure of the adsorbates. A balanced contribution of dispersion and electrostatic stabilizing effects determines the interaction mechanisms, accounting for a whole contribution of 88-90%. The electrostatic contribution emerges from the favorable alignment of the PS-MPs and EDs dipoles upon interaction due to the mild charge transfer between them in solution. In contrast, the dispersion contribution emerges from electron-electron interactions due to the permanent dipoles in adsorbates and adsorbents. Furthermore, thermochemical analyses clarify the role of temperature and pressure effects on the relative adsorption stability among EDs in aquatic environments. Therefore, modeling the adsorption process contributes to new knowledge on the sorption properties of PS-MPs, providing a mechanistic basis to understand the cotransport of pollutants in water environments and their impacts on environmental pollution.

Improving Lurasidone Hydrochloride's Solubility and Stability by Higher-Order Complex Formation with Hydroxypropyl-β-cyclodextrin

The biopharmaceutical classification system groups low-solubility drugs into two groups: II and IV, with high and low permeability, respectively. Most of the new drugs developed for common pathologies present solubility issues. This is the case of lurasidone hydrochloride-a drug used for the treatment of schizophrenia and bipolar depression. Likewise, the stability problems of some drugs limit the possibility of preparing them in liquid pharmaceutical forms where hydrolysis and oxidation reactions can be favored. Lurasidone hydrochloride presents the isoindole-1,3-dione ring, which is highly susceptible to alkaline hydrolysis, and the benzisothiazole ring, which is susceptible to a lesser extent to oxidation. Herein, we propose to study the increase in the solubility and stability of lurasidone hydrochloride by the formation of higher-order inclusion complexes with hydroxypropyl-β-cyclodextrin. Several stoichiometric relationships were studied at between 0.5 and 3 hydroxypropyl-β-cyclodextrin molecules per drug molecule. The obtained products were characterized, and their solubility and stability were assessed. According to the obtained results, the formation of inclusion complexes dramatically increased the solubility of the drug, and this increased with the increase in the inclusion ratio. This was associated with the loss of crystalline state of the drug, which was in an amorphous state according to infrared spectroscopy, calorimetry, and X-ray analysis. This was also correlated with the stabilization of lurasidone by the cyclodextrin inhibiting its recrystallization. Phase solubility,¹H-NMR, and docking computational characterization suggested that the main stoichiometric ratio was 1:1; however, we cannot rule out a 1:2 ratio, where a second cyclodextrin molecule could bind through the isoindole-1,3-dione ring, improving its stability as well. Finally, we can conclude that the formation of higher-order inclusion complexes of lurasidone with hydroxypropyl-β-cyclodextrin is a successful strategy to increase the solubility and stability of the drug.

Biochemical characterization of Peumus boldus fruits: Insights of its antioxidant properties through a theoretical approach

Peumus boldus is an endemic tree species from Chile whose leaves have been the focus of study for decades given that their infusions are reported to relieve rheumatic symptoms, headache, dyspepsia, urinary tract inflammation, and symptoms of other illnesses. These health properties have been studied mainly using leaves and bark, then it is relevant to know more about these properties in different parts of the plant. Considering the importance of P. boldus fruits in the diet of some rural populations, we analyzed their properties to explore its impact on the Chilean population health. Liquid chromatography and mass spectrometry analysis confirmed the presence of alkaloids such as boldine, although aporphine N-methyl-laurotetanine was the most abundant. In addition, flavonoids catechin, chrysin and quercetin were also found in the extract. Cytotoxicity and anti-inflammatory activities of the fruit extract were invitro tested by using a murine macrophage cell model, observing that a diluted fraction of the extract was not cytotoxic, but showed anti-inflammatory activity, which is likely attributed to antioxidants activities. By means of quantum chemical calculations, we calculated the redox potential of the respective alkaloids and flavonoids found in the extract. Results suggest a synergistic effect between alkaloids and flavonoids, where boldine and N-methyl-laurotetanine showed similar antioxidant properties. Finally, we present a description of the oxidation mechanisms for both groups of molecules which will sustain P. boldus fruit biological properties, in order to give this kind of fruits scientific value focusing on human health.

Closed-shell d10–d10 in [AuCl(CNR)]n and [AuCl(CO)]n (n = 1, 2; R = –H, –CH3, –Cy) complexes: quantum chemistry study of their electronic and optical properties

The [AuCl(CNR)] and [AuCl(CO)] (R = –H, –CH3, –Cy) complexes were modeled and their electronic and optical properties described.

Exploration of the Interaction Strength at the Interface of Anionic Chalcogen Anchors and Gold (111)-Based Nanomaterials

Nowadays, the use of sulfur-based ligands to modify gold-based materials has become a common trend. Here, we present a theoretical exploration of the modulation of the chalcogenides-gold interaction strength, using sulfur, selenium, and tellurium as anchor atoms. To characterize the chalcogenide-gold interaction, we designed a nanocluster of 42 gold atoms (Au₄₂) to model a gold surface (111) and a series of 60 functionalized phenyl-chalcogenolate ligands to determine the ability of electron-donor and -withdrawing groups to modulate the interaction. The analysis of the interaction was performed by using energy decomposition analysis (EDA), non-covalent interactions index (NCI), and natural population analysis (NPA) to describe the charge transfer processes and to determine data correlation analyses. The results revealed that the magnitudes of the interaction energies increase following the order S < Se < Te, where this interaction strength can be augmented by electron-donor groups, under the donor-acceptor character the chalcogen-gold interaction. We also found that the functionalization in meta position leads to better control of the interaction strength than the ortho substitution due to the steric and inductive effects involved when functionalized in this position.

Theoretical exploration of the forces governing the interaction between gold-phthalocyanine and gold surface clusters

Here we aim to explore the nature of the forces governing the adsorption of gold-phthalocyanine on gold substrates. For this, we designed computational models of metal-free phthalocyanine and gold-phthalocyanine deposited over a gold metallic surface represented by cluster models of different sizes and geometries. Thereby, we were able to determine the role of the metal center and of the size of the substrate in the interaction process. For this purpose, we worked within the framework provided by density functional theory, were the inclusion of the semi-empirical correction of the dispersion forces of Grimme's group was indispensable. It has been shown that the interaction between molecules and surfaces is ruled by van der Waals attractive forces, which determine the stabilization of the studied systems and their geometric properties. Their contribution was characterized by energy decomposition analysis and through the visualization of the dispersion interactions by means of the NCI methodology. Moreover, calculations of Density of States (DOS) showed that the molecule-surface system displays a metal-organic interface evidenced by changes in their electronic structure, in agreement with a charge transfer process found to take place between the interacting parts.

Electronic and optical properties of [Au(CH3CSS)]4 cluster. A quantum chemistry study

The [Au(dta)]₄ (dta = dithioacetate, S₂CCH₃) cluster is modeled and the electronic and optical properties described.

Adsorption/desorption process of formaldehyde onto iron doped graphene: a theoretical exploration from density functional theory calculations

The interaction of formaldehyde (H₂CO) onto Fe-doped graphene (FeG) was studied in detail from density functional theory calculations and electronic structure analyses. Our aim was to obtain insights into the adsorption, desorption and sensing properties of FeG towards H₂CO, a hazardous organic compound. The adsorption of H₂CO was shown to be energetically stable onto FeG, with adsorption energies of up to 1.45 eV and favored in different conformations. This interaction was determined to be mostly electrostatic in nature, where the oxygen plays an important role in this contribution; besides, our quantum molecular dynamics results showed the high stability of the FeG-H₂CO interaction at ambient temperature (300 K). All the interactions were determined to be accompanied by an increase in the HOMO-LUMO energy gap with respect to the isolated adsorbent, indicating that FeG is highly sensitive to H₂CO with respect to pristine graphene. Finally, it was found that external electric fields of 0.04-0.05 a.u. were able to induce the pollutant desorption from the adsorbent, allowing the adsorbent reactivation for repetitive applications. These results indicate that FeG could be a promising candidate for adsorption/sensing platforms of H₂CO.

Oxidized and Si-doped graphene: emerging adsorbents for removal of dioxane

The adsorption properties of oxidized graphene (GO) and Si-doped graphene (SiG) towards 1,4-dioxane were theoretically characterized.

Theoretical exploration of seleno and tellurophenols as promising alternatives to sulfur ligands for anchoring to gold (111) materials

Selenium and tellurium ligands are proposed as improved alternatives to sulfur ligands as a new strategy to anchor functional molecules to gold based materials.

Catalytic aspects of metallophthalocyanines adsorbed on gold-electrode. Theoretical exploration of the binding nature role

We report a computational study of supramolecular complexes of metallophthalocyanines (MPcs, M = Fe, Co, Cu) on gold substrates, and the effect of the substrate on their electrocatalytic properties at the DFT and DFT-D3 levels.

Mechanistic insights into the dehalogenation reaction of fluoroacetate/fluoroacetic acid

Fluoroacetate is a toxic compound whose environmental accumulation may represent an important contamination problem, its elimination is therefore a challenging issue. Fluoroacetate dehalogenase catalyzes its degradation through a two step process initiated by an S(N)2 reaction in which the aspartate residue performs a nucleophilic attack on the carbon bonded to the fluorine; the second step is hydrolysis that releases the product as glycolate. In this paper, we present a study based on density functional theory calculations of the S(N)2 initiation reaction modeled through the interaction between the substrate and the propionate anion as the nucleophile. Results are analyzed within the framework of the reaction force and using the reaction electronic flux to identify and characterize the electronic activity that drives the reaction. Our results reveal that the selective protonation of the substrate catalyzes the reaction by decreasing the resistance of the structural and electronic reorganization needed to reach the transition state. Finally, the reaction energy is modulated by the degree of stabilization of the fluoride anion formed after the S(N)2 reaction. In this way, a site-induced partial protonation acts as a chemical switch in a key process that determines the output of the reaction.

Theoretical study on interactions of fluorinated organomercurials with arene and gold fragments

We report a computational study of [Hg(C₆F₅)₂]₂–{L}, [Hg₃(o-C₆F₄)₃]₂·{L} (L = naphthalene, biphenyl, fluorene) and [Hg₃(o-C₆F₄)₃]{Au₃(μ-C(OEt)NC₆H₄CH₃)₃}_n (n = 1, 2) adducts at the HF, MP2, DFT and DFT-D3 levels.

Computational studies of the metal-binding site of the wild-type and the H46R mutant of the copper, zinc superoxide dismutase

Impairment of the Zn(II)-binding site of the copper, zinc superoxide dismutase (CuZnSOD) protein is involved in a number of hypotheses and explanations for the still unknown toxic gain of function mutant varieties of CuZnSOD that are associated with familial forms of amyotrophic lateral sclerosis (ALS). In this work, computational chemistry methods have been used for studying models of the metal-binding site of the ALS-linked H46R mutant of CuZnSOD and of the wild-type variety of the enzyme. By comparing the energy and electronic structure of these models, a plausible explanation for the effect of the H46R mutation on the zinc site is obtained. The computational study clarifies the role of the D124 and D125 residues for keeping the structural integrity of the Zn(II)-binding site, which was known to exist but its mechanism has not been explained. Earlier results suggest that the explanation for the impairment of the Zn(II)-site proposed in this work may be useful for understanding the mechanism of action of the ALS-linked mutations in CuZnSOD in general.

A computationally efficient and reliable bond order measure

Bond order indexes are useful measures that connect quantum mechanical results with chemical understanding. One of these measures, the natural bond order index, based on the natural resonance theory procedure and part of the natural bond orbital analysis tools, has been proved to yield reliable results for many systems. The procedure's computational requirements, nevertheless, scales so highly with the number of functions in the basis set and the delocalization of the system, that the calculation of this bond order is limited to small or medium size molecules. We present in this work a bond order index, the first order perturbation theory bond order (fopBO), which is based on and strongly connected to the natural bond orbital analysis tools. We present the methodology for the calculation of the fopBO index and a number of test calculations that shows that it is as reliable as the natural bond orbital index, with the same weak sensitivity to variations among commonly used basis sets and, as opposed to the natural bond order index, suitable for the study of large systems, such as most of those of biological interest.