On the variation of cluster core characteristics by an endohedral atom. Shape variation in 8-ce [EAu4(PPh3)4]2+ (E = N, P, As, Sb) clusters.

Atomically precise gold superatoms have attracted interest owing to their suitable use as building blocks for cluster-assembled materials, favoring ordered structures with advanced properties. In this sense, expanding their versatility is a relevant issue for controlling their properties and retaining a specific nuclearity. Interestingly, the reported structure for isoelectronic [Au4N(PPh3)4]+ and [Au4Sb(PPh3)4]+ clusters denotes two contrasting shapes featuring a tetrahedral and square pyramidal structure, respectively. Herein, we further explore the [Au4E(PPh3)4]+ (E = N, P, As, Sb) series in order to evaluate energetic and structural factors determining the overall shape. Our results show a favorable [Au4(PPh3)4]4+/E3- interaction energy, predicting particular patterns in their UV-vis spectrum. Thus, the use of dopant atoms is enabled to vary the core shape and, in turn, to modify the cluster properties, which serve as a structural control, in addition to ligand-based and size approaches.

Biological Activity of Complexes Involving Nitro-Containing Ligands and Crystallographic-Theoretical Description of 3,5-DNB Complexes.

Drug resistance in infectious diseases developed by bacteria and fungi is an important issue since it is necessary to further develop novel compounds with biological activity that counteract this problem. In addition, new pharmaceutical compounds with lower secondary effects to treat cancer are needed. Coordination compounds appear to be accessible and promising alternatives aiming to overcome these problems. In this review, we summarize the recent literature on coordination compounds based on nitrobenzoic acid (NBA) as a ligand, its derivatives, and other nitro-containing ligands, which are widely employed owing to their versatility. Additionally, an analysis of crystallographic data is presented, unraveling the coordination preferences and the most effective crystallization methods to grow crystals of good quality. This underscores the significance of elucidating crystalline structures and utilizing computational calculations to deepen the comprehension of the electronic properties of coordination complexes.

Antifungal activity of Co(II) and Cu(II) complexes containing 1,3-bis(benzotriazol-1-yl)-propan-2-ol on the growth and virulence traits of fluconazole-resistant Candida species: synthesis, DFT calculations, and biological activity.

Relevant virulence traits in Candida spp. are associated with dimorphic change and biofilm formation, which became an important target to reduce antifungal resistance. In this work, Co(II) complexes containing a benzotriazole derivative ligand showed a promising capacity of reducing these virulence traits. These complexes exhibited higher antifungal activities than the free ligands against all the Candida albicans and non-albicans strains tested, where compounds 2 and 4 showed minimum inhibitory concentration values between 15.62 and 125 µg mL-1. Moreover, four complexes (2-5) of Co(II) and Cu(II) with benzotriazole ligand were synthesized. These compounds were obtained as air-stable solids and characterized by melting point, thermogravimetric analysis, infrared, Raman and ultraviolet/visible spectroscopy. The analysis of the characterization data allowed us to identify that all the complexes had 1:1 (M:L) stoichiometries. Additionally, Density Functional Theory calculations were carried out for 2 and 3 to propose a probable geometry of both compounds. The conformer Da of 2 was the most stable conformer according to the Energy Decomposition Analysis; while the conformers of 3 have a fluxional behavior in this analysis that did not allow us to determine the most probable conformer. These results provide an important platform for the design of new compounds with antifungal activities and the capacity to attack other target of relevance to reduce antimicrobial resistance.

Cl@Si20X20 cages: evaluation of encapsulation nature, structural rigidity, and 29Si-NMR patterns using relativistic DFT calculations.

The experimental characterization of Cl@Si20 endohedral clusters, featuring different ligands such as [Cl@Si20H20]- (1) [Cl@Si20H12Cl8]- (2), and [Cl@Si20Cl20]- (3), provides insight into the variable encapsulation environment for chloride anions. The favorable formation of such species enables the evaluation of the encapsulation nature and the role of the inner anion in the rigidity of the overall cluster. Our results show a sizable interaction which increases as -66.7, -100.8, and -130.3 kcal mol-1 from 1 to 3, respectively, featuring electrostatic character. The orbital interaction involves 3p-Cl → Si20X20 and 3s-Cl → Si20X20 charge transfer channels and a slight contribution from London dispersion-type interactions. These results show that the inner bonding environment can be modified by the choice of exobonded ligands. Moreover, 29Si-NMR parameters are depicted in terms of the chemical shift anisotropy (CSA), leading to a strong variation of the three principal tensor components (δ11, δ22, δ33), unraveling the origin of the experimental 29Si-NMR chemical shift (δiso) differences along the given series. Thus, the Si20 cage is a useful template to further evaluate different environments for encapsulating atomic species.

From 8- to 18-Cluster Electrons Superatoms: Evaluation via DFT Calculations of the Ligand-Protected W@Au12(dppm)6 Cluster Displaying Distinctive Electronic and Optical Properties.

The iconic W@Au12 icosahedral bare cluster reaches the favorable closed-shell superatomic electron configuration 1S2 1P6 1D10, making it an 18-cluster electron (18-ce) superatom. Here, we pursue the evaluation of a ligand-protected counterpart based on the construction of a fully phosphine-protected [W@Au12(dppm)6] cluster strongly related to the characterized [Au13(dppm)6]5+ homometallic counterpart. The later cluster has the same total number of valence electrons as the former but is considered an 8-ce superatom with 1S2 1P6 configuration. The fundamental differences between 8- and 18-ce species are investigated. The character of the frontier orbitals varies from 1P/1D in the 8-ce case to a 1D/ligand for 18-ce species, enabling an efficient charge transfer toward the ligands upon irradiation, being interesting for electron injection in optoelectronic devices and black absorbers applications. Excited-state properties are also revisited, showing different geometrical and electronic structure variations between 8- and 18-ce species. Moreover, the continuum between the 8- and 18-ce limits has been explored by varying the nature of the encapsulated dopant between group 6 and group 11. The transition between the 8- and 18-ce counts can be formally situated between Pt (8-ce) and Ir (18-ce). Thus, 18-ce derivatives obtained as doped counterparts of homometallic gold clusters can introduce useful alternatives to achieve different properties in related structural motifs, which can be further explored owing to their extension of the well-established versatility of current gold nanoclusters.

Switch from local to global aromatic character in Möbius carbon nanobelts upon dioxidation. Evaluation of magnetic behavior in neutral and charged species.

Here we show that recent Möbius carbon nanobelts (MCNBs) can be switched from a local to a global aromatic behavior upon dioxidation. Hence, large aromatic structures can be achieved by the choice of the charge states, giving rise to shielding cone characteristics extended within the overall structure at the nanoscale regime, pushing the limit of aromatic circuits to 198 π-electrons.

Enabling dual aromaticity in fused nanobelts: evaluation of the magnetic behavior of fused [10]CPP units.

Cyclo-para-phenylene (CPP) nanobelt structures with curved π-surfaces are of relevance in the development of desirable building units for materials science. Dimeric [10]CPP motifs have been reported ([10]SCPP), extending the individual features to fused nanobelts sharing structural components. Our results indicate a local-aromatic behavior of the neutral dimeric motif, leading to a switched-on character upon di- and tetra-oxidation resulting in the formation of two long-ranged shielding regions at the center of each [10]CPP fused unit. This evaluation shows the ability to enable two global aromatic circuits to compromise the overall carbon backbone, instead of being located exclusively at each phenylene ring. Thus, fused nanobelt structures are able to sustain a dual global aromatic behavior, which can be switched-on via oxidation, leading to more complex aromatic species at the nanoscale.

Machine learning approach to discovery of small molecules with potential inhibitory action against vasoactive metalloproteases.

With the advancement of combinatorial chemistry and big data, drug repositioning has boomed. In this sense, machine learning and artificial intelligence techniques offer a priori information to identify the most promising candidates. In this study, we combine QSAR and docking methodologies to identify compounds with potential inhibitory activity of vasoactive metalloproteases for the treatment of cardiovascular diseases. To develop this study, we used a database of 191 thermolysin inhibitor compounds, which is the largest as far as we know. First, we use Dragon's molecular descriptors (0-3D) to develop classification models using Bayesian networks (Naive Bayes) and artificial neural networks (Multilayer Perceptron). The obtained models are used for virtual screening of small molecules in the international DrugBank database. Second, docking experiments are carried out for all three enzymes using the Autodock Vina program, to identify possible interactions with the active site of human metalloproteases. As a result, high-performance artificial intelligence QSAR models are obtained for training and prediction sets. These allowed the identification of 18 compounds with potential inhibitory activity and an adequate oral bioavailability profile, which were evaluated using docking. Four of them showed high binding energies for the three enzymes, and we propose them as potential dual ACE/NEP inhibitors for the control of blood pressure. In summary, the in silico strategies used here constitute an important tool for the early identification of new antihypertensive drug candidates, with substantial savings in time and money.

Reply to 'Comment on "Structural characterization, reactivity, and vibrational properties of silver clusters: A new global minimum for Ag16"' by P. V. Nhat, N. T. Si, L. V. Duong and M. T. Nguyen, Phys. Chem. Chem. Phys., 2021, 23, DOI: D1CP00646K.

Recently, P. V. Nhat et al., have discussed and commented on our article (DOI: 10.1039/D0CP04018E) for the case of the most stable structure of Ag15. They have found a new most stable structure (labeled as 15-1) in comparison to the putative global minimum reported by us, which is a four layered 1-4-6-4 stacking structure with a C2v point group (15-2). In this reply, we have performed a larger structure search which allowed us to confirm the results of Nhat et al. The results show the existence of multiple isoenergetic isomers with similar structure motifs for the Ag15 system, increasing the problem complexity to locate the global minimum. The results in regard to the structure and electronic properties of the new lowest energy structure are discussed.

Theoretical Evaluation of Novel Thermolysin Inhibitors from Bacillus thermoproteolyticus. Possible Antibacterial Agents.

The search for new antibacterial agents that could decrease bacterial resistance is a subject in continuous development. Gram-negative and Gram-positive bacteria possess a group of metalloproteins belonging to the MEROPS peptidase (M4) family, which is the main virulence factor of these bacteria. In this work, we used the previous results of a computational biochemistry protocol of a series of ligands designed in silico using thermolysin as a model for the search of antihypertensive agents. Here, thermolysin from Bacillus thermoproteolyticus, a metalloprotein of the M4 family, was used to determine the most promising candidate as an antibacterial agent. Our results from docking, molecular dynamics simulation, molecular mechanics Poisson-Boltzmann (MM-PBSA) method, ligand efficiency, and ADME-Tox properties (Absorption, Distribution, Metabolism, Excretion, and Toxicity) indicate that the designed ligands were adequately oriented in the thermolysin active site. The Lig783, Lig2177, and Lig3444 compounds showed the best dynamic behavior; however, from the ADME-Tox calculated properties, Lig783 was selected as the unique antibacterial agent candidate amongst the designed ligands.

Heterobimetallic Catalysts for the Thermal Decomposition of Ammonium Perchlorate: Efficient Burning Rate Catalysts for Solid Rocket Motors and Missiles.

We show the synthesis and characterization of four heterobimetallic compounds derived from s-indacene of general formula [{(CO)3Mn}-s-Ic-{MCp*}]q with M = Fe, Co, Ni, and Ru; q = 0, 1+. The complexes reported here were characterized by 1H and 13C NMR, elemental analysis and FT-IR. Additionally, the X-ray crystal structure of [(CO)3Mn-s-Ic-FeCp*] (1) and Mössbauer spectra are reported. The heterobimetallic compounds exhibit higher quasireversible redox potentials compared with ferrocene and catocene under the same reaction conditions. The complexes were tested as catalysts on the thermal decomposition of ammonium perchlorate examined by a differential scanning calorimetry technique to study their catalytic behavior. Compound (1) causes a decrease of ammonium perchlorate's decomposition temperature to 315 °C, consequently increasing the heat release by 138 J·g-1. Conversely, [{(CO)3Mn}-s-Ic'-{CoCp*}] (2) presents a higher heat release (2462 J·g-1), comparable to catocene.

Full recombinant flagellin B from Vibrio anguillarum (rFLA) and its recombinant D1 domain (rND1) promote a pro-inflammatory state and improve vaccination against P. salmonis in Atlantic salmon (S. salar).

Flagellin is the major component of the flagellum, and a ligand for Toll-like receptor 5. As reported, recombinant flagellin (rFLA) from Vibrio anguillarum and its D1 domain (rND1) are able to promote in vitro an upregulation of pro-inflammatory genes in gilthead seabream (Sparus aurata) and rainbow trout (Oncorhynchus mykiss) macrophages. This study evaluated the in vitro and in vivo stimulatory/adjuvant effect for rFLA and rND1 during P. salmonis vaccination in Atlantic salmon (Salmo salar). We demonstrated that rFLA and rND1 are molecules able to generate an acute upregulation of pro-inflammatory cytokines (IL-1ß, IL-8, IL-12ß), allowing the expression of genes associated with T-cell activation (IL-2, CD4, CD8ß), and differentiation (IFNγ, IL-4/13, T-bet, Eomes, GATA3), in a differential manner, tissue/time dependent way. Altogether, our results suggest that rFLA and rND1 are valid candidates to be used as an immuno-stimulant or adjuvants with existing vaccines in farmed salmon.

Structural characterization, reactivity, and vibrational properties of silver clusters: a new global minimum for Ag16.

In the present work, the lowest energy structures and electronic properties of Agn clusters up to n = 16 are investigated using a successive growth algorithm coupled with density functional theory calculations (DFT). In the literature, a number of putative global minimum structures for silver clusters have been reported by using different approaches, but a comparative study for n = 15-16 has not been undertaken so far. Here, we perform a comparative study using the PW91/cc-pVDZ-PP level to more precisely determine the optimal configuration. For Ag15, the most stable configuration is a four layered 1-4-6-4 stacking structure with C2v symmetry. For Ag16 a new most stable form is found with a 1-4-2-5-1-3 stacking structure in the singlet state, slightly more stable than the putative global minimum reported. By means of the electrostatic potential, the new putative global minimum has been found to be more reactive, and the active sites of the clusters were identified and confirmed with the interaction energy. The electronic and vibrational properties are found to be in good agreement with the available experimental data. Theoretical data on the infrared spectra of the clusters is also provided.

Evaluation of new antihypertensive drugs designed in silico using Thermolysin as a target.

The search for new therapies for the treatment of Arterial hypertension is a major concern in the scientific community. Here, we employ a computational biochemistry protocol to evaluate the performance of six compounds (Lig783, Lig1022, Lig1392, Lig2177, Lig3444 and Lig6199) to act as antihypertensive agents. This protocol consists of Docking experiments, efficiency calculations of ligands, molecular dynamics simulations, free energy, pharmacological and toxicological properties predictions (ADME-Tox) of the six ligands against Thermolysin. Our results show that the docked structures had an adequate orientation in the pocket of the Thermolysin enzymes, reproducing the X-ray crystal structure of Inhibitor-Thermolysin complexes in an acceptable way. The most promising candidates to act as antihypertensive agents among the series are Lig2177 and Lig3444. These compounds form the most stable ligand-Thermolysin complexes according to their binding free energy values obtained in the docking experiments as well as MM-GBSA decomposition analysis calculations. They present the lowest values of Ki, indicating that these ligands bind strongly to Thermolysin. Lig2177 was oriented in the pocket of Thermolysin in such a way that both OH of the dihydroxyl-amino groups to establish hydrogen bond interactions with Glu146 and Glu166. In the same way, Lig3444 interacts with Asp150, Glu143 and Tyr157. Additionally, Lig2177 and Lig3444 fulfill all the requirements established by Lipinski Veber and Pfizer 3/75 rules, indicating that these compounds could be safe compounds to be used as antihypertensive agents. We are confident that our computational biochemistry protocol can be used to evaluate and predict the behavior of a broad range of compounds designed in silicoagainst a protein target.

Interactions of 2-phenyl-benzotriazole xenobiotic compounds with human Cytochrome P450-CYP1A1 by means of docking, molecular dynamics simulations and MM-GBSA calculations.

2-phenyl-benzotriazole xenobiotic compounds (PBTA-4, PBTA-6, PBTA-7 and PBTA-8) that were previously isolated and identified in waters of the Yodo river, in Japan (Nukaya et al., 2001; Ohe et al., 2004; Watanabe et al., 2001) were characterized as powerful pro-mutagens. In order to predict the activation mechanism of these pro-mutagens, we designed a computational biochemistry protocol, which includes, docking experiments, molecular dynamics simulations and free energy decomposition calculations to obtain information about the interaction of 2-phenyl-benzotriazole molecules into the active center of cytochrome P450-CYP1A1 (CYP1A1). Molecular docking calculations using AutoDock Vina software shows that PBTAs are proportionally oriented in the pocket of CYP1A1, establishing π-π stacking attractive interactions between the triazole group and the Phe224, as well as, the hydrogen bonds of the terminal NH2 over the benzotriazole units with the Asn255 and Ser116 amino acids. Molecular dynamics simulations using NAMD package showed that these interactions are stable along 100.0 ns of trajectories. Into this context, free binding energy calculations employing the MM-GBSA approach, shows that some differences exists among the interaction of PBTAs with CYP1A1, regarding the solvation, electrostatic and van der Waals interaction energy components. These results suggest that PBTA molecules might be activated by CYP1A1. Thus, enhancing their mutagenicity when compared with the pro-mutagen parent species.

Influence of Ag(+) on the Magnetic Response of [2.2.2]Paracyclophane: NMR Properties of a Prototypical Organic Host for Cation Binding Based on DFT Calculations.

The complexation of metal cations into a host-guest situation is particularly well exemplified by [2.2.2]paracyclophane and Ag(I), which leads to a strong cation-π interaction with a specific face of the host molecule. Through this study we sought a deeper understanding of the effects the metal center has on the NMR spectroscopic properties of the prototypical organic host, generating theoretical reasons for the observed experimental results with an aim to determine the role of the cation-π interaction in a host-guest scenario. From an analysis of certain components of the induced magnetic field and the (13)C NMR shielding tensor under its own principal axis system (PAS), the local and overall magnetic behavior can be clearly described. Interestingly, the magnetic response of such a complex exhibits a large axis-dependent behavior, which leads to an overall shielding effect for the coordinating carbon atoms and a deshielding effect for the respective uncoordinated counterparts, evidence that complements previous experimental results. This proposed approach can be useful to gain further insight into the local and overall variation of NMR shifts for host-guest pairs involving both inorganic and organic hosts.

Calculated molecular properties of triangular tribenzo and perfluoro-tribenzo trimercuronin macrocycles.

Trimeric perfluoro-ortho-phenylene mercury(II) cluster is a prototypical example of a macrocyclic multidentate Lewis acid. In this study we report the electronic structure, the calculated absorption and vibrational spectra via all-electron scalar and spin-orbit relativistic DFT calculations for [Hg(o-C6H4)]3 (1), [Hg(o-C6F4)]3 (2), and the dimeric form of 2, ([Hg(o-C6F4)]3)2 (3). Due to the inclusion of the spin-orbit interaction, double point groups were used (D3h* and D3d*). The calculations suggest small paratropic ring currents at the center of 1 and being smaller for 2 due to the withdrawn properties of the perfluorated ligand. The luminescent properties of the solid state of 2 are well represented by the postulated model of dimer 3, which mimic the solid state, where the proposed mechanism involves a vibronically coupled emission process. The calculated lambda(absorption)max of 3 show an intense peak at 347 nm, which compares well with the reported band at 355 nm; also, the calculated lambda(emission)= 431 nm is close to the experimental value of 440 nm. Moreover, the calculated structural changes of the first excited state (3*) are reflected in the large value of the calculated Stoke shifts of 84 nm, which is in quite good agreement with the value of 85 nm extracted from the experimental data.