An influence of electronic structure theory method, thermodynamic and implicit solvation corrections on the organic carbonates conformational and binding energies

An impact of an electronic structure or force field method, gas-phase thermodynamic correction, and continuum solvation model on organic carbonate clusters (S)n conformational and binding energies is explored. None of the tested force field (GFN-FF, GAFF, MMFF94) and standard semiempirical methods (PM3, AM1, RM1, PM6, PM6-D3, PM6-D3H4, PM7) can reproduce reference RI-SCS-MP2 conformational energies. Tight-binding GFNn-xTB methods provide more realistic conformational energies which are accurate enough to discard the least stable conformers. The effect of thermodynamic correction is moderate and can be ignored if the gas phase conformational stability ranking is a goal. The influence of continuum solvation is stronger, especially if reinforced with the Gibbs free energy thermodynamic correction, and results in the reduced spread of conformational energies. The cluster formation binding energies strongly depend on a particular approach to vibrational thermochemistry with the difference between traditional harmonic and modified scaled rigid - harmonic oscillator approximations reaching 10 kcal mol-1.

Beyond chemical structures: lessons and guiding principles for the next generation of molecular databases

Databases of molecules and materials are indispensable for advancing chemical research, especially when enriched with electronic structure information from quantum chemistry methods like density functional theory. In this perspective, we review and analyze the current landscape of materials and molecular databases containing quantum chemical data. Our analysis reveals that the materials community has significantly benefited from data platforms such as the Materials Project, which seamlessly integrate chemical structures, electronic structure data, and open-source software. Conversely, quantum chemical data for molecular systems remains largely fragmented across individual datasets, lacking the comprehensive framework of a unified database. We distilled insights from these existing data resources into seven guiding principles termed QUANTUM, which build upon the foundational FAIR principles of data sharing (Findable, Accessible, Interoperable, and Reusable). These principles are aimed at advancing the development of molecular databases into robust, integrated data platforms. We conclude with an outlook on both short- and long-term objectives, guided by these QUANTUM principles, to foster future advancements in molecular quantum databases and enhance their utility for the research community.

Atomically precise rhodium-indium carbonyl nanoclusters: synthesis, characterization, crystal structure and electron-sponge features

In this paper we present the investigation of the reactivity of [Rh7(CO)16]3- with InCl3, with the aim of expanding the more general study that allowed us to obtain, among other species, the icosahedral [Rh12E(CO)27]n- (n = 4 when E = Ge or Sn; n = 3 when E = Sb or Bi) family of clusters. Indeed, the study resulted in the isolation and characterization of the analogous In-centred icosahedral [Rh12In(CO)28]3- nanocluster (1), which is isoelectronic and isostructural with the [Rh12E(CO)27]n- congeners. During the course of the reaction two more new species, namely the octahedral [Rh6(CO)15InCl3]2- (2) and the dimeric [{Rh6(CO)15InCl2}2]2- (3) have also been identified. The reaction between [Rh7(CO)16]3- and InCl3 proved to be poorly selective; nevertheless, by fine tuning some reaction parameters it was possible to drive the reaction more towards one product or the other. Alternatively, [Rh6(CO)15InCl3]2- can be more selectively prepared by reacting either [Rh5(CO)15]- or, less efficiently, [Rh6(CO)15]2- with InCl3. As for the dimeric [{Rh6(CO)15InCl2}2]2- species, this was only isolated by carrying out the reaction with [Rh7(CO)16]3- under inert atmosphere, as opposed to under CO. All clusters were characterized by IR spectroscopy and ESI-MS, and their molecular structures were fully established by single-crystal X-ray diffraction studies. The [Rh12In(CO)28]3- species was also analysed by EDS via SEM, and further investigated through in situ infrared spectroelectrochemistry and CV experiments to check its multivalence nature. Indeed, [Rh12In(CO)28]3- can reversibly undergo two monoelectronic oxidation and one bi-electronic reduction processes, behaving like an electron sponge and, thus, giving rise to the further [Rh12In(CO)28]n- derivatives (n = 1, 2 and 5). These results parallel the findings for the [Rh12E(CO)27]n- series. The geometry variations of the metal framework associated with the changes in the cluster negative charge were investigated by means of DFT calculations.

N-Indolyl diiron vinyliminium complexes exhibit antiproliferative effects in cancer cells associated with disruption of mitochondrial homeostasis, ROS scavenging, and antioxidant activity

The indole scaffold has been established as a key organic moiety for developing new drugs; on the other hand, a range of diiron bis-cyclopentadienyl complexes have recently emerged for their promising anticancer potential. Here, we report the synthesis of novel diiron complexes with an indole-functionalized vinyliminium ligand (2-5) and an indole-lacking analogue for comparative purposes (6), which were characterized by analytical and spectroscopic techniques. Complexes 2-6 are substantially stable in DMSO‑d6 and DMEM-d solutions at 37 °C (8% average degradation after 48 h) and display a balanced hydrophilic/lipophilic behaviour (LogPow values in the range -0.32 to 0.47), associated with appreciable water solubility. The complexes display selective antiproliferative potency towards several cancer cells in monolayer cultures, mainly in the low micromolar range, with reduced toxicity towards noncancerous epithelial cells. Thus, the cytotoxicity of the complexes is comparable to or better than clinically used metallopharmaceutical cisplatin. Comparing the antiproliferative activity obtained for complexes containing different ligands, we confirmed the importance of the indolyl group in the mechanism of antiproliferative activity of these complexes. Cell-based mechanistic studies suggest that the investigated diiron vinyliminium complexes (DVCs) show cytostatic rather than cytotoxic effects and subsequently induce a population of cells to undergo apoptosis. Furthermore, the molecular mechanism of action involves interactions with mitochondrial DNA and proteins, the reactive oxygen species (ROS)-scavenging properties and antioxidant activity of these complexes in cancer cells. This study highlights the importance of DVCs to their cancer cell activity and reinforces their prospective therapeutic potential as anticancer agents.

Highly Reduced Ruthenium Carbide Carbonyl Clusters: Synthesis, Molecular Structure, Reactivity, Electrochemistry, and Computational Investigation of [Ru6C(CO)15]4

The reaction of [Ru6C(CO)16]2- (1) with NaOH in DMSO resulted in the formation of a highly reduced [Ru6C(CO)15]4- (2), which was readily protonated by acids, such as HBF4·Et2O, to [HRu6C(CO)15]3- (3). Oxidation of 2 with [Cp2Fe][PF6] or [C7H7][BF4] in CH3CN resulted in [Ru6C(CO)15(CH3CN)]2- (5), which was quantitatively converted into 1 after exposure to CO atmosphere. The reaction of 2 with a mild methylating agent such as CH3,I afforded the purported [Ru6C(CO)14(COCH3)]3- (6). By employing a stronger reagent, that is, CF3SO3CH3, a mixture of [HRu6C(CO)16]- (4), [H3Ru6C(CO)15]- (7), and [Ru6C(CO)15(CH3CNCH3)]- (8) was obtained. The molecular structures of 2-5, 7, and 8 were determined by single-crystal X-ray diffraction as their [NEt4]4[2]·CH3CN, [NEt4]3[3], [NEt4][4], [NEt4]2[5], [NEt4][7], and [NEt4][8]·solv salts. The carbyne-carbide cluster 6 was partially characterized by IR spectroscopy and ESI-MS, and its structure was computationally predicted using DFT methods. The redox behavior of 2 and 3 was investigated by electrochemical and IR spectroelectrochemical methods. Computational studies were performed in order to unravel structural and thermodynamic aspects of these octahedral Ru-carbide carbonyl clusters displaying miscellaneous ligands and charges in comparison with related iron derivatives.

Triazine Chalcogenones from Thiocyanate or Selenocyanate Addition to Tetrazine Ligands in Ruthenium Arene Complexes

The chemistry of 1,2,4,5-tetrazines has attracted considerable interest both from a synthetic and applicative standpoint. Recently, regioselective reactions with alkynes and alkenes have been reported to be favored once the tetrazine ring is coordinated to Re(I), Ru(II), and Ir(III) centers. Aiming to further explore the effects of metal coordination, herein, we unveil the unexplored reactivity of tetrazines with chalcogenocyanate anions. Thus, ruthenium(II) tetrazine complexes, [RuCl{κ²N-3-(2-pyridyl)-6-R-1,2,4,5-tetrazine}(η⁶-arene)]⁺ (arene = p-cymene, R = H, [1a]⁺, R = Me, [1b]⁺, R = 2-pyridyl, [1c]⁺; arene = C₆Me₆, R = H, [1d]⁺, R = Me, [1e]⁺; PF₆^- salts), reacted quantitatively and in mild conditions with M(ECN) salts (M = Na, K, Bu₄N; E = O, S, Se). The addition of thiocyanate or selenocyanate to the tetrazine ligand is regioselective and afforded, via N₂ release, 1,2,4-triazine-5-chalcogenone heterocycles, the one with selenium being unprecedented. The novel ruthenium complexes [RuCl{κ²N-(2-pyridyl)}{triazine chalcogenone}(η⁶-arene)] 2a-e (sulfur), 3b, 3d, and 3e (selenium) were characterized by analytical (CHNS analyses, conductivity), spectroscopic (IR, multinuclear and two-dimensional (2D) NMR), and spectrometric (electrospray ionization mass spectrometry (ESI-MS)) techniques. According to density functional theory (DFT) calculations, the nucleophilic attack of SCN^- on the tetrazine ring is kinetically driven. Compound 2b is selectively and reversibly mono-protonated on the triazine ring by HCl or other strong acids, affording a single tautomer. When reactions of chalcogenocyanates were performed on the 2,2'-bipyridine (bpy) complex [RuCl(bpy)(η⁶-p-cymene)]⁺, the chloride substitution products [Ru(ECN)(bpy)(η⁶-p-cymene)]⁺ (E = O, [4]⁺; E = S, [5]⁺; E = Se, [6]⁺) were obtained in 82-90% yields (PF₆^- salts). Combined spectroscopic data (IR, ¹H/¹³C/⁷⁷Se NMR) was revealed to be a useful tool to study the linkage isomerism of the chalcogenocyanate ligand in [4-6]⁺.

Conformational energies of microsolvated Na+ clusters with protic and aprotic solvents from GFNn-xTB methods

Performance of contemporary tight-binding semiempirical GFNn-xTB methods for the conformational energies of singly charged sodium clusters Na⁺ (S)_n (n = 4-8) with 3 protic and 8 aprotic solvents is examined against the reference RI-MP2/CBS method. The median Pearson correlation coefficients of ρ = 0.84 (GFN2-xTB) and ρ = 0.82 (GFN1-xTB) do not give the clear preference to any tested approach. GFN1-xTB method demonstrates more stable performance than its GFN2-xTB successor with the average mean absolute errors (MAEs)/mean signed errors (MSEs) of 1.2/0.2 and 2.3/1.6 kcal mol^-1 , respectively. Conformational energies produced by the computationally efficient DFT functional PBE and double-ζ basis set complemented with -D3(BJ) dispersion correction are suitable for the preliminary sampling (median ρ = 0.93), but should be used with a caution for the calculations of the average ensemble properties (MAE/MSE = 1.7/1.1 kcal mol^-1 ). Higher-ranking PBE0-D3(BJ) and ωB97M-V with triple-ζ basis sets yield significantly lower MAEs/MSEs of 0.55/0.20 and 0.51/0.23 kcal mol^-1 , respectively.