Search Results (31)

We studied the boron-based composite cluster B₈Al₃⁺ doped with Al atoms. The global minimum structure of the B₈Al₃⁺ cluster is a three-layer structure, consisting of three parts: an Al₂ unit, a B₈ ring and an isolated Al atom. Charge calculations analysis shows that the cluster can be expressed as [Al]⁺[B₈]²⁻[Al₂]²⁺, has 6π/6σ double aromaticity and follows the (4n+2) Hückel rule. Born–Oppenheimer molecular dynamics (BOMD) simulation shows that the B₈Al₃⁺ cluster has dynamic fluxionality properties. Remarkably, at the single-point coupled cluster singles, doubles and triples (CCSD(T)) level, the energy barrier for intramolecular rotation is merely 0.19 kcal mol⁻¹. [B₈]²⁻ molecular wheels have magical 6π/6σ double aromaticity properties, providing a continuous cloud of delocalized electrons, which is a key factor in the dynamic fluxionality of the cluster. The B₈Al₃⁺ cluster provides a new example of dynamic structural fluxionality in molecular systems. Full article

The development of transition metal clusters is an active area of research in inorganic chemistry, as they can be used as catalysts to perform chemically or biologically relevant reactions. Computational chemistry, employing density functional theory (DFT), plays a key role in rationalizing the electronic structure and properties of transition metal clusters. This article reviews recent quantum chemical studies of Mo₃S₄M clusters (M = Fe, Co, Ni), their CO- or N₂-bound variants, and metal–hydride clusters. The ground state of the cluster systems was computed, and properties such as metal–metal bonding, orbital interactions, fluxional behavior of ligands, spectroscopy, and reaction mechanisms were rationalized and compared with available experimental results. Our research findings evidence that computational studies employing quantum chemical methods can guide experimental researchers to develop novel transition metal clusters for potential applications in catalysis. Full article

Small Li⁺Ar_n clusters are employed in this work as model systems to study microsolvation. Although first and second solvation shells are expected to be the most relevant ones for this type of atomic solvents, it is also interesting to explore larger clusters in order to identify the influence of external atoms on structural and thermodynamic properties. In this work, we perform a global geometry optimization for ${\mathrm{Li}}^{+}$${\mathrm{Ar}}_n$ clusters (with n = 41–100) and parallel tempering Monte Carlo (PTMC) simulations for some selected sizes. The results show that global minimum structures of large clusters always have 6 argon atoms in the first solvation shell while maintaining the number of 14 or 16 argon atoms in the second one. By contrast, third and fourth solvation shells vary significantly the number of argon atoms with the cluster size, and other shells can hardly be assigned due to the reduced influence of ${\mathrm{Li}}^{+}$ on the external argon atoms for large clusters. In turn, PTMC calculations show that the melting of the most external solvation shells of large microsolvation clusters occurs at $T\sim 50\mathrm{K}$, which is independent of cluster size. Structural transitions can be observed between quasi-degenerated structures at low temperatures. Moreover, the present results highlight the fluxional character of the external solvation shells of these large ${\mathrm{Li}}^{+}$${\mathrm{Ar}}_n$ clusters, which may be seen as typical “snowball” structures. Full article

The tetrafluoroborate salt of the cationic Cu(I) complex [Cu(CHpz₃)(PPh₃)]⁺, where CHpz₃ is the tridentate N-donor ligand tris(pyrazol-1-yl)methane and PPh₃ is triphenylphosphine, was synthesized through a displacement reaction on the acetonitrile complex [Cu(NCCH₃)₄][BF₄]. The compound crystallizes in the monoclinic P2₁/c space group. The single-crystal X-ray diffraction revealed that the copper(I) centre is tetracoordinated, with a disposition of the donor atoms surrounding the metal centre quite far from the ideal tetrahedral geometry, as confirmed by continuous shape measures and by the τ₄ parameter. The intermolecular interactions at the solid state were investigated through the Hirshfeld surface analysis, which highlighted the presence of several non-classical hydrogen bonds involving the tetrafluoroborate anion. The electronic structure of the crystal was modelled using plane-wave DFT methods. The computed band gap is around 2.8 eV and separates a metal-centred valence band from a ligand-centred conduction band. NMR spectroscopy indicated the fluxional behaviour of the complex in CDCl₃ solution. The geometry of the compound in the presence of chloroform as implicit solvent was simulated by means of DFT calculations, together with possible mechanisms related to the fluxionality. The reversible dissociation of one of the pyrazole rings from the Cu(I) coordination sphere resulted in an accessible process. Full article

Studies of the rotational barrier energy of the amide bond using quantum computing and nuclear magnetic resonance (NMR) are focused mainly on its use as a model of the peptide bond. The results of these studies are valuable not only in terms of the fundamental conformational properties of amide bonds, but also in the design of molecular machines, which have recently attracted interest. We investigate the fluxionality of the amide and enamide bonds of compound 3-[(E)-(dimethylamino)methylidene]-1,1-dimethylurea using advanced dynamic NMR experiments and a theoretical evaluation of the density functional theory (DFT) calculation. The dynamic NMR study shows restricted rotation around the amide group (16.4 kcal/mol) and a very high barrier around the enamine group (18.6 kcal/mol). In a structurally similar compound, (E)-3-(dimethylamino)-N,N-dimethylacrylamide (N atom is replaced by CH), the amide barrier is 12.4 kcal/mol and the enamine barrier is 11.7 kcal/mol. The DFT studies of both compounds reveal the electronic origin of this phenomenon. Theoretical calculations reveal the origin of the higher enamine barrier. The better delocalization of the lone pair of electrons on the end nitrogen atom into the antibonding orbital of the neighboring C–N double bond leads to the better stabilization of the ground state, and this leads to a greater increase in the enamine barrier. Full article

A series of phosphorus and selenium peri-substituted acenaphthene species with the phosphino group oxidized by O, S, and Se has been isolated and fully characterized, including by single-crystal X-ray diffraction. The P(V) and Se(II) systems showed fluxional behavior in solution due to the presence of two major rotamers, as evidenced with solution NMR spectroscopy. Using Variable-Temperature NMR (VT NMR) and supported by DFT (Density Functional Theory) calculations and solid-state NMR, the major rotamers in the solid and in solution were identified. All compounds showed a loss of the through-space J_PSe coupling observed in the unoxidized P(III) and Se(II) systems due to the sequestration of the lone pair of the phosphine, which has been previously identified as the major contributor to the coupling pathway. Full article

The octahydridotriborate anion plays a crucial role in the field of polyhedral boron chemistry, facilitating the synthesis of higher boranes and the preparation of diverse transition metal complexes. Among the stable forms of this anion, CsB₃H₈ (or (n-C₄H₉)₄N)[B₃H₈] have been identified. These salts serve as valuable precursors for the synthesis of metallaboranes, wherein the triborate anion acts as a ligand coordinating to the metal center. In this study, we have successfully synthesized a novel rhodatetraborane dihydride, [Rh(η²-B₃H₈)(H)₂(PPh₃)₂] (1), which represents a Rh(III) complex featuring a bidentate chelate ligand fasormed by B₃H₈⁻. Extensive characterization of this rhodatetraborane complex has been performed using NMR spectroscopy in solution and X-ray diffraction analysis in the solid state. Notably, the complex exhibits intriguing fluxional behavior, which has been investigated using NMR techniques. Moreover, we have explored the reactivity of complex 1 towards pyridine (py) and dimethylphenylphosphine (PMe₂Ph). Our findings highlight the labile nature of this four-vertex rhodatetraborane as it undergoes disassembly upon attack from the corresponding Lewis base, resulting in the formation of borane adducts, LBH₃, where L = py, PMe₂Ph. Furthermore, in these reactions, we report the characterization of new cationic hydride complexes, such as [Rh(H)₂(PPh₃)₂ (py)]⁺ (2) and [Rh(H)₂(PMe₂Ph)₄]⁺. Notably, the latter complex has been characterized as the octahydridotriborate salt [Rh(H)₂(PMe₂Ph)₄][B₃H₈] (3), which extends the scope of rhodatetraborane derivatives. Full article

Locally advanced rectal cancer (LARC) has traditionally been treated with trimodality therapy consisting of neoadjuvant radiation +/− chemotherapy, surgery, and adjuvant chemotherapy. There is currently a clinical need for biomarkers to predict treatment response and outcomes, especially during neoadjuvant therapy. Liquid biopsies in the form of circulating tumour cells (CTCs) and circulating nucleic acids in particular microRNAs (miRNA) are novel, the latter also being highly stable and clinically relevant regulators of disease. We studied a prospective cohort of 52 patients with LARC, and obtained samples at baseline, during treatment, and post-treatment. We enumerated CTCs during chemoradiation at these three time-points, using the Isoflux^TM (Fluxion Biosciences Inc., Alameda, CA, USA) CTC Isolation and detection platform. We then subjected the isolated CTCs to miRNA expression analyses, using a panel of 106 miRNA candidates. We identified CTCs in 73% of patients at baseline; numbers fell and miRNA expression profiles also changed during treatment. Between baseline and during treatment (week 3) time-points, three microRNAs (hsa-miR-95, hsa-miR-10a, and hsa-miR-16-1*) were highly differentially expressed. Importantly, hsa-miR-19b-3p and hsa-miR-483-5p were found to correlate with good response to treatment. The latter (hsa-miR-483-5p) was also found to be differentially expressed between good responders and poor responders. These miRNAs represent potential predictive biomarkers, and thus a potential miRNA-based treatment strategy. In this study, we demonstrate that CTCs are present and can be isolated in the non-metastatic early-stage cancer setting, and their associated miRNA profiles can potentially be utilized to predict treatment response. Full article

Doping alkali metals into boron clusters can effectively compensate for the intrinsic electron deficiency of boron and lead to interesting boron-based binary clusters, owing to the small electronegativity of the former elements. We report on the computational design of a three-layered sandwich cluster, Na₅B₇, on the basis of global-minimum (GM) searches and electronic structure calculations. It is shown that the Na₅B₇ cluster can be described as a charge-transfer complex: [Na₄]²⁺[B₇]³⁻[Na]⁺. In this sandwich cluster, the [B₇]³⁻ core assumes a molecular wheel in shape and features in-plane hexagonal coordination. The magic 6π/6σ double aromaticity underlies the stability of the [B₇]³⁻ molecular wheel, following the (4n + 2) Hückel rule. The tetrahedral Na₄ ligand in the sandwich has a [Na₄]²⁺ charge-state, which is the simplest example of three-dimensional aromaticity, spherical aromaticity, or superatom. Its 2σ electron counting renders σ aromaticity for the ligand. Overall, the sandwich cluster has three-fold 6π/6σ/2σ aromaticity. Molecular dynamics simulation shows that the sandwich cluster is dynamically fluxional even at room temperature, with a negligible energy barrier for intramolecular twisting between the B₇ wheel and the Na₄ ligand. The Na₅B₇ cluster offers a new example for dynamic structural fluxionality in molecular systems. Full article

Multiple fluxional processes of 6-monomethylcyclohexenylmanganese tricarbonyl [(6-MeC₆H₈)Mn(CO)₃, complex 1] and 5-monomethylcyclohexenylmanganese tricarbonyl [(5-MeC₆H₈)Mn(CO)₃, complex 2] have been explored using density functional theory (DFT) computations. The contributions of four agostomers—1, 2, 3, and 4—to the (MeC₆H₈)Mn(CO)₃ exchange processes were revealed. The computational results demonstrated that the 1, 2-agostic isomerization only occurred via the η⁴-diene hydride transition state (TS-1-2, 14.0 kcal/mol), which is consistent with the experimentally proposed high-energy exchange process (16.0 kcal/mol). Excellent agreement is observed (R² = 0.9862) when comparing the computed and experimentally observed variable temperature ¹H NMR chemical shifts. With these results, important insights into the role of agostic interaction in the homogeneous catalysis process could be made, especially with regard to transition metal catalyzed C-H activation. Full article

Catalytic systems based on sub-nanoclusters deposited over different supports are promising for very relevant chemical transformations such as many electrocatalytic processes as the ORR. These systems have been demonstrated to be very fluxional, as they are able to change shape and interconvert between each other either alone or in the presence of adsorbates. In addition, an accurate representation of their catalytic activity requires the consideration of ensemble effects and not a single structure alone. In this sense, a reliable theoretical methodology should assure an accurate and extensive exploration of the potential energy surface to include all the relevant structures and with correct relative energies. In this context, we applied DFT in conjunction with global optimization techniques to obtain and analyze the characteristics of the many local minima of Pt₆ sub-nanoclusters over a carbon-based support (graphene)—a system with electrocatalytic relevance. We also analyzed the magnetism and the charge transfer between the clusters and the support and paid special attention to the dependence of dispersion effects on the ensemble characteristics. We found that the ensembles computed with and without dispersion corrections are qualitatively similar, especially for the lowest-in-energy clusters, which we attribute to a (mainly) covalent binding to the surface. However, there are some significant variations in the relative stability of some clusters, which would significantly affect their population in the ensemble composition. Full article

A density functional theory study is performed to determine the stability and bonding in the neon dimer inside the B₃₀N₃₀ fullerene cage, the fluxional B₄₀ cage, and within non-fluxional cages such as B₁₂N₁₂ and C₆₀. The nature of bonding in the Ne₂ encapsulated B₄₀ is compared with the that in other cages in an attempt to determine whether any possible alterations are brought about by the dynamical nature of the host cage apart from the associated confinement effects. The bonding analysis includes the natural bond order (NBO), Bader’s Atoms-in-Molecules electron density analysis (AIM), and energy decomposition analysis (EDA), revealing the non-covalent nature of the interactions between the Ne atoms and that between the Ne and the cage atoms. The formation of all the Ne₂@cage systems is thermochemically unfavourable, the least being that for the B₃₀N₃₀ cage, which can easily be made favourable at lower temperatures. The Ne-Ne distance is lowest in the smallest cage and increases as the cage size increase due to steric relaxation experienced by the dimer. The dynamical picture of the systems is investigated by performing ab initio molecular dynamics simulations using the atom-centred density matrix propagation (ADMP) technique, which shows the nature of the movement of the dimer inside the cages, and by the fact that since it moves as a single entity, a weak bonding force holds them together, apart from their proven kinetic stability. Full article

We systematically explore the potential energy surface of the B₃Al₄⁺ combination of atoms. The putative global minimum corresponds to a structure formed by an Al₄ square facing a B₃ triangle. Interestingly, the dynamical behavior can be described as a Reuleaux molecular triangle since it involves the rotation of the B₃ triangle at the top of the Al₄ square. The molecular dynamics simulations, corroborating with the very small rotational barriers of the B₃ triangle, show its nearly free rotation on the Al₄ ring, confirming the fluxional character of the cluster. Moreover, while the chemical bonding analysis suggests that the multicenter interaction between the two fragments determines its fluxionality, the magnetic response analysis reveals this cluster as a true and fully three-dimensional aromatic system. Full article

The search of a putative physiological electron acceptor for thiocyanate dehydrogenase (TcDH) newly discovered in the thiocyanate-oxidizing bacteria Thioalkalivibrio paradoxus revealed an unusually large, single-heme cytochrome c (CytC552), which was co-purified with TcDH from the periplasm. Recombinant CytC552, produced in Escherichia coli as a mature protein without a signal peptide, has spectral properties similar to the endogenous protein and serves as an in vitro electron acceptor in the TcDH-catalyzed reaction. The CytC552 structure determined by NMR spectroscopy reveals significant differences compared to those of the typical class I bacterial cytochromes c: a high solvent accessible surface area for the heme group and so-called “intrinsically disordered” nature of the histidine-rich N- and C-terminal regions. Comparison of the signal splitting in the heteronuclear NMR spectra of oxidized, reduced, and TcDH-bound CytC552 reveals the heme axial methionine fluxionality. The TcDH binding site on the CytC552 surface was mapped using NMR chemical shift perturbations. Putative TcDH-CytC552 complexes were reconstructed by the information-driven docking approach and used for the analysis of effective electron transfer pathways. The best pathway includes the electron hopping through His528 and Tyr164 of TcDH, and His83 of CytC552 to the heme group in accordance with pH-dependence of TcDH activity with CytC552. Full article

The adsorption of helium or hydrogen on cationic triphenylene (TPL, C₁₈H₁₂), a planar polycyclic aromatic hydrocarbon (PAH) molecule, and of helium on cationic 1,3,5-triphenylbenzene (TPB, C₂₄H₁₈), a propeller-shaped PAH, is studied by a combination of high-resolution mass spectrometry and classical and quantum computational methods. Mass spectra indicate that He_nTPL⁺ complexes are particularly stable if n = 2 or 6, in good agreement with the quantum calculations that show that for these sizes, the helium atoms are strongly localized on either side of the central carbon ring for n = 2 and on either side of the three outer rings for n = 6. Theory suggests that He₁₄TPL⁺ is also particularly stable, with the helium atoms strongly localized on either side of the central and outer rings plus the vacancies between the outer rings. For He_nTPB⁺, the mass spectra hint at enhanced stability for n = 2, 4 and, possibly, 11. Here, the agreement with theory is less satisfactory, probably because TPB⁺ is a highly fluxional molecule. In the global energy minimum, the phenyl groups are rotated in the same direction, but when the zero-point harmonic correction is included, a structure with one phenyl group being rotated opposite to the other two becomes lower in energy. The energy barrier between the two isomers is very small, and TPB⁺ could be in a mixture of symmetric and antisymmetric states, or possibly even vibrationally delocalized. Full article