Na6MCl8 rock-salt compounds with M = Mg, Ca, Ba, Zn, Sr as components for solid-state sodium ion batteries.

We investigate a new series of rock-salt type structures, Na6MCl8 with M = Mg, Ca, Ba, Zn and Sr using advanced atomistic simulations. Calculated results show a direct relationship between the size of the M2+ cation and lattice parameters as well as the defect formation energy variation. The NaCl Schottky defect type is highly favourable, and the Na6BaCl8 structure possesses the lowest values of defect formation energies. These structures are predicted to be mechanically stable and ductile, implying their compatibility with possible use as electrodes/electrolytes. The Na6MCl8 structures exhibit semiconductor characteristics with an energy gap ranging between 4.1-4.6 eV, which differs from the previous value of Na6MgCl8. A 3D migration pathway is identified in each rock-salt structure. Despite the small variation of the Na diffusivity and conductivity at 250 K within the structures considered, the Na6BaCl8 is characterized by the highest conductivity at 250 K, while the Na6MgCl8 structure has the highest conductivity and diffusivity values. The outstanding properties predicted for a Na ion battery suggest future development of synthetic strategies for their actual preparation.

A theoretical study of the oxidation of benzene by manganese oxide clusters: formation of quinone intermediates.

Manganese oxides (MnxOy) have been widely applied in various chemical industrial processes owing to their long lifetime, low cost and high abundance. They have been used as co-reactants for the elimination of volatile organic compounds (VOCs); however, their oxidation mechanism is not clearly established. In this theoretical study, interaction capacities between benzene (C6H6) and MnxOy clusters, which were modeled with MnO2 and Mn2O3 molecules, were investigated by quantum chemical computations using density functional theory (DFT) with the PBE-D3 functional. The interaction capacity between C6H6 and MnxOy was evaluated, and the probing of the initial stage of the C6H6 oxidation at a molecular level offers an in-depth oxidation reaction path. Interaction energies computed in several spin states, along with the analysis of the electron distribution using the quantum theory of atoms in molecules, natural bond orbital and Wiberg bond index techniques as well as local softness values and MO energies of fragments, point out that the interaction between C6H6 and Mn2O3 is stronger than that with MnO2, amounting to -43 and -35 kcal mol-1, respectively, and the metal atom is identified as the primary active site. During the oxide cluster-assisted oxidation, benzene firstly undergoes an oxidation reaction by active oxygen to generate intermediates such as hydroquinone and benzoquinone. The pathway involving p-benzoquinone as the product (noted as PR1) is the most energetically favored one through a transition structure lying at 19 kcal mol-1, below the energy reference of the reactants, leading to an energy barrier significantly lower than that of 36 kcal mol-1 found for the gas phase oxidation reaction with molecular oxygen without the assistance of the oxide clusters. Potential energy profiles illustrating the reaction paths and molecular mechanisms were described in detail.

Design and synthesis of novel ß-carboline-bisindole hybrids as potential anticancer agents.

We are reporting a short and convenient pathway for the synthesis of novel ß-carboline-bisindole hybrid compounds from relatively cheap and commercially available chemicals such as tryptamine, dialdehydes and indoles. These newly designed compounds can also be prepared in high yields with the tolerance of many functional groups under mild conditions. Notably, these ß-carboline-bisindole hybrid compounds exhibited some promising applications as anticancer agents against the three common cancer cell lines MCF-7 (breast cancer), SK-LU-1 (lung cancer), and HepG2 (liver cancer). The two best compounds 5b and 5g inhibited the aforementioned cell lines with the same range of the reference Ellipticine at less than 2 µM. A molecular docking study to gain more information about the interactions between the synthesized molecules and the kinase domain of the EGFR was performed. Therefore, this finding can have significant impacts on the development of future research in medicinal chemistry and drug discovery.

A theoretical screening of phytochemical constituents from Millettia brandisiana as inhibitors against acetylcholinesterase.

Alzheimer's disease is one of the causes associated with the early stages of dementia. Nowadays, the main treatment available is to inhibit the actions of the acetylcholinesterase (AChE) enzyme, which has been identified as responsible for the disease. In this study, computational methods were used to examine the structure and therapeutic ability of chemical compounds extracted from Millettia brandisiana natural products against AChE. This plant is commonly known as a traditional medicine in Vietnam and Thailand for the treatment of several diseases. Furthermore, machine learning helped us narrow down the choice of 85 substances for further studies by molecular docking and molecular dynamics simulations to gain deeper insights into the interactions between inhibitors and disease proteins. Of the five top-choice substances, γ-dimethylallyloxy-5,7,2,5-tetramethoxyisoflavone emerges as a promising substance due to its large free binding energy to AChE and the high thermodynamic stability of the resulting complex.

Imidazole[1,5-a]pyridine derivatives as EGFR tyrosine kinase inhibitors unraveled by umbrella sampling and steered molecular dynamics simulations.

Although the use of the tyrosine kinase inhibitors (TKIs) has been proved that it can save live in a cancer treatment, the currently used drugs bring in many undesirable side-effects. Therefore, the search for new drugs and an evaluation of their efficiency are intensively carried out. Recently, a series of eighteen imidazole[1,5-a]pyridine derivatives were synthetized by us, and preliminary analyses pointed out their potential to be an important platform for pharmaceutical development owing to their promising actions as anticancer agents and enzyme (kinase, HIV-protease,…) inhibitors. In the present theoretical study, we further analyzed their efficiency in using a realistic scenario of computational drug design. Our protocol has been developed to not only observe the atomistic interaction between the EGFR protein and our 18 novel compounds using both umbrella sampling and steered molecular dynamics simulations, but also determine their absolute binding free energies. Calculated properties of the 18 novel compounds were in detail compared with those of two known drugs, erlotinib and osimertinib, currently used in cancer treatment. Inspiringly the simulation results promote three imidazole[1,5-a]pyridine derivatives as promising inhibitors into a further step of clinical trials.

Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics.

To ensure that an external force can break the interaction between a protein and a ligand, the steered molecular dynamics simulation requires a harmonic restrained potential applied to the protein backbone. A usual practice is that all or a certain number of protein's heavy atoms or Cα atoms are fixed, being restrained by a small force. This present study reveals that while fixing both either all heavy atoms and or all Cα atoms is not a good approach, while fixing a too small number of few atoms sometimes cannot prevent the protein from rotating under the influence of the bulk water layer, and the pulled molecule may smack into the wall of the active site. We found that restraining the Cα atoms under certain conditions is more relevant. Thus, we would propose an alternative solution in which only the Cα atoms of the protein at a distance larger than 1.2 nm from the ligand are restrained. A more flexible, but not too flexible, protein will be expected to lead to a more natural release of the ligand.

Correction: A topological path to the formation of a quasi-planar B70 boron cluster and its dianion.

Correction for 'A topological path to the formation of a quasi-planar B70 boron cluster and its dianion' by Pinaki Saha et al., Phys. Chem. Chem. Phys., 2024, https://doi.org/10.1039/d2cp05452c.

A reinvestigation of the boron cluster B15+/0/-: a benchmark of density functionals and consideration of aromaticity models.

This study presents a thorough reinvestigation of the B15+/0/- isomers, first employing coupled-cluster theory CCSD(T) calculations to validate the performance of different DFT functionals. The B15+ cation has two planar lowest-lying isomers, while the first 3D isomer is less stable than the global minimum by ∼10 kcal mol-1. The PBE functional, within this benchmark survey, has proved to be reliable in predicting relative energies for boron isomers. Other functionals such as the TPSSh, PBE0 and HSE06 result in good energy ordering of isomers but warrant reconsideration when distinguishing between 2D and 3D forms. Caution is needed for structures having high spin contamination, as it may lead to significant errors. The anomalously lower stability of the B15- anion with respect to its neighbours, in terms of electron detachment energy, was explained through a competition between both rectangle and disk models for its geometry. This elucidates its stability with 12 electrons in rectangle model and instability with 10 electrons in disk-shaped structure, emphasizing the value of employing such geometric models. The proximity of the σ* LUMO to the π HOMO also contributes to the weakening of the B15- stability.

Binding Mechanism and Surface-Enhanced Raman Scattering of the Antimicrobial Sulfathiazole on Gold Nanoparticles.

A combined study using the surface-enhanced Raman scattering (SERS) technique and quantum chemical calculations was carried out to elucidate the adsorption behavior of sulfathiazole, an antibiotic drug, on gold nanoparticles. The tetrahedral Au20 cluster was used as a simple model to mimic a nanostructured gold surface. Computations using density functional theory with the PBE functional were performed in both the gas phase and aqueous medium using a continuum model. The drug is found to bind to the Au metals via the nitrogen of the thiazole ring. The interaction is also partially stabilized by the ring-surface π coupling rather than a sideway adsorption as previously proposed. In an aqueous solution, the drug molecule mainly exists as a deprotonated form, which gives rise to a much greater affinity toward Au nanoparticles as compared to the neutral forms. The drug adsorption further induces a significant alteration on the energy gap of the gold cluster Aun, which could result in an electrical noise. Notable SERS signals below 1600 cm-1, which result from a coupling of several vibrations including the ring breathing, C-C stretching, and N-H bending, could be employed for both qualitative and quantitative detection and assessment of sulfathiazole at trace concentrations.

Formation of pyramidal structures through mixing gold and platinum atoms: the AuxPty2+ clusters with x + y = 10.

The geometric and electronic structures of a small series of mixed gold and platinum AuxPty2+ clusters, with x + y = 10, were investigated using quantum chemical methods. A consistent tetrahedral pyramid structure emerges, displaying two patterns of structural growth by a notable critical point at y = 5. This affects the clusters' electron population, chemical bonding, and stability. For the Pt-doped Au clusters with y values from 2 to 5, the bonds enable Pt atoms to assemble into symmetric line, triangle, quadrangle, and tetragonal pyramidal Pty blocks, respectively. For the Au-doped Pt clusters, with larger values of y > 5, the structures are more relaxed and the d electrons of Pt atoms become delocalized over more centers, leading to lower symmetry structures. A certain aromaticity arising from delocalization of d electrons over the multi-center framework in the doped Pt clusters contributes to their stability, with Pt102+ at y = 10 exhibiting the highest stability. While the ground electronic state of the neutral platinum atom [Xe]. 4f145d96s1 leads to a triplet state (3D3), the total magnetic moments of AuxPty2+ are large increasing steadily from 0 to 10 µB and primarily located on Pt atoms, corresponding to the increase of the number of Pt atoms from 0 to 10 and significantly enhancing the magnetic moments. An admixture of both Au and Pt atoms thus emerges as an elegant way of keeping a small pyramidal structure but bringing in a high and controllable magnetic moment.

Electron density mapping of boron clusters via convolutional neural networks to augment structure prediction algorithms.

Determination and prediction of atomic cluster structures is an important endeavor in the field of nanoclusters and thereby in materials research. To a large extent the fundamental properties of a nanocluster are mainly governed by its molecular structure. Traditionally, structure elucidation is achieved using quantum mechanics (QM) based calculations that are usually tedious and time consuming for large nanoclusters. Various structural prediction algorithms have been reported in the literature (CALYPSO, USPEX). Although they tend to accelerate the structure exploration, they still require the aid of QM based calculations for structure evaluation. This makes the structure prediction process quite a computationally expensive affair. In this paper, we report on the creation of a convolutional neural network model, which can give relatively accurate energies for the ground state of nanoclusters from the promolecule density on the fly and could thereby be utilized for aiding structure prediction algorithms. We tested our model on dataset consisting of pure boron nanoclusters of varying sizes.

Theoretical approaches to defect mechanisms and transport properties of compounds used for electrodes and solid-state electrolytes in alkali-ion batteries.

The transition from fossil fuels to cleaner energies employing different renewable sources constitutes one of the primary worldwide challenges. The search for appropriate solutions is becoming more urgent in view of the severe consequences of climate change. As for a perspective, stationary energy storage, alkali-ion batteries and hybrid supercapacitors are, among others, considered as efficient and affordable solutions. Alkali-ion batteries have proved to be the most investigated products in the past decade including optimizations for cost, energy density and safety. In this Perspective, a computational approach and its applicability in the inverse material design are presented. This approach includes density functional theory calculations, force field-based determinations and both static and molecular dynamics simulations. As for an illustration, the main properties of a selected series of battery materials, including oxides and sulfides Li2SiO3, Li2SnO3, SrSnO3, and A2B6X13 (A = Li+, Na+, K+; B = Ti4+, Sn4+; X = O2-, S2-), and mixed halide antiperovskite A3OX (A = Li+, Na+; X = Cl-, Br-) are explored in depth using these theoretical approaches. Doping strategies, new dopant incorporation mechanism, treatment with alkali insertion/de-insertion cycle in electrodes, transport properties, as well as thermodynamic stability, are discussed. Theoretical approaches reveal that the oxygen-sulfur exchange in alkali hexatitanates and hexastannates induces remarkable improvement of the required properties for electrode and electrolyte materials. In addition, doping of Li2SiO3 with low Na-concentration enhances the room temperature Li-diffusivity by a reduction of the activation energy. The effects of transition-metal and divalent dopants on the defect chemistry and transport properties of Li2SnO3 are also disclosed. The interstitial trivalent doping mechanism is a friendly synthesis strategy to improve the large-scale diffusion in Li2SnO3. The potential of SrSnO3 as an anode in alkali-ion batteries, and the influence of a particular grain boundary in nanocrystalline antiperovskite A3OX are also revealed by using advanced atomistic simulations. The computational approaches described here provide us with a convenient tool for the determination of the properties of battery materials with high accuracy and for the prediction of characteristics of a new generation of alkali battery materials that could be used in improved technologies.

Small chromium-doped silicon clusters CrSin: structures, IR spectra, charge effect, magnetism and chirality.

A series of small chromium-doped silicon clusters CrSin with n = 3-10 in the cationic, neutral and anionic charge states were investigated using quantum chemical methods. The CrSin+ cations with n = 6-10 were produced in the gas phase and characterized by far-IR multiple photon dissociation (IR-MPD) spectroscopy. Good agreement between experimental spectra in the 200-600 cm-1 frequency range and those determined for the lowest-energy isomers by density functional theory calculations (B3P86/6-311+G(d)) provide a strong support for the geometrical assignments. An extensive structural comparison for the three different charge states shows that the structural growth mechanism inherently depends on the charge. While the structures of the cationic clusters are preferentially formed by addition of the Cr dopant to the corresponding pure silicon cluster, it favors substitution in both the neutral and anionic counterparts. The Si-Cr bonds of the studied CrSin+/0/- clusters are polar covalent. Apart from a basket-like Cr@Si9- and an endohedral Cr@Si10- cage, the Cr dopant takes an exohedral position and bears a large positive charge in the clusters. The exohedrally doped clusters also have a high spin density on Cr, manifesting the fact that the intrinsic magnetic moment of the transition metal dopant is well conserved. Three CrSin clusters have a pair of enantiomeric isomers in their ground state, namely the cationic n = 9 and the neutral and anionic n = 7. Those can be distinguished from each other by their electronic circular dichroism spectra, calculated using time-dependent density functional theory. Those enantiomers, being intrinsically chiral inorganic compounds, might be used as building blocks of optical-magnetic nanomaterials because of their high magnetic moments and ability to rotate the plane of polarization.

A topological path to the formation of a quasi-planar B70 boron cluster and its dianion.

In view of the competing assignments regarding the most stable isomer of the B70 boron cluster including the quasi-planar and bilayer structures, we reinvestigated the structural motifs of B70 using a genetic algorithm for structure search (MEGA) in conjunction with density functional theory computations using the PBE functional. The quasi-planar structure was also constructed using the topological leapfrog algorithm. The latter search aimed to give us unique insight into its formation and the growth pattern of boron clusters. Also, the di-anionic state of B70 was explored. Our extensive search suggested a competition between the quasi-planar, tubular and bilayer isomers for the ground state of B70 in both neutral and dianionic states. While the bilayer form is more stable in the neutral state, the quasi-planar counterpart becomes more stable in the dianionic B702-. The stability arises due to the fact that the B702- dianion possesses 50 π electrons that satisfy the disk aromaticity model rule. These results tend to extend the stabilization of the quasi-planar structure upon negative charge addition previously found in small size boron clusters to larger sizes.

A new look at the structure of the neutral Au18 cluster: hollow versus filled golden cage.

The geometry of the neutral Au18 gold cluster was probed by a combination of quantum chemical calculations and far-infrared multiple photon dissociation (FIR-MPD) spectroscopy of a Kr messenger complex. Two low-lying isomers are identified to potentially contribute to the experimental IR spectrum, both being derived from a star-like Au17 structure upon capping with one extra Au atom either inside (18_1) or outside (18_5) the star. In particular, the present detection of structure 18_1 by DFT computations where a golden cage encapsulates an endohedral Au atom, is intriguing as a stable core-shell isomer has, to our knowledge, never been found before for such small neutral gold clusters. DFT and local coupled-cluster (DLPNO and PNO-CCSD(T)) computations indicate that both Au18 isomers are close to each other, within ∼3 kcal mol-1, on the energy scale. Although the exact energy ordering is again method-dependent and remains, at present, inconclusive, the most striking spectral signatures of both isomers are related to vibrational modes localized at atoms capping the inner pentaprism sub-structure that result in prominent peaks centered at ∼80 cm-1, close to the most prominent experimental feature found at 78 cm-1. The calculated IR spectra of both core-shell and hollow isomers are very similar to each other and both agree comparably well with the experimental FIR-MPD spectra of the Au18Kr1,2 complexes.

Facile iodine-promoted synthesis of bis(1-imidazo[1,5-a]pyridyl)arylmethanes and exploration of applications.

A practical strategy for the iodine-promoted synthesis of bis(1-imidazo[1,5-a]pyridyl)arylmethane and its derivatives has been developed. These compounds exhibit high cytotoxicity toward various cancer cell lines and moreover they are promising ligands for the Cu-catalysed synthesis of quinolines.

Binding mechanism and SERS spectra of 5-fluorouracil on gold clusters.

The adsorption behaviour of the 5-fluorouracil (5FU) on small gold clusters Au N with N = 6, 8, 20 was evaluated by means of density functional theory using the PBE-D3 functional in combination with a mixed basis set, i.e. cc-pVDZ-PP for gold atoms and cc-pVTZ for non-metal elements. The binding energies between 5FU and gold clusters were determined in the range of 16-24 and 11-19 kcal/mol in gas-phase and aqueous media, respectively. The corresponding Gibbs energies were found to be around -7 to -10 kcal/mol in vacum and sigificantly reduced to -1 to -6 kcal/mol in water solution, indicating that both the association and dissociation processes are likely spontaneous. An analysis on the charge density difference tends to confirm the existence of a charge transfer from the 5FU molecule to Au atoms. Analysis of the surface-enhanced Raman scattering (SERS) spectra of 5FU adsorbed on the Au surfaces shows that the stretching vibrations of N-H and C=O bonds play a major role in the SERS phenomenon. A mechanism for the drug releasing from the gold surfaces is also proposed. The process is triggered by either the low pH in cancerous tumors or the presence of cysteine residues in protein matrices.

Formation of the quasi-planar B56 boron cluster: topological path from B12 and disk aromaticity.

Formation and stability of the B56 boron cluster were investigated using a topological approach and the disk aromaticity model. An extensive global energy minimum search for the B56 system which was carried out by means of the Mexican Enhanced Genetic Algorithm (MEGA) in conjunction with density functional theory computations, confirms a quasi-planar structure as its energetically most stable isomer. Such a structural motif is derived by applying a topological leapfrog operation to a B12 form. Its high thermodynamic stability can be explained by the disk aromaticity model in which the delocalization of its π orbitals can be assigned to the levels of a particle in a circular box with the [(1σ)2 (1π)4 (1δ)4 (1φ)4 (2σ)2 (1γ)4 (2π)4 (2δ)4 (1η)4 (2φ)4 (1θ)2] electronic configuration. This π delocalization is confirmed by other delocalization indices. While the B56 has a similar electron delocalization to that of the quasi-planar B50, they have opposite magnetic ring current properties because of the symmetry selection rules of their HOMO-LUMO electronic transitions. The π delocalization in the boron clusters is larger at long distances as compared to carbon clusters at similar sizes, but such a trend is reversed at shorter distances.

Unravelling the alkali transport properties in nanocrystalline A3OX (A = Li, Na, X = Cl, Br) solid state electrolytes. A theoretical prediction.

Transport properties of the halogeno-alkali oxides A3OX (A = Li, Na, X = Cl, Br) nanocrystalline samples with the presence of ∑3(111) grain boundaries were computed using large-scale molecular dynamic simulations. Results on the diffusion/conduction process show that these nanocrystalline samples are characterized with higher activation energies as compared to previous theoretical studies, but closer to experiment. Such a performance can be attributed to the larger atomic density at the ∑3(111) grain boundary regions within the nanocrystals. Despite a minor deterioration of transport properties of the mixed cation Li2NaOX and Na2LiOX samples, these halogeno-alkali oxides can also be considered as good inorganic solid electrolytes in both Li- and Na-ion batteries.

First-row transition metal doped germanium clusters Ge16M: some remarkable superhalogens.

A theoretical study of geometric and electronic structures, stability and magnetic properties of both neutral and anionic Ge16M0/- clusters with M being a first-row 3d transition metal atom, is performed using quantum chemical approaches. Both the isoelectronic Ge16Sc- anion and neutral Ge16Ti that have a perfect Frank-Kasper tetrahedral T d shape and an electron shell filled with 68 valence electrons, emerge as magic clusters with an enhanced thermodynamic stability. The latter can be rationalized by the simple Jellium model. Geometric distortions from the Frank-Kasper tetrahedron of Ge16M having more or less than 68 valence electrons can be understood by a Jahn-Teller effect. Remarkably, DFT calculations reveal that both neutral Ge16Sc and Ge16Cu can be considered as superhalogens as their electron affinities (≥3.6 eV) exceed the value of the halogen atoms and even that of icosahedral Al13. A detailed view of the magnetic behavior of Ge16M0/- clusters shows that the magnetic moments of the atomic metals remain large even when they are quenched upon doping. When M goes from Sc to Zn, the total spin magnetic moment of Ge16M0/- increases steadily and reaches the maximum value of 3 µ B with M = Mn before decreasing towards the end of the first-row 3d block metals. Furthermore, the IR spectra of some tetrahedral Ge16M are also predicted.