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.

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.

The smallest triple-ring tubular gold clusters M2@Au15 with M = Mo, W: stability, electronic properties and nonlinear optical response.

The smallest triple ring tube-like gold clusters M2@Au15q with M = Mo, W and q = 1, 0, -1 are reported for the first time. Incorporation of an M2 dimer results in a remarkable modification of both atomic and electronic structures of the gold host. While the bare Au15 cluster exhibits a 3D cage shape, the doubly doped clusters M2@Au15 in all charge states are found to prefer a tubular form composed of three five-membered Au rings in an anti-prism arrangement and stabilized by an M2 unit placed inside the tube-like Au15 gold framework. The equilibrium geometry of both M2@Au15 and M2@Au15- is not much modified upon electron detachment from or attachment to their pure gold counterpart. The anion M2@Au15- with 28 itinerant electrons establishes an electron shell configuration of 1S21P61D102S21F8, in which the 1F shell splits into four different sub-levels. These stable clusters are thus not magic. Computed results on the first and second hyper-polarizability parameters of the doped clusters show a strong dependence on the charge. Overall, the neutral M2@Au15 is found to exhibit a particularly strong nonlinear optical (NLO) response. These clusters can also be extended to 1D nanowires, providing helpful guidance for the design of novel gold-based nanowires with rich optoelectronic properties.

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.

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.

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.

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.

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.

Boron Silicon B2Si3q and B3Si2p Clusters: The Smallest Aromatic Ribbons.

The small binary boron silicon clusters B2Si3q with q going from -2 to +2 and B3Si2p with p varying from -3 to +1 were reinvestigated using quantum chemical methods. The thermodynamic stability of these smallest ribbon structures is governed by both Hückel and ribbon models for aromaticity. The more negative the cluster charge, the more ribbon character is shown. In contrast, the more positive the charge state, the more pronounced the Hückel character becomes. The ribbon aromaticity character can also be classified into ribbon aromatic, semiaromatic, antiaromatic, and triplet aromatic when the electron configuration of a ribbon structure is described as [...π2(n+1)σ2n], [...π2n+1σ2n], [...π2nσ2n], and [...π2n+1σ2n-1], respectively. Geometry optimizations of the B2Si3 lowest-energy structure by some density functional theory (DFT) functionals result in a nonplanar shape because it possesses an antiaromatic ribbon character. However, its π aromaticity assigned by the Hückel rule is stronger in such a way that several other DFT and coupled-cluster theory CCSD(T) calculations show that B2Si3 is indeed stable in a planar form (Cs). A new global equilibrium structure for the anion B2Si32-, which is a ribbon semiaromatic species, was identified. Some benchmark tests were also carried out to evaluate the performance of popular methods for the treatment of binary B-Si clusters. At odds with some previous studies, we found that with reference to the high accuracy CCSD(T)/CBS method, the hybrid TPSSh functional is reliable for a structure search, whereas the hybrid B3LYP functional is more suitable for simulations of some experimental spectroscopic results.

Evolution of Vibrational Spectra in the Manganese-Silicon Clusters Mn2Sin, n = 10, 12, and 13, and Cationic [Mn2Si13].

A comparison of DFT-computed and measured infrared spectra reveals the ground state structures of a series of gas-phase silicon clusters containing a common Mn2 unit. Mn2Si12 and [Mn2Si13]+ are both axially symmetric, allowing for a clean separation of the vibrational modes into parallel (a1) and perpendicular (e1) components. Information about the Mn-Mn and Mn-Si bonding can be extracted by tracing the evolution of these modes as the cluster increases in size. In [Mn2Si13]+, where the antiprismatic core is capped on both hexagonal faces, a relatively simple spectrum emerges that reflects a pseudo-D6d geometry. In cases where the cluster is more polar, either because there is no capping atom in the lower face (Mn2Si12) or the capping atom is present but displaced off the principal axis (Mn2Si13), the spectra include additional features derived from vibrational modes that are forbidden in the parent antiprism.

Another look at energetically quasi-degenerate structures of the gold cluster Au27 q with q = 1, 0, -1.

Quantum chemical computations were used to reinvestigate the geometries, spectroscopic, and energetic properties of the gold clusters Au27 q in three charge states (q = 1, 0, -1). Density functional theory (DFT) and the domain-based local pair natural orbital modification of the coupled-cluster theory DLPNO-CCSD(T) calculations revealed that, at variance with earlier reports in the literature, while the anion Au27 - tends to exist in a tube-like form, both the lowest-energy Au27 and Au27 + isomers exhibit a pyramidal shape. However, several isomers were found to lie very close in energy, thus rendering a structural transition and their coexistence easy to occur. More specifically, the equilibrium geometry of the neutral Au27 is a core-shell pyramid-like structure with one gold atom located inside. We also identified a novel ground state for the anion Au27 - and located for the first time the global minimum of the cation Au27 + . The vertical detachment energies of the neutral and anionic states were also computed and used to assign the available experimental photoelectron spectra. Although many Au27 isomers were predicted to be energetically quasi-degenerate, the corresponding distinctive vibrational signatures can be used as fingerprints for the identification of cluster geometrical features.

Structure, stability and bonding of the leapfrog B24 0 ,±1,±2.

Two new structural motifs of the B24 clusters are constructed by use of the leapfrog transformation. The resulting leapfrog B24 has either a bowl shape with a square vacancy or a quasi-planar 2D close-packed triangular boron sheet. The neutral and ionic forms of the latter are found to be more stable than their homologous leapfrog bowl clusters, with the exception of the dicationic B24 +2 . While the leapfrog isomer is less stable than the tubular double ring in the neutral state, it becomes competitive in some ionic states. The nucleus independent chemical shift, electron localization function, ring current maps and the electronic structure of leapfrog B24 clusters reveal them to behave as aromatics.

Comment on 'Structural characterization, reactivity and vibrational properties of silver clusters: a new global minimum for Ag16' by P. L. Rodríguez-Kessler, A. R. Rodríguez-Domínguez, D. MacLeod Carey and A. Muñoz-Castro, Phys. Chem. Chem. Phys., 2020, 22, 27255, DOI: D0CP04018E.

A recent paper by Rodríguez-Kessler et al., Phys. Chem. Chem. Phys., 2020, 22, 27255-27262, reported not only results of quantum chemical computations (using the PW91 density functional) on Ag16 clusters as emphasized in the article's title, but also on the Ag15 size. These authors confirmed previous results obtained by McKee and Samokhvalov (J. Phys. Chem. A, 2017, 121, 5018-5028 using the M06 density functional) that the most stable isomer of Ag15 is a C2v structure. We wish to point out that two low symmetry isomers of Ag15 that have a similar energy content are even lower in energy than their reported C2v global minimum. The relative energies between low-lying Ag15 isomers were again found to be method-dependent, and within the expected accuracy of DFT and CCSD(T) methods they could be considered as energetically degenerate, and likely coexist in a molecular beam. The new lower-energy Ag15 isomers appear to fit more consistently within the structural evolution of small silver clusters.

The binary boron lithium clusters B12Lin with n = 1-14: in search for hydrogen storage materials.

Molecular structures and properties of the binary clusters containing twelve boron atoms mixed with n lithium atoms, B12Lin with n = 1-14, were investigated using density functional theory with the TPSSh functional and the 6-311+G(d) basis set. Energetic parameters including relative energies, average binding energies and second-order energies of the entire series were predicted using the coupled-cluster theory (U)CCSD(T) in conjunction with the cc-pVTZ basis set. Several lowest-lying isomers were determined for each size B12Lin whose energies differ from each other by <3 kcal mol-1, except for n = 1, 2 and 4 (≤5 kcal mol-1), and particularly n = 8 (∼13 kcal mol-1). Electronic structure and chemical bonding in some specific sizes such as B12Li4, B12Li8 and B12Li14 were analyzed in detail. We established the electron shells of some magic clusters such as the B12Li4 cone for which we proposed a mixed cone-disk electron shell model. Thanks to both the phenomenological shell and Clemenger-Nilsson models, B12Li8 which contains a specific set of shells of 44 valence electrons is a high stability species. The arrangement of Li atoms around a fullerene B12 framework shows that the mixed B12Li8 emerges as the most suitable of this cluster series to adsorb molecular hydrogen. Up to 32 H2 molecules can strongly be attached to the B12Li8 cluster which is thus predicted to be a realistic candidate for hydrogen storage material with gravimetric density reaching up to a theoritical limit of 26 wt%. Attachment of the fifth H2 molecule to each Li atom of B12Li8 results in weaker average bonds but can give rise to a total of 40 H2 molecules, corresponding to 30 wt% of hydrogen.

The lowest-energy structure of the gold cluster Au10: planar vs. nonplanar?

The onset of the transition from 2D to 3D structures in pure gold clusters remains a matter of continuing debate. In this theoretical study we revisit several planar and non-planar structural motifs of the size Au10 with the aim to clarify this issue. Computations using a long-range corrected exchange-correlation functional LC-BLYP, coupled-cluster theories CCSD(T) and PNO-LCCSD(T)-F12 reveal that, at variance with previous reports on the preference of a planar elongated hexagon, both planar and nonplanar isomers of the neutral Au10 are energetically degenerated up to 300 K. Its 3D equilibrium geometry is a core-shell structure which can be built up from a trigonal prism by capping four extra Au atoms outside. A comparison to the available experimental vibrational spectra allows us to argue that both lowest-lying 2D and 3D isomers of Au10 likely coexist in the molecular beam during measurement of its FIR spectra. This result also suggests that the 2D-3D transition of neutral gold clusters occurs at the size Au10.

Theoretical Study of the Binding of the Thiol-Containing Cysteine Amino Acid to the Silver Surface Using a Cluster Model.

Computational approaches within the framework of density functional theory (DFT) were employed to elucidate the binding mechanism of the cysteine amino acid on silver nanoparticles using several small silver clusters Agn with n = 2-10 as surface models. The long-range corrected LC-BLYP functional and correlation consistent basis sets cc-pVTZ-PP and cc-pVTZ were used to determine the structural features, energetics, and spectroscopic and electronic properties of the resulting complexes. In vacuum and highly acidic conditions, cysteine molecules prefer to adsorb on silver clusters via their amine group. In aqueous solution, the thiolate head turns out to be the most energetically favorable binding site. The cysteine affinity of silver clusters is greatly altered in different conditions, i.e., acidic solution < vacuum < aqueous solution, and is strongly dependent on the cluster size. As compared to free clusters, the frontier orbital energy gap of the ones capped by cysteine is significantly improved, which corresponds to stronger stability, especially in aqueous solution. The analysis of frontier orbitals also reveals that both forward and backward electron donations exhibit comparable contributions to the enhancement of stabilizing interactions. As for an application, a chemical enhancement mechanism of the surface-enhanced Raman scattering (SERS) procedure of cysteine by silver clusters was also analyzed.

Theoretical Aspects of Nonconventional Hydrogen Bonds in the Complexes of Aldehydes and Hydrogen Chalcogenides.

Hydrogen bonds (H-bonds) in the complexes between aldehydes and hydrogen chalcogenides, XCHO...nH2Z with X = H, F, Cl, Br, and CH3, Z = O, S, Se, and Te, and n = 1,2, were investigated using high-level ab initio calculations. The Csp2-H...O H-bonds are found to be about twice as strong as the Csp2-H...S/Se/Te counterparts. Remarkably, the S/Se/Te-H...S/Se/Te H-bonds are 4.5 times as weak as the O-H...O ones. The addition of the second H2Z molecule into binary systems induces stronger complexes and causes a positive cooperative effect in ternary complexes. The blue shift of Csp2-H stretching frequency involving the Csp2-H...Z H-bond sharply increases when replacing one H atom in HCHO by a CH3 group. In contrast, when one H atom in HCHO is substituted with a halogen, the magnitude of blue-shifting of the Csp2-H...Z H-bond becomes smaller. The largest blue shift up to 92 cm-1 of Csp2-H stretching frequency in Csp2-H...O H-bond in CH3CHO...2H2O has rarely been observed and is much greater than that in the cases of the Csp2-H...S/Se/Te ones. The Csp2-H blue shift of Csp2-H...Z bonds in the halogenated aldehydes is converted into a red shift when H2O is replaced by a heavier analogue, such as H2S, H2Se, or H2Te. The stability and classification of nonconventional H-bonds including Csp2-H...Se/Te, Te-H...Te, and Se/Te-H...O have been established for the first time.

SERS Chemical Enhancement of 2,4,5-Trichlorophenoxyacetic Acid Adsorbed on Silver Substrate.

Surface-enhanced Raman spectroscopy (SERS) was employed to gain an understanding of the chemical enhancement mechanism of 2,4,5-trichlorophenoxyacetic acid (2,4,5-T), an Agent Orange, adsorbed on a silver substrate surface. Experimental measurements were performed using a micro-Raman spectrophotometer with an excitation wavelength of 532 nm and successfully detected 2,4,5-T at a relatively low concentration of 0.4 nM. Density functional theory (DFT) calculations on the interactions of the 2,4,5-T molecule with some small silver clusters, Agn with n = 4, 8, and 20, as well as with extended Ag surfaces, demonstrate that the most stable adsorption configuration is formed via coordination of Cl9 sites and carbonyl C═O group on the 2,4,5-T ligand to the Ag atoms on surfaces. Analyses of charge transfer mechanism and frontier orbitals distributions show an electron transfer from 2,4,5-T to the cluster in the ground state, and an inversed trend occurs for the excited singlet state process, consequently leading to a chemical enhancement of SERS signals. The obtained results are of importance for subsequent work in guiding the design of mobile sensors specifically used for services of rapid screening and detection of these toxic compounds present in the environment, as well as agricultural and food products. Extensive computations pointed out that small silver clusters, in particular of Ag20 size, can be used as appropriate models for a metal nanoparticle surface.