Boron Silicon B2Si3q and B3Si2p Clusters: The Smallest Aromatic Ribbons

The small binary boron silicon clusters B₂Si₃^q with q going from -2 to +2 and B₃Si₂^p 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⁺¹σ^2n-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 (C_s). A new global equilibrium structure for the anion B₂Si₃^2-, 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.

Unexpected structures of the Au17 gold cluster: the stars are shining

The Au₁₇ gold cluster was experimentally produced in the gas phase and characterized by its vibrational spectrum recorded using far-IR multiple photon dissociation (FIR-MPD) of Au₁₇Kr. DFT and coupled-cluster theory PNO-LCCSD(T)-F12 computations reveal that, at odds with most previous reports, Au₁₇ prefers two star-like forms derived from a pentaprism added by two extra Au atoms on both top and bottom surfaces of the pentaprism, along with five other Au atoms each attached on a lateral face. A good agreement between calculated and FIR-MPD spectra indicates a predominant presence of these star-like isomers. Stabilization of a star form arises from strong orbital interactions of an Au₁₂ core with a five-Au-atom string.

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 Ge₁₆M^0/− 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 Ge₁₆M^0/− 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 Ge₁₆M^0/− 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.

A theoretical study of geometric and electronic structures, stability and magnetic properties of both neutral and anionic Ge₁₆M^0/− clusters with M being a first-row 3d transition metal atom, is performed using quantum chemical approaches.

Evolution of Vibrational Spectra in the Manganese-Silicon Clusters Mn2Sin, n = 10, 12, and 13, and Cationic [Mn2Si13]. J Phys Chem A 2022;126:1617-1626. [PMID: 35238570 PMCID: PMC9084549 DOI: 10.1021/acs.jpca.1c10027]

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-D_6d 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.

Correction: The binary aluminum scandium clusters Al x Sc y with x + y = 13: when is the icosahedron retained?

Correction for ‘The binary aluminum scandium clusters Al_xSc_y with x + y = 13: when is the icosahedron retained?’ by Ngo Tuan Cuong et al., RSC Adv., 2021, 11, 40072–40084. DOI: 10.1039/D1RA06994B.

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 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 C_sp2-H...O H-bonds are found to be about twice as strong as the C_sp2-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 C_sp2-H stretching frequency involving the C_sp2-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 C_sp2-H...Z H-bond becomes smaller. The largest blue shift up to 92 cm^-1 of C_sp2-H stretching frequency in C_sp2-H...O H-bond in CH₃CHO...2H₂O has rarely been observed and is much greater than that in the cases of the C_sp2-H...S/Se/Te ones. The C_sp2-H blue shift of C_sp2-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 C_sp2-H...Se/Te, Te-H...Te, and Se/Te-H...O have been established for the first time.

Generation and reactivity of an elusive base-stabilised phosphinidene

Reduction of phosphorus dichloride 6, supported by the diaryloxyphenyl group (OCO) featuring two bulky phenoxy wingtips, by PMe₃, generates a reactive intermediate that behaves as a base-stabilized phosphinidene (OCO)P (5). Warming up a solution of this species in toluene to room temperature results in trimerization to give the isolable cyclic triphosphine [(OCO)P]₃, whereas in situ trapping with 2,3-dimethylbutadiene-1,3 afforded a 3,4-dimethylphospholene-3. Investigation of the reduction of 6 by the phosphine PMe₃ by NMR led to the observation of a persistent species between -10 °C and 10 °C. A DFT study of this process suggests that this compound cannot be the proposed phosphinidene 5, and is more likely the diphosphine (OCO)ClP-PCl(OCO) (12). Attempted reduction of 5 by the bulky carbene IPr resulted in unusual electrophilic substitution in the carbene olefin backbone by the chlorophosphinyl group.

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.

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, B₁₂Li_n 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 B₁₂Li_n 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.

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, Ag_n 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.

An octacoordinated Nb atom in the NbAl8H8+ cluster

The NbAl₈H₈⁺ cluster was formed in a molecular beam and characterized by mass spectrometry and infrared spectroscopy. Density functional theory calculations show the lowest-energy isomer is a high symmetry singlet with the Nb atom placed at the center of a distorted hexagonal Al ring and coordinated by two AlH moieties, therefore exhibiting octacoordination. The unprecedented high-symmetric geometry is attributed to the 20 valence electrons; the central Nb atom adheres to the 18-electron rule and two additional delocalized electrons stabilize the hexagonal ring.

Adsorption/Desorption Behaviors and SERS Chemical Enhancement of 6-Mercaptopurine on a Nanostructured Gold Surface: The Au20 Cluster Model

Computational approaches are employed to elucidate the binding mechanism and the SERS phenomenon of 6-mercaptopurine (6MP) adsorbed on the tetrahedral Au20 cluster as a simple model for a nanostructured gold surface. Computations are carried out in both vacuum and aqueous environments using a continuum model. In the gaseous phase and neutral conditions, interaction of 6MP with the gold cluster is mostly dominated by a covalent Au-S bond and partially stabilized by the Au⋅⋅⋅H-N coupling. However, in acidic solution, the nonconventional Au⋅⋅⋅H-S hydrogen-bond becomes the most favorable binding mode. The 6MP affinity for gold clusters decreases in the order of vacuum > neutral solution > acidic medium. During the adsorption, the energy gap of Au20 substantially declines, leading to an increase in its electrical conductivity, which can be converted to an electrical noise. Moreover, such interaction is likely a reversible process and triggered by either the low pH in sick tissues or the presence of cysteine residues in protein matrices. While N-H bending and stretching vibrations play major roles in the SERS phenomenon of 6MP on gold surfaces in neutral solution, the strongest enhancement in acidic environment is mostly due to an Au⋅⋅⋅H-S coupling, rather than an aromatic ring-gold surface π overlap as previously proposed.

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 C_2v 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 C_2v 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.

Gold nanoclusters as prospective carriers and detectors of pramipexole

Pramipexole (PPX) is known in the treatment of Parkinson's disease and restless legs syndrome. We carried out a theoretical investigation on pramipexole–Au cluster interactions for the applications of drug delivery and detection. Three Au_N clusters with sizes N = 6, 8 and 20 were used as reactant models to simulate the metallic nanostructured surfaces. Quantum chemical computations were performed in both gas phase and aqueous environments using density functional theory (DFT) with the PBE functional and the cc-pVDZ-PP/cc-pVTZ basis set. The PPX drug is mainly adsorbed on gold clusters via its nitrogen atom of the thiazole ring with binding energies of ca. −22 to −28 kcal mol⁻¹ in vacuum and ca. −18 to −24 kcal mol⁻¹ in aqueous solution. In addition to such Au–N covalent bonding, the metal–drug interactions are further stabilized by electrostatic effects, namely hydrogen-bond NH⋯Au contributions. Surface-enhanced Raman scattering (SERS) of PPX adsorbed on the Au surfaces and its desorption process were also examined. In comparison to Au₈, both Au₆ and Au₂₀ clusters undergo a shorter recovery time and a larger change of energy gap, being possibly conducive to electrical conversion, thus signaling for detection of the drug. A chemical enhancement mechanism for SERS procedure was again established in view of the formation of nonconventional hydrogen interactions Au⋯H–N. The binding of PPX to a gold cluster is expected to be reversible and triggered by the presence of cysteine residues in protein matrices or lower-shifted alteration of environment pH. These findings would encourage either further theoretical probes to reach more accurate views on the efficiency of pramipexole–Au interactions, or experimental attempts to build appropriate gold nanostructures for practical trials, harnessing their potentiality for applications.

Gold clusters as prospective carriers and detectors of pramipexole.

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 Ag_n 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.

Enhanced Li-ion transport in divalent metal-doped Li2SnO3

The improvement of Li-ion transport properties and doping engineering in Li-ion batteries are currently active research topics in the search for next-generation energy storage devices. In this theoretical work, the intrinsic defect formation and transport properties of divalent metal-doped Li2SnO3, which is being considered as an electrode and coating electrode material, are explored using atomistic simulations. Defect formation simulations reveal that all divalent dopants (Zn, Sc, Cd and Eu) occupy the Li site with charge compensation through Li vacancies. Molecular dynamics simulations show that the divalent dopants significantly reduce the activation energy for ionic diffusion and conduction compared to the undoped sample. The effects of both grains and grain boundaries on the Li-ion transport properties are investigated. Our calculated results demonstrate a marked improvement in the properties of Li2SnO3 that can be achieved either in current commercial and next-generation Li-ion battery technologies through divalent doping in mono- and polycrystalline Li2SnO3 samples.

A theoretical design of bipolar host materials for blue phosphorescent OLED

A series of host molecules have been designed and characterized for use in phosphorescent organic light-emitting diode devices. The parent host molecule was modified by adding nitrogen-containing group at different positions. The first triplet excited (T₁) and first singlet excited (S₁) states energies, frontier orbital energy levels, reorganization energies and injection barriers of the molecules designed were calculated in comparison to those of the reference host, emitter, hole and electron transport materials. Interestingly, our results suggest that addition of nitrogen group into the dibenzothiophene by a N-C linkage increases the triplet energy separation and decreases the injection barriers making them suitable for use as blue phosphorescent materials.

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.

The binary aluminum scandium clusters AlxScy with x + y = 13: when is the icosahedron retained?

Geometrical and electronic structures of the 13-atom clusters Al_xSc_y with x + y = 13, as well as their thermodynamic stabilities were investigated using DFT calculations. Both anionic and neutral isomers of Al_xSc_y were found to retain an icosahedral shape of both Al₁₃ and Sc₁₃ systems in which an Al atom occupies the endohedral central position of the icosahedral cage, irrespective of the number of Al atoms present. Such a phenomenon occurs to maximize the number of stronger Al–Al and Sc–Al bonds instead of the weaker Sc–Sc bonds. NBO analyses were applied to examine their electron configurations and rationalize the large number of open shells and thereby high multiplicities of the mixed clusters having more than three Sc atoms. The SOMOs are the molecular orbitals belonged to the irreducible representations of the symmetry point group of the clusters studied, rather than to the cluster electron shells. Evaluation of the average binding energies showed that the thermodynamic stability of Al_xSc_y clusters is insignificantly altered as the number y goes from 0 to 7 and then steadily decreases when y attains the 7–13 range. Increase of the Sc atom number also reduces the electron affinities of the binary Al_xSc_y clusters, and thus they gradually lose the superhalogen characteristics with respect to the pure Al₁₃.

The icosahedral structure of the Al_xSc_y clusters with x + y = 13.

Autocatalysis in Formose Reaction and Formation of RNA Nucleosides

Understanding of the abiotic formation of nucleosides under geochemical conditions is currently a major scientific challenge. In this study, free radical pathways for formation of RNA nucleosides with canonical nucleobases are proposed for the first time. The pathways proceed with relatively low energy barriers for the formation of ribose as well as all RNA nucleosides. The formose reaction proceeds either with or without Ca²⁺ and CaOH⁺ cations. An autocalytic cycle for the formation of both glycolaldehyde and glyceraldehyde is identified when Ca²⁺ or CaOH⁺ cations are involved in the reaction. The results suggest that Ca²⁺ cations are not involved in the formation of ribose from glyceraldehyde. In addition, these pathways lead to the formation of dihydroxyacetone and d-erythrose. Calculated results show that the glycosidic bond can be formed abiotically between the d-ribose and the nucleobase, where d-ribose forms a cyclic free radical that subsequently reacts with the neutral nucleobase. Involvement of proper nucleobase tautomer is important for the formation of RNA nucleosides. Our approaches provide a solution for the long-standing question of how the glycosidic bond is formed under the abiotic conditions with low energy barriers. The pathways for formation of the sugars without a catalyst are relevant to the formation of sugars in interstellar clouds. On the other hand, the autocalysis in the formose reaction followed by the formation of the nucleosides is appropriate for the abiotic synthesis taking place in the presence of water in the early Earth environment. The Ca²⁺ and CaOH⁺ cations appear to be the first nonenzymatic catalytic systems for formation of biomolecules.