Lowest-lying Isomers Research Articles

The silicon doped B10Si2 and isovalent boron clusters: Quasi-degenerate 2D and 3D isomers and electron model for rectangular cuboid

The DFT/PBE functional and coupled-cluster theory CCSD(T) computations were used to explore properties of the isovalent B12H2, B11SiH and B10Si2 clusters. Diverse approaches for analysing quasi-degenerate isomers pointed out that while the ribbon-like isomer achieves aromaticity, its spatial effects diminish it with increasing ribbon size. Doping of two H atoms into B12 does not reduce the σ aromaticity of B12H12. Remarkably, the lowest-lying isomer of B10Si2 exhibits a novel 3D structure whose shape and electrons can be simulated by a rectangular cuboid. The spectrum of the whole set of valence electron of this 3D B10Si2 was elucidated by this model.

Conformational Preference of Lithium Polysulfide Clusters Li2Sx (x = 4-8) in Lithium-Sulfur Batteries.

Structures are of fundamental importance for diverse studies of lithium polysulfide clusters, which govern the performance of lithium-sulfur batteries. The ring-like geometries were regarded as the most stable structures, but their physical origin remains elusive. In this work, we systematically explored the minimal structures of Li2Sx (x = 4-8) clusters to uncover the driving force for their conformational preferences. All low-lying isomers were generated by performing global searches using the ABCluster program, and the ionic nature of the Li···S interactions was evidenced with the energy decomposition analysis based on the block-localized wave function (BLW-ED) approach and further confirmed with the quantum theory of atoms in molecule (QTAIM). By analysis of the contributions of various energy components to the relative stability with the references of the lowest-lying isomers, the controlling factor for isomer preferences was found to be the polarization interaction. Notably, although the electrostatic interaction dominates the binding energies, it contributes favorably to the relative stabilities of most isomers. The Li+···Li+ distance is identified as the key geometrical parameter that correlates with the strength of the polarization of the Sx2- fragment imposed by the Li+ cations. Further BLW-ED analyses reveal that the cooperativity of the Li+ cations primarily determines the relative strength of the polarization.

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.

Cr2 Gen - (n = 15-20) clusters with two Cr atoms exhibited antiferromagnetic coupling.

In this work, we investigated the structural evolution, electronic and magnetic properties of Cr2 Gen - clusters for n = 15-20 by using density functional theory (DFT) calculations. Low-energy structures for these clusters were fully searched through a self-developed genetic algorithm code combined with DFT calculations. The calculations show that all the two Cr atoms prefer to stay together to form a strong CrCr bond, which-except for size 20-is shorter than the nearest neighbor distance in Cr bulk. Sizes 15 and 16 adopt a wheel-like structure as the structural motif with the extra Ge atoms capped on the top, while larger sizes (n = 17-20) prefer fullerene-like Cr2 @Ge12 motifs. From the results of the average binding energies of Cr2 Gen - , one can conclude that it is easier to form larger size clusters. In these lowest-lying isomers except for size 16, the two Cr atoms contribute opposite magnetic moments for the total magnetic moments of 1 μB , showing an antiferromagnetic state.

Properties of Naked Silver Clusters with Up to 100 Atoms as Found with Embedded-Atom and Density-Functional Calculations.

The structural and energetic properties of small silver clusters Agn with n = 2-100 atoms are reported. For n = 2-100 the embedded atom model for the calculation of the total energy of a given structure in combination with the basin-hopping search strategy for an unbiased structure optimization has been used to identify the energies and structures of the three energetically lowest-lying isomers. These optimized structures for n = 2-11 were subsequently studied further through density-functional-theory calculations. These calculations provide additional information on the electronic properties of the clusters that is lacking in the embedded-atom calculations. Thereby, also quantities related to the catalytic performance of the clusters are studied. The calculated properties in comparison to other available theoretical and experimental data show a good agreement. Previously unidentified magic (i.e., particularly stable) clusters have been found for n>80. In order to obtain a more detailed understanding of the structural properties of the clusters, various descriptors are used. Thereby, the silver clusters are compared to other noble metals and show some similarities to both copper and nickel systems, and also growth patterns have been identified. All vibrational frequencies of all the clusters have been calculated for the first time, and here we focus on the highest and lowest frequencies. Structural effects on the calculated frequencies were considered.

Stability and hydrogen storage properties of Sc6O8 and Y6O8 cage-like complexes

To study the dihydrogen storage capacity of Sc6O8 and Y6O8 complexes, the stability and hydrogen adsorption behavior have been investigated by using density functional theoretical calculations. The lowest-lying isomers are cage-like complexes Sc6O801 and Y6O801, which are energetically much low-lying by at least 40.43 kcal/mol than the other isomers, respectively. Sc6O801 can adsorb 26H2 with gravimetric uptake capacity of 11.64 wt%. The average adsorption energy (ΔEave) is 0.12 eV/H2, which is in the reversible adsorption range. The Y6O801 seem have little ability to adsorb hydrogen molecules, because the ΔEave Y6O801 (1H2) is just only 0.065 eV. However, the binding capacity increases with the number of adsorbed H2 increasing. Y6O801 can adsorb 32H2 with ΔEave of 0.11 eV/H2, and the gravimetric uptake capacity is 8.89 wt%. Various characterization methods indicate that both transition metals and nonmetals in Sc6O801 and Y6O801 can effectively adsorb hydrogen molecules, and these two compounds can be regarded as candidate materials of dihydrogen adsorption under suitable condition.

The Au12 Gold Cluster: Preference for a Non-Planar Structure

The transition point from a two-dimensional (2D) to a three-dimensional (3D) structure in a series of small gold clusters remains a topic of continuing debate. In the present study, coupled-cluster CCSD(T) and DFT calculations are performed to re-examine the relative energies of several low-lying isomers of Au12, aiming to shed new light on this issue. At odds with many previous reports on the preference of a planar di-capped elongated-hexagon structure, the Au12 size is found to energetically prefer a globular cup-like form with C2v symmetry. While DFT results are not able to assign the most stable form of Au12 as the relative energies between the lowest-lying isomers are strongly functional-dependent, coupled-cluster theory calculations point out the preference of a 3D structure for having a D3h symmetry. Such a prediction is further supported by a comparison of the vibrational spectra computed using the revTPSS density functional with the available experimental infrared ones that were previously recorded from the far-IR multiple photon dissociation (FIR-MPD) experiment.

Potassium Binding Interactions with Aliphatic Amino Acids: Thermodynamic and Entropic Effects Analyzed via a Guided Ion Beam and Computational Study.

Noncovalent interactions between alkali metals and amino acids are critical for many biological processes, especially for proper function of protein ion channels; however, many precise binding affinities between alkali metals and amino acids still need to be measured. This study addresses this need by using threshold collision-induced dissociation with a guided ion beam tandem mass spectrometer to measure binding affinities between potassium cations and the aliphatic amino acids: Gly, Ala, hAla, Val, Leu, and Ile. These measurements are supplemented by theoretical calculations and include commentary on effects of enthalpy, entropy, and structural preference. Notably, all levels of theory indicate that the lowest-lying isomers at 298 K have K+ binding to the carbonyl oxygen in either a monodentate ([CO]) or bidentate ([CO,OH]) fashion, isomers that are linked in a double-well potential. This complicates the analysis of the data, although does not greatly influence the final results. Analysis of the resulting cross sections includes accounting for multiple ion-molecule collisions, internal energy of reactant ions, and unimolecular decay rates. The resulting experimental bond dissociation energies generally increase as the polarizability of the amino acid increases, results that agree well with quantum chemical calculations done at the B3LYP, B3P86, and MP2(full) levels of theory, with B3LYP-GD3BJ predicting systematically larger values.

Conjugation trumps cumulation: the global minimum on the C3H4O surface

Methylketene (CHCHCO) and acrolein (CHCHCHO) have received considerable attention from both theoreticians and experimentalists. In a number of computational studies, it has been identified that both isomers sit alongside their dissociation products , at the bottom of the potential energy surface with energies very close to each another. The most striking feature from preliminary calculations is that the relative energy difference between methylketene and trans-acrolein ( 0.8–3.4 kJ/mol) changes with respect to choice of reference geometry, correlation treatment, and basis set expansion. While the thermodynamic profile favours trans-acrolein as the lowest-lying isomer, it is difficult to estimate the quality of the currently available results, which are determined with a variety of methods. At higher levels of theory together with reducing basis set incompleteness methylketene might be the true minimum on the CHO potential energy surface. In addition to their being almost isoenergetic, much interest in these CHO isomers stems from an astrochemical standpoint. The discovery of both cis and trans-acrolein in the interstellar medium has led to speculation that methylketene may also be present. While thermodynamically methylketene proves to be a good candidate for extra-terrestrial observation, as yet there have been no reports of its detection. To this end, by applying the best correlation treatment that has been used for this species, using by far the most elaborate and accurate basis sets (up to sextuple-zeta quality), we establish the relative ordering and energetic difference between methylketene and trans-acrolein to within chemical accuracy (within 1 kJ/mol). We find the inclusion of zero-point energy, explicit core-correlation, and augmentation with diffuse functions have significant effects in determining the relative energy difference of the isomers, and assignment of the CHO global minimum.

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.

Nonrigid water octamer: Computations with the 8-cube.

A 8-cube model of the fully nonrigid water octamer is considered within the 8-dimensional hyperoctahedral wreath product group with 10,321,920 operations and 185 irreducible representations by employing computational and mathematical techniques. For the two lowest-lying isomers of (H2 O)8 with D2d and S4 symmetries of a rigid (H2 O)8 , correlation tables and nuclear spin statistics are constructed for the tunneling splittings of the rotational levels are computed by a computational matrix polynomial generating function technique combined with Möbius inversion, and the relationship to the 8-cube multinomials are pointed out. Multinomial generating functions combined with the induced representation techniques are employed to compute and construct the nuclear spin species, nuclear spin statistical weights and tunneling splittings of rovibronic levels. We have also computed the spin statistical weights and tunneling splittings of the rotational levels for a semirigid water octamer within the wreath product Oh [S2 ] consisting of 12,288 operations.

A theoretical research of dihydrogen storage in ScxNy (x+y=4) compounds

The dihydrogen storage capacity of ScxNy (x + y = 4) compounds have been theoretically investigated at different levels. At B3LYP-D3/6-311G(3df,3pd) level, ScN3 has multiple isomers with similar energies, which is an interference of hydrogen storage research. Sc2N2 and Sc3N has four and three isomers, respectively. For both systems, the lowest-lying isomers are planar Sc2N201 and Sc3N 01, which are energetically much low-lying by at least 20 kcal/mol than the other isomers, respectively. Sc3N 01 can adsorb 8H2 with gravimetric uptake capacity of 9.77 wt %. It satisfies the target specified by US DOE, however, some hydrogen molecules will dissociate and bond atomically on scandium atoms. The strong binding energy (0.66 eV/H2) exceeds the reversible adsorption range (0.1–0.4 eV/H2), which will cause high operating temperature to desorb hydrogen during the application process. Sc2N201 can adsorb 9H2 in the molecular form. The H2 gravimetric uptake capacity of Sc2N201 (9H2) (13.33 wt %) exceeds the target set by US Department of Energy, moreover, its average adsorption energy (0.32 eV/H2) is in the reversible adsorption range. The interaction of Sc2N201 with H2 molecules is considered by means of the bond critical points (bcp) in the quantum theory of atoms in molecules (QTAIM). The Gibbs free energy corrected adsorption energy points that the adsorption of Sc2N201(9H2) is energetically favorable below 240 K. Therefore, in ScxNy (x + y = 4), the planar compound Sc2N201 is more suitable to be a dihydrogen adsorption material.

Au2Si20: a honeycomb-shaped structure with short Au−Au single bond at the centre coordinated by twelve Si5 pentagons and reinforced by strong Au−Si interactions and aromaticity

Investigating the structures and properties of large-sized silicon clusters doped with multiple Au atoms can provide valuable microscopic information for gold-catalyzed high-quality Si nanowire and Au−Si alloying reactions, and also for the production of cluster-assembled functional materials. In this work, a quantum chemical investigation on the structural and electronic properties of double Au atoms doped Si20 cluster using density functional theory calculations was performed. The lowest-lying isomers of (The meaning of the acronym: refers to Au2Si20 cluster with a negative charge, neutral state, and a positive charge, respectively.) were found to all adopt a C 2h symmetric Au2-endohedral honeycomb-shaped structure consisting of twelve Si5 pentagons. Interestingly, in the anionic, neutral, and cationic Au2Si20, twelve Si5 pentagons can be stabilised by two Au atoms. The two Au atoms in tend to occupy high coordinate sites and exhibit strong aurophilic interactions. In addition, the Au−Si bonds show both covalent and ionic bonding characters. Moreover, , Au2Si20, and are all aromatic.

B3Ge12: a aromatic molecular sandwich-shaped structure with short B−B single bonds coordinated by a Ge12 hexagonal prism and reinforced by σ + π double delocalised bonding patterns

The geometrical structures and bonding properties of anionic, neutral, and cationic B3Ge12 clusters are investigated by quantum chemical calculations. The lowest-lying isomer of anion is found to have a distorted B-endohedral pentagonal prism with two face-capping B atoms and two face-capping Si atoms. In particular, anion is an outstanding superatom cluster with closed-shell electronic configuration of 1S21P61D102S21F142P61G18 on the principle of jellium model. Global minimum of B3Ge12 neutral adopts a D 3h symmetric hexagonal prismatic structure with a B3 triangle at the centre being parallel to the two hexagons and has strong B–B bonding interactions, being very close to the typical B−B single bond. cation has a similar structural feature with its neutral corresponding counterpart. Moreover, the nucleus-independent chemical shift (NICS), aromatic stabilisation energy (ASE), and multicenter bond index calculations suggest B3Ge12 neutral to be aromatic. Furthermore, the molecular orbitals reveal that B3Ge12 neutral exhibits σ plus π double bonding characters. Electrons are transferred from Ge12 framework to B atoms in terms of natural population analysis (NPA), atoms in molecules (AIM), and atomic dipole moment corrected Hirshfeld (ADCH) population analyses.

Dinuclear Metal-Mediated Guanine–Uracil Base Pairs: Theoretical Studies of GUM22+ (M = Cu, Ag, and Au) Ions

Dinuclear metal-mediated hetero base pairs with the d10–d10 closed-shell interactions have significant stability. It is interesting to identify whether coinage metal-mediated Wobble base pairs are also stable. Geometric and electronic structures of the lowest-lying isomers of GUM22+ (G = guanine, U = uracil, M = Cu, Ag, and Au) cluster ions were investigated with density functional theory. In the lowest-lying isomers of these dinuclear metal-mediated base pairs, the 2-oxo-4-hydroxy-trans-N1H isomer of uracil is derived from the canonical tautomer of uracil by the hydrogen atom transfer. M22+ cations remain as an unbroken unit and interact with the G···U ligand through two sets of closely linear N···M···O units, while the reciprocal hydrogen bonds between the Wobble base pair (G–U) are entirely substituted by the M–N or M–O interactions in these complexes. The atoms in molecules and EDA–NOCV calculations really reveal that the σ interactions in GUM22+ cations are the paramount term of ΔEOrb. The obtained instantaneous interaction energies ΔEint and bond dissociation energies of the metal–ligand interactions give the trend of the bond strength as Cu > Au > Ag.

Formation of the quasi-planar B50 boron cluster: topological path from B10 and disk aromaticity.

The lowest-lying isomer of the B50 boron cluster is confirmed to have a quasi-planar shape with two hexagonal holes. By applying a topological (leap-frog) dual operation followed by boron capping, we demonstrated that such a quasi-planar structure actually comes from the smallest elongated B102-, and its high thermodynamic stability is due to its inherent disk aromaticity arising from its 32 valent π electrons that fully occupy a disk configuration of [(1σ)2(1π)4(1δ)4(2σ)2(1φ)4(2π)4(1γ)4(2δ)4(1η)4]. The aromatic character of the quasi-planar B50 is further supported by a strong diatropic magnetic current flow. The sudden appearance of a quasi-planar B50 again points out that the growth pattern of pure boron clusters is still far from being completely understood.

Structural evolution and bonding properties of (n = 4-12) clusters: Size-selected anion photoelectron spectroscopy and theoretical calculations.

Size-selected anion photoelectron spectroscopy and theoretical calculations were used to investigate the structural evolution and bonding properties of BSin -/0 (n = 4-12) clusters. The results showed that the B atom in BSi4-12 -/0 prefers to occupy the high coordination sites to form more B-Si bonds. The lowest-lying isomers of BSi4-7 -/0 primarily adopt bowl-shaped based geometries, while those of BSi8-12 -/0 are mainly dominated by prismatic based geometries. For anionic clusters, BSi11 - is the critical size of the endohedral structure, whereas BSin neutrals form the B-endohedral structure at n = 9. Interestingly, both anionic and neutral BSi11 have a D 3h symmetric tricapped tetragonal antiprism structure with the B atom at the center and exhibit 3D aromaticity. The BSi11 - anion possesses σ plus π doubly delocalized bonding characters. The natural population analysis charge distributions on the B atom are related with the structural evolution of BSin - and the B-Si interactions.

A dinuclear Cu(i)-mediated complex: Theoretical studies of the G2Cu2 4+ cluster ion.

Recently, the T-Hg(ii)2-A base pair containing two equivalents of Hg(ii) has been prepared and characterized experimentally, which implies that there might exist considerable stable metal-mediated base pairs holding two neighbouring metal centers. Here we report a quantum chemical study on geometries, electronic structures, and bonding of various G2Cu2 4+ (G = guanine) isomers including one di-copper(i) unit. Different density functional methods [Becke 3-parameter-Lee-Yang-Parr, Perdew-Becke-Ernzerhof, Becke-Perdew, Density Functional Theory with Dispersion Corrections (DFT-D)] assign ambiguous relative energies to these isomers with the singlet and triplet states. High-level ab initio [domain-based local pair natural orbital (DLPNO) coupled-cluster with single and double excitations and DLPNO-coupled-cluster with single, double, and perturbative triple excitations] calculations confirm that the lowest-lying isomer of the G2Cu2 4+ ion has C 2h symmetry with the singlet state and is comparable to the singly and doubly charged homologues (G2Cu2 + and G2Cu2 2+). The extended transition state (ETS)-natural orbitals for the chemical valence (ETS-NOCV) calculations point out that it has larger instantaneous interaction energy and bond dissociation energy than the corresponding singly and doubly charged complexes due to its relatively stronger attractive energies and weaker Pauli repulsion. The orbital interactions in the quadruply charged cluster chiefly come from Cu2 4+ ← G⋯G π donations. The results may help the understanding of the bonding properties of other potential metal-base pair complexes with the electron transfer.

Solvation of barium atoms and singly charged cations in acetonitrile clusters.

The size distributions of neutral and cationic Ba x (CH3CN) n (x = 0, +1; n ≤ 7) clusters, as produced by a standard laser vaporization-supersonic expansion pick-up source, were determined from molecular beam experiments. The size distribution for cations is in the range of n = 1-7, whereas only the n = 1 complex is observed for neutral clusters, and these two features are unaffected by the variables controlling the performance of the cluster source. The distinct behavior is compatible with the expected charge-dipole interactions in the ionic species, which are stronger than the dipole induced-dipole interactions at play in neutral clusters, and it is corroborated by the relative magnitude of the theoretical successive binding energies (SBEs) for the lowest-lying isomers of cationic and neutral clusters with n = 1-5, as computed at the density functional theory level. The theoretical results also allow for the rationalization of the bimodal Ba+(CH3CN)1-7 size distribution, featuring an apparent minimum at n = 3, in terms of chiefly 6s-5d σ hybridization of the Ba+ ions, which ultimately leads to a relatively small third SBE for the Ba+(CH3CN)3 complex, as compared to those for n = 1, 2, and 4. Additional Born-Oppenheimer molecular dynamics simulations on the Ba+(CH3CN)2-4 clusters suggest that all of the ligands are coordinated to the Ba+ ion and prevent considering completion of the first solvent shell as responsible for the bimodal size distribution.

Structural evolution and bonding properties of Au2Sin-/0 (n = 1-7) clusters: Anion photoelectron spectroscopy and theoretical calculations.

The photoelectron spectra of Au2Sin- (n = 1-7) clusters were measured, and the structural evolution and bonding properties of Au2Si1-7- anions and their corresponding neutral counterparts were investigated by theoretical calculations. The two Au atoms in Au2Si1-7-/0 prefer to occupy low coordinate sites and form fewer Au-Si bonds. The aurophilic interaction is fairly weak in these clusters. The most stable structures of both Au2Sin- anions and Au2Sin neutrals can be described as the two Au atoms interacting with the Sin frameworks. The most stable isomers of Au2Sin- anions are in spin doublet states, while those of the neutral clusters are in spin singlet states. The lowest-lying isomers of Au2Si1-/0 have C2v symmetric V-shaped structures. The global minimum of the Au2Si2- anion has a D2h symmetric planar rhombus structure, while that of the Au2Si2 neutral adopts a C2v symmetric dibridged structure. In Au2Si3-/0, the two Au atoms independently interact with the different Si-Si bonds of the Si3 triangular structure. The global minima of Au2Si4-7-/0 primarily adopt prismatic based geometries. Interestingly, Au2Si6-/0 have significant 3D aromaticity and possess σ plus π double bonding characters, which play important roles in their structural stability.