Global Minimum Structure Research Articles

Effects of manganese doping on the structure evolution of small-sized boron clusters

Atomic doping of clusters is known as an effective approach to stabilize or modify the structures and properties of resulting doped clusters. We herein report the effect of manganese (Mn) doping on the structure evolution of small-sized boron (B) clusters. The global minimum structures of both neutral and charged Mn doped B cluster (n = 10–20 and Q = 0, ±1) have been proposed through extensive first-principles swarm-intelligence based structure searches. It is found that Mn doping has significantly modified the grow behaviors of B clusters, leading to two novel structural transitions from planar to tubular and then to cage-like B structures in both neutral and charged species. Half-sandwich-type structures are most favorable for small (n ⩽ 13) clusters and gradually transform to Mn-centered double-ring tubular structures at clusters with superior thermodynamic stabilities compared with their neighbors. Most strikingly, endohedral cages become the ground-state structures for larger (n ⩾ 19) clusters, among which adopts a highly symmetric structure with superior thermodynamic stability and a large HOMO-LUMO gap of 4.53 eV. The unique stability of the endohedral cage is attributed to the geometric fit and formation of 18-electron closed-shell configuration. The results significantly advance our understanding about the structure and bonding of B-based clusters and strongly suggest transition-metal doping as a viable route to synthesize intriguing B-based nanomaterials.

Assessing the stable conformations of ibuprofen in solution by means of Residual Dipolar Couplings

Detailing the conformational equilibria between global and local minimum energy structures of anti-inflammatory α-arylpropionic acids directly in solution is of the utmost importance for a better understanding of the structure-activity relationships, hence providing valuable clues for rational structure-based drug design studies. Here the conformational preferences of the widely used pharmaceutical ibuprofen were investigated in solution by NMR spectroscopy in weakly ordering phases. A thorough theoretical treatment of the anisotropic interactions that are relevant for NMR spectra led to a conformational model characterized by six pairs of symmetry-related conformers, in particular four couples of gauche structures, with a total probability of 93%, and 2 couples of trans structures, counting for the remaining 7%.

SGO: A fast engine for ab initio atomic structure global optimization by differential evolution

As the high throughout calculations and material genome approaches become more and more popular in material science, the search for optimal ways to predict atomic global minimum structure is a high research priority. This paper presents a fast method for global search of atomic structures at ab initio level. The structures global optimization (SGO) engine consists of a high-efficiency differential evolution algorithm, accelerated local relaxation methods and a plane-wave density functional theory code running on GPU machines. The purpose is to show what can be achieved by combining the superior algorithms at the different levels of the searching scheme. SGO can search the global-minimum configurations of crystals, two-dimensional materials and quantum clusters without prior symmetry restriction in a relatively short time (half or several hours for systems with less than 25 atoms), thus making such a task a routine calculation. Comparisons with other existing methods such as minima hopping and genetic algorithm are provided. One motivation of our study is to investigate the properties of magnetic systems in different phases. The SGO engine is capable of surveying the local minima surrounding the global minimum, which provides the information for the overall energy landscape of a given system. Using this capability we have found several new configurations for testing systems, explored their energy landscape, and demonstrated that the magnetic moment of metal clusters fluctuates strongly in different local minima.

The Influence of Carbon Doping on the Structures, Properties, and Stability of Beryllium Clusters

The global minimum structures of the carbon‐doped Ben (n = 1–12) clusters are obtained at the B3PW91/6‐311+G(d) level and compared with those of pure beryllium clusters. It is found that the carbon dopant prefers to be located outside the host Ben cage and tends to be tetracoordinated. The evolution of the electronic and energetic properties of BenC is studied using the QCISD(T) method. Results show that the introduction of carbon doping strengthens intracluster interaction of beryllium clusters. Besides, the Be3C and Be8C clusters, with their particular stability, are considered as magic‐number clusters in the BenC series. Molecular‐orbital (MO) analysis indicates that both clusters have fully filled electron shells, whereas the contribution of the carbon atomic orbital leads to MO energy‐level disorder of the BenC clusters.

A Fukui function-guided genetic algorithm. Assessment on structural prediction of Sin (n = 12-20) clusters.

Theoretical studies are essential for the structural characterization of clusters, when it comes to rationalize their unique size-dependent properties and composition. However, the rapid growth of local minima on the potential energy surface (PES), with respect to cluster size, makes the candidate identification a challenging undertaking. In this article, we introduce a hybrid strategy to explore the PES of clusters. This proposal involves the use of a biased initial population of a genetic algorithm procedure. Each individual in this population is built by assembling small fragments, according to the best matching of the Fukui function. The performance of a genetic algorithm procedure. The performance of the method is assessed on the PES exploration of medium-sized Sin clusters (n = 12-20). The most relevant results are: (a) the method converges at almost half of the time used by the canonical version of the GA and, (b) in all the studied cases, with the exception of Si13 and Si16 , the method allowed to identify the global minimum (GM) and other important low-lying structures. Additionally, the apparent deficiency of the proposal to identify the GM was corrected when a Si atom, or other low-lying isomers, were considered to build the clusters. © 2017 Wiley Periodicals, Inc.

On the structure of the simplest triselenide compound model and the stabilizing effect of water molecules

This study provides a molecular view of the simplest triselenide compound model, the hydrogen triselenide radical (HSe3) with Density Functional Theory (DFT), Møller–Plesset perturbation theory, and Coupled-Cluster theory. An analysis of the H–Se–Se–Se dihedral angle indicated barrier energies for the cis (1.8kcalmol−1) and trans (1.4kcalmol−1) configurations, which confirms the gauche conformation as the global minimum structure in the ground state with hydrogen atom out of plane. The central and the edge selenium–selenium bond lengths were predicted as 2.214–2.274 and 2.350–2.420Å, respectively, while an exploration of the edge Se–Se bond predicted a large polarized σ-bond revealing Wiberg (1.32) and Mayer order (1.31) bond order indices enhancing this feature. The influence of the population method on the prediction of the atomic charge distribution, the spin density, and the electric dipole moment was investigated. The harmonic and anharmonic vibrational frequency modes were also analyzed here. Moreover, the interaction between HSe3 and water molecules was investigated in order to explore the structural, electronic, and spectroscopic properties of monohydrated and dihydrated structures [HSe3(H2O)n; n=1,2]. Natural bond orbital (NBO) analysis and a topological analysis with the quantum theory of atoms in molecules (QTAIM) were employed to understand how the intermolecular interactions stabilize the triselenide compound.

On the electronic structures and s/p-orbital aromaticity in the Hg3Al3+/−, Hg3Al3Li, and Hg3Al3Be+ clusters

The equilibrium geometries, harmonic vibrational frequencies, stabilities, and chemical bonding of the low-lying states for all-metal Hg3Al3+/−, Hg3Al3Li, and Hg3Al3Be+ clusters are investigated using 2nd order Møller–Plesset perturbation theory. The extensive search for the global minimum structures of Hg3Al3+/− at the MP2 level of theory with 6-311++G∗ basis set for Al and CEP-121G basis set for Hg reveals that the ground states of the Hg3Al3+ and Hg3Al3− clusters are all singlet state 1A′ with Cs symmetry. A detailed molecular orbital (MO) analysis reveals that the Hg3Al3+ (Cs, 1A′) cation and Hg3Al3− (Cs, 1A′) anion possess double aromaticity (simultaneous presence of σ- and π-aromaticity). The hexagonal pyramidal-type Hg3Al3Li and Hg3Al3Be+ complexes containing the Hg3Al3− ligand reveal that the Hg3Al3− structural units are preserved in the Hg3Al3Li and Hg3Al3Be+ complexes, which also possess corresponding aromatic characters.

Neural network potentials for dynamics and thermodynamics of gold nanoparticles.

For understanding the dynamical and thermodynamical properties of metal nanoparticles, one has to go beyond static and structural predictions of a nanoparticle. Accurate description of dynamical properties may be computationally intensive depending on the size of nanoparticle. Herein, we demonstrate the use of atomistic neural network potentials, obtained by fitting quantum mechanical data, for extensive molecular dynamics simulations of gold nanoparticles. The fitted potential was tested by performing global optimizations of size selected gold nanoparticles (Aun, 17 ≤ n ≤ 58). We performed molecular dynamics simulations in canonical (NVT) and microcanonical (NVE) ensembles on Au17, Au34, Au58 for a total simulation time of around 3 ns for each nanoparticle. Our study based on both NVT and NVE ensembles indicate that there is a dynamical coexistence of solid-like and liquid-like phases near melting transition. We estimate the probability at finite temperatures for set of isomers lying below 0.5 eV from the global minimum structure. In the case of Au17 and Au58, the properties can be estimated using global minimum structure at room temperature, while for Au34, global minimum structure is not a dominant structure even at low temperatures.

Analysis and Investigation of Electronic Transport Coulomb Blockade in Al68 Based on DFT

Electronic transport properties in an Al cluster are investigated theoretically in this paper. We propose a possible illustration of Coulomb blockade based on variable electrostatic potential (ESP). Density functional theory (DFT) was used to achieve the global minimum structure and wave function for analyzing the ESP and density of states (DOS) of Al68 in different charged states. Al68 is able to contain multiple electrons. According to the calculation of systematic energy and surface ESP, respectively, the surface of Al68 presents a 0–6.33 eV ESP barrier after electron injection, which is 0 eV at first. The probability density of flow of electrons was calculated under one‐dimensional model with double barriers. Expected results were obtained, containing a nonlinear relationship between J and V and flow density steps. Moreover, an assumption is proposed associated with nonlinear conductance phenomenon of zero‐dimensional nanomaterials. Significantly, Al films with different thicknesses were prepared by the low vacuum physical vapor deposition (LVPVD) method, exhibiting novel fluorescent behaviors. In addition, the I–V curve of a 25‐nm Al film exhibited two steps at 7 and 27 V, respectively, which meant that the step effect was caused by Coulomb blockade, in accordance with the theoretical calculation.

Puzzle of magnetic moments of Ni clusters revisited using quantum Monte Carlo method.

The puzzle of the magnetic moments of small nickel clusters arises from the discrepancy between values predicted using density functional theory (DFT) and experimental measurements. Traditional DFT approaches underestimate the magnetic moments of nickel clusters. Two fundamental problems are associated with this puzzle, namely, calculating the exchange-correlation interaction accurately and determining the global minimum structures of the clusters. Theoretically, the two problems can be solved using quantum Monte Carlo (QMC) calculations and the ab initio random structure searching (AIRSS) method correspondingly. Therefore, we combined the fixed-moment AIRSS and QMC methods to investigate the magnetic properties of Nin (n = 5-9) clusters. The spin moments of the diffusion Monte Carlo (DMC) ground states are higher than those of the Perdew-Burke-Ernzerhof ground states and, in the case of Ni8-9, two new ground-state structures have been discovered using the DMC calculations. The predicted results are closer to the experimental findings, unlike the results predicted in previous standard DFT studies.

Low-energy structures of clusters modeled with competing repulsive and either long- or moderate short-range attractive interactions

We have employed an evolutionary algorithm (EA) to study the low-energy landscape of clusters modeled with a potential which is composed by an attractive Morse function and a repulsive Yukawa component. Since the range of the Morse potential is controlled by a single parameter (ρ), this has been varied between 3 and 14 to study its influence on the lowest-energy structure. The present results show that shorter-ranged attractive potentials tend to magnify the effect of the repulsive Yukawa function on the global minimum structure. Due to the higher energy-barriers, the short-range attractive interactions produce low-energy dissociated structures at smaller cluster sizes than long-range potentials. As a consequence of this, global minimum structures of clusters involving short-range attractive potentials tend to be elongated in order to reduce the number of second nearest-neighbor particles that usually correspond to a very repulsive contribution for the interaction energy. In addition, Bernal spirals and beaded-necklace motifs are often observed for potentials with a short-range attractive component, while long-ranged interactions can hardly support such structures. We have also searched for the global minima of the N=13 binary clusters formed by various combinations of the ρ-parameter in the Morse potential. Most of such binary clusters are unstable in relation to the corresponding N=13 homogeneous aggregates, and the structure tend to assume the usual icosahedral shape (especially for the cases involving the longer-range potentials) with particles associated to lower ρ-values preferentially located on the surface.

Discerning Near-Isoergic Isomers. A Matrix Isolation Infrared and ab Initio Study of the Propargyl Alcohol Dimers.

This study reports the first infrared spectroscopic investigation of the dimers of propargyl alcohol (PA) using matrix isolation infrared spectroscopy and ab initio computations. Computations indicated a number of isomers for the dimer, with the two most stable structures being nearly isoergic. Interestingly, our matrix isolation experiments were able to discern both of these isomers, which were corroborated by computations performed at the M06-2X/6-311++G(d,p) level. Identifying these two isomers was significant, since the two most stable and near-isoergic isomers can be expected to play an important role in the structure of the propargyl alcohol ices, an understanding of which is of significant importance in the study of astrochemical environments. The global minimum structure differed from its near-isoergic local minimum, in the dimer architecture; the former making a three-point hydrogen-bonded contact, O-H···O, O-H···π, and C-H···π, and the latter having two. The global minimum had been observed in molecular beam experiments, though not the near-isoergic local minimum. In both isomers, the propargyl alcohol monomer units were in their gauche conformation. AIM and NBO analyses were also performed to understand the nature of interaction in the dimers. The results of this study may well have significant implications in interpreting the PA spectra in astrochemical environments.

Structural evolution and bonding of phosphorus-doped silicon clusters SinPm−/0/+ with n = 1–10, m = 1, 2

The geometrical evolution, electronic structure and thermodynamic stability of a series of singly-doped SinP and doubly-doped SinP2 silicon clusters with n=1–10, in the neutral, cationic and anionic states were systematically investigated using DFT computations. The global minimum structures were identified using different search approaches. The isoelectronic structures including the neutral SinP, the cation Sin−1P2+ and the anion Sin+1− exhibit a similar shape. Structural evolution of doubly P-doped SinP2 was found to adopt a substitution mechanism rather than a caption pathway. Dissociation energies for various channels of SinP2 clusters point out that the fragmentations generating P2 atoms plus the corresponding Sin host is the most preferred process. The closed-shell species Si4P−, Si3P2, Si7P− and Si6P2 are found to have high thermodynamic stability with large binding energies and second-order difference energies. Their enhanced stability can be rationalized in terms of the Jellium shell model. The aromatic character was probed using the ring current maps of electron densities. The planar SiP2, Si2P− and Si3P− clusters feature an aromatic character, whereas only the five-membered plane of the bipyramid-like structures involving Si6P− and Si5P2 are locally aromatic.

DFT Global Optimization of Gas-Phase Subnanometer Ru–Pt Clusters

The global optimization of subnanometer Ru–Pt binary nanoalloys in the size range 2–8 atoms is systematically investigated using the Birmingham Parallel Genetic Algorithm (BPGA). The effect of size and composition on the structures, stabilities and mixing properties of Ru–Pt nanoalloys are discussed. The results revealed that the maximum mixing tendency is achieved for 40–50% Ru compositions. Global minimum structures show that the Ru atoms prefer to occupy central and core positions and maximize coordination number and the number of strong Ru–Ru bonds.

Prediction of hypervalent molecules: investigation on MnC (M = Li, Na, K, Rb and Cs; n = 1-8) clusters.

New hypervalent molecules have emerged from a systematic exploration of the structure and bonding of MnC (M = Li, Na, K, Rb and Cs; n = 1-8) clusters via an unbiased CALYPSO structure investigation combined with density functional theory. The global minimum structures are obtained at the B3LYP/6-311+G* and CCSD(T)/6-311+G* levels of theory. The observed growth behavior clearly indicates that the ground state of MnC (M = Li, Na, K, Rb and Cs; n = 1-8) is transformed from a planar to a three-dimensional (3D) structure at n = 4. A maximum of six alkali atoms can be bound atomically to a carbon atom. The determination of the averaged binding energies Eb(n), fragmentation energies ΔE(n) and HOMO-LUMO energy gaps unambiguously supports the stability of M6C. This indicated conclusively that 6 is a magic Li-coordination number for C. The nature of bonding is further investigated by an insightful analysis of the highest occupied molecular orbital (HOMO) and the topology of chemical bonds for the most stable clusters. In the final step, electron localization functions (ELF) and density of states (DOS) are determined in order to consolidate the acquired information on the studied electronic structures.

Identification of the smallest peptide with a zwitterion as the global minimum: a first-principles study on arginine-containing peptides.

Zwitterions are believed to play an important role in determining the structures, properties and functions of peptides and proteins. However, the smallest peptide with a zwitterionic structure as the global minimum in the gas phase is still not yet identified. In this study, an effective step-by-step strategy has been used to characterize the stable conformers of arginine-containing peptides arginylalanine (ArgAla) and arginylserine (ArgSer). Energy calculations at the DSD-PBEP86-D3BJ/aug-cc-pVTZ level and further extrapolation to the complete basis set (CBS) limit have confirmed, for the first time, that ArgSer appears to be a promising candidate as the smallest peptide with a zwitterionic global minimum structure. First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra and X-ray photoelectron spectra (XPS) at C, N and O K-edges, as well as for infrared (IR) spectra of these arginine-containing peptides. Notable spectral differences were found which enable the unambiguous identification of different neutral forms in future experiments. Our study thus provides valuable insights into the structural stability of zwitterions with the increase of molecular size and illustrates the competition between the canonical and zwitterionic isomers.

Planar B38- and B37- clusters with a double-hexagonal vacancy: molecular motifs for borophenes.

Boron clusters have been found to exhibit a variety of interesting electronic, structural, and bonding properties. Of particular interest are the recent discoveries of the 2D hexagonal B36-/0 which led to the concept of borophenes and the 3D fullerene-like B40-/0 which marked the onset of borospherene chemistry. Here, we present a joint photoelectron spectroscopic and first-principles study of B37- and B38-, which are in the transition size range between the 2D borophene-type clusters and the 3D borospherenes. These two clusters are found to possess highly stable 2D global-minimum structures consisting of a double-hexagonal vacancy. Detailed bonding analyses reveal that both B37- and B38- are all-boron analogues of coronene (C24H12) with a unique delocalized π system, featuring dual π aromaticity. These clusters with double hexagonal vacancies can be viewed as molecular motifs for the χ3-borophene which is the most stable form of borophenes recently synthesized on an Ag(111) substrate.

A universal mechanism of the planar boron rotors B11-, B13+, B15+, and B19-: inner wheels rotating in pseudo-rotating outer bearings.

Planar boron clusters B11-, B13+, B15+, and B19- have been introduced recently as molecular Wankel motors or tank treads. Here we present a universal mechanism for these dynamically fluxional clusters; that is, they are molecular rotors with inner wheels that rotate almost freely in pseudo-rotating outer bearings, analogous to rotating molecules trapped in pseudo-rotating cages. This mechanism has significant quantum mechanical consequences: the global-minimum structures of the clusters have C2v symmetry, whereas the wheels rotating in pseudo-rotating bearings generate rosette-type shapes with D9h, D10h, D11h, and D13h symmetries. The related rotational/pseudo-rotational energies appear with characteristic band structures, effecting the dynamics.

Ab Initio Calculations on some Antiepileptic Drugs such as Phenytoin, Phenbarbital, Ethosuximide and Carbamazepine

This research deals with some antiepileptic agents that are used to treat antiepileptic seizures. Stable conformational structures corresponding to potential energy minima for each molecule are determined in the gas phase with both Hartree-Fock and density functional methods. Polarizable continuum models have been employed to assess solvent effects on the activity of global minimum structures, and each molecule has become stabilized with increasing solvent dielectric constant. To examine structure-activity relationships, electron propagator calculations of ionization energies, electron affinities, and corresponding energy gaps with the Outer Valence Green’s Function (OVGF) and Partial Third Order (P3) approximations have also been performed to compare with Koopmans’s Theorem results. The best correlation between logED50 and electron affinity values, with a linear regression coefficient of 0.98 and a standard deviation of 0.19, is obtained for Koopmans’s Theorem with the 6-311++g** basis set in chloroform.

Growth patterns, shapes, and electronic properties of mixed SimGen clusters with [formula omitted

A global optimization method in combination with the density-functional tight-binding approach is used to determine all putative global minimum energy structures for mixed silicon-germanium clusters SimGen with n+m⩽30. All obtained structures are re-optimized with first-principles density-functional calculations and the influence of the composition on the shapes is studied. Several extraordinary stable structures are identified and it is shown that the stability correlates with the ‘prolateness’ of the cluster. However, it was not possible to relate the electronic properties to a single structural property like shape, composition, or local atomic environment.