An Efficient Growth Pattern Algorithm (GrowPAL) for Cluster Structure Prediction.

Identifying the lowest energy isomers in large clusters is a major challenge. Here, we introduce the Growth Pattern Algorithm (GrowPAL), a new approach that generates initial seeds composed of n+1 atoms from the system with n atoms through an interstitial-type addition (I-type) mechanism. We evaluated the effectiveness of GrowPAL on Lennard-Jones (LJ) clusters with up to n = 80 atoms, verifying the algorithm's ability to find challenging minima such as LJ38 and the partially icosahedral LJ69 with fewer optimizations than existing methods. In addition, we discuss the advantages and limitations of GrowPAL using our deconstruction scheme, which identifies "forebears" structures to study growth pathways. Having evaluated the strengths and weaknesses of GrowPAL, we employed it to explore Sutton-Chen clusters containing 5 to 80 atoms, uncovering three new lowest energy forms. We then applied GrowPAL to boron clusters containing 8 to 15 atoms, successfully identifying all reported minima. Overall, GrowPAL offers a practical solution for efficiently identifying global minima in hierarchical systems, thereby reducing computational costs.

Breaking the plane: B5H5 is a three-dimensional structure.

In this study, we delved into the structure of B5H5 and questioned some of its accepted assumptions. By exploring the potential energy surface, we found a new three-dimensional structure as the global minimum. This finding is in contrast with the previously hypothesized planar and cage-like models. Our exploration extends to the kinetic stability of various B5H5 isomers, offering insights into the dynamic behavior of these molecules.

Structural and optical properties of the Agn-tyrosine complexes (n = 3-12): a density functional theory study.

We study the optical properties of Agn (n = 3-12) neutral clusters and their coordination with a tyrosine (Tyr) molecule. A global search strategy coupled with density functional theory (DFT) computations explored the potential energy surface. Adsorption energy calculations predicted that Tyr coordination stabilizes the metal clusters, favouring the Agn-Tyr complexes with an even number of silver atoms. For the Agn low-lying isomers, the general shape and the major transitions of the calculated time dependent-DFT (TD-DFT) absorption spectra align with those of previous reports measured in an argon environment. We use the analysis of non-covalent interactions to identify the specific interactions between each silver cluster and functional groups of Tyr. The TD-DFT absorption spectra for the Agn-Tyr complexes showed that Tyr significantly modifies the optical properties of the coordinated silver clusters and affects the smaller systems to a greater extent. The optical absorption results of the bare Agn clusters and the Agn-Tyr complexes are compared and discussed in detail.

Unveiling the electronic and structural consequences of removing two electrons from B12H122.

The notion that a regular icosahedron is unattainable in neutral B12H12 has persisted for nearly 70 years. This is because 24 valence electrons are used for B-H bonds, while another 24 electrons are necessary to maintain the deltahedron, unlike the 26 used in the dianion. According to Wade-Mingos rules, the neutral system should be a deltahedron with a capped face. Nevertheless, our exploration of the potential energy surface of B12H12 reveals that the global minimum is a closed-shell form with an H2 unit attached to a boron vertex of B12H10, preserving the deltahedral boron skeleton.

Reconsidering the Structures of C2 Al4 - and C2 Al5.

The study of C2 Al4 -/0 and C2 Al5 -/0 was conducted using anion photoelectron spectroscopy and quantum chemical computations. The present findings reveal that C2 Al4 - has a boat-like structure, with a single C2 unit surrounded by four aluminum atoms. In contrast, the neutral C2 Al4 species adopts a D2h planar structure with two planar tetracoordinate carbon (ptC) units, consistent with previous reports. Furthermore, the global minimum isomer of C2 Al5 - adopts a D3h symmetry, where the C2 unit interacts with five aluminum atoms. It was also found that a lower symmetry structure of C2 Al5 - , where all five aluminum atoms are located on the same side of the C2 unit, albeit slightly higher in energy compared to the D3h structure. These computations show that the D3h structure of C2 Al5 - is highly stable, exhibiting a large HOMO-LUMO gap.

CAl11-: a molecular rotor with a quasi-planar tetracoordinate carbon.

In this work, we analyzed the bonding and fluxional character of the global minimum of CAl11-. Its structure is formed by two stacked layers, one of them resembles the well-known planar tetracoordinate carbon CAl4 on top of a hexagonal Al@Al6 wheel. Our results show that the CAl4 fragment rotates freely around the central axis. The exceptional stability and fluxionality of CAl11- derive from its particular electron distribution.

Dismantlement of ammonia upon interaction with Ben (n ≤ 10) clusters.

The interaction of ammonia with Ben (n < 1-10) clusters has been investigated by density functional theory and ab initio calculations. The main conclusion is that, regardless of the size of the Be cluster, neither the structure of ammonia nor that of the Be clusters are preserved due to a systematic dissociation of its NH bonds and a spontaneous H-shift toward the available Be atoms. This H migration not only leads to rather stable BeH bonds, but dramatically enhances the strength of the BeN bonds as well. Accordingly, the maximum stability is found for the interaction with the beryllium trimer, leading to a complex with three NBe and three BeH bonds. Another maximum in stability, although lower than that reached for n = 3, is found for the Be heptamer, since from n = 6, a new NBe bond is formed, so that complexes from n = 6 to n = 10 are characterized by the formation of a NBe4 moiety, whose stability reaches a maximum at n = 7. The bonding characteristics of the different species formed are analyzed by means of AIM, NBO, ELF and AdNDP approaches.

Acid Dissociation in (HX)n (H2 O)n Clusters (X=F, Cl, Br, I; n=2, 3).

In this work, we analyze the interactions between two or three hydrogen halide molecules and the same number of water moieties through a systematic exploration of their potential energy surfaces. Our results indicate that the most stable HF and HCl aggregates do not experience dissociation of any of the acid fragments, even with three water molecules. In contrast, in the HBr and HI clusters, one of the acid fragments does dissociate. While the global minimum of (HBr)3 (H2 O)3 is a hydrogen-bridged bihalide anion (BrHBr- ), which is persistent at temperatures up to 203 K, the lowest energy structure of (HI)3 (H2 O)3 has a separated ion pair, but the motif with a bihalide anion (IHI- ) is only 0.2 kcal mol-1 above the global minimum. Among the more stable structures is a broad spectrum of contacts, including water⋯water, HX⋯water, and HX⋯HX hydrogen bonds, halogen bonds, ionic and long-range X⋯H contacts.

γ-Valerolactone Production from Levulinic Acid Hydrogenation Using Ni Supported Nanoparticles: Influence of Tungsten Loading and pH of Synthesis.

γ-Valerolactone (GVL) has been considered an alternative as biofuel in the production of carbon-based chemicals; however, the use of noble metals and corrosive solvents has been a problem. In this work, Ni supported nanocatalysts were prepared to produce γ-Valerolactone from levulinic acid using methanol as solvent at a temperature of 170 °C utilizing 4 MPa of H2. Supports were modified at pH 3 using acetic acid (CH3COOH) and pH 9 using ammonium hydroxide (NH4OH) with different tungsten (W) loadings (1%, 3%, and 5%) by the Sol-gel method. Ni was deposited by the suspension impregnation method. The catalysts were characterized by various techniques including XRD, N2 physisorption, UV-Vis, SEM, TEM, XPS, H2-TPR, and Pyridine FTIR. Based on the study of acidity and activity relation, Ni dispersion due to the Lewis acid sites contributed by W at pH 9, producing nanoparticles smaller than 10 nm of Ni, and could be responsible for the high esterification activity of levulinic acid (LA) to Methyl levulinate being more selective to catalytic hydrogenation. Products and by-products were analyzed by 1H NMR. Optimum catalytic activity was obtained with 5% W at pH 9, with 80% yield after 24 h of reaction. The higher catalytic activity was attributed to the particle size and the amount of Lewis acid sites generated by modifying the pH of synthesis and the amount of W in the support due to the spillover effect.

Effects of Temperature on Enantiomerization Energy and Distribution of Isomers in the Chiral Cu13 Cluster.

In this study, we report the lowest energy structure of bare Cu13 nanoclusters as a pair of enantiomers at room temperature. Moreover, we compute the enantiomerization energy for the interconversion from minus to plus structures in the chiral putative global minimum for temperatures ranging from 20 to 1300 K. Additionally, employing nanothermodynamics, we compute the probabilities of occurrence for each particular isomer as a function of temperature. To achieve that, we explore the free energy surface of the Cu13 cluster, employing a genetic algorithm coupled with density functional theory. Moreover, we discuss the energetic ordering of isomers computed with various density functionals. Based on the computed thermal population, our results show that the chiral putative global minimum strongly dominates at room temperature.

Planar tetracoordinate fluorine atoms.

Among the list of planar tetracoordinate atoms, fluorine is missing. So far, there are no theoretical or experimental reports suggesting their existence. Herein, we introduce the first six combinations (FIn4 +, FTl4 +, FGaIn3 +, FIn2Tl2 +, FIn3Tl+, and FInTl3 +) whose global minima contain a planar tetracoordinate fluorine. The bonding analyses indicate that the interactions between the fluorine and the peripheral atoms are significantly electrostatic, which is also reflected in the electronic delocalization. As opposed to other planar tetracoordinate systems with carbon, nitrogen, or oxygen atoms, the fluorine in the ptFs does not act as a σ-acceptor, restraining any back-donation. On the other hand, σ-electrons show a diatropic response, which would characterize these clusters as σ-aromatic.

Molecular Docking and Dynamics Simulation of Protein ß-Tubulin and Antifungal Cyclic Lipopeptides.

To elucidate interactions between the antifungal cyclic lipopeptides iturin A, fengycin, and surfactin produced by Bacillus bacteria and the microtubular protein ß-tubulin in plant pathogenic fungi (Fusarium oxysporum, Colletrotrichum gloeosporioides, Alternaria alternata, and Fusarium solani) in molecular docking and molecular dynamics simulations, we retrieved the structure of tubulin co-crystallized with taxol from the Protein Data Bank (PDB) (ID: 1JFF) and the structure of the cyclic lipopeptides from PubChem (Compound CID: 102287549, 100977820, 10129764). Similarity and homology analyses of the retrieved ß-tubulin structure with those of the fungi showed that the conserved domains shared 84% similarity, and the root mean square deviation (RMSD) was less than 2 Å. In the molecular docking studies, within the binding pocket, residues Pro274, Thr276, and Glu27 of ß-tubulin were responsible for the interaction with the cyclic lipopeptides. In the molecular dynamics analysis, two groups of ligands were formed based on the number of poses analyzed with respect to the RMSD. Group 1 was made up of 10, 100, and 500 poses with distances 0.080 to 0.092 nm and RMSDs of 0.10 to 0.15 nm. For group 2, consisting of 1000 poses, the initial and final distance was 0.1 nm and the RMSDs were in the range of 0.10 to 0.30 nm. These results suggest that iturin A and fengycin bind with higher affinity than surfactin to ß-tubulin. These two lipopeptides may be used as lead compounds to develop new antifungal agents or employed directly as biorational products to control plant pathogenic fungi.

Bonding and Mobility of Alkali Metals in Helicenes.

In this work, we analyze the interactions of alkali metal cations with [6]- and [14]helicene and the cation mobility of therein. We found that the distortion of the carbon skeleton is the reason that some of the structures which are local minima for the smallest cations are not energetically stable for K+ , Rb+ , and Cs+ . Also, the most favorable complexes are those where the cation is interacting with two rings forming a metallocene-like structure, except for the largest cation Cs+ , where the distortion provoked by the size of the cation destabilizes the complex. As far as mobility is concerned, the smallest cations, particularly Na+ , are the ones that can move most efficiently. In [6]helicene, the mobility is limited by the capture of the cation forming the metallocene-like structure. In larger helicenes, the energy barriers for the cation to move are similar both inside and outside the helix. However, complexes with the cation between two layers are more energetically favored so that the movement will be preferred in that region. The bonding analysis reveals that interactions with no less than 50 % of orbital contribution are taking place for the series of E+ -[6]helicene. Particularly, the complexes of Li+ show remarkable orbital character (72.5-81.6 %).

Structure and Bonding in CE5- (E=Al-Tl) Clusters: Planar Tetracoordinate Carbon versus Pentacoordinate Carbon.

The structure, bonding, and stability of clusters with the empirical formula CE5- (E=Al-Tl) have been analyzed by means of high-level computations. The results indicate that, whereas aluminum and gallium clusters have C2v structures with a planar tetracoordinate carbon (ptC), their heavier homologues prefer three-dimensional C4v forms with a pentacoordinate carbon center over the ptC one. The reason for such a preference is a delicate balance between the interaction energy of the fifth E atom with CE4 and the distortion energy. Moreover, bonding analysis shows that the ptC systems can be better described as CE4- , with 17-valence electrons interacting with E. The ptC core in these systems exhibits double aromatic (both σ and π) behavior, but the σ contribution is dominating.

How Many Water Molecules Does it Take to Dissociate HCl?

The potential energy surfaces of the HCl(H2O)n (n is the number of water molecules) clusters are systematically explored using density functional theory and high-level ab initio computations. On the basis of electronic energies, the number of water molecules needed for HCl dissociation is four as reported by some experimental groups. However, this number is five owing to the inclusion of entropic factors. Wiberg bond indices are calculated and analyzed, and the results provide a quadratic correlation and classification of clusters according to the nondissociated, partially dissociated, and fully dissociated character of the H-Cl bond. Our computations show that if temperature is not controlled during the experiment, the values obtained for the dipole moment (or for any measurable property) are susceptible to change, providing a different picture of the number of water molecules needed for HCl dissociation in a nanoscopic droplet.

How strong are the metallocene-metallocene interactions? Cases of ferrocene, ruthenocene, and osmocene.

An exhaustive exploration of the potential energy surfaces of ferrocene, ruthenocene and osmocene dimers has been performed. Our computations involving dispersion show that only four different isomers are present in each metallocene dimer. The collective action of small interaction energies of dispersive nature leads to a dissociation energy of 7.5 kcal mol(-1) for the ferrocene dimer. Dispersion has strong effects on the geometrical parameters, reducing the M···M distances by almost 1 Å. Our results also reveal that inclusion of entropic factors modifies the relative stability of the complexes. The nature of bonding is examined using the energy decomposition analysis and the non-covalent interaction index. Both analyses indicate that dispersion is the major contributing factor in stabilizing a metallocene dimer.

Effects of Co doping on the metamagnetic states of the ferromagnetic fcc Fe-Co alloy.

The evolution of the metamagnetic states in the ferromagnetic face centered cubic (fcc) Fe(1-x)Co(x) alloy as a function of Co concentration has been studied by means of first-principles calculations. The ground state properties were obtained using the full-potential linear augmented plane wave method and the generalized gradient approximation for the exchange-correlation functional. The alloying was modeled using the virtual crystal approximation and the magnetic states were obtained from the calculations of the total energy as a function of the spin moment, using the fixed spin moment method. For ferromagnetic fcc Fe, the binding-energy curve shows metamagnetic behavior, with two minima corresponding to a small-volume, low-spin (LS) state and a large-volume, high-spin (HS) state, which are separated by a small energy (E(LS) ≲ E(HS)). The evolution of the magnetic moment, the exchange integral (J), and the binding-energy curve is analyzed in the whole range of Co concentrations (x). The magnetic moment corresponding to the HS state decreases monotonically from 2.6 µ(B)/atom in fcc Fe to 1.7 µ(B)/atom in fcc Co. In contrast, the exchange integral for the HS state shows a maximum at around x = 0.45. The thermal dependence of the lattice parameter is evaluated with a method based on statistical mechanics using the binding-energy curve as an effective potential. It is observed that the behavior of the lattice parameter with temperature is tuned by Co doping, from negative thermal expansion in fcc Fe to positive thermal expansion in fcc Co, through the modification of the energetics of the metamagnetic states.