AUTOMATON: A Program That Combines a Probabilistic Cellular Automata and a Genetic Algorithm for Global Minimum Search of Clusters and Molecules.

A novel program for the search of global minimum structures of atomic clusters and molecules in the gas phase, AUTOMATON, is introduced in this work. This program involves the following: first, the generation of an initial population, using a simplified probabilistic cellular automaton method, which allows easy control of the adequate distribution of atoms in space; second, the fittest individuals are selected to evolve, through genetic operations (mating and mutations), until the best candidate for a global minimum surfaces. In addition, we propose a simple way to build the descendant structures by establishing a ranking of genes to be inherited. Thus, by means of a chemical formula checker procedure, genes are transferred to the offspring, ensuring that they always have the appropriate type and number of atoms. It is worth noting that a fraction of the fittest group is subject to mutation operations. This program also includes algorithms to identify duplicate structures: one based on geometric similarity and another on the similar distribution of atomic charges. The effectiveness of the program was evaluated in a group of 45 molecules, considering organic and organometallic compounds (benzene, cyclopentadienyl anion, and ferrocene), Zintl ion clusters [Sn9- m- nGe mBi n](4- n)- ( n = 1-4 and m = 0-(9- n)), star-shaped clusters (Li7E5+, E = BH, C, Si, Ge) and a variety of boron-based clusters. The global minimum and the lowest-energy isomers reported in the literature were found for all the cases considered in this article. These results successfully prove AUTOMATON's effectiveness on the identification of energetically preferred structures of a wide variety of chemical species.

Which NICS method is most consistent with ring current analysis? Assessment in simple monocycles.

The aromaticity of benzene, Al4 2- cluster, cyclopropane, borazine and planar cyclooctatetraene (COT) was analyzed according to different strategies based on nucleus-independent chemical shift (NICS) computations. The analysis of NICS-components evolution along the main molecular axis seems to be the most adequate and simplest strategy to predict the aromatic or antiaromatic character of the studied systems. Moreover, the analysis of the σ- and π-electron contributions to the out-of-plane component of NICS (NICS zz ) leads to the same qualitative and quantitative conclusions previously obtained by the analysis of the magnetically induced ring current densities.

Exploiting electronic strategies to stabilize a planar tetracoordinate carbon in cyclic aromatic hydrocarbons.

A new approach to stabilize compounds containing a planar tetracoordinate carbon (ptC), embedded in aromatic hydrocarbons, is presented herein. This is achieved by using ligands that promote the formation of a 3c-2e σ-bond with the ptC under two conditions: without altering the sp2 hybridization of the aromatic carbons; and containing empty orbitals perpendicular to the aromatic ring to participate in the aromatic π-electronic delocalization.

Comparison among four different ways to condense the Fukui function.

Four different ways to condense the Fukui function are compared. Three of them perform a numerical integration over different basins to define the condensed Fukui function, and the other one is the most traditional Fukui function using Mulliken population analysis. The basins are chosen to be the basins of the electron density (AIM), the basins of the electron localization function (ELF), and the basins of the Fukui function itself. The use of the last two basins is new and presented for the first time here. It is found that the last three methods yield results which are stable against a change in the basis set. The condensed Fukui function using the basins of the ELF is not able to give information on the reactivity of an acceptor molecule. In general, the condensed Fukui function using the basins of the density or the basins of the Fukui function describe the reactivity trends well. The latter is preferred, because it only contains information about the Fukui function itself and it gives the right information for donor as well as acceptor centers.

Sigma-pi separation of the electron localization function and aromaticity.

The electron localization function (ELF) has been separated in its sigma and pi components. The topological analysis of the new ELFsigma and ELFpi functions has been used to quantify the concept of resonance. The highest bifurcation values of these functions describe in a correct way the aromaticity of classical ring molecules and some new aromatic compounds as B6CO6, Al4(2-), and N5-. In the case of Al4(2-), an important sigma delocalization contribution has been found, which is in agreement with previous interpretation.