A Practical Algorithm to Solve the Near-Congruence Problem for Rigid Molecules and Clusters.

We present an improved algorithm to solve the near-congruence problem for rigid molecules and clusters based on the iterative application of assignment and alignment steps with biased Euclidean costs. The algorithm is formulated as a quasi-local optimization procedure with each optimization step involving a linear assignment (LAP) and a singular value decomposition (SVD). The efficiency of the algorithm is increased by up to 5 orders of magnitude with respect to the original unbiased noniterative method and can be applied to systems with hundreds or thousands of atoms, outperforming all state-of-the-art methods published so far in the literature. The Fortran implementation of the algorithm is available as an open source library (https://github.com/qcuaeh/molalignlib) and is suitable to be used in global optimization methods for the identification of local minima or basins.

Assessment of Simultaneous Global Optimization of Geometry and Total Spin of Small Iron Clusters.

In this work, simultaneous global optimization of geometry and total spin of small iron clusters Fen (3 ≤ n ≤ 40) is assessed using Simulated Annealing (SA) simulations with forces calculated at the DFT-based Tight-Binding (DFTB) level of theory. In order to optimize the total spin, the occupancies of α and ß densities were allowed to relax at each SA step, resulting in a continuous variation of the total spin along the trajectory. The behavior and performance of the procedure were investigated running two series of 10 independent "long" molecular dynamics simulations and one series of 100 independent "short" simulations. Cluster structures optimized with the assessed methodology reproduced geometries and magnetic moments reported in a previous work very well where multiple fixed total spin and geometries of iron clusters were individually probed, and for some clusters, more stable global minima were found. Other properties such as binding energies and second energy differences were also calculated in order to compare with previously reported theoretical and experimental values. The few mismatches were found to be driven by quasi degenerated ground states with different magnetic moments or by states with crossing free energies at high temperatures.

Mechanosynthesis of Photochromic Oligophenyleneimines: Optical, Electrochemical and Theoretical Studies.

In this work, two oligophenyleneimines type pentamers with terminal aldehydes, designated as DAFCHO (4,4'-((((((2,5-bis(octyloxy)-1,4-phenylene)bis(methanylylidene))bis(azanyl ylidene))bis(9H-fluorene-7,2-diyl))bis(azanylylidene))bis(methanylylidene))bis(2,5-bis(octyloxy) benzaldehyde)) and FDACHO (4,4'-((((((2,5-bis(octyloxy)-1,4-phenylene)bis(methanylylidene))bis (azanylylidene))bis(4,1-phenylene))bis(azanylylidene))bis(methanylylidene))bis(2,5-bis(octyloxy) benzaldehyde)) were synthesized by mechanochemistry method using 2,5-bis(octyloxy) terephtal aldehyde and 2,7-diaminofluorene or 1,4-phenylenediamine. All compounds were spectroscopically characterized using ¹H and 13C-NMR, FT-IR and mass spectrometry MALDITOF. The optical properties of the compounds were analyzed by UV-vis spectroscopy using different solvents. We observed that DAFCHO and FDACHO exhibit interesting photochromic properties when they are dissolved in chloroform and exposed to sunlight for 3, 5 and 10 min. The value of the energy band gap was calculated from the absorption spectra without irradiation Egap(optical). It was 2.50 eV for DAFCHO in chloroform solution, and it decreased to 2.34 eV when it is in films. For FDACHO, it was 2.41 eV in solution and 2.27 eV in film. HOMO (Highest Occupied Molecular Orbital), LUMO (Lowest Unoccupied Molecular Orbital) and Egap(electrochemical) values were obtained by electrochemical studies. The results indicate that the compounds can be considered as organic semiconductors since their values are 2.35 eV for DAFCHO and 2.06 eV for FDACHO. The structural and electronic properties of the compounds were corroborated with a DFT (Density Functional Theory) study.

Transition-state searches in metal clusters by first-principle methods.

Elucidation of the chemical reactivity of metal clusters is often cumbersome due to the nonintuitive structures of the corresponding transition states. In this work, a hierarchical transition-state algorithm as implemented in the deMon2k code has been applied to locate transition states of small sodium clusters with 6-10 atoms. This algorithm combines the so-called double-ended interpolation method with the uphill trust region method. The minimum structures needed as input were obtained from Born-Oppenheimer molecular dynamics simulations. To connect the found transition states with the corresponding minimum structures, the intrinsic reaction coordinates were calculated. This work demonstrates how nonintuitive rearrangement mechanisms can be studied in metal clusters.

The discovery of unexpected isomers in sodium heptamers by Born-Oppenheimer molecular dynamics.

This work presents a density functional study of neutral, cationic, and anionic sodium cluster heptamers. The cluster structures were optimized with the local density approximation as well as with the generalized gradient approximation. For the neutral and cationic clusters new unexpected isomers are found closed in energy to the well known ground state structures. In the case of the neutral heptamer the new isomer was first noticed by inspection of a first-principles Born-Oppenheimer molecular dynamics (BOMD) simulations at 300 K. A structure alignment algorithm is presented which facilitates the discovery of new structures from such BOMD simulations. With this algorithm the structural evolution of the two low-lying isomers of the neutral, cationic, and anionic heptamer was analyzed at different temperatures. This work demonstrates the capability of reasonably long (approximately 100 ps) first-principles BOMD simulations to explore the potential energy landscape of metallic clusters.