The complex build algorithm to set up starting structures of lanthanoid complexes with stereochemical control for molecular modeling.

When handling metallic centers of higher coordination numbers, one is commonly deluded with the presumption that any assembled metal complex geometry (including a crystallographic one) is good enough as a starting structure for computational chemistry calculations; all oblivious to the fact that such a structure is nothing short of just one out of several, sometimes dozens, or even thousands of other stereoisomers. Moreover, coordination chirality, so frequently present in complexes of higher coordination numbers, is another often overlooked property, rarely recognized as such. The Complex Build algorithm advanced in this article has been designed with the purpose of generating starting structures for molecular modeling calculations with full stereochemical control, including stereoisomer complete identification and coordination chirality recognition.

Application of a quantum genetic algorithm and QTAIM analysis in the study of structural and electronic properties of neutral bimetallic clusters NaLi (4 ≤ x + y ≤ 10).

Alloy clusters of NaLi (4 ≤ x + y ≤ 10) are studied by exploring the potential energy surface in the ab initio MP2 level with the support of a quantum genetic algorithm (QGA). In some cases, the structures have been also refined with DFT and coupled-cluster methods. The general trends of sodium-lithium structures are in line with previous studies.

A New Genetic Algorithm Approach Applied to Atomic and Molecular Cluster Studies.

A new procedure is suggested to improve genetic algorithms for the prediction of structures of nanoparticles. The strategy focuses on managing the creation of new individuals by evaluating the efficiency of operators ( , ,…, ) in generating well-adapted offspring. This is done by increasing the creation rate of operators with better performance and decreasing that rate for the ones which poorly fulfill the task of creating favorable new generation.

Stereoisomerism in Lanthanide Complexes: Enumeration, Chirality, Identification, Random Coordination Ratios.

The concept of random coordination ratios, RCRs, is advanced for lanthanide complexes. RCRs describe the relative probabilities of occurrence of subsets of stereoisomers of same-symmetry point groups in the limiting situation when energetic effects are equivalent. We then introduce a method to uniquely identify the stereoisomer of the coordination polyhedron of a given crystallographic structure and introduce a notation that fully characterizes its stereochemistry in an unambiguous manner, from which absolute configuration naturally follows.

Genetic algorithms coupled with quantum mechanics for refinement of force fields for RNA simulation: a case study of glycosidic torsions in the canonical ribonucleosides.

We report the use of genetic algorithms (GA) as a method to refine force field parameters in order to determine RNA energy. Quantum-mechanical (QM) calculations are carried out for the isolated canonical ribonucleosides (adenosine, guanosine, cytidine and uridine) that are taken as reference data. In this particular study, the dihedral and electrostatic energies are reparametrized in order to test the proposed approach, i.