Development of the molecular graphics package MOLEKEL and its application to selected problems in organic and organometallic chemistry

MOLEKEL est un logiciel d'infographie moléculaire qui a été développé pour visualiser interactivement différents modèles de structures et de propriétés moléculaires. Leur représentation graphique est construite à partir des résultats numériques obtenus par des programmes externes de chimie physique pour lesquels des interfaces ont été implémentées. Les caractéristiques essentielles de ce logiciel résident dans sa grande convivialité, dans la haute qualité graphique des images qu'il permet d'obtenir et dans sa flexibilité en vue de traiter des problèmes chimiques très variés. Deux applications illustrent les possibilités de MOLEKEL: une étude de la distribution de densité de spin dans le biradical bis-nitroxide 1,3,5,7-tétraméthyl-2,6-diazaadamantane N,N'-dioxyl et une modélisation de l'attaque électrophile sur le complexe organométallique ([nu]⁵-C₅H₅)Ru(CO)(PPh₃)(H)

Combined Visualization of Contour Levels and 3D Volumes in Molecular Graphics

A new formalism has been developed to combine the representation of contour levels in arbitrary planes with the visualization of chemical properties as color-coded molecular envelopes or as isovalue rendered surfaces. This tool, which is characterized by a totally interactive and user-friendly input, has been integrated within our basic molecular graphics package MOLEKEL, which is used for molecular modeling applications on- graphics workstations. After an overview of the design and practical implementation of this development, several applications are presented which underline its flexibility and utility in modeling the structure and reactivity of various chemical systems, ranging from pyrrole to Cr(benzene)(CO)3 and C60 fullerene derivatives

Recent developments in molecular graphics : visualization of chemical structures and properties

As three-dimensional models of chemical objects are essential tools for understanding their intimate structure and function, nowadays molecular graphics techniques allow building, visualizing, and manipulating, of complex molecular structures and their related properties. This paper presents several developments recently achieved in this field, namely: the representation of macromolecular structures such as proteins; the modelization of molecular envelopes as dot surfaces, mesh surfaces, and solid models; the evaluation and visualization of color-coded reactivity indices based on intermolecular interaction energies. The last application is shown to be particularly useful in several applications, such as molecular recognition and drug design

Calculation and visualization of a reactivity index for organometallics based on the extended Hückel model

Calculated as the sum of electrostatic, charge-transfer and exchange-repulsion components derived from extended Hückel wavefunctions, the intermolecular interaction energies between an organometallic substrate S and an incoming reactant R are used as a reactivity index to describe electrophilic and nucleophilic addition or substitution mechanisms. In order to facilitate the interpretation, the values of this local index are mapped onto the molecular surface of S by means of a standard colour or grey-scale code, which allows the possible directions and sites of attack to be visualized rapidly. When applied to important reaction mechanisms such as (i) protonation of ferrocene and iron pentacarbonyl and (ii) nucleophilic attack on arene-V (CO)4+ and butadiene Fe(CO)3, this combination of quantum-chemical and molecular-graphics techniques is shown to describe adequately their high regioselectivity