Jean Devillers

Distance Dependence of the NaCl(100) AFM Images

Constant-altitude AFM images of the NaCl(100) surface are calculated from a fully relaxed molecular-mechanic approach using a diamond tip apex. Three different ranges of the z tip-apex-to-surface distance have been found. For 2.5 A < z < 5 A, the apparent corrupgation is recorded from the normal force component. For intermediate z (1.4 A < z < 2.5 A), a surface image can be formed by measuring the lateral force because the normal corrugation decreases due to surface deformation. At even smaller distances (z < 1.4 A), a contrast reversal phenomenon occurs just before the surface destruction.

Theoretical study of the atomic-force-microscopy imaging process on the NaCl(001) surface

Based on a fully relaxed molecular-mechanics approach, we present a complete series of atomic force microscopy images of the NaCl(001) surface. For a given atomic structure of a diamond probe-tip [111] oriented, we analyze the results obtained from the two usual imaging modes either based on the monitoring of lateral or vertical forces. By accounting for the atomic relaxation of the whole system for any tip-sample configuration, we were able to get new insights about the achievement of atomic resolution on such substrates. Depending on the tip-sample distance range, the scanning of the NaCl(001) surface results in completely different behaviors associated with these two imaging modes. At very short distance we observed an increase of the apparent corrugation when working with the lateral force mode. The perturbations generated in the images by the presence of localized defects (vacancy and monoatomic step) are also analyzed within this model. These last calculations clearly indicate the fundamental role p...

Molecular structure of 2-Amino-5-(1-methyl-5-nitro-2-imidazolyl)-1,3,4-thiadiazol (Megazol) and related compounds: A concerted study using X-ray crystallography, molecular mechanics, and semiempirical methods

A structural study of three nitroimidazoles was carried out using molecular mechanics, semiempirical methods, and X-ray crystallography. Structural features which might account for the high efficiency of1 (Megazol) as an antiparasitic drug and its opposite, the inactivity of its regiomers2 and3 were examined, i.e., coplanarity of the two rings, preferred conformations, and rotational barriers around the pivot bond between the two rings. For the three compounds an antiperiplanar conformation is preferred for the N(CH3) and C-S bonds. For compounds1 and3, the rings are coplanar, with2 being somewhat twisted. The geometry obtained by molecular mechanics for compound1 is in excellent agreement with the X-ray structure, and greater confidence can be placed in this method than in semiempirical ones. Similarities observed on the LUMO positions, as well as rotational barriers lead to the conclusion that the differences in biological activity of these compounds do not rely on their ground state properties but rather on their subsequent reactions with oxygen. In addition, the calculations revealed significant structural information of a family of biological importance (nitroimidazoles) and constitute a comparative test for the MM2, AM1, and PM3 methods.

Scaling Force and Corrugation in AFM Image Calculations: The Graphite Surface

Extending the AFM-MM2 technique, a model is proposed to calculate AFM images with a good prediction of the force and the corrugation compared to the measured ones. The long-range attractive interactions between the tip body, the bulk surface, the tip apex and the surface scanned are now taken into account in optimizing, at the molecular mechanical level, the surface and tip apex atom positions upon tip approach and tip scanning. For the graphite surface, this leads to an accessible attractive-force range down to -7.7 nN and to a calculated surface corrugation larger than 0.2 A even at low forces.

Molecular mechanics: Use of an extended version of the MM2 program for pentacoordinated phosphorus compounds. 2. Conformational analysis of substituted bicyclic phosphoranes with a PH2 group

Allingers program MM2 extended to pentacoordinated phosphorus compounds was used for a conformational study of substituted bicyclophosphoranes containing a PH2 group. The results agree with NMR data and show that the difference in steric energies between the conformations of lowest energies determines whether the rings are in a single conformation or not.

Molecular mechanics: Extension of the MM2 program to pentacoordinate phosphorus compounds. 1. Conformational study of the bicyclic phosphoranes of the type R-P(H)N(CH2-CH2-O2 (R=H, Me, Ph)

Extension of Allingers program MM2 [21] to pentacoordinate phosphorus compounds has been performed, tested, and used for a conformational study of the bicyclic phosphoranes R-P(H)N(CH2-CH2-O)2 with R = H, Me, and Ph. Conformations of low energy and barriers between them agree well with the interpretation of NMR results in terms of flexibility of the rings with an exception for R = Ph. In that case, one possible explanation could be the lack of modeling of a special stereoelectronic interaction of the oxygen lone pairs with the phenyl ring.