Jean-Pierre Doucet

13C NMR measurement of hydrogen bonding effects for hydroxylic compounds: relationships between the OH stretching frequencies, the chemical shifts of proton donor group and electron reorganization

Abstract The carbon chemical shifts induced by hydrogen bonding have been measured for complexes between phenol, methanol, benzylic alcohol and π or n bases. Linear relationships are obtained between corrected induced chemical shifts and the IR frequency shifts ΔνOH but reverse slopes result for C-1 sp2 and sp3 carbons.

SIRS-SS: A System for simulating IR/Raman spectra. 1. Substructure/subspectrum correlation

An IR/RAMAN spectra simulation system is reported. The development of this software was based on the substructure/subspectrum relationships established for four different structural classes: small molecules, special fragments, atom-centered FRELs, and bond-centered FRELs (FREL: Fragment centered on an Environment which is Limited). Four corresponding knowledge-bases (now, at a pilot stage) are constructed from usual correlation charts or data analyses of large populations of compounds using data mining techniques.

Hydrogen Bonding Effects on Electron Population and 13C Chemical Shift of Base: Alcohol Pyridine Complexes

Abstract The carbon chemical shifts of pyridine associated to various aliphatic and aromatic alcohols are measured. Actual effects of hydrogen bonding formation on 13c shifts, have been characterized by evaluating in first, anisotropy and non specific medium effects. Linear relationships are obtained between 13C shifts and the IR frequency shifts. Positive slopes are observed for C-β and C-γ in agreement with the electron population change, but a reverse slope results for C-α carbon.

Grid stage modelling functions and molecular vector graphics

A polymodelling system (POLYMOD) is presented for varied 2D or 3D displays of chemical shapes, whether structural (molecular volumes distances, surfaces...) or electronic (molecular electrostatic potential, electron densities ...). The POLYMOD system manages reversible correspondences between calculation and representation spaces by immersing the molecules studied in a unique represetation space structured by a 3D grid box. This box, called COOBOX, defined by its point internal coordinates, is used to transform other coordinates into its own. Direct multi-slice images along thex, y, z axis provide access to a variety of derived operations around a molecular shape or set of shapes disposed in various manners. Interactive sub systems ensure Boolean operations and compare property shapes through the 3D grid. Clear separation of graphic routine and of downstream modelling programs leads to rapid and original generation of varied images (subimages, direct or composite images) which are then available for simulation strategies.

13C NMR Measurement of Hydrogen Bonding Effects for Benzylic Alcohol- Φ Or N Base Complexes : Relationship Between the Oh Stretching Frequencies and the Chemical Shifts of Proton Donor Groups

Abstract The carbon shifts induced by hydrogen bonding have been measured for complexes between benzylic alcohol and Φ or n bases (from benzene to collidine) of largely varied strengths. Linear relationships are obtained between corrected induced shifts and the IR frequency shifts ΔνOH but reverse slopes result for the C-1 and C-α carbons of benzylic alcohol.

Ring perception: proof of a formula calculating the number of the smallest rings in connected graphs

A general mathematical proof of a formula proposed and used by Fan et al. for calculating the number of the smallest rings in their smallest set of the smallest rings search algorithm is reported. This proof generalizes this formula to all connected cyclic graphs.

Measurement and Interpretation of Ethanol 13C Chemical Shifts Variations in Different Organic Solvents - Comparison with Aqueous Solvent

Abstract The carbon chemical shifts of ethanol are measured in varied aqueous and organic solvents. We determine the hydrogen bonding effect between alcohol and bases by correcting the experimental values from anisotropy and non specific medium effects.

MolDIA: XML based system of molecular diversity analysis towards virtual screening and QSPR.

In this paper a new chemoinformatics tool for Molecular Diversity Analysis (MolDIA) is introduced. The objective of this system is the analysis of molecular similarity and diversity through the treatment of structural and physicochemical information. Current needs for chemical databases include the analysis, the management and the retrieval of chemical information. The implementation of eXtended Markup Languages (XML) is proposed as a basis for representing and structuring the chemical information contained in data structures and databases. The adequate descriptor vector and related physicochemical properties have been defined and constructed. The benefits of XML in chemoinformatics are discussed, as well as, the applications of this system in a virtual screening environment. †Presented at CMTPI 2005: Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (Shanghai, China, October 29–November 1, 2005).

The Role of Imagery and Animation in Molecular Graphics

Abstract Molecular graphics (MG) is nowadays an essential component of the basic tools used in computer-assisted chemistry. As such, it is employed in numerous applications where its role consists not only in building and visualizing chemical models, but also in simulating complex situations resulting from the dynamic properties of chemical systems. By reviewing some of these applications developed in our laboratories, this paper presents several basic techniques used in MG, the emphasis being placed on the important role played by both imagery and animation.

Molecular shape embedding in a grid stage: modelling and animation

A computer system is proposed for bi or tri-dimensional graphic display of various structural shapes (molecular bodies) and property shape representations (one electron properties, electrostatic potential…). Calculation spaces, linked to molecular coordinates, are jointly handled within a unique representation space structured as a 3 D stage or grid Box. The Box fixed coordinates ensure Boolean and geometric operations through interactive graphic sub-systems. Direct images, subimages and composite images can be generated, as well as processed data and/or images. The polymodelling system presented — POLYMOD — leads to rapid and original animation operations on modelizations based on lengthy calculations.