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Research
Activities
Quantum
molecular modeling of biomolecules.
Foldamers,
Conceptual DFT.
My
modeling activity can take place at the macromolecular level
(oligomers conformational space analysis) and also at the
molecular level (understanding of the interactions within the
monomers). There is also a theoretical interest in studying
these molecules : the comprehension of the reactivity of the
functions which are new to
the biomolecular field. This is achieved by using the tools of
conceptual DFT.
Electronic
density topological analysis & hydrogen bonding.
Hydrogen
bonding studies are of utmost importance in the field of
biomolecules. I am using the topological analysis of the
electronic density to assess their strength and
nature.
This tool is especially efficient when the hydrogen bonding
network is ambiguous : Nucleosides present intramolecular
hydrogen bonds of the C-H...O type. Another example is the
guanine tetrads, where the nucleic bases are linked by
bifurcated hydrogen bonds.
Science
and Technology Studies .
Activities of modeling in computational
chemistry.
Computational
chemistry (which could be defined as the use of computer
resources to solve problems in chemistry) is a scientific
discipline that emerged at the same time that computers became
available in research laboratories, and developed with the
graphics terminal, in the 70s and 80s. When computers became
personal, ie a device in the research lab accessible to non
specialists, an upheaval appeared in the scientific community:
the scientists who were designing the molecular modeling
software (the developers) were not any more the same people than
those who performed the calculations (the users). Thus, in the
80s and 90s, the problem of the distribution of the software
arose, and tensions appeared in the community. Should the
software be shared freely? Should it be sold? Should the code
source be open? Could (and should) academic institutions benefit
from a "technology transfer"? Depending on what kind
of licensing? The computational chemistry community was also
involved with two major industries: the computer manufacturers
and the pharmaceutical industry, the latter becoming a potential
market for the former through modeling software.To
account for the strategies, tensions, and changes over time in
the community, this work explores The Computational Chemistry
List (CCL), a mailing list created in 1991 to provide a
discussion board to the fledgling community. For twenty years,
it has been used as an opinions forum and a platform for
scientific exchange. Since its inception, through the archives
of its thousands of threaded conversations, the mailing list is
a valuable corpus from a STS point of view, with its
"trolls" and "flame wars" particularly
helpful in revealing the tensions and controversies within the
community.
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Recent
publications & communications
A.
Hocquet, “RTFM! La chimie computationnelle, une communauté
loin du libre”, in “Histoires et Cultures du libre”,
Paloque Bergès et Masutti Eds., Framabook, Paris, 2013,
in press.
Communication
at the Conference of the Society for the History of Tecgnology ;
Special Interest Group Computers, Information & Society.
“RTFM!
Computational Chemists and Software Distribution”,
Copenhague, October 2012
Communication
at the Workshop “Internet dans l'histoire, Histoire de
l'Internet” of the Société pour l'Histoire des médias,
Paris, May 2012
Communication
at the “Communicating
Science and Technology II: From the 15th century to the present”
conference.
maison française d'Oxford, “RTFM!
Les « mailing lists » en tant que nouvelles formes de
communication entre scientifiques”
Paris, March
2012
Communication
at the
“Commission d'histoire
de la chimie
moderne” internationl
conference, “The
Computational Chemistry List: Comprendre les chimistes
computationnels à travers leurs échanges au sein d'une mailing
list” , Paris, June
2011
Dabbagh
H.A., Rasti E., Le Grel P., Hocquet A.,"DFT, ab initio,
NMR, and NBO analyses of Nα-substituted hydrazino acetamides:
Experimental vs theoretical values", 2010, Tetrahedron, 66,
13, 2322-2330.
The
"hydrazinoturn" hydrogen bonding network in
hydrazinopeptides and aza-beta3-peptides as probed by an AIM
topological analysis of the electronic density. Cyrille Simo,
Arnaud Salaün, Clément Arnarez, Lucie Delemotte, Alexandre
Haegy, Ali Kachmar, Adèle D. Laurent, Jennifer Thomas, Brigitte
Jamart-Grégoire, Philippe Le Grel and Alexandre Hocquet, J.
Mol. Struct. (THEOCHEM), 869, 2008, 41-46.
"A
conceptual DFT study of hydrazino peptides: Assessment of the
nucleophilicity of the nitrogen atoms by means of the dual
descriptor Δf(r)" C. Morell, A. Hocquet, A. Grand, B.
Jamart-Grégoire, J. Mol. Stuct. (THEOCHEM), 849, 2008, 46-51.
(Abstract)
« Pratiques
de modélisation : liens entre le chimiste théoricien et
l'ordinateur » : Communication at the Journées d'histoire
de la chimie, September 2007.
"A
conceptual DFT study of N-amino and hydrazino peptides :
Assesment of the nucleophilicity of the nitrogen atoms by means
of the dual descriptor Df(r)
" : Poster
at the ECCC11
conference, April 2007.
"N-(3-Amino-1H-isoindol-1-ylidene)-R-carbohydrazides
and Their Amide-Type Isomerism" O. Hordiyenko, A. Biitseva,
M. Kornilov, N. Brosse, A. Hocquet, B. Jamart-Grégoire, O.
Shishkin, R. Zubatyuk Eur. J. Org. Chem., 12, 2006, 2833-2842.
Abstract
"Interaction
of sodium and potassium ions with sandwiched cytosine-,
guanine-, thymine-, and uracil-base tetrads" M. Meyer, A.
Hocquet, J. Sühnel, J. Comput. Chem., 26, 2005, 352-364
Abstract
"N-aminopeptides
as peptidonucleic acids building blocks : a DFT and AIM study"
: Poster au congrès ECCC10,
2005.
"Intramolecular
interactions along the reaction path in the keto-enol
tautomerism: Fukui functions as local softnesses and charges as
local hardness" A. Hocquet, A. Toro-Labbé, H. Chermette,
J. Mol. Stuct. (THEOCHEM), 686, 2004, 213-218.
(Abstract)
"L
-nucleotides and 8-methylguanine of
d(C1m8G2C3G4C5LG6LC7G8C9G10)2 act cooperatively to promote a
left-handed helix under physiological salt conditions" I.
Cherrak, O. Mauffret, F. Santamaria, A. Hocquet, M. Ghomi, B.
Rayner, S. Fermandjian, Nucleic Acids Research, 2003, Vol. 31,
No. 23 6986-6995. (Abstract)
Poster
au congrès Horizons
in hydrogen bond research à Berlin, 2003.
"An
AIM topological analysis of Guanine tetrads interacting with
metals" G. Louit, A. Hocquet, M. Ghomi, M. Meyer, J.
Suehnel , Phys. Chem. Comm. , 2003, 6, 1-5.
(Abstract)
"Are
Guanine tetrads stabilised by bifurcated hydrogen bonds ? An AIM
topological analysis of the electronic density" G. Louit,
A. Hocquet, M. Ghomi, M. Meyer, J. Suehnel , Phys. Chem. Comm.,
2002, 5 (15), 94-98. (Abstract)
"Intramolecular
hydrogen bonding in ribonucleosides : an AIM topological study
of the electronic density" G. Louit, A. Hocquet M. Ghomi,
Physical Chemistry Chemical Physics, 2002, 3843-3848. (Abstract)
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