Download this list:
 |
 |
 |
List of scientific publications |
1. Research Articles
2000
- M. Baaden, P. Granger and A. Strich; "Dependence of isotropic shift averages and nuclear shielding tensors on the internal rotation of the functional group X about the C-X bond in seven simple vinylic derivatives H2C=CH-X.", Mol. Phys., 98, 2000, 329-342.
- B. Lambert, V. Jacques, A. Shivanyuk, S. E. Matthews, A. Tunayar, M. Baaden, G. Wipff, V. Böhmer, J. F. Desreux; "Calix{4}arenes as selective extracting agents. An NMR dynamic and conformational investigation of the lanthanide(III) and thorium(IV) complexes.", Inorg. Chem., 39, 2000, 2033-2041.
- M. Baaden, F. Berny, C. Boehme, N. Muzet, R. Schurhammer and G. Wipff; "Interaction of trivalent lanthanide cations with phosphoryl derivatives, amide, anisole, pyridine and triazine ligands: a quantum mechanics study.", J. Alloys & Compounds, 303-304, 2000, 104-111.
- M. Baaden, F. Berny, N. Muzet, L. Troxler, G. Wipff; "Interfacial features of assisted liquid-liquid extraction of uranyl and cesium salts: a molecular dynamics investigation.", in Calixarenes for Separations, 2000, edited by G. Lumetta, R. D. Rogers, and A. S. Gopalan (Oxford University Press, New York), ACS Symposium Series 757, pp. 71-85.
- M. Baaden, G. Wipff, M. R. Yaftian, M. Burgard and D. Matt; "Cation coordination by calix{4}arenes bearing amide and/or phosphine oxide pendant groups: how many arms are needed to bind Li+ vs Na+ ? A combined NMR and molecular dynamics study.", J. chem. Soc., Perkin Trans. 2., 2000, 1315-1321.
- M. Baaden, F. Berny, G. Wipff and C. Madic; "A molecular dynamics and quantum mechanics study of M3+ lanthanide cation solvation by acetonitrile: the role of cation size, counterions and polarization effects investigated.", J. Phys. Chem. A, 104, 2000, 7659-7671.
- M. Baaden, F. Berny, N. Muzet, R. Schurhammer and G. Wipff; "Separation of radioactive cations by liquid-liquid extraction: computer simulations of water / oil solutions of salts and ionophores.", in Proceedings of the Euradwaste 1999 conference, 2000, edited by C. Davies (EC, Luxemburg), pp. 390-393.
- L. Troxler, M. Baaden, V. Böhmer and G. Wipff; "Complexation of M3+ lanthanide cations by calix{4}arene-CMPO ligands: a molecular dynamics study in methanol solution and at a water / chloroform interface.", Supramol. Chem., 12, 2000, 27-51.
2001
- M. Baaden, F. Berny and G. Wipff; "The chloroform / TBP / aqueous nitric acid interfacial system: a molecular dynamics investigation.", J. Mol. Liq., 90, 2001, 1-9.
- M. Baaden, M. Burgard, C. Boehme and G. Wipff; "Lanthanide cation binding to a phosphoryl-calix{4}arene: the importance of solvent and counterions investigated by molecular dynamics and quantum mechanical simulations", Phys. Chem. Chem. Phys., 3, 2001, 1317-1325
- M. Baaden, M. Burgard, and G. Wipff; "TBP at the water - oil interface: the effect of TBP concentration and water acidity investigated by molecular dynamics simulations", J. Phys. Chem. B, 105, 2001, 11131-11141
2002
- M. Baaden, R. Schurhammer and G. Wipff; "Molecular dynamics study of the uranyl extraction by TBP: demixing of water / 'oil' / TBP solutions with a comparison of supercritical CO2 and chloroform.", J. Phys. Chem. B, 106, 2002, 434-441
2003
- M. Baaden, F. Berny, R. Schurhammer, C. Madic and G. Wipff; "Theoretical studies on lanthanide cation extraction by picolinamides: ligand-cation interactions and interfacial behavior.", Solv. Extr. Ion Exch., 21, 2003, 199-219
- J. D. Campbell, P. C. Biggin, M. Baaden and M. S. P. Sansom; "Extending the structure of an ABC transporter to atomic resolution: modelling and simulation studies of Msba.", Biochemistry, 42, 2003, 3666-3673
- M. Baaden, C. Meier and M. S. P. Sansom; "A molecular dynamics investigation of mono- and dimeric states of the outer membrane enzyme Ompla.", J. Mol. Biol., 331, 2003, 177-189
2004
- J. D. Faraldo-Gómez, L. R. Forrest, M. Baaden, P. J. Bond, C. Domene, G. Patargias, J. Cuthbertson and M. S. P. Sansom; "Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.", Proteins, 57, 2004, 783-791
- M. Baaden M and M. S. P. Sansom "OMPT: Molecular Dynamics simulations of an outer membrane enzyme.", Biophys. J., 87, 2004, 2942-2953
2005
- R. J. Law, C. Capener, M. Baaden, P. J. Bond, J. Campbell, G. Patargias, Y. Arinaminpathy and M. S. P. Sansom; "Membrane protein structure quality in molecular dynamics simulation.", J.Mol.Graph.Model., 24 2005, 157-165
2007
- K. Tai, M. Baaden, S. Murdock, B. Wu, M. Hong Ng, S. Johnston,
R. Boardman, H. Fangohr, K. Cox, J. W. Essex and M. S. P. Sansom;
"Three hydrolases and a transferase:
Comparative analysis of active-site dynamics via the BioSimGrid
database.", J.Mol.Graph.Model., 25 2007,
896-902
Online access to available Full-Text articles:
2. Other scientific publications
1999
- M. Baaden "Molecular Modeling with the ChemOffice Ultra 4.5
program suite.", published on web, 1999, CambridgeSoft
Corporation.
Download a PDF version of the CambridgeSoft web site:
|
ChemOffice Ultra 4.5 Review |
2000
- M. Baaden "Etudes de molécules
extractantes en solution et aux interfaces liquide-liquide: aspects
structuraux et mécanistiques des effets de synergie",
Ph.D. Thesis, 2000, Université Louis Pasteur,
Strasbourg (N°: 3630), 2 vol., 218/42 pages.
Download a PDF version of the thesis:
|
PhD thesis, vol. 1 (6.9MB) |
|
PhD thesis, vol. 2 (73.6MB) |
2002
- M. Baaden, F. Berny, G. Wipff; Contribution to the AMBER
Parameter Database
Accessible online at http://pharmacy.man.ac.uk/amber/.
3. Scientific Presentations and Posters [up to 2005]
1999
- M. Baaden, M. Burgard, D. Matt and G. Wipff, "Selective extraction of lanthanide cations by
tetra-phosphineoxide substituted calix{4}arenes: a molecular
dynamics study at a water/chloroform interface."
- Meeting of the SFC-Grand Est, Strasbourg, France, January 21-22, 1999.
- Annual meeting of the GDR PRACTIS, Avignon, France, Febuary 25th, 1999.
- Journée de l'école doctorale de Chimie Physique of Strasbourg, France, April, 1999.
- PRACTIS Atelier "Modélisation", Seyssins, France, November 25th 1999.
- M. Baaden, M. Burgard, D. Matt and G. Wipff, "Selective extraction of lanthanide cations by
tetra-phosphineoxide substituted calix{4}arenes: a molecular
dynamics study at a water/chloroform interface."
- Short presentation, Journée de l'école doctorale de Chimie Physique of Strasbourg, France, April, 1999.
- M. Baaden, "Solvation of M3+ lanthanide cations
in acetonitrile solution"
- Seminar lecture, Strasbourg, France, May, 1999.
- M. Baaden, L. Troxler and G. Wipff, "Interfacial
aspects in liquid-liquid ion extraction."
- Lecture, 26th International conference on solution chemistry (26ICSC), Fukuoka, Japan, 27 July 1999.
- A. Strich, M. Baaden and P. Granger, "Dependence
of Isotropic Shift Averages and Nuclear Shielding Tensors on the
Internal Rotation of the Functional Group X about the C-X bond in
Seven Simple Vinylic Derivatives H2C=CH-X."
- 6ème Ecole d'Eté de Physico-Chimie Théorique, Marly-le Roi, September 6-10, 1999.
- 11th European seminar on computational methods in quantum chemistry, Zakopane, Poland, September 23-25, 1999.
- 2ème rencontre des Chimistes Théoriciens du Grand Est, Reims, October 15th 1999.
2000
- M. Baaden, F. Berny, N. Muzet, R. Schurhammer and G. Wipff,
"Computer
Modeling of liquid - liquid ion extraction."
- Euradwaste '99, Luxembourg, November 15-18, 1999.
- PRACTIS Atelier "Modélisation", Seyssins, France, November 25th 1999.
- 2nd COST D11 workshop on supramolecular chemistry, Strasbourg, France, December 10-12, 1999.
- Journées PRACTIS, Villeneuve-lès-Avignon, February 17-18, 2000.
- M. Baaden, "Etudes de molécules
extractantes en solution: aspects structuraux et
mécanistiques des effets de synergie"
- Doctoriales d'Alsace 1999, Mittelwihr, France, November 1999.
- Journées PRACTIS, Villeneuve-lès-Avignon, February 17-18, 2000.
- M. Baaden, L. Troxler and G. Wipff, "Interfacial
aspects in liquid-liquid ion extraction."
- Seminar lecture, Oxford, England, 9 June 2000.
- M. Baaden, "Energy profiles for interface
crossing in liquid-liquid ion extraction."
- Seminar lecture, Zurich, Switzerland, 24 May 2000.
- M. Baaden, "Energy profiles for interface
crossing in liquid-liquid ion extraction."
- CECAM workshop on challenges in Free energy calculations, Lyon, France, 22 June 2000.
2001
- M. Baaden, M. S. P. Sansom, "Barrels & corks
in a computer, modelling bacterial iron transport systems."
- Poster presentation at the Biochemical Society Meeting, University of York, 17-19 December 2001. (Biochemical Soc. Trans. Part 1, 30, 2002, A44)
- M. Baaden, "Modelling the ligand-gated protein
channel and ferric enterobactin receptor FepA."
- Seminar, Mathematical Biology Division, National Institute for Medical Research, London, 4 December 2001.
- M. Baaden, "Modélisation de la
protéine membranaire FepA, transporteur bactérien du
fer."
- Seminar, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris, 18 October 2001.
- M. Baaden, M. S. P. Sansom, "Modelling the FepA protein, a bacterial iron transporter in the outer membrane."
- M. Baaden, various seminar lectures, Oxford, England.
2002
- M. Baaden, M. S. P. Sansom, "Barrels & corks
in a computer, modelling bacterial iron transport systems."
- Poster presentation at the 46th Annual Meeting of the Biophysical Society, San Francisco, 23-27 February 2002. (Biophys. J. Part 2, 82, 2002, 2610)
- M. Baaden, "Modelling the ligand-gated protein
channel and ferric enterobactin receptor FepA."
- Seminar, Laboratory of Molecular Biophysics, Oxford, 5 February 2002
- M. Baaden, M. S. P. Sansom, "Understanding bacterial iron transport."
2003
- M. Baaden, C. Meier and M. S. P. Sansom; "Molecular dynamics simulations of outer membrane phospholipase A."
- M. Baaden, "La dynamique moléculaire in silico."
- M. Baaden, M. S. P. Sansom, "Les protéines membranaires Ompla et Fepa."
- M. Baaden, "Protéines membranaires
à repliement 'tonneau béta' - modélisation et
dynamique moléculaire de l'enzyme OmplA et du transporteur
bactérien du fer FepA."
- Seminar, Institut Européen de Chimie et Biologie, Bordeaux, 4 April 2003.
- M. S. P. Sansom, P.Bond, M. Baaden, J.D. Faraldo-Gómez,
S. Deol, C. Meier, K. Cox, "Simulation of
Outer Membrane Proteins."
- Poster presentation at the Gordon Research Conference "Protons & Membrane Reactions", Ventura, CA, United States, 23-28 February 2003.
2004
- M. Baaden, C. Meier and M. S. P. Sansom; "Molecular dynamics simulations of outer membrane phospholipase A."
- M. Baaden, "Molecular dynamics
simulations of outer membrane phospholipase A."
- Seminar, Woolf lab, Johns-Hopkins University School of Medicine, Baltimore, 20 February 2004.
- Seminar, Osman lab, Mount Sinai School of Medicine, New York, 23 February 2004.
- Seminar, Roux lab, Weill Medical College of Cornell University, New York, 26 February 2004.
- M. Baaden, "Dynamique moléculaire de OmplA, une phospholipase de la membrane externe bactérienne."
- M. Baaden, M. S. P. Sansom, "La
protéine membranaire Ompla."
- Seminar, Ben Msik Sciences Faculty, Casablanca, Morocco, 16 June 2004.
2005
- M. Baaden, M. S. P. Sansom; "Molecular Dynamics Simulations of an Outer Membrane Enzyme."
- J. D. Faraldo-Gómez, L. R. Forrest, M. Baaden, P. J. Bond, C. Domene, G. Patargias, J. Cuthbertson, M. S. P. Sansom; "On the convergence of the conformational sampling in molecular dynamics simulations of membrane proteins."
- M. S. P. Sansom, K. Tai, B. Wu, S. Khalid, M. Baaden; "BioSimGRID: Application to Analysis of Membrane Protein Simulations."
- M. Baaden; "Utilisation de VMD et OpenDX."
- Presentation at the Journée Visualisation Scientifique, IDRIS, Orsay, France, 8 March 2005.
- M. Baaden; "Le système SHAMAN:
Système HAptique pour MAnipulation Nanoscopique."
- Seminar, CEA/DIF Centre DAM-Île de France Bruyères-le-Chatel, 14 April 2005.
- R. Chater, D. Perahia, K. A. Chihab, S. Moussamih, A. Adlouni,
M. Baaden, K. Zakrzewska, R. Lavery, M. El Messal, A. Kettani;
"Modélisation moléculaire des mutations
du récepteur des lipoprotéines de faible
densité impliquées dans l'hypercholesterolémie
familiale au Maroc"
Download abstracts:
Download talk as Quicktime movie:
 |
Talk 1999.4 ("Interfacial aspects in liquid-liquid ion extraction.") (20.0MB) |
Download PDF versions of posters:
