Lehrstuhl für Theoretische Chemie


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Quantum Chemistry

Protein Modeling

ab initio MD / Material Science

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(Graduate & Undergraduate)



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Dr. Marcus Böckmann


Contact Information


Dr. Marcus Böckmann
Lehrstuhl für Theoretische Chemie
Ruhr-Universität Bochum
D-44780 Bochum
Germany
Phone: +49-(0)-234-32-26749
Fax: +49-(0)-234-32-14945
E-mail: Marcus.Boeckmann@theochem.ruhr-uni-bochum.de


General Research Profile

The research portfolio comprises broad experience in the three distinguished fields of quantum chemistry (PhD Thesis w/ Prof. Martin Klessinger , WWU Münster), protein modeling (contract research w/ CHEOPS software company), and ab-initio molecular dynamics with special focus on nonadiabatic transitions in photochemical reactions (Volkswagen Stiftung: funding initiative "New Conceptual Approaches to Modeling and Simulation of Complex Soft and Condensed Matter" ).






Quantum Chemistry

- ab intio HF and DFT methods & semiempirical methods
- configuration interaction (CI) methods : MNDOC-CI, CASSCF/CASPT2
- spineigenfunctions & spin-orbit coupling
    ( the algorithm based on Rumer functions now to be found in the
      ORCA program package of Prof. Frank Neese's group (Bonn))
- second quantisation, group theory

Selected Publications

  • "Spin-Orbit Coupling in Organic Molecules: A Semiempirical Configuration Interaction Approach Toward Triplet State Reactivity"
    M. Böckmann, M. Klessinger, and M.C. Zerner
    J. Phys. Chem., 100, 10570-10579 (1996)
  • "Modellrechnungen zur Stereoselektivität der Triplett-Photoreaktion von 1,2-Dimethyltrimethylen"
    M. Böckmann and M. Klessinger
    Angew. Chem. Int. Ed. Engl., 35, 2502-2504 (1996)
    ( Angew. Chem., 108, 2681-2685 (1996) )




Protein Modeling

- preparation of x-ray structure for use in MD simulations (-> protein structure):
    o  invalid N/O/C assignments in ASN/GLN/HIS
    o  illegal deviations from Engh/Huber) parameters,
    o  automated detection of protonation state for basic/acidic residues
    o  automated addition of H w/ optimised hydrogen bond network
- protein structure solvation:
    o  validation of crystallographic water molecules
    o  algorithm for optimised positioning of water molecules
- contact analysis for fast & efficient evaluation of trajectory data
- docking algorithm w/ flexible sidechains/substrate
- homology modeling

Selected Publications

... sorry, but contract research is orthogonal to scientific publications.
  • "Simulations of a G protein-coupled receptor homology model
      predict dynamic features and a ligand binding site"
    S. Wolff, M. Böckmann, U. Höweler, J. Schlitter, and K. Gerwert
    FEBS Letters, 582, 3335-3342 (2008)




ab initio MD / materials science

- DFT based Car-Parrinello and Born-Oppenheimer molecular dynamics
- nonadiabatic effects triggered by photoexcitation
- multiscale methods bridging multiple time and length scales

Selected Publications

  • "Multiscale modelling of mesoscopic phenomena triggered by quantum events: light-driven azo-materials and beyond"
    M. Böckmann, D. Marx, C. Peter, L. DelleSite, K. Kremer, and N.L. Doltsinis
    Phys. Chem. Chem. Phys., 13, 7585-8052 (2011)
  • "Unraveling a Chemically Enhanced Photoswitch: Bridged Azobenzene"
    M. Böckmann, N.L. Doltsinis, and D. Marx
    Angew. Chem. Int. Ed. Engl., 49, 3382-3384 (2010)
  • "Nonadiabatic Hybrid Quantum and Molecular Mechanic Simulations
      of Azobenzene Photoswitching in Bulk Liquid Environment"
    M. Böckmann, N.L. Doltsinis, and D. Marx
    J. Phys. Chem. A, 114, 745-754 (2010)

Selected Talks

  • "Recent Method&Code Developments:
      Bochum Contributions to the official CPMD distribution"
    CPMD Developers Meeting 2010, Zürich (Switzerland), December 2010
  • "Nonadiabatic MD Simulation of Photoswitchable Materials"
    109. Bunsentagung, Bielefeld (Germany), May 2010
  • "Nonadiabatic Multiscale Simulation of Photoswitchable Materials"
    VW Status Symposium, Mainz (Germany), September 2009
  • "Photoisomerisation of Azobenzene: Novel Mechanistic Insight
      from nonadiabatic QM/MM Molecular Dynamics in the Condensed Phase"
    44th Symposium on Theoretical Chemistry, Ramsau (Austria), September 2008






Recommended Books

Biochemistry:

  • "Biochemical Pathways"
    G. Michal, Spektrum Akademischer Verlag, 1999

  • "Biochemistry"
    D. Voet and J. G. Voet, Wiley & Sons, 2000, 2004

  • "The Cell: A Molecular Approach"
    G. M. Cooper and R. E. Hausmann, Palgrave Macmillan, 2000,2009

  • "Allgemeine u. spezielle Pharmakologie und Toxikologie",
    K. Aktories, U. Förstermann, F. B. Hofmann, and K. Starke (eds.), Urban&Fischer / Elsevier, 2002,2006,2009

X-ray Crystallography:

  • "Accurate Bond and Angle Parameters for X-ray Protein Structure Refinement"
    R. A. Engh and R. Huber    Act. Cryst., A47, 392-400 (1991)
    (not quiet a book, but of outstanding importance!)

Theoretical Chemistry:

  • "Modern Quantum Chemistry",
    A. Szabo and N.S. Ostlund, McGraw-Hill, 1982.

  • "Second Quantized Approach to Quantum Chemistry",
    P. R. Surjan, Springer, 1989.

  • "Electronic Structure Calculations for Solids and Molecules",
    J. Kohanoff, Cambridge, 2006.

  • "Elektronenstruktur organischer Moleküle.
      Grundbegriffe quantenmechanischer Betrachtungsweisen",
    M. Klessinger, Wiley-VCH, 1982, 1997.

  • "Aufbau der Moleküle",
    F. Engelke, Teubner, 1992.

ab-initio Molecular Dynamics:

  • "Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods",
    D. Marx and J. Hutter, Cambridge, 2009.

  • "Statistical Mechanics: Theory and Molecular Simulation",
    M. E. Tuckerman, Oxford, 2010.

  • "Numerical Simulation in Molecular Dynamics",
    M. Griebel, G. Zumbusch, and S. Knapek, Springer, 2007.

Theoretical Physics:

  • "Grundkurs: Theoretische Physik" (Vol. 1 - 8)
    Wolfgang Nolting, Springer, 1992, 2010/2011.

  • "Computational Physics"
    Franz J. Vesely, Kluver Academic/Plenum Publishers, 1993,2000.

Mathematics:

  • "Mathematical Methods of Classical Mechanics"
    I. Arnold, Springer, 2nd ed. 1989.

  • "Dynamical Theory of Crystal Lattices"
    M. Born and K. Huang, Oxford (Reprint), 1954, 1988.

  • "Group Theory and its Application to Physical Problems"
    Morton Hamermesh, Dover (Reprint), 1963, 1989.

  • "Tensor Calculus"
    J.L. Synge and A. Schild, Dover (Reprint), 1969, 1978.


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