Photographer: Bernd Ensing

dr. ir. B. (Bernd) Ensing


  • Faculty of Science
    Van 't Hoff Institute for Molecular Sciences
  • Visiting address
    Science Park A
    Science Park 904  Room number: C2.238
  • Postal address:
    Postbus  94157
    1090 GD  Amsterdam
  • B.Ensing@uva.nl
    T: 0205255067

See also my personal webpage: http://www.acmm.nl/ensing 

Electron and proton transfer in solution

Protons and electrons are very light particles that can move with a high velocity, but in practice their transfer is strongly affected by the medium. The conductivity is governed by the solvent fluctuations. Confinement of the solvent in one or more dimensions affects the transfer mechanism. The solvent reorganization free energy is an important part of both the redox potential and the acidity constants of acceptor solutes.

 

 

 

Signal Transduction in Photoactive Proteins

Photoactive proteins are light sensors that allow plants to turn their leafs toward the sun and allow animals (and people) to see. They form the perfect study ground to understand how (sensor) proteins work, because they can simply be activated with a flash of (laser) light, after which their functioning is probed.

 

 

 

Hybrid Molecular Dynamics

We have developed a hybrid molecular dynamics method that is multiscale in both space and in time. This is particularly useful for large systems for which overall only a coarsegrained description is feasible. The hybrid MD method allows molecules to adapt their representation, between a fully atomistic and a coarsegrained resolution, on the fly in a smooth manner.

 

 

 

 

Finding the lowest free energy path

Chemical reactions are rare events on the picosecond time scale available to ab initio dynamics simulations. Using the metadynamics method we can nevertheless probe the multi-dimensional free energy landscape underlying (concerted) reactions. The lowest free energy path in this landscape provides important insight into the mechanism and rate of reactions.

 

 

 

 

Solvent effect on chemical reactions

PhD thesis work with prof. E.J. Baerends
Solvent effects can have a very large influence on the thermodynamics and the kinetics of chemical reactions in water. We used Car-Parrinello molecular dynamics simulations to study these effects on prototypical organic reactions and on certain transition metal catalyzed oxidation reactions (Fenton chemistry).

2018

  • Woutersen, S., Ensing, B., Hilbers, M., Zhao, Z., & Angell, C. A. (2018). A liquid-liquid transition in supercooled aqueous solution related to the HDA-LDA transition. Science, 359(6380), 1127-1130. DOI: 10.1126/science.aao7049 
  • Zhang, W., Innocenti, G., Oulego, P., Gitis, V., Wu, H., Ensing, B., ... Shiju, N. R. (2018). Highly Selective Oxidation of Ethyl Lactate to Ethyl Pyruvate Catalyzed by Mesoporous Vanadia-Titania. ACS Catalysis, 8(3), 2365-2374. DOI: 10.1021/acscatal.7603843 
  • Zhang, W., Innocenti, G., Oulego, P., Gitis, V., Wu, H., Ensing, B., ... Shiju, N. R. (2018). Highly Selective Oxidation of Ethyl Lactate to Ethyl Pyruvate Catalyzed by Mesoporous Vanadia–Titania. ACS Catalysis, 2365-2374. DOI: 10.1021/acscatal.7b03843 
  • Zhang, W., Ensing, B., Rothenberg, G., & Shiju, R. N. (2018). Designing effective solid catalysts for biomass conversion: Aerobic oxidation of ethyl lactate to ethyl pyruvate. Green Chemistry. DOI: 10.1039/C8GC00032H 

2017

  • Liu, L., Lukose, B., & Ensing, B. (2017). Hydrogen Activation by Frustrated Lewis Pairs Revisited by Metadynamics Simulations. The Journal of Physical Chemistry. C, 121(4), 2046-2051. DOI: 10.1021/acs.jpcc.6b09991 

2016

  • De Meyer, T., Ensing, B., Rogge, S. M. J., De Clerck, K., Meijer, E. J., & Van Speybroeck, V. (2016). Acidity Constant (pK(a)) Calculation of Large Solvated Dye Molecules: Evaluation of Two Advanced Molecular Dynamics Methods. ChemPhysChem, 17(21), 3447-3459. DOI: 10.1002/cphc.201600734 
  • van den Ende, J. A., Ensing, B., & Cuppen, H. M. (2016). Energy barriers and mechanisms in solid-solid polymorphic transitions exhibiting cooperative motion. CrystEngComm, 18(23), 4420-4430. DOI: 10.1039/c5ce02550h  [details] 
  • Tiwari, A., & Ensing, B. (2016). Reactive trajectories of the Ru2+/3+ self-exchange reaction and the connection to Marcus' theory. Faraday Discussions, 195, 291-310.
  • De Wispelaere, K., Wondergem, C. S., Ensing, B., Hemelsoet, K., Meijer, E. J., Weckhuysen, B. M., ... Ruiz-Martı́nez, J. (2016). Insight into the Effect of Water on the Methanol-to-Olefins Conversion in H-SAPO-34 from Molecular Simulations and in Situ Microspectroscopy. ACS Catalysis, 6(3), 1991-2002. DOI: 10.1021/acscatal.5b02139  [details] 

2015

  • Homsi Brandeburgo, W., Thijmen van der Post, S., Meijer, E. J., & Ensing, B. (2015). On the slowdown mechanism of water dynamics around small amphiphiles. Physical Chemistry Chemical Physics, 17(38), 24968-24977. DOI: 10.1039/c5cp03486h  [details] 
  • Burtch, N. C., Torres-Knoop, A., Foo, G. S., Leisen, J., Sievers, C., Ensing, B., ... Walton, K. S. (2015). Understanding DABCO Nanorotor Dynamics in Isostructural Metal-Organic Frameworks. The Journal of Physical Chemistry Letters, 6(5), 812-816. DOI: 10.1021/jz502653y  [details] 
  • De Wispelaere, K., Ensing, B., Ghysels, A., Meijer, E. J., & van Van Speybroeck, V. (2015). Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics. Chemistry - A European Journal, 21(26), 9385-9396. DOI: 10.1002/chem.201500473  [details] 
  • van den Ende, J. A., Smets, M. M. H., de Jong, D. T., Brugman, S. J. T., Ensing, B., Tinnemans, P. T., ... Cuppen, H. M. (2015). Do solid-to-solid polymorphic transitions in DL-norleucine proceed through nucleation? Faraday Discussions, 179, 421-436. DOI: 10.1039/c4fd00214h  [details] 

2014

2013

  • Franssen, N. M. G., Ensing, B., Hegde, M., Dingemans, T. J., Norder, B., Picken, S. J., ... de Bruin, B. (2013). On the "Tertiary Structure" of Poly-Carbenes; Self-Assembly of sp(3)-Carbon-Based Polymers into Liquid-Crystalline Aggregates. Chemistry - A European Journal, 19(35), 11577-11589. DOI: 10.1002/chem.201301403  [details] 
  • Kılıç, M., & Ensing, B. (2013). First and second one-​electron reduction of lumiflavin in water - A first principles molecular dynamics study. Journal of Chemical Theory and Computation, 9(9), 3889-3899. DOI: 10.1021/ct400088g  [details] 

2012

2011

  • Liu, Z., Ensing, B., & Moore, P. B. (2011). Quantitative assessment of force fields on both low-energy conformational basins and transition-state regions of the (phi-psi) space. Journal of Chemical Theory and Computation, 7(2), 402-419. DOI: 10.1021/ct100395n  [details] 
  • Nielsen, S. O., Moore, P. B., & Ensing, B. (2011). Comment on "Adaptive multiscale molecular dynamics of macromolecular fluids'': reply. Physical Review Letters, 107(9). DOI: 10.1103/PhysRevLett.107.099802  [details] 

2010

  • Ensing, B., & Nielsen, S. O. (2010). Multiscale molecular dynamics and the reverse mapping problem. In T. Dumitrica (Ed.), Trends in computational nanomechanics: transcending length and time scales (pp. 25-59). (Challenges and advances in computational chemistry and physics; No. 9). Dordrecht: Springer. DOI: 10.1007/978-1-4020-9785-0_2  [details] 
  • Lechner, W., Rogal, J., Juraszek, J., Ensing, B., & Bolhuis, P. G. (2010). Nonlinear reaction coordinate analysis in the reweighted path ensemble. Journal of Chemical Physics, 133(17), 174110. DOI: 10.1063/1.3491818  [details] 
  • Rogal, J., Lechner, W., Juraszek, J., Ensing, B., & Bolhuis, P. G. (2010). The reweighted path ensemble. Journal of Chemical Physics, 133(17), 174109. DOI: 10.1063/1.3491817  [details] 
  • Schor, M., Ensing, B., & Bolhuis, P. G. (2010). A simple coarse-grained model for self-assembling silk-like protein fibers. Faraday Discussions, 144, 127-141. DOI: 10.1039/b901608b  [details] 
  • Lau, J. K. C., & Ensing, B. (2010). Hydrolysis of cisplatin—a first-principles metadynamics study. Physical Chemistry Chemical Physics, 12(35), 10348-10355. DOI: 10.1039/b918301a  [details] 
  • Nielsen, S. O., Bulo, R. E., Moore, P. B., & Ensing, B. (2010). Recent progress in adaptive multiscale molecular dynamics simulations of soft matter. Physical Chemistry Chemical Physics, 12(39), 12401-12414. DOI: 10.1039/c004111d  [details] 
  • Nielsen, S. O., Moore, P. B., & Ensing, B. (2010). Adaptive multiscale molecular dynamics of macromolecular fluids. Physical Review Letters, 105(23), 237802. DOI: 10.1103/PhysRevLett.105.237802  [details] 

2009

  • Bulo, R. E., Ensing, B., Sikkema, J., & Visscher, L. (2009). Toward a practical method for adaptive QM/MM simulations. Journal of Chemical Theory and Computation, 5(9), 2212-2221. DOI: 10.1021/ct900148e  [details] 

2007

  • Ensing, B., Nielsen, S. O., Moore, P. B., Klein, M. L., & Parrinello, M. (2007). Energy conservation in adaptive hybrid atomistic/coarse-grain molecular dynamics. Journal of Chemical Theory and Computation, 3, 1100-1105. DOI: 10.1021/ct600323n 
  • De Vivo, M., Ensing, B., Dal Peraro, M., Gomez, G. A., Christianson, D. W., & Klein, M. L. (2007). Proton shuttles and phosphatase activity in soluble epoxide hydrolase. Journal of the American Chemical Society, 129, 387-394. DOI: 10.1021/ja066150c 
  • Nielsen, S. O., Ensing, B., Moore, P. B., & Klein, M. L. (2007). Coarse grained-to-atomistic mapping algorithm: a tool for multiscale simulations. In R. B. Ross, & S. Mohanty (Eds.), Multiscale Simulation Methods for Nanomaterials (pp. 73-88). Hoboken, NJ, USA.: John Wiley & Sons, Inc.. DOI: 10.1002/9780470191675.ch5 

2006

  • Ensing, B., De Vivo, M., Liu, Z., Moore, P. B., & Klein, M. L. (2006). Metadynamics as a tool for exploring the free energy landscape of chemical reactions. Accounts of Chemical Research, 39, 73-81. DOI: 10.1021/ar040198i 
  • Blumberger, J., Ensing, B., & Klein, M. L. (2006). Formamide hydrolysis in alkaline aqueous solution: Insights from ab-initio metadynamics calculations. Angewandte Chemie, International Edition, 45, 2893-2897. DOI: 10.1002/anie.200600283 
  • Khurana, E., Nielsen, S. O., Ensing, B., & Klein, M. L. (2006). Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents. The journal of Physical Chemistry. B, 110, 18965-18972. DOI: 10.1021/jp057471y 

2005

  • Ensing, B., & Klein, M. L. (2005). Perspective on the reactions between F- and CH3CH2F: the free energy landscape of the E2 and SN2 reaction channels. Proceedings of the National Academy of Sciences of the United States of America, 102, 6755-6759. DOI: 10.1073/pnas.0408094102 
  • Ensing, B., Laio, A., Parrinello, M., & Klein, M. L. (2005). A recipe for the computation of the free energy barrier and lowest free energy path of concerted reactions. The journal of Physical Chemistry. B, 109, 6676-6687. DOI: 10.1021/jp045571i 
  • Lopez, C. F., Nielsen, S. O., Ensing, B., Moore, P. B., & Klein, M. L. (2005). Structure and dynamics of model pore insertion into a membrane. Biophysical Journal, 88, 3083-3094. DOI: 10.1529/biophysj.104.053769 
  • Nielsen, S. O., Ensing, B., Ortiz, V., Moore, P. B., & Klein, M. L. (2005). Lipid bilayer perturbations around a transmembrane nanotube: a coarse grain molecular dynamics study. Biophysical Journal, 88, 3822-3828. DOI: 10.1529/biophysj.104.057703 

2004

  • Ensing, B., Buda, F., Gribnau, M. C. M., & Baerends, E. J. (2004). Methane to methanol oxidation by the hydrated iron(IV)oxo species in aqueous solution; a combined DFT and Car-Parrinello molecular dynamics study. Journal of the American Chemical Society, 126, 4355-4365. DOI: 10.1021/ja038865a 
  • Ensing, B., Laio, A., Gervasio, F. L., Parrinello, M., & Klein, M. L. (2004). A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion. Journal of the American Chemical Society, 126, 9492-9493. DOI: 10.1021/ja048285t 
  • De Vivo, M., Ensing, B., & Klein, M. L. (2004). Computational study of phosphatase activity in soluble epoxide hydrolase: high efficiency through a water bridge mediated proton shuttle. Journal of the American Chemical Society, 127, 11226-11227. DOI: 10.1021/ja053049j 

2003

  • Ensing, B., Buda, F., & Baerends, E. J. (2003). Fenton-like chemistry in water: Oxidation catalysis by Fe(III) and H2O2. The Journal of Physical Chemistry. A, 107, 5722-5731. DOI: 10.1021/jp0267149 
  • Buda, F., Ensing, B., Gribnau, M. C. M., & Baerends, E. J. (2003). O-2 evolution in the Fenton reaction. Chemistry - A European Journal, 9, 3436-3444. DOI: 10.1002/chem.200204444 

2002

  • Ensing, B., & Baerends, E. J. (2002). Reaction path sampling of the reaction between iron(II) and hydrogen peroxide in aqueous solution. The Journal of Physical Chemistry. A, 106, 7902-7910. DOI: 10.1021/jp025833l 
  • Ensing, B., Buda, F., Bloechl, P. E., & Baerends, E. J. (2002). A Car-Parrinello study of the formation of oxidizing intermediates from Fentons reagent in aqueous solution. Physical Chemistry Chemical Physics, 4, 3619-3627. DOI: 10.1039/b201864k 

2001

2000

  • Gritsenko, O. V., Ensing, B., Schipper, P. R. T., & Baerends, E. J. (2000). Comparison of the accurate Kohn-Sham solution with the generalized gradient approximations (GGAs) for the SN2 reaction F- + CH3F -> FCH3 + F-: A qualitative rule to predict success or failure of GGAs. The Journal of Physical Chemistry. A, 8558-8565. DOI: 10.1021/jp001061m 

1998

  • Hermansson, K., Baudin, M., Ensing, B., Alfredsson, M., & Wojcik, M. (1998). A combined molecular dynamics-ab initio study of hydrogen molecule adsorption on ideal, relaxed and temperature-reconstructed MgO (111) surfaces. Journal of Chemical Physics, 109, 7515-7521. DOI: 10.1063/1.477409 

Award

  • Ensing, B. (2016): HRSMC Fellowship.

Others

  • Ensing, B. (visiting researcher) (2016): Catalan Institute of Nanoscience and Nanotechnology (ICN2) of the Autonomous University of Barcelona (UAB) (visiting an external academic institution).
  • Ensing, B. (participant) (12-12-2016 - 16-12-2016): Graduate winter school for Theoretical Chemistry and Spectroscopy (organising a conference, workshop, ...).

2014

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  • No ancillary activities

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