Dr. Ir. Bernd Ensing

Postal address:
Van 't Hoff Institute for Molecular Sciences
University of Amsterdam
PO Box 94157
1090 GD Amsterdam, The Netherlands

Visiting address:
Science Park 904
1098 XH Amsterdam

room: C2.238
phone: (+31) 20 525 5067
email: b.ensinguva.nl

In the news

Peer reviewed publications

  1. Double Helical Conformation and Extreme Rigidity in a Rodlike Polyelectrolyte.
    Ying Wang, Yadong He, Zhou Yu, Jianwei Gao, Stephanie T. Brinck, Carla Slebodnick, Gregory B. Fahs, Curt J. Zanelotti, Maruti Hegde, Robert B. Moore, Bernd Ensing, Theo J. Dingemans, Rui Qiao, and Louis A. Madsen
    Nature Communications accepted (2019), DOI: 10.1038/s41467-019-08756-3
  2. The Puzzle of the Intramolecular Hydrogen Bond of Dibenzoylmethane Resolved by Molecular Dynamics Simulations.
    Mihajlo Etinski and Bernd Ensing
    J. Phys. Chem. A 122 (2018), 5945 – 5954 DOI: 10.1021/acs.jpca.8b01930
  3. Advances in enhanced sampling along adaptive paths of collective variables.
    Alberto Pérez de Alba Ortíz, Ambuj Tiwari, Rakesh C. Puthenkalathil, and Bernd Ensing
    J. Chem. Phys. 149 (2018), 072320 DOI: 10.1063/1.5027392
  4. Mechanisms behind the enhancement of thermal properties of graphene nanofluids.
    Maria del Rocio Rodríguez-Laguna, Alejandro Castro-Alvarez, Marinanna Sledzinska, Jeremie Maire, Francesca Costanzo, Bernd Ensing, Miguel Pruneda, Pablo Ordejón, Clivia M. Sotomayor Torres, Pedro Gómez-Romero and Emigdio Chávez-Ángel
    Nanoscale accepted (2018), DOI:10.1039/C8NR02762E
  5. Reaction Mechanism of Hydrogen Activation by Frustrated Lewis Pairs.
    Lei Liu, Binit Lukose, Pablo Jaque, Bernd Ensing
    Green Energy & Environment accepted (2018), DOI:10.1016/j.gee.2018.06.001
  6. Impact of Ligand Flexibility and Solvent on the O-O bond formation step in a highly active Ru Water Oxidation Catalyst.
    Nitish Govindarajan, Ambuj Tiwari, Bernd Ensing, and Evert Jan Meijer
    Communication in Inorg. Chem. 57 (2018), 13063 – 13066 DOI: 10.1021/acs.inorgchem.8b00619
  7. A liquid-liquid transition in supercooled aqueous solution related to the HDA-LDA transition.
    Sander Woutersen, Bernd Ensing, Michiel Hilbers, Zuofeng Zhao, and C. Austen Angell
    Science 359 (2018), 1127 – 1131 DOI: 10.1126/science.aao7049
  8. A free energy landscape of CO2 capture by frustrated Lewis pairs.
    Lei Liu, Binit Lukose, and Bernd Ensing
    ACS Catalysis 8 (2018), 3376 – 3381 DOI: 10.1021/acscatal.7b04072
  9. Designing effective solid catalysts for biomass conversion: Aerobic oxidation of ethyl lactate to ethyl pyruvate.
    Wei Zhang, Bernd Ensing, Gadi Rothenberg and Raveendran N Shiju
    Advance Article in Green Chemistry 20 (2018), 1866 – 1873 DOI: 10.1039/C8GC00032H
  10. Highly selective oxidation of ethyl lactate to ethyl pyruvate catalysed by mesoporous vanadia–titania.
    Wei Zhang, Giada Innocenti, Paula Oulego, Vitaly Gitis, Hai-Hong Wu; Bernd Ensing, Fabrizio Cavani, Gadi Rothenberg, N. Raveendran Shiju
    ACS Catalysis 8 (2018), 2365 – 2374 DOI: 10.1021/acscatal.7b03843
  11. Hydrogen activation by frustrated Lewis pairs revisited by metadynamics simulations.
    Lei Liu, Binit Lukose and Bernd Ensing
    J. Phys. Chem. C 121 (2017), 2046 - 2051 DOI:10.1021/acs.jpcc.6b09991
  12. Reactive trajectories of the Ru2+/3+ self-exchange reaction and the connection to Marcus’ theory.
    Ambuj Tiwari and Bernd Ensing
    Cover article in Faraday Discuss. 195 (2016), 291 - 310 DOI:10.1039/C6FD00132G
  13. Acidity constant (pKa) calculation of large solvated dye molecules: evaluation of two advanced molecular dynamics methods.
    Thierry De Meyer, Bernd Ensing, Sven M. J. Rogge, Karen De Clerck, Evert Jan Meijer and Veronique Van Speybroeck
    ChemPhysChem 17 (2016), 3447 - 3459 DOI:10.1002/cphc.201600734R1
  14. Energy barriers and mechanisms in solid-solid polymorphic transitions exhibiting cooperative motion.
    Joost A. van den Ende, Bernd Ensing, and Herma M. Cuppen
    CrystEngComm 18 (2016), 4420 - 4430 DOI:10.1039/C5CE02550H
  15. Insight in the effect of water on the methanol-to-olefins conversion in H-SAPO-34 from molecular simulations and in-situ micro-spectroscopy.
    Kristof De Wispelaere, Caterina S. Wondergem, Bernd Ensing, Karen Hemelsoet, Evert Jan Meijer, Bert M. Weckhuysen, Veronique Van Speybroeck, and Javier Ruiz-Martínez
    ACS Catalysis 6 (2016), 1991 - 2002 DOI:/10.1021/acscatal.5b02139
  16. On the slowdown mechanism of water dynamics around small amphiphiles.
    Wagner H. Brandeburgo, Sietse T. van der Post, Evert Jan Meijer, and Bernd Ensing
    Phys. Chem. Chem. Phys. 17 (2015), 24968 - 24977 DOI:/10.1039/c5cp03486h
  17. Complex reaction environments and competing reaction mechanisms in zeolite catalysis: insights from advanced molecular dynamics.
    Kristof De Wispelaere, Bernd Ensing, An Ghysels, Evert Jan Meijer, and Veronique Van Speybroeck
    Chem. Eur. J. 21 (2015), 9385 - 9396 DOI:/10.1002/chem.201500473
  18. Do solid-to-solid polymorphic transitions in DL-norleucine proceed through nucleation?
    Joost A. van den Ende, Mireille M. H. Smets, Daniël T. de Jong, Sander J. T. Brugman, Bernd Ensing, Paul T. Tinnemans, Hugo Meekes, and Herma M. Cuppen
    Faraday Discuss. 179 (2015), 421 - 436 DOI:/10.1039/C4FD00214H
  19. Understanding DABCO nanorotor dynamics in isostructural metal-organic frameworks.
    Nicholas Burtch, Ariana Torres-Knoop, Guo Shiou Foo, Johannes Leisen, Carsten Sievers, Bernd Ensing, David Dubbeldam, Krista Walton
    J. Phys. Chem. Lett. 6 (2015), 812 - 816 DOI:/10.1021/jz502653y
  20. Local orientational ordering in liquids revealed by resonant vibrational energy transfer.
    Matthijs R. Panman, Daniel J. Shaw, Bernd Ensing, and Sander Woutersen
    Phys. Rev. Lett. 113 (2014), 207801 DOI:/10.1103/PhysRevLett.113.207801
  21. Acidity constants of lumiflavin from first principles molecular dynamics simulations.
    Murat Kılıç and Bernd Ensing
    Phys. Chem. Chem. Phys. 16 (2014), 18993 - 19000 DOI:/10.1039/c4cp01450b
  22. Interaction of H2 with a double walled armchair nanotube by first principles calculations.
    Francesca Costanzo, Bernd Ensing, Roberto Scipioni, Francesco Ancilotto, and Pier Luigi Silvestrelli
    J. Phys. Chem. C 118 (2014), 15816 - 15824 DOI: 10.1021/jp503693q
  23. Comment on Communication: Benzene dimer - The free energy landscape [J. Chem. Phys. 139, 201102 (2013)].
    Ad van der Avoird, Rafal Podeszwa, Bernd Ensing and Krzysztof Szalewicz
    J. Chem. Phys. 140 (2014), 227101 DOI: 10.1063/1.4882015 Supplementary Material
  24. First and second one-electron reduction of lumiflavin in water - A first principles molecular dynamics study.
    Murat Kılıç and Bernd Ensing
    J. Chem. Theory Comput. 9 (2013), 3889 - 3899 DOI:/10.1021/ct400088g
  25. On the "tertiary Structure" of poly-Carbenes; self-assembly of sp3-carbon based polymers into liquid-crystalline aggregates.
    Nicole M. G. Franssen, Bernd Ensing, Maruti Hegde, Theo Dingemans, Ben Norder, Stephen J. Picken, Gert O. R. Alberda van Ekenstein, Ernst van Eck, Johannes A. A. W. Elemans, Mark Vis, Joost N. H. Reek and Bas de Bruin
    Cover article in Chem. Eur. J. 19 (2013), 11577 - 11589 DOI:10.1002/chem.201301403
  26. On the polarity of buckminsterfullerene with a water molecule inside.
    Bernd Ensing, Francesca Costanzo, and Pier Luigi Silvestrelli
    J. Phys. Chem. A 116 (2012), 12184 - 12188 DOI: 10.1021/jp311161q
  27. Hamiltonian adaptive hybrid atomistic/coarse-grain molecular dynamics.
    Bernd Ensing, Alessandro Laio, and Steven O. Nielsen
    Publication series of the John von Neumann Institute for Computing 46 (2013), 95 - 110, isbn13: 9783893368495 http://juser.fz-juelich.de/record/132949/
  28. Path finding on high-dimensional free energy landscapes.
    Grisell Díaz Leines and Bernd Ensing
    Phys. Rev. Lett. 109 (2012), 020601 DOI: 10.1103/PhysRevLett.109.020601
  29. Quantitative assessment of force fields on both low-energy conformational basins and transition-state regions of the (φ, ψ) space.
    Zhiwei Liu, Bernd Ensing, and Preston B. Moore
    J. Chem. Theory. Comput. 7 (2011), 402 - 419 DOI: 10.1021/ct100395n
  30. A Reply to the Comment by M. Praprotnik et al.
    Steven O. Nielsen, Preston B. Moore, Bernd Ensing
    Phys. Rev. Lett. 107 (2011), 099802 DOI: 10.1103/PhysRevLett.107.099802
  31. Recent progress in multiscale molecular dynamics simulation of soft matter.
    Steven O. Nielsen, Rosa E. Bulo, Preston B. Moore, Bernd Ensing
    Invited Perspective and cover article Phys. Chem. Chem. Phys. 12 (2010), 12401 - 12412 DOI: 10.1039/c004111d
  32. Adaptive multiscale molecular dynamics of macromolecular fluids.
    Steven O. Nielsen, Preston B. Moore, and Bernd Ensing
    Phys. Rev. Lett. 105 (2010), 237802 DOI: 10.1103/PhysRevLett.105.237802
  33. Smooth capping of short-range repulsive forces in hybrid atomistic/coarse-grain molecular dynamics simulation.
    Bernd Ensing
    Proceedings of Multiscale Materials Modeling 5 (2010), 47 - 53 MMM2010_MathematicalMethods.pdf
  34. Non-linear reaction coordinate analysis in the reweighted path ensemble.
    Wolfgang Lechner, Jutta Rogal, Jarek Juraszek, Bernd Ensing, and Peter Bolhuis
    J. Chem. Phys. 133 (2010), 174110 DOI: 10.1063/1.3491818
  35. The reweighted path ensemble.
    Jutta Rogal, Wolfgang Lechner, Jarek Juraszek, Bernd Ensing, and Peter Bolhuis
    J. Chem. Phys. 133 (2010), 174109 DOI: 10.1063/1.3491817
  36. Multiscale molecular dynamics and the reverse mapping problem.
    Bernd Ensing and Steven O. Nielsen
    Book chapter in Trends in Computational Nanomechanics (Challenges and Advances in Computational Chemistry and Physics, Volume 9) edited by T. Dumitrica (Springer, 2010), p. 25 - 60 DOI: 10.1007/978-1-4020-9785-0_2
  37. Hydrolysis of cisplatin - a first-principles metadyamics study.
    Justin Kai-Chi Lau and Bernd Ensing
    Phys. Chem. Chem. Phys. 12 (2010) 10348 - 10355 , DOI: 10.1039/b918301a
  38. A simple coarse-grained model for self-assembling silk-like protein fibers.
    Marieke Schor, Bernd Ensing, and Peter G. Bolhuis
    Faraday Discuss. 144 (2010), 127 - 141, DOI: 10.1039/b901608b
  39. Toward a practical method for adaptive QM/MM simulations.
    Rosa E. Bulo, Bernd Ensing, Jetze Sikkema, and Lucas Visscher
    J. Chem. Theory Comput. 5 (2009), 2212 - 2221, DOI: 10.1021/ct900148e
  40. Energy conservation in adaptive hybrid atomistic/coarse-grain molecular dynamics.
    Bernd Ensing, Steven O. Nielsen, Preston B. Moore, Michael L. Klein, and Michele Parrinello
    J. Chem. Theory Comput. 3 (2007), 1100 - 1105, DOI: 10.1021/ct600323n
  41. Proton shuttles and phosphatase activity in soluble epoxide hydrolase.
    Marco De Vivo, Bernd Ensing, Matteo Dal Peraro, German A. Gomez, David W. Christianson, and Michael L. Klein
    J. Am. Chem. Soc. 129 (2007) 387 - 394 DOI: 10.1021/ja066150c
  42. Coarse grained-to-atomistic mapping algorithm: a tool for multiscale simulations.
    Steven O. Nielsen, Bernd Ensing, Preston B. Moore, and Michael L. Klein
    Book chapter in Multiscale Simulation Methods for Nanomaterials, R. B. Ross and S. Mohanty, Editors. 2007, John Wiley & Sons, Inc., Hoboken, NJ, USA DOI: 10.1002/9780470191675.ch5
  43. Self-assembling cyclic peptides: molecular dynamics studies of dimers in polar and nonpolar solvents.
    Ekta Khurana, Steven O. Nielsen, Bernd Ensing, and Michael L. Klein
    J. Phys. Chem. B 110 (2006), 18965 - 18972 DOI: 10.1021/jp057471y
  44. Formamide hydrolysis in alkaline aqueous solution: Insights from ab-initio metadynamics calculations.
    Jochen Blumberger, Bernd Ensing, and Michael L. Klein
    Communication in Angewandte Chemie Int. Edit. 45 (2006), 2893 - 2897 DOI: 10.1002/anie.200600283
  45. Metadynamics as a tool for exploring the free energy landscape of chemical reactions.
    Bernd Ensing, Marco De Vivo, Zhiwei Liu, Preston Moore, and Michael L. Klein
    Acc. Chem. Res. 39 (2006), 73 - 81 DOI: 10.1021/ar040198i
  46. Perspective on the reactions between F- and CH3CH2F: the free energy landscape of the E2 and SN2 reaction channels.
    Bernd Ensing and Michael L. Klein
    Cover article in Proc. Natl. Acad. Sci., USA 102 (2005), 6755 - 6759 DOI: 10.1073/pnas.0408094102
  47. A recipe for the computation of the free energy barrier and lowest free energy path of concerted reactions.
    Bernd Ensing, Alessandro Laio, Michele Parrinello and Michael L. Klein
    J. Phys. Chem. B 109 (2005), 6676 - 6687 DOI: 10.1021/jp045571i
  48. Lipid bilayer perturbations around a transmembrane nanotube: a coarse grain molecular dynamics study.
    Steve O. Nielsen, Bernd Ensing, Vanessa Ortiz, Preston B. Moore, and Michael L. Klein
    Cover article in Biophys. J. 88 (2005), 3822 - 3828 DOI: 10.1529/biophysj.104.057703
  49. Structure and dynamics of model pore insertion into a membrane.
    Carlos F. Lopez, Steve O. Nielsen, Bernd Ensing, Preston B. Moore, and Michael L. Klein
    Cover article in Biophys. J. 88 (2005), 3083 - 3094 DOI: 10.1529/biophysj.104.053769
  50. Computational study of phosphatase activity in soluble epoxide hydrolase: high efficiency through a water bridge mediated proton shuttle.
    Marco De Vivo, Bernd Ensing, and Michael L. Klein
    Communication in J. Am. Chem. Soc. 127 (2004), 11226 - 11227 DOI: 10.1021/ja053049j
  51. A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion.
    Bernd Ensing, Alessandro Laio, Francesco L. Gervasio, Michele Parrinello, and Michael L. Klein
    Communication in J. Am. Chem. Soc. 126 (2004), 9492 - 9493 DOI: 10.1021/ja048285t
  52. Methane to methanol oxidation by the hydrated iron(IV)oxo species in aqueous solution; a combined DFT and Car-Parrinello molecular dynamics study.
    Bernd Ensing, Francesco Buda, Michiel C.M. Gribnau, and Evert Jan Baerends
    J. Am. Chem. Soc. 126 (2004), 4355 - 4365 DOI: 10.1021/ja038865a
  53. O-2 evolution in the Fenton reaction.
    Francesco Buda, Bernd Ensing, Michiel C.M. Gribnau, and Evert Jan Baerends
    Chem.Eur. J. 9 (2003), 3436 - 3444 DOI: 10.1002/chem.200204444
  54. Fenton-like chemistry in water: Oxidation catalysis by Fe(III) and H2O2.
    Bernd Ensing, Francesco Buda, and Evert Jan Baerends
    J. Phys. Chem. A. 107 (2003), 5722 - 5731 DOI: 10.1021/jp0267149
  55. Reaction path sampling of the reaction between iron(II) and hydrogen peroxide in aqueous solution.
    Bernd Ensing and Evert Jan Baerends
    J. Phys. Chem. A. 106 (2002), 7902 - 7910 DOI: 10.1021/jp025833l
  56. A Car-Parrinello study of the formation of oxidizing intermediates from Fentons reagent in aqueous solution.
    Bernd Ensing, Francesco Buda, Peter E. Bloechl, and Evert Jan Baerends
    Phys. Chem. Chem. Phys. 4 (2002), 3619 - 3627 DOI: 10.1039/b201864k
  57. Chemical involvement of solvent water molecules in elementary steps of the Fenton oxidation reaction.
    Bernd Ensing, Francesco Buda, Peter E. Bloechl, and Evert Jan Baerends
    Communication in Angewandte Chemie Int. Edit., 40 (2001), 2893 - 2895 DOI: 10.1002/1521-3757(20010803)113:15<2977::AID-ANGE2977>3.0.CO;2-Q
  58. DFT study of the active intermediate in the Fenton reaction.
    Francesco Buda, Bernd Ensing, Michiel C.M. Gribnau, and Evert Jan Baerends
    Chem. Eur. J. 7 (2001), 2775 - 2783 DOI: 10.1002/1521-3765(20010702)7:13<2775::AID-CHEM2775>3.0.CO;2-6
  59. Solvation effects on the SN2 reaction between CH3Cl and Cl- in water.
    Bernd Ensing, Evert Jan Meijer, Peter E. Bloechl, and Evert Jan Baerends
    J. Phys. Chem. A, 105 (2001), 3300 - 3310 DOI: 10.1021/jp003468x
  60. 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.
    Oleg V. Gritsenko, Bernd Ensing, Pieter R.T. Schipper, and Evert Jan Baerends
    J. Phys. Chem. A 104 (2000), 8558 - 8565 DOI: 10.1021/jp001061m
  61. A combined molecular dynamics-ab initio study of hydrogen molecule adsorption on ideal, relaxed and temperature-reconstructed MgO (111) surfaces.
    Micael Baudin, Kersti Hermansson, Bernd Ensing, Maria Alfredsson, and Mark Wojcik
    J. Chem. Phys. 109 (1998), 7515 - 7521 DOI: 10.1063/1.477409

PhD theses supervised

  1. Murat Kılıç
    Molecular simulation in electrochemistry – Electron and proton transfer reactions mediated by flavins in different molecular environments, 1-10-2014
  2. Grisell Díaz Leines
    Path-metadynamics, A computational study of conformational transitions in proteins, 15-11-2013
  3. Justin Kai Chi Lau
    Quantum Chemical Studies of Anti-Cancer Complexes, 5-12-2007 http://e-collection.library.ethz.ch/view/eth:30697