Our research areas


Responsive molecular units, such as molecular switches and motors, can undergo precise structural changes that alter chemical and physical properties at the atomic scale. These transformations are triggered by external stimuli like light, heat, or mechanical force. Understanding the intrinsic properties of these molecules is key to uncovering the fundamental principles that govern stimuli-driven dynamics at the molecular level. These insights not only deepen our knowledge of how molecules behave but also pave the way for designing more complex and functional molecular systems. Our research group uses atomistic simulations to explore these dynamic processes and reveal the underlying mechanisms that drive molecular responsiveness.


Selective publications:

  1. Photoinduced Forward and Backward Pedalo-Type Motion of a Molecular Switch; I. Conti, W. J. Buma, M. Garavelli, S. Amirjalayer, J. Phys. Chem. Lett., 2020, 11, 4741.
  2. Light on the Structural Evolution of Photoresponsive Molecular Switches in Electronically Excited States; S. Amirjalayer, W. J. Buma, Chem. Eur. J., 2019, 25, 6252.
  3. Photoinduced Pedalo-Type Motion in an Azodicarboxamide-Based Molecular Switch; S. Amirjalayer, A. Martinez-Cuezva, J. Berna, S. Woutersen, W. J. Buma,  Angew. Chem. Int. Ed., 2018, 57, 1792. 
  4. Direct observation of a dark state in the photocycle of a light-driven molecular motor; S. Amirjalayer, A. Cnossen, W. R. Browne, B. L. Feringa, W. J. Buma, S. Woutersen, J. Phys. Chem. A 2016, 120, 8606. 
  5. Fast photodynamics of azobenzene probed by scanning excited-state potential energy surfaces using slow spectroscopy; E. M.M. Tan, S. Amirjalayer, S. Smolarek, A. Vdovin, F. Zerbetto, W. J. Buma, Nature Commun. 2015 , 6:5860.

The structure of molecular-based materials is a fundamental aspect in determining their functionality. At the heart of this lies how molecules assemble, often through self-organization, and how ordered or amorphous structures grow. Understanding the interactions, organization, and evolution of individual molecules, especially at surfaces or within solvent environments, is crucial to controlling the structure and resulting properties of larger molecular assemblies. These processes often rely on delicate balances of non-covalent interactions and spatial constraints. To elucidate the structural and dynamic properties at the atomic level and to identify the key factors that govern structure formation, our team employs advanced simulation techniques. By revealing these underlying mechanisms, we aim to guide the molecular engineering of functional architectures.


Selective publications:

  1. The electron-rich and nucleophilic N-heterocyclic imines on metal surfaces: binding modes and interfacial charge transfer; J. Ren, M. Das, H. Osthues, M. Nyenhuis, B. Schulze Lammers, E. Kolodzeiski, H. Mönig, S. Amirjalayer, H. Fuchs, N. L. Doltsinis, F. Glorius, J. Am. Chem. Soc. 2024, 146, 7288.
  2. Cooperation of N-Heterocyclic Carbenes on a Gold Surface; S. Amirjalayer, A. Bakker, M, Freitag, F. Glorius, H. Fuchs, Angew. Chem. Int. Ed. 2020, 59, 21230.
  3. Elucidating the Binding Modes of N-Heterocyclic Carbenes on a Gold Surface; A. Bakker, A. Timmer, E. Kolodzeiski, M. Freitag, H. Y. Gao, H. Mönig, S. Amirjalayer, F. Glorius, H. Fuchs, J. Am. Chem. Soc. 2018, 140, 11889.
  4. Elucidating the Impact of Molecular Motors on Their Solvation Environment; E. Kolodzeiski, S. Amirjalayer, J. Phys. Chem. B, 2020, 124, 10879.
  5. Surface polarity and self-structured nanogrooves collaborative oriented molecular packing for high crystallinity towards efficient charge transport; D. Ji, X. Xu, L. Jiang, S. Amirjalayer, L. Jiang, Y. Zhen, Y. Zou, Y. Yao, H. Dong, J. Yu, H. Fuchs, W. Hu, J. Am. Chem. Soc., 2017, 139, 2734.

Responsive materials derive their unique functionality from the interplay of precise arrangement and dynamic behaviour of molecular building blocks. Through molecular engineering, these materials can be tailored to respond to external stimuli resulting in designated and on-demand functionality for applications such as soft robotic, photonics, smart membranes, and catalysis. Our research group develops interatomic atomic potentials, using genetic algorithms and machine learning approaches, to efficiently and accurately capture coupled, cooperative and collective dynamic at the different length and time scales. By providing a mechanistic insight and revealing how molecular-level phenomena translate into functionality, we aim to contribute to the rational development of programmable and stimuli-responsive materials.


Selective publications:

  1. Dynamic Network of Intermolecular Interactions in Metal-Organic Frameworks functionalized by Molecular Machines E. Kolodzeiski, S. Amirjalayer, Science Adv. 2022, 8, eabn4426.
  2. On the molecular mechanism of a photo-responsive phase change memory, S. Amirjalayer, Adv. Theory Simul. 2021, 4 2100017.
  3. Understanding the molecular origin of the collective movement in a diarylethene-based photo-responsive actuator S. Amirjalayer, ChemPhysChem, 2021, 22, 1658.
  4. Collective structural properties of embedded molecular motors in functionalized Metal-Organic Framework,  E. Kolodzeiski, S. Amirjalayer, Phys. Chem. Chem. Phys. 2021, 23, 4728.
  5. Atomistic Insight into the Host-Guest Interaction of a Photo-Responsive Metal-Organic Framework E. Kolodzeiski, S. Amirjalayer, Chem. Eur. J. 2020, 26, 1263.

Recent Research Highlights 

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2019

Light on the Structural Evolution of Photoresponsive Molecular Switches in Electronically Excited States

S. Amirjalayer*, W. J. Buma*, Chem. Eur. J., 2019, DOI: 10.1002/chem.201805810 ("Hot Paper").(*corresponding author)


Understanding the mechanocatalytic conversion of biomass: One‐step reaction mechanism by mechanical force

S. Amirjalayer*, H. Fuchs, D. Marx, Angew. Chem. Int. Ed. 2019, 58, 5232. (*corresponding author)


2018

Quantitative assessment of intermolecular interactions by atomic force microscopy imaging using copper oxide tips

H. Mönig, S. Amirjalayer, A. Timmer, Z. Hu, L. Liu, O. Díaz Arado, M. Cnudde, C. A. Strassert, W. Ji, M. Rohlfing, H. Fuchs, Nature Nanotechnology Advance Online Publication, DOI: 10.1038/s41565-018-0104-4.


Photoinduced Pedalo-Type Motion in an Azodicarboxamide-Based Molecular Switch

S. Amirjalayer*, A. Martinez-Cuezva, J. Berna, S. Woutersen*, W. J. Buma*,  Angew. Chem. Int. Ed., 2018, 57, 1792. (*corresponding author)


2017

Ballbot-type motion of N-heterocyclic carbenes on gold surfaces

G. Wang, A. Rühling, S. Amirjalayer, M. Knor, J. B. Ernst, H.-J Gao, H.-Y. Gao, C. Richter, N. L. Doltsinis, F. Glorius, H. Fuchs, Nature Chemistry, 2017, 9, 152.


Surface polarity and self-structured nanogrooves collaborative oriented molecular packing for high crystallinity towards efficient charge transport

D. Ji*, X. Xu*, L. Jiang*, S. Amirjalayer*, L. Jiang, Y. Zhen, Y. Zou, Y. Yao, H. Dong, J. Yu, H. Fuchs, W. Hu, J. Am. Chem. Soc., 2017, 139, 2734. (*co-first author)


2016

Direct observation of a dark state in the photocycle of a light-driven molecular motor

S. Amirjalayer*, A. Cnossen, W. R. Browne, B. L. Feringa, W. J. Buma, S. Woutersen, J. Phys. Chem. A 2016, 120, 8606. (*corresponding author)


Influence of Pore Dimension on the Host–Guest Interaction in Metal–Organic Frameworks

S. Amirjalayer*, R. Schmid, J. Phys. Chem. C 2016, 120, 27319. (*corresponding author)


An iron-iron hydrogenase mimic with appended electron reservoir for efficient proton reduction in aqueous media

R. Becker, S. Amirjalayer, P. Li, S. Woutersen, J. N.H. Reek, Science Advances 2016, 2, e1501014. 


2015

Fast photodynamics of azobenzene probed by scanning excited-state potential energy surfaces using slow spectroscopy

E. M.M. Tan, S. Amirjalayer, S. Smolarek, A. Vdovin, F. Zerbetto, W. J. Buma, Nature Commun. 2015 , 6:5860.