Our research goal is to transfer external stimuli into functionality on the molecular level. We focus on controlling intermolecular interactions in host-guest systems such as Metal-Organic Frameworks and at hybrid interfaces by light. Combining multiscale simulations with experimental methods - in particular time-resolved vibrational spectroscopy and scanning probe techniques - we investigate dynamic phenomena ranging from directed molecular motion to electron transfer processes and self-assembly mechanisms in well-defined molecular environments. Using this approach we study in particular the dynamics of photo-responsive molecular units with an emphasis on molecular machines. By correlating the dynamic phenomena on the molecular level with the resulting functionality of the molecular systems (e.g. photo-catalysis or selective drug release), we aim to derive new concepts for the development of smart stimuli-responsive nanomaterials.

Recent Research Highlights 


47. 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. FuchsNature Nanotechnology Advance Online Publication, DOI: 10.1038/s41565-018-0104-4.

46. 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)

45. Photo- and Electrochemical Properties of CO2 Reducing Ru- Re-pyridyl Based Catalysts

L. Frayne, N. Das, A. Paul, S. Amirjalayer, W. J. Buma, S. Woutersen, C. Long, J. G. Vos, M. T. Pryce, ChemPhotoChem 2018 , 2, 323.


44. 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.

43. 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)

42. Intermolecular on- Surface σ-Bond Metathesis

H.-Y. Gao*, P. A. Held*, S. Amirjalayer*, L. Liu, A. Timmer, B. Schirmer, O. D. Arado, H. Mönig, C. Mück-Lichtenfeld, J. Neugebauer, A. Studer, H. Fuchs, J. Am. Chem. Soc., 2017, 139, 7012. (*co-first author)

41. High-resolution gas-phase spectroscopy of a single-bond axle rotary motor

E. Maltseva, S. Amirjalayer, A. Cnossen, W. R. Browne, B. L. Feringa , W. J. Buma, Tetrahedron, 2017, 73, 4887.

40. Ultrafast dynamics and solvent-dependent deactivation kinetics of BODIPY molecular rotors

T. Suhina, S. Amirjalayer, S. Woutersen D. Bonn, A. M. Brouwer, Phys. Chem. Chem. Phys., 2017, 19, 19998.

39. High-resolution spectroscopic studies of electronically excited states of 1,8-naphthalic anhydride and 1,8-naphthalimide: a delicate interplay between one ππ* and two nπ* states

E. Maltseva, S. Amirjalayer, W. J. Buma, Phys. Chem. Chem. Phys., 2017, 19, 5861.


38. 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)

37. 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)

36. 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. 

35. Understanding molecular self-assembly of a diol compound by considering competitive interactions

O. Díaz Arado, M. Luft, H. Mönig*, P. A. Held, A. Studer, S. Amirjalayer*, H. Fuchs,  Phys. Chem. Chem. Phys. 2016, 18, 27390. (*corresponding author)

34. Excited-State Decay Pathways of Molecular Rotors: Twisted Intermediate or Conical Intersection?

T. Suhina, S. Amirjalayer, B. Mennucci, S. Woutersen, M. Hilbers, D. Bonn, A. M. Brouwer, J. Phys. Chem. Lett., 2016, 7, 4285.


33. Photochemistry and Electrochemistry of [(CO)5MC(OMe)Me](M = Cr or W) Explained Using Low-temperature Matrix Isolation, Picosecond Infrared Spectroscopy, Cyclic Voltammetry, and Time-dependent Density Functional Theory

S. McMahon, S. Amirjalayer, Y. Halpin, W. J. Buma, S. Woutersen, C. Long, A. D. Rooney, M. T. Pryce, Dalton Trans., 2015, 44, 15424.

(Publication was selected for the inside front cover picture Dalton Transactions Vol. 44 (35).)  

32. 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.

31. Stereoselective formation of coordination polymers with 1,4-diaminonaphthalene on various Cu substrates

M. Knor, H.-Y. Gao, S. Amirjalayer, A. Studer, H. Fuchs, Chem. Commun., 2015, 51, 10854.

30. Two-dimensional vibrational spectroscopy of Arg+···Glu− salt bridges in peptides: Evidence for two distinct types of hydrogen-bond geometry

A. Huerta-Viga, S. Amirjalayer, S. R. Domingos, H. Meuzelaar, A. Rupenyan, S. Woutersen, J. Chem. Phys., 2015, 142, 212444.

29. Isoreticular isomerism in 4,4- connected paddle-wheel metal–organic frameworks: structural prediction by the reverse topological approach

S. Bureekaew, V. Balwani, S. Amirjalayer, R. Schmid, CrystEngComm, 2015, 17, 344.  

(This article is part of the themed collection: Metal-Organic Frameworks and Hybrid Materials)

pre 2015

28. S. Amirjalayer, M. Tafipolsky , R. Schmid, “Surface Termination of the Metal-Organic Framework HKUST-1: A Theoretical Investigation”, J. Phys. Chem. Lett., 2014, 5, 3206.


27. J. Conyard, I. A. Heisler, W. R. Browne, B. L. Feringa, S. Amirjalayer*, W. J. Buma, S. Woutersen, S. R. Meech*, “Ultrafast Excited State Dynamics in 9,9’- Bifluorenylidene“,J. Phys. Chem. A, 2014, 118, 5961. (*corresponding author)


26. P. Li*, S. Amirjalayer*, F. Hartl, M. Lutz, B. de Bruin, R. Becker, S. Woutersen, J. N. H. Reek, “Direct Probing of Photo-induced Electron Transfer in a Self- assembled Biomimetic [2Fe2S]-Hydrogenase Complex using Ultrafast Vibrational Spectroscopy”, Inorg. Chem, 2014, 53, 5373. (* co-first-authors)


25. A. Huerta-Viga, S. R. Domingos, S. Amirjalayer, S. Woutersen, “A salt-bridge structure in solution revealed by 2D-IR spectroscopy”, Phys. Chem. Chem. Phys.,2014, 16, 15784.


24. S. R. Domingos, A. Huerta-Viga, L. Baij, S. Amirjalayer, D. A. E. Dunnebier, A. J. C. Walters, M. Finger, L. A. Nafie , B. de Bruin, W. J. Buma , S. Woutersen, “Amplified Vibrational Circular Dichroism as a Probe of Local Biomolecular Structure”, J. Am. Chem. Soc., 2014, 136, 3530.


23. T. H. van der Loop, F. Ruesink, S. Amirjalayer, H. J. Sanders, W. Jan Buma, S. Woutersen, "Unraveling the Mechanism of a Reversible Photo-Activated Molecular Proton Crane" J. Phys. Chem. B, 2014, 118, 12965.


22. M. Wehring, P.C.M.M. Magusin, S. Amirjalayer, R. Schmid, F. Stallmach, "Ferrocene in the metal–organic framework MOF-5 studied by homo- and heteronuclear correlation NMR and MD simulation", Micropor. Mesopor. Mater., 2014, 186, 130.


21. J. C. Manton, S. Amirjalayer, A. C. Coleman, S. McMahon, E. C. Harvey, G. M. Greetham, I. P. Clark, W. J. Buma, S. Woutersen, M. T. Pryce C. Long, "Excited state evolution towards ligand loss and ligand chelation at group 6 metal carbonyl centres",Dalton Trans. 2014, 43, 17797. 

(This article is part of the themed collection: Spectroscopy of Inorganic Excited States.)


20. E. M. M. Tan, S. Amirjalayer, P. Mazzella, B. H. Bakker, J. H. van Maarseveen, H. Bieraugel, W. J. Buma, “Molecular Beam and ab Initio Studies of Photoactive Yellow Protein Chromophores: Influence of the Thioester Functionality and Single Bond Rotation”, J. Phys. Chem. B, 2014, 118, 12395.


19. S. R. Domingos, S. Roeters, S. Amirjalayer, Z. Yu, S. Hecht, S. Woutersen, “Elucidating the backbone conformation of photoswitchable foldamers using vibrational circular dichroism”, Phys. Chem. Chem. Phys., 2013, 15, 17263.


18. E. M.M. Tan, S. Amirjalayer, S. Smolarek, A. Vdovin, A. M. Rijs, W. J. Buma, “Conformational heterogeneity of methyl-4- hydroxycinnamate: a gas-phase UV-IR spectroscopic study”, J. Phys. Chem. B, 2013, 117, 4798.


17. E. M. M. Tan, S. Amirjalayer, B. H Bakker, W. J. Buma, “Excited-state dynamics of Photoactive Yellow Protein chromophores elucidated by high-resolution spectroscopy and ab initio calculations”, Faraday Discuss., 2013, 163, 321.


16. S. Bureekaew, S. Amirjalayer, M. Tafipolsky, C. Spickermann, T. Kanchan Roy, R. Schmid, “MOF-FF – A flexible first-principles derived force field for metal-organic frameworks”, Phys. Status Solidi B, 2013, 250, 1128.


15. H. Noei, O. Kozachuk, S. Amirjalayer, S. Bureekaew, M. Kauer, R. Schmid, B. Marler, M. Muhler, R. A. Fischer, Y. Wang, “CO Adsorption on a Mixed-Valence Ruthenium Metal-Organic Framework Studied by UHV-FTIR Spectroscopy and DFT Calculations”, J. Phys. Chem. C, 2013, 4, 5658.


14. H. Noei, S. Amirjalayer, M. Müller, R. Schmid, M. Muhler, R. A. Fischer, Y. Wang, “Low-Temperature CO Oxidation over Cu-Based Metal–Organic Frameworks Monitored by FTIR Spectroscopy”, ChemCatChem, 2012, 4, 755.

(Publication was selected for the cover picture ChemCatChem 6/2012)


13. S. Bureekaew, S. Amirjalayer, R. Schmid, “Orbital directing effects in copper and zinc based paddle-wheel metal organic frameworks: the origin of flexibility”, J. Mater. Chem., 2012, 22, 10249.


12. S. Amirjalayer, M. Tafipolsky, R. Schmid, “Adsorption of Hydrocarbons in Metal– Organic Frameworks: A Force Field Benchmark on the Example of Benzene in Metal– Organic Framework 5”, J. Phys. Chem. C, 2012, 116, 15369.


11. S. Amirjalayer, R. Snurr, R. Schmid, “Prediction of Structure and Properties of Boron- Based Covalent Organic Frameworks by a First-Principles Derived Force Field”, J. Phys. Chem. C, 2012, 116, 4921.


10. S. Amirjalayer, M. Tafipolsky, R. Schmid, J. Phys. Chem. C, “Exploring Network Topologies of Copper Paddle-Wheel based Metal-Organic Frameworks with a First Principles Derived Force Field”, 2011, 115, 15133.


9. S. Hertel, M. Wehring, S. Amirjalayer, M. Gratz, J. Lincke, H. Krautscheid, R. Schmid, F. Stallmach, ”NMR studies of benzene mobility in metal-organic framework MOF-5”, Eur. Phys. J. Appl. Phys., 2011, 55, 20702.


8. V. Gwildies, T. Thiede, S. Amirjalayer, L. Alsamman, A. Devi, R.A. Fischer, “All- Nitrogen Coordinated Amidinato/Imido Complexes of Molybdenum and Tungsten: Syntheses and Characterization”, Inorg. Chem., 2010, 49, 8487.


7. M. Tafipolsky, S. Amirjalayer, R. Schmid, “First-Prinicples-Derived Force Field for Copper Paddle-Wheel-Based Metal-Organic Frameworks”, J. Phys. Chem. C, 2010, 114, 14402.


6. M. Tafipolsky, S. Amirjalayer, R. Schmid, “Atomistic Theoretical Models for Nanoporous Hybrid Materials”, Micropor. Mesopor. Mater., 2010, 129, 304. (Invited review).


5. S. Amirjalayer, R. Schmid, “Mechanism of Benzene Diffusion in MOF-5: A Molecular Dynamics Investigation”, Micropor. Mesopor. Mater., 2009, 125, 90.


4. S. Amirjalayer, R. Schmid, “Conformational Isomerism in the Isoreticular Metal Organic Framework Family: A Force Field Investigation”, J. Phys. Chem. C, 2008, 112, 14980.


3. S. Amirjalayer, M. Tafipolsky, R. Schmid, “Molecular dynamics simulation of benzene diffusion in MOF-5: Importance of lattice dynamics”, Angew. Chem. Int. Ed., 2007, 46, 463. (Selected as very important paper (VIP)).


2. M. Tafipolsky, S. Amirjalayer, R. Schmid, “Ab initio parametrized MM3 force field for the metal-organic framework MOF-5”, J. Comp. Chem., 2007, 28, 1169.


1. S. Hermes, F. Schröder, S. Amirjalayer, R. Schmid, R. A. Fischer, “Loading of porous metal-organic open frameworks with organometallic CVD precursors: inclusion compounds of the type [LnM](a)@MOF-5”, J. Mater. Chem., 2006, 16, 2464.