Head of the Group

Dr. rer. nat. Matthias Stein, M.Sc.
Dr. rer. nat. Matthias Stein, M.Sc.
Phone: +49 391 6110 436
Fax: +49 391 6110 403
Room: S1.17

Contact Person

Stephanie Geyer
Stephanie Geyer
Phone: +49 391 6110 461
Fax: +49 391 6110 551
Room: S1.12

Group page

Molecular Simulations and Design
View all information on the group Molecular Simulations and Design, research focus, projects and people.

Publications

Publications MSD group

Journal Article (59)

  1. 2020
    MPG.PuRe
    DOI
    Journal Article
    Creutznacher, R.; Schulze, E.; Wallmann, G.; Peters, T.; Stein, M.; Mallagaray, A.: Chemical-Shift Perturbations Reflect Bile Acid Binding to Norovirus Coat Protein - Recognition Comes in Different Flavors. ChemBioChem: A European Journal of Chemical Biology (accepted)
  2. 2019
    MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Dreimann, J. M.; Kohls, E.; Warmeling, H. F. W.; Stein, M.; Guo, L. F.; Garland, M.; Dinh, T. N.; Vorholt, A. J.: In Situ Infrared Spectroscopy as a Tool for Monitoring Molecular Catalyst for Hydroformylation in Continuous Processes. ACS Catalysis 9, pp. 4308 - 4319 (2019)
  3. MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Edler, E.; Stein, M.: Recognition and stabilization of geranylgeranylated human Rab5 by the GDP Dissociation Inhibitor (GDI). Small GTPases 10 (3), pp. 227 - 242 (2019)
  4. MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Jameel, F.; Kohls, E.; Stein, M.: Mechanism and Control of the Palladium-Catalyzed Alkoxycarbonylation of Oleochemicals from Sustainable Sources. ChemCatChem 11, pp. 1 - 14 (2019)
  5. MPG.PuRe
    DOI
    post-print
    Journal Article
    Kanan, T.; Kanan, D.; Erol, I.; Yazdi, S.; Stein, M.; Durdagi, S.: Targeting the NF-κB/IκBα complex via fragment-based E-Pharmacophore virtual screening and binary QSAR models. Journal of Molecular Graphics and Modelling 86, pp. 264 - 277 (2019)
  6. MPG.PuRe
    DOI
    post-print
    Journal Article
    Melnikov, S.; Stein, M.: Solvation and Dynamics of CO2 in Aqueous Alkanolamine Solutions. ACS Sustainable Chemistry & Engineering 7 (1), pp. 1028 - 1037 (2019)
  7. MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Melnikov, S.; Stein, M.: The effect of CO2 loading on alkanolamine absorbents in aqueous solutions. Physical Chemistry Chemical Physics 21, pp. 18386 - 18392 (2019)
  8. MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Münzberg, E.; Stein, M.: Structure and Dynamics of Mono- vs. Doubly Lipidated Rab5 in Membranes. International Journal of Molecular Sciences 20 (19), 4773 (2019)
  9. MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Petrenko, A.; Stein, M.: Toward a Molecular Reorganization Energy-Based Analysis of Third- Order Nonlinear Optical Properties of Polymethine Dyes and J‑Aggregates. The Journal of Physical Chemistry A 123 (43), pp. 9321 - 9327 (2019)
  10. MPG.PuRe
    DOI
    Journal Article
    Pullen, S.; Maji, S.; Stein, M.; Ott, S.: Restricted rotation of an Fe(CO)2(PL3)-subunit in [FeFe]-hydrogenase active site mimics by intramolecular ligation. Dalton Transactions 48 (18), 5939, pp. 5933 (2019)
  11. 2018
    MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Boz, E.; Tüzün, N. S.; Stein, M.: Computational investigation of the control of the thermodynamics and microkinetics of the reductive amination reaction by solvent coordination and a co-catalyst. RSC Advances 8, pp. 36662 - 36674 (2018)
  12. MPG.PuRe
    DOI
    post-print
    Journal Article
    Buchholz, H. K.; Stein, M.: Accurate Lattice Energies of Organic Molecular Crystals from Periodic Turbomole Calculations. Journal of Computational Chemistry 39 (19), pp. 1335 - 1343 (2018)
  13. MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Escorcia Cabrera, A. M.; Stein, M.: QM/MM Investigation of the Role of a Second Coordination Shell Arginine in [NiFe]-Hydrogenases. Frontiers in Chemistry (6), 164 (2018)
  14. MPG.PuRe
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    publisher-version
    Journal Article
    Kumar, V.; Naumann, M.; Stein, M.: Computational Studies on the Inhibitor Selectivity of Human JAMM Deubiquitinylases Rpn11 and CSN5. Frontiers in Chemistry 6, 480 (2018)
  15. MPG.PuRe
    DOI
    Journal Article
    Melnikov, S.; Stein, M.: Molecular Dynamics Study of the Solution Structure, Clustering, and Diffusion of Four Aqueous Alkanolamines. The Journal of Physical Chemistry B 122 (10), pp. 2769 - 2778 (2018)
  16. MPG.PuRe
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    publisher-version
    Journal Article
    Pandey, I. K.; Natarajan, M.; Faujdar, H.; Hussain, F.; Stein, M.; Kaur-Ghumaan, S.: Intramolecular stabilization of a catalytic [FeFe]-hydrogenase mimic investigated by experiment and theory. Dalton Transactions 47, pp. 4941 - 4949 (2018)
  17. MPG.PuRe
    DOI
    post-print
    Journal Article
    Salmas, R. E.; Seeman, P.; Stein, M.; Durdagi, S.: Structural Investigation of the Dopamine-2 Receptor Agonist Bromocriptine Binding to Dimeric D2HighR and D2LowR States. Journal of Chemical Information and Modeling 58 (4), pp. 826 - 836 (2018)
  18. MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Salmas, R. E.; Is, Y. S.; Durdagi, S.; Stein, M.; Yurtsever, M.: A QM protein–ligand investigation of antipsychotic drugs with the dopamine D2 Receptor (D2R). Journal of Biomolecular Structure and Dynamics 36 (10), pp. 2668 - 2677 (2018)
  19. MPG.PuRe
    DOI
    Journal Article
    Schulze, E.; Stein, M.: Simulation of Mixed Self-Assembled Monolayers on Gold: Effect of Terminal Alkyl Anchor Chain and Monolayer Composition. The Journal of Physical Chemistry B 122, pp. 7699 - 7710 (2018)
  20. 2017
    MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Buchholz, H. K.; Hylton, R. K.; Brandenburg, J. G.; Seidel-Morgenstern, A.; Lorenz, H.; Stein, M.; Price, S. L.: Thermochemistry of racemic and enantiopure molecular crystals for predicting enantiomer separation. Crystal Growth & Design 17 (9), pp. 4676 - 4686 (2017)
  21. MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Edler, E.; Stein, M.: Probing the druggability of membrane-bound Rab5 by molecular dynamics simulations. Journal of Enzyme Inhibition and Medicinal Chemistry 32 (1), pp. 434 - 443 (2017)
  22. MPG.PuRe
    DOI
    post-print
    supplementary-material
    Journal Article
    Edler, E.; Schulze, E.; Stein, M.: Membrane localization and dynamics of geranylgeranylated Rab5 hypervariable region. Biochimica et Biophysica Acta (BBA) - Biomembranes 1859 (8), pp. 1335 - 1349 (2017)
  23. MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Kohls, E.; Stein, M.: Vibrational scaling factors for RH(I) carbonyl compounds in homogeneous cataylsis. Contributions: MASA, Section of Natural, Mathematical & Biotechnical Sciences 38 (1), pp. 43 - 56 (2017)
  24. MPG.PuRe
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    publisher-version
    Journal Article
    Kohls, E.; Stein, M.: The thermochemistry of long chain olefin isomers during hydroformylation. New Journal of Chemistry 41 (15), pp. 7347 - 7355 (2017)
  25. MPG.PuRe
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    post-print
    Journal Article
    Lemberg, M.; Sadowski, G.; Gerlach, M.; Kohls, E.; Stein, M.; Hamel, C.; Seidel-Morgenstern, A.: Predicting Solvent Effects on the 1-dodecene Hydroformylation Reaction Equilibrium. AIChE-Journal 63 (10), pp. 4576 - 4585 (2017)
  26. MPG.PuRe
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    publisher-version
    Journal Article
    Natarajan, M.; Faujdar, H.; Mobin, S. M.; Stein, M.; Kaur-Ghumaan, S.: A mononuclear iron carbonyl complex [Fe(μ-bdt)(CO)2(PTA)2] with bulky phosphine ligands: a model for the [FeFe] hydrogenase enzyme active site with an inverted redox potential. Dalton Transactions 46 (30), pp. 10050 - 10056 (2017)
  27. MPG.PuRe
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    publisher-version
    Journal Article
    Petrenko, A.; Stein, M.: Distal [FeS]-Cluster Coordination in [NiFe]-Hydrogenase Facilitates Intermolecular Electron Transfer. International Journal of Molecular Sciences 18 (1), 100 (2017)
  28. MPG.PuRe
    DOI
    post-print
    Journal Article
    Salmas, R. E.; Stein, M.; Yurtsever, M.; Seeman, P.; Erol, I.; Mestanoglu, M.; Durdagi, S.: The signaling pathway of dopamine D2 receptor (D2R) activation using normal mode analysis (NMA) and the construction of pharmacophore models for D2R ligands. Journal of Biomolecular Structure and Dynamics 35 (9), pp. 2040 - 2048 (2017)
  29. MPG.PuRe
    DOI
    Journal Article
    Salmas, R. E.; Seeman, P.; Aksoydan, B.; Stein, M.; Yurtsever, M.; Durdagi, S.: Biological Insights of the Dopaminergic Stabilizer ACR16 at the Binding Pocket of Dopamine D2 Receptor. ACS Chemical Neuroscience 8 (4), pp. 826 - 836 (2017)
  30. MPG.PuRe
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    post-print
    Journal Article
    Salmas, R. E.; Seeman, P.; Aksoydan, B.; Erol, I.; Kantarcioglu, I.; Stein, M.; Yurtsever, M.; Durdagi, S.: Analysis of the Glutamate Agonist LY404,039 Binding to Nonstatic Dopamine Receptor D2 Dimer Structures and Consensus Docking. ACS Chemical Neuroscience 8 (6), pp. 1404 - 1415 (2017)
  31. MPG.PuRe
    DOI
    post-print
    post-print
    Journal Article
    Yazdi, S.; Naumann, M.; Stein, M.: Double Phosphorylation-Induced Structural Changes in the Signal-Receiving Domain of IκBα in Complex with NF-κB. Proteins: Structure, Function, and Bioinformatics 85 (1), pp. 17 - 29 (2017)
  32. 2016
    MPG.PuRe
    DOI
    Journal Article
    Durdagi, S.; Salmas, R. E.; Stein, M.; Yurtsever, M.; Seeman, P.: Binding Interactions of Dopamine and Apomorphine in D2High and D2Low States of Human Dopamine D2 Receptor Using Computational and Experimental Techniques. ACS Chemical Neuroscience 7 (2), pp. 185 - 195 (2016)
  33. MPG.PuRe
    DOI
    Journal Article
    Jörke, A.; Kohls, E.; Triemer, S.; Seidel-Morgenstern, A.; Hamel, C.; Stein, M.: Resolution of Structural Isomers of Complex Reaction Mixtures in Homogeneous Catalysis. Chemical Engineering and Processing 102, pp. 229 - 237 (2016)
  34. MPG.PuRe
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    publisher-version
    Journal Article
    Khandavilli, U. B. R.; Lusi, M.; Bhogala, B. R.; Maguire, A. R.; Stein, M.; Lawrence, S. E.: Diversity in a simple co-crystal: racemic and kryptoracemic behaviour. Chemical Communications 2016 (52), pp. 8309 - 8312 (2016)
  35. MPG.PuRe
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    publisher-version
    Journal Article
    Yazdi, S.; Stein, M.; Elinder, F.; Andersson, M.; Lindahl, E.: The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel. PLoS Computational Biology 12 (1), e1004704 (2016)
  36. 2015
    MPG.PuRe
    DOI
    Journal Article
    Chauhan, G.; Stein, M.; Seidel-Morgenstern, A.; Pant, K. K.; Nigam, K. D.P.: The thermodynamics and biodegradability of chelating agents upon metal extraction. Chemical Engineering Science 137, pp. 768 - 785 (2015)
  37. MPG.PuRe
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    Journal Article
    Hylton, R.; Tizzard, G. J.; Threlfall, T. L.; Ellis, A. L.; Coles, S. J.; Seaton, C. C.; Schulze, E.; Lorenz, H.; Seidel-Morgenstern, A.; Stein, M. et al.; Price, S. L.: Are the crystal structures of enantiopure and racemic mandelic acids determined by kinetics or thermodynamics? Journal of the American Chemical Society 137 (34), pp. 11095 - 11104 (2015)
  38. MPG.PuRe
    DOI
    Journal Article
    Petrenko, A.; Stein, M.: Molecular Reorganization Energy as a Key Determinant of J-Band Formation in J-Aggregates of Polymethine Dyes. The Journal of Physical Chemistry A 119 (26), pp. 6773 - 6780 (2015)
  39. MPG.PuRe
    DOI
    Journal Article
    Petrenko, A.; Stein, M.: Rates and Routes of Electron Transfer of [NiFe]-Hydrogenase in an Enzymatic Fuel Cell. The Journal of Physical Chemistry B 119 (43), pp. 3870 - 13882 (2015)
  40. MPG.PuRe
    DOI
    Journal Article
    Salmas, R. E.; Yurtsever, M.; Stein, M.; Durdagi, S.: Modeling and protein engineering studies of active and inactive states of human dopamine D2 receptor (D2R) and investigation of drug/receptor interactions. Molecular Diversity 19 (2), pp. 321 - 332 (2015)
  41. MPG.PuRe
    DOI
    publisher-version
    supplementary-material
    Journal Article
    Yazdi, S.; Durdagi, S.; Naumann, M.; Stein, M.: Structural modeling of the N-terminal signal–receiving domain of IκBα. frontiers in Molecular Biosciences 2, 32 (2015)
  42. 2014
    MPG.PuRe
    DOI
    Journal Article
    Chambers , G. M.; Mitra , J.; Rauchfuss, T. B.; Stein, M.: NiI/RuII Model for the Ni–L State of the [NiFe]Hydrogenases: Synthesis, Spectroscopy, and Reactivity. Inorganic Chemistry 53 (8), pp. 4243 - 4249 (2014)
  43. MPG.PuRe
    DOI
    post-print
    publisher-version
    Journal Article
    Edler, E.; Stein, M.: Spin‐State‐Dependent Properties of an Iron(III) Hydrogenase Mimic. European Journal of Inorganic Chemistry 2014 (22), pp. 3587 - 3599 (2014)
  44. MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Kaur-Ghumaan, S.; Stein, M.: [NiFe] hydrogenases: how close do structural and functional mimics approach the active site? Dalton Transactions 43 (25), pp. 9392 - 9405 (2014)
  45. MPG.PuRe
    DOI
    Journal Article
    Mirmohades, M.; Pullen, S.; Stein, M.; Maji, S.; Ott, S.; Hammarström, L.; Lomoth, R.: Direct Observation of Key Catalytic Intermediates in a Photoinduced Proton Reduction Cycle with a Diiron Carbonyl Complex. Journal of the American Chemical Society 136 (50), pp. 17366 - 17369 (2014)
  46. MPG.PuRe
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    publisher-version
    Journal Article
    Orthaber, A.; Karnahl, M.; Tschierlei, S.; Streich, D.; Stein, M.; Ott, S.: Coordination and conformational isomers in mononuclear iron complexes with pertinence to the [FeFe] hydrogenase active site. Dalton Transactions 43, pp. 4537 - 4549 (2014)
  47. 2013
    MPG.PuRe
    DOI
    Journal Article
    Erdem, Ö. F.; Stein, M.; Kaur-Ghumaan, S.; Reijerse, E. J.; Ott, S.; Lubitz, W.: Effect of Cyanide Ligands on the Electronic Structure of [FeFe] Hydrogenase Active-Site Model Complexes with an Azadithiolate Cofactor. Chemistry – A European Journal 19 (43), pp. 14566 - 14572 (2013)
  48. MPG.PuRe
    DOI
    Journal Article
    Stein, M.; Kaur-Ghumaan, S.: Microbial hydrogen splitting in the presence of oxygen. Biochemical Society Transactions 41 (5), pp. 1317 - 1324 (2013)
  49. MPG.PuRe
    DOI
    Journal Article
    Wang, W.; Nilges, M. J.; Rauchfuss, T. B.; Stein, M.: Isolation of a Mixed Valence Diiron Hydride: Evidence for a Spectator Hydride in Hydrogen Evolution Catalysis. Journal of the American Chemical Society 135 (9), pp. 3633 - 3639 (2013)
  50. 2012
    MPG.PuRe
    DOI
    publisher-version
    Journal Article
    Pandelia, M.-E.; Infossi, P.; Stein, M.; Guidici-Orticoni, M.-T.; Lubitz, W.: Spectroscopic characterization of the key catalytic intermediate Ni-C in the O2-tolerant [NiFe] hydrogenase I from Aquifex aeolicus: evidence of a weakly bound hydride. Chemical Communications 48 (6), pp. 823 - 825 (2012)
 
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