Publications

Articles in peer-reviewed journals:

  1. R. H. Tichauer, J. Feist, G. Groenhof
    Multi-scale dynamics simulations of molecular polaritons: The effect of multiple cavity modes on polariton relaxation
    J. Chem. Phys. 154 (2021) 104112
  2. E. Hulkko, S. Pikker, V. Tiainen, R. H. Tichauer, G. Groenhof, J. J. Toppari
    Effect of molecular Stokes shift on polariton dynamics
    J. Chem. Phys. 154 (2021) 154303
  3. R. Dods, P. Bath, D. Morozov, V. Ahlberg Gagner, D. Arnlund, H.-L. Luk, J. Kuebel, M. Maj, A. Vallejos, C. Wickstrand, R. Bosman, K. R. Beyerlein, G. Nelson, M. Liang, D. Milathianaki, J. Robinson, R. Harimoorthy, P. Berntsen, E. Malmerberg, L. Johansson, R. Andersson, S. Carbajo, E. Claesson, C. E. Conrad, P. Dahl, G. Hammarin, M. S. Hunter, C. Li, S. Lisova, A. Royant, C. Safari, A. Sharma, G. J. Williams, O. Yefanov, S. Westenhoff, J. Davidsson, D. P. DePonte, S. Boutet, A. Barty, G. Katona, G. Groenhof, G. Branden, R. Neutze
    Ultrafast structural changes within a photosynthetic reaction centre
    Nature 589 (2021) 310-314
  4. S. Mustalahti, D. Morozov, H. L. Luk, R. R. Pallerla, P. Myllyperkio, M. Pettersson, P. M. Pihko, G. Groenhof
    Photoactive Yellow Protein Chromophore Photoisomerizes around a Single Bond if the Double Bond is Locked
    J. Phys. Chem. Lett 11 (2020) 2177-2181
  5. E. Claesson, W. Y. Wahlgren, H. Takala, S. Pandey, L. Castillon, V. Kuznetsova, L. Henry, M. Panman, M. Carrillo, J. Kuebel, R. Nanekar, L. Isaksson, A. Nimmrich, A. Cellini, D. Morozov, M. Maj, M. Kurttila, R. Bosman, E. Nango, R. Tanaka, T. Tanaka, L. Fangjia, S. Iwata, S. Owada, K. Moffat, G. Groenhof, E. A. Stojkovic, J. A. Ihalainen, M. Schmidt, S. Westenhoff
    The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser
    Elife, 9 (2020) e53514
  6. G. Groenhof, V. Modi, D. Morozov
    Observe while it happens: catching photoactive proteins in the act with non-adiabatic molecular dynamics simulations
    Curr. Opin. Struct. Biol. 61 (2020) 106-112
  7. P. Dobrev, S. P. B. Vemulapalli, N. Nath, C. Griesinger, G. Groenhof, H. Grubmüller
    Probing the Accuracy of Explicit Solvent Constant pH Molecular Dynamics Simulations for Peptides
    J. Chem. Theory Comput. 16 (2020) 2561-2569

    Correction
    J. Chem. Theory Comput. 16 (2020) 4753-4753

  8. K. S. U. Kansanen, A. Asikainen, J. J. Toppari, G. Groenhof, T. T. Heikkilä
    Theory for stationary polariton response in the presence of vibrations
    Phys. Rev. B 100 (2019) 245426
  9. G. Groenhof, C. Climent, J. Feist, D. Morozov, J. J. Toppari
    Tracking Polariton Relaxation with Multiscale Molecular Dynamics Simulations
    J. Phys. Chem. Lett. 10 (2019) 5476-5483
  10. N. Amdursky, Y. Lin, N. Aho, G. Groenhof
    Exploring fast proton transfer events associated with lateral proton diffusion on the surface of membranes
    Proc. Natl. Acad. Sci. USA 116 (2019) 2443-2451
  11. V. Modi, S. Donnini, G. Groenhof, D. Morozov
    Protonation of the Biliverdin IXa Chromophore in the Red and Far-Red Photoactive States of Bacteriophytochrome
    J. Phys. Chem. B 123 (2019) 2325-2334
  12. G. Groenhof, J. J. Toppari
    Coherent Light Harvesting through Strong Coupling to Confined Light
    J. Phys. Chem. Lett. 9 (2018) 4848-4851
  13. M Priess, H. Goeddeke, G. Groenhof, L. V. Schaefer
    Molecular Mechanism of ATP Hydrolysis in an ABC Transporter
    ACS Cent. Sci. 4 (2018) 1334-1343
  14. L. T. Mix, E. C. Carroll, M. Morozov, J. Pan, W. R. Gordon, A. Philip, J. Fuzell, M. Kumauchi, I. van Stokkum, G. Groenhof, W. D. Hoff, D. S. Larsen
    Excitation-Wavelength-Dependent Photocycle Initiation Dynamics Resolve Heterogeneity in the Photoactive Yellow Protein from Halorhodospira halophila
    Biochemistry 117 (2018) 1733-1747
  15. T.-R. Tero, S. Malola, B. Koncz, E. Pohjolainen, S. Lautala, S. Mustalahti, P. Permi, G. Groenhof, M. Pettersson, H. Hakkinen
    Dynamic Stabilization of the Ligand-Metal Interface in Atomically Precise Gold Nanoclusters Au68 and Au144 Protected by Meta-Mercaptobenzoic Acid
    ACS Nano 11 (2017) 11872-11879

  16. H. L. Luk, J. Feist, J. J. Toppari, G. Groenhof
    Multi-Scale Molecular Dynamics Simulations of Polaritonic Chemistry
    J. Chem. Theory Comput. 13 (2017) 4324-4335

  17. E. Pohjolainen, S. Manola, G. Groenhof, H. Hakkinen
    Exploring strategies for labeling viruses with gold nanoclusters through non-equilibrium molecular dynamics simulations
    Bioconjugate Chem. 28 (2017) 2327-2339

  18. Z. Yin, L. Inhester, S. T. Veedu, W. Quevedo, A. Pietzsch, P. Wernet, G. Groenhof, A. Foehlisch, H. Grubmueller, S. A. Techert
    Cationic and Anionic Impact on the Electronic Structure of Liquid Water
    J. Phys. Chem. Lett. 8 (2017) 3759-3764

  19. S. Baieva, O. Hakamaa, G. Groenhof, T. T. Heikkila, J. J. Toppari
    Dynamics of strongly coupled modes between surface plasmon polaritons and photoactive molecules: the effect of the Stokes shift
    ACS Photonics 4 (2017) 28-37

  20. P. Dobrev, S. Donnini, G. Groenhof, H. Grubmueller
    An accurate three states model for amino acids with two chemically coupled titrating sites in explicit solvent atomistic constant pH simulations and pKa calculations
    J. Chem. Theory Comput. 13 (2017) 147-160

  21. T. Graen, L. Inhester, M. Clemens, H. Grubmueller, G. Groenhof
    The Low Barrier Hydrogen Bond in the Photoactive Yellow Protein: A Vacuum Artifact Absent in the Crystal and Solution
    J. Am. Chem. Soc. 138 (2016) 16620-16631

  22. K. Pande, C. D. M. Hutchison, G. Groenhof, A. Aquila, J. S. Robinson, J. Tenboer, S. Basu, S. Boutet, D. P. DePonte, M. Liang, T. A. White, N. A. Zatsepin, O. Yefanov, D. Morozov, D. Oberthuer, C. Gati, G. Subramanian, D. James, Y. Zhao, J. Koralek, J. Brayshaw, C. Kupitz, C. Conrad, S. Roy-Chowdhury, J. D. Coe, Markus Metz, P. Lourdu Xavier, T. D. Grant, J. E. Koglin, G. Ketawala, R. Fromme, V. Srajer, R. Henning, J. C. H. Spence, A. Ourmazd, P. Schwander, U. Weierstall, M. Frank, P. Fromme, A. Barty, H. N. Chapman, K. Moffat, J. J. van Thor, M. Schmidt
    Femtosecond Structural Dynamics Drives the Trans-to-Cis Isomerization in Photoactive Yellow Protein
    Science 352 (2016) 725-729
    See also our press release

  23. D. Morozov, G. Groenhof
    Hydrogen Bond Fluctuations Control Photochromism in a Reversibly Photo-Switchable Fluorescent Protein
    Angew. Chem. Int. Ed. 55 (2016) 576-578

  24. J. Koivisto, X. Chen, S. Donnini, T. Lahtinen, H. Hakkinen, G. Groenhof, M. Pettersson
    Acid-Base Properties and Surface Charge Distribution of the Water-Soluble Au102(pMBA)44 Nanocluster
    J. Phys. Chem. C 120 (2016) 10041-10050

  25. P. Edlund, H. Takala, E. Claesson, L. Henry, R. Dods, H. Lehtivuori, M. Panman, K. Pande, T. White, T. Nakane, O. Berntsson, E. Gustavsson, P. BÃ¥th, V. Modi, S. Roy-Chowdhury, J. Zook, P. Berntsen, S. Pandey, I. Poudyal, J. Tenboer, C. Kupitz, A. Barty, P. Fromme, J. D. Koralek, T. Tanaka, J. Spence, M. Liang, M. S. Hunter, S. Boutet, E. Nango, K. Moffat, G. Groenhof, J. Ihalainen, E. A. Stojkovic, M. Schmidt, S. Westenhof
    The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallograph
    Sci. Rep. 6 (2016) 35279

  26. S. Donnini, R. T. Ullmann, G. Groenhof, H. Grubmueller
    Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer
    J. Chem. Theory Comp. 12 (2016) 1040-1051

  27. E. Pohjolainen, X. Chen, S. Manola, G. Groenhof, H. HÃkkinen
    A Unified AMBER-Compatible Molecular Mechanics Force Field for Thiolate-Protected Gold Nanoclusters
    J. Chem. Theory Comp. 12 (2016) 1342-1350

  28. T. Kubar, K. Welke, G. Groenhof
    New QM/MM implementation of the DFTB3 method in the gromacs package
    J. Comp. Chem. 36 (2015) 1978-1989

  29. M. Kaucikas, A. Fitzpatrick, E. Bryan, A. Struve, R. Henning, I. Kosheleva, V. Srajer, G. Groenhof, J. J. van Thor
    Room temperature crystal structure of fast switching M159T mutant of the fluorescent protein Dronpa
    Proteins 83 (2015) 397-402

  30. A. N. Chernyshev, D. Morozov, J. Mutanen, V. Yu. Kukushkin, G. Groenhof, M. Haukka
    Weak intermolecular interactions promote blue luminescence of protonated 2,2-dipyridylamine salts
    J. Mat. Chem. C. 2 (2014) 8285-8294

  31. D. Arnlund, L. D. Johansson, C. Wickstrand, A. Barty, G. J. Williams, E. Malmerberg, J. Davidsson, D. Milathianaki, D. P. DePonte, R. L. Shoeman, D. Wang, D. James, G. Katona, S. Westenhoff, T. A. White, A. Aquila, S. Bari, P. Berntsen, M. Bogan, T. Brandt van Driel, R. B. Doak, K. Skov Kjaer, M. Frank, R. Fromme, I. Grotjohann, R. Henning, M. S. Hunter, R. A. Kirian, I. Kosheleva, C. Kupitz, M. Liang, A. V. Martin, M. Meedom Nielsen, M. Messerschmidt, M. M. Seibert, J. Sjohamn, F. Stellato, U. Weierstall, N. A. Zatsepin, J. C. H. Spence, P. Fromme, I. Schlichting, S. Boutet, G. Groenhof, H. N. Chapman, R. Neuze
    Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser
    Nat. Meth. 11 (2014) 923-926

  32. M. D. Davari, F. J. Avila Ferrer, D. Morozov, F. Santoro, G. Groenhof
    The lineshape of the electronic spectrum of the Green Fluorescent Protein chromophore, part I: gas phase
    ChemPhysChem 15 (2014) 3236-3245

  33. F. J. Avila Ferrer, M. D. Davari, D. Morozov, G. Groenhof, F. Santoro
    The lineshape of the electronic spectrum of the Green Fluorescent Protein, part II, solution phase
    ChemPhysChem 15 (2014) 3246-3257

  34. M. G. Wolf, H. Grubmueller, G. Groenhof
    Anomalous surface diffusion of protons on lipid membranes
    Biophys. J. 107 (2014) 76-87

  35. M. Boggio-Pasqua, G. Groenhof
    On the use of reduced active space CASSCF calculations
    Comp. Theor. Chem. 1040-1041 (2014) 6-13

  36. F. Knoch, D. Morozov, M. Boggio-Pasqua, G. Groenhof
    Steering the excited state dynamics of a photoactive yellow protein chromophore analogue with external electric fields
    Comp. Theor. Chem. 1040-1041 (2014) 120-125

  37. J. S. Hub, Bert. L. de Groot, H. Grubmueller, G. Groenhof
    Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge
    J. Chem. Theory. Comp. 10 (2014) 381-390

  38. M. G. Wolf, G. Groenhof
    Explicit proton transfer in classical molecular dynamics simulations
    J. Comp. Chem. 35 (2014) 657-671

  39. J. S. Hub, M. G. Wolf, C. Caleman, P. van Maaren, G. Groenhof, D. van der Spoel
    Thermodynamics of hydronium and hydroxide surface solvation
    Chem. Sci. 5 (2014) 1745-1749

  40. G. Groenhof
    Solving Chemical Problems with a Mixture of Quantum-Mechanical and Molecular Mechanics Calculations: Nobel Prize in Chemistry 2013 (highlight)
    Angew. Chem. Int. Ed. 52 (2013) 12489-12491

    Quantenmechanische und molekuelmechanische Rechnungen zur Loesung chemischer Probleme - der Chemie-Nobelpreis 2013 (highlight).
    Angew. Chem. 125 (2013) 12718-2720

  41. S. Faraji, G. Groenhof, A. Dreuw
    A Combined QM/MM Investigation on the Light-Driven Electron-Induced Repair of the (6-4) Tymine Dimer Catalyzed by DNA Photolyase
    J. Phys. Chem. B. 117 (2013) 10071-10079

  42. W. Li, S. A. Edwards, L. Lu, T. Kubar, S. P. Patil, H. Grubmueller, G. Groenhof, F. Graeter
    Force Distribution Analysis of Mechanochemically Reactive Dimethylcyclobutene
    Chem. Phys. Chem. 14 (2013) 2687-2697

  43. Bennett, W.F.D., Chen, A., Donnini, S., Groenhof, G., Tieleman, D.P.
    Constant pH simulations with the coarse-grained MARTINI model: application to oleic acid aggregates
    Canadian Journal of Chemistry 91 (2013) 839-846

  44. L. Inhester, G. Groenhof, H. Grubmueller
    Core hole screening and decay rates of double core ionized first row hydrides
    J. Chem. Phys. 138 (2013) 164304

  45. L. Vukovic, C. F. Burmeister, P. Kral, G. Groenhof
    Control Mechanisms of Photoisomerization in Protonated Schiff Bases
    J. Phys. Chem. Lett. 4 (2013) 1005-1011

  46. G. Groenhof
    Introduction to QM/MM simulations
    Meth. Mol. Biol. 924 (2013) 43-66

  47. M. G. Wolf, G. Groenhof
    Evaluating non-polarizable nucleic acids forcefield: A systematic comparison of the nucleobases hydration free energies and chloroform-to-water partition coefficients
    J. Comp. Chem. 33 (2012) 2225-2232

  48. M. Boggio-Pasqua, C. F. Burmeister, M. A. Robb, G. Groenhof
    Photochemical reactions in biological systems: probing the effect of the environment by means of hybrid quantum chemistry/molecular mechanics simulations (perspective)
    Phys. Chem. Chem. Phys. 14 (2012) 7912-7928

  49. L. Inhester, C. F. Burmeister, G. Groenhof, H. Grubmueler
    Auger spectrum of a water molecule after single and double core ionization
    J. Chem. Phys. 136 (2012) 144304

  50. M. Lopez, H. Vu, C. K. Wang, M. G. Wolf, G. Groenhof, A. Innocenti, C. T. Supuran, S.-A. Poulsen
    Promiscuity of Carbonic Anhydrase II. Unexpected Ester Hydrolysis of Carbohydrate-Based Sulfamate Inhibitors
    J. Am. Chem. Soc. 133 (2011) 18452-18462

  51. Boggio-Pasqua, M., Groenhof, G.
    Controlling the Photoreactivity of the Photoactive Yellow Protein Chromophore by Substituting at the p-Coumaric Acid Group
    J. Phys. Chem. B 115 (2011) 7021-7028.

  52. Donnini, S., Tegeler, F., Groenhof, G., Grubmueller, H.
    Constant pH Molecular Dynamics in Explicit Solvent with lambda-dynamics
    J. Chem. Theory Comput. 7 (2011) 1962-1978.

    Correction: J. Chem. Theory Comput. 9 (2013) 3261

  53. Woehri, A., G. Katona, L. C. Johansson, E. Fritz, E. Malmerberg, M. Andersson, J. Vincent, M. Eklund, M. Cammarata, M. Wulff, J. Davidsson, G. Groenhof and R. Neutze
    Light-induced structural changes in a photosynthetic reaction center caught by Laue diffraction
    Science, 328 (2010), 630-633.

  54. Brakemann, T., G. Weber, M. Andresen, G. Groenhof, A. C. Stiel, S. Trowitzsch, C. Eggeling, H. Grubmueller, S. W. Hell, M. Wahl and S. Jakobs
    Molecular basis of the light-driven switching of the photochromic fluorescent protein padron
    J. Biol. Chem. 285 (2010) 14603-14609

  55. M. G. Wolf, M. Hoefling, C. Aponte-Santamaria, H. Grubmueller, G. Groenhof
    g membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation
    J. Comput. Chem. 31 (2010) 2169-2174

  56. G. Groenhof, M. Boggio-Pasqua, M.A. Robb
    Computer Simulations of Photobiological Processes: the effect of the protein environment
    Adv. Quant. Chem. 59 (2010) 181-212

  57. M. Boggio-Pasqua, M.A. Robb, G. Groenhof
    Hydrogen bonding controls excited-state decay of the Photoactive Yellow Protein chromophore
    J. Am. Chem. Soc. 131 (2009) 13580-13581

  58. S. Donnini, A.W. Villa, G. Groenhof, A.E. Mark, R.K. Wierenga, A.H. Juffer
    Inclusion of ionization states of ligands in affinity calculations
    Proteins 76 (2009) 138-159

  59. E. Fabiano, G. Groenhof and W. Thiel
    Approximate switching algorithms for trajectory surface hopping
    Chem. Phys. 351 (2008) 111-116

  60. L.V. Schaefer, G. Groenhof, M. Boggio-Pasqua, M.A. Robb and H. Grubmueller
    Protein environment controls photoswitching of the asFP595 chromophore
    PLoS Comput. Biol. 4 (2008) e1000034

  61. G. Groenhof, L.V. Schaefer, M. Boggio-Pasqua, H. Grubmueller and M.A. Robb
    Arginine52 controls the photoisomerization process in photoactive yellow protein
    J. Am. Chem. Soc. 130 (2008) 3250-3251

  62. M. Boggio-Pasqua, G. Groenhof, L.V. Schaefer, H. Grubmueller and M.A. Robb
    Ultra-fast deactivation channel for thymine dimerization
    J. Am. Chem. Soc. 129 (2007) 10996-10997

  63. G. Groenhof, L.V. Schaefer, M. Boggio-Pasqua, M. Goette, H. Grubmueller and M.A. Robb
    Ultra-fast excited state decay of a cytosine-guanine basepair in DNA
    J. Am. Chem. Soc. 129 (2007) 6812-6819

  64. L.V. Schaefer, G. Groenhof, A.R. Klingen, G.M. Ullmann, M. Boggio-Pasqua, M.A. Robb and H. Grubmueller
    Photoswitching of the Fluorescent Protein asFP595: Mechanism, Proton Pathway, and Absorption Spectra
    Angew. Chem. Int. Ed. 119 (2007) 530-536

  65. S. Donnini, G. Groenhof, R.K. Wieringa, and A.H. Juffer
    The Planar Conformation of a Strained Proline Ring: a QM/MM Study
    Proteins 64 (2006) 700-710

  66. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark and H.J.C. Berendsen
    Gromacs: Fast, Flexible and Free
    J. Comput. Chem. 26 (2005) 1701-1718

  67. G. Groenhof, M. Bouxin-Cademartory, B. Hess, S.P. de Visser, H.J.C. Berendsen, M. Olivucci, A.E. Mark and M.A. Robb
    Photoactivation of the Photoactive Yellow Protein: Why photon absorption triggers a trans-to-cis isomerization of the chromophore in the protein
    J. Am. Chem. Soc. 126 (2004) 4228-4233

  68. G. Groenhof, M.F. Lensink, H.J.C. Berendsen and A.E. Mark
    Signal Transduction in the Photoactive Yellow Protein. II: Proton Transfer Initiates Conformational Changes
    Proteins 48 (2002) 212-223

  69. G. Groenhof, M.F. Lensink, J.G. Snijders, H.J.C. Berendsen and A.E. Mark
    Signal Transduction in the Photoactive Yellow Protein. I: Photon Absorption and the Isomerization of the Chromophore
    Proteins 48 (2002) 202-211

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