This includes preprints that have not been peer-reviewed and published.
Vester, J.; Carrasco-Busturia, D.; Ruud, K.; Rnigholm, M.; Olsen, J. M. H. Benchmarks and Workflow for Harmonic IR and Raman Spectra, 2024.
@misc{Vester2024benchmarks,
title = {Benchmarks and Workflow for Harmonic IR and Raman Spectra},
author = {Vester, J. and Carrasco-Busturia, D. and Ruud, K. and Rnigholm, M. and Olsen, J. M. H.},
year = {2024},
publisher = {ChemRxiv},
doi = {10.26434/chemrxiv-2024-5g38f},
url = {https://doi.org/10.26434/chemrxiv-2024-5g38f}
}
Vester, J.; Olsen, J. M. H. Assessing the Partial Hessian Approximation in QM/MM-Based Vibrational Analysis, 2024.
@misc{Vester2024assessing,
title = {Assessing the Partial Hessian Approximation in QM/MM-based Vibrational Analysis},
author = {Vester, J. and Olsen, J. M. H.},
year = {2024},
publisher = {ChemRxiv},
doi = {10.26434/chemrxiv-2024-63t4k},
url = {https://doi.org/10.26434/chemrxiv-2024-63t4k}
}
Kvedaravičiūtė, S.; Adjoua, O.; Ple, T.; Legardere, L.; Piquemal, J.-P.; Rothlisberger, U.; Olsen, J. M. H. A Fully Polarizable KS-DFT/AMOEBA Embedding Scheme for Plane Wave Basis Sets through the MiMiC Framework, 2024.
@misc{Kvedaraviciute2024afully,
title = {A fully polarizable KS-DFT/AMOEBA embedding scheme for plane wave basis sets through the MiMiC framework},
author = {Kvedaravičiūtė, S. and Adjoua, O. and Ple, T. and Legardere, L. and Piquemal, J.-P. and Rothlisberger, U. and Olsen, J. M. H.},
year = {2024},
publisher = {ChemRxiv},
doi = {10.26434/chemrxiv-2024-6sp7h},
url = {https://doi.org/10.26434/chemrxiv-2024-6sp7h}
}
Peer-reviewed publications
Antalík, A.; Levy, A.; Kvedaravičiūtė, S.; Johnson, S. K.; Carrasco-Busturia, D.; Raghavan, B.; Mouvet, F.; Acocella, A.; Das, S.; Gavini, V.; Mandelli, D.; Ippoliti, E.; Meloni, S.; Carloni, P.; Rothlisberger, U.; Olsen, J. M. H. MiMiC: A High-Performance Framework for Multiscale Molecular Dynamics Simulations. J. Chem. Phys.2024, 161, 022501.
@article{Antalik2024mimic,
author = {Antalík, A. and Levy, A. and Kvedaravičiūtė, S. and Johnson, S. K. and Carrasco-Busturia, D. and Raghavan, B. and Mouvet, F. and Acocella, A. and Das, S. and Gavini, V. and Mandelli, D. and Ippoliti, E. and Meloni, S. and Carloni, P. and Rothlisberger, U. and Olsen, J. M. H.},
title = {MiMiC: A High-Performance Framework for Multiscale Molecular Dynamics Simulations},
journal = {J. Chem. Phys.},
volume = {161},
pages = {022501},
year = {2024},
doi = {10.1063/5.0211053},
url = {https://doi.org/10.1063/5.0211053}
}
Carrasco-Busturia, D.; Ippoliti, E.; Meloni, S.; Rothlisberger, U.; Olsen, J. M. H. Multiscale Biomolecular Simulations in the Exascale Era. Curr. Opin. Struct. Biol.2024, 86, 102821.
@article{CarrascoBusturia2024Multiscale,
author = {Carrasco-Busturia, D. and Ippoliti, E. and Meloni, S. and Rothlisberger, U. and Olsen, J. M. H.},
title = {Multiscale Biomolecular Simulations in the Exascale Era},
journal = {Curr. Opin. Struct. Biol.},
volume = {86},
pages = {102821},
year = {2024},
doi = {10.1016/j.sbi.2024.102821},
url = {https://doi.org/10.1016/j.sbi.2024.102821}
}
Carrasco-Busturia, D.; Olsen, J. M. H. Polarizable Embedding Potentials through Molecular Fractionation with Conjugate Caps Including Hydrogen Bonds. J. Chem. Theory Comput.2023, 19, 6510–6520.
@article{CarrascoBusturia2023polarizable,
author = {Carrasco-Busturia, D. and Olsen, J. M. H.},
title = {{Polarizable Embedding Potentials through Molecular Fractionation with Conjugate Caps Including Hydrogen Bonds}},
journal = {J. Chem. Theory Comput.},
volume = {19},
pages = {6510--6520},
year = {2023},
doi = {10.1021/acs.jctc.3c00613},
url = {https://doi.org/10.1021/acs.jctc.3c00613}
}
Kvedaravičiūtė, S.; Carrasco-Busturia, D.; Møller, K. B.; Olsen, J. M. H. Polarizable Embedding without Artificial Boundary Polarization. J. Chem. Theory Comput.2023, 19, 5122–5141.
@article{Kvedaraviciute2023polarizable,
author = {Kvedaravičiūtė, S. and Carrasco-Busturia, D. and M\o{}ller, K. B. and Olsen, J. M. H.},
title = {{Polarizable Embedding without Artificial Boundary Polarization}},
journal = {J. Chem. Theory Comput.},
volume = {19},
pages = {5122--5141},
year = {2023},
doi = {10.1021/acs.jctc.3c00434},
url = {https://doi.org/10.1021/acs.jctc.3c00434}
}
Raghavan, B.; Schackert, F. K.; Levy, A.; Johnson, S. K.; Ippoliti, E.; Mandelli, D.; Olsen, J. M. H.; Rothlisberger, U.; Carloni, P. MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations. J. Chem. Inf. Model.2023, 63, 1406–1412.
@article{Raghavan2023mimicpy,
author = {Raghavan, B. and Schackert, F. K. and Levy, A. and Johnson, S. K. and Ippoliti, E. and Mandelli, D. and Olsen, J. M. H. and Rothlisberger, U. and Carloni, P.},
title = {{MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations}},
journal = {J. Chem. Inf. Model.},
volume = {63},
pages = {1406--1412},
year = {2023},
doi = {10.1021/acs.jcim.2c01620},
url = {https://doi.org/10.1021/acs.jcim.2c01620}
}
Wu, H.; Ma, Z.; Li, M.; Lu, H.; Tang, A.; Zhou, E.; Wen, J.; Sun, Y.; Tress, W.; Olsen, J. M. H.; Meloni, S.; Bo, Z.; Tang, Z. Impact of Donor Halogenation on Reorganization Energies and Voltage Losses in Bulk-Heterojunction Solar Cells. Energy Environ. Sci.2023, 16, 1277–1290.
@article{Wu2023impact,
author = {Wu, H. and Ma, Z. and Li, M. and Lu, H. and Tang, A. and Zhou, E. and Wen, J. and Sun, Y. and Tress, W. and Olsen, J. M. H. and Meloni, S. and Bo, Z. and Tang, Z.},
title = {{Impact of donor halogenation on reorganization energies and voltage losses in bulk-heterojunction solar cells}},
journal = {Energy Environ. Sci.},
volume = {16},
pages = {1277--1290},
doi = {10.1039/D3EE00174A},
url = {https://doi.org/10.1039/D3EE00174A},
year = {2023}
}
Church, J. R.; Olsen, J. M. H.; Schapiro, I. Induction Effects on the Absorption Maxima of Photoreceptor Proteins. Biophysics and Physicobiology2023, 20, e201007.
@article{Church2023induction,
author = {Church, J. R. and Olsen, J. M. H. and Schapiro, I.},
title = {{Induction effects on the absorption maxima of photoreceptor proteins}},
journal = {Biophysics and Physicobiology},
volume = {20},
pages = {e201007},
doi = {10.2142/biophysico.bppb-v20.s007},
url = {https://doi.org/10.2142/biophysico.bppb-v20.s007},
year = {2023}
}
Church, J. R.; Amoyal, G. S.; Borin, V. A.; Adam, S.; Olsen, J. M. H.; Schapiro, I. Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry. Chem. Eur. J.2022, 28, e202200139.
@article{Church2022deciphering,
author = {Church, J. R. and Amoyal, G. S. and Borin, V. A. and Adam, S. and Olsen, J. M. H. and Schapiro, I.},
title = {{Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry}},
journal = {Chem. Eur. J.},
volume = {28},
pages = {e202200139},
doi = {10.1002/chem.202200139},
url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/chem.202200139},
year = {2022}
}
Church, J. R.; Olsen, J. M. H.; Schapiro, I. The Impact of Retinal Configuration on the Protein–Chromophore Interactions in Bistable Jumping Spider Rhodopsin-1. Molecules2022, 27, 71.
@article{Church2022theimpact,
author = {Church, J. R. and Olsen, J. M. H. and Schapiro, I.},
title = {{The Impact of Retinal Configuration on the Protein--Chromophore Interactions in Bistable Jumping Spider Rhodopsin-1}},
journal = {Molecules},
volume = {27},
year = {2022},
pages = {71},
url = {https://www.mdpi.com/1420-3049/27/1/71},
doi = {10.3390/molecules27010071}
}
Kirsch, T.; Olsen, J. M. H.; Bolnykh, V.; Meloni, S.; Ippoliti, E.; Rothlisberger, U.; Cascella, M.; Gauss, J. Wavefunction-Based Electrostatic-Embedding QM/MM Using CFOUR through MiMiC. J. Chem. Theory Comput.2022, 18, 13–24.
@article{Kirsch2022wavefunction,
author = {Kirsch, T. and Olsen, J. M. H. and Bolnykh, V. and Meloni, S. and Ippoliti, E. and Rothlisberger, U. and Cascella, M. and Gauss, J.},
title = {{Wavefunction-Based Electrostatic-Embedding QM/MM Using CFOUR through MiMiC}},
journal = {J. Chem. Theory Comput.},
volume = {18},
pages = {13--24},
year = {2022},
doi = {10.1021/acs.jctc.1c00878},
url = {https://doi.org/10.1021/acs.jctc.1c00878}
}
Scheurer, M.; Reinholdt, P.; Olsen, J. M. H.; Dreuw, A.; Kongsted, J. Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees. J. Chem. Theory Comput.2021, 17, 3445–3454.
@article{Scheurer2021efficient,
author = {Scheurer, M. and Reinholdt, P. and Olsen, J. M. H. and Dreuw, A. and Kongsted, J.},
title = {{Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees}},
journal = {J. Chem. Theory Comput.},
volume = {17},
pages = {3445--3454},
year = {2021},
doi = {10.1021/acs.jctc.1c00225},
url = {https://doi.org/10.1021/acs.jctc.1c00225}
}
Dundas, K. O. H. M.; Beerepoot, M. T. P.; Ringholm, M.; Reine, S.; Bast, R.; List, N. H.; Kongsted, J.; Ruud, K.; Olsen, J. M. H. Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model. J. Chem Theory Comput.2021, 17, 3599–3617.
@article{Dundas2021harmonic,
author = {Dundas, K. O. H. M. and Beerepoot, M. T. P. and Ringholm, M. and Reine, S. and Bast, R. and List, N. H. and Kongsted, J. and Ruud, K. and Olsen, J. M. H.},
title = {{Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model}},
journal = {J. Chem Theory Comput.},
volume = {17},
pages = {3599--3617},
year = {2021},
doi = {10.1021/acs.jctc.0c01323},
url = {https://doi.org/10.1021/acs.jctc.0c01323}
}
Mroginski, M.-A.; Adam, S.; Amoyal, G. S.; Barnoy, A.; Bondar, A.-N.; Borin, V. A.; Church, J. R.; Domratcheva, T.; Ensing, B.; Fanelli, F.; Ferré, N.; Filiba, O.; Pedraza-González, L.; González, R.; González-Espinoza, C. E.; Kar, R. K.; Kemmler, L.; Kim, S. S.; Kongsted, J.; Krylov, A. I.; Lahav, Y.; Lazaratos, M.; NasserEddin, Q.; Navizet, I.; Nemukhin, A.; Olivucci, M.; Olsen, J. M. H.; Alba Ortíz, A. Pérez de; Pieri, E.; Rao, A. G.; Rhee, Y. M.; Ricardi, N.; Sen, S.; Solov’yov, I. A.; De Vico, L.; Wesolowski, T. A.; Wiebeler, C.; Yang, X.; Schapiro, I. Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochem. Photobiol.2021, 97, 243–269.
@article{Mroginski2021frontiers,
author = {Mroginski, M.-A. and Adam, S. and Amoyal, G. S. and Barnoy, A. and Bondar, A.-N. and Borin, V. A. and Church, J. R. and Domratcheva, T. and Ensing, B. and Fanelli, F. and Ferré, N. and Filiba, O. and Pedraza-González, L. and González, R. and González-Espinoza, C. E. and Kar, R. K. and Kemmler, L. and Kim, S. S. and Kongsted, J. and Krylov, A. I. and Lahav, Y. and Lazaratos, M. and NasserEddin, Q. and Navizet, I. and Nemukhin, A. and Olivucci, M. and Olsen, J. M. H. and Pérez de Alba Ortíz, A. and Pieri, E. and Rao, A. G. and Rhee, Y. M. and Ricardi, N. and Sen, S. and Solov'yov, I. A. and De Vico, L. and Wesolowski, T. A. and Wiebeler, C. and Yang, X. and Schapiro, I.},
title = {{Frontiers in Multiscale Modeling of Photoreceptor Proteins}},
journal = {Photochem. Photobiol.},
volume = {97},
pages = {243--269},
doi = {https://doi.org/10.1111/php.13372},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/php.13372},
year = {2021}
}
Reinholdt, P.; Jørgensen, F. K.; Kongsted, J.; Olsen, J. M. H. Polarizable Density Embedding for Large Biomolecular Systems. J. Chem. Theory Comput.2020, 16, 5999–6006.
@article{Reinholdt2020polarizable,
doi = {10.1021/acs.jctc.0c00763},
url = {https://doi.org/10.1021/acs.jctc.0c00763},
year = {2020},
volume = {16},
pages = {5999--6006},
author = {Reinholdt, P. and J{\o}rgensen, F. K. and Kongsted, J. and Olsen, J. M. H.},
title = {{Polarizable Density Embedding for Large Biomolecular Systems}},
journal = {J. Chem. Theory Comput.}
}
Capelli, R.; Lyu, W.; Bolnykh, V.; Meloni, S.; Olsen, J. M. H.; Rothlisberger, U.; Parrinello, M.; Carloni, P. Accuracy of Molecular Simulation-Based Predictions of k_off Values: A Metadynamics Study. J. Phys. Chem. Lett.2020, 11, 6373–6381.
@article{Capelli2020accuracy,
doi = {10.1021/acs.jpclett.0c00999},
url = {https://doi.org/10.1021/acs.jpclett.0c00999},
year = {2020},
volume = {11},
pages = {6373--6381},
author = {Capelli, R. and Lyu, W. and Bolnykh, V. and Meloni, S. and Olsen, J. M. H. and Rothlisberger, U. and Parrinello, M. and Carloni, P.},
title = {{Accuracy of Molecular Simulation-Based Predictions of $k_{off}$ Values: A Metadynamics Study}},
journal = {J. Phys. Chem. Lett.}
}
Rossano-Tapia, M.; Olsen, J. M. H.; Brown, A. Two-Photon Absorption Cross-Sections in Fluorescent Proteins Containing Non-Canonical Chromophores Using Polarizable QM/MM. Front. Mol. Biosci.2020, 7, 111.
@article{RossanoTapia2020twophoton,
doi = {10.3389/fmolb.2020.00111},
url = {https://doi.org/10.3389/fmolb.2020.00111},
year = {2020},
volume = {7},
pages = {111},
author = {Rossano-Tapia, M. and Olsen, J. M. H. and Brown, A.},
title = {{Two-Photon Absorption Cross-Sections in Fluorescent Proteins Containing Non-canonical Chromophores Using Polarizable {QM}/{MM}}},
journal = {Front. Mol. Biosci.}
}
Olsen, J. M. H.; Reine, S.; Vahtras, O.; Kjellgren, E.; Reinholdt, P.; Hjorth Dundas, K. O.; Li, X.; Cukras, J.; Ringholm, M.; Hedegård, E. D.; Di Remigio, R.; List, N. H.; Faber, R.; Cabral Tenorio, B. N.; Bast, R.; Pedersen, T. B.; Rinkevicius, Z.; Sauer, S. P. A.; Mikkelsen, K. V.; Kongsted, J.; Coriani, S.; Ruud, K.; Helgaker, T.; Jensen, H. J. A.; Norman, P. Dalton Project: A Python Platform for Molecular- and Electronic-Structure Simulations of Complex Systems. J. Chem. Phys.2020, 152, 214115.
@article{Olsen2020dalton,
doi = {10.1063/1.5144298},
url = {https://doi.org/10.1063/1.5144298},
year = {2020},
volume = {152},
pages = {214115},
author = {Olsen, J. M. H. and Reine, S. and Vahtras, O. and Kjellgren, E. and Reinholdt, P. and Hjorth Dundas, K. O. and Li, X. and Cukras, J. and Ringholm, M. and Hedeg{\aa}rd, E. D. and Di Remigio, R. and List, N. H. and Faber, R. and Cabral Tenorio, B. N. and Bast, R. and Pedersen, T. B. and Rinkevicius, Z. and Sauer, S. P. A. and Mikkelsen, K. V. and Kongsted, J. and Coriani, S. and Ruud, K. and Helgaker, T. and Jensen, H. J. Aa. and Norman, P.},
title = {{Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems}},
journal = {J. Chem. Phys.}
}
Saue, T.; Bast, R.; Gomes, A. S. P.; Jensen, H. J. A.; Visscher, L.; Aucar, I. A.; Di Remigio, R.; Dyall, K. G.; Eliav, E.; Fasshauer, E.; Fleig, T.; Halbert, L.; Hedegård, E. D.; Helmich-Paris, B.; Iliaš, M.; Jacob, C. R.; Knecht, S.; Laerdahl, J. K.; Vidal, M. L.; Nayak, M. K.; Olejniczak, M.; Olsen, J. M. H.; Pernpointner, M.; Senjean, B.; Shee, A.; Sunaga, A.; Stralen, J. N. P. van. The DIRAC Code for Relativistic Molecular Calculations. J. Chem. Phys.2020, 152, 204104.
@article{Saue2020thedirac,
doi = {10.1063/5.0004844},
url = {https://doi.org/10.1063/5.0004844},
year = {2020},
volume = {152},
pages = {204104},
author = {Saue, T. and Bast, R. and Gomes, A. S. P. and Jensen, H. J. {Aa}. and Visscher, L. and Aucar, I. A. and Di Remigio, R. and Dyall, K. G. and Eliav, E. and Fasshauer, E. and Fleig, T. and Halbert, L. and Hedeg{\aa}rd, E. D. and Helmich-Paris, B. and Ilia{\v{s}}, M. and Jacob, C. R. and Knecht, S. and Laerdahl, J. K. and Vidal, M. L. and Nayak, M. K. and Olejniczak, M. and Olsen, J. M. H. and Pernpointner, M. and Senjean, B. and Shee, A. and Sunaga, A. and van Stralen, J. N. P.},
title = {{The {DIRAC} code for relativistic molecular calculations}},
journal = {J. Chem. Phys.}
}
Chiariello, M. G.; Bolnykh, V.; Ippoliti, E.; Meloni, S.; Olsen, J. M. H.; Beck, T.; Rothlisberger, U.; Fahlke, C.; Carloni, P. Molecular Basis of CLC Antiporter Inhibition by Fluoride. J. Am. Chem. Soc.2020, 142, 7254–7258.
@article{Chiariello2020molecular,
doi = {10.1021/jacs.9b13588},
url = {https://doi.org/10.1021/jacs.9b13588},
year = {2020},
volume = {142},
pages = {7254--7258},
author = {Chiariello, M. G. and Bolnykh, V. and Ippoliti, E. and Meloni, S. and Olsen, J. M. H. and Beck, T. and Rothlisberger, U. and Fahlke, C. and Carloni, P.},
title = {{Molecular Basis of {CLC} Antiporter Inhibition by Fluoride}},
journal = {J. Am. Chem. Soc.}
}
Bolnykh, V.; Olsen, J. M. H.; Meloni, S.; Bircher, M. P.; Ippoliti, E.; Carloni, P.; Rothlisberger, U. MiMiC: Multiscale Modeling in Computational Chemistry. Front. Mol. Biosci.2020, 7, 45.
@article{Bolnykh2020mimic,
doi = {10.3389/fmolb.2020.00045},
url = {https://doi.org/10.3389/fmolb.2020.00045},
year = {2020},
volume = {7},
pages = {45},
author = {Bolnykh, V. and Olsen, J. M. H. and Meloni, S. and Bircher, M. P. and Ippoliti, E. and Carloni, P. and Rothlisberger, U.},
title = {{{MiMiC}: Multiscale Modeling in Computational Chemistry}},
journal = {Front. Mol. Biosci.}
}
Khah, A. M.; Reinholdt, P.; Olsen, J. M. H.; Kongsted, J.; Hättig, C. Avoiding Electron Spill-Out in QM/MM Calculations on Excited States with Simple Pseudopotentials. J. Chem. Theory Comput.2020, 16, 1373–1381.
@article{MarefatKhah2020avoiding,
doi = {10.1021/acs.jctc.9b01162},
url = {https://doi.org/10.1021/acs.jctc.9b01162},
year = {2020},
volume = {16},
pages = {1373--1381},
author = {Khah, A. M. and Reinholdt, P. and Olsen, J. M. H. and Kongsted, J. and H\"{a}ttig, C.},
title = {{Avoiding Electron Spill-Out in {QM}/{MM} Calculations on Excited States with Simple Pseudopotentials}},
journal = {J. Chem. Theory Comput.}
}
Reinholdt, P.; Kjellgren, E. R.; Steinmann, C.; Olsen, J. M. H. Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments. J. Chem. Theory Comput.2020, 16, 1162–1174.
@article{Reinholdt2019cost,
doi = {10.1021/acs.jctc.9b00616},
year = {2020},
volume = {16},
pages = {1162--1174},
url = {https://doi.org/10.1021/acs.jctc.9b00616},
author = {Reinholdt, P. and Kjellgren, E. R. and Steinmann, C. and Olsen, J. M. H.},
title = {{Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments}},
journal = {J. Chem. Theory Comput.}
}
Scheurer, M.; Reinholdt, P.; Kjellgren, E. R.; Olsen, J. M. H.; Dreuw, A.; Kongsted, J. CPPE: An Open-Source C++ and Python Library for Polarizable Embedding. J. Chem. Theory Comput.2019, 15, 6154–6163.
@article{Scheurer2019cppe,
doi = {10.1021/acs.jctc.9b00758},
url = {https://doi.org/10.1021/acs.jctc.9b00758},
year = {2019},
volume = {15},
pages = {6154--6163},
author = {Scheurer, M. and Reinholdt, P. and Kjellgren, E. R. and Olsen, J. M. H. and Dreuw, A. and Kongsted, J.},
title = {{CPPE: An Open-Source C++ and Python Library for Polarizable Embedding}},
journal = {J. Chem. Theory Comput.}
}
Bolnykh, V.; Olsen, J. M. H.; Meloni, S.; Bircher, M. P.; Ippoliti, E.; Carloni, P.; Rothlisberger, U. Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC. J. Chem. Theory Comput.2019, 15, 5601–5613.
@article{Bolnykh2019extreme,
doi = {10.1021/acs.jctc.9b00424},
url = {https://doi.org/10.1021/acs.jctc.9b00424},
year = {2019},
volume = {15},
pages = {5601--5613},
author = {Bolnykh, V. and Olsen, J. M. H. and Meloni, S. and Bircher, M. P. and Ippoliti, E. and Carloni, P. and Rothlisberger, U.},
title = {Extreme Scalability of {DFT}-based {QM}/{MM} {MD} Simulations Using {MiMiC}},
journal = {J. Chem. Theory Comput.}
}
Olsen, J. M. H.; Bolnykh, V.; Meloni, S.; Ippoliti, E.; Bircher, M. P.; Carloni, P.; Rothlisberger, U. MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry. J. Chem. Theory Comput.2019, 15, 3810–3823.
@article{Olsen2019mimic,
doi = {10.1021/acs.jctc.9b00093},
url = {https://doi.org/10.1021/acs.jctc.9b00093},
year = {2019},
volume = {15},
pages = {3810--3823},
author = {Olsen, J. M. H. and Bolnykh, V. and Meloni, S. and Ippoliti, E. and Bircher, M. P. and Carloni, P. and Rothlisberger, U.},
title = {{MiMiC}: A Novel Framework for Multiscale Modeling in Computational Chemistry},
journal = {J. Chem. Theory Comput.}
}
Scheurer, M.; Herbst, M. F.; Reinholdt, P.; Olsen, J. M. H.; Dreuw, A.; Kongsted, J. Polarizable Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems. J. Chem. Theory Comput.2018, 14, 4870–4883.
@article{Scheurer2018polarizable,
doi = {10.1021/acs.jctc.8b00576},
url = {https://doi.org/10.1021/acs.jctc.8b00576},
year = {2018},
volume = {14},
pages = {4870--4883},
author = {Scheurer, M. and Herbst, M. F. and Reinholdt, P. and Olsen, J. M. H. and Dreuw, A. and Kongsted, J.},
title = {Polarizable Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems},
journal = {J. Chem. Theory Comput.}
}
Steinmann, C.; Reinholdt, P.; Nørby, M. S.; Kongsted, J.; Olsen, J. M. H. Response Properties of Embedded Molecules through the Polarizable Embedding Model. Int. J. Quantum Chem.2018, 119, e25717.
@article{Steinmann2018response,
author = {Steinmann, C. and Reinholdt, P. and N\o{}rby, M. S. and Kongsted, J. and Olsen, J. M. H.},
title = {Response properties of embedded molecules through the polarizable embedding model},
year = {2018},
volume = {119},
pages = {e25717},
journal = {Int. J. Quantum Chem.},
doi = {10.1002/qua.25717}
}
Kjellgren, E. R.; Olsen, J. M. H.; Kongsted, J. Importance of Accurate Structures for Quantum Chemistry Embedding Methods: Which Strategy Is Better? J. Chem. Theory Comput.2018, 14, 4309–4319.
@article{Kjellgren2018importance,
doi = {10.1021/acs.jctc.8b00202},
url = {https://doi.org/10.1021/acs.jctc.8b00202},
year = {2018},
volume = {14},
pages = {4309--4319},
author = {Kjellgren, E. R. and Olsen, J. M. H. and Kongsted, J.},
title = {Importance of Accurate Structures for Quantum Chemistry Embedding Methods: Which Strategy Is Better?},
journal = {J. Chem. Theory Comput.}
}
Hršak, D.; Olsen, J. M. H.; Kongsted, J. Polarizable Density Embedding Coupled Cluster Method. J. Chem. Theory Comput.2018, 14, 1351–1360.
@article{Hrak2018polarizable,
doi = {10.1021/acs.jctc.7b01153},
url = {https://doi.org/10.1021/acs.jctc.7b01153},
year = {2018},
volume = {14},
pages = {1351--1360},
author = {Hr{\v{s}}ak, D. and Olsen, J. M. H. and Kongsted, J.},
title = {Polarizable Density Embedding Coupled Cluster Method},
journal = {J. Chem. Theory Comput.}
}
Fahleson, T.; Olsen, J. M. H.; Norman, P.; Rizzo, A. A QM/MM and QM/QM/MM Study of Kerr, Cotton–Mouton and Jones Linear Birefringences in Liquid Acetonitrile. Phys. Chem. Chem. Phys.2018, 20, 3831–3840.
@article{Fahleson2018a,
doi = {10.1039/c7cp07421b},
url = {https://doi.org/10.1039/c7cp07421b},
year = {2018},
volume = {20},
pages = {3831--3840},
author = {Fahleson, T. and Olsen, J. M. H. and Norman, P. and Rizzo, A.},
title = {A {QM}/{MM} and {QM}/{QM}/{MM} study of Kerr, Cotton{\textendash}Mouton and Jones linear birefringences in liquid acetonitrile},
journal = {Phys. Chem. Chem. Phys.}
}
Reinholdt, R.; Kongsted, J.; Olsen, J. M. H. Polarizable Density Embedding: A Solution to the Electron Spill-Out Problem in Multiscale Modeling. J. Phys. Chem. Lett.2017, 8, 5949–5958.
@article{Reinholdt2017polarizable,
doi = {10.1021/acs.jpclett.7b02788},
url = {https://doi.org/10.1021/acs.jpclett.7b02788},
year = {2017},
volume = {8},
pages = {5949--5958},
author = {Reinholdt, R. and Kongsted, J. and Olsen, J. M. H.},
title = {Polarizable Density Embedding: A Solution to the Electron Spill-Out Problem in Multiscale Modeling},
journal = {J. Phys. Chem. Lett.}
}
Nåbo, L. J.; Olsen, J. M. H.; Martı́nez T. J.; Kongsted, J. The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein. J. Chem. Theory Comput.2017, 13, 6230–6236.
@article{Nabo2017thequality,
doi = {10.1021/acs.jctc.7b00528},
url = {https://doi.org/10.1021/acs.jctc.7b00528},
year = {2017},
volume = {13},
pages = {6230--6236},
author = {N{\aa}bo, L. J. and Olsen, J. M. H. and Mart{\'{\i}}nez, T. J. and Kongsted, J.},
title = {{The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein}},
journal = {J. Chem. Theory Comput.}
}
Nørby, M. S.; Olsen, J. M. H.; Steinmann, C.; Kongsted, J. Modeling Electronic Circular Dichroism within the Polarizable Embedding Approach. J. Chem. Theory Comput.2017, 13, 4442–4451.
@article{Norby2017modeling,
doi = {10.1021/acs.jctc.7b00712},
url = {https://doi.org/10.1021/acs.jctc.7b00712},
year = {2017},
volume = {13},
pages = {4442--4451},
author = {N{\o}rby, M. S. and Olsen, J. M. H. and Steinmann, C. and Kongsted, J.},
title = {{Modeling Electronic Circular Dichroism within the Polarizable Embedding Approach}},
journal = {J. Chem. Theory Comput.}
}
Hršak, D.; Olsen, J. M. H.; Kongsted, J. Optimization and Transferability of Non-Electrostatic Repulsion in the Polarizable Density Embedding Model. J. Comput. Chem.2017, 38, 2108–2117.
@article{Hrsak2017optimization,
doi = {10.1002/jcc.24859},
url = {https://doi.org/10.1002/jcc.24859},
year = {2017},
volume = {38},
pages = {2108--2117},
author = {Hr{\v{s}}ak, D. and Olsen, J. M. H. and Kongsted, J.},
title = {{Optimization and transferability of non-electrostatic repulsion in the polarizable density embedding model}},
journal = {J. Comput. Chem.}
}
Olsen, J. M. H.; Hedegård, E. D. Modeling the Absorption Spectrum of the Permanganate Ion in Vacuum and in Aqueous Solution. Phys. Chem. Chem. Phys.2017, 19, 15870–15875.
@article{olsen2017modeling,
author = {Olsen, J. M. H. and Hedeg\aa{}rd, E. D.},
title = {{Modeling the absorption spectrum of the permanganate ion in vacuum and in aqueous solution}},
journal = {Phys. Chem. Chem. Phys.},
volume = {19},
pages = {15870--15875},
year = {2017},
doi = {10.1039/C7CP01194F},
url = {https://doi.org/10.1039/C7CP01194F}
}
Hedegård, E. D.; Bast, R.; Kongsted, J.; Olsen, J. M. H.; Jensen, H. J. \relax A. Relativistic Polarizable Embedding. J. Chem. Theory Comput.2017, 13, 2870–2880.
@article{hedegard2017relativistic,
author = {Hedeg\aa{}rd, E. D. and Bast, R. and Kongsted, J. and Olsen, J. M. H. and Jensen, H. J. {\relax Aa}.},
title = {{Relativistic Polarizable Embedding}},
journal = {J. Chem. Theory Comput.},
volume = {13},
pages = {2870--2880},
year = {2017},
doi = {10.1021/acs.jctc.7b00162},
url = {https://doi.org/10.1021/acs.jctc.7b00162}
}
Witzke, S.; List, N. H.; Olsen, J. M. H.; Steinmann, C.; Petersen, M.; Beerepoot, M. T. P.; Kongsted, J. An Averaged Polarizable Potential for Multiscale Modeling in Phospholipid Membranes. J. Comput. Chem.2017, 38, 601–611.
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author = {Witzke, S. and List, N. H. and Olsen, J. M. H. and Steinmann, C. and Petersen, M. and Beerepoot, M. T. P. and Kongsted, J.},
title = {{An averaged polarizable potential for multiscale modeling in phospholipid membranes}},
journal = {J. Comput. Chem.},
volume = {38},
pages = {601--611},
year = {2017},
doi = {10.1002/jcc.24718}
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Steinmann, C.; Bratholm, L. A.; Olsen, J. M. H.; Kongsted, J. Automated Fragmentation Polarizable Embedding Density Functional Theory (PE-DFT) Calculations of Nuclear Magnetic Resonance (NMR) Shielding Constants of Proteins with Application to Chemical Shift Predictions. J. Chem. Theory Comput.2017, 13, 525–536.
@article{steinmann2017automated,
author = {Steinmann, C. and Bratholm, L. A. and Olsen, J. M. H. and Kongsted, J.},
title = {{Automated Fragmentation Polarizable Embedding Density Functional Theory (PE-DFT) Calculations of Nuclear Magnetic Resonance (NMR) Shielding Constants of Proteins with Application to Chemical Shift Predictions}},
journal = {J. Chem. Theory Comput.},
volume = {13},
pages = {525--536},
year = {2017},
doi = {10.1021/acs.jctc.6b00965}
}
Steindal, A. H.; Beerepoot, M. T. P.; Ringholm, M.; List, N. H.; Ruud, K.; Kongsted, J.; Olsen, J. M. H. Open-Ended Response Theory with Polarizable Embedding: Multiphoton Absorption in Biomolecular Systems. Phys. Chem. Chem. Phys.2016, 18, 28339–28352.
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author = {Steindal, A. H. and Beerepoot, M. T. P. and Ringholm, M. and List, N. H. and Ruud, K. and Kongsted, J. and Olsen, J. M. H.},
title = {{Open-ended response theory with polarizable embedding: multiphoton absorption in biomolecular systems}},
journal = {Phys. Chem. Chem. Phys.},
year = {2016},
volume = {18},
pages = {28339--28352},
doi = {10.1039/C6CP05297E}
}
Nåbo, L. J.; Olsen, J. M. H.; List, N. H.; Solanko, L. M.; Wüstner, D.; Kongsted, J. Embedding beyond Electrostatics—The Role of Wave Function Confinement. J. Chem. Phys.2016, 145, 104102.
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author = {N\aa{}bo, L. J. and Olsen, J. M. H. and List, N. H. and Solanko, L. M. and W\"{u}stner, D. and Kongsted, J.},
title = {{Embedding beyond electrostatics---The role of wave function confinement}},
journal = {J. Chem. Phys.},
volume = {145},
pages = {104102},
year = {2016},
doi = {10.1063/1.4962367}
}
Nørby, M. S.; Steinmann, C.; Olsen, J. M. H.; Li, H.; Kongsted, J. Computational Approach for Studying Optical Properties of DNA Systems in Solution. J. Chem. Theory Comput.2016, 12, 5050–5057.
@article{norby2016computational,
author = {N\o{}rby, M. S. and Steinmann, C. and Olsen, J. M. H. and Li, H. and Kongsted, J.},
title = {{Computational Approach for Studying Optical Properties of DNA Systems in Solution}},
journal = {J. Chem. Theory Comput.},
volume = {12},
pages = {5050--5057},
year = {2016},
doi = {10.1021/acs.jctc.6b00706}
}
List, N. H.; Olsen, J. M. H.; Kongsted, J. Excited States in Large Molecular Systems through Polarizable Embedding. Phys. Chem. Chem. Phys.2016, 18, 20234–20250.
@article{list2016excited,
author = {List, N. H. and Olsen, J. M. H. and Kongsted, J.},
title = {{Excited states in large molecular systems through polarizable embedding}},
journal = {Phys. Chem. Chem. Phys.},
year = {2016},
volume = {18},
pages = {20234--20250},
doi = {10.1039/C6CP03834D}
}
Nørby, M. S.; Olsen, J. M. H.; Kongsted, J.; Jensen, H. J. \relax A. Multipole Moments for Embedding Potentials: Exploring Different Atomic Allocation Algorithms. J. Comp. Chem.2016, 37, 1887–1896.
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author = {N\o{}rby, M. S. and Olsen, J. M. H. and Kongsted, J. and Jensen, H. J. {\relax Aa}.},
title = {{Multipole moments for embedding potentials: Exploring different atomic allocation algorithms}},
journal = {J. Comp. Chem.},
volume = {37},
pages = {1887--1896},
year = {2016},
doi = {10.1002/jcc.24403}
}
Beerepoot, M. T. P.; Steindal, A. H.; List, N. H.; Kongsted, J.; Olsen, J. M. H. Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties. J Chem. Theory Comput.2016, 12, 1684–1695.
@article{beerepoot2016averaged,
author = {Beerepoot, M. T. P. and Steindal, A. H. and List, N. H. and Kongsted, J. and Olsen, J. M. H.},
title = {{Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties}},
journal = {J Chem. Theory Comput.},
volume = {12},
pages = {1684--1695},
year = {2016},
doi = {10.1021/acs.jctc.5b01000}
}
Rasmussen, E.; Olsen, J. M. H.; Solov’yov, I. Quantifying Electron Transfer Reactions in Biological Systems: What Interactions Play the Major Role? Scientific Reports2016, 5, 18446.
@article{rasmussen2015quantifying,
author = {Rasmussen, E. and Olsen, J. M. H. and Solov'yov, I.},
title = {{Quantifying electron transfer reactions in biological systems: what interactions play the major role?}},
journal = {Scientific Reports},
volume = {5},
pages = {18446},
year = {2016},
doi = {10.1038/srep18446}
}
Olsen, J. M. H.; List, N. H.; Kristensen, K.; Kongsted, J. Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials. J. Chem. Theory Comput.2015, 11, 1832–1842.
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author = {Olsen, J. M. H. and List, N. H. and Kristensen, K. and Kongsted, J.},
title = {{Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials}},
journal = {J. Chem. Theory Comput.},
volume = {11},
pages = {1832--1842},
year = {2015},
doi = {10.1021/acs.jctc.5b00078}
}
Hedegård, E. D.; Olsen, J. M. H.; Knecht, S.; Kongsted, J.; Jensen, H. J. \relax A. Polarizable Embedding with a Multiconfiguration Short-Range Density Functional Theory Linear Response Method. J. Chem. Phys.2015, 142, 114113.
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author = {Hedeg\aa{}rd, E. D. and Olsen, J. M. H. and Knecht, S. and Kongsted, J. and Jensen, H. J. {\relax Aa}.},
title = {{Polarizable embedding with a multiconfiguration short-range density functional theory linear response method}},
journal = {J. Chem. Phys.},
year = {2015},
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Olsen, J. M. H.; Steinmann, C.; Ruud, K.; Kongsted, J. Polarizable Density Embedding: A New QM/QM/MM-Based Computational Strategy. J. Phys. Chem. A2015, 119, 5344–5355.
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author = {Olsen, J. M. H. and Steinmann, C. and Ruud, K. and Kongsted, J.},
title = {{Polarizable Density Embedding: A New QM/QM/MM-Based Computational Strategy}},
journal = {J. Phys. Chem. A},
volume = {119},
pages = {5344--5355},
year = {2015},
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List, N. H.; Beerepoot, M. T. P.; Olsen, J. M. H.; Gao, B.; Ruud, K.; Jensen, H. J. \relax A.; Kongsted, J. Molecular Quantum Mechanical Gradients within the Polarizable Embedding Approach—Application to the Internal Vibrational Stark Shift of Acetophenone. J. Chem. Phys.2015, 142, 034119.
@article{list2015molecular,
author = {List, N. H. and Beerepoot, M. T. P. and Olsen, J. M. H. and Gao, B. and Ruud, K. and Jensen, H. J. {\relax Aa}. and Kongsted, J.},
title = {{Molecular quantum mechanical gradients within the polarizable embedding approach---Application to the internal vibrational Stark shift of acetophenone}},
journal = {J. Chem. Phys.},
year = {2015},
volume = {142},
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doi = {10.1063/1.4905909}
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Schwabe, T.; Beerepoot, M. T. P.; Olsen, J. M. H.; Kongsted, J. Analysis of Computational Models for an Accurate Study of Electronic Excitations in GFP. Phys. Chem. Chem. Phys.2015, 17, 2582–2588.
@article{schwabe2015analysis,
author = {Schwabe, T. and Beerepoot, M. T. P. and Olsen, J. M. H. and Kongsted, J.},
title = {{Analysis of computational models for an accurate study of electronic excitations in GFP}},
journal = {Phys. Chem. Chem. Phys.},
year = {2015},
volume = {17},
pages = {2582--2588},
doi = {10.1039/C4CP04524F}
}
Schmidt, J. A.; Olsen, J. M. H. Photodissociation of OCS: Deviations between Theory and Experiment, and the Importance of Higher Order Correlation Effects. J. Chem. Phys.2014, 141, 184310.
@article{schmidt2014photodissociation,
author = {Schmidt, J. A. and Olsen, J. M. H.},
title = {{Photodissociation of OCS: Deviations between theory and experiment, and the importance of higher order correlation effects}},
journal = {J. Chem. Phys.},
year = {2014},
volume = {141},
pages = {184310},
doi = {10.1063/1.4901426}
}
Aidas, K.; Angeli, C.; Bak, K. L.; Bakken, V.; Bast, R.; Boman, L.; Christiansen, O.; Cimiraglia, R.; Coriani, S.; Dahle, P.; Dalskov, E. K.; Ekström, U.; Enevoldsen, T.; Eriksen, J. J.; Ettenhuber, P.; Fernández, B.; Ferrighi, L.; Fliegl, H.; Frediani, L.; Hald, K.; Halkier, A.; Hättig, C.; Heiberg, H.; Helgaker, T.; Hennum, A. C.; Hettema, H.; Hjertenæs, E.; Høst, S.; Høyvik, I.-M.; Iozzi, M. F.; Jansík, B.; Jensen, H. J. A.; Jonsson, D.; Jørgensen, P.; Kauczor, J.; Kirpekar, S.; Kjærgaard, T.; Klopper, W.; Knecht, S.; Kobayashi, R.; Koch, H.; Kongsted, J.; Krapp, A.; Kristensen, K.; Ligabue, A.; Lutnæs, O. B.; Melo, J. I.; Mikkelsen, K. V.; Myhre, R. H.; Neiss, C.; Nielsen, C. B.; Norman, P.; Olsen, J.; Olsen, J. M. H.; Osted, A.; Packer, M. J.; Pawlowski, F.; Pedersen, T. B.; Provasi, P. F.; Reine, S.; Rinkevicius, Z.; Ruden, T. A.; Ruud, K.; Rybkin, V. V.; Sałek, P.; Samson, C. C. M.; Merás, A. S. de; Saue, T.; Sauer, S. P. A.; Schimmelpfennig, B.; Sneskov, K.; Steindal, A. H.; Sylvester-Hvid, K. O.; Taylor, P. R.; Teale, A. M.; Tellgren, E. I.; Tew, D. P.; Thorvaldsen, A. J.; Thøgersen, L.; Vahtras, O.; Watson, M. A.; Wilson, D. J. D.; Ziolkowski, M.; Ågren, H. The Dalton Quantum Chemistry Program System. WIREs Comput. Mol. Sci.2014, 4, 269–284.
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author = {Aidas, K. and Angeli, C. and Bak, K. L. and Bakken, V. and Bast, R. and Boman, L. and Christiansen, O. and Cimiraglia, R. and Coriani, S. and Dahle, P. and Dalskov, E. K. and Ekstr\"{o}m, U. and Enevoldsen, T. and Eriksen, J. J. and Ettenhuber, P. and Fern\'{a}ndez, B. and Ferrighi, L. and Fliegl, H. and Frediani, L. and Hald, K. and Halkier, A. and H\"{a}ttig, C. and Heiberg, H. and Helgaker, T. and Hennum, A. C. and Hettema, H. and Hjerten\ae{}s, E. and H\o{}st, S. and H\o{}yvik, I.-M. and Iozzi, M. F. and Jans\'{i}k, B. and Jensen, H. J. {Aa}. and Jonsson, D. and J\o{}rgensen, P. and Kauczor, J. and Kirpekar, S. and Kj\ae{}rgaard, T. and Klopper, W. and Knecht, S. and Kobayashi, R. and Koch, H. and Kongsted, J. and Krapp, A. and Kristensen, K. and Ligabue, A. and Lutn\ae{}s, O. B. and Melo, J. I. and Mikkelsen, K. V. and Myhre, R. H. and Neiss, C. and Nielsen, C. B. and Norman, P. and Olsen, J. and Olsen, J. M. H. and Osted, A. and Packer, M. J. and Pawlowski, F. and Pedersen, T. B. and Provasi, P. F. and Reine, S. and Rinkevicius, Z. and Ruden, T. A. and Ruud, K. and Rybkin, V. V. and Sa\l{}ek, P. and Samson, C. C. M. and de Mer\'{a}s, A. S\'{a}nchez and Saue, T. and Sauer, S. P. A. and Schimmelpfennig, B. and Sneskov, K. and Steindal, A. H. and Sylvester-Hvid, K. O. and Taylor, P. R. and Teale, A. M. and Tellgren, E. I. and Tew, D. P. and Thorvaldsen, A. J. and Th\o{}gersen, L. and Vahtras, O. and Watson, M. A. and Wilson, D. J. D. and Ziolkowski, M. and \AA{}gren, H.},
title = {{The Dalton quantum chemistry program system}},
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Poongavanam, V.; Olsen, J. M. H.; Kongsted, J. Binding Free Energy Based Structural Dynamics Analysis of HIV-1 RT RNase H-Inhibitor Complexes. Integr. Biol.2014, 6, 1010–1022.
@article{poongavanam2014binding,
author = {Poongavanam, V. and Olsen, J. M. H. and Kongsted, J.},
title = {{Binding free energy based structural dynamics analysis of HIV-1 RT RNase H-inhibitor complexes}},
journal = {Integr. Biol.},
year = {2014},
volume = {6},
pages = {1010--1022},
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}
Beerepoot, M. T. P.; Steindal, A. H.; Ruud, K.; Olsen, J. M. H.; Kongsted, J. Convergence of Environment Polarization Effects in Multiscale Modeling of Excitation Energies. Comp. Theor. Chem.2014, 1040-1041, 304–311.
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title = {Convergence of environment polarization effects in multiscale modeling of excitation energies},
journal = {Comp. Theor. Chem.},
volume = {1040-1041},
pages = {304--311},
year = {2014},
author = {Beerepoot, M. T. P. and Steindal, A. H. and Ruud, K. and Olsen, J. M. H. and Kongsted, J.},
doi = {10.1016/j.comptc.2014.03.022}
}
Pedersen, M. N.; Hedegård, E. D.; Olsen, J. M. H.; Kauczor, J.; Norman, P.; Kongsted, J. Damped Response Theory in Combination with Polarizable Environments: The Polarizable Embedding Complex Polarization Propagator Method. J. Chem. Theory Comput.2014, 10, 1164–1171.
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author = {Pedersen, M. N. and Hedeg\aa{}rd, E. D. and Olsen, J. M. H. and Kauczor, J. and Norman, P. and Kongsted, J.},
title = {{Damped Response Theory in Combination with Polarizable Environments: The Polarizable Embedding Complex Polarization Propagator Method}},
journal = {J. Chem. Theory Comput.},
volume = {10},
pages = {1164--1171},
year = {2014},
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Steinmann, C.; Olsen, J. M. H.; Kongsted, J. Nuclear Magnetic Shielding Constants from Quantum Mechanical/Molecular Mechanical Calculations Using Polarizable Embedding: Role of the Embedding Potential. J. Chem. Theory Comput.2014, 10, 981–988.
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author = {Steinmann, C. and Olsen, J. M. H. and Kongsted, J.},
title = {{Nuclear Magnetic Shielding Constants from Quantum Mechanical/Molecular Mechanical Calculations Using Polarizable Embedding: Role of the Embedding Potential}},
journal = {J. Chem. Theory Comput.},
volume = {10},
pages = {981--988},
year = {2014},
doi = {10.1021/ct400880n}
}
Sneskov, K.; Olsen, J. M. H.; Schwabe, T.; Hättig, C.; Christiansen, O.; Kongsted, J. Computational Screening of One- and Two-Photon Spectrally Tuned Channelrhodopsin Mutants. Phys. Chem. Chem. Phys.2013, 15, 7567–7576.
@article{sneskov2013computational,
title = {{Computational screening of one- and two-photon spectrally tuned channelrhodopsin mutants}},
author = {Sneskov, K. and Olsen, J. M. H. and Schwabe, T. and H\"{a}ttig, C. and Christiansen, O. and Kongsted, J.},
journal = {Phys. Chem. Chem. Phys.},
year = {2013},
volume = {15},
pages = {7567--7576},
doi = {10.1039/C3CP44350G}
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Beerepoot, M. T. P.; Steindal, A. H.; Kongsted, J.; Brandsdal, B. O.; Frediani, L.; Ruud, K.; Olsen, J. M. H. A Polarizable Embedding DFT Study of One-Photon Absorption in Fluorescent Proteins. Phys. Chem. Chem. Phys.2013, 15, 4735–4743.
@article{beerepoot2013polarizable,
title = {{A polarizable embedding DFT study of one-photon absorption in fluorescent proteins}},
author = {Beerepoot, M. T. P. and Steindal, A. H. and Kongsted, J. and Brandsdal, B. O. and Frediani, L. and Ruud, K. and Olsen, J. M. H.},
journal = {Phys. Chem. Chem. Phys.},
volume = {15},
pages = {4735--4743},
year = {2013},
doi = {10.1039/C3CP44659J}
}
Aidas, K.; Olsen, J. M. H.; Kongsted, J.; Ågren, H. Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics. J. Phys. Chem. B2013, 117, 2069–2080.
@article{aidas2013photoabsorption,
title = {{Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics}},
author = {Aidas, K. and Olsen, J. M. H. and Kongsted, J. and {\AA}gren, H.},
journal = {J. Phys. Chem. B},
volume = {117},
pages = {2069--2080},
year = {2013},
doi = {10.1021/jp311863x}
}
Murugan, N. A.; Olsen, J. M. H.; Kongsted, J.; Rinkevicius, Z.; Aidas, K.; Ågren, H. Amyloid Fibril-Induced Structural and Spectral Modifications in the Thioflavin-T Optical Probe. J. Phys. Chem. Lett.2012, 4, 70–77.
@article{murugan2012amyloid,
title = {{Amyloid Fibril-Induced Structural and Spectral Modifications in the Thioflavin-T Optical Probe}},
author = {Murugan, N. A. and Olsen, J. M. H. and Kongsted, J. and Rinkevicius, Z. and Aidas, K. and {\AA}gren, H.},
journal = {J. Phys. Chem. Lett.},
volume = {4},
pages = {70--77},
year = {2012},
doi = {10.1021/jz3018557}
}
List, N. H.; Olsen, J. M. H.; Jensen, H. J. A.; Steindal, A. H.; Kongsted, J. Molecular-Level Insight into the Spectral Tuning Mechanism of the DsRed Chromophore. J. Phys. Chem. Lett.2012, 3, 3513–3521.
@article{list2012molecular,
title = {{Molecular-Level Insight into the Spectral Tuning Mechanism of the DsRed Chromophore}},
author = {List, N. H. and Olsen, J. M. H. and Jensen, H. J. Aa. and Steindal, A. H. and Kongsted, J.},
journal = {J. Phys. Chem. Lett.},
volume = {3},
pages = {3513--3521},
year = {2012},
doi = {10.1021/jz3014858}
}
Steindal, A. H.; Olsen, J. M. H.; Ruud, K.; Frediani, L.; Kongsted, J. A Combined Quantum Mechanics/Molecular Mechanics Study of the One-and Two-Photon Absorption in the Green Fluorescent Protein. Phys. Chem. Chem. Phys.2012, 14, 5440–5451.
@article{steindal2012combined,
title = {{A Combined Quantum Mechanics/Molecular Mechanics Study of the One-and Two-Photon Absorption in the Green Fluorescent Protein}},
author = {Steindal, A. H. and Olsen, J. M. H. and Ruud, K. and Frediani, L. and Kongsted, J.},
journal = {Phys. Chem. Chem. Phys.},
volume = {14},
pages = {5440--5451},
year = {2012},
doi = {10.1039/C2CP23537D}
}
Schwabe, T.; Sneskov, K.; Olsen, J. M. H.; Kongsted, J.; Christiansen, O.; Hättig, C. PERI-CC2: A Polarizable Embedded RI-CC2 Method. J. Chem. Theory Comput.2012, 8, 3274–3283.
@article{schwabe2012peri,
title = {{PERI-CC2: A Polarizable Embedded RI-CC2 Method}},
author = {Schwabe, T. and Sneskov, K. and Olsen, J. M. H. and Kongsted, J. and Christiansen, O. and H{\"a}ttig, C.},
journal = {J. Chem. Theory Comput.},
volume = {8},
pages = {3274--3283},
year = {2012},
doi = {10.1021/ct3003749}
}
Steindal, A. H.; Olsen, J. M. H.; Frediani, L.; Kongsted, J.; Ruud, K. Parallelization of the Polarizable Embedding Scheme for Higher-Order Response Functions. Mol. Phys.2012, 110, 2579–2586.
@article{steindal2012parallelization,
title = {{Parallelization of the polarizable embedding scheme for higher-order response functions}},
author = {Steindal, A. H. and Olsen, J. M. H. and Frediani, L. and Kongsted, J. and Ruud, K.},
journal = {Mol. Phys.},
volume = {110},
pages = {2579--2586},
year = {2012},
doi = {10.1080/00268976.2012.721016}
}
List, N. H.; Olsen, J. M.; Rocha-Rinza, T.; Christiansen, O.; Kongsted, J. Performance of Popular XC-Functionals for the Description of Excitation Energies in GFP-like Chromophore Models. Int. J. Quant. Chem.2012, 112, 789–800.
@article{list2012performance,
title = {{Performance of popular XC-functionals for the description of excitation energies in GFP-like chromophore models}},
author = {List, N. H. and Olsen, J. M. and Rocha-Rinza, T. and Christiansen, O. and Kongsted, J.},
journal = {Int. J. Quant. Chem.},
volume = {112},
pages = {789--800},
year = {2012},
doi = {10.1002/qua.23059}
}
Olsen, J. M. H.; Kongsted, J. Molecular Properties through Polarizable Embedding. Adv. Quantum Chem.2011, 61, 107–143.
@article{olsen2011molecular,
title = {{Molecular Properties through Polarizable Embedding}},
author = {Olsen, J. M. H. and Kongsted, J.},
journal = {Adv. Quantum Chem.},
volume = {61},
pages = {107--143},
year = {2011},
note = {(book chapter)},
doi = {10.1016/B978-0-12-386013-2.00003-6}
}
Schwabe, T.; Olsen, J. M. H.; Sneskov, K.; Kongsted, J.; Christiansen, O. Solvation Effects on Electronic Transitions: Exploring the Performance of Advanced Solvent Potentials in Polarizable Embedding Calculations. J. Chem. Theory Comput.2011, 7, 2209–2217.
@article{schwabe2011solvation,
title = {{Solvation Effects on Electronic Transitions: Exploring the Performance of Advanced Solvent Potentials in Polarizable Embedding Calculations}},
author = {Schwabe, T. and Olsen, J. M. H. and Sneskov, K. and Kongsted, J. and Christiansen, O.},
journal = {J. Chem. Theory Comput.},
volume = {7},
pages = {2209--2217},
year = {2011},
doi = {10.1021/ct200258g}
}
Eriksen, J. J.; Olsen, J. M. H.; Aidas, K.; Ågren, H.; Mikkelsen, K. V.; Kongsted, J. Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts. A Case Study of L-Tryptophan in Aqueous Solution. J. Comp. Chem.2011, 32, 2853–2864.
@article{eriksen2011computational,
title = {{Computational protocols for prediction of solute NMR relative chemical shifts. A case study of \textsc{L}-tryptophan in aqueous solution}},
author = {Eriksen, J. J. and Olsen, J. M. H. and Aidas, K. and {\AA}gren, H. and Mikkelsen, K. V. and Kongsted, J.},
journal = {J. Comp. Chem.},
volume = {32},
year = {2011},
pages = {2853--2864},
doi = {10.1002/jcc.21867}
}
Zazza, C.; Olsen, J. M.; Kongsted, J. Solvatochromic Shifts vs Nanosolvation Patterns: Uracil in Water as a Test Case. Comp. Theor. Chem.2011, 974, 109–116.
@article{zazza2011solvatochromic,
title = {Solvatochromic shifts vs nanosolvation patterns: Uracil in water as a test case},
author = {Zazza, C. and Olsen, J. M. and Kongsted, J.},
journal = {Comp. Theor. Chem.},
volume = {974},
pages = {109--116},
year = {2011},
doi = {10.1016/j.comptc.2011.07.020}
}
Olsen, J. M.; Aidas, K.; Kongsted, J. Excited States in Solution through Polarizable Embedding. J. Chem. Theory Comput.2010, 6, 3721–3734.
@article{olsen2010excited,
title = {{Excited States in Solution through Polarizable Embedding}},
author = {Olsen, J. M. and Aidas, K. and Kongsted, J.},
journal = {J. Chem. Theory Comput.},
volume = {6},
pages = {3721--3734},
year = {2010},
doi = {10.1021/ct1003803}
}
Olsen, J. M.; Aidas, K.; Mikkelsen, K. V.; Kongsted, J. Solvatochromic Shifts in Uracil: A Combined MD-QM/MM Study. J. Chem. Theory Comput.2009, 6, 249–256.
@article{olsen2009solvatochromic,
title = {{Solvatochromic Shifts in Uracil: A Combined MD-QM/MM Study}},
author = {Olsen, J. M. and Aidas, K. and Mikkelsen, K. V. and Kongsted, J.},
journal = {J. Chem. Theory Comput.},
volume = {6},
pages = {249--256},
year = {2009},
doi = {10.1021/ct900502s}
}
Other publications
This includes other publications (co)authored by group members that do not include the group leader.
Vester, J.; Despré, V.; Kuleff, A. I. The Role of Symmetric Vibrational Modes in the Decoherence of Correlation-Driven Charge Migration. J. Chem. Phys.2023, 158, 104305.
@article{Vester2023therole,
author = {Vester, J. and Despr{\'{e}}, V. and Kuleff, A. I.},
title = {{The role of symmetric vibrational modes in the decoherence of correlation-driven charge migration}},
journal = {J. Chem. Phys.},
volume = {158},
pages = {104305},
year = {2023},
doi = {10.1063/5.0136681},
url = {https://doi.org/10.1063/5.0136681}
}
Lengvinaitė, D.; Kvedaraviciute, S.; Bielskutė, S.; Klimavicius, V.; Balevicius, V.; Mocci, F.; Laaksonen, A.; Aidas, K. Structural Features of the [C4mim][Cl] Ionic Liquid and Its Mixtures with Water: Insight from a 1H NMR Experimental and QM/MD Study. J. Phys. Chem. B2021, 125 (48), 13255–13266.
@article{Lengvinaite2021qmmmnmr,
author = {Lengvinaitė, D. and Kvedaraviciute, S. and Bielskutė, S. and Klimavicius, V. and Balevicius, V. and Mocci, F. and Laaksonen, A. and Aidas, K.},
title = {{Structural Features of the [C4mim][Cl] Ionic Liquid and Its Mixtures with Water: Insight from a 1H NMR Experimental and QM/MD Study}},
journal = {J. Phys. Chem. B},
volume = {125},
number = {48},
pages = {13255--13266},
year = {2021},
doi = {10.1021/acs.jpcb.1c08215},
url = {https://doi.org/10.1021/acs.jpcb.1c08215}
}
