Steric and Electronic origins of fluorescence in GFP and GFP-like proteins
Chey M. Jones, Nanna H. List, Todd J. Martinez.
J. Am. Chem. Soc. 2022, 144, 28, 12732
June 10, 2022
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Highlighted Publications
Probing Chirality across the Electromagnetic Spectrum with the Full Semi-classical Light–Matter Interaction
Martin van Horn, Trond Saue, and Nanna Holmgaard List,
J. Chem. Phys. 156, 054113 (2022)
January 10, 2022
Internal Conversion of the Anionic GFP Chromophore: In and Out of the I-twisted S1/S0 Conical Intersection Seam
Nanna H. List, Chey M. Jones and Todd J. Martínez,
Chem. Sci., 2022, 13,373
November 11, 2021
Predictions of Pre-edge Features in Time-Resolved Near-Edge X-ray Absorption Fine Structure Spectroscopy from Hole–Hole Tamm–Dancoff-Approximated Density Functional Theory
Edward G. Hohenstein, Jimmy K. Yu, Christoph Bannwarth, Nanna Holmgaard List, Alexander C. Paul, Sarai D. Folkestad, Henrik Koch, Todd J. Martínez,
J. Chem. Theory Comput. 2021, 17, 7120
October 8, 2021
Direct observation of ultrafast hydrogen bond strengthening in liquid water
Jie Yang, Riccardo Dettori, J. Pedro F. Nunes, Nanna H. List, Elisa Biasin, Martin Centurion, Zhijiang Chen, Amy A. Cordones, Daniel P. Deponte, Tony F. Heinz, Michael E. Kozina, Kathryn Ledbetter, Ming-Fu Lin, Aaron M. Lindenberg, Mianzhen Mo, Anders Nilsson, Xiaozhe Shen, Thomas J. A. Wolf, Davide Donadio, Kelly J. Gaffney, Todd J. Martinez, Xijie Wang,
Nature, 2021, 596, 531
August 25, 2021
Resolving the Ultrafast Dynamics of the Anionic Green Fluorescent Protein Chromophore in Water
C. M. Jones, N. H. List, T. J. Martínez,
Chem. Sci., 2021, 12, 11347
July 13, 2021
Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model
Karen Oda Hjorth Minde Dundas, Maarten T. P. Beerepoot, Magnus Ringholm, Simen Reine, Radovan Bast, Nanna Holmgaard List, Jacob Kongsted, Kenneth Ruud, and Jógvan Magnus Haugaard Olsen,
J. Chem. Theory Comput., 2021, 17, 3599
May 19, 2021
Probing competing relaxation pathways in malonaldehyde with transient X-ray absorption spectroscopy
Nanna Holmgaard List, Adrian L. Dempwolff, Andreas Dreuw, Patrick Norman, Todd J. Martinez,
Chem. Sci., 2020, 11, 4180
March 25, 2020
Local Electric Fields and Molecular Properties in Heterogeneous Environments Through Polarizable Embedding
N. H. List, H. J. Aa. Jensen, J. Kongsted,
Phys. Chem. Chem. Phys. 2016, 18, 10070
February 25, 2016
Full Publication list
Steric and Electronic origins of fluorescence in GFP and GFP-like proteins
June 10, 2022
Chey M. Jones, Nanna H. List, Todd J. Martinez.
J. Am. Chem. Soc. 2022, 144, 28, 12732
Probing Chirality across the Electromagnetic Spectrum with the Full Semi-classical Light–Matter Interaction
January 10, 2022
Martin van Horn, Trond Saue, and Nanna Holmgaard List,
J. Chem. Phys. 156, 054113 (2022)
Internal Conversion of the Anionic GFP Chromophore: In and Out of the I-twisted S1/S0 Conical Intersection Seam
November 11, 2021
Nanna H. List, Chey M. Jones and Todd J. Martínez,
Chem. Sci., 2022, 13,373
Predictions of Pre-edge Features in Time-Resolved Near-Edge X-ray Absorption Fine Structure Spectroscopy from Hole–Hole Tamm–Dancoff-Approximated Density Functional Theory
October 8, 2021
Edward G. Hohenstein, Jimmy K. Yu, Christoph Bannwarth, Nanna Holmgaard List, Alexander C. Paul, Sarai D. Folkestad, Henrik Koch, Todd J. Martínez,
J. Chem. Theory Comput. 2021, 17, 7120
Direct observation of ultrafast hydrogen bond strengthening in liquid water
August 25, 2021
Jie Yang, Riccardo Dettori, J. Pedro F. Nunes, Nanna H. List, Elisa Biasin, Martin Centurion, Zhijiang Chen, Amy A. Cordones, Daniel P. Deponte, Tony F. Heinz, Michael E. Kozina, Kathryn Ledbetter, Ming-Fu Lin, Aaron M. Lindenberg, Mianzhen Mo, Anders Nilsson, Xiaozhe Shen, Thomas J. A. Wolf, Davide Donadio, Kelly J. Gaffney, Todd J. Martinez, Xijie Wang,
Nature, 2021, 596, 531
Resolving the Ultrafast Dynamics of the Anionic Green Fluorescent Protein Chromophore in Water
July 13, 2021
C. M. Jones, N. H. List, T. J. Martínez,
Chem. Sci., 2021, 12, 11347
Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model
May 19, 2021
Karen Oda Hjorth Minde Dundas, Maarten T. P. Beerepoot, Magnus Ringholm, Simen Reine, Radovan Bast, Nanna Holmgaard List, Jacob Kongsted, Kenneth Ruud, and Jógvan Magnus Haugaard Olsen,
J. Chem. Theory Comput., 2021, 17, 3599
Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems
June 5, 2020
J. M. H. Olsen, S. Reine, O. Vahtras, E. Kjellgren, P. Reinholdt, K. O. H. Dundas, X. Li, J. Cukras, M. Ringholm, E. D. Hedegård, R. D. Remigio, N. H. List, R. Faber, B. N. C. Tenorio, R. Bast, T. B. Pedersen, Z. Rinkevicius, S. P. A. Sauer, K. V. Mikkelsen, J. Kongsted, S. Coriani, K. Ruud, T. Helgaker, H. J. Aa. Jensen, P. Norman,
J. Chem. Phys. 2020, 152, 214115
Beyond the Electric-Dipole Approximation in Simulations of X-Ray Absorption Spectroscopy: Lessons from Relativistic Theory
May 13, 2020
N. H. List, T. Melin, M. v. Horn, T. Saue,
J. Chem. Phys. 2020, 152, 184110
Probing competing relaxation pathways in malonaldehyde with transient X-ray absorption spectroscopy
March 25, 2020
Nanna Holmgaard List, Adrian L. Dempwolff, Andreas Dreuw, Patrick Norman, Todd J. Martinez,
Chem. Sci., 2020, 11, 4180
VeloxChem: A Python-driven density-functional theory program for spectroscopy simulations in high-performance computing environments
December 11, 2019
Z. Rinkevicius, X. Li, O. Vahtras, K. Ahmadzadeh, M. Brand, M. Ringholm, N. H. List, M. Scheurer, M. Scott, A. Dreuw, P. Norman,
WIREs Comput. Mol. Sci., 2019; e1457
Origin of DNA-Induced Circular Dichroism in a Minor-Groove Binder
October 2, 2017
N. H. List, J. Knoops, J. Rubio-Magnieto, J. Idé, D. Beljonne, P. Norman, M. Surin, M. Linares,
J. Am. Chem. Soc. 2017, 139, 14947
A Quantum-Mechanical Perspective on Linear Response Theory within Polarizable Embedding
June 16, 2017
N. H. List, P. Norman, J. Kongsted, H. J. Aa. Jensen,
J. Chem. Phys. 2017, 146, 234101
An Averaged Polarizable Potential for Multiscale Modeling in Phospholipid Membranes
February 3, 2017
S. Witzke, N. H. List, J. M. H. Olsen, C. Steinmann, M. Petersen, M. T. P. Beerepoot, J. Kongsted,
J. Comput. Chem. 2017, 38, 601
Computational Approach to Evaluation of Optical Properties of Membrane Probes
January 2, 2017
L. J. Nåbo, N. H. List, C. Steinmann, J. Kongsted,
J. Chem. Theory Comput. 2017, 13, 719
Open-ended Response Theory with Polarizable Embedding: Multiphoton Absorption in Biomolecular systems
September 19, 2016
A. H. Steindal, M. T. P. Beerepoot, M. Ringholm, N. H. List, K. Ruud, J. Kongsted, J. M. H.Olsen,
Phys. Chem. Chem. Phys. 2016, 18, 28339
Embedding beyond Electrostatics – The Role of Wave-Function Confinement
September 12, 2016
L. J. Nåbo, J. M. H. Olsen, N. H. List, L. M. Solanko, D. Wüstner, J. Kongsted,
J. Chem. Phys. 2016, 145, 104102
Excited states in Large Molecular Systems Through Polarizable Embedding
July 6, 2016
N. H. List, J. M. H. Olsen, J. Kongsted,
Phys. Chem. Chem. Phys. 2016, 18, 20234
Rotationally Averaged Linear Absorption Spectra Beyond the Electric-Dipole Approximation
June 8, 2016
N. H. List, T. Saue, P. Norman,
Mol. Phys. 2017, 115, 63
How far does a Receptor Influence Vibrational Properties of an Odorant?
March 25, 2016
A. Reese, N. H. List, J. Kongsted, I. Solov’yov,
PloS One 2016, DOI: 10.1371/journal.pone.0152345
Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties
March 3, 2016
M. T. P. Beerepoot, A. H. Steindal, N. H. List, J. Kongsted, J. M. H. Olsen,
J. Chem. Theory Comput. 2016, 12, 1684
Local Electric Fields and Molecular Properties in Heterogeneous Environments Through Polarizable Embedding
February 25, 2016
N. H. List, H. J. Aa. Jensen, J. Kongsted,
Phys. Chem. Chem. Phys. 2016, 18, 10070
Relation between Nonlinear Optical Properties of Push–Pull Molecules and Metric of Charge Transfer Excitations
July 17, 2015
N. H. List, R. Zaleśny, N. A. Murugan, J. Kongsted, W. Bartkowiak, H. Ågren,
J. Chem. Theory Comput. 2015, 11, 4182
Beyond the Electric-Dipole Approximation: A Formulation and Implementation of Molecular Response Theory for the Description of Absorption of Electromagnetic Field Radiation
June 29, 2015
N. H. List, J. Kauczor, T. Saue, H. J. Aa. Jensen, P. Norman,
J. Chem. Phys. 2015, 142, 244111
Benchmarking Two-Photon Absorption Cross Sections: Performance of CC2 and CAM-B3LYP
June 25, 2015
M. T. P. Beerepoot, D. H. Friese, N. H. List, J. Kongsted, K. Ruud,
Phys. Chem. Chem. Phys. 2015, 17, 19306
Design of New Fluorescent Cholesterol and Ergosterol Analogs: Insights from Theory
May 8, 2015
L. J. Nåbo, N. H. List, S. Witzke, D. Wüstner, H. Khandelia, J. Kongsted,
Biochim. Biophys. Acta Biomembr. 2015, 1848, 2188
Experimental and Computational Study of Solvent Effects on One- and Two-Photon Absorption Spectra of Chlorinated Harmines
April 9, 2015
D. Hršak, L. Holmegaard, A. S. Poulsen, N. H. List, J. Kongsted, M. P. Denofrio, R. Erra-Balsells, F. M. Cabrerizo, O. Christiansen, P. R. Ogilby,
Phys. Chem. Chem. Phys. 2015, 17, 12090
Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials
March 23, 2015
J. M. H. Olsen, N. H. List, K. Kristensen, J. Kongsted,
J. Chem. Theory Comput. 2015, 11, 1832
Molecular Quantum Mechanical Gradients within the Polarizable Embedding Approach — Application to the Internal Vibrational Stark Shift of Acetophenone
January 21, 2015
N. H. List, M. T. P. Beerepoot, J. M. H. Olsen, B. Gao, K. Ruud, H. J. Aa. Jensen, J. Kongsted,
J. Chem. Phys. 2015, 142, 034119
Lanczos-Driven Coupled-Cluster Damped Linear Response Theory for Molecules in Polarizable Environments
December 24, 2014
N. H. List, S. Coriani, J. Kongsted, O. Christiansen,
J. Chem. Phys. 2014, 141, 244107
Identifying the Hamiltonian Structure in Linear Response Theory
June 10, 2014
N. H. List, S. Coriani, O. Christiansen, J. Kongsted,
J. Chem. Phys. 2014, 140, 224103
Dehydroergosterol as an Analogue for Cholesterol: Why it Mimics Cholesterol So Well – or Does it?
June 3, 2014
M. Pourmousa, T. Róg, R. Mikkeli, I. Vattulainen, L. M. Solanko, D. Wüstner, N. H. List, J. Kongsted, M. Karttunen,
J. Phys. Chem. B 2014, 118, 7345
Effect of Chromophore Encapsulation on Linear and Non-Linear Optical Properties: The Case of ’miniSOG’, a Protein-Encased Flavin
January 7, 2014
N. H. List, F. M. Pimenta, L. Holmegaard, R. L. Jensen, M. Etzerodt, T. Schwabe, J. Kongsted, P. R. Ogilby, O. Christiansen,
Phys. Chem. Chem. Phys. 2014, 16, 9950
Toward Reliable Prediction of the Energy Ladder in Multichromophoric Systems: A Benchmark Study on the FMO Light-Harvesting Complex
September 18, 2013
N. H. List, C. Curutchet, S. Knecht, B. Mennucci, J. Kongsted,
J. Chem. Theory Comput. 2013, 9, 4928
The Multi-Configuration Self-Consistent Field Method within a Polarizable Embedded Framework
July 23, 2013
E. D. Hedegård, N. H. List, H. J. Aa. Jensen, J. Kongsted,
J. Chem. Phys. 2013, 139, 044101
A Unified Framework for the Polarizable Embedding and Continuum Methods within Multiconfigurational Self-Consistent Field Theory
July 23, 2013
N. H. List, H. J. Aa. Jensen, J. Kongsted, E. D. Hedegård,
Adv. Quantum Chem. 2013, 66, 195
Molecular-Level Insight into the Spectral Tuning Mechanism of the DsRed Chromophore
November 13, 2012
N. H. List, J. M. H. Olsen, H. J. Aa. Jensen, A. H. Steindal, J. Kongsted,
J. Phys. Chem. Lett. 2012, 3, 3513
A Click Chemistry Approach to Pleuromutilin Derivatives, Part 2: Conjugates with Acyclic Nucleosides and their Ribosomal Binding and Antibacterial Activity
January 26, 2012
I. Dreier, S. Kumar, H. Søndergaard, M. L. Rasmussen, L. H. Hansen, N. H. List, J. Kongsted, B. Vester, P. Nielsen,
J. Med. Chem. 2012, 55, 2067
Performance of popular XC-Functionals for the Description of Excitation Energies in GFP-Like Chromophore Models
April 11, 2011
N. H. List, J. M. H. Olsen, T. Rocha-Rinza, O. Christiansen, J. Kongsted,
Int. J. Quantum Chem. 2012, 112, 789