20092022

Research output per year

If you made any changes in Pure these will be visible here soon.

Research Output

Filter
Journal article
2020

Avoiding Electron Spill-Out in QM/MM Calculations on Excited States with Simple Pseudopotentials

Marefat Khah, A., Reinholdt, P., Olsen, J. M. H., Kongsted, J. & Hättig, C., 2020, In : Journal of Chemical theory and Computation. 16, 3, p. 1373-1381

Research output: Contribution to journalJournal articleResearchpeer-review

Binding and intracellular transport of 25-hydroxycholesterol by Niemann-Pick C2 protein

Petersen, D., Reinholdt, P., Szomek, M., Hansen, S. K., Poongavanam, V., Juhl, A. D., Heegaard, C. W., Krishnan, K., Fujiwara, H., Covey, D. F., Ory, D. S., Kongsted, J. & Wüstner, D., 1. Feb 2020, In : B B A - Biomembranes. 1862, 2, 14 p., 183063.

Research output: Contribution to journalJournal articleResearchpeer-review

2019

Combining polarizable embedding with the Frenkel exciton model: applications to absorption spectra with overlapping solute–solvent bands

Stendevad, J., Kongsted, J. & Steinmann, C., 1. Mar 2019, In : Theoretical Chemistry Accounts. 138, 3, 41.

Research output: Contribution to journalJournal articleResearchpeer-review

File
18 Downloads (Pure)

Computational Characterization of a Cholesterol-Based Molecular Rotor in Lipid Membranes

Reinholdt, P., Wind, S., Wüstner, D. & Kongsted, J., 2019, In : Journal of Physical Chemistry B. 123, 34, p. 7313-7326 14 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Computational Modeling Explains the Multi Sterol Ligand Specificity of the N-Terminal Domain of Niemann-Pick C1-Like 1 Protein

Poongavanam, V., Kongsted, J. & Wüstner, D., 2019, In : ACS Omega. 4, 25, p. 20894-20904 11 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
37 Downloads (Pure)

CPPE: An Open-Source C++ and Python Library for Polarizable Embedding

Scheurer, M., Reinholdt, P., Kjellgren, E. R., Haugaard Olsen, J. M., Dreuw, A. & Kongsted, J., 12. Nov 2019, In : Journal of Chemical Theory and Computation. 15, 11, p. 6154-6163 10 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Design, Synthesis and Biological Evaluation of Novel Galloyl Derivatives as HIV-1 RNase H Inhibitors

Gao, P., Wang, X., Sun, L., Cheng, X., Poongavanam, V., Kongsted, J., Álvarez, M., Luczkowiak, J., Pannecouque, C., Clercq, E. D., Lee, K-H., Chen, C-H., Liu, H., Menéndez-Arias, L., Liu, X. & Zhan, P., 1. Apr 2019, In : Chemical Biology & Drug Design. 93, 4, p. 582-589

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
39 Downloads (Pure)

Discovery of piperidine-substituted thiazolo[5,4-d]pyrimidine derivatives as potent and orally bioavailable HIV-1 non-nucleoside reverse transcriptase inhibitors

Kang, D., Zhao, T., Wang, Z., Feng, D., Zhang, H., Huang, B., Wu, G., Wei, F., Zhou, Z., Jing, L., Zuo, X., Tian, Y., Poongavanam, V., Kongsted, J., De Clercq, E., Pannecouque, C., Zhan, P. & Liu, X., 2019, In : Communications Chemistry. 2, 8 p., 74.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
78 Downloads (Pure)

Overview of Recent Strategic Advances in Medicinal Chemistry

Wu, G., Zhao, T., Kang, D., Zhang, J., Song, Y., Namasivayam, V., Kongsted, J., Pannecouque, C., De Clercq, E., Poongavanam, V., Liu, X. & Zhan, P., Nov 2019, In : Journal of Medicinal Chemistry. 62, 21, p. 9375-9414 40 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Photophysical investigation of two emissive nucleosides exhibiting gigantic stokes shifts

Stendevad, J., Hornum, M., Wüstner, D. & Kongsted, J., 17. Jun 2019, In : Photochemical and Photobiological Sciences. 18, 7, p. 1858-1865 8 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Rational Design of Nile Red Analogs for Sensing in Membranes

Prioli, S., Reinholdt, P., Hornum, M. & Kongsted, J., 12. Dec 2019, In : Journal of Physical Chemistry B. 123, 49, p. 10424-10432

Research output: Contribution to journalJournal articleResearchpeer-review

Rational design of novel fluorescent analogues of cholesterol: a "step-by-step" computational study

Bonvicini, A., Reinholdt, P., Tognetti, V., Joubert, L., Wüstner, D. & Kongsted, J., 24. Jun 2019, In : Physical Chemistry Chemical Physics. 21, 28, p. 15487-15503 17 p.

Research output: Contribution to journalJournal articleResearchpeer-review

The Journey of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) from Lab to Clinic

Namasivayam, V., Vanangamudi, M., Kramer, V. G., Kurup, S., Zhan, P., Liu, X., Kongsted, J. & Byrareddy, S. N., 23. May 2019, In : Journal of Medicinal Chemistry. 62, 10, p. 4851-4883

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
66 Downloads (Pure)
2018

Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models

Curutchet, C., Cupellini, L., Kongsted, J., Corni, S., Frediani, L., Steindal, A. H., Guido, C. A., Scalmani, G. & Mennucci, B., 2018, In : Journal of Chemical Theory and Computation. 14, 3, p. 1671–1681

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
104 Downloads (Pure)

Importance of Accurate Structures for Quantum Chemistry Embedding Methods: Which Strategy Is Better?

Kjellgren, E. R., Haugaard Olsen, J. M. & Kongsted, J., 2018, In : Journal of Chemical Theory and Computation. 14, 8, p. 4309-4319

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
92 Downloads (Pure)

Live-cell imaging of new polyene sterols for improved analysis of intracellular cholesterol transport

Modzel, M., Solanko, K. A., Szomek, M., Hansen, S. K., Dupont, A., Nåbo, L. J., Kongsted, J. & Wüstner, D., 2018, In : Journal of Microscopy. 271, 1, p. 36-48

Research output: Contribution to journalJournal articleResearchpeer-review

Modeling magnetic circular dichroism within the polarizable embedding approach

Nørby, M. S., Coriani, S. & Kongsted, J., 2018, In : Theoretical Chemistry Accounts. 137, 4, 8 p., 49.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
94 Downloads (Pure)
Open Access
File
63 Downloads (Pure)

One-Photon Absorption Properties from a Hybrid Polarizable Density Embedding/Complex Polarization Propagator Approach for Polarizable Solutions

Hršak, D., Nørby, M. S., Coriani, S. & Kongsted, J., 2018, In : Journal of Chemical Theory and Computation. 14, 4, p. 2145-2154

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
107 Downloads (Pure)

Polarizable Density Embedding Coupled Cluster Method

Hršak, D., Olsen, J. M. H. & Kongsted, J., 2018, In : Journal of Chemical Theory and Computation. 14, 3, p. 1351–1360

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
110 Downloads (Pure)

Polarizable Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems

Scheurer, M., Herbst, M. F., Reinholdt, P., Olsen, J. M. H., Dreuw, A. & Kongsted, J., 2018, In : Journal of Chemical Theory and Computation. 14, 9, p. 4870–4883

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
104 Downloads (Pure)

Structural design of intrinsically fluorescent oxysterols

Nåbo, L. J., Modzel, M., Krishnan, K., Covey, D. F., Fujiwara, H., Ory, D. S., Szomek, M., Khandelia, H., Wüstner, D. & Kongsted, J., 2018, In : Chemistry and Physics of Lipids. 212, p. 26–34

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
160 Downloads (Pure)

Structure-guided approach identifies a novel class of HIV-1 ribonuclease H inhibitors: Binding mode insights through magnesium complexation and site-directed mutagenesis studies

Poongavanam, V., Corona, A., Steinmann, C., Scipione, L., Grandi, N., Pandolfi, F., Di Santo, R., Costi, R., Esposito, F., Tramontano, E. & Kongsted, J., Mar 2018, In : MedChemComm. 9, 3, p. 562-575

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
110 Downloads (Pure)

The Reaction of Oxy Hemoglobin with Nitrite: Mechanism, Antioxidant-Modulated Effect, and Implications for Blood Substitute Evaluation

Hathazi, D., Scurtu, F., Bischin, C., Mot, A., Attia, A. A. A., Kongsted, J. & Silaghi-Dumitrescu, R., 2018, In : Molecules. 23, 2, 16 p., 350.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
165 Downloads (Pure)
2017

An averaged polarizable potential for multiscale modeling in phospholipid membranes

Witzke, S., List, N. H., Olsen, J. M. H., Steinmann, C., Petersen, M., Beerepoot, M. T. P. & Kongsted, J., 2017, In : Journal of Computational Chemistry. 38, 9, p. 601-611

Research output: Contribution to journalJournal articleResearchpeer-review

File
67 Downloads (Pure)

A quantum-mechanical perspective on linear response theory within polarizable embedding

List, N. H., Norman, P., Kongsted, J. & Jensen, H. J. A., 2017, In : Journal of Chemical Physics. 146, 23, 15 p., 234101.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
169 Downloads (Pure)

Assessing frequency-dependent site polarisabilities in linear response polarisable embedding

Nørby, M. S., Vahtras, O., Norman, P. & Kongsted, J., 2017, In : Molecular Physics. 115, 1-2, p. 39-47

Research output: Contribution to journalJournal articleResearchpeer-review

Computational approach to evaluation of optical properties of membrane probes

Nåbo, L. J., List, N. H., Svendsen, C. S. & Kongsted, J., 2017, In : Journal of Chemical Theory and Computation. 13, 2, p. 719–726

Research output: Contribution to journalJournal articleResearchpeer-review

Modeling Electronic Circular Dichroism within the Polarizable Embedding Approach

Nørby, M. S., Olsen, J. M. H., Steinmann, C. & Kongsted, J., 2017, In : Journal of Chemical Theory and Computation. 13, 9, p. 4442–4451

Research output: Contribution to journalJournal articleResearchpeer-review

File
109 Downloads (Pure)

Optimization and transferability of non-electrostatic repulsion in the polarizable density embedding model

Hrsak, D., Olsen, J. M. H. & Kongsted, J., 2017, In : Journal of Computational Chemistry. 38, 24, p. 2108-2117

Research output: Contribution to journalJournal articleResearchpeer-review

Relativistic Polarizable Embedding

Hedegård, E. D., Bast, R., Kongsted, J., Olsen, J. M. H. & Jensen, H. J. A., 2017, In : Journal of Chemical Theory and Computation. 13, 6, p. 2870-2880

Research output: Contribution to journalJournal articleResearchpeer-review

The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein

Nåbo, L. J., Olsen, J. M. H., Martínez, T. J. & Kongsted, J., 2017, In : Journal of Chemical Theory and Computation. 13, 12, p. 6230-6236

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
127 Downloads (Pure)

Very Strong Binding for a Neutral Calix[4]pyrrole Receptor Displaying Positive Allosteric Binding

Duedal, T., Nielsen, K., Olsen, G., Burgdorf Guldager Rasmussen, C., Kongsted, J., Levillain, E., Breton, T., Miyazaki, E., Takimiya, K., Bähring, S. & Jeppesen, J. O., 2017, In : Journal of Organic Chemistry. 82, 4, p. 2123–2128

Research output: Contribution to journalJournal articleResearchpeer-review

2016

Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties

Beerepoot, M., Steindal, A. H., List, N. H., Kongsted, J. & Olsen, J. M. H., Mar 2016, In : Journal of Chemical Theory and Computation. 12, 4, p. 1684-1695

Research output: Contribution to journalJournal articleResearchpeer-review

Binding affinity models for Falcipain inhibition based on the Linear Interaction Energy method

Poongavanam, V. & Kongsted, J., 2016, In : Journal of Molecular Graphics and Modelling. 70, p. 236-245

Research output: Contribution to journalJournal articleResearchpeer-review

Computational analysis of sterol ligand specificity of the Niemann Pick C2 protein

Poongavanam, V., Kongsted, J. & Wüstner, D., 2016, In : Biochemistry. 55, 36, p. 5165-5179

Research output: Contribution to journalJournal articleResearchpeer-review

Computational Approach for Studying Optical Properties of DNA Systems in Solution

Nørby, M. S., Svendsen, C. S., Olsen, J. M. H., Li, H. & Kongsted, J., 2016, In : Journal of Chemical Theory and Computation. 12, 10, p. 5050-5057

Research output: Contribution to journalJournal articleResearchpeer-review

Embedding beyond electrostatics: The role of wave function confinement

Nåbo, L. J., Olsen, J. M. H., Holmgaard List, N., Solanko, L. M., Wüstner, D. & Kongsted, J., 14. Sep 2016, In : The Journal of Chemical Physics. 145, 7 p., 104102.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
177 Downloads (Pure)

How Far Does a Receptor Influence Vibrational Properties of an Odorant?

Reese, A., List, N. H., Kongsted, J. & Solov'yov, I. A., 2016, In : P L o S One. 11, 3, 21 p., e0152345.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
167 Downloads (Pure)

Local electric fields and molecular properties in heterogeneous environments through polarizable embedding

List, N. H., Jensen, H. J. A. & Kongsted, J., 2016, In : Physical Chemistry Chemical Physics. 18, 15, p. 10070-10080

Research output: Contribution to journalJournal articleResearchpeer-review

Multipole moments for embedding potentials: Exploring different atomic allocation algorithms

Nørby, M. S., Olsen, J. M. H., Kongsted, J. & Jensen, H. J. A., 30. Jul 2016, In : Journal of Computational Chemistry. 37, 20, p. 1887-1896

Research output: Contribution to journalJournal articleResearchpeer-review

Open-ended response theory with polarizable embedding: Multiphoton absorption in biomolecular systems

Steindal, A. H., Beerepoot, M. T. P., Ringholm, M., List, N. H., Ruud, K., Kongsted, J. & Olsen, J. M. H., 2016, In : Physical Chemistry Chemical Physics. 18, 40, p. 28339-28352

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
150 Downloads (Pure)
2015

Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials

Olsen, J. M. H., List, N. H., Kristensen, K. & Kongsted, J., Mar 2015, In : Journal of Chemical Theory and Computation. 11, 4, p. 1832–1842

Research output: Contribution to journalJournal articleResearchpeer-review

A comparative study of binding affinities for 6,7-dimethoxy-4-pyrrolidylquinazolines as Phosphodiesterase 10A inhibitors using the linear interaction energy method

Kjellgren, E. R., Glue, O. E. S., Reinholdt, P., Meyer, J. E., Kongsted, J. & Poongavanam, V., 2015, In : Journal of Molecular Graphics and Modelling. 61, p. 44-52

Research output: Contribution to journalJournal articleResearchpeer-review

Analysis of computational models for an accurate study of electronic excitations in GFP

Schwabe, T., Beerepoot, M., Olsen, J. M. H. & Kongsted, J., 2015, In : Physical Chemistry Chemical Physics. 17, 4, p. 2582

Research output: Contribution to journalJournal articleResearchpeer-review

Benchmarking two-photon absorption cross secctions: Performance of CC2 and CAM-B3LYP

Beerepoot, M. T. P., Friese, D., List, N. H., Kongsted, J. & Ruud, K., 2015, In : Physical Chemistry Chemical Physics. 17, p. 19306-19314

Research output: Contribution to journalJournal articleResearchpeer-review

Biochemical and Computational Analysis of the Substrate Specificities of Cfr and RlmN Methyltransferases

Ntokou, E., Hansen, L. H., Kongsted, J. & Vester, B., 2015, In : P L o S One. 10, 12, 14 p., e0145655.

Research output: Contribution to journalJournal articleResearchpeer-review

Carotenoids and light-harvesting: from MRCI/DFT to the Tamm-Dancoff approximation

Andreussi, O., Knecht, S., Marian, C. M., Kongsted, J. & Mennucci, B., 2015, In : Journal of Chemical Theory and Computation. 11, 2, p. 655–666

Research output: Contribution to journalJournal articleResearchpeer-review