Jacob Kongsted - Publications

Affiliations: 
Department of Physics, Chemistry and Pharmacy University of Southern Denmark, Odense, Denmark 

138 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Reinholdt P, Wind S, Wüstner D, Kongsted J. Computational Characterization of a Cholesterol Based Molecular Rotor in Lipid Membranes. The Journal of Physical Chemistry. B. PMID 31381343 DOI: 10.1021/acs.jpcb.9b04967  0.32
2019 Bonvicini A, Reinholdt P, Tognetti V, Joubert L, Wüstner D, Kongsted J. Rational design of novel fluorescent analogues of cholesterol: a "step-by-step" computational study. Physical Chemistry Chemical Physics : Pccp. 21: 15487-15503. PMID 31259332 DOI: 10.1039/c9cp01902b  0.32
2019 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. Overview of Recent Strategic Advances in Medicinal Chemistry. Journal of Medicinal Chemistry. PMID 31050421 DOI: 10.1021/acs.jmedchem.9b00359  0.6
2019 Jiang X, Yu J, Zhou Z, Kongsted J, Song Y, Pannecouque C, Clercq E, Kang D, Poongavanam V, Liu X, Zhan P. Molecular design opportunities presented by solvent-exposed regions of target proteins. Medicinal Research Reviews. PMID 31002405 DOI: 10.1002/med.21581  0.6
2018 Gao P, Wang X, Sun L, Cheng X, Poongavanam V, Kongsted J, Álvarez M, Luczkowiak J, Pannecouque C, Clercq E, Lee KH, Chen CH, Liu H, Menéndez-Arias L, Liu X, et al. Design, Synthesis and Biological Evaluation of Novel Galloyl Derivatives as HIV-1 RNase H Inhibitors. Chemical Biology & Drug Design. PMID 30560566 DOI: 10.1111/cbdd.13455  0.6
2018 Reinholdt P, Nørby MS, Kongsted J. Modeling of Magnetic Circular Dichroism and UV/vis absorption spectra using Fluctuating Charges or Polarizable Embedding within a resonant-convergent response theory formalism. Journal of Chemical Theory and Computation. PMID 30407811 DOI: 10.1021/acs.jctc.8b00660  0.72
2018 Poongavanam V, Corona A, Steinmann C, Scipione L, Grandi N, Pandolfi F, Di Santo R, Costi R, Esposito F, Tramontano E, Kongsted J. Structure-guided approach identifies a novel class of HIV-1 ribonuclease H inhibitors: binding mode insights through magnesium complexation and site-directed mutagenesis studies. Medchemcomm. 9: 562-575. PMID 30108947 DOI: 10.1039/c7md00600d  1
2018 Scheurer M, Herbst MF, Reinholdt P, Olsen JMH, Dreuw A, Kongsted J. Polarizable Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems. Journal of Chemical Theory and Computation. PMID 30086234 DOI: 10.1021/acs.jctc.8b00576  0.72
2018 Kjellgren ER, Haugaard Olsen JM, Kongsted J. Importance of Accurate Structures for Quantum Chemistry Embedding Methods: Which Strategy Is Better? Journal of Chemical Theory and Computation. PMID 29969562 DOI: 10.1021/acs.jctc.8b00202  0.6
2018 Nielsen C, Nørby MS, Kongsted J, Solov'yov IA. Absorption Spectra of FAD Embedded in Cryptochromes. The Journal of Physical Chemistry Letters. 3618-3623. PMID 29905481 DOI: 10.1021/acs.jpclett.8b01528  0.72
2018 Hr Scaron Ak D, Nørby MS, Coriani S, Kongsted J. One-photon absorption properties from a hybrid Polarizable Density Embedding/Complex Polarization Propagator approach for polarizable solutions. Journal of Chemical Theory and Computation. PMID 29547283 DOI: 10.1021/acs.jctc.8b00155  0.72
2018 Hr Scaron Ak D, Olsen JMH, Kongsted J. The Polarizable Density Embedding Coupled Cluster Method. Journal of Chemical Theory and Computation. PMID 29444404 DOI: 10.1021/acs.jctc.7b01153  0.72
2018 Curutchet C, Cupellini L, Kongsted J, Corni S, Frediani L, Steindal AH, Guido CA, Scalmani G, Mennucci B. Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models. Journal of Chemical Theory and Computation. PMID 29439575 DOI: 10.1021/acs.jctc.7b00912  0.56
2017 Nåbo LJ, Modzel M, Krishnan K, Covey DF, Fujiwara H, Ory DS, Szomek M, Khandelia H, Wüstner D, Kongsted J. Structural design of intrinsically fluorescent oxysterols. Chemistry and Physics of Lipids. PMID 29287905 DOI: 10.1016/j.chemphyslip.2017.12.005  0.6
2017 Reinholdt P, Kongsted J, Olsen JMH. Polarizable Density Embedding: A Solution to the Electron Spill-Out Problem in Multiscale Modeling. The Journal of Physical Chemistry Letters. 8: 5949-5958. PMID 29178794 DOI: 10.1021/acs.jpclett.7b02788  0.72
2017 Nåbo LJ, Olsen JMH, Martínez TJ, 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. Journal of Chemical Theory and Computation. PMID 29099597 DOI: 10.1021/acs.jctc.7b00528  0.72
2017 Nørby MS, Olsen JMH, Steinmann C, Kongsted J. Modeling electronic circular dichroism within the polarizable embedding approach. Journal of Chemical Theory and Computation. PMID 28825811 DOI: 10.1021/acs.jctc.7b00712  1
2017 Hršak D, Olsen JMH, Kongsted J. Optimization and transferability of non-electrostatic repulsion in the polarizable density embedding model. Journal of Computational Chemistry. PMID 28643344 DOI: 10.1002/jcc.24859  0.72
2017 List NH, Norman P, Kongsted J, Jensen HJA. A quantum-mechanical perspective on linear response theory within polarizable embedding. The Journal of Chemical Physics. 146: 234101. PMID 28641427 DOI: 10.1063/1.4985565  0.68
2017 Hedegård ED, Bast R, Kongsted J, Olsen JMH, Jensen HJA. Relativistic Polarizable Embedding. Journal of Chemical Theory and Computation. PMID 28493714 DOI: 10.1021/acs.jctc.7b00162  0.72
2017 Witzke S, List NH, Olsen JM, Steinmann C, Petersen M, Beerepoot MT, Kongsted J. An averaged polarizable potential for multiscale modeling in phospholipid membranes. Journal of Computational Chemistry. PMID 28160294 DOI: 10.1002/jcc.24718  1
2017 Nåbo LJ, List NH, Steinmann C, Kongsted J. Computational approach to evaluation of optical properties of membrane probes. Journal of Chemical Theory and Computation. PMID 28042967 DOI: 10.1021/acs.jctc.6b01017  1
2016 Steinmann C, Bratholm LA, Olsen JM, Kongsted J. Automated Fragmentation Polarizable Embedding DFT Calculations of NMR Shielding Constants of Proteins with Application to Chemical Shift Predictions. Journal of Chemical Theory and Computation. PMID 27992211 DOI: 10.1021/acs.jctc.6b00965  1
2016 Poongavanam V, Kongsted J. Binding affinity models for Falcipain inhibition based on the Linear Interaction Energy method. Journal of Molecular Graphics & Modelling. 70: 236-245. PMID 27770746 DOI: 10.1016/j.jmgm.2016.06.008  0.6
2016 Steindal AH, Beerepoot MT, Ringholm M, List NH, Ruud K, Kongsted J, Olsen JM. Open-ended response theory with polarizable embedding: multiphoton absorption in biomolecular systems. Physical Chemistry Chemical Physics : Pccp. 18: 28339-28352. PMID 27722558 DOI: 10.1039/c6cp05297e  0.72
2016 Nåbo LJ, Olsen JM, Holmgaard List N, Solanko LM, Wüstner D, Kongsted J. Embedding beyond electrostatics-The role of wave function confinement. The Journal of Chemical Physics. 145: 104102. PMID 27634246 DOI: 10.1063/1.4962367  0.72
2016 Nørby MS, Steinmann C, Olsen JM, Li H, Kongsted J. Computational approach for studying optical properties of DNA systems in solution. Journal of Chemical Theory and Computation. PMID 27585250 DOI: 10.1021/acs.jctc.6b00706  1
2016 Poongavanam V, Kongsted J, Wüstner D. Computational Analysis of Sterol Ligand Specificity of the Niemann Pick C2 Protein. Biochemistry. 55: 5165-79. PMID 27533706 DOI: 10.1021/acs.biochem.6b00217  0.6
2016 List NH, Olsen JM, Kongsted J. Excited states in large molecular systems through polarizable embedding. Physical Chemistry Chemical Physics : Pccp. 18: 20234-50. PMID 27416749 DOI: 10.1039/c6cp03834d  0.72
2016 Reese A, List NH, Kongsted J, Solov'yov IA. How Far Does a Receptor Influence Vibrational Properties of an Odorant? Plos One. 11: e0152345. PMID 27014869 DOI: 10.1371/journal.pone.0152345  0.68
2016 List NH, Jensen HJ, Kongsted J. Local electric fields and molecular properties in heterogeneous environments through polarizable embedding. Physical Chemistry Chemical Physics : Pccp. 18: 10070-80. PMID 27007060 DOI: 10.1039/c6cp00669h  0.68
2016 Beerepoot MT, Steindal AH, List NH, Kongsted J, Olsen JM. Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties. Journal of Chemical Theory and Computation. 12: 1684-95. PMID 26938368 DOI: 10.1021/acs.jctc.5b01000  0.72
2016 Schwabe T, Beerepoot MT, Olsen JM, Kongsted J. Correction: Analysis of computational models for an accurate study of electronic excitations in GFP. Physical Chemistry Chemical Physics : Pccp. 18: 1349. PMID 26666172 DOI: 10.1039/c5cp90225h  0.72
2015 Steinmann C, Kongsted J. Electronic Energy Transfer in Polarizable Heterogeneous Environments: A Systematic Investigation of Different Quantum Chemical Approaches. Journal of Chemical Theory and Computation. 11: 4283-93. PMID 26575923 DOI: 10.1021/acs.jctc.5b00470  1
2015 List NH, Zaleśny R, Murugan NA, Kongsted J, Bartkowiak W, Ågren H. Relation between Nonlinear Optical Properties of Push-Pull Molecules and Metric of Charge Transfer Excitations. Journal of Chemical Theory and Computation. 11: 4182-4188. PMID 26575913 DOI: 10.1021/acs.jctc.5b00538  0.68
2015 Olsen JM, List NH, Kristensen K, Kongsted J. Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials. Journal of Chemical Theory and Computation. 11: 1832-42. PMID 26574389 DOI: 10.1021/acs.jctc.5b00078  0.72
2015 Kjellgren ER, Glue OE, Reinholdt P, Meyer JE, Kongsted J, Poongavanam V. A comparative study of binding affinities for 6,7-dimethoxy-4-pyrrolidylquinazolines as phosphodiesterase 10A inhibitors using the linear interaction energy method. Journal of Molecular Graphics & Modelling. 61: 44-52. PMID 26188794 DOI: 10.1016/j.jmgm.2015.06.010  0.6
2015 Beerepoot MT, Friese DH, List NH, Kongsted J, Ruud K. Benchmarking two-photon absorption cross sections: performance of CC2 and CAM-B3LYP. Physical Chemistry Chemical Physics : Pccp. 17: 19306-14. PMID 26139162 DOI: 10.1039/c5cp03241e  0.68
2015 Olsen JM, Steinmann C, Ruud K, Kongsted J. Correction to "Polarizable Density Embedding: A New QM/QM/MM-based Computational Strategy". The Journal of Physical Chemistry. A. 119: 6928. PMID 26103064 DOI: 10.1021/acs.jpca.5b05307  1
2015 Nåbo LJ, List NH, Witzke S, Wüstner D, Khandelia H, Kongsted J. Design of new fluorescent cholesterol and ergosterol analogs: Insights from theory. Biochimica Et Biophysica Acta. 1848: 2188-99. PMID 25963993 DOI: 10.1016/j.bbamem.2015.04.018  0.64
2015 Nåbo LJ, Madsen CS, Jensen KJ, Kongsted J, Astakhova K. Ultramild protein-mediated click chemistry creates efficient oligonucleotide probes for targeting and detecting nucleic acids. Chembiochem : a European Journal of Chemical Biology. 16: 1163-7. PMID 25940911 DOI: 10.1002/cbic.201500145  0.64
2015 Hršak D, Holmegaard L, Poulsen AS, List NH, Kongsted J, Denofrio MP, Erra-Balsells R, Cabrerizo FM, Christiansen O, Ogilby PR. Experimental and computational study of solvent effects on one- and two-photon absorption spectra of chlorinated harmines. Physical Chemistry Chemical Physics : Pccp. 17: 12090-9. PMID 25875497 DOI: 10.1039/c5cp00773a  0.68
2015 Hedegård ED, Kongsted J, Ryde U. Multiscale modeling of the active site of [fe] hydrogenase: the h2 binding site in open and closed protein conformations. Angewandte Chemie (International Ed. in English). 54: 6246-50. PMID 25867218 DOI: 10.1002/anie.201501737  0.64
2015 Hedegård ED, Olsen JM, Knecht S, Kongsted J, Jensen HJ. Polarizable embedding with a multiconfiguration short-range density functional theory linear response method. The Journal of Chemical Physics. 142: 114113. PMID 25796237 DOI: 10.1063/1.4914922  0.72
2015 Nielsen CB, Sørensen HO, Kongsted J. Comparison between theoretically and experimentally determined electronic properties: applications to two-photon singlet oxygen sensitizers. The Journal of Physical Chemistry. A. 119: 1906-16. PMID 25647309 DOI: 10.1021/jp5122849  0.64
2015 List NH, Beerepoot MT, Olsen JM, Gao B, Ruud K, Jensen HJ, Kongsted J. Molecular quantum mechanical gradients within the polarizable embedding approach--application to the internal vibrational Stark shift of acetophenone. The Journal of Chemical Physics. 142: 034119. PMID 25612701 DOI: 10.1063/1.4905909  0.72
2015 Olsen JM, Steinmann C, Ruud K, Kongsted J. Polarizable density embedding: a new QM/QM/MM-based computational strategy. The Journal of Physical Chemistry. A. 119: 5344-55. PMID 25594604 DOI: 10.1021/jp510138k  1
2015 Matczyszyn K, Olesiak-Banska J, Nakatani K, Yu P, Murugan NA, Zale?ny R, Roztoczy?ska A, Bednarska J, Bartkowiak W, Kongsted J, Ågren H, Samo? M. One- and two-photon absorption of a spiropyran-merocyanine system: experimental and theoretical studies. The Journal of Physical Chemistry. B. 119: 1515-22. PMID 25531561 DOI: 10.1021/jp5071715  0.64
2015 Schwabe T, Beerepoot MT, Olsen JM, Kongsted J. Analysis of computational models for an accurate study of electronic excitations in GFP. Physical Chemistry Chemical Physics : Pccp. 17: 2582-8. PMID 25494098 DOI: 10.1039/c4cp04524f  0.72
2014 Pedersen MN, Hedegård ED, Olsen JM, Kauczor J, Norman P, Kongsted J. Damped Response Theory in Combination with Polarizable Environments: The Polarizable Embedding Complex Polarization Propagator Method. Journal of Chemical Theory and Computation. 10: 1164-71. PMID 26580189 DOI: 10.1021/ct400946k  0.72
2014 Steinmann C, Olsen JM, Kongsted J. Nuclear Magnetic Shielding Constants from Quantum Mechanical/Molecular Mechanical Calculations Using Polarizable Embedding: Role of the Embedding Potential. Journal of Chemical Theory and Computation. 10: 981-8. PMID 26580177 DOI: 10.1021/ct400880n  1
2014 Murugan NA, Zaleśny R, Kongsted J, Ågren H. Chelation-Induced Quenching of Two-Photon Absorption of Azacrown Ether Substituted Distyryl Benzene for Metal Ion Sensing. Journal of Chemical Theory and Computation. 10: 778-88. PMID 26580052 DOI: 10.1021/ct400924u  0.68
2014 List NH, Coriani S, Kongsted J, Christiansen O. Lanczos-driven coupled-cluster damped linear response theory for molecules in polarizable environments. The Journal of Chemical Physics. 141: 244107. PMID 25554133 DOI: 10.1063/1.4903981  0.68
2014 Aidas K, Angeli C, Bak KL, Bakken V, Bast R, Boman L, Christiansen O, Cimiraglia R, Coriani S, Dahle P, Dalskov EK, Ekström U, Enevoldsen T, Eriksen JJ, Ettenhuber P, ... ... Kongsted J, et al. The Dalton quantum chemistry program system. Wiley Interdisciplinary Reviews. Computational Molecular Science. 4: 269-284. PMID 25309629 DOI: 10.1002/wcms.1172  0.64
2014 Murugan NA, Zale?ny R, Kongsted J, Nordberg A, Ågren H. Promising two-photon probes for in vivo detection of β amyloid deposits. Chemical Communications (Cambridge, England). 50: 11694-7. PMID 25141215 DOI: 10.1039/c4cc03897e  0.64
2014 Poongavanam V, Olsen JM, Kongsted J. Binding free energy based structural dynamics analysis of HIV-1 RT RNase H-inhibitor complexes. Integrative Biology : Quantitative Biosciences From Nano to Macro. 6: 1010-22. PMID 25119978 DOI: 10.1039/c4ib00111g  0.72
2014 Olsen ST, Arcisauskaite V, Hansen T, Kongsted J, Mikkelsen KV. Computational assignment of redox states to Coulomb blockade diamonds. Physical Chemistry Chemical Physics : Pccp. 16: 17473-8. PMID 25020007 DOI: 10.1039/c4cp02055c  0.72
2014 List NH, Coriani S, Christiansen O, Kongsted J. Identifying the Hamiltonian structure in linear response theory. The Journal of Chemical Physics. 140: 224103. PMID 24929370 DOI: 10.1063/1.4881145  0.68
2014 Poongavanam V, Steinmann C, Kongsted J. Inhibitor ranking through QM based chelation calculations for virtual screening of HIV-1 RNase H inhibition. Plos One. 9: e98659. PMID 24897431 DOI: 10.1371/journal.pone.0098659  1
2014 Pourmousa M, Róg T, Mikkeli R, Vattulainen L, Solanko LM, Wüstner D, List NH, Kongsted J, Karttunen M. Dehydroergosterol as an analogue for cholesterol: why it mimics cholesterol so well-or does it? The Journal of Physical Chemistry. B. 118: 7345-57. PMID 24893063 DOI: 10.1021/jp406883k  0.68
2014 Hede T, Murugan NA, Kongsted J, Leck C, Ågren H. Simulations of light absorption of carbon particles in nanoaerosol clusters. The Journal of Physical Chemistry. A. 118: 1879-86. PMID 24547982 DOI: 10.1021/jp412384j  0.4
2014 Waiker DK, Karthikeyan C, Poongavanam V, Kongsted J, Lozach O, Meijer L, Trivedi P. Synthesis, biological evaluation and molecular modelling studies of 4-anilinoquinazoline derivatives as protein kinase inhibitors. Bioorganic & Medicinal Chemistry. 22: 1909-15. PMID 24530227 DOI: 10.1016/j.bmc.2014.01.044  0.64
2014 Hedegård ED, Knecht S, Ryde U, Kongsted J, Saue T. Theoretical 57Fe Mössbauer spectroscopy: isomer shifts of [Fe]-hydrogenase intermediates. Physical Chemistry Chemical Physics : Pccp. 16: 4853-63. PMID 24468665 DOI: 10.1039/c3cp54393e  0.64
2014 Silva DL, Murugan NA, Kongsted J, Ã…gren H, Canuto S. Self-aggregation and optical absorption of stilbazolium merocyanine in chloroform. The Journal of Physical Chemistry. B. 118: 1715-25. PMID 24467553 DOI: 10.1021/jp411178h  0.4
2014 List NH, Pimenta FM, Holmegaard L, Jensen RL, Etzerodt M, Schwabe T, Kongsted J, Ogilby PR, Christiansen O. Effect of chromophore encapsulation on linear and nonlinear optical properties: the case of "miniSOG", a protein-encased flavin. Physical Chemistry Chemical Physics : Pccp. 16: 9950-9. PMID 24452275 DOI: 10.1039/c3cp54470b  0.64
2013 Murugan NA, Kongsted J, Ågren H. pH-Induced Modulation of One- and Two-Photon Absorption Properties in a Naphthalene-Based Molecular Probe. Journal of Chemical Theory and Computation. 9: 3660-9. PMID 26584119 DOI: 10.1021/ct400357t  0.68
2013 Hedegård ED, Kongsted J, Sauer SP. Validating and Analyzing EPR Hyperfine Coupling Constants with Density Functional Theory. Journal of Chemical Theory and Computation. 9: 2380-8. PMID 26583728 DOI: 10.1021/ct400171c  0.52
2013 List NH, Curutchet C, Knecht S, Mennucci B, Kongsted J. Toward Reliable Prediction of the Energy Ladder in Multichromophoric Systems: A Benchmark Study on the FMO Light-Harvesting Complex. Journal of Chemical Theory and Computation. 9: 4928-38. PMID 26583411 DOI: 10.1021/ct400560m  0.68
2013 Murugan NA, Olsen JM, Kongsted J, Rinkevicius Z, Aidas K, Ågren H. Amyloid Fibril-Induced Structural and Spectral Modifications in the Thioflavin-T Optical Probe. The Journal of Physical Chemistry Letters. 4: 70-7. PMID 26291214 DOI: 10.1021/jz3018557  0.72
2013 Wielgus M, Zaleśny R, Murugan NA, Kongsted J, Ågren H, Samoc M, Bartkowiak W. Two-photon solvatochromism II: Experimental and theoretical study of solvent effects on the two-photon absorption spectrum of reichardt's dye Chemphyschem. 14: 3731-3739. PMID 24106066 DOI: 10.1002/cphc.201300695  0.64
2013 Knecht S, Marian CM, Kongsted J, Mennucci B. On the photophysics of carotenoids: a multireference DFT study of peridinin. The Journal of Physical Chemistry. B. 117: 13808-15. PMID 24090414 DOI: 10.1021/jp4078739  0.64
2013 Poongavanam V, Kongsted J. Virtual screening models for prediction of HIV-1 RT associated RNase H inhibition. Plos One. 8: e73478. PMID 24066050 DOI: 10.1371/journal.pone.0073478  0.6
2013 Olesiak-Banska J, Matczyszyn K, Zaleśny R, Murugan NA, Kongsted J, Ågren H, Bartkowiak W, Samoc M. Revealing spectral features in two-photon absorption spectrum of hoechst 33342: A combined experimental and quantum-chemical study Journal of Physical Chemistry B. 117: 12013-12019. PMID 24016295 DOI: 10.1021/jp407144k  0.64
2013 Murugan NA, Apostolov R, Rinkevicius Z, Kongsted J, Lindahl E, Ågren H. Association dynamics and linear and nonlinear optical properties of an N-acetylaladanamide probe in a POPC membrane. Journal of the American Chemical Society. 135: 13590-7. PMID 23951997 DOI: 10.1021/ja407326n  0.68
2013 Hedegård ED, List NH, Jensen HJ, Kongsted J. The multi-configuration self-consistent field method within a polarizable embedded framework. The Journal of Chemical Physics. 139: 044101. PMID 23901954 DOI: 10.1063/1.4811835  0.68
2013 Sneskov K, Olsen JM, Schwabe T, Hättig C, Christiansen O, Kongsted J. Computational screening of one- and two-photon spectrally tuned channelrhodopsin mutants. Physical Chemistry Chemical Physics : Pccp. 15: 7567-76. PMID 23588588 DOI: 10.1039/c3cp44350g  0.72
2013 Beerepoot MTP, Steindal AH, Kongsted J, Brandsdal BO, Frediani L, Ruud K, Olsen JMH. A polarizable embedding DFT study of one-photon absorption in fluorescent proteins Physical Chemistry Chemical Physics. 15: 4735-4743. PMID 23426505 DOI: 10.1039/c3cp44659j  0.64
2013 Aidas K, Olsen JM, Kongsted J, Ågren H. Photoabsorption of acridine yellow and proflavin bound to human serum albumin studied by means of quantum mechanics/molecular dynamics. The Journal of Physical Chemistry. B. 117: 2069-80. PMID 23356863 DOI: 10.1021/jp311863x  0.72
2013 Frecus B, Rinkevicius Z, Murugan NA, Vahtras O, Kongsted J, Ågren H. EPR spin Hamiltonian parameters of encapsulated spin-labels: impact of the hydrogen bonding topology. Physical Chemistry Chemical Physics : Pccp. 15: 2427-34. PMID 23303199 DOI: 10.1039/c2cp43951d  0.68
2013 Aidas K, Ågren H, Kongsted J, Laaksonen A, Mocci F. A quantum mechanics/molecular dynamics study of electric field gradient fluctuations in the liquid phase. The case of Na+ in aqueous solution. Physical Chemistry Chemical Physics : Pccp. 15: 1621-31. PMID 23247548 DOI: 10.1039/c2cp41993a  0.72
2013 Curutchet C, Novoderezhkin VI, Kongsted J, Muñoz-Losa A, van Grondelle R, Scholes GD, Mennucci B. Energy flow in the cryptophyte PE545 antenna is directed by bilin pigment conformation. The Journal of Physical Chemistry. B. 117: 4263-73. PMID 22992117 DOI: 10.1021/jp305033d  0.64
2012 Schwabe T, Sneskov K, Haugaard Olsen JM, Kongsted J, Christiansen O, Hättig C. PERI-CC2: A Polarizable Embedded RI-CC2 Method. Journal of Chemical Theory and Computation. 8: 3274-83. PMID 26605734 DOI: 10.1021/ct3003749  0.68
2012 Li X, Rinkevicius Z, Kongsted J, Murugan NA, Ågren H. Binding Mechanism and Magnetic Properties of a Multifunctional Spin Label for Targeted EPR Imaging of Amyloid Proteins: Insight from Atomistic Simulations and First-Principles Calculations. Journal of Chemical Theory and Computation. 8: 4766-74. PMID 26605629 DOI: 10.1021/ct300606q  0.68
2012 Rinkevicius Z, Frecuş B, Murugan NA, Vahtras O, Kongsted J, Ågren H. Encapsulation Influence on EPR Parameters of Spin-Labels: 2,2,6,6-Tetramethyl-4-methoxypiperidine-1-oxyl in Cucurbit[8]uril. Journal of Chemical Theory and Computation. 8: 257-63. PMID 26592886 DOI: 10.1021/ct200816z  0.68
2012 List NH, Olsen JM, Jensen HJ, Steindal AH, Kongsted J. Molecular-Level Insight into the Spectral Tuning Mechanism of the DsRed Chromophore. The Journal of Physical Chemistry Letters. 3: 3513-21. PMID 26290981 DOI: 10.1021/jz3014858  0.72
2012 Murugan NA, Aidas K, Kongsted J, Rinkevicius Z, Ågren H. NMR spin-spin coupling constants in polymethine dyes as polarity indicators. Chemistry (Weinheim An Der Bergstrasse, Germany). 18: 11677-84. PMID 22887687 DOI: 10.1002/chem.201200270  0.72
2012 Hedegård ED, Kongsted J, Sauer SP. Improving the calculation of Electron Paramagnetic Resonance hyperfine coupling tensors for d-block metals. Physical Chemistry Chemical Physics : Pccp. 14: 10669-76. PMID 22785432 DOI: 10.1039/c2cp40969k  0.52
2012 Silva DL, Murugan NA, Kongsted J, Rinkevicius Z, Canuto S, Ågren H. The role of molecular conformation and polarizable embedding for one- and two-photon absorption of disperse orange 3 in solution. The Journal of Physical Chemistry. B. 116: 8169-81. PMID 22694126 DOI: 10.1021/jp3032034  0.68
2012 Eriksen JJ, Sauer SP, Mikkelsen KV, Jensen HJ, Kongsted J. On the importance of excited state dynamic response electron correlation in polarizable embedding methods. Journal of Computational Chemistry. 33: 2012-22. PMID 22685085 DOI: 10.1002/jcc.23032  0.72
2012 Steindal AH, Olsen JMH, 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 Physical Chemistry Chemical Physics. 14: 5440-5451. PMID 22407300 DOI: 10.1039/c2cp23537d  0.64
2012 Kupka T, Nieradka M, Stachów M, Pluta T, Nowak P, Kjær H, Kongsted J, Kaminsky J. Basis set convergence of indirect spin-spin coupling constants in the Kohn-Sham limit for several small molecules. The Journal of Physical Chemistry. A. 116: 3728-38. PMID 22401301 DOI: 10.1021/jp212588h  0.4
2012 Hansen SW, Stein PC, Sørensen A, Share AI, Witlicki EH, Kongsted J, Flood AH, Jeppesen JO. Quantification of the π-π interactions that govern tertiary structure in donor-acceptor [2]pseudorotaxanes. Journal of the American Chemical Society. 134: 3857-63. PMID 22280483 DOI: 10.1021/ja210861v  0.64
2012 Dreier I, Kumar S, Søndergaard H, Rasmussen ML, Hansen LH, List NH, Kongsted J, Vester B, Nielsen P. A click chemistry approach to pleuromutilin derivatives, part 2: Conjugates with acyclic nucleosides and their ribosomal binding and antibacterial activity Journal of Medicinal Chemistry. 55: 2067-2077. PMID 22280300 DOI: 10.1021/jm201266b  0.64
2012 Murugan NA, Kongsted J, Rinkevicius Z, Ågren H. Color modeling of protein optical probes. Physical Chemistry Chemical Physics : Pccp. 14: 1107-12. PMID 22134524 DOI: 10.1039/c1cp23060c  0.68
2011 Söderhjelm P, Kongsted J, Ryde U. Conformational Dependence of Isotropic Polarizabilities. Journal of Chemical Theory and Computation. 7: 1404-14. PMID 26610132 DOI: 10.1021/ct100714e  0.56
2011 Schwabe T, Olsen JM, Sneskov K, Kongsted J, Christiansen O. Solvation Effects on Electronic Transitions: Exploring the Performance of Advanced Solvent Potentials in Polarizable Embedding Calculations. Journal of Chemical Theory and Computation. 7: 2209-17. PMID 26606490 DOI: 10.1021/ct200258g  0.72
2011 Hedegård ED, Kongsted J, Sauer SP. Optimized Basis Sets for Calculation of Electron Paramagnetic Resonance Hyperfine Coupling Constants: aug-cc-pVTZ-J for the 3d Atoms Sc-Zn. Journal of Chemical Theory and Computation. 7: 4077-87. PMID 26598353 DOI: 10.1021/ct200587k  0.52
2011 Rinkevicius Z, Murugan NA, Kongsted J, Frecuş B, Steindal AH, Ågren H. Density Functional Restricted-Unrestricted/Molecular Mechanics Theory for Hyperfine Coupling Constants of Molecules in Solution. Journal of Chemical Theory and Computation. 7: 3261-71. PMID 26598160 DOI: 10.1021/ct2003572  0.68
2011 Kjaer H, Sauer SP, Kongsted J. The coupling constant polarizability and hyperpolarizabilty of 1J(NH) in N-methylacetamide, and its application for the multipole spin-spin coupling constant polarizability/reaction field approach to solvation. Journal of Computational Chemistry. 32: 3168-74. PMID 21953553 DOI: 10.1002/jcc.21897  0.52
2011 Sneskov K, Schwabe T, Christiansen O, Kongsted J. Scrutinizing the effects of polarization in QM/MM excited state calculations. Physical Chemistry Chemical Physics : Pccp. 13: 18551-60. PMID 21947164 DOI: 10.1039/c1cp22067e  0.68
2011 Eriksen JJ, Olsen JM, Aidas K, Ågren H, Mikkelsen KV, Kongsted J. Computational protocols for prediction of solute NMR relative chemical shifts. a case study of L-tryptophan in aqueous solution. Journal of Computational Chemistry. 32: 2853-64. PMID 21732391 DOI: 10.1002/jcc.21867  0.72
2011 Genheden S, Mikulskis P, Hu L, Kongsted J, Söderhjelm P, Ryde U. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration. Journal of the American Chemical Society. 133: 13081-92. PMID 21728337 DOI: 10.1021/ja202972m  0.64
2011 Arul Murugan N, Kongsted J, Rinkevicius Z, Aidas K, Mikkelsen KV, Ågren H. Hybrid density functional theory/molecular mechanics calculations of two-photon absorption of dimethylamino nitro stilbene in solution. Physical Chemistry Chemical Physics : Pccp. 13: 12506-16. PMID 21660320 DOI: 10.1039/c1cp20611g  0.72
2011 Rinkevicius Z, Murugan NA, Kongsted J, Aidas K, Steindal AH, Agren H. Density functional theory/molecular mechanics approach for electronic g-tensors of solvated molecules. The Journal of Physical Chemistry. B. 115: 4350-8. PMID 21449574 DOI: 10.1021/jp1108653  0.72
2011 Sneskov K, Schwabe T, Kongsted J, Christiansen O. The polarizable embedding coupled cluster method. The Journal of Chemical Physics. 134: 104108. PMID 21405157 DOI: 10.1063/1.3560034  0.68
2011 Steindal AH, Ruud K, Frediani L, Aidas K, Kongsted J. Excitation energies in solution: the fully polarizable QM/MM/PCM method. The Journal of Physical Chemistry. B. 115: 3027-37. PMID 21391548 DOI: 10.1021/jp1101913  0.72
2011 Curutchet C, Kongsted J, Muñoz-Losa A, Hossein-Nejad H, Scholes GD, Mennucci B. Photosynthetic light-harvesting is tuned by the heterogeneous polarizable environment of the protein. Journal of the American Chemical Society. 133: 3078-84. PMID 21322565 DOI: 10.1021/ja110053y  0.64
2011 Kjær H, Sauer SP, Kongsted J. Benchmarking the multipole shielding polarizability/reaction field approach to solvation against QM/MM: applications to the shielding constants of N-methylacetamide. The Journal of Chemical Physics. 134: 044514. PMID 21280755 DOI: 10.1063/1.3546033  0.52
2011 Rocha-Rinza T, Sneskov K, Christiansen O, Ryde U, Kongsted J. Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein. Physical Chemistry Chemical Physics : Pccp. 13: 1585-9. PMID 21132197 DOI: 10.1039/c0cp01075h  0.64
2011 Murugan NA, Kongsted J, Rinkevicius Z, Agren H. Demystifying the solvatochromic reversal in Brooker's merocyanine dye. Physical Chemistry Chemical Physics : Pccp. 13: 1290-2. PMID 21132167 DOI: 10.1039/c0cp01014f  0.4
2010 Genheden S, Kongsted J, Söderhjelm P, Ryde U. Nonpolar Solvation Free Energies of Protein-Ligand Complexes. Journal of Chemical Theory and Computation. 6: 3558-68. PMID 26617102 DOI: 10.1021/ct100272s  0.56
2010 Söderhjelm P, Kongsted J, Ryde U. Ligand Affinities Estimated by Quantum Chemical Calculations. Journal of Chemical Theory and Computation. 6: 1726-37. PMID 26615702 DOI: 10.1021/ct9006986  0.56
2010 Olsen JM, Aidas K, Mikkelsen KV, Kongsted J. Solvatochromic Shifts in Uracil: A Combined MD-QM/MM Study. Journal of Chemical Theory and Computation. 6: 249-56. PMID 26614335 DOI: 10.1021/ct900502s  0.72
2010 Sneskov K, Matito E, Kongsted J, Christiansen O. Approximate Inclusion of Triple Excitations in Combined Coupled Cluster/Molecular Mechanics: Calculations of Electronic Excitation Energies in Solution for Acrolein, Water, Formamide, and N-Methylacetamide. Journal of Chemical Theory and Computation. 6: 839-50. PMID 26613311 DOI: 10.1021/ct900641w  0.68
2010 Witzke S, Duelund L, Kongsted J, Petersen M, Mouritsen OG, Khandelia H. Inclusion of terpenoid plant extracts in lipid bilayers investigated by molecular dynamics simulations. The Journal of Physical Chemistry. B. 114: 15825-31. PMID 21070035 DOI: 10.1021/jp108675b  0.64
2010 Kjaer H, Sauer SP, Kongsted J. Benchmarking NMR indirect nuclear spin-spin coupling constants: SOPPA, SOPPA(CC2), and SOPPA(CCSD) versus CCSD. The Journal of Chemical Physics. 133: 144106. PMID 20949986 DOI: 10.1063/1.3483197  0.52
2010 Murugan NA, Kongsted J, Rinkevicius Z, Aidas K, Ågren H. Modeling the structure and absorption spectra of stilbazolium merocyanine in polar and nonpolar solvents using hybrid QM/MM techniques. The Journal of Physical Chemistry. B. 114: 13349-57. PMID 20925401 DOI: 10.1021/jp1060717  0.72
2010 Murugan NA, Kongsted J, Rinkevicius Z, Agren H. Breakdown of the first hyperpolarizability/bond-length alternation parameter relationship. Proceedings of the National Academy of Sciences of the United States of America. 107: 16453-8. PMID 20823263 DOI: 10.1073/pnas.1006572107  0.4
2010 Söderhjelm P, Kongsted J, Genheden S, Ryde U. Estimates of ligand-binding affinities supported by quantum mechanical methods. Interdisciplinary Sciences, Computational Life Sciences. 2: 21-37. PMID 20640794 DOI: 10.1007/s12539-010-0083-0  0.64
2010 Kuhlman TS, Kongsted J, Mikkelsen KV, Møller KB, Sølling TI. Interpretation of the ultrafast photoinduced processes in pentacene thin films. Journal of the American Chemical Society. 132: 3431-9. PMID 20175536 DOI: 10.1021/ja909166s  0.72
2010 Aidas K, Mikkelsen KV, Kongsted J. On the existence of the H3 tautomer of adenine in aqueous solution. Rationalizations based on hybrid quantum mechanics/molecular mechanics predictions. Physical Chemistry Chemical Physics : Pccp. 12: 761-8. PMID 20066363 DOI: 10.1039/b915604f  0.72
2009 Kongsted J, Söderhjelm P, Ryde U. How accurate are continuum solvation models for drug-like molecules? Journal of Computer-Aided Molecular Design. 23: 395-409. PMID 19444622 DOI: 10.1007/s10822-009-9271-6  0.64
2009 Møgelhøj A, Aidas K, Mikkelsen KV, Sauer SP, Kongsted J. Prediction of spin-spin coupling constants in solution based on combined density functional theory/molecular mechanics. The Journal of Chemical Physics. 130: 134508. PMID 19355752 DOI: 10.1063/1.3098255  0.72
2009 Pedersen TB, Kongsted J, Crawford TD, Ruud K. On the importance of vibrational contributions to small-angle optical rotation: Fluoro-oxirane in gas phase and solution. The Journal of Chemical Physics. 130: 034310. PMID 19173524 DOI: 10.1063/1.3054301  0.68
2009 Kongsted J, Ryde U. An improved method to predict the entropy term with the MM/PBSA approach. Journal of Computer-Aided Molecular Design. 23: 63-71. PMID 18781280 DOI: 10.1007/s10822-008-9238-z  0.64
2008 Kongsted J, Aidas K, Mikkelsen KV, Sauer SP. On the Accuracy of Density Functional Theory to Predict Shifts in Nuclear Magnetic Resonance Shielding Constants due to Hydrogen Bonding. Journal of Chemical Theory and Computation. 4: 267-77. PMID 26620658 DOI: 10.1021/ct700285j  0.72
2008 Hansen MB, Kongsted J, Toffoli D, Christiansen O. Vibrational contributions to indirect spin-spin coupling constants calculated via variational anharmonic approaches. The Journal of Physical Chemistry. A. 112: 8436-45. PMID 18707069 DOI: 10.1021/jp804306s  0.68
2008 Aidas K, Møgelhoj A, Nilsson EJ, Johnson MS, Mikkelsen KV, Christiansen O, Söderhjelm P, Kongsted J. On the performance of quantum chemical methods to predict solvatochromic effects: the case of acrolein in aqueous solution. The Journal of Chemical Physics. 128: 194503. PMID 18500876 DOI: 10.1063/1.2918537  0.72
2007 Aidas K, Møgelhøj A, Kjaer H, Nielsen CB, Mikkelsen KV, Ruud K, Christiansen O, Kongsted J. Solvent effects on NMR isotropic shielding constants. a comparison between explicit polarizable discrete and continuum approaches. The Journal of Physical Chemistry. A. 111: 4199-210. PMID 17474726 DOI: 10.1021/jp068693e  0.64
2007 Nielsen CB, Christiansen O, Mikkelsen KV, Kongsted J. Density functional self-consistent quantum mechanics/molecular mechanics theory for linear and nonlinear molecular properties: Applications to solvated water and formaldehyde. The Journal of Chemical Physics. 126: 154112. PMID 17461619 DOI: 10.1063/1.2711182  0.64
2007 Kongsted J, Nielsen CB, Mikkelsen KV, Christiansen O, Ruud K. Nuclear magnetic shielding constants of liquid water: insights from hybrid quantum mechanics/molecular mechanics models. The Journal of Chemical Physics. 126: 034510. PMID 17249887 DOI: 10.1063/1.2424713  0.64
2006 Paterson MJ, Kongsted J, Christiansen O, Mikkelsen KV, Nielsen CB. Two-photon absorption cross sections: an investigation of solvent effects. Theoretical studies on formaldehyde and water. The Journal of Chemical Physics. 125: 184501. PMID 17115759 DOI: 10.1063/1.2363997  0.64
2006 Osted A, Kongsted J, Mikkelsen KV, Astrand PO, Christiansen O. Statistical mechanically averaged molecular properties of liquid water calculated using the combined coupled cluster/molecular dynamics method. The Journal of Chemical Physics. 124: 124503. PMID 16599693 DOI: 10.1063/1.2176615  0.72
2006 Kongsted J, Pedersen TB, Jensen L, Hansen AE, Mikkelsen KV. Coupled cluster and density functional theory studies of the vibrational contribution to the optical rotation of (S)-propylene oxide. Journal of the American Chemical Society. 128: 976-82. PMID 16417389 DOI: 10.1021/ja056611e  0.64
2006 Falsig H, Gross A, Kongsted J, Osted A, Sloth M, Mikkelsen KV, Christiansen O. Uptake of phenol on aerosol particles. The Journal of Physical Chemistry. A. 110: 660-70. PMID 16405338 DOI: 10.1021/jp0536201  0.72
2005 Aidas K, Kongsted J, Osted A, Mikkelsen KV, Christiansen O. Coupled cluster calculation of the n --> pi* electronic transition of acetone in aqueous solution. The Journal of Physical Chemistry. A. 109: 8001-10. PMID 16834182 DOI: 10.1021/jp0527094  0.72
2004 Kongsted J, Osted A, Mikkelsen KV, Astrand PO, Christiansen O. Solvent effects on the n-->pi* electronic transition in formaldehyde: a combined coupled cluster/molecular dynamics study. The Journal of Chemical Physics. 121: 8435-45. PMID 15511167 DOI: 10.1063/1.1804957  0.72
2004 Kongsted J, Osted A, Mikkelsen KV, Christiansen O. Second harmonic generation second hyperpolarizability of water calculated using the combined coupled cluster dielectric continuum or different molecular mechanics methods. The Journal of Chemical Physics. 120: 3787-98. PMID 15268543 DOI: 10.1063/1.1642593  0.72
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