Jacob Kongsted

发表

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

Dalibor Hrsak, Jógvan Magnus H. Olsen, Jacob Kongsted, 2017, J. Comput. Chem..

Modelling spectroscopic properties of large molecular systems. The combined Density Functional Theory/Molecular Mechanics approach

Kurt V. Mikkelsen, Jacob Kongsted, Kestutis Aidas, 2007, J. Comput. Methods Sci. Eng..

Computational protocols for prediction of solute NMR relative chemical shifts. A case study of L‐tryptophan in aqueous solution

Kurt V. Mikkelsen, Jógvan Magnus H. Olsen, Jacob Kongsted, 2011, J. Comput. Chem..

Polarizable Density Embedding: A Solution to the Electron Spill-Out Problem in Multiscale Modeling.

Jacob Kongsted, Peter Reinholdt, Jógvan Magnus Haugaard Olsen, 2017, The journal of physical chemistry letters.

Modeling the Sterol-Binding Domain of Aster-A Provides Insight into Its Multiligand Specificity

Daniel Wüstner, Jacob Kongsted, Peter Reinholdt, 2020, J. Chem. Inf. Model..

Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems.

Roberto Di Remigio, Xin Li, Trygve Helgaker, 2020, The Journal of chemical physics.

An averaged polarizable potential for multiscale modeling in phospholipid membranes

Jógvan Magnus H. Olsen, Jacob Kongsted, Casper Steinmann, 2017, J. Comput. Chem..

Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes

Jacob Kongsted, Nina P. L. Junager, Kira Astakhova, 2016, Sensors.

An improved method to predict the entropy term with the MM/PBSA approach

Jacob Kongsted, Ulf Ryde, U. Ryde, 2009, J. Comput. Aided Mol. Des..

Models to identification.

Jacob Kongsted, Casper Steinmann, Vasanthanathan Poongavanam, 2014 .

How accurate are continuum solvation models for drug-like molecules?

Jacob Kongsted, Pär Söderhjelm, Ulf Ryde, 2009, J. Comput. Aided Mol. Des..

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

Maximilian Scheurer, Andreas Dreuw, Jacob Kongsted, 2019, Journal of chemical theory and computation.

Multipole moments for embedding potentials: Exploring different atomic allocation algorithms

Jógvan Magnus H. Olsen, Jacob Kongsted, Jógvan Magnus Haugaard Olsen, 2016, J. Comput. Chem..

Basis set error estimation for DFT calculations of electronic g‐tensors for transition metal complexes

Jacob Kongsted, Morten N. Pedersen, Erik D. Hedegård, 2014, J. Comput. Chem..

Response properties of embedded molecules through the polarizable embedding model

Jacob Kongsted, Casper Steinmann, Peter Reinholdt, 2018, International Journal of Quantum Chemistry.

On the importance of excited state dynamic response electron correlation in polarizable embedding methods

Kurt V. Mikkelsen, Jacob Kongsted, Janus Juul Eriksen, 2012, J. Comput. Chem..

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

Jacob Kongsted, Stephan P. A. Sauer, Hanna Kjær, 2011, J. Comput. Chem..

Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees

Maximilian Scheurer, Andreas Dreuw, Jacob Kongsted, 2021 .

A combined quantum mechanics/molecular mechanics study of the one- and two-photon absorption in the green fluorescent protein.

Luca Frediani, Kenneth Ruud, Jacob Kongsted, 2012, Physical chemistry chemical physics : PCCP.

Estimates of ligand-binding affinities supported by quantum mechanical methods

Jacob Kongsted, Samuel Genheden, Pär Söderhjelm, 2010, Interdisciplinary Sciences: Computational Life Sciences.

The polarizable embedding coupled cluster method.

Jacob Kongsted, Tobias Schwabe, Ove Christiansen, 2011, Journal of Chemical Physics.

Two-photon solvatochromism II: experimental and theoretical study of solvent effects on the two-photon absorption spectrum of Reichardt's dye.

Jacob Kongsted, Marek Samoc, Hans Ågren, 2013, Chemphyschem : a European journal of chemical physics and physical chemistry.

Statistical mechanically averaged molecular properties of liquid water calculated using the combined coupled cluster/molecular dynamics method.

Jacob Kongsted, Ove Christiansen, Kurt V Mikkelsen, 2006, The Journal of chemical physics.

Coupled Cluster/Molecular Mechanics Method: Implementation and Application to Liquid Water

Kurt V. Mikkelsen, Jacob Kongsted, Ove Christiansen, 2003 .

Automatic generation of force fields and property surfaces for use in variational vibrational calculations of anharmonic vibrational energies and zero-point vibrational averaged properties.

Jacob Kongsted, Ove Christiansen, J. Kongsted, 2006, The Journal of chemical physics.

Molecular Properties through Polarizable Embedding

Jacob Kongsted, Jógvan Magnus Haugaard Olsen, J. Kongsted, 2011 .

Polarizable embedding with a multiconfiguration short-range density functional theory linear response method.

Jacob Kongsted, Jógvan Magnus Haugaard Olsen, Stefan Knecht, 2015, The Journal of chemical physics.

Excited States in Solution through Polarizable Embedding

Jacob Kongsted, Kestutis Aidas, Jógvan Magnus Haugaard Olsen, 2010 .

Ligand Affinities Estimated by Quantum Chemical Calculations.

Jacob Kongsted, Pär Söderhjelm, Ulf Ryde, 2010, Journal of chemical theory and computation.

Polarizable Density Embedding Coupled Cluster Method.

Jacob Kongsted, Jógvan Magnus Haugaard Olsen, J. Kongsted, 2018, Journal of chemical theory and computation.

Vibrational and thermal effects on the dipole polarizability of methane and carbon tetrachloride from vibrational structure calculations.

Jacob Kongsted, Ove Christiansen, J. Kongsted, 2007, The Journal of chemical physics.

Molecular quantum mechanical gradients within the polarizable embedding approach--application to the internal vibrational Stark shift of acetophenone.

Kenneth Ruud, Jacob Kongsted, Bin Gao, 2015, The Journal of chemical physics.

Linear Response Properties of Liquid Water Calculated Using CC2 and CCSD within Different Molecular Mechanics Methods

Kurt V. Mikkelsen, Jacob Kongsted, Ove Christiansen, 2004 .

Nonpolar Solvation Free Energies of Protein-Ligand Complexes.

Jacob Kongsted, Samuel Genheden, Pär Söderhjelm, 2010, Journal of chemical theory and computation.

Dalton, a molecular electronic structure program, Release Dalton2011

Paweł Sałek, Elias Rudberg, Luca Frediani, 2011 .

Density Functional Restricted-Unrestricted/Molecular Mechanics Theory for Hyperfine Coupling Constants of Molecules in Solution.

Jacob Kongsted, Zilvinas Rinkevicius, Hans Ågren, 2011, Journal of chemical theory and computation.

A theoretical study of the reaction between CH3S(OH)CH3 and O2

Ian Barnes, Kurt V. Mikkelsen, Jacob Kongsted, 2004 .

Linear response functions for coupled cluster/molecular mechanics including polarization interactions

Kurt V. Mikkelsen, Jacob Kongsted, Ove Christiansen, 2003 .

Solvatochromic Shifts in Uracil: A Combined MD-QM/MM Study.

Jacob Kongsted, Jógvan Magnus Haugaard Olsen, K. Mikkelsen, 2010, Journal of chemical theory and computation.

Overview of Recent Strategic Advances in Medicinal Chemistry.

Peng Zhan, Yuning Song, Dongwei Kang, 2019, Journal of medicinal chemistry.

Prediction and rationalization of the pH dependence of the activity and stability of family 11 xylanases.

Jan H. Jensen, Jacob Kongsted, Ulf Ryde, 2007, Biochemistry.

On the photophysics of carotenoids: a multireference DFT study of peridinin.

Benedetta Mennucci, Jacob Kongsted, Stefan Knecht, 2013, The journal of physical chemistry. B.

Revealing spectral features in two-photon absorption spectrum of Hoechst 33342: a combined experimental and quantum-chemical study.

Jacob Kongsted, Joanna Olesiak-Banska, Katarzyna Matczyszyn, 2013, The journal of physical chemistry. B.

Density functional self-consistent quantum mechanics/molecular mechanics theory for linear and nonlinear molecular properties: Applications to solvated water and formaldehyde.

Jacob Kongsted, Ove Christiansen, Kurt V Mikkelsen, 2007, The Journal of chemical physics.

Solvent effects on NMR isotropic shielding constants. a comparison between explicit polarizable discrete and continuum approaches.

Kenneth Ruud, Jacob Kongsted, Kestutis Aidas, 2007, The journal of physical chemistry. A.

Excited states in large molecular systems through polarizable embedding.

Jacob Kongsted, Jógvan Magnus Haugaard Olsen, Nanna Holmgaard List, 2016, Physical chemistry chemical physics : PCCP.

Design, synthesis, and biologic evaluation of novel galloyl derivatives as HIV‐1 RNase H inhibitors

Peng Zhan, Jacob Kongsted, Luis Menéndez-Arias, 2019, Chemical biology & drug design.

Computational Approach for Studying Optical Properties of DNA Systems in Solution.

Jacob Kongsted, Casper Steinmann, Jógvan Magnus Haugaard Olsen, 2016, Journal of chemical theory and computation.

Polarizable density embedding: a new QM/QM/MM-based computational strategy.

Kenneth Ruud, Jacob Kongsted, Casper Steinmann, 2015, The journal of physical chemistry. A.

The QM/MM approach for wavefunctions, energies and response functions within self-consistent field and coupled cluster theories

Kurt V. Mikkelsen, Jacob Kongsted, Ove Christiansen, 2002 .

The multi-configuration self-consistent field method within a polarizable embedded framework.

Jacob Kongsted, J. Kongsted, N. List, 2013, The Journal of chemical physics.

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

Jacob Kongsted, Nanna Holmgaard List, J. Kongsted, 2016, Physical chemistry chemical physics : PCCP.

Damped Response Theory in Combination with Polarizable Environments: The Polarizable Embedding Complex Polarization Propagator Method.

Jacob Kongsted, Patrick Norman, Jógvan Magnus Haugaard Olsen, 2014, Journal of chemical theory and computation.

Transition-State Docking of Flunitrazepam and Progesterone in Cytochrome P450.

Lars Olsen, Patrik Rydberg, Jacob Kongsted, 2008, Journal of chemical theory and computation.

Theoretical 57Fe Mössbauer spectroscopy: isomer shifts of [Fe]-hydrogenase intermediates.

Jacob Kongsted, Ulf Ryde, Stefan Knecht, 2014, Physical chemistry chemical physics : PCCP.

Breakdown of the first hyperpolarizability/bond-length alternation parameter relationship

Jacob Kongsted, Zilvinas Rinkevicius, N Arul Murugan, 2010, Proceedings of the National Academy of Sciences.

Interpretation of the ultrafast photoinduced processes in pentacene thin films.

Kurt V. Mikkelsen, Jacob Kongsted, Theis I. Sølling, 2010, Journal of the American Chemical Society.

Performance of popular XC‐functionals for the description of excitation energies in GFP‐like chromophore models

Jacob Kongsted, Ove Christiansen, Jógvan Magnus Haugaard Olsen, 2012 .

Benchmarking two-photon absorption cross sections: performance of CC2 and CAM-B3LYP.

Kenneth Ruud, Jacob Kongsted, K. Ruud, 2015, Physical chemistry chemical physics : PCCP.

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

Jacob Kongsted, Patrick Norman, Nanna Holmgaard List, 2017, The Journal of chemical physics.

Chelation-Induced Quenching of Two-Photon Absorption of Azacrown Ether Substituted Distyryl Benzene for Metal Ion Sensing.

Jacob Kongsted, Hans Ågren, Robert Zaleśny, 2014, Journal of chemical theory and computation.

On the existence of the H3 tautomer of adenine in aqueous solution. Rationalizations based on hybrid quantum mechanics/molecular mechanics predictions.

Jacob Kongsted, Kestutis Aidas, Kurt V Mikkelsen, 2010, Physical chemistry chemical physics : PCCP.

Failures of TDDFT in describing the lowest intramolecular charge-transfer excitation in para-nitroaniline

Kurt V. Mikkelsen, Jacob Kongsted, Ove Christiansen, 2013 .

Density functional theory/molecular mechanics approach for electronic g-tensors of solvated molecules.

Jacob Kongsted, Zilvinas Rinkevicius, Kestutis Aidas, 2011, The journal of physical chemistry. B.

The Dalton quantum chemistry program system

Luca Frediani, Thomas Kjærgaard, Trygve Helgaker, 2013, Wiley interdisciplinary reviews. Computational molecular science.

Binding free energy based structural dynamics analysis of HIV-1 RT RNase H-inhibitor complexes.

Jacob Kongsted, Jógvan Magnus Haugaard Olsen, Vasanthanathan Poongavanam, 2014, Integrative biology : quantitative biosciences from nano to macro.

Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration.

Jacob Kongsted, Samuel Genheden, Pär Söderhjelm, 2011, Journal of the American Chemical Society.

Association dynamics and linear and nonlinear optical properties of an N-acetylaladanamide probe in a POPC membrane.

Erik Lindahl, Jacob Kongsted, Zilvinas Rinkevicius, 2013, Journal of the American Chemical Society.

Solvation Effects on Electronic Transitions: Exploring the Performance of Advanced Solvent Potentials in Polarizable Embedding Calculations.

Jacob Kongsted, Tobias Schwabe, Ove Christiansen, 2011, Journal of chemical theory and computation.

Excitation energies in solution: the fully polarizable QM/MM/PCM method.

Luca Frediani, Kenneth Ruud, Jacob Kongsted, 2011, The journal of physical chemistry. B.

The combined multiconfigurational self-consistent-field/molecular mechanics wave function approach

Kurt V. Mikkelsen, Jacob Kongsted, Peter R. Ogilby, 2001 .

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

Jacob Kongsted, Vasanthanathan Poongavanam, Vasanthanathan Poongavanam, 2016, Journal of molecular graphics & modelling.

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.

Jacob Kongsted, Casper Steinmann, Lars Andersen Bratholm, 2017, Journal of chemical theory and computation.

On the Accuracy of Density Functional Theory to Predict Shifts in Nuclear Magnetic Resonance Shielding Constants due to Hydrogen Bonding.

Jacob Kongsted, Kestutis Aidas, Stephan P A Sauer, 2008, Journal of chemical theory and computation.

Electronic Energy Transfer in Polarizable Heterogeneous Environments: A Systematic Investigation of Different Quantum Chemical Approaches.

Jacob Kongsted, Casper Steinmann, J. Kongsted, 2015, Journal of chemical theory and computation.

Color modeling of protein optical probes.

Jacob Kongsted, Zilvinas Rinkevicius, Hans Ågren, 2012, Physical chemistry chemical physics : PCCP.

Molecular design opportunities presented by solvent‐exposed regions of target proteins

Peng Zhan, Erik De Clercq, Yuning Song, 2019, Medicinal research reviews.

Embedding beyond electrostatics-The role of wave function confinement.

Daniel Wüstner, Jacob Kongsted, Lukasz M. Solanko, 2016, The Journal of chemical physics.

The role of molecular conformation and polarizable embedding for one- and two-photon absorption of disperse orange 3 in solution.

Sylvio Canuto, Jacob Kongsted, Zilvinas Rinkevicius, 2012, The journal of physical chemistry. B.

The Second-Order Polarization Propagator Approximation (SOPPA) method coupled to the polarizable continuum model

Daniel Wüstner, Jacob Kongsted, Lukasz M. Solanko, 2014 .

Nuclear magnetic shielding constants of liquid water: insights from hybrid quantum mechanics/molecular mechanics models.

Kenneth Ruud, Jacob Kongsted, Ove Christiansen, 2007, The Journal of chemical physics.

Scrutinizing the effects of polarization in QM/MM excited state calculations.

Jacob Kongsted, Tobias Schwabe, Ove Christiansen, 2011, Physical chemistry chemical physics : PCCP.