Journal of Chemical Theory and Computation, 1549-9618

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  1. 2019
  2. Temperature Dependence of Intrinsically Disordered Proteins in Simulations: What are We Missing?

    S. Jephthah, Staby, L., Kragelund, B. B. & M. Skepö, 2019, In : Journal of Chemical Theory and Computation. 15, 4, p. 2672-2683 12 p.

    Research output: Contribution to journalArticle

  3. 2018
  4. Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations

    Wang, M., Mei, Y. & Ulf Ryde, 2018 Oct 26, In : Journal of Chemical Theory and Computation. 14, p. 6613 6622 p.

    Research output: Contribution to journalArticle

  5. Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations

    Ulf Ryde, Olsson, M. & Steinmann, C., 2018 May 17, In : Journal of Chemical Theory and Computation. 14, p. 3228 3237 p.

    Research output: Contribution to journalArticle

  6. 2017
  7. Relativistic Polarizable Embedding

    Erik Donovan Hedegård, Bast, R., Kongsted, J., Olsen, J. M. H. & Jensen, H. J. A., 2017 Jun 13, In : Journal of Chemical Theory and Computation. 13, 6, p. 2870-2880 11 p.

    Research output: Contribution to journalArticle

  8. Comparison of QM/MM Methods To Obtain Ligand-Binding Free Energies

    Olsson, M. A. & Ulf Ryde, 2017 May 9, In : Journal of Chemical Theory and Computation. 13, 5, p. 2245-2253 9 p.

    Research output: Contribution to journalArticle

  9. Optimized long-range corrected density functionals for electronic and optical properties of bare and ligated CdSe quantum dots

    Bokareva, O. S., Shibl, M. F., Al-Marri, M. J., T. Pullerits & Kühn, O., 2017, In : Journal of Chemical Theory and Computation. 13, 1, p. 110-116 7 p.

    Research output: Contribution to journalArticle

  10. 2016
  11. Does the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems?

    Fouda, A. & Ulf Ryde, 2016 Nov 8, In : Journal of Chemical Theory and Computation. 12, 11, p. 5667-5679 13 p.

    Research output: Contribution to journalArticle

  12. Method for Slater-Type Density Fitting for Intermolecular Electrostatic Interactions with Charge Overlap. I. the Model

    Öhrn, A., Hermida-Ramon, J. M. & Gunnar Karlström, 2016 May 10, In : Journal of Chemical Theory and Computation. 12, 5, p. 2298-2311 14 p.

    Research output: Contribution to journalArticle

  13. Optimal Displacement Parameters in Monte Carlo Simulations

    Hebbeker, P., Linse, P. & Schneider, S., 2016 Apr 12, In : Journal of Chemical Theory and Computation. 12, 4, p. 1459-1465 7 p.

    Research output: Contribution to journalArticle

  14. 2015
  15. Molecular Dynamics Simulations and Neutron Reflectivity as an Effective Approach To Characterize Biological Membranes and Related Macromolecular Assemblies

    Darre, L., Iglesias-Fernandez, J., Kohlmeyer, A., Hanna Wacklin & Domene, C., 2015, In : Journal of Chemical Theory and Computation. 11, 10, p. 4875-4884

    Research output: Contribution to journalArticle

  16. 2014
  17. Robust Estimation of Diffusion-Optimized Ensembles for Enhanced Sampling

    Tian, P., Jonsson, S., Ferkinghoff-Borg, J., Krivov, S. V., Lindorff-Larsen, K., Anders Irbäck & Boomsma, W., 2014, In : Journal of Chemical Theory and Computation. 10, 2, p. 543-553

    Research output: Contribution to journalArticle

  18. 2013
  19. Analytical Gradients of Hartree-Fock Exchange with Density Fitting Approximations

    Boström, J., Aquilante, F., Pedersen, T. B. & Lindh, R., 2013, In : Journal of Chemical Theory and Computation. 9, 1, p. 204-212

    Research output: Contribution to journalArticle

  20. Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction

    Li, J., Mata, R. A. & Ulf Ryde, 2013, In : Journal of Chemical Theory and Computation. 9, 3, p. 1799-1807

    Research output: Contribution to journalArticle

  21. Understanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins

    Van Severen, M-C., Ulf Ryde, Parisel, O. & Piquernal, J-P., 2013, In : Journal of Chemical Theory and Computation. 9, 5, p. 2416-2424

    Research output: Contribution to journalArticle

  22. 2012
  23. Coupled Cluster and Moller-Plesset Perturbation Theory Calculations of Noncovalent Intermolecular Interactions using Density Fitting with Auxiliary Basis Sets from Cholesky Decompositions

    Boström, J., Pitonak, M., Aquilante, F., Neogrady, P., Pedersen, T. B. & Lindh, R., 2012, In : Journal of Chemical Theory and Computation. 8, 6, p. 1921-1928

    Research output: Contribution to journalArticle

  24. Improving the Efficiency of Protein-Ligand Binding Free-Energy Calculations by System Truncation

    Genheden, S. & Ulf Ryde, 2012, In : Journal of Chemical Theory and Computation. 8, 4, p. 1449-1458

    Research output: Contribution to journalArticle

  25. Subtle Monte Carlo Updates in Dense Molecular Systems

    Bottaro, S., Boomsma, W., Johansson, K. E., Andreetta, C., Hamelryck, T. & Ferkinghoff-Borg, J., 2012, In : Journal of Chemical Theory and Computation. 8, 2, p. 695-702

    Research output: Contribution to journalArticle

  26. 2011
  27. Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

    Hu, L. & Ulf Ryde, 2011, In : Journal of Chemical Theory and Computation. 7, 8, p. 2452-2463

    Research output: Contribution to journalArticle

  28. Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies

    Genheden, S. & Ulf Ryde, 2011, In : Journal of Chemical Theory and Computation. 7, 11, p. 3768-3778

    Research output: Contribution to journalArticle

  29. Conformational Dependence of Isotropic Polarizabilities

    Pär Söderhjelm, Kongsted, J. & Ulf Ryde, 2011, In : Journal of Chemical Theory and Computation. 7, 5, p. 1404-1414

    Research output: Contribution to journalArticle

  30. On the Convergence of QM/MM Energies

    Hu, L., Soederhjelm, P. & Ulf Ryde, 2011, In : Journal of Chemical Theory and Computation. 7, 3, p. 761-777

    Research output: Contribution to journalArticle

  31. 2010
  32. Calibration of Cholesky Auxiliary Basis Sets for Multiconfigurational Perturbation Theory Calculations of Excitation Energies

    Boström, J., Delcey, M., Aquilante, F., Serrano-Andres, L., Pedersen, T. B. & Lindh, R., 2010, In : Journal of Chemical Theory and Computation. 6, 3, p. 747-754

    Research output: Contribution to journalArticle

  33. Fast Proton Titration Scheme for Multiscale Modeling of Protein Solutions

    Reis Teixeira, A. A., Mikael Lund & Barroso da Silva, F. L., 2010, In : Journal of Chemical Theory and Computation. 6, 10, p. 3259-3266

    Research output: Contribution to journalArticle

  34. Ligand affinities estimated by quantum chemical calculations

    Pär Söderhjelm, Kongsted, J. & Ulf Ryde, 2010, In : Journal of Chemical Theory and Computation. 6, 5, p. 1726-1737

    Research output: Contribution to journalArticle

  35. Nonpolar Solvation Free Energies of Protein-Ligand Complexes

    Genheden, S., Kongsted, J., Pär Söderhjelm & Ulf Ryde, 2010, In : Journal of Chemical Theory and Computation. 6, 11, p. 3558-3568

    Research output: Contribution to journalArticle

  36. Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations

    Genheden, S., Diehl, C., Mikael Akke & Ulf Ryde, 2010, In : Journal of Chemical Theory and Computation. 6, 7, p. 2176-2190

    Research output: Contribution to journalArticle

  37. 2009
  38. Ab Initio Density Fitting: Accuracy Assessment of Auxiliary Basis Sets from Cholesky Decompositions

    Boström, J., Aquilante, F., Bondo Pedersen, T. & Lindh, R., 2009, In : Journal of Chemical Theory and Computation. 5, 6, p. 1545-1553

    Research output: Contribution to journalArticle

  39. Location of Two Seams in the Proximity of the C-2v pi pi Minimum Energy Path of Formaldehyde

    De Vico, L. & Lindh, R., 2009, In : Journal of Chemical Theory and Computation. 5, 1, p. 186-191

    Research output: Contribution to journalArticle

  40. Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities

    Pär Söderhjelm, Husberg, C., Strambi, A., Olivucci, M. & Ulf Ryde, 2009, In : Journal of Chemical Theory and Computation. 5, 3, p. 649-658

    Research output: Contribution to journalArticle

  41. 2008
  42. Embedding fragment ab initio model potentials in CASSCF/CASPT2 calculations of doped solids: Implementation and applications

    Swerts, B., Chibotaru, L. F., Lindh, R., Seijo, L., Barandiaran, Z., Clima, S., Pierloot, K. & Hendrickx, M. F. A., 2008, In : Journal of Chemical Theory and Computation. 4, 4, p. 586-594

    Research output: Contribution to journalArticle

  43. On the accuracy of density functional theory to predict shifts in nuclear magnetic resonance shielding constants due to hydrogen bonding

    Kongsted, J., Aidas, K., Mikkelsen, K. V. & Sauer, S. P. A., 2008, In : Journal of Chemical Theory and Computation. 4, 2, p. 267-277

    Research output: Contribution to journalArticle

  44. Proton transfer at metal sites in proteins studied by quantum mechanical free-energy perturbations

    Kaukonen, M., Pär Söderhjelm, Heimdal, J. & Ulf Ryde, 2008, In : Journal of Chemical Theory and Computation. 4, 6, p. 985-1001

    Research output: Contribution to journalArticle

  45. Sulfoxide, sulfur, and nitrogen oxidation and dealkylation by cytochrome P450

    Rydberg, P., Ulf Ryde & Olsen, L., 2008, In : Journal of Chemical Theory and Computation. 4, 8, p. 1369-1377

    Research output: Contribution to journalArticle

  46. Transition-state docking of flunitrazepam and progesterone in cytochrome P450

    Rydberg, P., Hansen, S. M., Kongsted, J., Norrby, P-O., Olsen, L. & Ulf Ryde, 2008, In : Journal of Chemical Theory and Computation. 4, 4, p. 673-681

    Research output: Contribution to journalArticle

  47. 2007
  48. General transition-state force field for cytochrome p450 Hydroxylation

    Rydberg, P., Olsen, L., Norrby, P-O. & Ulf Ryde, 2007, In : Journal of Chemical Theory and Computation. 3, 5, p. 1765-1773

    Research output: Contribution to journalArticle

  49. Many-body polarization, a cause of asymmetric solvation of ions and quadrupoles

    Öhrn, A. & Gunnar Karlström, 2007, In : Journal of Chemical Theory and Computation. 3, 6, p. 1993-2001

    Research output: Contribution to journalArticle

  50. 2006
  51. Quantum Chemical Study of the Influence of Anchor-Cum-Spacer Groups on Femtosecond Electron Transfer Times in Dye-Sensitized Semiconductor Nanocrystals

    Petter Persson, Lundqvist, M. J., Ernstorfer, R., Goddard III, W. A. & Willig, F., 2006, In : Journal of Chemical Theory and Computation. 2, 2, p. 441-451

    Research output: Contribution to journalArticle

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