Journal of Chemical Theory and Computation, 1549-9618

Tidskrift

Fler filtreringsmöjligheter
  1. 2019
  2. Host-Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations

    Wang, M., Mei, Y. & Ulf Ryde, 2019, I : Journal of Chemical Theory and Computation. 15, 4, s. 2659-2671

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  3. Temperature Dependence of Intrinsically Disordered Proteins in Simulations: What are We Missing?

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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

    Wang, M., Mei, Y. & Ulf Ryde, 2018 okt 26, I : Journal of Chemical Theory and Computation. 14, s. 6613 6622 s.

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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

    Ulf Ryde, Olsson, M. & Steinmann, C., 2018 maj 17, I : Journal of Chemical Theory and Computation. 14, s. 3228 3237 s.

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  7. 2017
  8. How Many Conformations Need to Be Sampled to Obtain Converged QM/MM Energies? the Curse of Exponential Averaging

    Ulf Ryde, 2017 nov 14, I : Journal of Chemical Theory and Computation. 13, 11, s. 5745-5752 8 s.

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  9. Relativistic Polarizable Embedding

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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

    Olsson, M. A. & Ulf Ryde, 2017 maj 9, I : Journal of Chemical Theory and Computation. 13, 5, s. 2245-2253 9 s.

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  11. 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, I : Journal of Chemical Theory and Computation. 13, 1, s. 110-116 7 s.

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  12. 2016
  13. Does the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems?

    Fouda, A. & Ulf Ryde, 2016 nov 8, I : Journal of Chemical Theory and Computation. 12, 11, s. 5667-5679 13 s.

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  14. 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 maj 10, I : Journal of Chemical Theory and Computation. 12, 5, s. 2298-2311 14 s.

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  15. Optimal Displacement Parameters in Monte Carlo Simulations

    Hebbeker, P., Linse, P. & Schneider, S., 2016 apr 12, I : Journal of Chemical Theory and Computation. 12, 4, s. 1459-1465 7 s.

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  16. Potential Energy Surface of the Chromium Dimer Re-re-revisited with Multiconfigurational Perturbation Theory

    Vancoillie, S., Per-Åke Malmqvist & Valera Veryazov, 2016, I : Journal of Chemical Theory and Computation. 12, 4, s. 1647–1655

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  17. 2015
  18. 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, I : Journal of Chemical Theory and Computation. 11, 10, s. 4875-4884

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  19. Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment

    Henriques, J., Cragnell, C. & Marie Skepö, 2015, I : Journal of Chemical Theory and Computation. 11, 7, s. 3420-3431

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  20. 2014
  21. Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability

    Genheden, S., Mikael Akke & Ulf Ryde, 2014, I : Journal of Chemical Theory and Computation. 10, 1, s. 432-438

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  22. 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, I : Journal of Chemical Theory and Computation. 10, 2, s. 543-553

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  23. 2013
  24. Accurate reaction energies in proteins obtained by combining QM/MM and large QM calculations

    Hu, L., Pär Söderhjelm & Ulf Ryde, 2013, I : Journal of Chemical Theory and Computation. 9, s. 640-649

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  25. Analysis of Protein Dynamics Simulations by a Stochastic Point Process Approach

    Bertil Halle & Filip Persson, 2013, I : Journal of Chemical Theory and Computation. 9, 6, s. 2838-2848

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  26. Analytical Gradients of Hartree-Fock Exchange with Density Fitting Approximations

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  27. Effect of geometry optimisations on QM-cluster and QM/MM studies of reaction energies in proteins

    Sumner, S., Pär Söderhjelm & Ulf Ryde, 2013, I : Journal of Chemical Theory and Computation. 9, 9, s. 4205-4214

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  29. 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, I : Journal of Chemical Theory and Computation. 9, 5, s. 2416-2424

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  30. 2012
  31. 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, I : Journal of Chemical Theory and Computation. 8, 6, s. 1921-1928

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  33. Subtle Monte Carlo Updates in Dense Molecular Systems

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  34. 2011
  35. Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  37. Conformational Dependence of Isotropic Polarizabilities

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  38. On the Convergence of QM/MM Energies

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  39. Structural Anisotropy in Polar Fluids Subjected to Periodic Boundary Conditions

    Joakim Stenhammar, Gunnar Karlström & Linse, P., 2011, I : Journal of Chemical Theory and Computation. 7, 12, s. 4165-4174

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  40. 2010
  41. 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, I : Journal of Chemical Theory and Computation. 6, 3, s. 747-754

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  43. Ligand affinities estimated by quantum chemical calculations

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  44. Nonpolar Solvation Free Energies of Protein-Ligand Complexes

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  46. 2009
  47. Ab Initio Density Fitting: Accuracy Assessment of Auxiliary Basis Sets from Cholesky Decompositions

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  50. 2008
  51. Cholesky decomposition-based multiconfiguration second-order perturbation theory (CD-CASPT2): Application to the spin-state energetics of Co-III(diiminato)(NPh)

    Aquilante, F., Per-Åke Malmqvist, Pedersen, T., Ghosh, A. & Roos, B., 2008, I : Journal of Chemical Theory and Computation. 4, 5, s. 694-702

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  52. 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, I : Journal of Chemical Theory and Computation. 4, 4, s. 586-594

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  53. 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, I : Journal of Chemical Theory and Computation. 4, 2, s. 267-277

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  56. 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, I : Journal of Chemical Theory and Computation. 4, 4, s. 673-681

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  57. 2007
  58. General transition-state force field for cytochrome p450 Hydroxylation

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

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

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

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  60. 2006
  61. 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, I : Journal of Chemical Theory and Computation. 2, 2, s. 441-451

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  62. 2005
  63. Accurate QM/MM free energy calculations of enzyme reactions: Methylation by catechol O-methyltransferase

    Rod, T. & Ulf Ryde, 2005, I : Journal of Chemical Theory and Computation. 1, 6, s. 1240-1251

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

  64. New general tools for constrained geometry optimizations

    De Vico, L., Olivucci, M. & Lindh, R., 2005, I : Journal of Chemical Theory and Computation. 1, 5, s. 1029-1037

    Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift