Journal: Journal of Chemical Theory and Computation

Abbreviation

J Chem Theory Comput

Publisher

American Chemical Society

Journal Volumes

ISSN

1549-9618
1549-9626

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Publications 1 - 10 of 200
  • Relaxation Matrix Analysis of Spin Diffusion for the NMR Structure Calculation with eNOEs
    Item type: Journal Article
    Orts, Julien; Vögeli, Beat; Riek, Roland (2012)
    Journal of Chemical Theory and Computation
  • A Nonorthogonal State-Interaction Approach for Matrix Product State Wave Functions
    Item type: Journal Article
    Knecht, Stefan; Keller, Sebastian; Autschbach, Jochen; et al. (2016)
    Journal of Chemical Theory and Computation
  • Explicitly Correlated Electronic Structure Calculations with Transcorrelated Matrix Product Operators
    Item type: Journal Article
    Baiardi, Alberto; Lesiuk, Michal; Reiher, Markus (2022)
    Journal of Chemical Theory and Computation
    In this work, we present the first implementation of the transcorrelated electronic Hamiltonian in an optimization procedure for matrix product states by the density matrix renormalization group (DMRG) algorithm. In the transcorrelation ansatz, the electronic Hamiltonian is similarity-transformed with a Jastrow factor to describe the cusp in the wave function at electron-electron coalescence. As a result, the wave function is easier to approximate accurately with the conventional expansion in terms of one-particle basis functions and Slater determinants. The transcorrelated Hamiltonian in first quantization comprises up to three-body interactions, which we deal with in the standard way by applying robust density fitting to two- and three-body integrals entering the second-quantized representation of this Hamiltonian. The lack of hermiticity of the transcorrelated Hamiltonian is taken care of along the lines of the first work on transcorrelated DMRG [J. Chem. Phys. 2020, 153, 164115] by encoding it as a matrix product operator and optimizing the corresponding ground state wave function with imaginary-time time-dependent DMRG. We demonstrate our quantum chemical transcorrelated DMRG approach at the example of several atoms and first-row diatomic molecules. We show that transcorrelation improves the convergence rate to the complete basis set limit in comparison to conventional DMRG. Moreover, we study extensions of our approach that aim at reducing the cost of handling the matrix product operator representation of the transcorrelated Hamiltonian.
  • The Role of Force Fields and Water Models in Protein Folding and Unfolding Dynamics
    Item type: Journal Article
    Fischer, Anna-Lena M.; Tichy, Anna; Kokot, Janik; et al. (2024)
    Journal of Chemical Theory and Computation
    Protein folding is a fascinating, not fully understood phenomenon in biology. Molecular dynamics (MD) simulations are an invaluable tool to study conformational changes in atomistic detail, including folding and unfolding processes of proteins. However, the accuracy of the conformational ensembles derived from MD simulations inevitably relies on the quality of the underlying force field in combination with the respective water model. Here, we investigate protein folding, unfolding, and misfolding of fast-folding proteins by examining different force fields with their recommended water models, i.e., ff14SB with the TIP3P model and ff19SB with the OPC model. To this end, we generated long conventional MD simulations highlighting the perks and pitfalls of these setups. Using Markov state models, we defined kinetically independent conformational substates and emphasized their distinct characteristics, as well as their corresponding state probabilities. Surprisingly, we found substantial differences in thermodynamics and kinetics of protein folding, depending on the combination of the protein force field and water model, originating primarily from the different water models. These results emphasize the importance of carefully choosing the force field and the respective water model as they determine the accuracy of the observed dynamics of folding events. Thus, the findings support the hypothesis that the water model is at least equally important as the force field and hence needs to be considered in future studies investigating protein dynamics and folding in all areas of biophysics.
  • A novel Hamiltonian replica exchange MD protocol to enhance protein conformational space sampling
    Item type: Journal Article
    Affentranger, Roman; Tavernelli, Ivano; Iorio, Ernesto E. Di (2006)
    Journal of Chemical Theory and Computation
  • Alchemical Free-Energy Calculations by Multiple-Replica -Dynamics: The Conveyor Belt Thermodynamic Integration Scheme
    Item type: Journal Article
    Hahn, David F.; Hünenberger, Philippe H. (2019)
    Journal of Chemical Theory and Computation
  • An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles
    Item type: Journal Article
    Keller, Bettina; Hünenberger, Philippe H.; van Gunsteren, Wilfred F. (2011)
    Journal of Chemical Theory and Computation
  • Solvation Free Energies in Subsystem Density Functional Theory
    Item type: Journal Article
    Bensberg, Moritz; Türtscher, Paul Lorenz; Unsleber, Jan Patrick; et al. (2022)
    Journal of Chemical Theory and Computation
    For many chemical processes the accurate description of solvent effects are vitally important. Here, we describe a hybrid ansatz for the explicit quantum mechanical description of solute-solvent and solvent-solvent interactions based on subsystem density functional theory and continuum solvation schemes. Since explicit solvent molecules may compromise the scalability of the model and transferability of the predicted solvent effect, we aim to retain both, for different solutes as well as for different solvents. The key for the transferability is the consistent subsystem decomposition of solute and solvent. The key for the scalability is the performance of subsystem DFT for increasing numbers of subsystems. We investigate molecular dynamics and stationary point sampling of solvent configurations and compare the resulting (Gibbs) free energies to experiment and theoretical methods. We can show that with our hybrid model reaction barriers and reaction energies are accurately reproduced compared to experimental data.
  • Hydrolysis of the Anticancer Drug Cisplatin:  Pitfalls in the Interpretation of Quantum Chemical Calculations
    Item type: Journal Article
    Lau, Justin Kai-Chi; Deubel, Dirk V. (2006)
    Journal of Chemical Theory and Computation
  • Path Integral Metadynamics
    Item type: Journal Article
    Quhe, Ruge; Nava, Marco; Tiwary, Pratyush; et al. (2015)
    Journal of Chemical Theory and Computation
Publications 1 - 10 of 200