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  1. Article ; Online: A Brief Scientific Autobiography of Roland Lindh.

    Lindh, Roland

    The journal of physical chemistry. A

    2024  Volume 128, Issue 16, Page(s) 3049–3050

    Language English
    Publishing date 2024-04-25
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.4c01500
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Smooth Things Come in Threes: A Diabatic Surrogate Model for Conical Intersection Optimization.

    Fdez Galván, Ignacio / Lindh, Roland

    Journal of chemical theory and computation

    2023  Volume 19, Issue 11, Page(s) 3418–3427

    Abstract: The optimization of conical intersection structures is complicated by the nondifferentiability of the adiabatic potential energy surfaces. In this work, we build a pseudodiabatic surrogate model, based on Gaussian process regression, formed by three ... ...

    Abstract The optimization of conical intersection structures is complicated by the nondifferentiability of the adiabatic potential energy surfaces. In this work, we build a pseudodiabatic surrogate model, based on Gaussian process regression, formed by three smooth and differentiable surfaces that can adequately reproduce the adiabatic surfaces. Using this model with the restricted variance optimization method results in a notable decrease of the overall computational effort required to obtain minimum energy crossing points.
    Language English
    Publishing date 2023-05-16
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.3c00389
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: A Story of Three Levels of Sophistication in SCF/KS-DFT Orbital Optimization Procedures.

    Sethio, Daniel / Azzopardi, Emily / Fdez Galván, Ignacio / Lindh, Roland

    The journal of physical chemistry. A

    2024  Volume 128, Issue 12, Page(s) 2472–2486

    Abstract: In this work, three versions of self-consistent field/Kohn-Sham density functional theory (SCF/KS-DFT) orbital optimization are described and benchmarked. The methods are a modified version of the geometry version of the direct inversion in the iterative ...

    Abstract In this work, three versions of self-consistent field/Kohn-Sham density functional theory (SCF/KS-DFT) orbital optimization are described and benchmarked. The methods are a modified version of the geometry version of the direct inversion in the iterative subspace approach (which we call r-GDIIS), the modified restricted step rational function optimization method (RS-RFO), and the novel subspace gradient-enhanced Kriging method combined with restricted variance optimization (S-GEK/RVO). The modifications introduced are aimed at improving the robustness and computational scaling of the procedures. In particular, the subspace approach in S-GEK/RVO allows the application to SCF/KS-DFT optimization of a machine learning technique that has proven to be successful in geometry optimizations. The performance of the three methods is benchmarked for a large number of small- to medium-sized organic molecules, at equilibrium structures and close to a transition state, and a second set of molecules containing closed- and open-shell transition metals. The results indicate the importance of the resetting technique in boosting the performance of the r-GDIIS procedure. Moreover, it is demonstrated that already at the inception of the subspace version of GEK to optimize SCF wave functions, it displays superior and robust convergence properties as compared to those of the standard state-of-the-art SCF/KS-DFT optimization methods.
    Language English
    Publishing date 2024-03-14
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.3c07647
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: On the role of symmetry in XDW-CASPT2.

    Battaglia, Stefano / Lindh, Roland

    The Journal of chemical physics

    2021  Volume 154, Issue 3, Page(s) 34102

    Abstract: Herewith, we propose two new exponents for the recently introduced XDW-CASPT2 method [S. Battaglia and R. Lindh, J. Chem. Theory Comput. 16, 1555-1567 (2020)], which fix one of the largest issues hindering this approach. By using the first-order ... ...

    Abstract Herewith, we propose two new exponents for the recently introduced XDW-CASPT2 method [S. Battaglia and R. Lindh, J. Chem. Theory Comput. 16, 1555-1567 (2020)], which fix one of the largest issues hindering this approach. By using the first-order effective Hamiltonian coupling elements, the weighting scheme implicitly takes into account the symmetry of the states, thereby averaging Fock operators only if the zeroth-order wave functions interact with each other. The use of Hamiltonian couplings also provides a physically sounder approach to quantitate the relative weights; however, it introduces new difficulties when these rapidly die off to zero. The improved XDW-CASPT2 method is critically tested on several systems of photochemical relevance, and it is shown that it succeeds in its original intent of maintaining MS-CASPT2 accuracy for the evaluation of transition energies and at the same time providing smooth potential energy surfaces around near-degenerate points akin to XMS-CASPT2.
    Language English
    Publishing date 2021-01-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3113-6
    ISSN 1089-7690 ; 0021-9606
    ISSN (online) 1089-7690
    ISSN 0021-9606
    DOI 10.1063/5.0030944
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Bonn / Germany

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  5. Article ; Online: Analytic First-Order Derivatives of (X)MS, XDW, and RMS Variants of the CASPT2 and RASPT2 Methods.

    Nishimoto, Yoshio / Battaglia, Stefano / Lindh, Roland

    Journal of chemical theory and computation

    2022  Volume 18, Issue 7, Page(s) 4269–4281

    Abstract: Crossings between states involve complex electronic structures, making the accurate characterization of the crossing point difficult. In this study, the analytic derivatives of three complete active space second-order perturbation theory (CASPT2) ... ...

    Abstract Crossings between states involve complex electronic structures, making the accurate characterization of the crossing point difficult. In this study, the analytic derivatives of three complete active space second-order perturbation theory (CASPT2) variants as well as an extension of the restricted active space (RASPT2) are developed. These variants are applied to locating minimum energy conical intersections. Our results demonstrate that the three CASPT2 variants predict qualitatively similar results, but a recently developed variant, the rotated multistate CASPT2 (RMS-CASPT2), is least sensitive to the number of states considered in the calculation. We demonstrate that CASPT2 and the reference self-consistent field calculations predict qualitatively different energetics and bond lengths.
    MeSH term(s) Quantum Theory
    Language English
    Publishing date 2022-06-14
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.2c00301
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Extended Dynamically Weighted CASPT2: The Best of Two Worlds.

    Battaglia, Stefano / Lindh, Roland

    Journal of chemical theory and computation

    2020  Volume 16, Issue 3, Page(s) 1555–1567

    Abstract: We introduce a new variant of the complete active space second-order perturbation theory (CASPT2) method that performs similarly to multistate CASPT2 (MS-CASPT2) in regions of the potential energy surface where the electronic states are energetically ... ...

    Abstract We introduce a new variant of the complete active space second-order perturbation theory (CASPT2) method that performs similarly to multistate CASPT2 (MS-CASPT2) in regions of the potential energy surface where the electronic states are energetically well separated and is akin to extended MS-CASPT2 (XMS-CASPT2) in case the underlying zeroth-order references are near-degenerate. Our approach follows a recipe analogous to that of XMS-CASPT2 to ensure approximate invariance under unitary transformations of the model states and a dynamic weighting scheme to smoothly interpolate the Fock operator between state-specific and state-average regimes. The resulting extended dynamically weighted CASPT2 (XDW-CASPT2) methodology possesses the most desirable features of both MS-CASPT2 and XMS-CASPT2, that is, the ability to provide accurate transition energies and correctly describe avoided crossings and conical intersections. The reliability of XDW-CASPT2 is assessed on a number of molecular systems. First, we consider the dissociation of lithium fluoride, highlighting the distinctive characteristics of the new approach. Second, the invariance of the theory is investigated by studying the conical intersection of the distorted allene molecule. Finally, the relative accuracy in the calculation of vertical excitation energies is benchmarked on a set of 26 organic compounds. We found that XDW-CASPT2, albeit being only approximately invariant, produces smooth potential energy surfaces around conical intersections and avoided crossings, performing equally well to the strictly invariant XMS-CASPT2 method. The accuracy of vertical transition energies is almost identical to MS-CASPT2, with a mean absolute deviation of 0.01-0.02 eV, in contrast to 0.12 eV for XMS-CASPT2.
    Language English
    Publishing date 2020-02-21
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.9b01129
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Regularized CASPT2: an Intruder-State-Free Approach.

    Battaglia, Stefano / Fransén, Lina / Fdez Galván, Ignacio / Lindh, Roland

    Journal of chemical theory and computation

    2022  Volume 18, Issue 8, Page(s) 4814–4825

    Abstract: In this work we present a new approach to fix the intruder-state problem (ISP) in CASPT2 based on ... ...

    Abstract In this work we present a new approach to fix the intruder-state problem (ISP) in CASPT2 based on σ
    Language English
    Publishing date 2022-07-25
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.2c00368
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Minimum-Energy Conical Intersections by Compressed Multistate Pair-Density Functional Theory.

    Calio, Paul B / Hermes, Matthew R / Bao, Jie J / Galván, Ignacio Fdez / Lindh, Roland / Truhlar, Donald G / Gagliardi, Laura

    The journal of physical chemistry. A

    2024  Volume 128, Issue 9, Page(s) 1698–1706

    Abstract: Compressed multistate pair-density functional theory (CMS-PDFT) is a multistate version of multiconfiguration pair-density functional theory that can capture the correct topology of coupled potential energy surfaces (PESs) around conical intersections. ... ...

    Abstract Compressed multistate pair-density functional theory (CMS-PDFT) is a multistate version of multiconfiguration pair-density functional theory that can capture the correct topology of coupled potential energy surfaces (PESs) around conical intersections. In this work, we develop interstate coupling vectors (ISCs) for CMS-PDFT in the
    Language English
    Publishing date 2024-02-26
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.3c07048
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Restricted-Variance Constrained, Reaction Path, and Transition State Molecular Optimizations Using Gradient-Enhanced Kriging.

    Fdez Galván, Ignacio / Raggi, Gerardo / Lindh, Roland

    Journal of chemical theory and computation

    2020  Volume 17, Issue 1, Page(s) 571–582

    Abstract: Gaussian process regression has recently been explored as an alternative to standard surrogate models in molecular equilibrium geometry optimization. In particular, the gradient-enhanced Kriging approach in association with internal coordinates, ... ...

    Abstract Gaussian process regression has recently been explored as an alternative to standard surrogate models in molecular equilibrium geometry optimization. In particular, the gradient-enhanced Kriging approach in association with internal coordinates, restricted-variance optimization, and an efficient and fast estimate of hyperparameters has demonstrated performance on par or better than standard methods. In this report, we extend the approach to constrained optimizations and transition states and benchmark it for a set of reactions. We compare the performance of the newly developed method with the standard techniques in the location of transition states and in constrained optimizations, both isolated and in the context of reaction path computation. The results show that the method outperforms the current standard in efficiency as well as in robustness.
    Language English
    Publishing date 2020-12-31
    Publishing country United States
    Document type Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.0c01163
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  10. Article ; Online: Unravelling the mechanism of pH-regulation in dinoflagellate luciferase.

    Kamerlin, Natasha / Delcey, Mickaël G / Lindh, Roland

    International journal of biological macromolecules

    2020  Volume 164, Page(s) 2671–2680

    Abstract: Dinoflagellates are the dominant source of bioluminescence in coastal waters. The luminescence reaction involves the oxidation of luciferin by a luciferase enzyme, which only takes place at low pH. The pH-dependence has previously been linked to four ... ...

    Abstract Dinoflagellates are the dominant source of bioluminescence in coastal waters. The luminescence reaction involves the oxidation of luciferin by a luciferase enzyme, which only takes place at low pH. The pH-dependence has previously been linked to four conserved histidines. It has been suggested that their protonation might induce a conformational change in the enzyme, thereby allowing substrate access to the binding pocket. Yet, the precise mechanism of luciferase activation has remained elusive. Here, we use computational tools to predict the open structure of the luciferase in Lingulodinium polyedra and to decipher the nature of the opening mechanism. Through accelerated molecular dynamics simulations, we demonstrate that the closed-open conformational change likely takes place via a tilt of the pH-regulatory helix-loop-helix domain. Moreover, we propose that the molecular basis for the transition is electrostatic repulsion between histidine-cation pairs, which destabilizes the closed conformation at low pH. Finally, by simulating truncated mutants, we show that eliminating the C-terminus alters the shape of the active site, effectively inactivating the luciferase.
    MeSH term(s) Dinoflagellida/chemistry ; Dinoflagellida/enzymology ; Dinoflagellida/genetics ; Hydrogen-Ion Concentration ; Luciferases/chemistry ; Luciferases/genetics ; Luciferases/metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Mutation ; Protein Conformation ; Protein Domains ; Protozoan Proteins/chemistry ; Protozoan Proteins/metabolism
    Chemical Substances Protozoan Proteins ; Luciferases (EC 1.13.12.-)
    Language English
    Publishing date 2020-08-19
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2020.08.071
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    In stock of ZB MED Cologne/Königswinter

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