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Lindh, Roland, ProfessorORCID iD iconorcid.org/0000-0001-7567-8295
Publications (10 of 197) Show all publications
Sankari, A., Stråhlman, C., Sankari, R., Partanen, L., Laksman, J., Kettunen, J. A., . . . Sorensen, S. L. (2020). Non-radiative decay and fragmentation in water molecules after 1a1-14a1 excitation and core ionization studied by [electron-energy-resolved electron–ion coincidence spectroscopy. Journal of Chemical Physics, 152(7), Article ID 074302.
Open this publication in new window or tab >>Non-radiative decay and fragmentation in water molecules after 1a1-14a1 excitation and core ionization studied by [electron-energy-resolved electron–ion coincidence spectroscopy
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2020 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 152, no 7, article id 074302Article in journal (Refereed) Published
National Category
Theoretical Chemistry Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-404397 (URN)10.1063/1.5141414 (DOI)
Available from: 2020-02-19 Created: 2020-02-19 Last updated: 2020-03-09Bibliographically approved
Li, C., Lindh, R. & Evangelista, F. A. (2019). Dynamically weighted multireference perturbation theory: Combining the advantages of multi-state and state-averaged methods. Journal of Chemical Physics, 150(14), Article ID 144107.
Open this publication in new window or tab >>Dynamically weighted multireference perturbation theory: Combining the advantages of multi-state and state-averaged methods
2019 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 14, article id 144107Article in journal (Refereed) Published
Abstract [en]

We introduce two new approaches to compute near-degenerate electronic states based on the driven similarity renormalization group (DSRG) framework. The first approach is a unitary multi-state formalism based on the DSRG (MS-DSRG), whereby an effective Hamiltonian is built from a set of state-specific solutions. The second approach employs a dynamic weighting parameter to smoothly interpolate between the multi-state and the state-averaged DSRG schemes. The resulting dynamically weighted DSRG (DW-DSRG) theory incorporates the most desirable features of both multi-state approaches (ability to accurately treat many states) and state-averaged methods (correct description of avoided crossings and conical intersections). We formulate second-order perturbation theories (PT2) based on the MS-and DW-DSRG and study the potential energy curves of LiF, the conical intersection of the two lowest singlet states of NH3, and several low-lying excited states of benzene, naphthalene, and anthracene. The DW-DSRG-PT2 predicts the correct avoided crossing of LiF and avoids artifacts produced by the corresponding state-specific and multi-state theories. Excitation energies of the acenes computed with the DW-DSRG-PT2 are found to be more accurate than the corresponding state-averaged values, showing a small dependence on the number of states computed.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-382850 (URN)10.1063/1.5088120 (DOI)000464451300010 ()30981256 (PubMedID)
Funder
Swedish Research Council, 2016-03398Wenner-Gren Foundations
Available from: 2019-05-22 Created: 2019-05-22 Last updated: 2019-05-22Bibliographically approved
Guo, M., Källman, E., Pinjari, R. V., Couto, R. C., Sörensen, L. K., Lindh, R., . . . Lundberg, M. (2019). Fingerprinting Electronic Structure of Heme Iron by Ab Initio Modeling of Metal L-Edge X-ray Absorption Spectra. Journal of Chemical Theory and Computation, 15(1), 477-489
Open this publication in new window or tab >>Fingerprinting Electronic Structure of Heme Iron by Ab Initio Modeling of Metal L-Edge X-ray Absorption Spectra
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2019 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, no 1, p. 477-489Article in journal (Refereed) Published
Abstract [en]

The capability of the multiconfigurational restricted active space approach to identify electronic structure from spectral fingerprints is explored by applying it to iron L-edge X-ray absorption spectroscopy (XAS) of three heme systems that represent the limiting descriptions of iron in the Fe-O-2 bond, ferrous and ferric [Fe(P)(ImH)(2)](0/1+) (P = porphine, ImH = imidazole), and Fe-II(P). The level of agreement between experimental and simulated spectral shapes is calculated using the cosine similarity, which gives a quantitative and unbiased assignment. Further dimensions in fingerprinting are obtained from the L-edge branching ratio, the integrated absorption intensity, and the edge position. The results show how accurate ab initio simulations of metal L-edge XAS can complement calculations of relative energies to identify unknown species in chemical reactions.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-375846 (URN)10.1021/acs.jctc.8b00658 (DOI)000455558200043 ()30513204 (PubMedID)
Funder
Swedish Research Council, 2012-3924Swedish Research Council, 2016-03398Knut and Alice Wallenberg Foundation, KAW-2013.0020Carl Tryggers foundation Swedish National Infrastructure for Computing (SNIC), snic2016-1-464
Available from: 2019-02-01 Created: 2019-02-01 Last updated: 2019-02-01Bibliographically approved
Häse, F., Fernández Galván, I., Aspuru-Guzik, A., Lindh, R. & Vacher, M. (2019). How machine learning can assist the interpretation of ab initio molecular dynamics simulations and conceptual understanding of chemistry. Chemical Science, 10(8), 2298-2307
Open this publication in new window or tab >>How machine learning can assist the interpretation of ab initio molecular dynamics simulations and conceptual understanding of chemistry
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2019 (English)In: Chemical Science, ISSN 2041-6520, Vol. 10, no 8, p. 2298-2307Article in journal (Refereed) Published
Abstract [en]

Molecular dynamics simulations are often key to the understanding of the mechanism, rate and yield of chemical reactions. One current challenge is the in-depth analysis of the large amount of data produced by the simulations, in order to produce valuable insight and general trends. In the present study, we propose to employ recent machine learning analysis tools to extract relevant information from simulation data without a priori knowledge on chemical reactions. This is demonstrated by training machine learning models to predict directly a specific outcome quantity of ab initio molecular dynamics simulations - the timescale of the decomposition of 1,2-dioxetane. The machine learning models accurately reproduce the dissociation time of the compound. Keeping the aim of gaining physical insight, it is demonstrated that, in order to make accurate predictions, the models evidence empirical rules that are, today, part of the common chemical knowledge. This opens the way for conceptual breakthroughs in chemistry where machine analysis would provide a source of inspiration to humans.

Place, publisher, year, edition, pages
The Royal Society of Chemistry, 2019
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-372043 (URN)10.1039/C8SC04516J (DOI)000459331200004 ()
Funder
Swedish Research Council, 2016-03398
Available from: 2019-01-04 Created: 2019-01-04 Last updated: 2019-08-01Bibliographically approved
Sørensen, L. K., Kieri, E., Srivastav, S., Lundberg, M. & Lindh, R. (2019). Implementation of a semiclassical light-matter interaction using the Gauss–Hermite quadrature: A simple alternative to the multipole expansion. Physical Review A: covering atomic, molecular, and optical physics and quantum information, 99(1), Article ID 013419.
Open this publication in new window or tab >>Implementation of a semiclassical light-matter interaction using the Gauss–Hermite quadrature: A simple alternative to the multipole expansion
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2019 (English)In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 99, no 1, article id 013419Article in journal (Refereed) Published
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-375867 (URN)10.1103/PhysRevA.99.013419 (DOI)000455815000010 ()
Available from: 2019-01-16 Created: 2019-02-04 Last updated: 2019-02-14Bibliographically approved
Giussani, A., Farahani, P., Martinez-Muñoz, D., Lundberg, M., Lindh, R. & Roca-Sanjuan, D. (2019). Molecular Basis of the Chemiluminescence Mechanism of Luminol. Chemistry - A European Journal, 25(20), 5202-5213
Open this publication in new window or tab >>Molecular Basis of the Chemiluminescence Mechanism of Luminol
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2019 (English)In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 25, no 20, p. 5202-5213Article in journal (Refereed) Published
Abstract [en]

Light emission from luminol is probably one of the most popular chemiluminescence reactions due to its use in forensic science, and has recently displayed promising applications for the treatment of cancer in deep tissues. The mechanism is, however, very complex and distinct possibilities have been proposed. By efficiently combining DFT and CASPT2 methodologies, the chemiluminescence mechanism has been studied in three steps: 1)luminol oxygenation to generate the chemiluminophore, 2)a chemiexcitation step, and 3)generation of the light emitter. The findings demonstrate that the luminol double-deprotonated dianion activates molecular oxygen, diazaquinone is not formed, and the chemiluminophore is formed through the concerted addition of oxygen and concerted elimination of nitrogen. The peroxide bond, in comparison to other isoelectronic chemical functionalities (-NH-NH-, -N--N--, and -S-S-), is found to have the best chemiexcitation efficiency, which allows the oxygenation requirement to be rationalized and establishes general design principles for the chemiluminescence efficiency. Electron transfer from the aniline ring to the OO bond promotes the excitation process to create an excited state that is not the chemiluminescent species. To produce the light emitter, proton transfer between the amino and carbonyl groups must occur; this requires highly localized vibrational energy during chemiexcitation.

Place, publisher, year, edition, pages
WILEY-V C H VERLAG GMBH, 2019
Keywords
CASPT2, cancer, density functional calculations, electron transfer, chemiluminescence, reaction mechanisms
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-387214 (URN)10.1002/chem.201805918 (DOI)000468855200014 ()30720222 (PubMedID)
Funder
Swedish Research Council, 2016-033989
Available from: 2019-06-25 Created: 2019-06-25 Last updated: 2019-06-25Bibliographically approved
Fernández Galván, I., Vacher, M., Alavi, A., Angeli, C., Aquilante, F., Autschbach, J., . . . Lindh, R. (2019). OpenMolcas: From Source Code to Insight. Journal of Chemical Theory and Computation, 15(11), 5925-5964
Open this publication in new window or tab >>OpenMolcas: From Source Code to Insight
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2019 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 15, no 11, p. 5925-5964Article in journal (Refereed) Published
Abstract [en]

In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2019
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-398580 (URN)10.1021/acs.jctc.9b00532 (DOI)000497260300014 ()31509407 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation, KAW-2013.0020Swedish Research Council, 2012-3924Swedish Research Council, 2016-03398Swedish Research Council, VR 2015-03956EU, Horizon 2020, 658173EU, European Research CouncilStiftelsen Olle Engkvist ByggmästareNIH (National Institute of Health), GM126627 01German Research Foundation (DFG), BO 4915/1-1
Available from: 2019-12-09 Created: 2019-12-09 Last updated: 2019-12-09Bibliographically approved
Khamesian, M., Fernández Galván, I., Delcey, M. G., Sørensen, L. K. & Lindh, R. (2019). Spectroscopy of linear and circular polarized ligth with the exact semiclassical light–matter interaction. In: David A. Dixon (Ed.), Annual Reports in Computational Chemistry: Volume 15: (pp. 39-76). Elsevier
Open this publication in new window or tab >>Spectroscopy of linear and circular polarized ligth with the exact semiclassical light–matter interaction
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2019 (English)In: Annual Reports in Computational Chemistry: Volume 15 / [ed] David A. Dixon, Elsevier, 2019, p. 39-76Chapter in book (Refereed)
Abstract [en]

We present the theory and the analytical and numerical solution for the calculation of the oscillator and rotatory strengths of molecular systems using a state-specific formalism. For a start, this is done in the context of the exact semiclassical light–matter interaction in association with electronic wave functions expanded in a Gaussian basis. The reader is guided through the standard approximations of the field, e.g., the use of commutators, truncation of Taylor expansions, and the implications of these are discussed in parallel. Expressions for the isotropically averaged values are derived, recovering the isotropic oscillator strength in terms of the transition electric-dipole moment, and the isotropic rotatory strength in terms of the transition electric-dipole and magnetic-dipole moments. This chapter gives a detailed description of the computation of the integrals over the plane wave in association with Gaussian one-particle basis sets. Finally, a brief description is given of how the computed oscillator and rotatory strengths are related to the quantities commonly used and discussed in experimental studies.

Place, publisher, year, edition, pages
Elsevier, 2019
Series
Annual Reports in Computational Chemistry ; 15
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-398676 (URN)10.1016/bs.arcc.2019.08.004 (DOI)978-0-12-817119-6 (ISBN)
Available from: 2019-12-09 Created: 2019-12-09 Last updated: 2019-12-16Bibliographically approved
Sand, A. M., Hoyer, C. E., Sharkas, K., Kidder, K. M., Lindh, R., Truhlar, D. G. & Gagliard, L. (2018). Analytic Gradients for Complete Active Space Pair-Density Functional Theory. Journal of Chemical Theory and Computation, 14(1), 126-138
Open this publication in new window or tab >>Analytic Gradients for Complete Active Space Pair-Density Functional Theory
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2018 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 14, no 1, p. 126-138Article in journal (Refereed) Published
Abstract [en]

Analytic gradient routines are a desirable feature for quantum mechanical methods, allowing for efficient determination of equilibrium and transition state structures and several other molecular properties. In this work, we present analytical gradients for multiconfiguration pair-density functional theory (MC-PDFT) when used with a state-specific complete active space self-consistent field reference wave function. Our approach constructs a Lagrangian that is variational in all wave function parameters. We find that MC-PDFT locates equilibrium geometries for several small- to medium-sized organic molecules that are similar to those located by complete active space second-order perturbation theory but that are obtained with decreased computational cost.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2018
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-341587 (URN)10.1021/acs.jctc.7b00967 (DOI)000419998300012 ()29211966 (PubMedID)
Funder
Swedish Research Council, 2016-03398
Available from: 2018-02-12 Created: 2018-02-12 Last updated: 2018-02-12Bibliographically approved
Tamayo-Mendoza, T., Kreisbeck, C., Lindh, R. & Aspuru-Guzik, A. (2018). Automatic Differentiation in Quantum Chemistry with Applications to Fully Variational Hartree-Fock. ACS CENTRAL SCIENCE, 4(5), 559-566
Open this publication in new window or tab >>Automatic Differentiation in Quantum Chemistry with Applications to Fully Variational Hartree-Fock
2018 (English)In: ACS CENTRAL SCIENCE, ISSN 2374-7943, Vol. 4, no 5, p. 559-566Article in journal (Refereed) Published
Abstract [en]

Automatic differentiation (AD) is a powerful tool that allows calculating derivatives of implemented algorithms with respect to all of their parameters up to machine precision, without the need to explicitly add any additional functions. Thus, AD has great potential in quantum chemistry, where gradients are omnipresent but also difficult to obtain, and researchers typically spend a considerable amount of time finding suitable analytical forms when implementing derivatives. Here, we demonstrate that AD can be used to compute gradients with respect to any parameter throughout a complete quantum chemistry method. We present DiffiQult, a Hartree-Fock implementation, entirely differentiated with the use of AD tools. DiffiQult is a software package written in plain Python with minimal deviation from standard code which illustrates the capability of AD to save human effort and time in implementations of exact gradients in quantum chemistry. We leverage the obtained gradients to optimize the parameters of one-particle basis sets in the context of the floating Gaussian framework.

Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2018
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-358092 (URN)10.1021/acscentsci.7b00586 (DOI)000434851700009 ()29806002 (PubMedID)
Funder
Swedish Research Council, 2016-03398
Available from: 2018-08-24 Created: 2018-08-24 Last updated: 2018-08-24Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0001-7567-8295

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