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Lindh, Roland, ProfessorORCID iD iconorcid.org/0000-0001-7567-8295
Publications (10 of 194) Show all publications
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
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
Vacher, M., Fernández Galván, I., Ding, B.-W., Schramm, S., Berraud-Pache, R., Naumov, P., . . . Lindh, R. (2018). Chemi- and Bioluminescence of Cyclic Peroxides. Chemical Reviews, 118(15), 6927-6974
Open this publication in new window or tab >>Chemi- and Bioluminescence of Cyclic Peroxides
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2018 (English)In: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 118, no 15, p. 6927-6974Article, review/survey (Refereed) Published
Abstract [en]

Bioluminescence is a phenomenon that has fascinated mankind for centuries. Today the phenomenon and its sibling, chemiluminescence, have impacted society with a number of useful applications in fields like analytical chemistry and medicine, just to mention two. In this review, a molecular-orbital perspective is adopted to explain the chemistry behind chemiexcitation in both chemi- and bioluminescence. First, the uncatalyzed thermal dissociation of 1,2-dioxetane is presented and analyzed to explain, for example, the preference for triplet excited product states and increased yield with larger nonreactive substituents. The catalyzed fragmentation reaction and related details are then exemplified with substituted 1,2-dioxetanone species. In particular, the preference for singlet excited product states in that case is explained. The review also examines the diversity of specific solutions both in Nature and in artificial systems and the difficulties in identifying the emitting species and unraveling the color modulation process. The related subject of excited-state chemistry without light absorption is finally discussed. The content of this review should be an inspiration to human design of new molecular systems expressing unique light-emitting properties. An appendix describing the state-of-the-art experimental and theoretical methods used to study the phenomena serves as a complement.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-357512 (URN)10.1021/acs.chemrev.7b00649 (DOI)000441475900002 ()29493234 (PubMedID)
Funder
Swedish Research Council, 2016-03398Wenner-Gren Foundations
Note

PMID: 29493234

Available from: 2018-08-16 Created: 2018-08-16 Last updated: 2018-11-12Bibliographically approved
Berraud-Pache, R., Lindh, R. & Navizet, I. (2018). QM/MM Study of the Formation of the Dioxetanone Ring in Fireflies through a Superoxide Ion. Journal of Physical Chemistry B, 122(20), 5173-5182
Open this publication in new window or tab >>QM/MM Study of the Formation of the Dioxetanone Ring in Fireflies through a Superoxide Ion
2018 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 20, p. 5173-5182Article in journal (Refereed) Published
Abstract [en]

The bioluminescence emission from fireflies is an astounding tool to mark and view cells. However, the bioluminescent mechanism is not completely deciphered, limiting the comprehension of key processes. We use a theoretical approach to study for the first time the arrival of a dioxygen molecule inside the fireflies protein and one path of the formation of the dioxetanone ring, the high-energy intermediate precursor of the bioluminescence. To describe this reaction step, a joint approach combining classical molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations is used. The formation of the dioxetanone ring has been studied for both singlet and triplet states with the help of MS-CASPT2 calculations. We also emphasize the role played by the proteinic environment in the formation of the dioxetanone ring. The results obtained shed some light on an important reaction step and give new insights concerning the bioluminescence in fireflies.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-357566 (URN)10.1021/acs.jpcb.8b00642 (DOI)000433403500005 ()29659277 (PubMedID)
Funder
Swedish Research Council, 2016-03398
Available from: 2018-08-17 Created: 2018-08-17 Last updated: 2018-08-17Bibliographically approved
Aspuru-Guzik, A., Lindh, R. & Reiher, M. (2018). The Matter Simulation (R)evolution. ACS CENTRAL SCIENCE, 4(2), 144-152
Open this publication in new window or tab >>The Matter Simulation (R)evolution
2018 (English)In: ACS CENTRAL SCIENCE, ISSN 2374-7943, Vol. 4, no 2, p. 144-152Article in journal (Refereed) Published
Abstract [en]

To date, the program for the development of methods and models for atomistic and continuum simulation directed toward chemicals and materials has reached an incredible degree of sophistication and maturity. Currently, one can witness an increasingly rapid emergence of advances in computing, artificial intelligence, and robotics. This drives us to consider the future of computer simulation of matter from the molecular to the human length and time scales in a radical way that deliberately dares to go beyond the foreseeable next steps in any given discipline. This perspective article presents a view on this future development that we believe is likely to become a reality during our lifetime.

National Category
Materials Chemistry
Identifiers
urn:nbn:se:uu:diva-351271 (URN)10.1021/acscentsci.7b00550 (DOI)000426613700006 ()
Funder
Swedish Research Council, 2016-03398
Available from: 2018-06-04 Created: 2018-06-04 Last updated: 2018-06-04Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0001-7567-8295

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