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Publications (10 of 17) Show all publications
Fernández Galván, I., Gustafsson, H. & Vacher, M. (2019). Chemiexcitation without the Peroxide Bond?: Replacing oxygen with other heteroatoms. ChemPhotoChem, 3(9), 957-967
Open this publication in new window or tab >>Chemiexcitation without the Peroxide Bond?: Replacing oxygen with other heteroatoms
2019 (English)In: ChemPhotoChem, ISSN 2367-0932, Vol. 3, no 9, p. 957-967Article in journal (Refereed) Published
Abstract [en]

Chemiexcitation is the population of electronic excited states from the electronic ground state via radiationless non-adiabatic transitions upon thermal activation. The subsequent emission of the excess of energy in the form of light is called chemiluminescence or bioluminescence when occurring in living organisms. Key intermediates in these reactions have been shown to contain a high-energy (often cyclic) peroxide which decomposes. The simplest molecules, 1,2-dioxetane and 1,2-dioxetanone, have thus been used extensively both theoretically and experimentally as model systems to understand the underlying mechanisms of chemiexcitation. An outstanding question remains whether the peroxide bond is a necessity and whether equivalent processes could happen in other simple molecules not containing an OO bond. In the present work, the decomposition reactions of four analogs of 1,2-dioxetane not containing a peroxide bond, the 1,2-oxazetidine anion, the 1,2-diazetidine anion, (neutral) 1,2-oxazetidine and 1,2-dithietane, have been studied theoretically using ab initio multicongurational methods. In particular, the reaction energy barriers and spin-orbit coupling strengths were calculated; the electronic degeneracy was studied and compared to the case of 1,2-dioxetane to assess the potentiality of chemiexcitation in the analog molecules.

Keywords
chemiexcitation, chemiluminescence, 1.2-dioxetane, ab initio calculations, computational photochemistry
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-372040 (URN)10.1002/cptc.201800232 (DOI)000487014600032 ()
Funder
Swedish Research Council, 2016-03398Swedish National Infrastructure for Computing (SNIC)
Available from: 2019-01-04 Created: 2019-01-04 Last updated: 2019-10-31Bibliographically approved
Delcey, M. G., Sörensen, L. K., Vacher, M., Couto, R. C. & Lundberg, M. (2019). Efficient calculations of a large number of highly excited states for multiconfigurational wavefunctions. Journal of Computational Chemistry, 40(19), 1789-1799
Open this publication in new window or tab >>Efficient calculations of a large number of highly excited states for multiconfigurational wavefunctions
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2019 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 40, no 19, p. 1789-1799Article in journal (Refereed) Published
Abstract [en]

Electronically excited states play important roles in many chemical reactions and spectroscopic techniques. In quantum chemistry, a common technique to solve excited states is the multiroot Davidson algorithm, but it is not designed for processes like X-ray spectroscopy that involves hundreds of highly excited states. We show how the use of a restricted active space wavefunction together with a projection operator to remove low-lying electronic states offers an efficient way to reach single and double-core-hole states. Additionally, several improvements to the stability and efficiency of the configuration interaction (CI) algorithm for a large number of states are suggested. When applied to a series of transition metal complexes the new CI algorithm does not only resolve divergence issues but also leads to typical reduction in computational time by 70%, with the largest savings for small molecules and large active spaces. Together, the projection operator and the improved CI algorithm now make it possible to simulate a wide range of single- and two-photon spectroscopies.

Place, publisher, year, edition, pages
WILEY, 2019
Keywords
configuration interaction, excited states, X-ray spectroscopy, multiconfigurational wavefunction, computational cost
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-387717 (URN)10.1002/jcc.25832 (DOI)000470013600006 ()30938847 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation, KAW-2013.0020Carl Tryggers foundation Stiftelsen Olle Engkvist Byggmästare
Available from: 2019-06-25 Created: 2019-06-25 Last updated: 2019-06-25Bibliographically 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
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
Polyak, I., Jenkins, A. J., Vacher, M., Bouduban, M. E. F., Bearpark, M. J. & Robb, M. A. (2018). Charge migration engineered by localisation: electron-nuclear dynamics in polyenes and glycine. Molecular Physics, 116(19-20), 2474-2489
Open this publication in new window or tab >>Charge migration engineered by localisation: electron-nuclear dynamics in polyenes and glycine
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2018 (English)In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 116, no 19-20, p. 2474-2489Article in journal (Refereed) Published
Abstract [en]

We demonstrate that charge migration can be ‘engineered’ in arbitrary molecular systems if a single localised orbital – that diabatically follows nuclear displacements – is ionised. Specifically, we describe the use of natural bonding orbitals in Complete Active Space Configuration Interaction (CASCI) calculations to form cationic states with localised charge, providing consistently well-defined initial conditions across a zero point energy vibrational ensemble of molecular geometries. In Ehrenfest dynamics simulations following localised ionisation of -electrons in model polyenes (hexatriene and decapentaene) and -electrons in glycine, oscillatory charge migration can be observed for several femtoseconds before dephasing. Including nuclear motion leads to slower dephasing compared to fixed-geometry electron-only dynamics results. For future work, we discuss the possibility of designing laser pulses that would lead to charge migration that is experimentally observable, based on the proposed diabatic orbital approach.

KEYWORDS: Ehrenfest method, coupled electron-nuclear dynamics, charge migration, localised orbital

Place, publisher, year, edition, pages
Taylor & Francis, 2018
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-357515 (URN)10.1080/00268976.2018.1478136 (DOI)000442634600008 ()
Available from: 2018-08-16 Created: 2018-08-16 Last updated: 2018-11-20Bibliographically 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
Kunnus, K., Harlang, T., Kjaer, K. S., Vacher, M., Vanko, G., Haldrup, K., . . . Gaffney, K. (2018). Coherent structural dynamics observed with femtosecond Fe K alpha and K beta X-ray emission spectroscopies. Paper presented at 256th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nanoscience, Nanotechnology and Beyond, AUG 19-23, 2018, Boston, MA. Abstract of Papers of the American Chemical Society, 256
Open this publication in new window or tab >>Coherent structural dynamics observed with femtosecond Fe K alpha and K beta X-ray emission spectroscopies
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2018 (English)In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 256Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
AMER CHEMICAL SOC, 2018
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-370052 (URN)000447609103560 ()
Conference
256th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nanoscience, Nanotechnology and Beyond, AUG 19-23, 2018, Boston, MA
Available from: 2018-12-20 Created: 2018-12-20 Last updated: 2018-12-20Bibliographically approved
Jenkins, A. J., Spinlove, K. E., Vacher, M., Worth, G. A. & Robb, M. A. (2018). The Ehrenfest method with fully quantum nuclear motion (Qu-Eh): Application to charge migration in radical cations. Journal of Chemical Physics, 149(9), Article ID 094108.
Open this publication in new window or tab >>The Ehrenfest method with fully quantum nuclear motion (Qu-Eh): Application to charge migration in radical cations
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2018 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 149, no 9, article id 094108Article in journal (Refereed) Published
Abstract [en]

An algorithm is described for quantum dynamics where an Ehrenfest potential is combined with fully quantum nuclear motion (Quantum-Ehrenfest, Qu-Eh). The method is related to the single-set variational multi-configuration Gaussian approach (vMCG) but has the advantage that only a single quantum chemistry computation is required at each time step since there is only a single time-dependent potential surface. Also shown is the close relationship to the “exact factorization method.” The quantum Ehrenfest method is compared with vMCG for study of electron dynamics in a modified bismethylene-adamantane cation system. Illustrative examples of electron-nuclear dynamics are presented for a distorted allene system and for HCCI+ where one has a degenerate Π system.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-360026 (URN)10.1063/1.5038428 (DOI)000444043600010 ()30195291 (PubMedID)
Available from: 2018-09-08 Created: 2018-09-08 Last updated: 2018-11-20Bibliographically approved
Sanchez-Gonzalez, A., Micaelli, P., Olivier, C., Barillot, T. R., Ilchen, M., Lutman, A. A., . . . Marangos, J. P. (2017). Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning. Nature Communications, 8, Article ID 15461.
Open this publication in new window or tab >>Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning
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2017 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 15461Article in journal (Refereed) Published
Abstract [en]

Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate. Here, we present a technique for circumventing this limitation. Employing a machine learning strategy, we can accurately predict X-ray properties for every shot using only parameters that are easily recorded at high-repetition rate, by training a model on a small set of fully diagnosed pulses. This opens the door to fully realizing the promise of next-generation high-repetition rate X-ray lasers.

Place, publisher, year, edition, pages
Nature Publishing Group, 2017
National Category
Condensed Matter Physics
Identifiers
urn:nbn:se:uu:diva-327226 (URN)10.1038/ncomms15461 (DOI)000402745000001 ()28580940 (PubMedID)
Available from: 2017-08-25 Created: 2017-08-25 Last updated: 2017-11-29Bibliographically approved
Vacher, M., Brakestad, A., Karlsson, H. O., Fernández Galván, I. & Lindh, R. (2017). Dynamical Insights into the Decomposition of 1,2-Dioxetane. Journal of Chemical Theory and Computation, 13(6), 2448-2457
Open this publication in new window or tab >>Dynamical Insights into the Decomposition of 1,2-Dioxetane
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2017 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 13, no 6, p. 2448-2457Article in journal (Refereed) Published
Abstract [en]

Chemiluminescence in 1,2-dioxetane occurs through a thermally activated decomposition reaction into two formaldehyde molecules. Both ground-state and nonadiabatic dynamics (including singlet excited states) of the decomposition reaction have been simulated, starting from the first O–O bond-breaking transition structure. The ground-state dissociation occurs between t = 30 fs and t = 140 fs. The so-called entropic trap leads to frustrated dissociations, postponing the decomposition reaction. Specific geometrical conditions are necessary for the trajectories to escape from the entropic trap and for dissociation to be possible. The singlet excited states participate as well in the trapping of the molecule: dissociation including the nonadiabatic transitions to singlet excited states now occurs from t = 30 fs to t = 250 fs and later. Specific regions of the seam of the So/S1 conical intersections that would "retain" the molecule for longer on the excited state have been identified.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-329717 (URN)10.1021/acs.jctc.7b00198 (DOI)000403530100009 ()28437611 (PubMedID)
Funder
Swedish Research Council, 2012-3910
Available from: 2017-10-02 Created: 2017-10-02 Last updated: 2017-10-02Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0001-9418-6579

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