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Schalk, O., Galiana, J., Geng, T., Larsson, T., Thomas, R., Fernández Galván, I., . . . Vacher, M. (2020). Competition between ring-puckering and ring-opening excited state reactions exemplified on 5H-furan-2-one and derivatives. Journal of Chemical Physics, 152(6), Article ID 064301.
Open this publication in new window or tab >>Competition between ring-puckering and ring-opening excited state reactions exemplified on 5H-furan-2-one and derivatives
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2020 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 152, no 6, article id 064301Article in journal (Refereed) Published
Abstract [en]

The influence of ring-puckering on the light-induced ring-opening dynamics of heterocyclic compounds was studied on the sample 5-membered ring molecules γ-valerolactone and 5H-furan-2-one using time-resolved photoelectron spectroscopy and ab initio molecular dynamics simulations. In γ-valerolactone, ring-puckering is not a viable relaxation channel and the only available reaction pathway is ring-opening, which occurs within one vibrational period along the C—O bond. In 5H-furan-2-one, the C=C double bond in the ring allows for ring-puckering which slows down the ring-opening process by about 150 fs while only marginally reducing its quantum yield. This demonstrates that ring-puckering is an ultrafast process, which is directly accessible upon excitation and which spreads the excited state wave packet quickly enough to influence even the outcome of an otherwise expectedly direct ring-opening reaction.

National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-404396 (URN)10.1063/1.5129366 (DOI)000522040400014 ()32061211 (PubMedID)
Funder
Swedish Research CouncilKnut and Alice Wallenberg FoundationWenner-Gren FoundationsSwedish National Infrastructure for Computing (SNIC)
Available from: 2020-02-19 Created: 2020-02-19 Last updated: 2020-05-06Bibliographically approved
Norell, J., Odelius, M. & Vacher, M. (2020). Ultrafast dynamics of photo-excited 2-thiopyridone: Theoretical insights into triplet state population and proton transfer pathways. STRUCTURAL DYNAMICS-US, 7(2), Article ID 024101.
Open this publication in new window or tab >>Ultrafast dynamics of photo-excited 2-thiopyridone: Theoretical insights into triplet state population and proton transfer pathways
2020 (English)In: STRUCTURAL DYNAMICS-US, ISSN 2329-7778, Vol. 7, no 2, article id 024101Article in journal (Refereed) Published
Abstract [en]

Ultrafast non-adiabatic dynamics of the small heteroaromatic compound 2-thiopyridone has been studied with surface hopping simulations based on multi-configurational quantum chemistry. Initial excitation of the bright S-2(pi,pi*) state is found to promptly relax to S-1(n, pi*) through in-plane motion. The subsequent dynamics are oppositely driven by out-of-plane motion, which results in both complex population transfers among all the available states and intersystem crossing predominantly through the "El-Sayed forbidden" S-1(n, pi*) to T-2(n, pi*) channel, through significant mixing of electronic excitation characters. Despite this complexity, the femto- to picosecond triplet population, expected from several spectroscopic measurements, is well described as a simple exponential decay of the singlet state manifold. No proton transfer is found in the reported trajectories, but two mechanisms for its possible mediation in previously reported experiments are proposed based on the observed structural dynamics: (i) ultrafast intra-molecular transfer driven by the initially coherent in-plane motion and (ii) inter-molecular solvent-mediated transfer driven by the out-of-plane modes that dominate the later motion.

Place, publisher, year, edition, pages
AMER INST PHYSICS, 2020
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-409656 (URN)10.1063/1.5143228 (DOI)000521264300001 ()32206689 (PubMedID)
Funder
Swedish Research Council, VR 2015-03956Swedish National Infrastructure for Computing (SNIC), SNIC2019-1-9Carl Tryggers foundation , CTS18:285
Available from: 2020-04-29 Created: 2020-04-29 Last updated: 2020-04-29Bibliographically approved
Kunnus, K., Vacher, M., Harlang, T. C. B., Kjaer, K. S., Haldrup, K., Biasin, E., . . . Gaffney, K. J. (2020). Vibrational wavepacket dynamics in Fe carbene photosensitizer determined with femtosecond X-ray emission and scattering. Nature Communications, 11(1), Article ID 634.
Open this publication in new window or tab >>Vibrational wavepacket dynamics in Fe carbene photosensitizer determined with femtosecond X-ray emission and scattering
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2020 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 11, no 1, article id 634Article in journal (Refereed) Published
Abstract [en]

The non-equilibrium dynamics of electrons and nuclei govern the function of photoactive materials. Disentangling these dynamics remains a critical goal for understanding photoactive materials. Here we investigate the photoinduced dynamics of the [Fe(bmip)2]2+ photosensitizer, where bmip = 2,6-bis(3-methyl-imidazole-1-ylidine)-pyridine, with simultaneous femtosecond-resolution Fe Kα and Kβ X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS). This measurement shows temporal oscillations in the XES and XSS difference signals with the same 278 fs period oscillation. These oscillations originate from an Fe-ligand stretching vibrational wavepacket on a triplet metal-centered (3MC) excited state surface. This 3MC state is populated with a 110 fs time constant by 40% of the excited molecules while the rest relax to a 3MLCT excited state. The sensitivity of the Kα XES to molecular structure results from a 0.7% average Fe-ligand bond length shift between the 1 s and 2p core-ionized states surfaces.

National Category
Physical Chemistry Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-407449 (URN)10.1038/s41467-020-14468-w (DOI)000513245600024 ()32005815 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation, KAW-2013.0020Knut and Alice Wallenberg Foundation, KAW 2014.0370EU, European Research Council, ERCStG-259709Stiftelsen Olle Engkvist ByggmästareEuropean Regional Development Fund (ERDF), VEKOP-2.3.2-16-2017-00015Carl Tryggers foundation
Available from: 2020-03-25 Created: 2020-03-25 Last updated: 2020-03-25Bibliographically approved
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
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