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Ertan, E., Lundberg, M., Sörensen, L. K. & Odelius, M. (2020). Setting the stage for theoretical x-ray spectra of the H2S molecule with multi-configurational quantum chemical calculations of the energy landscape. Journal of Chemical Physics, 152(9), Article ID 094305.
Open this publication in new window or tab >>Setting the stage for theoretical x-ray spectra of the H2S molecule with multi-configurational quantum chemical calculations of the energy landscape
2020 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 152, no 9, article id 094305Article in journal (Refereed) Published
Abstract [en]

In the H2S molecule, the interplay between different core levels can be investigated in great detail in relation to x-ray spectroscopy, which requires a theory for interpretation. Hence, valence and core excitations into the two antibonding molecular orbitals of the H2S molecule have been calculated within a multi-configurational wave function framework. Scanning along the S-H stretching coordinates, we derive potential energy surfaces and transition dipole moments involving the ground state and core and valence excited states. Both valence excitations and the S1s(-1) and S2p(-1) core excitations show pairs of dissociative and bound electronic states. These pairs of states are nearly degenerate in H2S at the ground state geometry. The close degeneracy together with conical intersections makes H2S an interesting target for x-ray spectroscopy involving ultra-fast dissociation influenced by non-adiabatic transitions and interference. For future investigations with x-ray absorption spectroscopy (XAS) and resonant inelastic x-ray scattering (RIXS), it is valuable to compare H2S with the water molecule, which exhibits state-selective gating to different vibrational modes [R. C. Couto et al., Nat. Commun. 8, 14165 (2017)] in its well-separated O1s(-1) core excited states. The dense manifolds of the S2p(-1) core excited states will complicate the analysis of K-alpha edge RIXS, but dynamical effects could be evaluated through detuning and by comparing with L edge XAS. In L edge RIXS, the dynamical effects will be more pronounced due to the longer lifetime of the S2p(-1) core excited states compared to the S1s(-1) core excited states.

Place, publisher, year, edition, pages
AMER INST PHYSICS, 2020
National Category
Theoretical Chemistry Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-408531 (URN)10.1063/1.5145139 (DOI)000519569400002 ()
Funder
Swedish Research Council, Dnr 2015-03956Knut and Alice Wallenberg Foundation, KAW-2013-0020
Available from: 2020-04-09 Created: 2020-04-09 Last updated: 2020-04-09Bibliographically 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
Kayser, Y., Milne, C., Juranic, P., Sala, L., Czapla-Masztafiak, J., Follath, R., . . . Szlachetkc, J. (2019). Core-level nonlinear spectroscopy triggered by stochastic X-ray pulses. Nature Communications, 10, Article ID 4761.
Open this publication in new window or tab >>Core-level nonlinear spectroscopy triggered by stochastic X-ray pulses
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2019 (English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 4761Article in journal (Refereed) Published
Abstract [en]

Stochastic processes are highly relevant in research fields as different as neuroscience, economy, ecology, chemistry, and fundamental physics. However, due to their intrinsic unpredictability, stochastic mechanisms are very challenging for any kind of investigations and practical applications. Here we report the deliberate use of stochastic X-ray pulses in two-dimensional spectroscopy to the simultaneous mapping of unoccupied and occupied electronic states of atoms in a regime where the opacity and transparency properties of matter are subject to the incident intensity and photon energy. A readily transferable matrix formalism is presented to extract the electronic states from a dataset measured with the monitored input from a stochastic excitation source. The presented formalism enables investigations of the response of the electronic structure to irradiation with intense X-ray pulses while the time structure of the incident pulses is preserved.

Place, publisher, year, edition, pages
Nature Publishing Group, 2019
National Category
Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-399093 (URN)10.1038/s41467-019-12717-1 (DOI)000490982100001 ()31628306 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation, KAW-2013.0020
Available from: 2019-12-16 Created: 2019-12-16 Last updated: 2019-12-16Bibliographically 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
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
Jayasinghe-Arachchige, V. M., Hu, Q., Sharma, G., Paul, T. J., Lundberg, M., Quinonero, D., . . . Prabhakar, R. (2019). Hydrolysis of Chemically Distinct Sites of Human Serum Albumin by Polyoxometalate: A Hybrid QM/MM (ONIOM) Study. Journal of Computational Chemistry, 40(1), 51-61
Open this publication in new window or tab >>Hydrolysis of Chemically Distinct Sites of Human Serum Albumin by Polyoxometalate: A Hybrid QM/MM (ONIOM) Study
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2019 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 40, no 1, p. 51-61Article in journal (Refereed) Published
Abstract [en]

In this study, mechanisms of hydrolysis of all four chemically diverse cleavage sites of human serum albumin (HSA) by [Zr(OH) (PW11O39)](4-)(ZrK) have been investigated using the hybrid two-layer QM/MM (ONIOM) method. These reactions have been proposed to occur through the following two mechanisms: internal attack (IA) and water assisted (WA). In both mechanisms, the cleavage of the peptide bond in the Cys392-Glu393 site of HSA is predicted to occur in the rate-limiting step of the mechanism. With the barrier of 27.5 kcal/mol for the hydrolysis of this site, the IA mechanism is found to be energetically more favorable than the WA mechanism (barrier = 31.6 kcal/mol). The energetics for the IA mechanism are in line with the experimentally measured values for the cleavage of a wide range of dipeptides. These calculations also suggest an energetic preference (Cys392-Glu393, Ala257-Asp258, Lys313-Asp314, and Arg114-Leu115) for the hydrolysis of all four sites of HSA. (C) 2018 Wiley Periodicals, Inc.

Keywords
polyoxometalates, human serum albumin, peptide hydrolysis, reaction mechanism, QM/MM (ONIOM) method
National Category
Theoretical Chemistry Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-372750 (URN)10.1002/jcc.25528 (DOI)000452421800005 ()30238478 (PubMedID)
Available from: 2019-01-15 Created: 2019-01-15 Last updated: 2019-01-15Bibliographically 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
Blachucki, W., Kayser, Y., Czapla-Masztafiak, J., Guo, M., Juranic, P., Kavcic, M., . . . Szlachetko, J. (2019). Inception of electronic damage of matter by photon-driven post-ionization mechanisms. Structural Dynamics, 6(2), Article ID 024901.
Open this publication in new window or tab >>Inception of electronic damage of matter by photon-driven post-ionization mechanisms
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2019 (English)In: Structural Dynamics, ISSN 2329-7778, Vol. 6, no 2, article id 024901Article in journal (Refereed) Published
Abstract [en]

"Probe-before-destroy" methodology permitted diffraction and imaging measurements of intact specimens using ultrabright but highly destructive X-ray free-electron laser (XFEL) pulses. The methodology takes advantage of XFEL pulses ultrashort duration to outrun the destructive nature of the X-rays. Atomic movement, generally on the order of >50 fs, regulates the maximum pulse duration for intact specimen measurements. In this contribution, we report the electronic structure damage of a molecule with ultrashort X-ray pulses under preservation of the atoms' positions. A detailed investigation of the X-ray induced processes revealed that X-ray absorption events in the solvent produce a significant number of solvated electrons within attosecond and femtosecond timescales that are capable of coulombic interactions with the probed molecules. The presented findings show a strong influence on the experimental spectra coming from ionization of the probed atoms' surroundings leading to electronic structure modification much faster than direct absorption of photons. This work calls for consideration of this phenomenon in cases focused on samples embedded in, e.g., solutions or in matrices, which in fact concerns most of the experimental studies.

National Category
Atom and Molecular Physics and Optics Physical Chemistry
Identifiers
urn:nbn:se:uu:diva-383884 (URN)10.1063/1.5090332 (DOI)000466710000011 ()31041363 (PubMedID)
Funder
Knut and Alice Wallenberg Foundation, KAW-2013.0020
Available from: 2019-05-29 Created: 2019-05-29 Last updated: 2019-05-29Bibliographically 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
Lundberg, M. & Delcey, M. G. (2019). Multiconfigurational Approach to X-ray Spectroscopy of Transition Metal Complexes. In: Ewa Broclawik; Tomasz Borowski; Mariusz Radoń (Ed.), Transition Metals in Coordination Environments: Computational chemistry and catalysis viewpoints. Springer
Open this publication in new window or tab >>Multiconfigurational Approach to X-ray Spectroscopy of Transition Metal Complexes
2019 (English)In: Transition Metals in Coordination Environments: Computational chemistry and catalysis viewpoints / [ed] Ewa Broclawik; Tomasz Borowski; Mariusz Radoń, Springer, 2019Chapter in book (Refereed)
Abstract [en]

Close correlation between theoretical modeling and experimental spectroscopy allows for identification of the electronic and geometric structure of a system through its spectral fingerprint. This is can be used to verify mechanistic proposals and is a valuable complement to calculations of reaction mechanisms using the total energy as the main criterion. For transition metal systems, X-ray spectroscopy offers a unique probe because the core-excitation energies are element specific, which makes it possible to focus on the catalytic metal. The core hole is atom-centered and sensitive to the local changes in the electronic structure, making it useful for redox active catalysts. The possibility to do time-resolved experiments also allows for rapid detection of metastable intermediates. Reliable fingerprinting requires a theoretical model that is accurate enough to distinguish between different species and multiconfigurational wavefunction approaches have recently been extended to model a number of X-ray processes of transition metal complexes. Compared to ground-state calculations, modeling of X-ray spectra is complicated by the presence of the core hole, which typically leads to multiple open shells and large effects of spin–orbit coupling. This chapter describes how these effects can be accounted for with a multiconfigurational approach and outline the basic principles and performance. It is also shown how a detailed analysis of experimental spectra can be used to extract additional information about the electronic structure.

Place, publisher, year, edition, pages
Springer, 2019
Series
Computational Chemistry and Catalysis Viewpoints, ISSN 2542-4491 ; 29
Keywords
Electronic structure - Coordination complexes - Metal–ligand bonding - Molecular orbital theory - Restricted active space
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-376635 (URN)10.1007/978-3-030-11714-6 (DOI)978-3-030-11713-9 (ISBN)978-3-030-11714-6 (ISBN)
Available from: 2019-02-07 Created: 2019-02-07 Last updated: 2019-08-08Bibliographically approved
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ORCID iD: ORCID iD iconorcid.org/0000-0002-1312-1202

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