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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
Yan, J. J., Kroll, T., Baker, M. L., Wilson, S. A., Decréau, R., Lundberg, M., . . . Solomon, E. I. (2019). Resonant inelastic X-ray scattering determination of the electronic structure of oxyhemoglobin and its model complex. Proceedings of the National Academy of Sciences of the United States of America, 116(8), 2854-2859
Open this publication in new window or tab >>Resonant inelastic X-ray scattering determination of the electronic structure of oxyhemoglobin and its model complex
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2019 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 8, p. 2854-2859Article in journal (Refereed) Published
Abstract [en]

The electronic structure of the heme oxy-iron center in oxyhemoglobin and oxymyoglobin has been the subject of debate for decades. Various experimental and computational methods have been used to study this system, leading to conflicting conclusions. This study uses X-ray spectroscopy to directly probe the iron center in the highly delocalized oxyhemoglobin and its model compound to define the electronic structure and understand the differences between the protein and the model. This study settles a longstanding debate in bioinorganic chemistry and provides insight into heme iron–oxygen binding, the key first step in many biocatalytic processes.Hemoglobin and myoglobin are oxygen-binding proteins with S = 0 heme FeO28 active sites. The electronic structure of these sites has been the subject of much debate. This study utilizes Fe K-edge X-ray absorption spectroscopy (XAS) and 1s2p resonant inelastic X-ray scattering (RIXS) to study oxyhemoglobin and a related heme FeO28 model compound, [(pfp)Fe(1-MeIm)(O2)] (pfp = meso-tetra(α,α,α,α-o-pivalamido-phenyl)porphyrin, or TpivPP, 1-MeIm = 1-methylimidazole) (pfpO2), which was previously analyzed using L-edge XAS. The K-edge XAS and RIXS data of pfpO2 and oxyhemoglobin are compared with the data for low-spin FeII and FeIII [Fe(tpp)(Im)2]0/+ (tpp = tetra-phenyl porphyrin) compounds, which serve as heme references. The X-ray data show that pfpO2 is similar to FeII, while oxyhemoglobin is qualitatively similar to FeIII, but with significant quantitative differences. Density-functional theory (DFT) calculations show that the difference between pfpO2 and oxyhemoglobin is due to a distal histidine H bond to O2 and the less hydrophobic environment in the protein, which lead to more backbonding into the O2. A valence bond configuration interaction multiplet model is used to analyze the RIXS data and show that pfpO2 is dominantly FeII with 6–8% FeIII character, while oxyhemoglobin has a very mixed wave function that has 50–77% FeIII character and a partially polarized Fe–O2 π-bond.

Place, publisher, year, edition, pages
National Academy of Sciences, 2019
Keywords
X-ray spectroscopy, resonant inelastic X-ray scattering, DFT, oxyhemoglobin, electronic structure
National Category
Inorganic Chemistry
Identifiers
urn:nbn:se:uu:diva-376521 (URN)10.1073/pnas.1815981116 (DOI)000459074400018 ()
Funder
Marcus and Amalia Wallenberg Foundation
Available from: 2019-02-06 Created: 2019-02-06 Last updated: 2019-08-01Bibliographically approved
Lundberg, M. & Wernet, P. (2019). Resonant Inelastic X-ray Scattering (RIXS) Studies in Chemistry:: Present and Future (2ed.). In: Jaeschke, E., Khan, S., Schneider, J.R., Hastings, J.B. (Ed.), Synchrotron Light Sources and Free-Electron Lasers: Accelerator Physics, Instrumentation and Science Applications. Springer
Open this publication in new window or tab >>Resonant Inelastic X-ray Scattering (RIXS) Studies in Chemistry:: Present and Future
2019 (English)In: Synchrotron Light Sources and Free-Electron Lasers: Accelerator Physics, Instrumentation and Science Applications / [ed] Jaeschke, E., Khan, S., Schneider, J.R., Hastings, J.B., Springer, 2019, 2Chapter in book (Refereed)
Abstract [en]

This chapter illustrates how resonant inelastic x-ray scattering (RIXS) is used to address questions in chemistry, with special focus on the electronic structure and catalytic activity of first row transition metals. RIXS is a two-photon process that is the x-ray equivalent of resonance Raman spectroscopy. The final states correspond to vibrational, valence electronic or even core excitations. In addition to the advantages of a local element-selective x-ray spectroscopic probe, RIXS gives new information compared to single-photon x-ray absorption and x-ray emission experiments. Metal L-edge RIXS shows intense metal-centered ligand- field transitions, even in cases where they are spin or parity forbidden in optical absorption spectroscopy. By selecting different resonances by appropriately tuning the incident energy, it is possible to isolate different ligand-field and charge-transfer transitions. The observation of a large number of electronic states that can be properly assigned, sometimes with the help of theoretical methods, gives novel opportunities to quantify metal-ligand interactions and their contributions to reactivity. RIXS in the K pre-edge can be used to obtain L- and M-edge like spectra including insight into charge-transfer excitations all with the advantages of a hard x-ray probe. Finally, it is shown how time-resolved RIXS down to the femtosecond timescale probes the orbitals of transient reaction intermediates. The usefulness of RIXS in chemistry is shown for a diverse set of systems, including coordination complexes, metal enzymes, and nanoparticles.

Place, publisher, year, edition, pages
Springer, 2019 Edition: 2
Keywords
X-ray free-electron laser - Resonant inelastic x-ray scattering - RIXS - Coordination complex - Metalloprotein - Nanoparticle - Ligand- field excitation - Covalency - Transient intermediate - Transition metals - Electronic structure calculations
National Category
Accelerator Physics and Instrumentation Atom and Molecular Physics and Optics
Identifiers
urn:nbn:se:uu:diva-376638 (URN)978-3-319-04507-8 (ISBN)9783319143958 (ISBN)
Available from: 2019-02-07 Created: 2019-02-07 Last updated: 2019-08-08Bibliographically approved
Esmieu, C., Guo, M., Redman, H. J., Lundberg, M. & Berggren, G. (2019). Synthesis of a miniaturized [FeFe] hydrogenase model system. Dalton Transactions, 48(7), 2280-2284
Open this publication in new window or tab >>Synthesis of a miniaturized [FeFe] hydrogenase model system
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2019 (English)In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 48, no 7, p. 2280-2284Article in journal (Refereed) Published
Abstract [en]

The reaction occurring during artificial maturation of [FeFe] hydrogenase has been recreated using molecular systems. The formation of a miniaturized [FeFe] hydrogenase model system, generated through the combination of a [4Fe4S] cluster binding oligopeptide and an organometallic Fe complex, has been monitored by a range of spectroscopic techniques. A structure of the final assembly is suggested based on EPR and FTIR spectroscopy in combination with DFT calculations. The capacity of this novel H-cluster model to catalyze H-2 production in aqueous media at mild potentials is verified in chemical assays.

Place, publisher, year, edition, pages
ROYAL SOC CHEMISTRY, 2019
National Category
Inorganic Chemistry Theoretical Chemistry
Identifiers
urn:nbn:se:uu:diva-379261 (URN)10.1039/c8dt05085f (DOI)000459626400004 ()30667428 (PubMedID)
Funder
Swedish Research Council, 621-2014-5670Swedish Research Council Formas, 213-2014-880EU, European Research Council, 714102Wenner-Gren Foundations
Available from: 2019-03-15 Created: 2019-03-15 Last updated: 2019-03-15Bibliographically approved
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Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-1312-1202

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