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  • 1.
    Agarwala, Hemlata
    et al.
    Department of Chemistry - Ångström Laboratories, Uppsala University Box 523, 75120, Uppsala, Sweden; Present address: Technical University of Munich (TUM), Campus Straubing for Biotechnology and Sustainability, Uferstraße 53, 94315, Straubing, Germany.
    Chen, Xiaoyu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Lyonnet, Julien R.
    Department of Chemistry - Ångström Laboratories, Uppsala University Box 523, 75120, Uppsala, Sweden; Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Tarragona, 43007, Spain.
    Johnson, Ben A.
    Department of Chemistry - Ångström Laboratories, Uppsala University Box 523, 75120, Uppsala, Sweden; Present address: Technical University of Munich (TUM), Campus Straubing for Biotechnology and Sustainability, Uferstraße 53, 94315, Straubing, Germany.
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Ott, Sascha
    Department of Chemistry - Ångström Laboratories, Uppsala University Box 523, 75120, Uppsala, Sweden.
    Alternating Metal-Ligand Coordination Improves Electrocatalytic CO2 Reduction by a Mononuclear Ru Catalyst**2023In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 62, no 17, article id e202218728Article in journal (Refereed)
    Abstract [en]

    Molecular electrocatalysts for CO2-to-CO conversion often operate at large overpotentials, due to the large barrier for C−O bond cleavage. Illustrated with ruthenium polypyridyl catalysts, we herein propose a mechanistic route that involves one metal center that acts as both Lewis base and Lewis acid at different stages of the catalytic cycle, by density functional theory in corroboration with experimental FTIR. The nucleophilic character of the Ru center manifests itself in the initial attack on CO2 to form [Ru-CO2]0, while its electrophilic character allows for the formation of a 5-membered metallacyclic intermediate, [Ru-CO2CO2]0,c, by addition of a second CO2 molecule and intramolecular cyclization. The calculated activation barrier for C−O bond cleavage via the metallacycle is decreased by 34.9 kcal mol−1 as compared to the non-cyclic adduct in the two electron reduced state of complex 1. Such metallacyclic intermediates in electrocatalytic CO2 reduction offer a new design feature that can be implemented consciously in future catalyst designs.

  • 2.
    Ahmadzadeh, Karan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Benchmarking Two-Photon Absorption Cross Sections: A Comparative study goingbeyond the generalized gradient approximationManuscript (preprint) (Other academic)
    Abstract [en]

    We present a a benchmark study on density functional approximation (DFA) per-formances for predicting two-photon absorption (TPA) strengths in π-conjugatedmolecules containing electron-donating/-accepting moieties. We have incorporateda variety of meta-generalized gradient approximation (meta-GGA) functionals, in-cluding SCAN, MN15, and M06-2X, to assess their accuracy in describing the TPAproperties of the chosen set of 48 organic molecules. Quadratic response theory is em-ployed for these functionals, and their performance is compared with the previouslystudied DFAs and the coupled-cluster CC2 model (RI-CC2) is used as a reference. Adetailed analysis of the meta-GGA functionals’ performance is provided, focusing ontheir ability to capture the key electronic and structural features of the π-conjugatedsystems. Furthermore, we discuss the implications of our findings for the design ofnew materials with tailored two-photon activity and the development of more accu-rate and efficient computational methods for TPA predictions

  • 3.
    Ahmadzadeh, Karan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Efficient Calculation of Nonlinear Spectroscopic Properties within the Time-Dependent Density Functional Theory Approximation2023Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis introduces a novel computational scheme tailored for efficient calculations of nonlinear spectroscopic observables. First, a derivation and implementation of an algorithm designed to harness the linearity of the Fock matrix construction in calculating two-photon absorption cross-sections within the self-consistent field approximation is presented. Subsequently, this computational scheme is extended to the density functional theory approximation for functionals belonging to the generalized gradient approximation. Lastly the derivation and implementation of the nonlinear exchange-correlation kernel for functionals belonging to the meta generalized gradient approximation are presented for the first time.

    Collectively, the advancements presented in this thesis contribute new methodologies and insights to the computational realm of nonlinear spectroscopic calculations, offering the potential for large-scale theoretical spectroscopy calculations at the level of density functional theory.

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  • 4.
    Ahmadzadeh, Karan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Efficient Kohn–Sham density-functional theory implementation of isotropicspectroscopic observables associated with cubic response functions going beyond thegeneralized gradient approximationManuscript (preprint) (Other academic)
    Abstract [en]

    Within the density Kohn–Sham density functional theory approximation, computa-tionally tractable expressions for the isotropic second-order hyperpolarizability havebeen derived and implemented for the calculation of two-photon absorption crosssections with meta-GGA functionals for the very first time. The tensor average for-mulation presented in this work allows for the evaluation of isotropic damped cubicresponse functions using only ∼3.3 % (one-photon off-resonance regions) and ∼10%(one-photon resonance regions) of the number of kernel integrations required whenexplicitly calculating all the needed individual tensor components of the cubic re-sponse function.1 

  • 5.
    Ahmadzadeh, Karan
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Kaunas Univ Technol, Fac Math & Nat Sci, Dept Phys, LT-51368 Kaunas, Lithuania..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Efficient Kohn-Sham density-functional theory implementation of isotropic spectroscopic observables associated with quadratic response functions2022In: Electronic Structure, E-ISSN 2516-1075, Vol. 4, no 4, article id 044004Article in journal (Refereed)
    Abstract [en]

    For general exchange-correlation functionals with a dependence on the local spin densities and spin-density gradients, we provide computationally tractable expressions for the tensor-averaged quadratic response functions pertinent to the experimental observables in second-harmonic generation (SHG). We demonstrate how the tensor-averaged quantities can be implemented with reference to a derived minimal number of first- and second-order perturbed Fock matrices. Our consideration has the capability of treating a situation of resonance enhancement as it is based on damped response theory and allows for the evaluation of tensor-averaged resonant-convergent quadratic response functions using only similar to 25% (one-photon off-resonance regions) and similar to 50% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of SHG intensities in the one-photon off-resonance region are provided for a sample of makaluvamine derivatives recognized for their large nonlinear optical responses as well as a benchmark set of small- and medium-sized organic molecules.

  • 6.
    Ahmadzadeh, Karan
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Zaleśny, Robert
    Wyb. Wyspiańskiego 27.
    Toward Accurate Two-Photon Absorption Spectrum Simulations: Exploring the Landscape beyond the Generalized Gradient Approximation2024In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 15, no 4, p. 969-974Article in journal (Refereed)
    Abstract [en]

    In this Letter, we present a pioneering analysis of the density functional approximations (DFAs) beyond the generalized gradient approximation (GGA) for predicting two-photon absorption (2PA) strengths of a set of push-pull π-conjugated molecules. In more detail, we have employed a variety of meta-generalized gradient approximation (meta-GGA) functionals, including SCAN, MN15, and M06-2X, to assess their accuracy in describing the 2PA properties of a chosen set of 48 organic molecules. Analytic quadratic response theory is employed for these functionals, and their performance is compared against the previously studied DFAs and reference data obtained at the coupled-cluster CC2 level combined with the resolution-of-identity approximation (RI-CC2). A detailed analysis of the meta-GGA functional performance is provided, demonstrating that they improve upon their predecessors in capturing the key electronic features of the π-conjugated two-photon absorbers. In particular, the Minnesota functional MN15 shows very promising results as it delivers pleasingly accurate chemical rankings for two-photon transition strengths and excited-state dipole moments.

  • 7.
    Andersen, Josefine
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Tech Univ Denmark, DTU Chem, Kemitorvet Bldg 207, DK-2800 Lyngby, Denmark.
    Haettig, Christof
    Ruhr Univ Bochum, Arbeitsgrp Quantenchem, D-44780 Bochum, Germany..
    Coriani, Sonia
    Tech Univ Denmark, DTU Chem, Kemitorvet Bldg 207, DK-2800 Lyngby, Denmark..
    Stepanek, Petr
    Univ Oulu, Fac Sci, NMR Res Unit, POB 3000, FI-90014 Oulu, Finland..
    Insights into localization, energy ordering, and substituent effect in excited states of azobenzenes from coupled cluster calculations of nuclear spin-induced circular dichroism2024In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 26, no 12, p. 9179-9196Article in journal (Refereed)
    Abstract [en]

    Nuclear spin-induced circular dichroism (NSCD) is a molecular effect of differential absorption of left- and right-circularly polarized light due to nuclear spins in the molecule. In this work, new tools for its calculation are presented. Specifically, analytic expressions for the computation of the 000000001111110000 000001110000001100 000010000000110110 000010001001100010 000100001011000100 000010010011001100 000001100110110000 000000001110001000 011000001100011000 011100011100011000 000010110100110000 000011100011100000 K term of NSCD have been derived and implemented for the second-order coupled cluster singles and doubles (CC2) model. NSCD results obtained thereby for three derivatives of azobenzenes have been compared with results from time-dependent density functional theory (TD-DFT). The complementary information that could be obtained from NSCD measurements compared to NMR for these three species is discussed. Due to its sensitivity to the local electronic structure, nuclear spin-induced circular dichroism can be used to gain insight into properties of excited states. New computational tools for its calculation are presented.

  • 8. Arja, K.
    et al.
    Selegård, R.
    Paloncyova, Marketa
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Linares, M.
    Lindgren, M.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Aili, D.
    Nilsson, K. P. R.
    Self-Assembly of Chiro-Optical Materials from Nonchiral Oligothiophene-Porphyrin Derivatives and Random Coil Synthetic Peptides2023In: ChemPlusChem, E-ISSN 2192-6506, Vol. 88, no 1, article id e202200262Article in journal (Refereed)
    Abstract [en]

    Biomimetic chiral optoelectronic materials can be utilized in electronic devices, biosensors and artificial enzymes. Herein, this work reports the chiro-optical properties and architectural arrangement of optoelectronic materials generated from self-assembly of initially nonchiral oligothiophene−porphyrin derivatives and random coil synthetic peptides. The photo-physical- and structural properties of the materials were assessed by absorption-, fluorescence- and circular dichroism spectroscopy, as well as dynamic light scattering, scanning electron microscopy and theoretical calculations. The materials display a three-dimensional ordered helical structure and optical activity that are observed due to an induced chirality of the optoelectronic element upon interaction with the peptide. Both these properties are influenced by the chemical composition of the oligothiophene−porphyrin derivative, as well as the peptide sequence. We foresee that our findings will aid in developing self-assembled optoelectronic materials with dynamic architectonical accuracies, as well as offer the possibility to generate the next generation of materials for a variety of bioelectronic applications. 

  • 9.
    Banerjee, Ambar
    et al.
    Department of Physics, Stockholm University, AlbaNova University Center, SE-106 91 Stockholm, Sweden; Department of Physics and Astronomy, X-ray Photon Science, Uppsala University, Ångströmlaboratoriet, Lägerhyddsvägen 1, 75120 Uppsala, Sweden, Lägerhyddsvägen 1.
    Da Cruz, Vinícius Vaz
    Institute Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz Center Berlin for Materials and Energy, 12489 Berlin, Germany.
    Ekholm, Victor
    MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden.
    Såthe, Conny
    MAX IV Laboratory, Lund University, SE-221 00 Lund, Sweden.
    Rubensson, Jan Erik
    Department of Physics and Astronomy, X-ray Photon Science, Uppsala University, Ångströmlaboratoriet, Lägerhyddsvägen 1, 75120 Uppsala, Sweden, Lägerhyddsvägen 1.
    Ignatova, Nina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Gel'mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Institute Methods and Instrumentation for Synchrotron Radiation Research, Helmholtz Center Berlin for Materials and Energy, Berlin, Germany.
    Odelius, Michael
    Department of Physics, Stockholm University, AlbaNova University Center, SE-106 91 Stockholm, Sweden.
    Simulating fluorine K -edge resonant inelastic x-ray scattering of sulfur hexafluoride and the effect of dissociative dynamics2023In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 108, no 2, article id 023103Article in journal (Refereed)
    Abstract [en]

    We report on a computational study of resonant inelastic x-ray scattering (RIXS), at different fluorine K-edge resonances of the SF6 molecule, and corresponding nonresonant x-ray emission. Previously measured polarization dependence in RIXS is reproduced and traced back to the local σ and π symmetry of the molecular orbitals and corresponding states involved in the RIXS process. Also electron-hole coupling energies are calculated and related to experimentally observed spectator shifts. The role of dissociative S-F bond dynamics is explored to model detuning of RIXS spectra at the |F1s-16a1g1) resonance, which shows challenges to accurately reproduce the required steepness for core-excited potential energy surface. We show that the RIXS spectra can only be properly described by considering breaking of the global inversion symmetry of the electronic wave function and core-hole localization, induced by vibronic coupling. Due to the core-hole localization we have symmetry forbidden transitions, which lead to additional resonances and changing width of the RIXS profile.

  • 10.
    Barreau, Lou
    et al.
    Department of Chemistry, University of California, Berkeley, California 94720, USA; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
    Ross, Andrew D.
    Department of Chemistry, University of California, Berkeley, California 94720, USA; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
    Kimberg, Victor
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Krasnov, Pavel
    International Research Center of Spectroscopy and Quantum Chemistry-IRC SQC, Siberian Federal University, Krasnoyarsk 660041, Russia.
    Blinov, Svyatoslav
    International Research Center of Spectroscopy and Quantum Chemistry-IRC SQC, Siberian Federal University, Krasnoyarsk 660041, Russia.
    Neumark, Daniel M.
    Department of Chemistry, University of California, Berkeley, California 94720, USA; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
    Leone, Stephen R.
    Department of Chemistry, University of California, Berkeley, California 94720, USA; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; Department of Physics, University of California, Berkeley, California 94720, USA.
    Core-excited states of Formula Presented probed with soft-x-ray femtosecond transient absorption of vibrational wave packets2023In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 108, no 1, article id 012805Article in journal (Refereed)
    Abstract [en]

    A vibrational wavepacket in Formula Presented is created by impulsive stimulated Raman scattering with a few-cycle infrared pulse and mapped simultaneously onto five sulfur core-excited states using table-top soft x-ray transient absorption spectroscopy between 170 to 200 eV. The femtosecond vibrations induce real-time energy shifts of the x-ray absorption, whose amplitude depend strongly on the nature of the core-excited state. The pump laser intensity is used to control the number of vibrational states in the superposition, thereby accessing core-excited levels for various extensions of the S-F stretching motion. This enables the determination of the relative core-level potential energy gradients for the symmetric stretching mode, in good agreement with TDDFT calculations. This experiment demonstrates a new means of characterizing core-excited potential energy curves.

  • 11.
    Bhowmick, Asmit
    et al.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Hussein, Rana
    Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany.
    Bogacz, Isabel
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Simon, Philipp S.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Ibrahim, Mohamed
    Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany; Institute of Molecular Medicine, University of Lübeck, Lübeck, Germany.
    Chatterjee, Ruchira
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Doyle, Margaret D.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Cheah, Mun Hon
    Molecular Biomimetics, Department of Chemistry — Ångström, Uppsala University, Uppsala, Sweden.
    Fransson, Thomas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Chernev, Petko
    Molecular Biomimetics, Department of Chemistry — Ångström, Uppsala University, Uppsala, Sweden.
    Kim, In Sik
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Makita, Hiroki
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Dasgupta, Medhanjali
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Kaminsky, Corey J.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Zhang, Miao
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Gätcke, Julia
    Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany.
    Haupt, Stephanie
    Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany.
    Nangca, Isabela I.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Keable, Stephen M.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Aydin, A. Orkun
    Molecular Biomimetics, Department of Chemistry — Ångström, Uppsala University, Uppsala, Sweden.
    Tono, Kensuke
    Japan Synchrotron Radiation Research Institute, Hyogo, Japan; RIKEN SPring-8 Center, Hyogo, Japan.
    Owada, Shigeki
    Japan Synchrotron Radiation Research Institute, Hyogo, Japan; RIKEN SPring-8 Center, Hyogo, Japan.
    Gee, Leland B.
    Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
    Fuller, Franklin D.
    Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
    Batyuk, Alexander
    Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
    Alonso-Mori, Roberto
    Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
    Holton, James M.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA; SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
    Paley, Daniel W.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Moriarty, Nigel W.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Mamedov, Fikret
    Molecular Biomimetics, Department of Chemistry — Ångström, Uppsala University, Uppsala, Sweden.
    Adams, Paul D.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Bioengineering, University of California, Berkeley, CA, USA.
    Brewster, Aaron S.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Dobbek, Holger
    Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany.
    Sauter, Nicholas K.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Bergmann, Uwe
    Department of Physics, University of Wisconsin–Madison, Madison, WI, USA.
    Zouni, Athina
    Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany.
    Messinger, Johannes
    Molecular Biomimetics, Department of Chemistry — Ångström, Uppsala University, Uppsala, Sweden; Department of Chemistry, Umeå University, Umeå, Sweden.
    Kern, Jan
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Yano, Junko
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Yachandra, Vittal K.
    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
    Structural evidence for intermediates during O2 formation in photosystem II2023In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 617, no 7961, p. 629-636Article in journal (Refereed)
    Abstract [en]

    In natural photosynthesis, the light-driven splitting of water into electrons, protons and molecular oxygen forms the first step of the solar-to-chemical energy conversion process. The reaction takes place in photosystem II, where the Mn4CaO5 cluster first stores four oxidizing equivalents, the S0 to S4 intermediate states in the Kok cycle, sequentially generated by photochemical charge separations in the reaction center and then catalyzes the O–O bond formation chemistry1–3. Here, we report room temperature snapshots by serial femtosecond X-ray crystallography to provide structural insights into the final reaction step of Kok’s photosynthetic water oxidation cycle, the S3→[S4]→S0 transition where O2 is formed and Kok’s water oxidation clock is reset. Our data reveal a complex sequence of events, which occur over micro- to milliseconds, comprising changes at the Mn4CaO5 cluster, its ligands and water pathways as well as controlled proton release through the hydrogen-bonding network of the Cl1 channel. Importantly, the extra O atom Ox, which was introduced as a bridging ligand between Ca and Mn1 during the S2→S3 transition4–6, disappears or relocates in parallel with Yz reduction starting at approximately 700 μs after the third flash. The onset of O2 evolution, as indicated by the shortening of the Mn1–Mn4 distance, occurs at around 1,200 μs, signifying the presence of a reduced intermediate, possibly a bound peroxide.

  • 12.
    Björk, Linnea
    et al.
    Department of Physics Chemistry and Biology Linköping University SE-581 83 Linköping Sweden.
    Shirani, Hamid
    Department of Physics Chemistry and Biology Linköping University SE-581 83 Linköping Sweden.
    Todarwal, Yogesh
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Vidal, Ruben
    Department of Pathology and Laboratory Medicine Indiana University School of Medicine Indianapolis 46202 Indiana USA.
    Ghetti, Bernardino
    Department of Pathology and Laboratory Medicine Indiana University School of Medicine Indianapolis 46202 Indiana USA.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Klingstedt, Therése
    Department of Physics Chemistry and Biology Linköping University SE-581 83 Linköping Sweden.
    Nilsson, K. Peter R.
    Department of Physics Chemistry and Biology Linköping University SE-581 83 Linköping Sweden.
    Distinct Heterocyclic Moieties Govern the Selectivity of Thiophene‐Vinylene‐Based Ligands towards Aβ or Tau Pathology in Alzheimer's Disease2023In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, Vol. 26, no 41, p. e202300583-Article in journal (Refereed)
    Abstract [en]

    Distinct aggregated proteins are correlated with numerous neurodegenerative diseases and the development of ligands that selectively detect these pathological hallmarks is vital. Recently, the synthesis of thiophene-based optical ligands, denoted bi-thiophene-vinyl-benzothiazoles (bTVBTs), that could be utilized for selective assignment of tau pathology in brain tissue with Alzheimer's disease (AD) pathology, was reported. Herein, we investigate the ability of these ligands to selectively distinguish tau deposits from aggregated amyloid-β (Aβ), the second AD associated pathological hallmark, when replacing the terminal thiophene moiety with other heterocyclic motifs. The selectivity for tau pathology was reduced when introducing specific heterocyclic motifs, verifying that specific molecular interactions between the ligands and the aggregates are necessary for selective detection of tau deposits. In addition, ligands having certain heterocyclic moieties attached to the central thiophene-vinylene building block displayed selectivity to aggregated Aβ pathology. Our findings provide chemical insights for the development of ligands that can distinguish between aggregated proteinaceous species consisting of different proteins and might also aid in creating novel agents for clinical imaging of tau pathology in AD.

  • 13.
    Blinov, Svyatoslav N.
    et al.
    International Research Center of Spectroscopy and Quantum Chemistry - IRC SQC, Siberian Federal University, 660041 Krasnoyarsk, Russia.
    Kimberg, Victor V.
    International Research Center of Spectroscopy and Quantum Chemistry - IRC SQC, Siberian Federal University, 660041 Krasnoyarsk, Russia.
    Krasnov, Pavel O.
    International Research Center of Spectroscopy and Quantum Chemistry - IRC SQC, Siberian Federal University, 660041 Krasnoyarsk, Russia.
    Gelmukhanov, Faris Kh
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. International Research Center of Spectroscopy and Quantum Chemistry - IRC SQC, Siberian Federal University, 660041 Krasnoyarsk, Russia.
    Polyutov, Sergey P.
    International Research Center of Spectroscopy and Quantum Chemistry - IRC SQC, Siberian Federal University, 660041 Krasnoyarsk, Russia.
    Mapping molecular potentials using pump-probe spectroscopy of vibrational wave packets' revival2023In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 108, no 1, article id 013104Article in journal (Refereed)
    Abstract [en]

    In this study, we investigate the nuclear dynamics in nitrogen monoxide after valence ionization by a pump pulse and subsequent probing with a time-delayed x-ray pulse. We calculate the development of the resulting vibrational wave packet, taking into account three different ionization mechanisms: one-photon, multiphoton, and tunneling ionization. Using a two-time propagation method, we solve the nonstationary nuclear Schrödinger equation to obtain time-resolved x-ray absorption spectra (TRXAS), considering the finite duration of the probe pulse. Our simulations show that the TRXAS profile accurately reflects the vibrational wave packets' trajectory in the cationic ground state. Additionally, we find that the TRXAS evolution is highly sensitive to small changes in the probed potential energy curve, making it a useful tool for reconstructing molecular potentials and determining anharmonicity and equilibrium bond length. This method can be applied to other polyatomic molecules and pump mechanisms.

  • 14.
    Brand, Manuel
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Implementation of complex polarization propagator theory for linear response properties of large molecular systems2022Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Since its beginning, the remarkable development from the first commercially available computers toward exascale supercomputers just within the span of a lifetime has been closely intertwined with the perpetual quest for the utilization of the arising computing power for the avail of theoretical chemistry. With the aim of further pushing the limits of computationally accessible molecular system sizes, this thesis includes the presentation of programming efforts, which brought forth two quantum chemical software codes, as well as a range of ab initio studies on carbon-based systems, enabled by the former.

    The VeloxChem and Gator programs, developed for spectroscopy simulations at the level of density-functional theory (DFT) and correlated wave function methods, respectively, employ a hybrid message passing interface (MPI)/open multiprocessing (OpenMP) parallelization scheme embedded in a modular program structure written in a Python/C++ layered fashion for the execution in contemporary high-performance computing (HPC) environments. Included numerical solvers for the evaluation of real and complex linear response functions in combination with the parallel construction of auxiliary Fock matrices enable the efficient calculation of one-photon absorption or electronic circular dichroism (CD) spectra in the ultraviolet/visible (UV/vis) or X-ray spectral region, as well as van der Waals C6 dispersion coefficients.

    Employing the VeloxChem program in two comprehensive investigations, the C6 dispersion coefficients of carbon fullerenes up to a system size of C540 and the CD spectra of carbohelicenes ranging from CH[5] to CH[30] have been calculated at the DFT level of theory. The revealed non-additive scaling with respect to the number of carbon atoms of N2.2 in the former and nontrivial CD band progressions, arguably linked to the number of overlapping layers in the helical conjugated systems, in the latter rectify the current conception in their respective fields.

    In a benchmark for the Gator program on a series of guanine oligomers, the full UV/vis spectrum for a tetrad was calculated at the level of a second-order algebraic-diagrammatic construction (ADC(2)) scheme in just under 15 hours by efficient employment of 32,768 central processing unit (CPU) cores.

    Exceeding the limit of 10,000 and 1,000 contracted basis functions for a treatment with the DFT and ADC(2) methods, respectively, these practical examples demonstrate the capability of VeloxChem and Gator to harness vast computational resources made available by contemporary and future HPC systems and thereby routinely address scopes of system sizes that were previously out of reach.

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  • 15.
    Brand, Manuel
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Ruprecht Karls Univ Heidelberg, Interdisciplinary Ctr Sci Comp, D-69120 Heidelberg, Germany..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Efficient and Parallel Implementation of Real and Complex Response Functions Employing the Second-Order Algebraic-Diagrammatic Construction Scheme for the Polarization Propagator2023In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 20, no 1, p. 103-113Article in journal (Refereed)
    Abstract [en]

    We present the implementation of an efficient matrix-folded formalism for the evaluation of complex response functions and the calculation of transition properties at the level of the second-order algebraic-diagrammatic construction (ADC(2)) scheme. The underlying algorithms, in combination with the adopted hybrid MPI/OpenMP parallelization strategy, enabled calculations of the UV/vis spectra of a guanine oligomer series ranging up to 1032 contracted basis functions, thereby utilizing vast computational resources from up to 32,768 CPU cores. Further analysis of the convergence behavior of the involved iterative subspace algorithms revealed the superiority of a frequency-separated treatment of response equations even for a large spectral window, including 101 frequencies. We demonstrate the applicability to general quantum mechanical operators by the first reported electronic circular dichroism spectrum calculated with a complex polarization propagator approach at the ADC(2) level of theory.

  • 16.
    Brand, Manuel
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Efficient parallel implementation of complex response functions employing the algebraic-diagrammatic construction schemeManuscript (preprint) (Other academic)
    Abstract [en]

    We present the derivation and implementation of an efficient matrix-folded formalism for the evaluation of complex response functions at the level of the second-order algebraic-diagrammatic construction ADC(2) scheme. The adopted hybrid MPI/OpenMP parallelization strategy enables the utilization of vast computational resources without significant performance losses as demonstrated by consistent size-scalings for the computationally most demanding steps obtained from calculations of the UV/vis spectra of a guanine oligomer series ranging up to 1,032 contracted basis functions. Further analysis of the convergence behavior of the involved iterative subspace algorithm revealed the superiority of a frequency-separated treatment of response equations even for a large spectral window including 101 frequencies. We demonstrate the applicability to general quantum mechanical operators by the first reported electric circular dichroism spectrum calculated with the complex polarization propagator approach at the ADC(2) level of theory.

  • 17.
    Brumboiu, Iulia E.
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Ericsson, L. K.
    Blazinic, V.
    Hansson, R.
    Opitz, A.
    Brena, B.
    Moons, E.
    Photooxidation of PC60BM: new insights from spectroscopy2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 42, p. 25753-25766Article in journal (Refereed)
    Abstract [en]

    This joint experimental-theoretical spectroscopy study of the fullerene derivative PC60BM ([6,6]-phenyl-C60-butyric acid methyl ester) aims to improve the understanding of the effect of photooxidation on its electronic structure. We have studied spin-coated thin films of PC60BM by X-ray Photoelectron Spectroscopy (XPS), Near-edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy, and Fourier Transform Infrared Spectroscopy (FTIR), before and after intentional exposure to simulated sunlight in air for different lengths of time. The π* resonance in the C1s NEXAFS spectrum was found to be a very sensitive probe for the early changes to the fullerene cage, while FTIR spectra, in combination with O1s NEXAFS spectra, enabled the identification of the oxidation products. The changes observed in the spectra obtained by these complementary methods were compared with the corresponding Density Functional Theory (DFT) calculated single-molecule spectra of a large set of in silico generated oxidation products of PC60BM where oxygen atoms were attached to the C60 cage. This comparison confirms that photooxidation of PC60BM disrupts the conjugation of the fullerene cage by a transition from sp2 to sp3-hybridized carbon and causes the formation of several oxidation products, earlier proposed for C60. The agreement between experimental and calculated IR spectra suggests moreover the presence of dicarbonyl and anhydride structures on the fullerene cage, in combination with cage opening at the adsorption site. By including PC60BM with physisorbed O2 molecules on the cage in our theoretical description in order to model oxygen diffused through the film, the experimental O1s XPS and O1s NEXAFS spectra could be reproduced.

  • 18.
    Chakraborty, Pratip
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Couto, Rafael Carvalho
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Holmgaard List, Nanna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Deciphering Methylation Effects on S2(ππ*) Internal Conversion in the Simplest Linear α,β-Unsaturated Carbonyl2023In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 127, no 25, p. 5360-5373Article in journal (Refereed)
    Abstract [en]

    Chemical substituents can influence photodynamics by altering the location of critical points and the topography of the potential energy surfaces (electronic effect) and by selectively modifying the inertia of specific nuclear modes (inertial effects). Using nonadiabatic dynamics simulations, we investigate the impact of methylation on S2(ππ*) internal conversion in acrolein, the simplest linear α,β-unsaturated carbonyl. Consistent with time constants reported in a previous time-resolved photoelectron spectroscopy study, S2 → S1 deactivation occurs on an ultrafast time scale (∼50 fs). However, our simulations do not corroborate the sequential decay model used to fit the experiment. Instead, upon reaching the S1 state, the wavepacket bifurcates: a portion undergoes ballistic S1 → S0 deactivation (∼90 fs) mediated by fast bond-length alternation motion, while the remaining decays on the picosecond time scale. Our analysis reveals that methyl substitution, generally assumed to mainly exert inertial influence, is also manifested in important electronic effects due to its weak electron-donating ability. While methylation at the β C atom gives rise to effects principally of an inertial nature, such as retarding the twisting motion of the terminal −CHCH3 group and increasing its coupling with pyramidalization, methylation at the α or carbonyl C atom modifies the potential energy surfaces in a way that also contributes to altering the late S1-decay behavior. Specifically, our results suggest that the observed slowing of the picosecond component upon α-methylation is a consequence of a tighter surface and reduced amplitude along the central pyramidalization, effectively restricting the access to the S1/S0-intersection seam. Our work offers new insight into the S2(ππ*) internal conversion mechanisms in acrolein and its methylated derivatives and highlights site-selective methylation as a tuning knob to manipulate photochemical reactions.

  • 19.
    Chakraborty, Pratip
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States.
    Liu, Y.
    McClung, S.
    Weinacht, T.
    Matsika, S.
    Nonadiabatic Excited State Dynamics of Organic Chromophores: Take-Home Messages2022In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 126, no 36, p. 6021-6031Article in journal (Refereed)
    Abstract [en]

    Nonadiabatic excited state dynamics are important in a variety of processes. Theoretical and experimental developments have allowed for a great progress in this area, while combining the two is often necessary and the best approach to obtain insight into the photophysical behavior of molecules. In this Feature Article we use examples of our recent work combining time-resolved photoelectron spectroscopy with theoretical nonadiabatic dynamics to highlight important lessons we learned. We compare the nonadiabatic excited state dynamics of three different organic molecules with the aim of elucidating connections between structure and dynamics. Calculations and measurements are compared for uracil, 1,3-cyclooctadiene, and 1,3-cyclohexadiene. The comparison highlights the role of rigidity in influencing the dynamics and the difficulty of capturing the dynamics accurately with calculations. 

  • 20.
    Chakraborty, Pratip
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Matsika, Spiridoula
    Department of Chemistry, Temple University, Philadelphia, Pennsylvania, USA.
    Time-resolved photoelectron spectroscopy via trajectory surface hopping2024In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, E-ISSN 1759-0884, Vol. 14, no 3, article id e1715Article, review/survey (Refereed)
    Abstract [en]

    Time-resolved photoelectron spectroscopy is a powerful pump-probe technique which can probe nonadiabatic dynamics in molecules. Interpretation of the experimental signals however requires input from theoretical simulations. Advances in electronic structure theory, nonadiabatic dynamics, and theory to calculate the ionization yields, have enabled accurate simulation of time-resolved photoelectron spectra leading to successful applications of the technique. We review the basic theory and steps involved in calculating time-resolved photoelectron spectra, and highlight successful applications. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Theoretical and Physical Chemistry > Spectroscopy.

  • 21.
    Cheng, Xiao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Multiplet computation methods for core level X-ray spectroscopy of transition metal and rare earth elements2023Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    With the development of new generation synchrotron facilities, the performances of various X-ray spectroscopies have become more advanced. In order to interpret the X-ray spectrum experiments of various novel materials related to transition metal and rare earth elements, new advanced theoretical methods are required. The present thesis incorporates four modus operandi based on the classic multiplet theory to study the core level X-ray spectroscopy of transition metal and rare earth element. The four approaches consist of new methods developed from classic multiplet approach to high level first-principles method assisted multiplet calculation. Some methods are selected from previous researches and some are invented by original researches. These methods are integrated together to form a complete set of multiplet computational methods. This set of multiplet computational methods can perform calculations on various X-ray spectroscopies such as XAS, XPS, XES and RIXS related to the core-level electron. These wide range of spectroscopic methods coupled to different multiplet theory approaches serve as efficient tools to understand the electronic structure of metal sites and their unique contribution to the physical/chemical properties of the materials.

    The thesis creatively improves the classic multiplet theory on several aspects: (1) the relation between crystal field parameters and local structure factors; (2) the difficulty of processing point group symmetry branching chain in low symmetric structure; (3) the first-principles calculation of semi-empirical parameters. Four modus operandi are presented in this thesis: the first is the classic multiplet theory consisting of the multiplet effect, crystal field effect and charge transfer effect via several semi-empirical parameters as description for these effects. The second level multiplet theoretical approach analyze the crystal field potential matrix in various symmetries according to the point group symmetry branching rules. Then the crystal field effect parameters used in classic multiplet theory are linked analytically to the specific structural factors such as bond length and angles. This approach is a good tool to study the structural distortion from higher to lower order symmetry with analysis of X-ray spectral feature changes in experiment. The third modus operandi adopts large cluster model consisting of point charges at equivalent atoms position to simulate the crystal field effect on the center metal site. This approach handles low order symmetric crystal field with long range effect in multiplet calculation in an easier way than the classic multiplet theory. The fourth modus operandi initially studies the system of interest in first-principles calculation for the electronic wavefunctions. Then the electronic wavefunctions are used to derive the maximally localized Wannier functions at metal/ligand sites. The analysis of these Wannier functions provide a lot of semi-empirical parameters required in the classic multiplet calculation approach in a first-principles way. This modus operandi has substantially resolved the problem of finding the best set of semi-empirical parameters to fit the calculated X-ray spectrum with experimental data.

    In order to study the core electrons of the light elements (such as C/N/O) around center metal ions, a theoretical calculation method used to study the core electrons' vibrationally-resolved X-ray spectroscopy is also introduced as a complementary research and applied to C1s core ionized XPS calculation as an example.

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  • 22.
    Cheng, Xiao
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Department of Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden ; Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720.
    Guo, Jinghua
    Glans, Per-Anders
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China.
    The High-Spin and Low-Spin States of Co(III) Ion in Co3O4 Studied by X-ray Absorption SpectroscopyManuscript (preprint) (Other academic)
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  • 23.
    Cheng, Xiao
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China.
    Guo, Jinghua
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China.
    Multiplet Ligand-Field Calculation of Co L-edge X-ray Absorption Spectrum using Parameters from DFT Wannier FunctionsManuscript (preprint) (Other academic)
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  • 24.
    Cheng, Xiao
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China.
    Guo, Jinghua
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China.
    Multiplet Ligand-Field Calculation of Co L-edge X-ray Absorption Spectrum using Parameters from DFT Wannier Functions AnalysisManuscript (preprint) (Other academic)
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  • 25.
    Cheng, Xiao
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, 230026 Hefei, China.
    Wei, Minrui
    Tian, Guangjun
    Hua, Weijie
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, 230026 Hefei, China.
    High-Resolution Vibrationally-Resolved X-ray Photoelectron Spectra of Linear Alkanes CnH2n+2 (n=1-8)Manuscript (preprint) (Other academic)
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  • 26.
    Cheng, Xiao
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, 230026 Hefei, China.
    Wei, Minrui
    Tian, Guangjun
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, 230026 Hefei, China.
    Hua, Weijie
    High-Resolution Vibrationally-Resolved X-ray Photoelectron Spectra of Linear Alkanes C$_{n}$H$_{2n+2}$ ($n$=1-8)Manuscript (preprint) (Other academic)
  • 27.
    Cheng, Xiao
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, 230026 Hefei, China;Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
    Wei, Minrui
    MIIT Key Laboratory of Semiconductor Microstructure and Quantum Sensing, Department of Applied Physics, School of Science, Nanjing University of Science and Technology, 210094 Nanjing, China.
    Tian, Guangjun
    Key Laboratory for Microstructural Material Physics of Hebei Province, School of Science, Yanshan University, Qinhuangdao 066004, China.
    Luo, Yi
    Hefei National Laboratory for Physical Science at the Microscale, University of Science and Technology of China, 230026 Hefei, China.
    Hua, Weijie
    MIIT Key Laboratory of Semiconductor Microstructure and Quantum Sensing, Department of Applied Physics, School of Science, Nanjing University of Science and Technology, 210094 Nanjing, China.
    Vibrationally-Resolved X-ray Photoelectron Spectra of Six Polycyclic Aromatic Hydrocarbons from First-Principles Simulations2022In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 126, no 33, p. 5582-5593Article in journal (Refereed)
    Abstract [en]

    Vibrationally resolved C 1s X-ray photoelectron spectra (XPS) of a series of six polycyclic aromatic hydrocarbons (PAHs; phenanthrene, coronene, naphthalene, anthracene, tetracene, and pentacene) were computed by combining the full core hole density functional theory and the Franck–Condon simulations with the inclusion of the Duschinsky rotation effect. Simulated spectra of phenanthrene, coronene, and naphthalene agree well with experiments both in core binding energies (BEs) and profiles, which validate the accuracy of our predictions for the rest molecules with no high-resolution experiments. We found that three types of carbons i (inner C), p (peripheral C bonded to three C atoms), and h (peripheral C bonded to an H atom) show decreasing BEs. In linear PAHs (the latter four), h-type carbons further split into h1 or h2 (on inner or edge benzene ring) subtypes with chemical shifts of ca. 0.2–0.4 eV. All major Franck–Condon-active modes are characterized to be in-plane vibrations: low-frequency (<800 cm–1) C–C ring deformation modes play an essential role in determining the peak asymmetries; and for each h-type carbon a high-frequency (ca. 3600 cm–1) C*–H stretching mode is responsible for the high-energy tail. We found that core ionization leads to reduction of all C*–C and C*–H bond lengths and ring deformation with a definite direction. Based on theoretical spectra of four linear PAHs, we found asymptotic relations and anticipated possible spectral features for even larger linear PAHs. Our calculations provide accurate reference spectra for XPS characterizations of PAHs, which are useful in understanding the vibronic coupling effects in this family. 

  • 28.
    Colozza, Noemi
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry. Univ Roma Tor Vergata, Dept Chem Sci & Technol, Via Ric Sci, I-00133 Rome, Italy..
    Casanova, Ana
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Fernandez-Perez, Bibiana M.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Crespo, Gaston A.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Flores, Gabriel A.
    Florida Int Univ, Dept Chem & Biochem, 11200 SW 8th St, Miami, FL 33199 USA.;Florida Int Univ, Biomol Sci Inst, 11200 SW 8th St, Miami, FL 33199 USA..
    Kavallieratos, Konstantinos
    Florida Int Univ, Dept Chem & Biochem, 11200 SW 8th St, Miami, FL 33199 USA.;Florida Int Univ, Biomol Sci Inst, 11200 SW 8th St, Miami, FL 33199 USA..
    Juan Angel, de Gracia Triviño
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Cuartero, Maria
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Insights into Tripodal Tris(pyrazolyl) Compounds as Ionophores for Potentiometric Ammonium Ion Sensing2022In: ChemElectroChem, E-ISSN 2196-0216, Vol. 9, no 18, article id e202200716Article in journal (Refereed)
    Abstract [en]

    The decentralisation of accurate determination of the ammonium ion (NH4+) is relevant for environmental monitoring (i. e., nitrogen cycle) and certain clinical applications (e. g., kidney and liver diseases). Potentiometric ionophore-based sensors are one alternative for these purposes in terms of versatile implementation, though the potassium ion (K+) is known to be a major source of interference. We herein investigate the use of three different tripodal tris(pyrazolyl) compounds derived from 1,3,5-triethylbenzene as NH4+ ionophores. A complete set of potentiometric experiments together with theoretical simulations reveals suitable analytical performance while demonstrating a suppression of the K+ interference given the formation of an adequate cavity in the ionophore to host NH4+ over K+ in the membrane environment. The results support the use of these electrodes in the analytical detection of NH4+ in a wide range of samples with variable contents.

  • 29.
    Cui, Jun Jie
    et al.
    School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710119, China.
    Cheng, Yongjun
    School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710119, China.
    Wang, Xin
    School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710119, China.
    Li, Zheng
    State Key Laboratory for Mesoscopic Physics and Collaborative Innovation Center of Quantum Matter, School of Physics, Peking University, Beijing 100871, China; Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China, Shanxi; Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, China.
    Rohringer, Nina
    Center for Free-Electron Laser Science CFEL, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany.
    Kimberg, Victor
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Zhang, Song Bin
    School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710119, China.
    Proposal for Observing XUV-Induced Rabi Oscillation Using Superfluorescent Emission2023In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 131, no 4, article id 043201Article in journal (Refereed)
    Abstract [en]

    Intense x-ray and extreme ultraviolet (XUV) light sources have been available for decades, however, due to weak nonlinear interaction in the XUV photon energy range, observation of Rabi oscillation induced by XUV pulse remains a very challenging experimental task. Here we suggest a scheme where photoionization of a He medium by an intense XUV pump pulse is followed by a strong population inversion and Rabi oscillation at the He+(1s-3p) transition and is accompanied by superfluorescence (SF) of the 7.56 eV pulse at the He+(3p-2s) transition. Our numerical simulations show that the Rabi oscillation at the He+(1s-3p) transition induced by an XUV pulse with photon energy 48.36 eV results in significant signatures in the SF spectra, allowing us to identify and characterize the XUV induced Rabi-oscillatory regime. The proposed scheme provides a sensitive tool to monitor and control ultrafast nonlinear dynamics in atoms and molecules triggered by intense XUV.

  • 30.
    De Gracia Triviño, Juan Angel
    et al.
    Department of Microtechnology and Nanoscience - MC2, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.
    Delcey, Mickael G
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Division of Theoretical Chemistry, Department of Chemistry, Lund University, SE-223 62 Lund, Sweden.
    Wendin, Göran
    Department of Microtechnology and Nanoscience - MC2, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.
    Complete Active Space Methods for NISQ Devices: The Importance of Canonical Orbital Optimization for Accuracy and Noise Resilience2023In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 19, no 10, p. 2863-2872Article in journal (Refereed)
    Abstract [en]

    To avoid the scaling of the number of qubits with the size of the basis set, one can divide the molecular space into active and inactive regions, which is also known as complete active space methods. However, selecting the active space alone is not enough to accurately describe quantum mechanical effects such as correlation. This study emphasizes the importance of optimizing the active space orbitals to describe correlation and improve the basis-dependent Hartree-Fock energies. We will explore classical and quantum computation methods for orbital optimization and compare the chemically inspired ansatz, UCCSD, with the classical full CI approach for describing the active space in both weakly and strongly correlated molecules. Finally, we will investigate the practical implementation of a quantum CASSCF, where hardware-efficient circuits must be used and noise can interfere with accuracy and convergence. Additionally, we will examine the impact of using canonical and noncanonical active orbitals on the convergence of the quantum CASSCF routine in the presence of noise.

  • 31.
    De Oliveira, Danilo Hirabae
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Biler, Michal
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Mim, Carsten
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Biomedical Engineering and Health Systems, Structural Biotechnology.
    Nilebäck, Linnea
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Kvick, Mathias
    Spiber Technol AB, SE-11428 Stockholm, Sweden..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Linares, Mathieu
    Linköping Univ, Lab Organ Elect, SE-58183 Linköping, Sweden.;Linköping Univ, Sci Visualizat Grp, ITN, SE-58183 Linköping, Sweden..
    Hedhammar, My
    KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Silk Assembly against Hydrophobic Surfaces?Modeling and Imaging of Formation of Nanofibrils2023In: ACS Applied Bio Materials, E-ISSN 2576-6422, Vol. 6, no 3, p. 1011-1018Article in journal (Refereed)
    Abstract [en]

    A detailed insight about the molecular organization behind spider silk assembly is valuable for the decoding of the unique properties of silk. The recombinant partial spider silk protein 4RepCT contains four poly-alanine/glycine-rich repeats followed by an amphiphilic C-terminal domain and has shown the capacity to self-assemble into fibrils on hydrophobic surfaces. We herein use molecular dynamic simulations to address the structure of 4RepCT and its different parts on hydrophobic versus hydrophilic surfaces. When 4RepCT is placed in a wing arrangement model and periodically repeated on a hydrophobic surface, fi-sheet structures of the poly-alanine repeats are preserved, while the CT part is settled on top, presenting a fibril with a height of similar to 7 nm and a width of similar to 11 nm. Both atomic force microscopy and cryo-electron microscopy imaging support this model as a possible fibril formation on hydrophobic surfaces. These results contribute to the understanding of silk assembly and alignment mechanism onto hydrophobic surfaces.

  • 32. Dreuw, A.
    et al.
    Fransson, Thomas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Using core-hole reference states for calculating X-ray photoelectron and emission spectra2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084Article in journal (Refereed)
    Abstract [en]

    For the calculation of core-ionization energies (IEs), X-ray photoelectron spectra (XPS), and X-ray emission spectra (XES), a commonly applied approach is to use non-Aufbau reference states with a core-hole as either final (IE and XPS) or initial (XES) state. However, such reference states can introduce numerical instabilities in post-HF methods, relating to the denominator of the energy corrections involved. This may become arbitrarily close to zero if a negative virtual orbital is present, e.g. a core-hole, leading to near-singularities. The resulting instabilities lead to severe convergence issues of the calculation schemes and, in addition, can strongly affect both energies and intensities, with oscillator strengths seen to reach values up to 4 × 107. For the K-edge we propose freezing the highest-energy virtual orbitals which contribute to any denominator below a threshold of 0.1 Hartree. Stable and reliable spectra are then produced, with minimal influence due to freezing energetically high-lying virtual orbitals (typically removing &lt;5% of the total number of MOs). The developed protocol is here tested for Møller-Plesset perturbation theory and for the algebraic diagrammatic construction scheme for the polarization propagator, and it is also relevant for coupled cluster theory and other related methods.

  • 33.
    Fransson, Thomas
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Delcey, Mickael G
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Brumboiu, Iulia Emilia
    Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, 87-100 Toruń, Poland.
    Hodecker, Manuel
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Dreuw, Andreas
    Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany, Im Neuenheimer Feld 205.
    Rhee, Young Min
    Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    eChem: A Notebook Exploration of Quantum Chemistry2023In: Journal of Chemical Education, ISSN 0021-9584, E-ISSN 1938-1328, Vol. 100, no 4, p. 1664-1671Article in journal (Refereed)
    Abstract [en]

    The eChem project features an e-book published as a web page (10.30746/978-91-988114-0-7), collecting a repository of Jupyter notebooks developed for the dual purpose of explaining and exploring the theory underlying computational chemistry in a highly interactive manner as well as providing a tutorial-based presentation of the complex workflows needed to simulate embedded molecular systems of real biochemical and/or technical interest. For students ranging from beginners to advanced users, the eChem book is well suited for self-directed learning, but workshops led by experienced instructors and targeting student bodies with specific needs and interests can readily be formed from its components. This has been done by using eChem as the base for a workshop directed toward graduate students learning the theory and practices of quantum chemistry, resulting in very positive assessment of the interactive nature of this framework. The members of the eChem team are engaged in both education and research, and as a mirroring activity, we develop the open-source software upon which this e-book is predominantly based. The overarching vision and goal of our work is to provide a science- and education-enabling software platform for quantum molecular modeling on contemporary and future high-performance computing systems, and to document the resulting development and workflows in the eChem book.

  • 34.
    Gel'mukhanov, Faris
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. International Research Center of Spectroscopy and Quantum Chemistry - IRC SQC, Siberian Federal University, 660041 Krasnoyarsk, Russia.
    Liu, Ji Cai
    School of Mathematics and Physics, North China Electric Power University, 102206 Beijing, China; Hebei Key Laboratory of Physics and Energy Technology, North China Electric Power University, 071000 Baoding, China.
    Krasnov, Pavel
    International Research Center of Spectroscopy and Quantum Chemistry - IRC SQC, Siberian Federal University, 660041 Krasnoyarsk, Russia.
    Ignatova, Nina
    International Research Center of Spectroscopy and Quantum Chemistry - IRC SQC, Siberian Federal University, 660041 Krasnoyarsk, Russia.
    Rubensson, Jan Erik
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120 Uppsala, Sweden.
    Kimberg, Victor
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Nonlocal resonant inelastic x-ray scattering2023In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 108, no 5, article id 052820Article in journal (Refereed)
    Abstract [en]

    In the description of resonant inelastic x-ray scattering (RIXS) from inversion-symmetric molecules the small core-level splitting is typically neglected. However, the spacing Δ between gerade and ungerade core levels in homonuclear diatomic molecules can be comparable with the lifetime broadening of the intermediate core-excited state Γ. We show that when Δ∼Γ the scattering becomes nonlocal in the sense that x-ray absorption at one atomic site is followed by emission at the other one. This is manifested in an unusual dependence of the RIXS cross section on the sum of the momenta of incoming and outgoing x-ray photons k+k′, contrary to the normal k-k′ dependence in the conventional local RIXS theory. The nonlocality of the scattering influences strongly the scattering angle and excitation energy dependence of the intensity ratio between parity forbidden and allowed RIXS channels. Numerical simulations for N2 show that this effect can readily be measured at present-day x-ray radiation facilities.

  • 35.
    Gonzalez-Sanchez, Marina
    et al.
    Univ Autoonoma Madrid, Organ Chem Dept, Nanostruct Mol Syst & Mat Grp, Madrid 28049, Spain..
    Mayoral, Mariia J.
    Univ Complutense Madrid, Dept Inorgan Chem, Madrid 28040, Spain..
    Vazquez-Gonzalez, Violeta
    Univ Autoonoma Madrid, Organ Chem Dept, Nanostruct Mol Syst & Mat Grp, Madrid 28049, Spain..
    Paloncyova, Marketa
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Palackyy Univ Olomouc, Czech Adv Technol & Res Inst CATRIN, Reg Ctr Adv Technol & Mat, Olomouc 77900, Czech Republic..
    Sancho-Casado, Irene
    Univ Autoonoma Madrid, Organ Chem Dept, Nanostruct Mol Syst & Mat Grp, Madrid 28049, Spain..
    Aparicio, Fatima
    Univ Autoonoma Madrid, Organ Chem Dept, Nanostruct Mol Syst & Mat Grp, Madrid 28049, Spain..
    de Juan, Alberto
    Univ Autoonoma Madrid, Organ Chem Dept, Nanostruct Mol Syst & Mat Grp, Madrid 28049, Spain..
    Longhi, Giovanna
    Univ Brescia, Dept Mol & Translat Med, I-25123 Brescia, Italy..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Linares, Mathieu
    Linköping Univ, Lab Organ Elect, S-58183 Linköping, Sweden.;Linköping Univ, Swedish Esci Res Ctr SeRC, S-58183 Linköping, Sweden.;Linköping Univ, Sci Visualizat Grp, ITN, Campus Norrköping, S-58183 Linköping, Sweden..
    Gonzalez-Rodriguez, David
    Univ Autoonoma Madrid, Organ Chem Dept, Nanostruct Mol Syst & Mat Grp, Madrid 28049, Spain.;Univ Autonoma Madrid, Inst Adv Res Chem Sci IAdChem, Madrid 28049, Spain..
    Stacked or Folded?: Impact of Chelate Cooperativity on the Self-Assembly Pathway to Helical Nanotubes from Dinucleobase Monomers2023In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 145, no 32, p. 17805-17818Article in journal (Refereed)
    Abstract [en]

    Self-assembled nanotubesexhibit impressive biologicalfunctionsthat have always inspired supramolecular scientists in their effortsto develop strategies to build such structures from small moleculesthrough a bottom-up approach. One of these strategies employs moleculesendowed with self-recognizing motifs at the edges, which can undergoeither cyclization-stacking or folding-polymerizationprocesses that lead to tubular architectures. Which of these self-assemblypathways is ultimately selected by these molecules is, however, oftendifficult to predict and even to evaluate experimentally. We showhere a unique example of two structurally related molecules substitutedwith complementary nucleobases at the edges (i.e., G:C and A:U) for which the supramolecular pathway takenis determined by chelate cooperativity, that is, by their propensityto assemble in specific cyclic structures through Watson-Crickpairing. Because of chelate cooperativities that differ in severalorders of magnitude, these molecules exhibit distinct supramolecularscenarios prior to their polymerization that generate self-assemblednanotubes with different internal monomer arrangements, either stackedor coiled, which lead at the same time to opposite helicities andchiroptical properties.

  • 36.
    Hansen, Nicolai S.B.
    et al.
    Department of Chemistry, Technical University of Denmark, Kgs. Lyngby 2800 Denmark.
    Monda, Fabrizio
    Department of Chemistry, Technical University of Denmark, Kgs. Lyngby 2800 Denmark.
    Bro, Frederik Simonsen
    Department of Chemistry, Technical University of Denmark, Kgs. Lyngby 2800 Denmark.
    Liu, Xiyue
    Department of Chemistry, Technical University of Denmark, Kgs. Lyngby 2800 Denmark.
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Madsen, Robert
    Department of Chemistry, Technical University of Denmark, Kgs. Lyngby 2800 Denmark.
    Development and mechanistic investigation of the dehydrogenation of alcohols with an iron(iii) salen catalyst2023In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 21, no 23, p. 4794-4800Article in journal (Refereed)
    Abstract [en]

    The iron(iii) salen complex (R,R)-N,N′-bis(salicylidene)-1,2-cyclohexanediamineiron(iii) chloride has been developed as a catalyst for the acceptorless dehydrogenation of alcohols. The complex catalyzes the direct synthesis of imines in good yields from different primary alcohols and amines with the liberation of hydrogen gas. The mechanism has been investigated experimentally with labelled substrates and theoretically with density functional theory calculations. In contrast to the corresponding manganese(iii) salen-catalyzed dehydrogenation, it has not been possible to identify a homogeneous catalytic pathway with the iron complex. Instead, poisoning experiments with trimethylphosphine and mercury indicated that the catalytically active species are heterogeneous small iron particles.

  • 37.
    He, Qinggang
    et al.
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Environm Energy Technol Div, Berkeley, CA 94720 USA.
    Cheng, Xiao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
    Wang, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Qiao, Ruimin
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA.
    Yang, Wanli
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA.
    Guo, Jinghua
    Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Adv Light Source, Berkeley, CA 94720 USA.
    Electrochemical and spectroscopic characterization of a dicobalt macrocyclic Pacman complex in the catalysis of the oxygen reduction reaction in acid media2013In: Journal of Porphyrins and Phthalocyanines, ISSN 1088-4246, E-ISSN 1099-1409, Vol. 17, no 4, p. 252-258Article in journal (Refereed)
    Abstract [en]

    The dicobalt complex [Co-2(L-2)] of a Schiff-base pyrrole macrocycle adopts a Pacman structure in solution and the solid state and shows much greater catalytic activity and selectivity for the four-electron oxygen reduction reaction (ORR) than the mononuclear cobalt phthalocyanine (CoPc) counterpart. Soft X-ray absorption spectroscopy (XAS) shows that the Co center in Co-2(L-2) is of the same valence as mononuclear CoPc. However, the former complex shows higher unoccupied Co 3d density which is believed to be beneficial for electron transfers. Furthermore, the XAS data suggests that the crystal fields for Co-2(L-2) and CoPc are different, and that an interaction remains between two Co atoms in Co-2(L-2). DFT calculations imply that the sterically hindered, cofacial structure of the dicobalt complex is critical for the operation of the four-electron reaction pathway during the ORR.

  • 38. Hillers-Bendtsen, A. E.
    et al.
    Todarwal, Yogesh
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Pittelkow, M.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Mikkelsen, K. V.
    Modeling Absorption and Emission Spectroscopies of Symmetric and Asymmetric Azaoxahelicenes in Vacuum and Solution2022In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 126, no 37, p. 6467-6472Article in journal (Refereed)
    Abstract [en]

    Helicenes are of general interest due to the significant chiral signals in both absorption- and emission-based spectroscopy. Herein, the spectroscopic properties of four recently synthesized azaoxahelicenes are studied using density functional theory methods. The azaoxahelicenes have 7, 9, 10, and 13 units and one to two complete turns of the structure. UV-vis absorption and electronic circular dichroism spectra are determined both in vacuum and in solution using explicit solvation through a combined molecular dynamics/polarizable embedding framework. Additionally, emission and circularly polarized luminescence spectra are determined based on vibronic calculations. The resulting spectra are in good agreement with the experimentally available data, highlighting that both absorption- and emission-based spectra of the systems can be modeled computationally such that reliable predictions can be made for systems that are yet to be synthesized. 

  • 39.
    Hillers-Bendtsen, Andreas Erbs
    et al.
    Univ Copenhagen, Dept Chem, DK-2100 Copenhagen O, Denmark..
    Todarwal, Yogesh
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Mikkelsen, Kurt V.
    Univ Copenhagen, Dept Chem, DK-2100 Copenhagen O, Denmark..
    Dynamical Effects of Solvation on Norbornadiene/Quadricyclane Systems2024In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 128, no 13, p. 2602-2610Article in journal (Refereed)
    Abstract [en]

    Molecules that can undergo reversible chemical transformations following the absorption of light, the so-called molecular photoswitches, have attracted increasing attention in technologies, such as solar energy storage. Here, the optical and thermochemical properties of the photoswitch are central to its applicability, and these properties are influenced significantly by solvation. We investigate the effects of solvation on two norbornadiene/quadricyclane photoswitches. Emphasis is put on the energy difference between the two isomers and the optical absorption as these are central to the application of the systems in solar energy storage. Using a combined classical molecular dynamics and quantum mechanical/molecular mechanical computational scheme, we showcase that the dynamic effects of solvation are important. In particular, it is found that standard implicit solvation models generally underestimate the energy difference between the two isomers and overestimate the strength of the absorption, while the explicit solvation spectra are also less red-shifted than those obtained using implicit solvation models. We also find that the absorption spectra of the two systems are strongly correlated with specific dihedral angles. Altogether, this highlights the importance of including the dynamic effects of solvation.

  • 40.
    Holmgaard List, Nanna
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Stanford Univ, Dept Chem, Stanford, CA 94305 USA.;Stanford Univ, PULSE Inst, Stanford, CA 94305 USA.;SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Jones, Chey M.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.;Stanford Univ, PULSE Inst, Stanford, CA 94305 USA.;SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Martinez, Todd J.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.;Stanford Univ, PULSE Inst, Stanford, CA 94305 USA.;SLAC Natl Accelerator Lab, 2575 Sand Hill Rd, Menlo Pk, CA 94025 USA..
    Internal conversion of the anionic GFP chromophore: in and out of the I-twisted S-1/S-0 conical intersection seam2022In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 13, no 2, p. 373-385Article in journal (Refereed)
    Abstract [en]

    The functional diversity of the green fluorescent protein (GFP) family is intimately connected to the interplay between competing photo-induced transformations of the chromophore motif, anionic p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI-). Its ability to undergo Z/E-isomerization is of particular importance for super-resolution microscopy and emerging opportunities in optogenetics. Yet, key dynamical features of the underlying internal conversion process in the native HBDI- chromophore remain largely elusive. We investigate the intrinsic excited-state behavior of isolated HBDI- to resolve competing decay pathways and map out the factors governing efficiency and the stereochemical outcome of photoisomerization. Based on non-adiabatic dynamics simulations, we demonstrate that non-selective progress along the two bridge-torsional (i.e., phenolate, P, or imidazolinone, I) pathways accounts for the three decay constants reported experimentally, leading to competing ultrafast relaxation primarily along the I-twisted pathway and S-1 trapping along the P-torsion. The majority of the population (similar to 70%) is transferred to S-0 in the vicinity of two approximately enantiomeric minima on the I-twisted intersection seam (MECI-Is). Despite their sloped, reactant-biased topographies (suggesting low photoproduct yields), we find that decay through these intersections leads to products with a surprisingly high quantum yield of similar to 30%. This demonstrates that E-isomer generation results at least in part from direct isomerization on the excited state. A photoisomerization committor analysis reveals a difference in intrinsic photoreactivity of the two MECI-Is and that the observed photoisomerization is the combined result of two effects: early, non-statistical dynamics around the less reactive intersection followed by later, near-statistical behavior around the more reactive MECI-I. Our work offers new insight into internal conversion of HBDI- that both establishes the intrinsic properties of the chromophore and enlightens principles for the design of chromophore derivatives and protein variants with improved photoswitching properties.

  • 41.
    Hua, Weijie
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Nanjing Univ Sci & Technol, Sch Phys, Dept Appl Phys, MIIT Key Lab Semicond Microstruct & Quantum Sensin, Nanjing 210094, Peoples R China.;Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA.
    MCNOX: A code for computing and interpreting ultrafast nonlinear X-ray spectra of molecules at the multiconfigurational level2024In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 296, article id 109016Article in journal (Refereed)
    Abstract [en]

    This work describes a program for computing and analyzing the ultrafast (attosecond and femtosecond) nonlinear X-ray spectra of molecules at the multiconfigurational quantum chemistry level, called MCNOX. It is aimed at cutting-edge current and future photochemistry/photophysics applications enabled by X-ray free-electron lasers and high harmonic generation light sources. It can compute steady-state X-ray absorption spectroscopy (XAS) and three types of ultrafast nonlinear X-ray spectra: transient XAS, all-X-ray four-wave mixing, and stimulated Raman spectra. It is especially capable of picking out major electronic transitions, and further computing the natural transition orbitals for these transitions, which help finally yield the physical and chemical insights from complex signals. Following a research paradigm of "electronic structure-*molecular dynamics-*signal", in this paper, methods for the former two steps are reviewed, and then the theory, implementations, and technical details for signal simulations are presented along illustrative examples on uracil.

  • 42.
    Idebohn, Veronica
    et al.
    Univ Gothenburg, Dept Phys, Origovgen 6B, S-41258 Gothenburg, Sweden..
    Linguerri, Roberto
    Univ Gustave Eiffel, COSYS IMSE, 5 Bd Descartes, F-77454 Champs Sur Marne, France..
    Cornetta, Lucas M.
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden.;Univ Estadual Campinas, Gleb Wataghin Inst Phys, Dept Appl Phys, Campinas, Brazil..
    Olsson, Emelie
    Univ Gothenburg, Dept Phys, Origovgen 6B, S-41258 Gothenburg, Sweden..
    Wallner, Mans
    Univ Gothenburg, Dept Phys, Origovgen 6B, S-41258 Gothenburg, Sweden..
    Squibb, Richard J.
    Univ Gothenburg, Dept Phys, Origovgen 6B, S-41258 Gothenburg, Sweden..
    Couto, Rafael Carvalho
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Karlsson, Leif
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Nyman, Gunnar
    Univ Gothenburg, Dept Chem & Mol Biol, Kemigarden 4, SE-41296 Gothenburg, Sweden..
    Hochlaf, Majdi
    Univ Gustave Eiffel, COSYS IMSE, 5 Bd Descartes, F-77454 Champs Sur Marne, France..
    Eland, John H. D.
    Univ Oxford, Dept Chem, Phys & Theoret Chem Lab, South Parks Rd, Oxford OX1 3QZ, England..
    Ågren, Hans
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Feifel, Raimund
    Univ Gothenburg, Dept Phys, Origovgen 6B, S-41258 Gothenburg, Sweden..
    Symmetry breaking in core-valence double ionisation of allene2023In: Communications Chemistry, E-ISSN 2399-3669, Vol. 6, no 1, article id 137Article in journal (Refereed)
    Abstract [en]

    Allene serves as a model to study multiple ionization of organic molecules. Here, the authors use synchrotron radiation-based multi-particle coincidence techniques and high-level ab initio calculations to propose a simple physical model to elucidate the symmetry breaking in core-valence double ionization of allene. Conventional electron spectroscopy is an established one-electron-at-the-time method for revealing the electronic structure and dynamics of either valence or inner shell ionized systems. By combining an electron-electron coincidence technique with the use of soft X-radiation we have measured a double ionisation spectrum of the allene molecule in which one electron is removed from a C1s core orbital and one from a valence orbital, well beyond Siegbahns Electron-Spectroscopy-for-Chemical-Analysis method. This core-valence double ionisation spectrum shows the effect of symmetry breaking in an extraordinary way, when the core electron is ejected from one of the two outer carbon atoms. To explain the spectrum we present a new theoretical approach combining the benefits of a full self-consistent field approach with those of perturbation methods and multi-configurational techniques, thus establishing a powerful tool to reveal molecular orbital symmetry breaking on such an organic molecule, going beyond Lowdins standard definition of electron correlation.

  • 43.
    Juan Angel, de Gracia Triviño
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Operando Condition Reaction Modeling Shows Highly Dynamic Attachment of Oligomeric Ruthenium Catalysts2023In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 13, no 2, p. 1270-1279Article in journal (Refereed)
    Abstract [en]

    To increase the stability and current density of molecular-catalyst-based electroanodes for water oxidation, immobilization of the catalysts at the electrode surface is a common strategy. A prominent example is the oligomerized Ru(tda) molecular catalyst, which showed outstanding current densities even at neutral pH values. One of the most challenging aspects of immobilized catalysts is to understand the interaction between the catalyst and the surface under operando conditions. Experiments are often performed under model conditions, and computational methods to study reaction steps are typically limited to a few hundred atoms. In this study, we combined three computational methods, density functional theory electronic structure computations, molecular dynamics for large-scale simulations of the catalyst-solid interaction, and empirical valence bond for reaction modeling the catalyst at the interface of a large carbon support and a phosphate water buffer. These techniques allowed us to explore the combined effects of solvent, hydrophobic directionality, and electric field on the attachment and reactivity of a Ru(tda) pentamer at a graphene surface. Our simulations have a perfect agreement with the experimental characterization under model conditions. However, we find that under operando conditions, where the catalyst is oxidized to the active RuV state, with a phosphate-containing electrolyte and an applied electric field, the attachment is completely reversed compared to the model conditions with RuII and organic solvents. This reversed attachment leads to a water-excluded region close to the active RuV═O center. The EVB reaction modeling showed that the reaction could still proceed to form an O-O bond via an oxide relay mechanism, where a dangling carboxylate reacts with the oxo via nucleophilic attack. We find that the activation energies are identical in water solution and at the electrode surface, showing how this mechanism is key to highly active molecular water oxidation catalysts immobilized on surfaces. Since attachment to surfaces could have a strong, and often negative, influence on the reactions, this study provides a guideline on how to model reactions without compromising the complexity of the electrode environment.

  • 44.
    Kragh Sørensen, Lasse
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Uppsala Univ, Dept Phys & Astron, SE-75120 Uppsala, Sweden.;Univ Southern Denmark, Univ Lib, DK-5230 Odense M, Denmark..
    Khrennikov, Daniil E.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem, Krasnoyarsk 660041, Russia..
    Gerasimov, Valeriy S.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem, Krasnoyarsk 660041, Russia.;RAS, Fed Res Ctr KSC SB, Inst Computat Modelling, Krasnoyarsk 660036, Russia..
    Ershov, Alexander E.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem, Krasnoyarsk 660041, Russia.;RAS, Fed Res Ctr KSC SB, Inst Computat Modelling, Krasnoyarsk 660036, Russia..
    Polyutov, Sergey P.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem, Krasnoyarsk 660041, Russia.;RAS, Fed Res Ctr KSC SB, Inst Computat Modelling, Krasnoyarsk 660036, Russia.;Fed Siberian Res Clin Ctr FMBA Russia, Kolomenskaya 660037, Russia..
    Karpov, Sergey
    RAS, Fed Res Ctr KSC SB, LV Kirensky Inst Phys, Krasnoyarsk 660036, Russia..
    Agren, Hans
    Uppsala Univ, Dept Phys & Astron, SE-75120 Uppsala, Sweden..
    Nature of the Anomalous Size Dependence of Resonance Red Shifts in Ultrafine Plasmonic Nanoparticles2022In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 126, no 39, p. 16804-16814Article in journal (Refereed)
    Abstract [en]

    Plasmonic red shifts of nanoparticles are commonly used in imaging technologies to probe the character of local environments, and the understanding of their dependence on size, shape, and surrounding media has therefore become an important target for research. The red shift of plasmon resonances changes character at about 8-10 nm of size for spherical gold nanoparticles-above this value, the red shift progresses linearly with particle size, while below this size, the red shift changes nonlinearly and more strongly with size. Using an atomistic discrete interaction model, we have studied the special properties of the nanoparticle surface layers and discovered its importance for ultrafine plasmonic nanoparticles and their red shifts. We find that the physical origin for the specific properties inherent to the surface layer of atoms near the nanoparticle boundary is related to the anisotropy of the local environment of atoms in this layer by other atoms. The anisotropy changes the conditions for light-induced nonlocal interactions of neighboring atoms with each other and with the incident radiation compared to the atoms located in the particle core with isotropic nearest surroundings by other atoms. The local anisotropy of the nanoparticle crystal lattice is a geometric factor that increases toward its boundary and that is the most fundamental factor underlying the physical differences between the nanoparticle surface layer and the core material. It is shown that the inflexion point at 8-10 nm is due to a change in the dominant physical origin of the red shift -from chaotization of atomically light-induced dipoles within the surface layer in the case of ultrafine nanoparticles to retardation effects for large nanoparticles in which the relative volume of the surface layer decreases rapidly to a negligible value with increasing nanoparticle size. The patterns revealed are the basis for predicting the manifestation of surface layer effects in ultrafine plasmonic nanoparticles of different and of different materials.

  • 45.
    Kuzmin, Julius
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Röckl, Johannes L.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Schwarz, Nils
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Djossou, Jonas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Ahumada, Guillermo
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Lundberg, Helena
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Electroreductive Desulfurative Transformations with Thioethers as Alkyl Radical Precursors2023In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 62, no 39, article id e202304272Article in journal (Refereed)
    Abstract [en]

    Thioethers are highly prevalent functional groups in organic compounds of natural and synthetic origin but remain remarkably underexplored as starting materials in desulfurative transformations. As such, new synthetic methods are highly desirable to unlock the potential of the compound class. In this vein, electrochemistry is an ideal tool to enable new reactivity and selectivity under mild conditions. Herein, we demonstrate the efficient use of aryl alkyl thioethers as alkyl radical precursors in electroreductive transformations, along with mechanistic details. The transformations proceed with complete selectivity for C(sp3)−S bond cleavage, orthogonal to that of established transition metal-catalyzed two-electron routes. We showcase a hydrodesulfurization protocol with broad functional group tolerance, the first example of desulfurative C(sp3)−C(sp3) bond formation in Giese-type cross-coupling and the first protocol for electrocarboxylation of synthetic relevance with thioethers as starting materials. Finally, the compound class is shown to outcompete their well-established sulfone analogues as alkyl radical precursors, demonstrating their synthetic potential for future desulfurative transformations in a one-electron manifold.

  • 46.
    Labrador-Páez, Lucia
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics. Univ Complutense Madrid, Dept Phys Chem, Madrid 28040, Spain..
    Kostiv, Uliana
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Liu, Qingyun
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Li, Yuanyuan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Biocomposites.
    Agren, Hans
    Uppsala Univ, Dept Phys & Astron, SE-75120 Uppsala, Sweden..
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Liu, Haichun
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Excitation Pulse Duration Response of Upconversion Nanoparticles and Its Applications2022In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 13, no 48, p. 11208-11215Article in journal (Refereed)
    Abstract [en]

    Lanthanide-doped upconversion nanoparticles (UCNPs) have rich photophysics exhibiting complex luminescence kinetics. In this work, we thoroughly investigated the luminescence response of UCNPs to excitation pulse durations. Analyzing this response opens new opportunities in optical encoding/decoding and the assignment of transitions to emission peaks and provides advantages in applications of UCNPs, e.g., for better optical sectioning and improved luminescence nanothermometry. Our work shows that monitoring the UCNP luminescence response to excitation pulse durations (while keeping the duty cycle constant) by recording the average luminescence intensity using a low-time resolution detector such as a spectrometer offers a powerful approach for significantly extending the utility of UCNPs.

  • 47.
    Li, Ge
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Computational comparison of Ru(bda)(py)2 and Fe(bda)(py)2 as water oxidation catalysts2022In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 51, no 22, p. 8618-8624Article in journal (Refereed)
    Abstract [en]

    Ru(bda)(py)2 (bda = 2,2′-bipyridine-6,6′-dicarboxylate, py = pyridine) has been a significant milestone in the development of water oxidation catalysts. Inspired by Ru(bda)(py)2 and aiming to reduce the use of noble metals, iron (Fe) was introduced to replace the Ru catalytic center in Ru(bda)(py)2. In this study, density functional theory (DFT) calculations were performed on Fe- and Ru(bda)(py)2 catalysts, and a more stable 6-coordinate Fe(bda)(py)2 with one carboxylate group of bda disconnecting with Fe was found. For the first time, theoretical comparisons have been conducted on these three catalysts to compare their catalytic performances, such as reduction potentials and energy profiles of the radical coupling process. Explanations for the high potential of [FeIII(bda)(py)2-H2O]+ and reactivity of [FeV(bda)(py)2-O]+ have been provided. This study can provide insights on Fe(bda)(py)2 from a computational perspective if it is utilized as a water oxidation catalyst. 

  • 48.
    Li, Jiachen
    et al.
    Zhejiang Univ, Dept Chem, Hangzhou 310027, Peoples R China..
    Chen, Hao
    Zhejiang Univ, Dept Chem, Hangzhou 310027, Peoples R China..
    Kang, Zhengzhong
    Zhejiang Univ, Dept Chem, Hangzhou 310027, Peoples R China..
    Liu, Yingchun
    Zhejiang Univ, Dept Chem, Hangzhou 310027, Peoples R China..
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Wang, Qi
    Zhejiang Univ, Dept Chem, Hangzhou 310027, Peoples R China..
    Fan, Jie
    Zhejiang Univ, Dept Chem, Hangzhou 310027, Peoples R China..
    A combined computational and experimental approach predicts thrombin adsorption to zeolites2023In: Colloids and Surfaces B: Biointerfaces, ISSN 0927-7765, E-ISSN 1873-4367, Vol. 221, p. 113007-, article id 113007Article in journal (Refereed)
    Abstract [en]

    Robust protein-nanomaterial surface analysis is important, but also a challenge. Thrombin plays an important role in the coagulant activity of protein corona mediated by Ca2+ ion exchanged zeolites. However, the mech-anism for this modulation remains unresolved. In this study, we proposed a combined computational and experimental approach to determine the adsorbed sites and orientations of thrombin binding to Ca2+-exchanged LTA-type (CaA) zeolite. Specifically, fourteen ensembles of simulated annealing molecular dynamics (SAMD) simulations and experimental surface residues microenvironment analysis were used to reduce the starting orientations needed for further molecular dynamics (MD) simulations. The combined MD simulations and pro -coagulant activity characterization also reveal the consequent corresponding deactivation of thrombin on CaA zeolite. It is mainly caused by two aspects: (1) the secondary structure of thrombin can change after its adsorption on the CaA zeolite. (2) The positively charged area of thrombin mediates the preferential interaction between thrombin and CaA zeolite. Some thrombin substrate sites are thus blocked by zeolite after its adsorption. This study not only provides a promising method for characterizing the protein-nanoparticle interaction, but also gives an insight into the design and application of zeolite with high procoagulant activity.

  • 49.
    Li, Jiachen
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology. Zhejiang Univ, Dept Chem, Hangzhou 310027, Peoples R China..
    Wang, Qi
    Zhejiang Univ, Dept Chem, Hangzhou 310027, Peoples R China..
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Binding modes of prothrombin cleavage site sequences to the factor Xa catalytic triad: Insights from atomistic simulations2022In: Computational and Structural Biotechnology Journal, E-ISSN 2001-0370, Vol. 20, p. 5401-5408Article in journal (Refereed)
    Abstract [en]

    Prothrombin is a key zymogen of the coagulation process and can be converted to thrombin by the prothrombinase complex, which consists of factor Xa (FXa), cofactor Va (FVa), and phospholipids. Prothrombin can be activated at two cleavage sites, R271 and R320, which generates two intermediates: prethrombin-2 via the initial cleavage at R271, and meizothrombin via the first cleavage at R320. Several mechanisms have been proposed to explain this activation preference, but the role of cleavage site sequences in prothrombin activation has not been thoroughly investigated. Here, we used an advanced sampling technique, parallel tempering metadynamics with a well-tempered ensemble (PTMetaDWTE), to study the binding modes of prothrombin cleavage site sequences R266AIEGRTATSEY277 (denoted as Pep271) and S315YIDGRIVEGSD326 (denoted as Pep320) to the FXa catalytic triad. Our study indicates that there exist three binding modes for Pep271 to the FXa catalytic triad but only one binding mode for Pep320 to the FXa catalytic triad. Further molecular dynamics simulations revealed that due to the strong electrostatic interactions, especially the H-bond interactions and salt bridges formed between Pep320 and FXa, the binding mode in the Pep320-FXa system is more stable than the binding modes in the Pep271-FXa system. In view of experimental observations and our results that there exists only one binding mode for Pep320 to the FXa catalytic triad and especially R320 in Pep320 can stably bind to the FXa catalytic triad, we believe that the first cleavage at R320 is favored.

  • 50.
    Li, Junhao
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Tang, Yun
    Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Meilong Road 130, 200237 Shanghai, P.R. China.
    Li, Weihua
    Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Meilong Road 130, 200237 Shanghai, P.R. China.
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Theoretical Chemistry and Biology.
    Mechanistic Insights into the Regio‐ and Stereoselectivities of Testosterone and Dihydrotestosterone Hydroxylation Catalyzed by CYP3A4 and CYP19A12020In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 26, no 28, p. 6214-6223Article in journal (Refereed)
    Abstract [en]

    The hydroxylation of nonreactive C−H bonds can be easily catalyzed by a variety of metalloenzymes, especially cytochrome P450s (P450s). The mechanism of P450 mediated hydroxylation has been intensively studied, both experimentally and theoretically. However, understanding the regio‐ and stereoselectivities of substrates hydroxylated by P450s remains a great challenge. Herein, we use a multi‐scale modeling approach to investigate the selectivity of testosterone (TES) and dihydrotestosterone (DHT) hydroxylation catalyzed by two important P450s, CYP3A4 and CYP19A1. For CYP3A4, two distinct binding modes for TES/DHT were predicted by dockings and molecular dynamics simulations, in which the experimentally identified sites of metabolism of TES/DHT can access to the catalytic center. The regio‐ and stereoselectivities of TES/DHT hydroxylation were further evaluated by quantum mechanical and ONIOM calculations. For CYP19A1, we found that sites 1β, 2β and 19 can access the catalytic center, with the intrinsic reactivity 2β>1β>19. However, our ONIOM calculations indicate that the hydroxylation is favored at site 19 for both TES and DHT, which is consistent with the experiments and reflects the importance of the catalytic environment in determining the selectivity. Our study unravels the mechanism underlying the selectivity of TES/DHT hydroxylation mediated by CYP3A4 and CYP19A1 and is helpful for understanding the selectivity of other substrates that are hydroxylated by P450s.

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