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  • 1. Banerjee, Ambar
    et al.
    Jay, Raphael M.
    Leitner, Torsten
    Wang, Ru-Pan
    Harich, Jessica
    Stefanuik, Robert
    Coates, Michael R.
    Stockholm University, Faculty of Science, Department of Physics.
    Beale, Emma V.
    Kabanova, Victoria
    Kahraman, Abdullah
    Wach, Anna
    Ozerov, Dmitry
    Arrell, Christopher
    Milne, Christopher
    Johnson, Philip J. M.
    Cirelli, Claudio
    Bacellar, Camila
    Huse, Nils
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Wernet, Philippe
    Accessing metal-specific orbital interactions in C–H activation with resonant inelastic X-ray scattering2024In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 15, no 7, p. 2398-2409Article in journal (Refereed)
    Abstract [en]

    Photochemically prepared transition-metal complexes are known to be effective at cleaving the strong C–H bonds of organic molecules in room temperature solutions. There is also ample theoretical evidence that the two-way, metal to ligand (MLCT) and ligand to metal (LMCT), charge-transfer between an incoming alkane C–H group and the transition metal is the decisive interaction in the C–H activation reaction. What is missing, however, are experimental methods to directly probe these interactions in order to reveal what determines reactivity of intermediates and the rate of the reaction. Here, using quantum chemical simulations we predict and propose future time-resolved valence-to-core resonant inelastic X-ray scattering (VtC-RIXS) experiments at the transition metal L-edge as a method to provide a full account of the evolution of metal–alkane interactions during transition-metal mediated C–H activation reactions. For the model system cyclopentadienyl rhodium dicarbonyl (CpRh(CO)2), we demonstrate, by simulating the VtC-RIXS signatures of key intermediates in the C–H activation pathway, how the Rh-centered valence-excited states accessible through VtC-RIXS directly reflect changes in donation and back-donation between the alkane C–H group and the transition metal as the reaction proceeds via those intermediates. We benchmark and validate our quantum chemical simulations against experimental steady-state measurements of CpRh(CO)2 and Rh(acac)(CO)2 (where acac is acetylacetonate). Our study constitutes the first step towards establishing VtC-RIXS as a new experimental observable for probing reactivity of C–H activation reactions. More generally, the study further motivates the use of time-resolved VtC-RIXS to follow the valence electronic structure evolution along photochemical, photoinitiated and photocatalytic reactions with transition metal complexes.

  • 2.
    Baronio, Cesare M.
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Barth, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    The Amide I Spectrum of Proteins—Optimization of Transition Dipole Coupling Parameters Using Density Functional Theory Calculations2020In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 124, no 9, p. 1703-1714Article in journal (Refereed)
    Abstract [en]

    The amide I region of the infrared spectrum is related to the protein backbone conformation and can provide important structural information. However, the interpretation of the experimental results is hampered because the theoretical description of the amide I spectrum is still under development. Quantum mechanical calculations, for example, using density functional theory (DFT), can be used to study the amide I spectrum of small systems, but the high computational cost makes them inapplicable to proteins. Other approaches that solve the eigenvalues of the coupled amide I oscillator system are used instead. An important interaction to be considered is transition dipole coupling (TDC). Its calculation depends on the parameters of the transition dipole moment. This work aims to find the optimal parameters for TDC in three major secondary structures: α-helices, antiparallel β-sheets, and parallel β-sheets. The parameters were suggested through a comparison between DFT and TDC calculations. The comparison showed a good agreement for the spectral shape and for the wavenumbers of the normal modes for all secondary structures. The matching between the two methods improved when hydrogen bonding to the amide oxygen was considered. Optimal parameters for individual secondary structures were also suggested.

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  • 3.
    Bassan, Arianna
    Stockholm University, Faculty of Science, Department of Physics.
    Theoretical studies of mononuclear non-heme iron active sites2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The quantum chemical investigations presented in this thesis use hybrid density functional theory to shed light on the catalytic mechanisms of mononuclear non-heme iron oxygenases, accommodating a ferrous ion in their active sites. More specifically, the dioxygen activation process and the subsequent oxidative reactions in the following enzymes were studied: tetrahydrobiopterin-dependent hydroxylases, naphthalene 1,2-dioxygenase and α-ketoglutarate-dependent enzymes. In light of many experimental efforts devoted to the functional mimics of non-heme iron oxygenases, the reactivity of functional analogues was also examined.

    The computed energetics and the available experimental data served to assess the feasibility of the reaction mechanisms investigated. Dioxygen activation in tetrahydrobiopterin- and α-ketoglutarate-dependent enzymes were found to involve a high-valent iron-oxo species, which was then capable of substrate hydroxylation. In the case of naphthalene 1,2-dioxygenase, the reactivity of an iron(III)-hydroxperoxo species toward the substrate was investigated and compared to the biomimetic counterpart.

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  • 4.
    Bjelkmar, Pär
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Modeling of voltage-gated ion channels2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The recent determination of several crystal structures of voltage-gated ion channels has catalyzed computational efforts of studying these remarkable molecular machines that are able to conduct ions across biological membranes at extremely high rates without compromising the ion selectivity.

    Starting from the open crystal structures, we have studied the gating mechanism of these channels by molecular modeling techniques. Firstly, by applying a membrane potential, initial stages of the closing of the channel were captured, manifested in a secondary-structure change in the voltage-sensor. In a follow-up study, we found that the energetic cost of translocating this 310-helix conformation was significantly lower than in the original conformation. Thirdly, collaborators of ours identified new molecular constraints for different states along the gating pathway. We used those to build new protein models that were evaluated by simulations. All these results point to a gating mechanism where the S4 helix undergoes a secondary structure transformation during gating.

    These simulations also provide information about how the protein interacts with the surrounding membrane. In particular, we found that lipid molecules close to the protein diffuse together with it, forming a large dynamic lipid-protein cluster. This has important consequences for the understanding of protein-membrane interactions and for the theories of lateral diffusion of membrane proteins.

    Further, simulations of the simple ion channel antiamoebin were performed where different molecular models of the channel were evaluated by calculating ion conduction rates, which were compared to experimentally measured values. One of the models had a conductance consistent with the experimental data and was proposed to represent the biological active state of the channel.

    Finally, the underlying methods for simulating molecular systems were probed by implementing the CHARMM force field into the GROMACS simulation package. The implementation was verified and specific GROMACS-features were combined with CHARMM and evaluated on long timescales. The CHARMM interaction potential was found to sample relevant protein conformations indifferently of the model of solvent used.

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  • 5.
    Blomberg, Margareta R. A.
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Ädelroth, Pia
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Reduction of molecular oxygen in flavodiiron proteins - Catalytic mechanism and comparison to heme-copper oxidases2024In: Journal of Inorganic Biochemistry, ISSN 0162-0134, E-ISSN 1873-3344, Vol. 255, article id 112534Article in journal (Refereed)
    Abstract [en]

    The family of flavodiiron proteins (FDPs) plays an important role in the scavenging and detoxification of both molecular oxygen and nitric oxide. Using electrons from a flavin mononucleotide cofactor molecular oxygen is reduced to water and nitric oxide is reduced to nitrous oxide and water. While the mechanism for NO reduction in FDPs has been studied extensively, there is very little information available about O2 reduction. Here we use hybrid density functional theory (DFT) to study the mechanism for O2 reduction in FDPs. An important finding is that a proton coupled reduction is needed after the O2 molecule has bound to the diferrous diiron active site and before the O–O bond can be cleaved. This is in contrast to the mechanism for NO reduction, where both N–N bond formation and N–O bond cleavage occurs from the same starting structure without any further reduction, according to both experimental and computational results. This computational result for the O2 reduction mechanism should be possible to evaluate experimentally. Another difference between the two substrates is that the actual O–O bond cleavage barrier is low, and not involved in rate-limiting the reduction process, while the barrier connected with bond cleavage/formation in the NO reduction process is of similar height as the rate-limiting steps. We suggest that these results may be part of the explanation for the generally higher activity for O2 reduction as compared to NO reduction in most FDPs. Comparisons are also made to the O2 reduction reaction in the family of heme‑copper oxidases.

  • 6.
    C. Couto, Rafael
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Kowalewski, Markus
    Stockholm University, Faculty of Science, Department of Physics.
    Suppressing non-radiative decay of photochromic organic molecular systems in the strong coupling regime2022In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 24, no 32, p. 19199-19208Article in journal (Refereed)
    Abstract [en]

    The lifetimes of electronic excited states have a strong influence on the efficiency of organic solar cells. However, in some molecular systems a given excited state lifetime is reduced due to the non-radiative decay through conical intersections. Several strategies may be used to suppress this decay channel. The use of the strong light-matter coupling provided in optical nano-cavities is the focus of this paper. Here, we consider the meso–tert-butyl-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene molecule (meso–tert-butyl-BODIPY) as a showcase of how strong and ultrastrong coupling might help in the development of organic solar cells. The meso–tert-butyl-BODIPY is known for its low fluorescence yield caused by the non-radiative decay through a conical intersection. However, we show here that, by considering this system within a cavity, the strong coupling can lead to significant changes in the multidimensional landscape of the potential energy surfaces of meso–tert-butyl-BODIPY, suppressing almost completely the decay of the excited state wave packet back to the ground state. By means of multi configuration electronic structure calculations and nuclear wave packet dynamics, the coupling with the cavity is analyzed in-depth to provide further insight of the interaction. By fine-tuning the cavity field strength and resonance frequency, we show that one can change the nuclear dynamics in the excited state, and control the non-radiative decay. This may lead to a faster and more efficient population transfer or the suppression of it.

  • 7. Caldeweyher, Eike
    et al.
    Elkin, Masha
    Gheibi, Golsa
    Johansson, Magnus J.
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Sweden.
    Sko''ld, Christian
    Norrby, Per-Ola
    Hartwig, John F.
    Hybrid Machine Learning Approach to Predict the Site Selectivity of Iridium-Catalyzed Arene Borylation2023In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 145, no 31, p. 17367-17376Article in journal (Refereed)
    Abstract [en]

    The borylation of aryl and heteroaryl C–H bonds is valuable for the site-selective functionalization of C–H bonds in complex molecules. Iridium catalysts ligated by bipyridine ligands catalyze the borylation of the C–H bond that is most acidic and least sterically hindered in an arene, but predicting the site of borylation in molecules containing multiple arenes is difficult. To address this challenge, we report a hybrid computational model that predicts the Site of Borylation (SoBo) in complex molecules. The SoBo model combines density functional theory, semiempirical quantum mechanics, cheminformatics, linear regression, and machine learning to predict site selectivity and to extrapolate these predictions to new chemical space. Experimental validation of SoBo showed that the model predicts the major site of borylation of pharmaceutical intermediates with higher accuracy than prior machine-learning models or human experts, demonstrating that SoBo will be useful to guide experiments for the borylation of specific C(sp2)–H bonds during pharmaceutical development.

  • 8. Charry, Jorge
    et al.
    Moncada, Félix
    Stockholm University, Faculty of Science, Department of Physics. Universidad Nacional de Colombia, Colombia.
    Barborini, Matteo
    Pedraza-González, Laura
    Varella, Márcio T. do N.
    Tkatchenko, Alexandre
    Reyes, Andrés
    The three-center two-positron bond2022In: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 13, no 46, p. 13795-13802Article in journal (Refereed)
    Abstract [en]

    Computational studies have shown that one or more positrons can stabilize two repelling atomic anions through the formation of two-center positronic bonds. In the present work, we study the energetic stability of a system containing two positrons and three hydride anions, namely 2e+[H33−]. To this aim, we performed a preliminary scan of the potential energy surface of the system with both electrons and positrons in a spin singlet state, with a multi-component MP2 method, that was further refined with variational and diffusion Monte Carlo calculations, and confirmed an equilibrium geometry with D3h symmetry. The local stability of 2e+[H33−] is demonstrated by analyzing the vertical detachment and adiabatic energy dissociation channels. Bonding properties of the positronic compound, such as the equilibrium interatomic distances, force constants, dissociation energies, and bonding densities are compared with those of the purely electronic H3+ and Li3+ systems. Through this analysis, we find compelling similarities between the 2e+[H33−] compound and the trilithium cation. Our results strongly point out the formation of a non-electronic three-center two-positron bond, analogous to the well-known three-center two-electron counterparts, which is fundamentally distinct from the two-center two-positron bond [D. Bressanini, J. Chem. Phys., 2021, 155, 054306], thus extending the concept of positron bonded molecules.

  • 9. Chen, Dan
    et al.
    Ranganathan, Anirudh
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Ijzerman, Adriaan P.
    Siegal, Gregg
    Carlsson, Jens
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Complementarity between in Silico and Biophysical Screening Approaches in Fragment-Based Lead Discovery against the A(2A) Adenosine Receptor2013In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 53, no 10, p. 2701-2714Article in journal (Refereed)
    Abstract [en]

    Fragment-based lead discovery (FBLD) is becoming an increasingly important method in drug development. We have explored the potential to complement NMR-based biophysical screening of chemical libraries with molecular docking in FBLD against the A(2A) adenosine receptor (A(2A)AR), a drug target for inflammation and Parkinson's disease. Prior to an NMR-based screen of a fragment library against the A(2A)AR, molecular docking against a crystal structure was used to rank the same set of molecules by their predicted affinities. Molecular docking was able to predict four out of the five orthosteric ligands discovered by NMR among the top 5% of the ranked library, suggesting that structure-based methods could be used to prioritize among primary hits from biophysical screens. In addition, three fragments that were top-ranked by molecular docking, but had not been picked up by the NMR-based method, were demonstrated to be A2AAR ligands. While biophysical approaches for fragment screening are typically limited to a few thousand compounds, the docking screen was extended to include 328,000 commercially available fragments. Twenty-two top-ranked compounds were tested in radioligand binding assays, and 14 of these were A(2A)AR ligands with K-i values ranging from 2 to 240 mu M. Optimization of fragments was guided by molecular dynamics simulations and free energy calculations. The results illuminate strengths and weaknesses of molecular docking and demonstrate that this method can serve as a valuable complementary tool to biophysical screening in FBLD.

  • 10. Cho, Daeheum
    et al.
    Rouxel, Jérémy R.
    Kowalewski, Markus
    Stockholm University, Faculty of Science, Department of Physics.
    Lee, Jin Yong
    Mukamel, Shaul
    Imaging of transition charge densities involving carbon core excitations by all X-ray sum-frequency generation2019In: Philosophical Transactions. Series A: Mathematical, physical, and engineering science, ISSN 1364-503X, E-ISSN 1471-2962, Vol. 377, no 2145, article id 2017.0470Article in journal (Refereed)
    Abstract [en]

    X-ray diffraction signals from the time-evolving molecular charge density induced by selective core excitation of chemically inequivalent carbon atoms are calculated. A narrowband X-ray pulse selectively excites the carbon K-edge of the –CH3 or –CH2F groups in fluoroethane (CH3–CH2F). Each excitation creates a distinct core coherence which depends on the character of the electronic transition. Direct propagation of the reduced single-electron density matrix, using real-time time-dependent density functional theory, provides the time-evolving charge density following interactions with external fields. The interplay between partially filled valence molecular orbitals upon core excitation induces characteristic femtosecond charge migration which depends on the core–valence coherence, and is monitored by the sum-frequency generation diffraction signal.

  • 11. Choi, Seungwoo
    et al.
    Liu, Chang
    Stockholm University, Faculty of Science, Department of Physics. KTH Royal Institute of Technology, Sweden.
    Seo, Da Hye
    Im, Sang Won
    Kim, Ryeong Myeong
    Jo, Jaeyeon
    Kim, Jeong Won
    Park, Gyeong-Su
    Kim, Miyoung
    Brinck, Tore
    Nam, Ki Tae
    Kink-Controlled Gold Nanoparticles for Electrochemical Glucose Oxidation2024In: Nano Letters, ISSN 1530-6984, E-ISSN 1530-6992, Vol. 24, no 15, p. 4528-4536Article in journal (Refereed)
    Abstract [en]

    Enzymes in nature efficiently catalyze chiral organic molecules by elaborately tuning the geometrical arrangement of atoms in the active site. However, enantioselective oxidation of organic molecules by heterogeneous electrocatalysts is challenging because of the difficulty in controlling the asymmetric structures of the active sites on the electrodes. Here, we show that the distribution of chiral kink atoms on high-index facets can be precisely manipulated even on single gold nanoparticles; and this enabled stereoselective oxidation of hydroxyl groups on various sugar molecules. We characterized the crystallographic orientation and the density of kink atoms and investigated their specific interactions with the glucose molecule due to the geometrical structure and surface electrostatic potential.

  • 12.
    Coates, Michael R.
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Banerjee, Ambar
    Stockholm University, Faculty of Science, Department of Physics.
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Simulations of the Aqueous Brown-Ring Complex Reveal Fluctuations in Electronic Character2023In: Inorganic Chemistry, ISSN 0020-1669, E-ISSN 1520-510X, Vol. 62, p. 16854-16866Article in journal (Refereed)
    Abstract [en]

    Ab initio molecular dynamics (AIMD) simulations of the aqueous [Fe(H2O)(5)(NO)](2+) brown-ring complex in different spin states, in combination with multiconfigurational quantum chemical calculations, show a structural dependence on the electronic character of the complex. Sampling in the quartet and sextet ground states show that the multiplicity is correlated with the Fe-N distance. This provides a motivation for a rigid Fe-N scan in the isolated brown-ring complex to investigate how the multiconfigurational wave function and the electron density change around the FeNO moiety. Our results show that subtle changes in the Fe-N distance produce a large response in the electronic configurations underlying the quartet wave function. However, while changes in spin density and potential energy are pronounced, variations in charge are negligible. These trends within the FeNO moiety are preserved in structural sampling of the AIMD simulations, despite distortions present in other degrees of freedom in the bulk solution.

  • 13.
    Das, Sambit
    Stockholm University, Faculty of Science, Department of Physics.
    A theoretical perspective on photoinduced reactions - based on quantum chemical models and non-adiabatic molecular dynamics.2023Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The broad range of applications for photochemical reactions is the result of light-matter interaction at the electronic level. The diverse application of photochemistry in various fields, including photovoltaic materials, molecular switches, and biological systems are due to electronic and structural transformations induced by photoexcitation as well as molecular alteration due to electron and charge transfer. An improved understanding of these photochemical events is dependent on the fundamental theoretical evaluation, to model and analyze the ultrafast processes. The studies discussed in this thesis explore such theoretical implementation in two different frontiers.

    In the first study, dynamic simulations are performed to model the light-induced bond dissociation of phenyl azide. The surface hopping formalism, implemented under the semiclassical molecular dynamics approach helped in tracing the time evolution of the electronic and structural levels, involved in the photodissociation. In the second study, the time-dependent density functional theory has been applied to generate XA spectra of imidazole solutions. The theoretical assessments support experimental measurements and provide more insight into the core excitations and structural influence on the absorption spectra.   

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  • 14.
    Das, Sambit
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Banerjee, Ambar
    Stockholm University, Faculty of Science, Department of Physics.
    Theoretical simulations of the photodissociation of phenyl azideManuscript (preprint) (Other academic)
    Abstract [en]

    Excited state molecular dynamics simulations of the photoexcitation of phenyl azide have been performed. The semi-classical surface hopping approximation has enabled an unconstrained analysis of the electronic and nuclear degrees of freedom which contribute to the molecular dissociation of phenyl azide into phenyl nitrene and molecular nitrogen. The significance of the S2 state in leading the photodissociation has been established through electronic structure calculations, based on multiconfigurational schemes, and state population dynamics. The investigations on the structural dynamics have revealed the N-N bond separation to be accompanied by synchronous changes in the azide N-N-N bond angle. The 100 fs simulation results in a nitrene fragment that is electronically and vibrationally excited, thus forming a hot nitrene species in the singlet manifold.

  • 15.
    Das, Sambit
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Nibbering, Erik
    MAX BORN INSTITUTE for Nonlinear Optics and Short Pulse Spectroscopy.
    Zhang, Zhuang-Yan
    MAX BORN INSTITUTE for Nonlinear Optics and Short Pulse Spectroscopy.
    Winghart, Marc-Oliver
    MAX BORN INSTITUTE for Nonlinear Optics and Short Pulse Spectroscopy.
    Probing the electronic structure of imidazole complexes in solution with quantum chemistry and X-ray absorption spectroscopyManuscript (preprint) (Other academic)
    Abstract [en]

    By combing soft X-ray spectroscopy and theoretical calculations, characterization of the shared proton in the imidazole molecular complex has been done. With nitrogen core-level excitations as a sensitive reporter about the protonation status, a new absorption resonance is observed at a pH where exactly half of the imidazoles are protonated, right between the known absorptions of pure imidazole and pure imidazolium. Supported by TDDFT calculations, the spectral signature has been assigned to the sharing of the excess proton between two imidazole molecules in an asymmetric double minimum potential. Analysis of the discrete core excitations reveals shared electronic attributes between the molecular complex and individual monomers. The theoretical investigation also uncovers the influence of the shared proton on the intrinsic features and the overall spectral outcome.

  • 16.
    Doverstål, Mats
    Stockholm University, Faculty of Science.
    Experimental studies of dimers and clusters1994Doctoral thesis, comprehensive summary (Other academic)
  • 17. Ekimova, Maria
    et al.
    Kleine, Carlo
    Ludwig, Jan
    Ochmann, Miguel
    Agrenius, Thomas E. G.
    Kozari, Eve
    Pines, Dina
    Pines, Ehud
    Huse, Nils
    Wernet, Philippe
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Nibbering, Erik T. J.
    From Local Covalent Bonding to Extended Electric Field Interactions in Proton Hydration2022In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 61, no 46, article id e202211066Article in journal (Refereed)
    Abstract [en]

    Seemingly simple yet surprisingly difficult to probe, excess protons in water constitute complex quantum objects with strong interactions with the extended and dynamically changing hydrogen-bonding network of the liquid. Proton hydration plays pivotal roles in energy transport in hydrogen fuel cells and signal transduction in transmembrane proteins. While geometries and stoichiometry have been widely addressed in both experiment and theory, the electronic structure of these specific hydrated proton complexes has remained elusive. Here we show, layer by layer, how utilizing novel flatjet technology for accurate x-ray spectroscopic measurements and combining infrared spectral analysis and calculations, we find orbital-specific markers that distinguish two main electronic-structure effects: Local orbital interactions determine covalent bonding between the proton and neigbouring water molecules, while orbital-energy shifts measure the strength of the extended electric field of the proton. © 2022 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.

  • 18.
    Eriksson, Lars
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Grins, Jekabs
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Svensson, Gunnar
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    DFT predictions of Prussian Blue structures2018Conference paper (Refereed)
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  • 19.
    Fransson, Thomas
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Pettersson, Lars
    Stockholm University, Faculty of Science, Department of Physics.
    TDDFT and the X-ray absorption spectrum of liquid water: finding the “best” functionalManuscript (preprint) (Other academic)
    Abstract [en]

    We investigate the performance of time-dependent density functional theory (TDDFT) for reproducing high-level reference X-ray absorption spectra of liquid water. For this, we apply the integrated absolute difference (IAD) metric, previously used for X-ray emission spectra of liquid water [J. Chem. Theory Comput. 19, 7333-7342 (2023)], in order to investigate which exchange-correlation (xc) functionals yield TDDFT spectra in best agreement to reference, as well as to investigate the suitability of IAD for XAS spectrum calculations. It is seen that long-range corrected xc-functionals are required to yield good agreement with reference coupled cluster (CC) and algebraic-diagrammatic construction (ADC) spectra, with 100% asymptotic Hartree−Fock exchange resulting in the lowest IADs. The xc-functionals with best agreement to reference have been adopted for larger water clusters, yielding results in line with recently published coupled cluster theory, but which still show some discrepancies in the relative intensity of the features compared to experiment.

  • 20.
    Fransson, Thomas
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Pettersson, Lars G. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Calibrating TDDFT Calculations of the X-ray Emission Spectrum of Liquid Water: The Effects of Hartree-Fock Exchange2023In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 19, no 20, p. 7333-7342Article in journal (Refereed)
    Abstract [en]

    The structure and dynamics of liquid water continue to be debated, with insight provided by, among others, X-ray emission spectroscopy (XES), which shows a split in the high-energy 1b1 feature. This split is yet to be reproduced by theory, and it remains unclear if these difficulties are related to inaccuracies in dynamics simulations, spectrum calculations, or both. We investigate the performance of different methods for calculating XES of liquid water, focusing on the ability of time-dependent density functional theory (TDDFT) to reproduce reference spectra obtained by high-level coupled cluster and algebraic-diagrammatic construction scheme calculations. A metric for evaluating the agreement between theoretical spectra termed the integrated absolute difference (IAD), which considers the integral of shifted difference spectra, is introduced and used to investigate the performance of different exchange-correlation functionals. We find that computed spectra of symmetric and asymmetric model water structures are strongly and differently influenced by the amount of Hartree-Fock exchange, with best agreement to reference spectra for similar to 40-50%. Lower percentages tend to yield high density of contributing states, resulting in too broad features. The method introduced here is useful also for other spectrum calculations, in particular where the performance for ensembles of structures are evaluated.

  • 21.
    Fransson, Thomas
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Pettersson, Lars Gunnar Moody
    Stockholm University, Faculty of Science, Department of Physics.
    Evaluating the Impact of the Tamm–Dancoff Approximation on X-ray Spectrum Calculations2024In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 20, no 5, p. 2181-2191Article in journal (Refereed)
    Abstract [en]

    The impact of the Tamm–Dancoff approximation (TDA) for time-dependent density functional theory (TDDFT) calculations of X-ray absorption and X-ray emission spectra (XAS and XES) is investigated, showing small discrepancies in the excitation energies and intensities. Through explicit diagonalization of the TDDFT Hessian, XES was considered by using full TDDFT with a core-hole reference state. This has previously not been possible with most TDDFT implementations as a result of the presence of negative eigenvalues. Furthermore, a core–valence separation (CVS) scheme for XES is presented, in which only elements including the core-hole are considered, resulting in a small Hessian with the dimension of the number of remaining occupied orbitals of the same spin as the core-hole (CH). The resulting spectra are in surprisingly good agreement with the full-space counterpart, illustrating the weak coupling between the valence–valence and valence–CH transitions. Complications resulting from contributions from the discretized continuum are discussed, which can occur for TDDFT calculations of XAS and XES and for TDA calculations of XAS. In conclusion, we recommend that TDA be used when calculating X-ray emission spectra, and either CVS-TDA or CVS-TDDFT can be used for X-ray absorption spectra.

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  • 22.
    Fromager, Emmanuel
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Teichteil, Christian
    Maron, Laurent
    Extraction of shape-consistent spin-orbit pseudopotential from an effective spin-orbit parameter and application to the tellurium atom2006In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 106, no 3, p. 764-771Article in journal (Refereed)
    Abstract [en]

    A hybrid procedure to extract spin-orbit pseudo-potentials is proposed, taking information from both the orbital shape in the valence region and the atomic spin-orbit splitting. An effective atomic spin-orbit parameter is derived from a Dirac–Coulomb–Fock reference atomic calculation and is then used to extract the spin-orbit pseudo-potential. This method is tested for the ground-state configuration (5s25p4) of the tellurium atom.

  • 23. Furukawa, Masashi
    et al.
    Yamada, Taro
    Katano, Satoshi
    Kawai, Maki
    Ogasawara, Hirohito
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics.
    Geometrical characterization of adenine and guanine on Cu(110) by NEXAFS, XPS, and DFT calculation2007In: Surface Science, ISSN 0039-6028, E-ISSN 1879-2758, Vol. 601, no 23, p. 5433-5440Article in journal (Refereed)
    Abstract [en]

    Adsorption of purine DNA bases (guanine and adenine) on Cu(110) was studied by X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine-structure spectroscopy (NEXAFS), and density-functional theory (DFT) calculation. At coverages near 0.2 monolayers, Angular-resolved NEXAFS analysis revealed that adenine adsorbates lie almost flat and that guanine adsorbates are tilted up on the surface with the purine ring parallel to the atom rows of Cu(110). Referring to the previous studies on pyrimidine DNA bases [M. Furukawa, H. Fujisawa, S. Katano, H. Ogasawara, Y. Kim, T. Komeda, A. Nilsson, M. Kawai, Surf. Sci. 532-535 (2003) 261], the isomerization of DNA bases on Cu(110) was found to play an important role in the adsorption geometry. Guanine, thymine and cytosine adsorption have an amine-type nitrogen next to a carbonyl group, which is dehydrogenated into imine nitrogen on Cu(110). These bases are bonded by the inherent portion of -NH-CO- altered by conversion into enolic form and dehydrogenation. Adenine contains no CO group and is bonded to Cu(110) by participation of the inherent amine parts, resulting in nearly flatly-lying position.

  • 24.
    Granseth, Erik
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Structure, prediction, evolution and genome wide studies of membrane proteins2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    α-helical membrane proteins constitute 20-30% of all proteins in a cell and are involved in many essential cellular functions. The structure is only known for a few hundred of them, which makes structural models important. The most common structural model of a membrane protein is the topology which is a two-dimensional representation of the structure.

    This thesis is focused on three different aspects of membrane protein structure: improving structural predictions of membrane proteins, improving the level of detail of structural models and the concept of dual topology.

    It is possible to improve topology models of membrane proteins by including experimental information in computer predictions. This was first performed in Escherichia coli and, by using homology, it was possible to extend the results to 225 prokaryotic organisms. The improved models covered ~80% of the membrane proteins in E. coli and ~30% of other prokaryotic organisms.

    However, the traditional topology concept is sometimes too simple for complex membrane protein structures, which create a need for more detailed structural models. We created two new machine learning methods, one that predicts more structural features of membrane proteins and one that predicts the distance to the membrane centre for the amino acids. These methods improve the level of detail of the structural models.

    The final topic of this thesis is dual topology and membrane protein evolution. We have studied a class of membrane proteins that are suggested to insert either way into the membrane, i.e. have a dual topology. These protein families might explain the frequent occurrence of internal symmetry in membrane protein structures.

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  • 25.
    Gudem, Mahesh
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Kowalewski, Markus
    Stockholm University, Faculty of Science, Department of Physics.
    Cavity-Modified Chemiluminescent Reaction of Dioxetane2023In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 127, no 45, p. 9483-9494Article in journal (Refereed)
    Abstract [en]

    Chemiluminescence is a thermally activated chemical process that emits a photon of light by forming a fraction of products in the electronic excited state. A well-known example of this spectacular phenomenon is the emission of light in the firefly beetle, where the formation of a four-membered cyclic peroxide compound and subsequent dissociation produce a light-emitting product. The smallest cyclic peroxide, dioxetane, also exhibits chemiluminescence but with a low quantum yield as compared to that of firefly dioxetane. Employing the strong light–matter coupling has recently been found to be an alternative strategy to modify the chemical reactivity. In the presence of an optical cavity, the molecular degrees of freedom greatly mix with the cavity mode to form hybrid cavity–matter states called polaritons. These newly generated hybrid light–matter states manipulate the potential energy surfaces and significantly change the reaction dynamics. Here, we theoretically investigate the effects of a strong light–matter interaction on the chemiluminescent reaction of dioxetane using the extended Jaynes–Cummings model. The cavity couplings corresponding to the electronic and vibrational degrees of freedom have been included in the interaction Hamiltonian. We explore how the cavity alters the ground- and excited-state path energy barriers and reaction rates. Our results demonstrate that the formation of excited-state products in the dioxetane decomposition process can be either accelerated or suppressed, depending on the molecular orientation with respect to the cavity polarization.

  • 26.
    Gudem, Mahesh
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Kowalewski, Markus
    Stockholm University, Faculty of Science, Department of Physics.
    Controlling the Photostability of Pyrrole with Optical Nanocavities2021In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 125, no 5, p. 1142-1151Article in journal (Refereed)
    Abstract [en]

    Strong light-matter coupling provides a new strategy to manipulate the non-adiabatic dynamics of molecules by modifying potential energy surfaces. The vacuum field of nanocavities can couple strongly with the molecular degrees of freedom and form hybrid light-matter states, termed as polaritons or dressed states. The photochemistry of molecules possessing intrinsic conical intersections can be significantly altered by introducing cavity couplings to create new conical intersections or avoided crossings. Here, we explore the effects of optical cavities on the photo-induced hydrogen elimination reaction of pyrrole. Wave packet dynamics simulations have been performed on the two-state, two-mode model of pyrrole, combined with the cavity photon mode. Our results show how the optical cavities assist in controlling the photostability of pyrrole and influence the reaction mechanism by providing alternative dissociation pathways. The cavity effects have been found to be intensely dependent on the resonance frequency. We further demonstrate the importance of the vibrational cavity couplings and dipole-self interaction terms in describing the cavity-modified non-adiabatic dynamics.

  • 27.
    Holtkamp, Yannick
    et al.
    Constructor University 1 , Bremen, Germany.
    Kowalewski, Markus
    Stockholm University, Faculty of Science, Department of Physics.
    Jasche, Jens
    Stockholm University, Faculty of Science, The Oskar Klein Centre for Cosmo Particle Physics (OKC). Sorbonne Université, Paris, France; Institut d’Astrophysique de Paris, Paris, France.
    Kleinekathöfer, Ulrich
    Constructor University 1, Bremen, Germany.
    Machine-learned correction to ensemble-averaged wave packet dynamics2023In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 159, no 9, article id 094107Article in journal (Refereed)
    Abstract [en]

    For a detailed understanding of many processes in nature involving, for example, energy or electron transfer, the theory of open quantumsystems is of key importance. For larger systems, an accurate description of the underlying quantum dynamics is still a formidable task, and,hence, approaches employing machine learning techniques have been developed to reduce the computational effort of accurate dissipativequantum dynamics. A downside of many previous machine learning methods is that they require expensive numerical training datasets forsystems of the same size as the ones they will be employed on, making them unfeasible to use for larger systems where those calculationsare still too expensive. In this work, we will introduce a new method that is implemented as a machine-learned correction term to the socalled Numerical Integration of Schrödinger Equation (NISE) approach. It is shown that this term can be trained on data from small systemswhere accurate quantum methods are still numerically feasible. Subsequently, the NISE scheme, together with the new machine-learnedcorrection, can be used to determine the dissipative quantum dynamics for larger systems. Furthermore, we show that the newly proposedmachine-learned correction outperforms a previously handcrafted one, which, however, improves the results already considerably. 

  • 28. Huang, Congcong
    et al.
    Wikfeldt, Kjartan Thor
    Stockholm University, Faculty of Science, Department of Physics.
    Tokushima, Takashi
    Nordlund, Dennis
    Harada, Yoshi
    Bergmann, Uwe
    Niebuhr, M.
    Weiss, T. M.
    Horikawa, Y.
    Leetmaa, Mikael
    Stockholm University, Faculty of Science, Department of Physics.
    Ljungberg, Mathias P.
    Stockholm University, Faculty of Science, Department of Physics.
    Takahashi, Osamu
    Lentz, Annika
    Ojamäe, Lars
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Shin, Shik
    Pettersson, Lars G.M.
    Stockholm University, Faculty of Science, Department of Physics.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics.
    Reply to Soper "Fluctuations in water around a bimodal distribution of local hydrogen bonded structural motifs"2010In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 107, no 12, article id E45Article in journal (Refereed)
  • 29.
    Ivanov, Mikhail
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Lyubartsev, Alexander P.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Development of a bottom-up coarse-grained model for interactions of lipids with TiO2 nanoparticles2024In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 45, no 16, p. 1364-1379Article in journal (Refereed)
    Abstract [en]

    Understanding interactions of inorganic nanoparticles with biomolecules is important in many biotechnology, nanomedicine, and toxicological research, however, the size of typical nanoparticles makes their direct modeling by atomistic simulations unfeasible. Here, we present a bottom-up coarse-graining approach for modeling titanium dioxide (TiO2) nanomaterials in contact with phospholipids that uses the inverse Monte Carlo method to optimize the effective interactions from the structural data obtained in small-scale all-atom simulations of TiO2 surfaces with lipids in aqueous solution. The resulting coarse-grained models are able to accurately reproduce the structural details of lipid adsorption on different titania surfaces without the use of an explicit solvent, enabling significant computational resource savings and favorable scaling. Our coarse-grained simulations show that small spherical TiO2 nanoparticles (𝑟=2 nm) can only be partially wrapped by a lipid bilayer with phosphoethanolamine headgroups, however, the lipid adsorption increases with the radius of the nanoparticle. The current approach can be used to study the effect of the size and shape of TiO2 nanoparticles on their interactions with cell membrane lipids, which can be a determining factor in membrane wrapping as well as the recently discovered phenomenon of nanoquarantining, which involves the formation of layered nanomaterial–lipid structures.

  • 30.
    Jadoun, Deependra
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Gudem, Mahesh
    Stockholm University, Faculty of Science, Department of Physics.
    Kowalewski, Markus
    Stockholm University, Faculty of Science, Department of Physics.
    Capturing fingerprints of conical intersection: Complementary information of non-adiabatic dynamics from linear x-ray probes2021In: Structural Dynamics, E-ISSN 2329-7778, Vol. 8, no 3, article id 034101Article in journal (Refereed)
    Abstract [en]

    Many recent experimental ultrafast spectroscopy studies have hinted at non-adiabatic dynamics indicating the existence of conical intersections, but their direct observation remains a challenge. The rapid change of the energy gap between the electronic states complicated their observation by requiring bandwidths of several electron volts. In this manuscript, we propose to use the combined information of different x-ray pump-probe techniques to identify the conical intersection. We theoretically study the conical intersection in pyrrole using transient x-ray absorption, time-resolved x-ray spontaneous emission, and linear off-resonant Raman spectroscopy to gather evidence of the curve crossing.

  • 31.
    Johansson, Anna CV
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Solvation properties of proteins in membranes2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Knowledge about the insertion and stabilization of membrane proteins is a key step towards understanding their function and enabling membrane protein design. Transmembrane helices are normally quite hydrophobic to insert efficiently, but there are many exceptions with unfavorable polar or titratable residues. Since evolutionary conserved these amino acids are likely of paramount functional importance, e.g. the four arginines in the S4 voltage sensor helix of voltage-gated ion channels. This has lead to vivid discussion about their conformation, protonation state and cost of insertion. To address such questions, the main focus of this thesis has been membrane protein solvation in lipid bilayers, evaluated using molecular dynamics simulations methods.

    A main result is that polar and charged amino acids tend to deform the bilayer by pulling water/head-groups into the hydrophobic core to keep their hydrogen bonds paired, thus demonstrating the adaptiveness of the membrane to allow specific and quite complex solvation. In addition, this retained hydration suggests that the solvation cost is mainly due to entropy, not enthalpy loss. To further quantify solvation properties, free energy profiles were calculated for all amino acids in pure bilayers, with shapes correlating well with experimental in vivo values but with higher magnitudes. Additional profiles were calculated for different protonation states of the titratable amino acids, varying lipid composition and with transmembrane helices present in the bilayer. While the two first both influence solvation properties, the latter seems to be a critical aspect. When the protein fraction in the models resemble biological membranes, the solvation cost drops significantly - even to values compatible with experiment.

    In conclusion, by using simulation based methods I have been able to provide atomic scale explanations to experimental results, and in particular present a hypothesis for how the solvation of charged groups occurs.

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  • 32.
    Johansson, Erik M. J.
    et al.
    Uppsala universitet.
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Plogmaker, Stefan
    Uppsala universitet.
    Gorgoi, Mihaela
    Helmholtz Zentrum Berlin, BESSY II.
    Svensson, Svante
    Uppsala universitet.
    Siegbahn, Hans
    Uppsala universitet.
    Rensmo, Håkan
    Uppsala universitet.
    Spin-Orbit Coupling and Metal-Ligand Interactions in Fe(II), Ru(II), and Os(II) Complexes2010In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 114, no 22, p. 10314-10322Article in journal (Refereed)
    Abstract [en]

    The purpose of the present paper is to experimentally map the energy levels governing the trends observed in oxidation potentials and absorption spectra of M(bpy)32+ complexes (bpy = 2,2′-bipyridine, M = Fe(II), Ru(II), and Os(II)). Molecular films of the transition metal complexes were investigated with element specific methods using photoelectron spectroscopy (PES) at high kinetic energy using hard X-rays and by X-ray absorption spectroscopy (XAS). The results were compared to electronic structure calculations on the complexes and the ligand. The approach allows us to experimentally measure and interpret the energy levels in terms of spin−orbit coupling and metal−ligand interactions. Specifically, it was verified that the anomaly in the trend in oxidation potentials could be explained by a large spin−orbit coupling for the Os(bpy)32+. The influence of the different metal ions on the state formed upon light absorption was also investigated by N 1s X-ray absorption, and from the spectra we could determine the relative position of the levels originating from d−σ and π contributions. The results for the occupied and unoccupied electronic levels explain the lower energy of the MLCT transition of the Os(bpy)32+ in comparison to the Ru(bpy)32+.

  • 33.
    Josefsson, Ida
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Kunnus, Kristjan
    Schreck, Simon
    Föhlisch, Alexander
    de Groot, Frank
    Wernet, Philippe
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Ab Initio Calculations of X-ray Spectra: Atomic Multiplet and Molecular Orbital Effects in a Multiconfigurational SCF Approach to the L-Edge Spectra of Transition Metal Complexes2012In: The Journal of Physical Chemistry Letters, E-ISSN 1948-7185, Vol. 3, no 23, p. 3565-3570Article in journal (Refereed)
    Abstract [en]

    A new ab initio approach to the calculation of X-ray spectra is demonstrated. It combines a high-level quantum chemical description of the chemical interactions and local atomic multiplet effects. We show here calculated L-edge X-ray absorption (XA) and resonant inelastic X-ray scattering spectra for aqueous Ni2+ and XA spectra for a polypyridyl iron complex. Our quantum chemical calculations on a high level of accuracy in a post-Hartree–Fock framework give excellent agreement with experiment. This opens the door to reliable and detailed information on chemical interactions and the valence electronic structure in 3d transition-metal complexes also in transient excited electronic states. As we combine a molecular-orbital description with a proper treatment of local atomic electron correlation effects, our calculations uniquely allow, in particular, identifying the influence of interatomic chemical interactions versus intra-atomic correlations in the L-edge X-ray spectra.

  • 34.
    Karlsen, Elly Johanne
    Stockholm University.
    Quantum chemical studies of catalytic N₂O decomposition and NOx storage on metal oxides2003Doctoral thesis, comprehensive summary (Other academic)
  • 35. Kazakov, Vladimir
    et al.
    Sobko, Evgeny
    Zarembo, Konstantin
    Stockholm University, Nordic Institute for Theoretical Physics (Nordita). Copenhagen University, Denmark.
    Large-N Principal Chiral Model in Arbitrary External Fields2024In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 132, no 14, article id 141602Article in journal (Refereed)
    Abstract [en]

    We report the explicit solution for the vacuum state of the two-dimensional SU(N) principal chiral model at large for an arbitrary set of chemical potentials and any interaction strength, a unique result of such kind for an asymptotically free quantum field theory. The solution matches one-loop perturbative calculation at weak coupling, and in the opposite strong-coupling regime exhibits an emergent spacial dimension from the continuum limit of the SU(N) Dynkin diagram.

  • 36.
    Kim, Hyunho
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Saura, Patricia
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Pöverlein, Maximilian C.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Gamiz-Hernandez, Ana P.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Kaila, Ville R. I.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Quinone Catalysis Modulates Proton Transfer Reactions in the Membrane Domain of Respiratory Complex I2023In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 145, no 31, p. 17075-17086Article in journal (Refereed)
    Abstract [en]

    Complex I is a redox-driven proton pump that drives electron transport chains and powers oxidative phosphorylation across all domains of life. Yet, despite recently resolved structures from multiple organisms, it still remains unclear how the redox reactions in Complex I trigger proton pumping up to 200 Å away from the active site. Here, we show that the proton-coupled electron transfer reactions during quinone reduction drive long-range conformational changes of conserved loops and trans-membrane (TM) helices in the membrane domain of Complex I from Yarrowia lipolytica. We find that the conformational switching triggers a π → α transition in a TM helix (TM3ND6) and establishes a proton pathway between the quinone chamber and the antiporter-like subunits, responsible for proton pumping. Our large-scale (>20 μs) atomistic molecular dynamics (MD) simulations in combination with quantum/classical (QM/MM) free energy calculations show that the helix transition controls the barrier for proton transfer reactions by wetting transitions and electrostatic effects. The conformational switching is enabled by re-arrangements of ion pairs that propagate from the quinone binding site to the membrane domain via an extended network of conserved residues. We find that these redox-driven changes create a conserved coupling network within the Complex I superfamily, with point mutations leading to drastic activity changes and mitochondrial disorders. On a general level, our findings illustrate how catalysis controls large-scale protein conformational changes and enables ion transport across biological membranes. 

  • 37.
    Kiusalaas, Rein
    Stockholm University.
    Relation between phases present in master alloys of the Al-Ti-B type1986Doctoral thesis, monograph (Other academic)
  • 38.
    Larson, Jonas
    Stockholm University, Faculty of Science, Department of Physics. Universität zu Köln, Germany.
    Absence of Vacuum Induced Berry Phases without the Rotating Wave Approximation in Cavity QED2012In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 108, no 3, article id 033601Article in journal (Refereed)
    Abstract [en]

    We revisit earlier studies on Berry phases suggested to appear in certain cavity QED settings. It has been especially argued that a nontrivial geometric phase is achievable even in the situation of no cavity photons. We, however, show that such results hinge on imposing the rotating wave approximation (RWA), while without the RWA no Berry phases occur in these schemes. A geometrical interpretation of our results is obtained by introducing semiclassical energy surfaces which in a simple way brings out the phase-space dynamics. With the RWA, a conical intersection between the surfaces emerges and encircling it gives rise to the Berry phase. Without the RWA, the conical intersection is absent and therefore the Berry phase vanishes. It is believed that this is a first example showing how the application of the RWA in the Jaynes-Cummings model may lead to false conclusions, regardless of the mutual strengths between the system parameters.

  • 39.
    Larsson, Per
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Prediction, modeling, and refinement of protein structure2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Accurate predictions of protein structure are important for understanding many processes in cells. The interactions that govern protein folding and structure are complex, and still far from completely understood. However, progress is being made in many areas. Here, efforts to improve the overall quality of protein structure models are described. From a pure evolutionary perspective, in which proteins are viewed in the light of gradually accumulated mutations on the sequence level, it is shown how information from multiple sources helps to create more accurate models. A very simple but surprisingly accurate method for assigning confidence measures for protein structures is also tested. In contrast to models based on evolution, physics based methods view protein structures as the result of physical interactions between atoms. Newly implemented methods are described that both increase the time-scales accessible for molecular dynamics simulations almost 10-fold, and that to some extent might be able to refine protein structures. Finally, I compare the efficiency and properties of different techniques for protein structure refinement.

  • 40.
    Liao, Rongzhen
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Quantum Chemical Cluster Modeling of Enzymatic Reactions2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The Quantum chemical cluster approach has been shown to be quite powerful and efficient in the modeling of enzyme active sites and reaction mechanisms. In this thesis, the reaction mechanisms of several enzymes have been investigated using the hybrid density functional B3LYP. The enzymes studied include four dinuclear zinc enzymes, namely dihydroorotase, N-acyl-homoserine lactone hydrolase, RNase Z, and human renal dipeptidase, two trinuclear zinc enzymes, namely phospholipase C and nuclease P1, two tungstoenzymes, namely formaldehyde ferredoxin oxidoreductase and acetylene hydratase, aspartate α-decarboxylase, and mycolic acid cyclopropane synthase. The potential energy profiles for various mechanistic scenarios have been calculated and analyzed. The role of the metal ions as well as important active site residues has been discussed.

      In the cluster approach, the effects of the parts of the enzyme that are not explicitly included in the model are taken into account using implicit solvation methods.

      For all six zinc-dependent enzymes studied, the di-zinc bridging hydroxide has been shown to be capable of performing nucleophilic attack on the substrate. In addition, one, two, or even all three zinc ions participate in the stabilization of the negative charge in the transition states and intermediates, thereby lowering the barriers.

      For the two tungstoenzymes, several different mechanistic scenarios have been considered to identify the energetically most feasible one. For both enzymes, new mechanisms are proposed.

      Finally, the mechanism of mycolic acid cyclopropane synthase has been shown to be a direct methyl transfer to the substrate double bond, followed by proton transfer to the bicarbonate.

      From the studies of these enzymes, we demonstrate that density functional calculations are able to solve mechanistic problems related to enzymatic reactions, and a wealth of new insight can be obtained.

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  • 41.
    Light, Sara
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Investigations into the evolution of biological networks2006Doctoral thesis, monograph (Other academic)
    Abstract [en]

    Individual proteins, and small collections of proteins, have been extensively studied for at least two hundred years. Today, more than 350 genomes have been completely sequenced and the proteomes of these genomes have been at least partially mapped. The inventory of protein coding genes is the first step toward understanding the cellular machinery. Recent studies have generated a comprehensive data set for the physical interactions between the proteins of Saccharomyces cerevisiae, in addition to some less extensive proteome interaction maps of higher eukaryotes. Hence, it is now becoming feasible to investigate important questions regarding the evolution of protein-protein networks. For instance, what is the evolutionary relationship between proteins that interact, directly or indirectly? Do interacting proteins co-evolve? Are they often derived from each other? In order to perform such proteome-wide investigations, a top-down view is necessary. This is provided by network (or graph) theory.

    The proteins of the cell may be viewed as a community of individual molecules which together form a society of proteins (nodes), a network, where the proteins have various kinds of relationships (edges) to each other. There are several different types of protein networks, for instance the two networks studied here, namely metabolic networks and protein-protein interaction networks. The metabolic network is a representation of metabolism, which is defined as the sum of the reactions that take place inside the cell. These reactions often occur through the catalytic activity of enzymes, representing the nodes, connected to each other through substrate/product edges. The indirect interactions of metabolic enzymes are clearly different in nature from the direct physical interactions, which are fundamental to most biological processes, which constitute the edges in protein-protein interaction networks.

    This thesis describes three investigations into the evolution of metabolic and protein-protein interaction networks. We present a comparative study of the importance of retrograde evolution, the scenario that pathways assemble backward compared to the direction of the pathway, and patchwork evolution, where enzymes evolve from a broad to narrow substrate specificity. Shifting focus toward network topology, a suggested mechanism for the evolution of biological networks, preferential attachment, is investigated in the context of metabolism. Early in the investigation of biological networks it seemed clear that the networks often display a particular, 'scale-free', topology. This topology is characterized by many nodes with few interaction partners and a few nodes (hubs) with a large number of interaction partners. While the second paper describes the evidence for preferential attachment in metabolic networks, the final paper describes the characteristics of the hubs in the physical interaction network of S. cerevisiae.

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  • 42.
    Ljungberg, Mathias P.
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Pettersson, Lars G.M.
    Stockholm University, Faculty of Science, Department of Physics.
    Nilsson, Anders
    Stockholm University, Faculty of Science, Department of Physics.
    Vibrational interference effects in x-ray emission of a model water dimer: implications for the interpretation of the liquid spectrum2011In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 134, no 4, p. 044513-Article in journal (Refereed)
    Abstract [en]

    We apply the Kramers-Heisenberg formula to a model water dimer to discuss vibrational interference in the x-ray emission spectrum of the donor molecule for which the core-ionized potential energy surface is dissociative but bounded by the accepting molecule. A long core-hole life time leads to decay from Zundel-like, fully delocalized vibrational states in the intermediate potential without involvement of a specific dissociated component. Comparison is made to a model with an unbound intermediate state allowing dissociation to infinity which gives a sharp, fully dissociated feature and a broad molecular peak at long core-hole life time. The implications of the vibrational interference effect on the liquid water spectrum are discussed and it is proposed that this mainly gives rise to an isotope-dependent asymmetrical broadening of the lone pair peak.

  • 43.
    Lundberg, Marcus
    Stockholm University, Faculty of Science, Department of Physics.
    Challenges in Enzyme Catalysis - Photosystem II and Orotidine Decarboxylase: A Density Functional Theory Treatment2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Possibly the most fascinating biochemical mechanism remaining to be solved is the formation of oxygen from water in photosystem II. This is a critical part of the photosynthetic reaction that makes solar energy accessible to living organisms.

    The present thesis uses quantum chemistry, more specifically the density functional B3LYP, to investigate a mechanism where an oxyl radical bound to manganese is the active species in O-O bond formation. Benchmark calculations on manganese systems confirm that B3LYP can be expected to give accurate results. The effect of the self-interaction error is shown to be limited. Studies of synthetic manganese complexes support the idea of a radical mechanism. A manganese complex with an oxyl radical is active in oxygen formation while manganese-oxo complexes remain inactive. Formation of the O-O bond requires a spin transition but there should be no effect on the rate. Spin transitions are also required in many short-range electron-transfer reactions.

    Investigations of the superproficient enzyme orotidine decarboxylase support a mechanism that involves an invariant network of charged amino acids, acting together with at least two mobile water molecules.

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  • 44.
    Majhi, Debashis
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Stevensson, Baltzar
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Nguyen, Tran Tra Mi
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Edén, Mattias
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    1H and 13C chemical shift-structure effects in anhydrous β-caffeine and four caffeine-diacid cocrystals probed by solid-state NMR experiments and DFT calculations2024In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084Article in journal (Refereed)
    Abstract [en]

    By using density functional theory (DFT) calculations, we refined the H atom positions in the structures of β-caffeine (C), α-oxalic acid (OA; (COOH)2), α-(COOH)2·2H2O, β-malonic acid (MA), β-glutaric acid (GA), and I-maleic acid (ME), along with their corresponding cocrystals of 2 : 1 (2C–OA, 2C–MA) or 1 : 1 (C–GA, C–ME) stoichiometry. The corresponding 13C/1H chemical shifts obtained by gauge including projector augmented wave (GIPAW) calculations agreed overall very well with results from magic-angle-spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy experiments. Chemical-shift/structure trends of the precursors and cocrystals were examined, where good linear correlations resulted for all COO1H sites against the H⋯O and/or H⋯N H-bond distance, whereas a general correlation was neither found for the aliphatic/caffeine-stemming 1H sites nor any 13C chemical shift against either the intermolecular hydrogen- or tetrel-bond distance, except for the 13COOH sites of the 2C–OA, 2C–MA, and C–GA cocrystals, which are involved in a strong COOHN bond with caffeine that is responsible for the main supramolecular stabilization of the cocrystal. We provide the first complete 13C NMR spectral assignment of the structurally disordered anhydrous β-caffeine polymorph. The results are discussed in relation to previous literature on the disordered α-caffeine polymorph and the ordered hydrated counterpart, along with recommendations for NMR experimentation that will secure sufficient 13C signal-resolution for reliable resonance/site assignments.

  • 45.
    Melén, Karin
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Topology Prediction of Membrane Proteins: Why, How and When?2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Membrane proteins are of broad interest since they constitute a large fraction of the proteome in all organisms, up to 20-30%. They play a crucial role in many cellular processes mediating information flow and molecular transport across otherwise nearly impermeable membranes. Traditional three-dimensional structural analyses of membrane proteins are difficult to perform, which makes studies of other structural aspects important. The topology of an α-helical membrane protein is a two-dimensional description of how the protein is embedded in the membrane and gives valuable information on both structure and function.

    This thesis is focused on predicting the topology of α-helical membrane proteins and on assessing and improving the prediction accuracy. Reliability scores have been derived for a number of prediction methods, and have been integrated into the widely used TMHMM predictor. The reliability score makes it possible to estimate the trustworthiness of a prediction.

    Mapping the full topology of a membrane protein experimentally is time-consuming and cannot be done on a genome-wide scale. However, determination of the location of one part of a membrane protein relative to the membrane is feasible. We have analyzed the impact of incorporating such experimental information a priori into TMHMM predictions and show that the accuracy increases significantly. We further show that the C-terminal location of a membrane protein (inside or outside) is the optimal information to use as a constraint in the predictions.

    By combining experimental techniques for determining the C-terminal location of membrane proteins with topology predictions, we have produced reliable topology models for the majority of all membrane proteins in the model organisms E. coli and S. cerevisiae. The results were further expanded to ~15,000 homologous proteins in 38 fully sequenced eukaryotic genomes. This large set of reliable topology models should be useful, in particular as the structural data for eukaryotic membrane proteins is very limited.

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  • 46.
    Moncada, Félix
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Universidad Nacional de Colombia, Colombia.
    Quintero, William
    Posada, Edwin
    Pettersson, Lars Gunnar Moody
    Stockholm University, Faculty of Science, Department of Physics.
    Reyes, Andrés
    A nuclear configuration interaction approach to study nuclear spin effects: an application to ortho- and para-3He2@C602024In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 25, no 4, article id e202300498Article in journal (Refereed)
    Abstract [en]

    We introduce a non-orthogonal configuration interaction approach to investigate nuclear quantum effects on energies and densities of confined fermionic nuclei. The Hamiltonian employed draws parallels between confined systems and many-electron atoms, where effective non-Coulombic potentials represent the interactions of the trapped particles. One advantage of this method is its generality, as it offers the potential to study the nuclear quantum effects of various confined species affected by effective isotropic or anisotropic potentials. As a first application, we analyze the quantum states of two 3He atoms encapsulated in C60. At the Hartree–Fock level, we observe the breaking of spin and spatial symmetries. To ensure wavefunctions with the correct symmetries, we mix the broken-symmetry Hartree–Fock states within the non-orthogonal configuration interaction expansion. Our proposed approach predicts singly and triply degenerate ground states for the singlet (para-3He2@C60) and triplet (ortho-3He2@C60) nuclear spin configurations, respectively. The ortho-3He2@C60 ground state is 5.69 cm−1 higher in energy than the para-3He2@C60 ground state. The nuclear densities obtained for these states exhibit the icosahedral symmetry of the C60 embedding potential. Importantly, our calculated energies for the lowest 85 states are in close agreement with perturbation theory results based on a harmonic oscillator plus rigid rotor model of 3He2@C60

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  • 47. Mosaferi, Mohammadreza
    et al.
    Céolin, Denis
    Rueff, Jean-Pascal
    Selles, Patricia
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Björneholm, Olle
    Öhrwall, Gunnar
    Carniato, Stéphane
    Fingerprint of Dipole Moment Orientation of Water Molecules in Cu2+ Aqueous Solution Probed by X-ray Photoelectron Spectroscopy2024In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 146, no 14, p. 9836-9850Article in journal (Refereed)
    Abstract [en]

    The electronic structure and geometrical organization of aqueous Cu2+ have been investigated by using X-ray photoelectron spectroscopy (XPS) at the Cu L-edge combined with state-of-the-art ab initio molecular dynamics and a quantum molecular approach designed to simulate the Cu 2p X-ray photoelectron spectrum. The calculations offer a comprehensive insight into the origin of the main peak and satellite features. It is illustrated how the energy drop of the Cu 3d levels (≈7 eV) following the creation of the Cu 2p core hole switches the nature of the highest singly occupied molecular orbitals (MOs) from the dominant metal to the dominant MO nature of water. It is particularly revealed how the repositioning of the Cu 3d levels induces the formation of new bonding (B) and antibonding (AB) orbitals, from which shakeup mechanisms toward the relaxed H-SOMO operate. As highlighted in this study, the appearance of the shoulder near the main peak corresponds to the characteristic signature of shakeup intraligand (1a1 → H-SOMO(1b1)) excitations in water, providing insights into the average dipole moment distribution (≈36°) of the first-shell water molecules surrounding the metal ion and its direct impact on the broadening of the satellite. It is also revealed that the main satellite at 8 eV from the main peak corresponds to (metal/1b2 → H-SOMO(1b1) of water) excitations due to a bonding/antibonding (B/AB) interaction of Cu 3d levels with the deepest valence O2p/H1s 1b2 orbitals of water. This finding underscores the sensitivity of XPS to the electronic structure and orientation of the nearest water molecules around the central ion.

  • 48.
    Nilsson, Anders
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Nordlund, Dennis
    Stanford.
    Waluyo, Ira
    Stanford.
    Huang, Ningdong
    Stanford.
    Ogasawara, Hirohito
    Stanford.
    Kaya, Sarp
    Stanford.
    Bergmann, Uwe
    Stanford.
    Näslund, Lars-Åke
    Stanford.
    Öström, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Wernet, Philippe
    Helmholtz-Zentrum Berlin, Germany.
    Andersson, Klas J.
    Haldor-Topsoe.
    Schiros, Theanne
    Stockholm University, Faculty of Science, Department of Physics.
    Pettersson, Lars G.M.
    Stockholm University, Faculty of Science, Department of Physics.
    X-ray Absorption Spectroscopy and X-ray Raman Scattering of Water : an Experimental View2010In: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, E-ISSN 1873-2526, Vol. 177, p. 99-129Article in journal (Refereed)
    Abstract [en]

    Here we present a review of X-ray absorption spectroscopy and X-ray Raman scattering with the perspective to understand the spectra of water including changes with temperature, mass of the water molecule and presence of monovalent ions. The different detection schemes are discussed and it is concluded that transmission X-ray absorption measurements, using a small area where the thickness is uniform, and X-ray Raman scattering give the most reliable spectra. Different model systems are discussed such as the surface and bulk of ice and various adsorbed monolayer structures on metal surfaces

  • 49.
    Noack, Holger
    Stockholm University, Faculty of Science, Department of Physics.
    Biomimetic Iron Complexes involved in Oxygenation and Chlorination: A Theoretical Study2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biomimetic chemistry is directed towards the simulation of enzymatic reactivity with synthetic analogues. In this thesis a quantum chemical method has been employed to study the mechanism of highly reactive iron-oxo complexes involved in oxygenation and chlorination of organic substrates. The aim of this research is to gain greater understanding for the reactivity paradigm of the iron-oxo group.

    One reaction deals with the conversion of cyclohexane into adipic acid, a key chemical in industrial chemistry, catalyzed by an iron(II)-porphyrin complex in the presence of dioxygen. This process constitutes a ’green’ alternative to conventional adipic acid production, and is thus of great interest to synthetic chemistry. Another reaction investigated herein regards the selective chlorination observed for a new group of non-heme iron enzymes. With help of theoretical modeling it was possible to propose a mechanism that explains the observed selectivity. It is furthermore demonstrated how a biomimetic iron complex simulates the enzymatic reactivity by a different mechanism.

    Other topics covered in this thesis regard the structure-reactivity relationship of a binuclear iron complex and the intradiol C-C bond cleavage of catechol catalyzed by an iron(III) complex.

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  • 50.
    Norjmaa, Gantulga
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Rebek Jr., Julius
    Himo, Fahmi
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Modeling Amine Methylation in Methyl Ester Cavitand2024In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 30, no 13, article id e202303911Article in journal (Refereed)
    Abstract [en]

    Methylation of amines inside an introverted resorcinarene-based deep methyl ester cavitand is investigated by means of molecular dynamics simulations and quantum chemical calculations. Experimentally, the cavitand has been shown to bind a number of amines and accelerate the methylation reaction by more than four orders of magnitude for some of them. Eight different amines are considered in the present study, and the geometries and energies of their binding to the cavitand are first characterized and analyzed. Next, the methyl transfer reactions are investigated and the calculated barriers are found to be in generally good agreement with experimental results. In particular, the experimentally-observed rate acceleration in the cavitand as compared to the solution reaction is well reproduced by the calculations. The origins of this rate acceleration are analyzed by computational modifications made to the structure of the cavitand, and the role of the solvent is discussed.

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