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  • 1.
    Aderne, Rian E.
    et al.
    Pontificia Univ Catolic Rio Janeiro PUC Rio, BR-22453900 Rio De Janeiro, RJ, Brazil.
    Borges, Bruno Gabriel A. L.
    Univ Fed Rio Janeiro UFRJ, Inst Quim, BR-21941909 Rio De Janeiro, RJ, Brazil.
    Avila, Harold C.
    Univ Atlantic, Dept Phys, Atlantico, Colombia.
    von Kieseritzky, Fredrik
    Karolinska Inst, Dept Neurobiol Care Sci & Soc, Stockholm, Sweden.
    Hellberg, Jonas
    Chemtron AB, Bergkallavagen 37C, S-19279 Sollentuna, Sweden.
    Koehler, Marlus
    Univ Fed Parana UFPR, Dept Fis, BR-81531980 Curitiba, PR, Brazil.
    Cremona, Marco
    Pontificia Univ Catolic Rio Janeiro PUC Rio, BR-22453900 Rio De Janeiro, RJ, Brazil.
    Roman, Lucimara S.
    Univ Fed Parana UFPR, Dept Fis, BR-81531980 Curitiba, PR, Brazil.
    Araujo, Moyses
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Karlstad Univ, Dept Engn & Phys, S-65188 Karlstad, Sweden.
    Rocco, Maria Luiza M.
    Univ Fed Rio Janeiro UFRJ, Inst Quim, BR-21941909 Rio De Janeiro, RJ, Brazil.
    Marchiori, Cleber F. N.
    Karlstad Univ, Dept Engn & Phys, S-65188 Karlstad, Sweden.
    On the energy gap determination of organic optoelectronic materials: the case of porphyrin derivatives2022In: Materials Advances, E-ISSN 2633-5409, Vol. 3, no 3, p. 1791-1803Article in journal (Refereed)
    Abstract [en]

    The correct determination of the ionization potential (IP) and electron affinity (EA) as well as the energy gap is essential to properly characterize a series of key phenomena related to the applications of organic semiconductors. For example, energy offsets play an essential role in charge separation in organic photovoltaics. Yet there has been a lot of confusion involving the real physical meaning behind those quantities. Experimentally the energy gap can be measured by direct techniques such as UV-Vis absorption, or indirect techniques such as cyclic voltammetry (CV). Another spectroscopic method is the Reflection Electron Energy Loss Spectroscopy (REELS). Regarding data correlation, there is little consensus on how the REELS' energy gap can be interpreted in light of the energies obtained from other methodologies such as CV, UV-Vis, or photoemission. In addition, even data acquired using those traditional techniques has been misinterpreted or applied to derive conclusions beyond the limits imposed by the physics of the measurement. A similar situation also happens when different theoretical approaches are used to assess the energy gap or employed to explain outcomes from experiments. By using a set of porphyrin derivatives as model molecules, we discuss some key aspects of those important issues. The peculiar properties of these porphyrins demonstrate that even straightforward measurements or calculations performed in a group of very similar molecules need a careful interpretation of the outcomes. Differences up to 660 meV (similar to 190 meV) are found comparing REELS (electrochemical) measurements with UV-Vis energy gaps, for instance. From the theoretical point of view, a reasonable agreement with electrochemical measurements of the IP, EA, and the gap of the porphyrins is only obtained when the calculations involve the full thermodynamics of the redox processes. The purpose of this work is to shed light on the differences and similarities of those aforementioned characterization methods and provide some insight that might help one to develop a critical analysis of the different experimental and theoretical methodologies.

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  • 2.
    Agarwala, Hemlata
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Synthetic Molecular Chemistry. Tech Univ Munich TUM, Campus Straubing Biotechnol & Sustainabil,Uferstr, D-94315 Straubing, Germany..
    Chen, Xiaoyu
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth CBH, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Lyonnet, Julien R.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström. Barcelona Inst Sci & Technol, Inst Chem Res Catalonia ICIQ, Tarragona 43007, Spain..
    Johnson, Ben A.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström. Tech Univ Munich TUM, Campus Straubing Biotechnol & Sustainabil,Uferstr, D-94315 Straubing, Germany..
    Ahlquist, Marten
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth CBH, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden..
    Ott, Sascha
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Alternating Metal-Ligand Coordination Improves Electrocatalytic CO2 Reduction by a Mononuclear Ru Catalyst2023In: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 62, no 17Article 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.

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  • 3.
    Agback, M
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Lunell, S
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Hussenius, A
    Department of Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Matsson, O
    Department of Chemistry. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Theoretical studies of proton transfer reactions in 1-methylindene1998In: ACTA CHEMICA SCANDINAVICA, ISSN 0904-213X, Vol. 52, no 5, p. 541-548Article in journal (Refereed)
    Abstract [en]

    The base-catalysed 1,3-proton transfer reactions in 1-methylindene have been studied theoretically in polar (water) and unpolar (cyclohexane) solvents, respectively, for two different choices of bases, namely ammonia and trimethylamine (TMA), using the SM

  • 4.
    Agosta, Lorenzo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Brandt, Erik G.
    Stockholm Univ, Dept Mat & Environm Chem, S-10691 Stockholm, Sweden..
    Lyubartsev, Alexander
    Stockholm Univ, Dept Mat & Environm Chem, S-10691 Stockholm, Sweden..
    Improved Sampling in Ab Initio Free Energy Calculations of Biomolecules at Solid-Liquid Interfaces: Tight-Binding Assessment of Charged Amino Acids on TiO2 Anatase (101)2020In: Computation, E-ISSN 2079-3197, Vol. 8, no 1, article id 12Article in journal (Refereed)
    Abstract [en]

    Atomistic simulations can complement the scarce experimental data on free energies of molecules at bio-inorganic interfaces. In molecular simulations, adsorption free energy landscapes are efficiently explored with advanced sampling methods, but classical dynamics is unable to capture charge transfer and polarization at the solid-liquid interface. Ab initio simulations do not suffer from this flaw, but only at the expense of an overwhelming computational cost. Here, we introduce a protocol for adsorption free energy calculations that improves sampling on the timescales relevant to ab initio simulations. As a case study, we calculate adsorption free energies of the charged amino acids Lysine and Aspartate on the fully hydrated anatase (101) TiO2 surface using tight-binding forces. We find that the first-principle description of the system significantly contributes to the adsorption free energies, which is overlooked by calculations with previous methods.

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  • 5.
    Ahlstrand, Emma
    et al.
    Linnæus University Centre for Biomaterials Chemistry.
    Spångberg, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Friedman, Ran
    Interaction Energies Between Metal Ions (Zn2+ and Cd2+) and Biologically Relevant Ligands2013In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 113, no 23, p. 2554-2562Article in journal (Refereed)
    Abstract [en]

    Interactions between the group XII metals Zn2+ and Cd2+ and amino acid residues play an important role in biology due to the prevalence of the first and the toxicity of the second. Estimates of the interaction energies between the ions and relevant residues in proteins are however difficult to obtain. This study reports on calculated interaction energy curves for small complexes of Zn2+ or Cd2+ and amino acid mimics (acetate, methanethiolate, and imidazole) or water. Given that many applications and models (e.g., force fields, solvation models, etc.) begin with and rely on an accurate description of gas-phase interaction energies, this is where our focus lies in this study. Four density functional theory (DFT)-functionals and MP2 were used to calculate the interaction energies not only at the respective equilibrium distances but also at a relevant range of ion–ligand separation distances. The calculated values were compared with those obtained by CCSD(T). All DFT-methods are found to overestimate the magnitude of the interaction energy compared to the CCSD(T) reference values. The deviation was analyzed in terms of energy components from localized molecular orbital energy decomposition analysis scheme and is mostly attributed to overestimation of the polarization energy. MP2 shows good agreement with CCSD(T) [root mean square error (RMSE) = 1.2 kcal/mol] for the eight studied complexes at equilibrium distance. Dispersion energy differences at longer separation give rise to increased deviations between MP2 and CCSD(T) (RMSE = 6.4 kcal/mol at 3.0 Å). Overall, the results call for caution in applying DFT methods to metalloprotein model complexes even with closed-shell metal ions such as Zn2+ and Cd2+, in particular at ion–ligand separations that are longer than the equilibrium distances.

  • 6.
    Ahmad, Mariam
    et al.
    Univ Southern Denmark, Mads Clausen Inst, SDU Ctr Adv Photovolta & Thin Film Energy Devices, DK-6400 Sonderborg, Denmark.;Univ Southern Denmark, SDU Climate Cluster, DK-5230 Odense, Denmark..
    Cruguel, Herve
    Sorbonne Univ, Inst Nanosci Paris, CNRS, UMR 7588, F-75005 Paris, France..
    Ahmadpour, Mehrad
    Univ Southern Denmark, Mads Clausen Inst, SDU Ctr Adv Photovolta & Thin Film Energy Devices, DK-6400 Sonderborg, Denmark..
    Vannucchi, Noemi
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Sorbonne Univ, Inst Nanosci Paris, CNRS, UMR 7588, F-75005 Paris, France..
    Samie, Nahed Mohammad
    Sorbonne Univ, Inst Nanosci Paris, CNRS, UMR 7588, F-75005 Paris, France..
    Leuillet, Celine
    Sorbonne Univ, Inst Nanosci Paris, CNRS, UMR 7588, F-75005 Paris, France..
    Generalov, Alexander
    Lund Univ, MAX Lab 4, S-22100 Lund, Sweden..
    Li, Zheshen
    Aarhus Univ, Ctr Storage Ring Facil, Dept Phys & Astron, ISA, DK-8000 Aarhus C, Denmark..
    Madsen, Morten
    Univ Southern Denmark, Mads Clausen Inst, SDU Ctr Adv Photovolta & Thin Film Energy Devices, DK-6400 Sonderborg, Denmark.;Univ Southern Denmark, SDU Climate Cluster, DK-5230 Odense, Denmark..
    Witkowski, Nadine
    Sorbonne Univ, Inst Nanosci Paris, CNRS, UMR 7588, F-75005 Paris, France..
    Uncovering the Electronic State Interplay at Metal Oxide Electron Transport Layer/Nonfullerene Acceptor Interfaces in Stable Organic Photovoltaic Devices2023In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 15, no 47, p. 55065-55072Article in journal (Refereed)
    Abstract [en]

    The implementation of sputter-deposited TiOx as an electron transport layer in nonfullerene acceptor-based organic photovoltaics has been shown to significantly increase the long-term stability of devices compared to conventional solution-processed ZnO due to a decreased photocatalytic activity of the sputtered TiOx. In this work, we utilize synchrotron-based photoemission and absorption spectroscopies to investigate the interface between the electron transport layer, TiOx prepared by magnetron sputtering, and the nonfullerene acceptor, ITIC, prepared in situ by spray deposition to study the electronic state interplay and defect states at this interface. This is used to unveil the mechanisms behind the decreased photocatalytic activity of the sputter-deposited TiOx and thus also the increased stability of the organic solar cell devices. The results have been compared to similar measurements on anatase TiOx since anatase TiOx is known to have a strong photocatalytic activity. We show that the deposition of ITIC on top of the sputter-deposited TiOx results in an oxidation of Ti3+ species in the TiOx and leads to the emergence of a new O 1s peak that can be attributed to the oxygen in ITIC. In addition, increasing the thickness of ITIC on TiOx leads to a shift in the O 1s and C 1s core levels toward higher binding energies, which is consistent with electron transfer at the interface. Resonant photoemission at the Ti L-edge shows that oxygen vacancies in sputtered TiOx lie mostly in the surface region, which contrasts the anatase TiOx where an equal distribution between surface and subsurface oxygen vacancies is observed. Furthermore, it is shown that the subsurface oxygen vacancies in sputtered TiOx are strongly reduced after ITIC deposition, which can reduce the photocatalytic activity of the oxide, while the oxygen vacancies in model anatase TiOx are not affected upon ITIC deposition. This difference can explain the inferior photocatalytic activity of the sputter-deposited TiOx and thus also the increased stability of devices with sputter-deposited TiOx used as an electron transport layer.

  • 7.
    Ahmed, Taha
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Edvinsson, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Materials Science and Engineering, Solid State Physics.
    Optical Quantum Confinement in Ultrasmall ZnO and the Effect of Size on Their Photocatalytic Activity2020In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 124, no 11, p. 6395-6404Article in journal (Refereed)
    Abstract [en]

    Zinc oxide is a well-known metal oxide semiconductor with a wide direct band gap that offers a promising alternative to titanium oxide in photocatalytic applications. ZnO is studied here as quantum dots (QDs) in colloidal suspensions, where ultrasmall nanoparticles of ZnO show optical quantum confinement with a band gap opening for particles below 9 nm in diameter from the shift of the band edge energies. The optical properties of growing ZnO QDs are determined with Tauc analysis, and a system of QDs for the treatment and degradation of distributed threats is analyzed using an organic probe molecule, methylene blue, whose UV/vis spectrum is analyzed in some detail. The effect of optical properties of the QDs and the kinetics of dye degradation are quantified for low-dimensional ZnO materials in the range of 3-8 nm and show a substantial increase in photocatalytic activity compared to larger ZnO particles. This is attributed to a combined effect from the increased surface area as well as a quantum confinement effect that goes beyond the increased surface area. The results show a significantly higher photocatalytic activity for the QDs between 3 and 6 nm with a complete decolorization of the organic probe molecule, while QDs from 6 nm and upward in diameter show signs of competing reduction reactions. Our study shows that ultrasmall ZnO particles have a reactivity beyond that which is expected because of their increased surface area and also demonstrates size-dependent reaction pathways, which introduces the possibility for size-selective catalysis.

  • 8. Alemdar, E.
    et al.
    Poznanski, R. R.
    Cacha, L. A.
    Leisman, G.
    Brändas, Erkki J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    New insights into holonomic brain theory: implications for active consciousness2023In: Journal of Multiscale Neuroscience, E-ISSN 2653-4983, Vol. 2, no 1, p. 159-168Article in journal (Refereed)
    Abstract [en]

    This pioneering research on how specific molecules deep inside our brains form a dynamic information holarchy in phase space, linking mind and consciousness, is not only provocative but also revolutionary. Holonomic is a dynamic encapsulation of the holonic view that originates from the word “holon” and designates a holarchical rather than a hierarchical, dynamic brain organization to encompass multiscale effects. The unitary nature of consciousness being interconnected stems from a multiscalar organization of the brain. We aim to give a holonomic modification of the thermodynamic approach to the problem of consciousness using spatiotemporal intermittency. Starting with quasiparticles as the minimalist material composition of the dynamical brain where interferences patterns between incoherent waves of quasiparticles and their quantum-thermal fluctuations constrain the kinetic internal energy of endogenous molecules through informational channels of the negentropically-derived quantum potential. This indicates that brains are not multifractal involving avalanches but are multiscalar, suggesting that unlike the hologram, where the functional interactions occur in the spectral domain, the spatiotemporal binding is multiscalar because of self-referential amplification occurring via long-range correlative information. The associated negentropic entanglement permeates the unification of the functional information architecture across multiple scales. As such, the holonomic brain theory is suitable for active consciousness, proving that consciousness is not fundamental. The holonomic model of the brain’s internal space is nonmetric and nonfractal. It contains a multiscalar informational structure decoded by intermittency spikes in the fluctuations of the negentropically-derived quantum potential. It is therefore, a more realistic approach than the platonic models in phase space.

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  • 9.
    Almquist, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Mattsson, Ken
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Edvinsson, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    High-fidelity numerical solution of the time-dependent Dirac equation2014In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 262, p. 86-103Article in journal (Refereed)
  • 10.
    Almquist, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Mattsson, Ken
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Edvinsson, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Stable and accurate simulation of phenomena in relativistic quantum mechanics2013In: Proc. 11th International Conference on Mathematical and Numerical Aspects of Waves, Tunisia: ENIT , 2013, p. 213-214Conference paper (Other academic)
  • 11.
    Amidani, Lucia
    et al.
    Rossendorf Beamline ESRF European Synchrotron, F-38043 Grenoble, France.;Inst Resource Ecol, Helmholtz Zent Dresden Rossendorf, D-01328 Dresden, Germany..
    Dumas, Thomas
    Univ Montpellier, CEA, DES, ISEC, F-30207 Bagnols Sur Ceze, France..
    Shuh, David K.
    Lawrance Berkeley Natl Lab, Berkeley, CA 94720 USA..
    Butorin, Sergei M.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Condensed Matter Physics of Energy Materials.
    Sahle, Christoph J.
    ESRF, European Synchrotron, F-38043 Grenoble, France..
    Longo, Alessandro
    ESRF, European Synchrotron, F-38043 Grenoble, France..
    Kvashnina, Kristina O.
    Rossendorf Beamline ESRF European Synchrotron, F-38043 Grenoble, France.;Inst Resource Ecol, Helmholtz Zent Dresden Rossendorf, D-01328 Dresden, Germany..
    Oxygen K-Edge X-ray Absorption Spectra of ThO2 and CeO2: Experiment, Interpretation, and Structural Effects2023In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 127, no 6, p. 3077-3084Article in journal (Refereed)
    Abstract [en]

    Experimental oxygen K-edge spectra of ThO2 and CeO2 are presented and interpreted based on density functional theory (DFT). The contribution of d and f orbitals to the O Kedge spectrum is identified as well-distinguished peaks, the presence of which evidences the strong hybridization of Th and Ce metal centers with O orbitals. The sensitivity of the O K-edge to both f- and d-states in the absence of a core-hole on the metal ion results in an insightful overview of the electronic structure involved in the chemical bond. In particular, the large bandwidth of the Th 5f band as compared to the Ce 4f band is observed as a set of wider and more substantial set of peaks in the O K-edge, confirming the stronger hybridization of the former with O orbitals. The peak ascribed to the 5f band of ThO2 is found at higher energy than the 6d band, as predicted from DFT calculations on actinide dioxides. To highlight the sensitivity and the potential use of the O K-edge for the characterization of ThO2-based systems, the sensitivity of the spectrum to structural changes such as lattice expansion and size reduction are calculated and discussed.

  • 12.
    Ammothum Kandy, Akshay Krishna
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Linear models for multiscale materials simulations: Towards a seamless linking of electronic and atomistic models for complex metal oxides2021Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Multiscale modelling approaches, connecting data from electronic structure calculations all the way towards engineering continuum models, have become an important ingredient in modern materials science. Materials modelling in a broader sense is already amply used to address complex chemical problems in academic science, but also in many industrial sectors. As far as multiscale modelling is concerned, however, many challenges remain, in particular when it comes to coupling and linking the various levels along the multiscale ladder in a seamless and efficient fashion.        

    This thesis focusses on the development of new and efficient linear models to improve the quality and parameterisation processes of the two-body potentials used in empirical and semi-empirical methods within a multiscale materials modelling framework. In this regard, a machinery called curvature constrained splines (CCS) based on cubic splines to approximate general two-body potentials has been developed. The method is linear, and parameters can be easily solved in a least-square sense using a quadratic programming approach. Moreover, the objective function is  convex, implying that global minima can be readily found. This makes the optimisation process easy to handle and requires little to no human effort. Initial tests to validate the method were performed on molecular and bulk neon systems. Later, the method was extended to incorporate long-range interactions by including atomic charges. The capability of the method was demonstrated for ZnO polymorphs, and at the same time benchmarked towards the conventional  Buckingham potentials applied to the same problem. The results indicate that the CCS+Q method performs on par with the Buckingham approach, but is much faster and easier to parameterise. The merits of the method is further demonstrated with an exploration of size and shape dependent stability of CeO2 nanoparticles.

    Having established the framework of the CCS methodology, the method was further used to develop repulsive potentials for the semi-empirical self-consistent charge density functional tight binding (SCC-DFTB) method. The generation of the repulsive potentials is normally a tedious and time-consuming task. The  CCS methodology  makes this process significantly more efficient, and further provides new opportunities to explore the limits of the SCC-DFTB method. The development of repulsive potentials for bulk Si polymorphs showed that it is possible to retrieve a good description of each individual polymorph, but impossible to obtain an acceptable joint description of all polymorphs. The results indicated that a transferable repulsive potential needs to have coordination dependence, and by the  use of a many-body artificial neural network representation for the repulsive potential, it was indeed possible to obtain a global transferability. The CCS methodology was finally used to model a system of considerable chemical diversity and complexity, namely reduced CeO2 within the SCC-DFTB formalism. Here, the CCS framework facilitated the development of an efficient workflow that yielded a harmonized description of Ce ions in different oxidation states. In short, the introduced CCS-based workflow proved to extend the applicability of SCC-DFTB to complex oxide systems with correlated electronic states.               

    To conclude, the CCS methodology is demonstrated to be a versatile tool for efficient linking between (and within) electronic and atomistic models.

    List of papers
    1. CCS: A software framework to generate two-body potentials using Curvature Constrained Splines
    Open this publication in new window or tab >>CCS: A software framework to generate two-body potentials using Curvature Constrained Splines
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    2021 (English)In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 258, article id 107602Article in journal (Refereed) Published
    Abstract [en]

    We have developed an automated and efficient scheme for the fitting of data using Curvature Constrained Splines (CCS), to construct accurate two-body potentials. The approach enabled the construction of an oscillation-free, yet flexible, potential. We show that the optimization problem is convex and that it can be reduced to a standard Quadratic Programming (QP) problem. The improvements are demonstrated by the development of a two-body potential for Ne from ab initio data. We also outline possible extensions to the method. Program summary Program Title: CCS CPC Library link to program files: http://dx.doi.org/10.17632/7dt5nzxgbs.1 Developer's repository link:gttp://github.com/aksam432/CCS Licensing provisions: GPLv3 Programming language: Python External routines/libraries: NumPy, matplotlib, ASE, CVXOPT Nature of problem: Ab initio quantum chemistry methods are often computationally very expensive. To alleviate this problem, the development of efficient empirical and semi-empirical methods is necessary. Two-body potentials are ubiquitous in empirical and semi-empirical methods. Solution method: The CCS package provides a new strategy to obtain accurate two body potentials. The potentials are described as cubic splines with curvature constraints.

    Place, publisher, year, edition, pages
    ElsevierELSEVIER, 2021
    Keywords
    Two-body potential, Force field, Quadratic programming, Cubic splines, Python
    National Category
    Computer Sciences Condensed Matter Physics
    Identifiers
    urn:nbn:se:uu:diva-426306 (URN)10.1016/j.cpc.2020.107602 (DOI)000587360000039 ()
    Funder
    Swedish Research CouncileSSENCE - An eScience Collaboration
    Available from: 2020-11-30 Created: 2020-11-30 Last updated: 2024-01-15Bibliographically approved
    2. Development of efficient linearly parametrized force fields for ionic materials
    Open this publication in new window or tab >>Development of efficient linearly parametrized force fields for ionic materials
    (English)In: Article in journal (Other academic) In press
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-434542 (URN)
    Available from: 2021-02-10 Created: 2021-02-10 Last updated: 2021-02-10
    3. Curvature Constrained Splines for DFTB Repulsive Potential Parametrization
    Open this publication in new window or tab >>Curvature Constrained Splines for DFTB Repulsive Potential Parametrization
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    2021 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 17, no 3, p. 1771-1781Article in journal (Refereed) Published
    Abstract [en]

    The Curvature Constrained Splines (CCS) methodology has been used for fitting repulsive potentials to be used in SCC-DFTB calculations. The benefit of using CCS is that the actual fitting of the repulsive potential is performed through quadratic programming on a convex objective function. This guarantees a unique (for strictly convex) and optimum two-body repulsive potential in a single shot, thereby making the parametrization process robust, and with minimal human effort. Furthermore, the constraints in CCS give the user control to tune the shape of the repulsive potential based on prior knowledge about the system in question. Herein, we developed the method further with new constraints and the capability to handle sparse data. We used the method to generate accurate repulsive potentials for bulk Si polymorphs and demonstrate that for a given Slater-Koster table, which reproduces the experimental band structure for bulk Si in its ground state, we are unable to find one single two-body repulsive potential that can accurately describe the various bulk polymorphs of silicon in our training set. We further demonstrate that to increase transferability, the repulsive potential needs to be adjusted to account for changes in the chemical environment, here expressed in the form of a coordination number. By training a near-sighted Atomistic Neural Network potential, which includes many-body effects but still essentially within the first-neighbor shell, we can obtain full transferability for SCC-DFTB in terms of describing the energetics of different Si polymorphs.

    Place, publisher, year, edition, pages
    American Chemical Society (ACS), 2021
    National Category
    Materials Chemistry
    Identifiers
    urn:nbn:se:uu:diva-434543 (URN)10.1021/acs.jctc.0c01156 (DOI)000629135700038 ()33606527 (PubMedID)
    Funder
    Swedish Research CouncileSSENCE - An eScience CollaborationSwedish National Infrastructure for Computing (SNIC)German Research Foundation (DFG), RTG 2247
    Available from: 2021-02-10 Created: 2021-02-10 Last updated: 2024-01-15Bibliographically approved
    4. Accurate description of Ce 4f states in reduced ceria using SCC-DFTB+U simulations
    Open this publication in new window or tab >>Accurate description of Ce 4f states in reduced ceria using SCC-DFTB+U simulations
    (English)In: Article in journal (Other academic) In press
    National Category
    Materials Chemistry
    Identifiers
    urn:nbn:se:uu:diva-434544 (URN)
    Available from: 2021-02-10 Created: 2021-02-10 Last updated: 2021-02-10
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  • 13.
    Amrein, Beat Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Extending the Reach of Computational Approaches to Model Enzyme Catalysis2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Recent years have seen tremendous developments in methods for computational modeling of (bio-) molecular systems. Ever larger reactive systems are being studied with high accuracy approaches, and high-level QM/MM calculations are being routinely performed. However, applying high-accuracy methods to large biological systems is computationally expensive and becomes problematic when conformational sampling is needed. To address this challenge, classical force field based approaches such as free energy perturbation (FEP) and empirical valence bond calculations (EVB) have been employed in this work. Specifically:

    1. Force-field independent metal parameters have been developed for a range of alkaline earth and transition metal ions, which successfully reproduce experimental solvation free energies, metal-oxygen distances, and coordination numbers. These are valuable for the computational study of biological systems.

    2. Experimental studies have shown that the epoxide hydrolase from Solanum tuberosum (StEH1) is not only an enantioselective enzyme, but for smaller substrates, displays enantioconvergent behavior. For StEH1, two detailed studies, involving combined experimental and computational efforts have been performed: We first used trans-stilbene oxide to establish the basic reaction mechanism of this enzyme. Importantly, a highly conserved and earlier ignored histidine was identified to be important for catalysis. Following from this, EVB and experiment have been used to investigate the enantioconvergence of the StEH1-catalyzed hydrolysis of styrene oxide. This combined approach involved wildtype StEH1 and an engineered enzyme variant, and established a molecular understanding of enantioconvergent behavior of StEH1.

    3. A novel framework was developed for the Computer-Aided Directed Evolution of Enzymes (CADEE), in order to be able to quickly prepare, simulate, and analyze hundreds of enzyme variants. CADEE’s easy applicability is demonstrated in the form of an educational example.

    In conclusion, classical approaches are a computationally economical means to achieve extensive conformational sampling. Using the EVB approach has enabled me to obtain a molecular understanding of complex enzymatic systems. I have also increased the reach of the EVB approach, through the implementation of CADEE, which enables efficient and highly parallel in silico testing of hundreds-to-thousands of individual enzyme variants.

    List of papers
    1. Force Field Independent Metal Parameters Using a Nonbonded Dummy Model
    Open this publication in new window or tab >>Force Field Independent Metal Parameters Using a Nonbonded Dummy Model
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    2014 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 16, p. 4351-4362Article in journal (Refereed) Published
    Abstract [en]

    The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn2+, Zn2+, Mg2+, and Ca2+, as well as providing new parameters for Ni2+, Co2+, and Fe2+. In all the cases, we are able to reproduce both M2+-O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase 1 as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers.

    National Category
    Physical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-225523 (URN)10.1021/jp501737x (DOI)000335113600010 ()
    Funder
    Swedish National Infrastructure for Computing (SNIC), 2013/26-1
    Available from: 2014-06-23 Created: 2014-06-04 Last updated: 2018-12-03Bibliographically approved
    2. Expanding the catalytic triad in epoxide hydrolases and related enzymes
    Open this publication in new window or tab >>Expanding the catalytic triad in epoxide hydrolases and related enzymes
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    2015 (English)In: ACS Catalysis, ISSN 2155-5435, E-ISSN 2155-5435, Vol. 5, no 10, p. 5702-5713Article in journal (Refereed) Published
    Abstract [en]

    Potato epoxide hydrolase 1 exhibits rich enantio- and regioselectivity in the hydrolysis of a broadrange of substrates. The enzyme can be engineered to increase the yield of optically pureproducts, as a result of changes in both enantio- and regioselectivity. It is thus highly attractive inbiocatalysis, particularly for the generation of enantiopure fine chemicals and pharmaceuticals.The present work aims to establish the principles underlying the activity and selectivity of theenzyme through a combined computational, structural, and kinetic study, using the substratetrans-stilbene oxide as a model system. Extensive empirical valence bond simulations have beenperformed on the wild-type enzyme together with several experimentally characterized mutants.We are able to computationally reproduce the differences in activities between differentstereoisomers of the substrate, and the effects of mutations in several active-site residues. Inaddition, our results indicate the involvement of a previously neglected residue, H104, which iselectrostatically linked to the general base, H300. We find that this residue, which is highlyconserved in epoxide hydrolases and related hydrolytic enzymes, needs to be in its protonatedform in order to provide charge balance in an otherwise negatively-charged active site. Our datashow that unless the active-site charge balance is correctly treated in simulations, it is notpossible to generate a physically meaningful model for the enzyme that can accurately reproduceactivity and selectivity trends. We also expand our understanding of other catalytic residues,demonstrating in particular the role of a non-canonical residue, E35, as a “backup-base” in theabsence of H300. Our results provide a detailed view of the main factors driving catalysis andregioselectivity in this enzyme, and identify targets for subsequent enzyme design efforts.

    National Category
    Biochemistry and Molecular Biology
    Research subject
    Biochemistry
    Identifiers
    urn:nbn:se:uu:diva-260232 (URN)10.1021/acscatal.5b01639 (DOI)000362391500006 ()
    Funder
    EU, FP7, Seventh Framework Programme, 306474Swedish Research Council, 621-2011-6055, 621-2010-5145Swedish National Infrastructure for Computing (SNIC), 2015/16-12
    Available from: 2015-08-18 Created: 2015-08-18 Last updated: 2017-12-04Bibliographically approved
    3. Conformational Diversity and Enantioconvergence in Potato Epoxide Hydrolase 1
    Open this publication in new window or tab >>Conformational Diversity and Enantioconvergence in Potato Epoxide Hydrolase 1
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    2016 (English)In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 14, no 24, p. 5639-5651Article in journal (Refereed) Published
    Abstract [en]

    Potato epoxide hydrolase 1 (StEH1) is a biocatalytically important enzyme that exhibits rich enantio-and regioselectivity in the hydrolysis of chiral epoxide substrates. In particular, StEH1 has been demonstrated to enantioconvergently hydrolyze racemic mixes of styrene oxide (SO) to yield (R)-1-phenylethanediol. This work combines computational, crystallographic and biochemical analyses to understand both the origins of the enantioconvergent behavior of the wild-type enzyme, as well as shifts in activities and substrate binding preferences in an engineered StEH1 variant, R-C1B1, which contains four active site substitutions (W106L, L109Y, V141K and I155V). Our calculations are able to reproduce both the enantio-and regioselectivities of StEH1, and demonstrate a clear link between different substrate binding modes and the corresponding selectivity, with the preferred binding modes being shifted between the wild-type enzyme and the R-C1B1 variant. Additionally, we demonstrate that the observed changes in selectivity and the corresponding enantioconvergent behavior are due to a combination of steric and electrostatic effects that modulate both the accessibility of the different carbon atoms to the nucleophilic side chain of D105, as well as the interactions between the substrate and protein amino acid side chains and active site water molecules. Being able to computationally predict such subtle effects for different substrate enantiomers, as well as to understand their origin and how they are affected by mutations, is an important advance towards the computational design of improved biocatalysts for enantioselective synthesis.

    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-282015 (URN)10.1039/C6OB00060F (DOI)000378933400042 ()27049844 (PubMedID)
    Funder
    Swedish National Infrastructure for Computing (SNIC), 25/2-10EU, European Research Council, 306474;283570Swedish Research Council, 621-2011-6055Carl Tryggers foundation , CTS13:104
    Available from: 2016-04-01 Created: 2016-04-01 Last updated: 2017-11-30Bibliographically approved
    4. CADEE: Computer-Aided Directed Evolution of Enzymes
    Open this publication in new window or tab >>CADEE: Computer-Aided Directed Evolution of Enzymes
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    2017 (English)In: IUCrJ, E-ISSN 2052-2525, Vol. 4, no 1, p. 50-64Article in journal (Refereed) Published
    Abstract [en]

    The tremendous interest in enzymes as biocatalysts has led to extensive work in enzyme engineering, as well as associated methodology development. Here, a new framework for computer-aided directed evolution of enzymes (CADEE) is presented which allows a drastic reduction in the time necessary to prepare and analyze in silico semi-automated directed evolution of enzymes. A pedagogical example of the application of CADEE to a real biological system is also presented in order to illustrate the CADEE workflow.

    Keywords
    computational directed evolution, computational enzyme design, distributed computing, empirical valence bond, triosephosphate isomerase
    National Category
    Structural Biology Bioinformatics (Computational Biology) Theoretical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-314218 (URN)10.1107/S2052252516018017 (DOI)000392925800007 ()
    Funder
    EU, FP7, Seventh Framework Programme, 306474Knut and Alice Wallenberg FoundationThe Royal Swedish Academy of SciencesSwedish Research Council, 2015-04928Swedish National Infrastructure for Computing (SNIC), 2015/16-12
    Available from: 2017-01-31 Created: 2017-01-31 Last updated: 2022-09-28Bibliographically approved
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  • 14.
    Amrein, Beat Anton
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Runthala, Ashish
    Kamerlin, Shina C. Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    In Silico-Directed Evolution Using CADEE2018In: Computational Methods in Protein Evolution / [ed] T. Tobias Sikosek, Springer Science+Business Media, LLC, part of Springer Nature , 2018, p. 381-415Chapter in book (Other academic)
  • 15.
    Amrein, Beat Anton
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Steffen-Munsberg, Fabian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Szeler, Ireneusz
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Purg, Miha
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kulkarni, Yashraj
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kamerlin, Shina Caroline Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    CADEE: Computer-Aided Directed Evolution of Enzymes2017In: IUCrJ, E-ISSN 2052-2525, Vol. 4, no 1, p. 50-64Article in journal (Refereed)
    Abstract [en]

    The tremendous interest in enzymes as biocatalysts has led to extensive work in enzyme engineering, as well as associated methodology development. Here, a new framework for computer-aided directed evolution of enzymes (CADEE) is presented which allows a drastic reduction in the time necessary to prepare and analyze in silico semi-automated directed evolution of enzymes. A pedagogical example of the application of CADEE to a real biological system is also presented in order to illustrate the CADEE workflow.

    Download full text (pdf)
    fulltext
  • 16.
    Anders, Brakestad
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ab Initio Characterization of Conical Intersections Related to Chemiluminescence in Methylated 1,2-Dioxetanes2017Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
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    fulltext
  • 17.
    Andersson, Mauritz
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry.
    Quantum Dynamics of Molecular Systems and Guided Matter Waves2001Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Quantum dynamics is the study of time-dependent phenomena in fundamental processes of atomic and molecular systems. This thesis focuses on systems where nature reveals its quantum aspect; e.g. in vibrational resonance structures, in wave packet revivals and in matter wave interferometry. Grid based numerical methods for solving the time-dependent Schrödinger equation are implemented for simulating time resolved molecular vibrations and to compute photo-electron spectra, without the necessity of diagonalizing a large matrix to find eigenvalues and eigenvectors.

    Pump-probe femtosecond laser spectroscopy on the sodium potassium molecule, showing a vibrational period of 450 fs, is theoretically simulated. We find agreement with experiment by inclusion of the finite length laser pulse and finite temperature effects.

    Complicated resonance structures observed experimentally in photo-electron spectra of hydrogen- and deuterium chloride is analyzed by a numerical computation of the spectra. The dramatic difference in the two spectra arises from non-adiabatic interactions, i.e. the interplay between nuclear and electron dynamics. We suggest new potential curves for the 32Σ+ and 42Σ+ states in HCI+.

    It is possible to guide slow atoms along magnetic potentials like light is guided in optical fibers. Quantum mechanics dictates that matter can show wave properties. A proposal for a multi mode matter wave interferometer on an atom chip is studied by solving the time-dependent Schrödinger equation in two dimensions. The results verifies a possible route for an experimental realization.

    An improved representation for wave functions using a discrete set of coherent states is presented. We develop a practical method for computing the expansion coefficients in this non-orthogonal set. It is built on the concept of frames, and introduces an iterative method for computing a representation of the identity operator. The phase-space localization property of the coherent states gives adaptability and better sampling efficiency.

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    FULLTEXT01
  • 18.
    Anikina, Ekaterina
    et al.
    South Ural State Univ, Inst Nat Sci & Math, Chelyabinsk 454014, Russia.;Uppsala Univ, Dept Phys & Astron, Mat Theory Div, S-75120 Uppsala, Sweden..
    Hussain, Tanveer
    Univ Western Australia, Sch Mol Sci, Perth, WA 6009, Australia..
    Beskachko, Valery
    South Ural State Univ, Inst Nat Sci & Math, Chelyabinsk 454014, Russia..
    Bae, Hyeonhu
    Konkuk Univ, Dept Phys, Seoul 05029, South Korea..
    Lee, Hoonkyung
    Konkuk Univ, Dept Phys, Seoul 05029, South Korea..
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Uppsala UniKTH Royal Inst Technol, Appl Mat Phys, Dept Mat & Engn, S-10044 Stockholm, Sweden..
    Tunning Hydrogen Storage Properties of Carbon Ene-Yne Nanosheets through Selected Foreign Metal Functionalization2020In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 124, no 31, p. 16827-16837Article in journal (Refereed)
    Abstract [en]

    In this study, we have employed density functional theory with a range of van der Waals corrections to study geometries, electronic structures, and hydrogen (H-2) storage properties of carbon ene-yne (CEY) decorated with selected alkali (Na, K) and alkaline-earth metals (Mg, Ca). We found that all metals, except Mg, bind strongly by donating a major portion of their valence electrons to the CEY monolayers. Thermal stabilities of representative systems, Ca-decorated CEY monolayers, have been confirmed through ab initio molecular dynamics simulations (AIMD). We showed that each metal cation adsorbs multiple H-2 with binding energies (E-bind) considerably stronger than on pristine CEY. Among various metal dopants, Ca stands out with the adsorption of five H-2 per each Ca having E-bind values within the desirable range for effective adsorption/desorption process. The resulting gravimetric density for CEY@Ca has been found around 6.0 wt % (DFT-D3) and 8.0 wt % (LDA), surpassing the U.S. Department of Energy's 2025 goal of 5.5 wt %. The estimated H-2 desorption temperature in CEY@Ca exceeds substantially the boiling point of liquid nitrogen, which confirms its potential as a practical H-2 storage medium. We have also employed thermodynamic analysis to explore the H-2 adsorption/desorption mechanism at varied conditions of temperature and pressure for real-world applications.

  • 19.
    Ann Delgado, Alexis Antoinette
    et al.
    Southern Methodist Univ, Dept Chem, Dallas, TX 75275 USA..
    Sethio, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Matthews, Devin
    Southern Methodist Univ, Dept Chem, Dallas, TX 75275 USA..
    Oliveira, Vytor
    Inst Tecnol Aeronaut ITA, Dept Quim, Sao Jose Dos Campos, SP, Brazil..
    Kraka, Elfi
    Southern Methodist Univ, Dept Chem, Dallas, TX 75275 USA..
    Substituted hydrocarbon: a CCSD(T) and local vibrational mode investigation2021In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 119, no 21-22, article id e1970844Article in journal (Refereed)
    Abstract [en]

    Substituent effects on the carbon-carbon bonds of hydrocarbons have been a topic of interest within the past seven decades as resultant information would enable one to tune the activity of CC bonds. However, current assessments of the C equivalent to C, C=C, and C-C bond strength of acetylene, ethylene, and ethane as well as their derivatives rely on indirect measures such as bond length and bond dissociation enthalpy. In this work, we introduce a quantitative measure of the intrinsic strength of C equivalent to C, C=C, and C-C bonds for a set of 40 hydrocarbon systems consisting of 3 parent structures, 36 hydrocarbon derivatives involving CF3, CH3, CHO, F, NH2, or OH groups, and a conjugated system, based on vibrational spectroscopy. Local mode force constants k(a)(CC) were computed at the CCSD(T)/cc-pVTZ level of theory for systems 1-32 and 34-40 and CCSD(T)/cc-pVDZ for 33. From k(a)(CC), we derived related bond strength orders BSO n(CC) in order to provide quantitative measures of intrinsic bond strength. Topological electron density and natural population analyses were carried out as to analyze the nature of these bonds and complement bond strength measures. For substituted hydrocarbon systems, we found the strengthening/weakening of the CC bonds occurs as the covalent nature of the bond increases/decreases by means of varying charge delocalizations. Our findings provide new guidelines for desirably modulating C equivalent to C, C=C, and C-C bond strength and for the design of prospective pathways for bond cleavage reactions. [GRAPHICS] .

  • 20.
    Aquilante, Francesco
    et al.
    Ecole Polytech Fed Lausanne EPFL, Theory & Simulat Mat THEOS, CH-1015 Lausanne, Switzerland.;Ecole Polytech Fed Lausanne EPFL, Natl Ctr Computat Design & Discovery Novel Mat MA, CH-1015 Lausanne, Switzerland..
    Autschbach, Jochen
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Baiardi, Alberto
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Battaglia, Stefano
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Borin, Veniamin A.
    Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam Res, IL-9190401 Jerusalem, Israel..
    Chibotaru, Liviu F.
    Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium..
    Conti, Irene
    Univ Bologna, Dipartimento Chim Ind Toso Montanari, Viale Risorgimento 4, I-40136 Bologna, Italy..
    De Vico, Luca
    Univ Siena, Dipartimento Biotecnol Chim & Farm, Via Aldo Moro 2, I-53100 Siena, Italy..
    Delcey, Mickael G
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Ferre, Nicolas
    Aix Marseille Univ, CNRS, Inst Chim Radicalaire, Marseille, France..
    Freitag, Leon
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Garavelli, Marco
    Univ Bologna, Dipartimento Chim Ind Toso Montanari, Viale Risorgimento 4, I-40136 Bologna, Italy..
    Gong, Xuejun
    Natl Univ Singapore, Dept Chem, 3 Sci Dr 3, Singapore 117543, Singapore..
    Knecht, Stefan
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Larsson, Ernst D.
    Lund Univ, Div Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Malmqvist, Per Ake
    Lund Univ, Div Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Nenov, Artur
    Univ Bologna, Dipartimento Chim Ind Toso Montanari, Viale Risorgimento 4, I-40136 Bologna, Italy..
    Norell, Jesper
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Olivucci, Massimo
    Univ Siena, Dipartimento Biotecnol Chim & Farm, Via Aldo Moro 2, I-53100 Siena, Italy.;Bowling Green State Univ, Dept Chem, Bowling Green, OH 43403 USA..
    Pedersen, Thomas B.
    Univ Oslo, Dept Chem, Hylleraas Ctr Quantum Mol Sci, POB 1033 Blindern, N-0315 Oslo, Norway..
    Pedraza-Gonzalez, Laura
    Univ Siena, Dipartimento Biotecnol Chim & Farm, Via Aldo Moro 2, I-53100 Siena, Italy..
    Phung, Quan M.
    Nagoya Univ, Inst Transformat Biomol WPI ITbM, Chikusa Ku, Nagoya, Aichi 4648602, Japan..
    Pierloot, Kristine
    Katholieke Univ Leuven, Dept Chem, Celestijnenlaan 200F, B-3001 Leuven, Belgium..
    Reiher, Markus
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Schapiro, Igor
    Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam Res, IL-9190401 Jerusalem, Israel..
    Segarra-Marti, Javier
    Imperial Coll London, Dept Chem, Mol Sci Res Hub, White City Campus,80 Wood Lane, London W12 0BZ, England..
    Segatta, Francesco
    Univ Bologna, Dipartimento Chim Ind Toso Montanari, Viale Risorgimento 4, I-40136 Bologna, Italy..
    Seijo, Luis
    Univ Autonoma Madrid, Dept Quim, Inst Univ Ciencia Mat Nicolas Cabrera, Madrid 28049, Spain.;Univ Autonoma Madrid, Condensed Matter Phys Ctr IFIMAC, Madrid 28049, Spain..
    Sen, Saumik
    Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam Res, IL-9190401 Jerusalem, Israel..
    Sergentu, Dumitru-Claudiu
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Stein, Christopher J.
    Swiss Fed Inst Technol, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Ungur, Liviu
    Natl Univ Singapore, Dept Chem, 3 Sci Dr 3, Singapore 117543, Singapore..
    Vacher, Morgane
    Univ Nantes, Lab CEISAM UMR CNRS 6230, F-44300 Nantes, France..
    Valentini, Alessio
    Univ Liege, Res Unit MolSys, Theoret Phys Chem, Allee 6 Aout 11, B-4000 Liege, Belgium..
    Veryazov, Valera
    Lund Univ, Div Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Modern quantum chemistry with [Open]Molcas2020In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 152, no 21Article in journal (Refereed)
    Abstract [en]

    MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.

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  • 21.
    Aquilante, Francesco
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Autschbach, Jochen
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Carlson, Rebecca K.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Chibotaru, Liviu F.
    Katholieke Univ Leuven, Div Quantum & Phys Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium.;Katholieke Univ Leuven, INPAC, Inst Nanoscale Phys & Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium..
    Delcey, Mickael G.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    De Vico, Luca
    Univ Copenhagen, Dept Chem, Univ Pk 5, DK-2100 Copenhagen O, Denmark..
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ferre, Nicolas
    Univ Aix Marseille, CNRS, Inst Chim Radicalaire, Campus Etoile St Jerome Case 521,Ave Esc, F-13397 Marseille 20, France..
    Frutos, Luis Manuel
    Univ Alcala De Henares, Unidad Docente Quim Fis, E-28871 Madrid, Spain..
    Gagliardi, Laura
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Garavelli, Marco
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy.;Univ Lyon, CNRS, Ecole Normale Super Lyon, 46 Allee Italie, F-69364 Lyon 07, France..
    Giussani, Angelo
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Hoyer, Chad E.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Li Manni, Giovanni
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA.;Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany..
    Lischka, Hans
    Texas Tech Univ, Dept Chem & Biochem, Mem Circle & Boston, Lubbock, TX 79409 USA.;Univ Vienna, Inst Theoret Chem, Wahringerstr 17, A-1090 Vienna, Austria..
    Ma, Dongxia
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA.;Max Planck Inst Festkorperforsch, Heisenbergstr 1, D-70569 Stuttgart, Germany..
    Malmqvist, Per Ake
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Mueller, Thomas
    Forschungszentrum Julich, IAS, JSC, Wilhelm Johnen Str, D-52425 Julich, Germany..
    Nenov, Artur
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Olivucci, Massimo
    Univ Siena, Dept Biotechnol Chem & Pharm, Via Aldo Moro 2, I-53100 Siena, Italy.;Bowling Green State Univ, Dept Chem, 141 Overman Hall, Bowling Green, OH 43403 USA.;Univ Strasbourg, Inst Phys & Chim Mat Strasbourg, CNRS UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Univ Strasbourg, Labex NIE, CNRS, UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Hebrew Univ Jerusalem, Inst Chem, Fritz Haber Ctr Mol Dynam, IL-91904 Jerusalem, Israel..
    Pedersen, Thomas Bondo
    Univ Oslo, Dept Chem, Ctr Theoret & Computat Chem, POB 1033 Blindern, N-0315 Oslo, Norway..
    Peng, Daoling
    S China Normal Univ, Coll Chem & Environm, Guangzhou 510006, Guangdong, Peoples R China..
    Plasser, Felix
    Univ Vienna, Inst Theoret Chem, Wahringerstr 17, A-1090 Vienna, Austria..
    Pritchard, Ben
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Reiher, Markus
    ETH, Phys Chem Lab, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland..
    Rivalta, Ivan
    Univ Lyon, CNRS, Ecole Normale Super Lyon, 46 Allee Italie, F-69364 Lyon 07, France..
    Schapiro, Igor
    Univ Strasbourg, Inst Phys & Chim Mat Strasbourg, CNRS UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France.;Univ Strasbourg, Labex NIE, CNRS, UMR 7504, 23 Rue Loess, F-67034 Strasbourg, France..
    Segarra-Marti, Javier
    Univ Bologna, Dipartimento Chim G Ciamician, Via Selmi 2, IT-40126 Bologna, Italy..
    Stenrup, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Truhlar, Donald G.
    Univ Minnesota, Inst Supercomp, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Chem Theory Ctr, Minneapolis, MN 55455 USA..
    Ungur, Liviu
    Katholieke Univ Leuven, Div Quantum & Phys Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium.;Katholieke Univ Leuven, INPAC, Inst Nanoscale Phys & Chem, Celestijnenlaan 200F, B-3001 Heverlee, Belgium..
    Valentini, Alessio
    Univ Siena, Dept Biotechnol Chem & Pharm, Via Aldo Moro 2, I-53100 Siena, Italy..
    Vancoillie, Steven
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Veryazov, Valera
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Vysotskiy, Victor P.
    Lund Univ, Ctr Chem, Dept Theoret Chem, POB 124, S-22100 Lund, Sweden..
    Weingart, Oliver
    Univ Dusseldorf, Inst Theoret Chem & Computerchem, Univ Str 1, D-40225 Dusseldorf, Germany..
    Zapata, Felipe
    Univ Alcala De Henares, Unidad Docente Quim Fis, E-28871 Madrid, Spain..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table2016In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, no 5, p. 506-541Article in journal (Refereed)
    Abstract [en]

    In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.

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  • 22.
    Aquilante, Francesco
    et al.
    Univ Bologna, Dipartimento Chim G Ciamician, Bologna, Italy..
    Delcey, Mickael G.
    Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA USA.;Univ Calif Berkeley, Dept Chem, Kenneth S Pitzer Ctr Theoret Chem, Berkeley, CA 94720 USA..
    Pedersen, Thomas Bondo
    Univ Oslo, Dept Chem, Ctr Theoret & Computat Chem, Oslo, Norway..
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Uppsala Univ, Dept Chem Angstrom, Theoret Chem Programme, Uppsala, Sweden..
    Inner projection techniques for the low-cost handling of two-electron integrals in quantum chemistry2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 17-18, p. 2052-2064Article in journal (Refereed)
    Abstract [en]

    The density-fitting technique for approximating electron-repulsion integrals relies on the quality of auxiliary basis sets. These are commonly obtained through data fitting, an approach that presents some shortcomings. On the other hand, it is possible to derive auxiliary basis sets by removing elements from the product space of both contracted and primitive orbitals by means of a particular form of inner projection technique that has come to be known as Cholesky decomposition (CD). This procedure allows for on-the-fly construction of auxiliary basis sets that may be used in conjunction with any quantum chemical method, i.e. unbiased auxiliary basis sets. One key feature of these sets is that they represent the electron-repulsion integral matrix in atomic orbital basis with an accuracy that can be systematically improved. Another key feature is represented by the fact that locality of fitting coefficients is obtained even with the long-ranged Coulomb metric, as result of integral accuracy. Here we report on recent advances in the development of the CD-based density fitting technology. In particular, the implementation of analytical gradients algorithms is reviewed and the present status of local formulations - potentially linear scaling - is analysed in detail.

  • 23.
    Aquilante, Francesco
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Pedersen, Thomas Bondo
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Veryazov, Valera
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    MOLCAS—a software for multiconfigurational quantum chemistry calculations2013In: Wiley Interdisciplinary Reviews: Computational Molecular Science, ISSN 1759-0876, Vol. 3, no 2, p. 143-149Article in journal (Refereed)
    Abstract [en]

    At variance, with most of the quantum chemistry software presently available, MOLCAS is a package that is specialized in multiconfigurational wave function theory (MC-WFT) rather than density functional theory (DFT). Given the much higher algorithmic complexity of MC-WFT versus DFT, an extraordinary effort needs to be made from the programming point of view to achieve state-of-the-art performance for large-scale calculations. In particular, a robust and efficient implementation of the Cholesky decomposition techniques for handling two-electron integrals has been developed which is unique to MOLCAS. Together with this 'Cholesky infrastructure', a powerful and multilayer graphical and scripting user interface is available, which is an essential ingredient for the setup of MC-WFT calculations. These two aspects of the MOLCAS software constitute the focus of the present report.

  • 24.
    Arruda, Lucas M.
    et al.
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany.;Minist Educ Brazil, Capes Fdn, BR-70040020 Brasilia, DF, Brazil..
    Ali, Md Ehesan
    Inst Nano Sci & Technol, Phase 10,Sect 64, Mohali 160062, Punjab, India..
    Bernien, Matthias
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Hatter, Nino
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Nickel, Fabian
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Kipgen, Lalminthang
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Hermanns, Christian F.
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Bisswanger, Timo
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Loche, Philip
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Heinrich, Benjamin W.
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Franke, Katharina J.
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Oppeneer, Peter M.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Kuch, Wolfgang
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Surface-orientation- and ligand-dependent quenching of the spin magnetic moment of Co porphyrins adsorbed on Cu substrates2020In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 22, no 22, p. 12688-12696Article in journal (Refereed)
    Abstract [en]

    Porphyrin molecules are particularly interesting candidates for spintronic applications due to their bonding flexibility, which allows to modify their properties substantially by the addition or transformation of ligands. Here, we investigate the electronic and magnetic properties of cobalt octaethylporphyrin (CoOEP), deposited on copper substrates with two distinct crystallographic surface orientations, Cu(100) and Cu(111), with X-ray absorption spectroscopy (XAS) and X-ray magnetic circular dichroism (XMCD). A significant magnetic moment is present in the Co ions of the molecules deposited on Cu(100), but it is completely quenched on Cu(111). Heating the molecules on both substrates to 500 K induces a ring-closure reaction with cobalt tetrabenzoporphyrin (CoTBP) as reaction product. In these molecules, the magnetic moment is quenched on both surfaces. Our XMCD and XAS measurements suggest that the filling of the dz(2)orbital leads to a non-integer valence state and causes the quench of the spin moments on all samples except CoOEP/Cu(100), where the molecular conformation induces variations to the ligand field that lift the quench. We further employ density functional theory calculations, supplemented with on-site Coulomb correlations (DFT+U), to study the adsorption of these spin-bearing molecules on the Cu substrates. Our calculations show that charge transfer from the Cu substrates as well as charge redistribution within the Co 3d orbitals lead to the filling of the Co minority spin dz(2)orbital, causing a 'turning off' of the exchange splitting and quenching of the spin moment at the Co magnetic centers. Our investigations suggest that, by this mechanism, molecule-substrate interactions can be used to control the quenching of the magnetic moments of the adsorbed molecules.

  • 25.
    Arruda, Lucas M.
    et al.
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany;Minist Educ Brazil, CAPES Fdn, BR-70040020 Brasilia, DF, Brazil.
    Ali, Md. Ehesan
    Inst Nano Sci & Technol, Phase 10,Sect 64, Mohali 160062, Punjab, India.
    Bernien, Matthias
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany.
    Nickel, Fabian
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany.
    Kopprasch, Jens
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany.
    Czekelius, Constantin
    Heinrich Heine Univ Dusseldorf, Inst Organ Chem & Makromol Chem, Univ Str 1, D-40225 Dusseldorf, Germany.
    Oppeneer, Peter M.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Kuch, Wolfgang
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany.
    Modifying the Magnetic Anisotropy of an Iron Porphyrin Molecule by an on-Surface Ring-Closure Reaction2019In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 23, p. 14547-14555Article in journal (Refereed)
    Abstract [en]

    The magnetic properties of adsorbed metalloporphyrin molecules can be altered or tuned by the substrate, additional axial ligands, or changes to the molecules' macrocycle. These modifications influence the electronic configuration of the fourfold-coordinated central metal ion that is responsible for the metalloporphyrins' magnetic properties. We report a substantial increase in the effective spin moment obtained from sum-rule analysis of X-ray magnetic circular dichroism for an iron metalloporphyrin molecule on Au(111) through its conversion from iron(II)-octaethylporphyrin to iron(II)-tetrabenzoporphyrin in a surface-assisted ring-closure ligand reaction. Density functional theory calculations with additional strong Coulomb correlation (DFT+U) show that the on-surface reaction alters the conformation of the molecule, increasing its planarity and the ion-surface distance. A spin-Hamiltonian fit of the magnetization as a function of field reveals a substantial increase in the intra-atomic magnetic dipole term (T-z) and a decrease in the magnitude of the easy-plane anisotropy upon ring closure. This consequence of the ring closure demonstrates how new magnetic properties can be obtained from on-surface reactions, resulting here in significant modifications to the magnetic anisotropy of the Fe ion, and sheds light onto the molecule-substrate interaction in these systems.

  • 26.
    Aurbakken, Einar
    et al.
    Univ Oslo, Hylleraas Ctr Quantum Mol Sci, Dept Chem, N-0371 Oslo, Norway..
    Sverdrup Ofstad, Benedicte
    Univ Oslo, Hylleraas Ctr Quantum Mol Sci, Dept Chem, N-0371 Oslo, Norway..
    Kristiansen, Håkon Emil
    Univ Oslo, Hylleraas Ctr Quantum Mol Sci, Dept Chem, N-0371 Oslo, Norway..
    Sigmundson Schøyen, Øyvind
    Univ Oslo, Dept Phys, N-0371 Oslo, Norway..
    Kvaal, Simen
    Univ Oslo, Hylleraas Ctr Quantum Mol Sci, Dept Chem, N-0371 Oslo, Norway..
    Kragh Sørensen, Lasse
    Univ Southern Denmark, Univ Lib, DK-5230 Odense M, Denmark..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Bondo Pedersen, Thomas
    Univ Oslo, Hylleraas Ctr Quantum Mol Sci, Dept Chem, N-0371 Oslo, Norway..
    Transient spectroscopy from time-dependent electronic-structure theory without multipole expansions2024In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 109, no 1, article id 013109Article in journal (Refereed)
    Abstract [en]

    Based on the work done by an electromagnetic field on an atomic or molecular electronic system, a general gauge-invariant formulation of transient absorption spectroscopy is presented within the semiclassical approximation. Avoiding multipole expansions, a computationally viable expression for the spectral response function is derived from the minimal-coupling Hamiltonian of an electronic system interacting with one or more laser pulses described by a source-free, enveloped electromagnetic vector potential. With a fixed-basis expansion of the electronic wave function, the computational cost of simulations of laser-driven electron dynamics beyond the dipole approximation is the same as simulations adopting the dipole approximation. We illustrate the theory by time-dependent configuration interaction and coupled-cluster simulations of core-level absorption and circular dichroism spectra.

  • 27.
    Axelsson, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Marchiori, Cleber F. N.
    Karlstad Univ, Dept Engn & Phys, S-65188 Karlstad, Sweden..
    Huang, Ping
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Araujo, C. Moyses
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Karlstad Univ, Dept Engn & Phys, S-65188 Karlstad, Sweden..
    Tian, Haining
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry.
    Small Organic Molecule Based on Benzothiadiazole for Electrocatalytic Hydrogen Production2021In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 143, no 50, p. 21229-21233Article in journal (Refereed)
    Abstract [en]

    A small organic molecule 2,1,3-benzothiadiazole-4, 7-dicarbonitrile (BTDN) is assessed for electrocatalytic hydrogen evolution on glassy carbon electrode and shows a hydrogen production Faradaic efficiency of 82% in the presence of salicylic acid. The key catalytic intermediates of reduced species BTDN-center dot and protonated intermediates are characterized or hypothesized by using various spectroscopic methods and density functional theory (DFT)-based calculations. With the experimental and theoretical results, a catalytic mechanism of BTDN for electrocatalytic H-2 evolution is proposed.

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  • 28.
    Azuri, Ido
    et al.
    Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel.
    Ali, Md. Ehesan
    Inst Nano Sci & Technol, Phase 10, Sect 64, Mohali 160062, Punjab, India.
    Tarafder, Kartick
    Natl Inst Technol Karnataka, Dept Phys, Mangalore 575025, India.
    Oppeneer, Peter M.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Kronik, Leeor
    Weizmann Inst Sci, Dept Mat & Interfaces, IL-76100 Rehovot, Israel.
    Fe-porphyrin on Co(001) and Cu(001): A Comparative Dispersion-augmented Density Functional Theory Study2020In: Israel Journal of Chemistry, ISSN 0021-2148, Vol. 60, no 8-9, p. 870-875Article in journal (Refereed)
    Abstract [en]

    We present a comparative density functional theory (DFT) investigation of the interaction of the iron porphyrin (FeP) molecule with the metallic Co(001) and Cu(001) surfaces, with the aim of elucidating the effect of different choices for the treatment of dispersion. We compare a GGA+U approach, several flavors of dispersion-augmented terms, and two variants of the vdW-DF approach, which treats long-range correlation explicitly. For the Co surface, we find that all approaches predict chemisorption and a high-spin state, although vdW-DF functionals generally predict weaker bonds and weaker chemisorption. For the Cu surface, we find that the functionals augmented by pair-wise dispersion once again predict chemisorption and a preferred HS state, but the vdW-DF functionals predict physisorption and a LS state. These results demonstrate the importance of careful assessment of the level of theory at which dispersion is treated, as this may have significant quantitative and even qualitative effects on the predictions made. The results also call for additional experimental data for these systems.

  • 29.
    Bako, Imre
    et al.
    Hungarian Acad Sci, Res Ctr Nat Sci, Inst Organ Chem, Magyar Tudosok Korutja 2, H-1117 Budapest, Hungary.
    Daru, Janos
    Hungarian Acad Sci, Res Ctr Nat Sci, Inst Organ Chem, Magyar Tudosok Korutja 2, H-1117 Budapest, Hungary.
    Pothoczki, Szilvia
    Hungarian Acad Sci, Wigner Res Ctr Phys, Konkoly Thege M Ut 29-33, H-1121 Budapest, Hungary.
    Pusztai, Laszlo
    Hungarian Acad Sci, Wigner Res Ctr Phys, Konkoly Thege M Ut 29-33, H-1121 Budapest, Hungary;Kumamoto Univ, Int Res Org Adv Sci & Technol, Chuo Ku, 2-39-1 Kurokami, Kumamoto 8608555, Japan.
    Hermansson, Kersti
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Effects of H-bond asymmetry on the electronic properties of liquid water: An AIMD analysis2019In: Journal of Molecular Liquids, ISSN 0167-7322, E-ISSN 1873-3166, Vol. 293, article id 111579Article in journal (Refereed)
    Abstract [en]

    The effects of an asymmetric environment on the electronic properties of a water molecule in liquid water are in focus in this paper and were analysed from ab initio molecular dynamics simulations of liquid water at 300 and 350 K with the BLYP-D3 functional. We make the following observations. (1) The electronic DOS and the net molecular charge are more affected by the asymmetry of the water molecule's H-bond surroundings than by the number of H-bonded neighbours. The reverse is true for the dipole moment. (2) For all three properties, a 3-coordinated water molecule is more perturbed by accepting two H-bonds and donating one than by donating two and accepting one. (3) This order is not maintained in the calculated XES spectrum, which is less straightforward to interpret in terms of structure-property relationships than the DOS spectrum.

  • 30.
    Ballante, Flavio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection2018In: Rational Drug Design: Methods and Protocols / [ed] Thomas Mavromoustakos; Tahsin F. Kellici, New York, NY: Humana Press, 2018, p. 67-88Chapter in book (Refereed)
    Abstract [en]

    Main goal in drug discovery is the identification of drug-like compounds capable to modulate specific biological targets. Thus, the prediction of reliable binding poses of candidate ligands, through molecular docking simulations, represents a key step to be pursued in structure-based drug design (SBDD). Since the increasing number of resolved three-dimensional ligand-protein structures, together with the expansion of computational power and software development, the comprehensive and systematic use of experimental data can be proficiently employed to validate the docking performance. This allows to select and refine the protocol to adopt when predicting the binding pose of trial compounds in a target. Given the availability of multiple docking software, a comparative docking assessment in an early research stage represents a must-use step to minimize fails in molecular modeling. This chapter describes how to perform a docking assessment, using freely available tools, in a semiautomated fashion.

  • 31.
    Ballante, Flavio
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Protein-Ligand Interactions and Drug Design2021Collection (editor) (Refereed)
    Abstract [en]

    This detailed book collects modern and established computer-based methods aimed at addressing the drug discovery challenge from disparate perspectives by exploiting information on ligand-protein recognition. Beginning with methods that allow for the exploration of specific areas of chemical space and the designing of virtual libraries, the volume continues with sections on methods based on docking, quantitative models, and molecular dynamics simulations, which are employed for ligand discovery or development, as well as methods exploiting an ensemble of protein structures for the identification of potential protein targets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

    Authoritative and cutting-edge, Protein-Ligand Interactions and Drug Design provides detailed practical procedures of solid computer-aided drug design methodologies employed to rationalize and optimize protein-ligand interactions, for experienced researchers and novices alike.

  • 32.
    Banerjee, Ambar
    et al.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Coates, Michael R.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Kowalewski, Markus
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Wikmark, Hampus
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Jay, Raphael
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Wernet, Philippe
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics.
    Odelius, Michael
    Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, SE-10691 Stockholm, Sweden..
    Photoinduced bond oscillations in ironpentacarbonyl give delayed synchronous bursts of carbonmonoxide release2022In: Nature Communications, E-ISSN 2041-1723, Vol. 13, no 1, article id 1337Article in journal (Refereed)
    Abstract [en]

    Early excited state dynamics in the photodissociation of transition metal carbonyls determines the chemical nature of short-lived catalytically active reaction intermediates. However, time-resolved experiments have not yet revealed mechanistic details in the sub-picosecond regime. Hence, in this study the photoexcitation of ironpentacarbonyl Fe(CO)(5) is simulated with semi-classical excited state molecular dynamics. We find that the bright metal-to-ligand charge-transfer (MLCT) transition induces synchronous Fe-C oscillations in the trigonal bipyramidal complex leading to periodically reoccurring release of predominantly axial CO. Metaphorically the photoactivated Fe(CO)(5) acts as a CO geyser, as a result of dynamics in the potential energy landscape of the axial Fe-C distances and non-adiabatic transitions between manifolds of bound MLCT and dissociative metal-centered (MC) excited states. The predominant release of axial CO ligands and delayed release of equatorial CO ligands are explained in a unified mechanism based on the sigma*(Fe-C) anti-bonding character of the receiving orbital in the dissociative MC states. The photodissociation of transition metal carbonyls is involved in catalysis and synthetic processes. Here the authors, using semi-classical excited state molecular dynamics, observe details of the early stage dynamics in the photodissociation of Fe(CO)(5), including synchronous bursts of CO at periodic intervals of 90 femtoseconds.

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    FULLTEXT01
  • 33.
    Banerjee, Amitava
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Applied Materials Physics, Department of Materials and Engineering, Royal Institute of Technology (KTH), Stockholm, Sweden.
    Chakraborty, Sudip
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Discipline of Physics, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, India.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Discipline of Physics, Indian Institute of Technology (IIT) Indore, Indore, Madhya Pradesh, India.
    Reaction Coordinate Mapping of Hydrogen Evolution Mechanism on Mg3N2Monolayer2020Article in journal (Other academic)
    Abstract [en]

    In this work, we have envisaged the hydrogen evolution reaction (HER) mechanism on Mg3N2 monolayer based on electronic structure calculations within the framework of density functional theory (DFT) formalism. The semiconducting nature of Mg3N2 monolayer motivates us to investigate the HER mechanism on this sheet. We have constructed the reaction coordinate associated with HER mechanism after determining the hydrogen adsorption energy on Mg3N2 monolayer, while investigating all possible adsorption sites. After obtaining the adsorption energy, we subsequently obtain the adsorption free energy while adding zero point energy difference (Delta ZPE) and entropic contribution (T Delta S). We have not only confined our investigations to a single hydrogen, but have thoroughly observed the adsorption phenomena for increasing number of hydrogen atoms on the surface. We have determined the projected density of states (DOS) in order to find the elemental contribution in the valence band and conduction band regime for all the considered cases. We have also compared the work function value among all the cases, which quantifies the amount of energy required for taking an electron out of the surface. The charge transfer mechanism is also being investigated in order to correlate with the HER mechanism with amount of charge transfer. This is the first attempt on this material to the best of our knowledge, where theoretical investigation has been done to mapping the reaction coordinate of HER mechanism with the associated charge transfer process and the work function values, not only for single hydrogen adsorption, but also for increasing number of adsorbed hydrogen.

  • 34.
    Banerjee, Paramita
    et al.
    Indian Assoc Cultivat Sci, Dept Mat Sci, Kolkata 700032, India..
    Pathak, Biswarup
    Indian Inst Technol, Discipline Chem, Indore 452020, India..
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Das, G. P.
    Indian Assoc Cultivat Sci, Dept Mat Sci, Kolkata 700032, India..
    First principles design of Li functionalized hydrogenated h-BN nanosheet for hydrogen storage2016In: International journal of hydrogen energy, ISSN 0360-3199, E-ISSN 1879-3487, Vol. 41, no 32, p. 14437-14446Article in journal (Refereed)
    Abstract [en]

    Employing first principles density functional theory (DFT) based approach, the structure, stability and hydrogen storage efficiency of a hydrogenated hexagonal boron nitride sheet (BHNH chair conformer) functionalized by the lightest alkali metal atom Li has been explored here in details. Substituting one hydrogen atom from both B and N sides of BHNH sheet by a Li atom, we have found that Li becomes cationic and acts as a binding site to adsorb hydrogen molecules. The stability of this Li-substituted BHNH sheet has been indicated via Ab-initio Molecular Dynamics (AIMD) simulation upto 400 K. The binding energy (similar to 0.18-0.3 eV/H-2 molecule) and gravimetric density (similar to 6 wt %) (upto similar to 200 K) of the hydrogen molecules fall in the required window for practical hydrogen storage. AIMD simulation indicates complete dehydrogenation from this system occurs at similar to 400 K, thereby predicting the suitability of this system from the point of view of efficient hydrogen storage.

  • 35.
    Bao, Jie J.
    et al.
    Univ Minnesota, Chem Theory Ctr, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Hermes, Matthew R.
    Univ Chicago, James Franck Inst, Pritzker Sch Mol Engn, Dept Chem,Chicago Ctr Theoret Chem, 5640 S Ellis Ave, Chicago, IL 60637 USA.;Argonne Natl Lab, Lemont, IL 60439 USA..
    Scott, Thais R.
    Univ Chicago, James Franck Inst, Pritzker Sch Mol Engn, Dept Chem,Chicago Ctr Theoret Chem, 5640 S Ellis Ave, Chicago, IL 60637 USA.;Argonne Natl Lab, Lemont, IL 60439 USA..
    Sand, Andrew M.
    Butler Univ, Dept Chem & Biochem, Indianapolis, IN 46208 USA..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Gagliardi, Laura
    Univ Chicago, James Franck Inst, Pritzker Sch Mol Engn, Dept Chem,Chicago Ctr Theoret Chem, 5640 S Ellis Ave, Chicago, IL 60637 USA.;Argonne Natl Lab, Lemont, IL 60439 USA..
    Truhlar, Donald G.
    Univ Minnesota, Chem Theory Ctr, Dept Chem, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Analytic gradients for compressed multistate pair-density functional theory2022In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 120, no 19-20, article id e2110534Article in journal (Refereed)
    Abstract [en]

    Photochemical reactions often involve states that are closely coupled due to near degeneracies, for example by proximity to conical intersections. Therefore, a multistate method is used to accurately describe these states; for example, ordinary perturbation theory is replaced by quasidegenerate perturbation theory. Multiconfiguration pair-density functional theory (MC-PDFT) provides an efficient way to approximate the full dynamical correlation energy of strongly correlated systems, and we recently proposed compressed multistate pair-density functional theory (CMS-PDFT) to treat closely coupled states. In the present paper, we report the implementation of analytic gradients for CMS-PDFT in both OpenMolcas and PySCF, and we illustrate the use of these gradients by applying the method to the excited states of formaldehyde and phenol.

  • 36.
    Baryshnikov, Glib V.
    et al.
    Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China.;Linköping Univ, Dept Sci & Technol, Lab Organ Elect, SE-60174 Norrköping, Sweden.
    Valiev, Rashid R.
    Univ Helsinki, Dept Chem, Fac Sci, FIN-00014 Helsinki, Finland.
    Valiulina, Lenara I.
    Tomsk State Univ, Dept Opt & Spect, Tomsk 634050, Russia.
    Kurtsevich, Alexandr E.
    Tomsk State Univ, Dept Opt & Spect, Tomsk 634050, Russia.
    Kurten, Theo
    Univ Helsinki, Dept Chem, Fac Sci, FIN-00014 Helsinki, Finland.
    Sundholm, Dage
    Univ Helsinki, Dept Chem, Fac Sci, FIN-00014 Helsinki, Finland.
    Pittelkow, Michael
    Univ Copenhagen, Dept Chem, DK-2100 Copenhagen O, Denmark.
    Zhang, Jinglai
    Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China.
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China.
    Odd-Number Cyclo[n]Carbons Sustaining Alternating Aromaticity2022In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 126, no 16, p. 2445-2452Article in journal (Refereed)
    Abstract [en]

    Cyclo[n]carbons (n = 5, 7, 9,..., 29) composed from an odd number of carbon atoms are studied computationally at density functional theory (DFT) and ab initio complete active space self-consistent field (CASSCF) levels of theory to get insight into their electronic structure and aromaticity. DFT calculations predict a strongly delocalized carbene structure of the cyclo[n]carbons and an aromatic character for all of them. In contrast, calculations at the CASSCF level yield geometrically bent and electronically localized carbene structures leading to an alternating double aromaticity of the odd-number cyclo[n]carbons. CASSCF calculations yield a singlet electronic ground state for the studied cyclo[n]carbons except for C25, whereas at the DFT level the energy difference between the lowest singlet and triplet states depends on the employed functional. The BHandHLYP functional predicts a triplet ground state of the larger odd-number cyclo[n]carbons starting from n = 13. Current-density calculations at the BHandHLYP level using the CASSCFoptimized molecular structures show that there is a through-space delocalization in the cyclo[n]carbons. The current density avoids the carbene carbon atom, leading to an alternating double aromaticity of the oddnumber cyclo[n]carbons satisfying the antiaromatic [4k+1] and aromatic [4k+3] rules. C11, C15, and C19 are aromatic and can be prioritized in future synthesis. We predict a bond-shift phenomenon for the triplet state of the cyclo[n]carbons leading to resonance structures that have different reactivity toward dimerization.

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  • 37. Battaglia, Stefano
    et al.
    Fdez. Galván, Ignacio
    Lindh, Roland
    Multiconfigurational quantum chemistry: The CASPT2 method2023In: Theoretical and Computational Photochemistry: Fundamentals, Methods, Applications and Synergy with Experimental Approaches / [ed] Cristina García-Iriepa, Marco Marazzi, Amsterdam: Elsevier, 2023, p. 135-162Chapter in book (Refereed)
    Abstract [en]

    This chapter presents the theory behind the CASPT2 method and its adaptation to a multistate formalism. The chapter starts with an introduction to the theory of the CASPT2 method—an application of the Rayleigh-Schrödinger perturbation theory applied to the multiconfigurational reference function—as it was originally presented. In particular, we discuss the nature of the reference Hamiltonian and the first-order interacting space. This is followed by some detailed discussion with respect to the intruder state problem and various shift techniques to address this problem. Afterward, a longer review on alternative reference Hamiltonians, which to some degree or completely remove the intruder state problem, is put forward. Subsequently, the presently proposed multistate versions of the CASPT2 method are discussed in some detail. The chapter is concluded with a review of different benchmark assessments of the accuracy of the method and a qualified suggestion on the future development potentials of the approach.

  • 38.
    Battaglia, Stefano
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Fransén, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Regularized CASPT2: an Intruder-State-Free Approach2022In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 18, no 8, p. 4814-4825Article in journal (Refereed)
    Abstract [en]

    In this work we present a new approach to fix the intruder-state problem (ISP) in CASPT2 based on sigma p regularization. The resulting sigma(p)-CASPT2 method is compared to previous techniques, namely, the real and imaginary level shifts, on a theoretical basis and by performing a series of systematic calculations. The analysis is focused on two aspects, the effectiveness of sigma(p)-CASPT2 in removing the ISP and the sensitivity of the approach with respect to the input parameter. We found that sigma p- CASPT2 compares favorably with respect to previous approaches and that different versions, sigma(1)-CASPT2 and sigma(2)-CASPT2, have different potential application domains. This analysis also reveals the unsuitability of the real level shift technique as a general way to avoid the intruder-state problem.

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  • 39.
    Battaglia, Stefano
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Extended Dynamically Weighted CASPT2: The Best of Two Worlds2020In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 16, no 3, p. 1555-1567Article in journal (Refereed)
    Abstract [en]

    We introduce a new variant of the complete active A space second-order perturbation theory (CASPT2) method that performs similarly to multistate CASPT2 (MS-CASPT2) in regions of the potential energy surface where the electronic states are energetically well separated and is akin to extended MS-CASPT2 (XMS-CASPT2) in case the underlying zeroth-order references are near-degenerate. Our approach follows a recipe analogous to that of XMS-CASPT2 to ensure approximate invariance under unitary transformations of the model states and a dynamic weighting scheme to smoothly interpolate the Fock operator between state-specific and state-average regimes. The resulting extended dynamically weighted CASPT2 (XDW-CASPT2) methodology possesses the most desirable features of both MS-CASPT2 and XMS-CASPT2, that is, the ability to provide accurate transition energies and correctly describe avoided crossings and conical intersections. The reliability of XDW-CASPT2 is assessed on a number of molecular systems. First, we consider the dissociation of lithium fluoride, highlighting the distinctive characteristics of the new approach. Second, the invariance of the theory is investigated by studying the conical intersection of the distorted allene molecule. Finally, the relative accuracy in the calculation of vertical excitation energies is benchmarked on a set of 26 organic compounds. We found that XDW-CASPT2, albeit being only approximately invariant, produces smooth potential energy surfaces around conical intersections and avoided crossings, performing equally well to the strictly invariant XMS-CASPT2 method. The accuracy of vertical transition energies is almost identical to MS-CASPT2, with a mean absolute deviation of 0.01-0.02 eV, in contrast to 0.12 eV for XMS-CASPT2.

  • 40.
    Battaglia, Stefano
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    On the role of symmetry in XDW-CASPT22021In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 154, no 3, article id 034102Article in journal (Refereed)
    Abstract [en]

    Herewith, we propose two new exponents for the recently introduced XDW-CASPT2 method [S. Battaglia and R. Lindh, J. Chem. Theory Comput. 16, 1555-1567 (2020)], which fix one of the largest issues hindering this approach. By using the first-order effective Hamiltonian coupling elements, the weighting scheme implicitly takes into account the symmetry of the states, thereby averaging Fock operators only if the zeroth-order wave functions interact with each other. The use of Hamiltonian couplings also provides a physically sounder approach to quantitate the relative weights; however, it introduces new difficulties when these rapidly die off to zero. The improved XDW-CASPT2 method is critically tested on several systems of photochemical relevance, and it is shown that it succeeds in its original intent of maintaining MS-CASPT2 accuracy for the evaluation of transition energies and at the same time providing smooth potential energy surfaces around near-degenerate points akin to XMS-CASPT2.

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  • 41.
    Bayani, Amirhossein
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Larsson, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Inorganic Chemistry.
    Intercalation of Au Atoms into SiC(0001)/Buffer Interfaces: A First-Principles Density Functional Theory Study2020In: ACS Omega, E-ISSN 2470-1343, Vol. 5, no 24, p. 14842-14846Article in journal (Refereed)
    Abstract [en]

    The process of Au intercalation into a SiC/buffer interface has been theoretically investigated here by using density functional theory (DFT) and the nudged elastic band (NEB) method. Energy barriers were at first calculated (using NEB) for the transfer of an Au atom through a free-standing graphene sheet. The graphene sheet was either of a nondefect character or with a defect in the form of an enlarged hexagonal carbon ring. Defects in the form of single and double vacancies were also considered. Besides giving a qualitative prediction of the relative energy barriers for the corresponding SiC/buffer interfaces, some of the graphene calculations also proved evidence of energy minima close to the graphene sheet. The most stable Au positions within the SiC/buffer interface were, therefore, calculated by performing geometry optimization with Au in the vicinity of the buffer layer. Based on these NEB and DFT calculations, two factors were observed to have a great influence on the Au intercalation process: (i) energy barrier and (ii) preferential bonding of Au to the radical C atoms at the edges of the vacancies. The energy barriers were considerably smaller in the presence of vacancies. However, the Au atoms preferred to bind to the edge atoms of these vacancies when approaching the buffer layer. It can thereby be concluded that the Au intercalation will only occur for a nondefect buffer layer when using high temperature and/or by using high-energy impacts by Au atoms. For this type of Au intercalation, the buffer layer will become completely detached from the SiC surface, forming a single layer of graphene with an intact Dirac point.

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  • 42.
    Begunovich, Lyudmila V.
    et al.
    Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem IRC SQC, 26 Kirensky St, Krasnoyarsk 660074, Russia..
    Kuklin, Artem, V
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy. Siberian Fed Univ, Int Res Ctr Spect & Quantum Chem IRC SQC, 26 Kirensky St, Krasnoyarsk 660074, Russia.;Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Baryshnikov, Glib, V.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden.;Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Valiev, Rashid R.
    Natl Res Tomsk Polytech Univ, Res Sch Chem & Appl Biomed Sci, Lenin Ave 30, Tomsk 634050, Russia.;Univ Helsinki, Fac Sci, Dept Chem, FIN-00014 Helsinki, Finland..
    Ågren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Chemical and Bio-Molecular Physics. Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden.;Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Single-layer polymeric tetraoxa[8]circulene modified by s-block metals: toward stable spin qubits and novel superconductors2021In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 13, no 9, p. 4799-4811Article in journal (Refereed)
    Abstract [en]

    Tunable electronic properties of low-dimensional materials have been the object of extensive research, as such properties are highly desirable in order to provide flexibility in the design and optimization of functional devices. In this study, we account for the fact that such properties can be tuned by embedding diverse metal atoms and theoretically study a series of new organometallic porous sheets based on two-dimensional tetraoxa[8]circulene (TOC) polymers doped with alkali or alkaline-earth metals. The results reveal that the metal-decorated sheets change their electronic structure from semiconducting to metallic behaviour due to n-doping. Complete active space self-consistent field (CASSCF) calculations reveal a unique open-shell singlet ground state in the TOC-Ca complex, which is formed by two closed-shell species. Moreover, Ca becomes a doublet state, which is promising for magnetic quantum bit applications due to the long spin coherence time. Ca-doped TOC also demonstrates a high density of states in the vicinity of the Fermi level and induced superconductivity. Using the ab initio Eliashberg formalism, we find that the TOC-Ca polymers are phonon-mediated superconductors with a critical temperature T-C = 14.5 K, which is within the range of typical carbon based superconducting materials. Therefore, combining the proved superconductivity and the long spin lifetime in doublet Ca, such materials could be an ideal platform for the realization of quantum bits.

  • 43.
    Behzadi, Hadi
    et al.
    Department of Physical Chemistry, Faculty of Chemistry, Kharazmi University, 15719-14911, Tehran, Iran.
    Manzetti, Sergio
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Fjordforsk AS, N-6894 Midtun, Vangsnes, Norway.
    Darghai, Mayram
    Department of Chemistry, Faculty of Science, Imam Khomeini International University, Qazvin, Iran.
    Roonasi, Payman
    Department of Physical Chemistry, Faculty of Chemistry, Kharazmi University, 15719-14911, Tehran, Iran.
    Khalilnia, Zahra
    Department of Physical Chemistry, Faculty of Chemistry, Kharazmi University, 15719-14911, Tehran, Iran.
    Application of calculated NMR parameters, aromaticity indices and wavefunction properties for evaluation of corrosion inhibition efficiency of pyrazine inhibitors2018In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 1151, p. 34-40Article in journal (Refereed)
    Abstract [en]

    In light of the importance of developing novel corrosion inhibitors, a series of quantum chemical calculations were carried out to evaluate 15N chemical shielding CS tensors as well as aromaticity indexes including NICS, HOMA, FLU, and PDI of three pyrazine derivatives, 2-methylpyrazine (MP), 2-aminopyrazine (AP) and 2-amino-5-bromopyrazine (ABP). The NICS parameters have been shown in previous studies to be paramount to the prediction of anti-corrosion properties, and have been combined here with HOMA, FLU and PDI and detailed wavefunction analysis to determine the effects from bromination and methylation on pyrazine. The results show that the electron density around the nitrogens, represented by CS tensors, can be good indicators of anti-corrosion efficiency. Additionally, the NICS, FLU and PDI, as aromaticity indicators of molecule, are well correlated with experimental corrosion inhibition efficiencies of the studied inhibitors. Bader sampling and detailed wavefunction analysis shows that the major effects from bromination on the pyrazine derivatives affect the Laplacian of the electron density of the ring, delocalizing the aromatic electrons of the carbon atoms into lone pairs and increasing polarization of the Laplacian values. This feature is well agreement with empirical studies, which show that ABP is the most efficient anti-corrosion compound followed by AP and MP, a property which can be attributed and predicted by derivation of the Laplacian of the electron density of the ring nuclei. This study shows the importance of devising DFT methods for development of new corrosion inhibitors, and the strength of electronic and nuclear analysis, and depicts most importantly how corrosion inhibitors composed of aromatic moieties may be modified to increase anti-corrosive properties.

  • 44. Beinik, Igor
    et al.
    Hellström, Matti
    Jensen, Thomas
    Broqvist, Peter
    Lauritsen, Jeppe
    Cu wets the polar ZnO(0001)-Zn surface because of interaction with subsurface defectsArticle in journal (Refereed)
  • 45.
    Benatto, L.
    et al.
    Univ Fed Parana, Dept Fis, CP 19044, BR-81531980 Curitiba, Parana, Brazil.
    Marchiori, Cleber
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. Univ Fed Parana, Dept Fis, CP 19044, BR-81531980 Curitiba, Parana, Brazil.
    da Luz, M. G. E.
    Univ Fed Parana, Dept Fis, CP 19044, BR-81531980 Curitiba, Parana, Brazil.
    Koehler, M.
    Univ Fed Parana, Dept Fis, CP 19044, BR-81531980 Curitiba, Parana, Brazil.
    Electronic and structural properties of fluorene-thiophene copolymers as function of the composition ratio between the moieties: a theoretical study2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 31, p. 20447-20458Article in journal (Refereed)
    Abstract [en]

    Through theoretical analysis, we study relevant properties of some molecular structures formed by oligothiophenes (T) and dioctylfluorenes (F) units, commonly employed in the fabrication of different kinds of optical and electronic devices. For so, we first consider F-(T)(n)-F molecules with different numbers of thiophene rings (n). Among other characteristics, we calculate the dipole moment change between the ground and excited state ((ge)), a quantity that greatly influences the exciton dissociation and charge carrier mobility. We show that the planarity of the ground state geometry correlates (ge) to the exciton binding energy (E-b), with higher (ge)'s corresponding to lower E-b's when n > 3. We also unveil a relevant dependence of (ge) with the odd-even parity of n and that (ge) assumes higher values when the molecule is composed by bithiophene (instead of simple thiophenes) moieties in the syn-conformation (with the two heteroatoms pointing in the same direction). From molecules results, we then address larger systems, formed by different oligomers of F-T copolymers containing blocks of dioctylfluorenes and bithiophenes (T2). We systematic investigate their electronic and structural properties as function of the composition ratio between the T2 and F moieties. Similar to the molecules, we deduce that the magnitude of (ge) is higher for the syn conformer of the T2 unit. Moreover, the highest values of (ge) are achieved when the number of the T2 increases relative to a fixed number of the F units in the mer. Such behaviors are in agreement and actually can qualitative explain measurements in the literature on the quantum efficiency of charge carrier generation in F-T copolymers. The present findings can be helpful in designing novel materials with improved photoelectric responses.

  • 46.
    Bengtson, Charlotta
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Stenrup, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Sjöqvist, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Quantum nonlocality in the excitation energy transfer in the Fenna-Matthews-Olson complex2016In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 116, p. 1763-1771Article in journal (Refereed)
    Abstract [en]

    The Fenna-Matthews-Olson (FMO) complex - a pigment protein complex involved in photosynthesis in green sulfur bacteria - is remarkably efficient in transferring excitation energy from light harvesting antenna molecules to a reaction center. Recent experimental and theoretical studies suggest that quantum coherence and entanglement may play a role in this excitation energy transfer (EET). We examine whether bipartite quantum nonlocality, a property that expresses a stronger-than-entanglement form of correlation, exists between different pairs of chromophores in the FMO complex when modeling the EET by the hierarchically coupled equations of motion method. We compare the results for nonlocality with the amount of bipartite entanglement in the system. In particular, we analyze in what way these correlation properties are affected by different initial conditions. It is found that bipartite nonlocality only exists when the initial conditions are chosen in an unphysiological manner and probably is absent when considering the EET in the FMO complex in its natural habitat. It is also seen that nonlocality and entanglement behave quite differently in this system. In particular, for localized initial states, nonlocality only exists on a very short time scale and then drops to zero in an abrupt manner. As already known from previous studies, quantum entanglement between chromophore pairs on the other hand is oscillating and exponentially decaying and follow thereby a pattern more similar to the chromophore population dynamics. The abrupt disappearance of nonlocality in the presence of nonvanishing entanglement is a phenomenon we call nonlocality sudden death; a striking manifestation of the difference between these two types of correlations in quantum systems. 

  • 47.
    Bernes, E.
    et al.
    Univ Trieste, Dept Chem & Pharmaceut Sci, I-34127 Trieste, Italy..
    Fronzoni, G.
    Univ Trieste, Dept Chem & Pharmaceut Sci, I-34127 Trieste, Italy..
    Stener, M.
    Univ Trieste, Dept Chem & Pharmaceut Sci, I-34127 Trieste, Italy..
    Guarnaccio, A.
    ISM CNR, Inst Struct Matter, Tito, PZ, Italy.;ISM CNR, Inst Struct Matter, Trieste, Italy..
    Zhang, T.
    Beijing Inst Technol BIT, Sch Informat & Elect, MIIT Key Lab Low Dimens Quantum Struct & Devices, Beijing 100081, Peoples R China.;Uppsala Univ, Dept Phys & Astron, SE-75120 Uppsala, Sweden..
    Grazioli, C.
    IOM CNR, Lab TASC, Sincrotrone Trieste, I-34149 Trieste, Basovizza, Italy..
    Johansson, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy.
    Coreno, M.
    ISM CNR, Inst Struct Matter, Tito, PZ, Italy.;ISM CNR, Inst Struct Matter, Trieste, Italy..
    de Simone, M.
    IOM CNR, Lab TASC, Sincrotrone Trieste, I-34149 Trieste, Basovizza, Italy..
    Puglia, Carla
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Toffoli, D.
    Univ Trieste, Dept Chem & Pharmaceut Sci, I-34127 Trieste, Italy..
    S 2p and P 2p Core Level Spectroscopy of PPT Ambipolar Material and Its Building Block Moieties2020In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 124, no 127, p. 14510-14520Article in journal (Refereed)
    Abstract [en]

    The near-edge X-ray absorption fine structure (NEXAFS and X-ray photoelectron (XP) spectra of gas-phase 2,8-bis-(diphenylphosphoryl)dibenzo[b,d]thiophene (PPT) and triphenylphosphine oxide (TPPO) have been measured at the S and P L-II,L-III-edge regions. The time-dependent density functional theory (TDDFT) based on the relativistic two-component zeroth-order regular approximation approach has been used to provide an assignment of the experimental spectra, giving the contribution of the spin-orbit splitting and of the molecular-field splitting to the sulfur and phosphor binding energies. Computed XP and NEXAFS spectra agree well with the experimental measurements. In going from dibenzothiophene and TPPO to PPT, the nature of the most intense S 2p and P 2p NEXAFS features are preserved; this trend suggests that the electronic and geometric behaviors of the S and P atoms in the two building block moieties are conserved in the more complex system of PPT. This work enables us to shed some light onto the structure of the P-O bond, a still highly debated topic in the chemical literature. Since the S 2p and P 2p NEXAFS intensities provide specific information on the higher-lying localized sigma*(C-S) and sigma*(P-O) virtual MOs, we have concluded that P 3d AOs are not involved in the formation of the P-O bond. Moreover, the results support the mechanism of negative hyperconjugation, by showing that transitions toward sigma*(P-O) states occur at lower energies with respect to those toward it pi*(P-O) states.

  • 48.
    Berraud-Pache, Romain
    et al.
    Univ Paris Est, Lab Modelisat & Simulat Multi Echelle, MSME, UMR CNRS 8208,UPEM, 5 Bd Descartes, F-77454 Marne La Vallee, France.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Navizet, Isabelle
    Univ Paris Est, Lab Modelisat & Simulat Multi Echelle, MSME, UMR CNRS 8208,UPEM, 5 Bd Descartes, F-77454 Marne La Vallee, France.
    QM/MM Study of the Formation of the Dioxetanone Ring in Fireflies through a Superoxide Ion2018In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, no 20, p. 5173-5182Article in journal (Refereed)
    Abstract [en]

    The bioluminescence emission from fireflies is an astounding tool to mark and view cells. However, the bioluminescent mechanism is not completely deciphered, limiting the comprehension of key processes. We use a theoretical approach to study for the first time the arrival of a dioxygen molecule inside the fireflies protein and one path of the formation of the dioxetanone ring, the high-energy intermediate precursor of the bioluminescence. To describe this reaction step, a joint approach combining classical molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations is used. The formation of the dioxetanone ring has been studied for both singlet and triplet states with the help of MS-CASPT2 calculations. We also emphasize the role played by the proteinic environment in the formation of the dioxetanone ring. The results obtained shed some light on an important reaction step and give new insights concerning the bioluminescence in fireflies.

  • 49.
    Berwanger, Mailing
    et al.
    Univ Fed Santa Maria, Dept Fis, BR-97105900 Santa Maria, RS, Brazil;Inst Fed Educ Ciencia & Tecnol Rio Grande do Sul, BR-98200000 Ibiruba, RS, Brazil.
    Ahuja, Rajeev
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Piquini, Paulo Cesar
    Univ Fed Santa Maria, Dept Fis, BR-97105900 Santa Maria, RS, Brazil.
    HfS2 and TiS2 Monolayers with Adsorbed C, N, P Atoms: A First Principles Study2020In: Catalysts, E-ISSN 2073-4344, Vol. 10, no 1, article id 94Article in journal (Refereed)
    Abstract [en]

    First principles density functional theory was used to study the energetic, structural, and electronic properties of HfS2 and TiS2 materials in their bulk, pristine monolayer, as well as in the monolayer structure with the adsorbed C, N, and P atoms. It is shown that the HfS2 monolayer remains a semiconductor while TiS2 changes from semiconductor to metallic behavior after the atomic adsorption. The interaction with the external atoms introduces localized levels inside the band gap of the pristine monolayers, significantly altering their electronic properties, with important consequences on the practical use of these materials in real devices. These results emphasize the importance of considering the interaction of these 2D materials with common external atomic or molecular species.

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  • 50.
    Bhaduri, Anindya
    et al.
    Johns Hopkins Univ, Dept Civil Engn, Baltimore, MD 21218 USA.
    Gardner, Jasmine
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Abrams, Cameron F.
    Drexel Univ, Dept Chem & Biol Engn, Philadelphia, PA 19104 USA.
    Graham-Brady, Lori
    Johns Hopkins Univ, Dept Civil Engn, Baltimore, MD 21218 USA.
    Free energy calculation using space filled design and weighted reconstruction: a modified single sweep approach2020In: Molecular Simulation, ISSN 0892-7022, E-ISSN 1029-0435, Vol. 46, no 3, p. 193-206Article in journal (Refereed)
    Abstract [en]

    A modified single sweep approach is proposed for generating free energy landscapes. The approach replaces the use of temperature-accelerated molecular dynamics (TAMD) to generate centres in collective variable (CV) space at which mean forces are computed using restrained molecular dynamics (MD) simulations with a sequential space-filling design. This approach also modifies the radial basis function reconstruction step of the traditional single sweep approach and proposes a weighted reconstruction of the free energy surface using the previously generated mean forces. The modified approach is compared to the traditional single sweep (SS) approach on the (phi, psi) dihedral free-energy map of solvated alanine dipeptide (AD). It is found that the new approach results in a more accurate reconstructed free energy than does the traditional approach when compared to the directly-computed reference free energy landscape. It is shown that the increased accuracy of the overall map stems from the improved 1-dimensional space filling (projective) property of the proposed design compared to that of the TAMD generated centres. A further enhancement in the accuracy of the crucial lower energy regions is enabled by the introduction of weights in the reconstruction step that give more importance to lower energy-valued regions.

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