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  • 301.
    Larsson, Per-Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Fysiska institutionen. QUANTUM CHEMISTRY.
    Potential Energy Models for Organic Reactions2001Licentiatavhandling, monografi (Övrigt vetenskapligt)
  • 302.
    Larsson, Per-Erik
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kvantkemi.
    Salhi-Benachenhou, Nessima
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kvantkemi.
    Dong, Xicheng
    Lunell, Sten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kvantkemi.
    Quadricyclane Radical Cation Isomerization Reactions: A Theoretical Study2002Ingår i: International Journal of Quantum Chemistry, Vol. 90, s. 1388-1395Artikel i tidskrift (Refereegranskat)
  • 303.
    Larsson, Per-Erik
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kvantkemi.
    Salhi-Benachenhou, Nessima
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kvantkemi.
    Lunell, Sten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kvantkemi.
    Bicyclo[2.2.1]hepta-2-ene-5-yl-7-ylium Radical Cation: A Theoretical Validation of a Bishomoaromatic Radical Cation Intermediate2003Ingår i: Organic Letters, ISSN 1523-7060, E-ISSN 1523-7052, Vol. 5, nr 8, s. 1329-1331Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    [structure: see text] A natural bond orbital analysis of the distonic bicyclo[2.2.1]hepta-2-ene-5-yl-7-ylium radical cation interprets its structure and radical character by a three-center two-electron bond between C2, C3, and C7 (a bishomoaromatic stabilization) and a singly occupied orbital on C5, n(5). Moreover, B3LYP/6-311+G(d,p) ESR parameters, which agree excellently with experiment, are interpreted in terms of spin polarization in the natural hybrids of sigma(C5-H5), and a dual hyperconjugative effect involving n(5), sigma(C1-H1a), sigma(C1-H1b), and antibonding counterparts.

  • 304.
    Levamaki, Henrik
    et al.
    Univ Turku, Dept Phys & Astron, FI-20014 Turku, Finland;Turku Univ, Ctr Mat & Surfaces MatSurf, Turku, Finland.
    Nagy, Agnes
    Univ Debrecen, Dept Theoret Phys, H-4002 Debrecen, Hungary.
    Vilja, Iiro
    Univ Turku, Dept Phys & Astron, FI-20014 Turku, Finland;Turku Ctr Quantum Phys, Turku, Finland.
    Kokko, Kalevi
    Univ Turku, Dept Phys & Astron, FI-20014 Turku, Finland;Turku Univ, Ctr Mat & Surfaces MatSurf, Turku, Finland.
    Vitos, Levente
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori. Royal Inst Technol, Dept Mat Sci & Engn, Appl Mat Phys, SE-10044 Stockholm, Sweden;Hungarian Acad Sci, Wigner Res Ctr Phys, Inst Solid State Phys & Opt, POB 49, H-1525 Budapest, Hungary.
    Kullback-Leibler and relative Fisher information as descriptors of locality2018Ingår i: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 118, nr 12, artikel-id e25557Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Kullback-Leibler and relative Fisher information functionals are applied in studying deviation from local density approximation. The reduced density gradient s and the local kinetic energy parameter alpha are key ingredients of these new locality descriptors. The relative Kullback-Leibler information density contains extra knowledge as it is negative where the given probability density is smaller than the reference density. The relative Fisher information incorporates the highest order deviations from the uniform electron gas approximation.

  • 305. Levitina, T.
    et al.
    Brändas, Erkki J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Sampling formula for convolution with a prolate2008Ingår i: International Journal of Computer Mathematics, ISSN 0020-7160, E-ISSN 1029-0265, Vol. 85, nr 3-4, s. 487-496Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Eigenfunctions of the Finite Fourier Transform, often referred to as 'prolates', are band-limited and highly concentrated at a finite time-interval. Both features are acquired by the convolution of a band-limited function with a prolate. This permits interpolation of such a convolution by the Walter and Shen sampling formula in terms of prolates, although the Fourier transform of the convolution is not necessarily even continuous and the concentration interval is twice as large as that of a prolate. Rigorous error estimates are given as dependent on the truncation limits. The accuracy achieved is tested by numerical examples.

  • 306.
    Levitina, Tatiana
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Fysiska institutionen. ADVANCED INSTRUMENTATION AND MEASUREMENTS.
    Brändas, Erkki
    Multitaper Techniques and Filter Diagonalisation Methods: A Comparison2003Ingår i: International Journal of Theoretical Physics, ISSN ISSN 0020-7748, Vol. 42, nr 10, s. 2531-2544Artikel i tidskrift (Refereegranskat)
  • 307. Levitina, Tatiana
    et al.
    Brändas, Erkki J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Filter diagonalization with prolates. Descrete signal data.2009Ingår i: Proceedings of the 2009 international conference on computational and mathematical methods in science and engineering, Gijón (Asturias), Spain, June 30, July 1-3, 2009 / [ed] J. Vigo-Aguiar, 2009, s. 618-621Konferensbidrag (Övrigt vetenskapligt)
  • 308.
    Levitina, Tatiana
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Fysiska institutionen. ADVANCED INSTRUMENTATION AND MEASUREMENTS.
    Brändas, Erkki J.
    Numerical Multitaper Techniques and Filter Diagonalisation: A Comparison2003Ingår i: Proceedings of the International Conference of Computational Methods in Sciences and Engineering, World Scientific , 2003, s. 365-Konferensbidrag (Refereegranskat)
  • 309.
    Levitina, Tatiana
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Fysiska institutionen. ADVANCED INSTRUMENTATION AND MEASUREMENTS.
    Brändas, Erkki J.
    Numerical Quadrature Performed on the Generalized Prolate Spheroidal Functions2003Ingår i: Proceedings of the International Conference of Computational Methods in Sciences and Engineering, ISSN ISBN: 981-238-595-9, s. 360-364Artikel i tidskrift (Refereegranskat)
  • 310.
    Levitina, TV
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Fysiska institutionen, Kvantkemi.
    Brändas, EJ
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Fysiska institutionen, Kvantkemi.
    Angle dependent total cross sections and the optical theorem2001Ingår i: Computers and Chemistry, ISSN 0097-8485, E-ISSN 1879-0763, Vol. 25, nr 1, s. 55-67Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Cross sections are either represented by generalized asymptotical partial wave expansions or obtained as a spherical average of an appropriate differential cross section. In these cases it is usually assumed that the total scattering cross section, as a property of a scattering object, does not depend on the incident angles. This viewpoint is supported by common knowledge in connection with low energy scattering. However this unconscious belief is not always correct. In the present paper we will show that a non-spherical scatterer may exhibit strong dependence on the incident direction. To do this we will represent the scattering data of the most general potential, separable in ellipsoidal coordinates, in perturbed ellipsoidal (Lamé) wave functions. These functions arise when variables in the Schrödinger equation are separated in an ellipsoidal coordinate system. The Lamé wave functions are analogous to spherical- and Bessel functions in the case of spherical symmetry. We will expand the total scattering cross section and derive the optical theorem explicitly demonstrating the incident angle dependence for such a class of potentials. As an illustration we will present and display some calculations of the total cross section versus incident direction. Unexpected behavior will be discussed and explained. We also use results from classical acoustic scattering by a triaxial ellipsoid. The general character of the ellipsoidal coordinate system is emphasized.

  • 311.
    Levämäki, H.
    et al.
    Royal Inst Technol, Dept Mat Sci & Engn, Appl Mat Phys, SE-10044 Stockholm, Sweden..
    Vitos, Levente
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori. Royal Inst Technol, Dept Mat Sci & Engn, Appl Mat Phys, SE-10044 Stockholm, Sweden.;Wigner Res Ctr Phys, Res Inst Solid State Phys & Opt, H-1525 Budapest, Hungary..
    Electron localization function implementation in the exact muffin-tin orbitals method2021Ingår i: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 103, nr 3, artikel-id 035118Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report implementation of the electron localization function (ELF) within the exact muffin-tin orbitals (EMTO) formalism. The ELF is often used to study the nature of electronic bonding in different types of materials, and it is also an important ingredient in meta-generalized gradient approximations, which are one of the classes of exchange-correlation functionals. The correctness of the ELF implementation is verified with test calculations and comparison with previous literature results. The implementation supports not only regular ordered systems but also disordered systems that have been calculated using the coherent potential approximation method.

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  • 312.
    Li, Chenyang
    et al.
    Emory Univ, Dept Chem, Atlanta, GA 30322 USA;Emory Univ, Cherry Emerson Ctr Sci Computat, Atlanta, GA 30322 USA.
    Lindh, Roland
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Evangelista, Francesco A.
    Emory Univ, Dept Chem, Atlanta, GA 30322 USA;Emory Univ, Cherry Emerson Ctr Sci Computat, Atlanta, GA 30322 USA.
    Dynamically weighted multireference perturbation theory: Combining the advantages of multi-state and state-averaged methods2019Ingår i: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, nr 14, artikel-id 144107Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We introduce two new approaches to compute near-degenerate electronic states based on the driven similarity renormalization group (DSRG) framework. The first approach is a unitary multi-state formalism based on the DSRG (MS-DSRG), whereby an effective Hamiltonian is built from a set of state-specific solutions. The second approach employs a dynamic weighting parameter to smoothly interpolate between the multi-state and the state-averaged DSRG schemes. The resulting dynamically weighted DSRG (DW-DSRG) theory incorporates the most desirable features of both multi-state approaches (ability to accurately treat many states) and state-averaged methods (correct description of avoided crossings and conical intersections). We formulate second-order perturbation theories (PT2) based on the MS-and DW-DSRG and study the potential energy curves of LiF, the conical intersection of the two lowest singlet states of NH3, and several low-lying excited states of benzene, naphthalene, and anthracene. The DW-DSRG-PT2 predicts the correct avoided crossing of LiF and avoids artifacts produced by the corresponding state-specific and multi-state theories. Excitation energies of the acenes computed with the DW-DSRG-PT2 are found to be more accurate than the corresponding state-averaged values, showing a small dependence on the number of states computed.

  • 313.
    Li, Jibiao
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori. Yangtze Normal Univ, Chongqing Key Lab Extraordinary Bond Engn & Adv M, Chongqing, Peoples R China; Stockholm Univ, AlbaNova Univ Ctr, Dept Phys, Stockholm, Sweden.
    He, Xin
    Sichuan Univ Arts & Sci, Sch Intelligent Mfg, Dazhou, Peoples R China.
    Peng, Cheng
    Yangtze Normal Univ, Chongqing Key Lab Extraordinary Bond Engn & Adv M, Chongqing, Peoples R China.
    Ahuja, Rajeev
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Chemical Bonding of Unique CO on Fe(100)2018Ingår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, nr 16, s. 9062-9074Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    At low coverage, CO molecules are known to preferentially occupy the hollow sites of Fe(100) with considerably inclined molecular orientations. This CO configuration serves as the precursor state of CO dissociation, which is particularly important in several important catalytic reactions. In this study, we present a unique bonding picture of the precursor state from the spin, charge, and orbital perspectives. From the spin and orbital views, we show the antiferromagenetic nature of the adsorbate–metal coupling, where 2π magnetism prevails with a dominant spin-down channel. However, contrasting tendencies are found for the two 1π orbitals in two orthogonal directions: the 1π orbital in the vertical plane loses its symmetry, whereas the other 1π orbital remains intact with a preserved symmetry. The 1π symmetry in the vertical plane favors the 1π → 2π* excitation mechanism owing to the partial opening up of the 1π symmetry. In the charge perspective, we have identified a charge transfer mechanism involving the local structural IFeC–C–O motif, in which the surface slightly charges the adsorbate with additional partial electrons located at the surface Fe atoms bonded to the carbon end, whereas the charges of the metallic atoms beneath the IFeC–C–O motif are found to be depleted. In both the adsorbate and metal sides, the depletion of s electrons serves as a good measure of orbital repulsion and delocalization. Interestingly, the carbon and oxygen ends exhibit contrasting electron affinity with the metal surface: the carbon end is attractive, whereas the oxygen end is repulsive in terms of the contrasting charge rearrangement in the bonded metallic atoms.

  • 314.
    Li, Wan-Lu
    et al.
    Univ Calif Berkeley, Kenneth S Pitzer Theory Ctr, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA.;Lawrence Berkeley Natl Lab, Chem Sci Div, Berkeley, CA 94720 USA..
    Li, Yong
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström. Tsinghua Univ, Dept Chem, Beijing 100084, Peoples R China.;Tsinghua Univ, Engn Res Ctr Adv Rare, Earth Mat Minist Educ, Beijing 100084, Peoples R China.;Univ Bremen, Inst Appl & Phys Chem, D-28359 Bremen, Germany.;Univ Bremen, Ctr Environm Res & Sustainable Technol, D-28359 Bremen, Germany..
    Li, Jun
    Tsinghua Univ, Dept Chem, Beijing 100084, Peoples R China.;Tsinghua Univ, Engn Res Ctr Adv Rare, Earth Mat Minist Educ, Beijing 100084, Peoples R China.;Southern Univ Sci & Technol, Dept Chem, Shenzhen 518055, Peoples R China.;Southern Univ Sci & Technol, Guangdong Prov Key Lab Catalyt Chem, Shenzhen 518055, Peoples R China..
    Head-Gordon, Teresa
    Univ Calif Berkeley, Kenneth S Pitzer Theory Ctr, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Chem, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Bioengn & Chem & Biomol Engn, Berkeley, CA 94720 USA.;Lawrence Berkeley Natl Lab, Chem Sci Div, Berkeley, CA 94720 USA..
    How thermal fluctuations influence the function of the FeMo cofactor in nitrogenase enzymes2023Ingår i: CHEM CATALYSIS, ISSN 2667-1093, Vol. 3, nr 7, artikel-id 100662Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The catalytic mechanism of N2 fixation by nitrogenase remains unre-solved in how the strong N=N bond is activated and why the reduc-tive elimination of H2 is required. Here, we use density functional theory and physiologically relevant thermal simulations to elucidate the mechanism of the complete nitrogenase catalytic cycle. Over the accumulation of four reducing equivalents, we find that protons and electrons transfer to the FeMo cofactor to weaken and break its bridge Fe-S bond, leading to temporary H2S formation that exposes the Fe sites to weakly bind N2. Remarkably, we find that subsequent H2 formation is responsible for chemical activation to an N=N dou-ble bond accompanied by a low barrier for H2 release. We empha-size that finite temperature effects smooth out mechanistic differ-ences between DFT functionals observed at 0 K, thus leading to a consistent understanding as to why H formation is an obligatory step in N2 adsorption and activation.

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  • 315.
    Liao, Qinghua
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Strukturbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Enhanced sampling and free energy calculations for protein simulations2020Ingår i: Computational Approaches For Understanding Dynamical Systems: Protein Folding And Assembly / [ed] Strodel, B Barz, B, Academic Press, 2020, s. 177-213Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Molecular dynamics simulation is a powerful computational technique to study biomolecular systems, which complements experiments by providing insights into the structural dynamics relevant to biological functions at atomic scale. It can also be used to calculate the free energy landscapes of the conformational transitions to better understand the functions of the biomolecules. However, the sampling of biomolecular configurations is limited by the free energy barriers that need to be overcome, leading to considerable gaps between the timescales reached by MD simulation and those governing biological processes. To address this issue, many enhanced sampling methodologies have been developed to increase the sampling efficiency of molecular dynamics simulations and free energy calculations. Usually, enhanced sampling algorithms can be classified into methods based on collective variables (CV-based) and approaches which do not require predefined CVs (CV-free). In this chapter, the theoretical basis of free energy estimation is briefly reviewed first, followed by the reviews of the most common CV-based and CV-free methods including the presentation of some examples and recent developments. Finally, the combination of different enhanced sampling methods is discussed.

  • 316.
    Lindblad, Rebecka
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Oorganisk kemi. Lund Univ, Dept Phys, Box 118, SE-22100 Lund, Sweden.;Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Kjellsson, Ludvig
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik. European XFEL GmbH, Holzkoppel 4, D-22869 Schenefeld, Germany..
    Couto, Rafael Carvalho
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. Royal Inst Technol, Sch Chem Biotechnol & Hlth, Theoret Chem & Biol, SE-10691 Stockholm, Sweden..
    Timm, M.
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, Albert Einstein Str 15, D-12489 Berlin, Germany.;Tech Univ Berlin, Inst Opt & Atomare Phys, Hardenbergstr 36, D-10623 Berlin, Germany..
    Bulow, C.
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Zamudio-Bayer, V.
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, Albert Einstein Str 15, D-12489 Berlin, Germany..
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    von Issendorff, B.
    Albert Ludwigs Univ Freiburg, Phys Inst, Hermann Herder Str 3, D-79104 Freiburg, Germany..
    Lau, J. T.
    Helmholtz Zentrum Berlin Mat & Energie, Abt Hochempfindl Rontgenspektroskopie, Albert Einstein Str 15, D-12489 Berlin, Germany.;Albert Ludwigs Univ Freiburg, Phys Inst, Hermann Herder Str 3, D-79104 Freiburg, Germany..
    Sorensen, S. L.
    Lund Univ, Dept Phys, Box 118, SE-22100 Lund, Sweden..
    Carravetta, V.
    IPCF CNR, Via Moruzzi 1, I-56124 Pisa, Italy..
    Ågren, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik. Royal Inst Technol, Sch Chem Biotechnol & Hlth, Theoret Chem & Biol, SE-10691 Stockholm, Sweden.;Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Rubensson, Jan-Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik.
    X-Ray Absorption Spectrum of the N-2(+) Molecular Ion2020Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 124, nr 20, artikel-id 203001Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The x-ray absorption spectrum of N-2(+) in the K-edge region has been measured by irradiation of ions stored in a cryogenic radio frequency ion trap with synchrotron radiation. We interpret the experimental results with the help of restricted active space multiconfiguration theory. Spectroscopic constants of the l sigma(-1 2)(u)Sigma(+)(u) state, and the two 1 sigma(-1)(u) 3 sigma(-1)(g) 1 pi(y) (II alpha)-I-2 states are determined from the measurements. The charge of the ground state together with spin coupling involving several open shells give rise to double excitations and configuration mixing, and a complete breakdown of the orbital picture for higher lying core-excited states.

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  • 317.
    Linderberg, Jan
    et al.
    Aarhus University, Denmark.
    Brändas, Erkki
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Öhrn, Yngve
    Univeristy of Florida, USA.
    Sabin, John
    University of Florida, USA.
    Per-Olov Löwdin2017Ingår i: Advances in Quantum Chemistry: Löwdin Volume / [ed] John R. Sabin, Erkki J. Brändas, Elsevier, 2017, Vol. 74, s. 1-7Kapitel i bok, del av antologi (Refereegranskat)
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  • 318.
    Lindh, Roland
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Cholesky Decomposition of the two-electron integrals: A reliable tool for linear scaling methods?2006Ingår i: RECENT PROGRESS IN COMPUTATIONAL SCIENCES AND ENGINEERING, VOLS 7A AND 7B, 2006, Vol. 7A-BKonferensbidrag (Övrigt vetenskapligt)
  • 319.
    Lindh, Roland
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Farahani, Pooria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Roca-Sanjuan, Daniel
    Zapata, Felipe
    Non-adiabatic process in 1,2-dioxetane2014Ingår i: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 247Artikel i tidskrift (Övrigt vetenskapligt)
  • 320. Lindh, Roland
    et al.
    Fdez. Galván, Ignacio
    Molecular structure optimizations with Gaussian process regression2023Ingår i: Quantum Chemistry in the Age of Machine Learning / [ed] Pavlo O. Dral, Amsterdam: Elsevier, 2023, s. 391-428Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Molecular structure optimization is one of the most common tasks performed in computational chemistry. Many applications require locating special points in a potential energy surface: minima, saddle points, and others. Given that the calculation of energies and gradients with accurate quantum chemical methods is quite computationally demanding, one is often interested in finding these special points with a minimal number of energy evaluations. During the last decades, optimization methods and strategies based on a second-order expansion of the potential energy surface have been developed and perfectioned, reaching a high level of efficiency and robustness. These “conventional” methods are briefly described in this chapter. More recently, alternative models and methods applying machine learning techniques (and most significantly Gaussian process regression) are being proposed and developed, and already show superior characteristics with respect to the established methods. These new approaches are discussed, in particular the restricted variance optimization method is described in some detail. Practical examples include optimization of stable structures and transition states.

  • 321.
    Lindh, Roland
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Galvan, Ignacio
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Liu, Ya-Jun
    Roca-Sanjuan, Daniel
    Recent method developments and applications in computational photochemistry, chemiluminescene and bioluminescence2015Ingår i: Photochemistry: Volume 42 / [ed] Elisa Fasani, Angelo Albini, Royal Society of Chemistry, 2015, 42, s. 11-42Kapitel i bok, del av antologi (Övrigt vetenskapligt)
    Abstract [en]

    This review summarises and discusses the advances of computational photochemistry in 2012 and 2013 in both methodology and applications fields. The methodological developments of models and tools used to study and simulate non-adiabatic processes are highlighted. These developments can be summarised as assessment studies, new methods to locate conical intersections, tools for representation, interpretation and visualisation, new computational approaches and studies introducing simpler models to rationalise the quantum dynamics near and in the conical intersection. The applied works on the topics of photodissociation, photostability, photoisomerisations, proton/charge transfer, chemiluminescence and bioluminescence are summarised, and some illustrative examples of studies are analysed in more detail, particularly with reference to photostability and chemi/bioluminescence. In addition, theoretical studies analysing solvent effects are also considered. We finish this review with conclusions and an outlook on the future.

  • 322.
    Lindh, Roland
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Liu, Ya-Jun
    Roca-Sanjuan, Daniel
    Computational Photochemistry and Photophysics: the state of the art2012Ingår i: Photochemistry: Volume 40 / [ed] Angelo Albini, Elisa Fasani, Royal Society of Chemistry, 2012, 40, s. 42-72-Kapitel i bok, del av antologi (Övrigt vetenskapligt)
    Abstract [en]

    This review starts with the most basic concepts in photochemistry and photophysics, followed by a chronological introduction of theoretical methods and relevant applications in the history of computational photochemistry, along with the authors’ comments on the methodologies currently available for photochemical studies. Recent advances in the field are next summarized and discussed, focusing separately on methodology and computational techniques and some highlighted applied works carried out during the last two years on the topics of photodissociations, photostability, photodimerizations, photoisomerizations, proton/hydrogen transfer, photodecarboxylations, charge transport, bioexcimers, chemiluminescence and bioluminescence. We finish this review by conclusions and an outlook of the future.

  • 323. Lindh, Roland
    et al.
    Pedersen, Thomas B.
    Aquilante, Francesco
    PHYS 142-Cholesky decomposition in computational chemistry2008Konferensbidrag (Övrigt vetenskapligt)
  • 324. Lindh, Roland
    et al.
    Roos, Björn O.
    Malmqvist, Per Åke
    Verazov, Valera
    Widmark, Per-Olof
    Multiconfigurational Quantum Chemistry2016Bok (Refereegranskat)
  • 325.
    Linge, Darius
    et al.
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Gedgaudas, Marius
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Merkys, Andrius
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Sect Crystallog & Cheminformat, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Petrauskas, Vytautas
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Vaitkus, Antanas
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Sect Crystallog & Cheminformat, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Grybauskas, Algirdas
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Sect Crystallog & Cheminformat, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Paketuryte, Vaida
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Zubriene, Asta
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Zaksauskas, Audrius
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Mickeviciute, Aurelija
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Smirnoviene, Joana
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Baranauskiene, Lina
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Capkauskaite, Edita
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Dudutiene, Virginija
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Urniezius, Ernestas
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Konovalovas, Aleksandras
    Vilnius Univ, Inst Biosci, Life Sci Ctr, Dept Biochem & Mol Biol, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Kazlauskas, Egidijus
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Shubin, Kirill
    Latvian Inst Organ Synth, Aizkraukles St 21, LV-1006 Riga, Latvia..
    Schiöth, Helgi B.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Funktionell farmakologi och neurovetenskap.
    Chen, Wen-Yih
    Natl Cent Univ, Dept Chem & Mat Engn, 300 Zhongda Rd, Taoyuan 320, Taiwan..
    Ladbury, John E.
    Univ Leeds, Sch Mol & Cellular Biol, Leeds LS2 9JT, England..
    Grazulis, Saulius
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Sect Crystallog & Cheminformat, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    Matulis, Daumantas
    Vilnius Univ, Inst Biotechnol, Life Sci Ctr, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania..
    PLBD: protein-ligand binding database of thermodynamic and kinetic intrinsic parameters2023Ingår i: Database: The Journal of Biological Databases and Curation, E-ISSN 1758-0463, Vol. 2023, artikel-id baad040Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We introduce a protein-ligand binding database (PLBD) that presents thermodynamic and kinetic data of reversible protein interactions with small molecule compounds. The manually curated binding data are linked to protein-ligand crystal structures, enabling structure-thermodynamics correlations to be determined. The database contains over 5500 binding datasets of 556 sulfonamide compound interactions with the 12 catalytically active human carbonic anhydrase isozymes defined by fluorescent thermal shift assay, isothermal titration calorimetry, inhibition of enzymatic activity and surface plasmon resonance. In the PLBD, the intrinsic thermodynamic parameters of interactions are provided, which account for the binding-linked protonation reactions. In addition to the protein-ligand binding affinities, the database provides calorimetrically measured binding enthalpies, providing additional mechanistic understanding. The PLBD can be applied to investigations of protein-ligand recognition and could be integrated into small molecule drug design.

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  • 326.
    Liu, Ya-Jun
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för kvantkemi. Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi. Kvantkemi.
    Persson, Petter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för kvantkemi. Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi. Kvantkemi.
    Lunell, Sten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för kvantkemi. Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi. Kvantkemi.
    Multireference Calculations of the Phosphorescence and Photodissociation of Chlorobenzene2004Ingår i: Journal of Chemical Physics, Vol. 121, nr 11000Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Multireference complete active space self-consistent-field (CASSCF) and multireference CASSF second-order perturbation theory (MSCASPT2) calculations were performed on the ground state and a number of low-lying excited singlet and triplet states of chlorobenzene. The dual phosphorescence observed experimentally is clearly explained by the MSCASPT2 potential-energy curves. Experimental findings regarding the dissociation channels of chlorobenzene at 193, 248, and 266 nm are clarified from extensive theoretical information including all low-energy potential-energy curves.

  • 327.
    Liu, Ya-Jun
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för kvantkemi. Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi. Kvantkemi.
    Persson, Petter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för kvantkemi. Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi. Kvantkemi.
    Lunell, Sten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för kvantkemi. Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi. Kvantkemi.
    Theoretical Study of the Photodissociation of Low Lying Excited States of Hydrogen Peroxide2004Ingår i: Molecular Physics, Vol. 102, nr 2575Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In order to explain recent photofragmentation experiments of hydrogen peroxide, the vertical excitation energies, potential-energy curves and surfaces, harmonic vibrational frequencies, and transition moments for a number of low lying excited states were calculated. The accessibility of different photodissociation channels for different excitation wavelengths was discussed, on the basis of the calculated results.

  • 328. Liu, Ya-Jun
    et al.
    Roca-Sanjuan, Daniel
    Lindh, Roland
    Computational Photochemistry and Photophysics: the state of the art2012Ingår i: Photochemistry, The Royal Society of Chemistry , 2012, Vol. 40, s. 42-72Kapitel i bok, del av antologi (Övrigt vetenskapligt)
    Abstract [en]

    This review starts with the most basic concepts in photochemistry and photophysics, followed by a chronological introduction of theoretical methods and relevant applications in the history of computational photochemistry, along with the authors’ comments on the methodologies currently available for photochemical studies. Recent advances in the field are next summarized and discussed, focusing separately on methodology and computational techniques and some highlighted applied works carried out during the last two years on the topics of photodissociations, photostability, photodimerizations, photoisomerizations, proton/hydrogen transfer, photodecarboxylations, charge transport, bioexcimers, chemiluminescence and bioluminescence. We finish this review by conclusions and an outlook of the future.

  • 329.
    Lundberg, Marcus
    Stockholms universitet.
    Challenges in Enzyme Catalysis - Photosystem II and Orotidine Decarboxylase: A Density Functional Theory Treatment2005Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

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

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

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

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  • 330.
    Lundberg, Marcus
    Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo-ku, Kyoto 606-8103, Japan..
    Understanding Cross-Boundary Events in ONIOM QM:QM' Calculations2012Ingår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 33, nr 4, s. 406-415Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    QM:QM' models, where QM' is a fast molecular orbital method, offers advantages over standard quantum mechanics: molecular mechanics (QM:MM) models, especially in the description of charge transfer and mutual polarization between layers. The ONIOM QM:QM' scheme also allows for reactions across the layer boundary, but the understanding of these events is limited. To explain the factors that affect cross-boundary events, a set of proton transfer processes, including the acylation reaction in serine protease, have been investigated. For reactions inside out, that is, when a group breaks a bond in the high layer and forms a new bond with a group in the low layer, QM' methods that are overbinding relative to the QM method, for example, Hartree-Fock versus B3LYP, can severely overestimate the exothermicity of the reaction. This might lead to artificial reactivity across the QM:QM' boundary, a phenomenon called model escape. The accuracy for reactions that occur outside in, that is, when a group in the low layer forms a new bond with the high layer, is mainly determined by the QM' calculation. Cross-boundary reactions should generally be avoided in the present ONIOM scheme. Fortunately, a better understanding of these events makes it easy to design stable ONIOM QM:QM' models, for example, by choosing a proper model system. Importantly, an accurate description of cross-boundary reactions would open up possibilities to simulate chemical reactions without a priori limiting the reactivity in the design of the computational model. Challenges to implement a simulation scheme (ONIOM-XR) that can automatically handle chemical reactions between different layers are briefly discussed.

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  • 331.
    Lundberg, Marcus
    et al.
    Stockholm University.
    Blomberg, Margareta R. A.
    Siegbahn, Per E. M.
    Developing active site models of ODCase: from large quantum models to a QM/MM approach2004Ingår i: Topics in current chemistry, ISSN 0340-1022, E-ISSN 1436-5049, Vol. 238, s. 79-112Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The catalytic mechanism of orotidine monophosphate decarboxylase (ODCase) has been modeled using density functional theory with the B3LYP functional. Barriers for three different mechanisms have been calculated using large QM and QM/MM models. A concerted protonation mechanism where TS stabilization is provided only by the positive Lys93 has a high barrier around 35 kcal/mol. QM/MM calculations confirm the results obtained using QM models. For a base protonation mechanism, 02 protonation gives a barrier for decarboxylation of 26 kcal/mol. Extensions to this QM model indicate that the cost of protonation may be inderestimated and the support for the base protonation mechanism is uncertain. An initial QM/MM investigation of a stepwise mechanism, where water molecules seem to play an important role for TS stabilization, gives the most promising results with an estimated barrier of 22 kcal/mol.

  • 332.
    Lundberg, Marcus
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Borowski, Tomasz
    Polish Acad Sci, Jerzy Haber Inst Catalysis & Surface Chem, PL-30239 Krakow, Poland.
    Oxoferryl species in mononuclear non-heme iron enzymes: biosynthesis, properties and reactivity from a theoretical perspective2013Ingår i: Coordination chemistry reviews, ISSN 0010-8545, E-ISSN 1873-3840, Vol. 257, nr 1, s. 277-289Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Mononuclear non-heme iron enzymes perform a wide range of chemical reactions. Still, the catalytic mechanisms are usually remarkably similar, with formation of a key oxoferryl (Fe(IV)=O) intermediate through two well-defined steps. First, two-electron reduction of dioxygen occurs to form a peroxo species, followed by O-O bond cleavage. Even though the peroxo species have different chemical character in various enzyme families, the analogies between different enzymes in the group make it an excellent base for investigating factors that control metal-enzyme catalysis. We have used density-functional theory to model the complete chemical reaction mechanisms of several enzymes, e.g., for aromatic and aliphatic hydroxylation, chlorination, and oxidative ring-closure. Reactivity of the Fe(IV)=O species is discussed with focus on electronic and steric factors determining the preferred reaction path. Various spin states are compared, as well as the two reaction channels that stem from involvement of different frontier molecular orbitals of Fe(IV)=O. Further, the two distinctive species of Fe(IV)=O, revealed by Mossbauer spectroscopy, and possibly relevant for specificity of aliphatic chlorination, can be identified. The stability of the modeling results have been analyzed using a range of approaches, from active-site models to multi-scale models that include classical free-energy contributions. Large effects from an explicit treatment of the protein matrix (similar to 10 kcal/mol) can be observed for O-2 binding, electron-transfer and product release.

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  • 333.
    Lundberg, Marcus
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Delcey, Mickaël G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Multiconfigurational Approach to X-ray Spectroscopy of Transition Metal Complexes2019Ingår i: Transition Metals in Coordination Environments: Computational chemistry and catalysis viewpoints / [ed] Ewa Broclawik; Tomasz Borowski; Mariusz Radoń, Cham: Springer, 2019, s. 185-217Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

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

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  • 334.
    Lundberg, Marcus
    et al.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.
    Kroll, Thomas
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.
    DeBeer, Serena
    Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Bergmann, Uwe
    Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Wilson, Samuel A.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA.
    Glatzel, Pieter
    ESRF, F-38043 Grenoble 9, France.
    Nordlund, Dennis
    Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Hedman, Britt
    Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Hodgson, Keith Owen
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA; Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Solomon, Edward I.
    Stanford Univ, Dept Chem, Stanford, CA 94305 USA; Stanford Univ, SLAC Natl Accelerator Lab, Stanford Synchrotron Radiat Lightsource, Menlo Pk, CA 94025 USA.
    Metal-ligand Covalency of Iron Complexes from High-Resolution Resonant Inelastic X-ray Scattering2013Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 135, nr 45, s. 17121-17134Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Data from Kα resonant inelastic X-ray scattering (RIXS) have been used to extract electronic structure information, i.e., the covalency of metal–ligand bonds, for four iron complexes using an experimentally based theoretical model. Kα RIXS involves resonant 1s→3d excitation and detection of the 2p→1s (Kα) emission. This two-photon process reaches similar final states as single-photon L-edge (2p→3d) X-ray absorption spectroscopy (XAS), but involves only hard X-rays and can therefore be used to get high-resolution L-edge-like spectra for metal proteins, solution catalysts and their intermediates. To analyze the information content of Kα RIXS spectra, data have been collected for four characteristic σ-donor and π-back-donation complexes: ferrous tacn [FeII(tacn)2]Br2, ferrocyanide [FeII(CN)6]K4, ferric tacn [FeIII(tacn)2]Br3 and ferricyanide [FeIII(CN)6]K3. From these spectra metal–ligand covalencies can be extracted using a charge-transfer multiplet model, without previous information from the L-edge XAS experiment. A direct comparison of L-edge XAS and Kα RIXS spectra show that the latter reaches additional final states, e.g., when exciting into the eg (σ*) orbitals, and the splitting between final states of different symmetry provides an extra dimension that makes Kα RIXS a more sensitive probe of σ-bonding. Another key difference between L-edge XAS and Kα RIXS is the π-back-bonding features in ferro- and ferricyanide that are significantly more intense in L-edge XAS compared to Kα RIXS. This shows that two methods are complementary in assigning electronic structure. The Kα RIXS approach can thus be used as a stand-alone method, in combination with L-edge XAS for strongly covalent systems that are difficult to probe by UV/vis spectroscopy, or as an extension to conventional absorption spectroscopy for a wide range of transition metal enzymes and catalysts.

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  • 335.
    Lundberg, Marcus
    et al.
    Kyoto University.
    Morokuma, Keiji
    The ONIOM Method and its Applications to Enzymatic Reactions2009Ingår i: Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications / [ed] T.-S. Lee and D.M. York, Springer Verlag , 2009Kapitel i bok, del av antologi (Övrigt vetenskapligt)
  • 336.
    Lundberg, Marcus
    et al.
    Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
    Nishimoto, Y.
    Nagoya Univ, Grad Sch Sci, Dept Chem, Chikusa Ku, Nagoya, Aichi 4648601, Japan.
    Irle, S.
    Nagoya Univ, Grad Sch Sci, Dept Chem, Chikusa Ku, Nagoya, Aichi 4648601, Japan.
    Delocalization errors in a hubbard-€like model: Consequences for density-€functional tight-€binding calculations of molecular systems2012Ingår i: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 112, nr 6, s. 1701-1711Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    It has previously been shown that self-consistent-charge density-functional tight-binding (SCC-DFTB) suffers from a self-interaction error that leads to artificial stabilization of delocalized states. The effects of the error are similar to those appearing for many density functionals. In SCC-DFTB, the delocalization error is inherently related to the use of a Hubbard-like term to describe on-site charge interactions. The mathematical simplicity of this Hubbard-like term makes it easy to estimate if a complex system is subject to artificial stabilization of delocalized states and to quantitatively predict the delocalization error in the system energy at large fragment separation. The error is directly proportional to the on-site charge interaction term but decreases as the fragments become more asymmetric. The difference in orbital energies required to eliminate the delocalization error becomes equal to the Hubbard-like parameter of the fragment with the highest electron affinity. However, in most cases, the localized state will be favored by spin polarization, fragment repulsion, solvent effects, and large reorganization energies, in analogy to density functional theory, from which SCC-DFTB is derived. The presented analysis gives an early indication whether the standard approach is suitable, or if a different method is required to correct the delocalization error. In addition to cationic dimers, we discuss the effects of the delocalization error for asymmetric systems, bond dissociation of neutral molecules, and the description of mixed valence transition metal systems, exemplified by the enzyme cytochrome oxidase.

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  • 337.
    Lundqvist, Maria J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Quantum Chemical Modeling of Dye-Sensitized Titanium Dioxide: Ruthenium Polypyridyl and Perylene Dyes, TiO2 Nanoparticles, and Their Interfaces2006Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Quantum chemical calculations have been used to model dye-sensitized nanostructured titanium dioxide systems that can be used in solar cells for solar energy to electricity conversion. Structural, electronic and spectral properties of isolated dyes and both bare and dye-sensitized TiO2 have been calculated with density functional theory, providing detailed information about both the separate parts and the dye-TiO2 interface.

    The connection between the geometry, the ligand field splitting and the lifetime of the triplet metal-to-ligand charge transfer (MLCT) excited state has been explored for a series of ruthenium polypyridyl dyes. Moreover, the relative energetics of MLCT and metal centered triplet excited states have been studied for a number of such systems. It was found that small alterations of the polypyridyl ligands can result in significant changes in ligand field splitting and in the energetics of the triplet states.

    Attachment of the dyes to the TiO2 surface is achieved via anchor and spacer groups. The influence of such groups on various properties of the dye and their ability to act as mediators of photo-induced surface electron transfer has been studied. Delocalization of the lowest unoccupied dye orbital onto the spacer and/or anchor group indicates that certain unsaturated groups can mediate electron transfer.

    With a combination of methods that enables efficient computations and a scheme for construction of metal oxide clusters, chemical models for bare TiO2 nanocrystals in the 1-2 nm size range have been developed. The electronic structures show well-developed band structures with essentially no electronic band gap defect states.

    Atomistic models of the interface between TiO2 nanocrystals and Ru(II)-bis-terpyridine dyes, the so-called N3 dye as well as perylene dyes are reported. Electronic coupling strengths, which provide estimates for the electron injection times, are extracted from the interfacial electronic structure and the lowest electronic excitations are calculated.

    Delarbeten
    1. Structural and Spectral Investigation of Ruthenium(II) Polypyridyl Complexes by DFT Calculations
    Öppna denna publikation i ny flik eller fönster >>Structural and Spectral Investigation of Ruthenium(II) Polypyridyl Complexes by DFT Calculations
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    (Engelska)Ingår i: Inorganic ChemistryArtikel i tidskrift (Refereegranskat) Submitted
    Identifikatorer
    urn:nbn:se:uu:diva-95090 (URN)
    Tillgänglig från: 2006-11-09 Skapad: 2006-11-09 Senast uppdaterad: 2013-05-17Bibliografiskt granskad
    2. Ruthenium complexes of bipyridyl(pyridyl)alkane ligands: Effect of methylene or iso-propylene bridge on structural and photophysical properties
    Öppna denna publikation i ny flik eller fönster >>Ruthenium complexes of bipyridyl(pyridyl)alkane ligands: Effect of methylene or iso-propylene bridge on structural and photophysical properties
    Visa övriga...
    (Engelska)Manuskript (Övrig (populärvetenskap, debatt, mm))
    Identifikatorer
    urn:nbn:se:uu:diva-94851 (URN)
    Tillgänglig från: 2006-09-22 Skapad: 2006-09-22 Senast uppdaterad: 2011-03-21
    3. Calculated optoelectronic properties of Ruthenium tris-bipyridine dyes containing oligophenyleneethynylene rigid rod linkers in different chemical environments
    Öppna denna publikation i ny flik eller fönster >>Calculated optoelectronic properties of Ruthenium tris-bipyridine dyes containing oligophenyleneethynylene rigid rod linkers in different chemical environments
    2007 (Engelska)Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 8, s. 1487-1497Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Ruthenium tris-bipyridine dyes containing oligophenyleneethynylene (OPE) rigid rod linker groups ([Ru(bpy)3]2+, [Ru(bpy)2bpy-E-Ipa]2+, [Ru(bpy)2bpy-E-Ph-E-Ipa]2+, and [Ru(bpy)2bpy-E-Bco-E-Ipa]2+, where bpy = 2,2'-bipyridine, E = ethynylene, Ph = p-phenylene, Bco = bicyclo[2.2.2]octylene, and Ipa = isophthalic acid) have been investigated using DFT and TD-DFT calculations to elucidate the influence of the rigid rod on their optoelectronic properties. Experimentally observed differences in the optical absorption for the different complexes are discussed on the basis of TD-DFT simulated absorption spectra. A comparison of the calculated optoelectronic properties of [Ru(bpy)2bpy-E-Ph-E-Ipa]2+ in different chemical environments, that is, in different solvents and with or without counter ions, suggests that both the absorption spectra and the redox properties of the dyes with OPE rods are sensitive to the environment. The calculations show that spurious low-energy charge-transfer excitations present in the TD-DFT calculations of the extended systems in vacuum are removed when the environment is included in the calculations.

    Nationell ämneskategori
    Kemi
    Identifikatorer
    urn:nbn:se:uu:diva-94852 (URN)10.1021/jp064219x (DOI)000244348100013 ()17279731 (PubMedID)
    Tillgänglig från: 2006-09-22 Skapad: 2006-09-22 Senast uppdaterad: 2022-01-28Bibliografiskt granskad
    4. Spacer and anchor effects on the electronic coupling in Ruthenium-bis-terpyridine dye-sensitized TiO2 nanocrystals studied by DFT
    Öppna denna publikation i ny flik eller fönster >>Spacer and anchor effects on the electronic coupling in Ruthenium-bis-terpyridine dye-sensitized TiO2 nanocrystals studied by DFT
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    2006 (Engelska)Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 110, nr 41, s. 20513-20525Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Structural and electronic properties of TiO2 nanoparticles sensitized with a set of Ru(II)(tpy)2 based dyes have been investigated using density functional theory (DFT) calculations combined with time-dependent (TD) DFT calculations. The effects of carboxylic and phosphonic acid anchor groups, as well as a phenylene spacer group, on the optical properties of the dyes and the electronic interactions in the dye-sensitized TiO2 nanoparticles have been investigated. Inclusion of explicit counterions in the modeling shows that the description of the environment is important in order to obtain a realistic interfacial energy level alignment. A comparison of calculated electronic coupling strengths suggests that both the nature of the anchor group and the inclusion of the phenylene spacer group are capable of significantly influencing electron-transfer rates across the dye-metal oxide interface.

    Nationell ämneskategori
    Kemi
    Identifikatorer
    urn:nbn:se:uu:diva-94853 (URN)10.1021/jp064045j (DOI)000241192200066 ()17034238 (PubMedID)
    Tillgänglig från: 2006-09-22 Skapad: 2006-09-22 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
    5. DFT study of bare and dye-sensitized TiO2 clusters and nanocrystals
    Öppna denna publikation i ny flik eller fönster >>DFT study of bare and dye-sensitized TiO2 clusters and nanocrystals
    2006 (Engelska)Ingår i: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 106, nr 15, s. 3214-3234Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Structural and electronic properties of bare and dye-sensitized TiO2 clusters and nanoparticles with sizes of ?2 nm have been studied by density functional theory (DFT) calculations. Starting from truncated bulk lattice structures, the degree of structural reorganization, including the formation of Ti dbond O surface species, of bare TiO2 anatase nanocrystals, is found to be sensitive to the quality of the computational method. The electronic structures of optimized 1-2 nm nanoparticles show well-developed band structures with essentially no electronic bandgap defect states. Significant bandgap broadening due to quantum size effects is observed as the size of the nanocrystals is reduced from 2 nm to 1 nm in diameter, but further bandgap widening is limited by increasingly severe competing surface defect sites as the particles become smaller than ?1 nm in diameter. The applicability of the TiO2 nanocrystals in modeling the electronic structure and electronic coupling at dye-sensitized TiO2 nanocrystal interfaces has been investigated by attachment of pyridine to one of the nanoparticle models via phosphonic or carboxylic acid anchor groups.

    Nyckelord
    DFT, TiO2, cluster, nanocrystal, surface electron transfer
    Nationell ämneskategori
    Kemi
    Identifikatorer
    urn:nbn:se:uu:diva-94854 (URN)10.1002/qua.21088 (DOI)
    Tillgänglig från: 2006-09-22 Skapad: 2006-09-22 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
    6. Quantum chemical calculations of the influence of anchor-cum-spacer groups on femtosecond electron transfer times in dye-sensitized semiconductor nanocrystals
    Öppna denna publikation i ny flik eller fönster >>Quantum chemical calculations of the influence of anchor-cum-spacer groups on femtosecond electron transfer times in dye-sensitized semiconductor nanocrystals
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    2006 (Engelska)Ingår i: Journal of Chemical Theory and Computation, Vol. 2, nr 2, s. 441-451Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-94855 (URN)
    Tillgänglig från: 2006-09-22 Skapad: 2006-09-22 Senast uppdaterad: 2009-03-26Bibliografiskt granskad
    7. Calculated structural and electronic interactions of the Ruthenium dye N3 with a titanium dioxide nanocrystal
    Öppna denna publikation i ny flik eller fönster >>Calculated structural and electronic interactions of the Ruthenium dye N3 with a titanium dioxide nanocrystal
    2005 (Engelska)Ingår i: Journal of Physical Chemistry B, Vol. 109, nr 24, s. 11918-11924Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-94856 (URN)
    Tillgänglig från: 2006-09-22 Skapad: 2006-09-22 Senast uppdaterad: 2009-03-26Bibliografiskt granskad
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  • 338.
    Lundqvist, Maria J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Fysiska institutionen. Institutionen för kvantkemi. Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Theoretical Studies of Biochemical Reactions Involving Hydroxyl Radicals2002Licentiatavhandling, monografi (Övrigt vetenskapligt)
  • 339.
    Lunell, Sten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Kvantkemi: kemi utan provrör2009Ingår i: Annales Academiae regiae scientiarum Upsaliensis: ungl. Vetenskapssamhällets i Uppsala årsbok.Vol 37, 2007-2008, Stockholm: Kungl. Vetenskapssamhället i Uppsala , 2009, s. 111-115Kapitel i bok, del av antologi (Övrigt vetenskapligt)
  • 340.
    Lunell, Sten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för kvantkemi. Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi. Kvantkemi.
    Kvantmekanik - filosofi eller ingenjörskonst?2001Ingår i: Acta Academiæ Regiæ Scientiaum Upsaliensis, 2001, s. 295-299Kapitel i bok, del av antologi (Övrigt vetenskapligt)
  • 341.
    Luo, Jinghui
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Biophysical Structural Chemistry, University of Leiden.
    van Loo, Bert
    University of Cambridge, Department of Biochemistry.
    Kamerlin, Lynn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Beräknings- och systembiologi.
    Examining the promiscuous phosphatase activity of Pseudomonas aeruginosa arylsulfatase: A comparison to analogous phosphatases2012Ingår i: Proteins: Structure, Function and Bioinformatics, ISSN 1097-0134, Vol. 80, nr 4, s. 1211-1226Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Pseudomonas aeruginosa arylsulfatase (PAS) is a bacterial sulfatase capable ofhydrolyzing a range of sulfate esters. Recently, it has been demonstrated to also show very high proficiency for phosphate ester hydrolysis. Such proficient catalytic promiscuity is significant, as promiscuity has been suggested to play an important role in enzyme evolution. Additionally, a comparative study of the hydrolyses of the p-nitrophenyl phosphate and sulfate monoesters in aqueous solution has demonstrated that despite superficial similarities, the two reactions proceed through markedly different transition states with very different solvation effects, indicating that the requirements for the efficient catalysis of the two reactions by an enzyme will also be very different (and yet they are both catalyzed by thesame active site). This work explores the promiscuous phosphomonoesterase activity ofPAS. Specifically, we have investigated the identity of the most likely base for the initial activation of the unusual formylglycine hydrate nucleophile (which is common to many sulfatases), and demonstrate that a concerted substrate-as-base mechanism is fully consistent with the experimentally observed data. This is very similar to other related systems, and suggests that, as far as the phosphomonoesterase activity of PAS is concerned, the sulfatase behaves like a classical phosphatase, despite the fact that such a mechanism is unlikely to be available to the native substrate (based on pKa considerations and studies of model systems). Understanding such catalytic versatility can be used to design novel artificial enzymes that are far more proficient than the current generation ofdesigner enzymes. 

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  • 342.
    Mace, Amber
    et al.
    Stockholm Univ, Dept Mat & Environm Chem, SE-10691 Stockholm, Sweden.;Stockholm Univ, Berzelii Ctr EXSELENT Porous Mat, SE-10691 Stockholm, Sweden..
    Leetmaa, Mikael
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Laaksonen, Aatto
    Stockholm Univ, Dept Mat & Environm Chem, SE-10691 Stockholm, Sweden.;Stockholm Univ, Berzelii Ctr EXSELENT Porous Mat, SE-10691 Stockholm, Sweden..
    Temporal Coarse Graining of CO2 and N-2 Diffusion in Zeolite NaKA: From the Quantum Scale to the Macroscopic2015Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, nr 10, s. 4850-4860Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The kinetic CO2-over-N-2 sieving capabilities in narrow pore zeolites are dependent on the free-energy barriers of diffusion between the zeolite pores, which can be fine-tuned by altering the framework composition. An ab initio level of theory is necessary to accurately compute the energy barriers, whereas it is desirable to predict the macroscopic scale diffusion for industrial applications. Using ab initio molecular dynamics on the picosecond time scale, the free-energy barriers of diffusion can be predicted for different local pore properties in order to identify those that are rate-determining for the pore-to-pore diffusion. Specifically, we investigate the effects of the Na+-to-K+ exchange at the different cation sites and the CO, loading in Zeolite NaKA. These computed energy barriers are then used as input for the Kinetic Monte Carlo method, coarse graining the dynamic simulation steps to the pore-to-pore diffusion. With this approach, we simulate how the identified rate-determining properties as well as the application of skin-layer surface defects affect the diffusion driven uptake in a realistic Zeolite NaKA powder particle model on a macroscopic time scale. Lastly, we suggest a model by combining these effects, which provides an excellent agreement with the experimental CO2 and N-2 uptake behaviors presented by Liu et Commun. 2010, 46, 4502-4504).

  • 343.
    Magdau, Ioan-Bogdan
    et al.
    Univ Cambridge, Engn Lab, Trumpington St, Cambridge CB2 1PZ, England..
    Arismendi-Arrieta, Daniel J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Strukturkemi.
    Smith, Holly E.
    Univ Cambridge, Yusuf Hamid Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England..
    Grey, Clare P.
    Univ Cambridge, Yusuf Hamid Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England..
    Hermansson, Kersti
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Strukturkemi.
    Csanyi, Gabor
    Univ Cambridge, Engn Lab, Trumpington St, Cambridge CB2 1PZ, England..
    Machine learning force fields for molecular liquids: Ethylene Carbonate/Ethyl Methyl Carbonate binary solvent2023Ingår i: npj Computational Materials, E-ISSN 2057-3960, Vol. 9, artikel-id 146Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Highly accurate ab initio molecular dynamics (MD) methods are the gold standard for studying molecular mechanisms in the condensed phase, however, they are too expensive to capture many key properties that converge slowly with respect to simulation length and time scales. Machine learning (ML) approaches which reach the accuracy of ab initio simulation, and which are, at the same time, sufficiently affordable hold the key to bridging this gap. In this work we present a robust ML potential for the EC:EMC binary solvent, a key component of liquid electrolytes in rechargeable Li-ion batteries. We identify the necessary ingredients needed to successfully model this liquid mixture of organic molecules. In particular, we address the challenge posed by the separation of scale between intra- and inter-molecular interactions, which is a general issue in all condensed phase molecular systems.

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  • 344.
    Mahida, H. R.
    et al.
    Veer Narmad South Gujarat Univ, Dept Phys, Surat 395007, India.
    Singh, Deobrat
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Sonvane, Yogesh
    Sardar Vallabhbhai Natl Inst Technol, Dept Phys, Adv Mat Lab, Surat 395007, India.
    Gupta, Sanjeev K.
    St Xaviers Coll, Dept Phys & Elect, Computat Mat & Nanosci Grp, Ahmadabad 380009, Gujarat, India.
    Thakor, P. B.
    Veer Narmad South Gujarat Univ, Dept Phys, Surat 395007, India.
    Ahuja, Rajeev
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori. Royal Inst Technol KTH, Dept Mat Sci & Engn, Appl Mat Phys, S-10044 Stockholm, Sweden.
    Hydrogenation and oxidation enhances the thermoelectric performance of Si2BN monolayer2021Ingår i: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 45, nr 8, s. 3892-3900Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the present study, we have investigated the structural, electronic, and charge transport properties of pristine, hydrogenated, and oxidized Si2BN monolayers via first-principles calculations based on density functional theory (DFT). Hydrogenation and oxidation of Si2BN monolayer display negative binding energy therefore these structures are energetically favorable. The electronic band structure engineered by the hydrogenation and oxidation of the Si2BN monolayer transformed from metallic to semiconducting nature. Due to the hydrogenation and oxidation of Si2BN, the monolayer also changes from a planar structure to a non-planar structure. The hydrogenated and oxidized structures led to high thermoelectric performance as compared to the pristine Si2BN monolayer. When the Si2BN monolayer is hydrogenated and oxidized, its electronic figure of merit (ZTe) significantly enhanced from 0.45 to 0.99. The investigation results suggest a practical approach for improving the performance of thermoelectric properties of the Si2BN monolayer.

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  • 345.
    Mahyaeh, Iman
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Kvantmateriens teori.
    Köhler, Thomas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Black-Schaffer, Annica M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Kantian, Adrian
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori. Heriot Watt Univ, Inst Photon & Quantum Sci, SUPA, Edinburgh EH14 4AS, Midlothian, Scotland.
    Superconducting pairing from repulsive interactions of fermions in a flat-band system2022Ingår i: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 106, nr 12, artikel-id 125155Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Fermion systems with flat bands can boost superconductivity by enhancing the density of states at the Fermi level. We use quasiexact numerical methods to show that repulsive interactions between spinless fermions in a one-dimensional (1D) flat-band system, the Creutz ladder, give a finite pairing energy that increases with repulsion, though charge quasiorder remains dominant. Adding an attractive component shifts the balance in favor of superconductivity and the interplay of two flat bands further yields a remarkable enhancement of superconductivity, well outside of known paradigms for 1D fermions.

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    FULLTEXT01
  • 346.
    Malyi, Oleksandr, I
    et al.
    Univ Oslo, Ctr Mat Sci & Nanotechnol, Dept Phys, POB 1048, NO-0316 Oslo, Norway.
    Sopiha, Kostiantyn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Tekniska sektionen, Institutionen för teknikvetenskaper, Fasta tillståndets elektronik.
    Persson, Clas
    Univ Oslo, Ctr Mat Sci & Nanotechnol, Dept Phys, POB 1048, NO-0316 Oslo, Norway.
    Noble gas as a functional dopant in ZnO2019Ingår i: npj Computational Materials, E-ISSN 2057-3960, Vol. 5, artikel-id 38Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Owing to fully occupied orbitals, noble gases are considered to be chemically inert and to have limited effect on materials properties under standard conditions. However, using first-principles calculations, we demonstrate herein that the insertion of noble gas (i.e. He, Ne, or Ar) in ZnO results in local destabilization of electron density of the material driven by minimization of an unfavorable overlap of atomic orbitals of the noble gas and its surrounding atoms. Specifically, the noble gas defect (interstitial or substitutional) in ZnO pushes the electron density of its surrounding atoms away from the defect. Simultaneously, the host material confines the electron density of the noble gas. As a consequence, the interaction of He, Ne, or Ar with O vacancies of ZnO in different charge states q (ZnO:V-O(q)) affects the vacancy stability and their electronic structures. Remarkably, we find that the noble gas is a functional dopant that can delocalize the deep in-gap V-O(q) states and lift electrons associated with the vacancy to the conduction band.

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  • 347.
    Manni, Giovanni Li
    et al.
    Max Planck Inst Solid State Res, Elect Struct Theory Dept, D-70569 Stuttgart, Germany..
    Fernández Galván, Ignacio
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi.
    Alavi, Ali
    Max Planck Inst Solid State Res, Elect Struct Theory Dept, D-70569 Stuttgart, Germany.;Univ Cambridge, Yusuf Hamied Dept Chem, Cambridge CB2 1EW, England..
    Aleotti, Flavia
    Univ Bologna, Dept Ind Chem Toso Montanari, I-40136 Bologna, Italy..
    Aquilante, Francesco
    Ecole Polytech Fed Lausanne, Theory & Simulat Mat THEOS, CH-1015 Lausanne, Switzerland.;Ecole Polytech Fed Lausanne, Natl Ctr Computat Design & Discovery Novel Mat MA, CH-1015 Lausanne, Switzerland..
    Autschbach, Jochen
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA..
    Avagliano, Davide
    Univ Bologna, Dept Ind Chem Toso Montanari, I-40136 Bologna, Italy..
    Baiardi, Alberto
    Swiss Fed Inst Technol, Lab Phys Chem, CH-8093 Zurich, Switzerland..
    Bao, Jie J.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Battaglia, Stefano
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi. Univ Zurich, Dept Chem, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Birnoschi, Letitia
    Univ Manchester, Dept Chem, Manchester M13 9PL, Lancs, England..
    Blanco-Gonzalez, Alejandro
    Bowling Green State Univ, Chem Dept, Bowling Green, OH 43403 USA..
    Bokarev, Sergey I.
    Tech Univ Munich, Sch Nat Sci, Chem Dept, D-85748 Garching, Germany.;Univ Rostock, Inst Phys, D-18059 Rostock, Germany..
    Broer, Ria
    Univ Groningen, Zernike Inst Adv Mat, Theoret Chem, NL-9747 AG Groningen, Netherlands..
    Cacciari, Roberto
    Univ Siena, Dipartimento Biotecnol Chim & Farm, I-53100 Siena, Italy..
    Calio, Paul B.
    Univ Chicago, James Franck Inst, Pritzker Sch Mol Engn, Dept Chem,Chicago Ctr Theoret Chem, Chicago, IL 60637 USA..
    Carlson, Rebecca K.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Couto, Rafael Carvalho
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Div Theoret Chem & Biol, SE-10691 Stockholm, Sweden..
    Cerdan, Luis
    Univ Valencia, Inst Ciencia Mol, Paterna 46980, Spain.;CSIC, IO, Madrid 28006, Spain..
    Chibotaru, Liviu F.
    Katholieke Univ Leuven, Dept Chem, B-3001 Leuven, Belgium..
    Chilton, Nicholas F.
    Univ Manchester, Dept Chem, Manchester M13 9PL, Lancs, England..
    Church, Jonathan Richard
    Hebrew Univ Jerusalem, Inst Chem, IL-91904 Jerusalem, Israel..
    Conti, Irene
    Univ Bologna, Dept Ind Chem Toso Montanari, I-40136 Bologna, Italy..
    Coriani, Sonia
    Tech Univ Denmark, Dept Chem, DK-2800 Lyngby, Denmark..
    Cuellar-Zuquin, Juliana
    Univ Valencia, Inst Ciencia Mol, Paterna 46980, Spain..
    Daoud, Razan E.
    Univ Siena, Dipartimento Biotecnol Chim & Farm, I-53100 Siena, Italy..
    Dattani, Nike
    HPQC Labs, Waterloo, ON N2T 2K9, Canada.;HPQC Coll, Waterloo, ON N2T 2K9, Canada..
    Decleva, Piero
    Univ Trieste, CNR, IOM, I-34121 Trieste, Italy.;Univ Trieste, Dipartimento Sci Chim & Farmaceut, I-34121 Trieste, Italy..
    de Graaf, Coen
    Univ Rovira & Virgili, Dept Phys & Inorgan Chem, Tarragona 43007, Spain.;ICREA, Barcelona 08010, Spain..
    Delcey, Mickael G.
    KTH Royal Inst Technol, Sch Engn Sci Chem Biotechnol & Hlth, Div Theoret Chem & Biol, SE-10691 Stockholm, Sweden..
    De Vico, Luca
    Univ Siena, Dipartimento Biotecnol Chim & Farm, I-53100 Siena, Italy..
    Dobrautz, Werner
    Chalmers Univ Technol, Dept Chem & Chem Engn, S-41296 Gothenburg, Sweden..
    Dong, Sijia S.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Northeastern Univ, Dept Chem & Chem Biol, Dept Phys, Boston, MA 02115 USA.;Northeastern Univ, Dept Chem Engn, Boston, MA 02115 USA..
    Feng, Rulin
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA.;Fudan Univ, Dept Chem, Shanghai 200433, Peoples R China..
    Ferre, Nicolas
    Aix Marseille Univ, CNRS, UMR 7273, ICR, F-13013 Marseille, France..
    Filatov (Gulak), Michael
    Kyungpook Natl Univ, Dept Chem, Daegu 702701, South Korea..
    Gagliardi, Laura
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Chicago, James Franck Inst, Pritzker Sch Mol Engn, Dept Chem,Chicago Ctr Theoret Chem, Chicago, IL 60637 USA..
    Garavelli, Marco
    Univ Bologna, Dept Ind Chem Toso Montanari, I-40136 Bologna, Italy..
    Gonzalez, Leticia
    Univ Vienna, Inst Theoret Chem, Fac Chem, A-1090 Vienna, Austria..
    Guan, Yafu
    Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Dalian 116023, Peoples R China.;Chinese Acad Sci, Dalian Inst Chem Phys, Ctr Theoret Computat Chem, Dalian 116023, Peoples R China..
    Guo, Meiyuan
    SLAC Natl Accelerator Lab, SSRL, Menlo Pk, CA 94025 USA..
    Hennefarth, Matthew R.
    Univ Chicago, James Franck Inst, Pritzker Sch Mol Engn, Dept Chem,Chicago Ctr Theoret Chem, Chicago, IL 60637 USA..
    Hermes, Matthew R.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Chicago, James Franck Inst, Pritzker Sch Mol Engn, Dept Chem,Chicago Ctr Theoret Chem, Chicago, IL 60637 USA..
    Hoyer, Chad E.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Washington, Dept Chem, Seattle, WA 98195 USA..
    Huix-Rotllant, Miquel
    Aix Marseille Univ, CNRS, UMR 7273, ICR, F-13013 Marseille, France..
    Jaiswal, Vishal Kumar
    Univ Bologna, Dept Ind Chem Toso Montanari, I-40136 Bologna, Italy..
    Kaiser, Andy
    Univ Rostock, Inst Phys, D-18059 Rostock, Germany..
    Kaliakin, Danil S.
    Bowling Green State Univ, Chem Dept, Bowling Green, OH 43403 USA..
    Khamesian, Marjan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi.
    King, Daniel S.
    Univ Chicago, James Franck Inst, Pritzker Sch Mol Engn, Dept Chem,Chicago Ctr Theoret Chem, Chicago, IL 60637 USA..
    Kochetov, Vladislav
    Univ Rostock, Inst Phys, D-18059 Rostock, Germany..
    Krosnicki, Marek
    Kumaar, Arpit Arun
    HPQC Labs, Waterloo, ON N2T 2K9, Canada..
    Larsson, Ernst D.
    Lund Univ, Div Theoret Chem, Chem Ctr, SE-22100 Lund, Sweden..
    Lehtola, Susi
    Mol Sci Software Inst, Blacksburg, VA 24061 USA.;Univ Helsinki, Dept Chem, FI-00014 Helsinki, Finland..
    Lepetit, Marie-Bernadette
    Inst Neel, Condensed Matter Theory Grp, F-38042 Grenoble, France.;Inst Laue Langevin, Theory Grp, F-38042 Grenoble, France..
    Lischka, Hans
    Texas Tech Univ, Dept Chem & Biochem, Lubbock, TX 79409 USA..
    Rios, Pablo Lopez
    Max Planck Inst Solid State Res, Elect Struct Theory Dept, D-70569 Stuttgart, Germany..
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Ma, Dongxia
    Max Planck Inst Solid State Res, Elect Struct Theory Dept, D-70569 Stuttgart, Germany.;Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Mai, Sebastian
    Univ Vienna, Inst Theoret Chem, Fac Chem, A-1090 Vienna, Austria..
    Marquetand, Philipp
    Univ Vienna, Inst Theoret Chem, Fac Chem, A-1090 Vienna, Austria..
    Merritt, Isabella C. D.
    Nantes Univ, CNRS, CEISAM, F-44000 Nantes, France..
    Montorsi, Francesco
    Univ Bologna, Dept Ind Chem Toso Montanari, I-40136 Bologna, Italy..
    Morchen, Maximilian
    Swiss Fed Inst Technol, Lab Phys Chem, CH-8093 Zurich, Switzerland..
    Nenov, Artur
    Univ Bologna, Dept Ind Chem Toso Montanari, I-40136 Bologna, Italy..
    Nguyen, Vu Ha Anh
    Nishimoto, Yoshio
    Kyoto Univ, Grad Sch Sci, Kyoto 6068502, Japan..
    Oakley, Meagan S.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Olivucci, Massimo
    Bowling Green State Univ, Chem Dept, Bowling Green, OH 43403 USA.;Univ Siena, Dipartimento Biotecnol Chim & Farm, I-53100 Siena, Italy..
    Oppel, Markus
    Univ Vienna, Inst Theoret Chem, Fac Chem, A-1090 Vienna, Austria..
    Padula, Daniele
    Univ Siena, Dipartimento Biotecnol Chim & Farm, I-53100 Siena, Italy..
    Pandharkar, Riddhish
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Chicago, James Franck Inst, Pritzker Sch Mol Engn, Dept Chem,Chicago Ctr Theoret Chem, Chicago, IL 60637 USA..
    Phung, Quan Manh
    Plasser, Felix
    Loughborough Univ, Dept Chem, Loughborough LE11 3TU, Leics, England..
    Raggi, Gerardo
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi. Quantum Mat & Software LTD, London EC1V 2NX, England..
    Rebolini, Elisa
    Inst Laue Langevin, Sci Comp Grp, F-38042 Grenoble, France..
    Reiher, Markus
    Swiss Fed Inst Technol, Lab Phys Chem, CH-8093 Zurich, Switzerland..
    Rivalta, Ivan
    Univ Bologna, Dept Ind Chem Toso Montanari, I-40136 Bologna, Italy.;ENSL, CNRS, UMR 5182, Lab Chim, 46 Allee Italie, F-69364 Lyon, France..
    Roca-Sanjuan, Daniel
    Univ Valencia, Inst Ciencia Mol, Paterna 46980, Spain..
    Romig, Thies
    Univ Rostock, Inst Phys, D-18059 Rostock, Germany..
    Safari, Arta Anushirwan
    Max Planck Inst Solid State Res, Elect Struct Theory Dept, D-70569 Stuttgart, Germany..
    Sanchez-Mansilla, Aitor
    Univ Rovira & Virgili, Dept Phys & Inorgan Chem, Tarragona 43007, Spain..
    Sand, Andrew M.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Butler Univ, Dept Chem & Biochem, Indianapolis, IN 46208 USA..
    Schapiro, Igor
    Hebrew Univ Jerusalem, Inst Chem, IL-91904 Jerusalem, Israel..
    Scott, Thais R.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA.;Univ Chicago, James Franck Inst, Pritzker Sch Mol Engn, Dept Chem,Chicago Ctr Theoret Chem, Chicago, IL 60637 USA.;Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA..
    Segarra-Marti, Javier
    Univ Valencia, Inst Ciencia Mol, Paterna 46980, Spain..
    Segatta, Francesco
    Univ Bologna, Dept Ind Chem Toso Montanari, I-40136 Bologna, Italy..
    Sergentu, Dumitru-Claudiu
    SUNY Buffalo, Dept Chem, Buffalo, NY 14260 USA.;AI Cuza Univ Iasi, RECENT AIR, Lab RA 03, Iasi 700506, Romania..
    Sharma, Prachi
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Shepard, Ron
    Argonne Natl Lab, Chem Sci & Engn Div, Lemont, IL 60439 USA..
    Shu, Yinan
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Staab, Jakob K.
    Univ Manchester, Dept Chem, Manchester M13 9PL, Lancs, England..
    Straatsma, Tjerk P.
    Oak Ridge Natl Lab, Natl Ctr Computat Sci, Oak Ridge, TN 37831 USA.;Univ Alabama, Dept Chem & Biochem, Tuscaloosa, AL 35487 USA..
    Sorensen, Lasse Kragh
    Univ Southern Denmark, Univ Lib, DK-5230 Odense M, Denmark..
    Tenorio, Bruno Nunes Cabral
    Tech Univ Denmark, Dept Chem, DK-2800 Lyngby, Denmark..
    Truhlar, Donald G.
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Ungur, Liviu
    Natl Univ Singapore, Dept Chem, Singapore 117543, Singapore..
    Vacher, Morgane
    Nantes Univ, CNRS, CEISAM, F-44000 Nantes, France..
    Veryazov, Valera
    Lund Univ, Div Theoret Chem, Chem Ctr, SE-22100 Lund, Sweden..
    Voss, Torben Arne
    Univ Rostock, Inst Phys, D-18059 Rostock, Germany..
    Weser, Oskar
    Max Planck Inst Solid State Res, Elect Struct Theory Dept, D-70569 Stuttgart, Germany..
    Wu, Dihua
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Yang, Xuchun
    Bowling Green State Univ, Chem Dept, Bowling Green, OH 43403 USA..
    Yarkony, David
    Johns Hopkins Univ, Dept Chem, Baltimore, MD 21218 USA..
    Zhou, Chen
    Univ Minnesota, Dept Chem, Chem Theory Ctr, 207 Pleasant St SE, Minneapolis, MN 55455 USA.;Univ Minnesota, Minnesota Supercomp Inst, Minneapolis, MN 55455 USA..
    Zobel, J. Patrick
    Univ Vienna, Inst Theoret Chem, Fac Chem, A-1090 Vienna, Austria..
    Lindh, Roland
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Organisk kemi.
    The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry2023Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 19, nr 20, s. 6933-6991Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.

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  • 348. Manni, Giovanni Li
    et al.
    Ma, Dongxia
    Vogiatzis, Konstantinos
    Aquilante, Francesco
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Gagliardi, Laura
    Olsen, Jeppe
    New methods for strong correlation and the challenging case of the Cr dimer2014Ingår i: Abstracts of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 248Artikel i tidskrift (Övrigt vetenskapligt)
  • 349.
    Manzetti, Sergio
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Beräkningsbiologi och bioinformatik. Fjordforsk A/S.
    Tian, Lu
    Beijing Kein Res Ctr Nat Sci, Beijing 100022, Peoples R China.
    Addendum: Solvation Energies of Butylparaben, Benzo[a]pyrene diol epoxide, Perfluorooctanesulfonic acid, and DEHP in Complex with DNA Bases2018Ingår i: Chemical Research in Toxicology, ISSN 0893-228X, E-ISSN 1520-5010, Vol. 31, nr 8, s. 639-640Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    The bonding mechanisms between DEHP, PFOS, butylparaben and benzo[a]pyrene with the DNA were recently published [1] and showed intriguing mechanisms of complex formation between these priority pollutants and the gene core fragment of the p53 suppressor which were analyzed at the electronic level. The study supplied also important bonding data, including solvent model by molecular dynamics simulation and quantum chemical energies of electronic interaction between the pollutants and the DNA. It was however not included in this study the effect of the solvent on the electronic landscape of the molecules, which is the ultimate description of whether an interaction is truly favored by the ubiquitous solvent phase of water which participates in all cellular and biomolecular mechanisms and reactions and governs the structures of all biomolecules [2]⁠. It is for this reason that we wish to submit this addendum which finally defines the true energies of interaction of the published complexes [1]⁠ which includes the SMD solvation model [3]⁠. The calculations show that all complexes form under favorable energies when the SMD quantum chemical solvent model is included, and hence the necessary confirmation of the favorable effects of solvent on the potential energy landscape is confirmed for these geometries. Table 1 shows the bonding energies of the published complexes [1]⁠, which are here derived using the procedure using Gaussian16 A.03 package [4]⁠, where the geometries of complexes were optimized at B3LYP-D3(BJ)/6-311G* [5]⁠ level under SMD solvation model and a single point energy was derived to generate the energies.

  • 350.
    Marchiori, Cleber F. N.
    et al.
    Karlstad Univ, Dept Engn & Phys, S-65188 Karlstad, Sweden..
    Damas, Giane B.
    Linköping Univ, Dept Phys Chem & Biol, S-58330 Linköping, Sweden..
    Araujo, Moyses
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori. Karlstad Univ, Dept Engn & Phys, S-65188 Karlstad, Sweden..
    Tuning the photocatalytic properties of porphyrins for hydrogen evolution reaction: An in-silico design strategy2022Ingår i: Journal of Power Sources Advances, E-ISSN 2666-2485, Vol. 15, artikel-id 100090Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Porphyrins constitute a class of attractive materials for harvesting sunlight and promote chemical reactions following their natural activity for the photosynthetic process in plants. In this work, we employ an in-silico design strategy to propose novel porphyrin-based materials as photocatalysts for hydrogen evolution reaction (HER). More specifically, a set of meso-substituted porphyrins with donor-acceptor architecture are evaluated within the density functional theory (DFT) framework, according to these screening criteria: i) broad absorption spectrum in the ultraviolet-visible (UV-Vis) and near infrared (NIR) range, ii) suitable redox potentials to drive the uphill reaction that lead to molecular hydrogen formation, iii) low exciton binding free energy (E-b), and iv) low hydrogen binding free energy (delta G(H)), a quantity that should present low HER overpotentials, ideally delta G(H) = 0. The outcomes indicate that the Se-containing compound, where the donor ligands are attached to the porphyrin core by the spacer, outstands as the most promising candidate that is presented in this work. It displays a broad absorption in the visible and NIR regions to up to 1000 nm, suitable catalytic power, low E-b (in special in high dielectric constant environment, such as water) and the lowest delta G(H) = +0.082 eV. This is comparable, in absolute values, to the value exhibited by platinum (delta G(H) =-0.10 eV), one of the most efficient catalysts for HER.

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