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  • 1. Aaldering, L. J.
    et al.
    Poongavanam, V.
    Langkjær, N.
    Natarajan Arul, Murugan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Jørgensen, P. T.
    Wengel, J.
    Veedu, R. N.
    Development of an Efficient G-Quadruplex-Stabilised Thrombin-Binding Aptamer Containing a Three-Carbon Spacer Molecule2017Ingår i: ChemBioChem (Print), ISSN 1439-4227, E-ISSN 1439-7633, Vol. 18, nr 8, s. 755-763Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The thrombin-binding aptamer (TBA), which shows anticoagulant properties, is one of the most studied G-quadruplex-forming aptamers. In this study, we investigated the impact of different chemical modifications such as a three-carbon spacer (spacer-C3), unlocked nucleic acid (UNA) and 3′-amino-modified UNA (amino-UNA) on the structural dynamics and stability of TBA. All three modifications were incorporated at three different loop positions (T3, T7, T12) of the TBA G-quadruplex structure to result in a series of TBA variants and their stability was studied by thermal denaturation; folding was studied by circular dichroism spectroscopy and thrombin clotting time. The results showed that spacer-C3 introduction at the T7 loop position (TBA-SP7) significantly improved stability and thrombin clotting time while maintaining a similar binding affinity as TBA to thrombin. Detailed molecular modelling experiments provided novel insights into the experimental observations, further supporting the efficacy of TBA-SP7. The results of this study could provide valuable information for future designs of TBA analogues with superior thrombin inhibition properties. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  • 2.
    Aguilar, Xavier
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schliephake, Michael
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Vahtras, Olav
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Gimenez, Judit
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Scalability analysis of Dalton, a molecular structure program2013Ingår i: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 29, nr 8, s. 2197-2204Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a performance characterization and optimization of Dalton. We also propose a solution to avoid the master/worker design of Dalton to become a performance bottleneck for larger process numbers. With these improvements we obtain speedups of 4x, increasing the parallel efficiency of the code and being able to run in it in a much bigger number of cores.

  • 3.
    Aguilar, Xavier
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Schliephake, Michael
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Vahtras, Olav
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Gimenez, Judit
    Barcelona Supercomputing Center, Universitat Politecnica de Catalunya, Barcelona, Spain.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Scaling Dalton, a molecular electronic structure program2011Ingår i: Seventh International Conference on e-Science, e-Science 2011, 5-8 December 2011, Stockholm, Sweden, IEEE conference proceedings, 2011, s. 256-262Konferensbidrag (Refereegranskat)
    Abstract [en]

    Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a characterization and performance optimization of Dalton that increases the scalability and parallel efficiency of the application. We also propose asolution that helps to avoid the master/worker design of Daltonto become a performance bottleneck for larger process numbers and increase the parallel efficiency.

  • 4.
    Ahlquist, Mårten
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Fabrizi, G
    Cacchi, S
    Norrby, Per-Ola
    Technical University of Denmark.
    Palladium(0) alkyne complexes as active species: a DFT investigation2005Ingår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, nr 33, s. 4196-4198Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Alkynes have been found to be excellent ligands for Pd(0); the stability of a range of alkyne-Pd(0) complexes, and their reactivity in oxidative addition, have been investigated by DFT methods.

  • 5.
    Ahlquist, Mårten
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Fabrizi, Giancarlo
    Cacchi, Sandro
    Norrby, Per-Ola
    Technical Univeristy of Denmark.
    The mechanism of the phosphine-free palladium-catalyzed hydroarylation of alkynes2006Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 128, nr 39, s. 12785-12793Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The mechanism of the Pd-catalyzed hydroarylation and hydrovinylation reaction of alkynes has been studied by a combination of experimental and theoretical methods (B3LYP), with an emphasis on the phosphine-free version. The regioselectivity of the hydroarylation and hydrovinylation shows unexpected differences, which could be attributed mainly to the higher steric demand of the cyclohexenyl group as compared to the phenyl group. Hydroarylation of alpha,beta-acetylenic carbonyl substrates yields a very unusual anti-Michael selectivity, which is shown to result from reaction of the nonconjugated double bond, leaving the conjugation intact. In all cases were the regioselectivities reproduced by the calculations.

  • 6.
    Ahlquist, Mårten
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Norrby, Per-Ola
    Department of Chemistry, University of Gothenburg, Sweden.
    Dispersion and Back-Donation Gives Tetracoordinate [Pd(PPh3)4]2011Ingår i: Angewandte Chemie International Edition, ISSN 1433-7851, E-ISSN 1521-3773, Vol. 50, nr 49, s. 11794-11797Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    18e R.I.P. The apparent compliance of [Pd(PPh3)4] ("tetrakis") with the 18-electron rule is not due to an electronic preference on the central metal. Pd is valence-saturated already by two ligands. Further ligand addition gives a minor energy gain, and is only possible due to strong back-bonding. Dispersion corrections are needed for properly describing the interactions between the ligands.

  • 7.
    Ahlquist, Mårten S. G.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Norrby, Per-Ola
    Department of Chemistry, University of Gothenburg, Sweden.
    Dispersion and back-donation gives tetracoordinate Pd(PPh3)(4)2012Ingår i: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 243Artikel i tidskrift (Övrigt vetenskapligt)
  • 8.
    Ahlquist, Mårten S. G.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Wang, Ying
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Xue, Liqin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Sanchez-de-Armas, Rocio
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Proton transfers in first row transition metal complexes2013Ingår i: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 245, s. 1381-INOR-Artikel i tidskrift (Övrigt vetenskapligt)
  • 9. Ahlstrand, David A.
    et al.
    Polukeev, Alexey V.
    Marcos, Rocio
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ahlquist, Mårten S. G.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Wendt, Ola F.
    Csp(3)-H Activation without Chelation Assistance in an Iridium Pincer Complex Forming Cyclometallated Products2017Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 23, nr 8, s. 1748-1751Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Cyclometallation of 8-methylquinoline and 2-(dimethylamino)-pyridine in an iridium-based pincer complex is described. The C-H activation of 2-(dimethylamino) pyridine is not chelation assisted, which has not been described before for Csp(3)-H bonds in cyclometallation reactions. The mechanism of the cyclometallation of 2-(dimethylamino) pyridine was studied by DFT calculations and kinetic measurements.

  • 10.
    Ai, Yuejie
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Theoretical studies on photophysics and photochemistry of DNA2010Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Theoretical studies on biological systems like nucleic acid and protein have been widely developed in the past 50 years and will continue to be a topic of interest in forefronts of natural science. In addition to experimental science, computational modeling can give useful information and help us to understand biochemical issues at molecular, atomic and even electronic levels.

    Deoxyribonucleic acid (DNA), the hereditary basis of life’s genetic identity, has always been major topic of discussions since its structure was built in 1953. However, harmful UV radiation from sunlight can make damage to DNA molecules and eventually give rise to DNA damaging biological consequences, like mutagenesis, carcinogenesis, and cell death. Photostability, photodamage, and photorepair are of vital importance in the photophysics and photochemistry of DNA. In this thesis, we have applied high level computer-aided theoretical methods to explore the underlying mechanisms for these three critical issues of DNA. Special attentions are paid to the following aspects: the properties of the excited states, the design of relevant computational models and the effects of biological environments.

    We have systematically studied the excited state properties of DNA from single base to base pair and oligonucleotides, where the concerted base pairing and base stacking effects was found to play important roles in DNA photostability. The UV-light induced isomerization mechanism between two photoproducts of DNA photodamage has been revealed in different biological environments. In association with DNA photodamage, the related photorepair processes have been proposed for different lesions in photolyase which is a catalytic enzyme for DNA, and the calculated results well explained the experimental observations. In particular, the internal and external properties of flavin cofactors have been extensively studied by combining the electronic structure and spectroscopic calculations. We have examined the effects of the intramolecular hydrogen bond on spectroscopic properties of flavins. The good agreements with the experimental spectra indicated that the biological self-regulation acted critical role in these biological systems.

  • 11.
    Ai, Yuejie
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Cui, Ganglong
    Beijing Normal University.
    Fang, Qiu
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Fang, Weihai
    Beijing Normal University.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Exploring concerted effects of base pairing and stacking on the excited-state nature of DNA oligonucleotides by DFT and TD-DFT studies2011Ingår i: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 111, nr 10, s. 2366-2377Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have taken (dA)5, (dT)5, and (dA)5•(dT)5 as model systems to study concerted effects of base pairing and stacking on excited-state nature of DNA oligonucleotides using density functional theory (DFT) and time dependent DFTmethods. The spectroscopic states are determined to be of a partial A →A charge transfernature in the A•T oligonucleotides. The T → T charge-transfer transitionsproduce dark states, which are hidden in the energy region of the steady-stateabsorption spectra. This is different from the previous assignment that the T → Tcharge-transfer transition is responsible for a shoulder at the red side of the first strongabsorption band. The A →T charge-transfer states were predicted to have relativelyhigh energies in the A•T oligonucleotides. The present calculations predict that the T→A charge-transfer states are not involved in the spectra and excited-state dynamics ofthe A•T oligonucleotides. In addition, the influence of base pairing and stacking on thenature of the 1nΠ* and 1ΠΠ* states are discussed in detail.

  • 12. Ai, Yuejie
    et al.
    Li, Xin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ji, Yongfei
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Song, Wei-Guo
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Hydrophobicity and Hydrophilicity Balance Determines Shape Selectivity of Suzuki Coupling Reactions Inside Pd@meso-SiO2 Nanoreactor2016Ingår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, nr 19, s. 10244-10251Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Molecular sorting and catalysis directed by shape selectivity have been extensively applied in porous extended frameworks for a low-carbon, predictable, renewable component of modern industry. A comprehensive understanding of the underlying recognition mechanism toward different shapes is unfortunately still missing, owing to the lack of structural and dynamic information under operating conditions. We demonstrate here that such difficulties can be overcome by state-of-the-art molecular dynamics simulations which provide atomistic details that are not accessible experimentally, as exemplified by our interpretation for the experimentally observed aggregation induced shape selectivity for Suzuki C-C coupling reaction catalyzed by Pd particles in mesoporous silica. It is found that both aggregation ability and aggregating pattern of the reactants play the decisive role in controlling the shape selectivity, which are in turn determined by the balance between the hydrophobicity and hydrophilicity of the reactants, or in other words, by the balance between the noncovalent hydrogen bonding interaction and van der Waals forces. A general rule that allows prediction of the shape selectivity of a reactant has been proposed and verified against experiments. We show that molecular modeling is a powerful tool for rational design of new mesoporous systems and for the control of catalytic reactions that are important for the petrochemical industry.

  • 13.
    Ai, Yue-Jie
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Liao, Rongzhen
    Stockholm University.
    Chen, Shilu
    Beijing Institute of Technology.
    Hua, Wei-Jie
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Fang, Wei-Hai
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Repair of DNA Dewar Photoproduct to (6-4) photoproduct in (6-4) Photolyase2011Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 115, nr 37, s. 10976-10982Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Dewar photoproduct (Dewar PP) is the valence isomer of (6-4) photoproduct ((6-4)PP) in photodamaged DNA. Compared to the extensive studied CPD photoproducts, the underlying repair mechanisms for the (6-4)PP, and especially for the Dewar PP, are not well-established to date. In this paper, the repair mechanism of DNA Dewar photoproduct T(dew)C in (6-4) photolyase was elucidated using hybrid density functional theory. Our results showed that, during the repair process, the T(dew)C has to isomerize to T(6-4)C photolesion first via direct C6'-N3' bond cleavage facilitated by electron injection. This isomerization mechanism is energetically much more efficient than other possible rearrangement pathways. The calculations provide a theoretical interpretation to recent experimental observations.

  • 14.
    Ai, Yue-Jie
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Liao, Rong-Zhen
    Fang, Wei-Hai
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Theoretical studies on the isomerization mechanism of the ortho-green fluorescent protein chromophore2012Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 14, nr 38, s. 13409-13414Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present a systematic theoretical investigation on the overall ground state and excited-state isomerization reaction mechanism of ortho-green fluorescent protein chromophore (o-HBDI) using the density functional theory and the multireference methods. The calculated results and subsequent analysis suggest the possible isomerization mechanism for o-HBDI. By comparison with experimental observation and detailed analysis, it is concluded that as initiated by the excited-state intramolecular proton transfer reaction, the conical intersection between the ground state and the excited state along the C4-C5 single-bond rotational coordinate is responsible for the rapid deactivation of o-HBDI.

  • 15.
    Ai, Yuejie
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Tian, Guangjun
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Liao, Rongzhen
    Stockholm University.
    Zhang, Qiong
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Fang, Weihai
    Beijing Normal University.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Intrinsic property of flavin mononucleotide controls its optical spectra in three redox states2011Ingår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 12, nr 16, s. 2899-2902Artikel i tidskrift (Refereegranskat)
  • 16.
    Ai, Yue-Jie
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Tian, Guangjun
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Luo, Yi
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Role of non-Condon vibronic coupling and conformation change on two-photon absorption spectra of green fluorescent protein2013Ingår i: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 111, nr 9-11, s. 1316-1321Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Two-photon absorption spectra of green fluorescent proteins (GFPs) often show a blue-shift band compared to their conventional one-photon absorption spectra, which is an intriguing feature that has not been well understood. We present here a systematic study on one- and two-photon spectra of GFP chromophore by means of the density functional response theory and complete active space self-consistent field (CASSCF) methods. It shows that the popular density functional fails to provide correct vibrational progression for the spectra. The non-Condon vibronic coupling, through the localised intrinsic vibrational modes of the chromophore, is responsible for the blue-shift in the TPA spectra. The cis to trans isomerisation can be identified in high-resolution TPA spectra. Our calculations demonstrate that the high level ab initio multiconfigurational CASSCF method, rather than the conventional density functional theory is required for investigating the essential excited-state properties of the GFP chromophore.

  • 17. Aidas, Kestutis
    et al.
    Angeli, Celestino
    Bak, Keld L.
    Bakken, Vebjorn
    Bast, Radovan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Boman, Linus
    Christiansen, Ove
    Cimiraglia, Renzo
    Coriani, Sonia
    Dahle, Pal
    Dalskov, Erik K.
    Ekstrom, Ulf
    Enevoldsen, Thomas
    Eriksen, Janus J.
    Ettenhuber, Patrick
    Fernandez, Berta
    Ferrighi, Lara
    Fliegl, Heike
    Frediani, Luca
    Hald, Kasper
    Halkier, Asger
    Hattig, Christof
    Heiberg, Hanne
    Helgaker, Trygve
    Hennum, Alf Christian
    Hettema, Hinne
    Hjertenaes, Eirik
    Host, Stinne
    Hoyvik, Ida-Marie
    Iozzi, Maria Francesca
    Jansik, Branislav
    Jensen, Hans Jorgen Aa.
    Jonsson, Dan
    Jorgensen, Poul
    Kauczor, Joanna
    Kirpekar, Sheela
    Kjrgaard, Thomas
    Klopper, Wim
    Knecht, Stefan
    Kobayashi, Rika
    Koch, Henrik
    Kongsted, Jacob
    Krapp, Andreas
    Kristensen, Kasper
    Ligabue, Andrea
    Lutnaes, Ola B.
    Melo, Juan I.
    Mikkelsen, Kurt V.
    Myhre, Rolf H.
    Neiss, Christian
    Nielsen, Christian B.
    Norman, Patrick
    Olsen, Jeppe
    Olsen, Jogvan Magnus H.
    Osted, Anders
    Packer, Martin J.
    Pawlowski, Filip
    Pedersen, Thomas B.
    Provasi, Patricio F.
    Reine, Simen
    Rinkevicius, Zilvinas
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Ruden, Torgeir A.
    Ruud, Kenneth
    Rybkin, Vladimir V.
    Salek, Pawel
    Samson, Claire C. M.
    de Meras, Alfredo Sanchez
    Saue, Trond
    Sauer, Stephan P. A.
    Schimmelpfennig, Bernd
    Sneskov, Kristian
    Steindal, Arnfinn H.
    Sylvester-Hvid, Kristian O.
    Taylor, Peter R.
    Teale, Andrew M.
    Tellgren, Erik I.
    Tew, David P.
    Thorvaldsen, Andreas J.
    Thogersen, Lea
    Vahtras, Olav
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Watson, Mark A.
    Wilson, David J. D.
    Ziolkowski, Marcin
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    The Dalton quantum chemistry program system2014Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, Vol. 4, nr 3, s. 269-284Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.

  • 18. Aidas, Kestutis
    et al.
    Olsen, Jogvan Magnus H.
    Kongsted, Jacob
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics2013Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 7, s. 2069-2080Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores-acridine yellow and proflavin-located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site. The computational scheme adopted involves classical molecular dynamics simulations of the ligands bound to the protein and subsequent linear response polarizable embedding density functional theory calculations of the excitation energies. A polarizable embedding potential consisting of point charges fitted to reproduce the electrostatic potential and isotropic atomic polarizabilities computed individually for every residue of the protein was used in the linear response calculations. Comparing the calculated aqueous solution-to-protein shifts of maximum absorption energies to available experimental data, we concluded that the cationic proflavin chromophore is likely not to bind albumin at its drug binding site I nor at its heme binding site. Although agreement with experimental data could only be obtained in qualitative terms, our results clearly indicate that the difference in optical response of the two probes is due to deprotonation, and not, as earlier suggested, to different binding sites. The ramifications of this finding for design of molecular probes targeting albumin or other proteins is briefly discussed.

  • 19.
    Aidas, Kestutis
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Kongsted, Jacob
    Laaksonen, Aatto
    Mocci, Francesca
    A quantum mechanics/molecular dynamics study of electric field gradient fluctuations in the liquid phase. The case of Na+ in aqueous solution2013Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 5, s. 1621-1631Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Na-23 quadrupolar coupling constant of the Na+ ion in aqueous solution has been predicted using molecular dynamics simulations and hybrid quantum mechanics/molecular mechanics methods for the calculation of electric field gradients. The developed computational approach is generally expected to provide reliable estimates of the quadrupolar coupling constants of monoatomic species in condensed phases, and we show here that intermolecular polarization and non-electrostatic interactions are of crucial importance as they result in a 100% increased quadrupolar coupling constant of the ion as compared to a simpler pure electrostatic picture. These findings question the reliability of the commonly applied classical Sternheimer approximation for the calculations of the electric field gradient. As it can be expected from symmetry considerations, the quadrupolar coupling constants of the 5- and 6-coordinated Na+ ions in solution are found to differ significantly.

  • 20. Ai-Xi, Chen
    et al.
    Hong, Wang
    Duan, Sai
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Hai-Ming, Zhang
    Xin, Xu
    Li-Feng, Chi
    Potential-Induced Phase Transition of N-Isobutyryl-L-cysteine Monolayers on Au(111) Surfaces2017Ingår i: Wuli huaxue xuebao, ISSN 1000-6818, Vol. 33, nr 5, s. 1010-1016Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Functional solid substrates modified by self-assembled monolayers (SAMs) have potential applications in biosensors, chromatography, and biocompatible materials. The potential-induced phase transition of N-isobutyryl-L-cysteine (L-NIBC) SAMs on Au(111) surfaces was investigated by in-situ electrochemical scanning tunneling microscopy (EC-STM) in 0.1 mol.L-1 H2SO4 solution. The NIBC SAMs with two distinct structures (alpha phase and beta phase) can be prepared by immersing the Au(111) substrate in pure NIBC aqueous solution and NIBC solution controlled by phosphate buffer at pH 7, respectively. The as-prepared a phase and beta phase of NIBC SAMs show various structural changes under the control of electrochemical potentials of the Au(111) in H2SO4 solution. The a phase NIBC SAMs exhibit structural changes from ordered to disordered structures with potential changes from 0.7 V (vs saturated calomel electrode, SCE) to 0.2 V. However, the beta phase NIBC SAMs undergo structural changes from disordered structures (E < 0.3 V) to y phase (0.4 V < E < 0.5 V) and finally to the beta phase (0.5 V < E < 0.7 V). EC-STM images also indicate that the phase transition from the alpha phase NIBC SAMs to the a phase occurs at positive potential. Combined with density functional theory (DFT) calculations, the phase transition from the beta phase to the a phase is explained by the potential-induced break of bonding interactions between -COO- and the negatively charged gold surfaces.

  • 21. Aldongarov, Anuar
    et al.
    Irgibaeva, Irina
    Hermansson, Kersti
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Theoretical study on passivation of small CdS clusters2014Ingår i: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 112, nr 5-6, s. 674-682Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We use density functional theory quantum chemical calculations to model optical properties of small cadmium sulphide clusters in order to explore the formation of trap states and the possibility to achieve surface passivation. The addition of capping oxygen ions on the surface of the CdS quantum dots is found to passivate the single-bonded Cd atoms. Added Cu ions resulted in the formation of deep trap states for certain locations of the copper impurity, while removal of single-bonded Cd atoms by adding S or SH groups leads to a band gap increase.

  • 22. Ambre, Ram B.
    et al.
    Daniel, Quentin
    Fan, Ting
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Chen, Hong
    Zhang, Biaobiao
    Wang, Lei
    Ahlquist, Marten S. G.
    Duan, Lele
    Sun, Licheng
    Molecular engineering for efficient and selective iron porphyrin catalysts for electrochemical reduction of CO2 to CO2016Ingår i: CHEMICAL COMMUNICATIONS, ISSN 1359-7345, Vol. 52, nr 100, s. 14478-14481Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Iron porphyrins Fe-pE, Fe-mE, and Fe-oE were synthesized and their electrochemical behavior for CO2 reduction to CO has been investigated. The controlled potential electrolysis of Fe-mE gave exclusive 65% Faradaic efficiency (FE) whereas Fe-oE achieved quasi-quantitative 98% FE (2% H-2) for CO production.

  • 23. Ashaduzzaman, M.
    et al.
    Anto Antony, A.
    Arul Murugan, Natarajan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Deshpande, S. R.
    Turner, A. P. F.
    Tiwari, A.
    Studies on an on/off-switchable immunosensor for troponin T2015Ingår i: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 73Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Regeneration is a key goal in the design of immunosensors. In this study, we report the temperature-regulated interaction of N-isopropylacrylamide (PNIPAAm) functionalised cardiac troponin T (cTnT) with anti-cTnT. Covalently bonded PNIPAAm on an anti-cTnT bioelectrode showed on/off-switchability, regeneration capacity and temperature triggered sensitivity for cTnT. Above the lower critical solution temperature (LCST), PNIPAAm provides a liphophilic microenvironment with specific volume reduction at the bioelectrode surface, making available binding space for cTnT, and facilitating analyte recognition. Computational studies provide details about the structural changes occurring at the electrode above and below the LCST. Furthermore, free energies associated with the binding of cTnT with PNIPAAm at 25 (δG<inf>coil</inf>=-6.0Kcal/mole) and 37°C (δG<inf>globular</inf>=-41.0kcal/mole) were calculated to elucidate the interaction and stability of the antigen-antibody complex. The responsiveness of such assemblies opens the way for miniaturised, smart immuno-technologies with 'built-in' programmable interactions of antigen-antibody upon receiving stimuli.

  • 24. Ashaduzzaman, Md.
    et al.
    Deshpande, Swapneel R.
    Natarajan Arul, Murugan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Mishra, Yogendra Kumar
    Turner, Anthony P. F.
    Tiwari, Ashutosh
    On/off-switchable LSPR nano-immunoassay for troponin-T2017Ingår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikel-id 44027Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Regeneration of immunosensors is a longstanding challenge. We have developed a re-usable troponin-T (TnT) immunoassay based on localised surface plasmon resonance (LSPR) at gold nanorods (GNR). Thermosensitive poly(N-isopropylacrylamide) (PNIPAAM) was functionalised with anti-TnT to control the affinity interaction with TnT. The LSPR was extremely sensitive to the dielectric constant of the surrounding medium as modulated by antigen binding after 20 min incubation at 37 degrees C. Computational modelling incorporating molecular docking, molecular dynamics and free energy calculations was used to elucidate the interactions between the various subsystems namely, IgG-antibody (c. f., anti-TnT), PNIPAAM and/or TnT. This study demonstrates a remarkable temperature dependent immuno-interaction due to changes in the PNIPAAM secondary structures, i.e., globular and coil, at above or below the lower critical solution temperature (LCST). A series of concentrations of TnT were measured by correlating the lambda(LSPR) shift with relative changes in extinction intensity at the distinct plasmonic maximum (i. e., 832 nm). The magnitude of the red shift in lambda(LSPR) was nearly linear with increasing concentration of TnT, over the range 7.6 x 10(-15) to 9.1 x 10(-4) g/mL. The LSPR based nano-immunoassay could be simply regenerated by switching the polymer conformation and creating a gradient of microenvironments between the two states with a modest change in temperature.

  • 25. Awasthi, Saurabh
    et al.
    Murugan, N. Arul
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Saraswathi, N. T.
    Advanced Glycation End Products Modulate Structure and Drug Binding Properties of Albumin2015Ingår i: Molecular Pharmaceutics, ISSN 1543-8384, E-ISSN 1543-8392, Vol. 12, nr 9, s. 3312-3322Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The extraordinary ligand binding properties of albumin makes it a key player in the pharmacokinetics and pharmacodynamics of many vital drugs. Albumin is highly susceptible for nonenzymatic glycation mediated structural modifications, and there is a need to determine structural and functional impact of specific AGEs modifications. The present study was aimed toward determining the AGE mediated structure and function changes, primarily looking into the effect on binding affinity of drugs in the two major drug binding sites of albumin. The impact of the two most predominant AGEs modifications, i.e., carboxyethyllysine (CEL) and argpyrimidine (Arg-P), was studied on the basis of the combination of in vitro and in silico experiments. In vitro studies were carried out by AGEs modification of bovine serum albumin (BSA) for the formation of Arg-P and CEL followed by drug interaction studies. In silico studies involved molecular dynamics (MD) simulations and docking studies for native and AGEs modified BSAs. In particular the side chain modification was specifically carried out for the residues in the drug binding sites, i.e., Arg-194, Arg-196, Arg-198, and Arg-217, and Lys-204 (site I) and Arg-409 and Lys-413 (site II). The equilibrated structures of native BSA (n-BSA) and glycated BSA (G-BSA) as obtained from MD were used for drug binding studies using molecular docking approach. It was evident from the results of both in vitro and in silico drug interaction studies that AGEs modification results in the reduced drug binding affinity for tolbutamide (TLB) and ibuprofen (IBP) in sites I and II. Moreover, the AGEs modification mediated conformational changes resulted in the shallow binding pockets with reduced accessibility for drugs.

  • 26. Bacalum, Mihaela
    et al.
    Wang, Lina
    Boodts, Stijn
    Yuan, Peijia
    Leen, Volker
    Smisdom, Nick
    Fron, Eduard
    Knippenberg, Stefan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Fabre, Gabin
    Trouillas, Patrick
    Beljonne, David
    Dehaen, Wim
    Boens, Noel
    Ameloot, Marcel
    A Blue-Light-Emitting BODIPY Probe for Lipid Membranes2016Ingår i: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 32, nr 14, s. 3495-3505Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Here we describe a new BODIPY-based membrane probe (1) that provides an alternative to dialkylcarbocyanine dyes, such as DiI-C,8, that can be excited in the blue spectral region. Compound 1 has unbranched octadecyl chains at the 3,5 -positions and a meso-amino function. In organic solvents, the absorption and emission maxima of 1 are determined mainly by solvent acidity and dipolarity. The fluorescence quantum yield is high and reaches 0.93 in 2-propanol. The fluorescence decays are well fitted with a single -exponential in pure solvents and in small and giant unilamellar vesicles (GUV) with a lifetime of ca. 4 ns. Probe 1 partitions in the same lipid phase as DiI-C-18(5) for lipid mixtures containing sphingomyelin and for binary mixtures of dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC). The lipid phase has no effect on the fluorescence lifetime but influences the fluorescence anisotropy. The translational diffusion coefficients of 1 in GUVs and OLN-93 cells are of the same order as those reported for DiI-C-18. The directions of the absorption and transition dipole moments of 1 are calculated to be parallel. This is reflected in the high steady-state fluorescence anisotropy of 1 in high ordered lipid phases. Molecular dynamic simulations of 1 in a model of the DOPC bilayer indicate that the average angle of the transition moments with respect to membrane normal is ca. 70 degrees, which is comparable with the value reported for al DiI-C-18.

  • 27. Badri, Zahra
    et al.
    Pathak, Shubhrodeep
    Fliegl, Heike
    Rashidi-Ranjbar, Parviz
    Bast, Radovan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Marek, Radek
    Foroutan-Nejad, Gina
    Ruud, Kenneth
    All-Metal Aromaticity: Revisiting the Ring Current Model among Transition Metal Clusters2013Ingår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, nr 11, s. 4789-4796Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present new insight into the nature of aromaticity in metal clusters. We give computational arguments in favor of using the ring-current model over local indices, such as nucleus independent chemical shifts, for the determination of the magnetic aromaticity. Two approaches for estimating magnetically induced ring currents are employed for this purpose, one based on the quantum theory of atoms in molecules (QTAIM) and the other where magnetically induced current densities (MICD) are explicitly calculated. We show that the two-zone aromaticity/antiaromaticity of a number of 3d metallic clusters (Sc-3(-), Cu-3(+), and Cu-4(2-)) can be explained using the QTAIM-based magnetizabilities. The reliability of the calculated atomic and bond magnetizabilities of the metallic clusters are verified by comparison with MICD computed at the multiconfiguration self-consistent field (MCSCF) and density functional levels of theory. Integrated MCSCF current strength susceptibilities as well as a visual analysis of the calculated current densities confirm the interpretations based on the QTAIM magnetizabilities. In view of the new findings, we suggest a simple explanation based on classical electromagnetic theory to explain the anomalous magnetic shielding in different transition metal clusters. Our results suggest that the nature of magnetic aromaticity/antiaromaticity in transition-metal clusters should be assessed more carefully based on global indices.

  • 28. Baev, Alexander
    et al.
    Prasad, Paras N.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Samoc, Marek
    Wegener, Martin
    Metaphotonics: An emerging field with opportunities and challenges2015Ingår i: Physics reports, ISSN 0370-1573, E-ISSN 1873-6270, Vol. 594, s. 1-60Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Metaphotonics is an emerging multidisciplinary field that deals with manipulation of electro-magnetic fields in nanoengineered (meta)materials using both electric and magnetic interactions and their cross-coupling. It offers unprecedented control of both linear and nonlinear optical functions for applications ranging from optical switching, to negative- and near-zero refractive index metamaterials, to chiral bioimaging, to cloaking. However, realization of such applications requires physics-guided nanoengineering of appropriate artificial media with electro-magnetic properties at visible and infrared wavelengths that are tailored to surpass those of any naturally-occurring material. Here, we review metaphotonics with a broadened vision and scope, introduce potential applications, describe the role of theoretical physics through multiscale modeling, review the materials development and current status, and outline opportunities in this fertile emerging field.

  • 29. Bai, Linyi
    et al.
    Zhu, Liangliang
    Ang, Chung Yen
    Li, Xin
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Wu, Shaojue
    Zeng, Yongfei
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Zhao, Yanli
    Iron( III)-Quantity-Dependent Aggregation-Dispersion Conversion of Functionalized Gold Nanoparticles2014Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 20, nr 14, s. 4032-4037Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Developing gold nanoparticles (AuNPs) with well-designed functionality is highly desirable for boosting the performance and versatility of inorganic-organic hybrid materials. In an attempt to achieve ion recognition with specific signal expressions, we present here 4-piperazinyl-1,8-naphthalimide-functionalized AuNPs for the realization of quantitative recognition of Fe-III ions with dual (colorimetric and fluorescent) output. The research takes advantage of 1)quantity-controlled chelation-mode transformation of the piperazinyl moiety on the AuNPs towards Fe-III, thereby resulting in an aggregation-dispersion conversion of the AuNPs in solution, and 2)photoinduced electron transfer of a naphthaimide fluorophore on the AuNPs, thus leading to reversible absorption and emission changes. The functional AuNPs are also responsive to pH variations. This strategy for realizing the aggregation-dispersion conversion of AuNPs with returnable signal output might exhibit application potential for advanced nanoscale chemosensors.

  • 30.
    Balamurugan, Kanagasabai
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Natarajan Arul, Murugan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Langström, Bengt
    Nordberg, Agneta
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Siberian Federal University, Russian Federation.
    Effect of Alzheimer Familial Chromosomal Mutations on the Amyloid Fibril Interaction with Different PET Tracers: Insight from Molecular Modeling Studies2017Ingår i: ACS Chemical Neuroscience, ISSN 1948-7193, E-ISSN 1948-7193, Vol. 8, nr 12, s. 2655-2666Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Alzheimer's disease (AD) is the most common neurodegenerative disorder. Along with an increasing number of elderly worldwide, it poses a great challenge for the society and health care. Although sporadic AD is the common form of AD, 2-3% of the AD cases are expected to be due to mutations in the fi region of the amyloid precursor protein, which is referred to as autosomal dominant AD (ADAD). These mutations may cause changes in the secondary structure of the amyloid fi fibrils and may alter the fibrillization rate leading to changes in the disease development and could also affect the binding to tracers used in diagnosis. In particular, from some recent clinical studies using PET tracers for detection of fibrillar amyloids, it is evident that in ADAD patients with Arctic mutation no amyloid plaque binding can be detected with the "C Pittsburgh Compound B (C-11-PIB). However, for in vitro conditions, significant binding of H-3-PIB has been reported for the amyloid fibrils carrying the Arctic mutation. The aim of the present study is to investigate if there is any mutation specific binding of commonly used amyloid tracers, namely, florbetaben, florbetapir, FPIB, AZD4694, and AZD2184, by means of molecular modeling techniques. Other than Arctic, ADAD mutations, such as the Dutch, Italian, Iowa, and Flemish mutations, are considered in this study. We report that all tracers except florbetapir show reduced binding affinity toward amyloid beta fibrils with the Arctic mutation when compared to the native type. Moreover, florbetapir is the only tracer that binds to all mutants with increased affinity when compared to the native fibril. The results obtained from these studies could increase the understanding of the structural changes caused by mutation and concomitant changes in the interaction pattern of the PET tracers with the mutated variants, which in turn can be useful in selecting the appropriate tracers for the purpose of diagnosis as well as for designing new tracers with desirable properties.

  • 31.
    Balamurugan, Kanagasabai
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Natarajan Arul, Murugan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi (stängd 20110512). KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Multistep Modeling Strategy To Improve the Binding Affinity Prediction of PET Tracers to A beta(42): Case Study with Styrylbenzoxazole Derivatives2016Ingår i: ACS CHEMICAL NEUROSCIENCE, ISSN 1948-7193, Vol. 7, nr 12, s. 1698-1705Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Positron emission tomography (PET) tracers play an important role in the diagnosis of Alzheimer's disease, a condition that leads to progressive dementia and memory loss. A high binding affinity and specificity of the PET tracers to amyloid oligomers and fibrils are crucial for their successful application as diagnostic agents. In this sense, it is essential to design PET tracers with enhanced binding affinities, which can lead to more precise and earlier detection of Alzheimer's disease conditions. The application of in silico methodology for the design and development of efficient PET tracers may serve as an important route to improved Alzheimer's disease diagnosis. In this work, the performance of widely used computational methods is explored for predicting experimental binding affinities of styrylbenzoxazole (SB) derivatives against a common amyloid protofibril. By performing docking, molecular dynamics, and quantum chemistry calculations in sequence their combined predictive performance is explored. The present work emphasizes the merits as well as limitations of these simulation strategies in the realm of designing PET tracers for Alzheimer's disease diagnosis.

  • 32.
    Banerjee, Saikat
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, Nordic Institute for Theoretical Physics NORDITA. Institute for Materials Science, Los Alamos National Laboratory, USA.
    Fransson, J.
    Black-Schaffer, A. M.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Balatsky, A. V.
    Granular superconductor in a honeycomb lattice as a realization of bosonic Dirac material2016Ingår i: PHYSICAL REVIEW B, ISSN 2469-9950, Vol. 93, nr 13, artikel-id 134502Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We examine the low-energy effective theory of phase oscillations in a two-dimensional granular superconducting sheet where the grains are arranged in a honeycomb lattice structure. Using the example of graphene, we present evidence for the engineered Dirac nodes in the bosonic excitations: the spectra of the collective bosonic modes cross at the K and K' points in the Brillouin zone and form Dirac nodes. We show how two different types of collective phase oscillations are obtained and that they are analogous to the Leggett and the Bogoliubov-Anderson-Gorkov modes in a two-band superconductor. We show that the Dirac node is preserved in the presence of an intergrain interaction, despite induced changes of the qualitative features of the two collective modes. Finally, breaking the sublattice symmetry by choosing different on-site potentials for the two sublattices leads to a gap opening near the Dirac node, in analogy with fermionic Dirac materials. The Dirac node dispersion of bosonic excitations is thus expanding the discussion of the conventional Dirac cone excitations to the case of bosons. We call this case as a representative of bosonic Dirac materials (BDM), similar to the case of Fermionic Dirac materials extensively discussed in the literature.

  • 33.
    Banerjee, Saikat
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, Nordic Institute for Theoretical Physics NORDITA. Los Alamos Natl Lab, USA.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Balatsky, Alexander V.
    KTH, Centra, Nordic Institute for Theoretical Physics NORDITA.
    Landau-like states in neutral particles2016Ingår i: PHYSICAL REVIEW B, ISSN 2469-9950, Vol. 93, nr 23, artikel-id 235134Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We show the emergence of a new type of dispersion relation for neutral atoms with an interesting similarity to the spectrum of two-dimensional electrons in an applied perpendicular constant magnetic field. These neutral atoms can be confined in toroidal optical traps and give quasi-Landau spectra. In strong contrast to the equidistant infinitely degenerate Landau levels for charged particles, the spectral gap for such two-dimensional neutral particles increases in particular electric-field configurations. The idea in the paper is motivated by the development in cold atom experiments and builds on the seminal paper of Aharonov and Casher.

  • 34. Baryshnikov, G. V.
    et al.
    Minaev, B. F.
    Minaeva, V. A.
    Podgornaya, A. T.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Application of Bader's atoms in molecules theory to the description of coordination bonds in the complex compounds of Ca2+ and Mg2+ with methylidene rhodanine and its anion2012Ingår i: Russian journal of general chemistry, ISSN 1070-3632, E-ISSN 1608-3350, Vol. 82, nr 7, s. 1254-1262Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the framework of Bader's atoms in molecules theory a complete analysis of the distribution function of electron density in molecules of complexes of Ca2+ and Mg2+ with methylidene rhodanine and its anion was carried out. The role of mutual polarization of the metal cation and the ligand in the formation of coordination bonds was demonstrated. The accumulation of electron density in the interatomic space of coordination bonds is assumed to be a consequence of the deformation of the ligand electron shell under the influence of the cation electric field. Based on the magnitude and sign of the Laplacian and the electron energy density at the critical points of coordination bonds the interactions were classified the in terms of the atoms in molecules theory. The energy of the coordination bonds was evaluated using the Espinoza's formula. The stability of metal-containing rings was considered basing on the values of the bond ellipticity.

  • 35. Baryshnikov, G. V.
    et al.
    Minaev, Boris F.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Minaeva, V. A.
    Ning, Zhijun
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Zhang, Qiong
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Structure and Spectral Properties of Truxene Dye S52012Ingår i: Optics and Spectroscopy, ISSN 0030-400X, E-ISSN 1562-6911, Vol. 112, nr 2, s. 168-174Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    On the ground of functional theory with the B3LYP and BMK functionals, we have studied the structure and optical properties of a truxene dye sensitizer S5 for photoelectric transducers. Based on the calculations of the vertical excitations energy of the dye molecule and accounting the influence of the solvent, we have revealed a positive solvatochromic effect that is weak compared to results obtained in the vacuum approximation. We have studied new features describing stabilization of the planar structure of the cyanothiophene-acrylic fragment of the S5 dye.

  • 36.
    Baryshnikov, Gleb
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Bohdan Khmelnytsky National University, Ukraine.
    Minaev, Boris
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Bohdan Khmelnytsky National University, Ukraine.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Siberian Federal University, Russia.
    Theory and Calculation of the Phosphorescence Phenomenon2017Ingår i: Chemical Reviews, ISSN 0009-2665, E-ISSN 1520-6890, Vol. 117, nr 9, s. 6500-6537Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Phosphorescence is a phenomenon of delayed luminescence that corresponds to the radiative decay of the molecular triplet state. As a general property of molecules, phosphorescence represents a cornerstone problem of chemical physics due to the spin prohibition of the underlying triplet-singlet emission and because its analysis embraces a deep knowledge of electronic molecular structure. Phosphorescence is the simplest physical process which provides an example of spin-forbidden transformation with a characteristic spin selectivity and magnetic field dependence, being the model also for more complicated chemical reactions and for spin catalysis applications. The bridging of the spin prohibition in phosphorescence is commonly analyzed by perturbation theory, which considers the intensity borrowing from spin-allowed electronic transitions. In this review, we highlight the basic theoretical principles and computational aspects for the estimation of various phosphorescence parameters, like intensity, radiative rate constant, lifetime, polarization, zero-field splitting, and spin sublevel population. Qualitative aspects of the phosphorescence phenomenon are discussed in terms of concepts like structure-activity relationships, donor-acceptor interactions, vibronic activity, and the role of spin-orbit coupling under charge-transfer perturbations. We illustrate the theory and principles of computational phosphorescence by highlighting studies of classical examples like molecular nitrogen and oxygen, benzene, naphthalene and their azaderivatives, porphyrins, as well as by reviewing current research on systems like electrophosphorescent transition metal complexes, nucleobases, and amino acids. We furthermore discuss modern studies of phosphorescence that cover topics of applied relevance, like the design of novel photofunctional materials for organic light-emitting diodes (OLEDs), photovoltaic cells, chemical sensors, and bioimaging.

  • 37.
    Baryshnikov, Gleb V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Bohdan Khmelnytsky National University, Ukraine.
    Gawrys, Pawel
    Ivaniuk, Khrystyna
    Witulski, Bernhard
    Whitby, Richard J.
    Al-Muhammad, Ayham
    Minaev, Boris
    Cherpak, Vladyslav
    Stakhira, Pavlo
    Volyniuk, Dmytro
    Wiosna-Salyga, Gabriela
    Luszczynska, Beata
    Lazauskas, Algirdas
    Tamulevicius, Sigitas
    Grazulevicius, Juozas V.
    Nine-ring angular fused biscarbazoloanthracene displaying a solid state based excimer emission suitable for OLED application2016Ingår i: Journal of Materials Chemistry C, ISSN 2050-7526, E-ISSN 2050-7534, Vol. 4, nr 24, s. 5795-5805Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A new biscarbazoloanthracene consisting of nine fused aromatic rings, including two pyrrole units, has been obtained in a straightforward and convergent synthesis. Computational chemistry and conformational analysis revealed that the semiconductor's molecule is not planar, the two carbazole moieties being helical twisted from the plane of the anthracene unit. Photophysical and electrochemical measurements showed that this angular fused heteroacene has a low lying HOMO energy level with a wide band gap despite its extended pi-conjugated molecular framework. Based on its relatively low-lying HOMO level, the semiconductor promises a high environmental stability in comparison to other related linear fused acenes and heteroacenes. The biscarbazoloanthracene has been applied as the light emitting layer in a white light emitting diode (WOLED). It is proposed that the white OLED feature is due to dual light emission properties from the active semiconductor layer being based on both the molecular luminescence of the small molecule and a discrete excimer emission made possible by suitable aggregates in the solid state. Noteworthy, this is the first reported example of such a behavior observed in a small molecule heteroacene rather than an oligomer or a polymer.

  • 38. Baryshnikov, Gleb V.
    et al.
    Minaev, Boris F.
    Minaeva, Valentina A.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Baryshnikova, Alina T.
    Pittelkow, Michael
    DFT and QTAIM study of the tetra-tert-butyltetraoxa[8]circulene regioisomers structure2012Ingår i: Journal of Molecular Structure, ISSN 0022-2860, E-ISSN 1872-8014, Vol. 1026, s. 127-132Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The recently synthesized tetra-tert-butyltetraoxa[8]circulene regioisomers characterized by unusual solution-state aggregation behavior are calculated at the density functional theory (DFT) level with the quantum theory of atoms in molecules (QTAIMs) approach to the electron density distribution analysis. The presence of stabilizing intramolecular hydrogen bonds and hydrogen-hydrogen interactions in the studied molecules is predicted and the energies of these interactions are estimated with QTAIM. Occurrence of the CH center dot center dot center dot O bonds is detected by the single-crystal X-ray analysis for two regioisomers, obtained in high purity.

  • 39. Baryshnikov, Gleb V.
    et al.
    Minaev, Boris F.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Pittelkow, Michael
    Nielsen, Christian B.
    Salcedo, Roberto
    Nucleus-independent chemical shift criterion for aromaticity in pi-extended tetraoxa[8]circulenes2013Ingår i: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 19, nr 2, s. 847-850Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Recently synthesized pi-extended symmetrical tetraoxa[8]circulenes that exhibit electroluminescent properties were calculated at the density functional theory (DFT) level using the quantum theory of atoms in molecules (QTAIM) approach to electron density distribution analysis. Nucleus-independent chemical shift (NICS) indices were used to characterize the aromaticity of the studied molecules. The tetraoxa[8]circulene molecules were found to consist of two antiaromatic perimeters (according to the Huckel "4n" antiaromaticity rule) that include 8 and 24 pi-electrons. Conversely, NICS calculations demonstrated the existence of a common pi-extended system (distributed like a flat ribbon) in the studied tetraoxa[8]circulene molecules. Thus, these symmetrical tetraoxa[8]circulene molecules provide examples of diatropic systems characterized by the presence of induced diatropic ring currents.

  • 40.
    Baryshnikov, Gleb V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Bogdan Khmelnitsky Natl Univ.
    Valiev, Rashid R.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Tomsk State Univ; Tomsk Polytech Univ.
    Karaush, Nataliya N.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Minaeva, Valentina A.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Sinelnikov, Alexandr N.
    Pedersen, Stephan K.
    Pittelkow, Michael
    Minaev, Boris F.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Benzoannelated aza-, oxa- and azaoxa[8]circulenes as promising blue organic emitters2016Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, nr 40, s. 28040-28051Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the present work, we studied the synergetic effect of benzoannelation and NH/O-substitution for enhancing the absorption intensity in a series of novel designed benzoannelated aza- and oxa[8]circulenes. Semi-empirical estimations of the fluorescence rate constants allowed us to determine the most promising fluorophores among all the possible benzoannelated aza-, oxa- and mixed azaoza[8]circulenes. Among them, para-dibenzoannelated [8]circulenes demonstrated the most intense light absorption and emission due to the prevailing role of the linear acene chromophore. Calculated phi(fl) values are in complete agreement with experimental data for a number of already synthesized circulenes. Thus, we believe that the most promising circulenes designed in this study can demonstrate an intensive fluorescence in the case of their successful synthesis, which in turn could be extremely useful for the fabrication of future blue OLEDs. Special attention is devoted to the aromaticity features and peculiarities of the absorption spectra for the two highly-symmetrical (D-4h ground state symmetry) pi-isoelectronic species as well as the so-called tetrabenzotetraaza[8]circulene and tetrabenzotetraoxa[8]circulene molecules. Both of them are characterized by rich electronic spectra, which can be assigned only by taking into account the vibronic coarse structure of the first electronic absorption band; the 0-1 and 0-2 transitions were found to be active in the absorption spectrum in complete agreement with experimental data obtained for both energy and intensity. The corresponding promotive vibrational modes have been determined and their vibronic activity estimated using the Franck-Condon approximation.

  • 41.
    Baryshnikov, Gleb V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Department of Organic Chemistry, Bohdan Khmelnitsky National University, Ukraine.
    Valiev, Rashid R.
    Karaush, Nataliya N.
    Sundholm, Dage
    Minaev, Boris F.
    Aromaticity of the doubly charged [8]circulenes2016Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, nr 13, s. 8980-8992Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Magnetically induced current densities and current pathways have been calculated for a series of fully annelated dicationic and dianionic tetraphenylenes, which are also named [8]circulenes. The gauge including magnetically induced current (GIMIC) method has been employed for calculating the current density susceptibilities. The aromatic character and current pathways are deduced from the calculated current density susceptibilities showing that the neutral [8]circulenes have two concentric pathways with aromatic and antiaromatic character, respectively. The inner octatetraene core (the hub) is found to sustain a paratropic (antiaromatic) ring current, whereas the ring current along the outer part of the macrocycle (the rim) is diatropic (aromatic). The neutral [8]circulenes can be considered nonaromatic, because the sum of the ring-current strengths of the hub and the rim almost vanishes. The aromatic character of the doubly charged [8]circulenes is completely different: the dianionic [8]circulenes and the OC-, CH-, CH2-, SiH-, GeH-, SiH2-, and GeH2-containing dicationic species sustain net diatropic ring currents i.e., they are aromatic, whereas the O-, S-, Se-, NH-, PH- and AsH-containing dicationic [8]circulenes are strongly antiaromatic. The present study also shows that GIMIC calculations on the [8]circulenes provide more accurate information about the aromatic character than that obtained using local indices such as nuclear-independent chemical shifts (NICSs) and H-1 NMR chemical shifts.

  • 42.
    Baryshnikov, Gleb V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Bogdan Khmelnitsky National University, Ukraine; Tomsk State University, Russian Federation.
    Valiev, Rashid R.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Tomsk State University, Russian Federation; Tomsk Polytechnic University, Russian Federation.
    Minaev, Boris F.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Bogdan Khmelnitsky National University, Ukraine; Tomsk State University, Russian Federation.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    A computational study of aromaticity and photophysical properties of unsymmetrical azatrioxa[8]circulenes2017Ingår i: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 41, nr 7, s. 2717-2723Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Owing to their potential use in organic light-emitting diodes and field-effect transistors we present a theoretical study of a series of unsymmetrical azatrioxa[8]circulenes in order to explain the impact of outer substituents and benzoannelation on photophysical constants and aromaticity of these compounds in terms of spin-orbit coupling perturbation and magnetically-induced ring currents. It is argued that the S1-Tn inter-system crossing processes constitute the main deactivation pathways for the fluorescence quenching, something that is supported by a good agreement obtained with experimental data on fluorescence quantum yields. The concept of the gauge-including magnetically induced currents has been applied in order to estimate the role of substituents and benzoannelated fragments on the aromaticity and particularly on the overall balance between the diatropic “aromatic” and paratropic “antiaromatic” current strengths. While a variation of the substituents in the outer perimeter of the studied circulenes does not provide a clear effect on their aromaticity, it is demonstrated that an additional benzoannelation (π-extension) of the azatrioxa[8]circulene macrocycle induces a significant aromaticity enhancement.

  • 43.
    Baryshnikov, Gleb V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Tomsk State University, Russian Federation.
    Valiev, Rashid R.
    Minaev, Boris F.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Siberian Federal University, Russian Federation.
    Optical tuning of tetrabenzo[8]circulene derivatives through pseudorotational conformational isomerization2018Ingår i: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 151, s. 372-379Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In order to further search efficient [8]circulene materials for OLED applications we have theoretically investigated the structure and electronic, absorption spectra of functionalized tetrabenzo[8]circulenes with different substituents in the outer perimeter. These hydrocarbon materials complement the wide family of [8]circulenes which earlier have been demonstrated to possess promising emissive and exciplex-forming properties suitable for organic light emitting diodes. The hydrocarbon tetrabenzo[8]circulenes show saddle shape of the molecular skeleton which can exist in two different conformations with different curvatures of the macrocycle. The aromaticity, electronic structure and orbital pattern are found to be principally different for these two isomers, where the global minimum isomer is weakly antiaromatic and electronically less stable comparing with the non-aromatic local minimum structure. The absorption spectra are also very different: the global minimum structure is more active in the long-wavelength region while the local minimum isomer shows absorption only at short wavelengths. Our computational findings suggest a new concept for optical tuning of curved [8]circulenes through conformational isomerization and aromaticity control, thus through structural variations without changing the molecular composition. Based on this principle we have designed novel functionalized [8]circulenes with promising fluorescence activity.

  • 44.
    Baryshnikov, Gleb V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Valiev, Rashid R.
    Minaev, Boris F.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Substituent-sensitive fluorescence of sequentially N-alkylated tetrabenzotetraaza[8]circulenes2017Ingår i: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 41, nr 15, s. 7621-7625Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We explore the use of substituent-sensitive balance between fluorescence and non-radiative decay as a tool for optical tuning of promising materials for organic light emitting diode applications. A series of N-butylated tetrabenzotetraaza[8]circulenes is studied computationally in order to explain the gradual decrease of fluorescence intensity with the increase of the substituent number. The inter-system crossing probability is found to increase upon the gradual substitution of the circulene macrocycle as a result of the decrease of the S-1-T-1 energy gap due to the deformation of the tetrabenzotetraaza[8] circulenes and therefore the distortion of the pi-conjugation within the macrocycles. In contrast, the S-1-T-1 spin-orbit coupling matrix elements are quite insensitive to the number of outer substituents. As a result, the fluorescence-responsible pi pi(star) transition becomes less intense and the fluorescence rate constant decreases.

  • 45.
    Baryshnikov, Glib V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Bogdan Khmelnitsky Cherkasy National University, Ukraine.
    Bondarchuk, S. V.
    Minaeva, V. A.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Minaev, Boris F.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Bogdan Khmelnitsky Cherkasy National University, Ukraine.
    Solvatochromic effect in absorption and emission spectra of star-shaped bipolar derivatives of 1,3,5-triazine and carbazole. A time-dependent density functional study2017Ingår i: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 23, nr 2, artikel-id 55Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A series of three star-shaped compounds containing both donor (carbazole) and acceptor (2,4,6-triphenyl-1,3,5-triazine) moieties linked through various linking bridges was studied theoretically at the linear response TD-DFT level of theory to describe their absorption and fluorescence spectra. The concept of a localized charge-transfer excited state has been applied successfully to explain the observed strong solvatochromic effect in the emission spectra of the studied molecules, which can be utilized for the fabrication of color tunable solution-processable OLEDs. The concept is in particularly applicable to donor–acceptor species with a C3 symmetry point group where the static dipole moment changes dramatically upon electronic excitation. An important peculiarity of the studied molecules is that they are characterized by non-zero values of the HOMO and LUMO orbitals in the same common part of molecular space that provides a large electric dipole transition moment for both light absorption and emission. [Figure not available: see fulltext.]

  • 46.
    Baryshnikov, Glib V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Cherkasy National University, Ukraine.
    Minaev, B. F.
    Baryshnikova, A. T.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. Siberian Federal University, Russian Federation.
    A computational study of structural and magnetic properties of bi- and trinuclear Cu(II) complexes with extremely long Cu–-Cu distances2017Ingår i: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 491, s. 48-55Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Three recently synthesized copper(II) complexes with aroylhydrazones of trifluoroacetic and benzenecarboxylic acids (Dalton Trans., 2013, 42, 16878) have been computationally investigated by density functional theory within the broken symmetry approximation accounting for empirical dispersion corrections. A topological analysis of electron density distributions has been carried out using Bader's “quantum theory of atoms in molecules” formalism. The calculated values of spin-spin exchange for the studied dinuclear complexes indicate a very weak ferromagnetic coupling of the unpaired electrons in good agreement with experimental data. At the same time, the trinuclear copper(II) complex possesses a low-spin doublet ground state with one ferromagnetic and two antiferromagnetic spin projections between the triangular-positioned Cu2+ ions. The estimated values of the coupling constants for the spin-spin exchange in this trinuclear complex are in a good agreement with experimental observations. The calculations support a mechanism of exchange coupling through the aromatic links in these strongly spin-separated systems.

  • 47.
    Baryshnikov, Glib V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. V. D. Kuznetsov Siberian Physical-Technical Institute at National Research Tomsk State University, Russian Federation.
    Minaev, Boris F.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. V. D. Kuznetsov Siberian Physical-Technical Institute at National Research Tomsk State University, Russian Federation.
    Baryshnikova, A. A.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Anion-induced exchange interactions in binuclear complexes of Cu(II) with flexible hexadentate bispicolylamidrazone ligands2016Ingår i: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 661, s. 48-52Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Two recently synthesized copper(II) complexes with spacer-armed bispicolylamidrazone ligands have been theoretically studied at the density functional theory (DFT) level accounting for empirical dispersion correction and intrinsic anionic environment by perchlorate ions. The exchange parameter between the open-shell singlet and triplet states of the studied complexes has been estimated by broken symmetry DFT calculations. The mechanism of spin-spin exchange interaction between the unpaired electrons via the σ-bond aliphatic chain (Gusev et al., 2015) is confirmed. Instead, a anion-induced mechanism is proposed which means that the anionic grid participates in the exchange interaction between the unpaired electrons.

  • 48.
    Baryshnikov, Glib V.
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Minaeva, Valentina A.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Minaev, Boris F.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Grigoras, M.
    The Electronic Structure and Spectra of Triphenylamines Functionalized by Phenylethynyl Groups2018Ingår i: Optics and Spectroscopy, ISSN 0030-400X, E-ISSN 1562-6911, Vol. 124, nr 1, s. 57-64Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We study the features of the electronic structure and the IR, UV, and visible spectra of a series of triphenylamines substituted with phenylethynyl groups. The analysis is performed at the level of the density functional theory (DFT) and its nonstationary version in comparison with the experimental data of IR and electron spectroscopy. It is shown that, in the excited state, there is a change in the alternation of single, double, and triple bonds in accordance with the character of bonding and antibonding in the lowest vacant molecular orbital. The gradual introduction of additional phenylethynyl groups does not cause frequency shifts in the IR spectra of the molecules under study, but significantly affects the intensity of the corresponding IR bands. A similar effect is also observed in the electronic-absorption spectra of these compounds. This can be used for optical tuning of triphenylamines as promising materials for organic light-emitting diodes and solar cells.

  • 49. Bednarska, Joanna
    et al.
    Zalesny, Robert
    Murugan, N. Arul
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Bartkowiak, Wojciech
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Odelius, Michael
    Elucidating the Mechanism of Zn2+ Sensing by a Bipyridine Probe Based on Two-Photon Absorption2016Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, nr 34, s. 9067-9075Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this work, we examine, by means of computational methods, the mechanism of Zn2+ sensing by a bipyridine-centered, D-pi-A-pi-D-type-ratiometric molecular probe. According to recently published experimental data [Divya, K. P.; Sreejith, S.; Ashokkumar, P.; Yuzhan, K.; Peng, Q; Maji, S. K.; Tong, Y.; Yu, H.; Zhao, Y.; Ramamurthy, P.; Ajayaghosh, A. A ratiometric fluorescent molecular -probe with enhanced two-photon response upon Zn2+ binding for in vitro and in vivo: bioimaging.= Chem. Sci. 2014, S, 3469-3474], after coordination to zinc ions the -probe exhibits a large enhancement of the two -photon absorption cross section. The goal of our investigation was to elucidate the mechanism behind this phenomenon. For this purpose, linear and nonlinear optical properties of -the unbound (cation-free) and bound probe were calculated, including the influence of solute Solvent interactions, implicitly using a polarizable continuum model and exp-licitely employing the QM/MM approach. Because the results of the calculations indicate that many conformers of the probe are energetically accessible at room temperature in solution and hence contribute to the Signal, structurepteperty relationships were also taken into account. Results of our simulations-demonstrate that the one-photon absorption bands for both the unbound -and bound forms correspond to the bright pi -> pi* transition to the first excited state; which, on the other hand,. exhibits negligible two-photon activity. On the basis of the results of the quadratic respOnse calculations, we put forward-notion that it is the second excited state that gives the strong signal in the experimental nonlinear spectrum. To explain the differenCes in the two-photon absorption activity for the two lowest-lying excited states and nonlinear response enhancement upon binding, we employed the generalized few -state model including the ground, first, and- second excited states. The analysis of the optical channel suggests that the large two-photon response is due to the coordination -induced increase of the, transition- moment from the first to the second excited state.

  • 50. Bednarska, Joanna
    et al.
    Zalesny, Robert
    Tian, Guangjun
    Natarajan Arul, Murugan
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Bartkowiak, Wojciech
    Nonempirical Simulations of Inhomogeneous Broadening of Electronic Transitions in Solution: Predicting Band Shapes in One- and Two-Photon Absorption Spectra of Chalcones2017Ingår i: Molecules, ISSN 1420-3049, E-ISSN 1420-3049, Vol. 22, nr 10, artikel-id 1643Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have examined several approaches relying on the Polarizable Embedding (PE) scheme to predict optical band shapes for two chalcone molecules in methanol solution. The PE-TDDFT and PERI-CC2 methods were combined with molecular dynamics simulations, where the solute geometry was kept either as rigid, flexible or partly-flexible (restrained) body. The first approach, termed RBMD-PE-TDDFT, was employed to estimate the inhomogeneous broadening for subsequent convolution with the vibrationally-resolved spectra of the molecule in solution determined quantum-mechanically (QM). As demonstrated, the RBMD-PE-TDDFT/QM-PCM approach delivers accurate band widths, also reproducing their correct asymmetric shapes. Further refinement can be obtained by the estimation of the inhomogeneous broadening using the RBMD-PERI-CC2 method. On the other hand, the remaining two approaches (FBMD-PE-TDDFT and ResBMD-PE-TDDFT), which lack quantum-mechanical treatment of molecular vibrations, lead to underestimated band widths. In this study, we also proposed a simple strategy regarding the rapid selection of the exchange-correlation functional for the simulations of vibrationally-resolved one-and two-photon absorption spectra based on two easy-to-compute metrics.

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