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  • 151.
    Brändas, Erkki J
    et al.
    Uppsala University.
    Kryachko, Eugene S.
    Uppsala University.
    Fundamental World of Quantum Chemistry: A Tribute to the Memory of Per-Olov Löwdin: Volume I2003In: Fundamental World of Quantum Chemistry, Vol. I, p. 1-677Book (Refereed)
  • 152.
    Brändas, Erkki J
    et al.
    Uppsala University.
    Kryachko, Eugene S.
    Uppsala University.
    Fundamental World of Quantum Chemistry: A Tribute to the Memory of Per-Olov Löwdin: Volume II2003In: Fundamental World of Quantum Chemistry, Vol. II, p. 1-696Book (Refereed)
  • 153.
    Brändas, Erkki J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Materials Science. Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry.
    Levitina, Tatiana
    Filter Diagonalization: filtering and postprocessing with prolates.2009In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 180, no 9, p. 1448-1457Article in journal (Refereed)
    Abstract [en]

    A detailed account is given of a recent modification of the Filter Diagonalization technique that serves to analyze a signal spectrum within a selected energy range. Our approach employs for filtering the eigenfunctions of the Finite Fourier Transform, or prolates, which are superior to other filters due to their special properties. In particular, prolates are simultaneously band-limited and highly concentrated at a finite time-interval, producing filters with optimal accuracy. In addition both features are acquired by the convolution of a band-limited function with a prolate, that permits the latter to be interpolated via the Walter and Shen sampling formula, which essentially simplifies the supplementary computations. Rigorous filtering error estimates are obtained. Test calculations illustrate the facilities of the presented modification.

  • 154.
    Brändas, Erkki J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lunell, Sten
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Obituary: Osvaldo Goscinski (1938–2013)2015Other (Other academic)
  • 155.
    Brändas, Erkki J
    et al.
    Uppsala University.
    Öhrn, Yngve
    Uppsala University.
    International Journal of Quantum Chemistry2003In: International Journal of Quantum Chemistry, Vol. 91-95, no 1-6, p. 1-4000Other (Other scientific)
  • 156.
    Brändas, Erkki
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry. Kvantkemi.
    Kryachko, Eugene
    Preface: A Tribute Volume in Honour of Professor Osvaldo Goscinski2004In: Advances in Quantum Chemistry, ISSN 0065-3276, Vol. 47, p. xvii-xviiiArticle in journal (Other scientific)
  • 157.
    Brändas, Erkki
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics. ADVANCED INSTRUMENTATION AND MEASUREMENTS.
    Sabin, John R.
    Preface2003In: Advances in Quantum Chemistry, Elsevier Inc. , 2003, Vol. 43, p. xi-xiiChapter in book (Other academic)
  • 158.
    Brändas, Erkki
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Physics. Chemistry, Department of Biochemistry. QUANTUM CHEMISTRY.
    Öhrn, Yngve
    Aims & Scope International Journal of Quantum Chemistry2001In: International Journal Of Quantum Chemistry, Vol. 81, no 3Other (Other scientific)
  • 159. Bunta, Juraj
    et al.
    Dahlberg, Martin
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Korolev, Nikolai
    Laaksonen, Aatto
    Lohikoski, Raimo
    Lyubartsev, Alexander
    Pinak, Miroslav
    Schyman, Patric
    Solvating, manipulating, damaging, and repairing DNA in a computer2007In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 107, no 2, p. 279-291Article in journal (Refereed)
    Abstract [en]

    This work highlights four different topics in modeling of DNA: (i) the importance of water and ions together with the structure and function of DNA; the hydration structure around the ions appears to be the determining factor in the ion coordination to DNA, as demonstrated in the results of our MD simulations; (ii) how MD simulations can be used to simulate single molecule manipulation experiments as a complement to reveal the structural dynamics of the studied biomolecules; (iii) how damaged DNA can be studied in computer simulations; and (iv) how repair of damaged DNA can be studied theoretically.

  • 160.
    Bushnell, Eric A C
    et al.
    University of Windsor, Windsor, ON, N9B 3P4, Canada.
    Erdtman, Edvin
    Örebro University, School of Science and Technology.
    Llano, Jorge
    University of Windsor, Windsor, ON, N9B 3P4, Canada.
    Eriksson, Leif A.
    National University of Ireland, Galway, University Road, Galway, Ireland.
    Gauld, James W.
    University of Windsor, Windsor, ON, N9B 3P4, Canada.
    Computational insights into the first branching point in porphyrin biosynthesis: decarboxylation of ring D in URO–III by Uroporphyrinogen–III DecarboxylaseManuscript (preprint) (Other academic)
  • 161.
    Bushnell, Eric A. C.
    et al.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Erdtman, Edvin
    Örebro University, School of Science and Technology.
    Llano, Jorge
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Eriksson, Leif A.
    Örebro University, School of Science and Technology.
    Gauld, James W.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 5, p. 822-834Article in journal (Refereed)
    Abstract [en]

    In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate-limiting step was found to be the initial protontransfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various activesite residues as well as several other functional groups.

  • 162.
    Bushnell, Eric A. C.
    et al.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada.
    Erdtman, Edvin
    Örebro universitet, Akademin för naturvetenskap och teknik, Örebro Universitet, Örebro, Sweden.
    Llano, Jorge
    Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada.
    Eriksson, Leif A.
    Örebro universitet, Akademin för naturvetenskap och teknik; School of Chemistry, National University of Ireland, Galway, Ireland.
    Gauld, James W.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada.
    The first branching point in porphyrin biosynthesis: a systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen-III decarboxylase2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 5, p. 822-834Article in journal (Refereed)
    Abstract [en]

    In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen-III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen-III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1 at 298.15 K. The rate-limiting step was found to be the initial protontransfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various activesite residues as well as several other functional groups.

  • 163.
    Börjesson, Anders
    et al.
    University of Borås, School of Engineering.
    Erdtman, Edvin
    University of Borås, School of Engineering.
    Ahlström, Peter
    University of Borås, School of Engineering.
    Berlin, Mikael
    Andersson, Thorbjörn
    Bolton, Kim
    University of Borås, School of Engineering.
    Molecular modelling of oxygen and water permeation in polyethylene2013In: Polymer, ISSN 0032-3861, E-ISSN 1873-2291, Vol. 54, no 12, p. 2988-Article in journal (Refereed)
    Abstract [en]

    Monte Carlo and molecular dynamics simulations were performed to calculate solubility, S, and diffusion, D, coefficients of oxygen and water in polyethylene, and to obtain a molecular-level understanding of the diffusion mechanism. The permeation coefficient, P, was calculated from the product of S and D. The AMBER force field, which yields the correct polymer densities under the conditions studied, was used for the simulations, and it was observed that the results were not sensitive to the inclusion of atomic charges in the force field. The simulated S for oxygen and water are higher and lower than experimental data, respectively. The calculated diffusion coefficients are in good agreement with experimental data. Possible reasons for the discrepancy in the simulated and experimental solubilities, which results in discrepancies in the permeation coefficients, are discussed. The diffusion of both penetrants occurs mainly by large amplitude, infrequent jumps of the molecules through the polymer matrix.

  • 164.
    Börjesson, Anders
    et al.
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Erdtman, Edvin
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Ahlström, Peter
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Berlin, Mikael
    Tetra Pak Packaging Solutions AB, Ruben Rausings gata, Lund, Sweden.
    Andersson, Thorbjörn
    Tetra Pak Packaging Solutions AB, Ruben Rausings gata, Lund, Sweden.
    Bolton, Kim
    Högskolan i Borås, Institutionen Ingenjörshögskolan.
    Molecular modelling of oxygen and water permeation in polyethylene2013In: Polymer, ISSN 0032-3861, E-ISSN 1873-2291, Vol. 54, no 12, p. 2988-Article in journal (Refereed)
    Abstract [en]

    Monte Carlo and molecular dynamics simulations were performed to calculate solubility, S, and diffusion, D, coefficients of oxygen and water in polyethylene, and to obtain a molecular-level understanding of the diffusion mechanism. The permeation coefficient, P, was calculated from the product of S and D. The AMBER force field, which yields the correct polymer densities under the conditions studied, was used for the simulations, and it was observed that the results were not sensitive to the inclusion of atomic charges in the force field. The simulated S for oxygen and water are higher and lower than experimental data, respectively. The calculated diffusion coefficients are in good agreement with experimental data. Possible reasons for the discrepancy in the simulated and experimental solubilities, which results in discrepancies in the permeation coefficients, are discussed. The diffusion of both penetrants occurs mainly by large amplitude, infrequent jumps of the molecules through the polymer matrix.

  • 165.
    C. Couto, Rafael
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vaz da Cruz, Vinícius
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ertan, Emelie
    Eckert, Sebastian
    Fondell, Mattis
    Dantz, Marcus
    Kennedy, Brian
    Schmitt, Thorsten
    Pietzsch, Annette
    F. Guimarães, Freddy
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gel’mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Odelius, Michael
    Kimberg, Victor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Föhlisch, Alexander
    Selective gating to vibrational modes through resonant X-ray scattering2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, p. 14165-1-14165-7Article in journal (Refereed)
    Abstract [en]

    The dynamics of fragmentation and vibration of molecular systems with a large number of coupled degrees of freedom are key aspects for understanding chemical reactivity and properties. Here we present a resonant inelastic X-ray scattering (RIXS) study to show how it is possible to break down such a complex multidimensional problem into elementary components. Local multimode nuclear wave packets created by X-ray excitation to different core-excited potential energy surfaces (PESs) will act as spatial gates to selectively probe the particular ground-state vibrational modes and, hence, the PES along these modes. We demonstrate this principle by combining ultra-high resolution RIXS measurements for gas-phase water with state-of-the-art simulations.

  • 166.
    Cao, Hui
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Dynamic Effects on Electron Transport in Molecular Electronic Devices2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    HTML clipboardIn this thesis, dynamic effects on electron transport in molecular electronic devices are presented. Special attention is paid to the dynamics of atomic motions of bridged molecules, thermal motions of surrounding solvents, and many-body electron correlations in molecular junctions.

    In the framework of single-body Green’s function, the effect of nuclear motions on electron transport in molecular junctions is introduced on the basis of Born-Oppenheimer approximation. Contributions to electron transport from electron-vibration coupling are investigated from the second derivative of current-voltage characteristics, in which each peak is corresponding to a normal mode of the vibration. The inelastic-tunneling spectrum is thus a useful tool in probing the molecular conformations in molecular junctions. By taking account of the many-body interaction between electrons in the scattering region, both time-independent and time-dependent many-body Green’s function formula based on timedependent density functional theory have been developed, in which the concept of state of the system is used to provide insight into the correlation effect on electron transport in molecular devices.

    An effective approach that combines molecular dynamics simulations and first principles calculations has also been developed to study the statistical behavior of electron transport in electro-chemically gated molecular junctions. The effect of thermal motions of polar water molecules on electron transport at different temperatures has been found to be closely related to the temperature-dependent dynamical hydrogen bond network.

  • 167.
    Cao, Hui
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ma, Jing
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Statistical Behavior of Electrochemical Single Molecular Field Effect Transistor2009In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126Article in journal (Refereed)
  • 168.
    Carlsen, Henrik
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Physics, Department of Quantum Chemistry.
    Quantal trajectories and geometric phase1998Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis concerns the following topics: geometric phase in the context of Galilean invariance and quantum measurements, Rydberg states of hydrogen atoms, vibronic coupling in the <I>E Ä e Jahn-Teller system and realism in quantum computations. In the analyses the de Broglie-Bohm pilot-wave formulation of quantummechanics is mainly used.

    It is shown that geometric phase is not Galilean invariant. Experimental implications are discussed and it is found that the experiments performed to date are frame independent. An experiment which is in principle able to detect the noninvariance is sketched. By adopting the measurement theory of the pilot-wave formulation it is shown how the measurement induced geometric phase continuously emerges. The Samuel-Bhandari geometric phase is identified as the nonrandom part of the total geometric phase induced in the measurement.

    Ensembles of particles for a circular Rydberg wave packet are studied. The trajectories of pilot-wave particles are shown to accurately imitate the behaviour of the wave packet in the high quantum number limit. The nonclassical features of the wave packet are intuitively explained by the nonvanishing quantum potential.

    Vibronic coupling in the Longuet-Higgins model of the <I>E Ä e Jahn-Teller system is investigated by means of quantal trajectories. The pilot-wave picture provides an intuitive tool for discussing time-scales. An argument based on ergodicity leads to an understanding of the averaging procedure over the electronic motion which provides the approximate nuclear motion.

    The existence of efficient quantum algorithms triggers questions on Natures ability of storing and processing information during quantum computations. The role of elements of reality in quantum computations is addressed using quantal trajectories. It is found that there is a many-to-one relationship between quantal trajectories and performed computations when quantum parallelism is utilized.

  • 169. Carniato, Stéphane
    et al.
    Taïeb, Richard
    Kukk, Edwin
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Brena, Barbara
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    N-K near edge x-ray absorption fine structures of acetonitrile in gas phase2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 123, no 21, p. 214301-Article in journal (Refereed)
    Abstract [en]

     The dynamic processes of N(1s) core-hole excitation in gas-phase CH3CN molecule have been studied at both Hartree-Fock and hybrid density-functional theory levels. The vibrational structure is analyzed for fully optimized core-excited states. Frank-Condon factors are obtained using the linear coupling model for various potential surfaces. It is found that the vibrational profile of the N-K absorption can be largely described by a summation of two vibrational progressions: a structure-rich profile of nu((CN)) stretching mode and a large envelope of congestioned vibrational levels related to the strong (-C-CN) terminal bending bond. Excellent agreement between theoretical and experimental spectra is obtained.

  • 170.
    Carvalho Couto, Rafael
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Coupled electron-nuclear dynamics in inelastic X-ray scattering2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This Thesis is devoted to theoretical and experimental studies of resonant inelastic X-ray scattering (RIXS) of carbon monoxide and water molecules. Using state-of-the-art ab initio electronic structure calculations and a time-dependent wave packet formalism, we make a complete analysis of the experimental RIXS spectra of the two molecular systems. In the CO RIXS analysis, we are able to reproduce the RIXS experiment with an excellent accuracy. Interference between different RIXS channels corresponding to the scattering via orthogonal molecular orbitals in the core-excited state of CO is described. We show the complete breakdown of the Born-Oppenheimer approximation in the region where forbidden final Rydberg states are mixed with a valence allowed final state. Here we explain the formation of a spectral feature which was attributed to a single state in previous studies. Moreover, through an experimental-theoretical combination, we improve the minimum of the valence E’Π excited state potential, along with the coupling constant between two Rydberg states. We developed a new theoretical approach to describe triatomic molecules through the wave packet propagation formalism to study the water system, which reproduces with high accuracy the vibrational structure of the high-resolution experimental quasi-elastic RIXS spectra. We demonstrate that due to the vibrational mode coupling and anharmonicity of the ground and core-excited potential energy surfaces, different core-excited states in RIXS can be used as gates to probe different vibrational dynamics and to map the ground state potential. Isotopic substitution is investigated by theoretical simulations and important dynamical features are discussed, especially for the dissociative core-excited state, where a so-called “atomic” peak is formed. We show the strong potential of high-resolution RIXS experiments combined with high-level theoretical simulations for advanced studies of highly excited molecular states.

  • 171.
    Castleton, Christopher W. M.
    et al.
    Nottingham Trent Univ, Sch Sci & Technol, Nottingham NG11 8NS, England;Malardalen Univ, Div Phys & Math Nat Sci Didact, Box 883, SE-72123 Vasteras, Sweden.
    Lee, Amy
    Nottingham Trent Univ, Sch Sci & Technol, Nottingham NG11 8NS, England.
    Kullgren, Jolla
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Structural Chemistry.
    Benchmarking Density Functional Theory Functionals for Polarons in Oxides: Properties of CeO22019In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 123, no 9, p. 5164-5175Article in journal (Refereed)
    Abstract [en]

    We examine methods for studying polarons in metal oxides with density functional theory (DFT), using the example of cerium dioxide and the functionals, local density approximation + U (LDA+U), generalized gradient approximation + U (GGA+U) in the Perdew-Burke-Ernzerhof parametrization (PBE+U), as well as the hybrid functionals B3LYP, Heyd Scuseria Ernzerhof (HSE)03, HSE06, and PBEO. We contrast the four polaron energies commonly reported in different parts of the literature: formation energy, localization/relaxation energy, density-of-states level, and polaron-hopping activation barrier. Qualitatively, all these functionals predict "small" (Holstein) polarons on the scale of a single lattice site, although LDA +U and GGA+U are more effective than the hybrids at localizing the Ce 4f electrons. The improvements over pure LDA/GGA appear because of changes in the filled Ce 4f states when using LDA/GGA+U but due to changes in the empty Ce 4f states when using the hybrids. DFT is shown to have sufficient correlation to predict both adiabatic and (approximate) diabatic hopping barriers. Overall, LDA+U = 6 eV provides the best description in comparison to the experiment, followed by GGA+U = 5 eV. The hybrids are worse, tending to overestimate the gap and significantly underestimate the polaron-hopping barriers.

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

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

  • 173.
    Chen, Guanying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ohulchanskyy, T. Y.
    Liu, S.
    Law, W. -C
    Wu, F.
    Swihart, M. T.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Prasad, P. N.
    Core/shell NaGdF 4:Nd 3+/NaGdF 4 nanocrystals with efficient near-infrared to near-infrared downconversion photoluminescence for bioimaging applications2012In: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 6, no 4, p. 2969-2977Article in journal (Refereed)
    Abstract [en]

    We have synthesized core/shell NaGdF 4:Nd 3+/NaGdF 4 nanocrystals with an average size of 15 nm and exceptionally high photoluminescence (PL) quantum yield. When excited at 740 nm, the nanocrystals manifest spectrally distinguished, near-infrared to near-infrared (NIR-to-NIR) downconversion PL peaked at ∌900, ∌1050, and ∌1300 nm. The absolute quantum yield of NIR-to-NIR PL reached 40% for core-shell nanoparticles dispersed in hexane. Time-resolved PL measurements revealed that this high quantum yield was achieved through suppression of nonradiative recombination originating from surface states and cross relaxations between dopants. NaGdF 4:Nd 3+/NaGdF 4 nanocrystals, synthesized in organic media, were further converted to be water-dispersible by eliminating the capping ligand of oleic acid. NIR-to-NIR PL bioimaging was demonstrated both in vitro and in vivo through visualization of the NIR-to-NIR PL at ∌900 nm under incoherent lamp light excitation. The fact that both excitation and the PL of these nanocrystals are in the biological window of optical transparency, combined with their high quantum efficiency, spectral sharpness, and photostability, makes these nanocrystals extremely promising as optical biomaging probes.

  • 174.
    Chen, Guanying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ohulchanskyy, Tymish Y.
    Law, Wing Cheung
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Prasad, Paras N.
    Monodisperse NaYbF4: Tm3+/NaGdF4 core/shell nanocrystals with near-infrared to near-infrared upconversion photoluminescence and magnetic resonance properties2011In: NANOSCALE, ISSN 2040-3364, Vol. 3, no 5, p. 2003-2008Article in journal (Refereed)
    Abstract [en]

    We report core/shell NaYbF4 : Tm3+/NaGdF4 nanocrystals to be used as probes for bimodal near infrared to near infrared (NIR-to-NIR) upconversion photoluminescence (UCPL) and magnetic resonance (MR) imaging. The NaYbF4 : Tm3+ nanocrystals were previously reported to produce the intense NIR-to-NIR UCPL peaked at similar to 800 nm under excitation at similar to 975 nm. We have found that the growth of a NaGdF4 shell on surface of the NaYbF4 : Tm3+ nanocrystals results in the increase in the intensity of UCPL of Tm3+ ions by about 3 times. Unlike biexponential PL decay of NaYbF4 : Tm3+ nanocrystals, the PL decay of NaYbF4 : Tm3+/NaGdF4 core/shell nanocrystals is single exponential and of longer lifetime due to the suppression of surface quenching effects for Tm3+ PL. The growth of a NaGdF4 shell on surface of the NaYbF4 : Tm3+ nanocrystals also provides high MR relaxivity from paramagnetic Gd3+ ions contained in the shell. The T1-weighted MR signal of the (NaYbF4:2% Tm3+)/NaGdF4 nanoparticles was measured to be about 2.6 mM(-1)s(-1). Due to the combined presence of efficient optical and MR imaging capabilities, nanoprobes based on NaYbF4 : Tm3+/NaGdF4 fluoride nanophosphors can be considered as a promising platform for simultaneous bimodal PL and MR bioimaging.

  • 175.
    Chen, Shilu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Quantum Chemical Modeling of Binuclear Zinc Enzymes2008Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    In the present thesis, the reaction mechanisms of several di-zinc hydrolases have been explored using quantum chemical modeling of the enzyme active sites. The studied enzymes are phosphotriesterase (PTE), aminopeptidase from Aeromonas proteolytica (AAP), glyoxalase II (GlxII), and alkaline phosphatase (AP). All of them contain a binuclear divalent zinc core in the active site. The density functional theory (DFT) method B3LYP functional was employed in the investigations. The potential energy surfaces (PESs) for various reaction pathways have been mapped and the involved transition states and intermediates have been characterized. The hydrolyses of different types of substrates were examined, including phosphate esters (PTE and AP) and the substrates containing carbonyl group (AAP and GlxII). The roles of zinc ions and individual active-site residues were analyzed and general features of di-zinc enzymes have been characterized.

    The bridging hydroxide stabilized by two zinc ions has been confirmed to be capable of the nucleophile in the hydrolysis reactions. PTE, AAP, and GlxII all employ the bridging hydroxide as the direct nucleophile. Furthermore, it is shown that either one of or both zinc ions provide the main catalytic power by stabilizing the negative charge developing during the reaction and thereby lowering the barriers. In the cases of GlxII and AP, one of zinc ions also contributes to the catalysis by stabilizing the leaving group. These features perfectly satisfy the two requisites for the hydrolysis, i.e. sufficient nucleophilicity and stabilization of charge. A competing mechanism, in which the bridging hydroxide acts as a base, was shown to have significantly higher barrier in the case of PTE.

    For phosphate hydrolysis reactions, it is important to characterize the nature of the transition states involved in the reactions. Associative mechanisms were observed for both PTE and AP. The former uses a step-wise associative pathway via a penta-coordinated intermediate, while the latter proceeds through a concerted associative path via penta-coordinated transition states.

    Finally, with PTE as a test case, systematic evaluation of the computational performance of the quantum chemical modeling approach has been performed. This assessment, coupled with other results of this thesis, provide an effective demonstration of the usefulness and powerfulness of quantum chemical active-site modeling in the exploration of enzyme reaction mechanisms and in the characterization of the transition states involved.

  • 176. Chen, Shu-Feng
    et al.
    Liu, Ya-Jun
    Navizet, Isabelle
    Ferré, Nicolas
    Fang, Wei-Hai
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Quantum Chemistry.
    Systematic theoretical investigation on the light emitter of firefly2011In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, no 3, p. 798-803Article in journal (Refereed)
    Abstract [en]

    This is a systematic theoretical investigation on all the possible light emitters of firefly using multireference method. Six chemical forms of oxyluciferin (OxyLH2) molecules/anions were studied by a multi-state complete active space second order perturbation (MS-CASPT2) method in vacuum and DMSO. The calculated results and subsequent analysis excluded enol-OxyLH2, keto-OxyLH2 and enolate-OxyLH- as possible light emitters. The remaining three candidates, phenolate-enol-OxyLH-, phenolate-keto-OxyLH- and OxyL2-, were further investigated in protein by a MS-CASPT2/molecular mechanics (MM) study to explain the natural bioluminescence of firefly. By comparison of the MS-CASPT2/MM calculated results of phenolate-enol-OxyLH-, phenolate-keto-OxyLH- and OxyL2- with the experimental observation and detailed analysis, we concluded that the direct decomposition excited-state product of firefly dioxetanone in vivo and the only light emitter of firefly in natural bioluminescence is the first singlet exited state (S1) of phenolate-keto-OxyLH-.

  • 177. Chen, Shufeng
    et al.
    Navizet, Isabelle
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Liu, Yajun
    Ferre, Nicolas
    Bioluminescence of Obelin: identification of the light emitters using QM/MM models2014In: Luminescence (Chichester, England Print), ISSN 1522-7235, E-ISSN 1522-7243, Vol. 29, p. 19-19Article in journal (Other academic)
  • 178.
    Chen, Tao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Temperature effects on anharmonic infrared spectra of large compact polycyclic aromatic hydrocarbons2019In: Astronomy and Astrophysics, ISSN 0004-6361, E-ISSN 1432-0746, Vol. 622, article id A152Article in journal (Refereed)
    Abstract [en]

    Aims. Large compact polycyclic aromatic hydrocarbon molecules (PAHs) present special interest in the astrochemical community. A key issue in analyses of large PAHs is understanding the effect that temperature and anharmonicity have on different vibrational bands, and thus interpreting the infrared (IR) spectra for molecules under various conditions. Methods. Because of the huge amount of interactions/resonances in large PAHs, no anharmonic IR spectrum can be produced with static/time-independent ab initio method, especially for the molecules with D6h symmetry, e.g., coronene and circumcoronene. In this work, we performed molecular dynamics simulations to generate anharmonic IR spectra of coronene and circumcoronene. Results. The method is validated for small PAHs, i.e., naphthalene and pyrene. We find that the semiempirical method PM3 produces accurate band positions with an error <5 cm(-1). Furthermore, we calculate the spectra at multiple temperatures and find a clear trend toward band shifting and broadening.

  • 179.
    Chen, Tao
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Formation of polyynes and ring-polyyne molecules following fragmentation of polycyclic aromatic hydrocarbons2019In: Monthly notices of the Royal Astronomical Society, ISSN 0035-8711, E-ISSN 1365-2966, Vol. 486, no 2, p. 1875-1881Article in journal (Refereed)
    Abstract [en]

    In this work, we perform molecular dynamic (MD) simulations to investigate the stability and fragmentation processes of vibrationally excited linear polycyclic aromatic hydrocarbons (PAHs). The program of CP2K in combination with the semi-empirical method PM3 is utilized for the MD simulations. The simulations show that the formation of molecular hydrogens (H-2) is different than previous studies, in particular, different than compact PAHs. At high temperatures, linear PAHs tend to open aromatic rings and convert the sp(3) C-C or sp(2) C=C bonds to sp C C bonds by removing H-2; i.e. polyynes are formed in such process. Besides polyynes, PAHs attached with sp-bonded polyyne chains are commonly observed at high temperatures. We notice that due to the addition of flexible tails (polyynes), the ring-polyyne molecules do not dissociate for a long period of time at high temperatures. Such structures facilitate the molecules to survive in the harsh environment of the interstellar medium. In addition, the ring-polyyne structures induce dipole moments that could, in principle, be detected by radio astronomy.

  • 180. Chen, X.
    et al.
    Zhu, L.
    Wang, D.
    Zou, Q.
    Li, Xin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Chen, W.
    A unimolecular platform based on diarylethene with multiple stimuli-gated photochromism2019In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 164, p. 91-96Article in journal (Refereed)
    Abstract [en]

    The gated photochromic systems have attracted great interest in scientific researches due to their merits in the opto-electronic fields, whereas the multi-stimuli gating function in a unimolecular platform has rarely been addressed. Herein, a new strategy to realize multi-stimuli gated photochromic function was devised relying on a simple Schiff-based diarylethene derivative. The compound shows no photoswitching properties in solution under irradiation with any wavelength of light. It is noteworthy that mecury(II) ions, water and protons can trigger its photo-reactivity independently with different absorption changes, respectively. Therefore, a molecular logic circuit with four inputs, including mecury(II) ions, water, protons and UV light, was fabricated on the basis of the unimolecular platform, suggesting promise for application in multi-controlled photoswitchings. These results could be valuable for the further development of photoswitchings with multiple stimuli responses.

  • 181.
    Chen, Xing
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical Studies on Magnetic and Photochemical Properties of Organic Molecules2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The present thesis is concerned with the theoretical studies on magnetic and photochemical properties of organic molecules. The ab initio and first principles theories were employed to investigate the vibrational effects on the isotropic hyperfine coupling constant (HFCC) known as the critical parameter in electron paramagnetic resonance spectrum, the theoretical simulations of the vibronically resolved molecular spectra, the photo-induced reaction mechanism of α-santonin and the spin-forbidden reaction of triplet-state dioxygen with cofactor-free enzyme. The theoretical predictions shed light on the interpretation of experimental observations, the understanding of reaction mechanism, and importantly the guideline and perspective in respect of the popularized applications.

    We focused on the vibrational corrections to the isotropic HFCCs of hydrogen and carbon atoms in organic radicals. The calculations indicate that the vibrational contributions induce or enhance the effect of spin polarization. A set of rules were stated to guide experimentalist and theoretician in identification of the contributions from the molecular vibrations to HFCCs. And the coupling of spin density with vibrational modes in the backbone is significant and provides the insight into the spin density transfer mechanism in organic π radicals.

    The spectral characters of the intermediates in solid-state photoarrangement of α-santonin were investigated in order to well understand the underlying experimental spectra. The molecular spectra simulated with Franck-Condon principle show that the positions of the absorption and emission bands of photosantonic acid well match with the experimental observations and the absorption spectrum has a vibrationally resolved character.

    α-Santonin is the first found organic molecule that has the photoreaction activities. The photorearrangement mechanism is theoretically predicted that the low-lying excited state 1(nπ*) undergoing an intersystem crossing process decays to 3(ππ*) state in the Franck-Condon region. A pathway which is favored in the solid-state reaction requires less space and dynamic advantage on the excited-state potential energy surface (PES). And the other pathway is predominant in the weak polar solvent due to the thermodynamical and dynamical preferences. Lumisantonin is a critical intermediate derived from α-santonin photoreaction. The 3(ππ*) state plays a key role in lumisantonin photolysis. The photolytic pathway is in advantage of dynamics and thermodynamics on the triplet-state PES. In contrast, the other reaction pathway is facile for pyrolysis ascribed to a stable intermediate formed on the ground-state PES.

     The mechanism of the oxidation reaction involving cofactor-free enzyme and triplet-state dioxygen were studied. The theoretical calculations show that the charge-transfer mechanism is not a sole way to make a spin-forbidden oxidation allowed. It is more likely to take place in the reactant consisting of a non-conjugated substrate. The other mechanism involving the surface hopping between the triplet- and singlet-state PESs via a minimum energy crossing point (MECP) without a significant charge migration. The electronic state of MECP exhibits a mixed characteristic of the singlet and triplet states. The enhanced conjugation of the substrate slows down the spin-flip rate, and this step can in fact control the rate of the reaction that a dioxygen attaches to a substrate.

  • 182.
    Chen, Xing
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Theoretical studies on molecular magnetic properties2010Licentiate thesis, comprehensive summary (Other academic)
  • 183.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cao, Zexing
    Department of Chemistry, Xiamen Univeristy.
    Theoretical studies on the mechanism of α-santonin photo-induced rearrangement2012In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 13, no 1, p. 353-362Article in journal (Refereed)
    Abstract [en]

    α-Santonin is the first organic compound observed to feature a photoinduced rearrangement and is now known to undergo a series of photochemical processes under UV irradiation. On the basis of the considerable interest of this system as a prototype, and of the yet limited insights reached for the basic photo mechanisms, we calculate the high-level electronic structures and explore the potential energy surfaces (PES) of α-santonin in the ground and lowest-lying excited states, their couplings, and the possible photoinduced isomerization pathways. The calculations identify the low-lying singlet excited state 1(nπ*) accessible under light irradiation, which decays to the low-energy 3(ππ*) state through an intersystem crossing in the Franck–Condon region to initiate the photoinduced rearrangement. The initial reaction from the C3C5 bond coupling, which takes place on the 3(ππ*) state potential energy surface, leads to a three-membered alkyl-ring compound intermediate state INT. The following photochemical reactions have the possibility to arise from two distinct CC bond cleavages, C4C5 and C3C4, denoted as path A and path B. Path A is favored both dynamically on the excited-state PES and thermodynamically on the ground-state PES in vacuo. Experiments show that it also becomes the dominant photoinduced rearrangement process in the crystal, which can be explained by considering the requirement for less space and the stacking effect under the confined environment. Path B is dynamical advantaged both on the ground- and excited-state PESs in a weak polar solvent, such as dioxane. Once the biradical intermediate B-INT is accessible on the ground-state PES, the formation of the product B-P is almost barrier free.

  • 184.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ruud, Kenneth
    Centre ofTheoretical and computational Chemistry, Department of Chemistry, University of Tromsø.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vibrationally induced carbon hyperfine coupling constants: a reinterpretation of the McConnell relationManuscript (preprint) (Other academic)
  • 185.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, Guangjun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cao, Zexing
    Department of Chemistry, Xiamen Univeristy.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Spectral character of intermediate state in solid-state photoarrangement of alpha-santonin2012In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 405, p. 40-45Article in journal (Refereed)
    Abstract [en]

    The vibronically resolved spectra of an intermediate and a product involved in the photoreaction of alpha-santonin have been explored by the density functional theory and the post-SCF methodologies, and a detailed comparison of theory with experiment was conducted to obtain reliable assignments to the observed spectra. The predicted emission energies of photosantonic acid and a topochemical product are found to match with the experimental values reasonably. The further calculations manifest that the absorption spectrum of photosantonic acid exhibits vibrationally resolved features, while the absorption band of topochemical product without vibrational resolution is opposite to the experimental observation. These new computational findings lead to a revised assignment to the observed bands and provide a basis for experimentalists to draw a convinced reaction mechanism for the alpha-santonin photorearrangement.

  • 186.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ying, Fuming
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Wu, Wei
    Department of Chemsitry, Center for Theoretical Chemistry, and the State Kay Laboratory for Physical Chemistry of Solid Surfaces, Xiamen University, Xiamen 361005, China.
    Cao, Zexing
    Department of Chemistry, Center for Theoretical Chemsitry, and the State Key Laboratory for Physical Chemsitry of Solid Surfaces, Xiamen University, Xiamen 361005, China.
    Restricted-unrestricted density functional theory for hyperfine coupling constants: vanadium complexesManuscript (preprint) (Other academic)
  • 187.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Wei-Wei
    Department of Chemistry, Xiamen University.
    Liao, Rong-Zhen
    Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhao, Yi
    Department of Chemistry, Xiamen University.
    Cao, Zexing
    Department of Chemistry, Xiamen Univeristy.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical studies on reaction of cofactor-free enzyme with triplet oxygen moleculeManuscript (preprint) (Other academic)
  • 188. Cheng, Mu-Jeng
    et al.
    Nielsen, Robert J.
    Ahlquist, Mårten
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Goddard, William A., III
    Carbon-Oxygen Bond Forming Mechanisms in Rhenium Oxo-Alkyl Complexes2010In: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 29, no 9, p. 2026-2033Article in journal (Refereed)
    Abstract [en]

    Three C X bond formation mechanisms observed in the oxidation of (HBpz(3))ReO(R)(OTf) [HBpz(3) = hydrotris(1-pyrazolypborate; R = Me, Et, and iPr; OTf = OSO(2)CF(3)] by dimethyl sulfoxide (DMSO) were investigated using quantum mechanics (M06//B3LYP DFT) combined with solvation (using the PBF Poisson Boltzmann polarizable continuum solvent model). For R = Et we find the alkyl group is activated through alpha-hydrogen abstraction by external base OTf(-) with a free energy barrier of only 12.0 kcal/mol, leading to formation of acetaldehyde. Alternatively, ethyl migration across the M=O bond (leading to the formation of acetaldehyde and ethanol) poses a free energy barrier of 22.1 kcal/mol, and the previously proposed alpha-hydrogen transfer to oxo (a 2+2 forbidden reaction) poses a barrier of 44.9 kcal/mol. The rate-determining step to formation of the final product acetaldehyde is an oxygen atom transfer from DMSO to the ethylidene, with a free energy barrier of 15.3 kcal/mol. When R = iPr, the alkyl 1,2-migration pathway becomes the more favorable pathway (both kinetically and thermodynamically), with a free energy barrier (Delta G(double dagger) = 11.8 kcal/mol) lower than alpha-hydrogen abstraction by OTf(-) (Delta G(double dagger) = 13.5 kcal/mol). This suggests the feasibility of utilizing this type of migration to functionalize M-R to M-OR. We also considered the nucleophilic attack of water and ammonia on the Re-ethylidene alpha-carbon as a means of recovering two-electron-oxidized products from an alkane oxidation. Nucleophilic attack (with internal deprotonation of the nucleophile) is exothermic. However, the subsequent protonolysis of the Re alkyl bond (to liberate an alcohol or amine) poses a barrier of 37.0 or 42.4 kcal/mol, respectively. Where comparisons are possible, calculated free energies agree very well with experimental measurements.

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

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

  • 190. Christodoulou, C.
    et al.
    Giannakopoulos, A.
    Nardi, M. V.
    Ligorio, G.
    Oehzelt, M.
    Chen, L.
    Pasquali, L.
    Timpel, M.
    Giglia, A.
    Nannarone, S.
    Norman, P.
    Linares, M.
    Parvez, K.
    Müllen, K.
    Beljonne, D.
    Koch, N.
    Tuning the work function of graphene-on-quartz with a high weight molecular acceptor2014In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, no 9, p. 4784-4790Article in journal (Refereed)
    Abstract [en]

    Ultraviolet and X-ray photoelectron spectroscopies in combination with density functional theory (DFT) calculations were used to study the change in the work function (Φ) of graphene, supported by quartz, as induced by adsorption of hexaazatriphenylene-hexacarbonitrile (HATCN). Near edge X-ray absorption fine structure spectroscopy (NEXAFS) and DFT modeling show that a molecular-density-dependent reorientation of HATCN from a planar to a vertically inclined adsorption geometry occurs upon increasing surface coverage. This, in conjunction with the orientation-dependent magnitude of the interface dipole, allows one to explain the evolution of graphene Φ from 4.5 eV up to 5.7 eV, rendering the molecularly modified graphene-on-quartz a highly suitable hole injection electrode. © 2014 American Chemical Society.

  • 191.
    Ciobanu, C V
    et al.
    Ohio State Univ, Dept Phys, Columbus, OH 43210 USA.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Shavitt, I
    Ohio State Univ, Dept Phys, Columbus, OH 43210 USA.
    Singer, S J
    Ohio State Univ, Dept Phys, Columbus, OH 43210 USA.
    Structure and vibrational spectra of H(+)(H(2)O)(8): Is the excess proton in a symmetrical hydrogen bond?2000In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 113, no 13, p. 5321-5330, article id PII [S0021-9606(00)30735-8]Article in journal (Refereed)
    Abstract [en]

    The energetics, structure, and vibrational spectra of a wide variety of H + (H 2 O) 8 structures are calculated using density functional theory and second-order Møller–Plesset ab initio methods. In these isomers of H + (H 2 O) 8 the local environment of the excess proton sometimes resembles a symmetric H 5 O + 2 structure and sometimes H 3 O + , but many structures are intermediate between these two limits. We introduce a quantitative measure of the degree to which the excess proton resembles H 5 O + 2 or H 3 O + . Other bond lengths and, perhaps most useful, the position of certain vibrational bands track this measure of the symmetry in the local structure surrounding the excess proton. The general trend is for the most compact structures to have the lowest energy. However, adding zero-point energy counteracts this trend, making prediction of the most stable isomer impossible at this time. At elevated temperatures corresponding to recent experiments and atmospheric conditions (150–200 K), calculated Gibbs free energies clearly favor the least compact structures, in agreement with recent thermal simulations [Singer, McDonald, and Ojamäe, J. Chem. Phys. 112, 710 (2000)]. © 2000 American Institute of Physics.

  • 192.
    Cirera, Borja
    et al.
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain.
    Giménez-Agulló, Nelson
    Institute of Chemical Research of Catalonia, Barcelona Institute of Science and Technology, Avinguda Pa¨ısos Catalans 16, Tarragona, Spain.
    Björk, Jonas
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Martínez-Peña, Francisco
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain..
    Martin-Jimenez, Alberto
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain..
    Rodriguez-Fernandez, Jonathan
    Departamento de F´ısica de la Materia Condensada, Universidad Auto´noma de Madrid, c/Francisco Toma´s y Valiente.
    Pizarro, Ana M.
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco,Madrid, Spain..
    Otero, Roberto
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco, 28049 Madrid, Spain,Universidad Auto´noma de Madrid, c/Francisco Toma´s y Valiente.
    Gallego, José M.
    Instituto de Ciencia de Materiales de Madrid, c/ Sor Juana Ine´s de la Cruz 3, Cantoblanco,Madrid, Spain..
    Ballester, Pablo
    Institute of Chemical Research of Catalonia, Barcelona Institute of Science and Technology, Avinguda Pa¨ısos Catalans 16, Tarragona, Spain/Catalan Institutionfor Research and Advanced Studies, Passeig Lluis Companys 23, Barcelona, Spain..
    Galan-Mascaros, José R.
    Institute of Chemical Research of Catalonia, Barcelona Institute of Science and Technology, Avinguda Pa¨ısos Catalans 16, Tarragona, Spain/Catalan Institutionfor Research and Advanced Studies, Passeig Lluis Companys 23, Barcelona, Spain..
    Ecija, David
    IMDEA Nanoscience, c/Faraday 9, Cantoblanco, Madrid, Spain.
    Thermal selectivity of intermolecular versus intramolecular reactions on surfaces2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, no 11002Article in journal (Refereed)
    Abstract [en]

    On-surface synthesis is a promising strategy for engineering heteroatomic covalent nanoarchitectures with prospects in electronics, optoelectronics and photovoltaics. Here we report the thermal tunability of reaction pathways of a molecular precursor in order to select intramolecular versus intermolecular reactions, yielding monomeric or polymeric phthalocyanine derivatives, respectively. Deposition of tetra-aza-porphyrin species bearing ethyl termini on Au(111) held at room temperature results in a close-packed assembly. Upon annealing from room temperature to 275 °C, the molecular precursors undergo a series of covalent reactions via their ethyl termini, giving rise to phthalocyanine tapes. However, deposition of the tetra-aza-porphyrin derivatives on Au(111) held at 300 °C results in the formation and self-assembly of monomeric phthalocyanines. A systematic scanning tunnelling microscopy study of reaction intermediates, combined with density functional calculations, suggests a [2+2] cycloaddition as responsible for the initial linkage between molecular precursors, whereas the monomeric reaction is rationalized as an electrocyclic ring closure.

  • 193.
    Contreras, F.-Xabier
    et al.
    Heidelberg University.
    Ernst, Andreas M
    Heidelberg University.
    Haberkant, Per
    Heidelberg University.
    Björkholm, Patrik
    Stockholm University.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Gönen, Başak
    Tischer, Christian
    Heidelberg University.
    Elofsson, Arne
    Stockholm University.
    von Heijne, Gunnar
    Stockholm University.
    Thiele, Christoph
    Heidelberg University.
    Pepperkok, Rainer
    Heidelberg University.
    Wieland, Felix
    Heidelberg University.
    Brügger, Britta
    Heidelberg University.
    Molecular recognition of a single sphingolipid species by a protein's transmembrane domain2012In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 481, no 7382, p. 525-529Article in journal (Refereed)
    Abstract [en]

    Functioning and processing of membrane proteins critically depend on the way their transmembrane segments are embedded in the membrane. Sphingolipids are structural components of membranes and can also act as intracellular second messengers. Not much is known of sphingolipids binding to transmembrane domains (TMDs) of proteins within the hydrophobic bilayer, and how this could affect protein function. Here we show a direct and highly specific interaction of exclusively one sphingomyelin species, SM 18, with the TMD of the COPI machinery protein p24 (ref. 2). Strikingly, the interaction depends on both the headgroup and the backbone of the sphingolipid, and on a signature sequence (VXXTLXXIY) within the TMD. Molecular dynamics simulations show a close interaction of SM 18 with the TMD. We suggest a role of SM 18 in regulating the equilibrium between an inactive monomeric and an active oligomeric state of the p24 protein, which in turn regulates COPI-dependent transport. Bioinformatic analyses predict that the signature sequence represents a conserved sphingolipid-binding cavity in a variety of mammalian membrane proteins. Thus, in addition to a function as second messengers, sphingolipids can act as cofactors to regulate the function of transmembrane proteins. Our discovery of an unprecedented specificity of interaction of a TMD with an individual sphingolipid species adds to our understanding of why biological membranes are assembled from such a large variety of different lipids.

  • 194. Corchado, José C.
    et al.
    Sánchez, M. Luz
    Fernández Galván, Ignacio
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Martín, M. Elena
    Muñoz-Losa, Aurora
    Barata-Morgado, Rute
    Aguilar, Manuel A.
    Theoretical Study of Solvent Effects on the Ground and Low-Lying Excited Free Energy Surfaces of a Push–Pull Substituted Azobenzene2014In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, no 43, p. 12518-12530Article in journal (Refereed)
    Abstract [en]

    The ground and low-lying excited free energy surfaces of 4-amino-4'-cyano azobenzene, a molecule that has been proposed as building block for chiroptical switches, are studied in gas phase and a variety of solvents (benzene, chloroform, acetone, and water). Solvent effects on the absorption and emission spectra and on the cistrans thermal and photo isomerizations are analyzed using two levels of calculation: TD-DFT and CASPT2/CASSCF. The solvent effects are introduced using a polarizable continuum model and a QM/MM method, which permits one to highlight the role played by specific interactions. We found that, in gas phase and in agreement with the results found for other azobenzenes, the thermal cistrans isomerization follows a rotation-assisted inversion mechanism where the inversion angle must reach values close to 180 degrees but where the rotation angle can take almost any value. On the contrary, in polar solvents the mechanism is controlled by the rotation of the CN=NC angle. The change in the mechanism is mainly related to a better solvation of the nitrogen atoms of the azo group in the rotational transition state. The photoisomerization follows a rotational pathway both in gas phase and in polar and nonpolar solvents. The solvent introduces only small modifications in the n pi* free energy surface (S-1), but it has a larger effect on the pi pi* surface (S-2) that, in polar solvents, gets closer to S-1. In fact, the S-2 band of the absorption spectrum is red-shifted 0.27 eV for the trans isomer and 0.17 eV for the cis. In the emission spectrum the trend is similar: only S-2 is appreciably affected by the solvent, but in this case a blue shift is found.

  • 195. Coriani, S.
    et al.
    Christiansen, O.
    Fransson, T.
    Norman, P.
    Coupled-cluster response theory for near-edge x-ray-absorption fine structure of atoms and molecules2012In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 85, no 2, article id 022507Article in journal (Refereed)
    Abstract [en]

    Based on an asymmetric Lanczos-chain subspace algorithm, damped coupled cluster linear response functions have been implemented for the hierarchy of coupled cluster (CC) models including CC with single excitations (CCS), CC2, CC with single and double excitations (CCSD), and CCSD with noniterative triple corrected excitation energies CCSDR(3). This work is a first step toward the extension of these theoretical electronic structure methods of well-established high accuracy in UV-vis absorption spectroscopies to applications concerned with x-ray radiation. From the imaginary part of the linear response function, the near K-edge x-ray absorption spectra of neon, water, and carbon monoxide are determined and compared with experiment. Results at the CCSD level show relative peak intensities in good agreement with experiment with discrepancies in transition energies due to incomplete treatment of electronic relaxation and correlation that amount to 1-2 eV. With inclusion of triple excitations, errors in energetics are less than 0.9 eV and thereby capturing 90%, 95%, and 98% of the relaxation-correlation energies for C, O, and Ne, respectively. © 2012 American Physical Society.

  • 196. Coriani, S.
    et al.
    Fransson, T.
    Christiansen, O.
    Norman, P.
    Asymmetric-lanczos-chain-driven implementation of electronic resonance convergent coupled-cluster linear response theory2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 5, p. 1616-1628Article in journal (Refereed)
    Abstract [en]

    We present an implementation of the damped coupled-cluster linear response function based on an asymmetric Lanczos chain algorithm for the hierarchy of coupled-cluster approximations CCS (coupled-cluster singles), CC2 (coupled-cluster singles and approximate doubles), and CCSD (coupled-cluster singles and doubles). Triple corrections to the excitation energies can be included via the CCSDR(3) (coupled-cluster singles and doubles with noniterative-triples-corrected excitation energies) approximation. The performance and some of the potentialities of the approach are investigated in calculations of the visible/ultraviolet absorption spectrum and the dispersion of the real polarizability in near-resonant regions of pyrimidine, the near-edge absorption fine structure (NEXAFS) of ammonia, and the direct determination of the C 6 dipole-dipole dispersion coefficient of the benzene dimer. © 2012 American Chemical Society.

  • 197.
    Cornelissen, Tim D.
    et al.
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Biler, Michal
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Urbanaviciute, Indre
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Linares, Mathieu
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Kemerink, Martijn
    Linkoping Univ, Dept Phys Chem & Biol IFM, S-58183 Linkoping, Sweden..
    Kinetic Monte Carlo simulations of organic ferroelectrics2019In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, no 3, p. 1375-1383Article in journal (Refereed)
    Abstract [en]

    Ferroelectrics find broad applications, e.g. in non-volatile memories, but the switching kinetics in real, disordered, materials is still incompletely understood. Here, we develop an electrostatic model to study ferroelectric switching using 3D Monte Carlo simulations. We apply this model to the prototypical small molecular ferroelectric trialkylbenzene-1,3,5-tricarboxamide (BTA) and find good agreement between the Monte Carlo simulations, experiments, and molecular dynamics studies. Since the model lacks any explicit steric effects, we conclude that these are of minor importance. While the material is shown to have a frustrated antiferroelectric ground state, it behaves as a normal ferroelectric under practical conditions due to the large energy barrier for switching that prevents the material from reaching its ground state after poling. We find that field-driven polarization reversal and spontaneous depolarization have orders of magnitude different switching kinetics. For the former, which determines the coercive field and is relevant for data writing, nucleation occurs at the electrodes, whereas for the latter, which governs data retention, nucleation occurs at disorder-induced defects. As a result, by reducing the disorder in the system, the polarization retention time can be increased dramatically while the coercive field remains unchanged.

  • 198.
    Costa Felicissimo, Viviane
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Guimaraes, Freddy
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Coherent control of population of vibrational states by infrared pulsesManuscript (preprint) (Other academic)
  • 199.
    Cournia, Zoe
    et al.
    Academy of Athens, Greece.
    Allen, Toby W.
    University of California, USA ; RMIT University, Australia.
    Andricioaei, Ioan
    University of California, USA.
    Antonny, Bruno
    Université de Nice Sophia-Antipolis, France.
    Baum, Daniel
    Zuse Institute Berlin, Germany.
    Brannigan, Grace
    Rutgers University-Camden, USA.
    Buchete, Nicolae-Viorel
    University College Dublin, Ireland.
    Deckman, Jason T.
    University of California, USA.
    Delemotte, Lucie
    Temple University, USA.
    del Val, Coral
    University of Granada, Spain.
    Friedman, Ran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Gkeka, Paraskevi
    Academy of Athens, Greece.
    Hege, Hans-Christian
    Zuse Institute Berlin, Germany.
    Hénin, Jérôme
    IBPC and CNRS, France.
    Kasimova,, Marina A.
    Université de Lorraine, France ; Lomonosov Moscow State University, Russia.
    Kolocouris, Antonios
    University of Athens, Greece.
    Klein, Michael L.
    Temple University, USA.
    Khalid, Syma
    University of Southampton, UK.
    Lemieux, M. Joanne
    University of Alberta, Canada.
    Lindow, Norbert
    Zuse Institute Berlin, Germany.
    Mahua, Roy
    University of California, USA.
    Selent, Jana
    Universitat Pompeu Fabra, Spain.
    Tarek, Mounir
    Université de Lorraine, France ; CNRS SRSMC, France.
    Tofoleanu, Florentina
    University College Dublin, Ireland.
    Stefano, Vanni
    Université de Nice Sophia-Antipolis, Greece.
    Sinisa, Urban
    Johns Hopkins University School of Medicine, USA.
    Wales, David J.
    University of Cambridge, UK.
    Smith, Jeremy C.
    Oak Ridge National Laboratory, USA.
    Bondar, Ana-Nicoleta
    Freie Universität Berlin, Germany.
    Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory2015In: Journal of Membrane Biology, ISSN 0022-2631, E-ISSN 1432-1424, Vol. 248, no 4, p. 611-640Article in journal (Refereed)
    Abstract [en]

    Membrane proteins mediate processes that are fundamental for the flourishing of biological cells. Membrane-embedded transporters move ions and larger solutes across membranes; receptors mediate communication between the cell and its environment and membrane-embedded enzymes catalyze chemical reactions. Understanding these mechanisms of action requires knowledge of how the proteins couple to their fluid, hydrated lipid membrane environment. We present here current studies in computational and experimental membrane protein biophysics, and show how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins.

  • 200.
    Cronstrand, P.
    et al.
    Royal Institute of Technology, Sweden.
    Jansik, B.
    Royal Institute of Technology, Sweden.
    Jonsson, D.
    Mälardalen University, Department of Mathematics and Physics. Stockholm University, Sweden.
    Luo, Y.
    Mälardalen University, Department of Mathematics and Physics. Royal Institute of Technology, Sweden.
    Ågren, H.
    Mälardalen University, Department of Mathematics and Physics. Royal Institute of Technology, Sweden.
    Density functional theory calculations of three-photon absorption2004In: Journal of Chemical Physics, ISSN 0021-9606, Vol. 121, no 19, p. 9239-9246Article in journal (Refereed)
    Abstract [en]

    Three-photon absorption probabilities delta(3PA) have been calculated through application of a recently derived method for cubic response functions within density functional theory (DFT). Calculations are compared with Hartree-Fock (HF) and with a coupled cluster hierarchy of models in a benchmarking procedure. Except for cases having intermediate states near resonance, density functional theory is demonstrated to be in sufficient agreement with the highly correlated methods in order to qualify for predictions of delta(3PA). For the larger systems addressed, a set of acceptor A and donor D substituted pi-conjugated systems formed by trans-stilbene and dithienothiophene (DTT), we find noticeable differences in the magnitude of delta(3PA) between HF and DFT, although similar trends are followed. It is shown that the dipolar structures, TS-AD and DTT-AD, have substantially larger delta(3PA) than other types of modifications which is in accordance with observations for two-photon absorption. This is the first application of density functional theory to three-photon absorption beyond the use of few-state models.

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