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  • 201.
    Hua, Weijie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Gao, Bin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Li, Shuhua
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    X-ray absorption spectra of graphene from first-principles simulations2010In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 82, no 15, p. 155433-Article in journal (Refereed)
    Abstract [en]

    Near edge x-ray absorption fine-structure spectra of graphenes are calculated using hybrid density-functional theory with the equivalent core hole approximation, aiming to resolve the ongoing debate on the interpretation of corresponding experimental spectra. Effects of size, stacking, edges, and defects on the spectra have been analyzed in detail for both C 1s-pi* and C 1s-sigma* transitions. The infinite graphene sheet has been modeled by graphene nanoribbons of different size. The size dependence and convergence of the spectra have been revealed. It is found that the pi-pi interaction between layers have mainly effects on the C 1s-pi* transitions in two different energy regions. The stacking effect smears out the double-peaks structure of the first main pi* peak around 285 eV and results in blueshift of the second pi* structure by almost 2 eV. The calculations show that the pi spectrum of hydrogen saturated edge carbons is redshifted with respect to the central ones and that a new weak sigma* peak around 288 eV appears. The presence of defects can also introduce new spectral features in both pi and sigma regions.

  • 202.
    Hua, Weijie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Yamane, Hiroyuki
    Gao, Bin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Jiang, Jun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Li, Shuhua
    Kato, Hiroyuki S.
    Kawai, Maki
    Hatsui, Takaki
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Kosugi, Nobuhiro
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Systematic Study of Soft X-ray Spectra of Poly(Dg)center dot Poly(Dc) and Poly(Da)center dot Poly(Dt) DNA Duplexes2010In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, no 20, p. 7016-7021Article in journal (Refereed)
    Abstract [en]

    In the present work, we have undertaken a combined experimental and theoretical study of X-ray spectroscopies for DNA base pairs, more precisely near-edge X-ray absorption, X-ray emission, and resonant inelastic X-ray scattering applied to poly(dG)center dot poly(dC) and poly(dA)center dot poly(dT) DNA duplexes. We have derived several conclusions on the nature of these X-ray spectra: the stacking of pairs has very little influence on the spectra; the spectra of a DNA composed of mixed Watson-Crick base pairs are well reproduced by linear combinations of GC and AT base pairs involved; the amine and imine nitrogens show noticeable differences as building blocks in the absorption, emission, and resonant emission spectra. The calculated spectra are in good agreement with experimental results. The ramifications of these conclusions for the use of X-ray spectroscopy for DNA are discussed.

  • 203.
    Huang, Bingru
    et al.
    South China Normal Univ, South China Acad Adv Optoelect, Ctr Opt & Electromagnet Res, Guangdong Prov Key Lab Opt Informat Mat & Technol, Guangzhou 510006, Guangdong, Peoples R China.
    Bergstrand, Jan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Duan, Sai
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Zhan, Qiuqiang
    South China Normal Univ, South China Acad Adv Optoelect, Ctr Opt & Electromagnet Res, Guangdong Prov Key Lab Opt Informat Mat & Technol, Guangzhou 510006, Guangdong, Peoples R China.
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Liu, Haichun
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Overtone Vibrational Transition-Induced Lanthanide Excited-State Quenching in Yb3+/Er3+-Doped Upconversion Nanocrystals2018In: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 12, p. 10572-10575Article in journal (Refereed)
  • 204. Huang, J.
    et al.
    Xu, B.
    Jamshidi, Asgar
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Sun, L.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Strategiesto Improve Photovoltaic Performance of “Green” CuInS2 Quantum Dots: Hybrid Passivation vs Use of ZnS shellsManuscript (preprint) (Other academic)
  • 205.
    Huang, Jing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xu, Bo
    KTH, School of Chemical Science and Engineering (CHE), Chemistry. KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Yuan, Chunze
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Chen, Hong
    Sun, Junliang
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry. KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Improved Performance of Colloidal CdSe Quantum Dot-Sensitized Solar Cells by Hybrid Passivation2014In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 6, no 21, p. 18808-18815Article in journal (Refereed)
    Abstract [en]

    A hybrid passivation strategy is employed to modify the surface of colloidal CdSe quantum dots (QDs) for quantum dot-sensitized solar cells (QDSCs), by using mercaptopropionic acid (MPA) and iodide anions through a ligand exchange reaction in solution. This is found to be an effective way to improve the performance of QDSCs based on colloidal QDs. The results show that MPA can increase the coverage of the QDs on TiO2 electrodes and facilitate the hole extraction from the photoxidized QDs, and simultaneously, that the iodide anions can remedy the surface defects of the CdSe QDs and thus reduce the recombination loss in the device. This hybrid passivation treatment leads to a significant enhancement of the power conversion efficiency of the QDSCs by 41%. Furthermore, an optimal ratio of iodide ions to MPA was determined for favorable hybrid passivation; results show that excessive iodine anions are detrimental to the loading of the QDs. This study demonstrates that the improvement in QDSC performance can be realized by using a combination of different functional ligands to passivate the QDs, and that ligand exchange in solution effective approach to introduce can be an different ligands.

  • 206.
    Huang, Jing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Efficiency Enhancement of Solid-State Quantum Dot-Sensitized Solar Cells by Quality Optimizing of Colloidal CuInS2 Quantum DotsManuscript (preprint) (Other academic)
  • 207. Huang, Jing
    et al.
    Ågren, Hans
    Photovoltaic Performance Improvement Strategies for Colloidal CuInS2 QDs: Hybrid Passivation vs ZnS shellManuscript (preprint) (Other academic)
  • 208. Huang, Kai
    et al.
    Liu, Haichun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kraft, Marco
    Shikha, Swati
    Zheng, Xiang
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Würth, Christian
    Resch-Genger, Ute
    Zhang, Yong
    Protected excitation-energy reservoir for efficient upconversion luminescence2017In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 10, no 1, p. 250-259Article in journal (Refereed)
    Abstract [en]

    Lanthanide-doped upconversion nanoparticles (UCNPs) are of great interest for biomedical applications. Currently, the applicability of UCNP bionanotechnology is hampered by the general low luminescence intensity of UCNPs and inefficient energy transfer from UCNPs to surface-bound chromophores used e.g. for photodynamic therapy or analyte sensing. In this work, we address the low efficiency issue by developing versatile core-shell nanostructures, where high-concentration sensitizers and activators are confined in the core- and shell region, representatively for hexagonal NaYF4:Yb, Er UCNPs. After doping concentration optimization, the sensitizer-rich core, is able to harvest/accumulate more excitation energy and generate almost one order of magnitude higher luminescence intensity than conventional homogeneously doped nanostructures. At the same time, the activator ions located in the shell enable a ~6 times more efficient resonant energy transfer from UCNPs to surface-bound acceptor dye molecules due to the short distance between donor-acceptor pairs. Our work provides new insights into the rational design of UCNPs and will greatly increase the general applicability of upconversion nanotechnologies.

  • 209.
    Hugosson, Håkan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Quantum Mechanics: Molecular Mechanics Modeling of an Enzyme Catalytic Reaction2009In: Multiscale Modeling and Simulation in Science / [ed] Björn Engquist, Per Lötstedt, Olof Runborg, Berlin, Heidelberg: Springer Berlin/Heidelberg, 2009Chapter in book (Refereed)
  • 210.
    Hugosson, Håkan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Quantum mechanics/classical mechanics modeling of biological systems2009In: Multiscale Modeling and Simulation in Science, Springer Berlin/Heidelberg, 2009, p. 291-294Conference paper (Refereed)
    Abstract [en]

    The objective of the project was to give an overview and hands-on insight into modern biotechnological modeling in and across several scales (and dimensions), from Quantum Mechanics to Classical Mechanics, from Molecular Mechanics to Molecular Dynamics, and from Single Molecules to Biological Systems. Here we give a starting tour of using the classical Molecular Dynamics software package AMBER [1], and the quantum mechanical Car-Parrinello package CPMD ( www. cpmd.org ) [2]. Introductions to some useful visualization software software specialised for biological systems was also given (Visual Molecular Dynamics) [3]. The main focus of this project is to apply multi-scale, here the so-called QM/MM molecular dynamics, methods to a biological system. In current biophysical modeling two main branches exist; classical force-field MD and static QM calculations. Though both methods are regularly and successfully applied to biological systems, many intrinsic restrictions exist, some of which are greatly reduced or solved by using multi-scale QM/MM MD. In classical MD, the by-far most common approach, the potential energy surface is parametrized through a fitting to empirical and/or theoretical data. They are therefore intrinsically restricted to situations where no significant changes of the electronic structure occur, but for example chemical reactions can only be treated adequately by a quantum mechanical description. Further restrictions include that the force field parameters are pre-defined and do not change when the system changes, either from conformational changes or from changes in the local environment. Secondly, if one wishes to model e.g. metallic centers or more uncommon organic molecules, no parameters may be available and a sometimes arduous and non-trivial parametrization is necessary.

  • 211.
    Ignatova, Nina
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Siberian Federal University.
    da Cruz, Vinícius V.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Couto, Rafael C.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ertan, Emelie
    Stockholm university.
    Odelius, Michael
    Stockholm university.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Guimarães, Freddy F.
    Zimin, Andrei
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Siberian Federal University.
    Polyutov, Sergey
    Siberian Federal University.
    Gel’mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kimberg, Victor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Infrared-pump–x-ray-probe spectroscopy of vibrationally excited molecules2017In: Physical Review A, ISSN 2469-9926, Vol. 95, no 4, article id 042502Article in journal (Refereed)
    Abstract [en]

    We develop a theory of infrared (IR)-pump–x-ray-probe spectroscopy for molecular studies. We illustrate advantages of the proposed scheme by means of numerical simulations employing a vibrational wave packet technique applied to x-ray absorption and resonant inelastic x-ray scattering (RIXS) spectra of the water molecule vibrationally excited by a preceding IR field. The promotion of the vibrationally excited molecule to the dissociative 1a−114a1 and bound 1a−112b2 core-excited states with qualitatively different shapes of the potential energy surfaces creates nuclear wave packets localized along and between the OH bonds, respectively. The projection of these wave packets on the final vibrational states, governed by selection and propensity rules, results in spatial selectivity of RIXS sensitive to the initial vibrationally excited state, which makes it possible to probe selectively the ground state properties along different modes. In addition, we propose to use RIXS as a tool to study x-ray absorption from a selected vibrational level of the ground state when the spectral resolution is sufficiently high to resolve vibrational overtones. The proposed technique has potential applications for advanced mapping of multidimensional potential energy surfaces of ground and core-excited molecular states, for symmetry-resolved spectroscopy, and for steering chemical reactions.

  • 212.
    Ignatova, Nina
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Siberian Federal University.
    V. Cruz, Vinícius
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Couto, Rafael C.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ertan, Emelie
    Zimin, Andrey
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    F. Guimarães, Freddy
    Polyutov, Sergey
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kimberg, Victor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Odelius, Michael
    Gel’mukhanov, Faris
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Gradual collapse of nuclear wave functions regulated by frequency tuned X-ray scattering2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, no 43891Article in journal (Refereed)
    Abstract [en]

    As is well established, the symmetry breaking by isotope substitution in the water molecule results in localisation of the vibrations along one of the two bonds in the ground state. In this study we find that this localisation may be broken in excited electronic states. Contrary to the ground state, the stretching vibrations of HDO are delocalised in the bound core-excited state in spite of the mass difference between hydrogen and deuterium. The reason for this effect can be traced to the narrow “canyon-like” shape of the potential of the state along the symmetric stretching mode, which dominates over the localisation mass-difference effect. In contrast, the localisation of nuclear motion to one of the HDO bonds is preserved in the dissociative core-excited state . The dynamics of the delocalisation of nuclear motion in these core-excited states is studied using resonant inelastic X-ray scattering of the vibrationally excited HDO molecule. The results shed light on the process of a wave function collapse. After core-excitation into the state of HDO the initial wave packet collapses gradually, rather than instantaneously, to a single vibrational eigenstate.

  • 213.
    Jamshidi, Asgar
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Chmyrov, V.
    Widengren, J.
    Sun, L.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Green” Colloidal InP/ZnS Quantum Dot Sensitized Solar CellsManuscript (preprint) (Other academic)
  • 214.
    Jamshidi, Asgar
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Huang, J.
    Ji, Y.
    Chmyrov, V.
    Widengren, J.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Sun, L.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Synthesisof Cd-Free and Low Toxic Cu2GeS3-Inp Quantum Dots For Infrared Solar Cell ApplicationsManuscript (preprint) (Other academic)
  • 215.
    Jamshidi, Asgar
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Yuan, Chunze
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Chmyrov, V.
    Widengren, J.
    Sun, L.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Efficiency Enhanced Colloidal Mn-Doped Type II Core/Shell ZnSe/CdS Quantum Dot Sensitized Hybrid Solar Cells2015In: Journal of Nanomaterials, ISSN 1687-4110, E-ISSN 1687-4129, article id 921903Article in journal (Refereed)
    Abstract [en]

    Colloidal Mn-doped ZnSe/CdS core/shell quantum dots (QDs) are synthesized for the first time and employed as a strategy to boost the power conversion efficiency of quantum dot sensitized solar cells. By using Mn-doping as a band gap engineering tool for core/shell QDs an effective improvement of absorption spectra could be obtained. The mid-states generated by a proper Mn content alleviate carrier separation and enhance the electron injection rate, thus facilitating electron transport to the TiO2 substrate. It is demonstrated that a device constructed with 0.25% Mn-doped ZnSe/CdS leads to an enhancement of the electron injection rate and power conversion efficiency by 4 times and 1.3, respectively.

  • 216. Jana, Avijit
    et al.
    Bai, Linyi
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhao, Yanli
    Morphology Tuning of Self-Assembled Perylene. Monoimide from Nanoparticles to Colloidosomes with Enhanced Excimeric NIR Emission for Bioimaging2016In: ACS Applied Materials and Interfaces, ISSN 1944-8244, E-ISSN 1944-8252, Vol. 8, no 3, p. 2336-2347Article in journal (Refereed)
    Abstract [en]

    Organic near-infrared (NIR) fluorescent probes have been recognized as an emerging class of materials exhibiting a great potential in advanced bioanalytical applications. However, synthesizing such organic probes that could simultaneously work in the NIR spectral range and have large Stokes shift, high stability in biological systems, and high photostability have been proven challenging. In this work, aggregation induced excimeric NIR emission in aqueous media was observed from a suitably substituted perylene monoimide (PeIm) dye. Controlled entrapment of the dye into pluronic F127 micellar system to preserve its monomeric green emission in aqueous media was also established. The aggregation process of the PeIm dye to form organic nanoparticles (NPs) was evaluated experimentally by the means of transmission electron microscope imaging as well as theoretically by the molecular dynamics simulation studies. Tuning the morphology along with the formation of colloidosomes by the controlled self-aggregation of PeIm NPs in aqueous suspension was demonstrated successfully. Finally, both excimeric and monomeric emissive PeIm NPs as well as PeIm colloidosomes were employed for the bioimaging in vitro.

  • 217. Jana, Avijit
    et al.
    Nguyen, Kim Truc
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhu, Pengcheng
    Tan, Nguan Soon
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhao, Yanli
    Perylene-Derived Single-Component Organic Nanoparticles with Tunable Emission: Efficient Anticancer Drug Carriers with Real-Time Monitoring of Drug Release2014In: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 8, no 6, p. 5939-5952Article in journal (Refereed)
    Abstract [en]

    An organic nanoparticle-based drug delivery system with high drug loading efficacy (similar to 79 wt %) was developed using a perylene-derived photoremovable protecting group, namely, perylene-3,4,9,10-tetrayltetramethanol (Pe(OH)(4)). The anticancer drug chlorambucil was protected by coupling with Pe(OH)(4) to form photocaged nanoparticles (Pe(OH)(4)). The photorelease mechanism of chlorambucil from the Pe(Cbl)(4) conjugate was investigated experimentally by high-resolution mass spectrometry and theoretically by density functional theory calculations. The Pe(Cbl)(4) nanoparticles perform four important roles: (i) a nanocarrier for drug delivery, (ii) a phototrigger for drug release, (iii) a fluorescent chromophore for cell imaging, and (iv) a photoswitchable fluorophore for real-time monitoring of drug release. Tunable emission of the perylene-derived nanoparticles was demonstrated by comparing the emission properties of the Pe(OH)(4) and Pe(Cbl)(4) nanoparticles with perylene-3-ylmethanol. These nanoparticles were subsequently employed in cell imaging for investigating their intracellular localization. Furthermore, the in vivo toxicity of the Pe(OH)(4) nanoparticles was investigated using the mouse model. Histological tissue analysis of five major organs, i.e., heart, kidney, spleen, liver, and lung, indicates that the nanoparticles did not show any obvious damage to these major organs under the experimental conditions. The current research presents a successful example of integrating multiple functions into single-component organic nanoparticles for drug delivery.

  • 218. Jansik, B.
    et al.
    de Meras, Amjs
    Schimmelpfennig, B.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    A coupled-cluster study of lanthanum trihalide structures2002In: Journal of the Chemical Society. Dalton Transactions, ISSN 1472-7773, E-ISSN 1364-5447, no 24, p. 4603-4606Article in journal (Refereed)
    Abstract [en]

    Coupled-cluster calculations were carried at the CCSD(T)-level in order to determine the structures and vibrational spectra of the lanthanum trihalides LaF3 and LaCl3. Two different approaches were employed to describe scalar relativistic effects; the quasi-relativistic Effective Core Potential approach and the all-electron Douglas-Kroll approach. We find LaF3 to be of pyramidal structure and LaCl3 to be planar. The obtained vibrational frequencies accord well with experimental measurements except for the v(2) mode. This disagreement is attributed to the intrinsic uncertainty of harmonic frequencies of this fluxional mode as extracted from spectra which were obtained at high temperature and for matrix isolated species.

  • 219. Jansik, B.
    et al.
    Rizzo, A.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Response theory calculations of two-photon circular dichroism2005In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 414, no 06-apr, p. 461-467Article in journal (Refereed)
    Abstract [en]

    The feasibility of calculations of two-photon circular dichroism (TPA-CD) by means of response theory is demonstrated. The results from sample applications, involving the calculation of residues of appropriate frequency dependent quadratic response functions within a density functional theory model, show that the structural content of TPA-CD spectra is very different from both normal circular dichroism and two-photon absorption, indicating a unique fingerprinting functionality for chiral species. Combined with increased penetrability of the infrared exciting light and the confocal nature of two-photon absorption, this makes TPA-CD a useful tool for biomolecular identification.

  • 220. Jansik, B.
    et al.
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Jonsson, D.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cubic response functions in time-dependent density functional theory2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 5Article in journal (Refereed)
    Abstract [en]

    We present density-functional theory for time-dependent response functions up to and including cubic response. The working expressions are derived from an explicit exponential parametrization of the density operator and the Ehrenfest principle, alternatively, the quasienergy ansatz. While the theory retains the adiabatic approximation, implying that the time-dependency of the functional is obtained only implicitly-through the time dependence of the density itself rather than through the form of the exchange-correlation functionals-it generalizes previous time-dependent implementations in that arbitrary functionals can be chosen for the perturbed densities (energy derivatives or response functions). In particular, general density functionals beyond the local density approximation can be applied, such as hybrid functionals with exchange correlation at the generalized-gradient approximation level and fractional exact Hartree-Fock exchange. With our implementation the response of the density can always be obtained using the stated density functional, or optionally different functionals can be applied for the unperturbed and perturbed densities, even different functionals for different response order. As illustration we explore the use of various combinations of functionals for applications of nonlinear optical hyperpolarizabilities of a few centrosymmetric systems; molecular nitrogen, benzene, and the C-60 fullerene. Considering that vibrational, solvent, and local field factors effects are left out, we find in general that very good experimental agreement can be obtained for the second dynamic hyperpolarizability of these systems. It is shown that a treatment of the response of the density beyond the local density approximation gives a significant effect. The use of different functional combinations are motivated and discussed, and it is concluded that the choice of higher order kernels can be of similar importance as the choice of the potential which governs the Kohn-Sham orbitals.

  • 221. Jansik, B.
    et al.
    Schimmelpfennig, B.
    Norman, P.
    Macak, P.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Ohta, K.
    Relativistic effects on linear and non-linear polarizabilities of the furan homologues2003In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 633, no 03-feb, p. 237-246Article in journal (Refereed)
    Abstract [en]

    First principles calculations including relativistic effects are carried out for dipole moments, polarizabilities, first- and second-order hyperpolarizabilities for the series of furan homologues XC4H4, X = O, S, Se, Te, at three different levels of theory; time-dependent Dirac-Hartree-Fock (DHF), time-dependent Hartree-Fock with a Douglas-Kroll transformed one-component Hamiltonian, and time-dependent Hartree-Fock using effective-core potentials. By comparison with the corresponding non-relativistic results, the influence of relativistic effects on the properties as well as the accuracy of previously reported calculations on these molecules using effective-core potentials for selenium and tellurium can be addressed. The obtained results indicate that relativistic effects can be described with comparable accuracy at all three employed levels, and that non-scalar effects, which are explicitly treated only at the time-dependent DHF level, are of minor importance. Frequency dispersion and relativity are found to be additive at the single-determinant level. We find that relativistic effects cannot make up for the earlier identified mismatch between theory and experiment for the non-linear polarizabilities of the heavier homologues. A Bishop-Kirtman analysis of vibrational effects indicates that the same can be said about these.

  • 222. Jansik, B.
    et al.
    Schimmelpfennig, B.
    Norman, P.
    Mochizuki, Y.
    Luo, Yi
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Size, order, and dimensional relations for silicon cluster polarizabilities2002In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 106, no 2, p. 395-399Article in journal (Refereed)
    Abstract [en]

    Response theory calculations in the random phase approximation are applied to linear polarizabilities and second hyperpolarizabilities of 1-, 2-, and 3-dimensional hydrogen-terminated silicon clusters. Successive enlargement of the clusters to embody on the order of 50 silicon atoms plus bond-saturating hydrogen atoms allows for extrapolation to bulk values of individual silicon atom contributions in the 1D and 3D cases. Modern effective core potentials are shown to provide excellent approximations to the all-electron values in all cases; errors for both polarizabilities and hyperpolarizabilities are on the order of 1%. The findings indicate considerable time savings in predictions of the electric polarizability properties of elements beyond the first row atoms.

  • 223. Jansik, B.
    et al.
    Schimmelpfennig, B.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Relativistic study of vuv radiation properties from Kr-Xe gas mixtures2003In: Physical Review A. Atomic, Molecular, and Optical Physics, ISSN 1050-2947, E-ISSN 1094-1622, Vol. 67, no 4Article in journal (Refereed)
    Abstract [en]

    In an effort to obtain a microscopic understanding of the origin of vuv emission from inert heavy-atom gas mixtures we present results from relativistic calculations of the krypton-xenon spectrum in the 68 000 cm(-1) region. Calculations carried out on the interatomic interaction in the ground and in the low-lying spin-orbit excited states [0(-)(P-3(2)), 0(+)(P-3(1)), 1(P-3(1)), 1(P-3(2)), 2(P-3(1))] of the krypton-xenon dimer are presented. The calculations were executed in a two-step procedure in which the CCSD(T) model for the ground state and the CCSD response theory model for the excited states were used to obtain spin-free potential curves in the first step. A perturbational treatment of the spin-orbit interaction within the atomic mean-field approximation was applied in the next step. Large-core quasirelativistic effective core potentials with richly augmented valence basis sets and midbond functions were used. All calculations were corrected for basis set superposition errors by applying the counterpoise method. For all involved states, spin-orbit perturbed potential energy curves were computed and equilibrium geometries, potential well depths, and local extrema were determined. Vibrational analysis and Franck-Condon factors for the ground and 0(+)(P-3(1)),1(P-3(1)) states were also calculated. The geometry dependence of the electronic dipole transition matrix elements between all involved excited states and the ground state was investigated. Excitation energies and potentials were obtained that are in excellent agreement with results based on fitting to experimental data. Out of some earlier disparate experimental assignments of the character of the excited states of the KrXe complex, the present results adhere most closely to the ones presented by Pibel [J. Chem. Phys. 101, 10 242 (1994)]. Analyzed together with the experimental data, the theoretical results provide a clear picture of the organization of exciplex states and of the origin of strong vuv emission from these states that follows from binary collisions of the heavy inert Kr and Xe atoms.

  • 224.
    Jansik, Branislav
    et al.
    KTH, Superseded Departments, Biotechnology.
    Jonsson, D.
    Salek, Pawel
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Calculations of static and dynamic polarizabilities of excited states by means of density functional theory2004In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 121, no 16, p. 7595-7600Article in journal (Refereed)
    Abstract [en]

    We present density functional theory and calculations for excited state second order, static or dynamic, properties. The excited state properties are identified from a double residue of a cubic response function. The performance of various functionals, including the generalized gradient approximation and fractional exact Hartree-Fock exchange, is compared to coupled cluster calculations. Applications on excited state polarizabilities of s-tetrazine and pyrimidine show a good agreement with ab initio correlated, coupled cluster, results.

  • 225. Jansik, Branislav
    et al.
    Rizzo, Antonio
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ab initio study of the two-photon circular dichroism in chiral natural amino acids2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 2, p. 446-460Article in journal (Refereed)
    Abstract [en]

    Two-photon circular dichroism spectra calculated within an origin-invariant density functional theory approximation in the absorption region where the lowest electronic excited states appear are presented for all 19 essential amino acids in the gas phase. A comparison of intensities and characteristic features is made with the corresponding two-photon absorption and one-photon circular dichroism spectra for each species. Also, the contributions of the electric dipole, magnetic dipole, and electric quadrupole transitions to the rotational strengths are analyzed in some detail. The remarkable fingerprinting capabilities of the two-photon circular dichroism spectroscopy are highlighted.

  • 226. Jansik, Branislav
    et al.
    Rizzo, Antonio
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Champagne, Benoit
    Strong two-photon circular dichroism in helicenes: A theoretical investigation2008In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 4, no 3, p. 457-467Article in journal (Refereed)
    Abstract [en]

    Using a recently derived origin-invariant quadratic response approach combined with time-dependent density functional theory, four representative helicenes are shown to present a very strong two-photon circular dichroism (TPCD) response, which makes them candidates for the first experimental observation of a TPCD effect. The large response is attributed to the unique combination of chirality and electron delocalization. Comparison with electronic circular dichroism and two-photon absorption (TPA) shows that the three effects exhibit complementary features for unravelling the molecular structures. In particular, for the four (M)-helicenes studied here, the first, i.e., low-energy, dominant Cotton band is always negative, whereas for TPCD it is positive. From an analysis of the frontier orbitals describing most of the one-electron excitation vectors, the largest TPCD response of tetramethoxy-bisquinone-dithia-[7]-helicene has been attributed to the charge-transfer character of the excited state, like for the parent TPA effect. Moreover, the TPCD intensities are found to be mostly governed by the electric and magnetic dipole contributions, while the electric quadrupole terms are, on a relative basis, less important.

  • 227.
    Jansson, Emil
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Jha, Prakash Chandra
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Chain length dependence of singlet and triplet excited states of oligofluorenes: A density functional study2007In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 336, no 2-3, p. 91-98Article in journal (Refereed)
    Abstract [en]

    Using time dependent density functional theory, we investigate the chain length dependence of the energies of excited states of a series of conjugated 9,9-dihexylfluorene-2,7-diyl oligomers. Excited state optimization reveals that upon excitation the dihedral angle between two adjacent monomer units moves towards zero, forming a planar structure within the oligomer. The calculated energies of the optical transitions in absorption, fluorescence, phosphorescence and triplet-triplet absorption are compared with recently reported experimental data. The calculated as well as experimentally reported energies involved seem to saturate very fast as the chain length increases. The energy dispersion and saturation indicates that the triplet ground state is somewhat more confined than the first singlet excited state. Our calculated energies agree well with the experimental findings where available, showing small but systematic deviations.

  • 228.
    Jansson, Emil
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Jha, Prakash Chandra
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Density functional study of triazole and thiadiazole systems as electron transporting materials.2006In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 330, no 02-jan, p. 166-171Article in journal (Refereed)
    Abstract [en]

    Density functional theory has been used for the calculation of electronic structures, vertical electron affinities and intramolecular reorganization energies for bis-aryl substituted triazole and thiadiazole. The results obtained on the basis of the theoretical calculations indicate that the HOMO and LUMO energies of the substituted molecules can be tuned by changing the substituents as well as by changing the center atom. These changes lead to energy shifts in the order of 2-2.5 eV. The calculation and comparison of vertical electron affinities and intramolecular reorganization energies confirm that thiadiazole systems are interesting for electron transport properties. Taking a lesson from these substitutions, we further model the systems by twisting the molecular units along the central dihedral angle starting from the ideal structure and compare their HOMO-LUMO gap, electron affinity and reorganization energy. We find that by having simple substituents at proper positions one can control the reorganization energy, which in turn indicates that electron transport properties can be tuned.

  • 229.
    Jansson, Emil
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Minaev, Boris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Schrader, Sigurd
    echnische Fachhochschule Wildau, University of Applied Sciences.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Time-dependent density functional calculations of phosphorescence parameters for fac-tris(2-phenylpyridine) iridium2007In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 333, no 03-feb, p. 157-167Article in journal (Refereed)
    Abstract [en]

    fac-Tris(2-phenylpyridine) iridium [fac-Ir(PPY)(3)] produces strong phosphorescence and has therefore been used as materials in organic light emitting diodes to overcome the efficiency limit imposed by the formation of triplet excitons. Accounting for this circumstance we present in this paper a theoretical study of phosphorescence in the Ir(PPY)(3) complex. The spin-orbit coupling effects and the radiative lifetime in the high temperature limit (T) are calculated by time-dependent density functional theory using quadratic response technology in order to elucidate the main mechanism of the phosphorescence. It is found that the orbital structure of the T, state has a localized character and that the T1 -> S0 transition is determined mostly by charge transfer from one of the ligands to the metal. At the vertical S-0-T-1 excitation the triplet state is highly delocalized among all three ligands and has a mixed pi pi* and metal-to-ligand charge transfer character. The intensity borrowing from the S-0 to S-5 transitions is mostly responsible for the strong phosphorescence emission from the x and y spin sublevels. Our results concord with the experimental data on temperature and magnetic field dependence of the phosphorescence kinetics. The calculated radiative lifetime in the high temperature limit agrees well with the measured decay times (2 mu s) accounting for negligible non-radiative quenching of the lowest triplet state.

  • 230.
    Jansson, Emil
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Norman, Patrick
    Linköpings Universitet.
    Minaev, Boris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Evaluation of low-scaling methods for calculation of phosphorescence parameters2006In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 124, no 11Article in journal (Refereed)
    Abstract [en]

    In order to find a methodology that is a compromise between favorable computational scaling and tolerable errors, a series of nonrelativistic approaches for the calculation of radiative phosphorescence lifetimes are benchmarked against fully relativistic four-component results. The study of the a (3)A(2)-X (1)A(1) transition intensity in the series of H2CX molecules, where X is a chalcogene atom, X={O,S,Se,Te}, indicates a general good agreement between fully relativistic four-component and nonrelativistic perturbation-theoretical calculations. Among the nonrelativistic approaches, the scaled-charge spin-orbit operator approach is recognized as to provide transition matrix elements that are in good agreement with those obtained with the more elaborate Breit-Pauli and atomic mean field spin-orbit operators. This finding supports phosphorescence calculations using the available linear scaling technology for large complexes and, together with effective-core potentials, large complexes including heavy elements.

  • 231.
    Jena, Naresh K.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Lyne, ÅL.
    Natarajan Arul, Murugan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Birgisson, B.
    Atomic level simulations of the interaction of asphaltene with quartz surfaces: role of chemical modifications and aqueous environment2017In: Materials and Structures, ISSN 1359-5997, E-ISSN 1871-6873, Vol. 50, no 1, article id 99Article in journal (Refereed)
    Abstract [en]

    Understanding the properties of bitumen and its interaction with mineral aggregates is crucial for future strategies to improve roads and highways. Knowledge of basic molecular and electronic structures of bitumen, one out of the two main components of asphalt, poses a major step towards achieving such a goal. In the present work we employ atomistic simulation techniques to study the interaction of asphaltenes, a major constituent of bitumen, with quartz surfaces. As an effective means to tune adhesion or cohesion properties of asphaltenes and mineral surfaces, we propose chemical modification of the pristine asphaltene structure. By the choice of substituent and site of substitution we find that adhesion between the asphaltene molecule and the quartz surface can easily be improved at the same time as the cohesive interaction between the asphaltene units is reduced, while other substituents may lead to the opposite effect. We also provide insight at the molecular level into how water molecules affect interactions between asphaltenes and quartz. Our approach emphasizes a future role for advanced atomistic modeling to understand the properties of bitumen and suggest further improvements.

  • 232.
    Jha, Prakash Chandra
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Jansson, Emil
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Triplet energies of pi-conjugated polymers2006In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 424, no 03-jan, p. 23-27Article in journal (Refereed)
    Abstract [en]

    We report time-dependent density functional theory calculations of singlet-triplet splittings (S-0-T-1) and triplet-triplet (T-1-T-n) excitation energies of a range of conjugated polymers with relevance as light emitting diode materials. The errors obtained from the computed results are discussed in terms of maximum and mean deviation values in comparison with experimental data. The theoretical methodology shows in general a sufficient agreement to warrant its use for prediction of polymer (S-0-T-1) and (T-0-T-1) excitation energies. We confirm that spin contamination of the triplet state is not a serious problem when computing triplet-triplet spectra of organic oligomers.

  • 233.
    Jha, Prakash Chandra
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Polyzos, Ioannis
    Persephonis, Peter
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Two- and three-photon absorption of organic ionic pyrylium based materials2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 17Article in journal (Refereed)
    Abstract [en]

    Pyrylium dyes having the same basic chemical structure, differing only to a specific substituent, have been used as novel materials for multiphoton three-dimensional data storage. Electronic absorption spectra, two-photon and three-photon absorption properties of this class of pyrylium dyes, have been studied theoretically and compared to experimental results. The effects of the counteranion, the surrounding solvent, and electron releasing and electron withdrawing groups in specific positions of the basic structure have been explored in detail. It is argued that on grounds of the quality of experimental spectroscopic agreement, the computed two- and three-photon data may be used in pulse propagation simulations of three-dimensional recording in optical memories.

  • 234. Jha, Prakash Chandra
    et al.
    Minaev, Boris
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    One- and two-photon absorptions in asymmetrically substituted free-base porphyrins: A density functional theory study2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 7Article in journal (Refereed)
    Abstract [en]

    Electronic spectra and structures of a new family of free-base porphyrin (H2P) derivatives with 4-(diphenylamino)stilbene (DPAS) or 4,4(')-bis-(diphenylamino)stilbene (BDPAS) asymmetric substituents, recently synthesized and studied by Drobizhev [J. Phys. Chem. B 110, 9802 (2006)] are investigated by density functional theory (DFT) using modern density functionals and the 6-31G(*) basis set. The time-dependent DFT technique is applied for calculations of one- and two-photon absorption spectra, electric and magnetic dipole moments, and for prediction of electronic circular dichroism for these chiral molecules. The four-band absorption spectrum of the H2P molecule (Q(x), Q(y), 0-0 and 1-0 bands) is enhanced in single-bond-linked DPAS. This enhancement is explained by hyperconjugation of the almost orthogonal pi systems and by small charge-transfer admixtures. The effect is much stronger for the double-bond- and triple-bond-linked DPAS and BDPAS substituents where absorption in the Q region transforms into a two-band spectrum. These molecules with ethenyl and ethynyl bonding of the porphyrin and donor substituent show very strong two-photon absorption in the near-infrared region. DFT calculations explain this by more efficient conjugation between the H2P and DPAS (BDPAS) chromophores, since they are almost coplanar: "Gerade" states of the H2P molecule occur in the Soret region and transform into charge-transfer states with nonzero transition moments. They are responsible for the strong two-photon absorption effects. Mixing of excitations in both chromophores explains the broadening of the Soret band. Though the calculated two-photon absorption cross sections are overestimated, the qualitative trends are reproduced and help understanding the whole genesis of spectra of these asymmetrically substituted H2P derivatives.

  • 235.
    Jha, Prakash Chandra
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Modeling two photon absorption cross sections of open-shell systems2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 1Article in journal (Refereed)
    Abstract [en]

    We demonstrate the prospects of computing two photon absorption cross sections of open-shell systems by applying recently developed spin-restricted time-dependent density functional response theory using the pyrrole radical as an example. The spin multiplicity effects on two photon absorption cross sections of this species are investigated for the doublet, quartet, and sextet states. It is found that irrespective of the exchange-correlation functional employed, the two photon cross sections increase with the increase in spin multiplicity. This result indicates that two photon cross sections of paramagnetic compounds can be controlled by manipulating their spin states and this opens new possibilities for design of hybrid magneto-optical materials.

  • 236.
    Jha, Prakash Chandra
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Spin Multiplicity Dependence of Nonlinear Optical Properties2009In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 10, no 5, p. 817-823Article in journal (Refereed)
    Abstract [en]

    Open-shell spin-restricted time-dependent density functional theory is applied to explore the spin multiplicity dependence of linear and nonlinear optical properties. An open-shell neutral conjugated system, the CAN radical in the doublet X(2)A(2), quartet X(4)A(2), and sextet X(6)A(1) states, is chosen as a model system to illustrate various aspects of the theory. It is found that irrespective of the exchange-correlation functional employed, the components of the polarizability alpha(-omega,omega) and first hyperpolarizability beta(-2(omega,omega,omega) show very different dependency with respect to the multiplicity, with an increasing trend for higher spin states. This is rationalized by the decrease in conjugation and stability of the system with increasing multiplicity, and by the way the interaction between unpaired electrons and the external field is shielded by remaining electrons of the molecule. The study suggests the applicability of open-shell systems for frequency-dependent nonlinear optical properties and for the possibility of spin control for such properties.

  • 237. Jha, Prakash Chandra
    et al.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Seal, Prasenjit
    Chakrabarti, Swapan
    Searching of potential energy curves for the benzene dimer using dispersion-corrected density functional theory2008In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 10, no 19, p. 2715-2721Article in journal (Refereed)
    Abstract [en]

    The present work aims to establish the utility of dispersion-corrected density functional theory for potential energy curves of the benzene dimer, a problem that has received significant attention for a long time. The interaction energies of parallel-stacked, T-shaped and parallel-displaced benzene dimer configurations have been evaluated using both dispersion- and normal gradient-corrected Perdew-Burke-Ernzerhof functionals along with Dunning's augmented correlation-consistent polarized valence triple-zeta (aug-cc-pVTZ) basis functions and compared with explicit correlation methods. The potential energy curves for the parallel-stacked and parallel-displaced benzene dimers are in excellent agreement with highly accurate coupled cluster (CCSD( T)) results, while for the T-shaped benzene dimer the dispersion- corrected results show a distinct deviation, being closer in that case to the MP2 level of results. The overestimation of interaction energy in the T-shaped dimer may be attributed to the presence of a permanent dipole moment in this configuration and indicates a structural dependence of the dispersion- corrected density functional method.

  • 238. Jha, Prakash Chandra
    et al.
    Seal, Prasenjit
    Sen, Sabyasachi
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Chakrabarti, Swapan
    Static and dynamic polarizabilities of (CdSe)(n) (n=1-16) clusters2008In: Computational materials science, ISSN 0927-0256, E-ISSN 1879-0801, Vol. 44, no 2, p. 728-732Article in journal (Refereed)
    Abstract [en]

    Density functional theoretical calculations have been performed on small and medium-sized (CdSe)(n) (n = 1-16) clusters in order to evaluate the variation in electric polarizability and anisotropy in polarizability with increase in the cluster size at both static and Nd:YAG laser frequencies. The electric polarizability values at static frequency show a rapid decrease up to heptamer only with the exception observed for (CdSe)(5) clusters where a sudden increase in the polarizability value is observed. An even-odd oscillating behavior is observed in the anisotropy values between the dimer and heptamer CdSe clusters. Apart from polarizability and anisotropy calculations, the variation in the energy gap between the highest occupied molecular orbital and lowest unoccupied molecular orbital and second difference of energies with the cluster size have also been calculated. just like the anisotropy values, an even-odd oscillating behavior is also observed in the second difference value for the smaller CdSe clusters.

  • 239.
    Jha, Prakash Chandra
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Wang, Yanhua
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    A critical examination of two-photon absorption cross-sections of some reference dyes2006In: Proceedings of International Symposium on Biophotonics, Nanophotonics and Metamaterials, 2006, p. 56-59Conference paper (Refereed)
    Abstract [en]

    The electronic structure and one- and two-photon absorption spectra of four most commonly used Flurophores, namely Bis-MSB, Coumarin 307, Fluorescein and Rhodamine B has been theoretically calculated and compared with experimentally reported spectra. The possible reasons for discrepancies in two photon absorption cross-sections reported in the literature till date is discussed. Since, our calculations are independent of laser source and different calibration methods used by different experimental groups, it should provide, at least in principle., a good picture about the electronic structure. The effect of solvent on the electronic one photon as well as two photon absorption spectra is also obtained. Finally, we also discuss about the necessary precautions that one needs to take when they, compare their results with the one already reported in the literature.

  • 240. Jha, Prakash Chandra
    et al.
    Wang, Yanhua
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Two-photon absorption cross-sections of reference dyes: A critical examination2008In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 9, no 1, p. 111-116Article in journal (Refereed)
    Abstract [en]

    The electronic structure and one- and two-photon absorption spectra of four fluorophores, p-bis(o-methoxystyryl)benzene (Bis-MSB), coumarin 307, fluorescein and rhodomine B, commonly used as reference compounds for two-photon absorption spectra, hove been theoretically calculated and compared with available experimental data. The possible reasons for the wide discrepancies in two-photon absorption cross-sections reported in the literature are discussed on the basis of the theoretical findings. The role of a solvent environment on the electronic one- and two-photon absorption spectra is also studied. We highlight some necessary precautions that one needs to take when comparing literature results of two-photon absorption cross-sections.

  • 241. Jonsson, D.
    et al.
    Norman, P.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Rizzo, A.
    Coriani, S.
    Ruud, K.
    The Cotton-Mouton effect of gaseous CO2, N2O, OCS, and CS2. A cubic response multiconfigurational self-consistent field study2001In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 114, no 19, p. 8372-8381Article in journal (Refereed)
    Abstract [en]

    The hypermagnetizability and the hypermagnetizability anisotropy of CO2, N2O, OCS, and CS2 are computed at a wavelength of 632.8 nm using cubic response theory with multiconfigurational self-consistent field wave functions. The anisotropies of the electric dipole polarizability and of the magnetizability are also obtained. This allows us to study the temperature dependence of the Cotton-Mouton constant for all four molecules and thus to compare to the results of the experimental study by Kling and Huttner [Chem. Phys. Lett. 90, 207 (1984)]. We also assess the importance of pure and zero-point vibrational effects on the relevant molecular properties. In particular, we show that for CO2, OCS, and CS2, the pure vibrational effects to the hypermagnetizability anisotropy can be even more important than the electronic contribution.

  • 242. Jonsson, Dan
    et al.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Jansik, Branislav
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Salek, Pawel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Kohn–Sham Time-Dependent Density Functional Theory with Applications to Linear and Nonlinear Properties2006In: Nonlinear optical properties of matter: From molecules to condensed phases / [ed] Manthos G. Papadopoulos, Andrzej J. Sadlej, Jerzy Leszczynski., Springer Netherlands, 2006, p. 151-209Chapter in book (Refereed)
    Abstract [en]

    We review Kohn–Sham density-functional theory for time-dependent response functionsup to and including cubic response. The working expressions are derived from anexplicit exponential parametrization of the density operator and the Ehrenfest principle,alternatively the quasi-energy ansatz. While the theory retains the adiabatic approximation,implying that the time-dependency of the functional is obtained only implicitly—through the time-dependency of the density itself rather than through the form ofthe exchange-correlation functionals—our implementation generalizes previous timedependentapproaches in that arbitrary functionals can be chosen for the perturbed densities(energy derivatives or response functions). Thus, the response of the density canalways be obtained using the stated density functional, or optionally different functionalscan be applied for the unperturbed and perturbed densities, even different functionals fordifferent response order. In particular, general density functionals beyond the local densityapproximation can be applied, such as hybrid functionals with exchange–correlation atthe generalized gradient-approximation level and fractional exact Hartree–Fock exchange.We also review some recent progress in time-dependent density functional theory foropen-shell systems, in particular spin-restricted and spin restricted-unrestricted formalismsfor property calculations. We highlight a sample of applications of the theory

  • 243. Journel, L.
    et al.
    Guillemin, R.
    Stolte, W. C.
    Carniato, S.
    Taieb, R.
    Minkov, I.
    Gel'mukhanov, Faris
    KTH.
    Salek, P.
    Ågren, Hans
    KTH.
    Hudson, A.
    Lindle, D. W.
    Simon, M.
    Ultrafast nuclear motion in Cl 1s core-excited HCl and DCl probed by resonant inelastic X-ray scattering: Experiment and theory2007In: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, E-ISSN 1873-2526, Vol. 156, p. XLIV-XLIVArticle in journal (Other academic)
  • 244. Justino, L. L. G.
    et al.
    Luísa Ramos, M.
    Abreu, P. E.
    Charas, A.
    Morgado, J.
    Scherf, U.
    Minaev, B. F.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Burrows, H. D.
    Structural and electronic properties of poly(9,9-dialkylfluorene)-based alternating copolymers in solution: An NMR spectroscopy and density functional theory study2013In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 117, no 35, p. 17969-17982Article in journal (Refereed)
    Abstract [en]

    The structural and electronic properties of three alternating poly(9,9-dialkylfluorene) copolymers, poly[2,7-(9,9-bis(octyl)-fluorene)-alt- benzothiadiazole] (F8BT), poly[2,7-(9,9-bis(2′-ethylhexyl)-fluorene)-alt- thiophene S,S-dioxide] (PFTSO2), and poly[2,7-(9,9-bis(2′-ethylhexyl)- fluorene)-alt-1,4-phenylene] (PFP), containing, respectively, benzothiadiazole (BT), thiophene S,S-dioxide, and phenylene groups, have been investigated and compared to those of the homopolymer poly[2,7-(9,9-bis(2′-ethylhexyl)- fluorene)] (PF2/6). The NMR spectra and corresponding shielding tensors of the 1H and 13C nuclei have been studied in solution and are interpreted by density functional theory (DFT) with complete geometry optimization using the B3LYP functional. Particular emphasis is placed on the conformational behavior and electronic properties in the electronic ground state. In addition, time-dependent DFT is applied to obtain detailed insight into the character of selected excited states. A new TDDFT interpretation is presented for optical absorption spectra of singlet and triplet states that have previously been reported for these fluorene-based conjugated copolymers using photoexcitation and pulse radiolysis-energy transfer studies. As well as providing detailed assignment of excited states, the results show that the triplet excitation is slightly more localized than S1 excitation, in agreement with experimental observations. The DFT analysis provides a link between structure and NMR, optical, electronic properties, allowing optimization of the potential of such polymers for photovoltaic and electroluminescence applications.

  • 245.
    Kang, Yu
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Tu, Yaoquan
    Wang, Qi
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    On the Mechanism of Protein Adsorption onto Hydroxylated and Nonhydroxylated TiO2 Surfaces2010In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 114, no 34, p. 14496-14502Article in journal (Refereed)
    Abstract [en]

    Protein adsorption onto implant surfaces is of great importance for the regulation of implant bioactivity. Surface modification of implants is a promising way in the molecular design of biocompatible materials against nonspecific adsorption of proteins. On the basis of these fundamental facts, we focus in this work on the different behavior of protein adsorption on hydroxylated and nonhydroxylated rutile TiO2 (110) surfaces through molecular dynamics simulations. Our investigation indicates that the distribution of the water molecules at the interface induced by the surface modification plays an important role in the protein adsorption. The surface with modified hydroxyl groups was observed to have much greater affinity to the protein, as reflected by the larger protein-surface electrostatic interaction and by the larger amount of adsorbed residues. The highly ordered structure of the modified hydroxyl groups on the hydroxylated surface diminishes the possibility of hydrogen bond formation between the surface and the water molecules above it, which in turn makes it easier for the protein to move closer to the surface with hydroxyl modification.

  • 246. Kang, Yu
    et al.
    Zhang, Zhisen
    Shi, Hui
    Zhang, Junqiao
    Liang, Lijun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Zhejiang University, China .
    Wang, Qi
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tu, Yaoquan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Na+ and K+ ion selectivity by size-controlled biomimetic graphene nanopores2014In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 6, no 18, p. 10666-10672Article in journal (Refereed)
    Abstract [en]

    Because biological ionic channels play a key role in cellular transport phenomena, they have attracted extensive research interest for the design of biomimetic nanopores with high permeability and selectivity in a variety of technical applications. Inspired by the structure of K+ channel proteins, we designed a series of oxygen doped graphene nanopores of different sizes by molecular dynamics simulations to discriminate between K+ and Na+ channel transport. The results from free energy calculations indicate that the ion selectivity of such biomimetic graphene nanopores can be simply controlled by the size of the nanopore; compared to K+, the smaller radius of Na+ leads to a significantly higher free energy barrier in the nanopore of a certain size. Our results suggest that graphene nanopores with a distance of about 3.9 A between two neighboring oxygen atoms could constitute a promising candidate to obtain excellent ion selectivity for Na+ and K+ ions.

  • 247.
    Karaush, N. N.
    et al.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Minaeva, V. A.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Baryshnikov, Gleb V.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine.
    Minaev, Boris F.
    Bohdan Khmelnytsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Identification of tautomeric intermediates of a novel thiazolylazonaphthol dye - A density functional theory study2018In: Spectrochimica Acta Part A - Molecular and Biomolecular Spectroscopy, ISSN 1386-1425, E-ISSN 1873-3557, Vol. 203, p. 324-332Article in journal (Refereed)
    Abstract [en]

    The recently synthesized thiazolylazo dye, 1-(5-benzy1-1,3-thiazol-2-yl)diazenyllnaphthalene-2-ol called shortly BnTAN, is studied by density functional theory (DFT) in three tautomeric forms in order to explain the available H-1 NMR, UV-Vis and FTIR spectra. An experimentally observed IR band at 1678 cm(-1), assigned to the C=O bond stretching vibration, supports the notion that BnTAN retains in the less stable keto-form even in the solid state due to an ultrafast single-coordinate intramolecular proton transfer. This finding is also in a good agreement with an X-ray crystallography analysis which indicates an intermediate position of the proton between the OH and -N=N-groups. Calculations also show that some experimentally observed H-I NMR signals could be considered as being averaged values between theoretically calculated chemical shifts for the corresponding protons in the keto- and enol-tautomers. At the same time the UV-Vis spectra are almost insensitive to the tautomerization processes as the main single band absorption at 500 nm is present in all tautomers according to our TD DFT simulations. The minor differences in spectral features of the long-wavelength visible region are also noted and discussed with respect to the manifestation of the less stable tautomer form.

  • 248. Karaush, Nataliya N.
    et al.
    Baryshnikov, Gleb V.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Minaeva, Valentina A.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Minaev, Boris F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Recent progress in quantum chemistry of hetero[8]circulenes2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 17-18, p. 2218-2230Article in journal (Refereed)
    Abstract [en]

    This mini-review presents recent advances in theory of electronic and spectral properties of hetero[8]circulenes used as promising fluorescent emitters for organic light-emitting diodes. Special attention is paid to the possibility of their further functionalisation into one-dimensional and two-dimensional (2D) materials. Such materials are predicted to be useful ambipolar organic semiconductors showing high charge carrier mobility. The porous structure of hetero[8]circulene-based nano-arrays can also provide suitable hydrogen storage materials, biomimetic-type nanopores and ionic channels. They serve as a good example of the density functional theory application for design of stable 2D structures, which extends the family of graphene-like materials. [GRAPHICS] .

  • 249.
    Karaush, Nataliya N.
    et al.
    Bogdan Khmelnitsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    Baryshnikov, Gleb V.
    Bogdan Khmelnitsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Minaev, Boris F.
    Bogdan Khmelnitsky Natl Univ, Dept Chem & Nanomat Sci, UA-18031 Cherkassy, Ukraine..
    A theoretical study of new representatives of closed- and open-circle benzofuran and benzocyclopentadienone oligomers2018In: New Journal of Chemistry, ISSN 1144-0546, E-ISSN 1369-9261, Vol. 42, no 14, p. 11493-11505Article in journal (Refereed)
    Abstract [en]

    Owing to their potential use as materials for strong optical rotation, circular dichroism and circularly polarized luminescence, the structure and energetic stability of novel closed- and open-circle benzofuran and benzocyclopentadienone oligomers have been studied computationally using the DFT method. It is found that an extension of the macrocycle size (n = 10-30) for the closed-circle species leads to a gradual transformation of their structure from saddle- to helical- and then to a wing-like shape. At the same time, the smaller closed-circle representatives with n = 4 and 6 exhibit a bowl-shaped structure due to the high energy strain of their molecular structures. Application of the NICS (nucleus-independent chemical shift) criterion to the here studied open-circle benzofuran and benzocyclopentadienone species with planar linear, planar fan-shape and helical molecular topology indicates that for the planar benzofuran series the inner benzene ring is more aromatic than the outer hexagons, while the aromaticity of the outer and inner furan rings is insensitive to the molecular size variations. The replacement of the aromatic furan rings by antiaromatic cyclopentadienone fragments for the planar linear species leads to a decrease of aromaticity of the benzene rings from the edge to the center of the benzocyclopentadienone chain. On the other hand, for the planar fan-shape benzocyclopentadienone series a zigzag trend in the NICS values is observed for the benzene rings. Loss of planarity only slightly affects the aromaticity of the helical open-circle benzofuran and benzocyclopentadienone oligomers. We propose that an increase of the NICS indices for the outer and inner rings of the macromolecular helical species is due to the magnetic couplings between the superimposed benzene and furan/cyclopentadienone rings.

  • 250. Karaush, Nataliya N.
    et al.
    Valiev, Rashid R.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Tomsk State Univ.
    Baryshnikov, Gleb V.
    Minaev, Boris F.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    DFT simulation of the heteroannelated octatetraenes vibronic spectra with the Franck-Condon and Herzberg-Teller approaches including Duschinsky effect2015In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 459, p. 65-71Article in journal (Refereed)
    Abstract [en]

    Calculations of vibronic structure in the electronic absorption spectra are carried out for the series of heteroannelated octatetraenes on the basis of density functional theory method. Both Franck-Condon and Herzberg-Teller approaches have been used for estimation of frequency and intensity of vibronic bands in the simulated absorption spectra with respect to the S-0 -> S-1 electronic transition. The key result discussed in this work is that the electronic transition into the first singlet excited states is vibronicallyactive in the absorption spectra for all studied circulenes in a good agreement with experimental observations. We have confirmed our previous assumption that the first (low-lying) weak absorption maximum in the spectra of tetra-tert-butyltetraoxa[8] circulene and dithieno[3,4-b: 3',4'-d]thiophene-annelated cyclooctatetraene can be assigned just for the S-0 -> S-1 transition which produce the next more intense vibronic satellite. In the case of aza[8] circulenes the S-0 -> S-1 transition is symmetry allowed and the corresponding vibronic bands are less intense relative to 0-0 band. (C) 2015 Elsevier B.V. All rights reserved.

2345678 201 - 250 of 639
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