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  • 1201. Wheatley, James E.
    et al.
    Ohlin, C. Andre
    Chaplin, Adrian B.
    Solvent promoted reversible cyclometalation in a tethered NHC iridium complex2014In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 50, no 6, p. 685-687Article in journal (Refereed)
    Abstract [en]

    Reaction of [Ir(COD)(py-(IBu)-Bu-t)](+) (py-(IBu)-Bu-t = 3-tert-butyl-1-picolylimidazol-2-ylidene) with acetonitrile results in reversible intramolecular C-H bond activation of the NHC ligand and formation of [Ir(g(2):g 1-C8H13)(py-ItBu’)(NCMe)](+). Coordinated COD acts as an internal hydride acceptor and acetonitrile coordination offsets the otherwise unfavourable thermodynamics of the process.

  • 1202.
    Wiklander, Jesper G.
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Karlsson, Björn C. G.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Aastrup, Teodor
    Nicholls, Ian A.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Towards a synthetic avidin mimic2011In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 400, no 5, p. 1397-1404Article in journal (Refereed)
    Abstract [en]

    A series of streptavidin-mimicking molecularly imprinted polymers has been developed and evaluated for their biotin binding characteristics. A combination of molecular dynamics and NMR spectroscopy was used to examine potential polymer systems, in particular with the functional monomers methacrylic acid and 2-acrylamidopyridine. The synthesis of copolymers of ethylene dimethacrylate and one or both of these functional monomers was performed. A combination of radioligand binding studies and surface area analyses demonstrated the presence of selectivity in polymers prepared using methacrylic acid as the functional monomer. This was predicted by the molecular dynamics studies showing the power of this methodology as a prognostic tool for predicting the behavior of molecularly imprinted polymers.

  • 1203.
    Wilson, Michael A.
    et al.
    Department of Pharmaceutical Chemistry, University of California, San Francisco.
    Wei, Chenyu
    Department of Pharmaceutical Chemistry, University of California, San Francisco.
    Bjelkmar, Pär
    MS 239-4, Exobiology Branch, NASA Ames Research Center, Moffet Field, California.
    Wallace, B. A.
    Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck College, University of London.
    Pohorille, Andrew
    Department of Pharmaceutical Chemistry, University of California, San Francisco.
    Molecular Dynamics Simulation of the Antiamoebin Ion Channel: Linking Structure and Conductance2011In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 100, no 10, p. 2394-402Article in journal (Refereed)
    Abstract [en]

    Molecular-dynamics simulations were carried out to ascertain which of the potential multimeric forms of the transmembrane peptaibol channel, antiamoebin, is consistent with its measured conductance. Estimates of the conductance obtained through counting ions that cross the channel and by solving the Nernst-Planck equation yield consistent results, indicating that the motion of ions inside the channel can be satisfactorily described as diffusive. The calculated conductance of octameric channels is markedly higher than the conductance measured in single channel recordings, whereas the tetramer appears to be nonconducting. The conductance of the hexamer was estimated to be 115 ± 34 pS and 74 ± 20 pS, at 150 mV and 75 mV, respectively, in satisfactory agreement with the value of 90 pS measured at 75 mV. On this basis, we propose that the antiamoebin channel consists of six monomers. Its pore is large enough to accommodate K+ and Cl with their first solvation shells intact. The free energy barrier encountered by K+ is only 2.2 kcal/mol whereas Cl encounters a substantially higher barrier of nearly 5 kcal/mol. This difference makes the channel selective for cations. Ion crossing events are shown to be uncorrelated and follow Poisson statistics.

  • 1204. Witzke, Sarah
    et al.
    Holmgaard List, Nanna
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Olsen, Jogvan Magnus Haugaard
    Steinmann, Casper
    Petersen, Michael
    Beerepoot, Maarten T. P.
    Kongsted, Jacob
    An Averaged Polarizable Potential for Multiscale Modeling in Phospholipid Membranes2017In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 38, no 9, p. 601-611Article in journal (Refereed)
    Abstract [en]

    A set of average atom-centered charges and polarizabilities has been developed for three types of phospholipids for use in polarizable embedding calculations. The lipids investigated are 1,2-dimyristoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2oleoyl-sn-glycero-3-phosphocholine, and 1-palmitoyl-2-oleoylsn- glycerol-3-phospho-L-serine given their common use both in experimental and computational studies. The charges, and to a lesser extent the polarizabilities, are found to depend strongly on the molecular conformation of the lipids. Furthermore, the importance of explicit polarization is underlined for the description of larger assemblies of lipids, that is, membranes. In conclusion, we find that specially developed polarizable parameters are needed for embedding calculations in membranes, while common non-polarizable point-charge force fields usually perform well enough for structural and dynamical studies.

  • 1205.
    Wohlert, Jakob
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
    Edholm, Olle
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.
    The range and shielding of dipole-dipole interactions in phospholipid bilayers2004In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 87, no 4, p. 2433-2445Article in journal (Refereed)
    Abstract [en]

    In molecular dynamics simulations of lipid bilayers, the structure is sensitive to the precise treatment of electrostatics. The dipole-dipole interactions between headgroup dipoles are not long-ranged, but the area per lipid and, through it, other properties of the bilayer are very sensitive to the detailed balance between the perpendicular and in-plane components of the headgroup dipoles. This is affected by the detailed properties of the cutoff scheme or if long-range interactions are included by Ewald or particle-mesh Ewald techniques. Interaction between the in-plane components of the headgroup dipoles is attractive and decays as the inverse sixth power of distance. The interaction is screened by the square of a dielectric permittivity close to the value for water. Interaction between the components perpendicular to the membrane plane is repulsive and decays as the inverse third power of distance. These interactions are screened by a dielectric permittivity of the order 10. Thus, despite the perpendicular components being much smaller in magnitude than the in-plane components, they will dominate the interaction energies at large distances.

  • 1206.
    Wu, Min
    et al.
    Chalmers University of Technology, Gothenburg, Sweden.
    Farkas, Daniel
    Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; School of Science and Technology, Örebro University, Örebro, Sweden.
    Eriksson, Leif A.
    University of Gothenburg, Gothenburg, Sweden.
    Strid, Åke
    Örebro University, School of Science and Technology.
    Proline 411 biases the conformation of the intrinsically disordered plant UVR8 photoreceptor C27 domain altering the functional properties of the peptide2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 818Article in journal (Refereed)
    Abstract [en]

    UVR8 (UV RESISTANCE LOCUS 8) is a UV-B photoreceptor responsible for initiating UV-B signalling in plants. UVR8 is a homodimer in its signalling inactive form. Upon absorption of UV radiation, the protein monomerizes into its photoactivated state. In the monomeric form, UVR8 binds the E3 ubiquitin ligase COP1 (CONSTITUTIVELY PHOTOMORPHOGENIC 1), triggering subsequent UV-B-dependent photomorphogenic development in plants. Recent in vivoexperiments have shown that the UVR8 C-terminal region (aa 397-423; UVR8C27) alone is sufficient to regulate the activity of COP1. In this work, CD spectroscopy and NMR experiments showed that the UVR8C27domain was non-structured but gained secondary structure at higher temperatures leading to increased order. Bias-exchange metadynamics simulations were also performed to evaluate the free energy landscape of UVR8C27. An inverted free energy landscape was revealed, with a disordered structure in the global energy minimum. Flanking the global energy minimum, more structured states were found at higher energies. Furthermore, stabilization of the low energy disordered state was attributed to a proline residue, P411, as evident from P411A mutant data. P411 is also a key residue in UVR8 binding to COP1. UVR8C27is therefore structurally competent to function as a molecular switch for interaction of UVR8 with different binding partners since at higher free energies different structural conformations are being induced in this peptide. P411 has a key role for this function.

  • 1207.
    Wu, Min
    et al.
    University of Gothenburg, Gothenburg, Sweden.
    Strid, Åke
    Örebro University, School of Science and Technology.
    Eriksson, Leif
    University of Gothenburg, Gothenburg, Sweden.
    Prediction of the thre-dimensional structure of the plant UVR8 photoreceptor dimer, and the key residues in UV-B regulated signalling pathway2012In: Science and Technology Day 2012.: Poster exhibition, 2012, p. C28-C28Conference paper (Other academic)
    Abstract [en]

    See attachment

  • 1208.
    Wu, Min
    et al.
    Gothenburg University, Gothenburg, Sweden.
    Strid, Åke
    Örebro University, School of Science and Technology.
    Eriksson, Leif
    Gothenburg University, Gothenburg, Sweden.
    Umbrella sampling calculations of the bindning free energy in the UVR8 dimer.: key residues in uv-b regulated signalling pathway revealed using dft and md simulation methods2012In: Challenges in biomolecular modeling: from qm to coarse-graining. International Society of Quantum Biology and Pharmacology / [ed] Lennart Nilsson, Stockholm, 2012Conference paper (Refereed)
    Abstract [en]

    The dimeric UVR8 protein is a ultraviolet-B radiation (280-315 nm) photoreceptor that is responsible for the first step in UV-B regulation of gene expression in plants1. Its action comprises the actual absorption of the UV quanta by a Trp array in the protein, followed by monomerisation, and subsequent aggregation with downstream signaling components2. Quantum theoretical DFT calculationsa of excitation spectra of both a large cluster model involving seven tryptophans at the interface of the UVR8 proteins where they are intermixed with positive residues (mainly arginines) and a couple of tyrosines, and smaller fragments thereof, reveal that absorption maxima appearing in the 280-300 nm range for the full cluster result from interactions between the central tryptophans and surrounding arginines2. This observation provides an explanation for the experimentally measured action spectrum of the UVR8-dependent UV-B stimulation of HY5 transcription in mature A. thaliana leaf tissue3. Umbrella sampling methodb was used to calculate the binding free energy for the wild type UVR8 dimer and three of its mutants (R286A, R338A and R286A/R338A), in order to verify the key mutants able to disrupt the dimeric structure.

    See also attached document.

  • 1209.
    Wu, Min
    et al.
    University of Gothenburg, Gothenburg, Sweden.
    Strid, Åke
    Örebro University, School of Science and Technology.
    Eriksson, Leif A.
    University of Gothenburg, Gothenburg, Sweden.
    Development of non-standard arginine residue parameters for use with the AMBER force fields2013In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 584, p. 188-194Article in journal (Refereed)
    Abstract [en]

    Amino acid radicals are often involved as intermediates in biological processes, but are difficult to capture by experiment. Computational modeling can be employed to study the features of the species involved. The neutral arginyl radical has previously been detected experimentally using ECD and ETD spectroscopy. Protonation of the radical can occur on the guanidinium carbon, depending on the peptide structure and protein environment. Accurate force fields are essential for reproducing the conformational and dynamic behavior of these intermediates. New AMBER ff99 parameters for the arginyl radical and hydrogenated arginyl side chains are presented based on ab initio quantum chemical calculations. (c) 2013 Elsevier B.V. All rights reserved.

  • 1210.
    Wu, Min
    et al.
    University of Gothenburg, Gothenburg, Sweden.
    Strid, Åke
    Örebro University, School of Science and Technology.
    Eriksson, Leif A
    University of Gothenburg, Gothenburg, Sweden.
    Interactions and Stabilities of the UV RESISTANCE LOCUS8 (UVR8) protein dimer and its key mutants2013In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 53, no 7, p. 1736-1746Article in journal (Refereed)
    Abstract [en]

    The dimeric UVR8 protein is a ultraviolet-B radiation (280-315 nm) photoreceptor responsible for the first step in UV-B regulation of gene expression in plants. Its action comprises the actual absorption of the UV quanta by a tryptophan array at the protein-protein interface, followed by monomerisation, and subsequent aggregation with downstream signaling components. A crystal structure of the Arabidopsis thaliana tryptophan-rich wild type UVR8 protein dimer was recently published, showing the presence of several salt bridges involving arginines R146, R286, R338 and R354. In this work, molecular dynamics simulations in conjunction with umbrella sampling was used to calculate the binding free energy for the wild type UVR8 dimer and three of its mutants (R286A, R338A and R286A/R338A), in order to verify whether the key mutants are able to disrupt the dimeric structure as indicated experimentally.

  • 1211.
    Wu, Shiying
    et al.
    Department of Cell and Molecular Biology, Uppsala University.
    Chen, Yu
    Department of Cell and Molecular Biology, Uppsala University.
    Mao, Guanzhong
    Department of Cell and Molecular Biology, Uppsala University.
    Trobro, Stefan
    Department of Cell and Molecular Biology, Uppsala University.
    Kwiatkowski, Marek
    Department of Cell and Molecular Biology, Uppsala University.
    Kirsebom, Leif A.
    Department of Cell and Molecular Biology, Uppsala University.
    Transition-state stabilization in Escherichia coli ribonuclease P RNA-mediated cleavage of model substrates2014In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 42, no 1, p. 631-642Article in journal (Refereed)
    Abstract [en]

    We have used model substrates carrying modified nucleotides at the site immediately 5' of the canonical RNase P cleavage site, the -1 position, to study Escherichia coli RNase P RNA-mediated cleavage. We show that the nucleobase at -1 is not essential but its presence and identity contribute to efficiency, fidelity of cleavage and stabilization of the transition state. When U or C is present at -1, the carbonyl oxygen at C2 on the nucleobase contributes to transition-state stabilization, and thus acts as a positive determinant. For substrates with purines at -1, an exocyclic amine at C2 on the nucleobase promotes cleavage at an alternative site and it has a negative impact on cleavage at the canonical site. We also provide new insights into the interaction between E. coli RNase P RNA and the -1 residue in the substrate. Our findings will be discussed using a model where bacterial RNase P cleavage proceeds through a conformational-assisted mechanism that positions the metal(II)-activated H2O for an in-line attack on the phosphorous atom that leads to breakage of the phosphodiester bond.

  • 1212. Wu, Yue
    et al.
    Guo, Zhiqian
    Zhu, Wei-Hong
    Wan, Wei
    Zhang, Junji
    Li, Wenlong
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, He
    Li, Alexander D. Q.
    Photoswitching between black and colourless spectra exhibits resettable spatiotemporal logic2016In: Materials Horizons, ISSN 2051-6347, E-ISSN 2051-6355, Vol. 3, no 2, p. 124-129Article in journal (Refereed)
    Abstract [en]

    Logic is the key to computing. Traditionally, logic devices have been fabricated by the top-down approach, whose dimensions are drastically limited. The ultimate goal is to use molecular tailorability to design logics using the "bottom-up'' approach. Here we report an unprecedented photochromic molecule that undergoes unimolecular logic switching when excited anywhere in the entire UV-visible spectrum, thus a bottom-up, all-photonic, molecular logic gate. Specifically, these molecular photonic logics embedded in the polymer thin films function as the "AND'' or "OR'' gate at different temporal responses. To achieve high information-processing density, moreover, a ternary flip-flap-flop gate is realized in the molecular logic because the fact that this photochromic molecule can be photoswitched anywhere in its UV-vis spectrum enabled three different lasers (532, 473, and 561 nm) as the inputs to deliver the complex logic optical outputs.

  • 1213.
    Wu, Yunzhen
    et al.
    Dalian Univ Technol, Inst Energy Sci & Technol, DUT KTH Joint Educ & Res Ctr Mol Devices, State Key Lab Fine Chem, Dalian 116024, Peoples R China..
    Meng, Yanan
    Chinese Acad Sci, Changchun Inst Appl Chem, State Key Lab Rare Earth Resource Utilizat, Changchun 130022, Jilin, Peoples R China.;Univ Sci & Technol China, Sch Appl Chem & Engn, Hefei 230026, Anhui, Peoples R China..
    Hou, Jungang
    Dalian Univ Technol, Inst Energy Sci & Technol, DUT KTH Joint Educ & Res Ctr Mol Devices, State Key Lab Fine Chem, Dalian 116024, Peoples R China..
    Cao, Shuyan
    Dalian Univ Technol, Inst Energy Sci & Technol, DUT KTH Joint Educ & Res Ctr Mol Devices, State Key Lab Fine Chem, Dalian 116024, Peoples R China..
    Gao, Zhanming
    Dalian Univ Technol, Inst Energy Sci & Technol, DUT KTH Joint Educ & Res Ctr Mol Devices, State Key Lab Fine Chem, Dalian 116024, Peoples R China..
    Wu, Zhijian
    Chinese Acad Sci, Changchun Inst Appl Chem, State Key Lab Rare Earth Resource Utilizat, Changchun 130022, Jilin, Peoples R China..
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Orienting Active Crystal Planes of New Class Lacunaris Fe2PO5 Polyhedrons for Robust Water Oxidation in Alkaline and Neutral Media2018In: Advanced Functional Materials, ISSN 1616-301X, E-ISSN 1616-3028, Vol. 28, no 35, article id 1801397Article in journal (Refereed)
    Abstract [en]

    Developing efficient and stable oxygen evolution reaction (OER) electrocatalysts is essential for realizing sustainable energy conversion, such as solar fuels. Although modulating active sites and electron transfer is of great significance to boost electrocatalysis activity, it still remains a big challenge to desirably actualize this goal. Herein, engineering of active sites and electronic framework is implemented via oriented modulation of crystal planes and construction of lacunaris architecture supported by ammonification-elicited simultaneous incorporation of nitrogen and oxygen-defect strategy. The new class porous nitrogen-incorporated Fe2PO5 with oxygen-defect (N-Fe2PO5-x) polyhedron with dominantly exposed {110} reactive facets exhibits superior performance toward water oxidation, achieving current densities of 10 mA cm(-2) at quite low overpotentials of 235 and 315 mV in alkaline and neutral media, respectively. Furthermore, density functional theoretical calculations reveal the energetically favorable {110} planes of lower absorption energy of intermediates and remolding of electronic density framework arising from the ammoniated elicitation process, contributing to excellent OER performance of lacunaris N-Fe2PO5-x polyhedrons. This work may offer a feasible guideline for regulating active sites and electron transfer to develop low-cost and highly efficient OER electrocatalysts in energy conversion systems.

  • 1214. Wu, ZhiFang
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Li, Jing
    Hua, JianLi
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, He
    Influence of the Auxiliary Acceptor on the Absorption Response and Photovoltaic Performance of Dye-Sensitized Solar Cells2014In: Chemistry - An Asian Journal, ISSN 1861-4728, E-ISSN 1861-471X, Vol. 9, no 12, p. 3549-3557Article in journal (Refereed)
    Abstract [en]

    Three new dyes with a 2-(1,1-dicyanomethylene)rhodanine (IDR-I, -II, -III) electron acceptor as anchor were synthesized and applied to dye-sensitized solar cells. We varied the bridging molecule to fine tune the electronic and optical properties of the dyes. It was demonstrated that incorporation of auxiliary acceptors effectively increased the molar extinction coefficient and extended the absorption spectra to the near-infrared (NIR) region. Introduction of 2,1,3-benzothiadiazole (BTD) improved the performance by nearly 50%. The best performance of the dye-sensitized solar cells (DSSCs) based on IDR-II reached 8.53% (short-circuit current density (J(sc))=16.73mAcm(-2), open-circuit voltage (V-oc)=0.71V, fill factor (FF)=71.26%) at AM1.5 simulated sunlight. However, substitution of BTD with a group that featured the more strongly electron-withdrawing thiadiazolo[3,4-c]pyridine (PT) had a negative effect on the photovoltaic performance, in which IDR-III-based DSSCs showed the lowest efficiency of 4.02%. We speculate that the stronger auxiliary acceptor acts as an electron trap, which might result in fast combination or hamper the electron transfer from donor to acceptor. This inference was confirmed by electrical impedance analysis and theoretical computations. Theoretical analysis indicates that the LUMO of IDR-III is mainly localized at the central acceptor group owing to its strong electron-withdrawing character, which might in turn trap the electron or hamper the electron transfer from donor to acceptor, thereby finally decreasing the efficiency of electron injection into a TiO2 semiconductor. This result inspired us to select moderated auxiliary acceptors to improve the performance in our further study.

  • 1215. Xia, Songqin
    et al.
    Lousada, Claudio M.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Materials Technology.
    Mao, Huahai
    KTH, Superseded Departments (pre-2005), Materials Science and Engineering.
    Maier, Annika Carolin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Korzhavyi, Pavel A.
    KTH, Superseded Departments (pre-2005), Materials Science and Engineering.
    Sandström, Rolf
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Wang, Y.
    Zhang, Y.
    Erratum: Nonlinear oxidation behavior in pure Ni and Ni-containing entropic alloys (Front. Mater., (2018) 5, 53, 10.3389/fmats.2018.00053)2018In: Frontiers in Materials, ISSN 2296-8016, Vol. 5, article id 73Article in journal (Refereed)
    Abstract [en]

    In the original article, there was an error. An explanation should be inserted at the beginning of the section Thermodynamic Calculations, Paragraph 1, line 1: In this as well as the following paragraphs the authors refer to phases such as halite, spinel, corundum etc. It thereby solely referred to the structure type and not the respective mineral. In the original article, there was an error. The word "sfinancial" should be corrected to "financial" in the Acknowledgements section, Paragraph 1: The Carl Tryggers Stiftelse för Vetenskaplig Forskning is gratefully acknowledged for financial support. The authors apologize for these errors and state that they do not change the scientific conclusions of the article in any way. The original article has been updated.

  • 1216. Xie, H.
    et al.
    Liu, C.
    Yuan, Y.
    Zhou, T.
    Fan, Ting
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Lei, Q.
    Fang, W.
    Oxidation of phenyl and hydride ligands of bis(pentamethylcyclopentadienyl)hafnium derivatives by nitrous oxide via selective oxygen atom transfer reactions: Insights from quantum chemistry calculations2016In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 45, no 3, p. 1152-1159Article in journal (Refereed)
    Abstract [en]

    The mechanisms for the oxidation of phenyl and hydride ligands of bis(pentamethylcyclopentadienyl)hafnium derivatives (Cp∗ = η5-C5Me5) by nitrous oxide via selective oxygen atom transfer reactions have been systematically studied by means of density functional theory (DFT) calculations. On the basis of the calculations, we investigated the original mechanism proposed by Hillhouse and co-workers for the activation of N2O. The calculations showed that the complex with an initial O-coordination of N2O to the coordinatively unsaturated Hf center is not a local minimum. Then we proposed a new reaction mechanism to investigate how N2O is activated and why N2O selectively oxidize phenyl and hydride ligands of. Frontier molecular orbital theory analysis indicates that N2O is activated by nucleophilic attack by the phenyl or hydride ligand. Present calculations provide new insights into the activation of N2O involving the direct oxygen atom transfer from nitrous oxide to metal-ligand bonds instead of the generally observed oxygen abstraction reaction to generate metal-oxo species.

  • 1217. Xie, Zhen
    et al.
    Duan, Sai
    Wang, Chuan-Kui
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. University of Science and Technology of China.
    Lighting up long-range charge-transfer states by a localized plasmonic field2017In: Nanoscale, ISSN 2040-3364, E-ISSN 2040-3372, Vol. 9, no 46, p. 18189-18193Article in journal (Refereed)
    Abstract [en]

    The long-range charge-transfer states in a donor-acceptor system exhibit well separated electron-hole pairs, but are often difficult to achieve by optical means owing to a very small overlap between the wave functions of the donor and acceptor. We have found that the introduction of a spatially confined plasmon can enhance the transition probability to the long-range charge-transfer states as it can effectively break the intrinsic symmetry selection rule imposed on the system. Meanwhile, the intensity borrowed from local excitations could also be selectively promoted, allowing the manipulation of the excited quantum states. In addition, our calculations reveal that the donor and acceptor moieties can be unambiguously visualized in real space by tip-enhanced resonance Raman images. These findings can benefit light-harvesting and also be readily extended to diverse optical processes.

  • 1218.
    Xu, Bin
    et al.
    Soochow Univ, Peoples R China; Univ Arkansas, AR 72701 USA; Univ Arkansas, AR 72701 USA.
    Hellman, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Bellaiche, L.
    Univ Arkansas, AR 72701 USA.
    Order-disorder transition in the prototypical antiferroelectric PbZrO32019In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 100, no 2, article id 020102Article in journal (Refereed)
    Abstract [en]

    The prototypical antiferroelectric PbZrO3 has several unsettled questions, such as the nature of the antiferroelectric transition, a possible intermediate phase, and the microscopic origin of the Pbam ground state. Using first-principles calculations, we show that no phonon becomes truly soft at the cubic-to-Pbam transition temperature, and the order-disorder character of this transition is clearly demonstrated based on molecular dynamics simulations and potential energy surfaces. The out-of-phase octahedral tilting is an important degree of freedom, which can collaborate with other phonon distortions and form a complex energy landscape with multiple minima Candidates of the possible intermediate phase are suggested based on the calculated kinetic barriers between energy minima, and the development of a first-principles-based effective Hamiltonian. The use of this latter scheme further reveals that specific bilinear interactions between local dipoles and octahedral tiltings play a major role in the formation of the Pbam ground state, which contrasts with most of the previous explanations.

  • 1219.
    Xu, Weidong
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering. Nanjing Tech Univ NanjingTech, Peoples R China.
    Gao, Feng
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    The progress and prospects of non-fullerene acceptors in ternary blend organic solar cells2018In: Materials Horizons, ISSN 2051-6347, E-ISSN 2051-6355, Vol. 5, no 2, p. 206-221Article, review/survey (Refereed)
    Abstract [en]

    The rapid development of organic solar cells (OSCs) based on non-fullerene acceptors has attracted increasing attention during the past few years, with a record power conversion efficiency of over 13% in a binary bulk heterojunction architecture. This exciting development also enables new possibilities for ternary OSCs to further enhance their efficiency and stability. This review summarizes very recent developments of ternary OSCs, with a focus on blends involving non-fullerene acceptors. We also highlight the challenges and perspectives for further development of ternary blend organic solar cells.

  • 1220. Xue, Yuhan
    et al.
    Li, Junhao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Wu, Zengrui
    Liu, Guixia
    Tang, Yun
    Li, Weihua
    Computational insights into the different catalytic activities of CYP3A4 and CYP3A5 toward schisantherin E2019In: Chemical Biology and Drug Design, ISSN 1747-0277, E-ISSN 1747-0285, Vol. 93, no 5, p. 854-864Article in journal (Refereed)
    Abstract [en]

    The cytochromes CYP3A4 and CYP3A5 share 84% sequence identity, but they exhibit different catalytic activities toward some substrates. Schisantherin E (SE) was recently identified as a selective substrate of CYP3A5, which exhibited catalytic efficiency that was more than 23 times higher than CYP3A4. At present, however, the structural determinants responsible for the different catalytic activities of the two enzymes toward SE have not been fully understood. In this study, a combination of molecular docking, molecular dynamic simulations, and binding free energy calculation was performed on the CYP3A4/CYP3A5-SE systems to investigate the issue. The results demonstrate that Ser119 in CYP3A4 and Glu374 in CYP3A5 formed direct hydrogen bonding with SE, respectively. Additionally, one water molecule located between the B-C loop and the I helix mediated different hydrogen-bonding networks between CYP3A4/3A5 and SE. The residue differences (Phe/Leu108 and Leu/Phe210) triggered the distinct conformational changes of the Phe-cluster residues, especially Phe213 and Phe215, which formed stronger hydrophobic interactions with SE in CYP3A5. The calculated binding free energies were consistent with the experimental results.

  • 1221.
    Yanai, Takeshi
    et al.
    Inst Mol Sci, Dept Theoret & Computat Mol Sci, Okazaki, Aichi, Japan.;Grad Univ Adv Studies, Sch Phys Sci, Dept Funct Mol Sci, Okazaki, Aichi, Japan..
    Kurashige, Yuki
    Kobe Univ, Grad Sch Syst Informat, Kobe, Hyogo, Japan.;PRESTO, Japan Sci & Technol Agcy, Kawaguchi, Saitama, Japan.;Kyoto Univ, Grad Sch Sci, Dept Chem, Kyoto, Japan..
    Saitow, Masaaki
    Grad Univ Adv Studies, Sch Phys Sci, Dept Funct Mol Sci, Okazaki, Aichi, Japan.;Max Planck Inst Chem Energiekonvers, Stiftstr 34-36, D-45470 Mulheim, Germany..
    Chalupsky, Jakub
    Acad Sci Czech Republ, Inst Organ Chem & Biochem, Prague, Czech Republic..
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Malmqvist, Per-Åke
    Lund Univ, Dept Theoret Chem, Lund, Sweden..
    Influence of the choice of projection manifolds in the CASPT2 implementation2017In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 115, no 17-18, p. 2077-2085Article in journal (Refereed)
    Abstract [en]

    The Complete Active Space Second-Order Perturbation Theory (CASPT2) is well-established as a high-accuracy electronic structure method. It was originally implemented in the early 1990s to an efficient computer code in the molcas program suite, and this implementation has been extensively used as a standard tool. Here, we report a comparison of it against two independent computer-aided implementations of the CASPT2 method, revealing that the CASPT2 energies provided by the original code of molcas (version 8 or earlier) are inconsistent with the predictions of the lately developed computer-aided implementations. It is shown that this error is associated with the projections of the first-order equation onto the fully internally contracted multireference bases which are partially inconsistent between the left- and right-hand sides. The degree of the errors is assessed by performing illustrative CASPT2 calculations. The errors in total CASPT2 energies are demonstrated to be negligible relative to chemical accuracy in many cases, while there is a difficult case where they may substantially alter chemical description. The incorporation of the consistent projections into molcas has been carried out, which is available in the version 8 sp1.

  • 1222.
    Yang, Guomin
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology, Chemical Engineering.
    Neretnieks, Ivars
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology, Chemical Engineering.
    Moreno, Luis
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology.
    Wold, Susanna
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Density functional theory of electrolyte solutions in slit-like nanopores II. Applications to forces and ion exchange2016In: Applied Clay Science, ISSN 0169-1317, E-ISSN 1872-9053, Vol. 132, p. 561-570Article in journal (Refereed)
    Abstract [en]

    An extended reference fluid density approach/weighted correlation approximation (RFD/WCA) of density functional theory (DFT) for size-asymmetric electrolytes presented in part I is applied to calculate the forces and the ion exchange for Ca- and Na-montmorillonite systems in equilibrium with salt solutions. Our modeling shows that the DFT calculations are in excellent agreement with Monte Carlo simulations and experimental results. The results indicate that the ion size plays an important role in force-distance relation. Due to the excluded volume effect, the osmotic pressure curve predicted by DFT is shifted towards larger separation distances with increasing the diameter of counterions. Additionally, the interaction can be switched from attraction to repulsion with increasing diameter of counterions from standard to hydrated ionic size. Furthermore, the quantitative characterization of the exchange of calcium for sodium at room temperature on Wyoming bentonite is investigated with the DFT modeling in aqueous solutions at pH 7.0. It is found that a significant variation of the selectivity coefficient could be observed with the surface charge density, ionic diameter and interlayer separations. This implies that ion selectivity in compacted bentonite differs from that in dilute smectite dispersions.

  • 1223.
    Yin, S.
    et al.
    Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing.
    Peng, Q.
    Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing.
    Shuai, Z.
    Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing.
    Fang, W.
    Department of Chemistry, Beijing Normal University.
    Wang, Yanhua
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Aggregation-enhanced luminescence and vibronic coupling of silole molecules from first principles2006In: Physical Review B Condensed Matter, ISSN 0163-1829, E-ISSN 1095-3795, Vol. 73, no 20, p. 205409-Article in journal (Refereed)
    Abstract [en]

    Aggregate formation in molecular solids usually quenches the luminescence, a piece of bad news for molecular electronic devices. However, siloles present extremely high luminescent efficiency in solid state as well as in aggregation, but have almost no luminescence in solution. By employing a first-principles calculation to study excited states and vibronic couplings, we find that it is the low-frequency twisting motions of side rings which enhance the nonradiative decay. These motions can be suppressed either by solid-state packing, by aggregation formation in polar solvents, or by increasing the solvent viscosity; thereby, the radiative decay becomes dominant, resulting in peculiar aggregate-induced emission phenomena in siloles.

  • 1224.
    Ying, Fuming
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Application and development of quantum chemical methods. Density functional theory and valence bond theory2010Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis deals with two disjoint subdiciplines of quantum chemistry.  One isthe most used electronic structure method today, density functional theory(DFT), and the other one of the least used electronic structure methods,valence bond theory (VB).  The work on DFT is based on previous developments inthe department in density functional response theory and involves studies ofhyperfine coupling constants which are measured in electron paramagneticresonance experiments.  The method employed is a combination of arestricted-unrestriced approaches which allows for adequate description of spinpolarization without spin contamination, and spin-orbit corrections to accountfor heavy atom effects useing degenerate perturbation theory.  The work anvalence bond theory is a new theoretical approach to higher-order derivatives.The orbital derivatives are complicated by the fact that the wave functions areconstructed from determinants of non-orthogonal orbitals. An approach based onnon-orthogonal second-quantization in biorthogonal basis sets leads tostraightforward derivations without explicit references to overlap matrices.These formulas are relevant for future applications in time-dependent valencebond theory.

  • 1225.
    Yongfei, Ji
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Proton Coupled Hole Transfer for H2O and small organic molecules (CH3OH, HCOOH and HCOH) on AnataseTiO2(101) SurfaceManuscript (preprint) (Other academic)
  • 1226. Yue, Ling
    et al.
    Roca-Sanjuán, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ferré, Nicolas
    Liu, Ya-Jun
    Can the Closed-Shell DFT Methods Describe the Thermolysis of 1,2-Dioxetanone?2012In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 8, no 11, p. 4359-4363Article in journal (Refereed)
    Abstract [en]

    The chemiluminescent decomposition of 1,2-dioxetanone has in the past been studied by state-of-the-art multireference quantum chemical calculations, and a stepwise biradical mechanism was established. Recently, this decomposition has been reinvestigated, and a concerted mechanism has been proposed based on calculations performed at the closed-shell density functional theory (DFT) level of theory. In order to solve this apparent mechanistic contradiction, the present paper presents restricted and unrestricted DFT results obtained using functionals including different amounts of Hartree–Fock (HF) exchange, repeating and complementing the above-mentioned DFT calculations. The calculated results clearly indicate that the closed-shell DFT methods cannot correctly describe the thermolysis of 1,2-dioxetanone. It is found that unrestricted Kohn–Sham reaction energies and barriers are always lower than the ones obtained using a restricted formalism. Hence, from energy principles, the biradical mechanism is found to be prevailing in the understanding of the 1,2-dioxetanone thermolysis.

  • 1227. Zakrzewska, A.
    et al.
    Zaleśny, R.
    Kolehmainen, E.
    Ośmiałowski, B.
    Jȩdrzejewska, B.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Pietrzak, M.
    Substituent effects on the photophysical properties of fluorescent 2-benzoylmethylenequinoline difluoroboranes: A combined experimental and quantum chemical study Dedication: This publication is dedicated to the memory of Prof. Jerzy Pa̧czkowski.2013In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 99, no 3, p. 957-965Article in journal (Refereed)
    Abstract [en]

    In this study, we demonstrate a successful synergy between theory and experiment and report on the photophysical properties of a recently synthesized series of substituted 2-benzoylmethylenequinoline difluoroboranes with a view towards the effect of substitution on their properties. In general difluoroboranes are known to have a bright fluorescence but for some analogs the properties are not fully understood. Quantum chemistry methods have been applied in order to explain a complex structure of the absorption and emission spectra and to gain an insight into the charge redistribution upon the excitation of the investigated molecules. We demonstrate that the spectra of this important class of compounds can be satisfactorily simulated using quantum chemistry methods. In particular, the absorption and emission band structure was resolved and the spectral features were assigned to C-H wagging and skeletal vibrations of the polycyclic core.

  • 1228. Zara, Zeenat
    et al.
    Iqbal, Javed
    Bibi, Shamsa
    Sadaf, Sana
    Eliasson, Bertil
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Designing Benzodithiophene-Based Donor Materials with Favorable Photovoltaic Parameters for Bulk Heterojunction Organic Solar Cells2017In: CHEMISTRYSELECT, ISSN 2365-6549, Vol. 2, no 20, p. 5628-5639Article in journal (Refereed)
    Abstract [en]

    Computational study on four Acceptor-Donor-Acceptor (A-D-A) type of donor molecules namely, dimethyl cyanoacetate terthiophene di(methylthiophene) benzo[1,2-b: 4,5-b'] dithiophene (DMCATDMTBDT) (M1), methylrhodanine terthiophene di (methylthiophene) benzo[1,2-b: 4,5-b'] dithiophene (MRTDMTBDT) (M2), dimethyl cyanoacetate terthiophene di (fluoromethyl thiophene) benzo[1,2-b: 4,5-b'] dithiophene (DMCATDFMTBDT) (M3), and methylrhodanine terthiophene di (fluoromethyl thiophene) benzo[1,2-b: 4,5-b'] dithiophene (MRTDFMTBDT) (M4) was carried out and their photovoltaic properties were associated with methyl cyanoacetate terthiophene di (methoxy) benzo[1,2-b: 4,5-b'] dithiophene (DCAO3TBDT) (R1) and methylrhodanine terthiophene di (methoxy) benzo[1,2-b: 4,5-b'] dithiophene (DR3TBDT) (R2). For the geometry optimization DFT functional CAM B3LYP/6-31G(d) was found to be the best choice, hence TD-CAM B3LYP/631G(d) was opted for the calculation of excited state of the molecules. M3 and M4 represented appropriate frontier molecular orbital energy levels and broad absorption band. The reorganization energies of the designed molecules illustrated excellent charge mobility property. The lower le values as compared to lambda(i) illustrate that the designed donor molecules are better electron donors. M4 was found as champion molecules with the lowest le (0.01601) value. The Voc value of M3 and M4 are 2.74 eV and 2.63 eV respectively with respect to the energy levels of PC60BM (acceptor).

  • 1229.
    Zeng, Yong
    KTH, School of Biotechnology (BIO).
    Optical properties of active photonic materials2007Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    Because of the generation of polaritons, which are quasiparticles possessing the characteristics of both photonics and electronics, active photonic materials offer a possible solution to transfer electromagnetic energy below the diffraction limit and further increase the density of photonic integrated circuits. A theoretical investigation of these exciting materials is, therefore, very important for practical applications.

    Four different kinds of polaritons have been studied in this thesis, (1) surface polaritons of negative-index-material cylindric rods, (2) exciton polaritons of semiconductor quantum dots, (3) localized plasmon polaritons of metallic nanoshells, and (4) surface plasmon polaritons of subwavelength hole arrays in thin metal films. All these types of polaritons were found to strongly affect the optical properties of the studied active photonic materials. More specifically, (1) for two-dimensional photonic crystals composed of negative-index-material cylindric rods, the coupling among surface polaritons localized in the rods results in dispersionless anti-crossing bands; (2) for three-dimensional diamond-lattice quantum-dot photonic crystals, the exciton polariton resonances lead to the formation of complete band gaps in the dispersion relationships; (3) for metallic nanoshells, the thickness of the metal shell strongly modifies the localized plasmon polaritons, and therefore influences the degree of localization of the electromagnetic field inside the metallic nanoshells; (4) for subwavelength hole arrays in thin metal films, high-order surface-polariton Bloch waves contribute significantly to the efficient transmission.

    To numerically simulate these active photonic materials, we introduced three approaches, (1) an extended plane-wave-based transfer-matrix approach for negative- index-material media, (2) a plane-wave method for semiconductor quantum-dot photonic crystals, and (3) an auxiliary-differential-equation finite-difference time- domain approach for semiconductor quantum-dot arrays. A brief perspective is also given at the end of this thesis.

  • 1230.
    Zeng, Yong
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Chen, X. S.
    Lu, W.
    Optical limiting in defective quadratic nonlinear photonic crystals2006In: Journal of Applied Physics, ISSN 0021-8979, E-ISSN 1089-7550, Vol. 99, no 12, p. 123107-Article in journal (Refereed)
    Abstract [en]

    By using a nonlinear transfer matrix method and an iteration method, we investigated an optical limiting in a defective quadratic nonlinear photonic crystal under strong pump-depletion conditions. Due to a giant enhancement of the second harmonic (SH) generation induced by the strong localization of light near the defective band, the progress of the energy exchange from the forward fundamental frequency (FF) channel to the SH channels (both forward and backward) and the backward FF channel is speeded up. The structure can therefore be used as a high-efficient compact optical power limiter. We have also studied the effects of two important parameters of the defective nonlinear periodic structure, the number of the periods and the nonlinear efficiency of the composite material, on the optical limiting.

  • 1231.
    Zeng, Yong
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Fu, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Bengtsson, Mats
    KTH, School of Electrical Engineering (EES), Signal Processing.
    Chen, Xiaoshuang
    National Laboratory for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Science.
    Lu, Wei
    National Laboratory for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Science.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Finite-difference time-domain simulations of exciton-polariton resonances in quantum-dot arrays2008In: Optics Express, ISSN 1094-4087, E-ISSN 1094-4087, Vol. 16, no 7, p. 4507-4519Article in journal (Refereed)
    Abstract [en]

    The optical properties of nanosize quantum-dot (QD) arrays are found to vary significantly around the exciton resonance frequency of the QDs. In order to simulate the interactions between electromagnetic waves and QD arrays, a general auxiliary-differential-equation, finite-difference time-domain approach is introduced and utilized in this article. Using this numerical method, the exciton-polariton resonances of single-layer and double-layer GaAs QD arrays are studied. The optical properties of a single-layer QD array are found to be characterized by the Mie resonance of its constituent QDs, while a double-layer QD array is characterized by the quasi-dipole formed by two QDs positioned in each of the two layers.

  • 1232.
    Zeng, Yong
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Fu, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Chen, Xiaoshuang
    National Laboratory for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Science.
    Lu, Q.
    National Laboratory for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Science.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Optical properties of two-dimensional negative-phase-velocity-medium photonic crystals2006In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics: Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, ISSN 1063-651X, E-ISSN 1095-3787, Vol. 73, no 6, p. 066625-Article in journal (Refereed)
    Abstract [en]

    By an extended plane-wave-based transfer-matrix method, the photonic band structure and the corresponding transmission spectrum have been calculated for a two-dimensional photonic crystal composed of negative-phase-velocity-medium (NPVM) cylindrical rods. Dispersionless anticrossing bands in the two-dimensional NPVM periodic structure are generated by the couplings among surface polaritons localized in the NPVM rods. In part of the negative-phase-velocity frequency region, the photonic band structures of the NPVM photonic crystal are characterized by a topographical continuous dispersion relationship accompanied by many anticrossing bands. The effect of the filling fraction of the NPVM rods on the optical properties of photonic crystals has also been studied.

  • 1233.
    Zeng, Yong
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Fu, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Chen, Xiaoshuang
    National Laboratory for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Science.
    Lu, Wei
    National Laboratory for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Science.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Complete band gaps in three-dimensional quantum dot photonic crystals2006In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 74, no 11, p. 115325-Article in journal (Refereed)
    Abstract [en]

    Nonlocal investigations have been performed about exciton-photon couplings in three-dimensional quantum-dot (QD) photonic crystals and a complete photonic band gap has been found in the band structure of a diamond lattice. The width of such a band gap can be broadened by increasing the filling ratio of the QDs (increasing the QD radius or/and decreasing the lattice constant of the photonic crystal). By decomposing the diamond lattice into two interlacing face-centered-cubic (fcc) sublattices, we have found that by significantly modifying the QD radius in one fcc sublattice (the diamond lattice therefore changed to the zinc blende lattice), the band structure of the zinc blende lattice is in principle the sum of two individual fcc sublattices. However, a huge exciton-photon coupling is observed near the band gaps of the two individual fcc sublattices when the radii of the QDs in the two fcc sublattices approach each other, resulting in the complete band gaps of the diamond structure.

  • 1234.
    Zeng, Yong
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Fu, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Chen, Xiaoshuang
    National Laboratory for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Science.
    Lu, Wei
    National Laboratory for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Science.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Extended plane-wave-based transfer-matrix approach to simulating dispersive photonic crystals2006In: Solid State Communications, ISSN 0038-1098, E-ISSN 1879-2766, Vol. 139, no 7, p. 328-333Article in journal (Refereed)
    Abstract [en]

    It has been difficult to compute the band structures and transmission spectra for photonic crystals (PCs) with dispersive components included in the periodic units. Here we show that by using an extended plane-wave-based transfer-matrix method, we are able to formulate the problem for computing optical properties of dispersive PCs, including magnetic and left-handed PCs. This approach is very general, since it can treat PCs with arbitrary Bravais lattice composed of materials with arbitrary dielectric permittivities and magnetic permeabilities. Combined with the supercell method, this method can further simulate defective PCs such as PC-based waveguides and microcavities.

  • 1235.
    Zeng, Yong
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Fu, Ying
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Chen, Xiaoshuang
    National Laboratory for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Science.
    Lu, Wei
    National Laboratory for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Science.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Selective excitation of surface-polariton Bloch waves for efficient transmission of light through a subwavelength hole array in a thin metal film2007In: Physical Review B Condensed Matter, ISSN 0163-1829, E-ISSN 1095-3795, Vol. 76, no 3, p. 035427-Article in journal (Refereed)
    Abstract [en]

    Electromagnetic (EM) field was found to be able to transmit efficiently through a subwavelength hole array in a metal thin film at specific resonant frequencies. By analyzing the near-field distributions of EM fields in the array system, as well as the corresponding Fourier spectra, we show that the surface-polariton (SP) Bloch waves focus the energy of the incident plane-wave EM field to the vicinity of the hole at resonances (through SP scattering provided by the periodic hole). Furthermore, the wave vectors of the SP waves that contribute to the focusing effect are quantized as functions of the geometric shape of the holes in such a way that the focusing effect of the EM energy into the hole is maximal. The transmission efficiency and bandwidth at resonances are found to partially depend on the number of SP modes which contribute to the focusing effect.

  • 1236.
    Zhan, Shaoqi
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ahlquist, Mårten S. G.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Dynamics and Reactions of Molecular Ru Catalysts at Carbon Nanotube-Water Interfaces2018In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 140, no 24, p. 7498-7503Article in journal (Refereed)
    Abstract [en]

    Immobilization of molecular catalysts to electrode surfaces can improve the recyclability and electron transfer rates. The drawback is that most experimental techniques and theoretical methods are not applicable. Here we present results from a study of a ruthenium water oxidation catalyst [(RuO)-O-V(bda)L-2] in explicit water at a carbon nanotube water interface, forming the key O-O bond between two 128 atom catalysts, all fully dynamically. Our methodology is based on a recently developed empirical valence bond (EVB) model. We follow the key steps of the reaction including diffusion of the catalysts at the interface, formation of the prereactive dimer, and the bond formation between the two catalysts. On the basis of the calculated parameters, we compute the turnover frequency (TOF) at the experimental loading, in excellent agreement with the experiments. The key O-O bond formation was significantly retarded at the surface, and limiting components were identified that could be improved by catalyst modification.

  • 1237.
    Zhang, Feng
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Theoretical Studies on Kinetics of Molecular Excited States2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    HTML clipboardKinetics on molecular excited states is a challenging subject in the field of theoretical chemistry. This thesis pays attention to theoretical studies on kinetics of photo-induced processes, including photo-chemical reactions, radiative and non-radiative transitions (intersystem crossing and internal conversion) in molecular and bio-related systems.

    One- or multi- dimensional potential energy surfaces (PESs) not only provide qualitative mechanistic explanation for excited state decay, but also make it possible to perform kinetic simulations. We have constructed several types of PESs by using computational methods of high-accuracy for a variety of systems of interest. In particular, density functional theory (DFT) and couple cluster singles and doubles (CCSD) method are employed to build PESs of the ground and lowest triple states. For medium-sized molecules, the complete active space self-consistent (CASSCF) method is used for constructing the PESs of excited states.

    Various kinetic theories for the decay processes of excite states are briefly introduced, in particularly adiabatic and nonadiabatic Rice–Ramsperger–Kassel -Marcus (RRKM) approaches for the kinetics of nonradiative decay of excited 2-aminopridine molecule. Special attention has been devoted to Monte Carlo transition state theory which can provide an efficient way to predict the rate of nonradiative transitions of polyatomic molecules on multi-dimensional PESs. Examples of Monte Carlo simulations on the intersystem crossing of isocyanic acid and a model molecule of hexacoordinate heme, as well as internal conversion process for 2-amininopyridine dimer and the adenine-thymine base pair are presented.

  • 1238.
    Zhang, Feng
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ai, Yue-Jie
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fang, Wei-Hai
    Beijing Normal University.
    Nonradiative decay of the lowest excited singlet state of 2-aminopyridine is considerably faster than the radiative decay2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 14, p. 144315-Article in journal (Refereed)
    Abstract [en]

    Ab initio calculations reveal that radiative lifetime of the lowest excited singlet state of 2-aminopyridine (2AP) molecule should be around 20 ns, consistent with the molecules of the same type, but is about one order of magnitude larger than the claimed experimental fluorescent lifetime in recent years. A S1/S0 conical intersection close to the S1 state has been located which could be the possible nonradiative channel that is responsible for the fast decay observed in the experiment.

  • 1239.
    Zhang, Igor Ying
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Wu, Jianming
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xu, Xin
    Accurate Bond Dissociation Enthalpies by Using Doubly Hybrid XYG3 Functional2011In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 9, p. 1824-1838Article in journal (Refereed)
    Abstract [en]

    In this work, we examine the performance of XYG3, a newly developed doubly hybrid density functional (Zhang, Xu, and Goddard III, Proc Natl Acad Sci USA 2009, 106, 4963), to calculate covalent bond dissociation enthalpy (BDE). We use 5 atoms, 32 molecular radicals, and 116 closed-shell molecules to set up 142 bond dissociation reactions. For the total of 148 heats of formation (HOFs) and 142 BDEs, XYG3 leads to mean absolute deviations (MADs) of 1.45 and 1.87 kcal/mol, respectively. In comparison with some other functionals, MADs for HOFs are 2.31 (M06-2X), 2.98 (B2PLYP-D), 3.04 (BMK), 3.96 (B3LYP), 4.47 (B2PLYP), 5.42 (B2GP-PLYP), 6.46 (PBE0), and 29.93 kcal/mol (B3P86), and the corresponding errors for BDEs are 2.06 (M06-2X), 2.25 (BMK), 2.51 (B2PLYP-D), 2.89 (B2GP-PLYP), 3.30 (B3P86), 3.44 (B2PLYP), 3.87 (PBE0), and 6.14 kcal/mol (B3LYP). (C) 2011 Wiley Periodicals, Inc. J Comput Chem 32: 1824-1838, 2011

  • 1240.
    Zhang, Jun
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Wang, Jun
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Sandberg, Alexander
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Wu, Xiongyu
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Nyström, Sofie
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    LeVine, Harry III
    Sanders-Brown Center on Aging, University of Kentucky, KY 40536-0230, Lexington, USA..
    Konradsson, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Hammarström, Per
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Lindgren, Mikael
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering. Department of Physics, Norwegian University of Science and Technology, 7491, Trondheim, Norway..
    Intramolecular Proton and Charge Transfer of Pyrene-based trans-Stilbene Salicylic Acids Applied to Detection of Aggregated Proteins.2018In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 19, no 22, p. 3001-3009Article in journal (Refereed)
    Abstract [en]

    Two analogues to the fluorescent amyloid probe 2,5-bis(4'-hydroxy-3'-carboxy-styryl)benzene (X-34) were synthesized based on the trans-stilbene pyrene scaffold (Py1SA and Py2SA). The compounds show strikingly different emission spectra when bound to preformed Aβ1-42 fibrils. This remarkable emission difference is retained when bound to amyloid fibrils of four distinct proteins, suggesting a common binding configuration for each molecule. Density functional theory calculations show that Py1SA is twisted, while Py2SA is more planar. Still, an analysis of the highest occupied molecular orbitals (HOMOs) and lowest unoccupied molecular orbitals (LUMOs) of the two compounds indicates that the degree of electronic coupling between the pyrene and salicylic acid (SA) moieties is larger in Py1SA than in Py2SA. Excited state intramolecular proton transfer (ESIPT) coupled-charge transfer (ICT) was observed for the anionic form in polar solvents. We conclude that ICT properties of trans-stilbene derivatives can be utilized for amyloid probe design with large changes in emission spectra and decay times from analogous chemical structures depending on the detailed physical nature of the binding site.less thanbr /greater than (© 2018 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim.)

  • 1241.
    Zhang, Qiong
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova.
    Tu, Yaoquan
    A molecular dynamics study of the thermal response of crystalline cellulose I beta2011In: Cellulose (London), ISSN 0969-0239, E-ISSN 1572-882X, Vol. 18, no 2, p. 207-221Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations were performed to better understand the atomic details of thermal induced transitions in cellulose I beta. The latest version of the GLYCAM force field series (GLYCAM06) was used for the simulations. The unit cell parameters, density, torsion angles and hydrogen-bonding network of the crystalline polymer were carefully analyzed. The simulated data were validated against the experimental results obtained by X-ray diffraction for the crystal structure of cellulose I beta at room and high temperatures, as well as against the temperature-dependent IR measurements describing the variation of hydrogen bonding patterns. Distinct low and high temperature structures were identified, with a phase transition temperature of 475-500 K. In the high-temperature structure, all the origin chains rotated around the helix axis by about 30A degrees and the conformation of all hydroxymethyl groups changed from tg to either gt on origin chains or gg on center chains. The hydrogen-bonding network was reorganized along with the phase transition. Compared to the previously employed GROMOS 45a4 force field, GLYCAM06 yields data in much better agreement with experimental observations, which reflects that a cautious parameterization of the nonbonded interaction terms in a force field is critical for the correct prediction of the thermal response in cellulose crystals.

  • 1242. Zhang, Ru bo
    et al.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Effects of OH radical addition on proton transfer in the guanine-cytosine base pair2007In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 23, p. 6571-6576Article in journal (Refereed)
    Abstract [en]

    Double proton transfer (PT) reactions in guanine-cytosine OH radical adducts are studied by the hybrid density functional B3LYP approach. Concerted and stepwise proton-transfer processes are explored between N1(H) on guanine (G) and N3 on cytosine (C), and between N4(H) on C and O6 on G. All systems except GC6OH display a concerted mechanism. 8OHGC has the highest dissociation energy and is 1.2 kcal/mol more stable than the nonradical GC base pair. The origin of the interactions are investigated through the estimation of intrinsic acid-basic properties of the *OH-X monomer (X = G or C). Solvent effects play a significant role in reducing the dissociation energy. The reactions including *OH-C adducts have significantly lower PT barriers than both the nonradical GC pair and the *OH-G adducts. All reactions are endothermic, with the GC6OH --> GC6OHPT reaction has the lowest reaction energy (4.6 kcal/mol). In accordance with earlier results, the estimated NBO charges show that the G moiety carries a slight negative charge (and C a corresponding positive one) in each adduct. The formation of a partial ion pair may be a potential factor leading to the PT reactions being thermodynamically unfavored.

  • 1243. Zhang, Ru Bo
    et al.
    Gao, Feng xin
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Radical-induced damage in 3'dTMP: Insights into a mechanism for DNA strand cleavage2007In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 3, no 3, p. 803-810Article in journal (Refereed)
    Abstract [en]

    DNA strand scission and base release in 3‘dTMP, induced by H and OH radical addition to thymine, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular the mechanism of H atom transfer subsequent to radical formation, from C2‘ on the sugar to the C6 site on the base, is explored. Bulk solvation is found to lower the barrier by up to 5 kcal mol-1 and the reaction energy by up to 12 kcal mol-1 for the hydroxyl radical adducts. The strengths of the N1−C1‘(N1-glycosidic bond) and C3‘−O(P) bonds are calculated, showing that homolytic bond breaking processes are largely favored in both cases. The barrier for C3‘−O(P) bond rupture is approximately 18.2 kcal mol-1, and its breakage is preferred by 10−15 kcal mol-1 over that of N1-glycosidic bond cleavage in both the gas phase and solvents, which is consistent with the changes in C3‘−O(P) and N1−C1‘ bond lengths during the H transfer reactions. Mulliken spin densities, NPA charges, and vertical electron affinities are calculated to clarify the reactive properties of the intramolecular H-transfer radicals.

  • 1244.
    Zhang, T.
    et al.
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Brumboiu, I. E.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Grazioli, C.
    Sincrotrone Trieste, CNR, ISM, I-34149 Trieste, Basovizza, Italy..
    Guarnaccio, A.
    CNR, ISM, I-85050 Potenza, Italy..
    Coreno, M.
    Sincrotrone Trieste, CNR, ISM, I-34149 Trieste, Basovizza, Italy..
    de Simone, M.
    Sincrotrone Trieste, Lab TASC, CNR, IOM, I-34149 Trieste, Basovizza, Italy..
    Santagata, A.
    CNR, ISM, I-85050 Potenza, Italy..
    Rensmo, H.
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Brena, B.
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Lanzilotto, V.
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Puglia, C.
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Lone-Pair Delocalization Effects within Electron Donor Molecules: The Case of Triphenylamine and Its Thiophene-Analog2018In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, no 31, p. 17706-17717Article in journal (Refereed)
    Abstract [en]

    Triphenylamine (TPA) and its thiophene-analog, N,N-diphenyl-2-thiophenamine (DPTA), are both well-known as electron-donating molecules implemented in optoelectronic devices such as organic solar cells and LEDs. Comprehensive valence and core level photoelectron spectroscopy, as well as near edge X-ray absorption spectroscopy (NEXAFS), measurements have been performed on gas phase TPA and DPTA. The experimental results have been compared to density functional theory calculations, providing a detailed description of the molecular electronic structure. Specifically, the C 1s photoelectron lines of both TPA and DPTA were resolved in the different C atom contributions and their binding energies explained as the result of two counter-acting effects: (1) the electronegativity of the nitrogen atom (and sulfur atom in DPTA) and (2) the the N (and S in DPTA) lone-pair electrons. In addition, the C K-edge NEXAFS spectrum of DPTA reveals that the lowest unoccupied molecular orbital (LUMO) energy position is affected differently if the core hole site is on the phenyl compared to the thiophene ring. The electron-donating properties of these two molecules are largely explained by the significant contribution of the N lone-pair electrons (p(z)) to the highest occupied molecular orbital. The contribution to the LUMO and to the empty density of states of the sulfur of the thiophene ring in DPTA explains the better performance of donor-pi-acceptor molecules containing this moiety and implemented in photoenergy conversion devices.

  • 1245. Zhang, T.
    et al.
    Brumboiu, Iulia
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Lanzilotto, V.
    Luder, J.
    Grazioli, C.
    Giangrisostomi, E.
    Ovsyannikov, R.
    Sass, Y.
    Bidermane, I.
    Stupar, M.
    de Simone, M.
    Coreno, M.
    Ressel, B.
    Pedio, M.
    Rudolf, P.
    Brena, B.
    Puglia, C.
    Conclusively Addressing the CoPc Electronic Structure: A Joint Gas-Phase and Solid-State Photoemission and Absorption Spectroscopy Study2017In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 121, no 47, p. 26372-26378Article in journal (Refereed)
    Abstract [en]

    The occupied and empty densities of states of cobalt phthalocyanine (CoPc) were investigated by photoelectron and X-ray absorption spectroscopies in the gas phase and in thin films deposited on a Au(111) surface. The comparison between the gas-phase results and density functional theory single-molecule simulations confirmed that the CoPc ground state is correctly described by the (2)A(1g) electronic configuration. Moreover, photon-energy-dependent valence photoemission spectra of both the gas phase and thin film confirmed the atomic character of the highest occupied molecular orbital as being derived from the organic ligand, with dominant contributions from the carbon atoms. Multiplet ligand-field theory was employed to simulate the Co L-edge X-ray absorption spectroscopy results.

  • 1246.
    Zhang, Teng
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Brumboiu, Iulia E.
    KTH Royal Institute of Technology, Department of Theoretical Chemistry and Biology & Korea Advanced Institute of Science and Technology (KAIST), Department of Chemistry.
    Grazioli, Cesare
    ISM-CNR, Trieste LD2 Unit, Italy.
    Guarnaccio, Ambra
    ISM-CNR, Tito Scalo (Pz), Italy.
    Coreno, Marcello
    ISM-CNR, Trieste LD2 Unit, Italy.
    de Simone, Monica
    IOM-CNR, Laboratorio TASC, Sincrotrone Trieste, Basovizza, Trieste, Italy.
    Santagata, Antonio
    ISM-CNR, Tito Scalo (Pz), Italy.
    Rensmo, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Brena, Barbara
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Lanzilotto, Valeria
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Puglia, Carla
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Molecular and Condensed Matter Physics.
    Lone-Pair Delocalization Effects within Electron Donor Molecules: The Case of Triphenylamine and Its Thiophene-Analog2018In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 122, no 31, p. 17706-17717Article in journal (Refereed)
    Abstract [en]

    Triphenylamine (TPA) and its thiophene-analog, N,N-diphenyl-2-thiophenamine (DPTA), are both well-known as electron-donating molecules implemented in optoelectronic devices such as organic solar cells and LEDs. Comprehensive valence and core level photoelectron spectroscopy, as well as near edge X-ray absorption spectroscopy (NEXAFS), measurements have been performed on gas phase TPA and DPTA. The experimental results have been compared to density functional theory calculations, providing a detailed description of the molecular electronic structure. Specifically, the C 1s photoelectron lines of both TPA and DPTA were resolved in the different C atom contributions and their binding energies explained as the result of two counter-acting effects: (1) the electronegativity of the nitrogen atom (and sulfur atom in DPTA) and (2) the the N (and S in DPTA) lone-pair electrons. In addition, the C K-edge NEXAFS spectrum of DPTA reveals that the lowest unoccupied molecular orbital (LUMO) energy position is affected differently if the core hole site is on the phenyl compared to the thiophene ring. The electron-donating properties of these two molecules are largely explained by the significant contribution of the N lone-pair electrons (p(z)) to the highest occupied molecular orbital. The contribution to the LUMO and to the empty density of states of the sulfur of the thiophene ring in DPTA explains the better performance of donor-pi-acceptor molecules containing this moiety and implemented in photoenergy conversion devices.

  • 1247.
    Zhao, Ke
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Theoretical study on nonlinearoptical properties of organicchromophores in solutions2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Inter-molecular interactions have significant influences on linear and nonlinear optical properties of molecules including one- and two-photon absorptions, emissions, and various high order nonlinear polarizations. The related investigation has become an active and challenging research area. The theoretical structure-to-property relationship obtained from quantum chemical calculations of single organic conjugated molecules often can not be directly applied to real materials in condensed phases. One has to consider the effect of environment, that is, inter-molecular interactions, where the model systems experience in real experiments or applications. The change of molecular conformations under all kinds of interactions and its effects on linear and nonlinear optical properties are the central issue of this thesis.

    Special attentions have been paid to symmetrical diamino substituted distyrylbenzene chromophores with different torsional angles, two dipolar merocyanine dyes of various orientations, two isomers of a V-shaped 2-hydroxypyrimidine derivative and their various dimers, and the structural fluctuations of interacting polar chromophores in solutions. Quantum chemical methods in combination with molecular dynamics simulations have been employed to study molecular conformations and optical properties in solutions, in particular the solvent and aggregation effects on one- and two-photon absorption. More specifically, time-dependent density functional theory has been used for all electronic calculations, while the polarizable continuum model and supermolecule approach have also been employed to take into account solvent effects.

    Moreover, the propagation of an ultrashort laser pulse through a one-dimensional asymmetric organic molecular medium which possesses large permanent dipole moments has been simulated by solving full Maxwell-Bloch equations using predictor-corrector finite-difference time-domain method. We have focused on the supercontinuum generation of spectra and the formation of attosecond pulses.

  • 1248.
    Zhovtobriukh, Iurii
    et al.
    Stockholm Univ, FYSIKUM, AlbaNova Univ Ctr, SE-10691 Stockholm, Sweden..
    Norman, Patrick
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Pettersson, Lars G. M.
    Stockholm Univ, FYSIKUM, AlbaNova Univ Ctr, SE-10691 Stockholm, Sweden..
    X-ray absorption spectrum simulations of hexagonal ice2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 3, article id 034501Article in journal (Refereed)
    Abstract [en]

    We calibrate basis sets and performance of two theoretical approaches to compute X-ray absorption spectra (XAS) of condensed water by comparison to experiments on hexagonal ice Ih. We apply both the transition-potential half-core-hole approach and the complex polarization propagator using four different models of the crystal with increasing oxygen and proton disorder but find poor agreement with experiments. We note that there are large variations in experimental spectra depending on detection mode and how the ice samples were prepared, which leads us to critically investigate what structures were actually prepared and measured in each case. This is done by using a Monte Carlo-based fitting technique which fits the spectra based on a library of precomputed spectra and assigns weights to contributions from different model structures. These are then used to generate O-O and O-H radial distribution functions and tetrahedrality parameters associated with each of the measured spectra. We find that all spectra are associated with sharp peaks at the oxygen positions in the perfect lattice, but with significant disorder around these positions. We suggest that presently available XAS of hexagonal ice are not fully representative of the perfect crystalline lattice, but contain varying amounts of defects and possible contributions from low-density amorphous ice.

  • 1249. Zhu, L.
    et al.
    Ang, C. Y.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Nguyen, K. T.
    Tan, S. Y.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhao, Y.
    Luminescent color conversion on cyanostilbene-functionalized quantum dots via in-situ photo-tuning2012In: Advanced Materials, ISSN 0935-9648, E-ISSN 1521-4095, Vol. 24, no 29, p. 4020-4024Article in journal (Refereed)
    Abstract [en]

    Photo-responsive CdSe quantum dots functionalized with the cyanostilbene unit are synthesized. The as-prepared quantum dot hybrid reveals a photo-tunable dual fluorescent characteristic. White light emission can be generated in situ from the hybrid through photoirradiation to adjust the relative intensities of the two complementary emissions. Luminescent color conversion through yellow, white, and blue can be realized by varying the photoirradiation time.

  • 1250. Zhu, Liang-Liang
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ji, Feng-Yuan
    Ma, Xiang
    Wang, Qiao-Chun
    Tian, He
    Photolockable Ratiometric Viscosity Sensitivity of Cyclodextrin Polypseudorotaxane with Light-Active Rotor Graft2009In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 25, no 6, p. 3482-3486Article in journal (Refereed)
    Abstract [en]

    A prototype, based on light-active fluorescent rotor grafted to beta-cyclodextrin, shows a good solvent viscosity-sensitive behavior due to the environment-dependent nonradiative decay. With the reversible photoisomerization of the cyanostilbene unit, the viscosity sensitivity of the molecular rotor could be locked and activated, and the two switchable states can be distinguished by fluorescent signals. This cyclodextrin derivative was threaded to form a novel polypseudorotaxane. Such supramolecular assembly displays a lockable ratiometric fluorescent viscosity sensitivity with two emission channels: one aroused by fluorophore's intramolecular excimer without influenced by viscosity is used to gauge the concentration of the compound, while the other corresponding to the monomer's rotor fluorescence acts as a viscosity-sensitive signal and it can be shut off by UV irradiation.

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