| 1. |
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| 2. |
- Åhlund, John, et al.
(författare)
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The electronic structure of iron phthalocyanine probed by photoelectron and x-ray absorption spectroscopies and density functional theory calculations
- 2006
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 125:3, s. 034709-1-034709-7
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Tidskriftsartikel (refereegranskat)abstract
- A joint experimental and theoretical work to explain the electronic and geometrical structure of an in situ prepared film of iron phthalocyanine (FePc) on silicon (100) is presented. FePc molecular films have been characterized by core and valence photoemission spectroscopy (PES) and x-ray absorption spectroscopy (XAS), and the results have been interpreted and simulated by density functional theory (DFT) calculations. C1s and N1s PE spectra have been analyzed by taking into account all chemically nonequivalent C and N atoms in the molecule. In the Fe2p(3/2) spectra it has been possible to resolve two components that can be related to the open shell structure of the molecule. By valence PES and N1s XAS data, the geometrical orientation of the FePc molecules in the film could be determined. Our results indicate that for the FePc on Si(100), the molecules within the film are mainly standing on the surface. The experimental N1s XAS spectra are very well reproduced by the theoretical calculations, which are both angle and atomic resolved, giving a detailed description of the electronic and geometric structure of the FePc film. Furthermore, the asymmetry and the intensity angle variation of the first N1s XAS threshold feature could be explained by the presented DFT calculations as due to the chemical nonequivalence of the N atoms and the symmetry character of the lowest unoccupied molecular orbital.
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| 3. |
- Hu, Wei, 1985-
(författare)
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Theoretical Study on Chemical Structures and Stability of Molecules in Metallic Junctions
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis, we focus on the structural identification of the interface using surface enhanced Raman spectroscopy (SERS) and inelastic electron tunnelling scattering (IETS). Two different molecular junctions, namely gold/ trans-1,2-bis (4-pyridyl) ethylene/gold junction and gold/4,4'-bipyridine/gold junctions in various conditions were studied and the corresponding configurations were determined. The enhancement in SERS was also studied by employing the time-dependent density functional theory. Furthermore, we studied some properties of the interface, such as the stability of the adsorbates and charge transfer properties of molecular junctions. The decrease in the stability of molecules was found when adsorbed on metallic surface and trapped in metallic junctions. Our studies explained several puzzles and by rational design, more stable molecular devices were obtained.
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| 4. |
- Duan, Sai, et al.
(författare)
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Thermal effects on electronic properties of CO/Pt(111) in water
- 2013
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 15:32, s. 13619-13627
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Tidskriftsartikel (refereegranskat)abstract
- Structure and adsorption energy of carbon monoxide molecules adsorbed on the Pt(111) surfaces with various CO coverages in water as well as work function of the whole systems at room temperature of 298 K were studied by means of a hybrid method that combines classical molecular dynamics and density functional theory. We found that when the coverage of CO is around half monolayer, i.e. 50%, there is no obvious peak of the oxygen density profile appearing in the first water layer. This result reveals that, in this case, the external force applied to water molecules from the CO/Pt(111) surface almost vanishes as a result of the competitive adsorption between CO and water molecules on the Pt(111) surface. This coverage is also the critical point of the wetting/non-wetting conditions for the CO/Pt(111) surface. Averaged work function and adsorption energy from current simulations are consistent with those of previous studies, which show that thermal average is required for direct comparisons between theoretical predictions and experimental measurements. Meanwhile, the statistical behaviors of work function and adsorption energy at room temperature have also been calculated. The standard errors of the calculated work function for the water-CO/Pt(111) interfaces are around 0.6 eV at all CO coverages, while the standard error decreases from 1.29 to 0.05 eV as the CO coverage increases from 4% to 100% for the calculated adsorption energy. Moreover, the critical points for these electronic properties are the same as those for the wetting/non-wetting conditions. These findings provide a better understanding about the interfacial structure under specific adsorption conditions, which can have important applications on the structure of electric double layers and therefore offer a useful perspective for the design of the electrochemical catalysts.
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| 5. |
- Zhao, Ke, et al.
(författare)
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Molecular Dynamics and Quantum Chemistry Study on Conformations and Optical Properties of Hydrogen Bonded Dipolar Merocyanine Dyes
- 2009
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Ingår i: Journal of Physical Chemistry B. - Washington : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 113:30, s. 10271-10276
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Tidskriftsartikel (refereegranskat)abstract
- An earlier proposed strategy to orient two merocyanine dyes in the desirable head-to-tail parallel fashion through multiple hydrogen bonds has been examined by molecular dynamics simulations and quantum chemical calculations. Two different merocyanine dyes dissolved in chloroform solution under various conditions are simulated by molecular dynamics. It is found that two dipolar units can be well connected through various numbers of hydrogen bonds. Although the probability to form the desirable head-to-tail dimer is unfortunately small even under strong poling electric field and low temperature, the formation of unwanted antiparallel structure has been effectively reduced. Typical hydrogen bonded dimers obtained from molecular dynamics simulations have been studied by hybrid density functional calculations. It is found that only the most probable complex can lead to the optical absorption spectrum that is in close agreement with the corresponding experiments. Calculated results for dipole moments of ground and charge transfer states, as well as first hyperpolarizabilities, of three typical complexes have also been provided.
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| 6. |
- Ai, Yue-Jie, et al.
(författare)
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Theoretical Studies on Photoisomerizations of (6-4) and Dewar Photolesions in DNA
- 2010
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:44, s. 14096-14102
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Tidskriftsartikel (refereegranskat)abstract
- The (6-4) photoproduct ((6-4) PP) is one of the main lesions in UV-induced DNA damage. The (6-4) PP and its valence isomer Dewar photoproduct (Dewar PP) can have a great threat of mutation and cancer but gained much less attention to date. In this study, with density functional theory (DFT) and the complete active space self-consistent field (CASSCF) methods, the photoisomerization processes between the (6-4) PP and the Dewar PP in the gas phase, the aqueous solution, and the photolyase have been carefully examined. Noticeably, the solvent effect is treated with the CASPT2//CASSCF/Amber (QM/MM) method. Our calculations show that the conical intersection (Cl) points play a crucial role in the photoisomerization reaction between the (6-4) PP and the Dewar PP in the gas and the aqueous solution. The ultrafast internal conversion between the S-2 ((1)pi pi*) and the So states via a distorted intersection point is found to be responsible for the formation of the Dewar PP lesion at 313 nm, as observed experimentally. For the reversed isomeric process, two channels involving the "dark" excited states have been identified. In addition to the above passages, in the photolyase, a new electron-injection isomerization process as an efficient way for the photorepair of the Dewar PP is revealed.
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| 7. |
- Li, Li, et al.
(författare)
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Reversible Modification of CdSe-CdS/ZnS Quantum Dot Fluorescence by Surrounding Ca2+ Ions
- 2014
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 118:19, s. 10424-10433
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Tidskriftsartikel (refereegranskat)abstract
- It has been known for a long time that the fluorescence intensity of colloidal quantum dots (QDs) becomes modified when free ions are added to the QD solution. The consequences of removing free ions from the QD solution, however, have not been closely investigated. In this work we studied fluorescence from 3-mercaptopropionic acid (3-MPA) coated CdSe-CdS/ZnS core-multishell QDs when free Ca2+ ions were added to and subsequently removed from the QD solution. It was found that QD fluorescence intensity was reduced when Ca2+ ions were added to the QD solution, while the wavelength of the QD fluorescence peak remained unchanged. QD fluorescence recovered when the concentration of free Ca2+ ions in the QD solution was reduced by adding Ca2+ chelator (ethylene glycol tetraacetic acid, EGTA). It was further observed that the time of single QD fluorescence at on-state and QD fluorescence lifetimes were also reduced after adding Ca2+ and then recovered when EGTA was added. Theoretical study shows that a free Ca2+ ion can attach stably to the system of [QD + surface ligand], attract the photoexcited electron, and repel the photoexcited hole inside the QD core, leading to the reduction of the radiative recombination between the electron and hole, thereafter decreasing the QD fluorescence intensity, on-state time, and fluorescence lifetimes, as observed experimentally. To the best of our knowledge, this is a first study to show that the changes of QD optical properties are reversible under the influence of Ca2+ ions. We further estimated the equilibrium association constant pK(a) of our QDs with Ca2+, which is much larger than QDs with Mg2+, Na+, and K+, indicating the feasibility of developing a QD-based Ca2+ sensor.
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| 8. |
- Ai, Yue-Jie, et al.
(författare)
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Theoretical studies on the isomerization mechanism of the ortho-green fluorescent protein chromophore
- 2012
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 14:38, s. 13409-13414
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Tidskriftsartikel (refereegranskat)abstract
- We present a systematic theoretical investigation on the overall ground state and excited-state isomerization reaction mechanism of ortho-green fluorescent protein chromophore (o-HBDI) using the density functional theory and the multireference methods. The calculated results and subsequent analysis suggest the possible isomerization mechanism for o-HBDI. By comparison with experimental observation and detailed analysis, it is concluded that as initiated by the excited-state intramolecular proton transfer reaction, the conical intersection between the ground state and the excited state along the C4-C5 single-bond rotational coordinate is responsible for the rapid deactivation of o-HBDI.
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| 9. |
- Deng, Yunfeng, et al.
(författare)
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A comparative theoretical study on core-hole excitation spectra of azafullerene and its derivatives
- 2014
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 140:12, s. 124304-
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Tidskriftsartikel (refereegranskat)abstract
- The core-hole excitation spectra-near-edge x-ray absorption spectroscopy (NEXAFS), x-ray emission spectroscopy (XES), and x-ray photoelectron spectroscopy (XPS) shake-up satellites have been simulated at the level of density functional theory for the azafullerene C59N and its derivatives (C59N)(+), C59HN, (C59N)(2), and C59N-C-60, in which the XPS shake-up satellites were simulated using our developed equivalent core hole Kohn-Sham(ECH-KS) density functional theory approach [B. Gao, Z. Wu, and Y. Luo, J. Chem. Phys. 128, 234704 (2008)] which aims for the study of XPS shake-up satellites of large-scale molecules. Our calculated spectra are generally in good agreement with available experimental results that validates the use of the ECH-KS method in the present work. The nitrogen K-edge NEXAFS, XES, and XPS shake-up satellites spectra in general can be used as fingerprints to distinguish the azafullerene C59N and its different derivatives. Meanwhile, different carbon K-edge spectra could also provide detailed information of (local) electronic structures of different molecules. In particular, a peak (at around 284.5 eV) in the carbon K-edge NEXAFS spectrum of the heterodimer C59N-C-60 is confirmed to be related to the electron transfer from the C59N part to the C-60 part in this charge-transfer complex.
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| 10. |
- Dou, Jin-Hu, et al.
(författare)
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Atomically precise single-crystal structures of electrically conducting 2D metal-organic frameworks
- 2021
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Ingår i: Nature Materials. - : Springer Science and Business Media LLC. - 1476-1122 .- 1476-4660. ; 20, s. 222-228
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Tidskriftsartikel (refereegranskat)abstract
- Electrically conducting 2D metal-organic frameworks (MOFs) have attracted considerable interest, as their hexagonal 2D lattices mimic graphite and other 2D van der Waals stacked materials. However, understanding their intrinsic properties remains a challenge because their crystals are too small or of too poor quality for crystal structure determination. Here, we report atomically precise structures of a family of 2D pi-conjugated MOFs derived from large single crystals of sizes up to 200 mu m, allowing atomic-resolution analysis by a battery of high-resolution diffraction techniques. A designed ligand core rebalances the in-plane and out-of-plane interactions that define anisotropic crystal growth. We report two crystal structure types exhibiting analogous 2D honeycomb-like sheets but distinct packing modes and pore contents. Single-crystal electrical transport measurements distinctively demonstrate anisotropic transport normal and parallel to the pi-conjugated sheets, revealing a clear correlation between absolute conductivity and the nature of the metal cation and 2D sheet packing motif. Two-dimensional MOFs can possess porosity and electrical conductivity but are difficult to grow as single crystals. Here, by balancing in-plane and out-of-plane interactions, single crystals of sizes up to 200 mu m are grown, allowing in-plane transport measurements and atomic-resolution analysis.
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