| 1. |
- Snezhkova, O., et al.
(författare)
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Iron phthalocyanine on copper nitride: geometry, spin state, and modification by pyridine adsorption
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Using a monolayer of iron phthalocyanine adsorbed on the Au(111) surface and on a Cu(111)-supported two-dimensional copper nitride layer, we show how the modification of the support can influence the electronic and magnetic properties of an adsorbed transition metal complex. The two systems have been studied by a combination of electron spectroscopy and first principles theoretical calculations, which included modelling of the van der Waals interactions. For adsorption of iron phthalocyanine on the Cu(100)c(2x2)-2N/Cu(111) surface we find several different adsorbate structures at different surface sites, which all have very similar energies. Depending on the adsorption site - above a support nitrogen or a support copper atom - the spin magnetic moment of the molecular iron ion assumes different values. Although pyridine adsorption on the iron phthalocyanine monolayer reduces the spin magnetic moments for all phthalocyanine adsorption sites, the difference between the different sites persists: only for the iron phthalocyanine adsorbates with the central iron ion above a support nitrogen atom the spin is quenched completely, while a residual spin magnetic moment is found for the adsorption structures with the iron ion above a copper atom. The results illustrate clearly the relevance of the support as a ligand to the central ion.
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| 2. |
- Farronato, M., et al.
(författare)
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New Quadratic Self-Assembly of Double-Decker Phthalocyanine on Gold(111) Surface : From Macroscopic to Microscopic Scale
- 2018
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 122:46, s. 26480-26488
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Tidskriftsartikel (refereegranskat)abstract
- Unveiling the self-organization mechanism of semiconducting organic molecules onto metallic surfaces is the first step to design hybrid devices in which the self-assembling is exploited to tailor magnetic properties. In this study, double-decker rare-earth phthalocyanines, namely, lutetium phthalocyanine (LuPc2), are deposited on Au(111) gold surface forming large-scale self-assemblies. Global and local experimental techniques, namely, grazing incidence X-ray diffraction and scanning tunneling microscopy, supplemented by density functional theory calculations with van der Waals corrections, give insight into the molecular structural arrangement of the thin film and the self organization at the surface. Our results show unambiguously that the two plateaus of the double-decker phthalocyanine present a different rotation than the isolated molecule. This is evidenced by density functional theory simulations of optimized LuPc2 monolayer showing a perfect agreement with experimental findings. Moreover, the stabilized structure of double layers reveals an eclipsed configuration of the molecules in the stacking, having the ligand plateaus parallel to the gold surface. The high crystallinity of the molecular assembly and its weak electronic coupling with the metallic substrate is expected to open new perspective in magnetic devices.
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| 3. |
- Lüder, J., et al.
(författare)
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Electronic correlations revealed by hybrid functional and GW calculations in the anti-aromatic biphenylene molecule
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The biphenylene molecule is an interesting new candidate as a building block for advanced 2D materials. In this study, the molecular properties of biphenylene, like ionization potential and electron affinity, as well as the HOMO-LUMO gap were computed with the GW approach and with hybrid functional Density Functional Theory. B3LYP, HSE and HSE06 were compared as well as with the OT-RSH approach. The electronic structure of the valence states obtained by GW calculations and hybrid functionals was compared to experimental valence photoelectron spectroscopy data.
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| 4. |
- Lüder, J., et al.
(författare)
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Theory of X-ray spectroscopy of strongly correlated systems
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- X-ray absorption spectroscopy measured at the L-edge of transition metals (TMs) is a powerful element-selective tool providing direct information about the correlation effects in the 3d states. The theoretical modelling of the 2p to 3d excitation processes remains a challenge for contemporary ab initio electronic structure techniques, due to strong core-hole and multiplet effects influencing the spectra. In this work we present a realisation of the method combining the density functional theory with multiplet ligand field theory, proposed in Phys. Rev. B 85, 165113 (2012). The core of this approach is the solution of the single-impurity Anderson model (SIAM), parameterised from first principles.In our implementation, we adopt the dynamical mean-field theory and utilize the local Hamiltonian and the hybridisation function, projected onto TM 3d states, in order to construct the SIAM. We show that the current method can be used as an alternative to the construction of the Wannier functions. The developed computational scheme is applied to calculate the L-edge spectra for several TM monoxides. An excellent agreement between the theory and experiment is found for all studied systems. The possible extensions of the method as well as its limitations are discussed.
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| 5. |
- Lüder, Kai, 1963, et al.
(författare)
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In silico prediction of drug solubility: 2. Free energy of solvation in pure melts
- 2007
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 111:7, s. 1883-1892
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Tidskriftsartikel (refereegranskat)abstract
- The solubility of drugs in water is investigated in a series of papers and in the current work. The free energy of solvation, Delta G(vl)(center dot), of a drug molecule in its pure drug melt at 673.15 K (400 degrees C) has been obtained for 46 drug molecules using the free energy perturbation method. The simulations were performed in two steps where first the Coulomb and then the Lennard-Jones interactions were scaled down from full to no interaction. The results have been interpreted using a theory assuming that Delta G(vl)(center dot) = Delta G(cav) + E-LJ + E-C/2 where the free energy of cavity formation, Delta G(cav), in these pure drug systems was obtained using hard body theories, and E-LJ and E-C are the Lennard-Jones and Coulomb interaction energies, respectively, of one molecule with the other ones. Since the main parameter in hard body theories is the volume fraction, an equation of state approach was used to estimate the molecular volume. Promising results were obtained using a theory for hard oblates, in which the oblate axial ratio was calculated from the molecular surface area and volume obtained from simulations. The Coulomb term, E-C/2, is half of the Coulomb energy in accord with linear response, which showed good agreement with our simulation results. In comparison with our previous results on free energy of hydration, the Coulomb interactions in pure drug systems are weaker, and the van der Waals interactions play a more important role.
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| 6. |
- Lüder, Kai, 1963, et al.
(författare)
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In silico prediction of drug solubility. 3. Free energy of solvation in pure amorphous matter
- 2007
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 111:25, s. 7303-7311
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Tidskriftsartikel (refereegranskat)abstract
- The solubility of drugs in water is investigated in a series of papers. In this work, we address the process of bringing a drug molecule from the vapor into a pure drug amorphous phase. This step enables us to actually calculate the solubility of amorphous drugs in water. In our general approach, we, on one hand, perform rigorous free energy simulations using a combination of the free energy perturbation and thermodynamic integration methods. On the other hand, we develop an approximate theory containing parameters that are easily accessible from conventional Monte Carlo simulations, thereby reducing the computation time significantly. In the theory for solvation, we assume that Delta G(center dot) = Delta G(cav) + E-LJ + E-C/2, where the free energy of cavity formation, Delta G(cav), in pure drug systems is obtained using a theory for hard-oblate spheroids, and E-LJ and E-C are the Lennard-Jones and Coulomb interaction energies between the chosen molecule and the others in the fluid. The theoretical predictions for the free energy of solvation in pure amorphous matter are in good agreement with free energy simulation data for 46 different drug molecules. These results together with our previous studies support our theoretical approach. By using our previous data for the free energy of hydration, we compute the total free energy change of bringing a molecule from the amorphous phase into water. We obtain good agreement between the theory and simulations. It should be noted that to obtain accurate results for the total process, high precision data are needed for the individual subprocesses. Finally, for eight different substances, we compare the experimental amorphous and crystalline solubility in water with the results obtained by the proposed theory with reasonable success.
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| 7. |
- Totani, R., et al.
(författare)
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Core levels, valence band structures and unoccupied states of biphenylene films
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Biphenylene is a cyclic hydrocarbon made of two benzene rings connected by a cyclobutadiene ring. We performed a photoemission and near-edge absorption (PES and NEXAFS) spectroscopy investigation on biphenylene films of different thicknesses, deposited onto a Cu(111) crystal. By PES we studied the occupied core and valence levels, while NEXAFS gave us information on the unoccupied states. The obtained results have been compared to previous gas phase spectra and density functional theory (DFT) calculations on single biphenylene molecule to get insights in the film electronic structure and possible modification induces by the adsorption. Furthermore, NEXAFS results of biphenylene films of different thicknesses allowed the characterization of the molecular arrangement in the overlayer on the Cu surface and helped to clarify the substrate-molecule interactions.
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| 8. |
- Totani, R., et al.
(författare)
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Electronic structure investigation of biphenylene films
- 2017
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 146:5
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Tidskriftsartikel (refereegranskat)abstract
- Photoelectron Spectroscopy (PS) and Near-Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy have been used to investigate the occupied and empty density of states of biphenylene films of different thicknesses, deposited onto a Cu(111) crystal. The obtained results have been compared to previous gas phase spectra and single molecule Density Functional Theory (DFT) calculations to get insights into the possible modification of the molecular electronic structure in the film induced by the adsorption on a surface. Furthermore, NEXAFS measurements allowed characterizing the variation of the molecular arrangement with the film thickness and helped to clarify the substrate-molecule interaction. Published by AIP Publishing.
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| 9. |
- Westergren, J., et al.
(författare)
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In silico prediction of drug solubility: 1. Free energy of hydration
- 2007
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 111:7, s. 1872-1882
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Tidskriftsartikel (refereegranskat)abstract
- As a first step in the computational prediction of drug solubility the free energy of hydration, Delta G(vw)(center dot), in TIP4P water has been computed for a data set of 48 drug molecules using the free energy of perturbation method and the optimized potential for liquid simulations all-atom force field. The simulations were performed in two steps, where first the Coulomb and then the Lennard-Jones interactions between the solute and the water molecules were scaled down from full to zero strength to provide physical understanding and simpler predictive models. The results have been interpreted using a theory assuming Delta G(vw)(center dot) = A(MS)gamma + E-LJ + E-C/2 where A(MS) is the molecular surface area, gamma is the water-vapor surface tension, and E-LJ and E-C are the solute-water Lennard-Jones and Coulomb interaction energies, respectively. It was found that by a proper definition of the molecular surface area our results as well as several results from the literature were found to be in quantitative agreement using the macroscopic surface tension of TIP4P water. This is in contrast to the surface tension for water around a spherical cavity that previously has been shown to be dependent on the size of the cavity up to a radius of similar to 1 nm. The step of scaling down the electrostatic interaction can be represented by linear response theory.
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| 10. |
- Zhang, Teng, et al.
(författare)
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Conclusively Addressing the CoPc Electronic Structure : A Joint Gas-Phase and Solid-State Photoemission and Absorption Spectroscopy Study
- 2017
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 121:47, s. 26372-26378
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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