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  • 1.
    Al-Saidi, W A
    et al.
    University of Pittsburgh, USA .
    Asher, Sanford A
    University of Pittsburgh, USA .
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Resonance Raman Spectra of TNT and RDX Using Vibronic Theory, Excited-State Gradient, and Complex Polarizability Approximations2012In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, no 30, p. 7862-7872Article in journal (Refereed)
    Abstract [en]

    Geometries, UV absorption bands, and resonance Raman (RR) cross sections of TNT and RDX are investigated using density functional theory (DFT) in conjunction with the Coulomb attenuated B3LYP exchange-correlation functional. The absorption and RR spectra are determined with use of vibronic (VB) theory, excited-state gradient, and complex polarizability (CPP) approximations. We examined lowenergy isomers (two for TNT and four for RDX) whose energies differ by less than 1 kcal/mol, such that they would appreciably be populated at room temperature. The two TNT isomers differ by an internal rotation of the methyl group, while the four conformers of RDX differ by the arrangements of the nitro group relative to the ring. Our theoretical optical properties of the TNT and RDX isomers are in excellent agreement with experimental and recent CCSD-EOM results, respectively. For the two TNT isomers, the ultraviolet RR (UVRR) spectra are similar and in good agreement with recently measured experimental results. Additionally, the UVRR spectra computed using the excited-state and CPP approaches compare favorably with the VB theory results. On the other hand, the RR spectra of the RDX conformers differ from one another, reflecting the importance of the positioning of the NO2 groups with respect to the ring. In the gas phase or in solution, RDX would give a spectrum associated with a conformationally averaged structure. It is encouraging that the computed spectra of the conformers show similarities to recent measured RDX spectra in acetonitrile solution, and reproduce the 10-fold decrease in the absolute Raman cross sections of RDX compared to TNT for the observed 229 nm excitation. We show that in TNT and RDX vibrational bands that couple to NO2 or the ring are particularly resonance enhanced. Finally, the computed RDX spectra of the conformers present a benchmark for understanding the RR spectra of the solid-phase polymorphs of RDX.

  • 2.
    Borg, O. Anders
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Örebro University, Sweden.
    Durbeej, Bo
    University of Siena, Italy.
    Electron-transfer induced repair of 6-4 photoproducts in DNA: a computational study2007In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, no 12, p. 2351-2361Article in journal (Refereed)
    Abstract [en]

    The mechanism employed by DNA photolyase to repair 6-4 photoproducts in UV-damaged DNA is explored by means of quantum chemical calculations. Considering the repair of both oxetane and azetidine lesions, it is demonstrated that reduction as well as oxidation enables a reversion reaction by creating anionic or cationic radicals that readily fragment into monomeric pyrimidines. However, on the basis of calculated reaction energies indicating that electron transfer from the enzyme to the lesion is a much more favorable process than electron transfer in the opposite direction, it is suggested that the photoenzymic repair can only occur by way of an anionic mechanism. Furthermore, it is shown that reduction of the oxetane facilitates a mechanism involving cleavage of the C−O bond followed by cleavage of the C−C bond, whereas reductive fragmentation of the azetidine may proceed with either of the intermonomeric C–N and C–C bonds cleaved as the first step. From calculations on neutral azetidine radicals, a significant increase in the free-energy barrier for the initial fragmentation step upon protonation of the carbonylic oxygens is predicted. This effect can be attributed to protonation serving to stabilize reactant complexes more than transition structures.

  • 3.
    Classen, Thomas
    et al.
    Max-Planck-Institut für Festkörperforschung, Stuttgart, Germany.
    Lingenfelder, Magali
    Max-Planck-Institut für Festkörperforschung, Stuttgart, Germany.
    Wang, Yeliang
    Max-Planck-Institut für Festkörperforschung, Stuttgart, Germany.
    Chopra, Rishav
    Max-Planck-Institut für Festkörperforschung, Stuttgart, Germany.
    Virojanadara, Chariya
    Max-Planck-Institut für Festkörperforschung, Stuttgart, Germany .
    Starke, Ulrich
    Max-Planck-Institut für Festkörperforschung, Stuttgart, Germany.
    Constantini, Giovanni
    Max-Planck-Institut für Festkörperforschung, Stuttgart, Germany.
    Kern, Klaus
    Max-Planck-Institut für Festkörperforschung, Stuttgart, Germany.
    Fratesi, G.
    INFM-CNR DEMOCRITOS Theory@Elettra group and SISSA Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy .
    Fabris, S.
    INFM-CNR DEMOCRITOS Theory@Elettra group and SISSA Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy .
    Gironcoli, S.
    INFM-CNR DEMOCRITOS Theory@Elettra group and SISSA Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy .
    Baroni, S.
    INFM-CNR DEMOCRITOS Theory@Elettra group and SISSA Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy .
    Haq, S.
    Surface Science Research Centre, University of Liverpool, U.K. .
    Raval, R.
    Surface Science Research Centre, University of Liverpool, U.K..
    Hydrogen and Coordination Bonding Supramolecular Structures of Trimesic Acid on Cu(110)2007In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, no 49, p. 12589-12603Article in journal (Refereed)
    Abstract [en]

    The adsorption of trimesic acid (TMA) on Cu(110) has been studied in the temperature range between 130 and 550 K and for coverages up to one monolayer. We combine scanning tunneling microscopy (STM), low-energy electron diffraction (LEED), reflection absorption infrared spectroscopy (RAIRS), X-ray photoemission spectroscopy (XPS), and density functional theory (DFT) calculations to produce a detailed adsorption phase diagram for the TMA/Cu(110) system as a function of the molecular coverage and the substrate temperature. We identify a quite complex set of adsorption phases, which are determined by the interplay between the extent of deprotonation, the intermolecular bonding, and the overall energy minimization. For temperatures up to 280 K, TMA molecules are only partly deprotonated and form hydrogen-bonded structures, which locally exhibit organizational chirality. Above this threshold, the molecules deprotonate completely and form supramolecular metal−organic structures with Cu substrate adatoms. These structures exist in the form of single and double coordination chains, with the molecular coverage driving distinct phase transitions.

  • 4.
    dos Santos, Renato B.
    et al.
    University of Federal Bahia, Brazil .
    Rivelino, Roberto
    University of Federal Bahia, Brazil .
    de B. Mota, Fernando
    University of Federal Bahia, Brazil .
    Gueorguiev, Gueorgui Kostov
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, The Institute of Technology.
    Exploring Hydrogenation and Fluorination in Curved 2D Carbon Systems: A Density Functional Theory Study on Corannulene2012In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, no 36, p. 9080-9087Article in journal (Refereed)
    Abstract [en]

    Corannulene has been a useful prototype for studying C-based nanostructures as well as surface chemistry and reactivity of sp(2)-hybridized carbon-based materials. We have investigated fluorination and hydrogenation of corannulene carrying out density functional theory calculations. In general, the fluorination is energetically more favorable than hydrogenation of corannulene. The substitution of the peripheral H atoms in the corannulene molecule by F atoms leads to a larger cohesive energy gain than when F (or H) atoms are bonded to the hub carbon and bridge carbon sites of this molecule. As expected for doped C-based nanostructures, the hydrogenation or fluorination significantly changes the HOMO-LUMO gap of the system. We have obtained HOMO-LUMO gap variations of 0.13-3.46 eV for F-doped and 0.38-1.52 eV for H-doped systems. These variations strongly depend on the concentration and position of the incorporated F/H atoms, instead of the structural stability of the doped systems. Considering these calculations, we avoid practical difficulties associated with the addition/substitution reactions of larger curved two-dimensional (2D) carbon nanostructures, and we obtain a comprehensive and systematic understanding of a variety of F/H 2D doped systems.

  • 5.
    Dsouza, Raison
    et al.
    Max Planck Inst Struct and Dynam Matter, Germany.
    Cheng, Xinxin
    Max Planck Inst Struct and Dynam Matter, Germany; Univ Hamburg, Germany.
    Li, Zheng
    Max Planck Inst Struct and Dynam Matter, Germany.
    Miller, R. J. Dwayne
    Max Planck Inst Struct and Dynam Matter, Germany; Univ Hamburg, Germany; Univ Toronto, Canada.
    Kochman, Michal
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Oscillatory Photoelectron Signal of N-Methylmorpholine as a Test Case for the Algebraic-Diagrammatic Construction Method of Second Order2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 50, p. 9688-9700Article in journal (Refereed)
    Abstract [en]

    Motivated by recent progress in the application of time-resolved photoelectron spectroscopy (TRPES) to molecular Rydberg states, we report herein a detailed assessment of the performance of the second-order algebraic diagrammatic construction (ADC(2)) method in the simulation of their TRPES spectra. As the test case, we employ the tertiary aliphatic amine N-methylmorpholine (NMM), which is notable for the fact that the signal of its 3s state exhibits long-lived oscillations along the electron binding energy axis. The relaxation process of photoexcited NMM is simulated via the Born-Oppenheimer molecular dynamics method, and the resulting TRPES spectrum is generated on the basis of ionization energies and approximate Dyson orbital norms calculated with the continuum orbital technique. On the whole, the simulated TRPES spectrum achieves satisfactory agreement with experiment, which suggests that the ADC(2) method provides a realistic description of the potential energy surfaces of the relevant excited and ionized states. In particular, the simulations reproduce the fine oscillatory structure of the signal of the 3s state, and provide evidence to the effect that it results from a coherent vibrational wavepacket evolving along the deformation modes of the six-membered ring. However, it is found that ADC(2) underestimates electron binding energies by up to a few tenths of an electronvolt. The case of NMM demonstrates the usefulness of ADC(2) as a tool to aid the interpretation of the TRPES spectra of large organic molecules.

  • 6.
    Durbeej, Bo
    et al.
    Uppsala University, Sweden.
    Eriksson, Leif A.
    Örebro University, Sweden.
    Photodegradation of substituted stilbene compounds: what colors aging paper yellow?2005In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 109, no 25, p. 5677-5682Article in journal (Refereed)
    Abstract [en]

    Photodegradation of lignin is one of the major postprocessing problems in paper production, as this renders yellowing of the paper and reduced paper quality. In this study, we have explored the photochemical properties of substituted stilbene derivatives believed to be key chromophores in the photodegradation of lignin derived from cinnamyl alcohol. In particular, the present work focuses on the computation of UV/vis electronic absorption spectra for different methoxylated stilbenes and their proposed photodegradation products. All calculations were performed using the time-dependent formalism of density functional theory (TD-DFT) and the B3LYP hybrid functional. It is concluded that the methodology employed is capable of reproducing not only the overall spectra, but also subtle features owing to the effects of different substitution patterns. For the strongly absorbing first excited singlet state (HOMO  LUMO excitation) of the methoxylated stilbenes, the calculated transition energies are, albeit somewhat fortuitously, in excellent agreement with experimental data. The light-induced yellowing indirectly caused by the presence of stilbenes can be rationalized in terms of the absorption spectra of the resulting photodegraded o-quinones, for which distinct transitions in the 420–500 nm region of the visible spectrum lacking prior to degradation are observed.

  • 7.
    Engstrom, Maria
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Himo, F
    Linkoping Univ, Dept Phys, SE-58183 Linkoping, Sweden.
    Graslund, A
    Linkoping Univ, Dept Phys, SE-58183 Linkoping, Sweden.
    Minaev, B
    Linkoping Univ, Dept Phys, SE-58183 Linkoping, Sweden.
    Vahtras, O
    Linkoping Univ, Dept Phys, SE-58183 Linkoping, Sweden.
    Agren, H
    Linkoping Univ, Dept Phys, SE-58183 Linkoping, Sweden.
    Hydrogen bonding to tyrosyl radical analyzed by ab initio g-tensor calculations2000In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 104, no 21, p. 5149-5153Article in journal (Refereed)
    Abstract [en]

    Hydrogen bonding to the tyrosyl radical in ribonucleotide reductase (RNR) has been simulated by a complex between the phenoxyl radical and a water molecule. Multiconfigurational self-consistent field linear response theory was used to calculate the g-tensor of the isolated phenoxyl radical and of the phenoxyl-water model. The relevance of the model was motivated by the fact that spin density distributions and electron paramagnetic resonance (EPR) spectra of the phenoxyl and tyrosyl radicals are very similar. The calculated g-tensor anisotropy of the phenoxyl radical was comparable with experimental findings for tyrosyl in those RNRs where the H-bond is absent: g(x) = 2.0087(2.0087), g(y) = 2.0050(2.0042), and g(z) = 2.0025(2.0020), where the tyrosyl radical EPR data from Escherichia coli RNR are given in parentheses. The hydrogen bonding models reproduced a shift toward a lower g(x) value that was observed experimentally for mouse and herpes simplex virus RNR where the H-bond was detected by electron-nuclear double resonance after deuterium exchange. This decrease could be traced to lower angular momentum and spin-orbit coupling matrix elements between the ground B-2(1) and the first excited B-2(2) states (oxygen lone-pair n to pi(SOMO) excitation) upon hydrogen bonding in a linear configuration. The g(x) value was further decreased by hydrogen bonding in bent configurations due to a blue shift of this excitation.

  • 8.
    Erdtman, Edvin
    et al.
    Örebro universitet, Institutionen för naturvetenskap.
    Eriksson, Leif A.
    Örebro universitet, Institutionen för naturvetenskap.
    Theoretical study of 5-aminolevulinic acid tautomerization: a novel self-catalyzed mechanism2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 18, p. 4367-4374Article in journal (Refereed)
    Abstract [en]

    5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. In this study density functional theory calculations were performed on the tautomers of 5ALA and the tautomerization reaction mechanism from its enolic forms (5-amino-4-hydroxypent-3-enoic acid and 5-amino-4-hydroxypent-4-enoic acid) to the more stable 5ALA. The hydrated form 5-amino-4,4-dihydroxypentanoic acid was also studied. The lowest energy pathway of 5ALA tautomerization is by means of autocatalysis, in that an oxygen of the carboxylic group transfers the hydrogen atom as a "crane", with an activation energy of similar to 15 kcal/mol. This should be compared to the barriers of about 35 kcal/mol for water assisted tautomerization, and 60 kcal/mol for direct hydrogen transfer. For hydration of 5ALA, the water catalyzed activation barrier is found to be similar to 35 kcal/mol, approximately 5 kcal/mol lower than direct hydration.

  • 9.
    Fahleson, Tobias
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Kauczor, Joanna
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Santoro, Fabrizio
    CNR, Italy.
    Improta, Roberto
    CNR, Italy.
    Coriani, Sonia
    University of Trieste, Italy; Aarhus University, Denmark.
    TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 21, p. 5476-5489Article in journal (Refereed)
    Abstract [en]

    We present a computational study of the Magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil,thymine, and cytosine, Using the B3LYP and CAM-B3LYP functionals. Solvent effects, are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In, general; the computed spectra are found to be in good agreement with the experimental ones, aprt from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine base are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to,that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific,but they do not in general alter the qualitative shape of the spectra. The bands are dominated the-bright pi -greater than pi* transitions; and our calculations in solution nicely reproduce theft energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n -greater than pi* excitations, but they are too weak to be observed in the. experiment.

  • 10.
    Falklöf, Olle
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Inter-Excited State Phosphorescence in the Four-Component Relativistic Kohn–Sham Approximation: A Case Study on Lumiflavin2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 49, p. 11911-11921Article in journal (Refereed)
    Abstract [en]

    Electronic transitions from one excited state to another excited state of different spin symmetry play important roles in many biochemical reactions. Although recent years have seen much progress in the elucidation of nonradiative (intersystem crossing) relaxation mechanisms for such transitions, there is presently a scarcity of data available to assess whether also radiative (phosphorescence) mechanisms are relevant for these processes. Here, we demonstrate that the well-established ability of quantum chemical methods to describe intersystem crossing events between excited states, can be supplemented by the ability to also describe inter-excited state phosphorescence. Specifically, performing four-component relativistic time-dependent density functional theory calculations, we obtain rate constants for the radiative transitions from the absorbing 1(πHπL*) singlet state of lumiflavin to the 3(πHπL*), 3(nN2πL*) and 3(πH–1πL*) triplet states, and subsequently compare these results with rate constants calculated for the corresponding nonradiative transitions. Thereby, it is found that the radiative rate constants for these particular transitions are typically two to five orders of magnitude smaller than the nonradiative ones.

  • 11.
    Fang, Changfeng
    et al.
    Center for Optics Research and Engineering, Shandong University.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Calculation of Free-Energy Barriers with TD-DFT: A Case Study on Excited-State Proton Transfer in Indigo2019In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 123, no 40, p. 8485-8495Article in journal (Refereed)
    Abstract [en]

    The performance of time-dependent density functional theory (TD-DFT) for the calculation of excited states of molecular systems has been the subject of many benchmark studies. Often, these studies focus on excitation energies or, more recently, excited-state equilibrium geometries. In this work, we take a different angle by instead exploring how well TD-DFT reproduces experimental free-energy barriers of a well-known photochemical reaction: the excited-state proton transfer (ESPT) in indigo. Specifically, by exploiting the possibility of using TD-DFT to locate and compute free energies of first-order saddle points in excited states, we test the performance of several popular density functionals in reproducing recently determined experimental free-energy barriers for ESPT in indigo and in an N-hexyl substituted derivative thereof. Through the calculations, it is found that all of the tested functionals perform quite well, uniformly overestimating the experimental values by 1.4–3.5 (mean error) and 2.5–5.5 kcal mol–1 (maximum error) only. Given that these errors are not larger than those typically observed when barriers for ground-state proton transfer reactions are calculated in ground-state DFT, the results highlight the potential of TD-DFT to enable accurate modeling of ESPT reactions based on free energies and explicit localization of transition states.

  • 12.
    Fang, Changfeng
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Oruganti, Baswanth
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    How method-dependent are calculated differences between vertical, adiabatic, and 0-0 excitation energies?2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 23, p. 4157-4171Article in journal (Refereed)
    Abstract [en]

    Through a large number of benchmark studies, the performance of different quantum chemical methods in calculating vertical excitation energies is today quite well established. Furthermore, these efforts have in recent years been complemented by a few benchmarks focusing instead on adiabatic excitation energies. However, it is much less well established how calculated differences between vertical, adiabatic and 0-0 excitation energies vary between methods, which may be due to the cost of evaluating zero-point vibrational energy corrections for excited states. To fill this gap, we have calculated vertical, adiabatic, and 0-0 excitation energies for a benchmark set of molecules covering both organic and inorganic systems. Considering in total 96 excited states and using both TD-DFT with a variety of exchange-correlation functionals and the ab initio CIS and CC2 methods, it is found that while the vertical excitation energies obtained with the various methods show an average (over the 96 states) standard deviation of 0.39 eV, the corresponding standard deviations for the differences between vertical, adiabatic, and 0-0 excitation energies are much smaller: 0.10 (difference between adiabatic and vertical) and 0.02 eV (difference between 0-0 and adiabatic). These results provide a quantitative measure showing that the calculation of such quantities in photochemical modeling is well amenable to low-level methods. In addition, we also report on how these energy differences vary between chemical systems and assess the performance of TD-DFT, CIS, and CC2 in reproducing experimental 0-0 excitation energies.

  • 13.
    Huang, X.
    et al.
    Cherry L. Emerson Ctr. of Sci. Comp., Department of Chemistry, Emory University, Atlanta, GA 30322, United States.
    Cho, H.M.
    Department of Chemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, OH 43210, United States.
    Carter, S.
    Cherry L. Emerson Ctr. of Sci. Comp., Department of Chemistry, Emory University, Atlanta, GA 30322, United States, Department of Chemistry, University of Reading, Reading, United Kingdom.
    Ojamäe, Lars
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry .
    Bowman, J.M.
    Cherry L. Emerson Ctr. of Sci. Comp., Department of Chemistry, Emory University, Atlanta, GA 30322, United States.
    Singer, S.J.
    Department of Chemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, OH 43210, United States.
    Full dimensional quantum calculations of vibrational energies of H5O2+2003In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 107, no 37, p. 7142-7151Article in journal (Refereed)
    Abstract [en]

    The full dimensional (15 degrees-of-freedom) quantum calculations of vibrational energies of H5O2+ are reported using the global potential energy surface (OSS) of Ojamäe et al. (J. Chem. Phys. 1998, 109, 5547). One set of calculations uses the diffusion Monte Carlo (DMC) method with a highly flexible initial trial wave function. This method is limited to the ground vibrational state, but produces what we believe is a highly accurate, benchmark energy and wave function for that state. The DMC wave function is analyzed to identify coordinates that are strongly correlated in zero-point fluctuations. A simple harmonic model is developed to elucidate the energetic consequences of these correlations. The other set of calculations is based on the code MULTIMODE, which does configuration interaction (CI) calculations using a basis determined from a vibrational self-consistent field (VSCF) Hamiltonian, but which uses a representation of the potential with mode coupling limited to a maximum of four modes. Good agreement is obtained between the DMC and the CI MULTIMODE energies for the ground vibrational state. When less sophisticated theoretical treatments are applied, either variational Monte Carlo or vibrational self-consistent field, fairly large errors are found. Vibrationally excited-state energies obtained with MULTIMODE are also reported.

  • 14. Itagaki, Y
    et al.
    Sanderud, A
    Sagstuen, E
    Lund, Anders
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Chemical Physics .
    ENDOR study of N-14 hyperfine and quadrupole couplings of N2D4 center dot+ formed in deuterated Li(N2H5)SO4 single crystal2002In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 106, no 11, p. 2617-2622Article in journal (Refereed)
    Abstract [en]

    X-irradiated Li(N2D5)SO4 single crystals were investigated using EPR and ENDOR spectroscopy. The N-14-ENDOR spectra of the deuterated hydrazine radical cation N2D4.+ were clearly observed at 240 K. N-14 hyperfine (life) and nuclear quadrupole (nqc) tensors of the N2D4.+ cation were determined from angular variation ENDOR measurements in the three orthogonal planes of the crystal. The life tensor obtained for the two equivalent N-14 atoms is very close to that reported in a N2H5HC2O4 single crystal, and the present results support the previous conclusion that the cation has a planar structure at 240 K. The N-14 nqc tensor was estimated using semiempirical methods and also calculated from the field gradients in the LiHzS crystal as evaluated by density functional theory methods. The general agreement with experimental observations further supported the suggested geometrical structure of the N2H4.+ radical. The H-1 and N-14-ENDOR enhancements observed may be due to weakened dipolar interactions between N-14-D-2 and H-1-D-2 leading to increased T-ln relaxations of the N-14 and residual H-1 nuclei of the N2D4.+ cation (and/or other isotopomers) in the deuterated crystals as compared to those in the Li(N2H5)SO4 crystals.

  • 15. Jansik, B
    et al.
    Schimmelpfennig, B
    Norman, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics .
    Mochizuki, Y
    Luo, Y
    Agren, H
    Size, order, and dimensional relations for silicon cluster polarizabilities2002In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 106, no 2, p. 395-399Article in journal (Refereed)
    Abstract [en]

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

  • 16.
    Kochman, Michal
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Durbeej, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Theoretical Study of Ground- and Excited-State Charge Transfer in Fulvene-Based Donor-Acceptor Systems2019In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 123, no 31, p. 6660-6673Article in journal (Refereed)
    Abstract [en]

    Donor-acceptor systems based on fulvene as the electron-accepting moiety are typified by exotic, strongly polar electronic structures. In this contribution, ab initio calculations have been performed to explore the ground- and excited-state properties of an archetypal compound of this class, which incorporates the exocyclic carbon atom of fulvene into a tetramethylimidazoline-like five-membered ring. In the electronic ground state, the compound under study has a pronounced zwitterionic character and is best described as consisting of a negatively charged cyclopentadienyl ring linked covalently to a positively charged tetramethylimidazolium ring. Both of these rings can be considered as aromatic. The excess negative charge localized on the cyclopentadienyl ring is highly labile in the photochemical sense: the low-lying valence excited states exhibit varying degrees of reverse charge transfer, whereby electron density is transferred from the cyclopentadienyl ring back onto the tetramethylimidazolium ring. The topographies of the excited-state potential energy surfaces favor rapid and efficient internal conversion at an extended, fulvene-like S1/S0 conical intersection seam. As a consequence, the excited-state lifetime of this compound is predicted to be on the order of 100 fs. 

    The full text will be freely available from 2020-07-11 08:10
  • 17. Kumagai, J
    et al.
    Itagaki, Y
    Ishizuka, M
    Kumada, T
    Lund, Anders
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Chemical Physics .
    Miyazaki, T
    ESR, ENDOR, and ESEEM spectroscopy study on the local structure and motion of reactants: Highly selective tunneling radical abstraction in a neopentane-ethane mixture2001In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 105, no 14, p. 3652-3657Article in journal (Refereed)
    Abstract [en]

    Local structures and motions of radical reactants in highly selective tunneling abstraction reaction in neopentane-ethane mixture are investigated with CW-ESR, ENDOR, and ESEEM spectroscopy at different temperatures. H atoms produced by the radiolysis of neo-C5H12 in the neo-C5H12-C2H6 (2 mol %) mixtures above 40 K react selectively with the solute C2H6 to give ethyl radicals. The selective reaction is suppressed below 30 K. The local structures of neopentane matrix around neopentyl and ethyl radicals are approximately the same in the temperature range from 4.4 to 45 K. Although neopentyl radicals are rigidly trapped below 100 K, ethyl radicals in neopentane matrix begin to librate even at 6 K and increase the degree of motion up to 30 K, Finally, the librating motion of the ethyl radicals in neopentane matrix is vigorous above 40 K. The ethane molecule can take more favorable orientation for the hydrogen abstraction reaction by H atoms than rigid neopentane molecules by the vigorous libration motion, resulting in the selective reaction with H atoms.

  • 18.
    Lenz, Annika
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry . Linköping University, The Institute of Technology.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry . Linköping University, The Institute of Technology.
    Structures of the I-, II- and H-Methane Clathrates and the Ice−Methane Clathrate Phase Transition from Quantum-Chemical Modeling with Force-Field Thermal Corrections2011In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 115, no 23, p. 6169-6176Article in journal (Refereed)
    Abstract [en]

    Methane hydrates with the three clathrate structures I, II and H are studied by quantumchemicalmethods. The periodic B3LYP computations are combined with force-field methodsfor the thermal energy corrections. The pressure dependencies for the crystal structures, latticeenergies and guest molecule interactions are derived. Quantum-chemical geometryoptimizations predict too small cell volumes compared to experimental data, but includingzero-point energy and thermal energy the cell volume increases and the correct densities areobtained. Phase diagram for the three structures are investigated, and phase transitions werefound at 5 GPa for the MH-I–MH-II transition and at 10 GPa for the MH-II–MH-H transition.

  • 19.
    Lenz, Annika
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry . Linköping University, The Institute of Technology.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Physical Chemistry . Linköping University, The Institute of Technology.
    Theoretical IR spectra for water clusters (H2O)n (n = 6-22, 28, 30) and identification of spectral contributions from different H-Bond conformations in gaseous and liquid water2006In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 110, no 50, p. 13388-13393Article in journal (Refereed)
    Abstract [en]

    The vibrational IR spectra in the O-H stretching region are computed for water clusters containing 6-22, 28, and 30 molecules using quantum-chemical calculations (B3LYP and an augmented basis set). For the cluster with 20 molecules, several different structures were studied. The vibrational spectrum was partitioned into contributions from different molecules according to their coordination properties. The frequency shifts depend on the number of donated/accepted H-bonds primarily of the two molecules participating in the H-bond, but also of the surrounding molecules H-bonding to these molecules. The frequencies of H-bonds between two molecules of the same coordination type are spread over a broad interval. The most downshifted hydrogen-bond vibrations are those donated by a single-donor 3-coordinated molecule where the H-bond is accepted by a single-acceptor molecule. The H-bonded neighbors influence the downshift, and their contribution can be rationalized in the same way as for the central dimer. Single donors/acceptors cause larger downshifts than 4-coordinated molecules, and the least downshift is obtained for double donors/acceptors. This result is at variance with the conception that experimental liquid water spectra may be divided into components for which larger downshifts imply higher H-bond coordination. A mean spectral contribution for each coordination type for the donor molecule was derived and fitted to the experimental liquid water IR spectrum, which enabled an estimation of the distribution of H-bond types and average number of H-bonds (3.0 ± 0.2) in the liquid. © 2006 American Chemical Society.

  • 20.
    Liu, Yuan
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    C-C Stretching Raman Spectra and Stabilities of Hydrocarbon Molecules in Natural Gas Hydrates: A Quantum Chemical Study2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 49, p. 11641-11651Article in journal (Refereed)
    Abstract [en]

    The presence of specific hydrocarbon gas molecules in various types of water cavities in natural gas hydrates (NGHs) are governed by the relative stabilities of these encapsulated guest molecule-water cavity combinations. Using molecular quantum chemical dispersion-corrected hybrid density functional computations, the interaction (Delta E(host-)guest) and cohesive energies (Delta E-coh), enthalpies, and Gibbs free energies for the complexes of host water cages and hydrocarbon guest molecules are calculated at the pi B97X-D/6-311++G(2d,2p) level of theory. The zero-point energy effect of ?Ehost-guest and ?Ecoh is found to be quite substantial. The energetically optimal host-guest combinations for seven hydrocarbon gas molecules (CH4, C2H6, C3H6, C3H8, C4H8, i-C4H10, and n-C4H10) and various water cavities (D, ID, T, P, H, and I) in NGHs are found to be CH4@D, C2H6@T, C3H6@T, C3H8@T, C4H8@T/P/H, i-C4H10@H, and n-C4H10@H, as the largest cohesive energy magnitudes will be obtained with these host-guest combinations. The stabilities of various water cavities enclosing hydrocarbon molecules are evaluated from the computed cohesive Gibbs free energies: CH4 prefers to be trapped in a ID cage; C2H6 prefer T cages; C3H6 and C3H8 prefer T and H cages; C4H8 and i-C4H10 prefer H cages; and n-C4H10 prefer I cages. The vibrational frequencies and Raman intensities of the C-C stretching vibrational modes for these seven hydrocarbon molecules enclosed in each water cavity are computed. A blue shift results after the guest molecule is trapped from gas phase into various water cages due to the host-guest interactions between the water cage and hydrocarbon molecule. The frequency shifts to the red as the radius of water cages increases. The model calculations support the view that C-C stretching vibrations of hydrocarbon molecules in the water cavities can be used as a tool to identify the types of crystal phases and guest molecules in NGHs.

  • 21.
    Luo, Y
    et al.
    Royal Inst Technol, Div Theoret Chem, S-10044 Stockholm, Sweden Univ Stockholm, FYSIKUM, S-11385 Stockholm, Sweden Linkoping Univ, Dept Phys & Measurement Technol, S-58183 Linkoping, Sweden.
    Norman, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics .
    Macak, P
    Royal Inst Technol, Div Theoret Chem, S-10044 Stockholm, Sweden Univ Stockholm, FYSIKUM, S-11385 Stockholm, Sweden Linkoping Univ, Dept Phys & Measurement Technol, S-58183 Linkoping, Sweden.
    Agren, H
    Royal Inst Technol, Div Theoret Chem, S-10044 Stockholm, Sweden Univ Stockholm, FYSIKUM, S-11385 Stockholm, Sweden Linkoping Univ, Dept Phys & Measurement Technol, S-58183 Linkoping, Sweden.
    Solvent-induced two-photon absorption of a push-pull molecule2000In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 104, no 20, p. 4718-4722Article in journal (Refereed)
    Abstract [en]

    Solvent-induced two-photon absorption cross sections are calculated for a push-pull molecule in solutions using both self-consistent reaction field and internal finite field approaches. It is shown analytically and numerically that the results from the two methods can be connected through induced local reaction field factors. The two-photon cross sections of the studied push-pull polyene are found to be rather insensitive to the choice of cavity shape. The solvent dependence of the two-photon absorption displays a pattern different from that of the first hyperpolarizability.

  • 22.
    Maliarik, Mikhail
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology.
    Plyusnin, V.F.
    Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation.
    Grivin, V.P.
    Institute of Chemical Kinetics and Combustion, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russian Federation.
    Toth, I.
    Tóth, I., Department of Inorganic and Analytical Chemistry, University of Debrecen, Hungary.
    Glaser, J.
    Department of Chemistry, Royal Institute of Technology (KTH), Stockholm, Sweden.
    Photoinduced electron transfer via nonbuttressed metal-metal bonds. The photochemical study of binuclear complexes with platinum-thallium bonds2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 26, p. 5786-5793Article in journal (Refereed)
    Abstract [en]

    The photochemistry of binuclear metal-metal bonded complexes [(NC) 5Pt-Tl(Solv)x] (solv is water or dimethylsulfoxide) has been studied in aqueous and dimethylsulfoxide solutions. Both stationary and nanosecond laser flash photolysis have been carried out on the species. The metal-metal bonded complexes have been photolyzed by irradiation into the corresponding intense MMCT absorption bands. Photoexcitation results in the cleavage of the platinum-thallium bond and the formation of a solvated thallous ion and a cyano complex of platinum(IV), [Pt(CN)5(Solv)]-, in both cases. The species have been characterized by multinuclear NMR and optical spectroscopy. The products of the photoreaction indicate a complementary two-electron transfer occurring between platinum and thallium ions in the binuclear Pt-Tl species. Quantum yield values for the photodecomposition of the species have been determined. The intermediates of the photoinduced metal-to-metal electron transfer have been detected and characterized by optical spectroscopy. The kinetics of transient formation and decomposition have been studied, and mechanisms of the photoactivated redox reaction have been suggested. © 2008 American Chemical Society.

  • 23.
    Malysheva, Lyuba
    et al.
    Bogolyubo Institute for Theoretical Physics, Kyiv, Ukraine.
    Onipko, Alexander
    Bogolyubo Institute for Theoretical Physics, Kyiv, Ukraine.
    Liedberg, Bo
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics. Linköping University, The Institute of Technology.
    Ab Initio Modeling of Amide-Stabilized, Oligo(etylene glycol)-Terminated Self-Assemblies: In-SAM Molecular Geometry, Orientation, and Hydrogen Bonding2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 8, p. 1683-1687Article in journal (Other academic)
    Abstract [en]

    Under the constraint that sulfur atoms form a hexagonal (×)R30° overlayer on the (111) gold surface, the optimized geometry of periodic arrays of HS(CH2)3CONH−(CH2CH2O)3H molecules has been found ab initio, by exploiting the BP86 exchange-correlation functional with 6-31G and “general” basis sets. The obtained data suggests that several prominent features of in-SAM molecular geometry and orientation stand out from conclusions based on single-molecule modeling. In particular, changing of amide-related dihedrals is shown to dominate in adjustment of molecular constituents to the assembly environment and to result in a substantial shortening of the hydrogen bond distance between nearest-neighbor amides. First demonstrated here, the full account to the intermolecular interaction within periodic arrays of amide-bridged, oligo(ethylene glycol)-terminated alkanethiolates forms a new platform for arguable modeling of SAM apparent properties.

  • 24.
    Malysheva, Lyuba
    et al.
    bogolyubov Institute for Theoretical Physics.
    Onipko, Alexander
    Bogolyubov Institute for Theoretical Physics.
    Liedberg, Bo
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics .
    Ab Initio Modeling of Defect Signatures in Infrared Reflection - Absorption Spectra of SAMs Exposing Methyl- and Hydrogen-Terminated Oligo(ethylene glycols)2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, p. 728-736Article in journal (Refereed)
  • 25. McDonald, S
    et al.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Singer, Sherwin J.
    Graph theoretical generation and analysis of hydrogen-bonded structures with applications to the neutral and protonated water cube and dodecahedral clusters1998In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 102, no 17, p. 2824-2832Article in journal (Refereed)
    Abstract [en]

    Graph theoretical techniques are demonstrated to be of considerable use in the search for stable arrangements of water clusters. inspired by the so-called "ice rules" that govern which hydrogen-bond networks are physically possible in the condensed phase, we use graphical techniques to generate a multitude of local minima of neutral and protonated water clusters using oriented graph theory. Efficient techniques to precisely enumerate all possible hydrogen-bonding topologies are presented. Empirical rules regarding favorable water neighbor geometries are developed that indicate which of the multitude of hydrogen-bonding topologies available to large water clathrates (e.g., 30 026 for (H2O)(20)) are likely to be the most stable structures. The cubic (H2O)(8) and dodecahedral (H2O)(20) clusters and their protonated analogues are treated as examples. In these structures every molecule is hydrogen bonded to three others, which lends to hydrogen-bonding topology fixing the cluster geometry. Graphical techniques can also be applied to geometrically irregular structures as well. The enumerated oriented graphs are used to generate initial guesses for optimization using various potential models. The hydrogen-bonding topology was found to have a significant effect on cluster stability, even though the total number of hydrogen bonds is conserved. For neutral clusters, the relationship between oriented graphs and local minima of several potential models appears to be one-to-one. The stability of the different topologies is rationalized primarily in terms of the number of nearest neighbor pairs that both have a free OH bond. This lends to the identification of water dodecahedra of greatest stability.

  • 26.
    Milne, Bruce F.
    et al.
    University of Basque Country, Spain; University of Basque Country, Spain; DIPC, Spain; University of Coimbra, Portugal.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Resonant-Convergent PCM Response Theory for the Calculation of Second Harmonic Generation in Makaluvamines A-V: Pyrroloiminoquinone Marine Natural Products from Poriferans of Genus Zyzzya2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 21, p. 5368-5376Article in journal (Refereed)
    Abstract [en]

    The first-order hyperpolarizability, beta, has been calculated for a group Of marine natural products, the makaluvamines. These compounds possess a common Cationic pyrroloiminoquinone structure that is substituted to varying degrees. Calculations at the MP2 level indicate that makaluvamines possessing phenolic side Chains conjugated with the pyrroloiminoquinone moiety display large beta values, while breaking this conjugation leads to a dramatic decrease in the calculated hyperpolarizability. This is consistent with a charge-transfer donor-pi-acceptor (D-pi-A) structure type, characteristic of nonlinear optical Chromophores. Dynamic hyperpolarizabilities calculated using resonance-convergent time-dependent density functional theory coupled to polarizable continuum model (PCM) solvation suggest that significant resonance, enhancement, effects can be expected for incident radiation with wavelengths around 800 nm. The results of the current Work suggest that the pyrroloiminoquinone moiety represents a potentially useful new Chromophore subunit, in particular for the development of molecular probes for biological imaging. The introduction of solvent solute interactions in the theory is conventionally made in a density matrix formalism, and the Present work will provide detailed account of the approximations that need to be introduced in wave function theory, and our program implementation. The program implementation as such is achieved by a mere combination of existing modules from previous developments, and it is here only briefly reviewed.

  • 27.
    Minkov, I.
    et al.
    Theoretical Chemistry, Royal Institute of Technology, Roslagstullsbacken 15, S-106 91 Stockholm, Sweden.
    Gel'Mukhanov, F.
    Theoretical Chemistry, Royal Institute of Technology, Roslagstullsbacken 15, S-106 91 Stockholm, Sweden.
    Agren, H.
    Ågren, H., Theoretical Chemistry, Royal Institute of Technology, Roslagstullsbacken 15, S-106 91 Stockholm, Sweden.
    Friedlein, Rainer
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry .
    Suess, C.
    Salaneck, William R
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Surface Physics and Chemistry .
    Core excitations of biphenyl2005In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 109, no 7, p. 1330-1336Article in journal (Refereed)
    Abstract [en]

    High-resolution C(1s) near-edge X-ray absorption and X-ray photoionization spectra of the free biphenyl molecule are presented and theoretically analyzed in order to allow an assignment of the observed spectral features. Finite lifetime broadening, a high density of vibrational states, and a strong overlap of contributions from chemically different carbon atom sites only partially allow resolving the vibrational fine structure. However, the shape and width of the spectral profiles are strongly determined by both chemical shifts and vibronic effects. In particular, different from photoionization of valence levels, both types of core level spectra do not contain contributions from dihedral modes which are related to the twisting motion of the two phenyl rings. Contrary to naphthalene, C-H stretching modes are significantly enhanced in the core excitation spectra of biphenyl while the contributions from C-C stretching modes are reduced. © 2005 American Chemical Society.

  • 28.
    Mosyagin, Igor
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Hellman, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Olovsson, Weine
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Simak, Sergey
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Abrikosov, Igor
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. NUST MISIS, Russia.
    Highly Efficient Free Energy Calculations of the Fe Equation of State Using Temperature-Dependent Effective Potential Method2016In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, no 43, p. 8761-8768Article in journal (Refereed)
    Abstract [en]

    Free energy calculations at finite temperature based on ab initio molecular dynamics (AIMD) simulations have become possible, but they are still highly computationally demanding. Besides, achieving simultaneously high accuracy of the calculated results and efficiency of the computational algorithm is still a challenge. In this work we describe an efficient algorithm to determine accurate free energies of solids in simulations using the recently proposed temperature-dependent effective potential method (TDEP). We provide a detailed analysis of numerical approximations employed in the TDEP algorithm. We show that for a model system considered in this work, hcp Fe, the obtained thermal equation of state at 2000 K is in excellent agreement with the results of standard calculations within the quasiharmonic approximation.

  • 29. Nuzhdin, K.B.
    et al.
    Nesterov, S. V.
    Tyurin, D.A.
    Feldman, V.I.
    Wei, L.
    Lund, Anders
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Chemical Physics .
    Structure of radical cations of saturated heterocyclic compounds with two heteroatoms as studied by electron paramagnetic resonance, electron-nuclear double resonance, and density functional theory calculations2005In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 109, no 28, p. 6166-6173Article in journal (Refereed)
    Abstract [en]

    The radical cations of piperazine, morpholine, thiomorpholine, and thioxane were investigated by electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR) spectroscopy in a solid Freon matrix. Optimized geometry and magnetic parameters of the radical cations were calculated using a density functional theory (DFT)/Perdew-Burke-Ernzerhof (PBE) method. Both experimental and theoretical results suggest that all the studied species adopt chair (or distorted chair) conformations. No evidence for the boat conformers with intramolecular σ*-bonding between heteroatoms were obtained. In the cases of morpholine and thioxane, the oxygen atoms are characterized by relatively small spin populations, whereas a major part of spin density is located at N and S atoms, respectively. The thiomorpholine radical cation exhibits nearly equal spin population of N and S atoms. In most cases (except for thioxane), the calculated magnetic parameters agree with the experimental data reasonably well. © 2005 American Chemical Society.

  • 30.
    Owenius, Rikard
    et al.
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology.
    Engstrom, Maria
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Lindgren, M.
    Huber, M.
    Huygens Laboratory, MAT Group, Leiden University, P.O. Box 9504, 2300 RA Leiden, Netherlands.
    Influence of solvent polarity and hydrogen bonding on the EPR parameters of a nitroxide spin label studied by 9-GHz and 95-GHz EPR spectroscopy and DFT calculations2001In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 105, no 49, p. 10967-10977Article in journal (Refereed)
    Abstract [en]

    The isotropic and anisotropic hyperfine coupling constants and g-values of the nitroxide spin label (1-oxyl-2,2,5,5-tetramethylpyrroline-3-methyl)methanethiosulfonate (MTSSL) were determined from 9-GHz and 95-GHz electron paramagnetic resonance (EPR) measurements in various solvents with a large distribution in polarity and proticity. The parameters Aiso, giso, Azz, and gxx of MTSSL were found to be sensitive to changes in solvent properties, where A-values increased and g-values decreased due to increased solvent polarity or proticity. A linear correlation was found for the isotropic (giso, Aiso) and anisotropic (gxx, Azz) parameters, respectively. Furthermore, density functional theory (DFT) calculations of the same parameters were performed for a model spin label with the possibility to vary the dielectric constant (e) of the medium and the number of hydrogen bonds formed with the nitroxide oxygen. From a qualitative analysis of experimental and calculated results, it was possible to specify the causes of the parameter shifts in more detail. In the "apolar region" (e < 25), the sensitivity of Aiso and Azz to e is large. However, in the "polar region" (e > 25), the sensitivity to epsi, is small, and the shifts in Aiso and Azz are mainly determined by the proticity of the solvent. Methanol was found to form ~1 and water ~2 hydrogen bonds to the nitroxide on average. The DFT method determined the shifts in giso and gxx due to hydrogen bonding more accurately compared with the restricted open-shell Hartree-Fock method. The anisotropic spin label-solvent data can be used in the interpretation of rigid-limit data from spin-labeled proteins to gain further insight in local environmental properties.

  • 31.
    Passos Abreu, Ana Virginia
    et al.
    University of Brasilia, Brazil.
    Fernando Teixeira, Jonathan
    University of Brasilia, Brazil.
    Luciano de Almeida Fonseca, Antonio
    University of Brasilia, Brazil.
    Gargano, Ricardo
    University of Brasilia, Brazil.
    Magela e Silva, Geraldo
    University of Brasilia, Brazil.
    Ribeiro, Luiz Antonio
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering. University of Brasilia, Brazil.
    Impact of the Electron-Phonon Interactions on the Polaron Dynamics in Graphene Nanoribbons2016In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, no 27, p. 4901-4906Article in journal (Refereed)
    Abstract [en]

    The influence of the electron-phonon (e-ph) interactions on the filed-included polaron dynamics in armchair graphene nanoribbons (GNRs) is theoretically investigated in the scope of a two-dimensional tight-binding model. The results show that the localization of the polaronic charge increases when the strength of e-ph coupling also increases. Consequently, the polaron saturation velocity decreases for higher e-ph coupling strengths. Interestingly, the interplay between the e-ph coupling strength and the GNR width changes substantially the polaron dynamics properties.

  • 32.
    Ribeiro, Luiz Antonio
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Ferreira da Cunha, Wiliam
    University of Brasilia, Brazil .
    Magela e Silva, Geraldo
    University of Brasilia, Brazil .
    Temperature Effects on the Scattering of Polarons and Bipolarons in Organic Conductors2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 32, p. 6272-6277Article in journal (Refereed)
    Abstract [en]

    The scattering process between an electron-polaron and a hole-bipolaron has been simulated using a version of the Su-Schrieffer-Heeger (SSH) model modified to include an external electric field, Coulomb interactions, and temperature effects in the scope of nonadiabatic molecular dynamics. The simulations reveal remarkable details concerning the polaron-bipolaron recombination reaction. It is found that there exists a critical temperature regime below which a hole-bipolaron and a mixed state composed by an electron-polaron and an exciton are formed and a hole-bipolaron and a free electron are the resulting products of the collisional process, if the temperature is higher than the critical value. In addition, it is obtained that both channels depend sensitively on the strength of the applied electric field. These significant results may provide guidance to understand processes regarding electro-luminescence in polymer diodes.

  • 33.
    Ribeiro, Luiz Antonio
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Univ Brasilia, Brazil.
    Monteiro, Fabio Ferreira
    Univ Brasilia, Brazil.
    Enders, Bernhard Georg
    Univ Brasilia, Brazil.
    de Almeida Fonseca, Antonio Luciano
    Univ Brasilia, Brazil.
    Magela e Silva, Geraldo
    Univ Brasilia, Brazil.
    da Cunha, Wiliam Ferreira
    Univ Brasilia, Brazil.
    Dynamic Formation of Bipolaron-Exciton Complexes in Conducting Polymers2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 15, p. 3866-3872Article in journal (Refereed)
    Abstract [en]

    The recombination dynamics of two oppositely charged bipolarons within a single polymer chain is numerically studied in the scope of a one-dimensional tight-binding model that considers electron electron and electron-phonon (e-ph) interactions. By scanning among values of e-ph coupling and electric field, novel channels for the bipolaron recombination were yielded based on the interplay between these two parameters. The findings point to the formation of a compound species formed from the coupling between a bipolaron and an exciton. Depending on the electric field and e-ph coupling strengths, the recombination mechanism may yield two distinct products: a trapped (and almost neutral) or a moving (and partially charged) bipolaron-exciton. These results might enlighten the understanding of the electroluminescence processes in organic light-emitting devices.

  • 34.
    Sagstuen, E
    et al.
    Univ Oslo, Dept Phys, N-0316 Oslo, Norway Linkoping Univ, Dept Phys & Measurement Tech, S-58183 Linkoping, Sweden Chim Phys Lab, F-75005 Paris, France.
    Lund, Anders
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Chemical Physics .
    Itagaki, Y
    Univ Oslo, Dept Phys, N-0316 Oslo, Norway Linkoping Univ, Dept Phys & Measurement Tech, S-58183 Linkoping, Sweden Chim Phys Lab, F-75005 Paris, France.
    Maruani, J
    Univ Oslo, Dept Phys, N-0316 Oslo, Norway Linkoping Univ, Dept Phys & Measurement Tech, S-58183 Linkoping, Sweden Chim Phys Lab, F-75005 Paris, France.
    Weakly coupled proton interactions in the malonic acid radical: Single crystal ENDOR analysis and EPR simulation at microwave saturation2000In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 104, no 27, p. 6362-6371Article in journal (Refereed)
    Abstract [en]

    The alpha-proton hyperfine coupling observed by electron paramagnetic resonance (EPR) spectroscopy on the radical (CH)-C-.(COOH)(2) in irradiated crystals of malonic acid, CH2(COOH)(2), has served as a standard against which hundreds of observations of similar couplings have been held and scaled. The major doublet of the malonic acid radical is accompanied by less intense "forbidden" (f) alpha-proton transitions and "spin-flip" (s) transitions due to weakly interacting protons. Both s and f transition lines exhibit microwave power saturation behaviors different from that of the major doublet. At high microwave power, the prominence of these s and f lines may be misinterpreted as originating from different radical species. Computer simulations could help distinguish between the different cases, but no computer simulation programs taking into account the microwave power saturation case are commonly available. On the basis of classical line-shape theory, an algorithm describing the microwave power dependence of an EPR line shape has been developed and implemented in an existing simulation program. To test this new program, malonic acid was selected because of the simplicity of its EPR spectra. However, sufficiently detailed information about the hyperfine coupling parameters for a satisfactory simulation of the room-temperature data (including s and f lines) was not available in the literature. Therefore, a detailed room-temperature EPR/ENDOR study on a single crystal of malonic acid was performed. In addition to the major cc-proton coupling, seven weaker proton interactions have been characterized and partly identified. Simulations under nonsaturating conditions reproduce very well all features of the experimental EPR spectra. Simulations under saturating conditions similarly reproduce the power-dependent EPR spectra and yield information about the relaxation behavior of the radical system, which is amenable to verification using other spin-resonance methods.

  • 35. Sanderud, A
    et al.
    Sagstuen, E
    Itagaki, Y
    Lund, Anders
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Chemical Physics .
    EPR and ENDOR studies of deuteron hyperfine and quadrupole coupling in center dot CD(COOD)(2): Experimental and theoretical estimates of electric field gradients from an alpha-carbon2000In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 104, no 27, p. 6372-6379Article in journal (Refereed)
    Abstract [en]

    In single crystals of malonic acid grown from heavy water, the methylene protons have been partially exchanged with deuterons. Upon X irradiation at room temperature, the (CD)-C-.(COOD)(2) radical is formed in an amount comparable to the (CH)-C-.(COOD): radical species. In the present work, EPR and ENDOR analyses of the a-deuteron hyperfine coupling (hfc) and nuclear quadrupolar coupling (nqc) tensors at room temperature have been performed. The hyperfine coupling tensor is, when scaled with the differences in the nuclear g-factor, almost identical to the a-proton coupling of the (CH)-C-.(COOH)(2) radical at room temperature. The quadrupolar coupling tensor was found to be virtually coaxial with the hyperfine coupling tensor. The quadrupolar coupling constant is 149.8 +/- 1 kHz, and the asymmetry factor eta = 0.092 +/- 0.020. It is known that, at room temperature, the malonic acid radical exhibits thermal motion between two potential energy minima separated by about +/-12 degrees. Assuming that the observed hfe and nqc tensors are the result of thermal avenging between these two conformations of the radical, a simple two-site jump model was used to estimate the rigid-limit tensors. The most significant result obtained was for the nyc tensor, for which the calculations resulted in a quadrupolar coupling constant of 160 kHz and an asymmetry factor eta = 0.026. These values are fairly close to the nqc parameters for the methylene deuterons in malonic acid at low temperature. The quadrupolar coupling tensor has been theoretically modeled using Slater orbitals and formal electronic populations, as well as electron populations obtained from RHF/CI INDO-type calculations. The simple model to compute the electric field gradient at the alpha-deuteron caused by the charge distribution at the sp(2)-hybridized alpha-carbon was found to be as successful as more advanced methods. Furthermore, density functional theoretical (DFT) calculations for both the malonic acid radical and the native malonic acid molecule have been performed. Field gradients calculated by the DFT method significantly overestimate the quadrupolar tensors for both the alpha-deuteron of the radical and the methylene deuterons of the malonic acid molecule. Calculations using electron populations from the RHF/CI INDO calculations show that contributions to the quadrupolar coupling tensor from electrons and nuclei beyond the nearest-neighbor atom of the Jeuteron are significant.

  • 36.
    Shiotani, M.
    et al.
    Department of Applied Chemistry, Graduate School of Engineering, Hiroshima University, Higashi - Hiroshima 739-8527, Japan.
    Lund, Anders
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Chemical Physics .
    Lunell, S.
    Department of Quantum Chemistry, Uppsala University, S-751 20 Uppsala, Sweden.
    Williams, F.
    Department of Chemistry, University of Tennessee, Knoxville, TN 37996-1600.
    Structures of the hexafluorocyclopropane, octafluorocyclobutane, and decafluorocyclopentane radical anions probed by experimental and computational studies of anisotropic electron spin resonance (ESR) spectra2007In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, no 2, p. 321-338Article in journal (Refereed)
    Abstract [en]

    Anisotropic electron spin resonance (ESR) spectra are reported for the radical anions of hexafluorocyclopropane (c-C3F6-), octafluorocyclobutane (c-C4F8-), and decafluorocyclopentane (c-C5F10-) generated via ?-irradiation in plastically crystalline tetramethylsilane (TMS) and rigid 2-methyltetrahydrofuran (MTHF) matrices. By combining the analysis of these experimental ESR spectra involving anisotropic hyperfine (hf) couplings with a series of quantum chemical computations, the geometrical and electronic structure of these unusual perfluorocycloalkane radical anions have been characterized more fully than in previous studies that considered only the isotropic couplings. Unrestricted Hartree-Fock (UHF) computations with the 6-311+G(d,p) basis set predict planar ring structures for all three radical anions, the ground electronic states being 2A2? for c-C3F6- (D3h symmetry), 2A2u for c-C4F8- (D 4h), and 2A2? for c-C5F 10- (D5h), in which the respective six, eight, and ten 19F-atoms are equivalent by symmetry. A successful test of the theoretical computation is indicated by the fact that the isotropic 19F hf couplings computed by the B3LYP method with the 6-311+G(2df,p) basis set for the optimized geometries are in almost perfect agreement with the experimental values: viz., 19.8 mT (exp) vs 19.78 mT (calc) for c-C 3F6-, 14.85 mT (exp) vs 14.84 mT (calc) for c-C4F8-, 11.6 mT (exp) vs 11.65 mT (calc) for c-C5F10-. Consequently, the same computation method has been applied to calculate the almost axially symmetric anisotropic 19F hf couplings for the magnetically equivalent 19F atoms: (-4.90 mT, -4.84 mT, 9.75 mT) for c-C3F6-, (-3.54 mT, -3.48 mT, 7.02 mT) for c-C4F 8-, and (-2.62 mT, -2.56 mT, 5.18 mT) for c-C 5F10-. ESR spectral simulations performed using the computed principal values of the hf couplings and the spatial orientations of the 19F nuclei as input parameters reveal an excellent fit to the experimental anisotropic ESR spectra of c-C3F6-, c-C4F8-, and c-C 5F10-, thereby providing a convincing proof of the highly symmetric Dnh structures that are predicted for these negative ions. Furthermore, using the computed 19F principal values and their orientations, the effective 19F anisotropic hf couplings along the molecular symmetry axes were evaluated for c-C3F 6- and c-C4F8- and successfully correlated with the positions of the characteristic outermost features in both the experimental and calculated anisotropic spectra. In addition, the electronic excitation energies and oscillator strengths for the c-C3F6-, c-C4F8-, and c-C5F10- radical anions were computed for the first time using time-dependent density functional theory (TD-DFT) methods. © 2007 American Chemical Society.

  • 37.
    Shiotani, M.
    et al.
    Department of Applied Chemistry, Graduate School of Engineering, Hiroshima University, Higashi-Hiroshima 739-8527, Japan.
    Persson, P.
    Department of Quantum Chemistry, Uppsala University, 5-757 20 Uppsala, Sweden.
    Lunell, S.
    Department of Quantum Chemistry, Uppsala University, 5-757 20 Uppsala, Sweden.
    Lund, Anders
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Chemical Physics .
    Williams, F.
    Department of Chemistry, University of Tennessee, Knoxville, TN 37996-1600, United States.
    Structures of tetrafluorocyclopropene, hexafluorocyclobutene, octafluorocyclopentene and related perfluoroalkene radical anions revealed by electron spin resonance spectroscopic and computational studies2006In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 110, no 19, p. 6307-6323Article in journal (Refereed)
    Abstract [en]

    Isotropic and anisotropic ESR spectra were observed for the radical anions of hexafluorocyclobutene (c-C4F6-), octafluorocyclopentene (c-C5F8-) and perfluoro-2-butene (CF3CF=CFCF3-) in ?-irradiated plastically crystalline neopentane, tetramethylsilane (TMS) and TMS-d12 matrices, or the rigid 2-methyltetrahydrofuran (MTHF) matrix. The isotropic spectra of c-C4F6- and c-C5F8- are characterized by three different sets of pairs of 19F nuclei with the isotropic hyperfine (hf) splittings of 15.2 (2F), 6.5 (2F), 1.1 (2F) mT for oC4F 6- and 14.7 (2F), 7.4 (2F), 1.0 (2F) mT for c-C 5F8-. By comparison with the results of ab initio quantum chemical computations, the large triplet 19F hf splittings of ca. 15 mT are assigned to the two fluorines attached to the C=C bond. The UHF, B3LYP and MP2 computations predict that the geometrical structures of the perfluoroalkenes are strongly distorted by one-electron reduction to form their radical anions, c-C3F4-: C2 symmetry (2A state) ? C2v (1A1), c-C4F6-: C 1 (2A) ? C2v (1A1) and c-C5F8-: C1 (2A) ? Cs (1A'). The structural distortion arises from a mixing of the p* and higher-lying s* orbitals at the C=C carbons similar to that previously found for CF2=CF 2- with a C2h, distortion. The isotropic 19F hf splittings computed with the B3LYP method with 6-311+G(2df,p) basis set for the geometry optimized by the UHF and/or MP2 methods are within 6% error of the experimental values. The experimental anisotropic spectra of c-C4F6-, c-C5F8- and CF2=CF2- were satisfactorily reproduced by the ESR spectral simulation method using the computed hf principal values and orientation of 19F nuclei. In addition, the electronic excitation energies and oscillator strengths for the CF2=CF 2-, c-C3F4-, c-C 4F6- and c-C5F8- radical anions were computed for the first time by TD-DFT methods. © 2006 American Chemical Society.

  • 38.
    Sjöqvist, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Mikkelsen, Kurt V.
    University of Copenhagen, Denmark .
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    QM/MM-MD Simulations of Conjugated Polyelectrolytes: A Study of Luminescent Conjugated Oligothiophenes for Use as Biophysical Probes2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 19, p. 3419-3428Article in journal (Refereed)
    Abstract [en]

    A methodological development is reported for the study of luminescence properties of conjugated polyelectrolytes, encompassing systems in which dihedral rotational barriers are easily overcome at room temperature. The components of the model include (i) a molecular mechanics (MM) force field description of the solvent in its electronic ground state well as the chromophore in its electronic ground and excited states, (ii) a conformational sampling by means of classical molecular dynamics (MD) in the respective electronic states, and (in) ii) spectral response calculations by means of the quantum mechanics/molecular mechanics QM/MM approach. A detailed analysis of the combined polarization effects of the ionic moiety and the polar water solvent is presented. At an increased computational cost of 30% compared to a calculation excluding the solvent, the error in the transition wavelength of the dominant absorption band is kept as small as 1 nm as compared to the high-quality benchmark result, based largely on a QM description of the solvent. At a reduced computational cost the error of the same quantity is kept as small as 6 nm, with the cost reduction being the result of an effective description of the effects of the solvent by means of replacing the carboxylate ions with neutral hydrogens. In absorption spectroscopy, the obtained best theoretical results are in excellent agreement with the experimental benchmark measurement, regarding excitation energies as well as band intensities and profiles. In fluorescence spectroscopy, the experimental spectrum shows a vibrational progression that is not addressed by theory, but the theoretical band position is in excellent agreement with experiment, with a highly accurate description of the Stokes shift as a result.

  • 39.
    Sjöqvist, Jonas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Maria, Jerôme
    Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway.
    Simon, Rozalyn
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Linares, Mathieu
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    Nilsson, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology.
    Lindgren, Mikael
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, The Institute of Technology. Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway.
    Toward a molecular understanding of the detection of amyloid proteins with flexible conjugated oligothiophenes2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 42, p. 9820-9827Article in journal (Refereed)
    Abstract [en]

    Molecular and electronic structures and optical absorption properties of oligothiophenes used for spectral assignment of amyloid deposits have been investigated for a family of probes known as luminescent conjugated oligothiophenes (LCOs). Theoretical absorption spectra have been determined using conformational averaging, combining classical molecular dynamics (MD) simulations with quantum mechanical/molecular mechanics (QM/MM) time-dependent density functional theory (TD-DFT) spectrum calculations. Theoretical absorption spectra are in excellent agreement with experiments, showing average errors below 5 nm for absorption maxima. To couple observed properties to molecular structures, a measure of planarity is defined, revealing a strong correlation between the transition wavelength of the first and dominating electronically excited state and dihedral rotations. It is shown that from this correlation, predictions can be made of the absorption properties of probes based only on information from MD trajectories. We show experimentally that red shifts observed in the excitation maxima of LCOs when bound to amyloid protein aggregates are also evident in absorption spectra. We predict that these red shifts are due to conformational restriction of the LCO in a protein binding pocket, causing a planarization of the conjugated backbone. On the basis of our studies of planarity, it is shown that such shifts are both possible and realistic.

  • 40.
    Solheim, Harald
    et al.
    Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, Tromsø, Norway.
    Ruud, Kenneth
    Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, Tromsø, Norway.
    Coriani, Sonia
    Dipartimento di Scienze Chimiche, Università degli Studi di Trieste, Via L Giorgieri 1, I-34127 Trieste, Italy and Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, Blindern, Oslo, Norway.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
    The A and B terms of magnetic circular dichroism revisited2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 40, p. 9615-9618Article in journal (Other academic)
    Abstract [en]

    The temperature-independent part of the magnetic circular dichroism spectrum is conventionally divided into the Faraday A and B terms, where the A term is nonzero only for systems with degenerate states. We propose that this separation is abandoned in favor of a unified temperature-independent term. This proposal is based on complex polarization propagator calculations on three structurally similar porphyrins. These calculations also suggest that the Soret band of Zn-porphyrin is determined by an isolated degenerate 2Eu state. © 2008 American Chemical Society.

  • 41.
    Sukkaew, Pitsiri
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Danielsson, Örjan
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Ojamäe, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Growth Mechanism of SiC CVD: Surface Etching by H-2, H Atoms, and HCl2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 9, p. 2503-2512Article in journal (Refereed)
    Abstract [en]

    Silicon carbide is a wide bandgap semiconductor with unique characteristics suitable for high temperature and high power applications. Fabrication of SiC epitaxial layers is usually performed using chemical vapor deposition (CVD). In this work, we use quantum chemical density functional theory (B3LYP and M06-2X) and transition state theory to study etching reactions occurring on the surface of SiC during CVD in order to combine etching effects to the surface kinetic model for SiC CVD. H-2, H atoms and HCl gases are chosen in the study as the most likely etchants responsible for surface etching. We consider etchings of four surface sites, namely CH3(ads), SiH3CH2(ads), SiH2(CH2)(2)(ads), and SiH(CH2)(3)(ads), which represent four subsequent snapshots of the surface as the growth proceeds. We find that H atoms are the most effective etchant on CH3(ads) and SiH3CH2(ads), which represent the first and second steps of the growth. HCl and H-2 are shown to be much less effective than H atoms and produce the etching rate constants which are, similar to 10(4) and similar to 10(7) times slower. In comparison to CH3(ads), SiH3CH2(ads) is shown to be less stable and more susceptible to etchings. Unlike the first and second steps of the growth, the third and fourth steps (i.e., SiH2(CH2)(2)(ads) and SiH(CH2)(3)(ads)) are stable and much less susceptible to any of the three etchants considered. This implies that the growth species become more stable via forming Si-C bonds with another surface species. The formation of a larger surface cluster thus helps stabilizing the growth against etchings.

  • 42. Sylvester-Hvid, KO
    et al.
    Mikkelsen, KV
    Norman, Patrick
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Computational Physics .
    Jonsson, D
    Agren, H
    Sign change of hyperpolarizabilities of solvated water, revised: Effects of equilibrium and nonequilibrium solvation2004In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 108, no 41, p. 8961-8965Article in journal (Refereed)
    Abstract [en]

    The second harmonic and electro-optical responses for the water molecule in its liquid state are theoretically revised. The continuum, semicontinuum, and supermolecular solvation models are employed using quadratic response theory at the Hartree-Fock level, either in the equilibrium or nonequilibrium implementation. The experimentally observed sign change of the second harmonic response of water on liquefaction is reproduced using the supermolecular and semicontinuum model for both equilibrium and nonequilibrium solvation. The conclusions of a previous study, which rested upon linear response theory in an equilibrium implementation, are confirmed. Also, the assumption of Kleinman symmetry and dispersion is addressed.

  • 43.
    Yahiro, H.
    et al.
    Department of Applied Chemistry, Faculty of Engineering, Ehime University, Matsuyama 790-8577, Japan.
    Lund, Anders
    Linköping University, The Institute of Technology. Linköping University, Department of Physics, Chemistry and Biology, Chemical Physics .
    Aasa, R.
    Department of Molecular Biotechnology, Chalmers University of Technology, Lundberg Laboratory, P. O. Box 462, SE-405 30 Göteborg, Sweden.
    Benetis, N.P.
    Department of Applied Chemistry, Faculty of Engineering, Hiroshima University, Higashi-Hiroshima 739-8527, Japan.
    Shiotani, M.
    Department of Applied Chemistry, Faculty of Engineering, Hiroshima University, Higashi-Hiroshima 739-8527, Japan.
    Association forms of NO in sodium ion-exchanged A-type zeolite: Temperature-dependent Q-band EPR spectra2000In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 104, no 34, p. 7950-7956Article in journal (Refereed)
    Abstract [en]

    Nitrogen monoxide (NO) introduced into sodium ion-exchanged A-type (Na-A) zeolite was studied by temperature- and NO pressure-dependent EPR measurements at Q-band in the temperature range between 5 and 140 K. The experimental spectra were successfully utilized to determine accurate values of the g and A(14N) tensors of NO monoradical and the g tensors and zero field splitting (ZFS) parameters, D and E, of the NO-NO biradical. Two different EPR spectra corresponding to low and high temperature forms of the NO monoradical were observed when the NO pressure was low (PNO=3.1 kPa). Based on the g and A tensors, the former was attributed to a rigid form and the latter to a rotational form of the monoradical. For higher NO pressure, the biradical became dominant. The structure of the biradical was discussed in terms of the D and g tensors combined with the spectral line shape simulation method.

  • 44.
    Zheng, Kaibo
    et al.
    Lund University, Sweden .
    Zidek, Karel
    Lund University, Sweden .
    Abdellah, Mohamed
    Lund University, Sweden .
    Torbjornsson, Magne
    Lund University, Sweden .
    Chabera, Pavel
    Lund University, Sweden .
    Shao, Shuyan
    Linköping University, Department of Physics, Chemistry and Biology, Applied Physics. Linköping University, The Institute of Technology.
    Zhang, Fengling
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology.
    Pullerits, Tonu
    Lund University, Sweden .
    Fast Monolayer Adsorption and Slow Energy Transfer in CdSe Quantum Dot Sensitized ZnO Nanowires2013In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, no 29, p. 5919-5925Article in journal (Refereed)
    Abstract [en]

    A method for CdSe quantum dot (QD) sensitization of ZnO nanowires (NW) with fast adsorption rate is applied. Photoinduced excited state dynamics of the quantum dots in the case of more than monolayer coverage of the nanowires is studied. Transient absorption kinetics reveals an excitation depopulation process of indirectly attached quantum dots with a lifetime of similar to 4 ns. Photoluminescence and incident photon-to-electron conversion efficiency show that this process consists of both radiative e-h recombination and nonradiative excitation-to-charge conversion. We argue that the latter occurs via interdot energy transfer from the indirectly attached QDs to the dots with direct contact to the nanowires. From the latter, fast electron injection into ZnO occurs. The energy transfer time constant is found to be around 5 ns.

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