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  • 1. Al-Saidi, W. A.
    et al.
    Asher, S. A.
    Norman, Patrick
    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 low-energy 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 NO 2 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 NO 2 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. © 2012 American Chemical Society.

  • 2. Aziz, Emad F.
    et al.
    Grasjo, Johan
    Forsberg, Johan
    Andersson, Egil
    Soderstrom, Johan
    Duda, Laurent
    Zhang, Wenhua
    Yang, Jinglong
    Eisebitt, Stefan
    Bergstrom, Christel
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Nordgren, Joseph
    Eberhardt, Wolfgang
    Rubensson, Jan-Erik
    Photoinduced formation of N-2 molecules in ammonium compounds2007In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, no 39, p. 9662-9669Article in journal (Refereed)
    Abstract [en]

    Via fluorescence yield (FY) and resonant inelastic scattering spectroscopy in the soft X-ray range we find that soft X-rays induce formation of N-2 molecules in solid NH4Cl and in related compounds. The nitrogen molecules form weak bonds in NH4Cl, so that a substantial fraction of the molecules remains in the sample. From measurements of the FY as a function of exposure and temperature, the rates for the photochemical processes are estimated. At elevated temperatures (363 K), several nitrogen atoms are removed from the sample per incoming photon. At lower temperatures (233 K), the rate is reduced to around 0.02 nitrogen atoms for each incoming photon. Virtually all these atoms form N-2 molecules which are bound in the sample. The generality and implications of these results are briefly discussed.

  • 3.
    Baev, Alexander
    et al.
    KTH, Superseded Departments, Biotechnology.
    Rubio-Pons, Oscar
    KTH, Superseded Departments, Biotechnology.
    Gel'Mukhanov, Faris
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    Optical limiting properties of Zinc- and Platinum-based organometallic compounds2004In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 108, no 36, p. 7406-7416Article in journal (Refereed)
    Abstract [en]

    Optical power limiting is theoretically studied using an approach that combines quantum electronic structure calculations of multiphoton excitations and classical calculations of dynamical wave propagation. We illustrate the capability of such a combined approach by presenting results for a couple of organometallic compounds; basic metal-base porphyrins, vinylphenylamine porhyrin, and the so-called type IVc platinum compound. A comparative analysis of their electronic properties related to nonlinear absorption of electromagnetic radiation and their optical limiting capability has been performed based on dynamical simulations of the nonlinear pulse propagation taking account of resonant as well as off-resonant effects. Several key features and rate-limiting steps in the transmission have been examined in relation to various characteristics of the pulse. It is found that the resonant vs off-resonant conditions, the saturation conditions and the dephasing play critical roles for the nonlinear transmission. The saturation effects are sensitive to the pulse duration, the inter-system crossing rate and the quenching of the higher triplet state. The inter-system crossing rate has to be comparable with the inverse pulse duration in order to boost the stepwise two-photon channel associated with singlet-singlet followed by triplet-triplet transitions. It is illustrated that structure-to-property relations of the rate-limiting steps serve as important criteria for choices of compounds suitable for the application of interest.

  • 4. Bittererova, M.
    et al.
    Brinck, Tore
    KTH, Superseded Departments, Chemistry.
    Ostmark, H.
    Theoretical study of the triplet N-4 potential energy surface2000In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 104, no 51, p. 11999-12005Article in journal (Refereed)
    Abstract [en]

    The N-4 molecule in its triplet state has been studied using the DFT-B3LYP, CASSCF, and CCSD(T) computational methods. The previously reported C-s ((3)A ) minimum was not found to be stable using these methods. A D-2d ((3)A(1)) minimum was found to be the lowest energy triplet with a closed structure. This minimum is 20.2 kcal/mol higher in energy than T-d ((1)A(1)) N-4 at the CCSD(T)/cc-pVTZ//CCSD(T)/DZP level of theory. The barrier to dissociation has been estimated to ca. 7.5 kcal/mol from CAS(8,8)+MR-ACPF and CAS(8,8)+MR-AQCC calculations. CASSCF(12,12) calculations indicate that the open-chain N-4 Of C-2h (B-3(u)) symmetry is not stable. The open-chain C-s((3)A ) structure has been found to be a true minimum at all investigated levels of theory. It is 13.4 kcal/mol lower in energy than T-d ((1)A(1)) N-4 at the CCSD(T)/cc-pVTZ//CCSD(T)/DZP level.

  • 5.
    Blom, Hans
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Chmyrov, Andriy
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Hassler, Kai
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Davis, L.M.
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Triplet-State Investigations of Fluorescent Dyes at Dielectric Interfaces Using Total Internal Reflection Fluorescence Correlation Spectroscopy2009In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 113, no 19, p. 5554-5566Article in journal (Refereed)
    Abstract [en]

    The triplet-state kinetics of several fluorescent dyes used in ultrasensitive fluorescence microscopy are investigated using total internal reflection fluorescence correlation spectroscopy (TIR-FCS). A theoretical outline of the correlation analysis and the physical aspects of evanescent excitation and fluorescence emission at dielectric interfaces are given. From this analysis, the rates of intersystem crossing and triplet decay are deduced for fluorescein, ATTO 488, rhodamine 110, rhodamine 123, and rhodamine 6G in aqueous buffer solutions. All investigated dyes show slightly higher triplet rates at the dielectric interface compared to bulk solution measurements. We attribute this enhancement to possible modifications of the dyes’ photophysical properties near a dielectric interface. In the case of rhodamine 6G, the impact of changes in the dye concentration, ionic strength of the solvent, and potassium iodide concentration are also investigated. This leads to a better understanding of the influences of dye−dye, dye−solvent, and dye−surface interactions on the increased triplet intersystem crossing and triplet decay rates. The study shows that analysis of triplet-state kinetics by TIR-FCS not only results in a better understanding of how the photophysical properties of the dyes are affected by the presence of an interface, but also provides a means for probing the microenvironment near dielectric interfaces.

  • 6.
    Bondarchuk, Sergey V.
    et al.
    Bogdan Khmelnitsky Cherkasy National University, Ukraine.
    Minaev, Boris F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Bogdan Khmelnitsky Cherkasy National University, Ukraine .
    Theoretical Study of Relationships between Structural, Optical, Energetic, and Magnetic Properties and Reactivity Parameters of Benzidine and Its Oxidized Forms2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 38, p. 8872-8882Article in journal (Refereed)
    Abstract [en]

    Structural, topological, optical, energetic, and magnetic properties and reactivity parameters of benzidine, its radical cation, and its dication as well as molecular complexes of the benzicline dication with the F-, Cl-, Br-, I-, NO3-, HSO4-, and H2PO4- anions were calculated at the B3LYP/6-311++G(2d,2p) level of theory in the CH2Cl2 medium. The CAM-B3LYP functional (as the most reliable one) and the 6-311++G(3df,3pd) basis set were used for the UV-vis absorption spectra prediction. The obtained spectral results are in a good agreement with available experimental data. A number of the calculated global and local molecular properties, including several recently developed ones, (in general, more than 20 parameters), namely, lambda(max), the bond lengths and orders (l and L-A,L-B), adiabatic ionization energy (IEad), global electrophilicity index (omega), condensed electrophilic Fukui functions (f(+)) and dual descriptor (Delta f(A)), van der Waals molecular volume, nuclear independent chemical shifts (NICS) and QTAIM topological parameters were estimated in the critical points of the C(1)-C(1'), C(2)-C(3), and C(4)-N bonds as well as at the ring critical point. These quantities were found to be in a strong linear dependence (R-2 > 0.99 in most cases) with the number of detached electrons (N-el) from the benzidine molecule up to formation of the dication (N-el = 2). On one hand, a position of the long-wave absorption band (lambda(CT)) corresponding to the anion-to-cation charge transfer in the neutral complexes of the benzidine dication with anions, correlates with the Mulliken electronegativity of the anion (R-2 = 0.8646) and its adiabatic ionization energy (R-2 = 0.8054). On the other hand, the correlations with the anion charge in the complexes and the anion isotropic polarizability are rather poor (R-2 = 0.6392 and 0.3470, respectively). On the ground of the obtained strong relationships, one may recommend the calculated molecular properties as potentially preferable descriptors for the benzidine-based compounds in terms of the QSAR methodology.

  • 7.
    Brinck, Tore
    et al.
    KTH, Superseded Departments, Chemistry.
    Carlqvist, P.
    Holm, A. H.
    Daasbjerg, K.
    Solvation of sulfur-centered cations and anions in acetonitrile2002In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 106, no 37, p. 8827-8833Article in journal (Refereed)
    Abstract [en]

    The solvation of substituted phenylsulfenium ions and thiophenoxides in acetonitrile has been analyzed on the basis of experimental and theoretical data. Experimental solvation energies are obtained from previously reported oxidation and reduction potentials of the corresponding arylthiyl radicals in combination with theoretically calculated ionization potentials and electron affinities at the B3LYP/6-31+G(d) level. These calculations provide a consistent set of values in contrast to the data sets obtained in our previous paper (Larsen et al., J. Am. Chem. Soc. 2001, 123, 1723). The extracted solvation data show the expected substituent dependency for both kinds of ions, i.e., the absolute value of the solvation energy decreases as the charge becomes more delocalized. For the thiophenoxides there is good agreement between the experimental solvation energies and solvation energies computed using the polarizable continuum model (PCM). The solvation of the arylsulfenium ions, is much stronger than predicted by the PCM method. This can be attributed to the formation of a strong covalent bond of the Ritter type between the arylsulfenium ion and one molecule of acetonitrile. When this interaction is included in the solvation energy calculations by means of a combined supermolecule and PCM approach the experimental data are reproduced within a few kcal mol(-1). While the energy difference of the singlet and triplet spin states of the arylsulfenium ions is almost negligible in gas phase, the singlet cation is undoubtedly the dominating species in solution, since the triplet cation lacks the ability to form a covalent bond with acetonitrile.

  • 8.
    Brinck, Tore
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Lee, Hau-Nan
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Jonsson, Mats
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Nuclear Chemistry.
    Quantum Chemical Studies on the Thermochemistry of Alkyl and Peroxyl Radicals.1999In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 103, p. 7094-7104-Article in journal (Refereed)
  • 9.
    Cao, Weimin
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Materials Process Science.
    Delin, Anna
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Seetharaman, Seshadri
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Materials Process Science.
    Effect of electronic structure and magnetism on S adsorption on Fe (100) from first principlesIn: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215Article in journal (Other academic)
  • 10.
    Carlqvist, Peter
    et al.
    KTH, Superseded Departments, Chemistry.
    Ostmark, H.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    The stability of arylpentazoles2004In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 108, no 36, p. 7463-7467Article in journal (Refereed)
    Abstract [en]

    The stability of phenylpentazole along with para-substituted and ortho,para-substituted arylpentazoles have been studied using high-level density functional theory (DFT). The decomposition of arylpentazoles to N-2 and the corresponding azide is a first-order reaction, where the breaking of the N1-N2 bond is concomitant with cleavage of the N3-N4 bond. Calculations confirm that the stability of arylpentazoles increases with electron-donating groups and decreases with electron-withdrawing groups, in the para position, as found in experiments. The stabilizing effect of the electron-donating groups is shown to be due to a resonance interaction with the electron-withdrawing pentazole ring. Addition of solvation effects, using the polarizable continuum model to simulate the polar solvent methanol, increases the stability of arylpentazoles. This is due to a more polar ground state than transition state. The calculated free energies of activation for the arylpentazoles agree well with experimental results. From the calculations, the electron-withdrawing effect of the pentazole group is found to be similar to that of cyanide (-CN). Some new arylpentazoles with hydroxyl groups in the ortho position are proposed. These are predicted to be more stable than all previously synthesized neutral arylpentazoles.

  • 11. Carravetta, V.
    et al.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Symmetry Breaking and Hole Localization in Multiple Core Electron Ionization2013In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, no 31, p. 6798-6802Article in journal (Refereed)
    Abstract [en]

    Motivated by recent opportunitites to study hollow molecules with multiple core holes offered by X-ray free electron lasers, we revisit the core-hole localization and symmetry breaking problem, now studying ionization of more than one core electron. It is shown, using a N-2 molecule with one, two, three, and four core holes, for example, that in a multiconfigurational determination of the core ionization potentials employing a molecular point group with broken inversion symmetry, one particular configuration is sufficient to account for the symmetry breaking relaxation energy in an independent particle approximation in the case of one or three holes, whereas the choice of point group symmetry is unessential for two and four holes. The relaxation energy follows a quadratic dependence on the number of holes in both representations.

  • 12.
    Chattopadhyaya, Mausumi
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Murugan, N. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Origin of the Absorption Band of Bromophenol Blue in Acidic and Basic pH: Insight from a Combined Molecular Dynamics and TD-DFT/MM Study2016In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, no 36, p. 7175-7182Article in journal (Refereed)
    Abstract [en]

    We study the linear and nonlinear optical properties of a well-known acid base indicator, bromophenol blue (BPB), in aqueous solution by employing static and integrated approaches. In the static approach, optical properties have been calculated using time-dependent density functional theory (TD-DFT) on the fully relaxed geometries of the neutral and different unprotonated forms of BPB. Moreover, both closed and open forms of BPB were considered. In the integrated approach, the optical properties have been computed over many snapshots extracted from molecular dynamics simulation using a hybrid time-dependent density functional theory/molecular mechanics approach. The static approach suggests closed neutral double right arrow anionic interconversion as the dominant mechanism for the red shift in the absorption spectra of BPB due to a change from acidic to basic pH. It is found by employing an integrated approach that the two interconversions, namely open neutral double right arrow anionic and open neutral double right arrow dianionic, can contribute to the pH- dependent shift in the absorption spectra of BPB. Even though both static and integrated approaches reproduce the pH-dependent red shift in the absorption spectra of BPB, the latter one is suitable to determine both the spectra and spectral broadening. Finally, the computed static first hyperpolarizability for various protonated and deprotonated forms of BPB reveals that this molecule can be used as a nonlinear optical probe for pH sensing in addition to its highly exploited use as an optical probe.

  • 13.
    Chen, Xing
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Cao, Zexing
    Department of Chemistry, Xiamen Univeristy.
    Role of the 3(ππ*) state in photolysis of lumisantonin: insight from ab initio studies2011In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 115, no 26, p. 7815-7822Article in journal (Refereed)
    Abstract [en]

    The CASSCF and CASPT2 methodologies have been used to explore the potential energy surfaces of lumisantonin in the ground and low-lying triplet states along the photoisomerization pathways. Calculations indicate that the (n pi*) state is the accessible low-lying singlet state with a notable oscillator strength under an excitation wavelength of 320 nm and that it can effectively decay to the (3)(pi pi*) state through intersystem crossing in the region of minimum surface crossings with a notable spin-orbital coupling constant. The 3(pi pi*) state, derived from the promotion of an electron from the pi-type orbital mixed with the sigma orbital localized on the C-C bond in the three-membered alkyl ring to the pi* orbital of conjugation carbon atoms, plays a critical role in C-C bond cleavage. Based on the different C-C bond rupture patterns, the reaction pathways can be divided into paths A and B. Photolysis along path A arising from C1-C5 bond rupture is favorable because of the dynamic and thermodynamic preferences on the triplet excited-state PES. Path B is derived from the cleavage of the C5-C6 bond, leading first to a relatively stable species, compared to intermediate A-INT formed on the ground state PES. path B is relatively facile for the pyrolytic reaction. The present results provide a basis to interpret the experimental observations.

  • 14.
    Coullerez, Geraldine
    et al.
    KTH, Superseded Departments, Fibre and Polymer Technology.
    Carlmark, Anna
    KTH, Superseded Departments, Fibre and Polymer Technology.
    Malmström, Eva
    KTH, Superseded Departments, Fibre and Polymer Technology.
    Jonsson, Mats
    KTH, Superseded Departments, Chemistry.
    Understanding copper-based atom-transfer radical polymerization in aqueous media2004In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 108, no 35, p. 7129-7131Article in journal (Refereed)
    Abstract [en]

    This study investigates the mechanism of copper(I)-mediated living atom-transfer radical polymerization (ATRP) in aqueous media. It is shown that the ATRP apparent rate constant for polymerization of methoxycapped oligo(ethylene glycol) methacrylate (OEGMA) in water (k(P)(app)) at room temperature correlates with the redox potential (E-1/2) of the copper complexes. The results are discussed along with previously published results on the kinetics for bulk polymerization of methyl acrylate at 60 degreesC with the redox potentials measured in MeCN. The faster ATRP kinetics in water can mainly be attributed to a higher equilibrium concentration of propagating radicals [W] and to solvent effects on the rate of propagation k(p). It is shown that [R*] can be calculated from the redox properties of the alkyl halide and the copper complex. The values of [R*] in MeCN/bulk and in H2O were determined to be 8.2 x 10(-8) and 6.3 x 10(-5) M, respectively. The respective kp values are in good agreement with the literature values (3.6 x 10(3) M-1 s(-1) for OEGMA in water and 2.5 x 10(3) M-1 s(-1) for methyl acrylate in bulk).

  • 15.
    Coullerez, Geraldine
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Nuclear Chemistry. KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Malmström, Eva
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Jonsson, Mats
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Nuclear Chemistry.
    Solvent effects on the redox properties of Cu complexes used as mediators in atom transfer radical polymerization2006In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 110, no 34, p. 10355-10360Article in journal (Refereed)
    Abstract [en]

    Solvent effects on the redox properties of six Cu(I) complexes used as mediators in atom transfer radical polymerization (ATRP) have been studied using cyclic voltammetry. The six ligands used were tris[2(dimethylamino) ethyl] amine, N-(n-propyl)-2-pyridylmethanimine, N, N, N', N', N'-pentamethyldiethylenetriamine, 1,1,4,7,10,10-hexamethyl-triethylenetetramine, 2,2'-bipyridine, and 1,4,8,11-tetraaza-1,4,8,11-tetramethylcyclotetradecan. The solvents used were DMSO, DMF, MeCN, MeOH, IP, and BuOH. Significant solvent effects were observed and quantitatively analyzed in terms of Kamlet-Taft relationships. The resulting Kamlet-Taft equations were found to successfully describe the solvent effects and could thus be used as tools for the design of ATRP in new solvents. The solvent sensitivity of the different ligands and the nature of the solvent effects are also discussed to some extent.

  • 16. de Almeida, Katia Júlia
    et al.
    Ramalho, T. C.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Cesar, Amary
    Theoretical Study of Specific Solvent Effects on the Optical and Magnetic Properties of Copper(II) Acetylacetonate2011In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 115, no 8, p. 1331-1339Article in journal (Refereed)
    Abstract [en]

    Specific and basicity solvent effects on the visible near-infrared electronic transitions and the electron paramagnetic resonance (EPR) parameters of the copper(II) acetylacetonate complex, Cu(acac)(2), have been investigated at the density functional theory level. The computed absorption transitions as well as the EPR parameters show a strong dependence on the direct coordination environment around the Cu(II) complex. High solvatocromic shifts are observed for 3d-3d transitions, with the highest effect observed for the d(z2)-->d(xy) transition, which is red-shifted by 6000 cm(-1) and 9000 cm(-1) in water and pyridine solvent models, respectively. Compared to the electronic g-tensors, the hyperfine coupling constants of the Cu(acac)(2) complex show a more pronounced dependence on the effect of base strength of solvent. Overall, the present methodology satisfactorily models the solvent effect on the optical and magnetic properties of the Cu(acac)(2) complex, and theory and experiment agree sufficiently well to warrant the use of the computed optical and EPR parameters to elucidate the coordination environment of the Cu(II) systems in basic solutions.

  • 17. Di Remigio, Roberto
    et al.
    Bast, Radovan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. Université de Toulouse III (Paul Sabatier), France.
    Frediani, Luca
    Saue, Trond
    Four-Component Relativistic Calculations in Solution with the Polarizable Continuum Model of Solvation: Theory, Implementation, and Application to the Group 16 Dihydrides H2X (X = O, S, Se, Te, Po)2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 21, p. 5061-5077Article in journal (Refereed)
    Abstract [en]

    We present a formulation of four-component relativistic self-consistent field (SCF) theory for a molecular solute described within the framework of the polarizable continuum model (PCM) for solvation. The linear response function for a four-component PCM-SCF state is also derived, as well as the explicit form of the additional contributions to the first-order response equations. The implementation of such a four-component PCM-SCF model, as carried out in a development version of the DIRAC program package, is documented. In particular, we present the newly developed application programming interface PCMSolver used in the actual implementation with DIRAC. To demonstrate the applicability of the approach, we present and analyze calculations of solvation effects on the geometries, electric dipole moments, and static electric dipole polarizabilities for the group 16 dihydrides H2X (X = O, S, Se, Te, Po).

  • 18.
    Dinér, Peter
    Uppsala University.
    Superacid-Promoted Ionization of Alkanes Without Carbonium Ion Formation: A Density Functional Theory Study2012In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, no 40, p. 9979-9984Article in journal (Refereed)
  • 19. Eggeling, C.
    et al.
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Brand, L.
    Schaffer, J.
    Felekyan, S.
    Seidel, C. A. M.
    Analysis of photobleaching in single-molecule multicolor excitation and forster resonance energy transfer measurement2006In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 110, no 9, p. 2979-2995Article in journal (Refereed)
    Abstract [en]

    we investigated the influence of photobleaching in fluorescence experiments applying multicolor laser as well as Forster resonance energy transfer (FRET) mediated excitation using several red-emitting dyes frequently used in multicolor experiments or as FRET acceptors. The chosen dyes (cyanine 5 (Cy5), MR121, Alexa660, Alexa680, Atto647N, Atto655) have chemically distinct chromophore systems and can be excited at 650 nm. Several fluorescence analysis techniques have been applied to detect photobleaching and to disclose the underlying photophysics, all of which are based on single-molecule detection: (1) fluorescence correlation spectroscopy (FCS) of bulk solutions, (2) fluorescence cross-correlation of single-molecule trajectories, and (3) multiparameter fluorescence detection (MFD) of single-molecule events. The maximum achievable fluorescence signals as well as the survival times of the red dyes were markedly reduced under additional laser irradiation in the range of 500 nm. Particularly at excitation levels at or close to saturation, the 500 nm irradiation effectively induced transitions to higher excited electronic states on already excited dye molecules, leading to a pronounced bleaching reactivity. A theoretical model for the observed laser irradiance dependence of the fluorescence brightness of a Cy5 FRET acceptor dye has been developed introducing the full description of the underlying photophysics. The model takes into account acceptor as well as donor photobleaching from higher excited electronic states, population of triplet states, and energy transfer to both the ground and excited states of the acceptor dye. Also, photoinduced reverse intersystem crossing via higher excited triplet states is included, which was found to be very efficient for Cy5 attached to DNA. Comparing continuous wave (cw) and pulsed donor excitation, a strong enhancement of acceptor photobleaching by a factor of 5 was observed for the latter. Thus, in the case of fluorescence experiments utilizing multicolor pulsed laser excitation, the application of the appropriate timing of synchronized green and red laser pulses in an alternating excitation mode can circumvent excessive photobleaching. Moreover, important new single-molecule analysis diagnosis tools are presented: (1) For the case of excessive acceptor photobleaching, cross-correlation analysis of single-molecule trajectories of the fluorescence signal detected in the donor and acceptor detection channels and vice versa shows an anticorrelated exponential decay and growth, respectively. (2) The time difference, T-g - T-r of the mean observation times of all photons detected for the donor and acceptor detection channels within a single-molecule fluorescence burst allows one to identify and exclude molecules with an event of acceptor photobleaching. The presented single-molecule analysis methods can be constrained to, for example, FRET-active subpopulations, reducing bias from FRET-inactive molecules. The observations made are of strong relevance for and demand a careful choice of laser action in multicolor and FRET experiments, in particular when performed at or close to saturation.

  • 20. Engstrom, M.
    et al.
    Himo, Fahmi
    KTH, Superseded Departments, Biotechnology.
    Graslund, A.
    Minaev, B.
    Vahtras, Olav
    KTH, Superseded Departments, Biotechnology.
    Ågren, Hans
    KTH, Superseded Departments, Biotechnology.
    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.

  • 21. Fahleson, T.
    et al.
    Kauczor, J.
    Norman, P.
    Santoro, F.
    Improta, R.
    Coriani, S.
    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, apart 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 bases 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 by the bright π → π∗ transitions, and our calculations in solution nicely reproduce their energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n → π∗ excitations, but they are too weak to be observed in the experiment. © 2015 American Chemical Society.

  • 22. Falklöf, O.
    et al.
    Durbeej, B.
    Norman, Patrick
    Linköping University, Sweden.
    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, by 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, we 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 2 to 5 orders of magnitude smaller than the nonradiative ones.

  • 23.
    Fang, Qiu
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Han, Juan
    Jiang, Jieling
    Chen, Xuebo
    Fang, Weihai
    The Conical Intersection Dominates the Generation of Tropospheric Hydroxyl Radicals from NO2 and H2O2010In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 114, no 13, p. 4601-4608Article in journal (Refereed)
    Abstract [en]

    In the present work, we report a quantitative understanding on how to generate hydroxyl radicals from NO2 and H2O in the troposphere upon photoexcitation at 410 nm by using multiconfigurational perturbation theory and density functional theory. The conical intersections dominate the nonadiabatic relaxation processes after NO2 irradiated at similar to 410 nm in the troposphere and further control the generation of OH radical by means of hydrogen abstraction. In agreement with two-component fluorescence observed by laser techniques, there are two different photophysical relaxation channels along decreasing and increasing O-N-O angle of NO2. In the former case, the conical intersection between (B) over tilde B-2(1) and (A) over tilde B-2(2) (CI (B-2(2)/B-2(1)) first funnels NO2 out of the Franck-Condon region of (B) over tilde B-2(1) and relaxes to the (A) over tilde B-2(2) surface. Following the primary relaxation, the conical intersection between (A) over tilde B-2(2) and (X) over tilde (2)A(1) (CI(B-2(2)/(2)A(1))) drives NO2 to decay into highly vibrationally excited (X) over tilde (2)A(1) state that is more than 20 000 cm(-1) above zeroth-order vertical bar n(1),n(2),n(3) = 0 > vibrational level. In the latter case, increasing the O-N-O angle leads NO2 to relax to a minimum of (B) over tilde B-2(1) with a linear O-N-O arrangement. This minimum point is also funnel region between (B) over tilde B-2(1) and (X) over tilde (2)A(1) (CI(B-2(1)/(2)A(1))) and leads NO2 to relax into a highly vibrationally excited (X) over tilde (2)A(1) state. The high energetic level of vibrationally excited state has enough energy to overcome the barrier of hydrogen abstraction (40-50 kcal/mol) from water vapor, producing OH ((2)Pi(3/2)) radicals. The collision between NO2 and H2O molecules not only is a precondition of hydrogen abstraction but induces the faster internal conversion (CIIC) via conical intersections. The faster internal conversion favors more energy transfer from electronically excited states into highly vibrationally excited (X) over tilde (2)A(1) states. The collision (i.e., the heat motion of molecules) functions as the trigger and accelerator in the generation of OH radicals from NO2 and H2O in the troposphere.

  • 24.
    Fang, Qiu
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Liu, Ya-Jun
    Wavelength-Dependent Photodissociation of Benzoic Acid Monomer in alpha C-O Fission2010In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 114, no 1, p. 680-684Article in journal (Refereed)
    Abstract [en]

    In concert with the latest laser-induced fluorescence (LIF) experiment [Wei et al. J. Phys. Client. A 2008, 112, 4727], we investigated the photodissociation mechanics of the benzoic acid monomer (BAM) with alpha C-O fission by means of state-of-the-art ab initio calculations. Complete active space self-consistent-field (CASSCF) and multi reference CASSCF second-order perturbation theory (MSCASPT2) calculations were performed on the ground and a number of low-lying excited states of BAM. Our calculations indicated that alpha C-O fission from the S, state is in competition with the fission from the T-2 state upon the 266-284 nm wavelength photon. This differs from the conclusion of the previous theoretical investigation and clarified the vague experimental conclusion made earlier. According to Our calculations, alpha C-O fission mainly occurs at the T, state upon photoexcitation at 284-294 nm, and the photon with a wavelength longer than 294 nm is unable to present the alpha C-O fission. This conclusion agrees with the LIF experimental observation.

  • 25.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Baader, Wilhelm J.
    Unimolecular Decomposition Mechanism of 1,2-Dioxetanedione: Concerted or Biradical? That is the Question!2017In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 121, p. 1189-1194Article in journal (Refereed)
    Abstract [en]

    Determination of the ground- and excited-stateunimolecular decomposition mechanisms of 1,2-dioxetanedionegives a level of insight into bimolecular decomposition reactionsof this kind for which some experimental results are reported.Although a few studies have put some effort to describe abiradical mechanism of this decomposition, there is still no systematic study that proves an existence of a biradical character.In the present study, state-of-the-art high-level multistatemulticonfigurational reference second-order perturbation theorycalculations are performed to describe the reaction mechanismof 1,2-dioxetanedione in detail. The calculations indicate that thedecomposition of this four-membered ring peroxide containingtwo carbonyl carbon atoms occurs in concerted but notsimultaneous fashion, so-called “merged”, contrary to the caseof unimolecular 1,2-dioxetane and 1,2-dioxetanone decompositions where biradical reaction pathways have been calculated. Atthe TS of the ground-state surface, the system enters an entropic trapping region, where four singlet and four triplet manifoldsare degenerated, which can lead to the formation of triplet and singlet excited biradical species. However, these excited specieshave to overcome a second activation barrier for C−C bond cleavage for excited product formation, whereas the ground-stateenergy surface possesses only one TS. Thus our calculations indicate that the unimolecular decomposition of 1,2-dioxetanedioneshould not lead to efficient excited-state formation, in agreement with the lack of direct emission from the peroxyoxalate reaction.

  • 26.
    Felicissimo, V.C.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). Universidade Federal de Minas Gerais, Brazil.
    Cesar, A.
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Probing weak molecular orbital interactions in non-conjugated diene molecules by means of near-edge X-ray absorption spectroscopy2005In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 109, no 33, p. 7385-7395Article in journal (Refereed)
    Abstract [en]

    Carbon and oxygen near-edge X-ray absorption fine structure (NEXAFS) spectra of 1,4-cyclohexadiene, p-benzoquinone, norbornadiene, norbornadienone, and cis-cis-[4,4,2]propella-3,8-diene-11,12-dione were calculated by means of Hartree-Fock and hybrid density functional theory using the static-exchange (STEX) approximation. The NEXAFS spectra are used as a probe to identify weak molecular interactions between the two non-conjugated ethylenic pi* orbitals present in these molecules. We show that the X-ray absorption spectrum of 1,4-cyclohexadiene exhibits some particular spectral structures in the discrete energy region that evidence diene through-bond orbital interaction, whereas absorption peaks are identified in the norbornadiene and norbornadienone spectra that indicate effective through-space orbital interactions. The molecular structure of the cis-cis-[4,4,2]propella-3,8-diene-11,12-dione isomer is such that the indirect through-bond or through-space diene orbital interactions are too weak to be assigned by its C1s NEXAFS spectrum.

  • 27.
    Felicissimo, V.C.
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). Universidade Federal de Minas Gerais, Brazil.
    Guimaraes, F.F.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512). Universidade Federal de Minas Gerais, Brazil.
    Cesar, A.
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Proton transfer mediated by the vibronic coupling in oxygen core ionized states of glyoxalmonoxime studied by infrared-X-ray pump-probe spectroscopy.2006In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 110, no 47, p. 12805-12813Article in journal (Refereed)
    Abstract [en]

    The theory of IR-X-ray pump-probe spectroscopy beyond the Born-Oppenheimer approximation is developed and applied to the study of the dynamics of intramolecular proton transfer in glyoxalmonoxime leading to the formation of the tautomer 2-nitrosoethenol. Due to the IR pump pulses the molecule gains sufficient energy to promote a proton to a weakly bound well. A femtosecond X-ray pulse snapshots the wave packet route and, hence, the dynamics of the proton transfer. The glyoxalmonoxime molecule contains two chemically nonequivalent oxygen atoms that possess distinct roles in the hydrogen bond, a hydrogen donor and an acceptor. Core ionizations of these form two intersecting core-ionized states, the vibronic coupling between which along the OH stretching mode partially delocalizes the core hole, resulting in a hopping of the core hole from one site to another. This, in turn, affects the dynamics of the proton transfer in the core-ionized state. The quantum dynamical simulations of X-ray photoelectron spectra of glyoxalmonoxime driven by strong IR pulses demonstrate the general applicability of the technique for studies of intramolecular proton transfer in systems with vibronic coupling.

  • 28. Feyer, Vitaliy
    et al.
    Plekan, Oksana
    Richter, Robert
    Coreno, Marcello
    Vall-Llosera, Gemma
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Prince, Kevin C.
    Trofimov, Alexander B.
    Zaytseva, Irina L.
    Moskovskaya, Tatyana E.
    Gromov, Evgeniy V.
    Schirmer, Jochen
    Tautomerism in Cytosine and Uracil: An Experimental and Theoretical Core Level Spectroscopic Study2009In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 113, no 19, p. 5736-5742Article in journal (Refereed)
    Abstract [en]

    The O, N, and C 1s core level photoemission spectra of the nucleobases cytosine and uracil have been measured in the vapor phase, and the results have been interpreted via theoretical calculations. Our calculations accurately predict the relative binding energies of the core level features observed in the experimental photoemission results and provide a full assignment. In agreement with previous work, a single tautomer of uracil is populated at 405 K, giving rise to relatively simple spectra. At 450 K, three tautomers of cytosine, one of which may consist of two rotamers, are identified, and their populations are determined. This resolves inconsistencies between recent laser studies of this molecule in which the rare imino-oxo tautomer was not observed and older microwave spectra in which it was reported.

  • 29. Fiedler, Johannes
    et al.
    Thiyam, Priyadarshini
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Multiscale Materials Modelling. University of Oslo, Norway.
    Kurumbail, Anurag
    Burger, Friedrich A.
    Walter, Michael
    Persson, Clas
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering. University of Oslo, Norway.
    Brevik, Iver
    Parsons, Drew F.
    Bostrom, Mathias
    Buhmann, Stefan Y.
    Effective Polarizability Models2017In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 121, no 51, p. 9742-9751Article in journal (Refereed)
    Abstract [en]

    Theories for the effective polarizability of a small particle in a medium are presented using different levels of approximation: we consider the virtual cavity, real cavity, and the hard-sphere models as well as a continuous interpolation of the latter two. We present the respective hard-sphere and-cavity radii as obtained from density-functional simulations as well as the resulting effective polarizabilities at discrete Matsubara frequencies. This enables us to account for macroscopic media in van der Waals interactions between molecules in water and their Casimir-Polder interaction with an interface.

  • 30. Fristrup, Peter
    et al.
    Ahlquist, Mårten
    Department of Chemistry, Technical University of Denmark.
    Tanner, David
    Norrby, Per-Ola
    On the Nature of the Intermediates and the Role of Chloride Ions in Pd-Catalyzed Allylic Alkylations: Added Insight from Density Functional Theory2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 50, p. 12862-12867Article in journal (Refereed)
    Abstract [en]

    The reactivity of intermediates in palladium-catalyzed allylic alkylation was investigated using DFT (B3LYP) calculations including a PB-SCRF solvation model. In the presence of both phosphine and chloride ligands, the allyl intermediate is in equilibrium between a cationic eta(3)-allylPd complex with two phosphine ligands, the corresponding neutral complex with one phosphine and one chloride ligand, and a neutral eta(1)-allylPd complex with one chloride and two phosphine ligands. The eta(1)-complex is unreactive toward nucleophiles. The cationic eta(3)-complex is the intermediate most frequently invoked in the title reaction, but in the presence of halides, the neutral, unsymmetrically substituted eta(3)-CoMplex will be formed rapidly from anionic Pd(0) complexes in solution. Since the latter will prefer both leaving group ionization and reaction with nucleophiles in the position trans to phosphorus, it can rationalize the observed "memory effect" (a regioretention) in the title reaction, even in the absence of chiral ligands.

  • 31. Fromager, E.
    et al.
    Vallet, V.
    Schimmelpfennig, B.
    Macak, P.
    Privalov, Timofei
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Wahlgren, U.
    Spin-orbit effects in electron transfer in neptunyl(VI)-neptunyl(V) complexes in solution2005In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 109, no 22, p. 4957-4960Article in journal (Refereed)
    Abstract [en]

    The spin-orbit effects were investigated on the complexes involved in the electron self-exchange between Np(V) and Np(VI) in both the outer-sphere and inner-sphere mechanisms, the latter for binuclear complexes containing hydroxide, fluoride, and carbonate as bridging ligands. Results obtained with the variation-perturbation and the multireference single excitation spin-orbit Cl calculations are compared. Both effects due to different relaxations of spinors within a multiplet (spin-orbit relaxation) and scalar (electrostatic) relaxation effects in the excited states are accounted for in the latter scheme. The results show that the scalar (electrostatic) relaxation is well described by the single-excitation spin-orbit CI, and that spin-orbit relaxation effects are small in the Np complexes, as in the lighter d-transition elements but in contrast to the main group elements.

  • 32. Gardfeldt, K.
    et al.
    Jonsson, Mats.
    KTH, Superseded Departments, Chemistry.
    Is bimolecular reduction of Hg(II) complexes possible in aqueous systems of environmental importance2003In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 107, no 22, p. 4478-4482Article in journal (Refereed)
    Abstract [en]

    One-electron reduction potentials for Hg(II) complexes were calculated from experimental data obtained from pulse radiolysis experiments in order to investigate the importance of some reducing agents in the environment, i.e., HO2. and/or O-2(.-). Knowledge on such potentials is valuable to foresee reduction pathways for mercury species in different environmental surroundings. The behavior of an aqueous system containing different proportions of Hg2+/H2C2O4/Cl- in the presence of actinic light was also investigated. The one-electron reduction potentials for the Hg(II) species during the experimental conditions in this study were found to be below -0.45 V. Consequently, Hg(II) should not be reduced by HO2. or O-2(.-) under ambient conditions. Hence, the proposed aqueous phase reduction of Hg(II) species by O-2(.-)/HO2. should not be included in models describing the atmospheric transport and transformation of mercury. Results from the photolytical experiments show that reduction of Hg(II) may occur via photo fragmentation of an organic ligand, such as oxalate, bound to the metal.

  • 33.
    Gavrilyuk, Sergey
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Polyutov, Sergey
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Jha, Prakash Chandra
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Gelmukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Many-photon dynamics of photobleaching2007In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, p. 11961-11975Article in journal (Refereed)
    Abstract [en]

    A detailed dynamical theory of photobleaching by periodical sequences of laser pulses is presented. The theory is used for interpretation of recent experiments with pyrylium salts. Our simulations are based on first-principles simulations of photoabsorption cross-sections and on empirical rate constants. Two competitive channels of photobleaching, namely, photobleaching from the lowest excited singlet and triplet states and from higher excited states, are found to explain different intensity dependences of the photobleaching rates in different samples. The process includes two-photon excitation from the ground state to the first or second excited singlet states and one-photon excitation from the first singlet or triplet states to higher excited states. The fluorescence follows double-exponential dynamics with two characteristic times. The first and the shorter one is the equilibrium settling time between the ground and the lowest triplet states. The second characteristic time, the time of photobleaching, is responsible for the long-term dynamics. The effective rate of photobleaching from the first excited singlet and lowest triplet states depends differently on the irradiance in comparison with the photobleaching in higher states. The first channel is characterized by a quadratic intensity dependence in contrast to the second channel that shows a cubic dependence. The competition between these photobleaching channels is very sensitive to the rate constants as well as to the repetition rate, the pulse duration, and the peak intensity. The double-exponential decay of the fluorescence is explained by the spatial inhomogeneity C of the light beam. The findings in this work are discussed in terms of the possibility of using many-photon-induced photobleaching for new three-dimensional read-write devices.

  • 34. Glimsdal, E.
    et al.
    Norman, Patrick
    Linköping University, Sweden.
    Lindgren, M.
    Excitation and emission properties of platinum(II) acetylides at high and low concentrations2009In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 113, no 42, p. 11242-11249Article in journal (Refereed)
    Abstract [en]

    Photophysical properties of platinum(II) acetylides in tetrahydrofuran (THF) solutions and incorporated in poly (methyl methacrylate) (PMMA) glasses have been studied over a large concentration range from 10 /ÀM to 50 mM. In general, the luminescence properties of the studied chromophores in the liquid state were also maintained in the solid state, except for shorter decay times of 50-90 μs of the triplet state in the glass compared with 200-300 μs in solution at low concentrations. The phosphorescence line shapes were found to be independent of both the chromophore concentration and the environment (THF and PMMA). The triplet state lifetimes did not change with concentration in the solid-state case, whereas, in solution, the decay becomes shorter at increasing concentration. The latter effect could be modeled with an additional linear quenching rate, kq in the range of (1 to 7) × 107 M-1 s-1. Excitation spectra of the triplet state at high concentrations, in both solutions and solid glasses, showed additional excitation bands on the long wavelength side compared with the corresponding measurements at low concentrations. This indicates enhanced singlet-triplet coupling due to intermolecular electronic interactions that become important at concentrations of 0.1 to 1 mM and above.

  • 35. Goldstein, S.
    et al.
    Lind, Johan
    KTH, Superseded Departments, Chemistry.
    Merenyi, Gabor
    KTH, Superseded Departments, Chemistry.
    Reaction of organic peroxyl radicals with (NO2)-N-center dot and (NO)-N-center dot in aqueous solution: Intermediacy of organic peroxynitrate and peroxynitrite species2004In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 108, no 10, p. 1719-1725Article in journal (Refereed)
    Abstract [en]

    In this work, we studied the reactions of alkyl peroxyl radicals with (NO2)-N-. and (NO)-N-. using the pulse radiolysis technique. The rate constants for the reaction of (NO2)-N-. with (CH3)(2)C(OH)CH2OO., CH3OO. and c-C5H9OO. vary between 7 x 10(8) and 1.5 x 10(9) M-1 s(-1). The reaction produces relatively long-lived alkyl peroxynitrates, which are in equilibrium with the parent radicals and have no appreciable absorption above 270 nm. It is also shown that (NO)-N-. adds rapidly to (CH3)(2)C(OH)CH2OO. and CH3OO. to form alkyl peroxynitrites. The rate constants for these reactions were determined to be 2.8 x 10(9) and 3.5 x 10(9) M-1 s(-1), respectively. However, in contrast to alkyl peroxynitrates, alkyl peroxynitrites do not accumulate. Rather, they decompose rapidly via homolysis along the relatively weak O-O bond, initially forming a geminate pair. Most of this pair collapses in the cage to form an alkyl nitrate, RONO2, and about 14% diffuses out as free alkoxyl and (NO2)-N-. radicals. A thermokinetic analysis predicts the half-life of CH3OONO in water to be less than 1 mus, an estimate that agrees well with previous experimental findings of ours for other alkyl peroxynitrites. A comparison of aqueous and gaseous thermochemistry of alkyl peroxynitrates reveals that alkyl peroxyl radicals and the corresponding alkyl peroxynitrates are similarly solvated by water.

  • 36. Goldstein, S.
    et al.
    Samuni, A.
    Hideg, K.
    Merenyi, Gabor
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Nuclear Chemistry.
    Structure-activity relationship of cyclic nitroxides as SOD mimics and scavengers of nitrogen dioxide and carbonate radicals2006In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 110, no 10, p. 3679-3685Article in journal (Refereed)
    Abstract [en]

    Synthetic nitroxide antioxidants attenuate oxidative damage in various experimental models. Their protective effect reportedly depends on ring size and ring substituents and is greater for nitroxides having lower oxidation potential. The present study focuses on the kinetics and mechanisms of the reactions of piperidine, pyrrolidine and oxazolidine nitroxides with HO2 center dot/O-2(center dot-), (NO2)-N-center dot and CO3 center dot- radicals, which are key intermediates in many inflammatory and degenerative diseases. It is demonstrated that nitroxides are the most efficient scavengers of (NO2)-N-center dot at physiological pH (k = (3-9) x 10(8) M-1 s(-1)) and among the most effective metal-independent scavengers Of CO3 center dot- radicals (k = (2 - 6) x 10(8) M-1 s(-1)). Their reactivity toward HO2 center dot, though not toward center dot NO2 and CO3 center dot-, depends on the nature of the ring side-chain and particularly on the ring-size. All nitroxide derivatives react slowly with O-2(center dot-) and are relatively inefficient SOD mimics at physiological pH. Even piperidine nitroxides, having the highest SOD-like activity, demonstrate a catalytic activity of about 1000-fold lower than that of native SOD at pH 7.4. The present results do not indicate any correlation between the kinetics of HO2 center dot/O-2(center dot-), (NO2)-N-center dot, and CO3 center dot- removal by nitroxides and their protective activity against biological oxidative stress and emphasize the importance of target-oriented nitroxides, i.e., interaction between the biological target and specific nitroxides.

  • 37. Goldstein, Sara
    et al.
    Samuni, Amram
    Merenyi, Gabor
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Nuclear Chemistry.
    Kinetics of the reaction between nitroxide and thiyl radicals: Nitroxides as antioxidants in the presence of thiols2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 37, p. 8600-8605Article in journal (Refereed)
    Abstract [en]

    Cyclic nitroxides effectively protect cells, tissues, isolated organs, and laboratory animals from radical-induced damage. The present study focuses on the kinetics and mechanisms of the reactions of piperidine and pyrrolidine nitroxides with thiyl radicals, which are involved in free radical "repair" equilibria, but being strong oxidants can also produce cell damage. Thiyl radicals derived from glutathione, cysteine, and penicillamine were generated in water by pulse radiolysis, and the rate constants of their reactions with 2,2,6,6-tetramethylpiperidine-1-oxyl (TPO), 4-OH-TPO, and 3-carbamoyl-proxyl were determined to be (5-7) x 10(8) M-1 s(-1) at pH 5-7, independent of the structure of the nitroxide and the thiyl radical. It is suggested that the reaction of nitroxide (>NO center dot) with thiyl radical (RS center dot) yields an unstable adduct (>NOSR). The deprotonated form of this adduct decomposes via heterolysis of the N-O bond, yielding the respective amine (>NH) and sulfinic acid (RS(O)OH). The protonated form of the adduct decomposes via homolysis of the N-O bond, forming the aminium radical (>NH center dot+) and sulfinyl radical (RSO center dot), which by subsequent reactions involving thiol and nitroxide produce the respective amine and sulfonic acid (RS(O)(2)OH). Nitroxides that are oxidized to the respective oxoammonium cations (>N+=O) are recovered in the presence of NADH but not in the presence of thiols. This suggests that the reaction of >N+=O with thiols yields the respective amine. Two alternative mechanisms are suggested, where >N+=O reacts with thiolate (RS-) directly generating the adduct >NOSR or indirectly forming >NO center dot and RS center dot, which subsequently together yield the adduct >NOSR. Under physiological conditions the adduct is mainly deprotonated, and therefore nitroxides can detoxify thiyl radicals. The proposed mechanism can account for the protective effect of nitroxides against reactive oxygen- and nitrogen-derived species in the presence of thiols.

  • 38.
    Gong, Zu-Yong
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Duan, Sai
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, Guangjun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Guozhen
    Jiang, Jun
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Optical Excitation in Donor-Pt-Acceptor Complexes: Role of the Structure2016In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, no 20, p. 3547-3553Article in journal (Refereed)
    Abstract [en]

    The optical properties of the Pt complexes in the form of donor-metal-acceptor (D-M-A) were studied at the first-principles level. Calculated results show that for the frontier molecular orbitals (MOs) of a D-M-A structure the energies of unoccupied frontier MO can be mainly determined by the interaction between M and A, whereas the M-A and M-D interactions both determine the energies of occupied frontier MO. By developing a straightforward transition dipole decomposition method, we found that not only the local excitations in D but also those in A can significantly contribute to the charge-transfer (CT) excitation. Furthermore, the calculations also demonstrate that by tuning the dihedral angle between D and A the transition probability can be precisely controlled so as to broaden the spectrum region of photoabsorption. For the D-M-A molecule with a delocalized pi system in A, the CT excitation barely affects the electronic structures of metal, suggesting that the oxidation state of the metal can be kept during the excitation. These understandings for the optical properties of the D-M-A molecule would be useful for the design of dye-sensitized solar cells, photocatalysis, and luminescence systems.

  • 39. Ha, Dang Trinh
    et al.
    Wang, Y.
    Alcami, M.
    Itaelae, E.
    Kooser, K.
    Urpeainen, S.
    Huels, Michael A.
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Kukk, E.
    Martin, F.
    Fragmentation Dynamics of Doubly Charged Methionine Phase2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 8, p. 1374-1383Article in journal (Refereed)
    Abstract [en]

    The dependence of the fragmentation of doubly charged gas-phase methionine (C5H11NO2S) on the electronic-state character of the parent ion is studied experimentally by energy-resolved electron ion-ion coincidence spectroscopy. The parent dication electronic states are populated by Auger transitions following site-specific sulfur 2p core ionization. Two fragmentation channels are observed to be strongly dependent on the electronic states with vacancies in weakly bound molecular orbitals. All-electron calculations are applied to assign doubly charged final states of sulfur 2p core ionized methionine. In addition, the Car-Parrinello method is applied to model fragmentation dynamics of doubly charged methionine molecules with various initial temperatures to understand the typical characteristics of the molecular dissociation and partly to support the interpretation of experimental data.

  • 40. Hede, Thomas
    et al.
    Murugan, Natarajan Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Kongsted, Jacob
    Leck, Caroline
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Simulations of Light Absorption of Carbon Particles in Nanoaerosol Clusters2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 10, p. 1879-1886Article in journal (Refereed)
    Abstract [en]

    Black carbon soot (BS) is considered to be the second most contributing organic matter next to carbon dioxide for the global warming effect. There is, however, so far no consensus on the quantitative warming effect due to the increased distribution of black carbon in the atmosphere. A recent report (Science 2012, 337, 1078) suggests that due to BS there is only a few percentage enhancement in absorption of BS-immersed aerosols. To get proper interpretation of the available experimental data, it becomes essential to obtain details of the microscopic origin of the absorption and scattering processes of the aerosol clusters due to the presence of soot. However, so far, due to the large spatial scale and the need for a quantum mechanical description of the particles involved in the absorption and scattering, this quest has posed an insurmountable challenge. In the present work we propose the use of a multiscale integrated approach based on molecular dynamics and a quantum mechanical molecular mechanical method to model the optical property of molecules immersed in nanosized aerosol particles. We choose fluoranthene (FA) with varying cis-pinonic acid (CPA) impurity concentration as an illustrative example of application. We observe that normally FA tends to be on the surface of the nanoaerosols but in the presence of CPA impurities its spatial location changes to a core aggregate to some extent. We find that the absorption maximum is only slightly red-shifted in the presence of increased CPA concentrations and that the oscillator strengths are not altered significantly. The comparable values for the oscillator strengths of all the low energy excitations suggest that the absorption enhancement of the aerosol due to BS will not be substantial, which is in line with the recent experimental report in Science.

  • 41.
    Hermansson, Kersti
    KTH, Superseded Departments, Biotechnology.
    Blue-shifting hydrogen bonds2002In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 106, no 18, p. 4695-4702Article in journal (Refereed)
    Abstract [en]

    In this paper we put forward the idea that the various improper, blue-shifting hydrogen bond systems discussed in the literature are all of essentially the same nature and occur because of three necessary circumstances: (i) the presence of a negative dipole moment derivative, dmu(0)/dr(XH), for the isolated H-bond donor molecule; (ii) the interaction between such a molecule and any electron density concentration on the H-bond acceptor ( pi-system density, lone-pair density, ionic charge,...) which at large intermolecular distances gives rise to a field-dominated, modest vibrational blue shift; (iii) an additional blue shift due to electronic exchange overlap. The negative dipole moment derivative is a necessary but not sufficient condition for the formation of a blue-shifted H-bond: thus, the blue-shifting CH4, F3CH, and Cl3CH molecules and their relatives can also give rise to normal, red-shifted H-bonds. This is a logical extension of the blue-shifting property and occurs when the electric field from the acceptor is sufficiently strong at the intermolecular equilibrium distance (e.g., for F- and Cl- acceptors).

  • 42. Himo, Fahmi
    Density functional theory study of the beta-carotene radical cation2001In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 105, no 33, p. 7933-7937Article in journal (Refereed)
    Abstract [en]

    The hybrid density functional theory method B3LYP is employed to study the beta -carotene radical cation. The radical is characterized by means of its geometry, spin distribution, and isotropic and anisotropic hyperfine coupling constants. It is shown that the spin is delocalized over the whole pi -conjugated system, including the double bonds of the headgroups. This delocalization results in methyl hyperfine coupling constants lower than 9 MHz, in excellent agreement with recent experimental couplings of the carotene radical in Photosystem II and in vitro, but in conflict with previous theoretical calculations. It is also demonstrated that rotation of the headgroups can affect the properties of the radical, in particular the spin delocalization to the ring.

  • 43.
    Himo, Fahmi
    et al.
    KTH, Superseded Departments, Biotechnology.
    Noodleman, L.
    Blomberg, M. R. A.
    Siegbahn, P. E. M.
    Relative acidities of ortho-substituted phenols, as models for modified tyrosines in proteins2002In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 106, no 37, p. 8757-8761Article in journal (Refereed)
    Abstract [en]

    The effects of a variety of ortho-substituents (CH3, OH, OCH3, SH, SCH3, NH2, NO2, F, Cl, CN, and imidazole) on the acidity of phenol are investigated using hybrid density functional theory. Substitutions are made at the ortho-position to model modified tyrosine residues found in enzymes. Although the experimental trends are reproduced, the calculations tend to exaggerate the substituent effects. It is shown that the cysteine cross-link to tyrosine, present in the radical enzyme galactose oxidase, has a small effect on the pK(a) of the residue. The histidine cross-link present in cytochrome c oxidase, on the other hand, will contribute more to. lower the pKa. Comparing the substituent effects on the O-H bond strengths and the acidities, no simple correlation is found between the two.

  • 44. Hua, Shugui
    et al.
    Hua, Weijie
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Li, Shuhua
    An Efficient Implementation of the Generalized Energy-Based Fragmentation Approach for General Large Molecules2010In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 114, no 31, p. 8126-8134Article in journal (Refereed)
    Abstract [en]

    An efficient implementation of the generalized energy-based fragmentation (GEBF) approach (Li, W.; Li, S.; Jiang, Y. J Phys. Chem. A 2007, 111, 2193) for treating a wide range of large molecules is presented. In this implementation, the fragmentation process can be automatically done for a general molecule, with only some functional groups defined by users. A new and fast scheme is designed for the generation of various subsystems and the derivation of their coefficients. The newly implemented GEBF approach has been applied to several large molecules including proteins, nucleic acids, and supermolecules with fused aromatic rings. Test calculations within the Hartree-Fock (HF) and density functional theory (DFT) framework demonstrate that the GEBF approach can provide reasonably accurate ground-state energies and optimized structures, which are in good agreement with those from conventional HF or DFT calculations. The GEBF approach implemented in this work can now be employed by nonexpert users to compute energies, optimized structures, and some molecular properties at various ab initio levels for a broad range of large molecules on ordinary PC workstations.

  • 45.
    Hua, Weijie
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Tian, Guangjun
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fronzoni, Giovanna
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Stener, Mauro
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Fe L-Edge X-ray Absorption Spectra of Fe(II) Polypyridyl Spin Crossover Complexes from Time-Dependent Density Functional Theory2013In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, no 51, p. 14075-14085Article in journal (Refereed)
    Abstract [en]

    L-edge near-edge X-ray fine structure spectroscopy (NEXAFS) has become a powerful tool to study the electronic structure and dynamics of metallo-organic and biological compounds in solution. Here, we present a series of density functional theory calculations of Fe L-edge NEXAFS for spin crossover (SCO) complexes within the time-dependent framework. Several key factors that control the L-edge excitations have been carefully examined using an Fe(II) polypyridyl complex [Fe(tren(py)(3))](2+) (where tren(py)(3) = tris(2-pyridylmethyliminoethyl)amine) as a model system. It is found that the electronic spectra of the low-spin (LS, singlet), intermediate-spin (IS, triplet), and high-spin (HS, quintet) states have distinct profiles. The relative energy positions, but not the spectral profiles, of different spin states are sensitive to the choice of the functionals. The inclusion of the vibronic coupling leads to almost no visible change in the resulting NEXAFS spectra because it is governed only by low-frequency modes of less than 500 cm(-1). With the help of the molecular dynamics sampling in acetonitrile at 300 K, our calculations reveal that the thermal motion can lead to a noticeable broadening of the spectra. The main peak position is strongly associated with the length of the Fe-N bond.

  • 46. Huthwelker, T.
    et al.
    Malmström, Maria E.
    KTH, Superseded Departments, Chemical Engineering and Technology. Max-Planck-Institut für Chemie, Germany.
    Helleis, F.
    Moortgat, G. K.
    Peter, T.
    Kinetics of HCI uptake on ice at 190 and 203 K: implications for the microphysics of the uptake process2004In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 108, no 30, p. 6302-6318Article, review/survey (Refereed)
    Abstract [en]

    The uptake of HCl on vapor-deposited ice is investigated for HCl partial pressure p from 2 x 10(-8) to 10(-5) Torr at temperatures of 190 and 203 K in an especially designed Knudsen cell experiment. Two kinetic regimes can be distinguished experimentally: a long-lasting tailing which accounts for the major amount of the overall uptake and follows diffusion-like kinetics, gamma(t) proportional to t(-1/2) (gamma, uptake coefficient; t, time), and an initial period, where the uptake is higher than predicted by diffusion-like kinetics. The uptake kinetics are analyzed using analytical equations and also by full numerical simulation of simultaneous adsorption onto the surface and diffusion into the bulk. We derive the quantity H-d*D-1/2 (H-d*, effective Henry's law constant, D diffusion constant) and find H-d*D-1/2 proportional to p(-1/2), which implies that HCl dissociates upon uptake. The results for both analysis methods closely coincide. We suggest the use of a semiempirical parametrization for the total HCl uptake (molecules per geometric surface area) on vapor-deposited ice films as time dependent function n(t, p) = n(resid)(P) + C(T)(tp)(1/2), where C(T) is a constant which depends on temperature only. The compatibility of the residual, nondiffusive uptake, n(resid), with various adsorption isotherms is discussed. The analysis suggests that the experimentally observed diffusion-like kinetics dominates the overall trace gas uptake after a brief initial period. The diffusion-like kinetics must be considered when analyzing uptake experiments and when making applications to natural ice.

  • 47. Itala, Eero
    et al.
    Levola, Helena
    Ha, Dang Trinh
    Kooser, Kuno
    Rachlew, Elisabeth
    KTH, School of Engineering Sciences (SCI), Physics, Atomic and Molecular Physics.
    Kukk, Edwin
    Photofragmentation of Serine Following C 1s Core Ionization-Comparison with Cysteine2016In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, no 28, p. 5419-5426Article in journal (Refereed)
    Abstract [en]

    Photofragmentation pathways of doubly ionized serine molecules are investigated and compared with those of cysteine. The main motivation for the study is to investigate if an atomic substitution within the same group of elements, namely, replacing sulfur (in cysteine) with oxygen (in serine), causes a major change in the C 1s core ionization induced dissociation pattern in the molecules of an otherwise identical structure. The results show that in serine there is a single completely dominant fragmentation channel producing the (CNH2-4+, COH1-3+) pairs, whereas in cysteine there are also many other fragmentation channels. The employed experimental method was the photoelectron-photoion-photoion coincidence (PEPIPICO) technique combined with synchrotron radiation tuned to ionize desired core levels. Molecular dynamics calculations were also carried out in order to extract information on the fragmentation and the neutral final fragments.

  • 48. Jalilehvand, F.
    et al.
    Maliarik, M.
    Mink, J.
    Sandstrom, M.
    Ilyukhin, A.
    Glaser, Julius
    KTH, Superseded Departments, Chemistry.
    Structure studies of dimeric Pt-2(CN)(10) (4-) pentacyanoplatinum(III) and monomeric pentacyanoplatinum(IV) complexes by EXAFS, vibrational spectroscopy, and X-ray crystallography2002In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 106, no 14, p. 3501-3516Article in journal (Refereed)
    Abstract [en]

    The Structures of the dimeric bispentacyanoplatinate (III) (Pt-Pt) complex [Pt-2(CN)(10)](4-) and the pentacyanoplatinuni(IV) species [Pt(CN)(5)(OH)](2-), [Pt(CN)(5)(H2O)](-), and [Pt(CN)(5)I](2-) have been studied in aqueous solution by the EXAFS technique. A nonsupported Pt-Pt bond, 2.73(l) Angstrom, connects two Pt(CN)(5) entities in the dimer. Normal coordinate analyses have been made on the basis of the Raman spectra, and the force constants have been used for discussions of the bonding. The metal-metal stretching force constants for the [Pt-2(CN)(10)](4-) Complex, the [(NC)(5)Pt-TI(CN)(n)](n-) (n = 1, 2, and 3) complexes, and some other dimetallic complexes have been correlated with the metal-metal bond distances. In the [Pt(CN)(5)X](n-) complexes, the mean Pt-C bond distance of the pentacyanoplatinum group was found to increase, and the corresponding Pt-C force constants were found to decrease, with increasing donor ability of the ligand X in the order X = H2O, OH, I, and Pt(CN)(5). The crystal structures of the compounds Tl-2[Pt(CN)(5)(OH)] and K-2[Pt(CN)(5)I].0.6H(2)O were determined by single-crystal X-ray diffraction techniques and used for comparisons with the EXAFS models. The Pt-I bond distance of the [Pt(CN)(5)I](2)- complex is 2.676(2) Angstrom in the crystal structure and 2.66(1) Angstrom in solution by EXAFS. A method is described for estimating the force constant for the metal-metal bond stretch in dimetallic complexes with heavy metal atoms, based on the use of an effective spectroscopic mass of the metal atoms in a diatomic model. The 18-electron rule is found to be useful for rationalizing the structures of the metal-metal bonded cyano complexes and a guideline in searching for metal cyano complexes analogous to those currently described.

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

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

  • 50.
    Jonsson, Mats
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Nuclear Chemistry.
    Thermochemical Properties of Peroxides and Peroxyl Radicals1996In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 100, p. 6814-6818Article in journal (Refereed)
123 1 - 50 of 115
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