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  • 1. Abu-samha, M.
    et al.
    Børve, K. J.
    Harnes, J.
    Bergersen, Henrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och materialvetenskap.
    What Can C1s Photoelectron Spectroscopy Tell about Structure and Bonding in Clusters of Methanol and Methyl Chloride?2007Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 37, s. 8903-8909Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Single-component clusters of methanol and methyl chloride have been produced by adiabatic expansion, and their carbon Is photoelectron spectra were recorded using synchrotron radiation and a high-resolution electron analyzer. The experimental spectra are interpreted by means of theoretical models based on molecular dynamics simulations. The data are used to explore to what extent core-level photoelectron spectra may provide information on the bonding mechanism and the geometric structure of clusters of polar molecules. The results indicate that the cluster-to-monomer shift in ionization energy and also the width of the cluster peak may be used to distinguish between hydrogen bonding and weaker electrostatic interactions. Moreover, the larger width of the cluster peak in methanol clusters as compared to methyl chloride clusters is partly due to the structured surface of methanol clusters. Theoretical modeling greatly facilitates the analysis of core-level photoelectron spectra of molecular clusters.

  • 2.
    Ahlstrand, Emma
    et al.
    Linnus Univ, Dept Chem & Biomed Sci, S-39182 Kalmar, Sweden.;Linnus Univ, Ctr Biomat Chem, S-39182 Kalmar, Sweden..
    Hermansson, Kersti
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Strukturkemi.
    Friedman, Ran
    Linnus Univ, Dept Chem & Biomed Sci, S-39182 Kalmar, Sweden.;Linnus Univ, Ctr Biomat Chem, S-39182 Kalmar, Sweden..
    Interaction Energies in Complexes of Zn and Amino Acids: A Comparison of Ab Initio and Force Field Based Calculations2017Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 121, nr 13, s. 2643-2654Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Zinc plays important roles in structural stabilization of proteins, eniyine catalysis, and signal transduction. Many Zn binding sites are located at the interface between the protein and the cellular fluid. In aqueous solutions, Zn ions adopt an octahedral coordination, while in proteins zinc can have different coordinations, with a tetrahedral conformation found most frequently. The dynainics of Zn binding to proteins and the formation of complexes that involve Zn are dictated by interactions between Zn and its binding partners. We calculated the interaction energies between Zn and its ligands in complexes that mimic protein binding sites and in Zn complexes of water and one or two amino acid moieties, using quantum mechanics (QM) and molecular mechanics (MM). It was found that MM calculations that neglect or only approximate polarizability did not reproduce even the relative order of the QM interaction energies in these complexes. Interaction energies calculated with the CHARMM-Diode polarizable force field agreed better with the ab initio results,:although the deviations between QM and MM were still rather large (40-96 kcallmol). In order to gain further insight into Zn ligand interactions, the free energies of interaction were estimated by QM calculations with continuum solvent representation, and we performed energy decomposition analysis calculations to examine the characteristics of the different complexes. The ligand-types were found to have high impact on the relative strength of polarization and electrostatic interactions. Interestingly, ligand ligand interactions did not play a significant role in the binding of Zn. Finally) analysis of ligand exchange energies suggests that carboxylates could be exchanged with water molecules, which explains the flexibility in Zn:binding dynamics. An exchange between earboxylate (Asp/Glii) and imidazole (His) is less likely.

  • 3. Aziz, Emad F
    et al.
    Gråsjö, Johan
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaci.
    Forsberg, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Mjukröntgenfysik.
    Andersson, Egil
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Mjukröntgenfysik.
    Söderström, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Fysiska institutionen. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik.
    Duda, Laurent
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Fysiska institutionen.
    Zhang, Wenhua
    Yang, Jinglong
    Eisebitt, Stefan
    Bergström, Christel
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Farmaceutiska fakulteten, Institutionen för farmaci.
    Luo, Yi
    Nordgren, Joseph
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och materialvetenskap, Yt- och gränsskiktsvetenskap.
    Eberhardt, Wolfgang
    Rubensson, Jan-Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Fysiska institutionen.
    Photoinduced Formation of N2 Molecules in Ammonium Compounds2007Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 39, s. 9662-9669Artikel i tidskrift (Refereegranskat)
    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 N2 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 N2 molecules which are bound in the sample. The generality and implications of these results are briefly discussed.

  • 4. Barone, Giampaolo
    et al.
    Mastalerz, Remigius
    Reiher, Markus
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Nuclear quadrupole moment of Sn-1192008Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, nr 7, s. 1666-1672Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Second-order scalar-relativistic Douglas-Kroll-Hess density functional calculations of the electric field gradient, including an analytic correction of the picture change error, were performed for 34 tin compounds of which molecular structures and Sn-119 Mossbauer spectroscopy parameters are experimentally known. The components of the diagonalized electric field gradient tensor, V-xx,V-yy, V-zz, were used to determine the quantity V, which is proportional to the nuclear quadrupole splitting parameter Delta E. The slope of the linear correlation plot of the experimentally determined Delta E parameter versus the corresponding calculated V data allowed us to obtain an absolute value of the nuclear quadrupole moment Q of Sn-119 equal to Q = 13.2 +/- 0.1 fm(2). This is about 11% larger than the picture-change-error-affected value and in good agreement with previous estimates of the picture change error in compounds of similar atomic charge. Moreover, despite the variety of the tin compounds considered in this study, the new result is in excellent agreement with the previously determined most accurate value of Q for Sn-119 of Q = 12.8 +/- 0.7 fm(2), but with a noticeably narrower error bar. The reliability of the calibration method in the calculation of the Delta E parameter of tin compounds is within a margin of +/- 0.3 mm s(-1) when compared to experimental data and does not depend on the inclusion of the picture change correction in the density functional calculations but is essentially determined by the use of an atomic natural orbital relativistic core-correlated basis set for the description of the core electron density. The results obtained suggest that the present picture-change-corrected Douglas-Kroll-Hess approach provides reliable electric field gradients in the case of closed-shell metal compounds involving elements up to the fifth row of the periodic table for which spin-orbit coupling is negligible.

  • 5.
    Bergson, Göran
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för biokemi och organisk kemi, Organisk kemi II.
    Linderberg, Jan
    Is a Proposed Reaction Mechanism Free from Unnecessary Assumptions?: Occam's Razor Applied in a Mathematical Way To Complex First-Order Reaction Systems2008Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, nr 112, s. 4235-4240Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Following Occam's principle, a proposed reaction mechanism should not contain assumptions about the existence of reactive intermediates and reaction paths that are unnecessary for a full description and interpretation of the available facts. A mechanism refers, in this paper, to a proposed reaction scheme or network that represents the reactions supposed to be going on in a complex reaction system with observable species as well as unobservable reactive intermediates. The scope is limited here to (pseudo) first-order reactions and the steady-state approximation is invoked in order to relate unknown mechanistic rate constants to experimentally determined ones, and, when available, theoretically calculated quantities. When the resulting, nonlinear system of equations admits a unique solution within a physically reasonable domain, it is concluded that the reaction mechanism fulfills Occam's principle. Otherwise, there are many or no solutions. No subjective or qualitative arguments enter the procedure and the outcome is not negotiable.

  • 6. Bickelhaupt, F Matthias
    et al.
    Nagle, Jeffrey K
    Klemm, William L
    Role of s-p orbital mixing in the bonding and properties of second-period diatomic molecules.2008Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, nr 11, s. 2437-46Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Qualitative molecular orbital theory is widely used as a conceptual tool to understand chemical bonding. Symmetry-allowed orbital mixing between atomic or fragment orbitals of different energies can greatly complicate such qualitative interpretations of chemical bonding. We use high-level Amsterdam Density Functional calculations to examine the issue of whether orbital mixing for some familiar second-row homonuclear and heteronuclear diatomic molecules results in net bonding or antibonding character for a given molecular orbital. Our results support the use of slopes of molecular orbital energy versus bond distance plots (designated radial orbital-energy slope: ROS) as the most useful criterion for making this determination. Calculated atomic charges and frontier orbital properties of these molecules allow their acid-base chemistry, including their reactivities as ligands in coordination chemistry, to be better understood within the context of the Klopman interpretation of hard and soft acid-base theory. Such an approach can be extended to any molecular species.

  • 7.
    Borg, Anders
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Eriksson, Leif
    Durbeej, Bo
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Electron-transfer induced repair of 6-4 photoproducts in DNA: A computational study2007Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 12, s. 2351-2361Artikel i tidskrift (Refereegranskat)
    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.

  • 8.
    Borg, O. Anders
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Godinho, Sofia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Lundqvist, Maria
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Lunell, Sten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Persson, Petter
    A Computational Study on the Lowest Triplet State of Ruthenium Polypyridyl Complexes used in Artificial Photosynthesis2008Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, nr 19, s. 4470-4476Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The potential energy surfaces of the first excited triplet state of some ruthenium polypyridyl complexes were investigated by means of density functional theory. Focus was placed on the interaction between the geometrical changes accompanying the photoactivity of these complexes when used as antenna complexes in artificial photosynthesis and dye-sensitized solar cells and the accompanying changes in electronic structure. The loss process (3)MLCT --> (3)MC can be understood by means of ligand-field splitting, traced down to the coordination of the central ruthenium atom.

  • 9.
    Brumboiu, Iulia Emilia
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori. KTH Royal Inst Technol, Dept Theoret Chem & Biol, S-10691 Stockholm, Sweden; Korea Adv Inst Sci & Technol, Dept Chem, Daejeon 34141, South Korea.
    Haldar, Soumyajyoti
    Lüder, Johann
    Eriksson, Olle
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Herper, Heike C.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Brena, Barbara
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Sanyal, Biplab
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Ligand effects on the linear response Hubbard U: The case of transition metal phthalocyanines2019Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 123, nr 14, s. 3214-3222Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    It is established that density functional theory (DFT) + U is a better choice compared to DFT for describing the correlated electron metal center in organometallics. The value of the Hubbard U parameter may be determined from linear response, either by considering the response of the metal site alone or by additionally considering the response of other sites in the compound. We analyze here in detail the influence of ligand shells of increasing size on the U parameter calculated from the linear response for five transition metal phthalocyanines. We show that the calculated multiple-site U is larger than the single-site U by as much as 1 eV and the ligand atoms that are mainly responsible for this difference are the isoindole nitrogen atoms directly bonded to the central metal atom. This suggests that a different U value may be required for computations of chemisorbed molecules compared to physisorbed and gas-phase cases.

  • 10.
    Brumboiu, Iulia Emilia
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi.
    Totani, Roberta
    de Simone, Monica
    Coreno, Marcello
    Grazioli, Cesare
    Lozzi, Luca
    Herper, Heike C
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Sanyal, Biplab
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Eriksson, Olle
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Puglia, Carla
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik.
    Brena, Barbara
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Materialteori.
    Elucidating the 3d Electronic Configuration in Manganese Phthalocyanine2014Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, nr 5, s. 927-932Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    To shed light on the metal 3d electronic structure of manganese phthalocyanine, so far controversial, we performed photoelectron measurements both in the gas phase and as thin film. With the purpose of explaining the experimental results, three different electronic configurations close in energy to one another were studied by means of density functional theory. The comparison between the calculated valence band density of states and the measured spectra revealed that in the gas phase the molecules exhibit a mixed electronic configuration, while in the thin film, manganese phthalocyanine finds itself in the theoretically computed ground state, namely, the b2g1eg3a1g1b1g0 electronic configuration.

  • 11.
    Ciavardini, Alessandra
    et al.
    Univ Roma La Sapienza, Dipartimento Chim & Tecnol Farmaco, Ple A Moro 5, I-00185 Rome, Italy;Univ Roma Tor Vergata, Dipartimento Sci & Tecnol Chim, Via Ric Sci, I-00133 Rome, Italy;CERIC ERIC, Basovizza Area Sci Pk, I-34149 Trieste, Italy.
    Coreno, Marcello
    ISM CNR, Basovizza Area Sci Pk, I-34149 Trieste, Italy;Elettra Sincrotrone Trieste, Ss 14,Km 163,5, I-34149 Trieste, Italy.
    Callegari, Carlo
    Elettra Sincrotrone Trieste, Ss 14,Km 163,5, I-34149 Trieste, Italy.
    Spezzani, Carlo
    Elettra Sincrotrone Trieste, Ss 14,Km 163,5, I-34149 Trieste, Italy.
    De Ninno, Giovanni
    Elettra Sincrotrone Trieste, Ss 14,Km 163,5, I-34149 Trieste, Italy;Univ Nova Gor, Lab Quantum Opt, Vipayska 11c, SI-5270 Ajdovscina, Slovenia.
    Ressel, Barbara
    Elettra Sincrotrone Trieste, Ss 14,Km 163,5, I-34149 Trieste, Italy;Univ Nova Gor, Lab Quantum Opt, Vipayska 11c, SI-5270 Ajdovscina, Slovenia.
    Grazioli, Cesare
    IOM CNR, Lab TASV, Basovizza SS-14,Km 163-5, I-34012 Trieste, Italy.
    de Simone, Monica
    IOM CNR, Lab TASV, Basovizza SS-14,Km 163-5, I-34012 Trieste, Italy.
    Kivimäki, Antti
    IOM CNR, Lab TASV, Basovizza SS-14,Km 163-5, I-34012 Trieste, Italy;Lund Univ, MAX 4 Lab, POB 118, SE-22100 Lund, Sweden.
    Miotti, Paolo
    IFN CNR, Padova Res Unit, Via Trasea 7, I-35131 Padua, Italy.
    Frassetto, Fabio
    IFN CNR, Padova Res Unit, Via Trasea 7, I-35131 Padua, Italy.
    Poletto, Luca
    IFN CNR, Padova Res Unit, Via Trasea 7, I-35131 Padua, Italy.
    Puglia, Carla
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik.
    Fornarini, Simonetta
    Univ Roma La Sapienza, Dipartimento Chim & Tecnol Farmaco, Ple A Moro 5, I-00185 Rome, Italy.
    Pezzella, Marco
    Univ Roma La Sapienza, Dipartimento Chim, Ple A Moro 5, I-00185 Rome, Italy.
    Bodo, Enrico
    Univ Roma La Sapienza, Dipartimento Chim, Ple A Moro 5, I-00185 Rome, Italy.
    Piccirillo, Susanna
    Univ Roma Tor Vergata, Dipartimento Sci & Tecnol Chim, Via Ric Sci, I-00133 Rome, Italy.
    Ultra-Fast-VUV Photoemission Study of UV Excited 2-Nitrophenol2019Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 123, nr 7, s. 1295-1302Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The initial deactivation pathways of gaseous 2-nitrophenol excited at 268 nm were investigated by time-resolved photoelectron spectroscopy (TRPES) with femtosecond-VUV light, produced by a monochromatized high harmonic generation source. TRPES allowed us to obtain new, valuable experimental information about the ultrafast excited-state dynamics of 2-nitrophenol in the gas phase. In accord with recent ab initio on-the-fly nonadiabatic molecular dynamic simulations, our results validate the occurrence of an ultrafast intersystem crossing leading to an intermediate state that decays on a subpicosecond time scale with a branched mechanisms. Two decay pathways are experimentally observed. One probably involves proton transfer, leading to the most stable triplet aci-form of 2-nitrophenol; the second pathway may involve OH rotation. We propose that following intersystem crossing, an ultrafast fragmentation channel leading to OH or HONO loss could also be operative.

  • 12.
    Dahlstrand, Christian
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Fysikalisk-organisk kemi.
    Rosenberg, Martin
    Department of Chemistry, University of Copenhagen.
    Kilså, Kristine
    Department of Chemistry, University of Copenhagen.
    Ottosson, Henrik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Fysikalisk-organisk kemi.
    Exploration of the π-Electronic Structure of Singlet, Triplet, and Quintet States of Fulvenes and Fulvalenes Using the Electron Localization Function2012Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, nr 20, s. 5008-5017Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The singlet ground states and lowest triplet states of penta- and heptafulvene, their benzannulated derivatives, as well as the lowest quintet states of pentaheptafulvalenes, either the parent compound or compounds in which the two rings are intercepted by either an alkynyl or a phenyl segment, were investigated at the (U)OLYP/6-311G(d,p) density functional theory level. The influence of (anti)-aromaticity was analyzed by the structure-based aromaticity index HOMA, the harmonic oscillator model of aromaticity. The extent of (anti)aromatic character was also evaluated in terms of the pi-electron (de)localization as measured by the pi component of the electron localization function (ELF pi). The natural atomic orbital (NAO) occupancies were calculated in order to evaluate the degree of pi-electron shift caused by the opposing electron-counting rules for aromaticity in the electronic ground state (S-0; Hiickel's rule) and the first pi pi* excited triplet state (T-1; Baird's rule). Pentaheptafulvalene (5) shows a shift of 0.5 pi electrons from the 5-ring to the 7-ring when going from the S-0 state to the lowest quintet state (Qu(1)). The pentaheptafulvalene 5 and [5.6.7]quinarene 7 were also investigated in their 90 degrees twisted conformations. From our study it is apparent that excitation localization in fulvalenes, but not in fulvenes, to a substantial degree is determined by aromaticity localization to triplet biradical 4n pi-electron cycles. Isolated benzene rings in these compounds tend to remain as closed-shell 6 pi-electron cycles.

  • 13. De Vico, Luca
    et al.
    Liu, Ya-Jun
    Krogh, Jesper Wisborg
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Chemiluminescence of 1,2-dioxetane. Reaction mechanism uncovered2007Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 32, s. 8013-8019Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The thermal decomposition of 1,2-dioxetane and the associated production of chemiluminescent products, model for a wide range of chemiluminescent reactions, has been studied at the multistate multiconfigurational second-order perturbation level of theory. This study is in qualitative and quantitative agreement with experimental observations with respect to the activation energy and the observed increase of triplet and singlet excited products as substituents are added to the parent molecule. The, previously incomplete, reaction mechanism of the chemiluminescence of 1,2-dioxetane is now rationalized and described as mainly due to a particular form of entropic trapping.

  • 14.
    Dinér, Peter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Syntetisk organisk kemi.
    Superacid-Promoted Ionization of Alkanes Without Carbonium Ion Formation: A Density Functional Theory Study2012Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, nr 40, s. 9979-9984Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The carbonium ion has been suggested to be the intermediate in superacid-promoted reactions (SbF5-HF) such as hydrogen-deuterium exchange and in the electrophilic C-H cleavage into hydrogen and the carbenium ion. In this study, the superacid-promoted C-H cleavage into hydrogen and the carbenium ion was studied using density functional theory (B3LYP and M062X) and ab initio methods (MP2 and CCSD). The calculations suggest that the superacid-promoted C-H cleavage proceeds via a concerted transition state leading to hydrogen (H-2) and the carbenium ion without the formation of the elusive carbonium ion. The reactivity for the superacid promoted C-H cleavage decreases upon going from isobutane (tertiary) > propane (secondary) > isobutane (primary) > propane (primary) > ethane >> methane.

  • 15. Dourado, Daniel F. A. R.
    et al.
    Fernandes, Pedro Alexandrino
    Mannervik, Bengt
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Ramos, Maria Joao
    Isomerization of Delta(5)-Androstene-3,17-dione into Delta(4)-Androstene-3, 17-dione Catalyzed by Human Glutathione Transferase A3-3: A Computational Study Identifies a Dual Role for Glutathione2014Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, nr 31, s. 5790-5800Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Glutathione transferases (GSTs) are important enzymes in the metabolism of electrophilic xenobiotic and endobiotic toxic compounds. In addition, human GST A3-3 also catalyzes the double bond isomerization of Delta 5-androstene-3,17-dione (Delta(5)-AD) and Delta(5)-pregnene-3,20-dione (Delta(5)-PD), which are the immediate precursors of testosterone and progesterone. In fact, GST A3-3 is the most efficient human enzyme known to exist in the catalysis of these reactions. In this work, we have used density functional theory (DFT) calculations to propose a refined mechanism for the isomerization of Delta(5)-AD catalyzed by GST A3-3. In this mechanism the glutathione (GSH) thiol and Tyr9 catalyze the proton transfer from the Delta(5)-AD C4 atom to the Delta(5)-AD C6 atom, with a rate limiting activation energy of 15.8 kcal.mol(-1). GSH has a dual function, because it is also responsible for stabilizing the negative charge that is formed in the 03 atom of the enolate intermediate. The catalytic role of Tyr9 depends on significant conformational rearrangements of its side chain. Neither of these contributions to catalysis has been observed before. Residues Phe10, Leul11, Ala 208, and Ala 216 complete the list of the important catalytic residues. The mechanism detailed here is based on the GST A3-3:GSH:Delta(4)-AD crystal structure and is consistent with all available experimental data.

  • 16. Fernández García-Prieto, F.
    et al.
    Aguilar, M. A.
    Fdez. Galván, Ignacio
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Muñoz-Losa, A.
    Olivares del Valle, F. J.
    Sánchez, M. L.
    Martín, M. E.
    Substituent and Solvent Effects on the UV–vis Absorption Spectrum of the Photoactive Yellow Protein Chromophore2015Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, nr 21, s. 5504-5514Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Solvent effects on the UV–vis absorption spectra and molecular properties of four models of the photoactive yellow protein (PYP) chromophore have been studied with ASEP/MD, a sequential quantum mechanics/molecular mechanics method. The anionic trans-p-coumaric acid (pCA), thioacid (pCTA), methyl ester (pCMe), and methyl thioester (pCTMe) derivatives have been studied in gas phase and in water solution. We analyze the modifications introduced by the substitution of sulfur by oxygen atoms and hydrogen by methyl in the coumaryl tail. We have found some differences in the absorption spectra of oxy and thio derivatives that could shed light on the different photoisomerization paths followed by these compounds. In solution, the spectrum substantially changes with respect to that obtained in the gas phase. The n → π1* state is destabilized by a polar solvent like water, and it becomes the third excited state in solution displaying an important blue shift. Now, the π → π1* and π → π2* states mix, and we find contributions from both transitions in S1 and S2. The presence of the sulfur atom modulates the solvent effect and the first two excited states become practically degenerate for pCA and pCMe but moderately well-separated for pCTA and pCTMe.

  • 17. Gassner, Helmut
    et al.
    Probst, Michael
    Lauenstein, Albert
    Hermansson, Kersti
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Kemiska institutionen.
    Representation of intermolecular potential functions by neural networks1998Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 102, nr 24, s. 4596-4605Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have investigated how a neural network representation of intermolecular potential functions can be used to elevate some of the problems commonly encountered during fitting and application of analytical potential functions in computer simulations. For this purpose we applied feed-forward networks of various sizes to reproduce the three-body interaction energies in the system H(2)O-Al(3+)-H(2)O. In this highly polarizable system the three-body interaction terms are necessary for an accurate description of the system, and it proved difficult to fit an analytical function to them. Subsequently we performed Monte Carlo simulations on an Al(3+ )ion dissolved in water and compared the results obtained using the neural network type potential function with those using a conventional analytical potential. The performance and results of our calculations lead to the conclusion that, for suitable systems, the advantages of a neural network type representation of potential functions as a model-independent and "semiautomatic" potential function outweigh the disadvantages in computing speed and lack of interpretability.

  • 18.
    Guo, Meiyuan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Erik, Källman
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Sørensen, Lasse Kragh
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Delcey, Mickaël G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. Lawrence Berkeley Natl Lab, Div Chem Sci, Berkeley, CA 94720 USA.; Univ Calif Berkeley, Kenneth S Pitzer Ctr Theoret Chem, Dept Chem, Berkeley, CA 94720 USA.
    Pinjari, Rahul V.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi. School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, Maharashtra, India..
    Lundberg, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Molecular orbital simulations of metal 1s2p resonant inelastic X-ray scattering2016Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, nr 29, s. 5848-5855Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    For first-row transition metals, high-resolution 3d electronic structure information can be obtained using resonant inelastic X-ray scattering (RIXS). In the hard X-ray region, a K pre-edge (1s -> 3d) excitation can be followed by monitoring the dipole-allowed K alpha (2p -> 1s) or K beta (3p -> 1s) emission, processes labeled 1s2p or 1s3p RIXS. Here the restricted active space (RAS) approach, which is a molecular orbital method, is used for the first time to study hard X-ray RIXS processes. This is achieved by including the two sets of core orbitals in different partitions of the active space. Transition intensities are calculated using both first- and second-order expansions of the wave vector, including, but not limited to, electric dipoles and quadrupoles. The accuracy of the approach is tested for 1s2p RIXS of iron hexacyanides [Fe(CN)(6)](n-) in ferrous and ferric oxidation states. RAS simulations accurately describe the multiplet structures and the role of 2p and 3d spin-orbit coupling on energies and selection rules. Compared to experiment, relative energies of the two [Fe(CN)(6)](3-) resonances deviate by 0.2 eV in both incident energy and energy transfer directions, and multiplet splittings in [Fe(CN)(6)](4-) are reproduced within 0.1 eV. These values are similar to what can be expected for valence excitations. The development opens the modeling of hard X-ray scattering processes for both solution catalysts and enzymatic systems.

  • 19.
    Hamberg, Mathias
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Högenergifysik.
    Kashperka, Iryna
    Thomas, Richard D.
    Roueff, Evelyne
    Zhaunerchyk, Vitali
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi, Molekyl- och kondenserade materiens fysik.
    Danielsson, Mathias
    af Ugglas, Magnus
    Osterdahl, Fabian
    Vigren, Erik
    Kaminska, Magdalena
    Kallberg, Anders
    Simonsson, Ansgar
    Paal, Andras
    Gerin, Maryvonne
    Larsson, Mats
    Geppert, Wolf D.
    Experimental Studies of (HCO+)-C-13 Recombining with Electrons at Energies between 2-50 000 meV2014Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, nr 31, s. 6034-6049Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    An investigation into the dissociative recombination process for (HCO+)-C-13 using merged ion-electron beam methods has been performed at the heavy ion storage ring CRYRING, Stockholm, Sweden. We have measured the branching fractions of the different product channels at similar to 0 eV collision energy to be the following: CO + H 87 +/- 2%, OH + C 9 +/- 2%, and O + CH 4 +/- 2%. The formation of electronically excited CO in the dominant reaction channel has also been studied, and we report the following tentative branching fractions for the different CO product electronic states: CO(X (1)Sigma(+)) + H, 54 +/- 10%; CO(a (3)Pi) + H, 23 +/- 4%; and CO(a' (3)Sigma(+)) + H, 23 +/- 4%. The absolute cross section between similar to 2-50 000 meV was measured and showed resonance structures between 3 and 15 eV. The cross section was fitted in the energy range relevant to astrophysics, i.e., between 1 and 300 meV, and was found to follow the expression sigma = 1.3 +/- 0.3 X 10(-16) E-1.29 +/- 0.05 cm(2) and the corresponding thermal rate constant was determined to be k(T) = 2.0 +/- 0.4 X 10(-7)(T/300)(-0.79 +/- 0.05) cm(3) s(-1). Radioastronomical observations with the IRAM 30 m telescope of HCO+ toward the Red Rectangle yielded an upper column density limit of 4 X 10(11) cm(-2) of HCO+ at the 1 sigma level in that object, indicating that previous claims that the dissociative recombination of HCO+ plays an important role in the production of excited CO molecules emitting the observed Cameron bands in that object are not supported.

  • 20. Harnes, J.
    et al.
    Winkler, M.
    Lindblad, Andreas
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi, Oorganisk kemi.
    Saethre, L. J.
    Borve, K. J.
    Size of Free Neutral CO(2) Clusters from Carbon 1s Ionization Energies2011Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 115, nr 38, s. 10408-10415Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Free neutral CO(2) clusters were produced by adiabatic expansion and characterized by carbon 1s (C1s) photoelectron spectroscopy using synchrotron radiation. The shift in C1s ionization energy (IE) between the cluster and the monomer, i.e., Delta IE = IE(cluster) - IE(monomer), was found to vary systematically with the experimental conditions. A functional relationship is established between the mean cluster size in the beam, < N >, and Delta IE, in good agreement with theoretical calculations of shifts in ionization energy for model clusters. This makes it possible to use core-level photoelectron spectroscopy to monitor the mean cluster size and also to estimate < N > from expansion conditions.

  • 21.
    Hermansson, Kersti
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi, Strukturkemi.
    Gajewski, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Mitev, Pavlin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi.
    Origin of the OH Vibrational Blue Shift in the LiOH Crystal2008Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, nr 51, s. 13487-13494Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The O−H vibrational frequency in crystalline hydroxides is either upshifted or downshifted by its crystalline surroundings. In the LiOH crystal, the experimental gas-to-solid O−H frequency upshift (“blue shift”) is approximately +115 cm−1. Here plane-wave DFT calculations for the isotope-isolated LiOH crystal have been performed and we discuss the origin of the OH frequency upshift, and the nature of the OH group and the interlayer interactions. We find that (1) the vibrational frequency upshift originates from interactions within the LiOH layer; this OH upshift is slightly lessened by the interlayer interactions; (2) the interlayer O−H - - - H−O interaction is largely electrostatic in character (but there is no hydrogen bonding); (3) the gas-to-solid vibrational shift for OH in LiOH(s) and its subsystems qualitatively adheres to a parabola-like “frequency vs electric field strength” correlation curve, which has a maximum for a positive electric field, akin to the correlation curve earlier found in the literature for an isolated OH ion in an electric field.

  • 22.
    Häupl, Tilmann
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Fysikalisk-kemiska institutionen.
    Lomoth, Reiner
    Hammarström, Leif
    Femtosecund Dynamics of the Photoexcited Methyl Viologen Radical Cation2003Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 107, nr 4, s. 435-438Artikel i tidskrift (Refereegranskat)
  • 23. Karlsson, H O
    et al.
    Goscinski, O
    Correlation functions and thermal rate constants2001Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 105, nr 12, s. 2599-2603Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Thermal rate constants k(T) and cumulative reaction probabilities N(E) can be computed as a sum of correlation functions C-nm = <(n)/f((H) over tilde/phi (m)). In this paper we discuss the use of two different Krylov subspace methods to compute these correlation functions for large systems. The first approach is based on the Lanczos algorithm to transform the Hamiltonian to tridiagonal form. As shown by Mandelshtam (J. Chem, Phys. 1998, 108, 9999) and Chen and Guo (J, Chem. Phys. 1999, 111, 9944), ail correlation functions can be computed from a single recursion. The second approach treats a number of linear systems of equations using a Krylov subspace solver. Here the quasiminimal residual (QMR) method was used. For the first approach, we found that we needed the same number of Lanczos recursions as the size of the matrix. If Ilo re-orthogonalization is used, the number of recursions grows further. The linear solver approach, on the other hand, converges fast for each linear system, but many systems must be solved.

  • 24.
    Karlsson, Hans
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Reduced-order modeling, error estimation, and the role of the start-vector: The recursive residue generation method revisited2007Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 41, s. 10263-10268Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The recursive residue generation method (RRGM) [Wyatt, R. E. Adv. Chem. Phys. 1989, 73, 231] is rederived using the formalism of reduced-order modeling [Bai, Z. Appl. Numerical Math. 2002, 43, 9]. A stopping criteria for the RRGM recursions is proposed, on the basis of an expression for an upper bound to the absolute error [B ai, Z.; Ye, Q. Electron. Trans. Numerical Anal. 1998, 7, 1]. It is further pointed out that, in general, the start-vector has a negligible effect on the convergence of the RRGM.

  • 25. Kocevski, Vancho
    et al.
    Pejov, Ljupcho
    On the Assessment of Some New Meta-Hybrid and Generalized Gradient Approximation Functionals for Calculations of Anharmonic Vibrational Frequency Shifts in Hydrogen-Bonded Dimers2010Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 114, nr 12, s. 4354-4363Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The performance of some recently proposed DFT functionals by Truhlar’s group (mPW1B95, mPWLYP1W,PBELYP1W, and PBE1W [Dahlke, E. E.; Truhlar, D. G. J. Phys. Chem. B 2005, 109, 317. Zhao, Y.; Truhlar,D. G. J. Phys. Chem. A 2004, 108, 6908.]) was tested primarily with respect to computation of anharmonicvibrational frequency shifts upon hydrogen bond formation in small molecular/ionic dimers. Five hydrogenbondedsystems with varying hydrogen bond strengths were considered: methanol-fluorobenzene, phenol-carbonmonoxide in ground neutral (S0) and cationic (D0) electronic states, phenol-acetylene, and phenol-benzene(+).Anharmonic OH stretching frequency shifts were calculated from the computed vibrational potentials forfree and hydrogen-bonded proton-donor molecules. To test the basis set convergence properties, all calculationswere performed with 6-31++G(d,p) and 6-311++G(2df,2pd) basis sets. The mPW1B95 functional was foundto perform remarkably better in comparison to more standard functionals (such as B3LYP, mPW1PW91,PBE1PBE) in the case of neutral dimers. In the case of cationic dimers, however, this is not always the case.With respect to prediction of anharmonic OH stretching frequency shifts upon ionization of free phenol, allDFT levels of theory outperform MP2. Some other aspects of the functional performances with respect tocomputation of interaction and dissociation energies were considered as well.

  • 26. Kocevski, Vancho
    et al.
    Pejov, Ljupco
    Anharmonic Vibrational Frequency Shifts upon Interaction of Phenol(+) with the Open Shell Ligand O2: The Performance of DFT Methods versus MP22012Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, nr 8, s. 1939-1949Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Anharmonic vibrational frequency shifts of the phenol(+) O–H stretching mode upon complex formation with the open-shell ligand O2 were computed at several DFT and MP2 levels of theory, with various basis sets, up to 6-311++G(2df,2pd). It was found that all DFT levels of theory significantly outperform the MP2 method with this respect. The best agreement with the experimental frequency shift for the hydrogen-bonded minimum on the potential energy surfaces was obtained with the HCTH/407 functional (−93.7 cm–1 theoretical vs −86 cm–1 experimental), which is a significant improvement over other, more standard DFT functionals (such as, e.g., B3LYP, PBE1PBE), which predict too large downshifts (−139.9 and −147.7 cm–1, respectively). Good agreement with the experiment was also obtained with the mPW1B95 functional proposed by Truhlar et al. (−109.2 cm–1). We have attributed this trend due to the corrected long-range behavior of the HCTH/407 and mPW1B95 functionals, despite the fact that they have been designed primarily for other purposes. MP2 method, even with the largest basis set used, manages to reproduce only less than 50% of the experimentally detected frequency downshift for the hydrogen-bonded dimer. This was attributed to the much more significant spin contamination of the reference HF wave function (compared to DFT Kohn–Sham wave functions), which was found to be strongly dependent on the O–H stretching vibrational coordinate. All DFT levels of theory outperform MP2 in the case of computed anharmonic OH stretching frequency shifts upon ionization of the neutral phenol molecule as well. Besides the hydrogen-bonded minimum, DFT levels of theory also predict existence of two other minima, corresponding to stacked arrangement of the phenol(+) and O2 subunits. mPW1B95 and PBE1PBE functionals predict a very slight blue shift of the phenol(+) O–H stretching mode in the case of stacked dimer with the nearly perpendicular orientation of oxygen molecule with respect to the phenolic ring, which is entirely of electrostatic origin, in agreement with the experimental observations of an additional band in the IR photodissociation spectra of phenol(+)–O2 dimer [Patzer, A.; Knorke, H.; Langer, J.; Dopfer, O. Chem. Phys. Lett. 2008, 457, 298]. The structural features of the minima on the studied PESs were discussed in details as well, on the basis of NBO and AIM analyses.

  • 27.
    Kowalewski, Markus
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Avdelningen för beräkningsvetenskap. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Matematisk-datavetenskapliga sektionen, Institutionen för informationsteknologi, Tillämpad beräkningsvetenskap.
    Mikosch, Jochen
    Wester, Roland
    de Vivie-Riedle, Regina
    Nucleophilic substitution dynamics: Comparing wave packet calculations with experiment2014Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, s. 4661-4669Artikel i tidskrift (Refereegranskat)
  • 28.
    Lindh, Roland
    et al.
    Department of Theoretical Chemistry, Lund University.
    Bernhardsson, Anders
    Schütz, Martin
    Benzyne thermochemistry: A benchmark ab initio study1999Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 103, nr 48, s. 9913-9920Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The thermochemistry of the benzynes has been reinvestigated in a set of benchmark calculations including, e.g., multireference perturbation theory in combination with large basis sets up to correlation consistent polarized valence quadruple xi followed by basis set extrapolation procedures. The vibrational corrections have been deduced from multiconfiguration self-consistent field (MCSCF) calculations employing average atomic natural orbital basis sets. The quality of the isodesmic reactions has been investigated by analyzing the errors of the utilized methods in predicting the CH bond strengths and energies of the related molecules. It turns out that multireference third order perturbation theory, although occasionally better than second order, suffers from less systematic errors and thus is not as well suited for use in isodesmic reactions as the corresponding second order theory. The present extended calculations show that all the isodesmic reactions used in previous studies of the thermochemistry of the benzynes are adequate. Furthermore, it is demonstrated that multireference second order perturbation theory accurately reproduces the singlet-triplet energy splittings of the benzynes.

  • 29.
    Lindh, Roland
    et al.
    Department of Theoretical Chemistry, Lund University.
    Kraemer, Wolfgang P
    Kamper, Manfred
    On the thermodynamic stability of ArO41999Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 103, nr 41, s. 8295-8302Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The argon tetroxide molecule, ArO4, and the isoelectronically associated perchlorate, ClO4-, and sulfate, SO42-, ions are investigated on different levels of ab initio theory. The equilibrium structures, harmonic vibrational frequencies, and heats of formation are computed applying density functional theory, second order Moller-Plesset perturbation, singles and doubles coupled-cluster with triples corrections, and Bruekner’s doubles coupled-cluster with triples corrections methods in conjunction with various one-particle basis sets. The calculations demonstrate that the description of the bond characteristics in argon tetroxide is sensitive to the applied level of theory. A careful analysis of the global potential energy surface shows that a stationary point exists for the ArO4 complex corresponding to a local mininium. The calculated equilibrium Ar-O bond distance of 1.48 Angstrom for this structure is slightly longer than the corresponding bond length of the perchlorate ion. Harmonic frequencies for ArO4 obtained using Bruekner’s doubles coupled-cluster with triples corrections are found to have a similar pattern like those obtained for the isoelectronic series of ions SiO44-, PO43-, SO42-, ClO4-. Using the concept of an isodesmic reaction, the enthalpy of formation of ArO4 is determined to be endothermic by as much as 1236 kJ/mol. The present theoretically predicted strong endothermicity and the large Ar-O bond distance are in conflict with the monotonic trends obtained for the isoelectronic ions, but can be supported by other chemical extrapolation schemes.

  • 30.
    Lomoth, R
    et al.
    University of Leipzig.
    Naumov, S
    Brede, O
    Genuine pyrimidine radical cations generated by radiation-induced electron transfer to butyl chloride or acetone parent ions1999Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 103, nr 15, s. 2641-2648Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Radical cations of multiple methylated uracils and thymines were generated by electron transfer to parent ions of solvents of low polarity such as n-butyl chloride and acetone. Pulse radiolysis resulted in the transient optical absorption spectra of the pyrimidine radical cations (Py.+) which exhibit bands generally peaking around lambda = 400 nm and in acetone showing an additional band in the range of lambda(max) = 500-560 nm. The identification of the solute radical cations is based on the direct observation of the formation of Py.+ by electron transfer (k = (1-2) x 10(10) M(-1)s(-1)), the nucleophilic reaction with the counterion (e.g., Cl-), the relatively low reactivity with oxygen even for the fully methylated nitrogen groups (k < 2 x 10(8) M(-1)s(-1)), and the observation of a subsequent electron transfer from triphenylamine to the pyrimidine radical cations proceeding in a diffusion-controlled manner. The solvent dependence of the spectral shape of Py.+ was also studied in acetone/n-butyl chloride mixtures and was found to depend on the polarity of the surroundings. This phenomenon is explained in terms of a lactam-lactim-like tautomerism of the transient involving the whole plane molecule. Quantum chemical calculations support the experimental findings by explaining the spectral structure and enable the formulation of the lactims as either 1,4- or 3,4-localized.

  • 31.
    Lomoth, R
    et al.
    University of Leipzig.
    Naumov, S
    Brede, O
    Transients of the oxidation of pyrimidines with SO4•-: Structure and reactivity of the resulting radicals1999Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 103, nr 33, s. 6571-6579Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Depending on the methylation pattern, the reaction of SO4.- with various methylated pyrimidines yields radicals deprotonated at N(1) and C(5)-OH or C(6)-OH adduct radicals and probably allyl radicals by subsequent deprotonation at the C(5)-methyl group of the thymines. All of these radicals are derived from the initial SO4.- adducts on the pyrimidines that have lifetimes of several microseconds in the case of N(1)-methylated thymines. These transients could be taken for long lived pyrimidine radical cations. However, spectral and kinetic comparison with the pyrimidine radical cations generated by electron transfer in nonpolar solvents (butyl chloride, acetone) reveals the adduct nature of these transients. In the course of sulfate adduct decay, pyrimidine radical cations could be formed as nondetectable short-lived (tau < 20ns) intermediates rapidly reacting to the above-mentioned radical products. The reactivity of the SO4.- adducts, as well as that of the other pyrimidinyl radicals observed, was characterized by the subsequent oxidation of triphenylamine and di- or trimethoxybenzene, which supports the mechanistic interpretation given above. Hence there is no indication of long-lived pyrimidine radical cations under the conditions of the SO4.- oxidation of pyrimidines in aqueous solution.

  • 32.
    Lomoth, Reiner
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Fysikalisk-kemiska institutionen.
    Magnuson, Ann
    Xu, Yunhua
    Sun, Licheng
    Mixed-Valance Properties of an Acetate-Bridged Dinuclear Ruthenium (II,II) Complex2003Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 107, s. 4373-4380Artikel i tidskrift (Refereegranskat)
  • 33.
    Lomoth, Reiner
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Fysikalisk-kemiska institutionen.
    Magnusson, Ann
    Xu, Yunhua
    Sun, Licheng
    Mixed-Valance Properties of an Acetate-Bridged Dinuclear Ruthenium (II,II) Complex2003Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 107, s. 4373-4380Artikel i tidskrift (Refereegranskat)
  • 34.
    Lundqvist, Maria J.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Galoppini, Elena
    Meyer, Gerald J.
    Persson, Petter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fysikalisk och analytisk kemi, Kvantkemi.
    Calculated optoelectronic properties of Ruthenium tris-bipyridine dyes containing oligophenyleneethynylene rigid rod linkers in different chemical environments2007Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 8, s. 1487-1497Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ruthenium tris-bipyridine dyes containing oligophenyleneethynylene (OPE) rigid rod linker groups ([Ru(bpy)3]2+, [Ru(bpy)2bpy-E-Ipa]2+, [Ru(bpy)2bpy-E-Ph-E-Ipa]2+, and [Ru(bpy)2bpy-E-Bco-E-Ipa]2+, where bpy = 2,2'-bipyridine, E = ethynylene, Ph = p-phenylene, Bco = bicyclo[2.2.2]octylene, and Ipa = isophthalic acid) have been investigated using DFT and TD-DFT calculations to elucidate the influence of the rigid rod on their optoelectronic properties. Experimentally observed differences in the optical absorption for the different complexes are discussed on the basis of TD-DFT simulated absorption spectra. A comparison of the calculated optoelectronic properties of [Ru(bpy)2bpy-E-Ph-E-Ipa]2+ in different chemical environments, that is, in different solvents and with or without counter ions, suggests that both the absorption spectra and the redox properties of the dyes with OPE rods are sensitive to the environment. The calculations show that spurious low-energy charge-transfer excitations present in the TD-DFT calculations of the extended systems in vacuum are removed when the environment is included in the calculations.

  • 35.
    Markle, Todd F.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap.
    Tronic, T. A.
    Dipasquale, A. G.
    Kaminsky, W.
    Mayer, J. M.
    Effect of basic site substituents on concerted proton-electron transfer in hydrogen-bonded pyridyl-phenols2012Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, nr 50, s. 12249-12259Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Separated concerted proton-electron transfer (sCPET) reactions of two series of phenols with pendent substituted pyridyl moieties are described. The pyridine is either attached directly to the phenol (HOAr-pyX) or connected through a methylene linker (HOArCH2pyX) (X = 4-NO2, 5-CF3, 4-CH3, and 4-NMe2). Electron-donating and -withdrawing substituents have a substantial effect on the chemical environment of the transferring proton, as indicated by IR and 1H NMR spectra, X-ray structures, and computational studies. One-electron oxidation of the phenols occurs concomitantly with proton transfer from the phenolic oxygen to the pyridyl nitrogen. The oxidation potentials vary linearly with the pK a of the free pyridine (pyX), with slopes slightly below the Nerstian value of 59 mV/pKa. For the HOArCH2pyX series, the rate constants ksCPET for oxidation by NAr3 •+ or [Fe(diimine)3]3+ vary primarily with the thermodynamic driving force (ΔG° sCPET), whether ΔG° is changed by varying the potential of the oxidant or the substituent on the pyridine, indicating a constant intrinsic barrier λ. In contrast, the substituents in the HOAr-pyX series affect λ as well as ΔG°sCPET, and compounds with electron-withdrawing substituents have significantly lower reactivity. The relationship between the structural and spectroscopic properties of the phenols and their CPET reactivity is discussed.

  • 36.
    Mäkie, Peter
    et al.
    FOI, CBRN Defence and Security, Umeå.
    Westin, Gunnar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för materialkemi, Oorganisk kemi.
    Persson, Per
    Dept of Chemistry, Umeå University, Umeå.
    Österlund, Lars
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Tekniska sektionen, Institutionen för teknikvetenskaper, Fasta tillståndets fysik.
    Adsorption of Trimethyl Phosphate on Maghemite, Hematite, and Goethite Nanoparticles2011Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 115, nr 32, s. 8948-8959Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Adsorption of trimethyl phosphate (TMP) on well-characterized hematite, maghemite and goethite nanopartides was studied by in situ DRIFT spectroscopy as a model system for adsorption of organophosphorous (OP) compounds on iron minerals. The iron minerals were characterized by X-ray diffraction (XRD), Raman spectroscopy, transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), specific surface area, and pore size distribution. The minerals were found to consist of stoichimetrically and morphologically well-defined maghemite, hematite, and goethite nanoparticles. Analysis of in situ diffuse reflectance Fourier transform (DRIFT) spectroscopy shows that TMP bonds mainly to Lewis acid Fe sites through the O phosphoryl atom (-P=O-Fe) on hematite and maghemite. On goethite most TMP molecules bond to Bronstedt acid surface OH groups and form hydrogen bonded surface complexes. The vibrational mode analysis and uptake kinetics suggest two main reasons for the observed trend of reactivity toward TMP (hematite > maghemite > goethite): (i) larger number of accessible Lewis acid adsorption sites on hematite; (ii) stronger interaction between the Lewis acid Fe sites and the phosphoryl O atom on TAP for hematite and maghemite compared to goethite with concomitant formation of surface coordinated TMP and dimethyl phosphate intermediates. As a result, on the oxides a surface oxidation pathway dominates during the initial adsorption, which results in the formation of surface methoxy and formate. In contrast, on goethite a slower hydrolysis pathway is identified, which eventually yields phosphoric acid. The observed trends of the reactivity and analysis of the corresponding surface structure and particle morphology suggest an intimate relation between the surface chemistry of exposed crystal facets on the iron minerals. These results are important to understand OP surface chemistry on iron minerals.

  • 37.
    Norberg, Daniel
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kvantkemi.
    Larsson, Per-Erik
    Salhi-Benachenhou, Nessima
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kvantkemi.
    Rearrangement and hydrogen scrambling pathways of the toluene radical cation: A computational study2008Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, nr 20, s. 4694-4702Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A computational study is undertaken to provide a unified picture for various rearrangement reactions and hydrogen scrambling pathways of the toluene radical cation (1). The geometries are optimized with the BHandHLYP density functional, and the energies are computed with the ab initio CCSD(T) method, in conjunction with the 6-311+G(d,p) basis set. In particular, four channels have been located, which may account for hydrogen scrambling, as they are found to have overall barriers lower than the observed threshold for hydrogen dissociation. These are a stepwise norcaradiene walk involved in the Hoffman mechanism, a rearrangement of 1 to the methylenecyclohexadiene radical cation (5) by successive [1,2]-H shifts via isotoluene radical cations, a series of [ 1,2] -H shifts in the cycloheptatriene radical cation (4), and a concerted norcaradiene walk. In addition, we have also investigated other. pathways such as the suggested Dewar-Landman mechanism, Which proceeds through 5, via two consecutive [1,2]-H shifts. This pathway is, however, found to be inactive as it involves too high reaction barriers. Moreover, a novel rearrangement pathway that connects 5 to the norcaradiene radical cation (3) has also been located in this work.

  • 38.
    Norberg, Daniel
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för kvantkemi.
    Shiotani, Masaru
    Lunell, Sten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för kvantkemi.
    SH2 reaction vs. hydrogen abstraction/expulsion in methyl radical-methylsilane reactions: Effects of prereactive complex formation2008Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, nr 6, s. 1330-1338Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A quantum chemical study has been undertaken to elucidate the cause of the recently observed S(H)2 reaction between the deuterated methyl radical ((CD3)-C-center dot) and methylsilane (SiD3CH3) following the photolysis of CD3I. [Komaguchi, K.; Norberg, D.; Nakazawa, N.; Shiotani, M.; Persson, P.; Lunell, S. Chem. Phys. Lett. 2005, 410, 1-5.] It is found that the backside SH2 mechanism may proceed favorably for C-Si-C angles deviating with up to 40 degrees from linearity. The competitive hydrogen abstraction reaction is predicted to be active in the range of 90 degrees <= C-Si-C <= 135 degrees. For steeper attack angles, the frontside S(H)2 mechanism is activated. However, high barriers along the corresponding reaction paths probably make the frontside mechanism less important for the present S(H)2 reaction. A number of bound SiH3CH3/CH3I complexes have been located with the MP2 method. At the CCSD(T) level, a complex corresponding to the collinear arrangement where the methyl moiety of methyl iodide points toward the silicon, which is the most favorable conformation for the subsequent S(H)2 reaction with the backside mechanism, is found to be the most stable linear conformer. A complex with similar energy is found where the methyl moiety of methyl iodide points approximately toward an Si-H bond. However, because C-Si-C = 69.4 degrees in this complex, subsequent photolysis of methyl iodide would probably not lead to hydrogen abstraction with full efficiency. These findings could provide an explanation for the observed S(H)2 reaction.

  • 39. Osterman, Tomas
    et al.
    Abrahamsson, Maria
    Becker, Hans-Christian
    Hammarström, Leif
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Fysikalisk kemi.
    Persson, Petter
    Influence of Triplet State Multidimensionality on Excited State Lifetimes of Bis-tridentate Ru(II) Complexes: A Computational Study2012Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, nr 3, s. 1041-1050Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Calculated triplet excited state potential energy surfaces are presented for a set of three bis-tridentate Ru(II)-polypyridyl dies covering a wide range of room temperature excited state lifetimes: [Ru(II)(tpy)(2)](2+), 250 ps; [Ru(II)(bmp)(2)](2+), 15 ns; and [Ru(II)(dqp)(2)](2+), 3 mu s (tpy is 2,2':6',2 ''-terpyridine, bmp is 6-(2-picoly1)-2,2'-bipyridine, and dqp is 2,6-di(quinolin-8-yl)Fridine). The computational results provide a multidimensional view of the (3)MLCT-(3)MC transition for the investigated complexes. Recently reported results of significantly prolonged (3)MLCT excited state lifetimes of bis-tridentate Ru(II)-complexes, for example [Ru(II)(dqp)(2)](2+), are found to correlate with substantial differences in their triplet excited state multidimensional potential energy surfaces. In addition to identification of low-energy transition paths for (3)MLCT-(3)MC conversion associated with simultaneous elongation of two or more Ru-N bonds for all investigated complexes, the calculations also suggest significant differences in (3)MLCT state volume in the multidimensional reaction coordinate space formed from various combinations of Ru-N bond distance varix:ions. This is proposed to be an important aspect for understanding the large differences in experimentally observed (3)MLCT excited state lifetimes. The results demonstrate the advantage of considering multidimensional potential energy surfaces beyond the Franck-Condon region in order to predict photophysical and photochemical properties of bis-tridentate Ru(II)-polypyridyl dyes and related metal complexes.

  • 40.
    Panchmatia, Pooja M.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi.
    Ali, Md Ehesan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi.
    Sanyal, Biplab
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi.
    Oppeneer, Peter M.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Institutionen för fysik och astronomi.
    Halide Ligated Iron Porphines: A DFT plus U and UB3LYP Study2010Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 114, nr 51, s. 13381-13387Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We apply the density functional theory + U (DFT+U) and unrestricted hybrid functional DFT-UB3LYP methods to study the electronic structure and magnetic properties of two prototypical iron porphines: porphine chloride (FePCl) and difluoro iron(III-IV) porphine. Plain DFT within the generalized gradient approximation (GGA) implementation fails in describing the correct high-spin ground state of these porphine molecules, whereas DFT+U and UB3LYP provide an improved description. For a range of U values (4-8 eV), we compare the results of the DFT+U approach to those obtained previously with the hybrid functional (B3LYP) and with the CASPT2 approach. The DFT+U and UB3LYP methods successfully predict the molecular high spin (S = 5/2) ground state of FePCl, and also provide the nontrivial S = 3 high spin ground state for FePF2. For the latter six-coordinated Fe porphine, our DFT+U calculations show that the S = 2, S = 5/2, and S = 3 states are energetically very close together (differences of 30 meV). Nonetheless, S = 3 is obtained as the ground state of the whole molecule, in accordance with the spin expected from the electron count. Our DFT+U calculations show furthermore that the Fe 3d occupancy is similar for FePF2 and FePCl, i.e., DET+U does not support Fe(IV) for FePF2, but rather an Fe(III) porphyrin pi-cation radical species, with an Fe high spin S-Fe = 5/2, and an additional S = 1/2 stemming from spin density distributed over the porphine ring. This observation is also supported by our UB3LYP calculations.

  • 41. Pinsook, Udomsilp
    et al.
    Scheicher, Ralph H
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Fysiska institutionen, Fysik IV.
    Ahuja, Rajeev
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Fysiska sektionen, Fysiska institutionen, Fysik IV.
    Hannongbua, Supot
    Internal vibrations of the Li(NH3)4+ complex analyzed from ab initio, density functional theory, and the classical spring network model2008Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, nr 24, s. 5323-5326Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report our theoretical findings regarding internal vibrations of the Li(NH3)4+ complex which have been studied using three different methods, namely, a classical spring network model, density functional theory, and ab initio Hartree−Fock plus Møller−Plesset correlation energy correction truncated at second-order. The equilibrium Li···N and N···N distances are found to be 2.12 and 3.47 Å, respectively, in good agreement with the experimental data. The theoretically determined vibrational frequencies of the lowest modes are in good agreement with those extracted from inelastic X-ray scattering measurements. From group theory considerations, the internal vibrations of Li(NH3)4+ complexes resemble those of a tetrahedral object. Further experimental investigation is suggested.

  • 42. Raab, Juraj
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Wang, Xuefeng
    Andrews, Lester
    Gagliardi, Laura
    A combined experimental and theoretical study of uranium polyhydrides with new evidence for the large complex UH4(H-2)(6)2007Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 28, s. 6383-6387Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Several monouranium and diuranium polyhydride molecules were investigated using quantum chemical methods. The infrared spectra of uranium and hydrogen reaction products in condensed neon and pure hydrogen were measured and compared with previous argon matrix frequencies. The calculated molecular structures and vibrational frequencies were used to identify the species present in the matrix. Major new absorptions were observed and compared with the previous argon matrix study. Spectroscopic evidence was obtained for the novel complex, UH4(H-2)(6), which has potential interest as a metal hydride with a large number of hydrogen atoms bound to uranium. Our calculations show that the series of complexes UH4(H-2)(1,2,4,6) are stable.

  • 43. Roos, Björn O
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Cho, Han-Gook
    Andrews, Lester
    Agostic interaction in the methylidene metal dihydride complexes H2MCH2 (M = Y, Zr, Nb, Mo, Ru, Th, or U)2007Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 28, s. 6420-6424Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Multiconfigurational quantum chemical methods (complete active space self-consistent field (CASSCF)/second-order perturbation theory (CASPT2)) have been used to study the agostic interaction between the metal atom and H(C) in the methylidene metal dihydride complexes H2MCH2, where M is a second row transition metal or the actinide atoms Th or U. The geometry of some of these complexes is highly irregular due to the formation of a three center bond CH center dot center dot center dot M, where the electrons in the CH bond are delocalized onto empty or half empty orbitals of d- or f-type on the metal. No agostic interaction is expected when M = Y, where only a single bond with methylene can be formed, or when M = Ru, because of the lack of empty electron accepting metal valence orbitals. The largest agostic interaction is found in the Zr and U complexes.

  • 44. Roos, Björn O
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Malmqvist, Per-Åke
    Veryazov, Valera
    Widmark, Per-Olof
    Main group atoms and dimers studied with a new relativistic ANO basis set2004Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 108, nr 15, s. 2851-2858Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    New basis sets of the atomic natural orbital (ANO) type have been developed for the main group and rare gas atoms. The ANO’s have been obtained from the average density matrix of the ground and lowest excited states of the atom, the positive and negative ions, and the dimer at its equilibrium geometry. Scalar relativistic effects are included through the use of a Douglas-Kroll Hamiltonian. Multiconfigurational wave functions have been used with dynamic correlation included using second-order perturbation theory (CASSCF/CASPT2). The basis sets are applied in calculations of ionization energies, electron affinities, and excitation energies for all atoms and the ground-state potentials for the dimers. These calculations include spin-orbit coupling using the RASSCF State Interaction (RASSI-SO) method. The spin-orbit splitting for the lowest atomic term is reproduced with an accuracy of better than 0.05 eV, except for row 5, where it is 0.15 eV. Ionization energies and electron affinities have an accuracy better than 0.2 eV, and atomic polarizabilities for the spherical atoms are computed with errors smaller than 2.5%. Computed bond energies for the dimers are accurate to better than 0.15 eV in most cases (the dimers for row 5 excluded).

  • 45. Roos, Björn O
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Malmqvist, Per-Åke
    Veryazov, Valera
    Widmark, Per-Olof
    New relativistic ANO basis sets for transition metal atoms2005Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 109, nr 29, s. 6575-6579Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    New basis sets of the atomic natural orbital (ANO) type have been developed for the first, second, and third row transition metal atoms. The ANOs have been obtained from the average density matrix of the ground and lowest excited states of the atom, the positive and negative ions, and the atom in an electric field. Scalar relativistic effects are included through the use of a Douglas-Kroll-Hess Hamiltonian. Multiconfigurational wave functions have been used with dynamic correlation included using second order perturbation theory (CASSCF/CASPT2). The basis sets are applied in calculations of ionization energies, electron affinities, and excitation energies for all atoms and polarizabilities for spherically symmetric atoms. These calculations include spin-orbit coupling using a variation-perturbation approach. Computed ionization energies have an accuracy better than 0.2 eV in most cases. The accuracy of computed electron affinities is the same except in cases where the experimental values are smaller than 0.5 eV. Accurate results are obtained for the polarizabilities of atoms with spherical symmetry. Multiplet levels are presented for some of the third row transition metals.

  • 46. Roos, Björn O
    et al.
    Lindh, Roland
    Department of Theoretical Chemistry, Lund University.
    Malmqvist, Per-Åke
    Veryazov, Valera
    Widmark, Per-Olof
    Borin, Antonio Carlos
    New Relativistic Atomic Natural Orbital Basis Sets for Lanthanide Atoms with Applications to the Ce Diatom and LuF32008Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, nr 45, s. 11431-11435Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    New basis sets of the atomic natural orbital (ANO) type have been developed for the lanthanide atoms La-Lu. The ANOs have been obtained from the average density matrix of the ground and lowest excited states of the atom, the positive ions, and the atom in an electric field. Scalar relativistic effects are included through the use of a Douglas-Kroll-Hess Hamiltonian. Multiconfigurational wave functions have been used with dynamic correlation included using second-order perturbation theory (CASSCF/CASPT2). The basis sets are applied in calculations of ionization energies and some excitation energies. Computed ionization energies have an accuracy better than 0.1 eV in most cases. Two molecular applications are inluded as illustration: the cerium diatom and the LuF3 molecule. In both cases it is shown that 4f orbitals are not involved in the chemical bond in contrast to an earlier claim for the latter molecule.

  • 47.
    Ryderfors, Linus
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap.
    Mukhtar, Emad
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap.
    Johansson, Lennart B. -A.
    Excited-state symmetry and reorientation dynamics of perylenes in liquid solutions: Time-resolved fluorescence depolarization studies using one- and two-photon excitation2008Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, nr 26, s. 5794-5803Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The excited-state symmetry and molecular reorientation of perylene, 1,7-diazaperylene, and 2,5,8,1 1-tetratert-butylperylene have been studied by different fluorescence depolarization experiments. The first excited electronic singlet state was reached through one-photon excitation (OPE) and two-photon excitation (TPE). A 400 and 800 nm femtosecond laser pulse was used for this purpose, and data were collected by means of the time-correlated single-photon counting technique. It is found that the rotational correlation times for each perylene derivative are very similar in the OPE and TPE depolarization experiments. For the determination of the two-photon absorption tensor, a recently described theoretical model has been applied (Ryderfors et al. J. Phys. Chem. A 2007, 111, 11531). It was found that the two-photon process can be described by a 2 x 2 absorption tensor for which the components are solvent dependent and exhibit mixed vibronic character. In the dipole approximation this is compatible with a parity-forbidden two-photon absorption into the first excited singlet state.

  • 48.
    Ryderfors, Linus
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap.
    Mukhtar, Emad
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för fotokemi och molekylärvetenskap.
    Johansson, Lennart B.-Å.
    The Symmetry of Two-Photon Excited States as Determined by Time-Resolved Fluorescence Depolarisation Experiments2007Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 45, s. 11531-11539Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A new experimental and theoretical approach is presented for the quantitative determination and assignment of the two-photon absorption tensor of fluorophores dissolved in liquid solutions. Two linearly independent time-resolved fluorescence anisotropies and the two-photon polarization ratio were determined from experiments based on using the time-correlated single photon counting technique. The data were analyzed in a global manner under the assumption of prevailing diffusive molecular reorientations and when accounting for the influence of rapid unresolved reorientations. The method has been applied in fluorescence studies of perylene, two-photon excited at 800 nm. The analysis suggests that the two-photon transition is mediated via vibronic coupling including at least two vibrations of different symmetry, and also that the first singlet excited electronic state acts as a dominating intermediate state.

  • 49.
    Sandström, Niclas
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för biokemi och organisk kemi.
    Piqueras, Mari Carmen
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för biokemi och organisk kemi.
    Ottosson, Henirk
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för biokemi och organisk kemi.
    Crespo, Raül
    Electronic excitations of 1,4-disilyl-substituted 1,4-disilabicycloalkanes: A MS-CASPT2 study of the influence of cage size2007Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, nr 14, s. 2804-2810Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present a multistate complete active space second-order perturbation theory computational study aimed to predict the low-lying electronic excitations of four compounds that can be viewed as two disilane units connected through alkane bridges in a bicyclic cage. The analysis has focused on l,4-disilyl-l,4-disilabicyclo[2.2.1]heptane (la), l,4-bis(trimethylsilyl)-l,4- disilabicyclo[2.2.1]heptane (1b), l,4-disilyl-l,4-disilabicyclo[2.1.1]hexane (2a), and l,4-fcw(trimethylsilyl)-l,4-disilabicyclo[2.1.1]hexane (2b). The aim has been to find out the nature of the lowest excitations with significant oscillator strengths and to investigate how the cage size affects the excitation energies and the strengths of the transitions. Two different substituents on the terminal silicon atoms (H and CH3) were used in order to investigate the end group effects. The calculations show that the lowest allowed excitations are of the same character as that found in disilanes but now redshifted. As the cage size is reduced from a 1,4-disilabicyclo[2.2.1]heptane to a l,4-disilabicyclo[2.1.1]hexane, the Si'"Si through-space distance decreases from approximately 2.70 to 2.50 A and the lowest allowed transitions are red-shifted by up to 0.9 eV, indicating increased interaction between the two Si-Si bonds. The first ionization potential, which corresponds to ionization from the Si-Si a orbitals, is lower in Ib and 2b than in SiiMee by approximately 0.9 and 1.2 eV, respectively. Moreover, Ib and 2b, which have methyl substituents at the terminal Si atoms, have slightly lower excitation energies than the analogous species la and 2a.

  • 50.
    Schalk, O.
    et al.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Chem Phys, S-10691 Stockholm, Sweden..
    Stenrup, Michael
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen.
    Geng, T.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Chem Phys, S-10691 Stockholm, Sweden..
    Lindh, Roland
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Teoretisk kemi.
    Thomas, R. D.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Chem Phys, S-10691 Stockholm, Sweden..
    Feifel, R.
    Univ Gothenburg, Dept Phys, S-41296 Gothenburg, Sweden..
    Hansson, T.
    Stockholm Univ, AlbaNova Univ Ctr, Dept Chem Phys, S-10691 Stockholm, Sweden..
    Influence of Alkoxy Groups on the Photoinduced Dynamics of Organic Molecules Exemplified on Alkyl Vinyl Ethers2015Ingår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, nr 45, s. 11105-11112Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A series of different alkyl vinyl ethers is investigated to decipher the possible reaction channels upon photoexcitation to the pi 3s-Rydberg and the pi pi*-valence state at 200 nm using time-resolved photoelectron spectroscopy and on-the-fly time-dependent density functional theory dynamics simulations. The results indicate two possible relaxation pathways: (1) a radiationless decay through the pi pi*-state back to the ground state via torsion of the C=C double bond, in accordance with the dynamics found in ethylene; and (2) a fast dissociation of the C-O bond between the alkyl and the vinoxy group in the pi sigma*-state. The latter state can be accessed only after excitation to the pi 3s-Rydberg state (quantum yield of similar to 50% according to the dynamics simulations). Additionally, the excited state barrier leading to formation of a vinyl radical was found to be too high to be crossed. These results indicate that the dynamics of ethers crucially depend on the excitation wavelength and that the pi sigma*-state constitutes an important competitive reaction channel that leads to dissociation of the molecules.

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