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  • 1. Benetis, Nikolas P.
    et al.
    Dmitriev, Yurij
    Mocci, Francesca
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Rotation Dynamics Do Not Determine the Unexpected Isotropy of Methyl Radical EPR Spectra2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 35, p. 9385-9404Article in journal (Refereed)
    Abstract [en]

    A simple first-principles electronic structure computation, further qc (quantum chemistry) computation, of the methyl radical gives three equal hf (hyperfine) couplings for the three protons with the unpaired electron. The corresponding dipolar tensors were notably rhombic and had different orientations and regular magnitude components, as they should, but what the overall A-tensor was seen by the electron spin is a different story! The final g = (2.002993, 2.002993, 2.002231) tensor and the hf coupling results obtained in vacuum, at the B3LYP/EPRIII level of theory clearly indicate that in particular the above A = (-65.19, -65.19, 62.54) MHz tensor was axial to a first approximation without considering any rotational dynamics for the CH3. This approximation was not applicable, however, for the trifluoromethyl CF3 radical, a heavier and nonplanar rotor with very anisotropic hf coupling, used here for comparison. Finally, a derivation is presented explaining why there is actually no need for the CH3 radicals to consider additional rotational dynamics in order for the electron to obtain an axially symmetric hf (hyperfine) tensor by considering the simultaneous dipolar couplings of the three protons. An additional consequence is an almost isotropic A-tensor for the electron spin of the CH3 radical. To the best of our knowledge, this point has not been discussed in the literature before. The unexpected isotropy of the EPR parameters of CH3 was solely attributed to the rotational dynamics and was not clearly separated from the overall symmetry of the species. The present theoretical results allowed a first explanation of the forbidden satellite lines in the CH3 EPR spectrum. The satellites are a fingerprint of the radical rotation, helping thus in distinguishing the CH3 reorientation from quantum rotation at very low temperatures.

  • 2. Calabrese, Camilla
    et al.
    Vigorito, Annalisa
    Maris, Assimo
    Mariotti, Sergio
    Fathi, Pantea
    Stockholm University, Faculty of Science, Department of Physics.
    Geppert, Wolf D.
    Stockholm University, Faculty of Science, Department of Physics.
    Melandri, Sonia
    Millimeter Wave Spectrum of the Weakly Bound Complex CH2=CHCN center dot H2O: Structure, Dynamics, and Implications for Astronomical Search2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 48, p. 11674-11682Article in journal (Refereed)
    Abstract [en]

    The weakly bound 1:1 complex between acrylonitrile (CH2=-CHCN) and water has been characterized spectroscopically in the millimeter wave range (59.6-74.4 GHz) using a Free Jet Absorption Millimeter Wave spectrometer. Precise values of the rotational and quartic centrifugal distortion constants have been obtained from the measured frequencies of the normal and isotopically substituted water moiety (DOH, DOD, (HOH)-O-18). Structural parameters have been estimated from the rotational constants and their differences among isotopologues: the complex has a planar structure with the two subunits held together by a O-H center dot center dot center dot N (2.331(3) angstrom) and a C- H center dot center dot center dot O (2.508(4) angstrom) interaction. The ab initio intermolecular binding energy, obtained at the counterpoise corrected MP2/aug-cc-pVTZ level of calculation, is D-e = 24.4 kJ mol(-1)

  • 3. Crovetto, Luis
    et al.
    Paredes, Jose M.
    Rios, Ramon
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Talavera, Eva M.
    Avarez-Pez, Jose M.
    Photophysics of a xanthenic derivative dye useful as an ""On/Off"" fluorescence probe2007In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 111, no 51, p. 13311-13320Article in journal (Refereed)
    Abstract [en]

    The photophysical behavior of a new fluorescein derivative has been explored by using absorption and steady-state and time-resolved fluorescence measurements. The influence of ionic strength, as well as total buffer concentration, on both the absorbance and fluorescence has been investigated. The apparent acidity constant of the dye determined by absorbance is almost independent of the added buffer and salt concentrations. A semiempirical model is proposed to rationalize the variations in the apparent pK(a) values. The excited-state proton-exchange reaction around the physiological pH becomes reversible upon addition of phosphate buffer, inducing a pH-dependent change of the steady-state fluorescence and decay times. Fluorescence decay traces, collected as a function of total buffer concentration and pH, were analyzed by global compartmental analysis, yielding the following values of the rate constants describing excited-state dynamics: k(01) = 1.29 x 10(10) s(-1), k(02) = 4.21 x 10(8) s(-1), k(21)approximate to 3 x 10(6) M-1 s(-1), k(12)(B) = 6.40 x 10(8) M-1 s(-1), and k(21)(B) = 2.61 x 10(7) M-1 s(- 1). The decay rate constant values of k(01), k(21), and k(21)(B), along with the low molar absorption coefficient of the neutral form, mean that coupled decays are practically monoexponential at buffer concentrations higher than 0.02 M and any pH. Thus, the pH and buffer concentration can modulate the main lifetime of the dye.

  • 4.
    Dahlberg, Martin
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Arnold, Maliniak
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK), Physical Chemistry.
    Mennucci, Benedetta
    Department of Chemistry, University of Pisa.
    Marini, Alberto
    Department of Chemistry, University of Pisa.
    Quantum Chemical Modeling of the Cardiolipin Headgroup2010In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 114, no 12, p. 4375-4387Article in journal (Refereed)
    Abstract [en]

    Cardiolipin is a key lipid component in many biological membranes. Proton conduction and proton−lipid interactions on the membrane surface are thought to be central to mitochondrial energy production. However, details on the cardiolipin headgroup structure are lacking and the protonation state of this lipid at physiological pH is not fully established. Here we present ab initio DFT calculations of the cardiolipin (CL) headgroup and its 2′-deoxy derivative (dCL), with the aim of establishing a connection between structure and acid−base equilibrium in CL. Furthermore, we investigate the effects of solvation on the molecular conformations. In our model, both CL and dCL showed a significant gap between the two pKa values, with pKa2 above the physiological range, and intramolecular hydrogen bonds were found to play a central role in the conformations of both molecules. This behavior was also observed experimentally in CL. Structures derived from the DFT calculations were compared with those obtained experimentally, collected for CL in the Protein Data Bank, and conformations from previous as well as new molecular dynamics simulations of cardiolipin bilayers. Transition states for proton transfer in CL were investigated, and we estimate that protons can exchange between phosphate groups with an approximate 4−5 kcal/mol barrier. Computed NMR and IR spectral properties were found to be in reasonable agreement with experimental results available in the literature.

  • 5. Dourado, Daniel F. A. R.
    et al.
    Fernandes, Pedro Alexandrino
    Mannervik, Bengt
    Stockholm University, Faculty of Science, Department of Neurochemistry.
    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 Glutathione2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 31, p. 5790-5800Article in journal (Refereed)
    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.

  • 6. Ernst, Hanna A.
    et al.
    Wolf, Thomas J. A.
    Schalk, Oliver
    Stockholm University, Faculty of Science, Department of Physics. National Research Council of Canada, Canada.
    González-García, Núria
    Boguslavskiy, Andrey E.
    Stolow, Albert
    Olzmann, Matthias
    Unterreiner, Andreas-Neil
    Ultrafast Dynamics of o-Nitrophenol: An Experimental and Theoretical Study2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 35, p. 9225-9235Article in journal (Refereed)
    Abstract [en]

    The photolysis of o-nitrophenol (o-NP), a typical push pull molecule, is of current interest in atmospheric chemistry as a possible source of nitrous acid (HONO). To characterize the largely unknown photolysis mechanism, the dynamics of the lowest lying excited singlet state (S-1) of o-NP was investigated by means of femtosecond transient absorption spectroscopy in solution, time-resolved photoelectron spectroscopy (TRPES) in the gas phase and quantum chemical calculations. Evidence of the unstable aci-nitro isomer is provided both in the liquid and in the gas phase. Our results indicate that the Si state displays strong charge transfer character, which triggers excited state proton transfer from the OH to the NO2 group as evidenced by a temporal shift of 20 fs of the onset of the photoelectron spectrum. The proton transfer itself is found to be coupled to an out-of-plane rotation of the newly formed HONO group, finally leading to a conical intersection between Si and the ground state So. In solution, return to So within 0.2-0.3 ps was monitored by stimulated emission. As a competitive relaxation channel, ultrafast intersystem crossing to the upper triplet manifold on a subpicosecond time scale occurs both in solution and in the gas phase. Due to the ultrafast singlet dynamics, we conclude that the much discussed HONO split-off is likely to take place in the triplet manifold.

  • 7. Gagin, Anton
    et al.
    Yarevsky, Evgeny
    Salci, Moses
    Stockholm University, Faculty of Science, Department of Physics.
    Elander, Nils
    Stockholm University, Faculty of Science, Department of Physics.
    Eigen Energies and the Statistical Distributions of the Rovibrational Levels of the Bosonic van der Waals Argon Trimer2009In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 113, no 52, p. 14979-14986Article in journal (Refereed)
    Abstract [en]

    The eigen energies and the statistical distributions of the rovibrational levels (J = 0-2) of the bosonic van der Waals argon trimer were calculated using a full angular momentum three-dimensional finite element method. The influence of interatomic potentials on the vibrational levels and statistical properties of the trimer was discussed.

  • 8.
    Hamberg, Mathias
    et al.
    Stockholm University, Faculty of Science, Department of Physics. Uppsala University, Sweden.
    Kashperka, Iryna
    Stockholm University, Faculty of Science, Department of Physics.
    Thomas, Richard D.
    Stockholm University, Faculty of Science, Department of Physics.
    Roueff, Evelyne
    Zhaunerchyk, Vitali
    Stockholm University, Faculty of Science, Department of Physics. Uppsala University, Sweden.
    Danielsson, Mathias
    Stockholm University, Faculty of Science, Department of Physics.
    af Ugglas, Magnus
    Stockholm University, Faculty of Science, Department of Physics.
    Österdahl, Fabian
    Stockholm University, Faculty of Science, Department of Physics.
    Vigren, Erik
    Stockholm University, Faculty of Science, Department of Physics.
    Kaminska, Magdalena
    Källberg, Anders
    Stockholm University, Faculty of Science, Department of Physics.
    Simonsson, Ansgar
    Stockholm University, Faculty of Science, Department of Physics.
    Paál, Andras
    Stockholm University, Faculty of Science, Department of Physics.
    Gerin, Maryvonne
    Larsson, Mats
    Stockholm University, Faculty of Science, Department of Physics.
    Geppert, Wolf D.
    Stockholm University, Faculty of Science, Department of Physics.
    Experimental Studies of (HCO+)-C-13 Recombining with Electrons at Energies between 2-50 000 meV2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 31, p. 6034-6049Article in journal (Refereed)
    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.

  • 9. Harper, James K.
    et al.
    Tishler, Derek
    Richardson, David
    Lokvam, John
    Pendrill, Robert
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Widmalm, Göran
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Solid-State NMR Characterization of the Molecular Conformation in Disordered Methyl alpha-L-Rhamnofuranoside2013In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, no 26, p. 5534-5541Article in journal (Refereed)
    Abstract [en]

    A combination of solid-state C-13 NMR tensor data and DFT computational methods is utilized to predict the conformation in disordered methyl alpha-L-rhamnofuranoside. This previously uncharacterized solid is found to be crystalline and consists of at least six distinct conformations that exchange on the kHz time scale. A total of 66 model structures were evaluated, and six were identified as being consistent with experimental C-13 NMR data. All feasible structures have very similar carbon and oxygen positions and differ most significantly in OH hydrogen orientations. A concerted rearrangement of OH hydrogens is proposed to account for the observed dynamic disorder. This rearrangement is accompanied by smaller changes in ring conformation and is slow enough to be observed on the NMR time scale due to severe steric crowding among ring substituents. The relatively minor differences in non-hydrogen atom positions in the final structures suggest that characterization of a complete crystal structure by X-ray powder diffraction may be feasible.

  • 10.
    Hede, Thomas
    et al.
    Stockholm University, Faculty of Science, Department of Meteorology .
    Murugan, N. Arul
    Kongsted, Jacob
    Leck, Caroline
    Stockholm University, Faculty of Science, Department of Meteorology .
    Ågren, Hans
    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.

  • 11. Henschel, Henning
    et al.
    Acosta Navarro, Juan Camilo
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Yli-Juuti, Taina
    Kupiainen-Määttä, Oona
    Olenius, Tinja
    Ortega, Ismael K.
    Clegg, Simon L.
    Kurtén, Theo
    Riipinen, Ilona
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Vehkamäki, Hanna
    Hydration of Atmospherically Relevant Molecular Clusters: Computational Chemistry and Classical Thermodynamics2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 14, p. 2599-2611Article in journal (Refereed)
    Abstract [en]

    Formation of new particles through clustering of molecules from condensable vapors is a significant source for atmospheric aerosols. The smallest clusters formed in the very first steps of the condensation process are, however, not directly observable by experimental means. We present here a comprehensive series of electronic structure calculations on the hydrates of clusters formed by up to four molecules of sulfuric acid, and up to two molecules of ammonia or dimethylamine. Though clusters containing ammonia, and certainly dimethylamine, generally exhibit lower average hydration than the pure acid clusters, populations of individual hydrates vary widely. Furthermore, we explore the predictions obtained using a thermodynamic model for the description of these hydrates. The similar magnitude and trends of hydrate formation predicted by both methods illustrate the potential of combining them to obtain more comprehensive models. The stabilization of some clusters relative to others due to their hydration is highly likely to have significant effects on the overall processes that lead to formation of new particles in the atmosphere.

  • 12.
    Heshmat, Mojgan
    Stockholm University, Faculty of Science, Department of Organic Chemistry. Vrije Universiteit Amsterdam, The Netherlands.
    Unraveling the Origin of Solvent Induced Enantioselectivity in the Henry Reaction with Cinchona Thiourea as Catalyst2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 40, p. 7974-7982Article in journal (Refereed)
    Abstract [en]

    In this work, we report an energy decomposition and electronic structure analysis using DFT calculations for the C-C coupling step in the Henry reaction with cinchona thiourea as catalyst and DMF solvent to unravel the origin of enantioselectivity. We found that the conformation of flexible thiourea moiety is affected by the solvent, and in the preferred conformation of thiourea in strong Lewis basic DMF solvent, the N-H sites are in the opposite direction, i.e., in trans conformation. Hence, the thiourea moiety acts via single hydrogen bonding with substrates. The conformation of the substrates with respect to the forming C-C bond plays critical role to increase orbital interaction between two substrates and enhances hydrogen bond strength between substrates and catalyst, which in turn stabilizes the positive charge developing on the catalyst at the transition state for one of the enantiomers (S). Thus, the enantioselectivity has electronic structure origin. The stronger H-bond formation in the S enantiomer has been confirmed by the calculated IR spectra and is in agreement with thus far experimental and computational results.

  • 13.
    Heshmat, Mojgan
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Privalov, Timofei
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    H-2 Cleavage by Frustrated Lewis Pairs Characterized by the Energy Decomposition Analysis of Transition States: An Alternative to the Electron Transfer and Electric Field Models2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 36, p. 7202-7211Article in journal (Refereed)
    Abstract [en]

    Knowing that the Papai's electron transfer (ET) and the Grimme's electric field (EF) models draw attention to somewhat different physical aspects, we are going to systematically (re)examine interactions in the transition states (TSs) of the heterolytic H-2-cleavage by the Frustrated Lewis Pairs (FLPs). Our main vehicle is the quantitative energy decomposition analysis (EDA), a powerful method for elucidation of interactions, plus the analysis of molecular orbitals (MOs). Herein, the Lewis acid (LA) is B(C6F5)(3) and the Lewis bases (LBs) are tBu(3)P, (o-C6H4Me)(3)P, 2,6-lutidine, 2,4,6-lutidine, MeN=C(Ph)Me imine, MeN(H)-C(H)PhMe amine, THF, 1,4-dioxane, and acetone. For a series of the phosphorus-, nitrogen-, and oxygen-bearing LBs plus B(C6F5)(3), we will show that (i) neither the electrostatic nor the orbital interactions dominate but instead both are essential alongside the Pauli repulsion and (ii) the frontier molecular orbitals (FMOs) of a TS can arise not only from the push-pull molecular orbital scheme by Papai et al., which directly involves the occupied sigma and the empty sigma* MOs of H-2, but also from a more intricate but energetically more fitting orbital interactions which have escaped notice thus far.

  • 14.
    Heshmat, Mojgan
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Privalov, Timofei
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Structurally Flexible Oxocarbenium/Borohydride Ion Pair: Dynamics of Hydride Transfer on the Background of Conformational Roaming2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 23, p. 5098-5106Article in journal (Refereed)
    Abstract [en]

    We apply Born-Oppenheimer molecular dynamics to the practically significant [dioxane-H(+)-acetone]-[(C6F5)(3)B-H(-)] and [Et2O-H(+)-OCPr2][(C6F5)(3)B-H(-)] ion pair intermediates. Dynamics of hydride transfer in cation/anion ion pair takes place on the background of large amplitude configurational changes. Geometry of oxocarbenium/borohydride ion pairs is flexible, meaning that we uncover significant actual structural disorder at a finite temperature. Therefore, although the starting structure can be fairly close to the configurational area of the hydride transfer transition state (TS) and despite a low potential energy barrier (ca. 1.5 kcal/mol, according to the literature), already at T approximate to 325 K the system can remain ignorant of the TS region and move round and about (roam) in the configurational space for a period of time in the range between 10 and 100 ps. This indicates structural flexibility of oxocarbenium/borohydride ion pair on apparently a flat potential energy landscape of cation/anion interaction, and this has not been taken into consideration by the free energy estimations in static considerations made thus far. The difference between the dynamics-based representation of the system versus the static representation amounts to the difference between quasi-bimolecular versus unimolecular descriptions of the hydride transfer step.

  • 15.
    Heshmat, Mojgan
    et al.
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Privalov, Timofei
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    Surprisingly Flexible Oxonium/Borohydride Ion Pair Configurations2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 15, p. 3713-3727Article in journal (Refereed)
    Abstract [en]

    We investigate the geometry of oxonium/borohydride ion pairs [ether-H(+) ether] [LA-H(-)] with dioxane, THF, and Et2O as ethers and B(C6F5)(3) as the Lewis acid (LA). The question is about possible location of the disolvated proton [ether -H(+) -ether], with respect to the hydride of the structurally complex [LA -H(-)] anion. Using Born Oppenheimer molecular dynamics and a comparison of the potential and free energies of the optimized configurations, we show that herein considered ion pairs are much more flexible geometrically than previously thought. Conformers with different locations of cations with respect to anions are governed by a flat energy -landscape. We found a novel configuration in which oxonium is below [LA-11((-))], with respect to the direction of borane -> hydride vector, and the proton -hydride distance is ca. 6 A. With calculations of the vibrational spectra of [ether-H(+)-ether][(C6F5)(3)B-H(-)] for dioxane, THF, and Et2O as ethers, we investigate the manifestation of SSLB-type (short, strong, low -barrier) hydrogen bonding in the OHO motif of an oxonium cation.

  • 16. Isac, Dragos Lucian
    et al.
    Airinei, Anton
    Maftei, Dan
    Humelnicu, Ionel
    Mocci, Francesca
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK). Petru Poni Institute of Macromolecular Chemistry, Romania.
    Pinteala, Mariana
    On the Charge-Transfer Excitations in Azobenzene Maleimide Compounds: A Theoretical Study2019In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 123, no 26, p. 5525-5536Article in journal (Refereed)
    Abstract [en]

    Photoswitchable systems with charge-transfer (CT) transitions have gained much attention during the recent years because of their many emerging applications. CT transitions themselves are of fundamental importance from physical, chemical, engineering, and molecular modeling points of view because they depend on the modified intramolecular electronic structure. CT transitions in azobenzene (AB) were observed when substituted with the maleimide (MI) functional group. This work represents a systematic theoretical study of excited states of the AB MI structures of eight azo derivatives. In addition to the two main azo transitions (pi -> pi* and n -> pi*), our calculations show a CT occurring between the azo moiety as a donor and the MI group as an acceptor. The CT mechanism can be characterized based on both the number and the position of the MI fragments. MI groups in the azo structure result in low-energy transitions, changing the order of the main transitions by introducing a CT character. Calculations using both density functional theory (DFT) and high-end molecular orbital theories confirm the CT character of these derivatives, although the order of excited states was found to differ depending on the chosen level of theory. We present here the first theoretical investigation of the electronic excited states (n pi*CT and pi pi*CT) and corresponding transitions for this class of compounds. The computational results showed that the CT mechanism in AB MI derivatives can occur via two pathways: planar and twisted. Our findings are expected to be of substantial interest, especially in the area of molecular optoelectronics and in the design of responsive materials.

  • 17.
    Julin, Jan
    et al.
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Shiraiwa, Manabu
    Miles, Rachael E. H.
    Reid, Jonathan P.
    Poschl, Ulrich
    Riipinen, Ilona
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Mass Accommodation of Water: Bridging the Gap Between Molecular Dynamics Simulations and Kinetic Condensation Models2013In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, no 2, p. 410-420Article in journal (Refereed)
    Abstract [en]

    The condensational growth of submicrometer aerosol particles to climate relevant sizes is sensitive to their ability to accommodate vapor molecules, which is described by the mass accommodation coefficient. However, the underlying processes are not yet fully understood. We have simulated the mass accommodation and evaporation processes of water using molecular dynamics, and the results are compared to the condensation equations derived from the kinetic gas theory to shed light on the compatibility of the two. Molecular dynamics simulations were performed for a planar TIP4P-Ew water surface at four temperatures in the range 268-300 K as well as two droplets, with radii of 1.92 and 4.14 nm at T = 273.15 K. The evaporation flux from molecular dynamics was found to be in good qualitative agreement with that predicted by the simple kinetic condensation equations. Water droplet growth was also modeled with the kinetic multilayer model KM-GAP of Shiraiwa et al. [Atmos. Chem. Phys. 2012, 12, 2777]. It was found that, due to the fast transport across the interface, the growth of a pure water droplet is controlled by gas phase diffusion. These facts indicate that the simple kinetic treatment is sufficient in describing pure water condensation and evaporation. The droplet size was found to have minimal effect on the value of the mass accommodation coefficient. The mass accommodation coefficient was found to be unity (within 0.004) for all studied surfaces, which is in agreement with previous simulation work. Additionally, the simulated evaporation fluxes imply that the evaporation coefficient is also unity. Comparing the evaporation rates of the mass accommodation and evaporation simulations indicated that the high collision flux, corresponding to high supersaturation, present in typical molecular dynamics mass accommodation simulations can under certain conditions lead to an increase in the evaporation rate. Consequently, in such situations the mass accommodation coefficient can be overestimated, but in the present cases the corrected values were still close to unity with the lowest value at approximate to 10.99.

  • 18. Kelly, Orla
    et al.
    Calvert, Christopher R.
    Greenwood, Jason B.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Nielsen, Steen Brondsted
    Wyer, Jean A.
    Effects of Charge Location on the Absorptions and Lifetimes of Protonated Tyrosine Peptides in Vacuo2012In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, no 7, p. 1701-1709Article in journal (Refereed)
    Abstract [en]

    Nearby charges affect the electronic energy levels of chromophores, with the extent of the effect being determined by the magnitude of the charge and degree of charge-chromophore separation. The molecular configuration dictates the charge chromophore distance. Hence, in this study, we aim to assess how the location of the charge influences the absorption of a set of model protonated and diprotonated peptide ions, and whether spectral differences are large enough to be identified. The studied ions were the dipeptide YK, the tripeptide KYK (Y = tyrosine; K = lysine) and their complexes with 18-crown-6-ether (CE). The CE targets the ammonium group by forming internal ionic hydrogen bonds and limits the folding of the peptide. In the tripeptide, the distance between the chromophore and the backbone ammonium is enlarged relative to that in the dipeptide. Experiments were performed in an electrostatic ion storage ring using a tunable laser system, and action spectra based on lifetime measurements were obtained in the range from 210 to 310 nm. The spectra are all quite similar though there seems to be some changes in the absorption band between 210 and 250 nm, while in the lower energy band all ions had a maximum absorption at similar to 275 nm. Lifetimes after photoexcitation were found to shorten upon protonation and lengthen upon CE complexation, in accordance with the increased number of degrees of freedom and an increase in activation energies for dissociation as the mobile proton model is no longer operative.

  • 19.
    Kulyk, Kostiantyn
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Wolf, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Gatchell, Michael
    Stockholm University, Faculty of Science, Department of Physics. Universität Innsbruck, Austria.
    Giacomozzi, Linda
    Stockholm University, Faculty of Science, Department of Physics.
    Vegvari, Akos
    Kovalenko, Oleksandr
    de Ruette, Nathalie
    Stockholm University, Faculty of Science, Department of Physics.
    Wendt, Ola
    Zubarev, Roman
    Schmidt, T. Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Cederquist, Henrik
    Stockholm University, Faculty of Science, Department of Physics.
    Zettergren, Henning
    Stockholm University, Faculty of Science, Department of Physics.
    Collision Induced Dissociation of the retinal chromophore Schiff base from sub-eV to keV collision energiesIn: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215Article in journal (Refereed)
    Abstract [en]

    The gas-phase fragmentation of the protonated n-butylamine Schiff base of all-trans-retinal (NB-RPSB) was measured in low- and high-energy collisional activation modes. The protonated n-butyl β-ionone Schiff base (NB-BISB) peak at m/z = 248, known to be formed as a result of a complex gas-phase rearrangement reaction, has been reported to dominate in mass spectra of NB-RPSB after photo- and collisionally activated fragmentation processes. Earlier reported high-energy collision (50 keV) mass spectra have shown a broad distribution of the fragments with the peak at m/z = 248 present but not dominating. We observed the formation of a peak at m/z = 248 only in collisional activation of NB-RPSB parent ion below a few eV, which shows that the rearrangement process is extremely efficient and happens in a very narrow energy range. On the other hand, our high-energy collision induced dissociation experiments yielded fragmentation patterns, which are fully accounted for simple bond cleavages of the NB-RPSB molecular backbone. We do not observe any peak corresponding to the formation of NB-BISB in the 10 eV – 1 keV collision energy range. This leaves the question open why this fragment reappears in the mass spectra at much higher energies.

  • 20.
    Lenori, Francesca
    et al.
    Universitá di Perugia.
    Petrucci, Raffaelo
    Universitá di Perugia.
    Hickson, Kevin E.
    Université Bordeaux 1.
    Hamberg, Mathias
    Stockholm University, Faculty of Science, Department of Physics.
    Casavecchia, Piergiorgio
    Universitá di Perugia.
    Geppert, Wolf
    Stockholm University, Faculty of Science, Department of Physics.
    Crossed-Beam and Theoretical Studies of the S(1D) + C2H2 Reaction2009In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 113, p. 4330-Article in journal (Refereed)
    Abstract [en]

    The reaction dynamics of excited sulfur atoms, S(D-1), with acetylene has been investigated by the crossed-beam scattering technique with mass spectrometric detection and time-of-flight (TOF) analysis at the collision energy of 35.6 kJ mol(-1). These studies have been made possible by the development of intense continuous supersonic beams of S(P-3,D-1) atoms. From product angular and TOF distributions, center-of-mass product angular and translational energy distributions are derived. The S(D-1) + C2H2 reaction is found to lead to formation of HCCS (thioketenyl) + H, while the only other energetically allowed channels, those leading to CCS((3)Sigma(-), Delta) + H-2, are not observed to occur to an appreciable extent. The dynamics of the H-elimination channel is discussed and elucidated. The interpretation of the scattering results is assisted by synergic high-level ab initio electronic structure calculations of stationary points and product energetics for the C2H2S ground-state singlet potential energy surface. In addition, by exploiting the novel capability of performing product detection by means of a tunable electron-impact ionizer, we have obtained the first experimental information on the ionization energy of thioketenyl radical, HCCS, as synthesized in the reactive scattering experiment. This has been complemented by ab initio calculations of the adiabatic and vertical ionization energies for the ground-state radical. The theoretically derived value of 9.1 eV confirms very recent, accurate calculations and is corroborated by the experimentally determined ionization threshold of 8.9 +/- 0.3 eV for the internally warm HCCS produced from the title reaction.

  • 21.
    Lindén, Fredrik
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Alcaraz, Christian
    Ascenzi, Daniela
    Guillemin, Jean-Claude
    Koch, Leopold
    Lopes, Allan
    Polášek, Miroslav
    Romanzin, Claire
    Zabka, Jan
    Zymak, Illia
    Geppert, Wolf D.
    Stockholm University, Faculty of Science, Department of Physics.
    Is the Reaction of C3N- with C2H2 a Possible Process for Chain Elongation in Titan's Ionosphere?2016In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, no 27, p. 5337-5347Article in journal (Refereed)
    Abstract [en]

    The reaction of C3N- with acetylene was studied using three different experimental setups, a triple quadrupole mass spectrometer (Trento), a tandem quadrupole mass spectrometer (Prague), and the CERISES guided ion beam apparatus at Orsay. The process is of astrophysical interest because it can function as a chain elongation mechanism to produce larger anions that have been detected in Titan's ionosphere by the Cassini Plasma Spectrometer. Three major products of primary processes, C2H-, CN-, and C5N-, have been identified, whereby the production of the cyanide anion is probably partly due to collisional induced dissociation. The formations of all these products show considerable reaction thresholds and also display comparatively small cross sections. Also, no strong signals of anionic products for collision energies lower than 1 eV have been observed. Ab initio calculations have been performed to identify possible pathways leading to the observed products of the title reaction and to elucidate the thermodynamics of these processes. Although the productions of CN- and C5N- are exoergic, all reaction pathways have considerable barriers. Overall, the results of these computations are in agreement with the observed reaction thresholds. Due to the existence of considerable reaction enenrgy barriers and the small observed cross sections, the title reaction is not very likely to play major role in the buildup of large anions in cold environments like the interstellar medium or planetary and satellite ionospheres.

  • 22. Martini, Paul
    et al.
    Kranabetter, Lorenz
    Goulart, Marcelo
    Rasul, Bilal
    Gatchell, Michael
    Stockholm University, Faculty of Science, Department of Physics. Universität Innsbruck, Austria.
    Scheier, Paul
    Echt, Olof
    Atomic Gold Ions Clustered with Noble Gases: Helium, Neon, Argon, Krypton, and Xenon2019In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 123, no 44, p. 9505-9513Article in journal (Refereed)
    Abstract [en]

    High-resolution mass spectra of helium droplets doped with gold and ionized by electrons reveal HenAu+ cluster ions. Additional doping with heavy noble gases results in NenAu+, ArnAu+, KrnAu+, and XenAu+ cluster ions. The high stability predicted for covalently bonded Ar2Au+, Kr2Au+, and Xe2Au+ is reflected in their relatively high abundance. Surprisingly, the abundance of Ne2Au+, which is predicted to have zero covalent bonding character and no enhanced stability, features a local maximum, too. The predicted size and structure of complete solvation shells surrounding ions with essentially nondirectional bonding depends primarily on the ratio sigma* of the ion-ligand versus the ligand-ligand distance. For Au+ solvated in helium and neon, the ratio sigma* is slightly below 1, favoring icosahedral packing in agreement with a maximum observed in the corresponding abundance distributions at n = 12. HenAu+ appears to adopt two additional solvation shells of I-h symmetry, containing 20 and 12 atoms, respectively. For ArnAu+, with sigma* approximate to 0.67, one would expect a solvation shell of octahedral symmetry, in agreement with an enhanced ion abundance at n = 6. Another anomaly in the ion abundance at Ar9Au+ matches a local maximum in its computed dissociation energy.

  • 23. Matsuda, Akitaka
    et al.
    Fushitani, Mizuho
    Thomas, Richard D.
    Stockholm University, Faculty of Science, Department of Physics.
    Zhaunerchyk, Vitali
    Stockholm University, Faculty of Science, Department of Physics.
    Hishikawa, Akiyoshi
    Multiple Explosion Pathways of the Deuterated Benzene Trication in 9-fs Intense Laser Fields2009In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 113, no 11, p. 2254-2260Article in journal (Refereed)
    Abstract [en]

    The fragmentation of deuterated benzene (CA) in ultrashort intense laser fields (9 fs, 1 x 10(15) W/cm(2)) is studied by the ion-coincidence momentum imaging technique. Five two-body and eight three-body Coulomb explosion pathways from the trication (C6D63+), associated with the deprotonation and ring-opening reactions, are identified. It is found from the fragment momentum correlation that all the observed three-body explosion processes proceed sequentially via the two-body Coulomb explosion forming molecular dications, CmDn2+, with (m,n) = (6,5), (5,5), (5,4), (4,4), (4,3), and (3,3), which further dissociate into pairs of monocations. The branching ratio of the fragmentation pathways estimated from the number of the observed coincidence events indicates that the fragmentation is nonstatistical.

  • 24.
    Mijovilovich, Ana
    et al.
    Utrecht University, The Netherlands.
    Pettersson, Lars G.M.
    Stockholm University, Faculty of Science, Department of Physics.
    de Groot, Frank M.F.
    Utrecht University, The Netherlands.
    Weckhuysen, Bert M.
    Utrecht University, The Netherlands.
    Functional groups and sulfur K-edge XANES spectra: study of sulfides and disulfides2010In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 114, no 35, p. 9523-9528Article in journal (Refereed)
    Abstract [en]

    Sulfur K-edge XANES was measured for two divalent sulfurs (dibenzyl and benzyl phenyl) and two disulfides (dibenzyl and diphenyl). The absorption spectra could be assigned using density functional theory with the “half core hole” approximation for the core hole including relaxation of selected excited states at the absorption edge. Analysis of the molecular orbitals shows that the characteristic double peak of the dibenzyl disulfide arises as a consequence of the enhanced splitting of the LUMO (lowest unoccupied molecular orbital) and the LUMO + 1. Exchange of the ligand benzyl by phenyl introduces more transitions at the absorption edge, which enhance the broadening in the divalent sulfur and splitting of the peaks of the disulfide. It is shown that different ligand groups introduce significant differences in the absorption edge, which poses a problem for the speciation analysis when the ligand groups are not clearly defined.

  • 25. Miles, Rachael E. H.
    et al.
    Reid, Jonathan P.
    Riipinen, Ilona
    Stockholm University, Faculty of Science, Department of Applied Environmental Science (ITM).
    Comparison of Approaches for Measuring the Mass Accommodation Coefficient for the Condensation of Water and Sensitivities to Uncertainties in Thermophysical Properties2012In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 116, no 44, p. 10810-10825Article in journal (Refereed)
    Abstract [en]

    We compare and contrast measurements of the mass accommodation coefficient of water on a water surface made using ensemble and single particle techniques under conditions of supersaturation and subsaturation, respectively. In particular, we consider measurements made using an expansion chamber, a continuous flow streamwise thermal gradient cloud condensation nuclei chamber, the Leipzig Aerosol Cloud Interaction Simulator, aerosol optical tweezers, and electrodynamic balances. Although this assessment is not intended to be comprehensive, these five techniques are complementary in their approach and give values that span the range from near 0.1 to 1.0 for the mass accommodation coefficient. We use the same semianalytical treatment to assess the sensitivities of the measurements made by the various techniques to thermophysical quantities (diffusion constants, thermal conductivities, saturation pressure of water, latent heat, and solution density) and experimental parameters (saturation value and temperature). This represents the first effort to assess and compare measurements made by different techniques to attempt to reduce the uncertainty in the value of the mass accommodation coefficient. Broadly, we show that the measurements are consistent within the uncertainties inherent to the thermophysical and experimental parameters and that the value of the mass accommodation coefficient should be considered to be larger than 0.5. Accurate control and measurement of the saturation ratio is shown to be critical for a successful investigation of the surface transport kinetics during condensation/evaporation. This invariably requires accurate knowledge of the partial pressure of water, the system temperature, the droplet curvature and the saturation pressure of water. Further, the importance of including and quantifying the transport of heat in interpreting droplet measurements is highlighted; the particular issues associated with interpreting measurements of condensation/evaporation rates with varying pressure are discussed, measurements that are important for resolving the relative importance of gas diffusional transport and surface kinetics.

  • 26. Myllys, Nanna
    et al.
    Chee, Sabrina
    Olenius, Tinja
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Lawler, Michael
    Smith, James
    Molecular-Level Understanding of Synergistic Effects in Sulfuric Acid-Amine-Ammonia Mixed Clusters2019In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 123, no 12, p. 2420-2425Article in journal (Refereed)
    Abstract [en]

    The abundance and basicity of a stabilizing base have shown to be key factors in sulfuric acid driven atmospheric new-particle formation. However, since experiments indicate that a low concentration of ammonia enhances particle formation from sulfuric acid and dimethylamine, which is a stronger base, there must be additional factors affecting the particle formation efficiency. Using quantum chemistry, we provide a molecular-level explanation for the synergistic effects in sulfuric acid-dimethylamine-ammonia cluster formation. Because of the capability of ammonia to form more intermolecular interactions than dimethylamine, it can act as a bridge-former in sulfuric acid-dimethylamine clusters. In many cluster compositions, ammonia is more likely to be protonated than dimethylamine, although it is a weaker base. By nanoparticle formation rate simulations, we show that due to the synergistic effects, ammonia can increase the particle formation rate by up to 5 orders of magnitude compared to the two-component sulfuric acid-amine system.

  • 27. Myllys, Nanna
    et al.
    Olenius, Tinja
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Kurtén, Theo
    Vehkamäki, Hanna
    Riipinen, Ilona
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Elm, Jonas
    Effect of Bisulfate, Ammonia, and Ammonium on the Clustering of Organic Acids and Sulfuric Acid2017In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 121, no 25, p. 4812-4824Article in journal (Refereed)
    Abstract [en]

    We investigate the effect of the bisulfate anion HSO4-, ammonium cation NH4+, and ammonia NH3 on the clustering of sulfuric acid and pinic acid or 3-methyl-1,2,3-butanetricarboxylic acid (MBTCA). The systems were chosen based on their expected relevance in atmospheric new particle formation. Using quantum chemical methods together with kinetic calculations, we study the ability of these compounds to enhance cluster formation and growth. The cluster structures are obtained and frequencies are calculated using three different DFT functionals (M06-2X, PW91, and omega B97X-D) with the 6-31++G(d,p) basis set. The electronic energies are corrected using an accurate DLPNO-CCSD(T)/def2-QZVPP level of theory. The evaporation rates are evaluated based on the calculated Gibbs free energies. The interaction between the ions and sulfuric acid or carboxylic acid group is strong, and thereby small two-component ionic clusters are found to be very stable against evaporation. The presence of bisulfate stimulates the cluster formation through addition of the sulfuric acid, whereas the presence of ammonium favors the addition of organic acids. Bisulfate and ammonium enhance the first steps of cluster formation; however, at atmospheric conditions further cluster growth is limited due to the weak interaction and fast evaporation of the larger three-component clusters. On the basis of our results it is therefore unlikely that the studied organic acids and sulfuric acid, even together with bisulfate, ammonia, or ammonium can drive new-particle formation via clustering mechanisms. Other mechanisms such as chemical reactions are needed to explain observed new-particle formation events in the presence of oxidized organic compounds resembling the acids studied here.

  • 28. Myllys, Nanna
    et al.
    Ponkkonen, Tuomo
    Passananti, Monica
    Elm, Jonas
    Vehkämaki, Hanna
    Olenius, Tinja
    Stockholm University, Faculty of Science, Department of Environmental Science and Analytical Chemistry.
    Guanidine: A Highly Efficient Stabilizer in Atmospheric New-Particle Formation2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 20, p. 4717-4729Article in journal (Refereed)
    Abstract [en]

    The role of a strong organobase, guanidine, in sulfuric acid-driven new-particle formation is studied using state-of-the-art quantum chemical methods and molecular cluster formation simulations. Cluster formation mechanisms at the molecular level are resolved, and theoretical results on cluster stability are confirmed with mass spectrometer measurements. New-particle formation from guanidine and sulfuric acid molecules occurs without thermodynamic barriers under studied conditions, and clusters are growing close to a 1:1 composition of acid and base. Evaporation rates of the most stable clusters are extremely low, which can be explained by the proton transfers and symmetrical cluster structures. We compare the ability of guanidine and dimethylamine to enhance sulfuric acid-driven particle formation and show that more than 2000-fold concentration of dimethylamine is needed to yield as efficient particle formation as in the case of guanidine. At similar conditions, guanidine yields 8 orders of magnitude higher particle formation rates compared to dimethylamine. Highly basic compounds such as guanidine may explain experimentally observed particle formation events at low precursor vapor concentrations, whereas less basic and more abundant bases such as ammonia and amines are likely to explain measurements at high concentrations.

  • 29.
    Nozière, Barbara
    et al.
    Stockholm University, Faculty of Science, Department of Meteorology .
    Córdova, Armando
    Stockholm University, Faculty of Science, Department of Organic Chemistry.
    A Kinetic and Mechanistic Study of the Amino Acid Catalyzed Aldol Condensation of Acetaldehyde in Aqueous and Salt Solutions2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 13, p. 2827-2837Article in journal (Refereed)
    Abstract [en]

    The amino acid-catalyzed aldol condensation is of great interest in organic synthesis and natural environments such as atmospheric particles. But kinetic and mechanistic information on these reactions is limited. In this work, the kinetics of the aldol condensation of acetaldehyde in water and aqueous salt solutions (NaCl, CaCl2, Na2SO4, MgSO4), catalyzed by five amino acids (glycine, alanine, serine, arginine, and proline) at room temperature (295 ± 2K) has been studied. Monitoring the formation of three products, crotonaldehyde, 2,4-hexadienal, and 2,4,6-octatrienal by UV-Visible absorption over 200 – 1100 nm revealed two distinct kinetic regimes: at low amino acid concentrations (in all cases, below 0.1 M) the overall reaction was first order with respect to acetaldehyde and kinetically limited by the formation of the enamine intermediate. At larger amino acid concentrations (at least 0.3 M) the kinetics was second order and controlled by the C-C bond-forming step. The first-order rate constants increased linearly with amino acid concentration, consistent with the enamine formation. Inorganic salts further accelerated the enamine formation according to their pKb plausibly by facilitating the iminium and/or enamine formation. The rate constant of the C-C bond-forming step varied with the square of amino acid concentration, suggesting the involvement of two amino acid molecules. Thus, the reaction proceeded via a Mannich pathway. However, the contribution of an aldol pathway, first-order in amino acid, could not be excluded. Our results show that the rate constant for the self-condensation of acetaldehyde in aqueous atmospheric aerosols (up to 10 of mM of amino acids) is identical as in sulfuric acid 10 - 15 M (kI ~ 10-7 - 10-6 s-1), clearly illustrating the potential importance of amino acid catalysis in natural environments. This work also demonstrates that under usual laboratory conditions and in natural environments aldol condensation is likely to be kinetically controlled by the enamine formation. Notably, kinetic investigations of the C-C bond-forming addition step would only be possible with high concentrations of amino acids.

  • 30.
    Odelius, Michael
    Stockholm University, Faculty of Science, Department of Physics.
    Information content in O[1s] K-edge X-ray emission spectroscopy of liquid water.2009In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 113, no 29, p. 8176-81Article in journal (Refereed)
    Abstract [en]

    Does the fine-structure in oxygen K-edge X-ray emission (Fuchs et al. Phys. Rev. Lett. 2008, 100, 027801) imply that liquid water is a two-component mixture or is it the signature of a transient OH species arising in the core-excitation process? As with the interpretation of the X-ray absorption spectrum of liquid water, this question is also intensely discussed in the water and X-ray spectroscopy communities. X-ray emission is an independent probe of the electronic structure yielding complementary information on hydrogen bonding in liquid water. In this study, the angular anisotropy in the resonant inelastic soft X-ray scattering (resonant X-ray emission (XE)) spectrum of liquid water is simulated on the basis of ab initio molecular dynamics simulations to allow for direct comparison to recent experimental data (Forsberg et al. Phys. Rev. B 2009, 79, 132203). Theoretical simulations unequivocally show that the difference in angular anisotropy in the water lone-pair features is related to their fundamentally different origin. The high emission-energy peak is primarily due to the contribution from the out-of-plane (1b(1)) lone-pair in intact water molecules. On the other hand, the low emission-energy lone-pair peak originates from the bonding (3a(1)) state and is assigned to a transient OH species formed by ultrafast (<10 fs) photodissociation. The information in the XE spectrum on the structure of liquid water is limited and buried in features arising from excited state dynamics. In combination with available experimental data, the theoretical simulations settle a rising debate on the interpretation of resonant and nonresonant XE spectra of liquid water and there are strong implications for the XE spectroscopy of hydrogen-bonded liquids. The simulations show that the fine-structure in the XE spectrum of liquid water can be explained simply in terms of present day ab initio molecular dynamics simulations.

  • 31. Petrov, Oleg
    et al.
    Tosner, Zdenek
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Csöregh, Ingeborg
    Kowalewski, Jozef
    Sandström, Dick
    Dynamics of Chloromethanes in Cryptophane-E Inclusion Complexes: A H-2 Solid State NMR and X-ray Diffraction Study2005In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 109, no 20, p. 4442-4451Article in journal (Refereed)
    Abstract [en]

    In this paper, we present a variable temperature 2H solid-state NMR investigation of cryptophane-E:chloroform and cryptophane-E:dichloromethane inclusion complexes. The 2H line shapes and nuclear spin relaxation rates were analyzed in terms of the distribution of C−D bond orientations and the time scale of the guest dynamics. It was found that encaged chloroform produces broad 2H spectra, and that its reorientation is relatively slow with a correlation time of 0.17 μs at 292 K. In contrast, the 2H line shapes of encaged dichloromethane are narrow and the motion of this guest molecule is fast with a correlation time of 1.4 ps at 283 K. The 2H NMR data were complemented by an X-ray diffraction study of the cryptophane-E:dichloromethane structure, which was utilized in the analysis of the NMR parameters.

  • 32. Pitsevich, G.
    et al.
    Malevich, A.
    Kozlovskaya, E.
    Mahnach, E.
    Doroshenko, I.
    Pogorelov, V.
    Pettersson, Lars G. M.
    Stockholm University, Faculty of Science, Department of Physics.
    Sablinskas, V.
    Balevicius, V.
    MP4 Study of the Anharmonic Coupling of the Shared Proton Stretching Vibration of the Protonated Water Dimer in Equilibrium and Transition States2017In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 121, no 10, p. 2151-2165Article in journal (Refereed)
    Abstract [en]

    The structure and harmonic and anharmonic IR spectra of the protonated water dimer (PWD) were calculated in C-1,C- C-2.., and C-s, symmetry at the MP4/acc-pVTZ level of theory. We found that structure and IR spectra are practically identical in C-2 and C-1 symmetry, demonstrating that an equilibrium C-1 configuration of the PWD is not realized. Anharmonic coupling of the shared proton stretching-vibration with all other modes in the PWD in C-2 and C-s symmetry was the focus of this investigation. For this purpose, 28 two-dimensional potential energy surfaces (2D PES) were built at the MP4/acc-pVTZ level of theory and the corresponding vibrational Schrodinger equations were solved using the DVR method. Differences in the coupling of the investigated mode with other modes in the C-2 and C-s configurations, along with some factors that determine the red-or blue-shift of the stretching vibration frequency, were analyzed. We obtained a rather reasonable value of the stretching frequency of the bridging proton (1058.4 cm(-1)) unperturbed by Fermi resonance. The Fermi resonance between the fundamental vibration v7 and the combined vibration v(2) + v(6) of the same symmetry was analyzed through anharmonic second order perturbation theory calculations, as well as by 3D PES constructed using Q(2), Q(6), and Q(7) as normal coordinates. A significant (up to 50%) transfer of intensity from the fundamental vibration to the combined one was found. We have estimated the frequency of the bridging proton stretching vibration in the C-s configuration of the PWD based on calculations of the intrinsic anharmonicity and anharmonic double modes interactions at the MP4/acc-pVTZ level of theory (1261 cm(-1)).

  • 33. Plasson, Raphael
    et al.
    Brandenburg, Axel
    Stockholm University, Faculty of Science, Department of Astronomy. Stockholm University, Nordic Institute for Theoretical Physics (Nordita).
    Jullien, Ludovic
    Bersini, Hugues
    Autocatalyses2011In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 115, no 28, p. 8073-8085Article in journal (Refereed)
    Abstract [en]

    Autocatalysis is a fundamental concept, used in a wide range of domains. From the most general definition of autocatalysis, that is, a process in which a chemical compound is able to catalyze its own formation, several different systems can be described. We detail the different categories of autocatalyses and compare them on the basis of their mechanistic, kinetic, and dynamic properties. It is shown how autocatalytic patterns can be generated by different systems of chemical reactions. With the notion of autocatalysis covering a large variety of mechanistic realizations with very similar behaviors, it is proposed that the key signature of autocatalysis is its kinetic pattern expressed in a mathematical form.

  • 34.
    Rudbeck, Maria E.
    et al.
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Kumar, Saroj
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    Mroginski, Maria-Andrea
    Nilsson Lill, Sten O.
    Stockholm University, Faculty of Science, Department of Physics.
    Blomberg, Margareta R. A.
    Stockholm University, Faculty of Science, Department of Physics.
    Barth, Andreas
    Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
    The Infrared Spectrum of Phosphoenol Pyruvate: Computational and Experimental Studies2009In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 113, no 12, p. 2935-2942Article in journal (Refereed)
    Abstract [en]

    The infrared spectrum of phosphoenol pyruvate (PEP) in aqueous solution was studied experimentally and theoretically in its fully ionized, singly protonated and doubly protonated form. The density functional theory with the B3LYP functional and with the 6-31G(d,p), 6-31++G(d,p), and 6-311++G(d,p) basis sets were used in the theoretical study. The calculations with the two latter basis sets and the CPCM continuum model for water showed good agreement with the experiments except for vibrations assigned to hydroxyl groups. These needed to be modeled with explicit water molecules. The effects of deuteration and of 13C2,3 labeling of PEP were reproduced by the calculations.

  • 35.
    Ruiperez, Fernando
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Wahlgren, Ulf
    Stockholm University, Faculty of Science, Department of Physics.
    Charge Transfer in Uranyl(VI) Halides [UO2X4]2− (X = F, Cl, Br, and I). A Quantum Chemical Study of the Absorption Spectra2010In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 114, no 10, p. 3615-3621Article in journal (Refereed)
    Abstract [en]

    The electronic spectra of uranyl(VI) coordinated with four equatorial halide ligands, [UO2X4]2− (X = F, Cl, Br, and I), have been calculated at the all-electron level using the multiconfigurational CASPT2 method, with spin−orbit coupling included through the variational-perturbational method. The halide-to-uranyl charge-transfer states were taken into account in the calculation by including ligand orbitals in the active space. In order to do that, it is assumed that the charge transfer takes place from only one of the four ligands. Two models, which in principle can describe this, were investigated: the first one makes use of a localizing technique and the second one replaces three ligands by ab initio model potentials (AIMPs). The basis set dependence was investigated by using two different basis sets for the halides, of triple-ζ and quadruple-ζ quality. The localization procedure turned out to be strongly basis set dependent, and the most stable results were obtained with ab initio model potentials. The ground state is a closed shell singlet state, and the first excitation is from the bonding σu orbital on uranyl to the nonbonding δu orbitals, except for the [UO2I4]2− complex, where the first excited state has a mixed character of charge transfer from the I and the σu1u1 configuration. In [UO2F4]2− there is no charge transfer excitation below 50000 cm−1, while in [UO2Cl4]2− it appears around 33000 cm−1 and in [UO2Br4]2− around 23000 cm−1. A blueshift of the spectra, from F to I, is observed. The calculations compare reasonably well with available experimental results.

  • 36.
    Ruipérez, Fernando
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Danilo, Cécile
    Laboratoire PhLAM, Université des Sciences et Technologies de Lille 1.
    Real, Florent
    Laboratoire PhLAM, Université des Sciences et Technologies de Lille 1.
    Flament, Jean-Pierre
    Laboratoire PhLAM, Université des Sciences et Technologies de Lille 1.
    Vallet, Valérie
    Laboratoire PhLAM, Université des Sciences et Technologies de Lille 1.
    Wahlgren, Ulf
    Stockholm University, Faculty of Science, Department of Physics.
    An ab initio theoretical study of the electronic structure of UO2+ and [UO2(CO3)3]5-2009In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 113, p. 1420-1428Article in journal (Refereed)
    Abstract [en]

    The electronic spectra up to 50000 cm-1 of uranyl(V) both as a bare ion, UO21, and coordinated with three carbonate ligands, [UO2(CO3)3]5-, are presented. Solvent effects were treated by a nonequilibrium continuum solvent model. The transition energies were obtained at the spin-orbit level using relativistic wave function based multiconfigurational methods such as the complete active space self-consistent field method (CASSCF) and the complete active space with second-order perturbation theory (CASPT2) followed by a calculation of the spin-orbit effects at the variation-perturbation level. Earlier relativistic intermediate Hamiltonian Fock space coupled-cluster calculations on the spectrum of the bare uranyl(V) ion were extended to investigate the influence of electron correlation effects on spacings between the electronic states. This study is an attempt to contribute to an enhanced understanding of the electronic structure of actinyl ions. Both spectra show transitions within nonbonding orbitals and between nonbonding and antibonding orbitals as well as charge transfers from the uranyl oxygens to uranium. The ground state in UO2+ is found to be 2Φ5/2u, corresponding to the σu2φu1 configuration, while in [UO2(CO3)3]5-, it is 23/2u, arising from the σu2δu1 configuration. It is remarkable that the excited state corresponding to an excitation from the nonbonding δu to the uranyl antibonding 3πu* molecular orbital is significantly lower in energy in the carbonate complex, 6623 cm-1, than that in the bare ion, 17908 cm-1. The first ligand (carbonate) to metal charge-transfer excitation is estimated to occur above 50000 cm-1. The reported results compare favorably with experiment when available.

  • 37.
    Ruipérez, Fernando
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Wahlgren, Ulf
    Stockholm University, Faculty of Science, Department of Physics.
    Charge transfer in uranyl(VI) halides [UO2X4]2- (X = F, Cl, Br and I). A quantum chemical study of the absorption spectraIn: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215Article in journal (Refereed)
    Abstract [en]

    The electronic spectra of uranyl(VI) coordinated with four equatorial halide ligands, [UO2X4]2- (X = F, Cl, Br and I), have been calculated at the all-electron level using the multiconfigurational CASPT2 method, with spin-orbit coupling included through the variational-perturbational method. The halide-to-uranyl charge-transfer states were taken into account in the calculation by including ligand orbitals in the active space. In order to do that, it is assumed that the charge transfer takes place from only one of the four ligands. Two models which in principle can describe this were investigated: the first one makes use of a localizing technique and the second one replaces three ligands by ab initio model potentials (AIMPs). The basis set dependence was investigated by using two different basis sets for the halides, of triple-ζ and quadruple-ζ quality. The localization procedure turned out to be strongly basis set dependent, and the most stable results were obtained with ab initio model potentials. The ground state is a closed shell singlet state, and the first excitation is from the bonding σu orbital on uranyl to the nonbonding δu orbitals, except for the [UO2I4]2− complex, where the first excited state has a mixed character of charge transfer from the I and the σu1φu1 configuration. In [UO2F4]2− there is no charge transfer excitation below 50000 cm−1 , while in [UO2Cl4]2− it appears around 33000 cm−1 and in [UO2Br4]2− around 23000 cm−1 . A blueshift of the spectra, from F to I, is observed. The calculations compare reasonably well with available experimental results.

  • 38.
    Schalk, Oliver
    et al.
    Stockholm University, Faculty of Science, Department of Physics. University of Munich.
    Boguslavskiy, Andrei E.
    Schuurman, Michael S.
    Brogaard, Rasmus Y.
    Unterreiner, Andreas N.
    Wrona-Piotrowicz, Anna
    Werstiuk, Nick H.
    Stolow, Albert
    Substituent Effects on Dynamics at Conical Intersections: Cycloheptatrienes2013In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, no 40, p. 10239-10247Article in journal (Refereed)
    Abstract [en]

    Using selective methyl substitution, we study the effects of vibrational dynamics at conical intersections in unsaturated hydrocarbons. Here, we investigate the excited state nonadiabatic dynamics of cycloheptatriene (CHT) and its relation to dynamics in other polyenes by comparing CHT with 7-methyl CHT, 7-ethyl CHT, and perdeuterated CHT using time-resolved photoelectron spectroscopy and photoelectron anisotropy. Our results suggest that, upon pi pi*-excitation to the bright 2A state, we observe an early intersection with the dark 2A' state close to the Franck-Condon region with evidence of wavepacket bifurcation. This indicates that the wavepacket evolves on both states, likely along a planarization coordinate, with the majority of the flux undergoing nonadiabatic transition via conical intersections within 100 fs following light absorption. In CHT, large amplitude motion along the planarization coordinate improves the intra-ring pi-overlap, yielding a delocalized electronic density. However, substitutions in 7 position, chosen to modify the inertia of the planarization motion, did not markedly alter the first step in the sequential kinetic scheme. This suggests that there is a crossing of potential energy surfaces before planarization is achieved and, thus, nonadiabatic transition likely takes place far away from a local minimum.

  • 39.
    Schalk, Oliver
    et al.
    Stockholm University, Faculty of Science, Department of Physics. National Research Council Canada.
    Boguslavskiy, Andrey E.
    Anisotropy in Time-Resolved Photoelectron Spectroscopy in the Gas Phase2017In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 121, no 50, p. 9612-9618Article in journal (Refereed)
    Abstract [en]

    Transient absorption anisotropy is a well-established technique in time-resolved liquid phase spectroscopy. Here, we show how the technique is applied in the gas phase for time-resolved photoelectron spectroscopy and what type of additional information can be obtained as compared to other techniques. We exemplify its use by presenting results on rotational revivals in pyrazine after excitation at 324 nm and provide new insights into two recent experiments: (i) the difference between Rydberg and valence state excitation after one- and two photon absorption in butadiene and (ii) excitation to the two lowest lying vibronic modes of the degenerate pi 3p Rydberg state in 1-azabicyclo[2.2.0]octane. Going forward, we expect the technique to be used on a regular basis, especially with the advent of high harmonic probe sources and liquid beam setups where other techniques to extract polarization-dependent information such as velocity map imaging cannot easily be applied.

  • 40.
    Schalk, Oliver
    et al.
    Stockholm University, Faculty of Science, Department of Physics. University of Munich .
    Broman, Sören L.
    Petersen, Michael A.
    Khakhulin, Dmitry V.
    Brogaard, Rasmus Y.
    Nielsen, Mogens Brondsted
    Boguslavskiy, Andrey E.
    Stolow, Albert
    Solling, Theis I.
    On the Condensed Phase Ring-Closure of Vinylheptafulvalene and Ring-Opening of Gaseous Dihydroazulene2013In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, no 16, p. 3340-3347Article in journal (Refereed)
    Abstract [en]

    Dihydroazulenes are interesting because of their photoswitching behavior. While the ring-opening to vinylheptafulvalene (VHF) is light induced, the back reaction is known to proceed thermally. In the present paper, we show the first gas phase study of the ring-opening reaction of 2-phenyl-1,8a-dihydroazulene-1,1-dicarbonitrile (Ph-DHA) by means of time-resolved photoelectron spectroscopy which permits us to follow the ring-opening process. Moreover, we investigated s-trans-Ph-VHF in a series of transient absorption experiments, supported by ab initio computations, to understand the origin of the absence of light-induced ring-closure. The transient absorption results show a biexponential decay governed by a hitherto unknown state. This state is accessed within 1-2 ps and return to the ground state is probably driven through a cis-trans isomerization about the exocyclic C-1=C-2 double bond. The rapid decrease in potential energy disfavors internal rotation to s-cis-Ph-VHF, the structure that would precede the ring-closure reaction.

  • 41.
    Schalk, Oliver
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Geng, Ting
    Stockholm University, Faculty of Science, Department of Physics.
    Thompson, Travis
    Baluyot, Noel
    Thomas, Richard D.
    Stockholm University, Faculty of Science, Department of Physics.
    Tapavicza, Enrico
    Hansson, Tony
    Stockholm University, Faculty of Science, Department of Physics.
    Cyclohexadiene Revisited: A Time-Resolved Photoelectron Spectroscopy and ab Initio Study2016In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, no 15, p. 2320-2329Article in journal (Refereed)
    Abstract [en]

    We have reinvestigated the excited state dynamics of cyclohexa-1,3-diene (CHD) with time-resolved photoelectron spectroscopy and fewest switches surface hopping molecular dynamics based on linear response time dependent density functional theory after excitation to the lowest lying pi pi* (1B) state. The combination of both theory and experiment revealed several new results: First, the dynamics progress on one single excited state surface. After an incubation time of 35 +/- 10 fs on the excited state, the dynamics proceed to the ground state in an additional 60 +/- 10 fs, either via a conrotatory ring-opening to hexatriene or back to the CHD ground state. Moreover, ring-opening predominantly occurs when the wavepacket crosses the region of strong nonadiabatic coupling with a positive velocity in the bond alternation coordinate. After 100 fs, trajectories remaining in the excited state must return to the CHD ground state. This extra time delay induces a revival of the photoelectron signal and is an experimental confirmation of the previously formulated model of two parallel reaction channels with distinct time constants. Finally, our simulations suggest that after the initially formed cis-Z-cis HT rotamer the trans-Z-trans isomer is formed, before the thermodynamical equilibrium of three possible rotamers is reached after 1 ps.

  • 42.
    Schalk, Oliver
    et al.
    Stockholm University, Faculty of Science, Department of Physics. University of Copenhagen, Denmark.
    Larsen, M. A. B.
    Skov, A. B.
    Liisberg, M. B.
    Geng, Ting
    Stockholm University, Faculty of Science, Department of Physics.
    Sølling, T. I.
    Thomas, Richard D.
    Stockholm University, Faculty of Science, Department of Physics.
    Time-Resolved Photoelectron Studies of Thiophene and 2,5-Dimethylthiophene2018In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 122, no 45, p. 8809-8818Article in journal (Refereed)
    Abstract [en]

    The photoinduced dynamics of thiophene and 2,S-dimethylthiophene (2,5-DMT) were investigated upon excitation at 200 and 255 nm (2,5-DMT only) using time-resolved photoelectron spectroscopy and compared with results from ab initio coupled cluster calculations. For thiophene, depopulation of the initially excited B 2 (pi(3)pi(4)*) state to the lower-lying A(1) (pi(3)pi(4)*) state occurs within 25 +/- 20 fs, with a subsequent bifurcation into a ring-puckering channel and a ring-opening channel with lifetimes of 80 +/- 20 and 450 +/- 50 fs, respectively. For 2,5-DMT, the dynamics following excitation at 200 nm is described by a monoexponential decay with a time constant of 120 +/- 20 fs, while that following excitation at 255 nm is best fit by a biexponential decay with time constants of 115 +/- 20 fs and 15 +/- 3 ps, respectively. The fast signal observed after excitation of 2,5-DMT is assigned to the ring-opening channel, which is favored with respect to thiophene due to a lower excited-state barrier along the ring-opening coordinate and an increased inertia toward the ring-puckering channel. Coupled cluster calculations have been undertaken to compare the relaxation dynamics of thiophene to thiazole and isothiazole. For the latter two molecules, we find a strong gradient along the ring-opening coordinate in the Franck-Condon region of the initially populated pi pi* state and predict that ring-opening is the dominating relaxation channel after photoexcitation. We use the extracted information for a comparison of the thiophene dynamics with the light-induced processes observed in other five-membered heterocyclic molecules.

  • 43.
    Schalk, Oliver
    et al.
    Stockholm University, Faculty of Science, Department of Physics. University of Munich, Germany.
    Schuurman, Michael S.
    Wu, Guorong
    Lang, Peter
    Mucke, Melanie
    Feifel, Raimund
    Stolow, Albert
    Internal Conversion versus Intersystem Crossing: What Drives the Gas Phase Dynamics of Cyclic alpha,beta-Enones?2014In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 118, no 12, p. 2279-2287Article in journal (Refereed)
    Abstract [en]

    We investigate the competition between intersystem crossing (ISC) and internal conversion (IC) as nonradiative relaxation pathways in cyclic alpha,beta-unsaturated enones following excitation to their lowest lying (1)pi pi* state, by means of time-resolved photoelectron spectroscopy and ab initio computation. Upon excitation, the (1)pi pi* state of 2-cyclopentenone decays to the lowest lying (1)pi pi* state within 120 +/- 20 fs. Within 1.2 +/- 0.2 ps, the molecule subsequently decays to the triplet manifold and the singlet ground state, with quantum yields of 0.35 and 0.65, respectively. The corresponding dynamics in modified derivatives, obtained by selective methylation, show a decrease in both IC and ISC rates, with the quantum yields of ISC varying between 0.35 and 0.08. The rapid rates of ISC are explained by a large spin orbit coupling of 45-60 cm(-1) over an extended region of near degeneracy between the singlet and triplet state. Furthermore, the rate of IC is depressed by the existence of a well-defined minimum on the (1)n pi* potential energy surface. The nonadiabatic pathways evinced by the present results highlight the fact that these molecular systems conceptually represent intermediate cases between ultrafast dynamics mediated by vibrational motions at conical intersections versus those by statistical decay mechanisms.

  • 44.
    Schalk, Oliver
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Stenrup, M.
    Geng, Ting
    Stockholm University, Faculty of Science, Department of Physics.
    Lindh, R.
    Thomas, Richard D.
    Stockholm University, Faculty of Science, Department of Physics.
    Feifel, R.
    Hansson, Tony
    Stockholm University, Faculty of Science, Department of Physics.
    Influence of Alkoxy Groups on the Photoinduced Dynamics of Organic Molecules Exemplified on Alkyl Vinyl Ethers2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 45, p. 11105-11112Article in journal (Refereed)
    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.

  • 45. Schyman, Patric
    et al.
    Danielsson, Jonas
    Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
    Laaksonen, Aatto
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Theoretical study of the human DNA repair protein hOGG1 activity2005In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 109, no 8, p. 1713-1719Article in journal (Refereed)
    Abstract [en]

    We have examined the role of the catalytic lysine (Lys 249) in breaking the glycosidic bond of 8-oxoguanine in the enzyme human 8-oxoguanine DNA glycosylase. Until quite recently it has been assumed that this lysine acts as a nucleophile in an SN2 type of reaction after being activated through a donation of a proton to a strictly conserved aspartate, also located in the active site. However, evidence from crystallographic, as well as biochemical studies, questions this assumption mainly because the lysine is not ideally positioned for such an attack. In addition, the catalytic activity is preserved even after that aspartate is mutated to a residue not accepting protons, but still keeping the interactions in the active site. In this study, we have investigated several different reaction mechanisms to discover plausible ways where the lysine could assist in breaking the glycosidic bond. We use hybrid density functional theory to characterize both associative and dissociative pathways. We find that the smallest energetical barrier involves an SN1 type of mechanism where the lysine electrostatically stabilizes the dissociating base and then donates a proton with a very small barrier and then finally attacks the sugar ring to create the covalently bound protein−DNA intermediate complex. The SN2 mechanism also has a lower barrier than the “spontaneous” bond breaking but considerably above that of the SN1 reaction. However, in current conditions, the reactants placed in a conformation posed for an SN2 reaction is substantially more stable than if posed for the SN1 reaction, indicating that the active site has to bind stronger to the latter in order to achieve a full catalytic effect. An analysis of the polarization of the transition states shows that the polarization is largest for the SN1 reaction, indicating that this path will gain most by being placed in a prepolarized active site. These findings give further support to the hypothesis that a dissociative mechanism may be the preferred mode of action for this type of enzymes.

  • 46. Sekikawa, Taro
    et al.
    Schalk, Oliver
    Stockholm University, Faculty of Science, Department of Physics. Hokkaido University.
    Wu, Guorong
    Boguslavskiy, Andrey E.
    Stolow, Albert
    Initial Processes of Proton Transfer in Salicylideneaniline Studied by Time-Resolved Photoelectron Spectroscopy2013In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, no 14, p. 2971-2979Article in journal (Refereed)
    Abstract [en]

    Excited-state intramolecular proton transfer (ESIPT) in salicylideneaniline (SA) and selected derivatives substituted in the para position of the anilino group have been investigated by femtosecond time-resolved photoelectron spectroscopy (TRPES) and time-dependent density functional theory (TDDFT). SA has a twisted structure at the energetic minimum of the ground state, but ESIPT is assumed to take place through a planar structure, although this has not been fully established. The TRPES studies revealed that the excited-state dynamics within the S-1 band varied significantly with excitation wavelength. At finite temperatures, the ground state was found to sample a broad range of torsional angles, from planar to twisted. At lower photon energies (370 nm), only the planar ground-state molecules were excited, and the excited-state reaction took place within 50 fs. At higher energies (350 and 330 nm), predominantly twisted ground-state molecules were excited: they had to planarize before ESIPT could occur. This process was found to be slower in methylated SA but did not change significantly in the brominated and nitrated SAs. These substitution effects on the decay dynamics can be explained by modifications of the potential barriers, as predicted by the TDDFT calculations, and support the mechanism of a twisting motion of the anilino ring prior to ESIPT. The contribution of another pathway leading to internal conversion within the enol form was found to be minor at the excitation wavelengths considered here.

  • 47.
    Siegbahn, Per E.M.
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Blomberg, Margareta R.A.
    Stockholm University, Faculty of Science, Department of Physics.
    On the Proton Pumping Mechanism in Cytochrome c Oxidase2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, p. 12772-12780Article in journal (Refereed)
    Abstract [en]

    Two different issues, important for the pumping mechanism of cyctochrome c oxidase, have been addressed in the present study. One of them concerns the nature of two key proton transfer transition states. A simple electrostatic model is used to suggest that the transition state (TS) for transfer to the pump-site should be positively charged, while the one for transfer to the binuclear center should be charge-neutral. The character of the former TS will guarantee that the protons will be pumped to the outside and not return to the inside, while the neutral character of the latter one will allow transfer with a sufficiently low barrier. In the simple electrostatic analysis, leading to this qualitative picture of the pumping process, the results from the kinetic experiments are strictly followed, but it is at least as important to follow the fundamental requirements for pumping. In this perspective, the uncertainties in the quantitative analysis should be rather unimportant for the emerging qualitative picture of the pumping mechanism. The second problem addressed concerns the purpose of the K-channel. It is argued that the reason for the presence of the K-channel could be that protons cannot pass through the binuclear center at some stage of pumping. Barriers and water binding energies were computed using hybrid density functional theory (DFT) to investigate this question.

  • 48. Sun, Lu
    et al.
    Hede, Thomas
    Stockholm University, Faculty of Science, Department of Meteorology .
    Tu, Yaoquan
    Leck, Caroline
    Stockholm University, Faculty of Science, Department of Meteorology .
    Ågren, Hans
    Combined Effect of Glycine and Sea Salt on Aerosol Cloud Droplet Activation Predicted by Molecular Dynamics Simulations2013In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, no 41, p. 10746-10752Article in journal (Refereed)
    Abstract [en]

    The present study illustrates the combined effect of organic and inorganic compounds on cloud droplet nucleation and activation processes representative for the marine environment. Amino acids and sea salt are common marine cloud condensation nuclei (CCN) which act as a prerequisite for growth of cloud droplets. The chemical and physical properties of these CCN play a key role for interfacial properties such as surface tension, which is important for the optical properties of clouds and for heterogeneous reactions. However, there is a lack of detailed information and in situ measurements of surface tension of such nanosized droplets. Here we present a study of the combined effect of zwitterionic glycine (ZGLY) and sea salt in nanosized water droplets using molecular dynamics simulations, where particular emphasis is placed on the surface tension for the nanosized droplets. The critical supersaturation is estimated by the Kohler equation. It is found that dissolved sea salt interacts with ZGLY through a water bridge and weakens the hydrogen bonds among ZGLYs, which has a significant effect on both surface tension and water vapor supersaturation. Clusters of glycine mixed with sea salt deliquesce more efficiently and have higher growth factors.

  • 49.
    Thomas, R. D.
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Zhaunerchyk, Vitali
    Stockholm University, Faculty of Science, Department of Physics.
    Hellberg, Fredrik
    Stockholm University, Faculty of Science, Department of Physics.
    Ehlerding, Anneli
    Stockholm University, Faculty of Science, Department of Physics.
    Geppert, Wolf D.
    Stockholm University, Faculty of Science, Department of Physics.
    Bahati, E.
    Bannister, M. E.
    Fogle, M. R.
    Vane, C. R.
    Petrignani, A.
    Andersson, P. U.
    Ojekull, J.
    Pettersson, J. B. C.
    van der Zande, W. J.
    Larsson, M.
    Hot Water from Cold. The Dissociative Recombination of Water Cluster Ions2010In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 114, no 14, p. 4843-4846Article in journal (Refereed)
    Abstract [en]

    Dissociative recombination of the Zundel cation D(5)O(2)(+) almost exclusively produces D + 2 D(2)O with a maximum kinetic energy release of 5.1 eV. An imaging technique is used to investigate the distribution of the available reaction energy among these products. Analysis shows that as much as 4 eV can be stored internally by the molecular fragments, with a preference for producing highly excited molecular fragments, and that the deuteron shows a nonrandom distribution of kinetic energies. A possible mechanism and the implications for these observations are addressed.

  • 50.
    Thomas, Richard D.
    et al.
    Stockholm University, Faculty of Science, Department of Physics.
    Kashperka, Iryna
    Stockholm University, Faculty of Science, Department of Physics.
    Vigren, Erik
    Stockholm University, Faculty of Science, Department of Physics.
    Geppert, Wolf D.
    Stockholm University, Faculty of Science, Department of Physics.
    Hamberg, Mathias
    Stockholm University, Faculty of Science, Department of Physics.
    Larsson, Mats
    Stockholm University, Faculty of Science, Department of Physics.
    af Ugglas, Magnus
    Stockholm University, Faculty of Science, Department of Physics.
    Zhaunerchyk, Vitali
    Stockholm University, Faculty of Science, Department of Physics.
    Dissociative Recombination of CH4+2013In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 117, no 39, p. 9999-10005Article in journal (Refereed)
    Abstract [en]

    CH4+ is an important molecular ion in the astrochemistry of diffuse clouds, dense clouds, cometary comae, and planetary ionospheres However, the rate of one of the common destruction mechanisms for molecular ions in these regions, dissociative recombination (DR), is somewhat uncertain. Here, we present absolute measurements for the DR of CH4+ made using the heavy ion storage ring CRYRING hi Stockholm, Sweden. From our collision energy dependent cross sections, we infer a thermal rate constant of k(T-e) = 1.71(+/- 0.02) X 10(-6)(T-e/300)(-0.66(+/- 0.02)) cm(3) s(-1) over the region of electron temperatures 10 <= T-e <= 1000 K. At low collision energies, we have measured the branching fractions of the DR products to be CH4 (0.00 +/- 0.00); CH3 + H (0.18 +/- 0.03); CH2 + 2H (0.51 +/- 0.03); CH2 + H-2 (0.06 +/- 0.01); CH + H-2 + H (0.23 +/- 0.01); and CH + 2H(2) (0.02 +/- 0.01), indicating that two or more C-H bonds are broken in similar to 80% of all collisions.

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