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1.	Malysheva, Lyuba, et al. (author) Molecular Orientation in Helical and All-Trans Oligo(ethylene glycol)-Terminated Assemblies on Gold: Results of ab Initio Modeling 2005 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215 .- 1520-6106 .- 1520-5207. ; 109:34, s. 7788-7796 Journal article (peer-reviewed)abstract The structural properties of self-assembled monolayers (SAMs) of oligo(ethylene glycol) (OEG)-terminated and amide-containing alkanethiols (HS(CH2)15CONH(CH2CH2O)6H and related molecules with shorter alkyl or OEG portions) on gold are addressed. Optimized geometry of the molecular constituents, characteristic vibration frequencies, and transition dipole moments are obtained using density-functional theory methods with gradient corrections. These data are used to simulate IR reflection-absorption (RA) spectra associated with different OEG conformations. It is shown that the positions and relative intensities of all characteristic peaks in the fingerprint region are accurately reproduced by the model spectra within a narrow range of the tilt and rotation angles of the alkyl plane, which turns out to be nearly the same for the helical and all-trans OEG conformations. In contrast, the tilt of the OEG axis changes considerably under conformational transition from helical to all-trans OEG. By means of ab initio modeling, we also clarify other details of the molecular structure and orientation, including lateral hydrogen bonding, the latter of which is readily possessed by the SAMs in focus. These results are crucial for understanding phase and folding characteristics of OEG SAMs and other complex molecular assemblies. They are also expected to contribute to an improved understanding of the interaction with water, ions, and ultimately biological macromolecules.
2.	Mark, P, et al. (author) Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K 2001 In: JOURNAL OF PHYSICAL CHEMISTRY A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215 .- 1520-6106. ; 105:43, s. 9954-9960 Journal article (other academic/artistic)
3.	Abid, Abdul Rahman, et al. (author) Forming Bonds While Breaking Old Ones : Isomer-Dependent Formation of H3O+ from Aminobenzoic Acid During X-ray-Induced Fragmentation 2023 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 127:6, s. 1395-1401 Journal article (peer-reviewed)abstract Intramolecular hydrogen transfer, a reaction where donor and acceptor sites of a hydrogen atom are part of the same molecule, is a ubiquitous reaction in biochemistry and organic synthesis. In this work, we report hydronium ion (H3O+) production from aminobenzoic acid (ABA) after core-level ionization with soft X-ray synchrotron radiation. The formation of H3O+ during the fragmentation requires that at least two hydrogen atoms migrate to one of the oxygen atoms within the molecule. The comparison of two structural isomers, ortho- and meta-ABA, revealed that the production of H3O+ depends strongly on the structure of the molecule, the ortho-isomer being much more prone to produce H3O+. The isomer-dependency suggests that the amine group acts as a donor in the hydrogen transfer process. In the case of ortho-ABA, detailed H3O+ production pathways were investigated using photoelectron-photoion-photoion coincidence (PEPIPICO) spectroscopy. It was found that H3O+ can result from a direct two-body dissociation but also from sequential fragmentation processes.
4.	Ablyasova, Olesya S., et al. (author) Electronic Structure of the Complete Series of Gas-Phase Manganese Acetylacetonates by X-ray Absorption Spectroscopy 2023 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 127:34, s. 7121-7131 Journal article (peer-reviewed)abstract Metal centers in transition metal–ligand complexes occur in a variety of oxidation states causing their redox activity and therefore making them relevant for applications in physics and chemistry. The electronic state of these complexes can be studied by X-ray absorption spectroscopy, which is, however, due to the complex spectral signature not always straightforward. Here, we study the electronic structure of gas-phase cationic manganese acetylacetonate complexes Mn(acac)1–3+ using X-ray absorption spectroscopy at the metal center and ligand constituents. The spectra are well reproduced by multiconfigurational wave function theory, time-dependent density functional theory as well as parameterized crystal field and charge transfer multiplet simulations. This enables us to get detailed insights into the electronic structure of ground-state Mn(acac)1–3+ and extract empirical parameters such as crystal field strength and exchange coupling from X-ray excitation at both the metal and ligand sites. By comparison to X-ray absorption spectra of neutral, solvated Mn(acac)2,3 complexes, we also show that the effect of coordination on the L3 excitation energy, routinely used to identify oxidation states, can contribute about 40–50% to the observed shift, which for the current study is 1.9 eV per oxidation state.
5.	Abrahamsson, Erik, 1974, et al. (author) Dynamics of the O + CN Reaction and N + CO Scattering on Two Coupled Surfaces 2009 In: J. Phys. Chem. A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 113:52, s. 14824-14830 Journal article (peer-reviewed)abstract Spin−orbit coupling between the two collinear 2Π and 4Σ− potential energy surfaces for the NCO system are calculated using the RASSI method with CASSCF wave functions as basis set. The GDVR method has been used to interpolate a spin−orbit coupling surface. Wave packet and quasi-classical trajectory surface hopping calculations have been performed and compared for both the O(3P) + CN(X2Σ+) → N(4S) + CO(X1Σ+) reaction and for electronically inelastic scattering in the N + CO channels. The O + CN nonadiabatic reaction probabilities are small. The wavepacket study gives a resonance structure. Also for the N + CO electronically inelastic scattering the wave packet calculations give a distinct resonance structure with peak transition probabilities up to around 10%, which is somewhat lower than the trajectory surface hopping results.
6.	Abu-samha, M., et al. (author) What Can C1s Photoelectron Spectroscopy Tell about Structure and Bonding in Clusters of Methanol and Methyl Chloride? 2007 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 111:37, s. 8903-8909 Journal article (peer-reviewed)abstract Single-component clusters of methanol and methyl chloride have been produced by adiabatic expansion, and their carbon Is photoelectron spectra were recorded using synchrotron radiation and a high-resolution electron analyzer. The experimental spectra are interpreted by means of theoretical models based on molecular dynamics simulations. The data are used to explore to what extent core-level photoelectron spectra may provide information on the bonding mechanism and the geometric structure of clusters of polar molecules. The results indicate that the cluster-to-monomer shift in ionization energy and also the width of the cluster peak may be used to distinguish between hydrogen bonding and weaker electrostatic interactions. Moreover, the larger width of the cluster peak in methanol clusters as compared to methyl chloride clusters is partly due to the structured surface of methanol clusters. Theoretical modeling greatly facilitates the analysis of core-level photoelectron spectra of molecular clusters.
7.	Adams, Christopher, et al. (author) Vibrational Autodetachment from Anionic Nitroalkane Chains - From Molecular Signatures to Thermionic Emission 2019 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 123:40, s. 8562-8570 Journal article (peer-reviewed)abstract We report the kinetic energy distributions in electron autodetachment from nitroethane, 1-nitropropane, and 1-nitrobutane anions upon laser excitation of CH stretching modes measured using velocity map electron imaging. In striking contrast to the case of nitromethane, the kinetic energy distributions show almost no distinct vibrational features, and they can be described by thermionic emission, relating the shape of the distributions to the electron capture cross section of the neutral molecule. The data suggest that a classical description is warranted above ca. 20 meV electron kinetic energy. At lower energies, quantum effects suppress the attachment cross section.
8.	Ahlstrand, Emma, et al. (author) Interaction Energies in Complexes of Zn and Amino Acids : A Comparison of Ab Initio and Force Field Based Calculations 2017 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 121:13, s. 2643-2654 Journal article (peer-reviewed)abstract Zinc plays important roles in structural stabilization of proteins, eniyine catalysis, and signal transduction. Many Zn binding sites are located at the interface between the protein and the cellular fluid. In aqueous solutions, Zn ions adopt an octahedral coordination, while in proteins zinc can have different coordinations, with a tetrahedral conformation found most frequently. The dynainics of Zn binding to proteins and the formation of complexes that involve Zn are dictated by interactions between Zn and its binding partners. We calculated the interaction energies between Zn and its ligands in complexes that mimic protein binding sites and in Zn complexes of water and one or two amino acid moieties, using quantum mechanics (QM) and molecular mechanics (MM). It was found that MM calculations that neglect or only approximate polarizability did not reproduce even the relative order of the QM interaction energies in these complexes. Interaction energies calculated with the CHARMM-Diode polarizable force field agreed better with the ab initio results,:although the deviations between QM and MM were still rather large (40-96 kcallmol). In order to gain further insight into Zn ligand interactions, the free energies of interaction were estimated by QM calculations with continuum solvent representation, and we performed energy decomposition analysis calculations to examine the characteristics of the different complexes. The ligand-types were found to have high impact on the relative strength of polarization and electrostatic interactions. Interestingly, ligand ligand interactions did not play a significant role in the binding of Zn. Finally) analysis of ligand exchange energies suggests that carboxylates could be exchanged with water molecules, which explains the flexibility in Zn:binding dynamics. An exchange between earboxylate (Asp/Glii) and imidazole (His) is less likely.
9.	Aidas, Kestutis, et al. (author) Solvent effects on NMR isotropic shielding constants. A comparison between explicit polarizable discrete and continuum approaches 2007 In: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1520-5215. ; 111:20, s. 4199-4210 Journal article (peer-reviewed)abstract The gas-to-aqueous solution shifts of the O-17 and C-13 NMR isotropic shielding constants for the carbonyl chromophore in formaldehyde and acetone are investigated. For the condensed-phase problem, we use the hybrid density functional theory/molecular mechanics approach in combination with a statistical averaging over an appropriate number of solute-solvent configurations extracted from classical molecular dynamics simulations. The PBE0 exchange-correlation functional and the 6-311++G(2d,2p) basis set are used for the calculation of the shielding constants. London atomic orbitals are employed to ensure gauge-origin independent results. The effects of the bulk solvent molecules are found to be crucial in order to calculate accurate solvation shifts of the shielding constants. Very good agreement between the computed and experimental solvation shifts is obtained for the shielding constants of acetone when a polarizable water potential is used. Supermolecular results based on geometry-optimized molecular structures are presented. We also compare the results obtained with the polarizable continuum model to the results obtained using explicit MM molecules to model the bulk solvent effect.
10.	Al-Saidi, W. A., et al. (author) Resonance raman spectra of TNT and RDX using vibronic theory, excited-state gradient, and complex polarizability approximations 2012 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 116:30, s. 7862-7872 Journal article (peer-reviewed)abstract Geometries, UV absorption bands, and resonance Raman (RR) cross sections of TNT and RDX are investigated using density functional theory (DFT) in conjunction with the Coulomb attenuated B3LYP exchange-correlation functional. The absorption and RR spectra are determined with use of vibronic (VB) theory, excited-state gradient, and complex polarizability (CPP) approximations. We examined low-energy isomers (two for TNT and four for RDX) whose energies differ by less than 1 kcal/mol, such that they would appreciably be populated at room temperature. The two TNT isomers differ by an internal rotation of the methyl group, while the four conformers of RDX differ by the arrangements of the nitro group relative to the ring. Our theoretical optical properties of the TNT and RDX isomers are in excellent agreement with experimental and recent CCSD-EOM results, respectively. For the two TNT isomers, the ultraviolet RR (UVRR) spectra are similar and in good agreement with recently measured experimental results. Additionally, the UVRR spectra computed using the excited-state and CPP approaches compare favorably with the VB theory results. On the other hand, the RR spectra of the RDX conformers differ from one another, reflecting the importance of the positioning of the NO 2 groups with respect to the ring. In the gas phase or in solution, RDX would give a spectrum associated with a conformationally averaged structure. It is encouraging that the computed spectra of the conformers show similarities to recent measured RDX spectra in acetonitrile solution, and reproduce the 10-fold decrease in the absolute Raman cross sections of RDX compared to TNT for the observed 229 nm excitation. We show that in TNT and RDX vibrational bands that couple to NO 2 or the ring are particularly resonance enhanced. Finally, the computed RDX spectra of the conformers present a benchmark for understanding the RR spectra of the solid-phase polymorphs of RDX.
11.	Albinsson, Bo, 1963, et al. (author) Conformers of n-Si5Me12: A comparison of ab initio and molecular mechanics methods 1999 In: Journal of Physical Chemistry A. - 1089-5639 .- 1520-5215. ; 103:14, s. 2184-2196 Journal article (peer-reviewed)abstract Optimized geometries of the conformers of permethylated linear pentasilane, n-Si5Me12, were calculated by the HF/3-21G, MM3, MM2, and MM+ methods, which predict eight, nine, six, and six energetically distinct enantiomeric conformer pairs, respectively, at geometries representing various combinations of the anti (similar to 165 degrees), ortho (similar to 90 degrees), and gauche (similar to 55 degrees) SiSiSiSi dihedral angles in the backbone. The results of the MM2 and MM+ methods, based on the same force field, differ insignificantly. The barriers between conformers appear to be exaggerated by the molecular mechanics methods, particularly MM2. Contour maps showing the groundstate energy as a function of the full range of two backbone SiSiSiSi dihedral angles, with all other geometrical variables optimized, computed by each of the methods (only a limited range of angles near the anti,anti geometry in the case of HF/3-21G) are compared with each other and with analogous results for a model compound, Si4Me10. Conformer interconversion paths are discussed, and two meso transition states for enantiomer interconversion have been located at the HF/3-21G* level of calculation. At the eight HF/3-21G* optimized geometries, single-point energies (HF/6-31G* and MP2/6-31G) and vibrational frequencies (HF/3-21G) were computed. The predicted IR and Raman spectra suggest that about half of the expected conformers will be identifiable by vibrational spectroscopy under conditions of matrix isolation. Relative conformer energies calculated by the MM2 and HF methods are similar and favor the anti dihedral angles over gauche and ortho, in agreement with results of solution experiments. Those calculated by the hIM3 and HF methods are similar to each other and favor both anti and gauche dihedral angles nearly equally over ortho, in agreement with indications provided by gas-phase experiments. A rationalization of these solvent effects is proposed. The energies of the conformers of Si4Me10 and Si3Me12 were used to set up a system of additive increments at the MM2, MM3, HF/3-21G, HF/6-31G, and MP2/6-31G* levels of calculation, which can be used to predict conformational energies of longer permethylated oligosilanes. An intrinsic energy value is assigned to each of the a, o, and g dihedral angles, and interaction energy values are assigned to each combination of two dihedral angles. The interaction values follow the expected rules in that equal twist sense is favored for adjacent aa, ag, oo, and gg pairs, whereas opposite twist sense is generally favored for adjacent so and go pairs. The MM3-derived set of increments has been tested against results computed for Si6Me14 and found to perform well.
12.	Andersen, Christina, et al. (author) Atmospheric Chemistry of Tetrahydrofuran, 2-Methyltetrahydrofuran, and 2,5-Dimethyltetrahydrofuran : Kinetics of Reactions with Chlorine Atoms, OD Radicals, and Ozone 2016 In: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1089-5639. ; 120:37, s. 7320-7326 Journal article (peer-reviewed)abstract FTIR smog chamber techniques were used to study the kinetics of the gas-phase reactions of Cl atoms, OD radicals, and O3 with the five-membered ring-structured compounds tetrahydrofuran (C4H8O, THF), 2-methyltetrahydrofuran (CH3C4H7O, 2-MTHF), 2,5-dimethyltetrahydrofuran ((CH3)2C4H5O, 2,5-DMTHF), and furan (C4H4O). The rate coefficients determined using relative rate methods were kTHF+Cl = (1.96 ± 0.24) × 10-10, kTHF+OD = (1.81 ± 0.27) × 10-11, kTHF+O3 = (6.41 ± 2.90) × 10-21, k2-MTHF+Cl = (2.65 ± 0.43) × 10-10, k2-MTHF+OD = (2.41 ± 0.51) × 10-11, k2-MTHF+O3 = (1.87 ± 0.82) × 10-20, k2,5-DMTHF+OD = (4.56 ± 0.68) × 10-11, k2,5-DMTHF+Cl = (2.84 ± 0.34) × 10-10, k2,5-DMTHF+O3 = (4.58 ± 2.18), kfuran+Cl = (2.39 ± 0.27) × 10-10, and kfuran+O3 = (2.60 ± 0.31) × 10-18 molecules cm-3 s-1. Rate coefficients of the reactions with ozone were also determined using the absolute rate method under pseudo-first-order conditions. OD radicals, in place of OH radicals, were produced from CD3ONO to avoid spectral overlap of isopropyl and methyl nitrite with the reactants. The kinetics of OD radical reactions are expected to resemble the kinetics of OH radical reactions, and the rate coefficients of the reactions with OD radicals were used to calculate the atmospheric lifetimes with respect to reactions with OH radicals. The lifetimes of THF, 2-MTHF, and 2,5-DMTHF are approximately 15, 12, and 6 h, respectively.
13.	Andersen, J., et al. (author) Far-Infrared Investigation of the Benzene-Water Complex : The Identification of Large-Amplitude Motion and Tunneling Pathways 2020 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 124:3, s. 513-519 Journal article (peer-reviewed)abstract The far-infrared spectrum of the weakly OH···πhydrogen-bonded benzene-water complex has been studied in neon and argon matrices, below 30 K. The in-plane water libration has been observed in both neon and argon for H2O and D2O complexed with C6H6 and C6D6 but not for the corresponding complexes involving HDO. Both H2O and D2O can tunnel between the two possible hydrogen bonds. This is not possible for HDO. The reported far-infrared observations have implications for the interpretation of the previously obtained molecular beam microwave spectrum of the benzene-water complex.
14.	Andersson, Markus, 1981, et al. (author) Coordination of Imidazoles by Cu(II) and Zn(II) as Studied by NMR Relaxometry, EPR, far-FTIR Vibrational Spectroscopy and Ab Initio Calculations: Effect of Methyl Substitution 2010 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 114:50, s. 13146-13153 Journal article (peer-reviewed)abstract Synthetic imidazole ligands are typically substituted at the N-1 ((1)-Im) position while natural imidazole ligands are substituted at the C-4 ((4)-Im) position. To outline the difference in coordination properties, the methyl-substituted imidazoles Me(4)-Im and Me(1)-Im were complexed with CuCl2 and ZnCl2 and investigated by NMR relaxometry, electron paramagnetic resonance, far-Fourier transform IR vibrational spectroscopy, and ab initio calculations. Me(4)-Im, Me(1)-Im, and Im in excess form the usual tetragonal D-4h [CuL4X2] complexes with CuCl2 whereas the methylated imidazoles form pseudotetrahedral C-2v, complexes instead of the usual octahedral O-h [ZnIm(6)](2+) complex. All imidazoles display a high degree of covalence in the M-L sigma- and pi-bonds and the pi-interaction strength affects the relative energies of complexation. Opportunities to tailor complexes by the chemical properties of the substituents are envisaged due to the role of the inductive and hyperconjugative effects, rather than position.
15.	Andersson, M P, et al. (author) New scale factors for harmonic vibrational frequencies using the B3LYP density functional method with the triple-xi basis set 6-311+G(d,p) 2005 In: The Journal of Physical Chemistry Part A: Molecules, Spectroscopy, Kinetics, Environment and General Theory. - : American Chemical Society (ACS). - 1520-5215. ; 109:12, s. 2937-2941 Journal article (peer-reviewed)abstract We have calculated optimal frequency scaling factors for the B3LYP/ 6-311+G(d,p) method for fundamental vibrational frequencies on the basis of a set of 125 molecules. Using the new scaling factor, the vibrational frequencies calculated with the triple-zeta basis set 6-311+G(d,p) give significantly better accuracy than those calculated with the double-zeta 6-31G(d) basis set. Scale factors were also determined for low-frequency vibrations using the molecular set of 125 molecules and for zero-point energies using a smaller set of 40 molecules. We have studied the effect on the calculated vibrational frequencies for various combinations of diffuse and polarization functions added to the triple-zeta 6-311G basis set. The 6-311+G(d,p) basis set is found to give almost converged frequencies for most molecules, and we conclude that our optimum scaling factors are valid for the basis sets 6-311 G(d,p) to 6-311++G(3df,3pd). The new scale factors are 0.9679 for vibrational frequencies, 1.0100 for low-frequency vibrations, and 0.9877 for zero-point vibrational energies.
16.	Andersson, Patrik U, 1970, et al. (author) Carbon dioxide interactions with crystalline and amorphous ice surfaces 2004 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 108:21, s. 4627-4631 Journal article (peer-reviewed)abstract Carbon dioxide interactions with crystalline and amorphous water ice have been studied by time-resolved molecular beam techniques. CO2 collisions at thermal kinetic energies with ice in the temperature range 100-160 K result in efficient trapping on the ice surface followed by desorption. The desorption kinetics on crystalline ice at 100-125 K are well described by the Arrhenius equation with an activation energy of 0.22 +/- 0.02 eV and a preexponential factor of 10(13.32+/-0.57) s(-1). Below 120 K, CO2 populates strongly bonded sites on amorphous ice, resulting in surface residence times on the order of minutes at 100 K, and the desorption data can in this case not be explained by a simple first-order process. The results are compared to previous studies of gas-ice interactions, and the implications for heterogeneous processes in the terrestrial atmosphere are discussed.
17.	Andersson, Stefan, 1973, et al. (author) Comparison of quantum dynamics and quantum transition state theory estimates of the H + CH4 reaction rate. 2009 In: The journal of physical chemistry. A. - : American Chemical Society (ACS). - 1520-5215 .- 1089-5639. ; 113:16, s. 4468-78 Journal article (peer-reviewed)abstract Thermal rate constants are calculated for the H + CH(4) --> CH(3) + H(2) reaction employing the potential energy surface of Espinosa-Garcia (Espinosa-Garcia, J. J. Chem. Phys. 2002, 116, 10664). Two theoretical approaches are used. First, we employ the multiconfigurational time-dependent Hartree method combined with flux correlation functions. In this way rate constants in the range 225-400 K are obtained and compared with previous results using the same theoretical method but the potential energy surface of Wu et al. (Wu, T.; Werner, H.-J.; Manthe, U. Science 2004, 306, 2227). It is found that the Espinosa-Garcia surface results in larger rate constants. Second, a harmonic quantum transition state theory (HQTST) implementation of instanton theory is used to obtain rate constants in a temperature interval from 20 K up to the crossover temperature at 296 K. The HQTST estimates are larger than MCTDH ones by a factor of about three in the common temperature range. Comparison is also made with various tunneling corrections to transition state theory and quantum instanton theory.
18.	Andersson, Stefan, 1973, et al. (author) Computational studies of the kinetics of the C+NO and O+CN reactions 2003 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 107:28, s. 5439-5447 Journal article (peer-reviewed)abstract Thermal rate coefficients for the reactions C(3P) + NO(X2Π) → CN(X2Σ+) + O(3P), C(3P) + NO(X2Π) → CO(X1Σ+) + N(2D), and O(3P) + CN(X2Σ+) → CO(X1Σ+) + N(2D) in the temperature range from 5 to 5000 K have been obtained using quasiclassical trajectory calculations. Results are reported for two ab initio potential energy surfaces corresponding to states of 2A‘ and 2A‘ ‘ symmetry. Good agreement between calculated and experimental rate coefficients are obtained for the C + NO reactions for all temperatures, whereas the rate coefficient for the O + CN reaction at room temperature is larger than that found experimentally. The dynamics is considerably different on the two potential energy surfaces with the 2A‘ ‘ giving rate coefficients in better agreement with experiments. The quality of the potential energy surfaces are discussed in the light of new electronic structure calculations including spin−orbit coupling.
19.	Andersson, Åke, et al. (author) Indication of 310-Helix Structure in Gas-Phase Neutral Pentaalanine 2022 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 127:4, s. 938-45 Journal article (peer-reviewed)abstract We investigate the gas-phase structure of the neutral pentaalanine peptide. The IR spectrum in the 340-1820 cm-1 frequency range is obtained by employing supersonic jet cooling, infrared multiphoton dissociation, and vacuum-ultraviolet action spectroscopy. Comparison with quantum chemical spectral calculations suggests that the molecule assumes multiple stable conformations, mainly of two structure types. In the most stable conformation theoretically found, the N-terminus forms a C5 ring and the backbone resembles that of an 310-helix with two β-turns. Additionally, the conformational preferences of pentaalanine have been evaluated using Born-Oppenheimer molecular dynamics, showing that a nonzero simulation time step causes a systematic frequency shift.
20.	Andersson, Åke, et al. (author) IRMPD Spectroscopy of Homo- and Heterochiral Asparagine Proton-Bound Dimers in the Gas Phase 2021 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 125:34, s. 7449-7456 Journal article (peer-reviewed)abstract We investigate gas-phase structures of homo- and heterochiral asparagine proton-bound dimers with infrared multi-photon dissociation (IRMPD) spectroscopy and quantum-chemical calculations. Their IRMPD spectra are recorded at room temperature in the range of 500-1875 and 3000-3600 cm(-1). Both varieties of asparagine dimers are found to be charge-solvated based on their IRMPD spectra. The location of the principal intramolecular H-bond is discussed in light of harmonic frequency analyses using the B3LYP functional with GD3BJ empirical dispersion. Contrary to theoretical analyses, the two spectra are very similar.
21.	Andersson, Åke, et al. (author) Structure of Proton-Bound Methionine and Tryptophan Dimers in the Gas Phase Investigated with IRMPD Spectroscopy and Quantum Chemical Calculations 2020 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 124:12, s. 2408-2415 Journal article (peer-reviewed)abstract The structures of three proton-bound dimers (Met(2)H(+), MetTrpH(+), and Trp(2)H(+)) are investigated in the gas phase with infrared multiple photon disassociation (IRMPD) spectroscopy in combination with quantum chemical calculations. Their IRMPD spectra in the range of 600-1850 cm(-1) are obtained experimentally using an FT-ICR mass spectrometer and the CLIO free electron laser as an IR light source. The most abundant conformers are elucidated by comparing the IRMPD spectra with harmonic frequencies obtained at the B3LYPGD3BJ/6-311++G** level of theory. Discrepancies between the experimental and theoretical data in the region of 1500-1700 cm(-1) are attributed to the anharmonicity of the amino bending modes. We confirm the result of a previous IRMPD study that the structure of gas-phase Trp(2)H(+) is charge-solvated but find that there are more stable structures than originally reported (Feng, R.; Yin, H.; Kong, X. Rapid Commun. Mass Spectrom. 2016, 30, 24-28). In addition, gas-phase Met(2)H(+) and MetTrpH(+) have been revealed to have charge-solvated structures. For all three dimers, the most stable conformer is found to be of type A. The spectrum of Met(2)H(+), however, cannot be explained without some abundance of type B charge-solvated conformers as well as salt-bridged structures.
22.	Andreasson, Joakim, 1973, et al. (author) Efficient non-radiative deactivation and conformational flexibility of meso-diaryloctaalkylporphyrins in the excited triplet state 2000 In: Journal of Physical Chemistry A. - 1089-5639 .- 1520-5215. ; 104:41, s. 9307-9314 Journal article (peer-reviewed)abstract The excited triplet state deactivation of zinc(II) meso-diaryloctaalkylporphyrins (ZnDAOAP) has been studied over a wide temperature range using transient triplet-triplet absorption spectroscopy together with steady-state and time-resolved phosphorescence techniques, The results from transient absorption measurements show that the depopulation of the initially formed triplet state (T-1A state) is unusually fast at temperatures above 150 K. The efficiency of the deactivation originates from a spin allowed transition to a second tripler state (T-1B state), The transformation process T-1A-->T-1B is therefore the dominating deactivation channel of the T-1A state in this temperature range, and direct intersystem crossing T-1A-->S-0 makes negligible contribution. The subsequent ground-state recovery T-1B-->S-0 is also very efficient in comparison to many other porphyrins. Due to the substantial activation energy found for the transformation process, it most likely involves a conformational distortion of the porphyrin macrocycle. At low temperature, however, the relaxation of the T-1A State occurs by direct intersystem crossing to the ground state.
23.	Andreasson, Joakim, 1973, et al. (author) Photoinduced hole transfer from the triplet state in a porphyrin-based donor-bridge-acceptor system 2003 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 107:42, s. 8825-8833 Journal article (peer-reviewed)abstract The triplet excited-state deactivation of a gold porphyrin (AuP) in porphyrin-based donor-bridge-acceptor (D-B-A) systems has been studied. The results from room temperature and 80 K measurements are presented. The primary objectives have been to investigate whether electrons/electron holes or excitation energy could be transferred from (AuP)-Au-3 to the appended zinc porphyrin (ZnP) in the dimers. As the bridging chromophores in our D-B-A systems separate the ZnP and AuP moieties by 19 A edge-to-edge, we do not expect a significant contribution to either electron or energy transfer from a direct (through space) exchange mechanism. This gives us the opportunity to scrutinize how the bridging chromophores influence the transfer reactions. The results show that quenching of (AuP)-Au-3 occurs with high efficiency in the dimers that are connected by fully conjugated bridging chromophores, whereas no quenching is observed when the conjugation of the bridge is broken. We also observed that the decay of (AuP)-Au-3 is complex at temperatures below 110 K. In addition to the two previously published lifetimes on the order of some 10-100 mus, we have found a third lifetime on the nanosecond time scale.
24.	Apriliyanto, Yusuf Bramastya, et al. (author) Toward a Generalized Hückel Rule : The Electronic Structure of Carbon Nanocones 2021 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 125:45, s. 9819-9825 Journal article (peer-reviewed)abstract In this work, we investigate a particular class of carbon nanocones, which we name graphannulenes, and present a generalized Hückel rule (GHR) that predicts the character of their ground state based on simply the three topological indices that uniquely define them. Importantly, this rule applies to both flat and curved systems, encompassing a wide variety of known structures that do not satisfy the “classic” 4n + 2 rule such as coronene, corannulene, and Kekulene. We test this rule at the Hückel level of theory for a large number of systems, including structures that are convex and flat, with a saddle-like geometry, and at the CASSCF level of theory for a selected representative subset. All the performed calculations support the GHR that we propose in this work.
25.	Ashworth, Eleanor K., et al. (author) Complexation of Green and Red Kaede Fluorescent Protein Chromophores by a Zwitterion to Probe Electrostatic and Induction Field Effects 2022 In: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 126:7, s. 1158-1167 Journal article (peer-reviewed)abstract The photophysics of green fluorescent protein (GFP) and red Kaede fluorescent protein (rKFP) are defined by the intrinsic properties of the light-absorbing chromophore and its interaction with the protein binding pocket. This work deploys photodissociation action spectroscopy to probe the absorption profiles for a series of synthetic GFP and rKFP chromophores as the bare anions and as complexes with the betaine zwitterion, which is assumed as a model for dipole microsolvation. Electronic structure calculations and energy decomposition analysis using Symmetry-Adapted Perturbation Theory are used to characterize gas-phase structures and complex cohesion forces. The calculations reveal a preponderance for coordination of betaine to the phenoxide deprotonation site predominantly through electrostatic forces. Calculations using the STEOM-DLPNO-CCSD method are able to reproduce absolute and relative vertical excitation energies for the bare anions and anion–betaine complexes. On the other hand, treatment of the betaine molecule with a point-charge model, in which the charges are computed from some common electron density population analysis schemes, show that just electrostatic and point-charge induction interactions are unable to account for the betaine-induced spectral shift. The present methodology could be applied to investigate cluster forces and optical properties in other gas-phase ion–zwitterion complexes.

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