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  • 251.
    Elgammal, Karim
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Hugosson, Håkan W.
    Smith, Anderson D.
    KTH, School of Information and Communication Technology (ICT), Electronics, Integrated devices and circuits. Chalmers Institute of Technology, Sweden.
    Råsander, Mikael
    Bergqvist, Lars
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Uppsala University, Sweden.
    Density functional calculations of graphene-based humidity and carbon dioxide sensors: effect of silica and sapphire substrates2017In: Surface Science, ISSN 0039-6028, E-ISSN 1879-2758, Vol. 663, p. 23-30Article in journal (Refereed)
    Abstract [en]

    We present dispersion-corrected density functional calculations of water and carbon dioxide molecules adsorption on graphene residing on silica and sapphire substrates. The equilibrium positions and bonding distances for the molecules are determined. Water is found to prefer the hollow site in the center of the graphene hexagon, whereas carbon dioxide prefers sites bridging carbon-carbon bonds as well as sites directly on top of carbon atoms. The energy differences between different sites are however minute - typically just a few tenths of a millielectronvolt. Overall, the molecule-graphene bonding distances are found to be in the range 3.1-3.3 (A) over circle. The carbon dioxide binding energy to graphene is found to be almost twice that of the water binding energy (around 0.17 eV compared to around 0.09 eV). The present results compare well with previous calculations, where available. Using charge density differences, we also qualitatively illustrate the effect of the different substrates and molecules on the electronic structure of the graphene sheet.

  • 252.
    Elinder, Fredrik
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Madeja, Michael
    University of Munster, Germany; Goethe University of Frankfurt, Germany.
    Zeberg, Hugo
    Karolinska Institute, Sweden.
    Arhem, Peter
    Karolinska Institute, Sweden.
    Extracellular Linkers Completely Transplant the Voltage Dependence from Kv1.2 Ion Channels to Kv2.12016In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 111, no 8, p. 1679-1691Article in journal (Refereed)
    Abstract [en]

    The transmembrane voltage needed to open different voltage-gated K (Kv) channels differs by up to 50 mV from each other. In this study we test the hypothesis that the channels voltage dependences to a large extent are set by charged amino-acid residues of the extracellular linkers of the Kv channels, which electrostatically affect the charged amino-acid residues of the voltage sensor S4. Extracellular cations shift the conductance-versus-voltage curve, G(V), by interfering with these extracellular charges. We have explored these issues by analyzing the effects of the divalent strontium ion (Sr2+) on the voltage dependence of the G(V) curves of wild-type and chimeric Kv channels expressed in Xenopus oocytes, using the voltage-clamp technique. Out of seven Kv channels, Kv1.2 was found to be most sensitive to Sr2+ (50 mM shifted G(V) by +21.7 mV), and Kv2.1 to be the least sensitive (+7.8 mV). Experiments on 25 chimeras, constructed from Kv1.2 and Kv2.1, showed that the large Sr2+-induced G(V) shift of Kv1.2 can be transferred to Kv2.1 by exchanging the extracellular linker between S3 and S4 (L3/4) in combination with either the extracellular linker between S5 and the pore (L5/P) or that between the pore and S6 (LP/6). The effects of the linker substitutions were nonadditive, suggesting specific structural interactions. The free energy of these interactions was similar to 20 kJ/mol, suggesting involvement of hydrophobic interactions and/or hydrogen bonds. Using principles from double-layer theory we derived an approximate linear equation (relating the voltage shifts to altered ionic strength), which proved to well match experimental data, suggesting that Sr2+ acts on these channels mainly by screening surface charges. Taken together, these results highlight the extracellular surface potential at the voltage sensor as an important determinant of the channels voltage dependence, making the extracellular linkers essential targets for evolutionary selection.

  • 253. Elm, J.
    et al.
    Norman, P.
    Bilde, M.
    Mikkelsen, K. V.
    Computational study of the Rayleigh light scattering properties of atmospheric pre-nucleation clusters2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 22, p. 10883-10890Article in journal (Refereed)
    Abstract [en]

    The Rayleigh and hyper Rayleigh scattering properties of the binary (H 2SO4)(H2O)n and ternary (H 2SO4)(NH3)(H2O)n clusters are investigated using a quantum mechanical response theory approach. The molecular Rayleigh scattering intensities are expressed using the dipole polarizability α and hyperpolarizability β tensors. Using density functional theory, we elucidate the effect of cluster morphology on the scattering properties using a combinatorial sampling approach. We find that the Rayleigh scattering intensity depends quadratically on the number of water molecules in the cluster and that a single ammonia molecule is able to induce a high anisotropy, which further increases the scattering intensity. The hyper Rayleigh scattering activities are found to be extremely low. This study presents the first attempt to map the scattering of atmospheric molecular clusters using a bottom-up approach. This journal is © the Partner Organisations 2014.

  • 254. Elm, J.
    et al.
    Norman, P.
    Mikkelsen, K. V.
    Rayleigh light scattering properties of atmospheric molecular clusters consisting of sulfuric acid and bases2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 24, p. 15701-15709Article in journal (Refereed)
    Abstract [en]

    The Rayleigh light scattering properties of (H<inf>2</inf>SO<inf>4</inf>)<inf>a</inf>(NH<inf>3</inf>)<inf>b</inf> and (H<inf>2</inf>SO<inf>4</inf>)<inf>a</inf>((CH<inf>3</inf>)<inf>2</inf>NH)<inf>b</inf> atmospheric molecular clusters have been investigated using a response theory approach. Using density functional theory the molecular structures and stepwise formation free energies of clusters with a and b up to 4 have been re-investigated. The Rayleigh scattering intensities are calculated from the dipole polarizability tensor α using the CAM-B3LYP functional by applying linear response methods. The intrinsic scattering properties of (H<inf>2</inf>SO<inf>4</inf>)<inf>a</inf>(NH<inf>3</inf>)<inf>b</inf> and (H<inf>2</inf>SO<inf>4</inf>)<inf>a</inf>((CH<inf>3</inf>)<inf>2</inf>NH)<inf>b</inf> indicate that amine containing clusters scatter light significantly more efficiently then their ammonia containing counterparts. Using the Atmospheric Cluster Dynamics Code (ACDC) the steady state cluster concentrations are estimated and the effective scattering is calculated. The effective scattering is shown to be highly dependent on the estimated concentrations and indicates that there exist competitive pathways, such as nucleation and coagulation, which influence the cluster distributions. The frequency dependence of the scattering is found to depend on the cluster composition and show increased responses when clusters contain more bases than acid molecules. Based on structures obtained using semi-empirical molecular dynamics simulations the Rayleigh scattering properties of clusters with up to 20 acid-base pairs are evaluated. This study represents the first step towards gaining a fundamental understanding of the scattering properties of small atmospheric clusters in the ambient atmosphere. © the Owner Societies 2015.

  • 255.
    Elm, Jonas
    et al.
    University of Copenhagen, Denmark.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Mikkelsen, Kurt V.
    University of Copenhagen, Denmark.
    Rayleigh light scattering properties of atmospheric molecular clusters consisting of sulfuric acid and bases2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 24, p. 15701-15709Article in journal (Refereed)
    Abstract [en]

    The Rayleigh light scattering properties of (H2SO4)(a)(NH3)(b) and (H2SO4)(a)((CH3)(2)NH)(b) atmospheric molecular clusters have been investigated using a response theory approach. Using density functional theory the molecular structures and stepwise formation free energies of clusters with a and b up to 4 have been re-investigated. The Rayleigh scattering intensities are calculated from the dipole polarizability tensor a using the CAM-B3LYP functional by applying linear response methods. The intrinsic scattering properties of (H2SO4)(a)(NH3)(b) and (H2SO4)(a)((CH3)(2)NH)(b) indicate that amine containing clusters scatter light significantly more efficiently then their ammonia containing counterparts. Using the Atmospheric Cluster Dynamics Code (ACDC) the steady state cluster concentrations are estimated and the effective scattering is calculated. The effective scattering is shown to be highly dependent on the estimated concentrations and indicates that there exist competitive pathways, such as nucleation and coagulation, which influence the cluster distributions. The frequency dependence of the scattering is found to depend on the cluster composition and show increased responses when clusters contain more bases than acid molecules. Based on structures obtained using semi-empirical molecular dynamics simulations the Rayleigh scattering properties of clusters with up to 20 acid-base pairs are evaluated. This study represents the first step towards gaining a fundamental understanding of the scattering properties of small atmospheric clusters in the ambient atmosphere.

  • 256.
    Erdtman, Edvin
    Örebro University, School of Science and Technology.
    5-Aminolevulinic acid and derivatives thereof: properties, lipid permeability and enzymatic reactions2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    5-aminolevulinic acid (5-ALA) and derivatives thereof are widely usedprodrugs in treatment of pre-malignant skin diseases of the cancer treatmentmethod photodynamic therapy (PDT). The target molecule in 5-ALAPDTis protoporphyrin IX (PpIX), which is synthesized endogenously from5-ALA via the heme pathway in the cell. This thesis is focused on 5-ALA,which is studied in different perspectives and with a variety of computationalmethods. The structural and energetic properties of 5-ALA, itsmethyl-, ethyl- and hexyl esters, four different 5-ALA enols, and hydrated5-ALA have been investigated using Quantum Mechanical (QM) first principlesdensity functional theory (DFT) calculations. 5-ALA is found to bemore stable than its isomers and the hydrolysations of the esters are morespontaneous for longer 5-ALA ester chains than shorter. The keto-enoltautomerization mechanism of 5-ALA has been studied, and a self-catalysismechanism has been proposed to be the most probable. Molecular Dynamics(MD) simulations of a lipid bilayer have been performed to study themembrane permeability of 5-ALA and its esters. The methyl ester of 5-ALAwas found to have the highest permeability constant (PMe-5-ALA = 52.8 cm/s).The mechanism of the two heme pathway enzymes; Porphobilinogen synthase(PBGS) and Uroporphyrinogen III decarboxylase (UROD), have beenstudied by DFT calculations and QM/MM methodology. The rate-limitingstep is found to have a barrier of 19.4 kcal/mol for PBGS and 13.7kcal/mol for the first decarboxylation step in UROD. Generally, the resultsare in good agreement with experimental results available to date.

  • 257.
    Erdtman, Edvin
    Örebro universitet, Akademin för naturvetenskap och teknik.
    5-Aminolevulinic acid and derivatives thereof: properties, lipid permeability and enzymatic reactions2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    5-aminolevulinic acid (5-ALA) and derivatives thereof are widely usedprodrugs in treatment of pre-malignant skin diseases of the cancer treatmentmethod photodynamic therapy (PDT). The target molecule in 5-ALAPDTis protoporphyrin IX (PpIX), which is synthesized endogenously from5-ALA via the heme pathway in the cell. This thesis is focused on 5-ALA,which is studied in different perspectives and with a variety of computationalmethods. The structural and energetic properties of 5-ALA, itsmethyl-, ethyl- and hexyl esters, four different 5-ALA enols, and hydrated5-ALA have been investigated using Quantum Mechanical (QM) first principlesdensity functional theory (DFT) calculations. 5-ALA is found to bemore stable than its isomers and the hydrolysations of the esters are morespontaneous for longer 5-ALA ester chains than shorter. The keto-enoltautomerization mechanism of 5-ALA has been studied, and a self-catalysismechanism has been proposed to be the most probable. Molecular Dynamics(MD) simulations of a lipid bilayer have been performed to study themembrane permeability of 5-ALA and its esters. The methyl ester of 5-ALAwas found to have the highest permeability constant (PMe-5-ALA = 52.8 cm/s).The mechanism of the two heme pathway enzymes; Porphobilinogen synthase(PBGS) and Uroporphyrinogen III decarboxylase (UROD), have beenstudied by DFT calculations and QM/MM methodology. The rate-limitingstep is found to have a barrier of 19.4 kcal/mol for PBGS and 13.7kcal/mol for the first decarboxylation step in UROD. Generally, the resultsare in good agreement with experimental results available to date.

  • 258.
    Erdtman, Edvin
    et al.
    Akademin för textil, teknik och ekonomi, Högskolan i Borås, Borås, Sverige.
    Bohlén, Martin
    Akademin för textil, teknik och ekonomi, Högskolan i Borås, Borås, Sverige.
    Ahlström, Peter
    Akademin för textil, teknik och ekonomi, Högskolan i Borås, Borås, Sverige.
    Gkourmpis, Thomas
    Innovation & Technology, Borealis AB, Stenungsund, Sweden.
    Berlin, Mikael
    Tetra Pak Packaging Solutions AB, Ruben Rausings Gata, Lund, Sweden.
    Andersson, Thorbjörn
    Tetra Pak Packaging Solutions AB, Ruben Rausings Gata, Lund, Sweden.
    Bolton, Kim
    Akademin för textil, teknik och ekonomi, Högskolan i Borås, Borås, Sverige.
    A molecular-level computational study of the diffusion and solubility of water and oxygen in carbonaceous polyethylene nanocomposites2016In: Journal of Polymer Science Part B: Polymer Physics, ISSN 0887-6266, E-ISSN 1099-0488, Vol. 54, no 5, p. 589-602Article in journal (Refereed)
    Abstract [en]

    Monte Carlo and molecular dynamics simulations were performed to investigate the effect on the solubility, diffusion, and permeability of water and oxygen when adding graphene or single-walled carbon nanotubes (SWCNTs) to polyethylene (PE). When compared with pure PE, addition of graphene lowered the solubility of water, whereas at lower temperatures, the oxygen solubility increased because of the oxygen–graphene interaction. Addition of SWCNTs lowered the solubility of both water and oxygen when compared with pure PE. A detailed analysis showed that an ordered structure of PE is induced near the additive surface, which leads to a decrease in the diffusion coefficient of both penetrants in this region. The addition of graphene does not change the permeation coefficient of oxygen (in the direction parallel to the filler) and, in fact, may even increase this coefficient when compared with pure PE. In contrast, the water permeability is decreased when graphene is added to PE. The addition of SWCNTs decreases the permeability of both penetrants. Graphene can consequently be added to selectively increase the solubility and permeation of oxygen over water, at least at lower temperatures. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 589–602

  • 259. Erdtman, Edvin
    et al.
    Bohlén, Martin
    University of Borås, School of Engineering.
    Ahlström, Peter
    University of Borås, School of Engineering.
    Gkourmpis, Thomas
    Berlin, Mikael
    Andersson, Thorbjörn
    Bolton Kim, Kim
    University of Borås, School of Engineering.
    Permeation of water and oxygen through carbonaceous PE composites2014Conference paper (Refereed)
  • 260.
    Erdtman, Edvin
    et al.
    Örebro University, School of Science and Technology.
    Bushnell, Eric A. C.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Gauld, James W.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Eriksson, Leif A.
    School of Chemistry, National University of Ireland (NUI Galway), Galway, Ireland.
    Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase2011In: Computational and Theoretical Chemistry, ISSN 2210-271X, E-ISSN 2210-2728, Vol. 963, no 2-3, p. 479-489Article in journal (Refereed)
    Abstract [en]

    Schiff bases are common and important intermediates in many bioenzymatic systems. The mechanism by which they are formed, however,is dependent on the solvent, pH and other factors. In the present study we have used density functional theory methods in combination with appropriate chemical models to get a better understanding of the inherent chemistry of the formation of two Schiff bases that have been proposed to be involved in the catalytic mechanism of porphobilinogensynthase (PBGS), a key enzyme in the biosynthesis of porphyrins. More specifically, we have investigated the uncatalysed reaction of its substrate 5-aminolevulinic acid (5-ALA) with a lysine residue for theformation of the P-site Schiff base, and as possibly catalysed by the second active site lysine, water or the 5-ALA itself. It is found that cooperatively both the second lysine and the amino group of the initial 5-ALA itself are capable of reducing the rate-limiting energy barrier to14.0 kcal mol-1. We therefore propose these to be likely routes involved in the P-site Schiff-base formation in PBGS.

  • 261.
    Erdtman, Edvin
    et al.
    Örebro universitet, Akademin för naturvetenskap och teknik.
    Bushnell, Eric A. C.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Gauld, James W.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor ON, Canada.
    Eriksson, Leif A.
    School of Chemistry, National University of Ireland (NUI Galway), Galway, Ireland.
    Computational studies on Schiff-base formation: Implications for the catalytic mechanism of porphobilinogen synthase2011In: Computational and Theoretical Chemistry, ISSN 2210-271X, E-ISSN 2210-2728, Vol. 963, no 2-3, p. 479-489Article in journal (Refereed)
    Abstract [en]

    Schiff bases are common and important intermediates in many bioenzymatic systems. The mechanism by which they are formed, however,is dependent on the solvent, pH and other factors. In the present study we have used density functional theory methods in combination with appropriate chemical models to get a better understanding of the inherent chemistry of the formation of two Schiff bases that have been proposed to be involved in the catalytic mechanism of porphobilinogensynthase (PBGS), a key enzyme in the biosynthesis of porphyrins. More specifically, we have investigated the uncatalysed reaction of its substrate 5-aminolevulinic acid (5-ALA) with a lysine residue for theformation of the P-site Schiff base, and as possibly catalysed by the second active site lysine, water or the 5-ALA itself. It is found that cooperatively both the second lysine and the amino group of the initial 5-ALA itself are capable of reducing the rate-limiting energy barrier to14.0 kcal mol-1. We therefore propose these to be likely routes involved in the P-site Schiff-base formation in PBGS.

  • 262.
    Erdtman, Edvin
    et al.
    Örebro University, Department of Natural Sciences.
    dos Santos, Daniel J. V. A.
    Löfgren, Lennart
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer2008In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 463, no 1-3, p. 178-182Article in journal (Refereed)
    Abstract [en]

    5-Aminolevulinic acid (5ALA) and ester derivates thereof are used as prodrugs in photodynamic therapy (PDT). The behavior of 5ALA and three esters of 5ALA in a DPPC lipid bilayer is investigated. In particular, the methyl ester displays a very different free energy profile, where the highest barrier is located in the region with highest lipid density, while the others have their peak in the middle of the membrane, and also displays a considerably lower permeability coefficient than neutral 5ALA and the ethyl ester. The zwitterion of 5ALA has the highest permeability constant, but a significant free energy minimum in the polar head-group region renders an accumulation in this region.

  • 263.
    Erdtman, Edvin
    et al.
    Institutionen för naturvetenskap and Modelling and Simulation Research Center, Örebro University, Sweden.
    dos Santos, Daniel J. V. A.
    i. Med. UL/Institute for Medicine and Pharmaceutical Sciences, Faculty of Pharmacy, University of Lisbon. Av. Prof. Gama Pinto, Lisbon, Portugal.
    Löfgren, Lennart
    Head- and Neck Oncology Center, Örebro University Hospital, Örebro, Sweden.
    Eriksson, Leif A.
    Örebro universitet, Institutionen för naturvetenskap.
    Modelling the behavior of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer2008In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 463, no 1-3, p. 178-182Article in journal (Refereed)
    Abstract [en]

    5-Aminolevulinic acid (5ALA) and ester derivates thereof are used as prodrugs in photodynamic therapy (PDT). The behavior of 5ALA and three esters of 5ALA in a DPPC lipid bilayer is investigated. In particular, the methyl ester displays a very different free energy profile, where the highest barrier is located in the region with highest lipid density, while the others have their peak in the middle of the membrane, and also displays a considerably lower permeability coefficient than neutral 5ALA and the ethyl ester. The zwitterion of 5ALA has the highest permeability constant, but a significant free energy minimum in the polar head-group region renders an accumulation in this region.

  • 264.
    Erdtman, Edvin
    et al.
    Örebro University, Department of Natural Sciences.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Theoretical study of 5-aminolevulinic acid (5ALA) and some pharmaceutically important derivatives2007In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 434, no 1-3, p. 101-106Article in journal (Refereed)
    Abstract [en]

    5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. The addition of extracorporeal 5ALA and its alkyl ester derivatives are in current clinical use in photodynamical diagnostics and photodynamic therapy of tumors and skin disorders. In the current study density functional theory calculations are performed on 5ALA and its methyl, ethyl, and hexyl esters, in order to explore the basic chemical properties of these species. It is concluded that even in aqueous media the zwitterionic form of 5ALA is less stable than the non-zwitterionic one, that the local environment (lipid vs water) affects the energetics of reaction considerably, and that the hexyl species is most prone to hydrolysis of the three alkyl ester derivatives.

  • 265.
    Erdtman, Edvin
    et al.
    Örebro universitet, Institutionen för naturvetenskap.
    Eriksson, Leif A.
    Örebro universitet, Institutionen för naturvetenskap.
    Theoretical study of 5-aminolevulinic acid (5ALA) and some pharmaceutically important derivatives2007In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 434, no 1-3, p. 101-106Article in journal (Refereed)
    Abstract [en]

    5-Aminolevulinic acid (5ALA) is the key synthetic building block in protoporphyrin IX (PpIX), the heme chromophore in mitochondria. The addition of extracorporeal 5ALA and its alkyl ester derivatives are in current clinical use in photodynamical diagnostics and photodynamic therapy of tumors and skin disorders. In the current study density functional theory calculations are performed on 5ALA and its methyl, ethyl, and hexyl esters, in order to explore the basic chemical properties of these species. It is concluded that even in aqueous media the zwitterionic form of 5ALA is less stable than the non-zwitterionic one, that the local environment (lipid vs water) affects the energetics of reaction considerably, and that the hexyl species is most prone to hydrolysis of the three alkyl ester derivatives.

  • 266.
    Erdtman, Edvin
    et al.
    Örebro University, Department of Natural Sciences.
    Eriksson, Leif A.
    Örebro University, Department of Natural Sciences.
    Theoretical study of 5-aminolevulinic acid tautomerization: a novel self-catalyzed mechanism2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 18, p. 4367-4374Article in journal (Refereed)
    Abstract [en]

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

  • 267.
    Erdtman, Edvin
    et al.
    Örebro universitet, Institutionen för naturvetenskap.
    Eriksson, Leif A.
    Örebro universitet, Institutionen för naturvetenskap.
    Theoretical study of 5-aminolevulinic acid tautomerization: a novel self-catalyzed mechanism2008In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 112, no 18, p. 4367-4374Article in journal (Refereed)
    Abstract [en]

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

  • 268.
    Erdtman, Edvin
    et al.
    Örebro University, School of Science and Technology.
    Gauld, James W
    Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B.
    Eriksson, Leif A.
    School of Chemistry, NUI Galway, Galway, Ireland.
    Computational Insights into the Mechanism of Substrate Binding in Potphobilinogen SynthaseManuscript (preprint) (Other academic)
  • 269.
    Erdtman, Edvin
    et al.
    Örebro University, School of Science and Technology.
    Gauld, James W.
    Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B.
    Eriksson, Leif A.
    School of Chemistry, NUI Galway, Galway, Ireland.
    Modelling the mechanism of porphobilinogen synthaseManuscript (preprint) (Other academic)
  • 270.
    Erdtman, Edvin
    et al.
    University of Borås, School of Engineering.
    Gebäck, Tobias
    University of Borås, School of Engineering.
    Ahlström, Peter
    University of Borås, School of Engineering.
    Atomistic Modelling of Protein Superabsorbents2012Conference paper (Other academic)
  • 271.
    Erdtman, Edvin
    et al.
    University of Borås, School of Engineering.
    Gebäck, Tobias
    Ahlström, Peter
    University of Borås, School of Engineering.
    Computational modeling of Protein based super-absorbents from waste2011Conference paper (Other academic)
    Abstract [en]

    Hydrogels are used for various applications, for example as transporters in drug delivery, in control lenses, and as superabsorbent material in diapers.[1] Most synthetic produced hydrogels are based on synthetic polymers. Even though they are efficient and cheap, they are not biodegradable and sometimes even toxic. To produce more environmental friendly and biodegradable superabsorbent polymers (Bio- SAPs), other building blocks can be used, such as polysaccharides[2] and various protein structures, for example fish shells[3], collagen[4], soy protein[5] and egg protein[6]. Experimental studies at the University of Boras show that it is possible to produce Bio-SAPs from by-products of ethanol production from ligno-cellulose.[2, 6, 7] 2. Method We have studied the absorption properties of protein structures in silico as a comparison to experimental studies. The NPT Gibbs Ensemble Monte Carlo (GEMC) simulation scheme with two phases is used in order to calculate the absorption capacity of the protein. Pure water was simulated in the first GEMC-phase and the peptide in the second phase. The simulations were made with SPC/E water model [8] and the AMBER99 atomistic force field for the peptides [9]. Furthermore, mesoscopic studies with coarse grained force fields have been done. To facilitate faster computations, we used cell lists for the atom-atom interactions, configurational bias algorithm to build the water molecules and the peptide side-chains, and the cavity bias algorithm [10] for molecule insertions. Model peptides have been studied with varying secondary structure, temperature and protonation (pH). We also plan to study how cross-links affect the absorption. One of the peptides we study is a 20 amino acid long peptide called SSP1.[11] This peptide is designed to form a fibrous structure a hydrogel, and its structure is well defined. We have also studied a peptide which changes secondary structure when changing the pH, and concentration.[12] This makes it possible to compare absorption properties with respect to the secondary structure. 3. Conclusion We have simulated peptides with the Gibbs Ensemble Monte Carlo scheme in order to study the water absorption rate dependent of structure, charge, pH and temperature. This information is useful when developing new biodegradable superabsorbent materials.

  • 272.
    Eriksson, Emma S. E.
    et al.
    Department of Chemistry and Molecular Biology, University of Gothenburg.
    Erdtman, Edvin
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Eriksson, Leif A.
    Department of Chemistry and Molecular Biology, University of Gothenburg.
    Permeability of 5-aminolevulinic acid oxime derivatives in lipid membranes2016In: Theoretical Chemistry accounts, ISSN 1432-881X, E-ISSN 1432-2234, Vol. 135, no 1, p. 1-9Article in journal (Refereed)
    Abstract [en]

    The endogenous molecule 5-aminolevulinic acid (5ALA) and its methyl ester (Me-5ALA) have been used as prodrugs in photodynamic treatment of actinic keratosis and superficial non-melanoma skin cancers for over a decade. Recently, a novel set of 5ALA derivatives based on introducing a hydrolyzable oxime functionality was proposed and shown to generate considerably stronger onset of the photoactive molecule protoporphyrin IX (PpIX) in the cells. In the current work, we employ molecular dynamics simulation techniques to explore whether the higher intercellular concentration of PpIX caused by the oxime derivatives is related to enhanced membrane permeability, or whether other factors contribute to this. It is concluded that the oximes show overall similar accumulation at the membrane headgroup regions as the conventional derivatives and that the transmembrane permeabilities are in general close to that of 5ALA. The highest permeability of all compounds explored is found for Me-5ALA, which correlates with a considerably lower fee energy barrier at the hydrophobic bilayer center. The high PpIX concentration must hence be sought in other factors, where slow hydrolysis of the oxime functionality is a plausible reason, enabling stronger buildup of PpIX over time.

  • 273.
    Eriksson, Lars
    et al.
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Grins, Jekabs
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    Svensson, Gunnar
    Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
    DFT predictions of Prussian Blue structures2018In: DFT predictions of Prussian Blue structures, 2018Conference paper (Refereed)
  • 274.
    Eriksson, Leif A.
    et al.
    Örebro University, Department of Natural Sciences.
    Russo, Nino
    Ugalde, Jesus M.
    Second International Theoretical Biophysics Symposium, Örebro University, Sweden, June 28–July 1, 20052007In: International Journal of Quantum Chemistry, ISSN 0020-7608, E-ISSN 1097-461X, Vol. 107, no 2, p. 66p. 259-260Article in journal (Refereed)
  • 275.
    Eriksson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Photoluminescence Characteristics of III-Nitride Quantum Dots and Films2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    III-Nitride semiconductors are very promising in both electronics and optical devices. The ability of the III-Nitride semiconductors as light emitters to span the electromagnetic spectrum from deep ultraviolet light, through the entire visible region, and into the infrared part of the spectrum, is a very important feature, making this material very important in the field of light emitting devices. In fact, the blue emission from Indium Gallium Nitride (InGaN), which was awarded the 2014 Nobel Prize in Physics, is the basis of the common and important white light emitting diode (LED).

    Quantum dots (QDs) have properties that make them very interesting for light emitting devices for a range of different applications, such as the possibility of increasing device efficiency. The spectrally well-defined emission from QDs also allows accurate color reproduction and high-performance communication devices. The small size of QDs, combined with selective area growth allows for an improved display resolution. By control of the polarization direction of QDs, they can be used in more efficient displays as well as in traditional communication devices. The possibility of sending out entangled photon pairs is another QD property of importance for quantum key distribution used for secure communication.

    QDs can hold different exciton complexes, such as the neutral single exciton, consisting of one electron and one hole, and the biexciton, consisting of two excitons. The integrated PL intensity of the biexciton exhibits a quadratic dependence with respect to the excitation power, as compared to the linear power dependence of the neutral single exciton. The lifetime of the neutral exciton is 880 ps, whereas the biexciton, consisting of twice the number of charge carriers and lacks a dark state, has a considerably shorter lifetime of only 500 ps. The ratio of the lifetimes is an indication that the size of the QD is in the order of the exciton Bohr radius of the InGaN crystal making up these QDs in the InGaN QW.

    A large part of the studies of this thesis has been focused on InGaN QDs on top of hexagonal Gallium Nitride (GaN) pyramids, selectively grown by Metal Organic Chemical Vapor Deposition (MOCVD). On top of the GaN pyramids, an InGaN layer and a GaN capping layer were grown. From structural and optical investigations, InGaN QDs have been characterized as growing on (0001) facets on truncated GaN pyramids. These QDs exhibit both narrow photoluminescence linewidths and are linearly polarized in directions following the symmetry of the pyramids.

    In this work, the neutral single exciton, and the more rare negatively charged exciton, have been investigated. At low excitation power, the integrated intensity of the PL peak of the neutral exciton increases linearly with the excitation power. The negatively charged exciton, on the other hand, exhibits a quadratic power dependence, just like that of the biexciton. Upon increasing the temperature, the power dependence of the negatively charged exciton changes to linear, just like the neutral exciton. This change in power dependence is explained in terms of electrons in potential traps close to the QD escaping by thermal excitation, leading to a surplus of electrons in the vicinity of the QD. Consequently, only a single exciton needs to be created by photoexcitation in order to form a negatively charged exciton, while the extra electron is supplied to the QD by thermal excitation.

    Upon a close inspection of the PL of the neutral exciton, a splitting of the peak of just below 0.4 meV is revealed. There is an observed competition in the integrated intensity between these two peaks, similar to that between an exciton and a biexciton. The high energy peak of this split exciton emission is explained in terms of a remotely charged exciton. This exciton state consists of a neutral single exciton in the QD with an extra electron or hole in close vicinity of the QD, which screens the built-in field in the QD.

    The InGaN QDs are very small; estimated to be on the order of the exciton Bohr radius of the InGaN crystal, or even smaller. The lifetimes of the neutral exciton and the negatively charged exciton are approximately 320 ps and 130 ps, respectively. The ratio of the lifetimes supports the claim of the QD size being on the order of the exciton Bohr radius or smaller, as is further supported by power dependence results. Under the assumption of a spherical QD, theoretical calculations predict an emission energy shift of 0.7 meV, for a peak at 3.09 eV, due to the built-in field for a QD with a diameter of 1.3 nm, in agreement with the experimental observations.

    Studying the InGaN QD PL from neutral and charged excitons at elevated temperatures (4 K to 166 K) has revealed that the QDs are surrounded by potential fluctuations that trap charge carriers with an energy of around 20 meV, to be compared with the exciton trapping energy in the QDs of approximately 50 meV. The confinement of electrons close to the QD is predicted to be smaller than for holes, which accounts for the negative charge of the charged exciton, and for the higher probability of capturing free electrons. We have estimated the lifetimes of free electrons and holes in the GaN barrier to be 45 ps and 60 ps, in consistence with excitons forming quickly in the barrier upon photoexcitation and that free electrons and holes get trapped quickly in local potential traps close to the QDs. This analysis also indicates that there is a probability of 35 % to have an electron in the QD between the photoexcitation pulses, in agreement with a lower than quadratic power dependence of the negatively charged exciton.

    InN is an attractive material due to its infrared emission, for applications such as light emitters for communication purposes, but it is more difficult to grow with high quality and low doping concentration as compared to GaN. QDs with a higher In-composition or even pure InN is an interesting prospect as being a route towards increased quantum confinement and room temperature device operation. For all optical devices, p-type doping is needed. Even nominally undoped InN samples tend to be heavily n-type doped, causing problems to make pn-junctions as needed for LEDs. In our work, we present Mg-doped p-type InN films, which when further increasing the Mg-concentration revert to n-type conductivity. We have focused on the effect of the Mg-doping on the light emission properties of these films. The low Mg doped InN film is inhomogeneous and is observed to contain areas with n-type conductivity, so called n-type pockets in the otherwise p-type InN film. A higher concentration of Mg results in a higher crystalline quality and the disappearance of the n-type pockets. The high crystalline quality has enabled us to determine the binding energy of the Mg dopants to 64 meV. Upon further increase of the Mg concentration, the film reverts to ntype conductivity. The highly Mg doped sample also exhibits a red-shifted emission with features that are interpreted as originating from Zinc-Blende inclusions in the Wurtzite InN crystal, acting as quantum wells. The Mg doping is an important factor in controlling the conductivity of InN, as well as its light emission properties, and ultimately construct InN-based devices.

    In summary, in this thesis, both pyramidal InGaN QDs and InGaN QDs in a QW have been investigated. Novel discoveries of exciton complexes in these QD systems have been reported. Knowledge has also been gained about the challenging material InN, including a study of the effect of the Mg-doping concentration on the semiconductor crystalline quality and its light emission properties. The outcome of this thesis enriches the knowledge of the III-Nitride semiconductor community, with the long-term objective to improve the device performance of III-Nitride based light emitting devices.

  • 276.
    Erkki, Brändas and Yngve Öhrn
    Uppsala University.
    Quantum Systems in Chemistry and Physics VI2002In: International Journal of Quantum Chemistry, Vol. 89, no 4, p. 181-427Conference proceedings (editor) (Other scientific)
  • 277.
    Esmieu, Charlene
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics. CNRS, LCC, 205 Route Narbonne,BP 44099, F-31077 Toulouse 4, France.
    Guo, Meiyuan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Redman, Holly J.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Berggren, Gustav
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Molecular Biomimetics.
    Synthesis of a miniaturized [FeFe] hydrogenase model system2019In: Dalton Transactions, ISSN 1477-9226, E-ISSN 1477-9234, Vol. 48, no 7, p. 2280-2284Article in journal (Refereed)
    Abstract [en]

    The reaction occurring during artificial maturation of [FeFe] hydrogenase has been recreated using molecular systems. The formation of a miniaturized [FeFe] hydrogenase model system, generated through the combination of a [4Fe4S] cluster binding oligopeptide and an organometallic Fe complex, has been monitored by a range of spectroscopic techniques. A structure of the final assembly is suggested based on EPR and FTIR spectroscopy in combination with DFT calculations. The capacity of this novel H-cluster model to catalyze H-2 production in aqueous media at mild potentials is verified in chemical assays.

  • 278. Fahleson, T.
    et al.
    Kauczor, J.
    Norman, P.
    Coriani, S.
    The magnetic circular dichroism spectrum of the C 60 fullerene2013In: Molecular Physics, ISSN 0026-8976, E-ISSN 1362-3028, Vol. 111, no 9-11, p. 1401-1404Article in journal (Refereed)
    Abstract [en]

    The magnetic circular dichroism spectrum of the C60 fullerene has been determined with the use of Kohn-Sham density functional theory in conjunction with the CAM-B3LYP exchange-correlation functional. The experimental spectrum of Gasyna et al. [Chem. Phys. Lett. 183, 283 (1991)] covering the wavelength region above 200 nm is explained by the signal responses from the three lowest singlet states of T 1u symmetry. © 2013 Copyright Taylor and Francis Group, LLC.

  • 279. Fahleson, T.
    et al.
    Kauczor, J.
    Norman, P.
    Santoro, F.
    Improta, R.
    Coriani, S.
    TD-DFT investigation of the magnetic circular dichroism spectra of some purine and pyrimidine bases of nucleic acids2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 21, p. 5476-5489Article in journal (Refereed)
    Abstract [en]

    We present a computational study of the magnetic circular dichroism (MCD) spectra in the 200-300 nm wavelength region of purine and its derivative hypoxanthine, as well as of the pyrimidine bases of nucleic acids uracil, thymine, and cytosine, using the B3LYP and CAM-B3LYP functionals. Solvent effects are investigated within the polarizable continuum model and by inclusion of explicit water molecules. In general, the computed spectra are found to be in good agreement with the experimental ones, apart from some overall blue shifts. Both the pseudo-A term shape of the MCD spectra of the purines and the B term shape of the spectra of pyrimidine bases are reproduced. Our calculations also correctly reproduce the reversed phase of the MCD bands in purine compared to that of its derivatives present in nucleic acids. Solvent effects are sizable and system specific, but they do not in general alter the qualitative shape of the spectra. The bands are dominated by the bright π → π∗ transitions, and our calculations in solution nicely reproduce their energy differences, improving the estimates obtained in the gas phase. Shoulders are predicted for purine and uracil due to n → π∗ excitations, but they are too weak to be observed in the experiment. © 2015 American Chemical Society.

  • 280. Fahleson, T.
    et al.
    Norman, P.
    Coriani, S.
    Rizzo, A.
    Rikken, G. L. J. A.
    A density functional theory study of magneto-electric Jones birefringence of noble gases, furan homologues, and mono-substituted benzenes2013In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 139, no 19, article id 194311Article in journal (Refereed)
    Abstract [en]

    We report on the results of a systematic ab initio study of the Jones birefringence of noble gases, of furan homologues, and of monosubstituted benzenes, in the gas phase, with the aim of analyzing the behavior and the trends within a list of systems of varying size and complexity, and of identifying candidates for a combined experimental/theoretical study of the effect. We resort here to analytic linear and nonlinear response functions in the framework of time-dependent density functional theory. A correlation is made between the observable (the Jones constant) and the atomic radius for noble gases, or the permanent electric dipole and a structure/chemical reactivity descriptor as the para Hammett constant for substituted benzenes. © 2013 AIP Publishing LLC.

  • 281.
    Fahleson, Tobias
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Derivation and application of response functions for nonlinear absorption and dichroisms2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis is titled ’Derivation and application of response functions for nonlinear absorption and dichroisms’ and was written by Tobias Fahleson at the Division of Theoretical Chemistry & Biology at KTH Royal Institute of Technology in Sweden. It explores and expands upon theoretical means of quantifying a number of nonlinear spectroscopies, including two-photon absorption, resonant inelastic x-ray scattering, Jones birefringence, and magnetic circular dichroism. Details are provided for the derivation and program implementation of complex-valued (damped) cubic response functions that have been implemented in the quantum chemistry package DALTON [1], based on working equations formulated for an approximate-state wave function. This is followed by an assessment of the implementation. It is demonstrated how two-photon absorption (TPA) can be described either through second-order transition moments or the damped cubic response function. A set of illustrative TPA profiles are produced for smaller molecules. In addition, resonant inelastic x-ray scattering (RIXS) is explored in a similar manner as two-photon absorption. It is shown for small systems how RIXS spectra may be obtained using a reduced form of the cubic response function. Linear birefringences are investigated for noble gases, monosubstituted benzenes, furan homologues, and liquid acetonitrile. Regarding the noble gases, the Jones effect is shown to be proportional to a power series with respect to atomic radial sizes. For monosubstituted benzenes, a linear relation between the Jones birefringence and the empirical para-Hammett constant as well as the permanent electric dipole moment is presented. QM/MM protocols are applied for a pure acetonitrile liquid, including polarizable embedding and polarizable-density embedding models. The final chapter investigates magnetically induced circular dichroism (MCD). A question regarding relative stability of the first set of excited states for DNA-related molecular systems is resolved through MCD by exploiting the signed nature of circular dichroisms. Furthermore, to what extent solvent contributions affect MCD spectra and the effect on uracil MCD spectrum due to thionation is studied.

  • 282.
    Fahleson, Tobias
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Development and characterization of damped cubic response functions with application to two-photon absorption2015Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Molecular response to electromagnetic fields - static or optical - within a framework of perturbation theory diverges close to resonance with molecular transitionen energies, and need work-around solutions for real-valued response functions. This licentiate thesis deals with nonlinear response, with focus being on cubic polarizaibilities, and outlines the underlying mathematics for exact-state and approximatestate, complex-valued response functions applicable to quantum chemical computation. Such a complex-valued response theory is commonly known as dampedresponse theory, for which the response functions consists of a real and an imaginary component, each of them representing various spectroscopies in nature. In addition to the mathematics, the formulas have been implemented in the quantum chemical package DALTON, and several tests determining the integrity of the implementation has been conducted.

    The fourth and final major part of the thesis is concerned with applied nonlinear response theory, including not only cubic response functions, but also quadratic and linear response functions, some of which are of the more exotic character. Three spectroscopies have been investigated for small and medium-sized organic molecules and the neon atom: two-photon absorption (TPA), Jones birefringence (JB), and magnetic circular dichroism (MCD).

    The TPA part is a simple demonstration of capability of the damped cubic response code, for which neon is the example system. Perfect agreement is shown for the Ehrenfest approach and an independent implementation based on the quasienergy formalism.

    JB is an optical eect in which induced refractive anisotropy, by means of external electric and magnetic static elds, results in ellipticity of linearly polarized light beams. This part mainly discuss implications from a paper which the current author took part in. The paper ultimately attempts to indentify the general observable strength of the effect, and coincidentaly pin-point some particular system suitable for experiments. Among other finds, JB is found to be correlated to the electric dipole moment, and for monosubstituted benzenes, the para-Hammett constant.

    Finally, MCD is discussed based on three papers in which the present author is included. The elegant MCD solution to broad absorption peaks, for which it is desired to distinguish individual states, is demonstrated on adenine and three additional purine derivatives. A drawn out debate regarding relative stability of certain low-lying states could be settled by this method. Furthermore, appropriate description of solvation environment in conjunction with the exchange-correlation functionals B3LYP and CAM-B3LYP is investigated on purine and pyrimidine derivatives. CAM-B3LYP is found to be superior in terms of general prole shapes, while results regarding solvation model are rather inconclusive, although the results suggests some level of solvation model is appropriate, such as a polarizable continuum model or explicit solvation molecules.

  • 283.
    Fahleson, Tobias
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Kauczor, Joanna
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Santoro, Fabrizio
    CNR, Italy.
    Improta, Roberto
    CNR, Italy.
    Coriani, Sonia
    University of Trieste, Italy; Aarhus University, Denmark.
    TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 21, p. 5476-5489Article in journal (Refereed)
    Abstract [en]

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

  • 284.
    Fahleson, Tobias
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Norman, Patrick
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Resonant-convergent cubic response function in the random-phase approximation with application to two-photon absorption on neon in the ultraviolet-visible regionManuscript (preprint) (Other academic)
    Abstract [en]

    Damped cubic response functions are presented for exact-state and approximate-state methods eligible for quantum chemical computational applications. Proof of proper implementation is given, accompanied by a two-photon absorption example on neon in the ultraviolet-visible spectral region. The method accurately distinguish one- and two-photon resonances and exhibits spot-on agreement with other approaches.

  • 285.
    Fahleson, Tobias
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Resonant-convergent second-order nonlinear response functions at the levels of Hartree-Fock and Kohn-Sham density functional theory2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 147, no 14, article id 144109Article in journal (Refereed)
    Abstract [en]

    The second-order nonlinear (or cubic) response function is derived from the Ehrenfest theorem with inclusion made of the finite lifetimes of the excited states, representing the extension of the derivation of the quadratic response function in the same framework [P. Norman et al., J. Chem. Phys. 123, 194103 (2005)]. The resulting damped response functions are physically sound and converging also in near-resonance and resonance regions of the spectrum. Being an accurate approximation for small complex frequencies (defined as the sum of an optical frequency and an imaginary damping parameter), the polynomial expansion of the complex cubic response function in terms of the said frequencies is presented and used to validate the program implementation. In terms of approximate state theory, the computationally tractable expressions of the damped cubic response function are derived and implemented at the levels of Hartree-Fock and Kohn-Sham density functional theory. Numerical examples are provided in terms of studies of the intensity-dependent refractive index of para-nitroaniline and the two-photon absorption cross section of neon. For the latter property, a numerical comparison is made against calculations of the square of two-photon matrix elements that are identified from a residue analysis of the resonance-divergent quadratic response function.

  • 286. Fahleson, Tobias
    et al.
    Olsen, Jógvan Magnus Haugaard
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rizzo, Antonio
    A QM/MM and QM/QM/MM study of Kerr, Cotton--Mouton and Jones linear birefringences in liquid acetonitrile2017In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084Article in journal (Refereed)
    Abstract [en]

    QM/MM and QM/QM/MM protocols are applied to the ab initio study of the three linear bire-fringences Kerr, Cotton–Mouton, and Jones, as shown by acetonitrile in the gas and pureliquid phases. The relevant first-order properties as well as linear, quadratic, and cubicfrequency-dependent response functions were computed using time-dependent Kohn–Shamdensity-functional theory with use of the standard CAM-B3LYP functional. In the liquid phase,a series of room temperature (293.15 K) molecular dynamics snapshots were selected, for whichaveraged values of the observables were obtained at an optical wavelength of 632.8 nm. Thebirefringences were computed for electric and magnetic induction fields corresponding to the lab-oratory setup previously employed by Roth and Rikken in Phys. Rev. Lett. 85, 4478, (2000).Under these conditions, acetonitrile is shown to exhibit a weak Jones response — in fact roughly6.5 times smaller than the limit of detection of the apparatus employed in the measurementsmentioned above. A comparison is made with the corresponding gas-phase results and an as-sessment is made of the index of measureability, estimating the degree of overlap of the threebirefringences in actual measurements. For acetonitrile, it is shown that this index is a factorof 3.6 and 6.7 larger than that of methylcyclopentadienyl-Mn-tricarbonyl and cyclohexadienyl-Fe-tricarbonyl, respectively — two compounds reported in Phys. Rev. Lett. 85, 4478, (2000) to exhibita strong Jones signal.

  • 287. Fahleson, Tobias
    et al.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. Linköping University, Sweden.
    A Polarization Propagator for Nonlinear X-ray Spectroscopies2016In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 7, no 11, p. 1991-1995Article in journal (Refereed)
    Abstract [en]

    A complex polarization propagator approach has been developed to third order and implemented in density functional theory (DFT), allowing for the direct calculation of nonlinear molecular properties in the X-ray wavelength regime without explicitly addressing the excited-state manifold. We demonstrate the utility of this propagator method for the modeling of coherent near-edge X-ray two-photon absorption using, as an example, DFT as the underlying electronic structure model. Results are compared with the corresponding near edge X-ray absorption fine structure spectra, illuminating the differences in the role of symmetry, localization, and correlation between the two spectroscopies. The ramifications of this new technique for nonlinear X-ray research are briefly discussed.

  • 288. Falklöf, O.
    et al.
    Durbeej, B.
    Norman, Patrick
    Linköping University, Sweden.
    Inter-Excited-State Phosphorescence in the Four-Component Relativistic Kohn-Sham Approximation: A Case Study on Lumiflavin2015In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, no 49, p. 11911-11921Article in journal (Refereed)
    Abstract [en]

    Electronic transitions from one excited state to another excited state of different spin symmetry play important roles in many biochemical reactions. Although recent years have seen much progress in the elucidation of nonradiative (intersystem crossing) relaxation mechanisms for such transitions, there is presently a scarcity of data available to assess whether also radiative (phosphorescence) mechanisms are relevant for these processes. Here, we demonstrate that the well-established ability of quantum chemical methods to describe intersystem crossing events between excited states can be supplemented by the ability to also describe inter-excited-state phosphorescence. Specifically, by performing four-component relativistic time-dependent density functional theory calculations, we obtain rate constants for the radiative transitions from the absorbing 1(πHπL∗) singlet state of lumiflavin to the 3(πHπL∗), 3(nN2πL∗), and 3(πH-1πL∗) triplet states, and subsequently, we compare these results with rate constants calculated for the corresponding nonradiative transitions. Thereby, it is found that the radiative rate constants for these particular transitions are typically 2 to 5 orders of magnitude smaller than the nonradiative ones.

  • 289.
    Falklöf, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Chemistry. Linköping University, Faculty of Science & Engineering.
    Computational Studies of Photobiological Keto-Enol Reactions and Chromophores2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis presents computational chemistry studies of keto-enol reactions and chromophores of photobiological signicance.

    The rst part of the thesis is concerned with two protein-bound chromophores that, depending on the chemical conditions, can exist in a number of dierent ketonic and enolic forms. The rst chromophore is astaxanthin, which occurs in the protein complex responsible for the deep-blue color of lobster carapace. By investigating how dierent forms of astaxanthin absorb UV-vis radiation of dierent wavelengths, a model is presented that explains the origin of the dramatic color change from deep-blue to red upon cooking of live lobsters.

    The second chromophore is the oxyluciferin light emitter of fireflies, which is formed in the catalytic center of the enzyme firefly luciferase. To date, there is no consensus regarding which of the possible ketonic and enolic forms is the key contributor to the light emission. In the thesis, the intrinsic tendency of oxyluciferin to prefer one particular form over other possible forms is established through calculation of keto-enol and acid-base excited-state equilibrium constants in aqueous solution.

    The second part of the thesis is concerned with two families of biological photoreceptors: the blue-light-absorbing LOV-domain proteins and the red-light-absorbing phytochromes. Based on the ambient light environment, these proteins regulate physiological and developmental processes by switching between inactive and active conformations. In both families, the conversion of the inactive into the active conformation is triggered by a chemical reaction of the respective chromophore.

    The LOV-domain proteins bind a LOV-domain proteins bidn in flavin chromophore and regulate processes such as chloroplast relocation and phototropism in plants. An important step in the activation of these photoreceptors is a singlet-triplet transition between two electronically excited states of the flavin chromophore. In the thesis, this transition is used as a prototype example for illustrating, for the rst time, the ability of rst-principles methods to calculate rate constants of inter-excited state phosphorescence events.

    Phytochromes, in turn, bind bilin chromophores and are active in the regulation of processes like seed germination and  flowering time in plants. Following two systematic studies identifying the best way to model the UV-vis absorption and fluorescence spectra of these photoreceptors, it is demonstrated that steric interactions between the chromophore and the apoprotein play a decisive role for how phytochromes are activated by light.

  • 290.
    Fang, Qiu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Mechanistic photodissociation of small molecules explored by electronic structure calculation and dynamics simulation2011Doctoral thesis, comprehensive summary (Other academic)
  • 291.
    Farahani, Pooria
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Theoretical Studies of Ground and Excited State Reactivity2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    To exemplify how theoretical chemistry can be applied to understand ground and excited state reactivity, four different chemical reactions have been modeled. The ground state chemical reactions are the simplest models in chemistry. To begin, a route to break down halomethanes through reactions with ground state cyano radical has been selected. Efficient explorations of the potential energy surfaces for these reactions have been carried out using the artificial force induced reaction algorithm. The large number of feasible pathways for reactions of this type, up to eleven, shows that these seemingly simple reactions can be quite complex. This exploration is followed by accurate quantum dynamics with reduced dimensionality for the reaction between Cland PH2Cl. The dynamics indicate that increasing the dimensionality of the model to at least two dimensions is a crucial step for an accurate calculation of the rate constant. After considering multiple pathways on a single potential energy surface, various feasible pathways on multiple surfaces have been investigated. As a prototype of these reactions, the thermal decomposition of a four-membered ring peroxide compound, called 1,2-dioxetane, which is the simplest model of chemi- and bioluminescence, has been studied. A detailed description of this model at the molecular level can give rise to a unified understanding of more complex chemiluminescence mechanisms. The results provide further details on the mechanisms and allow to rationalize the high ratio of triplet to singlet dissociation products. Finally, a thermal decomposition of another dioxetane-like compound, called Dewar dioxetane, has been investigated. This study allows to understand the effect of conjugated double bonds adjacent to the dioxetane moiety in the chemiluminescence mechanism of dioxetane. Our studies illustrate that no matter how complex a system is, theoretical chemistry can give a level of insight into chemical processes that cannot be obtained from other methods.

  • 292.
    Farahani, Pooria
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Theoretical Studies of Seemingly Simple Chemical Reactions2013Licentiate thesis, comprehensive summary (Other academic)
  • 293.
    Farahani, Pooria
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Theoretical Studies of Solvent Effect on Normal Mode Analysis and Thermodynamic Properties of Zigzag (5, 0) Carbon Nanotube2011In: Fullerenes, nanotubes, and carbon nanostructures (Print), ISSN 1536-383X, E-ISSN 1536-4046, Vol. 19, p. 469-482Article in journal (Refereed)
    Abstract [en]

    Normal mode analysis is an important tool for studying the structure and dynamicsof nanosized systems. The vibrational frequencies obtained can be used to relateobserved spectra to the details of the molecular structure, dynamics and other thermodynamicproperties. It is important to understand the energetic, stability-dependentphysical properties of zigzag (5, 0) carbon nanotube. In this study we have employedsemi-empirical, DFT, molecular mechanic methods. Our results show that the processof introducing (5, 0) carbon nanotube to different dielectrics is energetically comparablein maximum energy; with increasing the dielectric, the energy declines and thestability increases. AM1and PM3 have the same results in the semi-empirical methodand have good agreement relative to each other.

  • 294.
    Farahani, Pooria
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström.
    Theoretical Study of the Chemiluminescence Mechanism of Dewar DioxetaneManuscript (preprint) (Other academic)
    Abstract [en]

    Light emission from the heating of Dewar benzene was first reported by McCapra (McCapra, PureAppl. Chem. 1970, 24, 611–629). Since most of the chemiluminescence reactions occur through anO-O cleavage, light observed through the thermal decomposition of Dewar benzene was suggested to becaused by the chemiluminescence mechanism of a dioxetane-based intermediate produced after oxidation.However, no prove of this proposal has been suggested so far and the details of the mechanism are thusunknown. In this paper, thermally activated decomposition mechanism of Dewar dioxetane has been studiedby the multiconfigurational CASPT2//CASSCF approach, and accurate reaction path descriptions havebeen provided for a two-step biradical mechanism consisting of O1-O’1and C2-C’2ruptures based onminimum energy path and intrinsic reaction coordinate computations. A radiationless decay path has beendetermined for the molecule along the excited triplet state, while in the excited singlet state the systemevolves toward an equilibrium structure that might be responsible of the light emission. This findingsprovide clues for rationalizing the observed light emission and point to higher efficiency of fluorescencethan triplet emission. Furthermore, the study allows to understand the effect of conjugated double bondsadjacent to the dioxetane moiety in the chemiluminescence mechanism of dioxetane.

  • 295.
    Farahani, Pooria
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Baader, Wilhelm J.
    Unimolecular Decomposition Mechanism of 1,2-Dioxetanedione: Concerted or Biradical? That is the Question!2017In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 121, p. 1189-1194Article in journal (Refereed)
    Abstract [en]

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

  • 296. Farahani, Pooria
    et al.
    Lundberg, Marcus
    Karlsson, Hans
    Ab initio quantum mechanical calculation of the reaction probability forthe Cl þ PH2Cl ! ClPH2 þ Cl reaction2013In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, p. 134-140Article in journal (Refereed)
    Abstract [en]

    The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantummolecular dynamics simulations have been performed to study the prototype reactionCl þ PH2Cl ! ClPH2 þ Cl, using one and two-dimensional models. A potential energy surface, showingan energy well for a transition complex, was generated using ab initio electronic structure calculations.The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensionalmodel displays involved resonance structures in the reaction probability. The reaction rate is almosttwo orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energeticerrors in the potential energy surface is estimated to affect the rate by only a factor of two. Thisshows that for these types of reactions it is more important to increase the dimensionality of the modelingthan to increase the accuracy of the electronic structure calculation.

  • 297.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Ab initio quantum mechanical calculation of the reaction probability for the Cl- + PH2Cl -> ClPH2 + Cl- reaction2013In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, p. 134-140Article in journal (Refereed)
    Abstract [en]

    The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2ClClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.

  • 298. Farahani, Pooria
    et al.
    Lundberg, Marcus
    Lindh, Roland
    Roca-Sanjuan, Daniel
    Theoretical study of the dark photochemistry of 1,3-butadiene via the chemiexcitation of Dewar dioxetane2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, p. 18653-18664Article in journal (Refereed)
    Abstract [en]

    Excited-state chemistry is usually ascribed to photo-induced processes, such as fluorescence, phosphorescence, and photochemistry, or to bio-and chemiluminescence, in which light emission originates from a chemical reaction. A third class of excited-state chemistry is, however, possible. It corresponds to the photochemical phenomena produced by chemienergizing certain chemical groups without light - chemiexcitation. By studying Dewar dioxetane, which can be viewed as the combination of 1,2-dioxetane and 1,3-butadiene, we show here how the photo-isomerization channel of 1,3-butadiene can be reached at a later stage after the thermal decomposition of the dioxetane moiety. Multi-reference multiconfigurational quantum chemistry methods and accurate reaction-path computational strategies were used to determine the reaction coordinate of three successive processes: decomposition of the dioxetane moiety, non-adiabatic energy transfer from the ground to the excited state, and finally non-radiative decay of the 1,3-butadiene group. With the present study, we open a new area of research within computational photochemistry to study chemically-induced excited-state chemistry that is difficult to tackle experimentally due to the short-lived character of the species involved in the process. The findings shall be of relevance to unveil "dark'' photochemistry mechanisms, which might operate in biological systems under conditions of lack of light. These mechanisms might allow reactions that are typical of photo-induced phenomena.

  • 299.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry. Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Lindh, Roland
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Roca-Sanjuan, Daniel
    Univ Valencia, Inst Ciencia Mol, ES-46071 Valencia, Spain.
    Theoretical study of the dark photochemistry of 1,3-butadiene via the chemiexcitation of Dewar dioxetane2015In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 17, no 28, p. 18653-18664Article in journal (Refereed)
    Abstract [en]

    Excited-state chemistry is usually ascribed to photo-induced processes, such as fluorescence, phosphorescence, and photochemistry, or to bio-and chemiluminescence, in which light emission originates from a chemical reaction. A third class of excited-state chemistry is, however, possible. It corresponds to the photochemical phenomena produced by chemienergizing certain chemical groups without light - chemiexcitation. By studying Dewar dioxetane, which can be viewed as the combination of 1,2-dioxetane and 1,3-butadiene, we show here how the photo-isomerization channel of 1,3-butadiene can be reached at a later stage after the thermal decomposition of the dioxetane moiety. Multi-reference multiconfigurational quantum chemistry methods and accurate reaction-path computational strategies were used to determine the reaction coordinate of three successive processes: decomposition of the dioxetane moiety, non-adiabatic energy transfer from the ground to the excited state, and finally non-radiative decay of the 1,3-butadiene group. With the present study, we open a new area of research within computational photochemistry to study chemically-induced excited-state chemistry that is difficult to tackle experimentally due to the short-lived character of the species involved in the process. The findings shall be of relevance to unveil "dark'' photochemistry mechanisms, which might operate in biological systems under conditions of lack of light. These mechanisms might allow reactions that are typical of photo-induced phenomena.

  • 300.
    Farahani, Pooria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Maeda, Satoshi
    Hokkaido Univ, Dept Chem, Fac Sci, Kita Ku, Sapporo, Hokkaido 0600810, Japan.
    Fancisco, Joseph S.
    Purdue Univ, Dept Chem, W Lafayette, IN 47907 USA.
    Lundberg, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Mechanisms for the Breakdown of Halomethanes through Reactions with Ground-State Cyano Radicals2015In: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 16, no 1, p. 181-190Article in journal (Refereed)
    Abstract [en]

    One route to break down halomethanes is through reactions with radical species. The capability of the artificial force-induced reaction algorithm to efficiently explore a large number of radical reaction pathways has been illustrated for reactions between haloalkanes (CX3Y; X=H, F; Y=Cl, Br) and ground-state (2Σ+) cyano radicals (CN). For CH3Cl+CN, 71 stationary points in eight different pathways have been located and, in agreement with experiment, the highest rate constant (108 s−1 M−1 at 298 K) is obtained for hydrogen abstraction. For CH3Br, the rate constants for hydrogen and halogen abstraction are similar (109 s−1 M−1), whereas replacing hydrogen with fluorine eliminates the hydrogen-abstraction route and decreases the rate constants for halogen abstraction by 2–3 orders of magnitude. The detailed mapping of stationary points allows accurate calculations of product distributions, and the encouraging rate constants should motivate future studies with other radicals.

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