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  • 1. Andrae, Johan C. G.
    et al.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Kalghatgi, G. T.
    HCCI experiments with toluene reference fuels modeled by a semidetailed chemical kinetic model2008In: Combustion and Flame, ISSN 0010-2180, E-ISSN 1556-2921, Vol. 155, no 4, p. 696-712Article in journal (Refereed)
    Abstract [en]

    A semidetailed mechanism (137 species and 633 reactions) and new experiments in a homogeneous charge conic pression ignition (HCCI) engine on the autoignition of toluene reference fuels are presented. Skeletal mechanisms for isooctane and n-heptane were added to a detailed toluene submechanism. The model shows generally good agreement with ignition delay times measured in a shock tube and a rapid compression machine and is sensitive to changes in temperature, pressure, and mixture strength. The addition of reactions involving the formation and destruction of benzylperoxide radical was crucial to modeling toluene shock tube data. Laminar burning velocities for benzene and toluene were well predicted by the model after some revision of the high-temperature chemistry. Moreover, laminar burning velocities of a real gasoline at 353 and 500 K Could be predicted by the model using a toluene reference fuel as a surrogate. The model also captures the experimentally observed differences in combustion phasing of toluene/n-heptane mixtures, compared to a primary reference fuel of the same research octane number, in HCCI engines as the intake pressure and temperature are changed. For high intake pressures and low intake temperatures, a sensitivity analysis at the moment of maximum heat release rate shows that the consumption of phenoxy radicals is rate-limiting when a toluene/n-heptane fuel is used, which makes this fuel more resistant to autoignition than the primary reference fuel. Typical CPU times encountered in zero-dimensional calculations were on the order of seconds and minutes in laminar flame speed calculations. Cross reactions between benzylperoxy radicals and n-heptane improved the model prediction,,; of shock tube experiments for phi = 1.0 and temperatures lower than 800 K for an n-heptane/toluene fuel mixture, but cross reactions had no influence on HCCI Simulations.

  • 2.
    Angelin, Marcus
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Rahm, Martin
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Fischer, Andreas
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Ramström, Olof
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Diastereoselective One-Pot Tandem Synthesis of 3-Substituted Isoindolinones: A Mechanistic Investigation2010In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 75, no 17, p. 5882-5887Article in journal (Refereed)
    Abstract [en]

    The mechanism of a base-catalyzed one-pot reaction of 2-cyanobenzaldehyde and primary nitroalkanes, to produce 3-substituted isoindolinones, has been investigated. A route starting with a nitroaldol (Henry) reaction, followed by a subsequent cyclization and rearrangement, was supported by intermediate analogue synthesis and DFT calculations. Direct diastereoselective crystallization from the reaction mixture was also achieved and studied for a number of substrates. Furthermore, the 3-substituted isoindolinones are an interesting group of compounds, both present important natural products, as well as being precursors to other valuable building blocks.

  • 3.
    Berglund, Per
    et al.
    KTH, Superseded Departments, Biotechnology.
    Branneby, Cecilia
    Svedendahl Humble, Maria
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Carlqvist, Peter
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Magnusson, Anders
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Aldol and Michael additions catalyzed by a rationally redesigned hydrolytic enzyme2003In: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 226, no 2, p. U155-U156Article in journal (Refereed)
  • 4.
    Besharat, Zahra
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Material Physics, MF. KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Halldin Stenlid, Joakim
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Soldemo, Markus
    KTH, School of Engineering Sciences (SCI), Applied Physics, Material Physics, MF.
    Marks, Kess
    Önsten, Anneli
    KTH, School of Engineering Sciences (SCI), Applied Physics, Material Physics, MF.
    Johnson, Magnus
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Öström, Henrik
    Weissenrieder, Jonas
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Göthelid, Mats
    KTH, School of Engineering Sciences (SCI), Applied Physics, Material Physics, MF.
    Dehydrogenation of methanol on Cu2O(100) and (111)2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 146, no 24Article in journal (Refereed)
    Abstract [en]

    Adsorption and desorption of methanol on the (111) and (100) surfaces of  Cu2O have been studied using high-resolution photoelectron spectroscopy in the temperature range 120–620 K, in combination with density functional theorycalculations and sum frequency generation spectroscopy. The bare (100) surfaceexhibits a (3,0; 1,1) reconstruction but restructures during the adsorption process into a Cu-dimer geometry stabilized by methoxy and hydrogen binding in Cu-bridge sites. During the restructuring process, oxygen atoms from the bulk that can host hydrogen appear on the surface. Heating transforms methoxy to formaldehyde, but further dehydrogenation is limited by the stability of the surface and the limited access to surface oxygen. The (√3 × √3)R30°-reconstructed (111) surface is based on ordered surface oxygen and copper ions and vacancies, which offers a palette of adsorption and reaction sites. Already at 140 K, a mixed layer of methoxy, formaldehyde, and CHxOy is formed. Heating to room temperature leaves OCH and CHx. Thus both CH-bond breaking and CO-scission are active on this  surface at low temperature. The higher ability to dehydrogenate methanol on (111) compared to (100) is explained by the multitude of adsorption sites and, in particular, the availability of surfaceoxygen.

  • 5. Bittererova, M.
    et al.
    Brinck, Tore
    KTH, Superseded Departments, Chemistry.
    Ostmark, H.
    Theoretical study of the singlet electronically excited states of N-42001In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 340, no 06-maj, p. 597-603Article in journal (Refereed)
    Abstract [en]

    Vertical excitation energies for the lowest eleven singlet states of T-d N-4 were calculated using the TD-DFT method with the B3LYP functional, and at the EOM-CCSD level of theory. The vertical excitation energies for the five lowest-lying excited states were also obtained using the state-averaged CASSCF, CASPT2, CASPT3, and MRCI + Q methods. Our results show that the five lowest-lying states are of valence character. EOM-CCSD/d-aug-cc-pVTZ calculations predict that there are two weakly allowed optical transitions of T-2 symmetry at 10.44 and 10.82 eV. The transition to the third T-2 state, which is predicted to be at 10.89 eV, has an oscillator strength about one order of magnitude higher.

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

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

  • 7. Bittererova, M.
    et al.
    Ostmark, H.
    Brinck, Tore
    KTH, Superseded Departments, Chemistry.
    A theoretical study of the azide (N-3) doublet states. A new route to tetraazatetrahedrane (N-4): N+N-3 -> N-42002In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 116, no 22, p. 9740-9748Article in journal (Refereed)
    Abstract [en]

    The potential energy surfaces for the low-lying doublet states of the azide radical (N-3) have been computed at the complete active space self-consistent field (CASSCF) level with the CAS(15,12) active space. The cc-pVTZ and aug-cc-pVTZ basis sets have been employed throughout the present work. Energies, geometries and harmonic frequencies were determined for the N-3 linear ground electronic state ((2)Pi(g)), a stable C-2v ring structure (B-2(1)), and a C-s transition state ((2)A(')) connecting the ring and linear structures. Other N-3 (C-2v) stationary points ((2)A(2), B-2(1), and (2)A(1)) have been characterized, as well. The vertical excitation energies for the doublet excited states of the N-3 linear ((2)Pi(g)) and stable ring (B-2(1)) isomers were calculated using CASSCF and multireference configuration interaction [MRCI-SD(Q)] methods. A new route to tetraazatetrahedrane [N-4(T-d)] has been proposed on the N-4 singlet potential energy surface within C-s symmetry. MRCI-SD(Q) calculations predict that N-4 (T-d) can be formed from atomic nitrogen in the D-2 state and N-3 (C-2v, B-2(1)) in a barrierless exothermic reaction. The energy difference (D-0) is 135.4 kcal/mol at the MRCI-SD(Q) level.

  • 8. Bittererova, M.
    et al.
    Ostmark, H.
    Brinck, Tore
    KTH, Superseded Departments, Chemistry.
    Ab initio study of the ground state and the first excited state of the rectangular (D-2h) N-4 molecule2001In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 347, no 03-jan, p. 220-228Article in journal (Refereed)
    Abstract [en]

    The dissociation pathway of D-2h N-4 has been investigated at the CASSCF level of theory. A new C-2v transition state to dissociation was found and characterized on the potential energy surface. The effective barrier of dissociation from D-2h N-4 to 2N(2) is estimated to 6.5 kcal/mol from MR-AQCCNTZ//CAS(12,12)/VTZ calculations. Vertical excitation energies and oscillator strengths for the lowest 20 singlet states of D-2h N-4 have been calculated using the EOM-CCSD method. The geometry of the first excited state B-1(3u), considered as the lowest optically accessible state, has been optimized and characterized at various computational levels. This state might be useful for detection of D-2h N-4 by means of laser-induced fluorescence (LIF) spectroscopy.

  • 9.
    Brandt, Erik G.
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Hellgren, Mikko
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Bergman, Tomas
    Edholm, Olle
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Molecular dynamics study of zinc binding to cysteines in a peptide mimic of the alcohol dehydrogenase structural zinc site2009In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 11, no 6, p. 975-983Article in journal (Refereed)
    Abstract [en]

    The binding of zinc (Zn) ions to proteins is important for many cellular events. The theoretical and computational description of this binding (as well as that of other transition metals) is a challenging task. In this paper the binding of the Zn ion to four cysteine residues in the structural site of horse liver alcohol dehydrogenase (HLADH) is studied using a synthetic peptide mimic of this site. The study includes experimental measurements of binding constants, classical free energy calculations from molecular dynamics (MD) simulations and quantum mechanical (QM) electron structure calculations. The classical MD results account for interactions at the molecular level and reproduce the absolute binding energy and the hydration free energy of the Zn ion with an accuracy of about 10%. This is insufficient to obtain correct free energy differences. QM correction terms were calculated from density functional theory (DFT) on small clusters of atoms to include electronic polarisation of the closest waters and covalent contributions to the Zn-S coordination bond. This results in reasonably good agreement with the experimentally measured binding constants and Zn ion hydration free energies in agreement with published experimental values. The study also includes the replacement of one cysteine residue to an alanine. Simulations as well as experiments showed only a small effect of this upon the binding free energy. A detailed analysis indicate that the sulfur is replaced by three water molecules, thereby changing the coordination number of Zn from four (as in the original peptide) to six (as in water).

  • 10.
    Branneby, Cecilia
    et al.
    KTH, Superseded Departments, Biotechnology.
    Carlqvist, Peter
    KTH, Superseded Departments, Chemistry.
    Hult, Karl
    KTH, Superseded Departments, Biotechnology.
    Brinck, Tore
    KTH, Superseded Departments, Chemistry.
    Berglund, Per
    KTH, Superseded Departments, Biotechnology.
    Aldol Additions with Mutant Lipase: Analysis by Experiments and Theoretical Calculations2004In: Journal of Molecular Catalysis B: Enzymatic, ISSN 1381-1177, E-ISSN 1873-3158, Vol. 31, no 4-6, p. 123-128Article in journal (Refereed)
    Abstract [en]

    A Ser105Ala mutant of Candida antarctica lipase B has previously been shown to catalyze aldol additions. Quantum chemical calculations predicted a reaction rate similar to that of natural enzymes, whereas experiments showed a much lower reaction rate. Molecular dynamics simulations, presented here, show that the low reaction rate is a consequence of the low frequencies of near attack complexes in the enzyme. Equilibrium was also considered as a reason for the slow product formation, but could be excluded by performing a sequential reaction to push the reaction towards product formation. In this paper, further experimental results are also presented, highlighting the importance of the entire active site for catalysis.

  • 11. Branneby, Cecilia
    et al.
    Carlqvist, Peter
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry (closed 20130101).
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Berglund, Per
    KTH, Superseded Departments, Biotechnology.
    Rational redesign of a lipase to an aldolase2003In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 42, no 28, p. 8633-8633Article in journal (Refereed)
  • 12.
    Branneby, Cecilia
    et al.
    KTH, Superseded Departments, Biotechnology.
    Carlqvist, Peter
    KTH, Superseded Departments, Chemistry.
    Magnusson, Anders
    KTH, Superseded Departments, Biotechnology.
    Hult, Karl
    KTH, Superseded Departments, Biotechnology.
    Brinck, Tore
    KTH, Superseded Departments, Chemistry.
    Berglund, Per
    KTH, Superseded Departments, Biotechnology.
    Carbon-Carbon Bonds by Hydrolytic Enzymes2003In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 125, no 4, p. 874-875Article in journal (Refereed)
    Abstract [en]

    Enzymes are efficient catalysts in synthetic chemistry, and their catalytic activity with unnatural substrates in organic reaction media is an area attracting much attention. Protein engineering has opened the possibility to change the reaction specificity of enzymes and allow for new reactions to take place in their active sites. We have used this strategy on the well-studied active-site scaffold offered by the serine hydrolase Candida antarctica lipase B (CALB, EC 3.1.1.3) to achieve catalytic activity for aldol reactions. The catalytic reaction was studied in detail by means of quantum chemical calculations in model systems. The predictions from the quantum chemical calculations were then challenged by experiments. Consequently, Ser105 in CALB was targeted by site-directed mutagenesis to create enzyme variants lacking the nucleophilic feature of the active site. The experiments clearly showed an increased reaction rate when the aldol reaction was catalyzed by the mutant enzymes as compared to the wild-type lipase. We expect that the new catalytic activity, harbored in the stable protein scaffold of the lipase, will allow aldol additions of substrates, which cannot be reached by traditional aldolases

  • 13.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Green Energetic Materials2014Collection (editor) (Other academic)
    Abstract [en]

    Since the end of the 20th century it has been increasingly realised that the use, or production, of many energetic materials leads to the release of substances which are harmful to both humans and the environment. To address this, the principles of green chemistry can be applied to the design of new products and their manufacturing processes, to create green energetic materials that are virtually free of environmental hazards and toxicity issues during manufacturing, storage, use and disposal. Active research is underway to develop new ingredients and formulations, green synthetic methods and non-polluting manufacturing processes. Green Energetic Materials provides a detailed account of the most recent research and developments in the field, including green pyrotechnics, explosives and propellants. From theoretical modelling and design of new materials, to the development of sustainable manufacturing processes, this book addresses materials already on the production line, as well as considering future developments in this evolving field. Topics covered include: • Theoretical design of green energetic materials • Development of green pyrotechnics • Green primary and secondary explosives • Oxidisers and binder materials for green propellants • Environmentally sustainable manufacturing technologies for energetic materials • Electrochemical methods for synthesis of energetic materials and waste remediation Green Energetic Materials is a valuable resource for academic, industrial and governmental researchers working on the development of energetic materials, for both military and civilian applications.

  • 14.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Introduction to Green Energetic Materials2014In: Green Energetic Materials, Wiley-Blackwell, 2014, p. 1-14Chapter in book (Refereed)
    Abstract [en]

    This chapter begins with a short summary of the history of energetic materials. It is emphasized that developments generally have been driven by the objectives of improving performance and safety of handling. In addition to these objectives, new materials should also be green. This requirement is considered in relation to green chemistry and other tools for improving the sustainability of new products. A definition of a green energetic materials from the principles of green chemistry is presented. The chapter goes on to analyze past and present attempts to introduce green propulsion technologies to civil space travel. This analysis shows that the development of a green propellant system and its associated engine system is a lengthy and expensive process. The chances of succeeding seem to largely depend on the size of the engine system.

  • 15.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Preface2014In: Green Energetic Materials, Wiley-Blackwell, 2014, p. xi-xiiChapter in book (Refereed)
  • 16.
    Brinck, Tore
    et al.
    KTH, Superseded Departments, Chemistry.
    Carlqvist, P.
    Holm, A. H.
    Daasbjerg, K.
    Solvation of sulfur-centered cations and anions in acetonitrile2002In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 106, no 37, p. 8827-8833Article in journal (Refereed)
    Abstract [en]

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

  • 17.
    Brinck, Tore
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Carlqvist, Peter
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Halldin Stenlid, Joakim
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Local Electron Attachment Energy and Its Use for Predicting Nucleophilic Reactions and Halogen Bonding2016In: JOURNAL OF PHYSICAL CHEMISTRY A, ISSN 1089-5639, Vol. 120, no 50, p. 10023-10032Article in journal (Refereed)
    Abstract [en]

    A new local property, the local electron attachment energy [E(r)], is introduced and is demonstrated to, be a useful guide to predict intermolecular interactions and chemical reactivity. The E(r) is analogous to the average local ionization energy but indicates susceptibility toward interactions with nucleophiles rather than electrophiles. The functional form E(r) is motivated based on Janak's theorem and the piecewise linear energy dependence of electron addition to atomic and molecular systems. Within the generalized Kohn-Sham method (GKS-DFT), only the virtual orbitals with negative eigenvalues contribute to E(r). In the, present study, E(r) has been computed from orbitals obtained from GKS-DFT computations with a hybrid exchange correlation functional. It is shown that E(r) computed on a molecular isodengty surface, E-S(r), reflects the regioselectivity and relative reactivity for nucleophilic aromatic substitution, nucleophilic addition to activated double bonds, and formation of halogen bonds. Good to excellent correlations between experimental or theoretical measures of interaction strengths and minima in E-S(r) (E-S,E-min) are demonstrated.

  • 18.
    Brinck, Tore
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Haeberlein, Markus
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Jonsson, Mats
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Nuclear Chemistry.
    A Computational Analysis of Substituent Effects on the O-H Bond Dissociation Energy in Phenols: Polar Versus Radical Effects1997In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 119, no 18, p. 4239-4244Article in journal (Refereed)
  • 19.
    Brinck, Tore
    et al.
    KTH, Superseded Departments, Chemistry.
    Jin, P.
    Ma, Y. G.
    Murray, J. S.
    Politzer, P.
    Segmental analysis of molecular surface electrostatic potentials: application to enzyme inhibition2003In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 9, no 2, p. 77-83Article in journal (Refereed)
    Abstract [en]

    We have recently shown that the anti-HIV activities of reverse transcriptase inhibitors can be related quantitatively to properties of the electrostatic potentials on their molecular surfaces. We now introduce the technique of using only segments of the drug molecules in developing such expressions. If an improved correlation is obtained for a given family of compounds, it would suggest that the segment being used plays a key role in the interaction. We demonstrate the procedure for three groups of drugs, two acting on reverse transcriptase and one on HIV protease. Segmental analysis is found to be definitely beneficial in one case, less markedly so in another, and to have a negative effect in the third. The last result indicates that major portions of the molecular surfaces are involved in the interactions and that the entire molecules need to be considered, in contrast to the first two examples, in which certain segments appear to be of primary importance. This initial exploratory study shows that segmental analysis can provide insight into the nature of the process being investigated, as well as possibly enhancing the predictive capability.

  • 20.
    Brinck, Tore
    et al.
    KTH, Superseded Departments, Chemistry.
    Larsen, A. G.
    Madsen, K. M.
    Daasbjerg, K.
    Solvation of carbanions in organic solvents: A test of the polarizable continuum model2000In: Journal of Physical Chemistry B, ISSN 1089-5647, Vol. 104, no 42, p. 9887-9893Article in journal (Refereed)
    Abstract [en]

    The solvation of carbanions in the solvents N,N-dimethylformamide (DMF) and tetrahydrofuran (THF) has been analyzed on the basis of experimental and theoretical data. Experimental solvation energies are obtained from present and previously reported electrochemical measurements of reduction potentials of the corresponding radicals. Theoretical solvation energies are obtained from quantum chemical calculations using the polarizable continuum model (PCM). It is found that the solvation energy is relatively independent of molecular size and structure for the saturated carbanions. This indicates that the negative charge is strongly localized to the anionic carbon. The conjugated carbanions have considerably lower absolute solvation energies (\ DeltaG degrees (sol)\) than the saturated carbanions. This is a consequence of the strong delocalization of the negative charge in the former group. The propargyl anion is also found to have a surprisingly low absolute solvation energy. However, high-level quantum chemical calculations show that the electronic structure has large contributions from two different resonance structures, CH=CCH2- and -CH=C=CH2, which results in a significant charge delocalization. There is good agreement between calculated and experimental solvation energies for both the conjugated and nonconjugated primary anions. However, the PCM method consistently underestimates the absolute solvation energies of the secondary and tertiary carbanions. This is attributed to an insufficient treatment of first-layer solvation effects in the method. According to the experimental measurements, the absolute solvation energies are on average 2-3 kcal mol(-1) lower in THF than in DMF. The theoretical data indicate a considerably larger solvent effect, 7-10 kcal mol(-1). The discrepancy between theory and experiment may partly be attributed to the use of a supporting electrolyte in the measurements, but the main cause seems to be that the short-range interaction tendencies of the solvent cannot be Fully characterized by its dielectric constant.

  • 21.
    Brinck, Tore
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Lee, Hau-Nan
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Jonsson, Mats
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Nuclear Chemistry.
    Quantum Chemical Studies on the Thermochemistry of Alkyl and Peroxyl Radicals.1999In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 103, p. 7094-7104-Article in journal (Refereed)
  • 22.
    Brinck, Tore
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Rahm, M.
    Theoretical Design of Green Energetic Materials: Predicting Stability, Detection, Synthesis and Performance2014In: Green Energetic Materials, Wiley-Blackwell, 2014, p. 15-44Chapter in book (Other academic)
    Abstract [en]

    The objective of this chapter is to illustrate the use of modern quantum chemical methods in the rational design of energetic materials with targeted properties. In the first part we discuss the methods that are used for prediction of thermochemical data, and for analysis of decomposition pathways and kinetic stabilities of new compounds. We also describe how quantum chemical methods can be used for predicting spectroscopic data, synthesis pathways, and performance characteristics of energetic materials. In the remaining part of the chapter we provide examples of the theoretical characterization of a number of compounds with promising properties for use in green propellants. Two of these, 1-nitro-2-oxo-3-amino-triazene and tetraazatetrahedrane, combine high kinetic stabilities with excellent propulsion performance.

  • 23. Bulat, Felipe A.
    et al.
    Toro-Labbé, Alejandro
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Murray, Jane S.
    Politzer, Peter
    Quantitative analysis of molecular surfaces: areas, volumes, electrostatic potentials and average local ionization energies2010In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 16, no 11, p. 1679-1691Article in journal (Refereed)
    Abstract [en]

    We describe a procedure for performing quantitative analyses of fields f(r) on molecular surfaces, including statistical quantities and locating and evaluating their local extrema. Our approach avoids the need for explicit mathematical representation of the surface and can be implemented easily in existing graphical software, as it is based on the very popular representation of a surface as collection of polygons. We discuss applications involving the volumes, surface areas and molecular surface electrostatic potentials, and local ionization energies of a group of 11 molecules.

  • 24.
    Caraballo, Remi
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Rahm, Martin
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Vongvilai, Pornrapee
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Ramström, Olof
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Phosphine-catalyzed disulfide metathesis2008In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, no 48, p. 6603-6605Article in journal (Refereed)
    Abstract [en]

    The reaction between disulfides and phosphines generates a reversible disulfide metathesis process.

  • 25.
    Caraballo, Rémi
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Deng, Lingquan
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Amorim, Luis
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Ramström, Olof
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    pH-Dependent Mutarotation of 1-Thioaldoses in Water. Unexpected Behavior of (2S)-D-Aldopyranoses2010In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 75, no 18, p. 6115-6121Article in journal (Refereed)
    Abstract [en]

    The pH-dependent mutarotation of 1-thioaldopyranoses in aqueous media has been investigated. Anomerization readily occurred at lower and neutral pH for all aldopyranoses studied, whereas mainly for (2S)-D-aldopyranoses at higher pH. 1-Thio-D-mannopyranose and 1-thio-D-altropyranose showed very strong pH dependence where the anomeric equilibrium ratios changed dramatically from a preference for the beta-anomer at lower pH to the alpha-anomer at higher pH.

  • 26. Carlqvist, P.
    et al.
    Eklund, R.
    Brinck, Tore
    KTH, Superseded Departments, Chemistry.
    A theoretical study of the uncatalyzed and BF3-assisted Baeyer-Villiger reactions2001In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 66, no 4, p. 1193-1199Article in journal (Refereed)
    Abstract [en]

    The mechanisms for the uncatalyzed and boron trifluoride (BF3) assisted Baeyer-Villiger reactions between acetone and hydrogen peroxide have been investigated using high level ab initio [MP2 and CCSD(T)] and density functional theory (B3LYP) methods. Both steps in the uncatalyzed reaction are found to have very high transition state energies. It is clear that detectable amounts of the Crieege intermediate or the products cannot be formed without the aid of a catalyst. The main function of BF3 in both the addition step and the rearrangement (migration) step is to facilitate proton transfer. In the addition step the complexation of hydrogen peroxide with BF3 leads to an increased acidity of the attacking OH group, while in the rearrangement step BF3 takes active part in the proton-transfer process. This latter step is found to be rate determining with an activation free energy of 17.7 kcal/mol in organic solution. The products of the reaction are BF2OH, hydrogen fluoride, and methyl acetate. Thus, BF3 is not directly regenerated from the reaction.

  • 27. Carlqvist, P.
    et al.
    Eklund, R.
    Hult, Karl
    KTH, Superseded Departments, Biochemistry and Biotechnology.
    Brinck, Tore
    KTH, Superseded Departments, Chemistry.
    Rational design of a lipase to accommodate catalysis of Baeyer-Villiger oxidation with hydrogen peroxide2003In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 9, no 3, p. 164-171Article in journal (Refereed)
    Abstract [en]

    The mechanism and potential energy surface for the Baeyer-Villiger oxidation of acetone with hydrogen peroxide catalyzed by a Ser105-Ala mutant of Candida antarctica Lipase B has been determined using ab initio and density functional theories. Initial substrate binding has been studied using an automated docking procedure and molecular dynamics simulations. Substrates were found to bind to the active site of the mutant. The activation energy for the first step of the reaction, the nucleophilic attack of hydrogen peroxide on the carbonyl carbon of hydrogen peroxide, was calculated to be 4.4 kcal mol(-1) at the B3LYP/6-31+G* level. The second step, involving the migration of the alkyl group, was found to be the rate-determining step with a computed activation energy of 19.9 kcal mol(-1) relative the reactant complex. Both steps were found to be lowered considerably in the reaction catalyzed by the mutated lipase, compared to the uncatalyzed reaction. The first step was lowered by 36.0 kcal mol(-1) and the second step by 19.5 kcal mol(-1). The second step of the reaction, the rearrangement step, has a high barrier of 27.7 kcal mol(-1) relative to the Criegee intermediate. This could lead to an accumulation of the intermediate. It is not clear whether this result is an artifact of the computational procedure, or an indication that further mutations of the active site are required.

  • 28.
    Carlqvist, Peter
    et al.
    KTH, Superseded Departments, Chemistry.
    Ostmark, H.
    Brinck, Tore
    KTH, Superseded Departments, Chemistry.
    Computational study of the amination of halobenzenes and phenylpentazole. A viable route to isolate the pentazolate anion?2004In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 69, no 9, p. 3222-3225Article in journal (Refereed)
    Abstract [en]

    Amination of halobenzenes, which proceeds via the benzyne intermediate (1), has been studied using quantum chemical methods. The computational data are in agreement with experimentally observed trends in reactivity and provide a qualitative explanation for the observed hydrogen isotope effects. To investigate if this is a viable way to isolate the pentazolate anion (2), the reactivities of the halobenzenes have been compared to phenylpentazole (3). The reaction energetics for phenylpentazole become favorable after complexation with Zn2+.

  • 29.
    Carlqvist, Peter
    et al.
    KTH, Superseded Departments, Chemistry.
    Ostmark, H.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    The stability of arylpentazoles2004In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 108, no 36, p. 7463-7467Article in journal (Refereed)
    Abstract [en]

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

  • 30.
    Carlqvist, Peter
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Svedendahl, Maria
    KTH, School of Biotechnology (BIO), Biochemistry.
    Branneby, Cecilia
    KTH, School of Biotechnology (BIO), Biochemistry.
    Hult, Karl
    KTH, School of Biotechnology (BIO), Biochemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Berglund, Per
    KTH, School of Biotechnology (BIO), Biochemistry.
    Exploring the Active-Site of a Rationally Redesigned Lipase for Catalysis of Michael-Type Additions2005In: ChemBioChem (Print), ISSN 1439-4227, E-ISSN 1439-7633, Vol. 6, p. 331-336Article in journal (Refereed)
    Abstract [en]

    Michael-type additions of various thiols and alpha,beta-unsaturated carbonyl compounds were performed in organic solvent catalyzed by wild-type and a rationally redesigned mutant of Candida antarctica lipase B. The mutant locks the nucleophilic serine 105 in the active-site; this results in a changed catalytic mechanism of the enzyme. The possibility of utilizing this mutant for Michael-type additions was initially explored by quantum-chemical calculations on the reaction between acrolein and methanethiol in a model system. The model system was constructed on the basis of docking and molecular-dynamics simulations and was designed to simulate the catalytic properties of the active site. The catalytic system was explored experimentally with a range of different substrates. The k(cat) values were found to be in the range of 10(-3) to 4 min(-1), similar to the values obtained with aldolase antibodies. The enzyme proficiency was 10(7). Furthermore, the Michael-type reactions followed saturation kinetics and were confirmed to take place in the enzyme active site.

  • 31.
    Dong, Hai
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Rahm, Martin
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Ramström, Olof
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Supramolecular Control in Carbohydrate Epimerization: Discovery of a New Anion Host−Guest System2008In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 130, p. 15270-15271Article in journal (Refereed)
    Abstract [en]

    A new anion-carbohydrate recognition system is described. Pyranosides with axial protons in 1-, 3-, and 5-position proved efficient, forming relatively strong complexes between the anion and the B-face of the carbohydrate. This system could furthermore be used in supramolecular control in Lattrell-Dax epimerization reactions, leading to either activation or deactivation effects.

  • 32.
    Dong, Hai
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Rahm, Martin
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Thota, Niranjan
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Deng, Lingquan
    KTH, School of Chemical Science and Engineering (CHE), Chemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Ramström, Olof
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Control of the ambident reactivity of the nitrite ion2013In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 11, no 4, p. 648-653Article in journal (Refereed)
    Abstract [en]

    In previous studies, it was reported that a neighbouring equatorial ester group is essential for a good yield of nitrite-mediated triflate inversion, whereas with neighbouring benzyl ether groups or axial ester groups, mixtures are generally produced. In the present study, the origin of this difference was addressed. The ambident reactivity of the nitrite ion has been found to be the cause of the complex product formation observed, which can be controlled by a neighbouring equatorial ester group. Both N-attack and O-attack occur in the absence of the ester group, whereas O-attack is favoured in its presence. A neighbouring group assistance mechanism is proposed, in addition to steric effects, based on secondary interactions between the neighbouring ester group and the incoming nucleophile. High-level quantum mechanical calculations were carried out in order to delineate this effect. The theoretical results are in excellent agreement with experiments, and suggest a catalytic role for the neighbouring equatorial ester group.

  • 33.
    Fidalgo, Alexandre Barreiro
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Dahlgren, Björn
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Jonsson, Mats
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Surface Reactions of H2O2, H-2, and O-2 in Aqueous Systems Containing ZrO22016In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 3, p. 1609-1614Article in journal (Refereed)
    Abstract [en]

    In radiolysis of water, three molecular products are formed (H2O2, O-2, and H-2). It has previously been shown that aqueous hydrogen peroxide is catalytically decomposed on many oxide surfaces and that the decomposition proceeds via the formation of surface-bound hydroxyl radicals. In this work, we have investigated the behavior of aqueous H-2 and O-2 in contact with ZrO2. Experiments were carried out in an autoclave with high H2 pressure and low O-2 pressure (40 and 0.2 bar, respectively). In the experiments the concentration of H-abstracting radicals was monitored as a function of time using tris(hydroxymethyl)aminomethane (Tris) as scavenger and the subsequent formation of formaldehyde to probe radical formation. The plausible formation of H2O2 was also monitored in the experiments. In addition, density functional theory (employing the hybrid PBE0 functional) was used to search for reaction pathways. The results from the,experiments show that hydrogen-abstracting radicals: are formed in the aqueous H2O2-system in contact with solid ZrO2. Formation of H2O2 is also detected, and the time dependent production of hydrogen-abstracting radicals follows the time-dependent H2O2 concentration, strongly:indicating that the radicals are produced upon catalytic decomposition of H2O2. The DFT study implies that H2O2 formation proceeds via a pathway where HO2 is a key intermediate. It is interesting to note that all the stable molecular products from aqueous radiolysis are precursors of quite intriguing radical reactions at water/oxide interfaces.

  • 34.
    Gracin, Sandra
    et al.
    KTH, Superseded Departments, Chemical Engineering and Technology.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Rasmuson, Åke C.
    KTH, Superseded Departments, Chemical Engineering and Technology.
    Prediction of Solubility of Solid Organic Compounds in Solvents by UNIFAC2002In: Industrial & Engineering Chemistry Research, ISSN 0888-5885, E-ISSN 1520-5045, Vol. 41, no 20, p. 5114-5124Article in journal (Refereed)
    Abstract [en]

    Predictions of solubility of nine different solid organic fine chemical compounds in water and organic solvents of relevance to industrial processing are examined. UNIFAC interaction parameters are taken from standard reference literature, extracted from liquid-vapor equilibria. For most systems, predicted solubilities deviate more than 15% from experimental values. Deviations are due to uncertainties in the estimation of the activity of the pure solid as well as to deficiencies in the estimation of activity coefficients in the solution. By comparison with results from ab initio quantum chemical calculations of the elecrostatic potential on the molecular surface of the solutes, it can be shown that a key assumption of the UNIFAC approach is not necessarily fulfilled. The properties of a functional group may depend significantly on the properties of the rest of the molecule.

  • 35.
    Gustafsson, Camilla
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Applied Physical Chemistry.
    Vassiliev, Serguei
    Department of Biological Sciences, Brock University, Ontario, Canada.
    Kürten, Charlotte
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Syrén, Per-Olof
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Brinck, Tore
    MD Simulations Reveal Complex Water Paths in Squalene–Hopene Cyclase: Tunnel-Obstructing Mutations Increase the Flow of Water in the Active Site2017In: ACS Omega, ISSN 2470-1343, Vol. 2, no 11, p. 8495-8506Article in journal (Refereed)
    Abstract [en]

    Squalene–hopene cyclase catalyzes the cyclization of squalene to hopanoids. A previous study has identified a network of tunnels in the protein, where water molecules have been indicated to move. Blocking these tunnels by site-directed mutagenesis was found to change the activation entropy of the catalytic reaction from positive to negative with a concomitant lowering of the activation enthalpy. As a consequence, some variants are faster and others are slower than the wild type (wt) in vitro under optimal reaction conditions for the wt. In this study, molecular dynamics (MD) simulations have been performed for the wt and the variants to investigate how the mutations affect the protein structure and the water flow in the enzyme, hypothetically influencing the activation parameters. Interestingly, the tunnel-obstructing variants are associated with an increased flow of water in the active site, particularly close to the catalytic residue Asp376. MD simulations with the substrate present in the active site indicate that the distance for the rate-determining proton transfer between Asp376 and the substrate is longer in the tunnel-obstructing protein variants than in the wt. On the basis of the previous experimental results and the current MD results, we propose that the tunnel-obstructing variants, at least partly, could operate by a different catalytic mechanism, where the proton transfer may have contributions from a Grotthuss-like mechanism.

  • 36. Haeffner, F.
    et al.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    How does methyllithium invert? A density functional study2001In: Organometallics, ISSN 0276-7333, E-ISSN 1520-6041, Vol. 20, no 24, p. 5134-5138Article in journal (Refereed)
    Abstract [en]

    Quantum chemical studies (B3LYP) of the inversion of methyllithium in both tetrameric and dimeric aggregates have been carried out. Results show that inversion occurs either via dissociation of the tetramer into the dimers, passage of a four-membered-ring transition state, and association of the dimers to form the inverted tetramer, or via a nonconcerted route involving an eight-membered-ring transition state. The activation energies of these two mechanisms are similar. However, the dissociative mechanism is ruled out by NMR experiments.

  • 37.
    Haeffner, Fredrik
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Barnham, Kevin J.
    Bush, Ashley I.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Generation of soluble oligomeric beta-amyloid species via copper catalyzed oxidation with implications for Alzheimer's disease: A DFT study2010In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 16, no 6, p. 1103-1108Article in journal (Refereed)
    Abstract [en]

    A mechanism for the oxidation of a dimeric beta-amyloid copper ion complex is proposed based on DFT calculations. It involves the Met35 residue, which is believed to be important in the neurotoxicity causing Alzheimer's disease. Oxidation of Met35 is found to proceed readily with dioxygen when two Met35 residues are close to each other and the copper ion. This indicates that oxidants, such as hydrogen peroxide, are not necessary for oxidation of beta-amyloid copper ion complexes. Understanding these processes could be pivotal in gaining more knowledge of this complex disease and for the development of therapeutic treatments.

  • 38.
    Hagberg, Daniel
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Marinado, Tannia
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Edvinsson, Tomas
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Boschloo, Gerrit
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Hagfeldt, Anders
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry (closed 20110630).
    Rhodanine Dyes for Dye Sensitized Solar Cells: Spectroscopy, Energy Levels and Photovoltaic Performance2009In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 11, p. 133-141Article in journal (Refereed)
    Abstract [en]

    Three new sensitizers for photoelectrochemical solar cells were synthesized consisting of a triphenylamine donor, a rhodanine-3-acetic acid acceptor and a polyene connection. The conjugation length was systematically increased, which resulted in two effects: first, it led to a red-shift of the optical absorption of the dyes, resulting in an improved spectral overlap with the solar spectrum. Secondly, the oxidation potential decreased systematically. The excited state levels were, however, calculated to be nearly stationary. The experimental trends were in excellent agreement with density functional theory (DFT) computations. The photovoltaic performance of this set of dyes as sensitizers in mesoporous TiO2 solar cells was investigated using electrolytes containing the iodide/triiodide redox couple. The dye with the best absorption characteristics showed the poorest solar cell efficiency, due to losses by recombination of electrons in TiO2 with triiodide. Addition of 4-tert butylpyridine to the electrolyte led to a strongly reduced photocurrent for all dyes due to a reduced electron injection efficiency, caused by a 0.15 V negative shift of the TiO2 conduction band potential.

  • 39.
    Hagberg, Daniel
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Marinado, Tannia
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Hagfeldt, Anders
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Brinck, Tove
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Linder, Mats
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Jiang, Xiao
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Gabrielsson, Erik
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Symmetric and Unsymmetric Donor Functionalization. Comparing Structural and Spectral Benefits of Chromophores for Dye Sensitized Solar Cells.2009In: Journal of Materials Chemistry, ISSN 0959-9428, E-ISSN 1364-5501, Vol. 19, p. 7232-7238Article in journal (Refereed)
    Abstract [en]

     

    A series of organic chromophores have been synthesized in order to investigate the benefits of structural versus spectral properties as well as the absorption properties and solar cell performance when introducing unsymmetrical substituents in the chromophore. Exceptionally high Voc was found for the symmetrical, structural benefited dye, which also gave the best overall solar cell performance.

     

  • 40.
    Hagberg, Daniel P.
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Marinado, Tannia
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Karlsson, Karl Martin
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Nonomura, Kazeteru
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Qin, Peng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Boschloo, Gerrit
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Hagfeldt, Anders
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Physical Chemistry.
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Tuning the HOMO and LUMO Energy Levels of Organic Chromophores For Dye Sensitized Solar Cells2007In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, no 72, p. 9550-9556Article in journal (Refereed)
    Abstract [en]

    A series of organic chromophores have been synthesized in order to approach optimal energy level composition in the TiO2-dye-iodide/triiodide system in the dye-sensitized solar cells. HOMO and LUMO energy level tuning is achieved by varying the conjugation between the triphenylamine donor and the cyanoacetic acid acceptor. This is supported by spectral and electrochemical experiments and TDDFT calculations. These results show that energetic tuning of the chromophores was successful and fulfilled the thermodynamic criteria for dye-sensitized solar cells, electrical losses depending on the size and orientation of the chromophores were observed.

  • 41.
    Halldin Stenlid, Joakim
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Extending the σ-Hole Concept to Metals: An Electrostatic Interpretation of the Nanostructural Effects in Gold and Platinum Catalysis2017In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126Article in journal (Refereed)
    Abstract [en]

    Crystalline surfaces of gold are chemically inert, whereas nanoparticles of gold are excellent catalysts for many reactions. The catalytic properties of nanostructured gold have been connected to increased binding affinities of reactant molecules to low-coordinated Au atoms. Here we show that the high reactivity at these sites is a consequence of the formation of σ-holes, i.e. maxima in the surface electrostatic potential (Vs,max) due to the overlap of mainly the valence s-orbitals when forming the bonding σ-orbitals. The σ-holes are binding sites for Lewis bases, and binding energies correlate with magnitudes of the Vs,max. For symmetrical Au clusters, of varying size, the most positive Vs,max are found at corners, edges, and surfaces (facets) and decreasing in that order. This is in agreement with the experimentally and theoretically observed dependence of catalytic activity on local structure. The density of σ-holes can explain the increasing catalytic activity with decreasing particle size also for other transition metal catalysts, such as platinum.

  • 42.
    Halldin Stenlid, Joakim
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Johansson, A. J.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    σ-Holes and σ-lumps direct the Lewis basic and acidic interactions of noble metal nanoparticles: Introducing regium bonds2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 4, p. 2676-2692Article in journal (Refereed)
    Abstract [en]

    Using local DFT-based probes for electrostatic as well as charge transfer/polarization interactions, we are able to characterize Lewis basic and acidic sites on copper, silver and gold nanoparticles. The predictions obtained using the DFT-probes are compared to the interaction energies of the electron donating (CO, H2O, NH3 and H2S) and the electron accepting (BH3, BF3, HCl [H-down] and Na+) compounds. The probes include the local electron attachment energy [E(r)], the average local ionization energy [Ī(r)], and the electrostatic potential [V(r)] and are evaluated on isodensity surfaces located at distances corresponding to typical interaction distances. These probes have previously been successful in characterizing molecular interactions. Good correlations are found between Lewis acidity and maxima in V(r), appearing as a consequence of σ-holes, as well as minima in E(r), of the noble metal nanoparticles. Similarly are Lewis basic sites successfully described by surface minima in V(r) and Ī(r); the former are indicative of σ-lumps, i.e. regions of enhanced σ-density. The investigated probes are anticipated to function as reliable tools in nanoparticle reactivity and interaction characterization, and may act as suitable descriptors in large-scale screenings for materials of specific properties, e.g. in heterogeneous catalysis. Because of the similarity between the noble metal nanoparticle's interactions with Lewis bases and the concepts of halogen and hydrogen bonding, a new class of bonds is introduced-regium bonds-taking place between a σ-hole of a Cu, Ag or Au compound and an electron donor.

  • 43.
    Halldin Stenlid, Joakim
    et al.
    KTH.
    Johansson, A. J.
    Leygraf, Christofer
    KTH.
    Brinck, Tore
    KTH.
    Atomic-scale modelling of copper corrosion in anoxic and sulphide containing water2017In: EUROCORR 2017 - The Annual Congress of the European Federation of Corrosion, 20th International Corrosion Congress and Process Safety Congress 2017, Asociace koroznich inzenyru z.s.- AKI - Czech Association of Corrosion Engineers , 2017Conference paper (Refereed)
  • 44.
    Halldin Stenlid, Joakim
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Johansson, Adam Johaness
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    σ-Holes on Transition Metal Nanoclusters and Their Influence on the Local Lewis Acidity2017In: Crystals, ISSN 2073-4352, Vol. 7, article id 222Article in journal (Refereed)
    Abstract [en]

    Understanding the molecular interaction behavior of transition metal nanoclusters lies at the heart of their efficient use in, e.g., heterogeneous catalysis, medical therapy and solar energy harvesting. For this purpose, we have evaluated the applicability of the surface electrostatic potential [VS(r)] and the local surface electron attachment energy [ES(r)] properties for characterizing the local Lewis acidity of a series of low-energy TM13 transition metal nanoclusters (TM = Au, Cu, Ru, Rh, Pd, Ir, Pt, Co), including also Pt7Cu6. The clusters have been studied using hybrid Kohn–Sham density functional theory (DFT) calculations. The VS(r) and ES(r), evaluated at 0.001 a.u. isodensity contours, are used to analyze the interactions with H2O. We find that the maxima of VS(r), σ-holes, are either localized or diffuse. This is rationalized in terms of the nanocluster geometry and occupation of the clusters’s, p and d valence orbitals. Our findings motivate a new scheme for characterizing σ-holes as σs (diffuse), σp (localized) or σd (localized) depending on their electronic origin. The positions of the maxima in VS(r) (and minima in ES(r)) are found to coincide with O-down adsorption sites of H2O, whereas minima in VS(r) leads to H-down adsorption. Linear relationships between VS,max (and ES,min) and H2O interaction energies are further discussed.

  • 45.
    Halldin Stenlid, Joakim
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Johansson, Adam Johannes
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Local Lewis Acidity of (TiO2)n n=7-10 Nanoparticles Characterized by DFT-Based DescriptorsManuscript (preprint) (Other academic)
  • 46.
    Halldin Stenlid, Joakim
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Johansson, Adam Johannes
    Swedish Nuclear Fuel and Waste Management Co (SKB).
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Searching for the thermodynamic limit - a DFT study of the step-wise water oxidation of the bipyramidal Cu-7 cluster2014In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 16, no 6, p. 2452-2464Article in journal (Refereed)
    Abstract [en]

    Oxidative degradation of copper in aqueous environments is a major concern in areas such as catalysis, electronics and construction engineering. A particular challenge is to systematically investigate the details of this process for non-ideal copper surfaces and particles under the conditions found in most real applications. To this end, we have used hybrid density functional theory to study the oxidation of a Cu-7 cluster in water solution. Especially, the role of a large water coverage is explored. This has resulted in the conclusion that, under atmospheric H-2 pressures, the thermodynamically most favored state of degradation is achieved upon the generation of four H-2 molecules (i.e. Cu-7 + 8H(2)O -> Cu-7(OH)(8) + 4H(2)) in both condensed and gas phases. This state corresponds to an average oxidation state below Cu(I). The calculations suggest that the oxidation reaction is slow at ambient temperatures with the water dissociation as the rate-limiting step. Our findings are expected to have implication for, among other areas, the copper catalyzed water-gas shift reaction, and for the general understanding of copper corrosion in aqueous environments.

  • 47.
    Halldin Stenlid, Joakim
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Johansson, Adam Johannes
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    sigma-Holes and sigma-lumps direct the Lewis basic and acidic interactions of noble metal nanoparticles: introducing regium bonds2018In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 20, no 4, p. 2676-2692Article in journal (Refereed)
    Abstract [en]

    Using local DFT-based probes for electrostatic as well as charge transfer/polarization interactions, we are able to characterize Lewis basic and acidic sites on copper, silver and gold nanoparticles. The predictions obtained using the DFT-probes are compared to the interaction energies of the electron donating (CO, H2O, NH3 and H2S) and the electron accepting (BH3, BF3, HCl [H-down] and Na+) compounds. The probes include the local electron attachment energy [E(r)], the average local ionization energy [% I(r)], and the electrostatic potential [V(r)] and are evaluated on isodensity surfaces located at distances corresponding to typical interaction distances. These probes have previously been successful in characterizing molecular interactions. Good correlations are found between Lewis acidity and maxima in V(r), appearing as a consequence of sigma-holes, as well as minima in E(r), of the noble metal nanoparticles. Similarly are Lewis basic sites successfully described by surface minima in V(r) and % I(r); the former are indicative of sigma-lumps, i.e. regions of enhanced sigma-density. The investigated probes are anticipated to function as reliable tools in nanoparticle reactivity and interaction characterization, and may act as suitable descriptors in large-scale screenings for materials of specific properties, e.g. in heterogeneous catalysis. Because of the similarity between the noble metal nanoparticle's interactions with Lewis bases and the concepts of halogen and hydrogen bonding, a new class of bonds is introduced - regium bonds - taking place between a sigma-hole of a Cu, Ag or Au compound and an electron donor.

  • 48.
    Halldin Stenlid, Joakim
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Johansson, Adam Johannes
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    σ-Holes and σ-Lumps Direct the Lewis Basic and Acidic Interactions of Noble Metal Nanoparticles: Introducing Regium BondsManuscript (preprint) (Other academic)
  • 49.
    Halldin Stenlid, Joakim
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Johansson, Adam Johannes
    Kloo, Lars
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Aqueous Solvation and Surface Oxidation of the Cu7 Nanoparticle: Insights from Theoretical Modeling2016In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 3, p. 1977-1988Article in journal (Refereed)
    Abstract [en]

    The current understanding on: the behavior of nano particles in solution is limited. We have studied tho effects of the aqueous environment on the anoxic oxidation of a Cu-7 riannpartide using a range of different computational solvation models. On the basis of a series of hydroxylated Cu-7(H2O)(y)(OH)x structures, the performance of standard continuum models have been compared to discrete models including up to, and beyond, the second solvation layer. Both full quantum chemical 4 (DFT: PBEO-D3) and QM/MM (PBEO/EPP1) computations were employed in the analysis. The Cu-7 structures were solvated in water nanodroplets and studied by molecular dynamics simulations. On the basis of the simulations, we were able to identify new modes of H2O interactions with the Cu(7)particle, modes that were previously considered unbeneficial. All solvation models favor the "Same equilibrium oxidation state corresponding to a Cu(I)OH surface species. However, for quantitative energy comparison of similar- systems, our results suggest the use of a combined water cinst07cniftinuum model including at least a first explicit solvation shell for energetic comparisons. Nevertheless, the second solvatiOn:thell is -important for identifying representative inner solvation shell structures.

  • 50.
    Halldin Stenlid, Joakim
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Johansson, Adam Johannes
    Leygraf, Christopher
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Brinck, Tore
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Applied Physical Chemistry.
    Computational Analysis of the Early Stage of Cuprous Oxide Sulphidation: A Top-Down Process2017In: Corrosion Engineering, Science and Technology, ISSN 1478-422X, E-ISSN 1743-2782, Vol. 52, no S1, p. 50-53Article in journal (Refereed)
    Abstract [en]

    The initial steps of Cu2O sulphidation to Cu2S have been studied using plane-wave density functional theory at the PBE-D3+U level of sophistication. Surface adsorption and dissociation of H2S and H2O, as well as the replacement reaction of lattice oxygen with sulphur, have been investigated for the most stable (111) and (100) surface facets under oxygen-lean conditions. We find that the (100) surface is more susceptible to sulphidation than the (111) surface, promoting both H2S adsorption, dissociation and the continued oxygen–sulphur replacement. The results presented in this proceeding bridge previous results from high-vacuum experiments on ideal surface to more realistic corrosion conditions and set the grounds for future mechanistic studies. Potential implications on the long-term final disposal of spent nuclear fuel are discussed.

123 1 - 50 of 115
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