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  • 1.
    Berglund, Per
    et al.
    KTH, Tidigare Institutioner, Bioteknologi.
    Branneby, Cecilia
    Svedendahl Humble, Maria
    KTH, Skolan för bioteknologi (BIO), Biokemi (stängd 20130101).
    Carlqvist, Peter
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi (stängd 20110630).
    Magnusson, Anders
    Hult, Karl
    KTH, Skolan för bioteknologi (BIO), Biokemi (stängd 20130101).
    Brinck, Tore
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi (stängd 20110630).
    Aldol and Michael additions catalyzed by a rationally redesigned hydrolytic enzyme2003Inngår i: Abstract of Papers of the American Chemical Society, ISSN 0065-7727, Vol. 226, nr 2, s. U155-U156Artikkel i tidsskrift (Fagfellevurdert)
  • 2.
    Branneby, Cecilia
    et al.
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Carlqvist, Peter
    KTH, Tidigare Institutioner                               , Kemi.
    Hult, Karl
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Brinck, Tore
    KTH, Tidigare Institutioner                               , Kemi.
    Berglund, Per
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Aldol Additions with Mutant Lipase: Analysis by Experiments and Theoretical Calculations2004Inngår i: Journal of Molecular Catalysis B: Enzymatic, ISSN 1381-1177, E-ISSN 1873-3158, Vol. 31, nr 4-6, s. 123-128Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 3. Branneby, Cecilia
    et al.
    Carlqvist, Peter
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi (stängd 20110630).
    Hult, Karl
    KTH, Skolan för bioteknologi (BIO), Biokemi (stängd 20130101).
    Brinck, Tore
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi (stängd 20110630).
    Berglund, Per
    KTH, Tidigare Institutioner, Bioteknologi.
    Rational redesign of a lipase to an aldolase2003Inngår i: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 42, nr 28, s. 8633-8633Artikkel i tidsskrift (Fagfellevurdert)
  • 4.
    Branneby, Cecilia
    et al.
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Carlqvist, Peter
    KTH, Tidigare Institutioner                               , Kemi.
    Magnusson, Anders
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Hult, Karl
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Brinck, Tore
    KTH, Tidigare Institutioner                               , Kemi.
    Berglund, Per
    KTH, Tidigare Institutioner                               , Bioteknologi.
    Carbon-Carbon Bonds by Hydrolytic Enzymes2003Inngår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 125, nr 4, s. 874-875Artikkel i tidsskrift (Fagfellevurdert)
    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

  • 5.
    Brinck, Tore
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Carlqvist, Peter
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Halldin Stenlid, Joakim
    KTH, Skolan för kemivetenskap (CHE), Kemi, Tillämpad fysikalisk kemi.
    Local Electron Attachment Energy and Its Use for Predicting Nucleophilic Reactions and Halogen Bonding2016Inngår i: JOURNAL OF PHYSICAL CHEMISTRY A, ISSN 1089-5639, Vol. 120, nr 50, s. 10023-10032Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 6.
    Carlqvist, Peter
    KTH, Tidigare Institutioner, Kemi.
    Applied Computational Chemistry: Exploring New Routes for Chemical Synthesis2004Doktoravhandling, med artikler (Annet vitenskapelig)
  • 7.
    Carlqvist, Peter
    et al.
    KTH, Tidigare Institutioner, Kemi.
    Ostmark, H.
    Brinck, Tore
    KTH, Tidigare Institutioner, Kemi.
    Computational study of the amination of halobenzenes and phenylpentazole. A viable route to isolate the pentazolate anion?2004Inngår i: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 69, nr 9, s. 3222-3225Artikkel i tidsskrift (Fagfellevurdert)
    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+.

  • 8.
    Carlqvist, Peter
    et al.
    KTH, Tidigare Institutioner, Kemi.
    Ostmark, H.
    Brinck, Tore
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi (stängd 20110630).
    The stability of arylpentazoles2004Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 108, nr 36, s. 7463-7467Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 9.
    Carlqvist, Peter
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi.
    Svedendahl, Maria
    KTH, Skolan för bioteknologi (BIO), Biokemi.
    Branneby, Cecilia
    KTH, Skolan för bioteknologi (BIO), Biokemi.
    Hult, Karl
    KTH, Skolan för bioteknologi (BIO), Biokemi.
    Brinck, Tore
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi.
    Berglund, Per
    KTH, Skolan för bioteknologi (BIO), Biokemi.
    Exploring the Active-Site of a Rationally Redesigned Lipase for Catalysis of Michael-Type Additions2005Inngår i: ChemBioChem (Print), ISSN 1439-4227, E-ISSN 1439-7633, Vol. 6, s. 331-336Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 10.
    Svedendahl, Maria
    et al.
    KTH, Tidigare Institutioner, Biokemi och biokemisk teknologi.
    Branneby, Cecilia
    Cambrex Karlskoga AB.
    Carlqvist, Peter
    KTH, Tidigare Institutioner, Kemi.
    Brinck, Tore
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi (stängd 20110630).
    Hult, Karl
    KTH, Tidigare Institutioner, Biokemi och biokemisk teknologi.
    Berglund, Per
    KTH, Tidigare Institutioner, Biokemi och biokemisk teknologi.
    Michael-type additions catalyzed by a rationally redesigned lipase2004Konferansepaper (Fagfellevurdert)
  • 11.
    Svedendahl, Maria
    et al.
    KTH, Tidigare Institutioner, Biokemi och biokemisk teknologi.
    Branneby, Cecilia
    KTH, Tidigare Institutioner, Biokemi och biokemisk teknologi.
    Carlqvist, Peter
    KTH, Tidigare Institutioner, Kemi.
    Hult, Karl
    KTH, Tidigare Institutioner, Biokemi och biokemisk teknologi.
    Brinck, Tore
    KTH, Tidigare Institutioner, Kemi.
    Berglund, Per
    KTH, Tidigare Institutioner, Biokemi och biokemisk teknologi.
    Expanding the Synthetic Scope of Hydrolytic Enzymes: Catalysis of Aldol- and Michael-Type Additions2004Konferansepaper (Fagfellevurdert)
  • 12.
    Svedendahl, Maria
    et al.
    KTH, Skolan för bioteknologi (BIO), Biokemi.
    Carlqvist, Peter
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi.
    Branneby, Cecilia
    KTH, Skolan för bioteknologi (BIO), Biokemi.
    Allnér, Olof
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi.
    Frise, Anton
    KTH, Skolan för kemivetenskap (CHE), Kemi, Fysikalisk kemi.
    Hult, Karl
    KTH, Skolan för bioteknologi (BIO), Biokemi.
    Berglund, Per
    KTH, Skolan för bioteknologi (BIO), Biokemi.
    Brinck, Tore
    Direct Epoxidation in Candida antarctica Lipase B Studied by Experiment and Theory2008Inngår i: ChemBioChem (Print), ISSN 1439-4227, E-ISSN 1439-7633, Vol. 9, nr 15, s. 2443-2451Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Candida antarctica lipase B (CALB) is a promiscuous serine hydrolase that, besides its native function, catalyzes different side reactions, such as direct epoxidation. A single-point mutant of CALB demonstrated a direct epoxidation reaction mechanism for the epoxidation of alpha,beta-unsaturated aldehydes by hydrogen peroxide in aqueous and organic solution. Mutation of the catalytically active Ser105 to alanine made the previously assumed indirect epoxidation reaction mechanism impossible. Gibbs free energies, activation parameters, and substrate selectivities were determined both computationally and experimentally. The energetics and mechanism for the direct epoxidation in CALB Ser105Ala were investigated that the reaction proceeds through a two step-mechanism with formation of an oxyanionic intermediate. The active-site residue His224 functions as a general acid-base catalyst with support from Asp187. Oxyanion stabilization is facilitated by two hydrogen bonds from Thr40.

1 - 12 of 12
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